Sample records for backcross inbred lines

  1. Efficient QTL detection for nonhost resistance in wild lettuce: backcross inbred lines versus F2 population

    PubMed Central

    Pelgrom, K.; Stam, P.; Lindhout, P.

    2008-01-01

    In plants, several population types [F2, recombinant inbred lines, backcross inbred lines (BILs), etc.] are used for quantitative trait locus (QTL) analyses. However, dissection of the trait of interest and subsequent confirmation by introgression of QTLs for breeding purposes has not been as successful as that predicted from theoretical calculations. More practical knowledge of different QTL mapping approaches is needed. In this recent study, we describe the detection and mapping of quantitative resistances to downy mildew in a set of 29 BILs of cultivated lettuce (L. sativa) containing genome segments introgressed from wild lettuce (L. saligna). Introgression regions that are associated with quantitative resistance are considered to harbor a QTL. Furthermore, we compare this with results from an already existing F2 population derived from the same parents. We identified six QTLs in our BIL approach compared to only three in the F2 approach, while there were two QTLs in common. We performed a simulation study based on our actual data to help us interpret them. This revealed that two newly detected QTLs in the BILs had gone unnoticed in the F2, due to a combination of recessiveness of the trait and skewed segregation, causing a deficit of the wild species alleles. This study clearly illustrates the added value of extended genetic studies on two different population types (BILs and F2) to dissect complex genetic traits. PMID:18251002

  2. Mapping quantitative trait loci for lint yield and fiber quality across environments in a Gossypium hirsutum × Gossypium barbadense backcross inbred line population.

    PubMed

    Yu, Jiwen; Zhang, Ke; Li, Shuaiyang; Yu, Shuxun; Zhai, Honghong; Wu, Man; Li, Xingli; Fan, Shuli; Song, Meizhen; Yang, Daigang; Li, Yunhai; Zhang, Jinfa

    2013-01-01

    Identification of stable quantitative trait loci (QTLs) across different environments and mapping populations is a prerequisite for marker-assisted selection (MAS) for cotton yield and fiber quality. To construct a genetic linkage map and to identify QTLs for fiber quality and yield traits, a backcross inbred line (BIL) population of 146 lines was developed from a cross between Upland cotton (Gossypium hirsutum) and Egyptian cotton (Gossypium barbadense) through two generations of backcrossing using Upland cotton as the recurrent parent followed by four generations of self pollination. The BIL population together with its two parents was tested in five environments representing three major cotton production regions in China. The genetic map spanned a total genetic distance of 2,895 cM and contained 392 polymorphic SSR loci with an average genetic distance of 7.4 cM per marker. A total of 67 QTLs including 28 for fiber quality and 39 for yield and its components were detected on 23 chromosomes, each of which explained 6.65-25.27% of the phenotypic variation. Twenty-nine QTLs were located on the At subgenome originated from a cultivated diploid cotton, while 38 were on the Dt subgenome from an ancestor that does not produce spinnable fibers. Of the eight common QTLs (12%) detected in more than two environments, two were for fiber quality traits including one for fiber strength and one for uniformity, and six for yield and its components including three for lint yield, one for seedcotton yield, one for lint percentage and one for boll weight. QTL clusters for the same traits or different traits were also identified. This research represents one of the first reports using a permanent advanced backcross inbred population of an interspecific hybrid population to identify QTLs for fiber quality and yield traits in cotton across diverse environments. It provides useful information for transferring desirable genes from G. barbadense to G. hirsutum using MAS.

  3. Effect of indica pedigree on eating and cooking quality in rice backcross inbred lines of indica and japonica crosses

    PubMed Central

    Fan, Mingyu; Wang, Xiaojing; Sun, Jian; Zhang, Qun; Xu, Zhengjin; Xu, Quan

    2017-01-01

    Amylopectin is one of the major determinants of rice (Oryza sativa L.) grain quality, and a large difference in amylopectin is found between two subspecies: japonica and indica. However, the relationship among rice grain quality, indica/japonica genetic background, and amylopectin has not been clearly established. In this study, a series of backcross inbred lines derived from the cross between japonica (cv. Sasanishiki) and indica (cv. Habataki) were used to survey eating and cooking quality (ECQ), rapid visco analyzer (RVA) profiles, and the chain length distribution of amylopectin. The frequency of indica pedigree (Fi) was calculated to analyze the effects of Fi on grain quality and amylopectin. The results showed that the Sasanishiki cultivar was markedly enriched in chain length with DP6-15 and DP34-45 compared to the Habataki. DP34-45 strongly correlated to RVA characteristics, cooking quality, and prolamin content. The Fi also has significant correlations to RVA characteristics and ECQ, but only significantly negative correlation to DP34-45. Seven quantitative trait loci (QTLs) corresponding to amylopectin were mapped, of which three were in agreement with previous findings. The results of this study provide valuable information for amylopectin characteristics in the offspring derived from the subspecies cross, and the novel QTLs may provide new insights to the identification of minor starch synthesis-related genes. PMID:29398938

  4. Marker-Assisted Introgression in Backcross Breeding Programs

    PubMed Central

    Visscher, P. M.; Haley, C. S.; Thompson, R.

    1996-01-01

    The efficiency of marker-assisted introgression in backcross populations derived from inbred lines was investigated by simulation. Background genotypes were simulated assuming that a genetic model of many genes of small effects in coupling phase explains the observed breed difference and variance in backcross populations. Markers were efficient in introgression backcross programs for simultaneously introgressing an allele and selecting for the desired genomic background. Using a marker spacing of 10-20 cM gave an advantage of one to two backcross generations selection relative to random or phenotypic selection. When the position of the gene to be introgressed is uncertain, for example because its position was estimated from a trait gene mapping experiment, a chromosome segment should be introgressed that is likely to include the allele of interest. Even for relatively precisely mapped quantitative trait loci, flanking markers or marker haplotypes should cover ~10-20 cM around the estimated position of the gene, to ensure that the allele frequency does not decline in later backcross generations. PMID:8978075

  5. Identification of QTLs for rice brown spot resistance in backcross inbred lines derived from a cross between Koshihikari and CH45.

    PubMed

    Matsumoto, Kengo; Ota, Yuya; Seta, Satomi; Nakayama, Yukinori; Ohno, Teppei; Mizobuchi, Ritsuko; Sato, Hiroyuki

    2017-12-01

    Rice brown spot (BS), caused by Bipolaris oryzae , is one of the major diseases of rice in Japan. Quantitative resistance has been observed in local cultivars (e.g., CH45), but no economically useful resistant variety has been bred. Using simple sequence repeat (SSR) polymorphic markers, we conducted quantitative trait locus (QTL) analysis of BS resistance in backcross inbred lines (BILs) from a cross between indica CH45 (resistant) and japonica Koshihikari (susceptible). On the basis of field disease evaluations in 2015 and 2016, four QTLs contributing to BS resistance were identified on chromosomes 2 ( qBSR2-kc ), 7 ( qBSR7-kc ), 9 ( qBSR9-kc ), and 11 ( qBSR11-kc ). The 'CH45' alleles at qBSR2-kc , qBSR7-kc , and qBSR11-kc and the 'Koshihikari' allele at qBSR9-kc increased resistance. The major QTL qBSR11-kc explained 23.0%-25.9% of the total phenotypic variation. Two QTLs ( qBSR9-kc and qBSR11-kc ) were detected in both years, whereas the other two were detected only in 2016. Genetic markers flanking these four QTLs will be powerful tools for marker-assisted selection to improve BS resistance.

  6. Assessment and genetic analysis of heavy metal content in rice grain using an Oryza sativa × O. rufipogon backcross inbred line population.

    PubMed

    Huang, De-Run; Fan, Ye-Yang; Hu, Biao-Lin; Xiao, Ye-Qing; Chen, Da-Zhou; Zhuang, Jie-Yun

    2018-03-01

    Heavy metal accumulation in rice is a growing concern for public health. Backcross inbred lines derived from an interspecific cross of Oryza sativa × O. rufipogon were grown in two distinct ecological locations (Hangzhou and Lingshui, China). The objective of this study was to characterise the contents of heavy metal in rice grains, and to identify quantitative trait loci (QTLs) for heavy metal contents. The contents of Ni, As, Pb, Cr and Hg in milled rice showed a significant decline as compared with those in brown rice, whereas the content of Cd showed little change. The concentration of heavy metal in rice grain varied greatly between the two environments. A total of 24 QTLs responsible for heavy metal contents were detected, including two for both the brown and milled rice, 13 for brown rice only, and nine for milled rice only. All the QTLs except two had the enhancing alleles derived from O. rufipogon. Sixteen QTLs were clustered in six chromosomal regions. Environmental variation plays an important role in the heavy metal contents in rice grain. QTLs detected in this study might be useful for breeding rice varieties with low heavy metal content. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  7. Identification of trait-improving quantitative trait loci for grain yield components from a dent corn inbred line in an advanced backcross BC2F2 population and comparison with its F2:3 population in popcorn.

    PubMed

    Li, Y L; Niu, S Z; Dong, Y B; Cui, D Q; Wang, Y Z; Liu, Y Y; Wei, M G

    2007-06-01

    Normal maize germplasm could be used to improve the grain yield of popcorn inbreds. Our first objective was to locate genetic factors associated with trait variation and make first assessment on the efficiency of advanced backcross quantitative trait locus (AB-QTL) analysis for the identification and transfer of favorable QTL alleles for grain yield components from the dent corn inbred. A second objective was to compare the detection of QTL in the BC2F2 population with results using F(2:3) lines of the same parents. Two hundred and twenty selected BC2F2 families developed from a cross between Dan232 and an elite popcorn inbred N04 were evaluated for six grain yield components under two environments, and genotyped by means of 170 SSR markers. Using composite interval mapping (CIM), a total of 19 significant QTL were detected. Eighteen QTL had favorable alleles contributed by the dent corn parent Dan232. Sixteen of these favorable QTL alleles were not in the same or near marker intervals with QTL for popping characteristics. Six QTL were also detected in the F(2:3) population. Improved N04 could be developed from 210 and 208 families with higher grain weight per plant and/or 100-grain weight, respectively, and 35 families with the same or higher popping expansion volume than N04. In addition, near isogenic lines containing detected QTL (QTL-NILs) for grain weight per plant and/or 100-grain weight could be obtained from 12 families. Our study demonstrated that the AB-QTL method can be applied to identify and manipulate favorable QTL alleles from normal corn inbreds and combine QTL detection and popcorn breeding efficiently.

  8. Mapping osmotic adjustment in an advanced back-cross inbred population of rice.

    PubMed

    Robin, S; Pathan, M S; Courtois, B; Lafitte, R; Carandang, S; Lanceras, S; Amante, M; Nguyen, H T; Li, Z

    2003-11-01

    Osmotic adjustment is one of several characters putatively associated with drought tolerance in rice. Indica cultivars are known to have a greater capacity for osmotic adjustment than japonica cultivars. We developed an advanced back-cross population using an indica donor, IR62266-42-6-2, to introgress osmotic adjustment into an elite japonica cultivar, IR60080-46A. One hundred and fifty BC(3)F(3) families were genotyped using microsatellites and RFLP markers, and a few candidate genes. We evaluated osmotic adjustment in these lines under greenhouse conditions using the re-hydration technique. Using the composite interval mapping technique, we detected 14 QTLs located on chromosomes 1, 2, 3, 4, 5, 7, 8 and 10 that together explained 58% of the phenotypic variability. Most, but not all, of the alleles with positive effects came from the donor parent. On chromosome 8, two QTLs were associated in repulsion. The QTL locations were in good agreement with previous studies on this trait on rice and in other cereals. Some BC(3)F(3) lines carried the favorable alleles at the two markers flanking up to four QTLs. Intercrossing these lines followed by marker-aided selection in their progenies will be necessary to recover lines with levels of osmotic adjustment equal to the donor parent. The advanced back-cross strategy appeared to be an appropriate method to accelerate the process of introgressing interesting traits into elite material.

  9. Recombinant inbred lines derived from potato interspecific hybrids

    USDA-ARS?s Scientific Manuscript database

    Recombinant inbred lines (RILs) offer new opportunities for mapping traits of interest to potato breeders. We are developing a set of six RILs, which will comprise a nested association mapping population. The common parent is M6, an inbred line of the diploid wild relative Solanum chacoense. Other g...

  10. Marker-assisted breeding for introgression of opaque-2 allele into elite maize inbred line BML-7.

    PubMed

    Krishna, M S R; Sokka Reddy, S; Satyanarayana, Sadam D V

    2017-07-01

    Improvement of quality protein maize (QPM) along with high content of lysine and tryptophan had foremost importance in maize breeding program. The efficient and easiest way of developing QPM hybrids was by backcross breeding in marker aided selection. Hence, the present investigation aimed at conversion of elite maize inbred line BML-7 into QPM line. CML-186 was identified to be a donor variety as it revealed high-quality polymorphism with BML-7 for opaque-2 gene specific marker umc1066. Non-QPM inbred line BML-7 was crossed with QPM donor CML-186 and produced F 1 followed by the development of BC 1 F 1 and BC 2 F 1 population. Foreground selection was carried out with umc1066 in F 1 , and selected plants were used for BC 1 F 1 and BC 2 F 1 populations. Two hundred plants were screened in both BC 1 F 1 and BC 2 F 1 population with umc1066 for foreground selection amino acid modifiers. Foreground selected plants for both opaque-2 and amino acid modifiers were screened for background selection for BML-7 genome. Recurrent parent genome (RPG) was calculated for BC 2 F 1 population plants. Two plants have shown with RPG 90-93% in two generation with back cross population. Two BC 2 F 2 populations resulted from marker recognized BC 2 F 1 individuals subjected toward foreground selection followed by tryptophan estimation. The tryptophan and lysine concentration was improved in all the plants. BC 2 F 2 lines developed from hard endosperm kernels were selfed for BC 2 F 2 lines and finest line was selected to illustrate the QPM version of BML-7, with 0.97% of tryptophan and 4.04% of lysine concentration in protein. Therefore, the QPM version of BML-7 line can be used for the development of single cross hybrid QPM maize version.

  11. Registration of maize inbred line GT603

    USDA-ARS?s Scientific Manuscript database

    GT603 (Reg. No. xxxx, PI xxxxxx) is a yellow dent maize (Zea mays L.) inbred line developed and released by the USDA-ARS Crop Protection and Management Research Unit in cooperation with the University of Georgia Coastal Plain Experiment Station in 2010. GT603 was developed through seven generations ...

  12. Sites of ozone sensitivity in diverse maize inbred lines

    USDA-ARS?s Scientific Manuscript database

    Tropospheric ozone (O3) is an air pollutant that costs ~$14-26 billion in global crop losses and is projected to worsen in the future. Potential sites of O3 sensitivity in maize were tested by growing 200 inbred lines, including the nested association mapping population founder lines, under ambient...

  13. Incorrect strain information for mouse cell lines: sequential influence of misidentification on sublines.

    PubMed

    Uchio-Yamada, Kozue; Kasai, Fumio; Ozawa, Midori; Kohara, Arihiro

    2017-03-01

    Misidentification or cross-contamination of cell lines can cause serious issues. Human cell lines have been authenticated by short tandem repeat profiling; however, mouse cell lines have not been adequately assessed. In this study, mouse cell lines registered with the JCRB cell bank were examined by simple sequence length polymorphism (SSLP) analysis to identify their strains. Based on comparisons with 7 major inbred strains, our results revealed their strains in 80 of 90 cell lines. However, 12 of the 80 cell lines (15%) were found to differ from registered information. Of them, 4 cell lines originated from the same mouse, which had been generated through mating between two different inbred strains. The genotype of the mouse sample had not been examined after the backcross, leading to strain misidentification in those cell lines. Although 8 other cell lines had been established as sublines of a BALB/c cell line, their SSLP profiles are similar to a Swiss cell line. This affects differences in genotypes between inbred and outbred strains. Because the use of inbred samples and interbreeding between strains are not involved in human materials, our results suggest that the cause and influence of misidentification in mouse cell lines are different from those in human.

  14. [Systematically induced effects of Tetranychus cinnabarinus infestation on chemical defense in Zea mays inbred lines].

    PubMed

    Zhu, Yu-xi; Yang, Qun-fang; Huang, Yu-bi; Li, Qing

    2015-09-01

    In the present study, we investigated the systematically induced production of defense-related compounds, including DIMBOA, total phenol, trypsin inhibitors (TI) and chymotrypsin inhibitor (CI), by Tetranychus cinnabarinus infestation in Zea mays. The first leaves of two corn in-bred line seedlings, the mite-tolerant line ' H1014168' and the mite-sensitive line 'H1014591', were sucked by T. cinnabarinus adult female for seven days, and then the contents of DIMBOA, total phenol, TI and CI were measured in the second leaf and in the roots, respectively. Results showed that as compared to the unsucked control, all contents of DIMBOA, total phenol, TI and CI induced by T. cinnabarinus sucking were significantly higher in the second leaf of both inbred lines as well as in the roots of the mite-tolerant 'H1014168'. However, in the roots of 'H1014591', these defense compounds had different trends, where there was a higher induction of TI and a lower level of total phenol than that of the healthy control, while had almost no difference in DIMBOA and CI. These findings suggested that the infestation of T. cinnabarinus could systematically induce accumulation of defense-related compounds, and this effect was stronger in the mite-tolerant inbred line than in the mite-sensitive inbred line.

  15. Development and Genetic Characterization of an Advanced Backcross-Nested Association Mapping (AB-NAM) Population of Wild × Cultivated Barley

    PubMed Central

    Nice, Liana M.; Steffenson, Brian J.; Brown-Guedira, Gina L.; Akhunov, Eduard D.; Liu, Chaochih; Kono, Thomas J. Y.; Morrell, Peter L.; Blake, Thomas K.; Horsley, Richard D.; Smith, Kevin P.; Muehlbauer, Gary J.

    2016-01-01

    The ability to access alleles from unadapted germplasm collections is a long-standing problem for geneticists and breeders. Here we developed, characterized, and demonstrated the utility of a wild barley advanced backcross-nested association mapping (AB-NAM) population. We developed this population by backcrossing 25 wild barley accessions to the six-rowed malting barley cultivar Rasmusson. The 25 wild barley parents were selected from the 318 accession Wild Barley Diversity Collection (WBDC) to maximize allelic diversity. The resulting 796 BC2F4:6 lines were genotyped with 384 SNP markers, and an additional 4022 SNPs and 263,531 sequence variants were imputed onto the population using 9K iSelect SNP genotypes and exome capture sequence of the parents, respectively. On average, 96% of each wild parent was introgressed into the Rasmusson background, and the population exhibited low population structure. While linkage disequilibrium (LD) decay (r2 = 0.2) was lowest in the WBDC (0.36 cM), the AB-NAM (9.2 cM) exhibited more rapid LD decay than comparable advanced backcross (28.6 cM) and recombinant inbred line (32.3 cM) populations. Three qualitative traits: glossy spike, glossy sheath, and black hull color were mapped with high resolution to loci corresponding to known barley mutants for these traits. Additionally, a total of 10 QTL were identified for grain protein content. The combination of low LD, negligible population structure, and high diversity in an adapted background make the AB-NAM an important tool for high-resolution gene mapping and discovery of novel allelic variation using wild barley germplasm. PMID:27182953

  16. Genome-Wide Patterns of Polymorphism in an Inbred Line of the African Malaria Mosquito Anopheles gambiae

    PubMed Central

    Turissini, David A.; Gamez, Stephanie; White, Bradley J.

    2014-01-01

    Anopheles gambiae is a major mosquito vector of malaria in Africa. Although increased use of insecticide-based vector control tools has decreased malaria transmission, elimination is likely to require novel genetic control strategies. It can be argued that the absence of an A. gambiae inbred line has slowed progress toward genetic vector control. In order to empower genetic studies and enable precise and reproducible experimentation, we set out to create an inbred line of this species. We found that amenability to inbreeding varied between populations of A. gambiae. After full-sib inbreeding for ten generations, we genotyped 112 individuals—56 saved prior to inbreeding and 56 collected after inbreeding—at a genome-wide panel of single nucleotide polymorphisms (SNPs). Although inbreeding dramatically reduced diversity across much of the genome, we discovered numerous, discrete genomic blocks that maintained high heterozygosity. For one large genomic region, we were able to definitively show that high diversity is due to the persistent polymorphism of a chromosomal inversion. Inbred lines in other eukaryotes often exhibit a qualitatively similar retention of polymorphism when typed at a small number of markers. Our whole-genome SNP data provide the first strong, empirical evidence supporting associative overdominance as the mechanism maintaining higher than expected diversity in inbred lines. Although creation of A. gambiae lines devoid of nearly all polymorphism may not be feasible, our results provide critical insights into how more fully isogenic lines can be created. PMID:25377942

  17. QTL analysis on rice grain appearance quality, as exemplifying the typical events of transgenic or backcrossing breeding

    PubMed Central

    Yan, Bao; Liu, Rongjia; Li, Yibo; Wang, Yan; Gao, Guanjun; Zhang, Qinglu; Liu, Xing; Jiang, Gonghao; He, Yuqing

    2014-01-01

    Rice grain shape and yield are usually controlled by multiple quantitative trait loci (QTL). This study used a set of F9–10 recombinant inbred lines (RILs) derived from a cross of Huahui 3 (Bt/Xa21) and Zhongguoxiangdao, and detected 27 QTLs on ten rice chromosomes. Among them, twelve QTLs responsive for grain shape/ or yield were mostly reproducibly detected and had not yet been reported before. Interestingly, the two known genes involved in the materials, with one insect-resistant Bt gene, and the other disease-resistant Xa21 gene, were found to closely link the QTLs responsive for grain shape and weight. The Bt fragment insertion was firstly mapped on the chromosome 10 in Huahui 3 and may disrupt grain-related QTLs resulting in weaker yield performance in transgenic plants. The introgression of Xa21 gene by backcrossing from donor material into receptor Minghui 63 may also contain a donor linkage drag which included minor-effect QTL alleles positively affecting grain shape and yield. The QTL analysis on rice grain appearance quality exemplified the typical events of transgenic or backcrossing breeding. The QTL findings in this study will in the future facilitate the gene isolation and breeding application for improvement of rice grain shape and yield. PMID:25320558

  18. QTL analysis on rice grain appearance quality, as exemplifying the typical events of transgenic or backcrossing breeding.

    PubMed

    Yan, Bao; Liu, Rongjia; Li, Yibo; Wang, Yan; Gao, Guanjun; Zhang, Qinglu; Liu, Xing; Jiang, Gonghao; He, Yuqing

    2014-09-01

    Rice grain shape and yield are usually controlled by multiple quantitative trait loci (QTL). This study used a set of F9-10 recombinant inbred lines (RILs) derived from a cross of Huahui 3 (Bt/Xa21) and Zhongguoxiangdao, and detected 27 QTLs on ten rice chromosomes. Among them, twelve QTLs responsive for grain shape/ or yield were mostly reproducibly detected and had not yet been reported before. Interestingly, the two known genes involved in the materials, with one insect-resistant Bt gene, and the other disease-resistant Xa21 gene, were found to closely link the QTLs responsive for grain shape and weight. The Bt fragment insertion was firstly mapped on the chromosome 10 in Huahui 3 and may disrupt grain-related QTLs resulting in weaker yield performance in transgenic plants. The introgression of Xa21 gene by backcrossing from donor material into receptor Minghui 63 may also contain a donor linkage drag which included minor-effect QTL alleles positively affecting grain shape and yield. The QTL analysis on rice grain appearance quality exemplified the typical events of transgenic or backcrossing breeding. The QTL findings in this study will in the future facilitate the gene isolation and breeding application for improvement of rice grain shape and yield.

  19. QTLs Analysis and Validation for Fiber Quality Traits Using Maternal Backcross Population in Upland Cotton.

    PubMed

    Ma, Lingling; Zhao, Yanpeng; Wang, Yumei; Shang, Lianguang; Hua, Jinping

    2017-01-01

    Cotton fiber is renewable natural fiber source for textile. Improving fiber quality is an essential goal for cotton breeding project. In present study, F 14 recombinant inbred line (RIL) population was backcrossed by the maternal parent to obtain a backcross (BC) population, derived from one Upland cotton hybrid. Three repetitive field trials were performed by randomized complete block design with two replicates in three locations in 2015, together with the BC population, common male parent and the RIL population. Totally, 26 QTLs in BC population explained 5.00-14.17% of phenotype variation (PV) and 37 quantitative trait loci (QTL) were detected in RIL population explaining 5.13-34.00% of PV. Seven common QTLs detected simultaneously in two populations explained PV from 7.69 to 23.05%. A total of 20 QTLs in present study verified the previous results across three environments in 2012. Particularly, qFL-Chr5-2 controlling fiber length on chromosome 5 explained 34.00% of PV, while qFL-Chr5-3 only within a 0.8 cM interval explained 13.93% of PV on average in multiple environments. These stable QTLs explaining great variation offered essential information for marker-assisted selection (MAS) to improve fiber quality traits. Lots of epistasis being detected in both populations acted as one of important genetic compositions of fiber quality traits.

  20. Two traditional maize inbred lines of contrasting technological abilities are discriminated by the seed flour proteome.

    PubMed

    Pinheiro, Carla; Sergeant, Kjell; Machado, Cátia M; Renaut, Jenny; Ricardo, Cândido P

    2013-07-05

    The seed proteome of two traditional maize inbred lines (pb269 and pb369) contrasting in grain hardness and in preferable use for bread-making was evaluated. The pb269 seeds, of flint type (i.e., hard endosperm), are preferably used by manufacturers, while pb369 (dent, soft endosperm) is rejected. The hypothesis that the content and relative amounts of specific proteins in the maize flour are relevant for such discrimination of the inbred lines was tested. The flour proteins were sequentially extracted following the Osborne fractionation (selective solubilization), and the four Osborne fractions were submitted to two-dimensional electrophoresis (2DE). The total amount of protein extracted from the seeds was not significantly different, but pb369 flour exhibited significantly higher proportions of salt-extracted proteins (globulins) and ethanol-extracted proteins (alcohol-soluble prolamins). The proteome analysis allowed discrimination between the two inbred lines, with pb269 demonstrating higher heterogeneity than pb369. From the 967 spots (358 common to both lines, 208 specific to pb269, and 401 specific to pb369), 588 were submitted to mass spectrometry (MS). Through the combined use of trypsin and chymotrypsin it was possible to identify proteins in 436 spots. The functional categorization in combination with multivariate analysis highlighted the most discriminant biological processes (carbohydrate metabolic process, response to stress, chitin catabolic process, oxidation-reduction process) and molecular function (nutrient reservoir activity). The inbred lines exhibited quantitative and qualitative differences in these categories. Differences were also revealed in the amounts, proportions, and distribution of several groups of storage proteins, which can have an impact on the organization of the protein body and endosperm hardness. For some proteins (granule-bound starch synthase-1, cyclophilin, zeamatin), a change in the protein solubility rather than in the

  1. Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines

    USDA-ARS?s Scientific Manuscript database

    Natural variation provides a powerful opportunity to study the genetic basis of biological traits. Brachypodium distachyon is a broadly distributed diploid model grass with a small genome and a large collection of diverse inbred lines. As a step towards understanding the genetic basis of the natura...

  2. Genetic mapping with an inbred line-derived F2 population in potato

    USDA-ARS?s Scientific Manuscript database

    Potato (Solanum tuberosum L.) is an important global food crop, for which tetrasomic inheritance and self-incompatibility have limited both genetic discovery and breeding gains. We report here on the creation of the first diploid inbred line-derived F2 population in potato, and demonstrate its utili...

  3. Cell wall composition and biomass recalcitrance differences within a genotypically diverse set of Brachypodium distachyon inbred lines

    DOE PAGES

    Cass, Cynthia L.; Lavell, Anastasiya A.; Santoro, Nicholas; ...

    2016-05-26

    Brachypodium distachyon ( Brachypodium) has emerged as a useful model system for studying traits unique to graminaceous species including bioenergy crop grasses owing to its amenability to laboratory experimentation and the availability of extensive genetic and germplasm resources. Considerable natural variation has been uncovered for a variety of traits including flowering time, vernalization responsiveness, and above-ground growth characteristics. However, cell wall composition differences remain underexplored. Therefore, we assessed cell wall-related traits relevant to biomass conversion to biofuels in seven Brachypodium inbred lines that were chosen based on their high level of genotypic diversity as well as available genome sequences andmore » recombinant inbred line (RIL) populations. Senesced stems plus leaf sheaths from these lines exhibited significant differences in acetyl bromide soluble lignin (ABSL), cell wall polysaccharide-derived sugars, hydroxycinnamates content, and syringyl:guaiacyl:p-hydroxyphenyl (S:G:H) lignin ratios. Free glucose, sucrose, and starch content also differed significantly in senesced stems, as did the amounts of sugars released from cell wall polysaccharides (digestibility) upon exposure to a panel of thermochemical pretreatments followed by hydrolytic enzymatic digestion. Correlations were identified between inbred line lignin compositions and plant growth characteristics such as biomass accumulation and heading date (HD), and between amounts of cell wall polysaccharides and biomass digestibility. Finally, stem cell wall p-coumarate and ferulate contents and free-sugars content changed significantly with increased duration of vernalization for some inbred lines. Taken together, these results show that Brachypodium displays substantial phenotypic variation with respect to cell wall composition and biomass digestibility, with some compositional differences correlating with growth characteristics. Moreover, besides influencing

  4. Cell wall composition and biomass recalcitrance differences within a genotypically diverse set of Brachypodium distachyon inbred lines

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Cass, Cynthia L.; Lavell, Anastasiya A.; Santoro, Nicholas

    Brachypodium distachyon ( Brachypodium) has emerged as a useful model system for studying traits unique to graminaceous species including bioenergy crop grasses owing to its amenability to laboratory experimentation and the availability of extensive genetic and germplasm resources. Considerable natural variation has been uncovered for a variety of traits including flowering time, vernalization responsiveness, and above-ground growth characteristics. However, cell wall composition differences remain underexplored. Therefore, we assessed cell wall-related traits relevant to biomass conversion to biofuels in seven Brachypodium inbred lines that were chosen based on their high level of genotypic diversity as well as available genome sequences andmore » recombinant inbred line (RIL) populations. Senesced stems plus leaf sheaths from these lines exhibited significant differences in acetyl bromide soluble lignin (ABSL), cell wall polysaccharide-derived sugars, hydroxycinnamates content, and syringyl:guaiacyl:p-hydroxyphenyl (S:G:H) lignin ratios. Free glucose, sucrose, and starch content also differed significantly in senesced stems, as did the amounts of sugars released from cell wall polysaccharides (digestibility) upon exposure to a panel of thermochemical pretreatments followed by hydrolytic enzymatic digestion. Correlations were identified between inbred line lignin compositions and plant growth characteristics such as biomass accumulation and heading date (HD), and between amounts of cell wall polysaccharides and biomass digestibility. Finally, stem cell wall p-coumarate and ferulate contents and free-sugars content changed significantly with increased duration of vernalization for some inbred lines. Taken together, these results show that Brachypodium displays substantial phenotypic variation with respect to cell wall composition and biomass digestibility, with some compositional differences correlating with growth characteristics. Moreover, besides influencing

  5. Identification of resistance to Maize rayado fino virus in maize inbred lines

    USDA-ARS?s Scientific Manuscript database

    Maize rayado fino virus (MRFV) is one of the most important virus diseases of maize in America. Severe yield losses, ranging from 10 to 50% in landraces to nearly 100% in contemporary cultivars, have been reported. Resistance has been reported in populations, but few inbred lines have been identifie...

  6. Characterization of early follicular cDNA library suggests evidence for genetic polymorphisms in the inbred strain C108 of Bombyx mori.

    PubMed

    Mills, D R; Goldsmith, M R

    2000-04-01

    Recent work towards the completion of a saturated molecular genetic linkage map for the lepidopteran silkworm, Bombyx mori (n = 28), has provided evidence for existing polymorphisms in the inbred strain C108. Two inbred parental strains, p50 and C108, were crossed to produce the F1 (P/C) hybrid offspring. The populations used in this project were comprised of a combination of 29 F2 (F1 x F1) and 31 reciprocal backcross (P/C x C/C, P/C x P/P) progeny. All restriction fragment length polymorphisms (RFLPs) for the initial analysis were hybridized with anonymous probes derived from a random early follicular cDNA (Rcf) library from Bombyx. A total of 19 Rcf probes were selected as showing scorable codominant polymorphic patterns when screened against F2 and backcross DNAs digested with the restriction enzymes EcoRI, HindIII, or PstI, and Southern blotted to nylon membranes for hybridization. Of the newly reported Rcf probes, 7 (37%) were characterized as producing 'simple' polymorphic patterns, while 12 (63%) were characterized as producing 'complex' polymorphic patterns. Further characterization of the complex patterns subdivided this group into two general classes: polymorphisms that contained an additional allele, and multiple bands that contained an easily scored two banded polymorphism. Because the extra allele class was limited to the (P/C x C/C) backcross progeny, it is suggested that the inbred parental strain C108 harbors polymorphic loci that are inherited in a simple Mendelian fashion. A genetic analysis discussing plausible origins and maintenance of these polymorphisms is presented.

  7. Germplasm enhancement of maize: A look into haploid induction and chromosomal doubling of haploids from temperate-adapted tropical sources

    USDA-ARS?s Scientific Manuscript database

    Doubled haploid technology is used to develop completely homozygous inbred lines, where each of the chromatids making up a chromosome pair are identical. Two inbred lines, PHB47 and PHZ51, were used to make backcrosses to 18 maize landraces, generating 36 populations. The landraces were chosen bas...

  8. Identification of multiple ear-colonizing insect and disease resistance in CIMMYT maize inbred lines with varying levels of silk maysin.

    PubMed

    Ni, Xinzhi; Krakowsky, Matthew D; Buntin, G David; Rector, Brian G; Guo, Baozhu; Snook, Maurice E

    2008-08-01

    Ninety four corn inbred lines selected from International Center for the Improvement of Maize and Wheat (CIMMYT) in Mexico were evaluated for levels of silk maysin in 2001 and 2002. Damage by major ear-feeding insects [i.e., corn earworm, Helicoverpa zea (Boddie) (Lepidoptera: Noctuidae); maize weevil, Sitophilus zeamais (Motschulsky) (Coleoptera: Curculionidae); brown stink bug, Euschistus servus (Say); southern green stink bugs, Nezara viridula (L.) (Heteroptera: Pentatomidae)], and common smut [Ustilago maydis DC (Corda)] infection on these inbred lines were evaluated in 2005 and 2006 under subtropical conditions at Tifton, GA. Ten inbred lines possessing good agronomic traits were also resistant to the corn earworm. The correlation between ear-feeding insect damage or smut infection and three phenotypic traits (silk maysin level, husk extension, and husk tightness of corn ears) was also examined. Corn earworm and stink bug damage was negatively correlated to husk extension, but not to either silk maysin levels or husk tightness. In combination with the best agronomic trait ratings that show the least corn earworm and stink bug damage, lowest smut infection rate, and good insect-resistant phenotypic traits (i.e., high maysin and good husk coverage and husk tightness), 10 best inbred lines (CML90, CML92, CML94, CML99, CML104, CML108, CML114, CML128, CML137, and CML373) were identified from the 94 lines examined. These selected inbred lines will be used for further examination of their resistance mechanisms and development of new corn germplasm that confers multiple ear-colonizing pest resistance.

  9. Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hirsch, Candice N.; Hirsch, Cory D.; Brohammer, Alex B.

    Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production of high-yielding hybrids, we generated a draft genome assembly of the inbred line PH207 to complement and compare with the existing B73 reference sequence. B73 is a founder of the Stiff Stalk germplasm pool, while PH207 is a founder of Iodent germplasm, both of which have contributed substantially to the production of temperate commercial maize and are combined to make heterotic hybrids. Comparison ofmore » these two assemblies revealed over 2500 genes present in only one of the two genotypes and 136 gene families that have undergone extensive expansion or contraction. Transcriptome profiling revealed extensive expression variation, with as many as 10,564 differentially expressed transcripts and 7128 transcripts expressed in only one of the two genotypes in a single tissue. Genotype-specific genes were more likely to have tissue/condition-specific expression and lower transcript abundance. The availability of a high-quality genome assembly for the elite maize inbred PH207 expands our knowledge of the breadth of natural genome and transcriptome variation in elite maize inbred lines across heterotic pools.« less

  10. Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize

    DOE PAGES

    Hirsch, Candice N.; Hirsch, Cory D.; Brohammer, Alex B.; ...

    2016-11-01

    Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production of high-yielding hybrids, we generated a draft genome assembly of the inbred line PH207 to complement and compare with the existing B73 reference sequence. B73 is a founder of the Stiff Stalk germplasm pool, while PH207 is a founder of Iodent germplasm, both of which have contributed substantially to the production of temperate commercial maize and are combined to make heterotic hybrids. Comparison ofmore » these two assemblies revealed over 2500 genes present in only one of the two genotypes and 136 gene families that have undergone extensive expansion or contraction. Transcriptome profiling revealed extensive expression variation, with as many as 10,564 differentially expressed transcripts and 7128 transcripts expressed in only one of the two genotypes in a single tissue. Genotype-specific genes were more likely to have tissue/condition-specific expression and lower transcript abundance. The availability of a high-quality genome assembly for the elite maize inbred PH207 expands our knowledge of the breadth of natural genome and transcriptome variation in elite maize inbred lines across heterotic pools.« less

  11. Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize[OPEN

    PubMed Central

    Soifer, Ilya; Barad, Omer; Shem-Tov, Doron; Baruch, Kobi; Lu, Fei; Hernandez, Alvaro G.; Wright, Chris L.; Koehler, Klaus; Buell, C. Robin; de Leon, Natalia

    2016-01-01

    Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production of high-yielding hybrids, we generated a draft genome assembly of the inbred line PH207 to complement and compare with the existing B73 reference sequence. B73 is a founder of the Stiff Stalk germplasm pool, while PH207 is a founder of Iodent germplasm, both of which have contributed substantially to the production of temperate commercial maize and are combined to make heterotic hybrids. Comparison of these two assemblies revealed over 2500 genes present in only one of the two genotypes and 136 gene families that have undergone extensive expansion or contraction. Transcriptome profiling revealed extensive expression variation, with as many as 10,564 differentially expressed transcripts and 7128 transcripts expressed in only one of the two genotypes in a single tissue. Genotype-specific genes were more likely to have tissue/condition-specific expression and lower transcript abundance. The availability of a high-quality genome assembly for the elite maize inbred PH207 expands our knowledge of the breadth of natural genome and transcriptome variation in elite maize inbred lines across heterotic pools. PMID:27803309

  12. Profiling polyphenols of two diploid strawberry (Fragaria vesca) inbred lines using UHPLC-HRMSn

    USDA-ARS?s Scientific Manuscript database

    Phenolic compounds in the fruits of two diploid strawberries (Fragaria vesca f. semperflorens) inbred lines-Ruegen F7-4 (a red fruited genotype) and YW5AF7 (a yellow fruited genotype) were characterized using ultra high-performance liquid chromatography in tandem with high resolution mass spectromet...

  13. Profiling polyphenols of two diploid strawberry (Fragaria vesca) inbred lines using UHPLC-HRMSn

    PubMed Central

    Sun, Jianghao; Liu, Xianjin; Yang, Tianbao; Slovin, Janet; Chen, Pei

    2013-01-01

    Phenolic compounds in the fruits of two diploid strawberries (Fragaria vesca f. semperflorens) inbred lines-Ruegen F7-4 (a red-fruited genotype) and YW5AF7 (a yellow-fruited genotype) were characterised using ultra-high-performance liquid chromatography coupled with tandem high-resolution mass spectrometry (UHPLC-HRMSn). The changes of anthocyanin composition during fruit development and between Ruegen F7-4 and YW5AF7 were studied. About 67 phenolic compounds, including taxifolin 3-O-arabinoside, glycosides of quercetin, kaempferol, cyanidin, pelargonidin, peonidin, ellagic acid derivatives, and other flavonols were identified in these two inbred lines. Compared to the regular octoploid strawberry, unique phenolic compounds were found in F. vesca fruits, such as taxifolin 3-O-arabinoside (both) and peonidin 3-O-malonylglucoside (Ruegen F7-4). The results provide the basis for comparative analysis of polyphenolic compounds in yellow and red diploid strawberries, as well as with the cultivated octoploid strawberries. PMID:24176345

  14. Yield and quality attributes of faba bean inbred lines grown under marginal environmental conditions of Sudan.

    PubMed

    Gasim, Seif; Hamad, Solafa A A; Abdelmula, Awadalla; Mohamed Ahmed, Isam A

    2015-11-01

    Faba beans (Vicia faba L.) represent an essential source of food protein for many people in Sudan, especially those who cannot afford to buy animal meat. The demand for faba bean seeds is greatly increased in recent years, and consequently its production area was extended southward where the climate is marginally suitable. Therefore, this study was aimed to evaluate seed yield and nutritional quality of five faba bean inbred lines grown under marginal environmental conditions of Sudan. The inbred lines have considerable (P ≤ 0.05) variability in yield and yield components, and seed chemical composition. The mean carbohydrate content was very high (501.1 g kg(-1)) and negatively correlated with seed yield, whereas the average protein content was relatively high (253.1 g kg(-1)) and positively correlated with seed yield. Globulin was the significant fraction (613.5 g kg(-1)protein) followed by albumin (200.2 g kg(-1)protein). Biplot analysis indicates that inbred lines Hudeiba/93-S5 and Ed-damar-S5 outscore other lines in terms of seed yield and nutritional quality. This study demonstrates that Hudeiba/93-S5 and Ed-damar-S5 are useful candidates in faba bean breeding program to terminate the protein deficiency malnutrition and provide healthy and nutritious meal for people living in subtropical areas.

  15. Genetic Analysis of Recombinant Inbred Lines For Sorghum Bicolor x Perennial S. Propinquum.

    USDA-ARS?s Scientific Manuscript database

    From an annual S. bicolor x perennial S. propinquum F2 population used in early-generation genetic analysis, we have produced and describe here a recombinant inbred line (RIL) population of 161 F5 genotypes that segregates for rhizomatousness and many other traits. The genetic map of the recombinant...

  16. Profiling polyphenols of two diploid strawberry (Fragaria vesca) inbred lines using UHPLC-HRMS(n.).

    PubMed

    Sun, Jianghao; Liu, Xianjin; Yang, Tianbao; Slovin, Janet; Chen, Pei

    2014-03-01

    Phenolic compounds in the fruits of two diploid strawberries (Fragaria vesca f. semperflorens) inbred lines-Ruegen F7-4 (a red-fruited genotype) and YW5AF7 (a yellow-fruited genotype) were characterised using ultra-high-performance liquid chromatography coupled with tandem high-resolution mass spectrometry (UHPLC-HRMS(n)). The changes of anthocyanin composition during fruit development and between Ruegen F7-4 and YW5AF7 were studied. About 67 phenolic compounds, including taxifolin 3-O-arabinoside, glycosides of quercetin, kaempferol, cyanidin, pelargonidin, peonidin, ellagic acid derivatives, and other flavonols were identified in these two inbred lines. Compared to the regular octoploid strawberry, unique phenolic compounds were found in F. vesca fruits, such as taxifolin 3-O-arabinoside (both) and peonidin 3-O-malonylglucoside (Ruegen F7-4). The results provide the basis for comparative analysis of polyphenolic compounds in yellow and red diploid strawberries, as well as with the cultivated octoploid strawberries. Published by Elsevier Ltd.

  17. Transpiration, and Nitrogen Uptake and Flow in Two Maize (Zea mays L.) Inbred Lines as Affected by Nitrogen Supply

    PubMed Central

    Niu, Junfang; Chen, Fanjun; Mi, Guohua; Li, Chunjian; Zhang, Fusuo

    2007-01-01

    Background and Aims The influence of two nitrogen (N) levels on growth, water relations, and N uptake and flow was investigated in two different inbred lines of maize (N-efficient Zi330 and N-inefficient Chen94-11) to analyse the differences in N uptake and cycling within a plant. Methods Xylem sap from different leaves of the inbred lines cultured in quartz sand was collected by application of pressure to the root system. Plant transpiration was measured on a daily basis by weighing five pots of each of the treatments. Key Results N-efficient Zi330 had a higher relative growth rate and water-use efficiency at both high (4 mm) and low (0·08 mm) N levels. At a high N level, the amount of N taken up was similar for the two inbred lines; the amount of N transported in the xylem and retranslocated in the phloem was slight greater in Chen94-11 than in Zi330. At a low N level, however, the total amount of N taken up, transported in the xylem and retranslocated in the phloem of Zi330 was 2·2, 2·7 and 2·7 times more, respectively, than that of Chen94-11. Independent of inbred line and N level, the amounts of N transported in the xylem and cycled in the phloem were far more than that taken up by roots at the same time. Low N supply shifted NO3−1 reduction towards the roots. The major nitrogenous compound in the xylem sap was NO3−1, when plants grew at the high N level, while amino acid-N was predominant when plants grew at the low N level. Conclusions The N-efficient maize inbred line Zi330 had a higher ability to take up N and cycle N within the plant than N-inefficient Chen94-11 when grown under N-deficiency. PMID:17088295

  18. Characterization of the Recombinant Inbred Line Population Derived from the Cross of Nipponbare/9311

    USDA-ARS?s Scientific Manuscript database

    As a part of the project entitled “Understanding the rice epigenome: From genes to genomes” funded by the National Science Foundation, a mapping population of 480 F6-8 recombinant inbred lines (RILs) derived from a cross of Nipponbare with 9311 (Nip/9311) was developed. Phenotyping important agronom...

  19. Evaluation of Combining Ability and Grain Quality of Quality Protein Maize Derived from U.S. Public Inbred Lines

    USDA-ARS?s Scientific Manuscript database

    Quality Protein Maize (QPM) has improved nutritional quality due to the opaque2 mutation as well as hard endosperm conferred by uncharacterized modifier genes. We have developed a series of QPM inbred lines based on crosses between public U.S. Corn Belt-adapted lines with QPM lines developed at the...

  20. Registration of a rice gene mapping population of Lemont X Jasmine 85 recombinant inbred lines

    USDA-ARS?s Scientific Manuscript database

    A mapping population developed from a cross of rice (Oryza sativa L.) tropical japonica cultivar ‘Lemont’ and indica cultivar ‘Jasmine 85’ was developed to facilitate genetic studies for important agronomic traits. The indica- and japonica-based rice recombinant inbred line (RIL) mapping population ...

  1. Depolymerization degree of water-extractable arabinoxylans in rye bread: characteristics of inbred lines used for breeding of bread cultivars.

    PubMed

    Cyran, Malgorzata R; Ceglińska, Alicja; Kolasińska, Irena

    2012-09-05

    The water-extractable arabinoxylans (WE AXs) present in rye bread govern its viscous properties, which may be related to reduced risk of cardiovascular diseases and diabetes. Breads made from rye cultivars generally exhibit higher AX-dependent extract viscosities (Cyran, M. R.; Saulnier, L. Food Chemistry2012, 131, 667-676) when compared with those produced from inbred lines used for their breeding. To give further details about this trend, the WE AXs were isolated from breads of lines and structurally characterized by HPSEC and (1)H NMR spectroscopy. The extract viscosities of endosperm and whole-meal breads were usually comparable, in contrast to those made from rye cultivars with higher viscosity of endosperm bread. The WE AXs present in breads obtained from inbred lines were characterized by the higher degradation degrees than those in breads from cultivars, as indicated by their HPSEC-RI profiles. This was associated with considerably lower proportions of 2-Xylp in their backbones. Besides, a level of endoxylanase activity in flours from inbred lines was much higher than that in flours from cultivars. Breeding of hybrid rye cultivars for production of high-viscosity bread requires the proper components. They may be preliminarily selected from populations with high WE AX contents and relatively low levels of endoxylanase activity by using the overall viscosity test for starting flours. However, further measurement of AX-dependent extract viscosity in test breads made from such lines may verify their usefulness completely.

  2. Development of the recombinant inbred line population of tropical japonica Lemont crossed with indica Jasmine 85

    USDA-ARS?s Scientific Manuscript database

    A recombinant inbred line (RIL) population of rice is routinely used in studying agronomically important genes, and is particularly useful for analyzing quantitative trait loci (QTL) since phenotypes can be assessed over years. Jasmine 85, a midseason aromatic long-grain indica rice cultivar develo...

  3. Genetic analyses of endoreduplication in Zea mays endosperm: evidence of sporophytic and zygotic maternal control.

    PubMed

    Dilkes, Brian P; Dante, Ricardo A; Coelho, Cintia; Larkins, Brian A

    2002-03-01

    Flow cytometry was used to assess the variability of endoreduplication in endosperms of maize inbred lines. Little variation was found between midwestern dent types, and high levels of endoreduplication were observed in popcorns. Endoreduplication is different between inbred lines by 13-18 days after pollination, and flow cytometric analysis of ploidy level was feasible until 20 DAP. To study the genetic regulation of endoreduplication, four inbreds were crossed to B73 and developing endosperms from both parental, reciprocal F(1), and backcross generations were subjected to flow cytometric analysis. Three measurements of endoreduplication were calculated from these data and analyzed as quantitative genetic traits. Multiple models of trait inheritance were considered including triploid, diploid, sporophytic maternal, and maternal and paternal zygotic nuclear inheritance. Maternal zygotic effects, often considered a form of parental imprinting, and maternal sporophytic effects were detected. To test the feasibility of introgressing a high endoreduplication phenotype into a midwestern dent inbred line, a backcross population was generated from B73 x Sg18. Parental and progeny endoreduplication levels were compared and heritabilities assessed. The heritabilities calculated from these data generally agree with the values calculated in the larger crossing experiments.

  4. Field screening of experimental corn hybrids and inbred lines for multiple ear-feeding insect resistance.

    PubMed

    Ni, Xinzhi; Xu, Wenwei; Krakowsky, Matthew D; Buntin, G David; Brown, Steve L; Lee, R Dewey; Coy, Anton E

    2007-10-01

    Identifying and using native insect resistance genes is the core of integrated pest management. In this study, 10 experimental corn, Zea mays L., hybrids and 10 inbred lines were screened for resistance to major ear-feeding insects in the southeastern Coastal Plain region of the United States during 2004 and 2005. Ear-feeding insect damage was assessed at harvest by visual damage rating for the corn earworm, Helicoverpa zea (Boddie), and by the percentage of kernels damaged by the maize weevil, Sitophilus zeamais Motschulsky, and stink bugs [combination of Euschistus servus (Say) and southern green stink bug, Nezara viridula (L.)]. Among the eight inbred lines and two control populations examined, C3S1B73-5b was resistant to corn earworm, maize weevil, and stink bugs. In contrast, C3S1B73-4 was resistant to corn earworm and stink bugs, but not to maize weevil. In a similar manner, the corn hybrid S1W*CML343 was resistant to all three ear-feeding insects, whereas hybrid C3S1B73-3*Tx205 was resistant to corn earworm and maize weevil in both growing seasons, but susceptible to stink bugs in 2005. The silk-feeding bioassay showed that corn earworm developed better on corn silk than did fall armyworm. Among all phenotypic traits examined (i.e., corn ear size, husk extension, and husk tightness), only corn ear size was negatively correlated to corn earworm damage in the inbred lines examined, whereas only husk extension (i.e., coverage) was negatively correlated to both corn earworm and maize weevil damage on the experimental hybrids examined. Such information could be used to establish a baseline for developing agronomically elite corn germplasm that confers multiple ear-feeding insect resistance.

  5. Genome-wide transcriptomic analysis of response to low temperature reveals candidate genes determining divergent cold-sensitivity of maize inbred lines.

    PubMed

    Sobkowiak, Alicja; Jończyk, Maciej; Jarochowska, Emilia; Biecek, Przemysław; Trzcinska-Danielewicz, Joanna; Leipner, Jörg; Fronk, Jan; Sowiński, Paweł

    2014-06-01

    Maize, despite being thermophyllic due to its tropical origin, demonstrates high intraspecific diversity in cold-tolerance. To search for molecular mechanisms of this diversity, transcriptomic response to cold was studied in two inbred lines of contrasting cold-tolerance. Microarray analysis was followed by extensive statistical elaboration of data, literature data mining, and gene ontology-based classification. The lines used had been bred earlier specifically for determination of QTLs for cold-performance of photosynthesis. This allowed direct comparison of present transcriptomic data with the earlier QTL mapping results. Cold-treated (14 h at 8/6 °C) maize seedlings of cold-tolerant ETH-DH7 and cold-sensitive ETH-DL3 lines at V3 stage showed strong, consistent response of the third leaf transcriptome: several thousand probes showed similar, statistically significant change in both lines, while only tens responded differently in the two lines. The most striking difference between the responses of the two lines to cold was the induction of expression of ca. twenty genes encoding membrane/cell wall proteins exclusively in the cold-tolerant ETH-DH7 line. The common response comprised mainly repression of numerous genes related to photosynthesis and induction of genes related to basic biological activity: transcription, regulation of gene expression, protein phosphorylation, cell wall organization. Among the genes showing differential response, several were close to the QTL regions identified in earlier studies with the same inbred lines and associated with biometrical, physiological or biochemical parameters. These transcripts, including two apparently non-protein-coding ones, are particularly attractive candidates for future studies on mechanisms determining divergent cold-tolerance of inbred maize lines.

  6. Genome-Wide Association Study Identifies Candidate Genes That Affect Plant Height in Chinese Elite Maize (Zea mays L.) Inbred Lines

    PubMed Central

    Wang, Jianjun; Liu, Changlin; Li, Mingshun; Zhang, Degui; Bai, Li; Zhang, Shihuang; Li, Xinhai

    2011-01-01

    Background The harvest index for many crops can be improved through introduction of dwarf stature to increase lodging resistance, combined with early maturity. The inbred line Shen5003 has been widely used in maize breeding in China as a key donor line for the dwarf trait. Also, one major quantitative trait locus (QTL) controlling plant height has been identified in bin 5.05–5.06, across several maize bi-parental populations. With the progress of publicly available maize genome sequence, the objective of this work was to identify the candidate genes that affect plant height among Chinese maize inbred lines with genome wide association studies (GWAS). Methods and Findings A total of 284 maize inbred lines were genotyped using over 55,000 evenly spaced SNPs, from which a set of 41,101 SNPs were filtered with stringent quality control for further data analysis. With the population structure controlled in a mixed linear model (MLM) implemented with the software TASSEL, we carried out a genome-wide association study (GWAS) for plant height. A total of 204 SNPs (P≤0.0001) and 105 genomic loci harboring coding regions were identified. Four loci containing genes associated with gibberellin (GA), auxin, and epigenetic pathways may be involved in natural variation that led to a dwarf phenotype in elite maize inbred lines. Among them, a favorable allele for dwarfing on chromosome 5 (SNP PZE-105115518) was also identified in six Shen5003 derivatives. Conclusions The fact that a large number of previously identified dwarf genes are missing from our study highlights the discovery of the consistently significant association of the gene harboring the SNP PZE-105115518 with plant height (P = 8.91e-10) and its confirmation in the Shen5003 introgression lines. Results from this study suggest that, in the maize breeding schema in China, specific alleles were selected, that have played important roles in maize production. PMID:22216221

  7. Differential hormonal and gene expression dynamics in two inbred sunflower lines with contrasting dormancy level.

    PubMed

    Roselló, Paula L; Vigliocco, Ana E; Andrade, Andrea M; Riera, Natalí V; Calafat, Mario; Molas, María L; Alemano, Sergio G

    2016-05-01

    Seed germination and dormancy are tightly regulated by hormone metabolism and signaling pathway. We investigated the endogenous content of abscisic acid (ABA), its catabolites, and gibberellins (GAs), as well as the expression level of certain ABA and GAs metabolic and signaling genes in embryo of dry and imbibed cypselas of inbred sunflower (Helianthus annuus L., Asteraceae) lines: B123 (dormant) and B91 (non-dormant). Under our experimental conditions, the expression of RGL2 gene might be related to the ABA peak in B123 line at 3 h of imbibition. Indeed, RGL2 transcripts are absent in dry and early embedded cypselas of the non-dormant line B91. ABA increase was accompanied by a significant ABA-Glucosyl ester (ABA-GE) and phaseic acid (PA) (two ABA catabolites) decrease in B123 line (3 h) which indicates that ABA metabolism seems to be more active in this line, and that it would be involved in the imposition and maintenance of sunflower seed dormancy, as it has been reported for many species. Finally, an increase of bioactive GAs (GA1 and GA3) occurs at 12 h of imbibition in both lines after a decrease in ABA content. This study shows the first report about the RGL2 tissue-specific gene expression in sunflower inbred lines with contrasting dormancy level. Furthermore, our results provide evidence that ABA and GAs content and differential expression of metabolism and signaling genes would be interacting in seed dormancy regulation through a mechanism of action related to embryo itself. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  8. Advanced backcross QTL mapping of resistance to Fusarium head blight and plant morphological traits in a Triticum macha × T. aestivum population.

    PubMed

    Buerstmayr, Maria; Lemmens, Marc; Steiner, Barbara; Buerstmayr, Hermann

    2011-07-01

    While many reports on genetic analysis of Fusarium head blight (FHB) resistance in bread wheat have been published during the past decade, only limited information is available on FHB resistance derived from wheat relatives. In this contribution, we report on the genetic analysis of FHB resistance derived from Triticum macha (Georgian spelt wheat). As the origin of T. macha is in the Caucasian region, it is supposed that its FHB resistance differs from other well-investigated resistance sources. To introduce valuable alleles from the landrace T. macha into a modern genetic background, we adopted an advanced backcross QTL mapping scheme. A backcross-derived recombinant-inbred line population of 321 BC(2)F(3) lines was developed from a cross of T. macha with the Austrian winter wheat cultivar Furore. The population was evaluated for Fusarium resistance in seven field experiments during four seasons using artificial inoculations. A total of 300 lines of the population were genetically fingerprinted using SSR and AFLP markers. The resulting linkage map covered 33 linkage groups with 560 markers. Five novel FHB-resistance QTL, all descending from T. macha, were found on four chromosomes (2A, 2B, 5A, 5B). Several QTL for morphological and developmental traits were mapped in the same population, which partly overlapped with FHB-resistance QTL. Only the 2BL FHB-resistance QTL co-located with a plant height QTL. The largest-effect FHB-resistance QTL in this population mapped at the spelt-type locus on chromosome 5A and was associated with the wild-type allele q, but it is unclear whether q has a pleiotropic effect on FHB resistance or is closely linked to a nearby resistance QTL.

  9. Molecular mapping of four blast resistance genes using recombinant inbred lines of 93-11 and nipponbare

    USDA-ARS?s Scientific Manuscript database

    Molecular mapping of new blast resistance genes is important for developing resistant rice cultivars using marker-assisted selection. In this study, 259 recombinant inbred lines (RILs) were developed from a cross between Nipponbare and 93-11, and were used to construct a 1165.8-cM linkage map with 1...

  10. Proteomic Analysis of Silk Viability in Maize Inbred Lines and Their Corresponding Hybrids.

    PubMed

    Ma, Zhihui; Qin, Yongtian; Wang, Yafei; Zhao, Xiaofeng; Zhang, Fangfang; Tang, Jihua; Fu, Zhiyuan

    2015-01-01

    A long period of silk viability is critical for a good seed setting rate in maize (Zea mays L.), especially for inbred lines and hybrids with a long interval between anthesis and silking. To explore the molecular mechanism of silk viability and its heterosis, three inbred lines with different silk viability characteristics (Xun928, Lx9801, and Zong3) and their two hybrids (Xun928×Zong3 and Lx9801×Zong3) were analyzed at different developmental stages by a proteomic method. The differentially accumulated proteins were identified by mass spectrometry and classified into metabolism, protein biosynthesis and folding, signal transduction and hormone homeostasis, stress and defense responses, and cellular processes. Proteins involved in nutrient (methionine) and energy (ATP) supply, which support the pollen tube growth in the silk, were important for silk viability and its heterosis. The additive and dominant effects at a single locus, as well as complex epistatic interactions at two or more loci in metabolic pathways, were the primary contributors for mid-parent heterosis of silk viability. Additionally, the proteins involved in the metabolism of anthocyanins, which indirectly negatively regulate local hormone accumulation, were also important for the mid-parent heterosis of silk viability. These results also might imply the developmental dependence of heterosis, because many of the differentially accumulated proteins made distinct contributions to the heterosis of silk viability at specific developmental stages.

  11. Genetic variation and population structure of maize inbred lines adapted to the mid-altitude sub-humid maize agro-ecology of Ethiopia using single nucleotide polymorphic (SNP) markers.

    PubMed

    Ertiro, Berhanu Tadesse; Semagn, Kassa; Das, Biswanath; Olsen, Michael; Labuschagne, Maryke; Worku, Mosisa; Wegary, Dagne; Azmach, Girum; Ogugo, Veronica; Keno, Tolera; Abebe, Beyene; Chibsa, Temesgen; Menkir, Abebe

    2017-10-12

    Molecular characterization is important for efficient utilization of germplasm and development of improved varieties. In the present study, we investigated the genetic purity, relatedness and population structure of 265 maize inbred lines from the Ethiopian Institute of Agricultural Research (EIAR), the International Maize and Wheat Improvement Centre (CIMMYT) and the International Institute of Tropical Agriculture (IITA) using 220,878 single nucleotide polymorphic (SNP) markers obtained using genotyping by sequencing (GBS). Only 22% of the inbred lines were considered pure with <5% heterogeneity, while the remaining 78% of the inbred lines had a heterogeneity ranging from 5.1 to 31.5%. Pairwise genetic distances among the 265 inbred lines varied from 0.011 to 0.345, with 89% of the pairs falling between 0.301 and 0.345. Only <1% of the pairs had a genetic distance lower than 0.200, which included 14 pairs of sister lines that were nearly identical. Relative kinship analysis showed that the kinship coefficients for 59% of the pairs of lines was close to zero, which agrees with the genetic distance estimates. Principal coordinate analysis, discriminant analysis of principal components (DAPC) and the model-based population structure analysis consistently suggested the presence of three groups, which generally agreed with pedigree information (genetic background). Although not distinct enough, the SNP markers showed some level of separation between the two CIMMYT heterotic groups A and B established based on pedigree and combining ability information. The high level of heterogeneity detected in most of the inbred lines suggested the requirement for purification or further inbreeding except those deliberately maintained at early inbreeding level. The genetic distance and relative kinship analysis clearly indicated the uniqueness of most of the inbred lines in the maize germplasm available for breeders in the mid-altitude maize breeding program of Ethiopia. Results from

  12. Integrated analysis of mRNA and miRNA expression profiling in rice backcrossed progenies (BC2F12) with different plant height

    PubMed Central

    Cao, Aqin; Jin, Jie; Li, Shaoqing

    2017-01-01

    Inter-specific hybridization and backcrossing commonly occur in plants. The use of progeny generated from inter-specific hybridization and backcrossing has been developed as a novel model system to explore gene expression divergence. The present study investigated the analysis of gene expression and miRNA regulation in backcrossed introgression lines constructed from cultivated and wild rice. High-throughput sequencing was used to compare gene and miRNA expression profiles in three progeny lines (L1710, L1817 and L1730), with different plant heights resulting from the backcrossing of introgression lines (BC2F12) and their parents (O. sativa and O. longistaminata). A total of 25,387 to 26,139 mRNAs and 379 to 419 miRNAs were obtained in these rice lines. More differentially expressed genes and miRNAs were detected in progeny/O. longistaminata comparison groups than in progeny/O. sativa comparison groups. Approximately 80% of the genes and miRNAs showed expression level dominance to O. sativa, indicating that three progeny lines were closer to the recurrent parent, which might be influenced by their parental genome dosage. Approximately 16% to 64% of the differentially expressed miRNAs possessing coherent target genes were predicted, and many of these miRNAs regulated multiple target genes. Most genes were up-regulated in progeny lines compared with their parents, but down-regulated in the higher plant height line in the comparison groups among the three progeny lines. Moreover, certain genes related to cell walls and plant hormones might play crucial roles in the plant height variations of the three progeny lines. Taken together, these results provided valuable information on the molecular mechanisms of hybrid backcrossing and plant height variations based on the gene and miRNA expression levels in the three progeny lines. PMID:28859136

  13. Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize

    USDA-ARS?s Scientific Manuscript database

    Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production of high-yielding hybrids, we generated a draft geno...

  14. The Genetic Basis of Plant Architecture in 10 Maize Recombinant Inbred Line Populations.

    PubMed

    Pan, Qingchun; Xu, Yuancheng; Li, Kun; Peng, Yong; Zhan, Wei; Li, Wenqiang; Li, Lin; Yan, Jianbing

    2017-10-01

    Plant architecture is a key factor affecting planting density and grain yield in maize ( Zea mays ). However, the genetic mechanisms underlying plant architecture in diverse genetic backgrounds have not been fully addressed. Here, we performed a large-scale phenotyping of 10 plant architecture-related traits and dissected the genetic loci controlling these traits in 10 recombinant inbred line populations derived from 14 diverse genetic backgrounds. Nearly 800 quantitative trait loci (QTLs) with major and minor effects were identified as contributing to the phenotypic variation of plant architecture-related traits. Ninety-two percent of these QTLs were detected in only one population, confirming the diverse genetic backgrounds of the mapping populations and the prevalence of rare alleles in maize. The numbers and effects of QTLs are positively associated with the phenotypic variation in the population, which, in turn, correlates positively with parental phenotypic and genetic variations. A large proportion (38.5%) of QTLs was associated with at least two traits, suggestive of the frequent occurrence of pleiotropic loci or closely linked loci. Key developmental genes, which previously were shown to affect plant architecture in mutant studies, were found to colocalize with many QTLs. Five QTLs were further validated using the segregating populations developed from residual heterozygous lines present in the recombinant inbred line populations. Additionally, one new plant height QTL, qPH3 , has been fine-mapped to a 600-kb genomic region where three candidate genes are located. These results provide insights into the genetic mechanisms controlling plant architecture and will benefit the selection of ideal plant architecture in maize breeding. © 2017 American Society of Plant Biologists. All Rights Reserved.

  15. Romanian Maize (Zea mays) Inbred Lines as a Source of Genetic Diversity in SE Europe, and Their Potential in Future Breeding Efforts

    PubMed Central

    Haș, Voichița; Haș, Ioan; Miclăuș, Mihai

    2013-01-01

    Maize has always been under constant human selection ever since it had been domesticated. Intensive breeding programs that resulted in the massive use of hybrids nowadays have started in the 60s. That brought significant yield increases but reduced the genetic diversity at the same time. Consequently, breeders and researchers alike turned their attention to national germplasm collections established decades ago in many countries, as they may hold allelic variations that could prove useful for future improvements. These collections are mainly composed of inbred lines originating from well-adapted local open pollinated varieties. However, there is an overall lack of data in the literature about the genetic diversity of maize in SE Europe, and its potential for future breeding efforts. There are no data, whatsoever, on the nutritional quality of the grain, primarily dictated by the zein proteins. We therefore sought to use the Romanian maize germplasm as an entry point in understanding the molecular make-up of maize in this part of Europe. By using 80 SSR markers, evenly spread throughout the genome, on 82 inbred lines from various parts of the country, we were able to decipher population structure and the existing relationships between those and the eight international standards used, including the reference sequenced genome B73. Corroborating molecular data with a standardized morphological, physiological, and biochemical characterization of all 90 inbred lines, this is the first comprehensive such study on the existing SE European maize germplasm. The inbred lines we present here are an important addition to the ever-shrinking gene pool that the breeding programs are faced-with, because of the allelic richness they hold. They may serve as parental lines in crosses that will lead to new hybrids, characterized by a high level of heterosis, nationwide and beyond, due to their existing relationship with the international germplasm. PMID:24392016

  16. Additive effects of two quantitative trait loci that confer Rhopalosiphum maidis (corn leaf aphid) resistance in maize inbred line Mo17

    PubMed Central

    Betsiashvili, Mariam; Ahern, Kevin R.; Jander, Georg

    2015-01-01

    Plants show considerable within-species variation in their resistance to insect herbivores. In the case of Zea mays (cultivated maize), Rhopalosiphum maidis (corn leaf aphids) produce approximately twenty times more progeny on inbred line B73 than on inbred line Mo17. Genetic mapping of this difference in maize aphid resistance identified quantitative trait loci (QTL) on chromosomes 4 and 6, with the Mo17 allele reducing aphid reproduction in each case. The chromosome 4 QTL mapping interval includes several genes involved in the biosynthesis of DIMBOA (2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one), a maize defensive metabolite that also is required for callose accumulation in response to aphid feeding. Consistent with the known association of callose with plant defence against aphids, R. maidis reproduction on B73×Mo17 recombinant inbred lines was negatively correlated with both DIMBOA content and callose formation. Further genetic mapping, as well as experiments with near-isogenic lines, confirmed that the Mo17 allele causes increased DIMBOA accumulation relative to the B73 allele. The chromosome 6 aphid resistance QTL functions independently of DIMBOA accumulation and has an effect that is additive to that of the chromosome 4 QTL. Thus, at least two separate defence mechanisms account for the higher level of R. maidis resistance in Mo17 compared with B73. PMID:25249072

  17. Proteomic Analysis of Silk Viability in Maize Inbred Lines and Their Corresponding Hybrids

    PubMed Central

    Wang, Yafei; Zhao, Xiaofeng; Zhang, Fangfang; Tang, Jihua; Fu, Zhiyuan

    2015-01-01

    A long period of silk viability is critical for a good seed setting rate in maize (Zea mays L.), especially for inbred lines and hybrids with a long interval between anthesis and silking. To explore the molecular mechanism of silk viability and its heterosis, three inbred lines with different silk viability characteristics (Xun928, Lx9801, and Zong3) and their two hybrids (Xun928×Zong3 and Lx9801×Zong3) were analyzed at different developmental stages by a proteomic method. The differentially accumulated proteins were identified by mass spectrometry and classified into metabolism, protein biosynthesis and folding, signal transduction and hormone homeostasis, stress and defense responses, and cellular processes. Proteins involved in nutrient (methionine) and energy (ATP) supply, which support the pollen tube growth in the silk, were important for silk viability and its heterosis. The additive and dominant effects at a single locus, as well as complex epistatic interactions at two or more loci in metabolic pathways, were the primary contributors for mid-parent heterosis of silk viability. Additionally, the proteins involved in the metabolism of anthocyanins, which indirectly negatively regulate local hormone accumulation, were also important for the mid-parent heterosis of silk viability. These results also might imply the developmental dependence of heterosis, because many of the differentially accumulated proteins made distinct contributions to the heterosis of silk viability at specific developmental stages. PMID:26630375

  18. Characterization of conditionally expressed mutants affecting age-specific survival in inbred lines of Drosophila melanogaster: lethal conditions and temperature-sensitive periods.

    PubMed Central

    Vermeulen, C J; Bijlsma, R

    2004-01-01

    The specific genetic basis of inbreeding depression is poorly understood. To address this question, two conditionally expressed lethal effects that were found to cause line-specific life span reductions in two separate inbred lines of Drosophila melanogaster were characterized phenotypically and genetically in terms of whether the accelerated mortality effects are dominant or recessive. The mortality effect in one line (I4) is potentially a temperature-sensitive semilethal that expresses in adult males only and is partially dominant. The other line (I10) responds as one would expect for a recessive lethal. It requires a cold shock for expression and is cold sensitive. Flies exhibiting this lethal condition responded as pupae and freshly eclosed imagoes. The effect is recessive in both males and females. The expression of the lethal effects in both lines is highly dependent upon environmental conditions. These results will serve as a basis for more detailed and mechanistic genetic research on inbreeding depression and are relevant to sex- and environment-specific effects on life span observed in quantitative trait loci studies using inbred lines. PMID:15280238

  19. Fine mapping of a dominantly inherited powdery mildew resistance major-effect QTL, Pm1.1, in cucumber identifies a 41.1 kb region containing two tandemly arrayed cysteine-rich receptor-like protein kinase genes

    USDA-ARS?s Scientific Manuscript database

    Powdery mildew (PM) is a severe fungal disease in cucumber, but the molecular genetic mechanisms of PM resistance in cucumber are still poorly understood. In this study, through marker-assisted backcrossing with an elite susceptible inbred line D8, we developed a single segment substitution line SSS...

  20. Identification of QTLs underlying seed micronutrients accumulation in 'MD96-5722' by 'Spencer' recombinant inbred lines of soybean

    USDA-ARS?s Scientific Manuscript database

    Genetic mapping of quantitative trait loci (QTL) associated with seed nutrition levels is almost non-existent. The objective of this study was to identify QTLs associated with seed micronutrients accumulation (concentration) in a population of 92 F5:7 recombinant inbred lines (RILs) that derived fro...

  1. Genetic regulation of cold-induced albinism in the maize inbred line A661

    PubMed Central

    Rodríguez, Víctor M.; Velasco, Pablo; Garrido, José L.; Revilla, Pedro; Ordás, Amando; Butrón, Ana

    2013-01-01

    In spite of multiple studies elucidating the regulatory pathways controlling chlorophyll biosynthesis and photosynthetic activity, little is known about the molecular mechanism regulating cold-induced chlorosis in higher plants. Herein the characterization of the maize inbred line A661 which shows a cold-induced albino phenotype is reported. The data show that exposure of seedlings to low temperatures during early leaf biogenesis led to chlorophyll losses in this inbred. A661 shows a high plasticity, recovering resting levels of photosynthesis activity when exposed to optimal temperatures. Biochemical and transcriptome data indicate that at suboptimal temperatures chlorophyll could not be fully accommodated in the photosynthetic antenna in A661, remaining free in the chloroplast. The accumulation of free chlorophyll activates the expression of an early light inducible protein (elip) gene which binds chlorophyll to avoid cross-reactions that could lead to the generation of harmful reactive oxygen species. Higher levels of the elip transcript were observed in plants showing a cold-induced albino phenotype. Forward genetic analysis reveals that a gene located on the short arm of chromosome 2 regulates this protective mechanism. PMID:23881393

  2. Combining ability of tropical and temperate inbred lines of popcorn.

    PubMed

    da Silva, V Q R; do Amaral Júnior, A T; Gonçalves, L S A; Freitas Júnior, S P; Candido, L S; Vittorazzi, C; Moterle, L M; Vieira, R A; Scapim, C A

    2010-08-31

    In Brazil, using combining ability of popcorn genotypes to achieve superior hybrids has been unsuccessful because the local genotypes are all members of the same heterotic group. To overcome this constraint, 10 lines (P(1) to P(10)) with different adaptations to tropical or temperate edaphoclimatic environments were used to obtain 45 F(1) hybrids in a complete diallel. These hybrids and three controls were evaluated in two environments in Rio de Janeiro State. Grain yield (GY), popping expansion (PE), plant height (PH), ear height (EH), and days to silking (FL) were evaluated in randomized complete blocks with three replications. Significant differences between genotypes (P inbred lines that improved GY were P(3) and P(4), unlike P(8), P(9) and P(10), which improved PE, and P(2), which improved both PE and GY. The additive effects were much more important for PE than for GY. The hybrid combinations gave positive estimates of heterosis for GY but not for PE.

  3. The Genetic Basis of Plant Architecture in 10 Maize Recombinant Inbred Line Populations1[OPEN

    PubMed Central

    Pan, Qingchun; Xu, Yuancheng; Peng, Yong; Zhan, Wei; Li, Wenqiang; Li, Lin

    2017-01-01

    Plant architecture is a key factor affecting planting density and grain yield in maize (Zea mays). However, the genetic mechanisms underlying plant architecture in diverse genetic backgrounds have not been fully addressed. Here, we performed a large-scale phenotyping of 10 plant architecture-related traits and dissected the genetic loci controlling these traits in 10 recombinant inbred line populations derived from 14 diverse genetic backgrounds. Nearly 800 quantitative trait loci (QTLs) with major and minor effects were identified as contributing to the phenotypic variation of plant architecture-related traits. Ninety-two percent of these QTLs were detected in only one population, confirming the diverse genetic backgrounds of the mapping populations and the prevalence of rare alleles in maize. The numbers and effects of QTLs are positively associated with the phenotypic variation in the population, which, in turn, correlates positively with parental phenotypic and genetic variations. A large proportion (38.5%) of QTLs was associated with at least two traits, suggestive of the frequent occurrence of pleiotropic loci or closely linked loci. Key developmental genes, which previously were shown to affect plant architecture in mutant studies, were found to colocalize with many QTLs. Five QTLs were further validated using the segregating populations developed from residual heterozygous lines present in the recombinant inbred line populations. Additionally, one new plant height QTL, qPH3, has been fine-mapped to a 600-kb genomic region where three candidate genes are located. These results provide insights into the genetic mechanisms controlling plant architecture and will benefit the selection of ideal plant architecture in maize breeding. PMID:28838954

  4. Induced cytomictic diversity in maize (Zea mays L.) inbred.

    PubMed

    Rai, Prashant Kumar; Kumar, Girjesh; Tripathi, Avinash

    2010-01-01

    Mutation breeding has been used for improving oligogenic and polygenic characters, disease resistance and quantitative characters including yielding ability. The cytological stability of maize inbred lines is an important consideration in view of their extensive use in genetics and plant breeding research. Investigation in Zea mays L. confirms that the migration of chromosomes is a real event that cannot be misunderstood as an artifact produced by fixation or mechanical injuries. During present investigation, we found that out of six inbred lines of Zea mays L. viz. CM-135, CM-136, CM-137, CM-138, CM-142 and CM-213 at various treatment doses of gamma irradiations viz. 200, 400 and 600 Gy, some of the plants of inbred line CM- 138 at 200 Gy dose displayed characteristic cytoplasmic connections during all the stages of meiosis. Four plants from this treatment set were found to be engaged in a rare phenomenon reported as "Cytomixis". It elucidates that in inbred of Zea mays L., induced cytomixis through gamma rays treatment may be considered to be a possible source of production of aneuploid and polyploid gametes. This phenomenon may have several applications in Zea mays L. improvement in the sense of diversity and ever yield potential.

  5. Histological and transcript analyses of intact somatic embryos in an elite maize (Zea mays L.) inbred line Y423.

    PubMed

    Liu, Beibei; Su, Shengzhong; Wu, Ying; Li, Ying; Shan, Xiaohui; Li, Shipeng; Liu, Hongkui; Dong, Haixiao; Ding, Meiqi; Han, Junyou; Yuan, Yaping

    2015-07-01

    Intact somatic embryos were obtained from an elite maize inbred line Y423, bred in our laboratory. Using 13-day immature embryos after self-pollination as explants, and after 4-5 times subculture, a large number of somatic embryos were detected on the surface of the embryonic calli on the medium. The intact somatic embryos were transferred into the differential medium, where the plantlets regenerated with shoots and roots forming simultaneously. Histological analysis and scanning electron micrographs confirmed the different developmental stages of somatic embryogenesis, including globular-shaped embryo, pear-shaped embryo, scutiform embryo, and mature embryo. cDNA-amplified fragment length polymorphism (cDNA-AFLP) was used for comparative transcript profiling between embryogenic and non-embryogenic calli of a new elite maize inbred line Y423 during somatic embryogenesis. Differentially expressed genes were cloned and sequenced. Gene Ontology analysis of 117 candidate genes indicated their involvement in cellular component, biological process and molecular function. Nine of the candidate genes were selected. The changes in their expression levels during embryo induction and regeneration were analyzed in detail using quantitative real-time PCR. Two full-length cDNA sequences, encoding ZmSUF4 (suppressor of fir 4-like protein) and ZmDRP3A (dynamin-related protein), were cloned successfully from intact somatic embryos of the elite inbred maize line Y423. Here, a procedure for maize plant regeneration from somatic embryos is described. Additionally, the possible roles of some of these genes during the somatic embryogenesis has been discussed. This study is a systematic analysis of the cellular and molecular mechanism during the formation of intact somatic embryos in maize. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

  6. Recurrent parent genome recovery analysis in a marker-assisted backcrossing program of rice (Oryza sativa L.).

    PubMed

    Miah, Gous; Rafii, Mohd Y; Ismail, Mohd R; Puteh, Adam B; Rahim, Harun A; Latif, Mohammad A

    2015-02-01

    Backcross breeding is the most commonly used method for incorporating a blast resistance gene into a rice cultivar. Linkage between the resistance gene and undesirable units can persist for many generations of backcrossing. Marker-assisted backcrossing (MABC) along with marker-assisted selection (MAS) contributes immensely to overcome the main limitation of the conventional breeding and accelerates recurrent parent genome (RPG) recovery. The MABC approach was employed to incorporate (a) blast resistance gene(s) from the donor parent Pongsu Seribu 1, the blast-resistant local variety in Malaysia, into the genetic background of MR219, a popular high-yielding rice variety that is blast susceptible, to develop a blast-resistant MR219 improved variety. In this perspective, the recurrent parent genome recovery was analyzed in early generations of backcrossing using simple sequence repeat (SSR) markers. Out of 375 SSR markers, 70 markers were found polymorphic between the parents, and these markers were used to evaluate the plants in subsequent generations. Background analysis revealed that the extent of RPG recovery ranged from 75.40% to 91.3% and from 80.40% to 96.70% in BC1F1 and BC2F1 generations, respectively. In this study, the recurrent parent genome content in the selected BC2F2 lines ranged from 92.7% to 97.7%. The average proportion of the recurrent parent in the selected improved line was 95.98%. MAS allowed identification of the plants that are more similar to the recurrent parent for the loci evaluated in backcross generations. The application of MAS with the MABC breeding program accelerated the recovery of the RP genome, reducing the number of generations and the time for incorporating resistance against rice blast. Copyright © 2014 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  7. A deleterious effect associated with UNH159 is attenuated in twin embryos of an inbred line of tilapia (Oreochromis aureus)

    USDA-ARS?s Scientific Manuscript database

    Offspring of a highly inbred gynogenetic line of Oreochromis aureus displayed 12-fold increase in twinning rate compared to the outbred population. Asymmetric conjoined twins which consist of a normal embryo attached to a malformed-atrophic twin were frequently encountered in both gynogenetic (90.7%...

  8. Reinventing potato as a diploid inbred line-based crop

    USDA-ARS?s Scientific Manuscript database

    The third most important food crop worldwide, potato, is a tetraploid outcrossing species propagated from tubers. Breeders have long been challenged by polyploidy, heterozygosity, and asexual reproduction. It has been assumed that tetraploidy is essential for high yield, the creation of inbred potat...

  9. Identification of genomic region controlling resistance to aflatoxin contamination in a peanut recombinant inbred line population (Tifrunner x GT-C20)

    USDA-ARS?s Scientific Manuscript database

    Aflatoxin contamination of peanut is a significant threat to global food safety. In this study we performed quantitative trait loci (QTL) analysis to identify peanut genomic regions contributing to aflatoxin contamination resistance in a recombinant inbred line (RIL) population derived from the Tifr...

  10. Genetic mapping of QTLs associated with seed macronutrients accumulation in 'MD96-5722' by 'Spencer' recombinant inbred lines of soybean

    USDA-ARS?s Scientific Manuscript database

    Research of genetic mapping of QTLs for macronutrient accumulation in soybean seed is limited. Therefore, the objective of this research was to identify QTLs related to macronutrients (N, C, S, P, K, Ca, and Mg) in seeds in 92 F5:7 recombinant inbred lines developed from a cross between MD 96-5722 (...

  11. Selection and phenotypic characterization of a core collection of Brachypodium distachyon inbred lines.

    PubMed

    Tyler, Ludmila; Fangel, Jonatan U; Fagerström, Alexandra Dotson; Steinwand, Michael A; Raab, Theodore K; Willats, William Gt; Vogel, John P

    2014-01-14

    The model grass Brachypodium distachyon is increasingly used to study various aspects of grass biology. A large and genotypically diverse collection of B. distachyon germplasm has been assembled by the research community. The natural variation in this collection can serve as a powerful experimental tool for many areas of inquiry, including investigating biomass traits. We surveyed the phenotypic diversity in a large collection of inbred lines and then selected a core collection of lines for more detailed analysis with an emphasis on traits relevant to the use of grasses as biofuel and grain crops. Phenotypic characters examined included plant height, growth habit, stem density, flowering time, and seed weight. We also surveyed differences in cell wall composition using near infrared spectroscopy (NIR) and comprehensive microarray polymer profiling (CoMPP). In all cases, we observed extensive natural variation including a two-fold variation in stem density, four-fold variation in ferulic acid bound to hemicellulose, and 1.7-fold variation in seed mass. These characterizations can provide the criteria for selecting diverse lines for future investigations of the genetic basis of the observed phenotypic variation.

  12. Mapping and validation of quantitative trait loci associated with concentrations of 16 elements in unmilled rice grain

    USDA-ARS?s Scientific Manuscript database

    In this study, quantitative trait loci (QTLs) affecting the concentrations of 16 elements in whole, unmilled rice (Oryza sativa L.) grain were identified. Two rice mapping populations, the ‘Lemont’ x ‘TeQing’ recombinant inbred lines (LT-RILs), and the TeQing-into-Lemont backcross introgression lin...

  13. Karyotype variability in tropical maize sister inbred lines and hybrids compared with KYS standard line

    PubMed Central

    Mondin, Mateus; Santos-Serejo, Janay A.; Bertäo, Mônica R.; Laborda, Prianda; Pizzaia, Daniel; Aguiar-Perecin, Margarida L. R.

    2014-01-01

    Maize karyotype variability has been extensively investigated. The identification of maize somatic and pachytene chromosomes has improved with the development of fluorescence in situ hybridization (FISH) using tandemly repeated DNA sequences as probes. We identified the somatic chromosomes of sister inbred lines that were derived from a tropical flint maize population (Jac Duro [JD]), and hybrids between them, using FISH probes for the 180-bp knob repeat, centromeric satellite (CentC), centromeric satellite 4 (Cent4), subtelomeric clone 4-12-1, 5S ribosomal DNA and nucleolus organizing region DNA sequences. The observations were integrated with data based on C-banded mitotic metaphases and conventional analysis of pachytene chromosomes. Heterochromatic knobs visible at pachynema were coincident with C-bands and 180-bp FISH signals on somatic chromosomes, and most of them were large. Variation in the presence of some knobs was observed among lines. Small 180-bp knob signals were invariant on the short arms of chromosomes 1, 6, and 9. The subtelomeric 4-12-1 signal was also invariant and useful for identifying some chromosomes. The centromere location of chromosomes 2 and 4 differed from previous reports on standard maize lines. Somatic chromosomes of a JD line and the commonly used KYS line were compared by FISH in a hybrid of these lines. The pairing behavior of chromosomes 2 and 4 at pachytene stage in this hybrid was investigated using FISH with chromosome-specific probes. The homologues were fully synapsed, including the 5S rDNA and CentC sites on chromosome 2, and Cent4 and subtelomeric 4-12-1 sites on chromosome 4. This suggests that homologous chromosomes could pair through differential degrees of chromatin packaging in homologous arms differing in size. The results contribute to current knowledge of maize global diversity and also raise questions concerning the meiotic pairing of homologous chromosomes possibly differing in their amounts of repetitive DNA

  14. Identification of five novel modifier loci of ApcMin harbored in the BXH14 recombinant inbred strain

    PubMed Central

    Siracusa, Linda D.

    2012-01-01

    Every year thousands of people in the USA are diagnosed with small intestine and colorectal cancers (CRC). Although environmental factors affect disease etiology, uncovering underlying genetic factors is imperative for risk assessment and developing preventative therapies. Familial adenomatous polyposis is a heritable genetic disorder in which individuals carry germ-line mutations in the adenomatous polyposis coli (APC) gene that predisposes them to CRC. The Apc Min mouse model carries a point mutation in the Apc gene and develops polyps along the intestinal tract. Inbred strain background influences polyp phenotypes in Apc Min mice. Several Modifier of Min (Mom) loci that alter tumor phenotypes associated with the Apc Min mutation have been identified to date. We screened BXH recombinant inbred (RI) strains by crossing BXH RI females with C57BL/6J (B6) Apc Min males and quantitating tumor phenotypes in backcross progeny. We found that the BXH14 RI strain harbors five modifier loci that decrease polyp multiplicity. Furthermore, we show that resistance is determined by varying combinations of these modifier loci. Gene interaction network analysis shows that there are multiple networks with proven gene–gene interactions, which contain genes from all five modifier loci. We discuss the implications of this result for studies that define susceptibility loci, namely that multiple networks may be acting concurrently to alter tumor phenotypes. Thus, the significance of this work resides not only with the modifier loci we identified but also with the combinations of loci needed to get maximal protection against polyposis and the impact of this finding on human disease studies. Abbreviations:APCadenomatous polyposis coliGWASgenome-wide association studiesQTLquantitative trait lociSNPsingle-nucleotide polymorphism. PMID:22637734

  15. [Effect of selenium deficiency on the F344 inbred line offspring rats' neuro-behavior, ability of learning and memory].

    PubMed

    Hong, Liang-Li; Tian, Dong-Ping; Su, Min; Shen, Xiu-Na; Gao, Yuxia

    2006-01-01

    To establish the selenium (Se) deficient animal model on F344 inbred line rats and observe the effects of a long-term Se-deficiency on the offspring's neuro-behavior, abilities of learning and memory. Feeding F344 inbred line rats on Se-deficient diet to establish Se-deficient animal model. For the offspring, the body weight, physiological indexes nervous reflections for growth and development were monitored during the early postnatal period. The Se-deficient diet contained less than 0.01 mg/kg and the glutathione peroxidase (GSH-Px) activity in blood of the Se-deficient group rats is lower than the Se-normal group after feeding on Se-deficient diet for 4 weeks. For the offspring, the birth weight and the body weight of Se-deficient group were obviously lower than the Se-normal group before weaning. Se-deficient offspring rats differed from Se-normal controls in lower scores in surface righting reflex (RR) test at postnatal 4th day after delivery, cliff avoidance test at postnatal 7th day and auditory acuity trial at postnatal 10th day respectively. But these differences disappear after a few days in the same tests. In addition, no significant differences between two groups in suspending test and walking ability test at postnatal 12th and 14th day. In open field test, Se-deficient male offspring stayed less time in the middle grid and moved less. In Morris water maze test, the Se-deficient offspring spent more time to find the hidden platform at the 6th and 9th training tests in the place navigation trial. Furthermore, the Se-deficient group spent less time in target quadrant when giving the spatial probe trial. A Se-deficient animal model have been established on F344 inbred line rats successfully. A long-term Se deficiency could retard the development of the offspring in uterus and after delivery. Se deficiency also decreased the offspring's abilities of spatial learning and memory in Morris water maze test and resulted in the male offspring's nervousness to new

  16. ROOT TRAITS AND NODULATION OF RECOMBINANT INBRED BEAN LINES FROM A ‘JAMAPA × CALIMA’ POPULATION INOCULATED WITH TWO STRAINS OF RHIZOBIUM

    USDA-ARS?s Scientific Manuscript database

    Bean cultivars of Andean and Middle American origin often have contrasting above-ground traits. Less is known, however, of possible differences in root traits of beans from different gene pools. Recombinant inbred lines (RIL) derived from a cross between the Andean cultivar ‘Calima’ and the Middle A...

  17. Incorporation of Bacterial Blight Resistance Genes Into Lowland Rice Cultivar Through Marker-Assisted Backcross Breeding.

    PubMed

    Pradhan, Sharat Kumar; Nayak, Deepak Kumar; Pandit, Elssa; Behera, Lambodar; Anandan, Annamalai; Mukherjee, Arup Kumar; Lenka, Srikanta; Barik, Durga Prasad

    2016-07-01

    Bacterial blight (BB) of rice caused by Xanthomonas oryzae pv. oryzae is a major disease of rice in many rice growing countries. Pyramided lines carrying two BB resistance gene combinations (Xa21+xa13 and Xa21+xa5) were developed in a lowland cultivar Jalmagna background through backcross breeding by integrating molecular markers. In each backcross generation, markers closely linked to the disease resistance genes were used to select plants possessing the target genes. Background selection was continued in those plants carrying resistant genes until BC(3) generation. Plants having the maximum contribution from the recurrent parent genome were selected in each generation and hybridized with the recipient parent. The BB-pyramided line having the maximum recipient parent genome recovery of 95% was selected among BC3F1 plants and selfed to isolate homozygous BC(3)F(2) plants with different combinations of BB resistance genes. Twenty pyramided lines with two resistance gene combinations exhibited high levels of tolerance against the BB pathogen. In order to confirm the resistance, the pyramided lines were inoculated with different X. oryzae pv. oryzae strains of Odisha for bioassay. The genotypes with combination of two BB resistance genes conferred high levels of resistance to the predominant X. oryzae pv. oryzae isolates prevalent in the region. The pyramided lines showed similarity with the recipient parent with respect to major agro-morphologic traits.

  18. The backcross sterility technique

    Treesearch

    V. C. Mastro; A. Pellegrini-Toole

    1991-01-01

    The sterile insect technique (SIT) and the induced inherited (F1) sterility technique have been investigated for a number of lepidopterous pests, including the gypsy moths. Another technique, backcross sterility, which could potentially prove as or more useful for control of pest species has been developed for the control of only one lepidopteran...

  19. Inbred decorated crickets exhibit higher measures of macroparasitic immunity than outbred individuals.

    PubMed

    Gershman, S N; Barnett, C A; Pettinger, A M; Weddle, C B; Hunt, J; Sakaluk, S K

    2010-09-01

    Inbreeding is assumed to have negative effects on fitness, including the reduced ability to withstand immune challenges. We examined the immunological consequences of inbreeding in decorated crickets, Gryllodes sigillatus, by comparing lytic activity, phenoloxidase (PO) activity, and encapsulation ability of crickets from eight inbred lines with that of crickets from the outbred founder population. Surprisingly, crickets from inbred lines had a greater encapsulation ability compared with crickets from the outbred population. We suggest that because inbred crickets have reduced reproductive effort, they may, therefore, have the option of devoting more resources to this form of immunity than outbred individuals. We also found that both inbred and outbred females had higher immunity than males in PO activity and implant darkness. This result supports the hypothesis that females should devote more effort to somatic maintenance and immunity than males. PO activity and implant darkness were heritable in both males and females, but lytic activity was only heritable in females. Males and females differed in the heritability of, and genetic correlations among, immune traits, suggesting that differences in selective pressures on males and females may have resulted in a sexual conflict over optimal immune trait values.

  20. Selection for Reduced Fusarium Ear Rot and Fumonisin Content in Advanced Backcross Maize Lines and Their Topcross Hybrids

    USDA-ARS?s Scientific Manuscript database

    Backcross breeding is an important method to improve elite cultivars for traits controlled by a small number of loci but has been used less frequently to improve quantitatively controlled traits. Resistances to Fusarium ear rot and contamination by the associated mycotoxin fumonisin in maize are qua...

  1. Identifying Rare FHB-Resistant Segregants in Intransigent Backcross and F2 Winter Wheat Populations.

    PubMed

    Clark, Anthony J; Sarti-Dvorjak, Daniela; Brown-Guedira, Gina; Dong, Yanhong; Baik, Byung-Kee; Van Sanford, David A

    2016-01-01

    Fusarium head blight (FHB), caused mainly by Fusarium graminearum Schwabe [telomorph: Gibberella zeae Schwein.(Petch)] in the US, is one of the most destructive diseases of wheat (Triticum aestivum L. and T. durum L.). Infected grain is usually contaminated with deoxynivalenol (DON), a serious mycotoxin. The challenge in FHB resistance breeding is combining resistance with superior agronomic and quality characteristics. Exotic QTL are widely used to improve FHB resistance. Success depends on the genetic background into which the QTL are introgressed, whether through backcrossing or forward crossing; QTL expression is impossible to predict. In this study four high-yielding soft red winter wheat breeding lines with little or no scab resistance were each crossed to a donor parent (VA01W-476) with resistance alleles at two QTL: Fhb1 (chromosome 3BS) and QFhs.nau-2DL (chromosome 2DL) to generate backcross and F2 progeny. F2 individuals were genotyped and assigned to 4 groups according to presence/ absence of resistance alleles at one or both QTL. The effectiveness of these QTL in reducing FHB rating, incidence, index, severity, Fusarium-damaged kernels (FDK) and DON, in F2-derived lines was assessed over 2 years. Fhb1 showed an average reduction in DON of 17.5%, and conferred significant resistance in 3 of 4 populations. QFhs.nau-2DL reduced DON 6.7% on average and conferred significant resistance in 2 of 4 populations. The combination of Fhb1 and QFhs.nau-2DL resistance reduced DON 25.5% across all populations. Double resistant lines had significantly reduced DON compared to double susceptible lines in 3 populations. Backcross derived progeny were planted in replicated yield trials (2011 and 2012) and in a scab nursery in 2012. Several top yielding lines performed well in the scab nursery, with acceptable DON concentrations, even though the average effect of either QTL in this population was not significant. Population selection is often viewed as an "all or nothing

  2. Descriptive statistics and correlation analysis of agronomic traits in a maize recombinant inbred line population.

    PubMed

    Zhang, H M; Hui, G Q; Luo, Q; Sun, Y; Liu, X H

    2014-01-21

    Maize (Zea mays L.) is one of the most important crops in the world. In this study, 13 agronomic traits of a recombinant inbred line population that was derived from the cross between Mo17 and Huangzao4 were investigated in maize: ear diameter, ear length, ear axis diameter, ear weight, plant height, ear height, days to pollen shed (DPS), days to silking (DS), the interval between DPS and DS, 100-kernel weight, kernel test weight, ear kernel weight, and kernel rate. Furthermore, the descriptive statistics and correlation analysis of the 13 traits were performed using the SPSS 11.5 software. The results providing the phenotypic data here are needed for the quantitative trait locus mapping of these agronomic traits.

  3. Inheritance of resistance to watermelon mosaic virus in the cucumber line TMG-1: tissue-specific expression and relationship to zucchini yellow mosaic virus resistance.

    PubMed

    Wai, T; Grumet, R

    1995-09-01

    The inbred cucumber (Cucumis sativus L.) line TMG-1 is resistant to three potyviruses:zucchini yellow mosaic virus (ZYMV), watermelon mosaic virus (WMV), and the watermelon strain of papaya ringspot virus (PRSV-W). The genetics of resistance to WMV and the relationship of WMV resistance to ZYMV resistance were examined. TMG-1 was crossed with WI-2757, a susceptible inbred line. F1, F2 and backcross progeny populations were screened for resistance to WMV and/or ZYMV. Two independently assorting factors conferred resistance to WMV. One resistance was conferred by a single recessive gene from TMG-1 (wmv-2). The second resistance was conferred by an epistatic interaction between a second recessive gene from TMG-1 (wmv-3) and either a dominant gene from WI-2757 (Wmv-4) or a third recessive gene from TMG-1 (wmv-4) located 20-30 cM from wmv-3. The two resistances exhibited tissue-specific expression. Resistance conferred by wmv-2 was expressed in the cotyledons and throughout the plant. Resistance conferred by wmv-3 + Wmv-4 (or wmv-4) was expressed only in true leaves. The gene conferring resistance to ZYMV appeared to be the same as, or tightly linked to one of the WMV resistance genes, wmv-3.

  4. Nonpermissiveness for mouse embryonic stem (ES) cell derivation circumvented by a single backcross to 129/Sv strain: establishment of ES cell lines bearing the Omd conditional lethal mutation.

    PubMed

    Kress, C; Vandormael-Pournin, S; Baldacci, P; Cohen-Tannoudji, M; Babinet, C

    1998-12-01

    The inbred mouse strain DDK carries a conditional early embryonic lethal mutation that is manifested when DDK females are crossed to males of other inbred strains but not in the corresponding reciprocal crosses. It has been shown that embryonic lethality could be assigned to a single genetic locus called Ovum mutant (Om), on Chromosome (Chr) 11 near Syca 1. In the course of our study of the molecular mechanisms underlying the embryonic lethality, we were interested in deriving an embryonic stem cell bearing the Om mutation in the homozygous state (Omd/Omd). However, it turned out that DDK is nonpermissive for ES cell establishment, with a standard protocol. Here we show that permissiveness could be obtained using Omd/Omd blastocysts with a 75% 129/Sv and 25% DDK genetic background. Several germline-competent Omd/Omd ES cell lines have been derived from blastocysts of this genotype. Such a scenario could be extended to the generation of ES cell lines bearing any mutation present in an otherwise nonpermissive mouse strain.

  5. Flooding tolerance in interspecific introgression lines containing chromosome segments from teosinte (Zea nicaraguensis) in maize (Zea mays subsp. mays).

    PubMed

    Mano, Y; Omori, F

    2013-10-01

    Nicaraguan teosinte (Zea nicaraguensis), a species found in frequently flooded areas, provides useful germplasm for breeding flooding-tolerant maize (Z. mays subsp. mays). The objective of this study was to select flooding-tolerant lines using a library of introgression lines (ILs), each containing a chromosome segment from Z. nicaraguensis in the maize inbred line Mi29. To produce the ILs, a single F1 plant derived from a cross between maize Mi29 and Z. nicaraguensis was backcrossed to Mi29 three times, self-pollinated four times and genotyped using simple sequence repeat markers. Flooding tolerance was evaluated at the seedling stage under reducing soil conditions. By backcrossing and selfing, a series of 45 ILs were developed covering nearly the entire maize genome. Five flooding-tolerant lines were identified from among the ILs by evaluating leaf injury. Among these, line IL#18, containing a Z. nicaraguensis chromosome segment on the long arm of chromosome 4, showed the greatest tolerance to flooding, suggesting the presence of a major quantitative trait locus (QTL) in that region. The presence of the QTL was verified by examining flooding tolerance in a population segregating for the candidate region of chromosome 4. There was no significant relationship between the capacity to form constitutive aerenchyma and flooding tolerance in the ILs, indicating the presence of other factors related to flooding tolerance under reducing soil conditions. A flooding-tolerant genotype, IL#18, was identified; this genotype should be useful for maize breeding. In addition, because the chromosome segments of Z. nicaraguensis in the ILs cover nearly the entire genome and Z. nicaraguensis possesses several unique traits related to flooding tolerance, the ILs should be valuable material for additional QTL detection and the development of flooding-tolerant maize lines.

  6. Flooding tolerance in interspecific introgression lines containing chromosome segments from teosinte (Zea nicaraguensis) in maize (Zea mays subsp. mays)

    PubMed Central

    Mano, Y.; Omori, F.

    2013-01-01

    Background and Aims Nicaraguan teosinte (Zea nicaraguensis), a species found in frequently flooded areas, provides useful germplasm for breeding flooding-tolerant maize (Z. mays subsp. mays). The objective of this study was to select flooding-tolerant lines using a library of introgression lines (ILs), each containing a chromosome segment from Z. nicaraguensis in the maize inbred line Mi29. Methods To produce the ILs, a single F1 plant derived from a cross between maize Mi29 and Z. nicaraguensis was backcrossed to Mi29 three times, self-pollinated four times and genotyped using simple sequence repeat markers. Flooding tolerance was evaluated at the seedling stage under reducing soil conditions. Key Results By backcrossing and selfing, a series of 45 ILs were developed covering nearly the entire maize genome. Five flooding-tolerant lines were identified from among the ILs by evaluating leaf injury. Among these, line IL#18, containing a Z. nicaraguensis chromosome segment on the long arm of chromosome 4, showed the greatest tolerance to flooding, suggesting the presence of a major quantitative trait locus (QTL) in that region. The presence of the QTL was verified by examining flooding tolerance in a population segregating for the candidate region of chromosome 4. There was no significant relationship between the capacity to form constitutive aerenchyma and flooding tolerance in the ILs, indicating the presence of other factors related to flooding tolerance under reducing soil conditions. Conclusions A flooding-tolerant genotype, IL#18, was identified; this genotype should be useful for maize breeding. In addition, because the chromosome segments of Z. nicaraguensis in the ILs cover nearly the entire genome and Z. nicaraguensis possesses several unique traits related to flooding tolerance, the ILs should be valuable material for additional QTL detection and the development of flooding-tolerant maize lines. PMID:23877074

  7. Use of molecular markers aids in the development of diverse inbred backcross lines in beit alpha cucumber (Cucumis sativus L.)

    USDA-ARS?s Scientific Manuscript database

    Beit Alpha cucumber (Cucumis sativus L.) is a Mediterranean fresh-market type with a relatively narrow genetic base. To broaden its base for plant improvement, 42 diverse accessions were compared employing a previously defined standard marker array to choose wide-based parental lines for use in bac...

  8. Use of molecular markers aids in the development of diverse inbred backcross lines in Beit Alpha cucumber (Cucumis sativus L.)

    USDA-ARS?s Scientific Manuscript database

    Beit Alpha cucumber (Cucumis sativus L.) is a Mediterranean fresh-market type with a relatively narrow genetic base. To broaden its base for plant improvement, 42 diverse accessions were compared employing a previously defined standard marker array to choose wide-based parental lines for use in bac...

  9. Evaluating hybrid poplar rooting. II. backcross breeding method exhibits exceptional promise

    Treesearch

    Ronald S., Jr. Zalesny; Don E. Riemenschneider; Richard B. Hall

    2002-01-01

    Backcross breeding uses two crosses to create genotypes with improved traits. The first cross establishes an F1 population, which is then used as the female parent in a set of second crosses. The male parent of the second cross is often a genotype well-adapted to local environments. A currently investigated backcross population is the result of...

  10. A SNP genetic linkage map based on the ‘Hamilton’ by ‘Spencer’ recombinant inbred line (RIL) population identified QTL for seed Isoflavone contents in soybean

    USDA-ARS?s Scientific Manuscript database

    Soybean is one of the most important crops worldwide for its protein, oil as well as the health beneficial phytoestrogens or isoflavone. This study reports a relatively dense SNP-Based genetic map based on ‘Hamilton’ by ‘Spencer’ recombinant inbred line (RIL) population and quantitative t...

  11. Functional Coding Variation in Recombinant Inbred Mouse Lines Reveals Novel Serotonin Transporter-Associated Phenotypes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Carneiro, Ana; Airey, David; Thompson, Brent

    The human serotonin (5-hydroxytryptamine, 5-HT) transporter (hSERT, SLC6A4) figures prominently in the etiology or treatment of many prevalent neurobehavioral disorders including anxiety, alcoholism, depression, autism and obsessive-compulsive disorder (OCD). Here we utilize naturally occurring polymorphisms in recombinant inbred (RI) lines to identify novel phenotypes associated with altered SERT function. The widely used mouse strain C57BL/6J, harbors a SERT haplotype defined by two nonsynonymous coding variants (Gly39 and Lys152 (GK)). At these positions, many other mouse lines, including DBA/2J, encode Glu39 and Arg152 (ER haplotype), assignments found also in hSERT. Synaptosomal 5-HT transport studies revealed reduced uptake associated with the GKmore » variant. Heterologous expression studies confirmed a reduced SERT turnover rate for the GK variant. Experimental and in silico approaches using RI lines (C57Bl/6J X DBA/2J=BXD) identifies multiple anatomical, biochemical and behavioral phenotypes specifically impacted by GK/ER variation. Among our findings are multiple traits associated with anxiety and alcohol consumption, as well as of the control of dopamine (DA) signaling. Further bioinformatic analysis of BXD phenotypes, combined with biochemical evaluation of SERT knockout mice, nominates SERT-dependent 5-HT signaling as a major determinant of midbrain iron homeostasis that, in turn, dictates ironregulated DA phenotypes. Our studies provide a novel example of the power of coordinated in vitro, in vivo and in silico approaches using murine RI lines to elucidate and quantify the system-level impact of gene variation.« less

  12. Expression Analysis of Stress-Related Genes in Kernels of Different Maize (Zea mays L.) Inbred Lines with Different Resistance to Aflatoxin Contamination

    PubMed Central

    Jiang, Tingbo; Zhou, Boru; Luo, Meng; Abbas, Hamed K.; Kemerait, Robert; Lee, Robert Dewey; Scully, Brian T.; Guo, Baozhu

    2011-01-01

    This research examined the expression patterns of 94 stress-related genes in seven maize inbred lines with differential expressions of resistance to aflatoxin contamination. The objective was to develop a set of genes/probes associated with resistance to A. flavus and/or aflatoxin contamination. Ninety four genes were selected from previous gene expression studies with abiotic stress to test the differential expression in maize lines, A638, B73, Lo964, Lo1016, Mo17, Mp313E, and Tex6, using real-time RT-PCR. Based on the relative-expression levels, the seven maize inbred lines clustered into two different groups. One group included B73, Lo1016 and Mo17, which had higher levels of aflatoxin contamination and lower levels of overall gene expression. The second group which included Tex6, Mp313E, Lo964 and A638 had lower levels of aflatoxin contamination and higher overall levels of gene expressions. A total of six “cross-talking” genes were identified between the two groups, which are highly expressed in the resistant Group 2 but down-regulated in susceptible Group 1. When further subjected to drought stress, Tex6 expressed more genes up-regulated and B73 has fewer genes up-regulated. The transcript patterns and interactions measured in these experiments indicate that the resistant mechanism is an interconnected process involving many gene products and transcriptional regulators, as well as various host interactions with environmental factors, particularly, drought and high temperature. PMID:22069724

  13. Resistance of Tripsacorn-introgressed maize lines to Sitophilus zeamais

    USDA-ARS?s Scientific Manuscript database

    The maize weevil, Sitophilus zeamais Motschulsky (Coleoptera: Curculionidae), is one of the major pests of maize worldwide. We tested one Tripsacorn-introgressed inbred maize line and 42 hybrid combinations between eleven public inbred lines and 16 different Tripsacorn-introgressed inbreds for resis...

  14. Haldane, Waddington and recombinant inbred lines: extension of their work to any number of genes.

    PubMed

    Samal, Areejit; Martin, Olivier C

    2017-11-01

    In the early 1930s, J. B. S. Haldane and C. H. Waddington collaborated on the consequences of genetic linkage and inbreeding. One elegant mathematical genetics problem solved by them concerns recombinant inbred lines (RILs) produced via repeated self or brother-sister mating. In this classic contribution, Haldane and Waddington derived an analytical formula for the probabilities of 2-locus and 3-locus RIL genotypes. Specifically, the Haldane-Waddington formula gives the recombination rate R in such lines as a simple function of the per generation recombination rate r. Interestingly, for more than 80 years, an extension of this result to four or more loci remained elusive. In 2015, we generalized the Haldane-Waddington self-mating result to any number of loci. Our solution used self-consistent equations of the multi-locus probabilities 'for an infinite number of generations' and solved these by simple algebraic operations. In practice, our approach provides a quantum leap in the systems that can be handled: the cases of up to six loci can be solved by hand while a computer program implementing our mathematical formalism tackles up to 20 loci on standard desktop computers.

  15. Variation in cell wall composition among forage maize (Zea mays L.) inbred lines and its impact on digestibility: analysis of neutral detergent fiber composition by pyrolysis-gas chromatography-mass spectrometry.

    PubMed

    Fontaine, Anne-Sophie; Bout, Siobhán; Barrière, Yves; Vermerris, Wilfred

    2003-12-31

    Cell wall digestibility is an important determinant of forage quality, but the relationship between cell wall composition and digestibility is poorly understood. We analyzed the neutral detergent fiber (NDF) fraction of nine maize inbred lines and one brown midrib3 mutant with pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS). Among 29 pyrolysis fragments that were quantified, two carbohydrate-derived and six lignin-derived fragments showed statistically significant genetic variation. The pyrolysis products 4-vinyl phenol and 2,6-dimethoxy-4-vinyl phenol were negatively correlated with digestibility, whereas furfural and 3-(4-hydroxyphenyl)-3-oxopropanal showed a positive correlation with digestibility. Linear discriminant analysis of the pyrolysis data resulted in the resolution of groups of inbred lines with different digestibility properties based on their chemical composition. These analyses reveal that digestibility is governed by complex interactions between different cell wall compounds, but that several pyrolysis fragments can be used as markers to distinguish between maize lines with different digestibility.

  16. Genotype × Environment Interactions of Yield Traits in Backcross Introgression Lines Derived from Oryza sativa cv. Swarna/Oryza nivara

    PubMed Central

    Balakrishnan, Divya; Subrahmanyam, Desiraju; Badri, Jyothi; Raju, Addanki Krishnam; Rao, Yadavalli Venkateswara; Beerelli, Kavitha; Mesapogu, Sukumar; Surapaneni, Malathi; Ponnuswamy, Revathi; Padmavathi, G.; Babu, V. Ravindra; Neelamraju, Sarla

    2016-01-01

    Advanced backcross introgression lines (BILs) developed from crosses of Oryza sativa var. Swarna/O. nivara accessions were grown and evaluated for yield and related traits. Trials were conducted for consecutive three seasons in field conditions in a randomized complete block design with three replications. Data on yield traits under irrigated conditions were analyzed using the Additive Main Effect and Multiplicative Interaction (AMMI), Genotype and Genotype × Environment Interaction (GGE) and modified rank-sum statistic (YSi) for yield stability. BILs viz., G3 (14S) and G6 (166S) showed yield stability across the seasons along with high mean yield performance. G3 is early in flowering with high yield and has good grain quality and medium height, hence could be recommended for most of the irrigated locations. G6 is a late duration genotype, with strong culm strength, high grain number and panicle weight. G6 has higher yield and stability than Swarna but has Swarna grain type. Among the varieties tested DRRDhan 40 and recurrent parent Swarna showed stability for yield traits across the seasons. The component traits thousand grain weight, panicle weight, panicle length, grain number and plant height explained highest genotypic percentage over environment and interaction factors and can be prioritized to dissect stable QTLs/ genes. These lines were genotyped using microsatellite markers covering the entire rice genome and also using a set of markers linked to previously reported yield QTLs. It was observed that wild derived lines with more than 70% of recurrent parent genome were stable and showed enhanced yield levels compared to genotypes with higher donor genome introgressions. PMID:27807437

  17. Highly efficient generation of GGTA1 biallelic knockout inbred mini-pigs with TALENs.

    PubMed

    Xin, Jige; Yang, Huaqiang; Fan, Nana; Zhao, Bentian; Ouyang, Zhen; Liu, Zhaoming; Zhao, Yu; Li, Xiaoping; Song, Jun; Yang, Yi; Zou, Qingjian; Yan, Quanmei; Zeng, Yangzhi; Lai, Liangxue

    2013-01-01

    Inbred mini-pigs are ideal organ donors for future human xenotransplantations because of their clear genetic background, high homozygosity, and high inbreeding endurance. In this study, we chose fibroblast cells from a highly inbred pig line called Banna mini-pig inbred line (BMI) as donor nuclei for nuclear transfer, combining with transcription activator-like effector nucleases (TALENs) and successfully generated α-1,3-galactosyltransferase (GGTA1) gene biallelic knockout (KO) pigs. To validate the efficiency of TALEN vectors, in vitro-transcribed TALEN mRNAs were microinjected into one-cell stage parthenogenetically activated porcine embryos. The efficiency of indel mutations at the GGTA1-targeting loci was as high as 73.1% (19/26) among the parthenogenetic blastocysts. TALENs were co-transfected into porcine fetal fibroblasts of BMI with a plasmid containing neomycin gene. The targeting efficiency reached 89.5% (187/209) among the survived cell clones after a 10 d selection. More remarkably 27.8% (58/209) of colonies were biallelic KO. Five fibroblast cell lines with biallelic KO were chosen as nuclear donors for somatic cell nuclear transfer (SCNT). Three miniature piglets with biallelic mutations of the GGTA1 gene were achieved. Gal epitopes on the surface of cells from all the three biallelic KO piglets were completely absent. The fibroblasts from the GGTA1 null piglets were more resistant to lysis by pooled complement-preserved normal human serum than those from wild-type pigs. These results indicate that a combination of TALENs technology with SCNT can generate biallelic KO pigs directly with high efficiency. The GGTA1 null piglets with inbred features created in this study can provide a new organ source for xenotransplantation research.

  18. Analysis of Natural Allelic Variation of Arabidopsis Seed Germination and Seed Longevity Traits between the Accessions Landsberg erecta and Shakdara, Using a New Recombinant Inbred Line Population1

    PubMed Central

    Clerkx, Emile J.M.; El-Lithy, Mohamed E.; Vierling, Elizabeth; Ruys, Gerda J.; Vries, Hetty Blankestijn-De; Groot, Steven P.C.; Vreugdenhil, Dick; Koornneef, Maarten

    2004-01-01

    Quantitative trait loci (QTL) mapping was used to identify loci controlling various aspects of seed longevity during storage and germination. Similar locations for QTLs controlling different traits might be an indication for a common genetic control of such traits. For this analysis we used a new recombinant inbred line population derived from a cross between the accessions Landsberg erecta (Ler) and Shakdara (Sha). A set of 114 F9 recombinant inbred lines was genotyped with 65 polymerase chain reaction-based markers and the phenotypic marker erecta. The traits analyzed were dormancy, speed of germination, seed sugar content, seed germination after a controlled deterioration test, hydrogen peroxide (H2O2) treatment, and on abscisic acid. Furthermore, the effects of heat stress, salt (NaCl) stress, osmotic (mannitol) stress, and natural aging were analyzed. For all traits one or more QTLs were identified, with some QTLs for different traits colocating. The relevance of colocation for mechanisms underlying the various traits is discussed. PMID:15122038

  19. Comparative quantitative trait locus mapping of maize flowering-related traits in an F2:3 and recombinant inbred line population.

    PubMed

    Liu, Y H; Yi, Q; Hou, X B; Zhang, X G; Zhang, J J; Liu, H M; Hu, Y F; Huang, Y B

    2016-06-30

    Flowering-related traits in maize are affected by complex factors and are important for the improvement of cropping systems in the maize zone. Quantitative trait loci (QTLs) detected using different materials and methods usually vary. In the present study, 266 maize (Zea mays) F2:3 families and 301 recombinant inbred lines (RIL) derived from a cross between 08-641 (founding parent from southeast China) and Ye478 (founding parent from China) were evaluated for four flowering-related traits, including days to tasseling (DTT), days to pollen shedding (DPS), days to silking (DTS), and anthesis-silking interval. Sixty-six QTLs controlling the target traits were detected in the F2:3 and RIL populations via single environment analysis and joint analysis across all environments (JAAE). The QTLs explained 0.8-13.47% of the phenotypic variation, with 12 QTLs explaining more than 10%. The results of meta-QTL (MQTL) analysis indicated that 41 QTLs could be integrated into 14 MQTLs. One MQTL included 2.9 QTLs, ranging from two to ten QTLs for one to three traits. QTLs, including MQTL1-1 and MQTL9-1, were detected across the F2:3 and RIL populations via SAE and JAAE. Among the MQTLs, nine QTLs were integrated into MQTL9-1 and affected DTT, DPS, and DTS, with the favored allele being derived from 08-641. MQTL3-2 showed high phenotypic variation and was suitable for fine mapping to determine the genetic mechanisms of flowering. MQTL3-2 could be applied to improve inbred lines using marker-assisted selection.

  20. Transcriptome analysis of two recombinant inbred lines of common bean contrasting for symbiotic nitrogen fixation

    PubMed Central

    Kamfwa, Kelvin; Zhao, Dongyan; Kelly, James D.

    2017-01-01

    Common bean (Phaseolus vulgaris L.) fixes atmospheric nitrogen (N2) through symbiotic nitrogen fixation (SNF) at levels lower than other grain legume crops. An understanding of the genes and molecular mechanisms underlying SNF will enable more effective strategies for the genetic improvement of SNF traits in common bean. In this study, transcriptome profiling was used to identify genes and molecular mechanisms underlying SNF differences between two common bean recombinant inbred lines that differed in their N-fixing abilities. Differential gene expression and functional enrichment analyses were performed on leaves, nodules and roots of the two lines when grown under N-fixing and non-fixing conditions. Receptor kinases, transmembrane transporters, and transcription factors were among the differentially expressed genes identified under N-fixing conditions, but not under non-fixing conditions. Genes up-regulated in the stronger nitrogen fixer, SA36, included those involved in molecular functions such as purine nucleoside binding, oxidoreductase and transmembrane receptor activities in nodules, and transport activity in roots. Transcription factors identified in this study are candidates for future work aimed at understanding the functional role of these genes in SNF. Information generated in this study will support the development of gene-based markers to accelerate genetic improvement of SNF in common bean. PMID:28192540

  1. An inbred line of the diploid strawberry Fragaria vesca f. semperflorens for genomic and molecular genetic studies in the Rosaceae

    PubMed Central

    2009-01-01

    Background The diploid woodland strawberry (Fragaria vesca) is an attractive system for functional genomics studies. Its small stature, fast regeneration time, efficient transformability and small genome size, together with substantial EST and genomic sequence resources make it an ideal reference plant for Fragaria and other herbaceous perennials. Most importantly, this species shares gene sequence similarity and genomic microcolinearity with other members of the Rosaceae family, including large-statured tree crops (such as apple, peach and cherry), and brambles and roses as well as with the cultivated octoploid strawberry, F. ×ananassa. F. vesca may be used to quickly address questions of gene function relevant to these valuable crop species. Although some F. vesca lines have been shown to be substantially homozygous, in our hands plants in purportedly homozygous populations exhibited a range of morphological and physiological variation, confounding phenotypic analyses. We also found the genotype of a named variety, thought to be well-characterized and even sold commercially, to be in question. An easy to grow, standardized, inbred diploid Fragaria line with documented genotype that is available to all members of the research community will facilitate comparison of results among laboratories and provide the research community with a necessary tool for functionally testing the large amount of sequence data that will soon be available for peach, apple, and strawberry. Results A highly inbred line, YW5AF7, of a diploid strawberry Fragaria vesca f. semperflorens line called "Yellow Wonder" (Y2) was developed and examined. Botanical descriptors were assessed for morphological characterization of this genotype. The plant line was found to be rapidly transformable using established techniques and media formulations. Conclusion The development of the documented YW5AF7 line provides an important tool for Rosaceae functional genomic analyses. These day-neutral plants have

  2. [Expression and distribution of xenoantigen alpha-Gal in intervertebral disk of Chinese banna minipig inbred line].

    PubMed

    Shou, Jian-guo; Mi, Jian-hong; Ying, Da-jun

    2002-09-01

    To investigate the expression and distribution of xenoantigen in intervertebral disk of Chinese banna minipig inbred line, and to study the availability of xenograft transplantation of intervertebral disk. Samples of intervertebral disk were collected from six Banna pigs of 8 to 11-month-old. The fixation, embedment and slice were performed. alpha-Gal specific binding lection (BSI-B4) were used as affinity reagents and affinity-immunohistochemistry assays (SABC methods and DAB stain) were conducted to detect the expression and distribution of xenoantigen (alpha-Gal). alpha-Gal was found in chondrocyte cell and chondrocyte-like cell in intervertebral disk which have the positive yellow-stained particulate aggradation. There was no stain in the matrix, elastic fiber and collagen fiber. The distribution of xenoantigen is locally in the tissue of intervertebral disk and its expression is weak. This suggests that the intervertebral disk of Banna pig may be alternative donor for xenotransplantation.

  3. [Genetic study on two maize male sterile mutants obtained by space mutagenesis].

    PubMed

    Li, Yu-Ling; Yu, Yong-Liang; Liu, Yan-Xia; Li, Xue-Hui; Fu, Jia-Feng

    2007-06-01

    Two maize male sterile mutants were selected from the offspring of four maize inbred lines, which were carried into space by the Shenzhou spaceship 4. Their genetic characteristic and stability was analyzed in present study. Crosses were made between the male sterile plants and fertile plants from the same line, and other inbred lines with normal cytoplasm. The ratios of the sterile plants with the fertile plants in their F1, F2 generations, and their reciprocal backcross generations with the male sterile plants were calculated. The results showed that the characteristic in male sterility was stable in different years, different seasons and different locations, and was inheritable from generation to generation. This male sterile was controlled by a single nuclear recessive gene. Since no pollens or a few malformed pollens existed in the anther of the sterile plants, it was a completely sterile type.

  4. Elevated ozone reduces photosynthetic carbon gain by accelerating leaf senescence of inbred and hybrid maize in a genotype-specific manner.

    PubMed

    Yendrek, Craig R; Erice, Gorka; Montes, Christopher M; Tomaz, Tiago; Sorgini, Crystal A; Brown, Patrick J; McIntyre, Lauren M; Leakey, Andrew D B; Ainsworth, Elizabeth A

    2017-12-01

    Exposure to elevated tropospheric ozone concentration ([O 3 ]) accelerates leaf senescence in many C 3 crops. However, the effects of elevated [O 3 ] on C 4 crops including maize (Zea mays L.) are poorly understood in terms of physiological mechanism and genetic variation in sensitivity. Using free air gas concentration enrichment, we investigated the photosynthetic response of 18 diverse maize inbred and hybrid lines to season-long exposure to elevated [O 3 ] (~100 nl L -1 ) in the field. Gas exchange was measured on the leaf subtending the ear throughout the grain filling period. On average over the lifetime of the leaf, elevated [O 3 ] led to reductions in photosynthetic CO 2 assimilation of both inbred (-22%) and hybrid (-33%) genotypes. There was significant variation among both inbred and hybrid lines in the sensitivity of photosynthesis to elevated [O 3 ], with some lines showing no change in photosynthesis at elevated [O 3 ]. Based on analysis of inbred line B73, the reduced CO 2 assimilation at elevated [O 3 ] was associated with accelerated senescence decreasing photosynthetic capacity and not altered stomatal limitation. These findings across diverse maize genotypes could advance the development of more O 3 tolerant maize and provide experimental data for parameterization and validation of studies modeling how O 3 impacts crop performance. © 2017 John Wiley & Sons Ltd.

  5. Recovery of maize (Zea mays L.) inbreds and hybrids from chilling stress of various duration: photosynthesis and antioxidant enzymes.

    PubMed

    Holá, Dana; Kocová, Marie; Rothová, Olga; Wilhelmová, Nad'a; Benesová, Monika

    2007-07-01

    The differences between two maize (Zea mays L.) inbred lines and their F1 hybrids in their response to chilling periods of various duration (1, 2, 3 or 4 weeks) and subsequent return to optimum temperatures were analysed by the measurement of the photosystem (PS) 1 and 2 activity, the photosynthetic pigments' content and the activity of antioxidant enzymes. The PS2 activity and the chlorophyll content decreased in plants subjected to 3 or 4 weeks of chilling, but not in those subjected to 1 or 2 weeks of chilling. This decrease was more pronounced in inbreds compared to their hybrids. The activity of superoxide dismutase did not much change with the increasing length of chilling period in the inbreds but decreased in the hybrids, the glutathione reductase activity increased in both types of genotypes but more in the inbred lines, while for ascorbate peroxidase and catalase the changes in parents-hybrids relationship did not show any specific trend. The PS1 activity and the carotenoids' content was not much affected.

  6. Genomic methylation and transcriptomic profiling provides insights into heading depression in inbred Brassica rapa L. ssp. pekinensis.

    PubMed

    Liu, Yan; Xu, Cui; Tang, Xuebing; Pei, Surui; Jin, Di; Guo, Minghao; Yang, Meng; Zhang, Yaowei

    2018-07-30

    Inbreeding depression is the reduction in fitness observed in inbred populations. In plants, it leads to disease, weaker resistance to adverse environmental conditions, inhibition of growth, and decrease of yield. To elucidate molecular mechanisms behind inbreeding depression, we compared global DNA methylation and transcriptome profiles of a normal and a highly inbred heading degenerated variety of the Chinese cabbage (Brassica rapa L. ssp. pekinensis). DNA methylation was reduced in inbred plants, suggesting a change in the epigenetic landscape. Transcriptome analysis by RNA-Seq revealed that genes in auxin-response and synthesis pathways were differentially expressed in the inbreeding depression lines. Interestingly, methylation levels of some of those genes were also changed. Furthermore, endogenous IAA content was decreased in inbred plants, in agreement with expression and methylation data. Chemical inhibition of auxin also replicated the degenerated phenotype in normal plants, while exogenous IAA application had no effect in inbred depression plants, suggesting a more complex mechanism. These data indicate DNA methylation-regulated auxin pathways play a role in establishing inbred depression phenotypes in plants. Our findings reveal new insights into inbreeding depression and leafy head development in Chinese cabbage. Copyright © 2018 Elsevier B.V. All rights reserved.

  7. Experimental hybridization and backcrossing reveal forces of reproductive isolation in Microbotryum

    PubMed Central

    2013-01-01

    Background Hybridization and reproductive isolation are central to the origin and maintenance of species, and especially for sympatric species, gene flow is often inhibited through barriers that depend upon mating compatibility factors. The anther-smut fungi (genus Microbotryum) serve as models for speciation in the face of sympatry, and previous studies have tested for but not detected assortative mating. In addition, post-mating barriers are indicated by reduced fitness of hybrids, but sources of those barriers (i.e. ecological maladaptation or genetic incompatibilities) have not yet been detected. Here, backcrossing experiments, specifically controlling for the fungal species origins of the mating compatibility factors, were used to investigate reproductive isolation in the recently-derived species Microbotryum lychnidis-dioicae and Microbotryum silenes-dioicae. Results Assortative mating was detected during backcrossing and was manifested by the preferential conjugation of the hybrid-produced gametes with non-hybrid gametes containing mating compatibility factors from the same parental species. Patterns of post-mating performance supported either a level of extrinsic isolation mechanism, where backcross progeny with a higher proportion of the pathogen genome adapted to the particular host environment were favored, or an infection advantage attributed to greater genetic contribution to the hybrid from the M. lychnidis-dioicae genome. Conclusion The use of controlled backcrossing experiments reveals significant species-specific mating type effects on conjugations between recently-derived sister species, which are likely to play important roles in both maintaining species separation and the nature of hybrids lineages that emerge in sympatry between Microbotryum species. PMID:24112452

  8. Independent genetic control of early and late stages of chemically induced skin tumors in a cross of a Japanese wild-derived inbred mouse strain, MSM/Ms.

    PubMed

    Okumura, Kazuhiro; Sato, Miho; Saito, Megumi; Miura, Ikuo; Wakana, Shigeharu; Mao, Jian-Hua; Miyasaka, Yuki; Kominami, Ryo; Wakabayashi, Yuichi

    2012-11-01

    MSM/Ms is an inbred mouse strain derived from a Japanese wild mouse, Mus musculus molossinus. In this study, we showed that MSM/Ms mice exhibit dominant resistance when crossed with susceptible FVB/N mice and subjected to the two-stage skin carcinogenesis protocol using 7,12-dimethylbenz(a)anthracene (DMBA)/ 12-O-tetradecanoylphorbol-13-acetate (TPA). A series of F1 backcross mice were generated by crossing p53(+/+) or p53(+/-) F1 (FVB/N × MSM/Ms) males with FVB/N female mice. These generated 228 backcross animals, approximately half of which were p53(+/-), enabling us to search for p53-dependent skin tumor modifier genes. Highly significant linkage for papilloma multiplicity was found on chromosomes 6 and 7 and suggestive linkage was found on chromosomes 3, 5 and 12. Furthermore, in order to identify stage-dependent linkage loci we classified tumors into three categories (<2mm, 2-6mm and >6mm), and did linkage analysis. The same locus on chromosome 7 showed strong linkage in groups with <2mm or 2-6mm papillomas. No linkage was detected on chromosome 7 to papillomas >6mm, but a different locus on chromosome 4 showed strong linkage both to papillomas >6mm and to carcinomas. This locus, which maps near the Cdkn2a/p19(Arf) gene, was entirely p53-dependent, and was not seen in p53 (+/-) backcross animals. Suggestive linkage conferring susceptibility to carcinoma was also found on chromosome 5. These results clearly suggest distinct loci regulate each stage of tumorigenesis, some of which are p53-dependent.

  9. Crop to wild introgression in lettuce: following the fate of crop genome segments in backcross populations

    PubMed Central

    2012-01-01

    Background After crop-wild hybridization, some of the crop genomic segments may become established in wild populations through selfing of the hybrids or through backcrosses to the wild parent. This constitutes a possible route through which crop (trans)genes could become established in natural populations. The likelihood of introgression of transgenes will not only be determined by fitness effects from the transgene itself but also by the crop genes linked to it. Although lettuce is generally regarded as self-pollinating, outbreeding does occur at a low frequency. Backcrossing to wild lettuce is a likely pathway to introgression along with selfing, due to the high frequency of wild individuals relative to the rarely occurring crop-wild hybrids. To test the effect of backcrossing on the vigour of inter-specific hybrids, Lactuca serriola, the closest wild relative of cultivated lettuce, was crossed with L. sativa and the F1 hybrid was backcrossed to L. serriola to generate BC1 and BC2 populations. Experiments were conducted on progeny from selfed plants of the backcrossing families (BC1S1 and BC2S1). Plant vigour of these two backcrossing populations was determined in the greenhouse under non-stress and abiotic stress conditions (salinity, drought, and nutrient deficiency). Results Despite the decreasing contribution of crop genomic blocks in the backcross populations, the BC1S1 and BC2S1 hybrids were characterized by a substantial genetic variation under both non-stress and stress conditions. Hybrids were identified that performed equally or better than the wild genotypes, indicating that two backcrossing events did not eliminate the effect of the crop genomic segments that contributed to the vigour of the BC1 and BC2 hybrids. QTLs for plant vigour under non-stress and the various stress conditions were detected in the two populations with positive as well as negative effects from the crop. Conclusion As it was shown that the crop contributed QTLs with either a

  10. Crop to wild introgression in lettuce: following the fate of crop genome segments in backcross populations.

    PubMed

    Uwimana, Brigitte; Smulders, Marinus J M; Hooftman, Danny A P; Hartman, Yorike; van Tienderen, Peter H; Jansen, Johannes; McHale, Leah K; Michelmore, Richard W; Visser, Richard G F; van de Wiel, Clemens C M

    2012-03-26

    After crop-wild hybridization, some of the crop genomic segments may become established in wild populations through selfing of the hybrids or through backcrosses to the wild parent. This constitutes a possible route through which crop (trans)genes could become established in natural populations. The likelihood of introgression of transgenes will not only be determined by fitness effects from the transgene itself but also by the crop genes linked to it. Although lettuce is generally regarded as self-pollinating, outbreeding does occur at a low frequency. Backcrossing to wild lettuce is a likely pathway to introgression along with selfing, due to the high frequency of wild individuals relative to the rarely occurring crop-wild hybrids. To test the effect of backcrossing on the vigour of inter-specific hybrids, Lactuca serriola, the closest wild relative of cultivated lettuce, was crossed with L. sativa and the F(1) hybrid was backcrossed to L. serriola to generate BC(1) and BC(2) populations. Experiments were conducted on progeny from selfed plants of the backcrossing families (BC(1)S(1) and BC(2)S(1)). Plant vigour of these two backcrossing populations was determined in the greenhouse under non-stress and abiotic stress conditions (salinity, drought, and nutrient deficiency). Despite the decreasing contribution of crop genomic blocks in the backcross populations, the BC(1)S(1) and BC(2)S(1) hybrids were characterized by a substantial genetic variation under both non-stress and stress conditions. Hybrids were identified that performed equally or better than the wild genotypes, indicating that two backcrossing events did not eliminate the effect of the crop genomic segments that contributed to the vigour of the BC(1) and BC(2) hybrids. QTLs for plant vigour under non-stress and the various stress conditions were detected in the two populations with positive as well as negative effects from the crop. As it was shown that the crop contributed QTLs with either a positive

  11. Locating a modifier gene of Ovum mutant through crosses between DDK and C57BL/6J inbred strains in mice.

    PubMed

    Tan, Jing; Song, Gen Di; Song, Jia Sheng; Ren, Shi Hao; Li, Chun Li; Zheng, Zhen Yu; Zhao, Wei Dong

    2016-06-01

    A striking infertile phenotype has been discovered in the DDK strain of mouse. The DDK females are usually infertile when crossed with males of other inbred strains, whereas DDK males exhibit normal fertility in reciprocal crosses. This phenomenon is caused by mutation in the ovum (Om) locus on chromosome 11 and known as the DDK syndrome. Previously, some research groups reported that the embryonic mortality deviated from the semilethal rate in backcrosses between heterozygous (Om/+) females and males of other strains. This embryonic mortality exhibited an aggravated trend with increasing background genes of other strains. These results indicated that some modifier genes of Om were present in other strains. In the present study, a population of N₂2 (Om/+) females from the backcrosses between C57BL/6J (B6) and F₁ (B6♀ × DDK♂) was used to map potential modifier genes of Om. Quantitative trait locus showed that a major locus, namely Amom1 (aggravate modifier gene of Om 1), was located at the middle part of chromosome 9 in mice. The Amom1 could increase the expressivity of Om gene, thereby aggravating embryonic lethality when heterozygous (Om/+) females mated with males of B6 strain. Further, the 1.5 LOD-drop analysis indicated that the confidence interval was between 37.54 and 44.46 cM, ~6.92 cM. Amom1 is the first modifier gene of Om in the B6 background.

  12. Efficiency gain of marker-assisted backcrossing by sequentially increasing marker densities over generations.

    PubMed

    Prigge, Vanessa; Melchinger, Albrecht E; Dhillon, Baldev S; Frisch, Matthias

    2009-06-01

    Expenses for marker assays are the major costs in marker-assisted backcrossing programs for the transfer of target genes from a donor into the genetic background of a recipient genotype. Our objectives were to (1) investigate the effect of employing sequentially increasing marker densities over backcross generations on the recurrent parent genome (RPG) recovery and the number of marker data points (MDP) required, and (2) determine optimum designs for attaining RPG thresholds of 93-98% with a minimum number of MDP. We simulated the introgression of one dominant target gene for genome models of sugar beet (Beta vulgaris L.) and maize (Zea mays L.) with varying marker distances of 5-80 cM and population sizes of 30-250 plants across BC(1) to BC(3) generations. Employing less dense maps in early backcross generations resulted in savings of over 50% in the number of required MDP compared with using a constant set of markers and was accompanied only by small reductions in the attained RPG values. The optimum designs were characterized by increasing marker densities and increasing population sizes in advanced generations for both genome models. We conclude that increasing simultaneously the marker density and the population size from early to advanced backcross generations results in gene introgression with a minimum number of required MDP.

  13. QTL mapping of fruit rot resistance to the plant pathogen Phytophthora capsici in a recombinant inbred line Capsicum annuum population.

    PubMed

    Naegele, R P; Ashrafi, H; Hill, T A; Chin-Wo, S Reyes; Van Deynze, A E; Hausbeck, M K

    2014-05-01

    Phytophthora capsici is an important pepper (Capsicum annuum) pathogen causing fruit and root rot, and foliar blight in field and greenhouse production. Previously, an F6 recombinant inbred line population was evaluated for fruit rot susceptibility. Continuous variation among lines and partial and isolate-specific resistance were found. In this study, Phytophthora fruit rot resistance was mapped in the same F6 population between Criollo del Morelos 334 (CM334), a landrace from Mexico, and 'Early Jalapeno' using a high-density genetic map. Isolate-specific resistance was mapped independently in 63 of the lines evaluated and the two parents. Heritability of the resistance for each isolate at 3 and 5 days postinoculation (dpi) was high (h(2) = 0.63 to 0.68 and 0.74 to 0.83, respectively). Significant additive and epistatic quantitative trait loci (QTL) were identified for resistance to isolates OP97 and 13709 (3 and 5 dpi) and 12889 (3 dpi only). Mapping of fruit traits showed potential linkage with few disease resistance QTL. The partial fruit rot resistance from CM334 suggests that this may not be an ideal source for fruit rot resistance in pepper.

  14. Shelf life determinants and enzyme activities of pearl millet: a comparison of changes in stored flour of hybrids, CMS lines, inbreds and composites.

    PubMed

    Goyal, Preeti; Chugh, L K

    2017-09-01

    Shelf life of pearl millet flour is very short because of rapid development of rancidity. This investigation was carried out in view of generating breeding material for development of low rancid pearl millet hybrids/varieties. Flour of twenty-one genotypes; seven hybrids, seven CMS lines, five inbreds and two composites stored in covered aluminium boxes at 37 °C for 30 days along with respective fresh flour was analysed for shelf life indicators/determinants. Crude fat content and fat acidity (FA) of fresh flour of the genotypes varied from 3.8 to 7.2% and 11 to 75 mg KOH/100 g d.m., respectively. FA in stored flour ranged between 180 and 330 mg KOH/100 g d.m. After storage, magnitude of decrease in pH of water extract of flour of the genotypes varied from 0.15 to 0.44. Activity of peroxidase (POX) varied from 378 to 588 units in control flour and irrespective of the genotypes decreased upon storage. Increase in FA (difference between FA of fresh and stored flour) rather total build up of FA was positively associated with crude fat content (r = 0.440*) indicated comparatively more prominent role of lipolytic enzymes. Chemical changes taking place in water soluble fraction of flour were independent of fat content as no correlation was discerned between fat content and decrease in pH. Among the hybrids, HHB 197 had lowest crude fat content (4.7%), lowest total build up FA (212 mg KOH/100 g d.m.), slowest increase in FA (191 mg KOH/100 g d.m.), least decrease in pH (0.31) of water soluble fraction flour during storage and lowest activity of POX in fresh flour (377 units/g d.m). Among all the tested CMS lines, inbreds and composites, HBL 11 showed pattern of quantitative changes in FA, pH and POX activity similar to the hybrid HHB 197 and was identified a promising inbred for developing low-rancid pearl millet variety or hybrid.

  15. Molecular and Functional Characterization of GR2-R1 Event Based Backcross Derived Lines of Golden Rice in the Genetic Background of a Mega Rice Variety Swarna

    PubMed Central

    Bollinedi, Haritha; S., Gopala Krishnan; Prabhu, Kumble Vinod; Singh, Nagendra Kumar; Mishra, Sushma; Khurana, Jitendra P.; Singh, Ashok Kumar

    2017-01-01

    Homozygous Golden Rice lines developed in the background of Swarna through marker assisted backcross breeding (MABB) using transgenic GR2-R1 event as a donor for the provitamin A trait have high levels of provitamin A (up to 20 ppm) but are dwarf with pale green leaves and drastically reduced panicle size, grain number and yield as compared to the recurrent parent, Swarna. In this study, we carried out detailed morphological, biochemical and molecular characterization of these lines in a quest to identify the probable reasons for their abnormal phenotype. Nucleotide blast analysis with the primer sequences used to amplify the transgene revealed that the integration of transgene disrupted the native OsAux1 gene, which codes for an auxin transmembrane transporter protein. Real time expression analysis of the transgenes (ZmPsy and CrtI) driven by endosperm-specific promoter revealed the leaky expression of the transgene in the vegetative tissues. We propose that the disruption of OsAux1 disturbed the fine balance of plant growth regulators viz., auxins, gibberellic acid and abscisic acid, leading to the abnormalities in the growth and development of the lines homozygous for the transgene. The study demonstrates the conserved roles of OsAux1 gene in rice and Arabidopsis. PMID:28068433

  16. Molecular and Functional Characterization of GR2-R1 Event Based Backcross Derived Lines of Golden Rice in the Genetic Background of a Mega Rice Variety Swarna.

    PubMed

    Bollinedi, Haritha; S, Gopala Krishnan; Prabhu, Kumble Vinod; Singh, Nagendra Kumar; Mishra, Sushma; Khurana, Jitendra P; Singh, Ashok Kumar

    2017-01-01

    Homozygous Golden Rice lines developed in the background of Swarna through marker assisted backcross breeding (MABB) using transgenic GR2-R1 event as a donor for the provitamin A trait have high levels of provitamin A (up to 20 ppm) but are dwarf with pale green leaves and drastically reduced panicle size, grain number and yield as compared to the recurrent parent, Swarna. In this study, we carried out detailed morphological, biochemical and molecular characterization of these lines in a quest to identify the probable reasons for their abnormal phenotype. Nucleotide blast analysis with the primer sequences used to amplify the transgene revealed that the integration of transgene disrupted the native OsAux1 gene, which codes for an auxin transmembrane transporter protein. Real time expression analysis of the transgenes (ZmPsy and CrtI) driven by endosperm-specific promoter revealed the leaky expression of the transgene in the vegetative tissues. We propose that the disruption of OsAux1 disturbed the fine balance of plant growth regulators viz., auxins, gibberellic acid and abscisic acid, leading to the abnormalities in the growth and development of the lines homozygous for the transgene. The study demonstrates the conserved roles of OsAux1 gene in rice and Arabidopsis.

  17. Construction of integrated linkage map of a recombinant inbred line population of white lupin (Lupinus albus L.)

    PubMed Central

    Vipin, Cina Ann; Luckett, David J.; Harper, John D.I.; Ash, Gavin J.; Kilian, Andrzej; Ellwood, Simon R.; Phan, Huyen T.T.; Raman, Harsh

    2013-01-01

    We report the development of a Diversity Arrays Technology (DArT) marker panel and its utilisation in the development of an integrated genetic linkage map of white lupin (Lupinus albus L.) using an F8 recombinant inbred line population derived from Kiev Mutant/P27174. One hundred and thirty-six DArT markers were merged into the first genetic linkage map composed of 220 amplified fragment length polymorphisms (AFLPs) and 105 genic markers. The integrated map consists of 38 linkage groups of 441 markers and spans a total length of 2,169 cM, with an average interval size of 4.6 cM. The DArT markers exhibited good genome coverage and were associated with previously identified genic and AFLP markers linked with quantitative trait loci for anthracnose resistance, flowering time and alkaloid content. The improved genetic linkage map of white lupin will aid in the identification of markers for traits of interest and future syntenic studies. PMID:24273424

  18. Hybrid sterility and evolution in Hawaiian Drosophila: differential gene and allele-specific expression analysis of backcross males.

    PubMed

    Brill, E; Kang, L; Michalak, K; Michalak, P; Price, D K

    2016-08-01

    The Hawaiian Drosophila are an iconic example of sequential colonization, adaptive radiation and speciation on islands. Genetic and phenotypic analysis of closely related species pairs that exhibit incomplete reproductive isolation can provide insights into the mechanisms of speciation. Drosophila silvestris from Hawai'i Island and Drosophila planitibia from Maui are two closely related allopatric Hawaiian picture-winged Drosophila that produce sterile F1 males but fertile F1 females, a pattern consistent with Haldane's rule. Backcrossing F1 hybrid females between these two species to parental species gives rise to recombinant males with three distinct sperm phenotypes despite a similar genomic background: motile sperm, no sperm (sterile), and immotile sperm. We found that these three reproductive morphologies of backcross hybrid males produce divergent gene expression profiles in testes, as measured with RNA sequencing. There were a total of 71 genes significantly differentially expressed between backcross males with no sperm compared with those backcross males with motile sperm and immotile sperm, but no significant differential gene expression between backcross males with motile sperm and backcross males with immotile sperm. All of these genes were underexpressed in males with no sperm, including a number of genes with previously known activities in adult testis. An allele-specific expression analysis showed overwhelmingly more cis-divergent than trans-divergent genes, with no significant difference in the ratio of cis- and trans-divergent genes among the sperm phenotypes. Overall, the results indicate that the regulation of gene expression involved in sperm production likely diverged relatively rapidly between these two closely related species.

  19. Genetic Analysis of Recombinant Inbred Lines for Sorghum bicolor × Sorghum propinquum

    PubMed Central

    Kong, Wenqian; Jin, Huizhe; Franks, Cleve D.; Kim, Changsoo; Bandopadhyay, Rajib; Rana, Mukesh K.; Auckland, Susan A.; Goff, Valorie H.; Rainville, Lisa K.; Burow, Gloria B.; Woodfin, Charles; Burke, John J.; Paterson, Andrew H.

    2013-01-01

    We describe a recombinant inbred line (RIL) population of 161 F5 genotypes for the widest euploid cross that can be made to cultivated sorghum (Sorghum bicolor) using conventional techniques, S. bicolor × Sorghum propinquum, that segregates for many traits related to plant architecture, growth and development, reproduction, and life history. The genetic map of the S. bicolor × S. propinquum RILs contains 141 loci on 10 linkage groups collectively spanning 773.1 cM. Although the genetic map has DNA marker density well-suited to quantitative trait loci mapping and samples most of the genome, our previous observations that sorghum pericentromeric heterochromatin is recalcitrant to recombination is highlighted by the finding that the vast majority of recombination in sorghum is concentrated in small regions of euchromatin that are distal to most chromosomes. The advancement of the RIL population in an environment to which the S. bicolor parent was well adapted (indeed bred for) but the S. propinquum parent was not largely eliminated an allele for short-day flowering that confounded many other traits, for example, permitting us to map new quantitative trait loci for flowering that previously eluded detection. Additional recombination that has accrued in the development of this RIL population also may have improved resolution of apices of heterozygote excess, accounting for their greater abundance in the F5 than the F2 generation. The S. bicolor × S. propinquum RIL population offers advantages over early-generation populations that will shed new light on genetic, environmental, and physiological/biochemical factors that regulate plant growth and development. PMID:23316442

  20. Genetic analysis of recombinant inbred lines for Sorghum bicolor × Sorghum propinquum.

    PubMed

    Kong, Wenqian; Jin, Huizhe; Franks, Cleve D; Kim, Changsoo; Bandopadhyay, Rajib; Rana, Mukesh K; Auckland, Susan A; Goff, Valorie H; Rainville, Lisa K; Burow, Gloria B; Woodfin, Charles; Burke, John J; Paterson, Andrew H

    2013-01-01

    We describe a recombinant inbred line (RIL) population of 161 F5 genotypes for the widest euploid cross that can be made to cultivated sorghum (Sorghum bicolor) using conventional techniques, S. bicolor × Sorghum propinquum, that segregates for many traits related to plant architecture, growth and development, reproduction, and life history. The genetic map of the S. bicolor × S. propinquum RILs contains 141 loci on 10 linkage groups collectively spanning 773.1 cM. Although the genetic map has DNA marker density well-suited to quantitative trait loci mapping and samples most of the genome, our previous observations that sorghum pericentromeric heterochromatin is recalcitrant to recombination is highlighted by the finding that the vast majority of recombination in sorghum is concentrated in small regions of euchromatin that are distal to most chromosomes. The advancement of the RIL population in an environment to which the S. bicolor parent was well adapted (indeed bred for) but the S. propinquum parent was not largely eliminated an allele for short-day flowering that confounded many other traits, for example, permitting us to map new quantitative trait loci for flowering that previously eluded detection. Additional recombination that has accrued in the development of this RIL population also may have improved resolution of apices of heterozygote excess, accounting for their greater abundance in the F5 than the F2 generation. The S. bicolor × S. propinquum RIL population offers advantages over early-generation populations that will shed new light on genetic, environmental, and physiological/biochemical factors that regulate plant growth and development.

  1. Evaluation of the Morpho-physiology characteristics of maize inbred lines introduced from CIMMYT to identify the best candidates for planting in acidic soil in Jasinga, Indonesia

    NASA Astrophysics Data System (ADS)

    Lubis, K.; Sutjahjo, S. H.; Syukur, M.; Trikoesoemaningtyas

    2016-08-01

    Technological developments and climate change have affected crop planting strategies. For example, maize production has expanded to sub-optimal lands, including acidic soil common in areas like Indonesia. Breeding programs have created inbred lines of maize introduced from CIMMYT; they were tested locally in acidic soils to determine their adaptability and tolerance mechanisms. Breeds CLA 46 and NEI 9008 were found to be excellent candidates for acidic soil due to their ASI, high number of grains per year, and suitable dry seed weight.

  2. Quantitative Trait Loci for Cold Tolerance of Rice Recombinant Inbred Lines in Low Temperature Environments

    PubMed Central

    Jiang, Wenzhu; Jin, Yong-Mei; Lee, Joohyun; Lee, Kang-Ie; Piao, Rihua; Han, Longzhi; Shin, Jin-Chul; Jin, Rong-De; Cao, Tiehua; Pan, Hong-Yu; Du, Xinglin; Koh, Hee-Jong

    2011-01-01

    Low temperature is one of the major environmental stresses in rice cultivation in high-altitude and high-latitude regions. In this study, we cultivated a set of recombinant inbred lines (RIL) derived from Dasanbyeo (indica) / TR22183 (japonica) crosses in Yanji (high-latitude area), Kunming (high-altitude area), Chuncheon (cold water irrigation) and Suwon (normal) to evaluate the main effects of quantitative trait loci (QTL) and epistatic QTL (E-QTL) with regard to their interactions with environments for coldrelated traits. Six QTLs for spikelet fertility (SF) were identified in three cold treatment locations. Among them, four QTLs on chromosomes 2, 7, 8, and 10 were validated by several near isogenic lines (NILs) under cold treatment in Chuncheon. A total of 57 QTLs and 76 E-QTLs for nine cold-related traits were identified as distributing on all 12 chromosomes; among them, 19 QTLs and E-QTLs showed significant interactions of QTLs and environments (QEIs). The total phenotypic variation explained by each trait ranged from 13.2 to 29.1% in QTLs, 10.6 to 29.0% in EQTLs, 2.2 to 8.8% in QEIs and 1.0% to 7.7% in E-QTL × environment interactions (E-QEIs). These results demonstrate that epistatic effects and QEIs are important properties of QTL parameters for cold tolerance at the reproductive stage. In order to develop cold tolerant varieties adaptable to wide-ranges of cold stress, a strategy facilitating marker-assisted selection (MAS) is being adopted to accumulate QTLs identified from different environments. PMID:22080374

  3. Genome-wide identification of gene expression in contrasting maize inbred lines under field drought conditions reveals the significance of transcription factors in drought tolerance

    PubMed Central

    Zhang, Xiaojing; Liu, Xuyang; Zhang, Dengfeng; Tang, Huaijun; Sun, Baocheng; Li, Chunhui; Hao, Luyang; Liu, Cheng; Li, Yongxiang; Shi, Yunsu; Xie, Xiaoqing; Song, Yanchun; Wang, Tianyu; Li, Yu

    2017-01-01

    Drought is a major threat to maize growth and production. Understanding the molecular regulation network of drought tolerance in maize is of great importance. In this study, two maize inbred lines with contrasting drought tolerance were tested in the field under natural soil drought and well-watered conditions. In addition, the transcriptomes of their leaves was analyzed by RNA-Seq. In total, 555 and 2,558 genes were detected to specifically respond to drought in the tolerant and the sensitive line, respectively, with a more positive regulation tendency in the tolerant genotype. Furthermore, 4,700, 4,748, 4,403 and 4,288 genes showed differential expression between the two lines under moderate drought, severe drought and their well-watered controls, respectively. Transcription factors were enriched in both genotypic differentially expressed genes and specifically responsive genes of the tolerant line. It was speculated that the genotype-specific response of 20 transcription factors in the tolerance line and the sustained genotypically differential expression of 22 transcription factors might enhance tolerance to drought in maize. Our results provide new insight into maize drought tolerance-related regulation systems and provide gene resources for subsequent studies and drought tolerance improvement. PMID:28700592

  4. The importance of site quality to backcross chestnut establishment success

    Treesearch

    C.C. Pinchot; A.A. Royo; M.P. Peters; S.E. Schlarbaum; S.L. Anagnostakis

    2017-01-01

    Short-term studies show that American chestnut (Castanea dentata) grows faster on mesic compared to xeric sites. Long-term impacts of site quality and corresponding moisture and nutrient availability on backcross chestnut establishment success and resistance to the chestnut blight fungus, Cryphonectria parasitica, however, have...

  5. Introgression of heat shock protein (Hsp70 and sHsp) genes into the Malaysian elite chilli variety Kulai (Capsicum annuum L.) through the application of marker-assisted backcrossing (MAB).

    PubMed

    Usman, Magaji G; Rafii, Mohd Y; Martini, Mohammad Y; Yusuff, Oladosu A; Ismail, Mohd R; Miah, Gous

    2018-03-01

    Backcrossing together with simple sequence repeat marker strategy was adopted to improve popular Malaysian chilli Kulai (Capsicum annuum L.) for heat tolerance. The use of molecular markers in backcross breeding and selection contributes significantly to overcoming the main drawbacks such as increase linkage drag and time consumption, in the ancient manual breeding approach (conventional), and speeds up the genome recovery of the recurrent parent. The strategy was adopted to introgress heat shock protein gene(s) from AVPP0702 (C. annuum L.), which are heat-tolerant, into the genetic profile of Kulai, a popular high-yielding chilli but which is heat sensitive. The parents were grown on seed trays, and parental screening was carried out with 252 simple sequence repeat markers. The selected parents were crossed and backcrossed to generate F 1 hybrids and backcross generations. Sixty-eight markers appeared to be polymorphic and were used to assess the backcross generation; BC 1 F 1 , BC 2 F 1 and BC 3 F 1 . The average recipient allele of the selected four BC 1 F 1 plants was 80.75% which were used to produce the BC 2 F 1 generation. BC 1 -P 7 was the best BC 1 F 1 plant because it had the highest recovery at 83.40% and was positive to Hsp-linked markers (Hsp70-u2 and AGi42). After three successive generations of backcrossing, the average genome recovery of the recurrent parent in the selected plants in BC 3 F 1 was 95.37%. Hsp gene expression analysis was carried out on BC 1 F 1 , BC 2 F 1 and BC 3 F 1 selected lines. The Hsp genes were found to be up-regulated when exposed to heat treatment. The pattern of Hsp expression in the backcross generations was similar to that of the donor parent. This confirms the successful introgression of a stress-responsive gene (Hsp) into a Kulai chilli pepper variety. Furthermore, the yield performance viz. plant height, number of fruits, fruit length and weight and total yield of the improved plant were similar with the recurrent

  6. Gibberellins Promote Brassinosteroids Action and Both Increase Heterosis for Plant Height in Maize (Zea mays L.)

    PubMed Central

    Hu, Songlin; Wang, Cuiling; Sanchez, Darlene L.; Lipka, Alexander E.; Liu, Peng; Yin, Yanhai; Blanco, Michael; Lübberstedt, Thomas

    2017-01-01

    Brassinosteroids (BRs) and Gibberellins (GAs) are two classes of plant hormones affecting plant height (PHT). Thus, manipulation of BR and GA levels or signaling enables optimization of crop grain and biomass yields. We established backcross (BC) families, selected for increased PHT, in two elite maize inbred backgrounds. Various exotic accessions used in the germplasm enhancement in maize project served as donors. BC1-derived doubled haploid lines in the same two elite maize inbred backgrounds established without selection for plant height were included for comparison. We conducted genome-wide association studies to explore the genetic control of PHT by BR and GA. In addition, we used BR and GA inhibitors to compare the relationship between PHT, BR, and GA in inbred lines and heterozygotes from a physiological and biological perspective. A total of 73 genomic loci were discovered to be associated with PHT, with seven co-localized with GA, and two co-localized with BR candidate genes. PHT determined in field trials was significantly correlated with seedling stage BR and GA inhibitor responses. However, this observation was only true for maize heterozygotes, not for inbred lines. Path analysis results suggest that heterozygosity increases GA levels, which in turn promote BR levels. Thus, at least part of heterosis for PHT in maize can be explained by increased GA and BR levels, and seedling stage hormone inhibitor response is promising to predict heterosis for PHT. PMID:28676808

  7. Do transgenesis and marker-assisted backcross breeding produce substantially equivalent plants? A comparative study of transgenic and backcross rice carrying bacterial blight resistant gene Xa21.

    PubMed

    Gao, Lifen; Cao, Yinghao; Xia, Zhihui; Jiang, Guanghuai; Liu, Guozhen; Zhang, Weixiong; Zhai, Wenxue

    2013-10-29

    The potential impact of genetically modified (GM) plants on human health has attracted much attention worldwide, and the issue remains controversial. This is in sharp contrast to the broad acceptance of plants produced by breeding through Marker Assisted Backcrossing (MAB). Focusing on transcriptome variation and perturbation to signaling pathways, we assessed the molecular and biological aspects of substantial equivalence, a general principle for food safety endorsed by the Food and Agricultural Organization and the World Health Organization, between a transgenic crop and a plant from MAB breeding. We compared a transgenic rice line (DXT) and a MAB rice line (DXB), both of which contain the gene Xa21 providing resistance to bacterial leaf blight. By using Next-Generation sequencing data of DXT, DXB and their parental line (D62B), we compared the transcriptome variation of DXT and DXB. Remarkably, DXT had 43% fewer differentially expressed genes (DEGs) than DXB. The genes exclusively expressed in DXT and in DXB have pathogen and stress defense functions. Functional categories of DEGs in DXT were comparable to that in DXB, and seven of the eleven pathways significantly affected by transgenesis were also perturbed by MAB breeding. These results indicated that the transgenic rice and rice from MAB breeding are substantial equivalent at the transcriptome level, and paved a way for further study of transgenic rice, e.g., understanding the chemical and nutritional properties of the DEGs identified in the current study.

  8. Do transgenesis and marker-assisted backcross breeding produce substantially equivalent plants? - A comparative study of transgenic and backcross rice carrying bacterial blight resistant gene Xa21

    PubMed Central

    2013-01-01

    Background The potential impact of genetically modified (GM) plants on human health has attracted much attention worldwide, and the issue remains controversial. This is in sharp contrast to the broad acceptance of plants produced by breeding through Marker Assisted Backcrossing (MAB). Results Focusing on transcriptome variation and perturbation to signaling pathways, we assessed the molecular and biological aspects of substantial equivalence, a general principle for food safety endorsed by the Food and Agricultural Organization and the World Health Organization, between a transgenic crop and a plant from MAB breeding. We compared a transgenic rice line (DXT) and a MAB rice line (DXB), both of which contain the gene Xa21 providing resistance to bacterial leaf blight. By using Next-Generation sequencing data of DXT, DXB and their parental line (D62B), we compared the transcriptome variation of DXT and DXB. Remarkably, DXT had 43% fewer differentially expressed genes (DEGs) than DXB. The genes exclusively expressed in DXT and in DXB have pathogen and stress defense functions. Functional categories of DEGs in DXT were comparable to that in DXB, and seven of the eleven pathways significantly affected by transgenesis were also perturbed by MAB breeding. Conclusions These results indicated that the transgenic rice and rice from MAB breeding are substantial equivalent at the transcriptome level, and paved a way for further study of transgenic rice, e.g., understanding the chemical and nutritional properties of the DEGs identified in the current study. PMID:24165682

  9. GWAS analysis using interspecific backcross progenies reveals superior blue catfish alleles responsible for strong resistance against enteric septicemia of catfish.

    PubMed

    Tan, Suxu; Zhou, Tao; Wang, Wenwen; Jin, Yulin; Wang, Xiaozhu; Geng, Xin; Luo, Jian; Yuan, Zihao; Yang, Yujia; Shi, Huitong; Gao, Dongya; Dunham, Rex; Liu, Zhanjiang

    2018-05-08

    Infectious diseases pose significant threats to the catfish industry. Enteric septicemia of catfish (ESC) caused by Edwardsiella ictaluri is the most devastating disease for catfish aquaculture, causing huge economic losses annually. Channel catfish and blue catfish exhibit great contrast in resistance against ESC, with channel catfish being highly susceptible and blue catfish being highly resistant. As such, the interspecific backcross progenies provide an ideal system for the identification of quantitative trait locus (QTL). We previously reported one significant QTL on linkage group (LG) 1 using the third-generation backcrosses, but the number of founders used to make the second- and third-generation backcross progenies was very small. Although the third-generation backcross progenies provided a greater power for fine mapping than the first-generation backcrosses, some major QTL for disease resistance may have been missing due to the small numbers of founders used to produce the higher generation backcrosses. In this study, we performed a genome-wide association study using first-generation backcrosses with the catfish 690 K SNP arrays to identify additional ESC disease resistance QTL, especially those at the species level. Two genomic regions on LG1 and LG23 were determined to be significantly associated with ESC resistance as revealed by a mixed linear model and family-based association test. Examination of the resistance alleles indicated their origin from blue catfish, indicating that at least two major disease resistance loci exist among blue catfish populations. Upon further validation, markers linked with major ESC disease resistance QTL should be useful for marker-assisted introgression, allowing development of highly ESC resistant breeds of catfish.

  10. Genetic analysis and identification of SSR markers associated with rice blast disease in a BC2F1 backcross population.

    PubMed

    Hasan, N; Rafii, M Y; Abdul Rahim, H; Nusaibah, S A; Mazlan, N; Abdullah, S

    2017-01-23

    Rice (Oryza sativa L.) blast disease is one of the most destructive rice diseases in the world. The fungal pathogen, Magnaporthe oryzae, is the causal agent of rice blast disease. Development of resistant cultivars is the most preferred method to achieve sustainable rice production. However, the effectiveness of resistant cultivars is hindered by the genetic plasticity of the pathogen genome. Therefore, information on genetic resistance and virulence stability are vital to increase our understanding of the molecular basis of blast disease resistance. The present study set out to elucidate the resistance pattern and identify potential simple sequence repeat markers linked with rice blast disease. A backcross population (BC 2 F 1 ), derived from crossing MR264 and Pongsu Seribu 2 (PS2), was developed using marker-assisted backcross breeding. Twelve microsatellite markers carrying the blast resistance gene clearly demonstrated a polymorphic pattern between both parental lines. Among these, two markers, RM206 and RM5961, located on chromosome 11 exhibited the expected 1:1 testcross ratio in the BC 2 F 1 population. The 195 BC 2 F 1 plants inoculated against M. oryzae pathotype P7.2 showed a significantly different distribution in the backcrossed generation and followed Mendelian segregation based on a single-gene model. This indicates that blast resistance in PS2 is governed by a single dominant gene, which is linked to RM206 and RM5961 on chromosome 11. The findings presented in this study could be useful for future blast resistance studies in rice breeding programs.

  11. Analysis of quantitative trait loci affecting chlorophyll content of rice leaves in a double haploid population and two backcross populations.

    PubMed

    Jiang, Gonghao; Zeng, Jing; He, Yuqing

    2014-02-25

    Chlorophyll content, one of the most important physiological parameters related to plant photosynthesis, is usually used to predict yield potential. To map the quantitative trait loci (QTLs) underlying the chlorophyll content of rice leaves, a double haploid (DH) population was developed from an indica/japonica (Zhenshan 97/Wuyujing 2) crossing and two backcross populations were established subsequently by backcrossing DH lines with each of their parents. The contents of chlorophyll a and chlorophyll b were determined by using a spectrophotometer to directly measure the leaf chlorophyll extracts. To determine the leaf chlorophyll retention along with maturation, all measurements were performed on the day of heading and were repeated 30 days later. A total of 60 QTLs were resolved for all the traits using these three populations. These QTLs were distributed on 10 rice chromosomes, except chromosomes 5 and 10; the closer the traits, the more clustering of the QTLs residing on common rice chromosomal regions. In general, the majority of QTLs that specify chlorophyll a content also play a role in determining chlorophyll b content. Strangely, chlorophyll content in this study was found mostly to be lacking or to have a negative correlation with yield. In both backcross F1 populations, overdominant (or underdominant) loci were more important than complete or partially dominant loci for main-effect QTLs and epistatic QTLs, thereby supporting previous findings that overdominant effects are the primary genetic basis for depression in inbreeding and heterosis in rice. Copyright © 2013 Elsevier B.V. All rights reserved.

  12. Sensitivity of inbred and selectively bred mice to ethanol.

    PubMed

    Smolen, A; Smolen, T N; van de Kamp, J L

    1987-01-01

    The Long-Sleep (LS) and Short-Sleep (SS) mice were bred for differences in sensitivity to ethanol as measured by duration of loss of the righting response (sleep time). The foundation population was a heterogeneous stock (HS) which was derived from a cross of eight inbred strains. Ethanol-induced sleep time and waking blood and brain ethanol levels were measured in the eight inbred strains, LS, SS and HS mice. The C3H and ISBI strains were quite resistant to ethanol as measured by sleep time, and only one, RIII, was very sensitive. Waking ethanol concentrations were similar for all of the inbreds, implying a narrow range of central nervous system sensitivity to ethanol. The HS mice had relatively short sleep times and blood ethanol levels equal to most of the inbred. The LS mice were significantly more, and the SS mice significantly less sensitive to ethanol than any of the inbreds or HS mice. These studies suggest that the extremes of CNS sensitivities to ethanol manifested by the LS and SS mice cannot be traced to any of the inbred strains, and must have arisen through the selection process by changes in allelic frequencies of those genes conferring ethanol sensitivity and resistance.

  13. Codominant expression of genes coding for different sets of inducible salivary polypeptides associated with parotid hypertrophy in two inbred mouse strains.

    PubMed

    López-Solís, Remigio O; Kemmerling, Ulrike

    2005-05-01

    Experimental mouse parotid hypertrophy has been associated with the expression of a number of isoproterenol-induced salivary proline-rich polypeptides (IISPs). Mouse salivary proline-rich proteins (PRPs) have been mapped both to chromosomes 6 and 8. Recently, mice of two inbred strains (A/Snell and A. Swiss) have been found to differ drastically in the IISPs. In this study, mice of both strains were used for cross-breeding experiments addressed to define the pattern of inheritance of the IISP phenotype and to establish whether the IISPs are coded on a single or on several chromosomes. The IISP phenotype of individual mice was assessed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of whole saliva collected after three daily stimulations by isoproterenol. Parental A/Snell and A. Swiss mice were homogeneous for distinctive strain-associated IISP-patterns. First filial generation (F1) mice obtained from the cross of A/Snell with A. Swiss mice expressed with no exception both the A/Snell and A. Swiss IISPs (coexpression). In the second filial generation (F2) both parental IISP phenotypes reappeared together with a majority of mice expressing the F1-hybrid phenotype (1:2:1 ratio). Backcrosses of F1 x A/Snell and F1 x A. Swiss produced offsprings displaying the F1 and the corresponding parental phenotypes with a 1:1 ratio. No recombinants were observed among F2 mice or among mice resulting from backcrosses. Thus, genes coding for the IISPs that are expressed differentially in both mouse strains are located on the same chromosome, probably at the same locus (alleles) or at quite closely linked loci (nonalleles). 2005 Wiley-Liss, Inc

  14. Transcriptome Analyses of Mosaic (MSC) Mitochondrial Mutants of Cucumber in a Highly Inbred Nuclear Background

    PubMed Central

    Mróz, Tomasz L.; Eves-van den Akker, Sebastian; Bernat, Agata; Skarzyńska, Agnieszka; Pryszcz, Leszek; Olberg, Madeline; Havey, Michael J.; Bartoszewski, Grzegorz

    2018-01-01

    Cucumber (Cucumis sativus L.) has a large, paternally transmitted mitochondrial genome. Cucumber plants regenerated from cell cultures occasionally show paternally transmitted mosaic (MSC) phenotypes, characterized by slower growth, chlorotic patterns on the leaves and fruit, lower fertility, and rearrangements in their mitochondrial DNAs (mtDNAs). MSC lines 3, 12, and 16 originated from different cell cultures all established using the highly inbred, wild-type line B. These MSC lines possess different rearrangements and under-represented regions in their mtDNAs. We completed RNA-seq on normalized and non-normalized cDNA libraries from MSC3, MSC12, and MSC16 to study their nuclear gene-expression profiles relative to inbred B. Results from both libraries indicated that gene expression in MSC12 and MSC16 were more similar to each other than MSC3. Forty-one differentially expressed genes (DEGs) were upregulated and one downregulated in the MSC lines relative to B. Gene functional classifications revealed that more than half of these DEGs are associated with stress-response pathways. Consistent with this observation, we detected elevated levels of hydrogen peroxide throughout leaf tissue in all MSC lines compared to wild-type line B. These results demonstrate that independently produced MSC lines with different mitochondrial polymorphisms show unique and shared nuclear responses. This study revealed genes associated with stress response that could become selection targets to develop cucumber cultivars with increased stress tolerance, and further support of cucumber as a model plant to study nuclear-mitochondrial interactions. PMID:29330162

  15. Identification of quantitative trait Loci for resistance to southern leaf blight and days to anthesis in a maize recombinant inbred line population.

    PubMed

    Balint-Kurti, P J; Krakowsky, M D; Jines, M P; Robertson, L A; Molnár, T L; Goodman, M M; Holl, J B

    2006-10-01

    ABSTRACT A recombinant inbred line population derived from a cross between the maize lines NC300 (resistant) and B104 (susceptible) was evaluated for resistance to southern leaf blight (SLB) disease caused by Cochliobolus heterostrophus race O and for days to anthesis in four environments (Clayton, NC, and Tifton, GA, in both 2004 and 2005). Entry mean and average genetic correlations between disease ratings in different environments were high (0.78 to 0.89 and 0.9, respectively) and the overall entry mean heritability for SLB resistance was 0.89. When weighted mean disease ratings were fitted to a model using multiple interval mapping, seven potential quantitative trait loci (QTL) were identified, the two strongest being on chromosomes 3 (bin 3.04) and 9 (bin 9.03-9.04). These QTL explained a combined 80% of the phenotypic variation for SLB resistance. Some time-point-specific SLB resistance QTL were also identified. There was no significant correlation between disease resistance and days to anthesis. Six putative QTL for time to anthesis were identified, none of which coincided with any SLB resistance QTL.

  16. QTL mapping of stalk bending strength in a recombinant inbred line maize population.

    PubMed

    Hu, Haixiao; Liu, Wenxin; Fu, Zhiyi; Homann, Linda; Technow, Frank; Wang, Hongwu; Song, Chengliang; Li, Shitu; Melchinger, Albrecht E; Chen, Shaojiang

    2013-09-01

    Stalk bending strength (SBS) is a reliable indicator for evaluating stalk lodging resistance of maize plants. Based on biomechanical considerations, the maximum load exerted to breaking (F max), the breaking moment (M max) and critical stress (σ max) are three important parameters to characterize SBS. We investigated the genetic architecture of SBS by phenotyping F max, M max and σ max of the fourth internode of maize plants in a population of 216 recombinant inbred lines derived from the cross B73 × Ce03005 evaluated in four environments. Heritability of F max, M max and σ max was 0.81, 0.79 and 0.75, respectively. F max and σ max were positively correlated with several other stalk characters. By using a linkage map with 129 SSR markers, we detected two, three and two quantitative trait loci (QTL) explaining 22.4, 26.1 and 17.2 % of the genotypic variance for F max, M max and σ max, respectively. The QTL for F max, M max and σ max located in adjacent bins 5.02 and 5.03 as well as in bin 10.04 for F max were detected with high frequencies in cross-validation. As our QTL mapping results suggested a complex polygenic inheritance for SBS-related traits, we also evaluated the prediction accuracy of two genomic prediction methods (GBLUP and BayesB). In general, we found that both explained considerably higher proportions of the genetic variance than the values obtained in QTL mapping with cross-validation. Nevertheless, the identified QTL regions could be used as a starting point for fine mapping and gene cloning.

  17. Comparative miRNAs analysis of Two contrasting broccoli inbred lines with divergent head-forming capacity under temperature stress.

    PubMed

    Chen, Chi-Chien; Fu, Shih-Feng; Norikazu, Monma; Yang, Yau-Wen; Liu, Yu-Ju; Ikeo, Kazuho; Gojobori, Takashi; Huang, Hao-Jen

    2015-12-01

    MicroRNAs (miRNAs) play a vital role in growth, development, and stress response at the post-transcriptional level. Broccoli (Brassica oleracea L. var italic) is an important vegetable crop, and the yield and quality of broccoli are decreased by heat stress. The broccoli inbred lines that are capable of producing head at high temperature in summer are unique varieties in Taiwan. However, knowledge of miRNAomes during the broccoli head formation under heat stress is limited. In this study, molecular characterization of two nearly isogenic lines with contrasting head-forming capacity was investigated. Head-forming capacity was better for heat-tolerant (HT) than heat-sensitive (HS) broccoli under heat stress. By deep sequencing and computational analysis, 20 known miRNAs showed significant differential expression between HT and HS genotypes. According to the criteria for annotation of new miRNAs, 24 novel miRNA sequences with differential expression between the two genotypes were identified. To gain insight into functional significance, 213 unique potential targets of these 44 differentially expressed miRNAs were predicted. These targets were implicated in shoot apical development, phase change, response to temperature stimulus, hormone and energy metabolism. The head-forming capacity of the unique HT line was related to autonomous regulation of Bo-FT genes and less expression level of heat shock protein genes as compared to HS. For the genotypic comparison, a set of miRNAs and their targets had consistent expression patterns in various HT genotypes. This large-scale characterization of broccoli miRNAs and their potential targets is to unravel the regulatory roles of miRNAs underlying heat-tolerant head-forming capacity.

  18. Evaluation of virus resistance and agronomic performance of rice cultivar ASD 16 after transfer of transgene against Rice tungro bacilliform virus by backcross breeding.

    PubMed

    Valarmathi, P; Kumar, G; Robin, S; Manonmani, S; Dasgupta, I; Rabindran, R

    2016-08-01

    Severe losses of rice yield in south and southeast Asia are caused by Rice tungro disease (RTD) induced by mixed infection of Rice tungro bacilliform virus (RTBV) and Rice tungro spherical virus (RTSV). In order to develop transgene-based resistance against RTBV, one of its genes, ORF IV, was used to generate transgenic resistance based on RNA-interference in the easily transformed rice variety Pusa Basmati-1, and the transgene was subsequently introgressed to rice variety ASD 16, a variety popular in southern India, using transgene marker-assisted selection. Here, we report the evaluation of BC3F4 and BC3F5 generation rice plants for resistance to RTBV as well as for agronomic traits under glasshouse conditions. The BC3F4 and BC3F5 generation rice plants tested showed variable levels of resistance, which was manifested by an average of twofold amelioration in height reduction, 1.5-fold decrease in the reduction in chlorophyll content, and 100- to 10,000-fold reduction in the titers of RTBV, but no reduction of RTSV titers, in three backcrossed lines when compared with the ASD 16 parent. Agronomic traits of some of the backcrossed lines recorded substantial improvements when compared with the ASD 16 parental line after inoculation by RTBV and RTSV. This work represents an important step in transferring RTD resistance to a susceptible popular rice variety, hence enhancing its yield in areas threatened by the disease.

  19. Quantitative trait loci underlying resistance to sudden death syndrome (SDS) in MD96-5722 by 'Spencer' recombinant inbred line population of soybean.

    PubMed

    Anderson, J; Akond, M; Kassem, M A; Meksem, K; Kantartzi, S K

    2015-04-01

    The best way to protect yield loss of soybean [Glycine max (L.) Merr.] due to sudden death syndrome (SDS), caused by Fusarium virguliforme (Aoki, O'Donnel, Homma & Lattanzi), is the development and use of resistant lines. Mapping quantitative trait loci (QTL) linked to SDS help developing resistant soybean germplasm through molecular marker-assisted selection strategy. QTL for SDS presented herein are from a high-density SNP-based genetic linkage map of MD 96-5722 (a.k.a 'Monocacy') by 'Spencer' recombinant inbred line using SoySNP6K Illumina Infinium BeadChip genotyping array. Ninety-four F 5:7 lines were evaluated for 2 years (2010 and 2011) at two locations (Carbondale and Valmeyer) in southern Illinois, USA to identify QTL controlling SDS resistance using disease index (DX). Composite interval mapping identified 19 SDS controlling QTL which were mapped on 11 separate linkage group (LG) or chromosomes (Chr) out of 20 LG or Chr of soybean genome. Many of these significant QTL identified in one environment/year were confirmed in another year or environment, which suggests a common genetic effects and modes of the pathogen. These new QTL are useful sources for SDS resistance studies in soybean breeding, complementing previously reported loci.

  20. Quantitative trait loci for response to ethanol in an intercontinental set of recombinant inbred lines of Drosophila melanogaster.

    PubMed

    Defays, Raquel; Bertoli, Carlos Ignacio

    2012-12-01

    Alcohol, a drug widely abused, impacts the central nervous system functioning of diverse organisms. The behavioral responses to acute alcohol exposure are remarkably similar among humans and fruit flies. In its natural environment, rich in fermentation products, the fruit fly Drosophila melanogaster encounters relatively high levels of ethanol. The effects of ethanol and its metabolites on Drosophila have been studied for decades, as a model for adaptive evolution. Although extensive work has been done for elucidating patterns of genetic variation, substantially less is known about the genomic regions or genes that underlie the genetic variation of this important trait. To identify regions containing genes involved in the responses to ethanol, we used a mapping population of recombinant inbred (RIL) lines to map quantitative trait loci (QTL) that affect variation in resistance and recovery from ethanol sedation in adults and ethanol resistance in larvae. We mapped fourteen QTL affecting the response to ethanol on the three chromosomes. Seven of the QTL influence the resistance to ethanol in adults, two QTL are related to ethanol-coma recovery in adults and five affect the survival to ethanol in larvae. Most of the QTL were trait specific, suggesting that overlapping but generally unique genetic architectures underlie each trait. Each QTL explained up to 16.8% of the genetic variance among lines. Potential candidate loci contained within our QTL regions were identified and analyzed. Copyright © 2012 Elsevier Inc. All rights reserved.

  1. Targeted Recombinant Progeny: a design for ultra-high resolution mapping of Quantitative Trait Loci in crosses between inbred or pure lines.

    PubMed

    Heifetz, Eliyahu M; Soller, Morris

    2015-07-07

    High-resolution mapping of the loci (QTN) responsible for genetic variation in quantitative traits is essential for positional cloning of candidate genes, and for effective marker assisted selection. The confidence interval (QTL) flanking the point estimate of QTN-location is proportional to the number of individuals in the mapping population carrying chromosomes recombinant in the given interval. Consequently, many designs for high resolution QTN mapping are based on increasing the proportion of recombinants in the mapping population. The "Targeted Recombinant Progeny" (TRP) design is a new design for high resolution mapping of a target QTN in crosses between pure, or inbred lines. It is a three-generation procedure generating a large number of recombinant individuals within a QTL previously shown to contain a QTN. This is achieved by having individuals that carry chromosomes recombinant across the target QTL interval as parents of a large mapping population; most of whom will therefore carry recombinant chromosomes targeted to the given QTL. The TRP design is particularly useful for high resolution mapping of QTN that differentiate inbred or pure lines, and hence are not amenable to high resolution mapping by genome-wide association tests. In the absence of residual polygenic variation, population sizes required for achieving given mapping resolution by the TRP-F2 design relative to a standard F2 design ranged from 0.289 for a QTN with standardized allele substitution effect = 0.2, mapped to an initial QTL of 0.2 Morgan to 0.041 for equivalent QTN mapped to an initial QTL of 0.02 M. In the presence of residual polygenic variation, the relative effectiveness of the TRP design ranges from 1.068 to 0.151 for the same initial QTL intervals and QTN effect. Thus even in the presence of polygenic variation, the TRP can still provide major savings. Simulation showed that mapping by TRP should be based on 30-50 markers spanning the initial interval; and on at least 50 or

  2. Comprehensive genotyping of the USA national maize inbred seed bank

    PubMed Central

    2013-01-01

    Background Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world. Results The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. More than half of the SNPs in the collection are rare. Although most rare alleles have been incorporated into public temperate breeding programs, only a modest amount of the available diversity is present in the commercial germplasm. Analysis of genetic distances shows population stratification, including a small number of large clusters centered on key lines. Nevertheless, an average fixation index of 0.06 indicates moderate differentiation between the three major maize subpopulations. Linkage disequilibrium (LD) decays very rapidly, but the extent of LD is highly dependent on the particular group of germplasm and region of the genome. The utility of these data for performing genome-wide association studies was tested with two simply inherited traits and one complex trait. We identified trait associations at SNPs very close to known candidate genes for kernel color, sweet corn, and flowering time; however, results suggest that more SNPs are needed to better explore the genetic architecture of complex traits. Conclusions The genotypic information described here allows this publicly available panel to be exploited by researchers facing the challenges of sustainable agriculture through better knowledge of the nature of genetic diversity. PMID:23759205

  3. Comprehensive genotyping of the USA national maize inbred seed bank.

    PubMed

    Romay, Maria C; Millard, Mark J; Glaubitz, Jeffrey C; Peiffer, Jason A; Swarts, Kelly L; Casstevens, Terry M; Elshire, Robert J; Acharya, Charlotte B; Mitchell, Sharon E; Flint-Garcia, Sherry A; McMullen, Michael D; Holland, James B; Buckler, Edward S; Gardner, Candice A

    2013-06-11

    Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world. The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. More than half of the SNPs in the collection are rare. Although most rare alleles have been incorporated into public temperate breeding programs, only a modest amount of the available diversity is present in the commercial germplasm. Analysis of genetic distances shows population stratification, including a small number of large clusters centered on key lines. Nevertheless, an average fixation index of 0.06 indicates moderate differentiation between the three major maize subpopulations. Linkage disequilibrium (LD) decays very rapidly, but the extent of LD is highly dependent on the particular group of germplasm and region of the genome. The utility of these data for performing genome-wide association studies was tested with two simply inherited traits and one complex trait. We identified trait associations at SNPs very close to known candidate genes for kernel color, sweet corn, and flowering time; however, results suggest that more SNPs are needed to better explore the genetic architecture of complex traits. The genotypic information described here allows this publicly available panel to be exploited by researchers facing the challenges of sustainable agriculture through better knowledge of the nature of genetic diversity.

  4. Effect of x-ray irradiation on maize inbred line B73 tissue cultures and regenerated plants

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wang, A.S.; Cheng, D.S.K.; Milcic, J.B.

    In order to enhance variation induced by the tissue culture process and to obtain agronomically desirable mutants, friable embryogenic tissue cultures of maize (Zea mays L.) inbred line B73 were x-ray irradiated with 11 doses (0-8.4 kilorads (kR)). Reductions in callus growth rate and embryogenic callus formation occurred with increasing x-ray doses 20 d and 3 months after irradiation. Callus irradiated with 0.8 kR showed a significant increase in growth rate and a 20% increase in embryogenic callus 9 months after irradiation. A total of 230 R/sub 0/ plants were regenerated for evaluation. Pollen fertility and seed set of R/submore » 0/ plants decreased with increasing x-ray dosage. Days to anthesis and plant height of R/sub 0/ plants varied among x-ray treatments but were generally reduced with higher dosages. The number of chromosomal aberrations increased with x-ray dosage. The R/sub 1/ seeds taken from R/sub 0/ plants were also grown and tested for mutant segregation. Plants regenerated from irradiated calli had a two- to 10-fold increase in mutations over plants regenerated from unirradiated control callus. Germination frequency of seeds from R/sub 0/ plants decreased with increasing x-ray dosage. Although chlorophyll mutants were most frequently observed, a number of vigorous plants with earlier anthesis date were also recovered.« less

  5. Genetic control of the honey bee (Apis mellifera) dance language: segregating dance forms in a backcrossed colony.

    PubMed

    Johnson, R N; Oldroyd, B P; Barron, A B; Crozier, R H

    2002-01-01

    We studied the genetic control of the dance dialects that exist in the different subspecies of honey bees (Apis mellifera) by observing the variation in dance form observed in a backcross between two lines that showed widely different dance dialects. To do this we generated the reciprocal of the cross performed by Rinderer and Beaman (1995), thus producing phenotypic segregation of dance forms within a single colony rather than between colonies. Our results are consistent with Rinderer and Beaman (1995) in that inheritance of the transition point from round dancing --> waggle dancing is consistent with control by a single locus with more than one allele. That is, we found one dance type to be dominant in the F(1), and observed a 1:1 segregation of dance in a backcross involving the F(1) and the recessive parent. However, we found some minor differences in dance dialect inheritance, with the most significant being an apparent reversal of dominance between our cross (for us "black" is the dominant dialect) and that of Rinderer and Beaman (1995) (they report "yellow" to be the dominant dialect). We also found that our black bees do not perform a distinct sickle dance, whereas the black bees used by Rinderer and Beaman (1995) did perform such a dance. However, our difference in dominance need not contradict the results of Rinderer and Beaman (1995), as there is no evidence that body color and dominance for dance dialect are linked.

  6. Transfer of Dicamba Tolerance from Sinapis arvensis to Brassica napus via Embryo Rescue and Recurrent Backcross Breeding.

    PubMed

    Jugulam, M; Ziauddin, Asma; So, Kenny K Y; Chen, Shu; Hall, J Christopher

    2015-01-01

    Auxinic herbicides (e.g. dicamba) are extensively used in agriculture to selectively control broadleaf weeds. Although cultivated species of Brassicaceae (e.g. Canola) are susceptible to auxinic herbicides, some biotypes of Sinapis arvensis (wild mustard) were found dicamba resistant in Canada. In this research, dicamba tolerance from wild mustard was introgressed into canola through embryo rescue followed by conventional breeding. Intergeneric hybrids between S. arvensis (2n = 18) and B. napus (2n = 38) were produced through embryo rescue. Embryo formation and hybrid plant regeneration was achieved. Transfer of dicamba tolerance from S. arvensis into the hybrid plants was determined by molecular analysis and at the whole plant level. Dicamba tolerance was introgressed into B. napus by backcrossing for seven generations. Homozygous dicamba-tolerant B. napus lines were identified. The ploidy of the hybrid progeny was assessed by flow cytometry. Finally, introgression of the piece of DNA possibly containing the dicamba tolerance gene into B. napus was confirmed using florescence in situ hybridization (FISH). This research demonstrates for the first time stable introgression of dicamba tolerance from S. arvensis into B. napus via in vitro embryo rescue followed by repeated backcross breeding. Creation of dicamba-tolerant B. napus varieties by this approach may have potential to provide options to growers to choose a desirable herbicide-tolerant technology. Furthermore, adoption of such technology facilitates effective weed control, less tillage, and possibly minimize evolution of herbicide resistant weeds.

  7. Correlation of intact sensibility and neuropathic pain-related behaviors in eight inbred and outbred rat strains and selection lines.

    PubMed

    Shir, Y; Zeltser, R; Vatine, J J; Carmi, G; Belfer, I; Zangen, A; Overstreet, D; Raber, P; Seltzer, Z

    2001-02-01

    In some rat strains, total hindpaw denervation triggers autotomy, a behavior of self mutilation presumably related to neuropathic pain. Partial sciatic ligation (PSL) in rats produces tactile allodynia and heat hyperalgesia but not autotomy. Our aims in this study were to examine: (1) whether sensibility of intact rats to noxious and non-noxious stimuli is strain-dependent; (2) whether sensibility of intact rats could predict levels of autotomy, or of allodynia and hyperalgesia in the PSL model; and (3) whether autotomy levels are correlated with levels of allodynia or hyperalgesia. Here we report that in two inbred rat strains (Lewis and Fisher 344), two outbred rat strains (Sabra and Sprague-Dawley) and four selection lines of rats (Genetically Epilepsy-Prone Rats, High Autotomy, Low Autotomy and Flinders Sensitive Line), tactile sensitivity and response duration to noxious heat of intact animals were strain-dependent. Levels of autotomy following hindpaw denervation and of allodynia and hyperalgesia in the PSL model were also strain-dependent. Thus, these traits are determined in part by genetic factors. Sensory sensibility of intact rats was not correlated with levels of autotomy following total denervation, or allodynia and hyperalgesia following partial denervation. We suggest that preoperative sensibility of intact rats is not a predictor of levels of neuropathic disorders following nerve injury. Likewise, no correlation was found between autotomy, allodynia and hyperalgesia, suggesting that neuropathic pain behaviors triggered by nerve injury of different etiologies are mediated by differing mechanisms.

  8. Inhibition of non-enzymatic glycation by silk extracts from a Mexican land race and modern inbred lines of maize (Zea mays).

    PubMed

    Farsi, Darius Arthur; Harris, Cory S; Reid, Lana; Bennett, Steffany A L; Haddad, Pierre S; Martineau, Louis C; Arnason, John Thor

    2008-01-01

    Non-enzymatic glycation and the accumulation of advanced glycation end products (AGEs) are associated with various disease states, including complications of diabetes and aging. Secondary metabolites from several plant species are known to inhibit non-enzymatic glycation and the formation of AGEs, including flavonoids found in the style (silk) of Zea mays (maize). Thirteen modern maize inbreds and one land race were tested for in vitro inhibition of non-enzymatic glycation of bovine serum albumin. Many of the tested extracts exhibited inhibitory activity, in particular the newest inbreds, which were bred for resistance to gibberella ear rot (Fusarium graminearum) and common smut (Ustilago maydis). The most active maize genotype (CO441), displaying an IC50 of 9.5 microg/mL, was more effective than aminoguanidine, a known inhibitor of glycation. Zapalote chico, a land race with high maysin content, showed only moderate inhibitory activity compared with the modern maize genotypes. Antiglycation activity was highly correlated with the total phenolic content of silk extracts and mildly correlated with resistance to certain fungal infections. The results identify modern resistant and high phenolic maize inbreds as promising candidates for the development of natural AGE inhibitors for the prevention and treatment of diabetic complications and the degenerative effects of aging. Copyright (c) 2007 John Wiley & Sons, Ltd.

  9. Construction and characterisation of near-isogenic Plutella xylostella (Lepidoptera: Plutellidae) strains resistant to Cry1Ac toxin.

    PubMed

    Zhu, Xun; Lei, Yanyuan; Yang, Yanjv; Baxter, Simon W; Li, Jianhong; Wu, Qingjun; Wang, Shaoli; Xie, Wen; Guo, Zhaojiang; Fu, Wei; Zhang, Youjun

    2015-02-01

    Resistance to insecticidal Bacillus thuringiensis (Bt) toxins has arisen in multiple populations of the worldwide Brassica pest Plutella xylostella (L.). To help elucidate the mechanism of resistance to Bt Cry1Ac toxin in a population from Florida, two pairs of near-isogenic lines (NILs) were developed. NILs were generated using either backcross or recombinant inbred line methodologies and evaluated for near-isogenicity with inter-simple-sequence-repeat (ISSR) markers. Backcross line BC6F4 maintained a similar level of Cry1Ac resistance to parental strain DBM1Ac-R (>5000-fold) yet showed 98.24% genetic similarity to the susceptible parental strain DBM1Ac-S. Single-pair backcrosses between DBM1Ac-S and BC6F4 revealed that Cry1Ac resistance was controlled by one recessive autosomal locus. BC6F4 exhibited high levels of cross-resistance to Cry1Ab and Cry1Ah but not to Cry1Ca or Cry1Ie. Near-isogenic strains were constructed to provide a reliable biological system to investigate the mechanism of Cry1Ac resistance in P. xylostella. These data suggest that resistance to Cry1Ac, Cry1Ab and Cry1Ah is probably caused by the alteration of a common receptor not recognised by Cry1Ca or Cry1Ie. Understanding Bt toxin cross-resistance provides valuable information to consider when developing pest control strategies to delay resistance evolution. © 2014 Society of Chemical Industry. © 2014 Society of Chemical Industry.

  10. Genotyping-by-sequencing highlights original diversity patterns within a European collection of 1191 maize flint lines, as compared to the maize USDA genebank.

    PubMed

    Gouesnard, Brigitte; Negro, Sandra; Laffray, Amélie; Glaubitz, Jeff; Melchinger, Albrecht; Revilla, Pedro; Moreno-Gonzalez, Jesus; Madur, Delphine; Combes, Valérie; Tollon-Cordet, Christine; Laborde, Jacques; Kermarrec, Dominique; Bauland, Cyril; Moreau, Laurence; Charcosset, Alain; Nicolas, Stéphane

    2017-10-01

    Genotyping by sequencing is suitable for analysis of global diversity in maize. We showed the distinctiveness of flint maize inbred lines of interest to enrich the diversity of breeding programs. Genotyping-by-sequencing (GBS) is a highly cost-effective procedure that permits the analysis of large collections of inbred lines. We used it to characterize diversity in 1191 maize flint inbred lines from the INRA collection, the European Cornfed association panel, and lines recently derived from landraces. We analyzed the properties of GBS data obtained with different imputation methods, through comparison with a 50 K SNP array. We identified seven ancestral groups within the Flint collection (dent, Northern flint, Italy, Pyrenees-Galicia, Argentina, Lacaune, Popcorn) in agreement with breeding knowledge. Analysis highlighted many crosses between different origins and the improvement of flint germplasm with dent germplasm. We performed association studies on different agronomic traits, revealing SNPs associated with cob color, kernel color, and male flowering time variation. We compared the diversity of both our collection and the USDA collection which has been previously analyzed by GBS. The population structure of the 4001 inbred lines confirmed the influence of the historical inbred lines (B73, A632, Oh43, Mo17, W182E, PH207, and Wf9) within the dent group. It showed distinctly different tropical and popcorn groups, a sweet-Northern flint group and a flint group sub-structured in Italian and European flint (Pyrenees-Galicia and Lacaune) groups. Interestingly, we identified several selective sweeps between dent, flint, and tropical inbred lines that co-localized with SNPs associated with flowering time variation. The joint analysis of collections by GBS offers opportunities for a global diversity analysis of maize inbred lines.

  11. QTL Mapping of Agronomic Waterlogging Tolerance Using Recombinant Inbred Lines Derived from Tropical Maize (Zea mays L) Germplasm

    PubMed Central

    Zaidi, Pervez Haider; Rashid, Zerka; Vinayan, Madhumal Thayil; Almeida, Gustavo Dias; Phagna, Ramesh Kumar; Babu, Raman

    2015-01-01

    Waterlogging is an important abiotic stress constraint that causes significant yield losses in maize grown throughout south and south-east Asia due to erratic rainfall patterns. The most economic option to offset the damage caused by waterlogging is to genetically incorporate tolerance in cultivars that are grown widely in the target agro-ecologies. We assessed the genetic variation in a population of recombinant inbred lines (RILs) derived from crossing a waterlogging tolerant line (CAWL-46-3-1) to an elite but sensitive line (CML311-2-1-3) and observed significant range of variation for grain yield (GY) under waterlogging stress along with a number of other secondary traits such as brace roots (BR), chlorophyll content (SPAD), % stem and root lodging (S&RL) among the RILs. Significant positive correlation of GY with BR and SPAD and negative correlation with S&RL indicated the potential use of these secondary traits in selection indices under waterlogged conditions. RILs were genotyped with 331 polymorphic single nucleotide polymorphism (SNP) markers using KASP (Kompetitive Allele Specific PCR) Platform. QTL mapping revealed five QTL on chromosomes 1, 3, 5, 7 and 10, which together explained approximately 30% of phenotypic variance for GY based on evaluation of RIL families under waterlogged conditions, with effects ranging from 520 to 640 kg/ha for individual genomic regions. 13 QTL were identified for various secondary traits associated with waterlogging tolerance, each individually explaining from 3 to 14% of phenotypic variance. Of the 22 candidate genes with known functional domains identified within the physical intervals delimited by the flanking markers of the QTL influencing GY and other secondary traits, six have previously been demonstrated to be associated with anaerobic responses in either maize or other model species. A pair of flanking SNP markers has been identified for each of the QTL and high throughput marker assays were developed to facilitate

  12. QTL mapping of agronomic waterlogging tolerance using recombinant inbred lines derived from tropical maize (Zea mays L) germplasm.

    PubMed

    Zaidi, Pervez Haider; Rashid, Zerka; Vinayan, Madhumal Thayil; Almeida, Gustavo Dias; Phagna, Ramesh Kumar; Babu, Raman

    2015-01-01

    Waterlogging is an important abiotic stress constraint that causes significant yield losses in maize grown throughout south and south-east Asia due to erratic rainfall patterns. The most economic option to offset the damage caused by waterlogging is to genetically incorporate tolerance in cultivars that are grown widely in the target agro-ecologies. We assessed the genetic variation in a population of recombinant inbred lines (RILs) derived from crossing a waterlogging tolerant line (CAWL-46-3-1) to an elite but sensitive line (CML311-2-1-3) and observed significant range of variation for grain yield (GY) under waterlogging stress along with a number of other secondary traits such as brace roots (BR), chlorophyll content (SPAD), % stem and root lodging (S&RL) among the RILs. Significant positive correlation of GY with BR and SPAD and negative correlation with S&RL indicated the potential use of these secondary traits in selection indices under waterlogged conditions. RILs were genotyped with 331 polymorphic single nucleotide polymorphism (SNP) markers using KASP (Kompetitive Allele Specific PCR) Platform. QTL mapping revealed five QTL on chromosomes 1, 3, 5, 7 and 10, which together explained approximately 30% of phenotypic variance for GY based on evaluation of RIL families under waterlogged conditions, with effects ranging from 520 to 640 kg/ha for individual genomic regions. 13 QTL were identified for various secondary traits associated with waterlogging tolerance, each individually explaining from 3 to 14% of phenotypic variance. Of the 22 candidate genes with known functional domains identified within the physical intervals delimited by the flanking markers of the QTL influencing GY and other secondary traits, six have previously been demonstrated to be associated with anaerobic responses in either maize or other model species. A pair of flanking SNP markers has been identified for each of the QTL and high throughput marker assays were developed to facilitate

  13. Divergence and inheritance of neocortical heterotopia in inbred and genetically-engineered mice.

    PubMed

    Toia, Alyssa R; Cuoco, Joshua A; Esposito, Anthony W; Ahsan, Jawad; Joshi, Alok; Herron, Bruce J; Torres, German; Bolivar, Valerie J; Ramos, Raddy L

    2017-01-18

    Cortical function emerges from the intrinsic properties of neocortical neurons and their synaptic connections within and across lamina. Neurodevelopmental disorders affecting migration and lamination of the neocortex result in cognitive delay/disability and epilepsy. Molecular layer heterotopia (MLH), a dysplasia characterized by over-migration of neurons into layer I, are associated with cognitive deficits and neuronal hyperexcitability in humans and mice. The breadth of different inbred mouse strains that exhibit MLH and inheritance patterns of heterotopia remain unknown. A neuroanatomical survey of numerous different inbred mouse strains, 2 first filial generation (F1) hybrids, and one consomic strain (C57BL/6J-Chr 1 A/J /NaJ) revealed MLH only in C57BL/6 mice and the consomic strain. Heterotopia were observed in numerous genetically-engineered mouse lines on a congenic C57BL/6 background. These data indicate that heterotopia formation is a weakly penetrant trait requiring homozygosity of one or more C57BL/6 alleles outside of chromosome 1. These data are relevant toward understanding neocortical development and disorders affecting neocortical lamination. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  14. [A Study of the Relationship Among Genetic Distances, NIR Spectra Distances, and NIR-Based Identification Model Performance of the Seeds of Maize Iinbred Lines].

    PubMed

    Liu, Xu; Jia, Shi-qiang; Wang, Chun-ying; Liu, Zhe; Gu, Jian-cheng; Zhai, Wei; Li, Shao-ming; Zhang, Xiao-dong; Zhu, De-hai; Huang, Hua-jun; An, Dong

    2015-09-01

    This paper explored the relationship among genetic distances, NIR spectra distances and NIR-based identification model performance of the seeds of maize inbred lines. Using 3 groups (total 15 pairs) of maize inbred lines whose genetic distaches are different as experimental materials, we calculates the genetic distance between these seeds with SSR markers and uses Euclidean distance between distributed center points of maize NIR spectrum in the PCA space as the distances of NIR spectrum. BPR method is used to build identification model of inbred lines and the identification accuracy is used as a measure of model identification performance. The results showed that, the correlation of genetic distance and spectra distancesis 0.9868, and it has a correlation of 0.9110 with the identification accuracy, which is highly correlated. This means near-Infrared spectrum of seedscan reflect genetic relationship of maize inbred lines. The smaller the genetic distance, the smaller the distance of spectrum, the poorer ability of model to identify. In practical application, near infrared spectrum analysis technology has the potential to be used to analyze maize inbred genetic relations, contributing much to genetic breeding, identification of species, purity sorting and so on. What's more, when creating a NIR-based identification model, the impact of the maize inbred lines which have closer genetic relationship should be fully considered.

  15. Leaf physiology and morphology of Castanea dentata (Marsh) Borkh., Castanea mollissima Blume, and three backcross breeding generations planted in the southern Appalachians, USA

    Treesearch

    Benjamin O. Knapp; G. Geoff Wang; Stacy L Clark; Lauren S. Pile; Scott E. Schlarbaum

    2014-01-01

    Backcross breeding programs have been used to transfer disease resistance and other traits from one forest tree species to another in order to meet restoration objectives. Evaluating the field performance of such material is critical for determining the success of breeding programs. In eastern North America, The American Chestnut Foundation has a backcross breeding...

  16. Interspecific hybridization, polyploidization, and backcross of Brassica oleracea var. alboglabra with B. rapa var. purpurea morphologically recapitulate the evolution of Brassica vegetables

    PubMed Central

    Zhang, Xiaohui; Liu, Tongjin; Li, Xixiang; Duan, Mengmeng; Wang, Jinglei; Qiu, Yang; Wang, Haiping; Song, Jiangping; Shen, Di

    2016-01-01

    Brassica oleracea and B. rapa are two important vegetable crops. Both are composed of dozens of subspecies encompassing hundreds of varieties and cultivars. Synthetic B. napus with these two plants has been used extensively as a research model for the investigation of allopolyploid evolution. However, the mechanism underlying the explosive evolution of hundreds of varieties of B. oleracea and B. rapa within a short period is poorly understood. In the present study, interspecific hybridization between B. oleracea var. alboglabra and B. rapa var. purpurea was performed. The backcross progeny displayed extensive morphological variation, including some individuals that phenocopied subspecies other than their progenitors. Numerous interesting novel phenotypes and mutants were identified among the backcross progeny. The chromosomal recombination between the A and C genomes and the chromosomal asymmetric segregation were revealed using Simple Sequence Repeats (SSR) markers. These findings provide direct evidence in support of the hypothesis that interspecific hybridization and backcrossing have played roles in the evolution of the vast variety of vegetables among these species and suggest that combination of interspecific hybridization and backcrossing may facilitate the development of new mutants and novel phenotypes for both basic research and the breeding of new vegetable crops. PMID:26727246

  17. Interspecific hybridization, polyploidization, and backcross of Brassica oleracea var. alboglabra with B. rapa var. purpurea morphologically recapitulate the evolution of Brassica vegetables.

    PubMed

    Zhang, Xiaohui; Liu, Tongjin; Li, Xixiang; Duan, Mengmeng; Wang, Jinglei; Qiu, Yang; Wang, Haiping; Song, Jiangping; Shen, Di

    2016-01-04

    Brassica oleracea and B. rapa are two important vegetable crops. Both are composed of dozens of subspecies encompassing hundreds of varieties and cultivars. Synthetic B. napus with these two plants has been used extensively as a research model for the investigation of allopolyploid evolution. However, the mechanism underlying the explosive evolution of hundreds of varieties of B. oleracea and B. rapa within a short period is poorly understood. In the present study, interspecific hybridization between B. oleracea var. alboglabra and B. rapa var. purpurea was performed. The backcross progeny displayed extensive morphological variation, including some individuals that phenocopied subspecies other than their progenitors. Numerous interesting novel phenotypes and mutants were identified among the backcross progeny. The chromosomal recombination between the A and C genomes and the chromosomal asymmetric segregation were revealed using Simple Sequence Repeats (SSR) markers. These findings provide direct evidence in support of the hypothesis that interspecific hybridization and backcrossing have played roles in the evolution of the vast variety of vegetables among these species and suggest that combination of interspecific hybridization and backcrossing may facilitate the development of new mutants and novel phenotypes for both basic research and the breeding of new vegetable crops.

  18. Impacts of using inbred animals in studies for detection of quantitative trait loci.

    PubMed

    Freyer, G; Vukasinovic, N; Cassell, B

    2009-02-01

    Effects of utilizing inbred and noninbred family structures in experiments for detection of quantitative trait loci (QTL) were compared in this simulation study. Simulations were based on a general pedigree design originating from 2 unrelated sires. A variance component approach of mapping QTL was applied to simulated data that reflected common family structures from dairy populations. Five different family structures were considered: FS0 without inbreeding, FS1 with an inbred sire from an aunt-nephew mating, FS2 with an inbred sire originating from a half-sib mating, FS3 and FS4 based on FS2 but containing an increased number of offspring of the inbred sire (FS3), and another extremely inbred sire with its final offspring (FS4). Sixty replicates each of the 5 family structures in 2 simulation scenarios each were analyzed to provide a praxis-like situation of QTL analysis. The largest proportion of QTL position estimates within the correct interval of 3 cM, best test statistic profiles and the smallest average bias were obtained from the pedigrees described by FS4 and FS2. The approach does not depend on the kind and number of genetic markers. Inbreeding is not a recommended practice for commercial dairy production because of possible inbreeding depression, but inbred animals and their offspring that already exist could be advantageous for QTL mapping, because of reduced genetic variance in inbred parents.

  19. Effect of Teosinte Cytoplasmic Genomes on Maize Phenotype

    PubMed Central

    Allen, James O.

    2005-01-01

    Determining the contribution of organelle genes to plant phenotype is hampered by several factors, including the paucity of variation in the plastid and mitochondrial genomes. To circumvent this problem, evolutionary divergence between maize (Zea mays ssp. mays) and the teosintes, its closest relatives, was utilized as a source of cytoplasmic genetic variation. Maize lines in which the maize organelle genomes were replaced through serial backcrossing by those representing the entire genus, yielding alloplasmic sublines, or cytolines were created. To avoid the confounding effects of segregating nuclear alleles, an inbred maize line was utilized. Cytolines with Z. mays teosinte cytoplasms were generally indistinguishable from maize. However, cytolines with cytoplasm from the more distantly related Z. luxurians, Z. diploperennis, or Z. perennis exhibited a plethora of differences in growth, development, morphology, and function. Significant differences were observed for 56 of the 58 characters studied. Each cytoline was significantly different from the inbred line for most characters. For a given character, variation was often greater among cytolines having cytoplasms from the same species than among those from different species. The characters differed largely independently of each other. These results suggest that the cytoplasm contributes significantly to a large proportion of plant traits and that many of the organelle genes are phenotypically important. PMID:15731518

  20. Differences in susceptibility of inbred mice to Bacillus anthracis.

    PubMed Central

    Welkos, S L; Keener, T J; Gibbs, P H

    1986-01-01

    Animal species differ in their resistance both to infection by Bacillus anthracis and to anthrax toxin. A mouse model was developed to study the basis of the host differences and the pathogenesis of infection. When mice were infected with the virulent B. anthracis strain Vollum 1B, low 50% lethal dose (LD50) values (5 to 30 spores) were found for all 10 strains of inbred mice tested. However, analysis of time-to-death data revealed significant differences among the strains, which could be divided into three groups: most susceptible (A/J and DBA/2J); least susceptible (CBA/J, BALB/cJ, and C57BR/cdJ); and intermediate (the remaining five strains). In contrast, the mice were distinctly susceptible or resistant to lethal infection by the toxigenic, nonencapsulated Sterne vaccine strain. The LD50 for the susceptible A/J and DBA/2J mice was approximately 10(3) spores of the Sterne strain, whereas the remaining eight relatively resistant strains were killed only by 10(6) or more spores. F1 hybrid and backcross studies suggested that resistance to the Sterne strain is determined by a single dominant gene or gene complex. Mice lethally infected with B. anthracis showed an acute course of infection, characterized by extensive gelatinous edema and large concentrations of bacilli in the blood and organs (e.g., 10(9) CFU/g of spleen). The susceptibility of A/J and CBA/J mice to intravenously injected anthrax toxin components appeared to differ from their susceptibility to infection. The toxin LD50 values for both strains were similar. However, CBA/J mice died sooner than did A/J mice, with mean time to death of 0.9 and 3.7 days, respectively, in mice given 4 LD50 of toxin. The mouse model appears to be useful in studies on host resistance to anthrax and on the pathogenesis of the infection. PMID:3081444

  1. [Intergration and epression of porcine endogenous retrovinus in the immortal cell line of Banna Minipig Inberd Line-Mesenhymal Stem Cells].

    PubMed

    Yu, Ping; Liu, Jin; Zhang, Li; Li, Shrng-Fu; Bu, Hong; Li, You-Ping; Cheng, Jing-Qui; Lu, Yan-Rong; Long, Dan

    2005-11-01

    To detect the integration and expression of porcine endogenous retrovirus (PERV) in the immortal cell line of Banna Minipig Inbred Line-Mesenchymal Stem Cells (BMI-MSCs). DNA and total RNA of the immortal cell line of BMI-MSCs were extracted and PCR, RT-PCR were performed to detect PERV-gag, pol and env gene, and the type of PERV was also detected. PERV-gag, pol and env gene were all detected in the primary culture and immortal cell line (passage 150 and passage 180) of BMI-MSCs, and the type of PERV was PERV-A, B. Functional expression of PERV-gag and pol mRNA was also detected. In this laboratory, PERV was not lost during the proceeding of pig inbred and since has been in long-term culture of pig cells in vitro. PERV has integrated into the genome of its natural host, and virus mRNA can effectively express. So it is very essential to evaluate the possibility of xenozoonoses in pig-to-human xenotransplantation.

  2. Chromosomal localization of Emv-16 and Emv-17, two closely linked ecotropic proviruses of RF/J mice.

    PubMed Central

    Buchberg, A M; Taylor, B A; Jenkins, N A; Copeland, N G

    1986-01-01

    Emv-16 and Emv-17, the two closely linked ecotropic proviral loci of RF/J mice, have been mapped to chromosome 1 between leaden, ln, and the mouse engrailed homeo-box locus, En-1, by using recombinant inbred strains and conventional backcross analysis. Images PMID:2878091

  3. Condition, innate immunity and disease mortality of inbred crows

    PubMed Central

    Townsend, Andrea K.; Clark, Anne B.; McGowan, Kevin J.; Miller, Andrew D.; Buckles, Elizabeth L.

    2010-01-01

    Cooperatively breeding American crows (Corvus brachyrhynchos) suffer a severe disease-mediated survival cost from inbreeding, but the proximate mechanisms linking inbreeding to disease are unknown. Here, we examine indices of nestling body condition and innate immunocompetence in relationship to inbreeding and disease mortality. Using an estimate of microsatellite heterozygosity that predicts inbreeding in this population, we show that inbred crows were in relatively poor condition as nestlings, and that body condition index measured in the first 2–33 days after hatching, in addition to inbreeding index, predicted disease probability in the first 34 months of life. Inbred nestlings also mounted a weaker response along one axis of innate immunity: the proportion of bacteria killed in a microbiocidal assay increased as heterozygosity index increased. Relatively poor body condition and low innate immunocompetence are two mechanisms that might predispose inbred crows to ultimate disease mortality. A better understanding of condition-mediated inbreeding depression can guide efforts to minimize disease costs of inbreeding in small populations. PMID:20444716

  4. Monoamines and glycogen levels in cerebral cortices of fast and slow methionine sulfoximine-inbred mice.

    PubMed

    Boissonnet, Arnaud; Hévor, Tobias; Landemarre, Ludovic; Cloix, Jean-François

    2013-05-01

    The experimental model of seizures which depends upon methionine sulfoximine (MSO) simulates the most striking form of human epilepsy. MSO generates epileptiform seizures in a large variety of animals, increases brain glycogen content and induces brain monoamines modifications. We selected two inbred lines of mice based upon their latency toward MSO-dependent seizures, named as MSO-Fast (sensitive), having short latency toward MSO, and MSO-Slow (resistant) with a long latency. We determined 13 monoamines and glycogen contents in brain cortices of the MSO-Fast and slow lines in order to determine the relationships with MSO-dependent seizures. The present data show that using these MSO-Fast and MSO-Slow inbred lines it could be demonstrated that: (1) in basal conditions the neurotransmitter 5-HT is significantly higher in MSO-Fast mice than in MSO-Slow ones; (2) MSO in both lines induced a significant increase in brain content of DOPAC (3,4-dihydroxyphenylacetic acid), HVA (homovanillic acid), MHPG (3-methoxy-4-hydroxyphenylglycol), and 5-HT (serotonin); a significant decrease in MSO-Slow mice in brain content of NME (normetepinephrine), and 5-HIAA (5-hydroxyindoleacetic acid) and the variation of other monoamines were not significant; (3) the brain glycogen content is significantly higher in MSO-Fast mice than in MSO-Slow ones, both in basal conditions and after MSO administration. From our data, we propose that brain glycogen content may constitute a defense against epileptic attack, as glycogen may be degraded down to glucose-6-phosphate that can be used to either postpone the epileptic attack or to provide neurons with energy when they needed it. Brain glycogen might therefore be considered as a molecule that can contribute to struggle seizures, at least in MSO-dependent seizure. The 5-HT content may constitute a defense against MSO-dependent epilepsy. Copyright © 2013 Elsevier B.V. All rights reserved.

  5. Mapping Stripe Rust Resistance in a BrundageXCoda Winter Wheat Recombinant Inbred Line Population

    PubMed Central

    Case, Austin J.; Naruoka, Yukiko; Chen, Xianming; Garland-Campbell, Kimberly A.; Zemetra, Robert S.; Carter, Arron H.

    2014-01-01

    A recombinant inbred line (RIL) mapping population developed from a cross between winter wheat (Triticum aestivum L.) cultivars Coda and Brundage was evaluated for reaction to stripe rust (caused by Puccinia striiformis f. sp. tritici). Two hundred and sixty eight RIL from the population were evaluated in replicated field trials in a total of nine site-year locations in the U.S. Pacific Northwest. Seedling reaction to stripe rust races PST-100, PST-114 and PST-127 was also examined. A linkage map consisting of 2,391 polymorphic DNA markers was developed covering all chromosomes of wheat with the exception of 1D. Two QTL on chromosome 1B were associated with adult plant and seedling reaction and were the most significant QTL detected. Together these QTL reduced adult plant infection type from a score of seven to a score of two reduced disease severity by an average of 25% and provided protection against race PST-100, PST-114 and PST-127 in the seedling stage. The location of these QTL and the race specificity provided by them suggest that observed effects at this locus are due to a complementation of the previously known but defeated resistances of the cultivar Tres combining with that of Madsen (the two parent cultivars of Coda). Two additional QTL on chromosome 3B and one on 5B were associated with adult plant reaction only, and a single QTL on chromosome 5D was associated with seedling reaction to PST-114. Coda has been resistant to stripe rust since its release in 2000, indicating that combining multiple resistance genes for stripe rust provides durable resistance, especially when all-stage resistance genes are combined in a fashion to maximize the number of races they protect against. Identified molecular markers will allow for an efficient transfer of these genes into other cultivars, thereby continuing to provide excellent resistance to stripe rust. PMID:24642574

  6. Evaluation of grain dimension and weight using backcross recombinant inbred lines (BRILs) between wild and domesticated Emmer wheat

    USDA-ARS?s Scientific Manuscript database

    Emmer wheat (Triticum turgidum ssp. dicoccum) represents the primitive situation in the domestication of AABB tetraploid wheat. As one of the earliest domesticated grain species, it was a principal crop in the development and spread of Neolithic agriculture in the Old World. Grain weight and dimensi...

  7. Evaluation of grain dimension and weight using backcross recombinant inbred lines (BRILs) between wild and domesticated emmer wheat

    USDA-ARS?s Scientific Manuscript database

    Emmer wheat (Triticum turgidum ssp. dicoccum) represents the primitive situation in the domestication of AABB tetraploid wheat. As one of the earliest domesticated grain species, it was a principal crop in the development and spread of Neolithic agriculture in the Old World. Grain weight and dimensi...

  8. Production of hybrids, amphiploids and backcross progenies between a cold-tolerant wild species, Erucastrum abyssinicum and crop brassicas.

    PubMed

    Rao, G U; Lakshmikumaran, M; Shivanna, K R

    1996-05-01

    Three intergeneric hybrids were produced between a cold-tolerant wild species, Erucastrum abyssinicum and three cultivated species of Brassica, B. juncea, B. carinata and B. oleracea, through ovary culture. The hybrids were characterized by morphology, cytology and DNA analysis. Amphiploidy was induced in all the F1 hybrids through colchicine treatment. Stable amphiploids and backcross progenies were obtained from two of the crosses, E. abyssinicum x B. juncea and E. abyssinicum x B. carinata. The amphiploid, E. abyssinicum x B. juncea was successfully used as a bridge species to produce hybrids with B. napus, B. campestris and B. nigra. These hybrids and backcross progenies provide useful genetic variability for the improvement of crop brassicas.

  9. Comparative performance of hybrid and elite inbred rice varieties with respect to their source-sink relationship.

    PubMed

    Haque, Md Moinul; Pramanik, Habibur Rahman; Biswas, Jiban Krishna; Iftekharuddaula, K M; Hasanuzzaman, Mirza

    2015-01-01

    Hybrid rice varieties have higher yield potential over inbred varieties. This improvement is not always translated to the grain yield and its physiological causes are still unclear. In order to clarify it, two field experiments were conducted including two popular indica hybrids (BRRI hybrid dhan2 and Heera2) and one elite inbred (BRRI dhan45) rice varieties. Leaf area index, chlorophyll status, and photosynthetic rate of flag leaf, postheading crop growth rate, shoot reserve translocation, source-sink relation and yield, and its attributes of each variety were comprehensively analyzed. Both hybrid varieties outyielded the inbred. However, the hybrids and inbred varieties exhibited statistically identical yield in late planting. Both hybrids accumulated higher amount of biomass before heading and exhibited greater remobilization of assimilates to the grain in early plantings compared to the inbred variety. Filled grain (%) declined significantly at delayed planting in the hybrids compared to elite inbred due to increased temperature impaired-inefficient transport of assimilates. Flag leaf photosynthesis parameters were higher in the hybrid varieties than those of the inbred variety. Results suggest that greater remobilization of shoot reserves to the grain rendered higher yield of hybrid rice varieties.

  10. Inbred guinea pig model of intrauterine infection with cytomegalovirus.

    PubMed

    Griffith, B P; McCormick, S R; Booss, J; Hsiung, G D

    1986-01-01

    Outbred guinea pigs have previously been utilized in an experimental model for the study of congenital infection with cytomegalovirus (CMV). Development of an inbred model of intrauterine CMV infection would allow analysis of the cells involved in CMV immunity, studies of transplacental CMV transfer, and investigation of the cellular immune factors that participate in intrauterine CMV infections. This study was therefore designed to assess the inbred guinea pig as a model for the study of congenital CMV infection. Intrauterine fetal and placental infection with CMV was demonstrated in inbred Strain 2 guinea pigs, and the maternal factors influencing transplacental transmission of CMV were evaluated. Infectious virus was recovered from placentas and offspring of mothers that experienced primary CMV infection during pregnancy, but not from placentas and offspring of mothers that were inoculated with CMV prior to pregnancy. However, histologic lesions consisting of focal necrosis and inflammation were seen in tissues of offspring from both groups of mothers. Inoculation of seronegative pregnant Strain 2 animals with low doses of virus (2.5 to 3.5 log10 TCID50) resulted in both placental and fetal CMV infection without significant maternal death. Infection of placentas and offspring occurred in utero regardless of the stage of pregnancy. In addition, infectious virus was detectable in fetal tissues at the time of maternal viremia but also later during the course of maternal infection, ie, 4 weeks after inoculation. These findings indicate that the inbred guinea pig model can be used to investigate the pathogenesis of intrauterine CMV infections.

  11. RiceCAP: Comparison of sheath blight QTLs in two Bengal/O. nivara advanced backcross mapping populations

    USDA-ARS?s Scientific Manuscript database

    Two advanced backcross populations were developed between a popular southern US tropical japonica rice (Oryza sativa L.) cultivar Bengal and two different of Oryza nivara (IRGC100898; IRGC104705) accessions to identify quantitative trait loci (QTLs) related to sheath blight (SB) disease resistance. ...

  12. Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population

    PubMed Central

    Schmitz, Robert J.; He, Yupeng; Valdés-López, Oswaldo; Khan, Saad M.; Joshi, Trupti; Urich, Mark A.; Nery, Joseph R.; Diers, Brian; Xu, Dong; Stacey, Gary; Ecker, Joseph R.

    2013-01-01

    Cytosine DNA methylation is one avenue for passing information through cell divisions. Here, we present epigenomic analyses of soybean recombinant inbred lines (RILs) and their parents. Identification of differentially methylated regions (DMRs) revealed that DMRs mostly cosegregated with the genotype from which they were derived, but examples of the uncoupling of genotype and epigenotype were identified. Linkage mapping of methylation states assessed from whole-genome bisulfite sequencing of 83 RILs uncovered widespread evidence for local methylQTL. This epigenomics approach provides a comprehensive study of the patterns and heritability of methylation variants in a complex genetic population over multiple generations, paving the way for understanding how methylation variants contribute to phenotypic variation. PMID:23739894

  13. Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population.

    PubMed

    Schmitz, Robert J; He, Yupeng; Valdés-López, Oswaldo; Khan, Saad M; Joshi, Trupti; Urich, Mark A; Nery, Joseph R; Diers, Brian; Xu, Dong; Stacey, Gary; Ecker, Joseph R

    2013-10-01

    Cytosine DNA methylation is one avenue for passing information through cell divisions. Here, we present epigenomic analyses of soybean recombinant inbred lines (RILs) and their parents. Identification of differentially methylated regions (DMRs) revealed that DMRs mostly cosegregated with the genotype from which they were derived, but examples of the uncoupling of genotype and epigenotype were identified. Linkage mapping of methylation states assessed from whole-genome bisulfite sequencing of 83 RILs uncovered widespread evidence for local methylQTL. This epigenomics approach provides a comprehensive study of the patterns and heritability of methylation variants in a complex genetic population over multiple generations, paving the way for understanding how methylation variants contribute to phenotypic variation.

  14. A genetic algorithm application in backcross breeding problem

    NASA Astrophysics Data System (ADS)

    Carnia, E.; Napitupulu, H.; Supriatna, A. K.

    2018-03-01

    In this paper we discuss a mathematical model of goat breeding strategy, i.e. the backcrossing breeding. The model is aimed to obtain a strategy in producing better variant of species. In this strategy, a female (doe) of a lesser quality goat, in terms of goat quality is bred with a male (buck) of an exotic goat which has a better goat quality. In this paper we will explore a problem on how to harvest the population optimally. A genetic algorithm (GA) approach will been devised to obtain the solution of the problem. We do several trials of the GA implementation which gives different set of solutions, but relatively close to each other in terms of the resulting total revenue, except a few. Further study need to be done to obtain GA solution that closer to the exact solution.

  15. Exploring the power of rice (O. sativa x O. rufipogon) chromosome segment substitution line libraries

    USDA-ARS?s Scientific Manuscript database

    Transgressive variation was reported as an increase in grain yield for several rice (Oryza sativa x O. rufipogon) advanced backcross mapping populations. The objective of this study was to develop chromosome segment substitution line (CSSL) libraries to further dissect the reported transgressive var...

  16. Mapping Blast and Sheath Blight QTL in an Advanced Backcross Bengal/O. nivara (Wild2) Population

    USDA-ARS?s Scientific Manuscript database

    An advanced backcross mapping population was developed from a cross between ‘Bengal’, a popular southern U.S. tropical japonica rice (Oryza sativa L.) cultivar, and an accession of the rice ancestral species, O. nivara Sharma & Shastry (IRGC104705). Previous studies identified this O. nivara accessi...

  17. [Cloning of Chinese Banna minipig inbred-line alpha1,3-galactosyltransferase gene and construction of its recombinant eukaryotic expression vector].

    PubMed

    Zhu, Shengming; Wang, Yanping; Zheng, Hong; Cheng, Jingqiu; Lu, Yanrong; Zeng, Yangzhi; Wang, Yu; Wang, Zhu

    2009-04-01

    This study sought to clone Chinese Banna minipig inbred-line (BMI) alpha1,3-galactosyltransferase (alpha1,3-GT) gene and construct its recombinant eukaryotic expression vector. Total RNA was isolated from BMI liver. Full length cDNA of alpha1,3-GT gene was amplified by RT-PCR and cloned into pMD18-T vector to sequence. Subsequently, alpha1,3-GT gene was inserted into pEGFP-N1 to construct eukaryotic expression vector pEGFP-N1-GT. Then the reconstructed plasmid pEGFP-N1-GT was transiently transfected into human lung cancer cell line A549. The expression of alpha1,3-GT mRNA in transfected cells was detected by RT-PCR. FITC-BS-IB4 lectin was used in the direct immunofluorescence method, which was performed to observe the alpha-Gal synthesis function of BMI alpha1,3-GT in transfected cells. The results showed that full length of BMI alpha1,3-GT cDNA was 1116 bp. BMI alpha1,3-GT cDNA sequence was highly homogenous with those of mouse and bovine, and was exactly the same as the complete sequence of those of swine, pEGFP-N1-GT was confirmed by enzyme digestion and PCR. The expression of alpha1,3-GT mRNA was detected in A549 cells transfected by pEGFP-N1-GT. The expression of alpha-Gal was observed on the membrane of A549 cells transfected by pEGFP-N1-GT. Successful cloning of BMI alpha1,3-GT cDNA and construction of its eukaryotic expression vector have established a foundation for further research and application of BMI alpha1,3-GT in the fields of xenotransplantation and immunological therapy of cancer.

  18. Marker-assisted introgression of opaque2 allele for rapid conversion of elite hybrids into quality protein maize.

    PubMed

    Hossain, Firoz; Muthusamy, Vignesh; Pandey, Neha; Vishwakarma, Ashish K; Baveja, Aanchal; Zunjare, Rajkumar U; Thirunavukkarasu, Nepolean; Saha, Supradip; Manjaiah, Kanchikeri M Manjaiah; Prasanna, Boddupalli M; Gupta, Hari S

    2018-03-01

    Maize is a valuable source of food and feed worldwide. Maize endosperm protein is, however nutritionally poor due to the reduced levels of two essential amino acids, lysine and tryptophan. In this study, recessive opaque2 (o2) allele that confers enhanced endosperm lysine and tryptophan, was introgressed using marker-assisted backcross breeding into three normal inbred lines (HKI323, HKI1105 and HKI1128). These are the parental lines of three popular medium-maturing single cross hybrids (HM4, HM8 and HM9) in India. Gene-based simple sequence repeat (SSR) markers (umc1066 and phi057) were successfully deployed for introgression of o2 allele. Background selection using genome-based SSRs helped in recovering > 96% of recurrent parent genome. The newly developed quality protein maize (QPM) inbreds showed modified kernels (25-50% opaqueness) coupled with high degree of phenotypic resemblance to the respective recipient lines, including grain yield. In addition, endosperm protein quality showed increased lysine and tryptophan in the inbreds to the range of 52-95% and 47-118%, respectively. The reconstituted QPM hybrids recorded significant enhancement of endosperm lysine (48-74%) and tryptophan (55-100%) in the endosperm. The QPM hybrids exhibited high phenotypic similarity with the original hybrids for morphological and yield contributing traits along with responses to some major diseases like turcicum leaf blight and maydis leaf blight. The grain yield of QPM hybrids was at par with their original versions under multilocation testing. These elite, high-yielding QPM hybrids with improved protein quality have been released and notified for commercial cultivation, and hold significant promise for improving nutritional security.

  19. Localization of the panhypopituitary dwarf mutation (df) on mouse chromosome 11 in an intersubspecific backcross.

    PubMed

    Buckwalter, M S; Katz, R W; Camper, S A

    1991-07-01

    Ames dwarf (df) is an autosomal recessive mutation characterized by severe dwarfism and infertility. This mutation provides a mouse model for panhypopituitarism. The dwarf phenotype results from failure in the differentiation of the cells which produce growth hormone, prolactin, and thyroid stimulating hormone. Using the backcross (DF/B-df/df X CASA/Rk) X DF/B-df/df, we confirmed the assignment of df to mouse chromosome 11 and demonstrated recombination between df and the growth hormone gene. This backcross is an invaluable resource for screening candidate genes for the df mutation. The df locus maps to less than 1 cM distal to Pad-1 (0.85 +/- 0.85 cM). Two new genes localized on mouse chromosome 11, Rpo2-1, and Edp-1, map to a region of conserved synteny with human chromosome 17. The localization of the alpha 1 adrenergic receptor, Adra-1, extends a known region of synteny conservation between mouse chromosome 11 and human chromosome 5, and suggests that a human counterpart to df would map to human chromosome 5.

  20. Global transcriptome analysis of the maize (Zea mays L.) inbred line 08LF during leaf senescence initiated by pollination-prevention

    PubMed Central

    Wang, Shunxi; Wu, Liuji; Ku, Lixia; Zhang, Jun; Song, Xiaoheng; Liu, Haiping

    2017-01-01

    In maize (Zea mays), leaf senescence acts as a nutrient recycling process involved in proteins, lipids, and nucleic acids degradation and transport to the developing sink. However, the molecular mechanisms of pre-maturation associated with pollination-prevention remain unclear in maize. To explore global gene expression changes during the onset and progression of senescence in maize, the inbred line 08LF, with severe early senescence caused by pollination prevention, was selected. Phenotypic observation showed that the onset of leaf senescence of 08LF plants occurred approximately 14 days after silking (DAS) by pollination prevention. Transcriptional profiling analysis of the leaf at six developmental stages during induced senescence revealed that a total of 5,432 differentially expressed genes (DEGs) were identified, including 2314 up-regulated genes and 1925 down-regulated genes. Functional annotation showed that the up-regulated genes were mainly enriched in multi-organism process and nitrogen compound transport, whereas down-regulated genes were involved in photosynthesis. Expression patterns and pathway enrichment analyses of early-senescence related genes indicated that these DEGs are involved in complex regulatory networks, especially in the jasmonic acid pathway. In addition, transcription factors from several families were detected, particularly the CO-like, NAC, ERF, GRAS, WRKY and ZF-HD families, suggesting that these transcription factors might play important roles in driving leaf senescence in maize as a result of pollination-prevention. PMID:28973044

  1. Global transcriptome analysis of the maize (Zea mays L.) inbred line 08LF during leaf senescence initiated by pollination-prevention.

    PubMed

    Wu, Liancheng; Li, Mingna; Tian, Lei; Wang, Shunxi; Wu, Liuji; Ku, Lixia; Zhang, Jun; Song, Xiaoheng; Liu, Haiping; Chen, Yanhui

    2017-01-01

    In maize (Zea mays), leaf senescence acts as a nutrient recycling process involved in proteins, lipids, and nucleic acids degradation and transport to the developing sink. However, the molecular mechanisms of pre-maturation associated with pollination-prevention remain unclear in maize. To explore global gene expression changes during the onset and progression of senescence in maize, the inbred line 08LF, with severe early senescence caused by pollination prevention, was selected. Phenotypic observation showed that the onset of leaf senescence of 08LF plants occurred approximately 14 days after silking (DAS) by pollination prevention. Transcriptional profiling analysis of the leaf at six developmental stages during induced senescence revealed that a total of 5,432 differentially expressed genes (DEGs) were identified, including 2314 up-regulated genes and 1925 down-regulated genes. Functional annotation showed that the up-regulated genes were mainly enriched in multi-organism process and nitrogen compound transport, whereas down-regulated genes were involved in photosynthesis. Expression patterns and pathway enrichment analyses of early-senescence related genes indicated that these DEGs are involved in complex regulatory networks, especially in the jasmonic acid pathway. In addition, transcription factors from several families were detected, particularly the CO-like, NAC, ERF, GRAS, WRKY and ZF-HD families, suggesting that these transcription factors might play important roles in driving leaf senescence in maize as a result of pollination-prevention.

  2. Genome-Wide QTL Mapping for Wheat Processing Quality Parameters in a Gaocheng 8901/Zhoumai 16 Recombinant Inbred Line Population.

    PubMed

    Jin, Hui; Wen, Weie; Liu, Jindong; Zhai, Shengnan; Zhang, Yan; Yan, Jun; Liu, Zhiyong; Xia, Xianchun; He, Zhonghu

    2016-01-01

    Dough rheological and starch pasting properties play an important role in determining processing quality in bread wheat (Triticum aestivum L.). In the present study, a recombinant inbred line (RIL) population derived from a Gaocheng 8901/Zhoumai 16 cross grown in three environments was used to identify quantitative trait loci (QTLs) for dough rheological and starch pasting properties evaluated by Mixograph, Rapid Visco-Analyzer (RVA), and Mixolab parameters using the wheat 90 and 660 K single nucleotide polymorphism (SNP) chip assays. A high-density linkage map constructed with 46,961 polymorphic SNP markers from the wheat 90 and 660 K SNP assays spanned a total length of 4121 cM, with an average chromosome length of 196.2 cM and marker density of 0.09 cM/marker; 6596 new SNP markers were anchored to the bread wheat linkage map, with 1046 and 5550 markers from the 90 and 660 K SNP assays, respectively. Composite interval mapping identified 119 additive QTLs on 20 chromosomes except 4D; among them, 15 accounted for more than 10% of the phenotypic variation across two or three environments. Twelve QTLs for Mixograph parameters, 17 for RVA parameters and 55 for Mixolab parameters were new. Eleven QTL clusters were identified. The closely linked SNP markers can be used in marker-assisted wheat breeding in combination with the Kompetitive Allele Specific PCR (KASP) technique for improvement of processing quality in bread wheat.

  3. Genome-Wide QTL Mapping for Wheat Processing Quality Parameters in a Gaocheng 8901/Zhoumai 16 Recombinant Inbred Line Population

    PubMed Central

    Jin, Hui; Wen, Weie; Liu, Jindong; Zhai, Shengnan; Zhang, Yan; Yan, Jun; Liu, Zhiyong; Xia, Xianchun; He, Zhonghu

    2016-01-01

    Dough rheological and starch pasting properties play an important role in determining processing quality in bread wheat (Triticum aestivum L.). In the present study, a recombinant inbred line (RIL) population derived from a Gaocheng 8901/Zhoumai 16 cross grown in three environments was used to identify quantitative trait loci (QTLs) for dough rheological and starch pasting properties evaluated by Mixograph, Rapid Visco-Analyzer (RVA), and Mixolab parameters using the wheat 90 and 660 K single nucleotide polymorphism (SNP) chip assays. A high-density linkage map constructed with 46,961 polymorphic SNP markers from the wheat 90 and 660 K SNP assays spanned a total length of 4121 cM, with an average chromosome length of 196.2 cM and marker density of 0.09 cM/marker; 6596 new SNP markers were anchored to the bread wheat linkage map, with 1046 and 5550 markers from the 90 and 660 K SNP assays, respectively. Composite interval mapping identified 119 additive QTLs on 20 chromosomes except 4D; among them, 15 accounted for more than 10% of the phenotypic variation across two or three environments. Twelve QTLs for Mixograph parameters, 17 for RVA parameters and 55 for Mixolab parameters were new. Eleven QTL clusters were identified. The closely linked SNP markers can be used in marker-assisted wheat breeding in combination with the Kompetitive Allele Specific PCR (KASP) technique for improvement of processing quality in bread wheat. PMID:27486464

  4. Metabolic profiling of two maize (Zea mays L.) inbred lines inoculated with the nitrogen fixing plant-interacting bacteria Herbaspirillum seropedicae and Azospirillum brasilense

    PubMed Central

    Brusamarello-Santos, Liziane Cristina; Gilard, Françoise; Brulé, Lenaïg; Quilleré, Isabelle; Gourion, Benjamin; Ratet, Pascal; Maltempi de Souza, Emanuel; Lea, Peter J.; Hirel, Bertrand

    2017-01-01

    Maize roots can be colonized by free-living atmospheric nitrogen (N2)-fixing bacteria (diazotrophs). However, the agronomic potential of non-symbiotic N2-fixation in such an economically important species as maize, has still not been fully exploited. A preliminary approach to improve our understanding of the mechanisms controlling the establishment of such N2-fixing associations has been developed, using two maize inbred lines exhibiting different physiological characteristics. The bacterial-plant interaction has been characterized by means of a metabolomic approach. Two established model strains of Nif+ diazotrophic bacteria, Herbaspirillum seropedicae and Azospirillum brasilense and their Nif- couterparts defficient in nitrogenase activity, were used to evaluate the impact of the bacterial inoculation and of N2 fixation on the root and leaf metabolic profiles. The two N2-fixing bacteria have been used to inoculate two genetically distant maize lines (FV252 and FV2), already characterized for their contrasting physiological properties. Using a well-controlled gnotobiotic experimental system that allows inoculation of maize plants with the two diazotrophs in a N-free medium, we demonstrated that both maize lines were efficiently colonized by the two bacterial species. We also showed that in the early stages of plant development, both bacterial strains were able to reduce acetylene, suggesting that they contain functional nitrogenase activity and are able to efficiently fix atmospheric N2 (Fix+). The metabolomic approach allowed the identification of metabolites in the two maize lines that were representative of the N2 fixing plant-bacterial interaction, these included mannitol and to a lesser extend trehalose and isocitrate. Whilst other metabolites such as asparagine, although only exhibiting a small increase in maize roots following bacterial infection, were specific for the two Fix+ bacterial strains, in comparison to their Fix- counterparts. Moreover, a number

  5. Metabolic profiling of two maize (Zea mays L.) inbred lines inoculated with the nitrogen fixing plant-interacting bacteria Herbaspirillum seropedicae and Azospirillum brasilense.

    PubMed

    Brusamarello-Santos, Liziane Cristina; Gilard, Françoise; Brulé, Lenaïg; Quilleré, Isabelle; Gourion, Benjamin; Ratet, Pascal; Maltempi de Souza, Emanuel; Lea, Peter J; Hirel, Bertrand

    2017-01-01

    Maize roots can be colonized by free-living atmospheric nitrogen (N2)-fixing bacteria (diazotrophs). However, the agronomic potential of non-symbiotic N2-fixation in such an economically important species as maize, has still not been fully exploited. A preliminary approach to improve our understanding of the mechanisms controlling the establishment of such N2-fixing associations has been developed, using two maize inbred lines exhibiting different physiological characteristics. The bacterial-plant interaction has been characterized by means of a metabolomic approach. Two established model strains of Nif+ diazotrophic bacteria, Herbaspirillum seropedicae and Azospirillum brasilense and their Nif- couterparts defficient in nitrogenase activity, were used to evaluate the impact of the bacterial inoculation and of N2 fixation on the root and leaf metabolic profiles. The two N2-fixing bacteria have been used to inoculate two genetically distant maize lines (FV252 and FV2), already characterized for their contrasting physiological properties. Using a well-controlled gnotobiotic experimental system that allows inoculation of maize plants with the two diazotrophs in a N-free medium, we demonstrated that both maize lines were efficiently colonized by the two bacterial species. We also showed that in the early stages of plant development, both bacterial strains were able to reduce acetylene, suggesting that they contain functional nitrogenase activity and are able to efficiently fix atmospheric N2 (Fix+). The metabolomic approach allowed the identification of metabolites in the two maize lines that were representative of the N2 fixing plant-bacterial interaction, these included mannitol and to a lesser extend trehalose and isocitrate. Whilst other metabolites such as asparagine, although only exhibiting a small increase in maize roots following bacterial infection, were specific for the two Fix+ bacterial strains, in comparison to their Fix- counterparts. Moreover, a number

  6. Genome characterization of the selected long- and short-sleep mouse lines.

    PubMed

    Dowell, Robin; Odell, Aaron; Richmond, Phillip; Malmer, Daniel; Halper-Stromberg, Eitan; Bennett, Beth; Larson, Colin; Leach, Sonia; Radcliffe, Richard A

    2016-12-01

    The Inbred Long- and Short-Sleep (ILS, ISS) mouse lines were selected for differences in acute ethanol sensitivity using the loss of righting response (LORR) as the selection trait. The lines show an over tenfold difference in LORR and, along with a recombinant inbred panel derived from them (the LXS), have been widely used to dissect the genetic underpinnings of acute ethanol sensitivity. Here we have sequenced the genomes of the ILS and ISS to investigate the DNA variants that contribute to their sensitivity difference. We identified ~2.7 million high-confidence SNPs and small indels and ~7000 structural variants between the lines; variants were found to occur in 6382 annotated genes. Using a hidden Markov model, we were able to reconstruct the genome-wide ancestry patterns of the eight inbred progenitor strains from which the ILS and ISS were derived, and found that quantitative trait loci that have been mapped for LORR were slightly enriched for DNA variants. Finally, by mapping and quantifying RNA-seq reads from the ILS and ISS to their strain-specific genomes rather than to the reference genome, we found a substantial improvement in a differential expression analysis between the lines. This work will help in identifying and characterizing the DNA sequence variants that contribute to the difference in ethanol sensitivity between the ILS and ISS and will also aid in accurate quantification of RNA-seq data generated from the LXS RIs.

  7. Characterization and performance of 16 new inbred lines of lettuce

    USDA-ARS?s Scientific Manuscript database

    The Agricultural Research Service, U.S. Department of Agriculture announces the release of sixteen breeding lines of lettuce (Lactuca sativa L.). Five (SM13-I1, SM13-I2, SM13-I3, SM13-I4, and SM13-I5) of the six iceberg breeding lines can be used for whole head or salad blend production; the sixth i...

  8. Manganese peroxidase from the white-rot fungus Phanerochaete chrysosporium is enzymatically active and accumulates to high levels in transgenic maize seed.

    PubMed

    Clough, Richard C; Pappu, Kameshwari; Thompson, Kevin; Beifuss, Katherine; Lane, Jeff; Delaney, Donna E; Harkey, Robin; Drees, Carol; Howard, John A; Hood, Elizabeth E

    2006-01-01

    Manganese peroxidase (MnP) has been implicated in lignin degradation and thus has potential applications in pulp and paper bleaching, enzymatic remediation and the textile industry. Transgenic plants are an emerging protein expression platform that offer many advantages over traditional systems, in particular their potential for large-scale industrial enzyme production. Several plant expression vectors were created to evaluate the accumulation of MnP from the wood-rot fungus Phanerochaete chrysosporium in maize seed. We showed that cell wall targeting yielded full-length MnP, whereas cytoplasmic localization resulted in multiple truncated peroxidase polypeptides as detected by immunoblot analysis. In addition, the use of a seed-preferred promoter dramatically increased the expression levels and reduced the negative effects on plant health. Multiple independent transgenic lines were backcrossed with elite inbred corn lines for several generations with the maintenance of high-level expression, indicating genetic stability of the transgene.

  9. Initial locomotor sensitivity to cocaine varies widely among inbred mouse strains.

    PubMed

    Wiltshire, T; Ervin, R B; Duan, H; Bogue, M A; Zamboni, W C; Cook, S; Chung, W; Zou, F; Tarantino, L M

    2015-03-01

    Initial sensitivity to psychostimulants can predict subsequent use and abuse in humans. Acute locomotor activation in response to psychostimulants is commonly used as an animal model of initial drug sensitivity and has been shown to have a substantial genetic component. Identifying the specific genetic differences that lead to phenotypic differences in initial drug sensitivity can advance our understanding of the processes that lead to addiction. Phenotyping inbred mouse strain panels are frequently used as a first step for studying the genetic architecture of complex traits. We assessed locomotor activation following a single, acute 20 mg/kg dose of cocaine (COC) in males from 45 inbred mouse strains and observed significant phenotypic variation across strains indicating a substantial genetic component. We also measured levels of COC, the active metabolite, norcocaine and the major inactive metabolite, benzoylecgonine, in plasma and brain in the same set of inbred strains. Pharmacokinetic (PK) and behavioral data were significantly correlated, but at a level that indicates that PK alone does not account for the behavioral differences observed across strains. Phenotypic data from this reference population of inbred strains can be utilized in studies aimed at examining the role of psychostimulant-induced locomotor activation on drug reward and reinforcement and to test theories about addiction processes. Moreover, these data serve as a starting point for identifying genes that alter sensitivity to the locomotor stimulatory effects of COC. © 2015 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.

  10. Characteristics of Sleep and Wakefulness inWild-Derived Inbred Mice

    PubMed Central

    HIYOSHI, Hideyuki; TERAO, Akira; OKAMATSU-OGURA, Yuko; KIMURA, Kazuhiro

    2014-01-01

    Genetic variations in the wild-derived inbred mouse strains are more diverse than that of classical laboratory inbred mouse strains, including C57BL/6J (B6). The sleep/wake and monoamine properties of six wild-derived inbred mouse strains (PGN2, NJL, BLG2, KJR, MSM, HMI) were characterized and compared with those of B6 mice. All examined mice were nocturnal and had a polyphasic sleep pattern with a “main sleep period” identified during the light period. However, there were three sleep/wake phenotypic differences between the wild-derived mouse strains and B6 strain. First, the amount of sleep during the dark phase was comparable with that of B6 mice. However, the amount of sleep during the light phase was more varied among strains, in particular, NJL and HMI had significantly less sleep compared with that of B6 mice. Second, PGN2, NJL, BLG2, and KJR mice showed a “highly awake period” (in which the hourly total sleep time was <10%) immediately after the onset of the dark period, which was not seen in B6 mice. Third, relative to that of B6 mice, PGN2 and KJR mice showed longer duration of wakefulness episodes during the 12-h dark phase. Differences in whole brain noradrenaline, dopamine, and 5-hydroxy-tryptamine contents between the wild-derived mouse strains and B6 strain were also found. These identified phenotypes might be potentially under strong genetic control. Hence, wild-derived inbred mice could be useful for identifying the genetic factors underlying the regulation of sleep and wakefulness. PMID:24770646

  11. Inheritance of height and maturity in crosses between pearl millet landraces and inbred Tift 85DB.

    PubMed

    Wilson, J P; Burton, G W; Bondari, K

    1990-11-01

    Over 300 landraces of pearl millet were collected in Burkina Faso and grown at the Coastal Plain Experiment Station in Tifton/GA. At Tifton, these landraces are predominantly tall and late-maturing. The photoperiod requirements of these landraces hinder evaluation of their performance in the field and their use in breeding programs. A conversion program has been initiated to transfer genes for dwarf stature and early flowering into the tall, late-maturing landraces. The inbred Tift 85DB is being used as a donor of genes for the dwarf and early characteristics, and was crossed to nine randomly selected landraces from Burkina Faso. The parents, F1, F2, and backcrosses to each parent were grown in the field and evaluated for plant height at anthesis and time in days from planting to anthesis. In general, plant height of F1s was taller than the tallest parent, and in all crosses the maturity of F1s was intermediate between the parents. Numbers of loci conferring height varied among crosses, ranging from 0 to 9.6, and averaged 1.6. Estimated numbers of loci conferring maturity ranged from 0 to 12.8 and averaged 3.4. Broad-sense heritability estimates for height and maturity averaged 60.2 and 65.7%, respectively. Corresponding narrow-sense estimates averaged 23.8 and 48.2%. Joint scaling tests revealed that additive-genetic effects were highly significant for both traits, but dominance and epistatic-genetic effects contributed to the inheritance of each trait in some crosses. The low gene numbers, high heritability estimates, and preponderance of additive-genetic effects suggest that selection for these traits should be effective.

  12. Screening of inbred popcorn lines for tolerance to low phosphorus.

    PubMed

    Santos, O J A P; Gonçalves, L S A; Scapim, C A; S M de Sousa, de; Castro, C R; Y Baba, V; de Oliveira, A L M

    2016-05-06

    Increasing phosphorus use efficiency in agriculture is essential for sustainable food production. Thus, the aims of this study were: i) to identify phosphorus use efficiency (PUE) in popcorn lines during the early plant stages, ii) to study the relationship between traits correlated with PUE, and iii) to analyze genetic diversity among lines. To accomplish this, 35 popcorn lines from Universidade Estadual de Maringá breeding program were studied. The experiment was conducted in a growth chamber using a nutrient solution containing two concentrations of phosphorus (P): 2.5 μM or low P (LP) and 250 μM or high P (HP). After 13 days in the nutrient solution, root morphology traits, shoot and root dry weight, and P content of the maize seedlings were measured. A deviance analysis showed there was a high level of genetic variability. An unweighted pair group method with arithmetic mean (UPGMA) clustering analysis identified three groups for the LP treatment (efficient, intermediate, and inefficient) and three groups for the HP treatment (responsive, moderately responsive, and unresponsive). The results of a principal component analysis and selection index were consistent with the UPGMA analysis, and lines 1, 2, 13, 17, 26, and 31 were classified as PUE.

  13. A genetic map of mouse chromosome 1 near the Lsh-Ity-Bcg disease resistance locus.

    PubMed

    Mock, B; Krall, M; Blackwell, J; O'Brien, A; Schurr, E; Gros, P; Skamene, E; Potter, M

    1990-05-01

    Isozyme and restriction fragment length polymorphism (RFLP) analyses of backcross progeny, recombinant inbred strains, and congenic strains of mice positioned eight genetic markers with respect to the Lsh-Ity-Bcg disease resistance locus. Allelic isoforms of Idh-1 and Pep-3 and RFLPs detected by Southern hybridization for Myl-1, Cryg, Vil, Achrg, bcl-2, and Ren-1,2, between BALB/cAnPt and DBA/2NPt mice, were utilized to examine the cosegregation of these markers with the Lsh-Ity-Bcg resistance phenotype in 103 backcross progeny. An additional 47 backcross progeny from a cross between C57BL/10ScSn and B10.L-Lshr/s mice were examined for the cosegregation of Myl-1 and Vil RFLPs with Lsh phenotypic differences. Similarly, BXD recombinant inbred strains were typed for RFLPs upon hybridization with Vil and Achrg. Recombination frequencies generated in the different test systems were statistically similar, and villin (Vil) was identified as the molecular marker closest (1.7 +/- 0.8 cM) to the Lsh-Ity-Bcg locus. Two other DNA sequences, nebulin (Neb) and an anonymous DNA fragment (D2S3), which map to a region of human chromosome 2q that is homologous to proximal mouse chromosome 1, were not closely linked to the Lsh-Ity-Bcg locus. This multipoint linkage analysis of chromosome 1 surrounding the Lsh-Ity-Bcg locus provides a basis for the eventual isolation of the disease gene.

  14. Transcriptome profiling of two maize inbreds with distinct responses to Gibberella ear rot disease to identify candidate resistance genes.

    PubMed

    Kebede, Aida Z; Johnston, Anne; Schneiderman, Danielle; Bosnich, Whynn; Harris, Linda J

    2018-02-09

    Gibberella ear rot (GER) is one of the most economically important fungal diseases of maize in the temperate zone due to moldy grain contaminated with health threatening mycotoxins. To develop resistant genotypes and control the disease, understanding the host-pathogen interaction is essential. RNA-Seq-derived transcriptome profiles of fungal- and mock-inoculated developing kernel tissues of two maize inbred lines were used to identify differentially expressed transcripts and propose candidate genes mapping within GER resistance quantitative trait loci (QTL). A total of 1255 transcripts were significantly (P ≤ 0.05) up regulated due to fungal infection in both susceptible and resistant inbreds. A greater number of transcripts were up regulated in the former (1174) than the latter (497) and increased as the infection progressed from 1 to 2 days after inoculation. Focusing on differentially expressed genes located within QTL regions for GER resistance, we identified 81 genes involved in membrane transport, hormone regulation, cell wall modification, cell detoxification, and biosynthesis of pathogenesis related proteins and phytoalexins as candidate genes contributing to resistance. Applying droplet digital PCR, we validated the expression profiles of a subset of these candidate genes from QTL regions contributed by the resistant inbred on chromosomes 1, 2 and 9. By screening global gene expression profiles for differentially expressed genes mapping within resistance QTL regions, we have identified candidate genes for gibberella ear rot resistance on several maize chromosomes which could potentially lead to a better understanding of Fusarium resistance mechanisms.

  15. Genetic relatedness of previously Plant-Variety-Protected commercial maize inbreds.

    PubMed

    Beckett, Travis J; Morales, A Jason; Koehler, Klaus L; Rocheford, Torbert R

    2017-01-01

    The emergence of high-throughput, high-density genotyping methods combined with increasingly powerful computing systems has created opportunities to further discover and exploit the genes controlling agronomic performance in elite maize breeding populations. Understanding the genetic basis of population structure in an elite set of materials is an essential step in this genetic discovery process. This paper presents a genotype-based population analysis of all maize inbreds whose Plant Variety Protection certificates had expired as of the end of 2013 (283 inbreds) as well as 66 public founder inbreds. The results provide accurate population structure information and allow for important inferences in context of the historical development of North American elite commercial maize germplasm. Genotypic data was obtained via genotyping-by-sequencing on 349 inbreds. After filtering for missing data, 77,314 high-quality markers remained. The remaining missing data (average per individual was 6.22 percent) was fully imputed at an accuracy of 83 percent. Calculation of linkage disequilibrium revealed that the average r2 of 0.20 occurs at approximately 1.1 Kb. Results of population genetics analyses agree with previously published studies that divide North American maize germplasm into three heterotic groups: Stiff Stalk, Non-Stiff Stalk, and Iodent. Principal component analysis shows that population differentiation is indeed very complex and present at many levels, yet confirms that division into three main sub-groups is optimal for population description. Clustering based on Nei's genetic distance provides an additional empirical representation of the three main heterotic groups. Overall fixation index (FST), indicating the degree of genetic divergence between the three main heterotic groups, was 0.1361. Understanding the genetic relationships and population differentiation of elite germplasm may help breeders to maintain and potentially increase the rate of genetic gain

  16. BXSB/long-lived is a recombinant inbred strain containing powerful disease suppressor loci.

    PubMed

    Haywood, Michelle E K; Gabriel, Luisa; Rose, S Jane; Rogers, Nicola J; Izui, Shozo; Morley, Bernard J

    2007-08-15

    The BXSB strain of recombinant inbred mice develops a spontaneous pathology that closely resembles the human disease systemic lupus erythematosus. Six non-MHC loci, Yaa, Bxs1-4, and Bxs6, have been linked to the development of aspects of the disease while a further locus, Bxs5, may be a BXSB-derived disease suppressor. Disease development is delayed in a substrain of BXSB, BXSB/MpJScr-long-lived (BXSB/ll). We compared the genetic derivation of BXSB/ll mice to the original strain, BXSB/MpJ, using microsatellite markers and single nucleotide polymorphisms across the genome. These differences were clustered and included two regions known to be important in the disease-susceptibility of these mice, Bxs5 and 6, as well as regions on chromosomes 5, 6, 9, 11, 12, and 13. We compared BXSB/ll to >20 strains including the BXSB parental SB/Le and C57BL/6 strains. This revealed that BXSB/ll is a separate recombinant inbred line derived from SB/Le and C57BL/6, but distinctly different from BXSB, that most likely arose due to residual heterozygosity in the BXSB stock. Despite the continued presence of the powerful disease-susceptibility locus Bxs3, BXSB/ll mice do not develop disease. We propose that the disappearance of the disease phenotype in the BXSB/ll mice is due to the inheritance of one or more suppressor loci in the differentially inherited intervals between the BXSB/ll and BXSB strains.

  17. Growth and formation of the foreleg skeleton inbred mice and rats under conditions of hypo-, normo- and hyperdynamia

    NASA Technical Reports Server (NTRS)

    Kogan, B. I.; Antipov, Y. S.

    1980-01-01

    Inbred 1 month old males of C57B 1/6, CBA, CC57Br/Mw interlinear hybrid mice of the first generation and rats of the August and Wistar lines were subjected to conditions of hypo-, normo- and hyperdynamia for 2 months. The statistically reliable dependence is shown between mechanical underloadings and overloadings and macro microscopic changes in the hind limb skeleton of animals. Genetic determination of growth and formation of the forelimb skeleton is established. Hereditary susceptibility and the phenomenon of heterosis are preserved under all motor conditions.

  18. Genetic-molecular characterization of backcross generations for sexual conversion in papaya (Carica papaya L.).

    PubMed

    Ramos, H C C; Pereira, M G; Pereira, T N S; Barros, G B A; Ferreguetti, G A

    2014-12-04

    The low number of improved cultivars limits the expansion of the papaya crop, particularly because of the time required for the development of new varieties using classical procedures. Molecular techniques associated with conventional procedures accelerate this process and allow targeted improvements. Thus, we used microsatellite markers to perform genetic-molecular characterization of papaya genotypes obtained from 3 backcross generations to monitor the inbreeding level and parental genome proportion in the evaluated genotypes. Based on the analysis of 20 microsatellite loci, 77 genotypes were evaluated, 25 of each generation of the backcross program as well as the parental genotypes. The markers analyzed were identified in 11 of the 12 linkage groups established for papaya, ranging from 1 to 4 per linkage group. The average values for the inbreeding coefficient were 0.88 (BC1S4), 0.47 (BC2S3), and 0.63 (BC3S2). Genomic analysis revealed average values of the recurrent parent genome of 82.7% in BC3S2, 64.4% in BC1S4, and 63.9% in BC2S3. Neither the inbreeding level nor the genomic proportions completely followed the expected average values. This demonstrates the significance of molecular analysis when examining different genotype values, given the importance of such information for selection processes in breeding programs.

  19. Development and genetic characterization of an Advanced Backcross-Nested Association Mapping (AB-NAM) population of wild × cultivated barley

    USDA-ARS?s Scientific Manuscript database

    The ability to access alleles from unadapted germplasm collections is a long-standing problem for geneticists and breeders. Here we developed, characterized, and demonstrated the utility of a wild barley advanced backcross-nested association mapping (AB-NAM) population. We developed this population ...

  20. The first research plantings of third-generation, third-backcross American chestnut (Castanea dentata) in the southeastern United States

    Treesearch

    Stacy Clark; S.E. Schlarbaum; F,V Saxton

    2014-01-01

    Production of American chestnut (Castanea dentata) resistant to the chestnut blight fungus (Cryphonectria parasitica) is being conducted currently through traditional breeding and genetic transformation. Sufficient material for field testing is currently available from The American Chestnut Foundation’s backcross breeding program. We planted approximately 4500 chestnut...

  1. Chromosome-wise dissection of the genome of the extremely big mouse line DU6i.

    PubMed

    Bevova, Marianna R; Aulchenko, Yurii S; Aksu, Soner; Renne, Ulla; Brockmann, Gudrun A

    2006-01-01

    The extreme high-body-weight-selected mouse line DU6i is a polygenic model for growth research, harboring many small-effect QTL. We dissected the genome of this line into 19 autosomes and the Y chromosome by the construction of a new panel of chromosome substitution strains (CSS). The DU6i chromosomes were transferred to a DBA/2 mice genetic background by marker-assisted recurrent backcrossing. Mitochondria and the X chromosome were of DBA/2 origin in the backcross. During the construction of these novel strains, >4000 animals were generated, phenotyped, and genotyped. Using these data, we studied the genetic control of variation in body weight and weight gain at 21, 42, and 63 days. The unique data set facilitated the analysis of chromosomal interaction with sex and parent-of-origin effects. All analyzed chromosomes affected body weight and weight gain either directly or in interaction with sex or parent of origin. The effects were age specific, with some chromosomes showing opposite effects at different stages of development.

  2. The Mouse Genomes Project: a repository of inbred laboratory mouse strain genomes.

    PubMed

    Adams, David J; Doran, Anthony G; Lilue, Jingtao; Keane, Thomas M

    2015-10-01

    The Mouse Genomes Project was initiated in 2009 with the goal of using next-generation sequencing technologies to catalogue molecular variation in the common laboratory mouse strains, and a selected set of wild-derived inbred strains. The initial sequencing and survey of sequence variation in 17 inbred strains was completed in 2011 and included comprehensive catalogue of single nucleotide polymorphisms, short insertion/deletions, larger structural variants including their fine scale architecture and landscape of transposable element variation, and genomic sites subject to post-transcriptional alteration of RNA. From this beginning, the resource has expanded significantly to include 36 fully sequenced inbred laboratory mouse strains, a refined and updated data processing pipeline, and new variation querying and data visualisation tools which are available on the project's website ( http://www.sanger.ac.uk/resources/mouse/genomes/ ). The focus of the project is now the completion of de novo assembled chromosome sequences and strain-specific gene structures for the core strains. We discuss how the assembled chromosomes will power comparative analysis, data access tools and future directions of mouse genetics.

  3. Enzyme markers in inbred rat strains: genetics of new markers and strain profiles.

    PubMed

    Adams, M; Baverstock, P R; Watts, C H; Gutman, G A

    1984-08-01

    Twenty-six inbred strains of the laboratory rat (Rattus norvegicus) were examined for electrophoretic variation at an estimated 97 genetic loci. In addition to previously documented markers, variation was observed for the enzymes aconitase, aldehyde dehydrogenase, and alkaline phosphatase. The genetic basis of these markers (Acon-1, Ahd-2, and Akp-1) was confirmed. Linkage analysis between 35 pairwise comparisons revealed that the markers Fh-1 and Pep-3 are linked. The strain profiles of the 25 inbred strains at 11 electrophoretic markers are given.

  4. Performance of container-grown seedlings of American chestnut backcross hybrids BC3 F3 generation in central Louisiana

    Treesearch

    Shi-Jean Susana Sung; Stacy L. Clark; Scott Schlarbaum; Daniel C. Dey; Daniel J. Leduc

    2016-01-01

    Seedlings from two families of the BC3F3 backcross generation of the American chestnut (Castanea dentata) and Chinese chestnut (C. mollissima) were cultured in 2013 in Missouri using the Root Production Method®, a container-based system used to avoid disease problems associated with...

  5. Evaluation of fall armyworm resistance in maize germplasm lines using visual leaf injury rating and predator survey

    USDA-ARS?s Scientific Manuscript database

    After examining ear-colonizing pest resistance, 20 maize lines from the USDA-ARS germplasm enhancement of Maize (GEM) Program were evaluated for whorl-feeding fall armyworm (FAW) (Spodoptera frugiperda) resistance using four maize inbred lines as the resistant and susceptible controls. Both FAW inju...

  6. Energy utilization and growth performance of chickens fed novel wheat inbred lines selected for different pentosan levels with and without xylanase supplementation

    PubMed Central

    Pirgozliev, V.; Rose, S. P.; Pellny, T.; Amerah, A. M.; Wickramasinghe, M.; Ulker, M.; Rakszegi, M.; Bedo, Z.; Shewry, P. R.; Lovegrove, A.

    2015-01-01

    Different F5 recombinant inbred lines from the cross Yumai 34 × Ukrainka were grown in replicated trials on a single site in one harvest year at Rothamsted Research. A total of 10 samples from those lines were harvested and used in a broiler experiment. Twenty nutritionally complete meal-form diets that had 630 g/kg of wheat with different amounts of pentosan, with and without exogenous xylanase supplementation, were used to compare broiler growth performance and determine apparent metabolizable energy corrected for N retention (AMEn). We examined the relationship between the nutritive value of the wheat samples and their chemical compositions and results of quality tests. The amounts of total and water soluble pentosans in wheat samples ranged from 36.7 to 48.0 g/kg DM, and 6.7 to 11.6 g/kg DM, respectively. The mean crude oil and protein contents of the wheat samples were 10.5 and 143.9 g/kg DM, respectively. The average determined value for the kinematic viscosity was 0.0018 mPa.s, and 2.1 mPa.s for the dynamic viscosity. The AMEn of the wheat-based diets had a maximum range of 0.47 MJ/kg DM within the ten wheat samples that were tested. Xylanase supplementation improved (P < 0.05) dietary AMEn, dry matter, and fat digestibility coefficients. There was a positive (P < 0.05) relationship between in vitro kinematic viscosity of the wheat samples and the total pentosan content. There was a negative relationship between the total pentosan content in the wheat and broiler growth performance. An increase by 10 g of pentosan per kg of wheat reduced (P < 0.001) daily feed intake and weight gain by 2.9 g and 3.5 g, respectively. The study shows that the feeding quality of wheat samples can be predicted by their total pentosan content. Supplementary xylanase improved energy and nutrient availability of all wheat samples that was independent of differences in pentosan content. PMID:25595480

  7. Shoot and Root Traits Contribute to Drought Resistance in Recombinant Inbred Lines of MD 23-24 × SEA 5 of Common Bean.

    PubMed

    Polania, Jose; Rao, Idupulapati M; Cajiao, Cesar; Grajales, Miguel; Rivera, Mariela; Velasquez, Federico; Raatz, Bodo; Beebe, Stephen E

    2017-01-01

    Drought is the major abiotic stress factor limiting yield of common bean ( Phaseolus vulgaris L.) in smallholder systems in Latin America and eastern and southern Africa; where it is a main source of protein in the daily diet. Identification of shoot and root traits associated with drought resistance contributes to improving the process of designing bean genotypes adapted to drought. Field and greenhouse studies were conducted at the International Center for Tropical Agriculture (CIAT), Palmira, Colombia to determine the relationship between grain yield and different shoot and root traits using a recombinant inbred lines (RILs) population (MD23-24 × SEA 5) of common bean. The main objectives of this study were to identify: (i) specific shoot and root morpho-physiological traits that contribute to improved resistance to drought and that could be useful as selection criteria in breeding beans for drought resistance; and (ii) superior genotypes with desirable shoot and root traits that could serve as parents in breeding programs that are aimed at improving drought resistance. A set of 121 bean genotypes (111 RILs, 2 parents, 8 checks) belonging to the Mesoamerican gene pool and one cowpea variety were evaluated under field conditions with two levels of water supply (irrigated and rainfed) over three seasons. To complement field studies, a greenhouse study was conducted using plastic cylinders with soil inserted into PVC pipes, to determine the relationship between grain yield obtained under field conditions with different root traits measured under greenhouse conditions. Resistance to drought stress was positively associated with a deeper and vigorous root system, better shoot growth, and superior mobilization of photosynthates to pod and seed production. The drought resistant lines differed in their root characteristics, some of them with a vigorous and deeper root system while others with a moderate to shallow root system. Among the shoot traits measured, pod

  8. Characterization of mature maize (Zea mays L.) root system architecture and complexity in a diverse set of Ex-PVP inbreds and hybrids.

    PubMed

    Hauck, Andrew L; Novais, Joana; Grift, Tony E; Bohn, Martin O

    2015-01-01

    The mature root system is a vital plant organ, which is critical to plant performance. Commercial maize (Zea mays L.) breeding has resulted in a steady increase in plant performance over time, along with noticeable changes in above ground vegetative traits, but the corresponding changes in the root system are not presently known. In this study, roughly 2500 core root systems from field trials of a set of 10 diverse elite inbreds formerly protected by Plant Variety Protection plus B73 and Mo17 and the 66 diallel intercrosses among them were evaluated for root traits using high throughput image-based phenotyping. Overall root architecture was modeled by root angle (RA) and stem diameter (SD), while root complexity, the amount of root branching, was quantified using fractal analysis to obtain values for fractal dimension (FD) and fractal abundance (FA). For each trait, per se line effects were highly significant and the most important contributor to trait performance. Mid-parent heterosis and specific combining ability was also highly significant for FD, FA, and RA, while none of the traits showed significant general combining ability. The interaction between the environment and the additive line effect was also significant for all traits. Within the inbred and hybrid generations, FD and FA were highly correlated (rp ≥ 0.74), SD was moderately correlated to FD and FA (0.69 ≥ rp ≥ 0.48), while the correlation between RA and other traits was low (0.13 ≥ rp ≥ -0.40). Inbreds with contrasting effects on complexity and architecture traits were observed, suggesting that root complexity and architecture traits are inherited independently. A more comprehensive understanding of the maize root system and the way it interacts with the environment will be useful for defining adaptation to nutrient acquisition and tolerance to stress from drought and high plant densities, critical factors in the yield gains of modern hybrids.

  9. Characterization of phenylpropanoid pathway genes within European maize (Zea mays L.) inbreds

    PubMed Central

    Andersen, Jeppe Reitan; Zein, Imad; Wenzel, Gerhard; Darnhofer, Birte; Eder, Joachim; Ouzunova, Milena; Lübberstedt, Thomas

    2008-01-01

    Background Forage quality of maize is influenced by both the content and structure of lignins in the cell wall. Biosynthesis of monolignols, constituting the complex structure of lignins, is catalyzed by enzymes in the phenylpropanoid pathway. Results In the present study we have amplified partial genomic fragments of six putative phenylpropanoid pathway genes in a panel of elite European inbred lines of maize (Zea mays L.) contrasting in forage quality traits. Six loci, encoding C4H, 4CL1, 4CL2, C3H, F5H, and CAD, displayed different levels of nucleotide diversity and linkage disequilibrium (LD) possibly reflecting different levels of selection. Associations with forage quality traits were identified for several individual polymorphisms within the 4CL1, C3H, and F5H genomic fragments when controlling for both overall population structure and relative kinship. A 1-bp indel in 4CL1 was associated with in vitro digestibility of organic matter (IVDOM), a non-synonymous SNP in C3H was associated with IVDOM, and an intron SNP in F5H was associated with neutral detergent fiber. However, the C3H and F5H associations did not remain significant when controlling for multiple testing. Conclusion While the number of lines included in this study limit the power of the association analysis, our results imply that genetic variation for forage quality traits can be mined in phenylpropanoid pathway genes of elite breeding lines of maize. PMID:18173847

  10. Genetic variation in salt tolerance during seed germination in a backcross inbred line population and advanced breeding lines derived from upland cotton x pima cotton

    USDA-ARS?s Scientific Manuscript database

    Seed germination is a crucial phase of the plant life cycle that affects its establishment and productivity. However, information on salt tolerance at this phase is limited. Pima cotton (Gossypium barbadense L.) may be more salt tolerant during germination than Upland cotton (G. hirsutum L.) based o...

  11. Analysis of antigen-induced changes in pulmonary mechanics in sensitized inbred rats.

    PubMed

    Holroyde, M C; Smith, S Y; Holme, G

    1982-05-01

    An inbred line of rats was derived which develop marked and consistent dyspnea following sensitization and then exposure to aerosolized antigen. This pulmonary response was investigated in detail by determining forced pulmonary mechanics to derive respiratory rate, peak expiratory flow rate (PEFR), forced vital capacity (FVC), forced expiratory volume in 0.1 s (FEV0.1), and maximal midexpiratory flow rate (MMFR). Challenging anesthetized rats for 5 min with an aerosol of 3% egg albumin produced minimal change in respiratory rate, a 20% fall in PEFR, a 50% fall in FVC, and a 30% decrease in FEV0.1 and MMFR. The response could be inhibited or reversed by salbutamol (0.5 mg/kg, i.v.) and aminophylline (25 mg/kg, i.v.) administered either before or after challenge. The pulmonary changes are consistent with antigen-induced asthma in the rats. The response shows similarities to human asthma and may provide a relevant experimental model.

  12. A novel intronic single nucleotide polymorphism in the myosin heavy polypeptide 4 gene is responsible for the mini-muscle phenotype characterized by major reduction in hind-limb muscle mass in mice.

    PubMed

    Kelly, Scott A; Bell, Timothy A; Selitsky, Sara R; Buus, Ryan J; Hua, Kunjie; Weinstock, George M; Garland, Theodore; Pardo-Manuel de Villena, Fernando; Pomp, Daniel

    2013-12-01

    Replicated artificial selection for high levels of voluntary wheel running in an outbred strain of mice favored an autosomal recessive allele whose primary phenotypic effect is a 50% reduction in hind-limb muscle mass. Within the High Runner (HR) lines of mice, the numerous pleiotropic effects (e.g., larger hearts, reduced total body mass and fat mass, longer hind-limb bones) of this hypothesized adaptive allele include functional characteristics that facilitate high levels of voluntary wheel running (e.g., doubling of mass-specific muscle aerobic capacity, increased fatigue resistance of isolated muscles, longer hind-limb bones). Previously, we created a backcross population suitable for mapping the responsible locus. We phenotypically characterized the population and mapped the Minimsc locus to a 2.6-Mb interval on MMU11, a region containing ∼100 known or predicted genes. Here, we present a novel strategy to identify the genetic variant causing the mini-muscle phenotype. Using high-density genotyping and whole-genome sequencing of key backcross individuals and HR mice with and without the mini-muscle mutation, from both recent and historical generations of the HR lines, we show that a SNP representing a C-to-T transition located in a 709-bp intron between exons 11 and 12 of the Myosin heavy polypeptide 4 (Myh4) skeletal muscle gene (position 67,244,850 on MMU11; assembly, December 2011, GRCm38/mm10; ENSMUSG00000057003) is responsible for the mini-muscle phenotype, Myh4(Minimsc). Using next-generation sequencing, our approach can be extended to identify causative mutations arising in mouse inbred lines and thus offers a great avenue to overcome one of the most challenging steps in quantitative genetics.

  13. Effectiveness of a detached‐leaf assay as a proxy for stem inoculations in backcrossed chestnut (Castanea) blight resistance breeding populations

    Treesearch

    N. R. LaBonte; J.R. McKenna; K. Woeste

    2016-01-01

    A recently developed detached-leaf blight resistance assay has generated interest because it could reduce the amount of time needed to evaluate backcrossed hybrid trees in the American chestnut blight resistance breeding programme. We evaluated the leaf inoculation technique on a sample of advanced progeny from the Indiana state chapter American Chestnut Foundation...

  14. Development of innovative techniques and principles that may be used as models to improve plant performance. Progress report

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hanna, W.W.; Burton, G.W.

    1984-06-01

    Dominant immunity to rust (Puccinia) and Piricularia leaf spot, a new stable A/sub 1/ cytoplasm and yield genes have been discovered in a single accession of P. monodii, a subspecies of pearl millet Pennisetum americanum. The useful genes were transferred to the best pearl millet inbreds using a backcrossing and screening system enhanced by controlling daylength, temperature, and breaking seed dormancy. Genes for fertility restoration, plant morphology, head characteristics and grain yield were transferred from the A' genome of P. purpureum (secondary gene pool) to pearl millet. This was made possible by doubling the chromosome number of the sterile triploidmore » between pearl millet and P. purpureum to produce fertile hexaploids. A number of hexaploids were backcrossed to pearl millet to find hexaploids that produced A' gametes to produce AA' 2n = 14 pearl millet plants. The value of the genes on the A' genome were not recognized before the AA' plants were produced because the B genome masked the characteristics on the A' genome in P. purpureum. In the tertiary gene pool, male and female fertile apomictic BC/sub 1/ plants were produced between pearl millet and P. orientale or P. squamulatum by manipulating chromosome levels or by producing trispecific hybrids. The development of fertile backcross plants in this gene pool is encouraging for further germplasm transfer research with emphasis on apomixis. The cytoplasm of P. schweinfurthii has been transferred to pearl millet. Mutations for early maturity and daylength insensitivity induced with mutagens have resulted in the development and release of early maturing inbreds Tift 23A/sub 1/E/sub 1/ and Tift 23B/sub 1/E/sub 1/.« less

  15. Genome-wide identification of copy number variations between two chicken lines that differ in genetic resistance to Marek’s disease

    USDA-ARS?s Scientific Manuscript database

    Background: Copy number variation (CNV) is a major source of genome polymorphism that directly contributes to phenotypic variation such as resistance to infectious diseases. Lines 63 and 72 are two highly inbred experimental chicken lines that differ greatly in susceptibility to Marek’s disease (MD)...

  16. Molecular analysis, cytogenetics and fertility of introgression lines from transgenic wheat to Aegilops cylindrica host.

    PubMed

    Schoenenberger, Nicola; Guadagnuolo, Roberto; Savova-Bianchi, Dessislava; Küpfer, Philippe; Felber, François

    2006-12-01

    Natural hybridization and backcrossing between Aegilops cylindrica and Triticum aestivum can lead to introgression of wheat DNA into the wild species. Hybrids between Ae. cylindrica and wheat lines bearing herbicide resistance (bar), reporter (gus), fungal disease resistance (kp4), and increased insect tolerance (gna) transgenes were produced by pollination of emasculated Ae. cylindrica plants. F1 hybrids were backcrossed to Ae. cylindrica under open-pollination conditions, and first backcrosses were selfed using pollen bags. Female fertility of F1 ranged from 0.03 to 0.6%. Eighteen percent of the sown BC1s germinated and flowered. Chromosome numbers ranged from 30 to 84 and several of the plants bore wheat-specific sequence-characterized amplified regions (SCARs) and the bar gene. Self fertility in two BC1 plants was 0.16 and 5.21%, and the others were completely self-sterile. Among 19 BC1S1 individuals one plant was transgenic, had 43 chromosomes, contained the bar gene, and survived glufosinate treatments. The other BC1S1 plants had between 28 and 31 chromosomes, and several of them carried SCARs specific to wheat A and D genomes. Fertility of these plants was higher under open-pollination conditions than by selfing and did not necessarily correlate with even or euploid chromosome number. Some individuals having supernumerary wheat chromosomes recovered full fertility.

  17. Shoot and Root Traits Contribute to Drought Resistance in Recombinant Inbred Lines of MD 23–24 × SEA 5 of Common Bean

    PubMed Central

    Polania, Jose; Rao, Idupulapati M.; Cajiao, Cesar; Grajales, Miguel; Rivera, Mariela; Velasquez, Federico; Raatz, Bodo; Beebe, Stephen E.

    2017-01-01

    Drought is the major abiotic stress factor limiting yield of common bean (Phaseolus vulgaris L.) in smallholder systems in Latin America and eastern and southern Africa; where it is a main source of protein in the daily diet. Identification of shoot and root traits associated with drought resistance contributes to improving the process of designing bean genotypes adapted to drought. Field and greenhouse studies were conducted at the International Center for Tropical Agriculture (CIAT), Palmira, Colombia to determine the relationship between grain yield and different shoot and root traits using a recombinant inbred lines (RILs) population (MD23–24 × SEA 5) of common bean. The main objectives of this study were to identify: (i) specific shoot and root morpho-physiological traits that contribute to improved resistance to drought and that could be useful as selection criteria in breeding beans for drought resistance; and (ii) superior genotypes with desirable shoot and root traits that could serve as parents in breeding programs that are aimed at improving drought resistance. A set of 121 bean genotypes (111 RILs, 2 parents, 8 checks) belonging to the Mesoamerican gene pool and one cowpea variety were evaluated under field conditions with two levels of water supply (irrigated and rainfed) over three seasons. To complement field studies, a greenhouse study was conducted using plastic cylinders with soil inserted into PVC pipes, to determine the relationship between grain yield obtained under field conditions with different root traits measured under greenhouse conditions. Resistance to drought stress was positively associated with a deeper and vigorous root system, better shoot growth, and superior mobilization of photosynthates to pod and seed production. The drought resistant lines differed in their root characteristics, some of them with a vigorous and deeper root system while others with a moderate to shallow root system. Among the shoot traits measured, pod

  18. Impact of the INBRE summer student mentored research program on undergraduate students in Arkansas.

    PubMed

    McSweeney, Jean C; Hudson, Teresa J; Prince, Latrina; Beneš, Helen; Tackett, Alan J; Miller Robinson, Caroline; Koeppe, Roger; Cornett, Lawrence E

    2018-03-01

    The Institutional Development Award (IDeA) program, housed within the National Institute for General Medical Sciences, administers the Networks of Biomedical Research Excellence (INBRE) as a strategic mission to broaden the geographic distribution of National Institutes of Health (NIH) funding within the United States. Undergraduate summer student mentored research programs (SSMRP) are a common feature of INBRE programs and are designed to increase undergraduate student interest in research careers in the biomedical sciences. Little information is available about student perspectives on how these programs impact their choices relative to education and careers. Therefore, we conducted qualitative interviews with 20 participants from the Arkansas INBRE SSMRP in the years 2002-2012. Each telephone interview lasted 30-45 min. An interview guide with a broad "grand tour" question was used to elicit student perspectives on SSMRP participation. Interviews were digitally recorded, then transcribed verbatim, and the transcript checked for accuracy. Content analysis and constant comparison were used to identify nine themes that were grouped into three temporal categories: before, during, and after the SSMRP experience. Students viewed the experience as positive and felt it impacted their career choices. They emphasized the value of mentoring in the program, and some reported maintaining a relationship with the mentor after the summer experience ended. Students also valued learning new laboratory and presentation skills and felt their research experience was enhanced by meeting students and scientists with a wide range of career interests. These data suggest that the Arkansas INBRE and the NIH IDeA program are successfully meeting the goal of increasing interest in research among undergraduates.

  19. SmartGrain: high-throughput phenotyping software for measuring seed shape through image analysis.

    PubMed

    Tanabata, Takanari; Shibaya, Taeko; Hori, Kiyosumi; Ebana, Kaworu; Yano, Masahiro

    2012-12-01

    Seed shape and size are among the most important agronomic traits because they affect yield and market price. To obtain accurate seed size data, a large number of measurements are needed because there is little difference in size among seeds from one plant. To promote genetic analysis and selection for seed shape in plant breeding, efficient, reliable, high-throughput seed phenotyping methods are required. We developed SmartGrain software for high-throughput measurement of seed shape. This software uses a new image analysis method to reduce the time taken in the preparation of seeds and in image capture. Outlines of seeds are automatically recognized from digital images, and several shape parameters, such as seed length, width, area, and perimeter length, are calculated. To validate the software, we performed a quantitative trait locus (QTL) analysis for rice (Oryza sativa) seed shape using backcrossed inbred lines derived from a cross between japonica cultivars Koshihikari and Nipponbare, which showed small differences in seed shape. SmartGrain removed areas of awns and pedicels automatically, and several QTLs were detected for six shape parameters. The allelic effect of a QTL for seed length detected on chromosome 11 was confirmed in advanced backcross progeny; the cv Nipponbare allele increased seed length and, thus, seed weight. High-throughput measurement with SmartGrain reduced sampling error and made it possible to distinguish between lines with small differences in seed shape. SmartGrain could accurately recognize seed not only of rice but also of several other species, including Arabidopsis (Arabidopsis thaliana). The software is free to researchers.

  20. Instability of the insertional mutation in CftrTgH(neoim)Hgu cystic fibrosis mouse model

    PubMed Central

    Charizopoulou, Nikoletta; Jansen, Silke; Dorsch, Martina; Stanke, Frauke; Dorin, Julia R; Hedrich, Hans-Jürgen; Tümmler, Burkhard

    2004-01-01

    Background A major boost to the cystic fibrosis disease research was given by the generation of various mouse models using gene targeting in embryonal stem cells. Moreover, the introduction of the same mutation on different inbred strains generating congenic strains facilitated the search for modifier genes. From the original CftrTgH(neoim)Hgu CF mouse model we have generated using strict brother × sister mating two inbred CftrTgH(neoim)Hgu mouse lines (CF/1 and CF/3). Thereafter, the insertional mutation was introgressed from CF/3 into three inbred backgrounds (C57BL/6, BALB/c, DBA/2J) generating congenic animals. In every backcross cycle germline transmission of the insertional mutation was monitored by direct probing the insertion via Southern RFLP. In order to bypass this time consuming procedure we devised an alternative PCR based protocol whereby mouse strains are differentiated at the Cftr locus by Cftr intragenic microsatellite genotypes that are tightly linked to the disrupted locus. Results Using this method we were able to identify animals carrying the insertional mutation based upon the differential haplotypic backgrounds of the three inbred strains and the mutant CftrTgH(neoim)Hgu at the Cftr locus. Moreover, this method facilitated the identification of the precise vector excision from the disrupted Cftr locus in two out of 57 typed animals. This reversion to wild type status took place without any loss of sequence revealing the instability of insertional mutations during the production of congenic animals. Conclusions We present intragenic microsatellite markers as a tool for fast and efficient identification of the introgressed locus of interest in the recipient strain during congenic animal breeding. Moreover, the same genotyping method allowed the identification of a vector excision event, posing questions on the stability of insertional mutations in mice. PMID:15102331

  1. [Genetic characteristics associated with drought tolerance of plant height and thousand-grain mass of recombinant inbred lines of wheat].

    PubMed

    Yang, De-Long; Zhang, Guo-Hong; Li, Xing-Mao; Xing, Hua; Cheng, Hong-Bo; Ni, Sheng-Li; Chen, Xiao-Ping

    2012-06-01

    A total of 120 recombinant inbred lines (RIL) derived from Chinese winter wheat cultivars Longjian 19xQ9086 and the two parents were taken as test materials to study the quantitative genetics characteristics of their plant height at different development stages, thousand-grain mass, as well as the correlations between the two traits under rainfed (drought stress) and well-watered conditions, and evaluate the genetic variation of the RIL. Under the two water conditions, the target traits of the RIL showed substantial transgressive segregation and great sensitivity to water condition. The drought stress coefficient of the plant height was higher at jointing stage, being up to 0.851. There was a significant positive correlation between the plant height at different development stages and the thousand-grain mass, and comparing with that at other growth stages, the plant height at jointing stage had a higher correlation coefficient with the thousand-grain mass (R2DS = 0.32, R2WW = 0.28). The plant height at both jointing and flowering stages had significant positive and direct effect but negative and indirect gross effect on the thousand-grain mass, while the plant height at heading and maturing stages was in adverse. The target traits showed a lower heritability ranged from 0.27 to 0.60. The numbers of the gene pairs controlling the thousand-grain mass were 10 under rainfed and 13 under well-watered conditions, while those of the gene pairs controlling the plant height at different development stages were 3-7 under rainfed and 4-14 under well-watered conditions, respectively. According to the clustering of the drought stress coefficient of plant height, the RIL could be classified into five subgroups, showing the abundant variation of the RIL in their phe- notypes and in the sensitivity to water condition. It was considered that the test RIL were appropriate for the study of the quantitative genetics of wheat drought resistance.

  2. Quantitative trait loci for maysin synthesis in maize (Zea mays L.) lines selected for high silk maysin content.

    PubMed

    Meyer, J D F; Snook, M E; Houchins, K E; Rector, B G; Widstrom, N W; McMullen, M D

    2007-06-01

    Maysin is a naturally occurring C-glycosyl flavone found in maize (Zea mays L.) silk tissue that confers resistance to corn earworm (Helicoverpa zea, Boddie). Recently, two new maize populations were derived for high silk maysin. The two populations were named the exotic populations of maize (EPM) and the southern inbreds of maize (SIM). Quantitative trait locus (QTL) analysis was employed to determine which loci were responsible for elevated maysin levels in inbred lines derived from the EPM and SIM populations. The candidate genes consistent with QTL position included the p (pericarp color), c2 (colorless2), whp1 (white pollen1) and in1 (intensifier1) loci. The role of these loci in controlling high maysin levels in silks was tested by expression analysis and use of the loci as genetic markers onto the QTL populations. These studies support p, c2 and whp1, but not in1, as loci controlling maysin. Through this study, we determined that the p locus regulates whp1 transcription and that increased maysin in these inbred lines was primarily due to alleles at both structural and regulatory loci promoting increased flux through the flavone pathway by increasing chalcone synthase activity.

  3. Reciprocal translocation of small numbers of inbred individuals rescues immunogenetic diversity.

    PubMed

    Grueber, Catherine E; Sutton, Jolene T; Heber, Sol; Briskie, James V; Jamieson, Ian G; Robertson, Bruce C

    2017-05-01

    Genetic rescue can reduce inbreeding depression and increase fitness of small populations, even when the donor populations are highly inbred. In a recent experiment involving two inbred island populations of the New Zealand South Island robin, Petroica australis, reciprocal translocations improved microsatellite diversity and individual fitness. While microsatellite loci may reflect patterns of genome-wide diversity, they generally do not indicate the specific genetic regions responsible for increased fitness. We tested the effectiveness of this reciprocal translocation for rescuing diversity of two immunogenetic regions: Toll-like receptor (TLR) and major histocompatibility complex (MHC) genes. We found that the relatively small number of migrants (seven and ten per island) effectively brought the characteristic TLR gene diversity of each source population into the recipient population. However, when migrants transmitted TLR alleles that were already present at high frequency in the recipient population, it was possible for offspring of mixed heritage to have decreased gene diversity compared to recipient population diversity prior to translocation. In contrast to TLRs, we did not observe substantial changes in MHC allelic diversity following translocation, with limited evidence of a decrease in differentiation, perhaps because most MHC alleles were observed at both sites prior to the translocation. Overall, we conclude that small numbers of migrants may successfully restore the diversity of immunogenetic loci with few alleles, but that translocating larger numbers of animals would provide additional opportunity for the genetic rescue of highly polymorphic immunity regions, such as the MHC, even when the source population is inbred. © 2017 John Wiley & Sons Ltd.

  4. Identification of quantitative trait loci affecting resistance to gastro-intestinal parasites in a double backcross population of Red Maasai and Dorper sheep

    USDA-ARS?s Scientific Manuscript database

    A genome-wide scan for quantitative trait loci (QTL) affecting gastrointestinal (GI) nematode resistance was completed using a double backcross sheep population derived from Red Maasai and Dorper ewes bred to F1 rams. These breeds were chosen, because Red Maasai sheep are known to be more tolerant ...

  5. Hypertensive renal disease: susceptibility and resistance in inbred hypertensive rat lines.

    PubMed

    Braun, Michael C; Herring, Stacy M; Gokul, Nisha; Monita, Monique; Bell, Rebecca; Hicks, M John; Wenderfer, Scott E; Doris, Peter A

    2013-10-01

    Spontaneously hypertensive rat (SHR) lines differ in their susceptibility to hypertensive end-organ disease and may provide an informative model of genetic risk of disease. Lines derived from the original SHR-B and SHR-C clades are highly resistant to hypertensive end-organ disease, whereas lines derived from the SHR-A clade were selected for stroke susceptibility and experience hypertensive renal disease. Here we characterize the temporal development of progressive renal injury in SHR-A3 animals consuming 0.3% sodium in the diet and drinking water. SHR-A3 rats demonstrate albuminuria, glomerular damage, tubulointerstitial injury, and renal fibrosis that emerge at 18 weeks of age and progress. Mortality of SHR-A3 animals was 50% at 40 weeks of age, and animals surviving to this age had reduced renal function. In contrast SHR-B2, which are 87% genetically identical to SHR-A3, are substantially protected from renal injury and demonstrate only moderate changes in albuminuria and renal histological injury over this time period. At 40 weeks of age, electron microscopy of the renal glomerulus revealed severe podocyte effacement in SHR-A3, but slit diaphragm architecture in SHR-B2 at this age was well preserved. Renal injury traits in the F1 and F2 progeny of an intercross between SHR-A3 and SHR-B2 were measured to determine heritability of renal injury in this model. Heritability of albuminuria, glomerular injury, and tubulointerstitial injury were estimated at 48.9, 66.5 and 58.6%, respectively. We assessed the relationship between blood pressure and renal injury measures in the F2 animals and found some correlation between these variables that explain up to 26% of the trait variation. Quantitative trait locus (QTL) mapping was performed using over 200 single nucleotide polymorphism markers distributed across the 13% of the genome that differs between these two closely related lines. Mapping of albuminuria, tubulointerstitial injury, and renal fibrosis failed to

  6. Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins

    USDA-ARS?s Scientific Manuscript database

    Decades of intensive tomato breeding using wild germplasm has resulted in genomes of domesticated accessions (Solanum lycopersicum) to be intertwined with introgressions from their wild relatives. Here we present the first whole genome sequences of two tomato inbreds Gh13 and BTI87, both carrying a ...

  7. Effects of temporal dynamics, nut weight and nut size on growth of American chestnut, Chinese chestnut and backcross generations in a commercial nursery

    Treesearch

    Cornelia Pinchot; Stacy Clark; Scott Schlarbaum; Arnold Saxton; Shi-Jean Sung; Frederick. Hebard

    2015-01-01

    Blight-resistant American chestnut (Castanea dentata) may soon be commercially available, but few studies have tested methods to produce high quality seedlings that will be competitive after planting. This study evaluated the performance of one American, one Chinese (C. mollissima), one second-generation backcross (BC3...

  8. A Novel Intronic Single Nucleotide Polymorphism in the Myosin heavy polypeptide 4 Gene Is Responsible for the Mini-Muscle Phenotype Characterized by Major Reduction in Hind-Limb Muscle Mass in Mice

    PubMed Central

    Kelly, Scott A.; Bell, Timothy A.; Selitsky, Sara R.; Buus, Ryan J.; Hua, Kunjie; Weinstock, George M.; Garland, Theodore; Pardo-Manuel de Villena, Fernando; Pomp, Daniel

    2013-01-01

    Replicated artificial selection for high levels of voluntary wheel running in an outbred strain of mice favored an autosomal recessive allele whose primary phenotypic effect is a 50% reduction in hind-limb muscle mass. Within the High Runner (HR) lines of mice, the numerous pleiotropic effects (e.g., larger hearts, reduced total body mass and fat mass, longer hind-limb bones) of this hypothesized adaptive allele include functional characteristics that facilitate high levels of voluntary wheel running (e.g., doubling of mass-specific muscle aerobic capacity, increased fatigue resistance of isolated muscles, longer hind-limb bones). Previously, we created a backcross population suitable for mapping the responsible locus. We phenotypically characterized the population and mapped the Minimsc locus to a 2.6-Mb interval on MMU11, a region containing ∼100 known or predicted genes. Here, we present a novel strategy to identify the genetic variant causing the mini-muscle phenotype. Using high-density genotyping and whole-genome sequencing of key backcross individuals and HR mice with and without the mini-muscle mutation, from both recent and historical generations of the HR lines, we show that a SNP representing a C-to-T transition located in a 709-bp intron between exons 11 and 12 of the Myosin heavy polypeptide 4 (Myh4) skeletal muscle gene (position 67,244,850 on MMU11; assembly, December 2011, GRCm38/mm10; ENSMUSG00000057003) is responsible for the mini-muscle phenotype, Myh4Minimsc. Using next-generation sequencing, our approach can be extended to identify causative mutations arising in mouse inbred lines and thus offers a great avenue to overcome one of the most challenging steps in quantitative genetics. PMID:24056412

  9. Comparative Evaluation of Two Vaccine Candidates against Experimental Leishmaniasis Due to Leishmania major Infection in Four Inbred Mouse Strains▿

    PubMed Central

    Benhnini, Fouad; Chenik, Mehdi; Laouini, Dhafer; Louzir, Hechmi; Cazenave, Pierre André; Dellagi, Koussay

    2009-01-01

    Experimental leishmaniasis in BALB/c and C57BL/6 mice are the most investigated murine models that were used for the preclinical evaluation of Leishmania vaccine candidates. We have previously described two new inbred mouse strains named PWK and MAI issued from feral founders that also support the development of experimental leishmaniasis due to L. major. In this study, we sought to determine whether different mouse inbred strains generate concordant or discordant results when used to evaluate the potential of Leishmania proteins to protect against experimental leishmaniasis. To this end, two Leishmania proteins, namely, LACK (for Leishmania homolog of receptor for activated C kinase) and LmPDI (for L. major protein disulfide isomerase) were compared for their capacity to protect against experimental leishmaniasis in PWK, MAI, BALB/c, and C57BL/6 inbred mouse strains. Our data show that the capacity of Leishmania proteins to confer protection depends on the mouse strain used, stressing the important role played by the genetic background in shaping the immune response against the pathogen. These results may have important implications for the preclinical evaluation of candidate Leishmania vaccines: rather than using a single mouse strain, a panel of different inbred strains of various genetic backgrounds should be tested in parallel. The antigen that confers protection in the larger range of inbred strains may have better chances to be also protective in outbred human populations and should be selected for clinical trials. PMID:19726616

  10. Comparative evaluation of two vaccine candidates against experimental leishmaniasis due to Leishmania major infection in four inbred mouse strains.

    PubMed

    Benhnini, Fouad; Chenik, Mehdi; Laouini, Dhafer; Louzir, Hechmi; Cazenave, Pierre André; Dellagi, Koussay

    2009-11-01

    Experimental leishmaniasis in BALB/c and C57BL/6 mice are the most investigated murine models that were used for the preclinical evaluation of Leishmania vaccine candidates. We have previously described two new inbred mouse strains named PWK and MAI issued from feral founders that also support the development of experimental leishmaniasis due to L. major. In this study, we sought to determine whether different mouse inbred strains generate concordant or discordant results when used to evaluate the potential of Leishmania proteins to protect against experimental leishmaniasis. To this end, two Leishmania proteins, namely, LACK (for Leishmania homolog of receptor for activated C kinase) and LmPDI (for L. major protein disulfide isomerase) were compared for their capacity to protect against experimental leishmaniasis in PWK, MAI, BALB/c, and C57BL/6 inbred mouse strains. Our data show that the capacity of Leishmania proteins to confer protection depends on the mouse strain used, stressing the important role played by the genetic background in shaping the immune response against the pathogen. These results may have important implications for the preclinical evaluation of candidate Leishmania vaccines: rather than using a single mouse strain, a panel of different inbred strains of various genetic backgrounds should be tested in parallel. The antigen that confers protection in the larger range of inbred strains may have better chances to be also protective in outbred human populations and should be selected for clinical trials.

  11. Selection of inbred maize (Zea mays L.) progenies by topcrosses conducted in contrasting environments.

    PubMed

    Rodrigues, C S; Pacheco, C A P; Guedes, M L; Pinho, R G V; Castro, C R

    2016-09-23

    The aim of this study was to identify inbred progenies of S 0:1 maize (Zea mays L.) plants that were efficient at a low level of technology and responsive at a high level of technology through the use of topcrosses. Two contrasting environments were created using two levels of base fertilization and topdressing, so that the levels of nitrogen, phosphorus, and potassium were applied four times higher in one environment than in the other. We used S 0:1 progenies derived from commercial hybrids in topcrosses with two testers (an elite line from the flint heterotic group and an elite line from the dent heterotic group). The progenies and three controls were evaluated in an augmented block design in Nossa Senhora das Dores, SE, Brazil in the 2010 crop season. The average grain yield in the high-technological level was 21.44% greater than that in the low-technological level. There were no changes in progeny behavior in the two technological levels for grain yield. The testers did not differ in the average grain yield of the progenies at the two technological levels. Therefore, it is possible to select progenies derived from commercial hybrids that have an efficient response to fertilization.

  12. QTL mapping for Mediterranean corn borer resistance in European flint germplasm using recombinant inbred lines

    PubMed Central

    2010-01-01

    Background Ostrinia nubilalis (ECB) and Sesamia nonagrioides (MCB) are two maize stem borers which cause important losses in temperate maize production, but QTL analyses for corn borer resistance were mostly restricted to ECB resistance and maize materials genetically related (mapping populations derived from B73). Therefore, the objective of this work was to identify and characterize QTLs for MCB resistance and agronomic traits in a RILs population derived from European flint inbreds. Results Three QTLs were detected for stalk tunnel length at bins 1.02, 3.05 and 8.05 which explained 7.5% of the RILs genotypic variance. The QTL at bin 3.05 was co-located to a QTL related to plant height and grain humidity and the QTL at bin 8.05 was located near a QTL related to yield. Conclusions Our results, when compared with results from other authors, suggest the presence of genes involved in cell wall biosynthesis or fortification with effects on resistance to different corn borer species and digestibility for dairy cattle. Particularly, we proposed five candidate genes related to cell wall characteristics which could explain the QTL for stalk tunnelling in the region 3.05. However, the small proportion of genotypic variance explained by the QTLs suggest that there are also many other genes of small effect regulating MCB resistance and we conclude that MAS seems not promising for this trait. Two QTLs detected for stalk tunnelling overlap with QTLs for agronomic traits, indicating the presence of pleitropism or linkage between genes affecting resistance and agronomic traits. PMID:20230603

  13. Genetic evaluation of recombinant inbred lines of rice (Oryza sativa L.) for grain zinc concentrations, yield related traits and identification of associated SSR markers.

    PubMed

    Bekele, Berhanu D; Naveen, G K; Rakhi, S; Shashidhar, H E

    2013-12-01

    The objectives of the present study were to evaluate genetic variability parameters, correlations that exist for grain Zn concentration and yield related traits and identification of SSR markers linked to these traits in rice. One hundred seventy six Recombinant Inbred Lines (RILs) of Azucena X Moromutant were grown at University of Agricultural Sciences, Bangalore in augmented experimental design during wet seasons of 2010 and 2011. The study revealed significant genetic variability for all the traits. Grain yield per plant and grain zinc concentration showed higher phenotypic and genotypic co-efficient of variation. Significant positive correlation was observed for grain yield per plant with number of productive tillers per plant (r = 0.5) and number of tillers per plant (r = 0.4). Grain zinc concentration showed negative correlation with grain yield per plant (r = - 0.27). The path-coefficient analysis indicated the positive direct effect of number of productive tillers per plant on grain yield per plant (0.514). Grain zinc concentration showed negative direct effect on grain yield per plant (-0.186). Single-marker analysis using 26 SSR markers on RILs mapping population showed that RM212, RM263, RM6832, RM152, RM21, RM234 and RM3331 had association with grain zinc concentration and other yield related traits. But validation of these markers on fifty two rice genotypes showed that only three markers RM263, RM152 and RM21 had association with grain zinc concentration. Therefore, the genetic information generated and molecular markers identified from this study could be used for zinc biofortification programmes in rice.

  14. Accumulation, speciation, and coordination of arsenic in an inbred line and a wild type cultivar of the desert plant species Chilopsis linearis (Desert willow).

    PubMed

    Castillo-Michel, Hiram A; Zuverza-Mena, Nubia; Parsons, Jason G; Dokken, Kenneth M; Duarte-Gardea, Maria; Peralta-Videa, Jose R; Gardea-Torresdey, Jorge L

    2009-03-01

    This study investigated the absorption of arsenic (As), sulfur (S), and phosphorus (P) in the desert plant Chilopsis linearis (Desert willow). A comparison between an inbred line (red flowered) and wild type (white flowered) plants was performed to look for differential responses to As treatment. One month old seedlings were treated for 7 days with arsenate (As(2)O(5), As(V)) at 0, 20, and 40 mg As(V)L(-1). Results from the ICP-OES analysis showed that at 20mg As(V)L(-1), red flowered plants had 280+/-11 and 98+/-7 mg As kg(-1) dry wt in roots and stems, respectively, while white flowered plants had 196+/-30 and 103+/-13 mg As kg(-1) dry wt for roots and stems. At this treatment level, the concentration of As in leaves was below detection limits for both plants. In red flowered plants treated with 40 mg As(V)L(-1), As was at 290+/-77 and 151+/-60 mg As kg(-1) in roots and stems, respectively, and not detected in leaves, whereas white flowered plants had 406+/-36, 213+/-12, and 177+/-40 mg As kg(-1) in roots, stems, and leaves. The concentration of S increased in all As treated plants, while the concentration of P decreased in roots and stems of both types of plants and in leaves of red flowered plants. X-ray absorption spectroscopy analyses demonstrated partial reduction of arsenate to arsenite in the form of As-(SX)(3) species in both types of plants.

  15. Strong genetic influences on measures of behavioral-regulation among inbred rat strains

    PubMed Central

    Richards, Jerry B.; Lloyd, David R.; Kuehlewind, Brandon; Militello, Leah; Paredez, Marita; Solberg -Woods, Leah; Palmer, Abraham A.

    2013-01-01

    A fundamental challenge for any complex nervous system is to regulate behavior in response to environmental challenges. Three measures of behavioral regulation were tested in a panel of 8 inbred rat strains. These measures were; 1) sensation seeking as assessed by locomotor response to novelty and the sensory reinforcing effects of light onset, 2) attention and impulsivity, as measured by a choice reaction time task, and 3) impulsivity as measured by a delay discounting task. Deficient behavioral regulation has been linked to a number of psychopathologies, including ADHD, Schizophrenia, Autism, drug abuse and eating disorders. Eight inbred rat strains (August Copenhagen Irish, Brown Norway, Buffalo, Fischer 344, Wistar Kyoto, Spontaneous Hypertensive Rat, Lewis, Dahl Salt Sensitive) were tested. With n=9 for each strain, we observed robust strain differences for all tasks; heritability was estimated between 0.43 and 0.66. Performance of the 8 inbred rat strains on the choice reaction time task was compared to the performance of out bred Sprague Dawley (n=28) and Heterogeneous strain rats (n=48). The results indicate a strong genetic influence on complex tasks related to behavioral regulation and indicate that some of measures tap common genetically-driven processes. Furthermore, our results establish the potential for future studies aimed at identifying specific alleles that influence variability for these traits. Identification of such alleles could contribute to our understanding of the molecular genetic basis of behavioral regulation, which is of fundamental importance and likely contributes to multiple psychiatric disorders. PMID:23710681

  16. Identification and validation of quantitative trait loci for seed yield, oil and protein contents in two recombinant inbred line populations of soybean.

    PubMed

    Wang, Xianzhi; Jiang, Guo-Liang; Green, Marci; Scott, Roy A; Song, Qijian; Hyten, David L; Cregan, Perry B

    2014-10-01

    Soybean seeds contain high levels of oil and protein, and are the important sources of vegetable oil and plant protein for human consumption and livestock feed. Increased seed yield, oil and protein contents are the main objectives of soybean breeding. The objectives of this study were to identify and validate quantitative trait loci (QTLs) associated with seed yield, oil and protein contents in two recombinant inbred line populations, and to evaluate the consistency of QTLs across different environments, studies and genetic backgrounds. Both the mapping population (SD02-4-59 × A02-381100) and validation population (SD02-911 × SD00-1501) were phenotyped for the three traits in multiple environments. Genetic analysis indicated that oil and protein contents showed high heritabilities while yield exhibited a lower heritability in both populations. Based on a linkage map constructed previously with the mapping population and using composite interval mapping and/or interval mapping analysis, 12 QTLs for seed yield, 16 QTLs for oil content and 11 QTLs for protein content were consistently detected in multiple environments and/or the average data over all environments. Of the QTLs detected in the mapping population, five QTLs for seed yield, eight QTLs for oil content and five QTLs for protein content were confirmed in the validation population by single marker analysis in at least one environment and the average data and by ANOVA over all environments. Eight of these validated QTLs were newly identified. Compared with the other studies, seven QTLs for seed yield, eight QTLs for oil content and nine QTLs for protein content further verified the previously reported QTLs. These QTLs will be useful for breeding higher yield and better quality cultivars, and help effectively and efficiently improve yield potential and nutritional quality in soybean.

  17. Genetic dissection of growth, wood basic density and gene expression in interspecific backcrosses of Eucalyptus grandis and E. urophylla

    PubMed Central

    2012-01-01

    Background F1 hybrid clones of Eucalyptus grandis and E. urophylla are widely grown for pulp and paper production in tropical and subtropical regions. Volume growth and wood quality are priority objectives in Eucalyptus tree improvement. The molecular basis of quantitative variation and trait expression in eucalypt hybrids, however, remains largely unknown. The recent availability of a draft genome sequence (http://www.phytozome.net) and genome-wide genotyping platforms, combined with high levels of genetic variation and high linkage disequilibrium in hybrid crosses, greatly facilitate the detection of quantitative trait loci (QTLs) as well as underlying candidate genes for growth and wood property traits. In this study, we used Diversity Arrays Technology markers to assess the genetic architecture of volume growth (diameter at breast height, DBH) and wood basic density in four-year-old progeny of an interspecific backcross pedigree of E. grandis and E. urophylla. In addition, we used Illumina RNA-Seq expression profiling in the E. urophylla backcross family to identify cis- and trans-acting polymorphisms (eQTLs) affecting transcript abundance of genes underlying QTLs for wood basic density. Results A total of five QTLs for DBH and 12 for wood basic density were identified in the two backcross families. Individual QTLs for DBH and wood basic density explained 3.1 to 12.2% of phenotypic variation. Candidate genes underlying QTLs for wood basic density on linkage groups 8 and 9 were found to share trans-acting eQTLs located on linkage groups 4 and 10, which in turn coincided with QTLs for wood basic density suggesting that these QTLs represent segregating components of an underlying transcriptional network. Conclusion This is the first demonstration of the use of next-generation expression profiling to quantify transcript abundance in a segregating tree population and identify candidate genes potentially affecting wood property variation. The QTLs identified in this

  18. The congenic normal R/APfd and jaundiced R/APfd-j/j rat strains: a new animal model of hereditary non-haemolytic unconjugated hyperbilirubinaemia due to defective bilirubin conjugation.

    PubMed

    Leyten, R; Vroemen, J P; Blanckaert, N; Heirwegh, K P

    1986-10-01

    In this paper the production of the R/APfd-j/j strain which is congenic with the R/APfd strain is reported. The R/APfd-j/j completely lacks hepatic bilirubin UDP-glucuronyltransferase activity, as do our GUNNXR/Pfd-j/j rat strain and various other stocks of GUNN rats (j/j) described in the literature. Our recombinant inbred strain GUNNXR/Pfd-j/j was produced from non-inbred GUNN (j/j) rats. This GUNNXR/Pfd-j/j rat was used as a donor of the jaundice gene j, the R/APfd rat serving as the recipient. After eight backcross-intercross cycles (16 generations) the R/APfd-j/j strain was obtained which is congenic with the R/APfd strain. Congenicity was demonstrated by various techniques including transplantation of skin tissue, strain-specific tumour cells and hepatocytes, the mixed lymphocyte reaction, and comparison of biochemical markers. The potential of the novel inbred strain of jaundiced rat, R/APfd-j/j, and the corresponding control strain R/APfd for biochemical and clinical studies of bilirubin metabolism are briefly discussed.

  19. Quantitative trait loci segregating in crosses between New Hampshire and White Leghorn chicken lines: I. egg production traits.

    PubMed

    Goraga, Z S; Nassar, M K; Brockmann, G A

    2012-04-01

    A genome scan was performed to detect chromosomal regions that affect egg production traits in reciprocal crosses between two genetically and phenotypically extreme chicken lines: the partially inbred line New Hampshire (NHI) and the inbred line White Leghorn (WL77). The NHI line had been selected for high growth and WL77 for low egg weight before inbreeding. The result showed a highly significant region on chromosome 4 with multiple QTL for egg production traits between 19.2 and 82.1 Mb. This QTL region explained 4.3 and 16.1% of the phenotypic variance for number of eggs and egg weight in the F(2) population, respectively. The egg weight QTL effects are dependent on the direction of the cross. In addition, genome-wide suggestive QTL for egg weight were found on chromosomes 1, 5, and 9, and for number of eggs on chromosomes 5 and 7. A genome-wide significant QTL affecting age at first egg was mapped on chromosome 1. The difference between the parental lines and the highly significant QTL effects on chromosome 4 will further support fine mapping and candidate gene identification for egg production traits in chicken. © 2011 The Authors, Animal Genetics © 2011 Stichting International Foundation for Animal Genetics.

  20. Improvement of Basmati rice varieties for resistance to blast and bacterial blight diseases using marker assisted backcross breeding.

    PubMed

    Ellur, Ranjith K; Khanna, Apurva; Yadav, Ashutosh; Pathania, Sandeep; Rajashekara, H; Singh, Vikas K; Gopala Krishnan, S; Bhowmick, Prolay K; Nagarajan, M; Vinod, K K; Prakash, G; Mondal, Kalyan K; Singh, Nagendra K; Vinod Prabhu, K; Singh, Ashok K

    2016-01-01

    Marker assisted backcross breeding was employed to incorporate the blast resistance genes, Pi2 and Pi54 and bacterial blight (BB) resistance genes xa13 and Xa21 into the genetic background of Pusa Basmati 1121 (PB1121) and Pusa Basmati 6. Foreground selection for target gene(s) was followed by arduous phenotypic and background selection which fast-tracked the recovery of recurrent parent genome (RPG) to an extent of 95.8% in one of the near-isogenic lines (NILs) namely, Pusa 1728-23-33-31-56, which also showed high degree of resemblance to recurrent parent, PB6 in phenotype. The phenotypic selection prior to background selection provided an additional opportunity for identifying the novel recombinants viz., Pusa 1884-9-12-14 and Pusa 1884-3-9-175, superior to parental lines in terms of early maturity, higher yield and improved quality parameters. There was no significant difference between the RPG recovery estimated based on SSR or SNP markers, however, the panel of SNPs markers was considered as the better choice for background selection as it provided better genome coverage and included SNPs in the genic regions. Multi-location evaluation of NILs depicted their stable and high mean performance in comparison to the respective recurrent parents. The Pi2+Pi54 carrying NILs were effective in combating a pan-India panel of Magnaporthe oryzae isolates with high level of field resistance in northern, eastern and southern parts of India. Alongside, the PB1121-NILs and PB6-NILs carrying BB resistance genes xa13+Xa21 were resistant against Xanthomonas oryzae pv. oryzae races of north-western, southern and eastern parts of the country. Three of NILs developed in this study, have been promoted to final stage of testing during the ​Kharif 2015 in the Indian National Basmati Trial. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  1. Evidence should trump intuition by preferring inbred strains to outbred stocks in preclinical research.

    PubMed

    Festing, Michael F W

    2014-01-01

    Inbred strains of mice such as C57BL and BALB/c are more widely used in published work than outbred stocks of mice such as ICR and CD-1. In contrast, outbred stocks of rats such as Wistar and Sprague-Dawley are more widely used than inbred strains such as F344 and LEW. The properties of inbred and outbred mice and rats are briefly reviewed, and it is concluded that, with some exceptions, there is a strong case for using inbred strains in most controlled experiments. This is because they are usually more uniform, so that fewer animals are usually needed to detect a specified response and they are more repeatable, because they are genetically defined (i.e., the strain can be identified using genetic markers) and less liable to genetic change. Yet many scientists continue to use outbred animals. In Daniel Kahneman's book "Thinking Fast and Slow" he explains that we can answer questions in 2 ways: "fast" by intuition or "slow" by analytical reasoning. The former method is instantaneous, requires no thought but is not evidence based. Analytical reasoning is evidence based but requires hard work, which we all avoid. He has found that "… when faced with a difficult question, we often answer an easier one instead, usually without noticing the substitution." The target question of whether to choose outbred or inbred strains in controlled experiments is a difficult one requiring knowledge of the characteristics of these strains and the principles of experimental design. A substitute question, "are humans and outbred stocks both genetically heterogeneous," is easily answered in the affirmative. It is likely that many scientists are intuitively answering the substitute question and are assuming that they have answered the target question. If so they may be using the wrong animals in their research. Nor is the fact that humans and outbred stocks are alike in being genetically heterogeneous a reason for using them. The whole concept of a "model" is that it is similar to the

  2. Agrobacterium- and Biolistic-Mediated Transformation of Maize B104 Inbred.

    PubMed

    Raji, Jennifer A; Frame, Bronwyn; Little, Daniel; Santoso, Tri Joko; Wang, Kan

    2018-01-01

    Genetic transformation of maize inbred genotypes remains non-routine for many laboratories due to variations in cell competency to induce embryogenic callus, as well as the cell's ability to receive and incorporate transgenes into the genome. This chapter describes two transformation protocols using Agrobacterium- and biolistic-mediated methods for gene delivery. Immature zygotic embryos of maize inbred B104, excised from ears harvested 10-14 days post pollination, are used as starting explant material. Disarmed Agrobacterium strains harboring standard binary vectors and the biolistic gun system Bio-Rad PDS-1000/He are used as gene delivery systems. The herbicide resistant bar gene and selection agent bialaphos are used for identifying putative transgenic type I callus events. Using the step-by-step protocols described here, average transformation frequencies (number of bialaphos resistant T 0 callus events per 100 explants infected or bombarded) of 4% and 8% can be achieved using the Agrobacterium- and biolistic-mediated methods, respectively. An estimated duration of 16-21 weeks is needed using either protocol from the start of transformation experiments to obtaining putative transgenic plantlets with established roots. In addition to laboratory in vitro procedures, detailed greenhouse protocols for producing immature ears as transformation starting material and caring for transgenic plants for seed production are also described.

  3. Whole Genome Sequence of Two Wild-Derived Mus musculus domesticus Inbred Strains, LEWES/EiJ and ZALENDE/EiJ, with Different Diploid Numbers

    PubMed Central

    Morgan, Andrew P.; Didion, John P.; Doran, Anthony G.; Holt, James M.; McMillan, Leonard; Keane, Thomas M.; de Villena, Fernando Pardo-Manuel

    2016-01-01

    Wild-derived mouse inbred strains are becoming increasingly popular for complex traits analysis, evolutionary studies, and systems genetics. Here, we report the whole-genome sequencing of two wild-derived mouse inbred strains, LEWES/EiJ and ZALENDE/EiJ, of Mus musculus domesticus origin. These two inbred strains were selected based on their geographic origin, karyotype, and use in ongoing research. We generated 14× and 18× coverage sequence, respectively, and discovered over 1.1 million novel variants, most of which are private to one of these strains. This report expands the number of wild-derived inbred genomes in the Mus genus from six to eight. The sequence variation can be accessed via an online query tool; variant calls (VCF format) and alignments (BAM format) are available for download from a dedicated ftp site. Finally, the sequencing data have also been stored in a lossless, compressed, and indexed format using the multi-string Burrows-Wheeler transform. All data can be used without restriction. PMID:27765810

  4. Microsatellite markers associated with resistance to Marek's disease in commercial layer chickens.

    PubMed

    McElroy, J P; Dekkers, J C M; Fulton, J E; O'Sullivan, N P; Soller, M; Lipkin, E; Zhang, W; Koehler, K J; Lamont, S J; Cheng, H H

    2005-11-01

    The objective of the current study was to identify QTL conferring resistance to Marek's disease (MD) in commercial layer chickens. To generate the resource population, 2 partially inbred lines that differed in MD-caused mortality were intermated to produce 5 backcross families. Vaccinated chicks were challenged with very virulent plus (vv+) MD virus strain 648A at 6 d and monitored for MD symptoms. A recent field isolate of the MD virus was used because the lines were resistant to commonly used older laboratory strains. Selective genotyping was employed using 81 microsatellites selected based on prior results with selective DNA pooling. Linear regression and Cox proportional hazard models were used to detect associations between marker genotypes and survival. Significance thresholds were validated by simulation. Seven and 6 markers were significant based on proportion of false positive and false discovery rate thresholds less than 0.2, respectively. Seventeen markers were associated with MD survival considering a comparison-wise error rate of 0.10, which is about twice the number expected by chance, indicating that at least some of the associations represent true effects. Thus, the present study shows that loci affecting MD resistance can be mapped in commercial layer lines. More comprehensive studies are under way to confirm and extend these results.

  5. Cytological study of radiation induced alterations in cytoplasmic factors controlling male sterility in corn. Progress report, February 28, 1973--December 1, 1973

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Edwardson, J.R.

    1973-01-01

    Cytoplasmic male sterile accessions, other than T-type, are being backcrossed to adapted maintainer and restorer inbred corn lines. Fertile selections from gamma -irradiated T-type corn continue to exhibit resistance to infection by race-T of Helminthosporium maydis in field and greenhouse tests. Cytological comparisons of these fertile selections and T-sterile, maintainer, and restorer lines are continuing. Dominant male sterility and its suppression in S-cytoplasm corn is being investigated. lnduction of cytoplasmic male sterility in normal cytoplasm corn and suppression of susceptibility to Helminthosporium maydis infection in T cytoplasm corn is being attempted with chemical mutagens. Consistent differences in cytoplasmic inclusions inmore » sterile and maintainer Vicia faba were observed. Consistent differences in mitochondria were observed in cytological comparisons of normal and sterile corn. These abnormal mitochondria and non-Mendelian plastid abnormalities in corn, sorghum, tobacco, and petunia will be used in studying the fertilization process. Investigations of the properties of Datura Q-virus are near completion. Cytological and serological studies indicate the Q-virus is a strain of tobacco streak virus. Graft-transmission of cytoplasmic male sterility is being attempted in sunflower. (auth)« less

  6. The relative contribution of target-site mutations in complex acaricide resistant phenotypes as assessed by marker assisted backcrossing in Tetranychus urticae.

    PubMed

    Riga, Maria; Bajda, Sabina; Themistokleous, Christos; Papadaki, Stavrini; Palzewicz, Maria; Dermauw, Wannes; Vontas, John; Leeuwen, Thomas Van

    2017-08-23

    The mechanisms underlying insecticide and acaricide resistance in insects and mites are often complex, including additive effects of target-site insensitivity, increased metabolism and transport. The extent to which target-site resistance mutations contribute to the resistance phenotype is, however, not well studied. Here, we used marker-assisted backcrossing to create 30 congenic lines carrying nine mutations (alone, or in combination in a few cases) associated with resistance to avermectins, pyrethroids, mite growth inhibitors and mitochondrial complex III inhibitors (QoI) in a polyphagous arthropod pest, the spider mite Tetranychus urticae. Toxicity tests revealed that mutations in the voltage-gated sodium channel, chitin synthase 1 and cytochrome b confer high levels of resistance and, when fixed in a population, these mutations alone can result in field failure of acaricide treatment. In contrast, although we confirmed the implication of mutations in glutamate-gated chloride channels in abamectin and milbemectin insensitivity, these mutations do not lead to the high resistance levels that are often reported in abamectin resistant strains of T. urticae. Overall, this study functionally validates reported target-site resistance mutations in T. urticae, by uncoupling them from additional mechanisms, allowing to finally investigate the strength of the conferred phenotype in vivo.

  7. Genotypic gain with simultaneous selection of production, nutrition, and culinary traits in cowpea crosses and backcrosses using mixed models.

    PubMed

    Oliveira, D G; Rocha, M M; Damasceno-Silva, K J; Sá, F V; Lima, L R L; Resende, M D V

    2017-08-17

    The aim of this study was to estimate the genotypic gain with simultaneous selection of production, nutrition, and culinary traits in cowpea crosses and backcrosses and to compare different selection indexes. Eleven cowpea populations were evaluated in a randomized complete block design with four replications. Fourteen traits were evaluated, and the following parameters were estimated: genotypic variation coefficient, genotypic determination coefficient, experimental quality indicator and selection reliability, estimated genotypic values ​​- BLUE, genotypic correlation coefficient among traits, and genotypic gain with simultaneous selection of all traits. The genotypic gain was estimated based on tree selection indexes: classical, multiplicative, and the sum of ranks. The genotypic variation coefficient was higher than the environmental variation coefficient for the number of days to start flowering, plant type, the weight of one hundred grains, grain index, and protein concentration. The majority of the traits presented genotypic determination coefficient from medium to high magnitude. The identification of increases in the production components is associated with decreases in protein concentration, and the increase in precocity leads to decreases in protein concentration and cooking time. The index based on the sum of ranks was the best alternative for simultaneous selection of traits in the cowpea segregating populations resulting from the crosses and backcrosses evaluated, with emphasis on the F 4 BC 12 , F 4 C 21 , and F 4 C 12 populations, which had the highest genotypic gains.

  8. Identification of full-length proviral DNA of porcine endogenous retrovirus from Chinese Wuzhishan miniature pigs inbred.

    PubMed

    Ma, Yuyuan; Lv, Maomin; Xu, Shu; Wu, Jianmin; Tian, Kegong; Zhang, Jingang

    2010-07-01

    Existence of porcine endogenous retrovirus (PERV) hinders pigs to be used in clinical xenotransplantation to alleviate the shortage of human transplants. Chinese miniature pigs are potential organ donors for xenotransplantation in China. However, so far, an adequate level of information on the molecular characteristics of PERV from Chinese miniature pigs has not been available. We described here the cloning and characterization of full-length proviral DNA of PERV from Chinese Wuzhishan miniature pigs inbred (WZSP). Full-length nucleotide sequences of PERV-WZSP and other PERVs were aligned and phylogenetic tree was constructed from deduced amino-acid sequences of env. The results demonstrated that the full-length proviral DNA of PERV-WZSP belongs to gammaretrovirus and shares high similarity with other PERVs. Sequence analysis also suggested that different patterns of LTR existed in the same porcine germ line and partial PERV-C sequence may recombine with PERV-A sequence in LTR. (c) 2008 Elsevier Ltd. All rights reserved.

  9. Population parameters for resistance to Fusarium graminearum and Fusarium verticillioides ear rot among large sets of early, mid-late and late maturing European maize (Zea mays L.) inbred lines.

    PubMed

    Löffler, Martin; Kessel, Bettina; Ouzunova, Milena; Miedaner, Thomas

    2010-03-01

    Infection of maize ears with Fusarium graminearum (FG) and Fusarium verticillioides (FV) reduces yield and quality by mycotoxin contamination. Breeding and growing varieties resistant to both Fusarium spp. is the best alternative to minimize problems. The objectives of our study were to draw conclusions on breeding for ear rot resistance by estimating variance components, heritabilities and correlations between resistances to FV and FG severity and to investigate different inoculation methods. In 2007 and 2008, three maturity groups (early, mid-late, late) each comprising about 150 inbred lines were tested in Germany, France, Italy, and Hungary according to their maturity group. They were silk channel inoculated by FG (early) and FV (all groups). In the late maturity group, additionally kernel inoculation was applied in a separate trial. The percentage of mycelium coverage on the ear was rated at harvest (0-100%). Significant (P < 0.01) genotypic variances of ear rot severity were found in all groups. Inoculation was superior to natural infection because of higher disease severities and heritabilities. In early maturing flints and dents, FG caused significantly (P < 0.01) higher ear rot severity than FV (61.7 and 55.1% FG vs. 18.2 and 11.1% FV ear rot severity, respectively). FV inoculation in Southern Europe (mid-late, late) resulted in similar means between 10.3 and 14.0%. Selection is complicated by significant (P < 0.01) genotype x environment interactions. Correlation between FG and FV severity was moderate in flints and dents (r = 0.59 and 0.49, respectively) but lines resistant to both fungi exist. We conclude that chances for selecting improved European elite maize material within the existing germplasms is promising by multi-environmental inoculation trials.

  10. Inbred Strain-Specific Effects of Exercise in Wild Type and Biglycan Deficient Mice

    PubMed Central

    Wallace, Joseph M.; Golcuk, Kurtulus; Morris, Michael D.; Kohn, David H.

    2010-01-01

    Biglycan (bgn)-deficient mice (KO) have defective osteoblasts which lead to changes in the amount and quality of bone. Altered tissue strength in C57BL6/129 (B6;129) KO mice, a property which is independent of tissue quantity, suggests that deficiencies in tissue quality are responsible. However, the response to bgn-deficiency is inbred strain-specific. Mechanical loading influences bone matrix quality in addition to any increase in bone mass or change in bone formation activity. Since many diseases influence the mechanical integrity of bone through altered tissue quality, loading may be a way to prevent and treat extracellular matrix deficiencies. C3H/He (C3H) mice consistently have a less vigorous response to mechanical loading vs. other inbred strains. It was therefore hypothesized that the bones from both wild type (WT) and KO B6;129 mice would be more responsive to exercise than the bones from C3H mice. To test these hypotheses at 11 weeks of age, following 21 consecutive days of exercise, we investigated cross-sectional geometry, mechanical properties, and tissue composition in the tibiae of male mice bred on B6;129 and C3H backgrounds. This study demonstrated inbred strain-specific compositional and mechanical changes following exercise in WT and KO mice, and showed evidence of genotype-specific changes in bone in response to loading in a gene disruption model. This study further shows that exercise can influence bone tissue composition and/or mechanical integrity without changes in bone geometry. Together, these data suggest that exercise may represent a possible means to alter tissue quality and mechanical deficiencies caused by many diseases of bone. PMID:20033775

  11. Identification of Quantitative Trait Loci Controlling Root and Shoot Traits Associated with Drought Tolerance in a Lentil (Lens culinaris Medik.) Recombinant Inbred Line Population

    PubMed Central

    Idrissi, Omar; Udupa, Sripada M.; De Keyser, Ellen; McGee, Rebecca J.; Coyne, Clarice J.; Saha, Gopesh C.; Muehlbauer, Fred J.; Van Damme, Patrick; De Riek, Jan

    2016-01-01

    Drought is one of the major abiotic stresses limiting lentil productivity in rainfed production systems. Specific rooting patterns can be associated with drought avoidance mechanisms that can be used in lentil breeding programs. In all, 252 co-dominant and dominant markers were used for Quantitative Trait Loci (QTL) analysis on 132 lentil recombinant inbred lines based on greenhouse experiments for root and shoot traits during two seasons under progressive drought-stressed conditions. Eighteen QTLs controlling a total of 14 root and shoot traits were identified. A QTL-hotspot genomic region related to a number of root and shoot characteristics associated with drought tolerance such as dry root biomass, root surface area, lateral root number, dry shoot biomass and shoot length was identified. Interestingly, a QTL (QRSratioIX-2.30) related to root-shoot ratio, an important trait for drought avoidance, explaining the highest phenotypic variance of 27.6 and 28.9% for the two consecutive seasons, respectively, was detected. This QTL was closed to the co-dominant SNP marker TP6337 and also flanked by the two SNP TP518 and TP1280. An important QTL (QLRNIII-98.64) related to lateral root number was found close to TP3371 and flanked by TP5093 and TP6072 SNP markers. Also, a QTL (QSRLIV-61.63) associated with specific root length was identified close to TP1873 and flanked by F7XEM6b SRAP marker and TP1035 SNP marker. These two QTLs were detected in both seasons. Our results could be used for marker-assisted selection in lentil breeding programs targeting root and shoot characteristics conferring drought avoidance as an efficient alternative to slow and labor-intensive conventional breeding methods. PMID:27602034

  12. High frequency fo X-Y chromosome dissociation in primary spermatocytes of F1 hybrids between Japanese wild mice (Mus musculus molossinus) and inbred laboratory mice.

    PubMed

    Imai, H T; Matsuda, Y; Shiroishi, T; Moriwaki, K

    1981-01-01

    In the hybrids between Japanese wild mice (Mus musculus molossinus) and inbred laboratory mice (BALB/c and B10.BR, which were probably derived from M. m. domesticus), the X and Y chromosomes dissociated precociously at the first meiotic metaphase in some 70% of spermatocytes; that percentage was only 8.9% in inbred laboratory mice and 21.1% in wild mice. X-Y dissociation began at least at early diakinesis and continued during metaphase I (MI). Some autosomes of the hybrid (10.1%) and BALB/c (10.6%) mice also dissociated precociously, but there was no distinctive correlation between X-Y and autosomal dissociation. In B10 or B6 congenic lines with a Y chromosome from wild M. m. molossinus, there was an apparent tendency for the percentage of precocious X-Y dissociation to decrease with an increasing number of back cross generations. Based on these observations we concluded that: 1. the X-Y dissociation found is genetically controlled, perhaps by multiple genes; 2. these genes are located on autosomes and are active only when they are heterozygous; 3. the frequent dissociation of the sex chromosomes neither affects male fertility nor induces non-disjunction of the X and Y chromosomes, though it significantly reduces testes weight.

  13. Phenotypic analysis of first-year traits in a pseudo-backcross {(slash x loblolly) x slash} and the ope-pollinated families of the pure-species progenitors

    Treesearch

    Patricio R. Munoz Del Valle; Dudley A. Huber; John R. Butnor

    2011-01-01

    A single test, including one pseudo-backcross (Pinus elliottii x Pinus taeda) x P. elliottii and openpollinated families of the pure species progenitors, was established in North Central Florida in December 2007 to study the transfer of the fast-growing characteristics from a P. taeda L. (loblolly pine) parent into the P. elliottii Engelm. (slash pine) background....

  14. Physiological and genetic analyses of inbred mouse strains with a type I iodothyronine 5' deiodinase deficiency.

    PubMed

    Berry, M J; Grieco, D; Taylor, B A; Maia, A L; Kieffer, J D; Beamer, W; Glover, E; Poland, A; Larsen, P R

    1993-09-01

    Inbred mouse strains differ in their capacity to deiodinate iododioxin and iodothyronines, with strains segregating into high or low activity groups. Metabolism of iododioxin occurs via the type I iodothyronine 5'deiodinase (5'DI), one of two enzymes that metabolize thyroxine (T4) to 3,5,3'-triiodothyronine (T3). Recombinant inbred strains derived from crosses between high and low activity strains exhibit segregation characteristic of a single allele difference. Hepatic and renal 5'DI mRNA in a high (C57BL/6J) and low (C3H/HeJ) strain paralleled enzyme activity and concentration, in agreement with a recent report. 5'DI-deficient mice had twofold higher serum free T4 but normal free T3 and thyrotropin. Brown adipose tissue 5'DII was invariant between the two strains. Southern analyses using a 5'DI probe identified a restriction fragment length variant that segregated with 5'DI activity in 33 of 35 recombinant inbred strains derived from four different pairs of high and low activity parental strains. Recombination frequencies using previously mapped loci allowed assignment of the 5'DI gene to mouse chromosome 4 and identified its approximate chromosomal position. We propose the symbol Dio1 to denote the mouse 5'DI gene. Conserved linkage between this segment of mouse chromosome 4 and human HSA1p predicts this location for human Dio1.

  15. High-throughput behavioral phenotyping of drug and alcohol susceptibility traits in the expanded panel of BXD recombinant inbred strains

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Philip, Vivek M; Ansah, T; Blaha, C,

    Genetic reference populations, particularly the BXD recombinant inbred strains, are a valuable resource for the discovery of the bio-molecular substrates and genetic drivers responsible for trait variation and co- ariation. This approach can be profitably applied in the analysis of susceptibility and mechanisms of drug and alcohol use disorders for which many predisposing behaviors may predict occurrence and manifestation of increased preference for these substances. Many of these traits are modeled by common mouse behavioral assays, facilitating the detection of patterns and sources of genetic co-regulation of predisposing phenotypes and substance consumption. Members of the Tennessee Mouse Genome Consortium havemore » obtained behavioral phenotype data from 260 measures related to multiple behavioral assays across several domains: self-administration, response to, and withdrawal from cocaine, MDMA, morphine and alcohol; novelty seeking; behavioral despair and related neurological phenomena; pain sensitivity; stress sensitivity; anxiety; hyperactivity; and sleep/wake cycles. All traits have been measured in both sexes and the recently expanded panel of 69 additional BXD recombinant inbred strains (N=69). Sex differences and heritability estimates were obtained for each trait, and a comparison of early (N = 32) and recent BXD RI lines was performed. Primary data is publicly available for heritability, sex difference and genetic analyses using www.GeneNetwork.org. These analyses include QTL detection and genetic analysis of gene expression. Stored results from these analyses are available at http://ontologicaldiscovery.org for comparison to other genomic analysis results. Together with the results of related studies, these data form a public resource for integrative systems genetic analysis of neurobehavioral traits.« less

  16. QTL detection for rice grain quality traits using an interspecific backcross population derived from cultivated Asian (O. sativa L.) and African (O. glaberrima S.) rice.

    PubMed

    Li, Jiming; Xiao, Jinhua; Grandillo, Silvana; Jiang, Longying; Wan, Yizhen; Deng, Qiyun; Yuan, Longping; McCouch, Susan R

    2004-08-01

    An interspecific advanced backcross population derived from a cross between Oryza sativa "V20A" (a popular male-sterile line used in Chinese rice hybrids) and Oryza glaberrima (accession IRGC No. 103544 from Mali) was used to identify quantitative trait loci (QTL) associated with grain quality and grain morphology. A total of 308 BC3F1 hybrid families were evaluated for 16 grain-related traits under field conditions in Changsha, China, and the same families were evaluated for RFLP and SSR marker segregation at Cornell University (Ithaca, N.Y.). Eleven QTL associated with seven traits were detected in six chromosomal regions, with the favorable allele coming from O. glaberrima at eight loci. Favorable O. glaberrima alleles were associated with improvements in grain shape and appearance, resulting in an increase in kernel length, transgressive variation for thinner grains, and increased length to width ratio. Oryza glaberrima alleles at other loci were associated with potential improvements in crude protein content and brown rice yield. These results suggested that genes from O. glaberrima may be useful in improving specific grain quality characteristics in high-yielding O. sativa hybrid cultivars.

  17. Limitation of Unloading in the Developing Grains Is a Possible Cause Responsible for Low Stem Non-structural Carbohydrate Translocation and Poor Grain Yield Formation in Rice through Verification of Recombinant Inbred Lines

    PubMed Central

    Li, Guohui; Pan, Junfeng; Cui, Kehui; Yuan, Musong; Hu, Qiuqian; Wang, Wencheng; Mohapatra, Pravat K.; Nie, Lixiao; Huang, Jianliang; Peng, Shaobing

    2017-01-01

    Remobilisation of non-structural carbohydrates (NSC) from leaves and stems and unloading into developing grains are essential for yield formation of rice. In present study, three recombinant inbred lines of rice, R91, R156 and R201 have been tested for source-flow-sink related attributes determining the nature of NSC accumulation and translocation at two nitrogen levels in the field. Compared to R91 and R156, R201 had lower grain filling percentage, harvest index, and grain yield. Meanwhile, R201 had significantly lower stem NSC translocation during grain filling stage. Grain filling percentage, harvest index, and grain yield showed the consistent trend with stem NSC translocation among the three lines. In comparison with R91 and R156, R201 had similarity in leaf area index, specific leaf weight, stem NSC concentration at heading, biomass, panicles m-2, spikelets per panicle, remobilization capability of assimilation in stems, sink capacity, sink activity, number and cross sectional area of small vascular bundles, greater number and cross sectional area of large vascular bundles, and higher SPAD, suggesting that source, flow, and sink were not the limiting factors for low stem NSC translocation and grain filling percentage of R201. However, R201 had significant higher stem and rachis NSC concentrations at maturity, which implied that unloading in the developing grains might result in low NSC translocation in R201. The results indicate that stem NSC translocation could be beneficial for enhancement of grain yield potential, and poor unloading into caryopsis may be the possible cause of low stem NSC translocation, poor grain filling and yield formation in R201. PMID:28848573

  18. Complementary DNA cloning, sequence analysis, and tissue transcription profile of a novel U2AF2 gene from the Chinese Banna mini-pig inbred line.

    PubMed

    Wang, S Y; Huo, J L; Miao, Y W; Cheng, W M; Zeng, Y Z

    2013-04-02

    U2 small nuclear RNA auxiliary factor 2 (U2AF2) is an important gene for pre-messenger RNA splicing in higher eukaryotes. In this study, the Banna mini-pig inbred line (BMI) U2AF2 coding sequence (CDS) was cloned, sequenced, and characterized. The U2AF2 complete CDS was amplified using the reverse transcription-polymerase chain reaction (RT-PCR) technique based on the conserved sequence information of cattle and known highly homologous swine expressed sequence tags. This novel gene was deposited into the National Center for Biotechnology Information database (Accession No. JQ839267). Sequence analysis revealed that the BMI U2AF2 coding sequence consisted of 1416 bp and encoded 471 amino acids with a molecular weight of 53.12 kDa. The protein sequence has high sequence homology with U2AF65 of 6 species - Homo sapiens (100%), Equus caballus (100%), Canis lupus (100%), Macaca mulatta (99.8%), Bos taurus (74.4%), and Mus musculus (74.4%). The phylogenetic tree analysis revealed that BMI U2AF65 has a closer genetic relationship with B. taurus U2AF65 than with U2AF65 of E. caballus, C. lupus, M. mulatta, H. sapiens, and M. musculus. RT-PCR analysis showed that BMI U2AF2 was most highly expressed in the brain; moderately expressed in the spleen, lung, muscle, and skin; and weakly expressed in the liver, kidney, and ovary. Its expression was nearly silent in the spinal cord, nerve fiber, heart, stomach, pancreas, and intestine. Three microRNA target sites were predicted in the CDS of BMI U2AF2 messenger RNA. Our results establish a foundation for further insight into this swine gene.

  19. The genetic rescue of two bottlenecked South Island robin populations using translocations of inbred donors.

    PubMed

    Heber, S; Varsani, A; Kuhn, S; Girg, A; Kempenaers, B; Briskie, J

    2013-02-07

    Populations forced through bottlenecks typically lose genetic variation and exhibit inbreeding depression. 'Genetic rescue' techniques that introduce individuals from outbred populations can be highly effective in reversing the deleterious effects of inbreeding, but have limited application for the majority of endangered species, which survive only in a few bottlenecked populations. We tested the effectiveness of using highly inbred populations as donors to rescue two isolated and bottlenecked populations of the South Island robin (Petroica australis). Reciprocal translocations significantly increased heterozygosity and allelic diversity. Increased genetic diversity was accompanied by increased juvenile survival and recruitment, sperm quality, and immunocompetence of hybrid individuals (crosses between the two populations) compared with inbred control individuals (crosses within each population). Our results confirm that the implementation of 'genetic rescue' using bottlenecked populations as donors provides a way of preserving endangered species and restoring their viability when outbred donor populations no longer exist.

  20. Gene interaction at seed-awning loci in the genetic background of wild rice.

    PubMed

    Ikemoto, Mai; Otsuka, Mitsuharu; Thanh, Pham Thien; Phan, Phuong Dang Thai; Ishikawa, Ryo; Ishii, Takashige

    2017-09-12

    Seed awning is one of the important traits for successful propagation in wild rice. During the domestication of rice by ancient humans, plants with awnless seeds may have been selected because long awns hindered collection and handling activities. To investigate domestication of awnless rice, QTL analysis for seed awning was first carried out using backcross recombinant inbred lines between Oryza sativa Nipponbare (recurrent parent) and O. rufipogon W630 (donor parent). Two strong QTLs were detected in the same regions as known major seed-awning loci, An-1 and RAE2. Subsequent causal mutation surveying and fine mapping confirmed that O. rufipogon W630 has functional alleles at both loci. The gene effects and interactions at these loci were examined using two backcross populations with reciprocal genetic backgrounds of O. sativa Nipponbare and O. rufipogon W630. As awn length in wild rice varied among seeds even in the same plant, awn length was measured based on spikelet position. In the genetic background of cultivated rice, the wild alleles at An-1 and RAE2 had awning effects, and plants having both wild homozygous alleles produced awns whose length was about 70% of those of the wild parent. On the other hand, in the genetic background of wild rice, the substitution of cultivated alleles at An-1 and RAE2 contributed little to awn length reduction. These results indicate that the domestication process of awnless seeds was complicated because many genes are involved in awn formation in wild rice.

  1. Sensitivity of Female Inbreds of Cucumis sativus to Sex Reversion by Gibberellin.

    PubMed

    Shifriss, O; George, W L

    1964-03-27

    Two female inbred cucumbers were developed by substituting gene Acr for acr in the genetic backgrounds of the monoecious races Marketer and Tokyo, which exhibit weak and strong male tendency respectively. Marketer females are resistant and Tokyo females are sensitive to sex reversion in response to treatments with gibberellin A(3). Resistance and sensitivity of this type appear to depend upon the genetic system which controls sex tendency.

  2. ActionMap: A web-based software that automates loci assignments to framework maps.

    PubMed

    Albini, Guillaume; Falque, Matthieu; Joets, Johann

    2003-07-01

    Genetic linkage computation may be a repetitive and time consuming task, especially when numerous loci are assigned to a framework map. We thus developed ActionMap, a web-based software that automates genetic mapping on a fixed framework map without adding the new markers to the map. Using this tool, hundreds of loci may be automatically assigned to the framework in a single process. ActionMap was initially developed to map numerous ESTs with a small plant mapping population and is limited to inbred lines and backcrosses. ActionMap is highly configurable and consists of Perl and PHP scripts that automate command steps for the MapMaker program. A set of web forms were designed for data import and mapping settings. Results of automatic mapping can be displayed as tables or drawings of maps and may be exported. The user may create personal access-restricted projects to store raw data, settings and mapping results. All data may be edited, updated or deleted. ActionMap may be used either online or downloaded for free (http://moulon.inra.fr/~bioinfo/).

  3. ActionMap: a web-based software that automates loci assignments to framework maps

    PubMed Central

    Albini, Guillaume; Falque, Matthieu; Joets, Johann

    2003-01-01

    Genetic linkage computation may be a repetitive and time consuming task, especially when numerous loci are assigned to a framework map. We thus developed ActionMap, a web-based software that automates genetic mapping on a fixed framework map without adding the new markers to the map. Using this tool, hundreds of loci may be automatically assigned to the framework in a single process. ActionMap was initially developed to map numerous ESTs with a small plant mapping population and is limited to inbred lines and backcrosses. ActionMap is highly configurable and consists of Perl and PHP scripts that automate command steps for the MapMaker program. A set of web forms were designed for data import and mapping settings. Results of automatic mapping can be displayed as tables or drawings of maps and may be exported. The user may create personal access-restricted projects to store raw data, settings and mapping results. All data may be edited, updated or deleted. ActionMap may be used either online or downloaded for free (http://moulon.inra.fr/~bioinfo/). PMID:12824426

  4. Simulation of the A-X and B-X transition emission spectra of the InBr molecule for diagnostics in low-pressure plasmas

    NASA Astrophysics Data System (ADS)

    Briefi, S.; Fantz, U.

    2011-04-01

    Inductively coupled low-pressure discharges containing InBr have been investigated spectroscopically. In order to obtain plasma parameters such as the vibrational and rotational temperature of the InBr molecule, the emission spectra of the A\\,^3\\!\\Pi_{0^+}\\rightarrow X\\,^1\\!\\Sigma_{0}^+ and the B\\,^3\\! \\Pi_{1}\\rightarrow X\\,^1\\!\\Sigma_{0}^+ transitions have been simulated. The program is based on the molecular constants and takes into account vibrational states up to v = 24. The required Franck-Condon factors and vibrationally resolved transition probabilities have been computed solving the Schrödinger equation using the Born-Oppenheimer approximation. The ground state density of the InBr molecule in the plasma has been determined from absorption spectra using effective transition probabilities for the A-X and B-X transition according to the vibrational population. The obtained densities agree well with densities derived from an Arrhenius type vapour pressure equation.

  5. Quantification of phenolic acids and antioxidant potential of inbred, hybrid and composite cultivars of maize under different nitrogen regimes.

    PubMed

    Ganie, Arshid Hussain; Yousuf, Peerzada Yasir; Ahad, Amjid; Pandey, Renu; Ahmad, Sayeed; Aref, Ibrahim M; Noor, Jewel Jameeta; Iqbal, Muhammad

    2016-11-01

    Maize (Zea mays L.) is a multipurpose crop, which is immensely used worldwide for its nutritional as well as medicinal properties. This study evaluates the effect of varying concentrations of nitrogen (N) on accumulation of phenolic acids and antioxidant activity in different maize cultivars, including inbreds, hybrids and a composite, which were grown in natural light under controlled temperature (30°C/20°C D/N) and humidity (80%), with sufficient (4.5mM) and low (0.05mM) nitrogen supply. Seeds of different cultivars were powdered and extracted in a methanol:water (80:20) mixture through reflux at 60-75°C, and the extracts obtained were subjected to high performance thin layer chromatography (HPTLC), using ethyl acetate: acetic acid: formic acid: water (109:16:12:31) solvent system for the separation of phenolic acids. Antioxidant activity of the extracts was determined by 2,2-diphenyl-1-picrylhydrazyl (DPPH) and H2O2-scavenging activity assays. At sufficient nitrogen condition, the contents of different phenolic acids were higher in the composite cultivar (8.7 mg g-1 d.wt. in gallic acid to 39.3 mg g-1 d.wt. in cinnamic and salicylic acids) than in inbreds and hybrids. Under low nitrogen condition, the phenolic acids contents declined significantly in inbreds and hybrids, but remained almost unaffected in the composite. The antioxidant activity was also the maximum in the composite, and declined similarly as phenolic acids under low nitrogen supply, showing a significant reduction in inbreds and hybrids only. Therefore, the maize composite has a potential for being used as a nutraceutical in human-health sector.

  6. Mapping Quantitative Trait Loci in Crosses between Outbred Lines Using Least Squares

    PubMed Central

    Haley, C. S.; Knott, S. A.; Elsen, J. M.

    1994-01-01

    The use of genetic maps based upon molecular markers has allowed the dissection of some of the factors underlying quantitative variation in crosses between inbred lines. For many species crossing inbred lines is not a practical proposition, although crosses between genetically very different outbred lines are possible. Here we develop a least squares method for the analysis of crosses between outbred lines which simultaneously uses information from multiple linked markers. The method is suitable for crosses where the lines may be segregating at marker loci but can be assumed to be fixed for alternative alleles at the major quantitative trait loci (QTLs) affecting the traits under analysis (e.g., crosses between divergent selection lines or breeds with different selection histories). The simultaneous use of multiple markers from a linkage group increases the sensitivity of the test statistic, and thus the power for the detection of QTLs, compared to the use of single markers or markers flanking an interval. The gain is greater for more closely spaced markers and for markers of lower information content. Use of multiple markers can also remove the bias in the estimated position and effect of a QTL which may result when different markers in a linkage group vary in their heterozygosity in the F(1) (and thus in their information content) and are considered only singly or a pair at a time. The method is relatively simple to apply so that more complex models can be fitted than is currently possible by maximum likelihood. Thus fixed effects and effects of background genotype can be fitted simultaneously with the exploration of a single linkage group which will increase the power to detect QTLs by reducing the residual variance. More complex models with several QTLs in the same linkage group and two-locus interactions between QTLs can similarly be examined. Thus least squares provides a powerful tool to extend the range of crosses from which QTLs can be dissected whilst at

  7. Quantitative trait loci that control body weight in DDD/Sgn and C57BL/6J inbred mice.

    PubMed

    Suto, Jun-Ichi; Kojima, Misaki

    2017-02-01

    Inbred DDD/Sgn mice are heavier than inbred C57BL/6J mice. In the present study, we performed quantitative trait loci (QTL) mapping for body weight using R/qtl in reciprocal F 2 male populations between the two strains. We identified four significant QTL on Chrs 1, 2, 5, and 17 (proximal region). The DDD/Sgn allele was associated with increased body weight at QTL on Chrs 1 and 5, and the DDD/Sgn allele was associated with decreased body weight at QTL on Chrs 2 and 17. A multiple regression analysis indicated that the detected QTL explain 30.94 % of the body weight variation. Because DDD/Sgn male mice have extremely high levels of circulating testosterone relative to other inbred mouse strains, we performed QTL mapping for plasma testosterone level to examine the effect of testosterone levels on body weight. We identified one suggestive QTL on Chr 5, which overlapped with body weight QTL. The DDD/Sgn allele was associated with increased testosterone level. Thus, we confirmed that there was a genetic basis for the changes in body weight and testosterone levels in male mice. These findings provide insights into the genetic mechanism by which body weight is controlled in male mice.

  8. Mapping of the bcl-2 oncogene on mouse chromosome 1.

    PubMed

    Mock, B A; Givol, D; D'Hoostelaere, L A; Huppi, K; Seldin, M F; Gurfinkel, N; Unger, T; Potter, M; Mushinski, J F

    1988-01-01

    Two bcl-2 alleles have been identified in inbred strains of mice by restriction fragment length polymorphism (RFLP). Analysis of a bcl-2 RFLP in a series of bilineal congenic strains (C.D2), developed as a tool for chromosomal mapping studies, revealed linkage of bcl-2 to the Idh-1/Pep-3 region of murine chromosome 1. The co-segregation of bcl-2 alleles with allelic forms of two other chromosome 1 loci, Ren-1,2 and Spna-1, in a set of back-cross progeny, positions bcl-2 7.8 cM centromeric from Ren-1,2.

  9. Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties

    PubMed Central

    Rostoks, Nils; Ramsay, Luke; MacKenzie, Katrin; Cardle, Linda; Bhat, Prasanna R.; Roose, Mikeal L.; Svensson, Jan T.; Stein, Nils; Varshney, Rajeev K.; Marshall, David F.; Graner, Andreas; Close, Timothy J.; Waugh, Robbie

    2006-01-01

    Genomewide association studies depend on the extent of linkage disequilibrium (LD), the number and distribution of markers, and the underlying structure in populations under study. Outbreeding species generally exhibit limited LD, and consequently, a very large number of markers are required for effective whole-genome association genetic scans. In contrast, several of the world's major food crops are self-fertilizing inbreeding species with narrow genetic bases and theoretically extensive LD. Together these are predicted to result in a combination of low resolution and a high frequency of spurious associations in LD-based studies. However, inbred elite plant varieties represent a unique human-induced pseudooutbreeding population that has been subjected to strong selection for advantageous alleles. By assaying 1,524 genomewide SNPs we demonstrate that, after accounting for population substructure, the level of LD exhibited in elite northwest European barley, a typical inbred cereal crop, can be effectively exploited to map traits by using whole-genome association scans with several hundred to thousands of biallelic SNPs. PMID:17085595

  10. Marker-assisted pyramiding of opaque2 and novel opaque16 genes for further enrichment of lysine and tryptophan in sub-tropical maize.

    PubMed

    Sarika, Konsam; Hossain, Firoz; Muthusamy, Vignesh; Zunjare, Rajkumar U; Baveja, Aanchal; Goswami, Rajat; Bhat, Jayant S; Saha, Supradip; Gupta, Hari S

    2018-07-01

    The improvement of protein quality in maize so far has been based on recessive opaque2 (o2) mutant that along with endosperm-modifiers led to development of quality protein maize (QPM). Recent discovery of nutritional benefits of recessive opaque16 (o16) mutant was of immense significance for further improvement of protein quality. In the present study, o16 was introgressed into o2-based parental inbreds (HKI161, HKI193-1, HKI193-2 and HKI163) of four commercial QPM hybrids (HQPM-1, HQPM-4, HQPM-5 and HQPM-7) released in India, using marker-assisted backcross breeding. Background selection led to high recovery of recurrent parent genome (RPG) to maximum of 95%, and introgressed progenies showed considerable phenotypic resemblance for plant-, ear- and grain- characteristics to their respective recurrent parents. Selection of markers for o2 and o16 led to development of pyramided lines (o2o2/o16o16) that possessed as high as 76% and 91% more lysine and tryptophan over the recurrent parents, respectively. Reconstituted hybrids showed an average enhancement of 49% and 60% in lysine and tryptophan over the original hybrids, with highest enhancement amounting 64% and 86%, respectively. This is first report of enhancement of both lysine and tryptophan by o16 in maize genotypes adaptable to sub-tropics. Moderate variation in lysine and tryptophan was also observed in pyramided lines. Multi-location evaluation of reconstituted hybrids revealed similar grain yield and attributing traits to their original versions. This study signified the role of o16 as supplementary to o2 for nutritional quality enhancement in maize, and improved elite inbreds and hybrids developed here hold great significance in maize biofortification programme. Copyright © 2018 Elsevier B.V. All rights reserved.

  11. Effects of inbreeding on economic traits of channel catfish.

    PubMed

    Bondari, K; Dunham, R A

    1987-05-01

    Inbred channel catfish (Ictalurus punctatus) were produced from two generations of full-sib matings to study the effect of inbreeding on reproduction, growth and survival. A randomly mated control line was propagated from the same base population to be used for the evaluation of the inbred fish. First generation inbred (I1) and control (C1) lines comprised five full-sib families each. Second generation inbred (I2) and control (C2) lines were produced by mating each male catfish from the I1 or C1 line to two females in sequence, one from the I1 and one from the C1 line. The design also produced two reciprocal outcross lines to be compared to their contemporary inbred and control lines. The coefficient of inbreeding for the inbred line increased from 0.25 in generation 1 to 0.375 in generation 2. The inbreeding coefficient was zero for all other lines. The resulting fish were performance tested in two locations, Tifton, Georgia and Auburn, Alabama and no genotype-environment interactions occurred. Results indicated that one generation of inbreeding increased number of days required for eggs to hatch by 21%, but did not significantly influence spawn weight or hatchability score. However, inbred females produced more eggs/kg body weight than control females. Two generations of full-sib mating in Georgia did not depress weight when expressed as a deviation to random controls but was depressed 13-16% when expressed as a deviation to half-sib out-crosses. Second generation inbreds produced in Alabama exhibited a 19% depression for growth rate when compared to either random or half-sib outcross controls. Survival rates at various age intervals was not decreased by inbreeding. The amount of inbreeding depression varied among families and between sexes.

  12. Response of rice to Al stress and identification of quantitative trait Loci for Al tolerance.

    PubMed

    Ma, Jian Feng; Shen, Renfang; Zhao, Zhuqing; Wissuwa, Matthias; Takeuchi, Yoshinobu; Ebitani, Takeshi; Yano, Masahiro

    2002-06-01

    Rice (Oryza sativa L.) shows the highest tolerance to Al toxicity among small-grain cereal crops, however, the mechanisms and genetics responsible for its high Al tolerance are not yet well understood. We investigated the response of rice to Al stress using the japonica variety Koshihikari in comparison to the indica variety Kasalath. Koshihikari showed higher tolerance at various Al concentrations than Kasalath. The Al content in root apexes was less in Koshihikari than in Kasalath, suggesting that exclusion mechanisms rather than internal detoxification are acting in Koshihikari. Al-induced secretion of citrate was observed in both Koshihikari and Kasalath, however, it is unlikely to be the mechanism for Al tolerance because there was no significant difference in the amount of citrate secreted between Koshihikari and Kasalath. Quantitative trait loci (QTLs) for Al tolerance were mapped in a population of 183 backcross inbred lines (BILs) derived from a cross of Koshihikari and Kasalath. Three putative QTLs controlling Al tolerance were detected on chromosomes 1, 2 and 6. Kasalath QTL alleles on chromosome 1 and 2 reduced Al tolerance but increased tolerance on chromosome 6. The three QTLs explained about 27% of the phenotypic variation in Al tolerance. The existence of QTLs for Al tolerance was confirmed in substitution lines for corresponding chromosomal segments.

  13. Genetic Influences on Survival Time After Severe Hemorrhage in Inbred Rat Strains

    DTIC Science & Technology

    2011-04-12

    technique (10, 41) immediately after insertion of the carotid catheter. A second incision was made in the skin in the medial aspect of the thigh to expose...rat strains. Both baseline and post hemorrhage mean arterial pres- sures (MAP) differed among inbred rat strains as did the decrease in MAP produced...measure for a given strain are different (P 0.05) between experiments for that strain. Mean arterial pressure (MAP) was recorded at 1 min prior to

  14. Genomic introgression mapping of field-derived multiple-anthelmintic resistance in Teladorsagia circumcincta

    PubMed Central

    Hallsworth-Pepin, Kymberlie; Martin, John; Mitreva, Makedonka

    2017-01-01

    Preventive chemotherapy has long been practiced against nematode parasites of livestock, leading to widespread drug resistance, and is increasingly being adopted for eradication of human parasitic nematodes even though it is similarly likely to lead to drug resistance. Given that the genetic architecture of resistance is poorly understood for any nematode, we have analyzed multidrug resistant Teladorsagia circumcincta, a major parasite of sheep, as a model for analysis of resistance selection. We introgressed a field-derived multiresistant genotype into a partially inbred susceptible genetic background (through repeated backcrossing and drug selection) and performed genome-wide scans in the backcross progeny and drug-selected F2 populations to identify the major genes responsible for the multidrug resistance. We identified variation linking candidate resistance genes to each drug class. Putative mechanisms included target site polymorphism, changes in likely regulatory regions and copy number variation in efflux transporters. This work elucidates the genetic architecture of multiple anthelmintic resistance in a parasitic nematode for the first time and establishes a framework for future studies of anthelmintic resistance in nematode parasites of humans. PMID:28644839

  15. Physiologic and endocrinologic characterization of male sex-biased diabetes in C57BLKS/J mice congenic for the fat mutation at the carboxypeptidease E locus.

    PubMed

    Leiter, E H; Kintner, J; Flurkey, K; Beamer, W G; Naggert, J K

    1999-02-01

    The fat gene in mice represents a recessive mutation at the carboxypeptidase E (Cpe) locus. The mutant allele (Cpe(fat)) encodes a highly unstable enzyme and produces an obesity phenotype characterized by attenuated processing of prohormones such as proinsulin that require this exopeptidase for full maturation. This article presents a preliminary physiologic and endocrinologic characterization of the stock of C57BLKS/LtJ-Cpe(fat)/Cpe(fat) mice at the backcross generation (N10) currently distributed by The Jackson Laboratory. Although previously reported not to be diabetogenic at N5, an additional five backcrosses to the C57BLKS/J background resulted in a male-biased development of both obesity and diabetes. Major differences distinguishing this mutant stock from the phenotypes produced by either the diabetes (Lepr(db)) or obese (Lep(ob)) mutations on the same inbred strain background are lack of hyperphagia and hypercorticism, sensitivity of diabetic males to exogenous insulin, and a milder and male-biased diabetes syndrome that is not associated with widespread beta-cell necrosis and islet atrophy, and that often remits with age.

  16. Hybrids between common and Antarctic minke whales are fertile and can back-cross.

    PubMed

    Glover, Kevin A; Kanda, Naohisa; Haug, Tore; Pastene, Luis A; Øien, Nils; Seliussen, Bjørghild B; Sørvik, Anne G E; Skaug, Hans J

    2013-04-15

    Minke whales are separated into two genetically distinct species: the Antarctic minke whale found in the southern hemisphere, and the common minke whale which is cosmopolitan. The common minke whale is further divided into three allopatric sub-species found in the North Pacific, southern hemisphere, and the North Atlantic. Here, we aimed to identify the genetic ancestry of a pregnant female minke whale captured in the North Atlantic in 2010, and her fetus, using data from the mtDNA control region, 11 microsatellite loci and a sex determining marker. All statistical parameters demonstrated that the mother was a hybrid displaying maternal and paternal contribution from North Atlantic common and Antarctic minke whales respectively. Her female fetus displayed greater genetic similarity to North Atlantic common minke whales than herself, strongly suggesting that the hybrid mother had paired with a North Atlantic common minke whale. This study clearly demonstrates, for the first time, that hybrids between minke whale species may be fertile, and that they can back-cross. Whether contact between these species represents a contemporary event linked with documented recent changes in the Antarctic ecosystem, or has occurred at a low frequency over many years, remains open.

  17. Strain difference in the immune response to hydralazine in inbred guinea-pigs

    PubMed Central

    Ellman, L.; Inman, J.; Green, Ira

    1971-01-01

    Guinea-pigs were immunized with hydralazine in Freund's complete adjuvant. A marked strain difference in the immune response involving both anti-hydralazine antibody and delayed hypersensitivity to hydralazine was observed in different strains of guinea-pigs: Hartley guinea-pigs and inbred strain 13 guinea-pigs were able to mount a vigorous immune response to the drug while inbred strain 2 guinea-pigs appeared to be `low or non-responders'. This difference could not be explained in terms of metabolism of the drug in that no differences in acetylation were observed. Breeding studies suggest that immune responsiveness to hydralazine is inherited in an autosomal dominant manner. The immune response to hydralazine may be controlled by a `specific immune response gene' which appears not to be linked to the major strain 13 histocompatibility gene. Anti-nuclear and anti-DNA antibodies could not be demonstrated at a time when the animals manifested a strong immune response to hydralazine. Thus, the development of auto-immune phenomena does not appear to be related to the development of an immune response to the drug in short term immunization. Hydralazine-protein conjugates were synthesized, radio-iodinated and used in a Farr technique for the measurement of anti-hydralazine antibody. These techniques for the assay of anti-hydralazine antibodies may be useful in clinical investigations. Imagesp933-a PMID:5316639

  18. Reaction of common bean lines and aggressiveness of Sclerotinia sclerotiorum isolates.

    PubMed

    Silva, P H; Santos, J B; Lima, I A; Lara, L A C; Alves, F C

    2014-11-07

    The aims of this study were to evaluate the reaction of common bean lines to white mold, the aggressiveness of different Sclerotinia sclerotiorum isolates from various common bean production areas in Brazil, and comparison of the diallel and GGE (genotype main effect plus genotype-by-environment interaction) biplot analysis procedures via study of the line-by-isolate interaction. Eleven common bean (Phaseolus vulgaris) lines derived from 3 backcross populations were used. Field experiments were performed in the experimental area of the Departamento de Biologia of the Universidade Federal de Lavras, Lavras, MG, Brazil, in the 2011 and 2012 dry crop season and 2011 winter crop season through a randomized block design with 3 replications. This study was also set up in a greenhouse. Inoculations were performed 28 days after sowing by means of the straw test method. The reaction of the bean lines to white mold was assessed according to a diagrammatic scale from 1 (plant without symptoms) to 9 (dead plant). Estimations of general reaction capacity (lines) and general aggressiveness capacity (isolates) indicated different horizontal levels of resistance in the lines and levels of aggressiveness in the isolates. Therefore, it was possible to select more resistant lines and foresee those crosses that are the most promising for increasing the level of resistance. It was also possible to identify the most aggressive isolates that were more efficient in distinguishing the lines. Both diallel and GGE biplot analyses were useful in identifying the genotypic values of lines and isolates.

  19. Comparison of neutrophil functions between two strains of inbred mice.

    PubMed

    Zhang, Xiaohuan; Zhao, Sainan; Sun, Luping; Li, Wenqing; Glogauer, Michael; Hu, Yan

    2016-12-01

    In this study, differences between two strains of inbred mice in aspects of neutrophil function, namely Rac1 expression, chemotaxis, nicotinamide adenine dinucleotide phosphate oxidase activity and formation of neutrophil extracellular traps (NETs), were determined. Neutrophils from CBA/CaH mice exhibited weaker Rac1 expression and a slower chemotactic gradient than BALB/c mice. Furthermore, PMA- or fMLP-stimulated neutrophils from CBA/CaH mice generated much less superoxide and NETs than similarly stimulated neutrophils from BALB/c mice. These findings suggest that neutrophils from BALB/c mice are functionally more efficient than those from CBA/CaH mice. © 2016 The Societies and John Wiley & Sons Australia, Ltd.

  20. M6: A diploid potato inbred line for use in breeding and genetics research

    USDA-ARS?s Scientific Manuscript database

    M6 is a vigorous, homozygous breeding line derived by self-pollinating the diploid wild potato relative Solanum chacoense for seven generations. While most wild Solanum species are self-incompatible, this clone is homozygous for the dominant self-incompatibility inhibitor gene Sli. It is homozygous ...

  1. Cocaine locomotor activation, sensitization and place preference in six inbred strains of mice

    PubMed Central

    2011-01-01

    Background The expanding set of genomics tools available for inbred mouse strains has renewed interest in phenotyping larger sets of strains. The present study aims to explore phenotypic variability among six commonly-used inbred mouse strains to both the rewarding and locomotor stimulating effects of cocaine in a place conditioning task, including several strains or substrains that have not yet been characterized for some or all of these behaviors. Methods C57BL/6J (B6), BALB/cJ (BALB), C3H/HeJ (C3H), DBA/2J (D2), FVB/NJ (FVB) and 129S1/SvImJ (129) mice were tested for conditioned place preference to 20 mg/kg cocaine. Results Place preference was observed in most strains with the exception of D2 and 129. All strains showed a marked increase in locomotor activity in response to cocaine. In BALB mice, however, locomotor activation was context-dependent. Locomotor sensitization to repeated exposure to cocaine was most significant in 129 and D2 mice but was absent in FVB mice. Conclusions Genetic correlations suggest that no significant correlation between conditioned place preference, acute locomotor activation, and locomotor sensitization exists among these strains indicating that separate mechanisms underlie the psychomotor and rewarding effects of cocaine. PMID:21806802

  2. Variable Suppression of Serum Thyroxine in Female Mice of Different Inbred Strains by Triiodothyronine Administered in Drinking Water

    PubMed Central

    Hamidi, Sepehr; Aliesky, Holly; Chen, Chun-Rong; Rapoport, Basil

    2010-01-01

    Background Recombinant-inbred mouse strains differ in their susceptibility to Graves'-like hyperthyroidism induced by immunization with adenovirus expressing the human thyrotropin (TSH) receptor. Because one genetic component contributing to this susceptibility is altered thyroid sensitivity to TSH receptor agonist stimulation, we wished to quantify thyroid responsiveness to TSH. For such studies, it is necessary to suppress endogenous TSH by administering L-3,5,3′-triiodothyronine (L-T3), with the subsequent decrease in serum thyroxine (T4) reflecting endogenous TSH suppression. Our two objectives were to assess in different inbred strains of mice (i) the extent of serum T4 suppression after L-T3 administration and (ii) the magnitude of serum T4 increase induced by TSH. Methods Mice were tail-bled to establish baseline-serum T4 before L-T3 administration. We initially employed a protocol of L-T3-supplemented drinking water for 7 days. In subsequent experiments, we injected L-T3 intraperitoneally (i.p.) daily for 3 days. Mice were then injected i.p. with bovine TSH (10 mU) and euthanized 5 hours later. Serum T4 was assayed before L-T3 administration, and before and after TSH injection. In some experiments, serum T3 and estradiol were measured in pooled sera. Results Oral L-T3 (3 or 5 μg/mL) suppressed serum T4 levels by 26%–64% in female BALB/c mice but >95% in males. T4 suppression in female B6 mice ranged from 0% to 90%. In C3H mice, L-T3 at 3 μg/mL was ineffective but 5 μg/mL achieved >80% serum T4 reduction. Unlike inbred mice, in outbred CF1 mice the same protocol was more effective: 83% in females and 100% suppression in males. The degree of T4 suppression was unrelated to baseline T4, T3, or estradiol, but was related to mouse weight and postmortem T3, with greater suppression in larger mice (outbred CF1 animals and inbred males). Among females with serum T4 suppression >80%, the increase in serum T4 after TSH injection was greater for BALB

  3. Significant improvement in cloning efficiency of an inbred miniature pig by histone deacetylase inhibitor treatment after somatic cell nuclear transfer.

    PubMed

    Zhao, Jianguo; Ross, Jason W; Hao, Yanhong; Spate, Lee D; Walters, Eric M; Samuel, Melissa S; Rieke, August; Murphy, Clifton N; Prather, Randall S

    2009-09-01

    The National Institutes of Health (NIH) miniature pig was developed specifically for xenotransplantation and has been extensively used as a large-animal model in many other biomedical experiments. However, the cloning efficiency of this pig is very low (<0.2%), and this has been an obstacle to the promising application of these inbred swine genetics for biomedical research. It has been demonstrated that increased histone acetylation in somatic cell nuclear transfer (SCNT) embryos, by applying a histone deacetylase (HDAC) inhibitor such as trichostatin A (TSA), significantly enhances the developmental competence in several species. However, some researchers also reported that TSA treatment had various detrimental effects on the in vitro and in vivo development of the SCNT embryos. Herein, we report that treatment with 500 nM 6-(1,3-dioxo-1H, 3H-benzo[de]isoquinolin-2-yl)-hexanoic acid hydroxyamide (termed scriptaid), a novel HDAC inhibitor, significantly enhanced the development of SCNT embryos to the blastocyst stage when NIH inbred fetal fibroblast cells (FFCs) were used as donors compared with the untreated group (21% vs. 9%, P < 0.05). Scriptaid treatment resulted in eight pregnancies from 10 embryo transfers (ETs) and 14 healthy NIH miniature pigs from eight litters, while no viable piglets (only three mummies) were obtained from nine ETs in the untreated group. Thus, scriptaid dramatically increased the cloning efficiency when using inbred genetics from 0.0% to 1.3%. In contrast, scriptaid treatment decreased the blastocyst rate in in vitro fertilization embryos (from 37% to 26%, P < 0.05). In conclusion, the extremely low cloning efficiency in the NIH miniature pig may be caused by its inbred genetic background and can be improved by alteration of genomic histone acetylation patterns.

  4. Did backcrossing contribute to the origin of hybrid edible bananas?

    PubMed Central

    De Langhe, Edmond; Hřibová, Eva; Carpentier, Sebastien; Doležel, Jaroslav; Swennen, Rony

    2010-01-01

    Background Bananas and plantains (Musa spp.) provide a staple food for many millions of people living in the humid tropics. The cultivated varieties (cultivars) are seedless parthenocarpic clones of which the origin remains unclear. Many are believed to be diploid and polyploid hybrids involving the A genome diploid M. acuminata and the B genome M. balbisiana, with the hybrid genomes consisting of a simple combination of the parental ones. Thus the genomic constitution of the diploids has been classified as AB, and that of the triploids as AAB or ABB. However, the morphology of many accessions is biased towards either the A or B phenotype and does not conform to predictions based on these genomic formulae. Scope On the basis of published cytotypes (mitochondrial and chloroplast genomes), we speculate here that the hybrid banana genomes are unbalanced with respect to the parental ones, and/or that inter-genome translocation chromosomes are relatively common. We hypothesize that the evolution under domestication of cultivated banana hybrids is more likely to have passed through an intermediate hybrid, which was then involved in a variety of backcrossing events. We present experimental data supporting our hypothesis and we propose a set of experimental approaches to test it, thereby indicating other possibilities for explaining some of the unbalanced genome expressions. Progress in this area would not only throw more light on the origin of one of the most important crops, but provide data of general relevance for the evolution under domestication of many other important clonal crops. At the same time, a complex origin of the cultivated banana hybrids would imply a reconsideration of current breeding strategies. PMID:20858591

  5. Effect of cytoplasmic diversity on post anthesis heat tolerance in wheat

    USDA-ARS?s Scientific Manuscript database

    The nuclear genomes of ten alloplasmic lines were substituted by backcrossing four or five times using ‘Karl 92’, ‘Ventnor’, ‘U1275’ and ‘Jagger’ as recurrent parents to study the cytoplasmic effects on heat tolerance. During the final backcross, reciprocal crosses were made to develop NILs (Near Is...

  6. Draft genome sequence of an inbred line of Chenopodium quinoa, an allotetraploid crop with great environmental adaptability and outstanding nutritional properties.

    PubMed

    Yasui, Yasuo; Hirakawa, Hideki; Oikawa, Tetsuo; Toyoshima, Masami; Matsuzaki, Chiaki; Ueno, Mariko; Mizuno, Nobuyuki; Nagatoshi, Yukari; Imamura, Tomohiro; Miyago, Manami; Tanaka, Kojiro; Mise, Kazuyuki; Tanaka, Tsutomu; Mizukoshi, Hiroharu; Mori, Masashi; Fujita, Yasunari

    2016-12-01

    Chenopodium quinoa Willd. (quinoa) originated from the Andean region of South America, and is a pseudocereal crop of the Amaranthaceae family. Quinoa is emerging as an important crop with the potential to contribute to food security worldwide and is considered to be an optimal food source for astronauts, due to its outstanding nutritional profile and ability to tolerate stressful environments. Furthermore, plant pathologists use quinoa as a representative diagnostic host to identify virus species. However, molecular analysis of quinoa is limited by its genetic heterogeneity due to outcrossing and its genome complexity derived from allotetraploidy. To overcome these obstacles, we established the inbred and standard quinoa accession Kd that enables rigorous molecular analysis, and presented the draft genome sequence of Kd, using an optimized combination of high-throughput next generation sequencing on the Illumina Hiseq 2500 and PacBio RS II sequencers. The de novo genome assembly contained 25 k scaffolds consisting of 1 Gbp with N50 length of 86 kbp. Based on these data, we constructed the free-access Quinoa Genome DataBase (QGDB). Thus, these findings provide insights into the mechanisms underlying agronomically important traits of quinoa and the effect of allotetraploidy on genome evolution. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  7. Draft genome sequence of an inbred line of Chenopodium quinoa, an allotetraploid crop with great environmental adaptability and outstanding nutritional properties

    PubMed Central

    Yasui, Yasuo; Hirakawa, Hideki; Oikawa, Tetsuo; Toyoshima, Masami; Matsuzaki, Chiaki; Ueno, Mariko; Mizuno, Nobuyuki; Nagatoshi, Yukari; Imamura, Tomohiro; Miyago, Manami; Tanaka, Kojiro; Mise, Kazuyuki; Tanaka, Tsutomu; Mizukoshi, Hiroharu; Mori, Masashi; Fujita, Yasunari

    2016-01-01

    Chenopodium quinoa Willd. (quinoa) originated from the Andean region of South America, and is a pseudocereal crop of the Amaranthaceae family. Quinoa is emerging as an important crop with the potential to contribute to food security worldwide and is considered to be an optimal food source for astronauts, due to its outstanding nutritional profile and ability to tolerate stressful environments. Furthermore, plant pathologists use quinoa as a representative diagnostic host to identify virus species. However, molecular analysis of quinoa is limited by its genetic heterogeneity due to outcrossing and its genome complexity derived from allotetraploidy. To overcome these obstacles, we established the inbred and standard quinoa accession Kd that enables rigorous molecular analysis, and presented the draft genome sequence of Kd, using an optimized combination of high-throughput next generation sequencing on the Illumina Hiseq 2500 and PacBio RS II sequencers. The de novo genome assembly contained 25 k scaffolds consisting of 1 Gbp with N50 length of 86 kbp. Based on these data, we constructed the free-access Quinoa Genome DataBase (QGDB). Thus, these findings provide insights into the mechanisms underlying agronomically important traits of quinoa and the effect of allotetraploidy on genome evolution. PMID:27458999

  8. Renal blood flow dynamics in inbred rat strains provides insight into autoregulation.

    PubMed

    A Mitrou, Nicholas G; Cupples, William A

    2014-01-01

    Renal autoregulation maintains stable renal blood flow in the face of constantly fluctuating blood pressure. Autoregulation is also the only mechanism that protects the delicate glomerular capillaries when blood pressure increases. In order to understand autoregulation, the renal blood flow response to changing blood pressure is studied. The steadystate response of blood flow is informative, but limits investigation of the individual mechanisms of autoregulation. The dynamics of autoregulation can be probed with transfer function analysis. The frequency-domain analysis of autoregulation allows investigators to probe the relative activity of each mechanism of autoregulation. We discuss the methodology and interpretation of transfer function analysis. Autoregulation is routinely studied in the rat, of which there are many inbred strains. There are multiple strains of rat that are either selected or inbred as models of human pathology. We discuss relevant characteristics of Brown Norway, Spontaneously hypertensive, Dahl, and Fawn-Hooded hypertensive rats and explore differences among these strains in blood pressure, dynamic autoregulation, and susceptibility to hypertensive renal injury. Finally we show that the use of transfer function analysis in these rat strains has contributed to our understanding of the physiology and pathophysiology of autoregulation and hypertensive renal disease.Interestingly all these strains demonstrate effective tubuloglomerular feedback suggesting that this mechanism is not sufficient for effective autoregulation. In contrast, obligatory or conditional failure of the myogenic mechanism suggests that this component is both necessary and sufficient for autoregulation.

  9. A non-synonymous SNP within the isopentenyl transferase 2 locus is associated with kernel weight in Chinese maize inbreds (Zea mays L.).

    PubMed

    Weng, Jianfeng; Li, Bo; Liu, Changlin; Yang, Xiaoyan; Wang, Hongwei; Hao, Zhuanfang; Li, Mingshun; Zhang, Degui; Ci, Xiaoke; Li, Xinhai; Zhang, Shihuang

    2013-07-05

    Kernel weight, controlled by quantitative trait loci (QTL), is an important component of grain yield in maize. Cytokinins (CKs) participate in determining grain morphology and final grain yield in crops. ZmIPT2, which is expressed mainly in the basal transfer cell layer, endosperm, and embryo during maize kernel development, encodes an isopentenyl transferase (IPT) that is involved in CK biosynthesis. The coding region of ZmIPT2 was sequenced across a panel of 175 maize inbred lines that are currently used in Chinese maize breeding programs. Only 16 single nucleotide polymorphisms (SNPs) and seven haplotypes were detected among these inbred lines. Nucleotide diversity (π) within the ZmIPT2 window and coding region were 0.347 and 0.0047, respectively, and they were significantly lower than the mean nucleotide diversity value of 0.372 for maize Chromosome 2 (P < 0.01). Association mapping revealed that a single nucleotide change from cytosine (C) to thymine (T) in the ZmIPT2 coding region, which converted a proline residue into a serine residue, was significantly associated with hundred kernel weight (HKW) in three environments (P <0.05), and explained 4.76% of the total phenotypic variation. In vitro characterization suggests that the dimethylallyl diphospate (DMAPP) IPT activity of ZmIPT2-T is higher than that of ZmIPT2-C, as the amounts of adenosine triphosphate (ATP), adenosine diphosphate (ADP), and adenosine monophosphate (AMP) consumed by ZmIPT2-T were 5.48-, 2.70-, and 1.87-fold, respectively, greater than those consumed by ZmIPT2-C. The effects of artificial selection on the ZmIPT2 coding region were evaluated using Tajima's D tests across six subgroups of Chinese maize germplasm, with the most frequent favorable allele identified in subgroup PB (Partner B). These results showed that ZmIPT2, which is associated with kernel weight, was subjected to artificial selection during the maize breeding process. ZmIPT2-T had higher IPT activity than ZmIPT2-C, and

  10. Development of male sterile Eruca sativa carrying a Raphanus sativus/Brassica oleracea cybrid cytoplasm.

    PubMed

    Nothnagel, Thomas; Klocke, Evelyn; Schrader, Otto; Linke, Bettina; Budahn, Holger

    2016-02-01

    Alloplasmic male sterile breeding lines of Eruca sativa were developed by intergeneric hybridization with CMS- Brassica oleracea, followed by recurrent backcrosses and determination of the breeding value. Male sterile breeding lines of rocket salad (Eruca sativa) were developed by intergeneric hybridization with cytoplasmic male sterile (CMS) cauliflower (Brassica oleracea) followed by recurrent backcrosses. Five amphidiploid F1 plants (2n = 2x = 20, CE), achieved by manual crosses and embryo rescue, showed an intermediate habit. The plants were completely male sterile and lacked seed set after pollination with the Eruca parent. Allotetraploid F1-hybrid plants (4n = 4x = 40, CCEE) obtained after colchicine treatment were backcrossed six times with pollen of the Eruca parent to select alloplasmic diploid E. sativa lines. The hybrid status and the nucleo-cytoplasmic constellation were continuously controlled by RAPD and Southern analysis during subsequent backcrosses. The ploidy level was investigated by flow cytometry and chromosome analysis. Premeiotic (sporophytic) and postmeiotic (pollen abortive) defects during the anther development were observed in the alloplasmic E. sativus plants in comparison to the CMS-cauliflower donor. No further incompatibilities were noticed between the CMS-inducing cybrid cytoplasm and the E. sativa nuclear genome. The final alloplasmic E. sativa lines were diploid with 2n = 2x = 22 chromosomes and revealed complete male sterility and restored female fertility. Plant vigor and yield potential of the CMS-E. sativa BC5 lines were comparable to the parental E. sativus line. In conclusion, the employed cybrid-cytoplasm has been proven as a vital source of CMS for E. sativa. The developed lines are directly applicable for hybrid breeding of rocket salad.

  11. Linkage of loci associated with two pigment mutations on mouse chromosome 13.

    PubMed

    Holcombe, R F; Stephenson, D A; Zweidler, A; Stewart, R M; Chapman, V M; Seidman, J G

    1991-08-01

    Progeny from one intra- and two inter-specific backcrosses between divergent strains of mice were typed to map multiple markers in relation to two pigment mutations on mouse chromosome 13, beige (bg) and pearl (pe). Both recessive mutants on a C57BL/6J background were crossed separately with laboratory strain PAC (M. domesticus) and the partially inbred M. musculus stock PWK. The intra- and inter-specific F1 hybrids were backcrossed to the C57BL/6J parental strain and DNA was prepared from progeny. Restriction fragment length polymorphisms were used to follow the segregation of alleles in the backcross offspring at loci identified with molecular probes. The linkage analysis defines the association between the bg and pe loci and the loci for the T-cell receptor gamma-chain gene (Tcrg), the spermatocyte specific histone gene (Hist1), the prolactin gene (Prl), the Friend murine leukaemia virus integration site 1 (Fim-1), the murine Hanukuh Factor gene (Muhf/Ctla-3) and the dihydrofolate reductase gene (Dhfr). This data confirms results of prior chromosomal mapping studies utilizing bg as an anchor locus, and provides previously unreported information defining the localization of the prolactin gene on mouse chromosome 13. The relationship of multiple loci in relation to pe is similarly defined. These results may help facilitate localization of the genes responsible for two human syndromes homologous with bg and pe, Chediak-Higashi syndrome and Hermansky-Pudlak syndrome.

  12. Significant Improvement in Cloning Efficiency of an Inbred Miniature Pig by Histone Deacetylase Inhibitor Treatment after Somatic Cell Nuclear Transfer1

    PubMed Central

    Zhao, Jianguo; Ross, Jason W.; Hao, Yanhong; Spate, Lee D.; Walters, Eric M.; Samuel, Melissa S.; Rieke, August; Murphy, Clifton N.; Prather, Randall S.

    2009-01-01

    The National Institutes of Health (NIH) miniature pig was developed specifically for xenotransplantation and has been extensively used as a large-animal model in many other biomedical experiments. However, the cloning efficiency of this pig is very low (<0.2%), and this has been an obstacle to the promising application of these inbred swine genetics for biomedical research. It has been demonstrated that increased histone acetylation in somatic cell nuclear transfer (SCNT) embryos, by applying a histone deacetylase (HDAC) inhibitor such as trichostatin A (TSA), significantly enhances the developmental competence in several species. However, some researchers also reported that TSA treatment had various detrimental effects on the in vitro and in vivo development of the SCNT embryos. Herein, we report that treatment with 500 nM 6-(1,3-dioxo-1H, 3H-benzo[de]isoquinolin-2-yl)-hexanoic acid hydroxyamide (termed scriptaid), a novel HDAC inhibitor, significantly enhanced the development of SCNT embryos to the blastocyst stage when NIH inbred fetal fibroblast cells (FFCs) were used as donors compared with the untreated group (21% vs. 9%, P < 0.05). Scriptaid treatment resulted in eight pregnancies from 10 embryo transfers (ETs) and 14 healthy NIH miniature pigs from eight litters, while no viable piglets (only three mummies) were obtained from nine ETs in the untreated group. Thus, scriptaid dramatically increased the cloning efficiency when using inbred genetics from 0.0% to 1.3%. In contrast, scriptaid treatment decreased the blastocyst rate in in vitro fertilization embryos (from 37% to 26%, P < 0.05). In conclusion, the extremely low cloning efficiency in the NIH miniature pig may be caused by its inbred genetic background and can be improved by alteration of genomic histone acetylation patterns. PMID:19386991

  13. Sex-Specific Genetic Loci for Femoral Neck Bone Mass and Strength Identified in Inbred COP and DA Rats

    PubMed Central

    Alam, Imranul; Sun, Qiwei; Liu, Lixiang; Koller, Daniel L; Carr, Lucinda G; Econs, Michael J; Foroud, Tatiana; Turner, Charles H

    2008-01-01

    Introduction Hip fracture is the most devastating osteoporotic fracture type with significant morbidity and mortality. Several studies in humans identified chromosomal regions linked to hip size and bone mass. Animal models, particularly the inbred rat, serve as complementary approaches for studying the genetic influence on hip fragility. The purpose of this study is to identify sex-independent and sex-specific quantitative trait loci (QTLs) for femoral neck density, structure, and strength in inbred Copenhagen 2331 (COP) and Dark Agouti (DA) rats. Materials and Methods A total of 828 (405 males and 423 females) F2 progeny derived from the inbred COP and DA strains of rats were phenotyped for femoral neck volumetric BMD (vBMD), cross-sectional area, polar moment of inertia (Ip), neck width, ultimate force, and energy to break. A whole genome screen was performed using 93 microsatellite markers with an average intermarker distance of 20 cM. Recombination-based marker maps were generated using MAPMAKER/EXP from the COP × DA F2 data and compared with published Rat Genome Database (RGD) maps. These maps were used for genome-wide linkage analyses to detect sex-independent and sex-specific QTLs. Results Significant evidence of linkage (p < 0.01) for sex-independent QTLs were detected for (1) femoral neck vBMD on chromosomes (Chrs) 1, 6, 10, and 12, (2) femoral neck structure on Chrs 5, 7, 10, and 18, and (3) biomechanical properties on Chrs 1 and 4. Male-specific QTLs were discovered on Chrs 2, 9, and 18 for total vBMD, on Chr 17 for trabecular vBMD, on Chr 9 for total bone area, and on Chr 15 for ultimate force. A female-specific QTL was discovered on Chr 2 for ultimate force. The effect size of the individual QTL varied between 1% and 4%. Conclusions We detected evidence that sex-independent and sex-specific QTLs contribute to hip fragility in the inbred rat. Several QTLs regions identified in this study are homologous to human chromosomal regions previously linked to

  14. Morpho-physiological characterization of cold-and pre-flowering drought tolerance in grain Sorghum (Sorghum bicolor L. Moench) inbreds

    USDA-ARS?s Scientific Manuscript database

    Aim: The relationships between early-season cold temperature germination and preflowering drought stress in eight grain sorghum inbreds were assessed using morphophysiological traits. Study Design: Field was laid out in a randomized complete block design. Place and Duration: The experiment was condu...

  15. Norepinephrine transporter: a candidate gene for initial ethanol sensitivity in inbred long-sleep and short-sleep mice.

    PubMed

    Haughey, Heather M; Kaiser, Alan L; Johnson, Thomas E; Bennett, Beth; Sikela, James M; Zahniser, Nancy R

    2005-10-01

    Altered noradrenergic neurotransmission is associated with depression and may contribute to drug abuse and alcoholism. Differential initial sensitivity to ethanol is an important predictor of risk for future alcoholism, making the inbred long-sleep (ILS) and inbred short-sleep (ISS) mice a useful model for identifying genes that may contribute to alcoholism. In this study, molecular biological, neurochemical, and behavioral approaches were used to test the hypothesis that the norepinephrine transporter (NET) contributes to the differences in ethanol-induced loss of righting reflex (LORR) in ILS and ISS mice. We used these mice to investigate the NET as a candidate gene contributing to this phenotype. The ILS and ISS mice carry different DNA haplotypes for NET, showing eight silent differences between allelic coding regions. Only the ILS haplotype is found in other mouse strains thus far sequenced. Brain regional analyses revealed that ILS mice have 30 to 50% lower [3H]NE uptake, NET binding, and NET mRNA levels than ISS mice. Maximal [3H]NE uptake and NET number were reduced, with no change in affinity, in the ILS mice. These neurobiological changes were associated with significant influences on the behavioral phenotype of these mice, as demonstrated by (1) a differential response in the duration of ethanol-induced LORR in ILS and ISS mice pretreated with a NET inhibitor and (2) increased ethanol-induced LORR in LXS recombinant inbred (RI) strains, homozygous for ILS in the NET chromosomal region (44-47 cM), compared with ISS homozygous strains. This is the first report to suggest that the NET gene is one of many possible genetic factors influencing ethanol sensitivity in ILS, ISS, and LXS RI mouse strains.

  16. Hamp1 mRNA and plasma hepcidin levels are influenced by sex and strain but do not predict tissue iron levels in inbred mice.

    PubMed

    McLachlan, Stela; Page, Kathryn E; Lee, Seung-Min; Loguinov, Alex; Valore, Erika; Hui, Simon T; Jung, Grace; Zhou, Jie; Lusis, Aldons J; Fuqua, Brie; Ganz, Tomas; Nemeth, Elizabeta; Vulpe, Chris D

    2017-11-01

    Iron homeostasis is tightly regulated, and the peptide hormone hepcidin is considered to be a principal regulator of iron metabolism. Previous studies in a limited number of mouse strains found equivocal sex- and strain-dependent differences in mRNA and serum levels of hepcidin and reported conflicting data on the relationship between hepcidin ( Hamp1 ) mRNA levels and iron status. Our aim was to clarify the relationships between strain, sex, and hepcidin expression by examining multiple tissues and the effects of different dietary conditions in multiple inbred strains. Two studies were done: first, Hamp1 mRNA, liver iron, and plasma diferric transferrin levels were measured in 14 inbred strains on a control diet; and second, Hamp1 mRNA and plasma hepcidin levels in both sexes and iron levels in the heart, kidneys, liver, pancreas, and spleen in males were measured in nine inbred/recombinant inbred strains raised on an iron-sufficient or high-iron diet. Both sex and strain have a significant effect on both hepcidin mRNA (primarily a sex effect) and plasma hepcidin levels (primarily a strain effect). However, liver iron and diferric transferrin levels are not predictors of Hamp1 mRNA levels in mice fed iron-sufficient or high-iron diets, nor are the Hamp1 mRNA and plasma hepcidin levels good predictors of tissue iron levels, at least in males. We also measured plasma erythroferrone, performed RNA-sequencing analysis of liver samples from six inbred strains fed the iron-sufficient, low-iron, or high-iron diets, and explored differences in gene expression between the strains with the highest and lowest hepcidin levels. NEW & NOTEWORTHY Both sex and strain have a significant effect on both hepcidin mRNA (primarily a sex effect) and plasma hepcidin levels (primarily a strain effect). Liver iron and diferric transferrin levels are not predictors of Hamp1 mRNA levels in mice, nor are the Hamp1 mRNA and plasma hepcidin levels good predictors of tissue iron levels, at least

  17. A major QTL corresponding to the Rk locus for resistance to root-knot nematodes in cowpea (Vigna unguiculata L. Walp.).

    PubMed

    Huynh, Bao-Lam; Matthews, William C; Ehlers, Jeffrey D; Lucas, Mitchell R; Santos, Jansen R P; Ndeve, Arsenio; Close, Timothy J; Roberts, Philip A

    2016-01-01

    Genome resolution of a major QTL associated with the Rk locus in cowpea for resistance to root-knot nematodes has significance for plant breeding programs and R gene characterization. Cowpea (Vigna unguiculata L. Walp.) is a susceptible host of root-knot nematodes (Meloidogyne spp.) (RKN), major plant-parasitic pests in global agriculture. To date, breeding for host resistance in cowpea has relied on phenotypic selection which requires time-consuming and expensive controlled infection assays. To facilitate marker-based selection, we aimed to identify and map quantitative trait loci (QTL) conferring the resistance trait. One recombinant inbred line (RIL) and two F2:3 populations, each derived from a cross between a susceptible and a resistant parent, were genotyped with genome-wide single nucleotide polymorphism (SNP) markers. The populations were screened in the field for root-galling symptoms and/or under growth-chamber conditions for nematode reproduction levels using M. incognita and M. javanica biotypes. One major QTL was mapped consistently on linkage group VuLG11 of each population. By genotyping additional cowpea lines and near-isogenic lines derived from conventional backcrossing, we confirmed that the detected QTL co-localized with the genome region associated with the Rk locus for RKN resistance that has been used in conventional breeding for many decades. This chromosomal location defined with flanking markers will be a valuable target in marker-assisted breeding and for positional cloning of genes controlling RKN resistance.

  18. An Unbiased Estimator of Gene Diversity with Improved Variance for Samples Containing Related and Inbred Individuals of any Ploidy

    PubMed Central

    Harris, Alexandre M.; DeGiorgio, Michael

    2016-01-01

    Gene diversity, or expected heterozygosity (H), is a common statistic for assessing genetic variation within populations. Estimation of this statistic decreases in accuracy and precision when individuals are related or inbred, due to increased dependence among allele copies in the sample. The original unbiased estimator of expected heterozygosity underestimates true population diversity in samples containing relatives, as it only accounts for sample size. More recently, a general unbiased estimator of expected heterozygosity was developed that explicitly accounts for related and inbred individuals in samples. Though unbiased, this estimator’s variance is greater than that of the original estimator. To address this issue, we introduce a general unbiased estimator of gene diversity for samples containing related or inbred individuals, which employs the best linear unbiased estimator of allele frequencies, rather than the commonly used sample proportion. We examine the properties of this estimator, H∼BLUE, relative to alternative estimators using simulations and theoretical predictions, and show that it predominantly has the smallest mean squared error relative to others. Further, we empirically assess the performance of H∼BLUE on a global human microsatellite dataset of 5795 individuals, from 267 populations, genotyped at 645 loci. Additionally, we show that the improved variance of H∼BLUE leads to improved estimates of the population differentiation statistic, FST, which employs measures of gene diversity within its calculation. Finally, we provide an R script, BestHet, to compute this estimator from genomic and pedigree data. PMID:28040781

  19. Characterization of health-related compounds in eggplant (Solanum melongena L.) lines derived from introgression of allied species.

    PubMed

    Mennella, Giuseppe; Rotino, Giuseppe L; Fibiani, Marta; D'Alessandro, Antonietta; Francese, Gianluca; Toppino, Laura; Cavallanti, Federica; Acciarri, Nazzareno; Lo Scalzo, Roberto

    2010-07-14

    The purpose of the present study was to investigate the levels of either the nutraceutical and health-promoting compounds or the antioxidant properties of innovative eggplant (Solanum melongena L.) genotypes tolerant and/or resistant to fungi, derived from conventional and non-conventional breeding methodologies (i.e., sexual interspecific hybridization, interspecific protoplast electrofusion, androgenesis, and backcross cycles) in comparison with their allied and cultivated parents. Chemical measures of soluble refractometric residue (SRR), glycoalkaloids (solamargine and solasonine), chlorogenic acid (CA), delphinidin 3-rutinoside (D3R), total phenols (TP), polyphenoloxidase (PPO) activity, antiradical activity on superoxide anion and hydroxyl radical were carried out in raw fruit and peel of 57 eggplant advanced introgression lines (ILs), of three eggplant recurrent genotypes and of three allied species during 2005 and 2006. The majority of the ILs, obtained after several backcross cycles, showed positive characteristics with respect to the allied parents such as good levels of SRR, CA, D3R, TP, PPO activity, the scavenging activity against superoxide anion and hydroxyl radical and, in particular, significantly (p

  20. Betaine deficiency in maize: Metabolic basis and relation to osmotic adjustment

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Rhodes, D.; Hanson, A.D.; Lerma, C.

    1990-05-01

    A single recessive gene causes betaine deficiency in certain maize inbred lines. As betaine may act as a cytosolic osmolyte, deficiency might be expected to reduce osmotic adjustment. Two near-isogenic maize lines differing for betaine, as well as groups of diverse betaine-containing and deficient inbreds, were tested under field water-stress conditions. The betaine-deficient isogenic line, and the group of deficient inbreds as a whole, showed significantly (P<0.05) less osmotic adjustment than their respective betaine-containing counterparts. When leaves from field-grown plants of the isogenic lines were supplied with ({sup 14}C)choline, the betaine-containing line produced ({sup 14}C)betaine whereas the deficient line didmore » not.« less

  1. Maternal heterozygosity and progeny fitness association in an inbred Scots pine population.

    PubMed

    Abrahamsson, S; Ahlinder, J; Waldmann, P; García-Gil, M R

    2013-03-01

    Associations between heterozygosity and fitness traits have typically been investigated in populations characterized by low levels of inbreeding. We investigated the associations between standardized multilocus heterozygosity (stMLH) in mother trees (obtained from12 nuclear microsatellite markers) and five fitness traits measured in progenies from an inbred Scots pine population. The traits studied were proportion of sound seed, mean seed weight, germination rate, mean family height of one-year old seedlings under greenhouse conditions (GH) and mean family height of three-year old seedlings under field conditions (FH). The relatively high average inbreeding coefficient (F) in the population under study corresponds to a mixture of trees with different levels of co-ancestry, potentially resulting from a recent bottleneck. We used both frequentist and Bayesian methods of polynomial regression to investigate the presence of linear and non-linear relations between stMLH and each of the fitness traits. No significant associations were found for any of the traits except for GH, which displayed negative linear effect with stMLH. Negative HFC for GH could potentially be explained by the effect of heterosis caused by mating of two inbred mother trees (Lippman and Zamir 2006), or outbreeding depression at the most heterozygote trees and its negative impact on the fitness of the progeny, while their simultaneous action is also possible (Lynch. 1991). However,since this effect wasn't detected for FH, we cannot either rule out that the greenhouse conditions introduce artificial effects that disappear under more realistic field conditions.

  2. Genetic characterization of the North Carolina State University maize lines

    USDA-ARS?s Scientific Manuscript database

    Since 1980, 150 North Carolina State University maize inbreds have been developed and released on the basis of superior performance for topcross yield and other traits of agronomic importance. During this time there has been great emphasis placed on breeding with exotic germplasm, with 86 NCSU inbr...

  3. Quantification of glucosinolates, anthocyanins, free amino acids, and vitamin C in inbred lines of cabbage (Brassica oleracea L.).

    PubMed

    Park, Suhyoung; Valan Arasu, Mariadhas; Lee, Min-Ki; Chun, Jin-Hyuk; Seo, Jeong Min; Lee, Sang-Won; Al-Dhabi, Naif Abdullah; Kim, Sun-Ju

    2014-02-15

    We profiled and quantified glucosinolates (GSLs), anthocyanins, free amino acids, and vitamin C metabolites in forty-five lines of green and red cabbages. Analysis of these distinct cabbages revealed the presence of 11 GSLs, 13 anthocyanins, 22 free amino acids, and vitamin C. GSL contents were varied amongst the different lines of cabbage. The total GSL content was mean 10.6 μmol/g DW, and sinigrin was the predominant GSL accounted mean 4.0 μmol/g DW (37.7% of the total) followed by glucoraphanin (1.9) and glucobrassicin (2.4). Amongst the 13 anthocyanins, cyanidin 3-(sinapoyl) diglucoside-5-glucoside levels were the highest. The amounts of total free amino acids in green cabbage lines ranged 365.9 mg/100g fresh weight (FW) to 1089.1mg/100g FW. Vitamin C levels were much higher in red cabbage line (129.9 mg/100g FW). Thus, the amounts of GSLs, anthocyanins, free amino acids, and vitamin C varied widely, and the variations in these compounds between the lines of cabbage were significant. Copyright © 2013 Elsevier Ltd. All rights reserved.

  4. Quantitative trait locus analysis of heterosis for plant height and ear height in an elite maize hybrid zhengdan 958 by design III.

    PubMed

    Li, Hongjian; Yang, Qingsong; Fan, Nannan; Zhang, Ming; Zhai, Huijie; Ni, Zhongfu; Zhang, Yirong

    2017-04-17

    Plant height (PH) and ear height (EH) are two important agronomic traits in maize selection breeding. F 1 hybrid exhibit significant heterosis for PH and EH as compared to their parental inbred lines. To understand the genetic basis of heterosis controlling PH and EH, we conducted quantitative trait locus (QTL) analysis using a recombinant inbreed line (RIL) based design III population derived from the elite maize hybrid Zhengdan 958 in five environments. A total of 14 environmentally stable QTLs were identified, and the number of QTLs for Z 1 and Z 2 populations was six and eight, respectively. Notably, all the eight environmentally stable QTLs for Z 2 were characterized by overdominance effect (OD), suggesting that overdominant QTLs were the most important contributors to heterosis for PH and EH. Furthermore, 14 environmentally stable QTLs were anchored on six genomic regions, among which four are trait-specific QTLs, suggesting that the genetic basis for PH and EH is partially different. Additionally, qPH.A-1.3, modifying about 10 centimeters of PH, was further validated in backcross populations. The genetic basis for PH and EH is partially different, and overdominant QTLs are important factors for heterosis of PH and EH. A major QTL qPH.A-1.3 may be a desired target for genetic improvement of maize plant height.

  5. Development of Near-Isogenic Lines in a Parthenogenetically Reproduced Thrips Species, Frankliniella occidentalis

    PubMed Central

    Yuan, Guangdi; Wan, Yanran; Li, Xiaoyu; He, Bingqing; Zhang, Youjun; Xu, Baoyun; Wang, Shaoli; Xie, Wen; Zhou, Xuguo; Wu, Qingjun

    2017-01-01

    Although near-isogenic lines (NILs) can standardize genetic backgrounds among individuals, it has never been applied in parthenogenetically reproduced animals. Here, through multiple rounds of backcrossing and spinosad screening, we generated spinosad resistant NILs in the western flower thrips, Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), with a haplo-diploid reproduction system. The resultant F. occidentalis NIL-R strain maintained a resistance ratio over 30,000-fold, which was comparable to its parental resistant strain, Spin-R. More importantly, F. occidentalis NIL-R shared 98.90% genetic similarity with its susceptible parental strain Ivf03. By developing this toolset, we are able to segregate individual resistance and facilitate the mechanistic study of insecticide resistances in phloem-feeding arthropods, a group of devastating pest species reproducing sexually as well as asexually. PMID:28348528

  6. Development of Near-Isogenic Lines in a Parthenogenetically Reproduced Thrips Species, Frankliniella occidentalis.

    PubMed

    Yuan, Guangdi; Wan, Yanran; Li, Xiaoyu; He, Bingqing; Zhang, Youjun; Xu, Baoyun; Wang, Shaoli; Xie, Wen; Zhou, Xuguo; Wu, Qingjun

    2017-01-01

    Although near-isogenic lines (NILs) can standardize genetic backgrounds among individuals, it has never been applied in parthenogenetically reproduced animals. Here, through multiple rounds of backcrossing and spinosad screening, we generated spinosad resistant NILs in the western flower thrips, Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), with a haplo-diploid reproduction system. The resultant F. occidentalis NIL-R strain maintained a resistance ratio over 30,000-fold, which was comparable to its parental resistant strain, Spin-R. More importantly, F. occidentalis NIL-R shared 98.90% genetic similarity with its susceptible parental strain Ivf03. By developing this toolset, we are able to segregate individual resistance and facilitate the mechanistic study of insecticide resistances in phloem-feeding arthropods, a group of devastating pest species reproducing sexually as well as asexually.

  7. Basal and induced granulopoiesis in outbred, F1 hybrid and inbred mice: can inbreeding depression influence the experimental practice?

    PubMed

    Hofer, Michal; Pospísil, Milan; Dusek, Ladislav; Holá, Jirina; Hoferová, Zuzana; Weiterová, Lenka

    2010-08-01

    In this study we examined differences in selected indices of granulopoiesis in outbred, F(1) hybrid and inbred mouse strains. Specifically, serum granulocyte colony-stimulating factor (G-CSF) levels, numbers of marrow granulocyte-macrophage progenitor cells and morphologically recognizable proliferative marrow granulocytic precursor cells were evaluated. These parameters were determined in untreated controls, and in mice exposed either to a non-specific stimulus (injection of saline) or to a granulopoiesis-enhancing stimulus (administration of a cyclooxygenase-2 inhibitor, meloxicam). Lower levels of G-CSF were detectable in the outbred ICR mice, which also demonstrated an enhanced response to both types of the stimuli. Considering the fact that outbred mice are closer to natural mammalian populations, including human ones, the possibility of using outbred mice, instead of the often used inbred strains, for experiments evaluating the effects of pharmacological interventions on hematopoiesis should be investigated.

  8. Detection of QTLs controlling fast kernel dehydration in maize (Zea mays L.).

    PubMed

    Qian, Y L; Zhang, X Q; Wang, L F; Chen, J; Chen, B R; Lv, G H; Wu, Z C; Guo, J; Wang, J; Qi, Y C; Li, T C; Zhang, W; Ruan, L; Zuo, X L

    2016-08-19

    In order to understand the effect of grain moisture of inbred lines at the silking and physiological maturity stages on kernel dehydration rate, 59 maize inbred lines from six subgroups were selected. Grain moisture was measured and QTLs associated with kernel dehydration were mapped. A rapid dehydration evaluation and association analysis revealed eight inbred lines with faster dehydration rate, including Yuanwu 02, K36, Zhonger/O2, Lo1125, Han 49, Qi 319, Hua 160, and PH4CV. A single sequence repeat analysis using 85 pairs detected five QTLs with phenotypic variation contribution ≥10% in the permanent F2 generation populations Zheng 58 x S1776 and Chang 7-2 x K1131, which had LOD threshold values ≥ 3 in both 2013 and 2014. The chromosome region of qFkdr7b had not previously been reported and is preliminarily identified as a new major QTL. A false positive field verification of grain dehydration rate of 53 inbred lines indicated that the screening result of the rapid dehydration inbred lines by specific amplification with marker Phi114 was most similar to the field assessment result, followed by markers Phi127 and Phi029. The rapid dehydration lines selected based on primer Phi114 amplification were also similar to the field dehydration rate and can thus be used for molecular marker-assisted selection. A significant effort is needed to improve stress resistance and shorten the growth period via fast kernel dehydration in intermediate materials of the inbred lines K36, Zhonger/ O2, Lo1125, Han 49, Hua 160, and PH4CV, and further using the selected lines for new combinations.

  9. Experimenter effects on behavioral test scores of eight inbred mouse strains under the influence of ethanol

    PubMed Central

    Bohlen, Martin; Hayes, Erika R.; Bohlen, Benjamin; Bailoo, Jeremy; Crabbe, John C.; Wahlsten, Douglas

    2016-01-01

    Eight standard inbred mouse strains were evaluated for ethanol effects on a refined battery of behavioral tests in a study that was originally designed to assess the influence of rat odors in the colony on mouse behaviors. As part of the design of the study, two experimenters conducted the tests, and the study was carefully balanced so that equal numbers of mice in all groups and times of day were tested by each experimenter. A defect in airflow in the facility compromised the odor manipulation, and in fact the different odor exposure groups did not differ in their behaviors. The two experimenters, however, obtained markedly different results for three of the tests. Certain of the experimenter effects arose from the way they judged behaviors that were not automated and had to be rated by the experimenter, such as slips on the balance beam. Others were not evident prior to ethanol injection but had a major influence after the injection. For several measures, the experimenter effects were notably different for different inbred strains. Methods to evaluate and reduce the impact of experimenter effects in future research are discussed. PMID:24933191

  10. Experimenter effects on behavioral test scores of eight inbred mouse strains under the influence of ethanol.

    PubMed

    Bohlen, Martin; Hayes, Erika R; Bohlen, Benjamin; Bailoo, Jeremy D; Crabbe, John C; Wahlsten, Douglas

    2014-10-01

    Eight standard inbred mouse strains were evaluated for ethanol effects on a refined battery of behavioral tests in a study that was originally designed to assess the influence of rat odors in the colony on mouse behaviors. As part of the design of the study, two experimenters conducted the tests, and the study was carefully balanced so that equal numbers of mice in all groups and times of day were tested by each experimenter. A defect in airflow in the facility compromised the odor manipulation, and in fact the different odor exposure groups did not differ in their behaviors. The two experimenters, however, obtained markedly different results for three of the tests. Certain of the experimenter effects arose from the way they judged behaviors that were not automated and had to be rated by the experimenter, such as slips on the balance beam. Others were not evident prior to ethanol injection but had a major influence after the injection. For several measures, the experimenter effects were notably different for different inbred strains. Methods to evaluate and reduce the impact of experimenter effects in future research are discussed. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Genetic variation of an acid phosphatase (Acp-2) in the laboratory rat: possible homology with mouse AP-1 and human ACP2.

    PubMed

    Bender, K; Bissbort, S; Kuhn, A; Nagel, M; Günther, E

    1986-02-01

    A genetic locus controlling the electrophoretic mobility of an acid phosphatase in the rat (Rattus norvegicus) is described. The locus, designed Acp-2, is not expressed in erythrocytes but is expressed in all other tissues studied. The product of Acp-2 hydrolyzes a wide variety of phosphate monoesters and is inhibited by L(+)-tartaric acid. Inbred rat strains have fixed either allele Acp-2a or allele Acp-2b. Codominant expression is observed in the respective F1 hybrids. Backcross progenies revealed the expected 1:1 segregation ratio. Possible loose linkage was found between the Acp-2 and the Pep-3 gene loci at a recombination frequency of 0.36 +/- 0.06.

  12. Genetic studies on experimental autoimmune gastritis induced by neonatal thymectomy using recombinant inbred strains between a high-incidence strain, BALB/c, and a low-incidence strain, DBA/2.

    PubMed Central

    Mori, Y; Hosono, M; Murakami, K; Katoh, H; Yoshikawa, Y; Kuribayashi, K; Kannagi, R; Sakai, M; Okuma, M; Masuda, T

    1991-01-01

    Thymectomy on day 3 after birth induced autoimmune gastritis (AIG) at the age of 2 months in 51-73% of BALB/c mice, and in only 3-5% of DBA/2 mice. AIG was detected by histological and serological (immunofluorescence staining for detecting anti-parietal cell autoantibody) examination. However, autoantibody was weakly positive in almost all of these DBA/2 mice when measured by ELISA using extract of murine gastric mucosa as the antigen. To investigate genetically the mechanism controlling the incidence of AIG, II recombinant inbred strains established by brother-sister mating of (BALB/c x DBA/2) F2 mice (C x D2 strains) were used. Among 26 markers tested, the Mls-1 locus on BALB/c chromosome 1 and the Hc locus coding a complement component (C5) on BALB/c chromosome 2 were found to be associated with high susceptibility to AIG. However, if one or both of the loci were of DBA/2 origin, mice showed medium or low susceptibility to AIG. For further analysis, F1, F2 and back-cross generations of these two strains were tested, but segregation of a single susceptibility or insusceptibility gene was not obtained. Taken together, it seems probable that two or more genes are involved in the induction mechanism of AIG. We did not detect C5 deposition in AIG lesions, nor complement-dependent cytotoxic antibody to parietal cells in serum from AIG mice. However, injection of irradiated spleen cells of DBA/2 mice into BALB/c mice thymectomized on day 3 augmented the incidence of AIG from 71 to 100%, but not that of oophoritis (33%). A relationship between Mls-1a determinants and the pathogenesis of AIG was further suggested from the fact that V beta 6 TcR-expressing T cells increased in number in AIG-bearing compared with normal BALB/c mice. Images Fig. 1 PMID:1901777

  13. Fine-structure mapping of the complex locus Odc-rs5 relative to Igk and distal loci.

    PubMed

    Richards-Smith, B A; Elliott, R W

    1992-01-01

    Odc-rs5 was previously identified as a complex locus closely linked to the Igk complex on mouse Chromosome (Chr) 6 and comprising at least five copies of a sequence related to the mRNA encoding ornithine decarboxylase (ODC) in the genomes of mice of some inbred strains and at least seven copies in others (Richards-Smith and Elliott, Mammalian Genome 2: 215, 1992). In the present study, Odc-rs5 was shown to be composed of at least seven copies of the ODC sequence in both the Odc-rs5a and Odc-rs5b haplotypes. Based upon the distribution of DNA restriction fragments (RFs) that had previously been associated with Odc-rs5a or Odc-rs5b among 42 mice of inbred laboratory strains having various haplotypes at Igk and in mice of two congenic strains [B6.PL-Ly-2a, Ly-3a(75NS)/Cy and B6.PL-Ly-2a,Ly-3a(85NS)/Cy] and a backcross-derived stock (NAK) known to be recombinant within Igk, a fine structure map of Odc-rs5 was deduced relative to Igk and more distal loci. Odc-rs5-derived RFs were located to three distinct regions within and/or distal to Igk and to a fourth site between (Ly-3, Ly-2) and Raf-1. Additionally, DNAs from 19 mice of inbred strains and random-bred stocks derived from wild progenitors trapped at various locations were analyzed and found to exhibit an unexpected variety of combinations of RFs associated with the two Odc-rs5 haplotypes most frequently observed among inbred laboratory strains of mice.

  14. Learning Strategy Selection in the Water Maze and Hippocampal CREB Phosphorylation Differ in Two Inbred Strains of Mice

    ERIC Educational Resources Information Center

    Sung, Jin-Young; Goo, June-Seo; Lee, Dong-Eun; Jin, Da-Qing; Bizon, Jennifer L.; Gallagher, Michela; Han, Jung-Soo

    2008-01-01

    Learning strategy selection was assessed in two different inbred strains of mice, C57BL/6 and DBA/2, which are used for developing genetically modified mouse models. Male mice received a training protocol in a water maze using alternating blocks of visible and hidden platform trials, during which mice escaped to a single location. After training,…

  15. Sterol balance and cholesterol absorption in inbred strains of rabbits hypo- or hyperresponsive to dietary cholesterol.

    PubMed

    Beynen, A C; Meijer, G W; Lemmens, A G; Glatz, J F; Versluis, A; Katan, M B; Van Zutphen, L F

    1989-06-01

    In 2 inbred strains of rabbits with high or low response of plasma cholesterol to dietary cholesterol, excretion of steroids in the feces and efficiency of cholesterol absorption were determined. Rates of whole-body cholesterol synthesis, measured as fecal excretion of bile acids and neutral steroids minus cholesterol intake, were similar in hypo- and hyperresponders fed a low-cholesterol (8 mumol/100 g) diet. Transfer of the rabbits to a high-cholesterol (182 mumol/100 g) diet caused an increase in fecal bile acid excretion in hypo- but not in hyperresponders. Dietary cholesterol did not affect neutral steroid excretion in either rabbit strain. Hyperresponders tended to accumulate more cholesterol in their body than did hyporesponders. After the rabbits were switched back from the high- to the low-cholesterol diet, rates of whole-body cholesterol synthesis were significantly higher in the hypo- than in the hyperresponders. With the use of the simultaneous oral administration of [3H]cholesterol and beta-[14C]sitosterol, hyperresponders were found to absorb significantly higher percentages of cholesterol than hyporesponders. It is concluded that the differences in stimulation of bile acid excretion after cholesterol feeding and the efficiency of cholesterol absorption are important determinants of the phenomenon of hypo- and hyperresponsiveness in the 2 inbred rabbit strains.

  16. Population genetic evidence for sex-specific dispersal in an inbred social spider.

    PubMed

    Smith, Deborah R; Su, Yong-Chao; Berger-Tal, Reut; Lubin, Yael

    2016-08-01

    Dispersal in most group-living species ensures gene flow among groups, but in cooperative social spiders, juvenile dispersal is suppressed and colonies are highly inbred. It has been suggested that such inbred sociality is advantageous in the short term, but likely to lead to extinction or reduced speciation rates in the long run. In this situation, very low levels of dispersal and gene flow among colonies may have unusually important impacts on fitness and persistence of social spiders. We investigated sex-specific differences in dispersal and gene flow among colonies, as reflected in the genetic structure within colonies and populations of the African social spider Stegodyphus dumicola Pocock, 1898 (Eresidae). We used DNA fingerprinting and mtDNA sequence data along with spatial mapping of colonies to compare male and female patterns of relatedness within and among colonies at three study sites. Samples were collected during and shortly after the mating season to detect sex-specific dispersal. Distribution of mtDNA haplotypes was consistent with proliferation of social nests by budding and medium- to long-distance dispersal by ballooning females. Analysis of molecular variance and spatial autocorrelation analyses of AFLPs showed high levels of genetic similarity within colonies, and STRUCTURE analyses revealed that the number of source populations contributing to colonies ranged from one to three. We also showed significant evidence of male dispersal among colonies at one site. These results support the hypothesis that in social spiders, genetic cohesion among populations is maintained by long-distance dispersal of female colony founders. Genetic diversity within colonies is maintained by colony initiation by multiple dispersing females, and adult male dispersal over short distances. Male dispersal may be particularly important in maintaining gene flow among colonies in local populations.

  17. Strain-dependent Differences in LTP and Hippocampus-dependent Memory in Inbred Mice

    PubMed Central

    Nguyen, Peter V.; Abel, Ted; Kandel, Eric R.; Bourtchouladze, Roussoudan

    2000-01-01

    Many studies have used “reverse” genetics to produce “knock-out” and transgenic mice to explore the roles of various molecules in long-term potentiation (LTP) and spatial memory. The existence of a variety of inbred strains of mice provides an additional way of exploring the genetic bases of learning and memory. We examined behavioral memory and LTP expression in area CA1 of hippocampal slices prepared from four different inbred strains of mice: C57BL/6J, CBA/J, DBA/2J, and 129/SvEms-+Ter?/J. We found that LTP induced by four 100-Hz trains of stimulation was robust and long-lasting in C57BL/6J and DBA/2J mice but decayed in CBA/J and 129/SvEms-+Ter?/J mice. LTP induced by one 100-Hz train was significantly smaller after 1 hr in the 129/SvEms-+Ter?/J mice than in the other three strains. Theta-burst LTP was shorter lasting in CBA/J, DBA/2J, and 129/SvEms-+Ter?/J mice than in C57BL/6J mice. We also observed specific memory deficits, among particular mouse strains, in spatial and nonspatial tests of hippocampus-dependent memory. CBA/J mice showed defective learning in the Morris water maze, and both DBA/2J and CBA/J strains displayed deficient long-term memory in contextual and cued fear conditioning tests. Our findings provide strong support for a genetic basis for some forms of synaptic plasticity that are linked to behavioral long-term memory and suggest that genetic background can influence the electrophysiological and behavioral phenotypes observed in genetically modified mice generated for elucidating the molecular bases of learning, memory, and LTP. PMID:10837506

  18. Genome-enabled prediction models for yield related traits in chickpea

    USDA-ARS?s Scientific Manuscript database

    Genomic selection (GS) unlike marker-assisted backcrossing (MABC) predicts breeding values of lines using genome-wide marker profiling and allows selection of lines prior to field-phenotyping, thereby shortening the breeding cycle. A collection of 320 elite breeding lines was selected and phenotyped...

  19. Characterization of a spontaneous disease of white leghorn chickens resembling progressive systemic sclerosis (scleroderma)

    PubMed Central

    1981-01-01

    University of California, Davis (UCD) line 200 White Leghorn Chickens spontaneously develop a syndrome that has many analogous features to human progressive systemic sclerosis. This syndrome is characterized by progressive involution of comb, dermal fibrosis, and distal polyarthritis. These three features occur within 6 wk after hatching, and are accompanied by a 40% mortality as a result of vaso-occlusive disease, with development of secondary infection of peripheral gangrenous lesions. Birds that survive greater than 2 mo after hatching progressively develop fibrosis of the esophagous and mononuclear infiltration of heart and kidney, with prominent occlusion of small and medium sized blood vessels. In addition, line 200 chickens develop rheumatoid factors, antinuclear antibodies, and antibodies to collagen, but do not have antibodies to thymocytes, DNA, or extractable nuclear antigens. Moreover, antinuclear antibodies when studied using HEp-2 cells as substrate demonstrate predominantly a speckled pattern. This syndrome of line 200 chickens is not detectable in F1 crosses to several UCD inbred lines. F1 X parental line BC1 backcrosses have an approximately 50% incidence of disease, suggesting that this syndrome is inherited as autosomal recessive. However, only 4% of F2 generation birds show abnormal symptoms, suggesting the presence of modifying genes. There is no appearance of IgG deposition, as determined by immunofluorescence, in either skin, blood vessels, esophagus, or heart. However, approximately 20% of chickens have a glomerulonephritis; this feature appears to be a terminal event and does not appear clinically significant. Although this syndrome of line 200 chickens has several features that are in sharp distinction to human scleroderma, the presence of common immunologic and pathologic denominators suggest that this spontaneous disease may be an appropriate model to develop a better understanding of autoimmune connective tissue diseases. PMID:7252423

  20. Genetic dissection of black grain rice by the development of a near isogenic line.

    PubMed

    Maeda, Hiroaki; Yamaguchi, Takuya; Omoteno, Motoyasu; Takarada, Takeshi; Fujita, Kenji; Murata, Kazumasa; Iyama, Yukihide; Kojima, Yoichiro; Morikawa, Makiko; Ozaki, Hidenobu; Mukaino, Naoyuki; Kidani, Yoshinori; Ebitani, Takeshi

    2014-06-01

    Rice (Oryza sativa L.) can produce black grains as well as white. In black rice, the pericarp of the grain accumulates anthocyanin, which has antioxidant activity and is beneficial to human health. We developed a black rice introgression line in the genetic background of Oryza sativa L. 'Koshihikari', which is a leading variety in Japan. We used Oryza sativa L. 'Hong Xie Nuo' as the donor parent and backcrossed with 'Koshihikari' four times, resulting in a near isogenic line (NIL) for black grains. A whole genome survey of the introgression line using DNA markers suggested that three regions, on chromosomes 1, 3 and 4 are associated with black pigmentation. The locus on chromosome 3 has not been identified previously. A mapping analysis with 546 F2 plants derived from a cross between the black rice NIL and 'Koshihikari' was evaluated. The results indicated that all three loci are essential for black pigmentation. We named these loci Kala1, Kala3 and Kala4. The black rice NIL was evaluated for eating quality and general agronomic traits. The eating quality was greatly superior to that of 'Okunomurasaki', an existing black rice variety. The isogenicity of the black rice NIL to 'Koshihikari' was very high.

  1. Genome-wide comparative transcriptome analysis of CMS-D2 and its maintainer and restorer lines in upland cotton.

    PubMed

    Wu, Jianyong; Zhang, Meng; Zhang, Bingbing; Zhang, Xuexian; Guo, Liping; Qi, Tingxiang; Wang, Hailin; Zhang, Jinfa; Xing, Chaozhu

    2017-06-08

    Cytoplasmic male sterility (CMS) conferred by the cytoplasm from Gossypium harknessii (D2) is an important system for hybrid seed production in Upland cotton (G. hirsutum). The male sterility of CMS-D2 (i.e., A line) can be restored to fertility by a restorer (i.e., R line) carrying the restorer gene Rf1 transferred from the D2 nuclear genome. However, the molecular mechanisms of CMS-D2 and its restoration are poorly understood. In this study, a genome-wide comparative transcriptome analysis was performed to identify differentially expressed genes (DEGs) in flower buds among the isogenic fertile R line and sterile A line derived from a backcross population (BC 8 F 1 ) and the recurrent parent, i.e., the maintainer (B line). A total of 1464 DEGs were identified among the three isogenic lines, and the Rf1-carrying Chr_D05 and its homeologous Chr_A05 had more DEGs than other chromosomes. The results of GO and KEGG enrichment analysis showed differences in circadian rhythm between the fertile and sterile lines. Eleven DEGs were selected for validation using qRT-PCR, confirming the accuracy of the RNA-seq results. Through genome-wide comparative transcriptome analysis, the differential expression profiles of CMS-D2 and its maintainer and restorer lines in Upland cotton were identified. Our results provide an important foundation for further studies into the molecular mechanisms of the interactions between the restorer gene Rf1 and the CMS-D2 cytoplasm.

  2. The locus Om, responsible for the DDK syndrome, maps close to Sigje on mouse chromosome 11.

    PubMed

    Baldacci, P A; Richoux, V; Renard, J P; Guénet, J L; Babinet, C

    1992-01-01

    The DDK inbred strain of mouse has a striking particularity: when DDK females are crossed to males of other strains they exhibit a reduced fertility, whereas the reciprocal crosses (non-DDK females x DDK males) are fertile (Wakasugi et al. 1967; Wakasugi 1973). The low fertility results from an early embryonic lethality, the F1 embryos dying near the late morula-early blastocyst stage. Genetic analyses (Wakasugi 1974) and nuclear and cytoplasmic transfers (Renard and Babinet 1986; Babinet et al. 1990; Mann 1986), have shown that the failure of the embroys to develop is due to an incompatibility between a DDK maternally encoded cytoplasmic product and the non-DDK paternal genome. In order to elucidate the genetic determinism of this embryonic lethality, we have analyzed the fertility of male progeny from a backcross BALB/c females x (BALB/c x DDK)F1 males and that of males from a set of recombinant inbred (RI) strains, established from DDK and BALB/c progenitors, when mated with DDK females. Our results indicate that a single locus, Om, is responsible for the DDK syndrome and is located on Chromosome (Chr) 11, very close to the Sigje locus.

  3. Assessing Autism-like Behavior in Mice: Variations in Social Interactions Among Inbred Strains.

    PubMed Central

    Bolivar, Valerie J.; Walters, Samantha R.; Phoenix, Jennifer L.

    2007-01-01

    Autism is a pervasive developmental disorder, with characteristics including impairments in reciprocal social interaction, impaired communication, and repetitive/stereotyped behaviors. Despite decades of research, the etiology of autism remains elusive. Thus, it is important that we pursue all avenues, in attempting to understand this complicated disorder. One such avenue is the development of animal models. While autism may be uniquely human, there are behavioral characteristics of the disorder that can be established in animal models. Evidence supports a genetic component for this disorder, and over the past few decades the mouse has been a highly valuable tool for the elucidation of pathways involved in many human disorders (e.g., Huntington’s disease). As a first step toward establishing a mouse model of autism, we studied same-sex social behavior in a number of inbred mouse strains. In Study 1, we examined intra-strain social behavior of male pairs after one mouse had 15 minutes prior exposure to the testing chamber. In Study 2, we evaluated intra-strain and inter-strain social behavior when both mice were naive to the testing chamber. The amount and type of social behavior seen differed between these studies, but overall there were general inbred strain differences in social behavior. Some strains were highly social (e.g., FVB/NJ, while others displayed low levels of social behavior (e.g., A/J, BTBR T+ tf/J). These strains may be useful in future genetic studies to determine specific genes involved in mouse social behavior, the findings of which should in turn help us to determine some of the genes involved in human social behavior and its disorders (e.g., autism). PMID:17097158

  4. Mapping and characterization of the new adult plant leaf rust resistance gene Lr77 derived from Santa Fe winter wheat.

    PubMed

    Kolmer, James A; Su, Zhenqi; Bernardo, Amy; Bai, Guihua; Chao, Shiaoman

    2018-07-01

    A new gene for adult plant leaf rust resistance in wheat was mapped to chromosome 3BL. This gene was designated as Lr77. 'Santa Fe' is a hard red winter cultivar that has had long-lasting resistance to the leaf rust fungus, Puccinia triticina. The objective of this study was to determine the chromosome location of the adult plant leaf rust resistance in Santa Fe wheat. A partial backcross line of 'Thatcher' (Tc) wheat with adult plant leaf rust resistance derived from Santa Fe was crossed with Thatcher to develop a Thatcher//Tc*2/Santa Fe F 6 recombinant inbred line (RIL) population. The RIL population and parental lines were evaluated for segregation of leaf rust resistance in three field plot tests and in an adult plant greenhouse test. A genetic map of the RIL population was constructed using 90,000 single-nucleotide polymorphism (SNP) markers with the Illumina Infinium iSelect 90K wheat bead array. A significant quantitative trait locus for reduction of leaf rust severity in all four tests was found on chromosome 3BL that segregated as a single adult plant resistance gene. The RILs with the allele from the resistant parent for SNP marker IWB10344 had lower leaf rust severity and a moderately resistant to moderately susceptible response compared to the susceptible RILs and Thatcher. The gene derived from Santa Fe on chromosome 3BL was designated as Lr77. Kompetitive allele-specific polymerase chain reaction assay markers linked to Lr77 on 3BL should be useful for selection of wheat germplasm with this gene.

  5. Characterization of central and peripheral components of the hypothalamus-pituitary-adrenal axis in the inbred Roman rat strains.

    PubMed

    Carrasco, Javier; Márquez, Cristina; Nadal, Roser; Tobeña, Adolfo; Fernández-Teruel, Albert; Armario, Antonio

    2008-05-01

    Several studies performed in outbred Roman high- and low-avoidance lines (RHA and RLA, respectively) have demonstrated that the more anxious line (RLA) is characterized by a higher hypothalamic-pituitary-adrenal (HPA) response to certain stressors than the less anxious one (RHA). However, inconsistent results have also been reported. Taking advantage of the generation of an inbred colony of RLA and RHA rats (RHA-I and RLA-I, respectively), we have characterized in the two strains not only resting and stress levels of peripheral HPA hormones but also central components of the HPA axis, including CRF gene expression in extra-hypothalamic areas. Whereas resting levels of ACTH and corticosterone did not differ between the strains, a greater response to a novel environment was found in RLA-I as compared to RHA-I rats. RLA-I rats showed enhanced CRF gene expression in the paraventricular nucleus (PVN) of the hypothalamus, with normal arginin-vasopressin gene expression in both parvocellular and magnocellular regions of the PVN. This enhanced CRF gene expression is not apparently related to altered negative corticosteroid feedback as similar levels of expression of brain glucorticoid and mineralocorticoid receptors were found in the two rat strains. CRF gene expression tended to be higher in the central amygdala and it was significantly higher in the dorsal region of the bed nucleus of stria terminalis (BNST) of RLA-I rats, while no differences appeared in the ventral region of BNST. Considering the involvement of CRF and the BNST in anxiety and stress-related behavioral alterations, the present data suggest that the CRF system may be a critical neurobiological substrate underlying differences between the two rat strains.

  6. Outbred CD1 mice are as suitable as inbred C57BL/6J mice in performing social tasks.

    PubMed

    Hsieh, Lawrence S; Wen, John H; Miyares, Laura; Lombroso, Paul J; Bordey, Angélique

    2017-01-10

    Inbred mouse strains have been used preferentially for behavioral testing over outbred counterparts, even though outbred mice reflect the genetic diversity in the human population better. Here, we compare the sociability of widely available outbred CD1 mice with the commonly used inbred C57BL/6J (C57) mice in the one-chamber social interaction test and the three-chamber sociability test. In the one-chamber task, intra-strain pairs of juvenile, non-littermate, male CD1 or C57 mice display a series of social and aggressive behaviors. While CD1 and C57 pairs spend equal amount of time socializing, CD1 pairs spend significantly more time engaged in aggressive behaviors than C57 mice. In the three-chamber task, sociability of C57 mice was less dependent on acclimation paradigms than CD1 mice. Following acclimation to all three chambers, both groups of age-matched male mice spent more time in the chamber containing a stranger mouse than in the empty chamber, suggesting that CD1 mice are sociable like C57 mice. However, the observed power suggests that it is easier to achieve statistical significance with C57 than CD1 mice. Because the stranger mouse could be considered as a novel object, we assessed for a novelty effect by adding an object. CD1 mice spend more time in the chamber with a stranger mouse than that a novel object, suggesting that their preference is social in nature. Thus, outbred CD1 mice are as appropriate as inbred C57 mice for studying social behavior using either the single or the three-chamber test using a specific acclimation paradigm. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  7. Introgression of a 4D chromosomal fragment into durum wheat confers aluminium tolerance

    PubMed Central

    Han, Chang; Ryan, Peter R.; Yan, ZeHong; Delhaize, Emmanuel

    2014-01-01

    Background and Aim Aluminium (Al3+) inhibits root growth of sensitive plant species and is a key factor that limits durum wheat (Triticum turgidum) production on acid soils. The aim of this study was to enhance the Al3+ tolerance of an elite durum cultivar by introgression of a chromosomal fragment from hexaploid wheat (Triticum aestivum) that possesses an Al3+ tolerance gene. Methods A 4D(4B) substitution line of durum wheat ‘Langdon’ was backcrossed to ‘Jandaroi’, a current semi-dwarf Australian durum. In the second backcross, using ‘Jandaroi’ as the recurrent parent, a seedling was identified where TaALMT1 on chromosome 4D was recombined with the Rht-B1b locus on chromosome 4B to yield an Al3+-tolerant seedling with a semi-dwarf habit. This seedling was used in a third backcross to generate homozygous sister lines with contrasting Al3+ tolerances. The backcrossed lines were characterized and compared with selected cultivars of hexaploid wheat for their Al3+ and Na+ tolerances in hydroponic culture as well as in short-term experiments to assess their growth on acid soil. Key Results Analysis of sister lines derived from the third backcross showed that the 4D chromosomal fragment substantially enhanced Al3+ tolerance. The ability to exclude Na+ from leaves was also enhanced, indicating that the chromosomal fragment possessed the Kna1 salt tolerance locus. Although Al3+ tolerance of seminal roots was enhanced in acid soil, the development of fine roots was not as robust as found in Al3+-tolerant lines of hexaploid wheat. Analysis of plant characteristics in the absence of Al3+ toxicity showed that the introgressed fragment did not affect total grain yield but reduced the weight of individual grains. Conclusions The results show that it is possible to increase substantially the Al3+ tolerance of an elite durum wheat cultivar by introgression of a 4D chromosomal fragment. Further improvements are possible, such as introducing additional genes to enhance

  8. Further Evidence for Selective Differences between Isoalleles in Drosophila

    PubMed Central

    Wills, Christopher; Phelps, Julia; Ferguson, Richard

    1975-01-01

    A number of separate strains of Drosophila pseudoobscura were inbred for 38 generations of brother-sister mating with forced heterozygosity for two alleles of either the octanol dehydrogenase or esterase-5 locus. Crosses were set up within each of these inbred lines such that simple mendelian ratios were expected, and eggs from these crosses were placed on media with additions of simple chemicals likely to interact with alleles of the two loci—octanol and ethanol for the ODH locus and tributyrin and triacetin for the E-5 locus. Similar crosses were set up involving parental flies with normally heterozygous genetic background as a control.—Significant deviations from mendelian expectation were observed in inbred E-5 flies grown on tributyrin, inbred ODH males grown on octanol, and inbred ODH females grown on ethanol. There was also a strong effect of octanol medium on males of one of the inbred E-5 lines, and a weak effect of tributyrin medium on ODH inbred females.—The probability that these results reflect interactions between these loci and the environment is assessed in the light of differences between the present results and those obtained at earlier stages of inbreeding. PMID:1126619

  9. Antioxidant Enzymatic Activities and Gene Expression Associated with Heat Tolerance in the Stems and Roots of Two Cucurbit Species (“Cucurbita maxima” and “Cucurbita moschata”) and Their Interspecific Inbred Line “Maxchata”

    PubMed Central

    Ara, Neelam; Nakkanong, Korakot; Lv, Wenhui; Yang, Jinghua; Hu, Zhongyuan; Zhang, Mingfang

    2013-01-01

    The elucidation of heat tolerance mechanisms is required to combat the challenges of global warming. This study aimed to determine the antioxidant enzyme responses to heat stress, at the enzymatic activity and gene expression levels, and to investigate the antioxidative alterations associated with heat tolerance in the stems and roots of squashes using three genotypes differing in heat tolerance. Plants of heat-tolerant “C. moschata”, thermolabile “C. maxima” and moderately heat-tolerant interspecific inbred line “Maxchata” genotypes were exposed to moderate (37 °C) and severe (42 °C) heat shocks. “C. moschata” exhibited comparatively little oxidative damage, with the lowest hydrogen peroxide (H2O2), superoxide (O2−) and malondialdehyde (MDA) contents in the roots compared to stems, followed by “Maxchata”. The enzyme activities of superoxide dismutase (SOD), ascorbate peroxidase (APX), catalase (CAT) and peroxidase (POD) were found to be increased with heat stress in tolerant genotypes. The significant inductions of FeSOD, MnSOD, APX2, CAT1 and CAT3 isoforms in tolerant genotypes suggested their participation in heat tolerance. The differential isoform patterns of SOD, APX and CAT between stems and roots also indicated their tissue specificity. Furthermore, despite the sequence similarity of the studied antioxidant genes among “C. maxima” and “Maxchata”, most of these genes were highly induced under heat stress in “Maxchata”, which contributed to its heat tolerance. This phenomenon also indicated the involvement of other unknown genetic and/or epigenetic factors in controlling the expression of these antioxidant genes in squashes, which demands further exploration. PMID:24336062

  10. Unpredictable chronic mild stress differentially impairs social and contextual discrimination learning in two inbred mouse strains.

    PubMed

    van Boxelaere, Michiel; Clements, Jason; Callaerts, Patrick; D'Hooge, Rudi; Callaerts-Vegh, Zsuzsanna

    2017-01-01

    Alterations in the social and cognitive domain are considered important indicators for increased disability in many stress-related disorders. Similar impairments have been observed in rodents chronically exposed to stress, mimicking potential endophenotypes of stress-related psychopathologies such as major depression disorder (MDD), anxiety, conduct disorder, and posttraumatic stress disorder (PTSD). Data from numerous studies suggest that deficient plasticity mechanisms in hippocampus (HC) and prefrontal cortex (PFC) might underlie these social and cognitive deficits. Specifically, stress-induced deficiencies in neural plasticity have been associated with a hypodopaminergic state and reduced neural plasticity persistence. Here we assessed the effects of unpredictable chronic mild stress (UCMS) on exploratory, social and cognitive behavior of females of two inbred mouse strains (C57BL/6J and DBA/2J) that differ in their dopaminergic profile. Exposure to chronic stress resulted in impaired circadian rhythmicity, sociability and social cognition in both inbred strains, but differentially affected activity patterns and contextual discrimination performance. These stress-induced behavioral impairments were accompanied by reduced expression levels of brain derived neurotrophic factor (BDNF) in the prefrontal cortex. The strain-specific cognitive impairment was coexistent with enhanced plasma corticosterone levels and reduced expression of genes related to dopamine signaling in hippocampus. These results underline the importance of assessing different strains with multiple test batteries to elucidate the neural and genetic basis of social and cognitive impairments related to chronic stress.

  11. Abiotic stress growth conditions induce different responses in kernel iron concentration across genotypically distinct maize inbred varieties

    PubMed Central

    Kandianis, Catherine B.; Michenfelder, Abigail S.; Simmons, Susan J.; Grusak, Michael A.; Stapleton, Ann E.

    2013-01-01

    The improvement of grain nutrient profiles for essential minerals and vitamins through breeding strategies is a target important for agricultural regions where nutrient poor crops like maize contribute a large proportion of the daily caloric intake. Kernel iron concentration in maize exhibits a broad range. However, the magnitude of genotype by environment (GxE) effects on this trait reduces the efficacy and predictability of selection programs, particularly when challenged with abiotic stress such as water and nitrogen limitations. Selection has also been limited by an inverse correlation between kernel iron concentration and the yield component of kernel size in target environments. Using 25 maize inbred lines for which extensive genome sequence data is publicly available, we evaluated the response of kernel iron density and kernel mass to water and nitrogen limitation in a managed field stress experiment using a factorial design. To further understand GxE interactions we used partition analysis to characterize response of kernel iron and weight to abiotic stressors among all genotypes, and observed two patterns: one characterized by higher kernel iron concentrations in control over stress conditions, and another with higher kernel iron concentration under drought and combined stress conditions. Breeding efforts for this nutritional trait could exploit these complementary responses through combinations of favorable allelic variation from these already well-characterized genetic stocks. PMID:24363659

  12. Derivation of Thymic Lymphoma T-cell Lines from Atm-/- and p53-/- Mice

    PubMed Central

    Jinadasa, Rasika; Balmus, Gabriel; Gerwitz, Lee; Roden, Jamie; Weiss, Robert; Duhamel, Gerald

    2011-01-01

    Established cell lines are a critical research tool that can reduce the use of laboratory animals in research. Certain strains of genetically modified mice, such as Atm-/- and p53-/- consistently develop thymic lymphoma early in life 1,2, and thus, can serve as a reliable source for derivation of murine T-cell lines. Here we present a detailed protocol for the development of established murine thymic lymphoma T-cell lines without the need to add interleukins as described in previous protocols 1,3. Tumors were harvested from mice aged three to six months, at the earliest indication of visible tumors based on the observation of hunched posture, labored breathing, poor grooming and wasting in a susceptible strain 1,4. We have successfully established several T-cell lines using this protocol and inbred strains ofAtm-/- [FVB/N-Atmtm1Led/J] 2 and p53-/- [129/S6-Trp53tm1Tyj/J] 5 mice. We further demonstrate that more than 90% of the established T-cell population expresses CD3, CD4 and CD8. Consistent with stably established cell lines, the T-cells generated by using the present protocol have been passaged for over a year. PMID:21490582

  13. Genetic mapping and legume synteny of aphid resistance in African cowpea (Vigna unguiculata L. Walp.) grown in California.

    PubMed

    Huynh, Bao-Lam; Ehlers, Jeffrey D; Ndeve, Arsenio; Wanamaker, Steve; Lucas, Mitchell R; Close, Timothy J; Roberts, Philip A

    The cowpea aphid Aphis craccivora Koch (CPA) is a destructive insect pest of cowpea, a staple legume crop in Sub-Saharan Africa and other semiarid warm tropics and subtropics. In California, CPA causes damage on all local cultivars from early vegetative to pod development growth stages. Sources of CPA resistance are available in African cowpea germplasm. However, their utilization in breeding is limited by the lack of information on inheritance, genomic location and marker linkage associations of the resistance determinants. In the research reported here, a recombinant inbred line (RIL) population derived from a cross between a susceptible California blackeye cultivar (CB27) and a resistant African breeding line (IT97K-556-6) was genotyped with 1,536 SNP markers. The RILs and parents were phenotyped for CPA resistance using field-based screenings during two main crop seasons in a 'hotspot' location for this pest within the primary growing region of the Central Valley of California. One minor and one major quantitative trait locus (QTL) were consistently mapped on linkage groups 1 and 7, respectively, both with favorable alleles contributed from IT97K-556-6. The major QTL appeared dominant based on a validation test in a related F2 population. SNP markers flanking each QTL were positioned in physical contigs carrying genes involved in plant defense based on synteny with related legumes. These markers could be used to introgress resistance alleles from IT97K-556-6 into susceptible local blackeye varieties by backcrossing.

  14. [Index screening and comprehensive evaluation of phenotypic traits of low nitrogen tolerance using BILs population derived from Dongxiang wild rice (Oryza rufipogon Griff)].

    PubMed

    Hu, Biao-lin; Li, Xia; Wan, Yong; Qiu, Zai-hui; Nie, Yuan-yuan; Xie, Jian-kun

    2015-08-01

    To identify the low nitrogen tolerance of Dongxiang wild rice (DXWR) and its progenies, ten phenotypic traits including plant height (PH), heading day (HD), panicle length (PL), number of effective tillers per plant (NETP), number of filled grains per panicle (NFGP), number of grains per panicle (NGP), grain density (GD), spikelet fertility (SF), 1000-grain mass (TGM) and grain yield per plant (GYP) were studied under normal and low nitrogen treatments, using backcross inbred lines (BILs) of Xieqingzao B//DXWR/Xieqingzao B in BC1 F12. Comprehensive evaluation on the low nitrogen tolerance of the BILs population was conducted using principal component analysis and the subordinate function. The evaluation results indicated that the low nitrogen tolerance of the line 116, 143 and 157 was the strongest, which could be served as the intermediate materials for genetic studies on the low nitrogen tolerance of DXWR and breeding for the low nitrogen tolerance in rice. The optimal regression equation of the low nitrogen tolerance in rice was established using stepwise regression analysis. The relative values of five traits including PH, NGP, SF, TGM and GYP were screened out and could be used as comprehensive evaluation indices for the low nitrogen tolerance in the whole growth stage. Therefore, more attention should be paid to the relative values of these five traits, especially for NGP and GYP, in the genetic improvement of the low nitrogen tolerance in rice.

  15. Specific immune response genes of new inbred strains of guinea pigs.

    PubMed

    Chiba, J; Egashira, Y

    1978-01-01

    Distribution of specific immune-response (Ir) genes controlling responsiveness to synthetic polypeptide antigens, homopolymer of poly-L-lysine (PLL), copolymer of L-glutamic acid and L-alanine (GA) and copolymer of L-glutamic acid and L-tyrosine (GT), and limiting doses of 2,4-dinitrophenyl guinea pig serum albumin (DNP-GPA) was surveyed in new inbred strains of guinea pigs, JY 1, JY 2, JY 9 and JY 10, established in this Institute. The PLL gene was not found in any of the guinea pigs. The GA gene was found in JY 1 and JY 2 guinea pigs and the GT gene in all the guinea pigs. The gene controlling responsiveness to low doses (1 microgram) of DNP-GPA was found in JY 1, JY 9 and JY 10 guinea pigs. The associated (Ia) antigens was discussed.

  16. Variation in heading date conceals quantitative trait loci for other traits of importance in breeding selection of rice

    PubMed Central

    Hori, Kiyosumi; Kataoka, Tomomori; Miura, Kiyoyuki; Yamaguchi, Masayuki; Saka, Norikuni; Nakahara, Takahiro; Sunohara, Yoshihiro; Ebana, Kaworu; Yano, Masahiro

    2012-01-01

    To identify quantitative trait loci (QTLs) associated with the primary target traits for selection in practical rice breeding programs, backcross inbred lines (BILs) derived from crosses between temperate japonica rice cultivars Nipponbare and Koshihikari were evaluated for 50 agronomic traits at six experimental fields located throughout Japan. Thirty-three of the 50 traits were significantly correlated with heading date. Using a linkage map including 647 single-nucleotide polymorphisms (SNPs), a total of 122 QTLs for 38 traits were mapped on all rice chromosomes except chromosomes 5 and 9. Fifty-eight of the 122 QTLs were detected near the heading date QTLs Hd16 and Hd17 and the remaining 64 QTLs were found in other chromosome regions. QTL analysis of 51 BILs having homozygous for the Koshihikari chromosome segments around Hd16 and Hd17 allowed us to detect 40 QTLs associated with 27 traits; 23 of these QTLs had not been detected in the original analysis. Among the 97 QTLs for the 30 traits measured in multiple environments, the genotype-by-environment interaction was significant for 44 QTLs and not significant for 53 QTLs. These results led us to propose a new selection strategy to improve agronomic performance in temperate japonica rice cultivars. PMID:23226082

  17. Ontogeny of con A and PHA responses of chicken blood cells in MHC-compatible lines 6(3) and 7(2).

    PubMed

    Fredericksen, T L; Gilmour, D G

    1983-06-01

    The development of T cell responsiveness to Con A and PHA was examined in two MHC-compatible inbred chicken lines, RPRL 6(3) and 7(2), at ages 2 to 118 days posthatching. These lines are respectively resistant or susceptible to Marek's disease, a naturally occurring, virally induced T cell lymphoma. Between-line comparisons were made of optimal in vitro responses of diluted serum-free blood cells to each mitogen in two groups of chicks tested over ages 2 to 63 and 41 to 118 days. Over 2 to 63 days, Con A responses increased with age at the same rate in each line, but 7(2) responses averaged 2.3 times higher than 6(3). The increase with age was dependent on blood lymphocyte counts, which also increased with age in parallel in both lines. In contrast, the between-line difference in responsiveness was dependent on intrinsic reactivity of cells as well as lymphocyte counts. Covariance analysis was used to estimate that line 7(2) was 1.4 times higher than 6(3) in intrinsic cell reactivity, after accounting for the effect of the twofold higher blood lymphocyte counts in 7(2), and that this intrinsic difference contributed almost one-half the total difference. Over 41 to 118 days Con A responses no longer increased with age, although lymphocyte counts were still increasing, and the line difference (2.6 times) was now almost entirely contributed by a 2.3-fold superiority of 7(2) blood cells in intrinsic reactivity. The line difference in PHA responses was the reverse of the above in young chicks, with 6(3) responses greater than 7(2) in spite of lower lymphocyte counts. In additional chicks tested over 5 to 26 days, intrinsic reactivity of 6(3) cells to PHA averaged 4.5 times higher than 7(2). There was an abrupt decline in intrinsic reactivity of line 6(3) blood cells between 26 and 41 days to a level equal with 7(2). After this age, line 7(2) responses were 1.8 times greater than those of 6(3), and this difference was dependent solely on lymphocyte count differences. The

  18. Electrophoretic variation in low molecular weight lens crystallins from inbred strains of rats.

    PubMed

    Donner, M E; Skow, L C; Kunz, H W; Gill, T J

    1985-10-01

    Analysis of rat lens soluble proteins by analytical isoelectric focusing detected two inherited electrophoretic differences in low molecular weight (LM) crystallins from inbred strains of rats (Rattus norvegicus). The polymorphic lens crystallins were shown to be similar to a genetically variant LM crystallin, LEN-1, previously described in mice (Mus musculus) and encoded on chromosome 1, at a locus linked to Pep-3 (dipeptidase). Linkage analysis demonstrated that the rat crystallin locus was loosely linked to Pep-3 at a recombination distance of 38 +/- 4.5 U. These data suggest the conservation of a large chromosomal region during the evolution of Rodentia and support the hypothesis that the gamma-crystallins are evolving more rapidly than alpha- or beta-crystallins.

  19. Dissociation of sensitivities to tumor promotion and progression in outbred and inbred SENCAR mice.

    PubMed

    Gimenez-Conti, I B; Bianchi, A B; Fischer, S M; Reiners, J J; Conti, C J; Slaga, T J

    1992-06-15

    The sensitivity of outbred SENCAR mice and inbred SENCAR (SSIN) mice to multistage carcinogenesis was studied. Tumors were induced using either 7,12-dimethylbenz[a]anthracene or N-methyl-N'-nitro-N-nitrosoguanidine as initiators and 12-O-tetradecanoylphorbol-13-acetate or benzoyl peroxide as promoting agents. Although the number of papillomas per mouse was higher in SSIN than in outbred SENCAR mice, the number of carcinomas observed in the SSIN strain was significantly lower regardless of the initiator or promoter used. It was also observed that the expression of markers of premalignant progression (i.e., dysplasia, expression of keratin K13, and loss of keratin K1 expression) was markedly suppressed in SSIN papillomas. After 50 wk of promotion with 12-O-tetradecanoylphorbol-13-acetate, the pattern of expression of K13 and K1 in SSIN mice was comparable to the pattern observed in outbred SENCAR mice after 10 to 20 wk of promotion with 12-O-tetradecanoylphorbol-13-acetate. It was also observed that 67% of the tumors induced in SSIN mice by initiation with 7,12-dimethylbenz[a]anthracene exhibited a mutation in codon 61 of the Ha-ras-1 gene. This latter finding suggests that the differences observed in tumor progression between the inbred strain and the outbred stock are not related to a genetic alteration in the Ha-ras-1 gene but rather to an independent event that we have postulated to involve a putative suppressor gene. The data reported here suggest that the putative gene(s) that confers susceptibility to tumor promotion was segregated from the gene(s) involved in tumor progression during selection and inbreeding of the SENCAR mouse stock.

  20. Genetic variance contributes to ingestive processes: a survey of eleven inbred mouse strains for fat (Intralipid) intake.

    PubMed

    Lewis, Sarah R; Dym, Cheryl; Chai, Christina; Singh, Amreeta; Kest, Benjamin; Bodnar, Richard J

    2007-01-30

    Genetic variation across inbred and outbred mouse strains have been observed for intake of sweet solutions, salts, bitter tastants and a high-fat diet. Our laboratory recently reported marked strain differences in the amounts and/or percentages of kilocalories of sucrose consumed among 11 inbred and one outbred mouse strains exposed to a wide range of nine sucrose concentrations (0.0001-5%) in two-bottle 24-h preference tests. To assess whether differences in fat intake were similarly associated with genetic variation, the present study examined intake of chow, water and an emulsified fat source (Intralipid) across nine different concentrations (0.00001-5%) in the same 11 inbred and 1 outbred mouse strains using two-bottle 24-h preference tests, which controlled for Intralipid concentration presentation effects, Intralipid and water bottle positions, and measurement of kilocalorie intake consumed as Intralipid or chow. Strains displayed differential increases in Intralipid intake relative to corresponding water with significant effects observed at the seven (BALB/cJ: 0.001% threshold sensitivity), four (AKR/J, C57BL/6J, DBA/2J, SWR/J: 0.5% threshold sensitivity), three (CD-1, C57BL/10J, SJL/J: 1% threshold sensitivity) and two (A/J, CBA/J, C3H/HeJ, 129P3/J: 2% threshold sensitivity) highest concentrations. In assessing the percentage of kilocalories consumed as Intralipid, SWR/J mice consumed significantly more at the three highest concentrations to a greater degree than BALB/cJ, C57BL/6J, CD-1, C3H/HeJ, DBA/J and 129P3/J strains which in turn consumed more than A/J, AKR/J, CBA/J, C57BL/10J and SJL/J mice. Relatively strong (h2 = 0.73-0.79) heritability estimates were obtained for weight-adjusted Intralipid intake at those concentrations (0.001-1%) that displayed the largest strain-specific effects in sensitivity to Intralipid. The identification of strains with diverging abilities to regulate kilocalorie intake when presented with high Intralipid concentrations

  1. Background controlled QTL mapping in pure-line genetic populations derived from four-way crosses

    PubMed Central

    Zhang, S; Meng, L; Wang, J; Zhang, L

    2017-01-01

    Pure lines derived from multiple parents are becoming more important because of the increased genetic diversity, the possibility to conduct replicated phenotyping trials in multiple environments and potentially high mapping resolution of quantitative trait loci (QTL). In this study, we proposed a new mapping method for QTL detection in pure-line populations derived from four-way crosses, which is able to control the background genetic variation through a two-stage mapping strategy. First, orthogonal variables were created for each marker and used in an inclusive linear model, so as to completely absorb the genetic variation in the mapping population. Second, inclusive composite interval mapping approach was implemented for one-dimensional scanning, during which the inclusive linear model was employed to control the background variation. Simulation studies using different genetic models demonstrated that the new method is efficient when considering high detection power, low false discovery rate and high accuracy in estimating quantitative trait loci locations and effects. For illustration, the proposed method was applied in a reported wheat four-way recombinant inbred line population. PMID:28722705

  2. Background controlled QTL mapping in pure-line genetic populations derived from four-way crosses.

    PubMed

    Zhang, S; Meng, L; Wang, J; Zhang, L

    2017-10-01

    Pure lines derived from multiple parents are becoming more important because of the increased genetic diversity, the possibility to conduct replicated phenotyping trials in multiple environments and potentially high mapping resolution of quantitative trait loci (QTL). In this study, we proposed a new mapping method for QTL detection in pure-line populations derived from four-way crosses, which is able to control the background genetic variation through a two-stage mapping strategy. First, orthogonal variables were created for each marker and used in an inclusive linear model, so as to completely absorb the genetic variation in the mapping population. Second, inclusive composite interval mapping approach was implemented for one-dimensional scanning, during which the inclusive linear model was employed to control the background variation. Simulation studies using different genetic models demonstrated that the new method is efficient when considering high detection power, low false discovery rate and high accuracy in estimating quantitative trait loci locations and effects. For illustration, the proposed method was applied in a reported wheat four-way recombinant inbred line population.

  3. The scent of inbreeding: a male sex pheromone betrays inbred males

    PubMed Central

    van Bergen, Erik; Brakefield, Paul M.; Heuskin, Stéphanie; Zwaan, Bas J.; Nieberding, Caroline M.

    2013-01-01

    Inbreeding depression results from mating among genetically related individuals and impairs reproductive success. The decrease in male mating success is usually attributed to an impact on multiple fitness-related traits that reduce the general condition of inbred males. Here, we find that the production of the male sex pheromone is reduced significantly by inbreeding in the butterfly Bicyclus anynana. Other traits indicative of the general condition, including flight performance, are also negatively affected in male butterflies by inbreeding. Yet, we unambiguously show that only the production of male pheromones affects mating success. Thus, this pheromone signal informs females about the inbreeding status of their mating partners. We also identify the specific chemical component (hexadecanal) probably responsible for the decrease in male mating success. Our results advocate giving increased attention to olfactory communication as a major causal factor of mate-choice decisions and sexual selection. PMID:23466986

  4. Several Classical Mouse Inbred Strains, Including DBA/2, NOD/Lt, FVB/N, and SJL/J, Carry a Putative Loss-of-Function Allele of Gpr84

    PubMed Central

    2013-01-01

    G protein–coupled receptor 84 (GPR84) is a 7-transmembrane protein expressed on myeloid cells that can bind to medium-chain free fatty acids in vitro. Here, we report the discovery of a 2-bp frameshift deletion in the second exon of the Gpr84 gene in several classical mouse inbred strains. This deletion generates a premature stop codon predicted to result in a truncated protein lacking the transmembrane domains 4-7. We sequenced Gpr84 exon 2 from 58 strains representing different groups in the mouse family tree and found that 14 strains are homozygous for the deletion. Some of these strains are DBA/1J, DBA/2J, FVB/NJ, LG/J, MRL/MpJ, NOD/LtJ, and SJL/J. However, the deletion was not found in any of the wild-derived inbred strains analyzed. Haplotype analysis suggested that the deletion originates from a unique mutation event that occurred more than 100 years ago, preceding the development of the first inbred strain (DBA), from a Mus musculus domesticus source. As GPR84 ostensibly plays a role in the biology of myeloid cells, it could be relevant 1) to consider the existence of this Gpr84 nonsense mutation in several mouse strains when choosing a mouse model to study immune processes and 2) to consider reevaluating data obtained using such strains. PMID:23616478

  5. Several classical mouse inbred strains, including DBA/2, NOD/Lt, FVB/N, and SJL/J, carry a putative loss-of-function allele of Gpr84.

    PubMed

    Perez, Carlos J; Dumas, Aline; Vallières, Luc; Guénet, Jean-Louis; Benavides, Fernando

    2013-01-01

    G protein-coupled receptor 84 (GPR84) is a 7-transmembrane protein expressed on myeloid cells that can bind to medium-chain free fatty acids in vitro. Here, we report the discovery of a 2-bp frameshift deletion in the second exon of the Gpr84 gene in several classical mouse inbred strains. This deletion generates a premature stop codon predicted to result in a truncated protein lacking the transmembrane domains 4-7. We sequenced Gpr84 exon 2 from 58 strains representing different groups in the mouse family tree and found that 14 strains are homozygous for the deletion. Some of these strains are DBA/1J, DBA/2J, FVB/NJ, LG/J, MRL/MpJ, NOD/LtJ, and SJL/J. However, the deletion was not found in any of the wild-derived inbred strains analyzed. Haplotype analysis suggested that the deletion originates from a unique mutation event that occurred more than 100 years ago, preceding the development of the first inbred strain (DBA), from a Mus musculus domesticus source. As GPR84 ostensibly plays a role in the biology of myeloid cells, it could be relevant 1) to consider the existence of this Gpr84 nonsense mutation in several mouse strains when choosing a mouse model to study immune processes and 2) to consider reevaluating data obtained using such strains.

  6. Effectiveness of the Ty-3 Introgression for Conferring Resistance in Recombinant Inbred Lines of Tomato to Bipartite Begomoviruses in Guatemala

    USDA-ARS?s Scientific Manuscript database

    Management of begomovirus-incited diseases on tomatoes in Guatemala continues to be a challenge and there continues to be a need to better understand the genetics of resistance to begomoviruses. In this study, the resistant line, Gh13, was crossed with the susceptible line, HUJ-VF, that lacked the ...

  7. Puroindoline genes introduced into durum wheat reduce milling energy and change milling behavior similar to soft common wheats

    USDA-ARS?s Scientific Manuscript database

    Grain physical characteristics and milling behavior of a durum wheat line in which both wild-type puroindoline alleles were translocated and stabilized after backcrossing (Svevo-Pin) were compared with the parent line (Svevo). The only observed differences between grain characteristics were the mech...

  8. Pollen germination and in vivo fertilization in response to high-temperature during flowering in hybrid and inbred rice.

    PubMed

    Shi, Wanju; Li, Xiang; Schmidt, Ralf C; Struik, Paul C; Yin, Xinyou; Jagadish, S V Krishna

    2018-01-15

    High-temperature during flowering in rice causes spikelet sterility and is a major threat to rice productivity in tropical and subtropical regions, where hybrid rice development is increasingly contributing to sustain food security. However, the sensitivity of hybrids to increasing temperature and physiological responses in terms of dynamic fertilization processes is unknown. To address these questions, several promising hybrids and inbreds were exposed to control temperature and high day-time temperature (HDT) in Experiment 1, and hybrids having contrasting heat tolerance were selected for Experiment 2 for further physiological investigation under HDT and high-night-time-temperature treatments. The day-time temperature played a dominant role in determining spikelet fertility compared with the night-time temperature. HDT significantly induced spikelet sterility in tested hybrids, and hybrids had higher heat susceptibility than the high-yielding inbred varieties. Poor pollen germination was strongly associated with sterility under high-temperature. Our novel observations capturing the series of dynamic fertilization processes demonstrated that pollen tubes not reaching the viable embryo sac was the major cause for spikelet sterility under heat exposure. Our findings highlight the urgent need to improve heat tolerance in hybrids and incorporating early-morning flowering as a promising trait for mitigating HDT stress impact at flowering. © 2018 John Wiley & Sons Ltd.

  9. Unpredictable chronic mild stress differentially impairs social and contextual discrimination learning in two inbred mouse strains

    PubMed Central

    van Boxelaere, Michiel; Clements, Jason; Callaerts, Patrick; D’Hooge, Rudi

    2017-01-01

    Alterations in the social and cognitive domain are considered important indicators for increased disability in many stress-related disorders. Similar impairments have been observed in rodents chronically exposed to stress, mimicking potential endophenotypes of stress-related psychopathologies such as major depression disorder (MDD), anxiety, conduct disorder, and posttraumatic stress disorder (PTSD). Data from numerous studies suggest that deficient plasticity mechanisms in hippocampus (HC) and prefrontal cortex (PFC) might underlie these social and cognitive deficits. Specifically, stress-induced deficiencies in neural plasticity have been associated with a hypodopaminergic state and reduced neural plasticity persistence. Here we assessed the effects of unpredictable chronic mild stress (UCMS) on exploratory, social and cognitive behavior of females of two inbred mouse strains (C57BL/6J and DBA/2J) that differ in their dopaminergic profile. Exposure to chronic stress resulted in impaired circadian rhythmicity, sociability and social cognition in both inbred strains, but differentially affected activity patterns and contextual discrimination performance. These stress-induced behavioral impairments were accompanied by reduced expression levels of brain derived neurotrophic factor (BDNF) in the prefrontal cortex. The strain-specific cognitive impairment was coexistent with enhanced plasma corticosterone levels and reduced expression of genes related to dopamine signaling in hippocampus. These results underline the importance of assessing different strains with multiple test batteries to elucidate the neural and genetic basis of social and cognitive impairments related to chronic stress. PMID:29166674

  10. [Molecular-genetic analysis of wheat (T. aestivum L.) genome with introgression of Ae. cylindrica Host genetic elements].

    PubMed

    Galaev, A V; Sivolap, Iu M

    2005-01-01

    Wheat-aegilops hybrid plants Triticum aestivum L. (2n = 42) x Aegilops cylindrica Host (2n = 28) were investigated with using microsatellite markers. In two BC1F9 lines some genome modifications connected with losing DNA fragments of initial variety or appearing of Aegilops genome elements were detected. In some investigated hybrids new amplicons lacking in parental plants were found. Substitution of wheat chromosomes for aegilops chromosomes was not revealed. Analysis of microsatellite loci in BC2F5 plants showed stable introgression of aegilops genetic elements into wheat; elimination of some transferred aegilops DNA fragments in the course of backcrossing; decreasing size of introgressive elements after backcrossing. Introgressive lines were classified according to genome changes.

  11. Bt-transgenic oilseed rape hybridization with its weedy relative, Brassica rapa.

    PubMed

    Halfhill, Matthew D; Millwood, Reginald J; Raymer, Paul L; Stewart, C Neal

    2002-10-01

    The movement of transgenes from crops to weeds and the resulting consequences are concerns of modern agriculture. The possible generation of "superweeds" from the escape of fitness-enhancing transgenes into wild populations is a risk that is often discussed, but rarely studied. Oilseed rape, Brassica napus (L.), is a crop with sexually compatible weedy relatives, such as birdseed rape (Brassica rapa (L.)). Hybridization of this crop with weedy relatives is an extant risk and an excellent interspecific gene flow model system. In laboratory crosses, T3 lines of seven independent transformation events of Bacillus thuringiensis (Bt) oilseed rape were hybridized with two weedy accessions of B. rapa. Transgenic hybrids were generated from six of these oilseed rape lines, and the hybrids exhibited an intermediate morphology between the parental species. The Bt transgene was present in the hybrids, and the protein was synthesized at similar levels to the corresponding independent oilseed rape lines. Insect bioassays were performed and confirmed that the hybrid material was insecticidal. The hybrids were backcrossed with the weedy parent, and only half the oilseed rape lines were able to produce transgenic backcrosses. After two backcrosses, the ploidy level and morphology of the resultant plants were indistinguishable from B. rapa. Hybridization was monitored under field conditions (Tifton, GA, USA) with four independent lines of Bt oilseed rape with a crop to wild relative ratio of 1200:1. When B. rapa was used as the female parent, hybridization frequency varied among oilseed rape lines and ranged from 16.9% to 0.7%.

  12. Ups and downs of a transcriptional landscape shape iron deficiency associated chlorosis of the maize inbreds B73 and Mo17

    PubMed Central

    2013-01-01

    Background Improving nutrient homeostasis is a major challenge of a sustainable maize cultivation, and cornerstone to ensure food supply for a growing world population. Although, iron constitutes an important nutrient, iron availability is limited. In this respect, iron deficiency associated chlorosis causes severe yield losses every year. Natural variation of the latter trait has yet not been addressed in maize and was therefore studied in the present analysis. Results In this study, we i) report about the contrasting chlorosis phenotypes of the inbreds B73 and Mo17 at 10 and 300 μM iron regime, ii) identified over 400 significantly regulated transcripts (FDR < 0.05) within both inbreds at these growth conditions by deep RNA-Sequencing, iii) linked the gained knowledge with QTL information about iron deficiency related traits within the maize intermated B73 by Mo17 (IBM) population, and iv) highlighted contributing molecular pathways. In this respect, several genes within methionine salvage pathway and phytosiderophore synthesis were found to present constitutively high expression in Mo17, even under sufficient iron supply. Moreover, the same expression pattern could be observed for two putative bHLH transcription factors. In addition, a number of differentially expressed genes showed a co-localisation with QTL confidence intervals for iron deficiency related traits within the IBM population. Conclusions Our study highlights differential iron deficiency associated chlorosis between B73 and Mo17 and represents a valuable resource for differentially expressed genes upon iron limitation and chlorosis response. Besides identifying two putative bHLH transcription factors, we propose that methionine salvage pathway and sterol metabolism amongst others; underlie the contrasting iron deficiency related chlorosis phenotype of both inbreds. Altogether, this study emphasizes a contribution of selected genes and pathways on natural trait variation within the IBM

  13. Multigenerational outbreeding effects in Chinook salmon (Oncorhynchus tshawytscha).

    PubMed

    Lehnert, Sarah J; Love, Oliver P; Pitcher, Trevor E; Higgs, Dennis M; Heath, Daniel D

    2014-08-01

    Outbreeding, mating between genetically divergent individuals, may result in negative fitness consequences for offspring via outbreeding depression. Outbreeding effects are of notable concern in salmonid research as outbreeding can have major implications for salmon aquaculture and conservation management. We therefore quantified outbreeding effects in two generations (F1 hybrids and F2 backcrossed hybrids) of Chinook salmon (Oncorhynchus tshawytscha) derived from captively-reared purebred lines that had been selectively bred for differential performance based on disease resistance and growth rate. Parental lines were crossed in 2009 to create purebred and reciprocal hybrid crosses (n = 53 families), and in 2010 parental and hybrid crosses were crossed to create purebred and backcrossed hybrid crosses (n = 66 families). Although we found significant genetic divergence between the parental lines (FST = 0.130), reciprocal F1 hybrids showed no evidence of outbreeding depression (hybrid breakdown) or favorable heterosis for weight, length, condition or survival. The F2 backcrossed hybrids showed no outbreeding depression for a suite of fitness related traits measured from egg to sexually mature adult life stages. Our study contributes to the current knowledge of outbreeding effects in salmonids and supports the need for more research to better comprehend the mechanisms driving outbreeding depression.

  14. The genetic architecture of NAFLD among inbred strains of mice

    PubMed Central

    Hui, Simon T; Parks, Brian W; Org, Elin; Norheim, Frode; Che, Nam; Pan, Calvin; Castellani, Lawrence W; Charugundla, Sarada; Dirks, Darwin L; Psychogios, Nikolaos; Neuhaus, Isaac; Gerszten, Robert E; Kirchgessner, Todd; Gargalovic, Peter S; Lusis, Aldons J

    2015-01-01

    To identify genetic and environmental factors contributing to the pathogenesis of non-alcoholic fatty liver disease, we examined liver steatosis and related clinical and molecular traits in more than 100 unique inbred mouse strains, which were fed a diet rich in fat and carbohydrates. A >30-fold variation in hepatic TG accumulation was observed among the strains. Genome-wide association studies revealed three loci associated with hepatic TG accumulation. Utilizing transcriptomic data from the liver and adipose tissue, we identified several high-confidence candidate genes for hepatic steatosis, including Gde1, a glycerophosphodiester phosphodiesterase not previously implicated in triglyceride metabolism. We confirmed the role of Gde1 by in vivo hepatic over-expression and shRNA knockdown studies. We hypothesize that Gde1 expression increases TG production by contributing to the production of glycerol-3-phosphate. Our multi-level data, including transcript levels, metabolite levels, and gut microbiota composition, provide a framework for understanding genetic and environmental interactions underlying hepatic steatosis. DOI: http://dx.doi.org/10.7554/eLife.05607.001 PMID:26067236

  15. Combined Metabolomic and Genetic Approaches Reveal a Link between the Polyamine Pathway and Albumin 2 in Developing Pea Seeds1[W][OA

    PubMed Central

    Vigeolas, Helene; Chinoy, Catherine; Zuther, Ellen; Blessington, Bernard; Geigenberger, Peter; Domoney, Claire

    2008-01-01

    Several legume seed proteins that are potentially allergenic, poorly digested by farm animals, and/or have undesirable functional properties, have been described. One of these is the albumin protein in pea (Pisum sativum) called PA2. A naturally occurring mutant line that lacks PA2 has been exploited in studies to determine the biological function of this nonstorage protein in seed development. The mutant, which has a small seed, a tall plant phenotype, and lacks most of the PA2-encoding genes, has been crossed with a standard cultivar, ‘Birte,’ which contains PA2 to give rise to a recombinant inbred (RI) population. An F3 line carrying the mutation and having a short plant phenotype has been used to generate backcross (BC) lines with ‘Birte.’ Despite having a lower albumin content, seeds from the mutant parent and RI lines lacking PA2 have an equivalent or higher seed nitrogen content. Metabolite profiling of seeds revealed major differences in amino acid composition and polyamine content in the two parent lines. This was investigated further in BC lines, where the effects of differences in seed size and plant height between the two parents were eliminated. Here, differences in polyamine synthesis were maintained as was a difference in total seed protein between the BC line lacking PA2 and ‘Birte.’ Analysis of enzyme activities in the pathways of polyamine synthesis revealed that the differences in spermidine content were attributable to changes in the overall activities of spermidine synthase and arginine decarboxylase. Although the genes encoding spermidine synthase and PA2 both localized to the pea linkage group I, the two loci were shown not to be closely linked and to have recombined in the BC lines. A distinct locus on linkage group III contains a gene that is related to PA2 but expressed predominantly in flowers. The results provide evidence for a role of PA2 in regulating polyamine metabolism, which has important functions in development

  16. Why develop O. sativa x O. rufipogon chromosome segment substitution line libraries?

    USDA-ARS?s Scientific Manuscript database

    Transgressive variation has been observed in rice (Oryza sativa) as an increase in grain yield in advanced backcross mapping populations derived from crosses between several adapted O. sativa varieties and a single accession (IRGC105491) of the ancestral parent, O. rufipogon. The phenomena of hybrid...

  17. Estimation of loci involved in non-shattering of seeds in early rice domestication.

    PubMed

    Ishikawa, Ryo; Nishimura, Akinori; Htun, Than Myint; Nishioka, Ryo; Oka, Yumi; Tsujimura, Yuki; Inoue, Chizuru; Ishii, Takashige

    2017-04-01

    Rice (Oryza sativa L.) is widely cultivated around the world and is known to be domesticated from its wild form, O. rufipogon. A loss of seed shattering is one of the most obvious phenotypic changes selected for during rice domestication. Previously, three seed-shattering loci, qSH1, sh4, and qSH3 were reported to be involved in non-shattering of seeds of Japonica-type cultivated rice, O. sativa cv. Nipponbare. In this study, we focused on non-shattering characteristics of O. sativa Indica cv. IR36 having functional allele at qSH1. We produced backcross recombinant inbred lines having chromosomal segments from IR36 in the genetic background of wild rice, O. rufipogon W630. Histological and quantitative trait loci analyses of abscission layer formation were conducted. In the analysis of quantitative trait loci, a strong peak was observed close to sh4. We, nevertheless, found that some lines showed complete abscission layer formation despite carrying the IR36 allele at sh4, implying that non-shattering of seeds of IR36 could be regulated by the combination of mutations at sh4 and other seed-shattering loci. We also genotyped qSH3, a recently identified seed-shattering locus. Lines that have the IR36 alleles at sh4 and qSH3 showed inhibition of abscission layer formation but the degree of seed shattering was different from that of IR36. On the basis of these results, we estimated that non-shattering of seeds in early rice domestication involved mutations in at least three loci, and these genetic materials produced in this study may help to identify novel seed-shattering loci.

  18. Comparative transcript profiling of alloplasmic male-sterile lines revealed altered gene expression related to pollen development in rice (Oryza sativa L.).

    PubMed

    Hu, Jihong; Chen, Guanglong; Zhang, Hongyuan; Qian, Qian; Ding, Yi

    2016-08-05

    Cytoplasmic male sterility (CMS) is an ideal model for investigating the mitochondrial-nuclear interaction and down-regulated genes in CMS lines which might be the candidate genes for pollen development in rice. In this study, a set of rice alloplasmic sporophytic CMS lines was obtained by successive backcrossing of Meixiang B, with three different cytoplasmic types: D62A (D type), ZS97A (WA type) and XQZ-A (DA type). Using microarray, the anther transcript profiles of the three indica rice CMS lines revealed 622 differentially expressed genes (DEGs) in each of the three CMS lines compared with the maintainer line Meixiang B. GO and MapMan analysis indicated that these DEGs were mainly involved in lipid metabolism and cell wall organization. Compared with the gene expression of sporophytic and gametophytic CMS lines, 303 DEGs were identified and 56 of them were down-regulated in all the CMS lines of rice. These down-regulated DEGs in the CMS lines were found to be involved in tapetum or cell wall formation and their suppressed expression might be related to male sterility. Weighted gene co-expression network analysis (WGCNA) revealed that two modules were significantly associated with male sterility and many hub genes that were differentially expressed in the CMS lines. A large set of putative genes involved in anther development was identified in the present study. The results will give some information for the nuclear gene regulation by different cytoplasmic genotypes and provide a rich resource for further functional research on the pollen development in rice.

  19. A genetic relationship between nitrogen use efficiency and seedling root traits in maize as revealed by QTL analysis.

    PubMed

    Li, Pengcheng; Chen, Fanjun; Cai, Hongguang; Liu, Jianchao; Pan, Qingchun; Liu, Zhigang; Gu, Riliang; Mi, Guohua; Zhang, Fusuo; Yuan, Lixing

    2015-06-01

    That root system architecture (RSA) has an essential role in nitrogen acquisition is expected in maize, but the genetic relationship between RSA and nitrogen use efficiency (NUE) traits remains to be elucidated. Here, the genetic basis of RSA and NUE traits was investigated in maize using a recombination inbred line population that was derived from two lines contrasted for both traits. Under high-nitrogen and low-nitrogen conditions, 10 NUE- and 9 RSA-related traits were evaluated in four field environments and three hydroponic experiments, respectively. In contrast to nitrogen utilization efficiency (NutE), nitrogen uptake efficiency (NupE) had significant phenotypic correlations with RSA, particularly the traits of seminal roots (r = 0.15-0.31) and crown roots (r = 0.15-0.18). A total of 331 quantitative trait loci (QTLs) were detected, including 184 and 147 QTLs for NUE- and RSA-related traits, respectively. These QTLs were assigned into 64 distinct QTL clusters, and ~70% of QTLs for nitrogen-efficiency (NUE, NupE, and NutE) coincided in clusters with those for RSA. Five important QTLs clusters at the chromosomal regions bin1.04, 2.04, 3.04, 3.05/3.06, and 6.07/6.08 were found in which QTLs for both traits had favourable effects from alleles coming from the large-rooted and high-NupE parent. Introgression of these QTL clusters in the advanced backcross-derived lines conferred mean increases in grain yield of ~14.8% for the line per se and ~15.9% in the testcross. These results reveal a significant genetic relationship between RSA and NUE traits, and uncover the most promising genomic regions for marker-assisted selection of RSA to improve NUE in maize. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  20. Effects of stacked quantitative resistances to downy mildew in lettuce do not simply add up.

    PubMed

    den Boer, Erik; Pelgrom, Koen T B; Zhang, Ningwen W; Visser, Richard G F; Niks, Rients E; Jeuken, Marieke J W

    2014-08-01

    In a stacking study of eight resistance QTLs in lettuce against downy mildew, only three out of ten double combinations showed an increased resistance effect under field conditions. Complete race nonspecific resistance to lettuce downy mildew, as observed for the nonhost wild lettuce species Lactuca saligna, is desired in lettuce cultivation. Genetic dissection of L. saligna's complete resistance has revealed several quantitative loci (QTL) for resistance with field infection reductions of 30-50 %. To test the effect of stacking these QTL, we analyzed interactions between homozygous L. saligna CGN05271 chromosome segments introgressed into the genetic background of L. sativa cv. Olof. Eight different backcross inbred lines (BILs) with single introgressions of 30-70 cM and selected predominately for quantitative resistance in field situations were intercrossed. Ten developed homozygous lines with stacked introgression segments (double combinations) were evaluated for resistance in the field. Seven double combinations showed a similar infection as the individual most resistant parental BIL, revealing epistatic interactions with 'less-than-additive' effects. Three double combinations showed an increased resistance level compared to their parental BILs and their interactions were additive, 'less-than-additive' epistatic and 'more-than-additive' epistatic, respectively. The additive interaction reduced field infection by 73 %. The double combination with a 'more-than-additive' epistatic effect, derived from a combination between a susceptible and a resistant BIL with 0 and 30 % infection reduction, respectively, showed an average field infection reduction of 52 %. For the latter line, an attempt to genetically dissect its underlying epistatic loci by substitution mapping did not result in smaller mapping intervals as none of the 22 substitution lines reached a similar high resistance level. Implications for breeding and the inheritance of L. saligna's complete

  1. Genome characterization of a breeding line derived from a cross between Oryza sativa and Oryza rufipogon.

    PubMed

    Keong, B P; Harikrishna, J A

    2012-02-01

    A preliminary screening was conducted on BC3F1 and BC4F1 backcross families developed from crossing Oryza sativa (MR219) and O. rufipogon (IRGC105491). Despite earlier results showing that O. rufipogon alleles (wild introgression) contributed to both number of panicles (qPPL-2) and tillers (qTPL-2) at loci RM250, RM208, and RM48 in line A20 of the BC2F2 population, we observed that wild introgression was lost at loci RM250 and RM208 but retained at locus RM48 in BC3F1 and BC4F1. Progeny tests conducted utilizing genotype and phenotype data on both BC4F1 and a reference population, BC2F7 (A20 line), did not show significant differences between groups having the MR219 allele and wild introgression at locus RM48. This suggests that there is no additive and transgressive effect of wild introgression in the BC3F1 and BC4F1 generated. The presence of wild introgression was largely due to gene contamination by cross-pollination during field breeding practices.

  2. Quantitative trait loci analysis of Verticillium wilt resistance in interspecific backcross populations of Gossypium hirsutum × Gossypium barbadense.

    PubMed

    Shi, Yuzhen; Zhang, Baocai; Liu, Aiying; Li, Wentan; Li, Junwen; Lu, Quanwei; Zhang, Zhen; Li, Shaoqi; Gong, Wankui; Shang, Haihong; Gong, Juwu; Chen, Tingting; Ge, Qun; Wang, Tao; Zhu, Heqin; Liu, Zhi; Yuan, Youlu

    2016-11-05

    Verticillium wilt (VW) caused by Verticillium dahliae (Kleb) is one of the most destructive diseases of cotton. The identification of highly resistant QTLs or genes in the whole cotton genome is quite important for developing a VW-resistant variety and for further molecular design breeding. In the present study, BC 1 F 1 , BC 1 S 1 , and BC 2 F 1 populations derived from an interspecific backcross between the highly resistant line Hai1 (Gossypium barbadense L.) and the susceptible variety CCRI36 (G. hirsutum L.) as the recurrent parent were constructed. Quantitative trait loci (QTL) related to VW resistance were detected in the whole cotton genome using a high-density simple sequence repeat (SSR) genetic linkage map from the BC 1 F 1 population, with 2292 loci covering 5115.16 centiMorgan (cM) of the cotton (AD) genome, and the data concerning VW resistance that were obtained from four dates of BC 2 F 1 in the artificial disease nursery and one date of BC 1 S 1 and BC 2 F 1 in the field. A total of 48 QTLs for VW resistance were identified, and 37 of these QTLs had positive additive effects, which indicated that the G. barbadense alleles increased resistance to VW and decreased the disease index (DI) by about 2.2-10.7. These QTLs were located on 19 chromosomes, in which 33 in the A subgenome and 15 QTLs in the D subgenome. The 6 QTLs were found to be stable. The 6 QTLs were consistent with those identified previously, and another 42 were new, unreported QTLs, of which 31 QTLs were from G. barbadense. By meta-analysis, 17 QTL hotspot regions were identified and 10 of them were new, unreported hotspot regions. 29 QTLs in this paper were in 12 hotspot regions and were all from G. barbadense. These stable or consensus QTL regions warrant further investigation to better understand the genetics and molecular mechanisms underlying VW resistance. This study provides useful information for further comparative analysis and marker-assisted selection in the breeding of disease

  3. Low sociability is associated with reduced size of the corpus callosum in the BALB/cJ inbred mouse strain.

    PubMed

    Fairless, Andrew H; Dow, Holly C; Toledo, Monica M; Malkus, Kristen A; Edelmann, Michele; Li, Hongzhe; Talbot, Konrad; Arnold, Steven E; Abel, Ted; Brodkin, Edward S

    2008-09-16

    The behavioral manifestations of autism, including reduced sociability (reduced tendency to seek social interaction), may be related to underdevelopment of the corpus callosum (CC). The BALB/cJ inbred mouse strain is a useful model system for testing the relationship between reduced sociability and CC underdevelopment. BALB/cJ mice show low levels of sociability, on average, but substantial intrastrain variability in sociability, as well as striking variability in CC development. This study tested the hypothesis that sociability is positively correlated with CC size within the BALB/cJ inbred strain. 30-day-old BALB/cJ and C57BL/6J mice were tested for sociability towards gonadectomized A/J stimulus mice in a social choice task. The size of the corpus callosum was measured histologically at the midsagittal plane. BALB/cJ mice showed a significant positive correlation between the tendency to sniff the stimulus mouse and size of the CC relative to brain weight. C57BL/6J mice showed consistently high levels of sociability and normal corpus callosum development. These results suggest that abnormal white matter structure is associated with deficits in sociability in BALB/cJ mice. Additional studies are warranted to elucidate the relationship between brain connectivity and sociability in this model system.

  4. Alterations and Abnormal Mitosis of Wheat Chromosomes Induced by Wheat-Rye Monosomic Addition Lines

    PubMed Central

    Fu, Shulan; Yang, Manyu; Fei, Yunyan; Tan, Feiquan; Ren, Zhenglong; Yan, Benju; Zhang, Huaiyu; Tang, Zongxiang

    2013-01-01

    Background Wheat-rye addition lines are an old topic. However, the alterations and abnormal mitotic behaviours of wheat chromosomes caused by wheat-rye monosomic addition lines are seldom reported. Methodology/Principal Findings Octoploid triticale was derived from common wheat T. aestivum L. ‘Mianyang11’×rye S. cereale L. ‘Kustro’ and some progeny were obtained by the controlled backcrossing of triticale with ‘Mianyang11’ followed by self-fertilization. Genomic in situ hybridization (GISH) using rye genomic DNA and fluorescence in situ hybridization (FISH) using repetitive sequences pAs1 and pSc119.2 as probes were used to analyze the mitotic chromosomes of these progeny. Strong pSc119.2 FISH signals could be observed at the telomeric regions of 3DS arms in ‘Mianyang11’. However, the pSc119.2 FISH signals were disappeared from the selfed progeny of 4R monosomic addition line and the changed 3D chromosomes could be transmitted to next generation stably. In one of the selfed progeny of 7R monosomic addition line, one 2D chromosome was broken and three 4A chromosomes were observed. In the selfed progeny of 6R monosomic addition line, structural variation and abnormal mitotic behaviour of 3D chromosome were detected. Additionally, 1A and 4B chromosomes were eliminated from some of the progeny of 6R monosomic addition line. Conclusions/Significance These results indicated that single rye chromosome added to wheat might cause alterations and abnormal mitotic behaviours of wheat chromosomes and it is possible that the stress caused by single alien chromosome might be one of the factors that induced karyotype alteration of wheat. PMID:23936213

  5. Exposure to chronic variable social stress during adolescence alters affect-related behaviors and adrenocortical activity in adult male and female inbred mice.

    PubMed

    Caruso, Michael J; Kamens, Helen M; Cavigelli, Sonia A

    2017-09-01

    Rodent models provide valuable insight into mechanisms that underlie vulnerability to adverse effects of early-life challenges. Few studies have evaluated sex differences in anxiogenic or depressogenic effects of adolescent social stress in a rodent model. Furthermore, adolescent stress studies often use genetically heterogeneous outbred rodents which can lead to variable results. The current study evaluated the effects of adolescent social stress in male and female inbred (BALB/cJ) mice. Adolescent mice were exposed to repeat cycles of alternating social isolation and social novelty for 4 weeks. Adolescent social stress increased anxiety-related behaviors in both sexes and depression-related behavior in females. Locomotion/exploratory behavior was also decreased in both sexes by stress. Previously stressed adult mice produced less basal fecal corticosteroids than controls. Overall, the novel protocol induced sex-specific changes in anxiety- and depression-related behaviors and corticoid production in inbred mice. The chronic variable social stress protocol used here may be beneficial to systematically investigate sex-specific neurobiological mechanisms underlying adolescent stress vulnerability where genetic background can be controlled. © 2017 Wiley Periodicals, Inc.

  6. Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers

    USDA-ARS?s Scientific Manuscript database

    Knowledge of germplasm diversity and relationships among elite breeding materials is fundamentally important in crop improvement. We genotyped 450 maize lines developed and/or widely used by CIMMYT breeding programs both in Kenya and Zimbabwe using 1065 SNP markers to (i) investigate population stru...

  7. PA-566, A Root-knot Nematode Resistant, Pimento-type Pepper

    USDA-ARS?s Scientific Manuscript database

    The Agricultural Research Service of the U.S. Department of Agriculture has released a new, open-pollinated, breeding line of a pimento-type pepper (Capsicum annuum) designated PA-566. The new breeding line is the product of a recurrent backcross breeding procedure to incorporate the dominant N roo...

  8. Elevated mutation rates in the germ line of first- and second-generation offspring of irradiated male mice

    PubMed Central

    Barber, Ruth; Plumb, Mark A.; Boulton, Emma; Roux, Isabelle; Dubrova, Yuri E.

    2002-01-01

    Mutation rates at two expanded simple tandem repeat loci were studied in the germ line of first- and second-generation offspring of inbred male CBA/H, C57BL/6, and BALB/c mice exposed to either high linear energy transfer fission neutrons or low linear energy transfer x-rays. Paternal CBA/H exposure to either x-rays or fission neutrons resulted in increased mutation rates in the germ line of two subsequent generations. Comparable transgenerational effects were observed also in neutron-irradiated C57BL/6 and x-irradiated BALB/c mice. The levels of spontaneous mutation rates and radiation-induced transgenerational instability varied between strains (BALB/c>CBA/H>C57BL/6). Pre- and postmeiotic paternal exposure resulted in similar increases in mutation rate in the germ line of both generations of CBA/H mice, which together with our previous results suggests that radiation-induced expanded simple tandem repeat instability is manifested in diploid cells after fertilization. The remarkable finding that radiation-induced germ-line instability persists for at least two generations raises important issues of risk evaluation in humans. PMID:11997464

  9. Detection of quantitative trait loci controlling grain zinc concentration using Australian wild rice, Oryza meridionalis, a potential genetic resource for biofortification of rice.

    PubMed

    Ishikawa, Ryo; Iwata, Masahide; Taniko, Kenta; Monden, Gotaro; Miyazaki, Naoya; Orn, Chhourn; Tsujimura, Yuki; Yoshida, Shusaku; Ma, Jian Feng; Ishii, Takashige

    2017-01-01

    Zinc (Zn) is one of the essential mineral elements for both plants and humans. Zn deficiency in human is one of the major causes of hidden hunger, a serious health problem observed in many developing countries. Therefore, increasing Zn concentration in edible part is an important issue for improving human Zn nutrition. Here, we found that an Australian wild rice O. meridionalis showed higher grain Zn concentrations compared with cultivated and other wild rice species. The quantitative trait loci (QTL) analysis was then performed to identify the genomic regions controlling grain Zn levels using backcross recombinant inbred lines derived from O. sativa 'Nipponbare' and O. meridionalis W1627. Four QTLs responsible for high grain Zn were detected on chromosomes 2, 9, and 10. The QTL on the chromosome 9 (named qGZn9), which showed the largest effect on grain Zn concentration was confirmed with the introgression line, which had a W1627 chromosomal segment covering the qGZn9 region in the genetic background of O. sativa 'Nipponbare'. Fine mapping of this QTL resulted in identification of two tightly linked loci, qGZn9a and qGZn9b. The candidate regions of qGZn9a and qGZn9b were estimated to be 190 and 950 kb, respectively. Furthermore, we also found that plants having a wild chromosomal segment covering qGZn9a, but not qGZn9b, is associated with fertility reduction. qGZn9b, therefore, provides a valuable allele for breeding rice with high Zn in the grains.

  10. Combined linkage and association mapping of flowering time in Sunflower (Helianthus annuus L.).

    PubMed

    Cadic, Elena; Coque, Marie; Vear, Felicity; Grezes-Besset, Bruno; Pauquet, Jerôme; Piquemal, Joël; Lippi, Yannick; Blanchard, Philippe; Romestant, Michel; Pouilly, Nicolas; Rengel, David; Gouzy, Jerôme; Langlade, Nicolas; Mangin, Brigitte; Vincourt, Patrick

    2013-05-01

    Association mapping and linkage mapping were used to identify quantitative trait loci (QTL) and/or causative mutations involved in the control of flowering time in cultivated sunflower Helianthus annuus. A panel of 384 inbred lines was phenotyped through testcrosses with two tester inbred lines across 15 location × year combinations. A recombinant inbred line (RIL) population comprising 273 lines was phenotyped both per se and through testcrosses with one or two testers in 16 location × year combinations. In the association mapping approach, kinship estimation using 5,923 single nucleotide polymorphisms was found to be the best covariate to correct for effects of panel structure. Linkage disequilibrium decay ranged from 0.08 to 0.26 cM for a threshold of 0.20, after correcting for structure effects, depending on the linkage group (LG) and the ancestry of inbred lines. A possible hitchhiking effect is hypothesized for LG10 and LG08. A total of 11 regions across 10 LGs were found to be associated with flowering time, and QTLs were mapped on 11 LGs in the RIL population. Whereas eight regions were demonstrated to be common between the two approaches, the linkage disequilibrium approach did not detect a documented QTL that was confirmed using the linkage mapping approach.

  11. Mitochondrial DNA transfer to the nucleus generates extensive insertion site variation in maize.

    PubMed

    Lough, Ashley N; Roark, Leah M; Kato, Akio; Ream, Thomas S; Lamb, Jonathan C; Birchler, James A; Newton, Kathleen J

    2008-01-01

    Mitochondrial DNA (mtDNA) insertions into nuclear chromosomes have been documented in a number of eukaryotes. We used fluorescence in situ hybridization (FISH) to examine the variation of mtDNA insertions in maize. Twenty overlapping cosmids, representing the 570-kb maize mitochondrial genome, were individually labeled and hybridized to root tip metaphase chromosomes from the B73 inbred line. A minimum of 15 mtDNA insertion sites on nine chromosomes were detectable using this method. One site near the centromere on chromosome arm 9L was identified by a majority of the cosmids. To examine variation in nuclear mitochondrial DNA sequences (NUMTs), a mixture of labeled cosmids was applied to chromosome spreads of ten diverse inbred lines: A188, A632, B37, B73, BMS, KYS, Mo17, Oh43, W22, and W23. The number of detectable NUMTs varied dramatically among the lines. None of the tested inbred lines other than B73 showed the strong hybridization signal on 9L, suggesting that there is a recent mtDNA insertion at this site in B73. Different sources of B73 and W23 were examined for NUMT variation within inbred lines. Differences were detectable, suggesting either that mtDNA is being incorporated or lost from the maize nuclear genome continuously. The results indicate that mtDNA insertions represent a major source of nuclear chromosomal variation.

  12. The Development of Quality Control Genotyping Approaches: A Case Study Using Elite Maize Lines.

    PubMed

    Chen, Jiafa; Zavala, Cristian; Ortega, Noemi; Petroli, Cesar; Franco, Jorge; Burgueño, Juan; Costich, Denise E; Hearne, Sarah J

    2016-01-01

    Quality control (QC) of germplasm identity and purity is a critical component of breeding and conservation activities. SNP genotyping technologies and increased availability of markers provide the opportunity to employ genotyping as a low-cost and robust component of this QC. In the public sector available low-cost SNP QC genotyping methods have been developed from a very limited panel of markers of 1,000 to 1,500 markers without broad selection of the most informative SNPs. Selection of optimal SNPs and definition of appropriate germplasm sampling in addition to platform section impact on logistical and resource-use considerations for breeding and conservation applications when mainstreaming QC. In order to address these issues, we evaluated the selection and use of SNPs for QC applications from large DArTSeq data sets generated from CIMMYT maize inbred lines (CMLs). Two QC genotyping strategies were developed, the first is a "rapid QC", employing a small number of SNPs to identify potential mislabeling of seed packages or plots, the second is a "broad QC", employing a larger number of SNP, used to identify each germplasm entry and to measure heterogeneity. The optimal marker selection strategies combined the selection of markers with high minor allele frequency, sampling of clustered SNP in proportion to marker cluster distance and selecting markers that maintain a uniform genomic distribution. The rapid and broad QC SNP panels selected using this approach were further validated using blind test assessments of related re-generation samples. The influence of sampling within each line was evaluated. Sampling 192 individuals would result in close to 100% possibility of detecting a 5% contamination in the entry, and approximately a 98% probability to detect a 2% contamination of the line. These results provide a framework for the establishment of QC genotyping. A comparison of financial and time costs for use of these approaches across different platforms is

  13. Aluminium tolerance of root hairs underlies genotypic differences in rhizosheath size of wheat (Triticum aestivum) grown on acid soil.

    PubMed

    Delhaize, Emmanuel; James, Richard A; Ryan, Peter R

    2012-08-01

    We found significant genetic variation in the ability of wheat (Triticum aestivum) to form rhizosheaths on acid soil and assessed whether differences in aluminium (Al(3+) ) tolerance of root hairs between genotypes was the physiological basis for this genetic variation. A method was developed to rapidly screen rhizosheath size in a range of wheat genotypes. Backcrossed populations were generated from cv Fronteira (large rhizosheath) using cv EGA-Burke (small rhizosheath) as the recurrent parent. A positive correlation existed between rhizosheath size on acid soil and root hair length. In hydroponic experiments, root hairs of the backcrossed lines with large rhizosheaths were more tolerant of Al(3+) toxicity than the backcrossed lines with small rhizosheaths. We conclude that greater Al(3+) tolerance of root hairs underlies the larger rhizosheath of wheat grown on acid soil. Tolerance of the root hairs to Al(3+) was largely independent of the TaALMT1 gene which suggests that different genes encode the Al(3+) tolerance of root hairs. The maintenance of longer root hairs in acid soils is important for the efficient uptake of water and nutrients. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

  14. BXD recombinant inbred strains participate in social preference, anxiety and depression behaviors along sex-differences in cytokines and tactile allodynia.

    PubMed

    López-Granero, Caridad; Antunes Dos Santos, Alessandra; Ferrer, Beatriz; Culbreth, Megan; Chakraborty, Sudipta; Barrasa, Angel; Gulinello, Maria; Bowman, Aaron B; Aschner, Michael

    2017-06-01

    Depression and anxiety are the most common psychiatric disorders, representing a major public health concern. Dysregulation of oxidative and inflammatory systems may be associated with psychiatric disorders, such as depression and anxiety. Due to the need to find appropriate animal models to the understanding of such disorders, we queried whether 2 BXD recombinant inbred (RI) mice strains (BXD21/TyJ RI and BXD84/RwwJ RI mice) and C57BL/6 wild-type mice show differential performance in depression and anxiety related behaviors and biomarkers. Specifically, we assessed social preference, elevated plus maze, forced swim, and Von Frey tests at 3-4 months-of-age, as well as activation of cytokines and antioxidant mRNA levels in the cortex at 7 months-of-age. We report that (1) the BXD84/RwwJ RI strain exhibits anxiety disorder and social avoidance-like behavior (2) BXD21/TyJ RI strain shows a resistance to depression illness, and (3) sex-dependent cytokine profiles and allodynia with elevated inflammatory activity were inherent to male BXD21/TyJ RI mice. In conclusion, we provide novel data in favor of the use of BXD recombinant inbred mice to further understand anxiety and depression disorders. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Severe inbreeding depression and no evidence of purging in an extremely inbred wild species--the Chatham Island black robin.

    PubMed

    Kennedy, Euan S; Grueber, Catherine E; Duncan, Richard P; Jamieson, Ian G

    2014-04-01

    Although evidence of inbreeding depression in wild populations is well established, the impact of genetic purging in the wild remains controversial. The contrasting effects of inbreeding depression, fixation of deleterious alleles by genetic drift, and the purging of deleterious alleles via natural selection mean that predicting fitness outcomes in populations subjected to prolonged bottlenecks is not straightforward. We report results from a long-term pedigree study of arguably the world's most inbred wild species of bird: the Chatham Island black robin Petroica traversi, in which conditions were ideal for purging to occur. Contrary to expectations, black robins showed a strong, negative relationship between inbreeding and juvenile survival, yielding lethal equivalents (2B) of 6.85. We also determined that the negative relationship between inbreeding and survival did not appear to be mediated by levels of ancestral inbreeding and may be attributed in part to unpurged lethal recessives. Although the black robin demographic history provided ideal conditions for genetic purging, our results show no clear evidence of purging in the major life-history trait of juvenile survival. Our results also show no evidence of fixation of deleterious alleles in juvenile survival, but do confirm that continued high levels of contemporary inbreeding in a historically inbred population could lead to additional severe inbreeding depression. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  16. Identification of minor effect QTLs for plant architecture related traits using super high density genotyping and large recombinant inbred population in maize (Zea mays).

    PubMed

    Wang, Baobao; Liu, Han; Liu, Zhipeng; Dong, Xiaomei; Guo, Jinjie; Li, Wei; Chen, Jing; Gao, Chi; Zhu, Yanbin; Zheng, Xinmei; Chen, Zongliang; Chen, Jian; Song, Weibin; Hauck, Andrew; Lai, Jinsheng

    2018-01-18

    Plant Architecture Related Traits (PATs) are of great importance for maize breeding, and mainly controlled by minor effect quantitative trait loci (QTLs). However, cloning or even fine-mapping of minor effect QTLs is very difficult in maize. Theoretically, large population and high density genetic map can be helpful for increasing QTL mapping resolution and accuracy, but such a possibility have not been actually tested. Here, we employed a genotyping-by-sequencing (GBS) strategy to construct a linkage map with 16,769 marker bins for 1021 recombinant inbred lines (RILs). Accurately mapping of well studied genes P1, pl1 and r1 underlying silk color demonstrated the map quality. After QTL analysis, a total of 51 loci were mapped for six PATs. Although all of them belong to minor effect alleles, the lengths of the QTL intervals, with a minimum and median of 1.03 and 3.40 Mb respectively, were remarkably reduced as compared with previous reports using smaller size of population or small number of markers. Several genes with known function in maize were shown to be overlapping with or close neighboring to these QTL peaks, including na1, td1, d3 for plant height, ra1 for tassel branch number, and zfl2 for tassel length. To further confirm our mapping results, a plant height QTL, qPH1a, was verified by an introgression lines (ILs). We demonstrated a method for high resolution mapping of minor effect QTLs in maize, and the resulted comprehensive QTLs for PATs are valuable for maize molecular breeding in the future.

  17. QTL mapping for grain yield, flowering time, and stay-green traits in sorghum with genotyping-by-sequencing markers

    USDA-ARS?s Scientific Manuscript database

    Molecular breeding can complement traditional breeding approaches to achieve genetic gains in a more efficient way. In the present study, genetic mapping was conducted in a sorghum recombinant inbred line (RIL) population developed from Tx436 (a non-stay-green high food quality inbred) × 00MN7645 (a...

  18. Resistance to Fusarium verticillioides and fumonisin accumulation in maize inbred lines involves an earlier and enhanced expression of lipoxygenase (LOX) genes.

    PubMed

    Maschietto, Valentina; Marocco, Adriano; Malachova, Alexandra; Lanubile, Alessandra

    2015-09-01

    Fusarium verticillioides causes ear rot in maize and contaminates the kernels with the fumonisin mycotoxins. It is known that plant lipoxygenase (LOX)-derived oxylipins regulate defence against pathogens and that the host-pathogen lipid cross-talk influences the pathogenesis. The expression profiles of fifteen genes of the LOX pathway were studied in kernels of resistant and susceptible maize lines, grown in field condition, at 3, 7 and 14 days post inoculation (dpi) with F. verticillioides. Plant defence responses were correlated with the pathogen growth, the expression profiles of fungal FUM genes for fumonisin biosynthesis and fumonisin content in the kernels. The resistant genotype limited fungal growth and fumonisin accumulation between 7 and 14 dpi. Pathogen growth became exponential in the susceptible line after 7 dpi, in correspondence with massive transcription of FUM genes and fumonisins augmented exponentially at 14 dpi. LOX pathway genes resulted strongly induced after pathogen inoculation in the resistant line at 3 and 7 dpi, whilst in the susceptible line the induction was reduced or delayed at 14 dpi. In addition, all genes resulted overexpressed before infection in kernels of the resistant genotype already at 3 dpi. The results suggest that resistance in maize may depend on an earlier activation of LOX genes and genes for jasmonic acid biosynthesis. Copyright © 2015 Elsevier GmbH. All rights reserved.

  19. Genetic rescue in an inbred Arctic fox (Vulpes lagopus) population.

    PubMed

    Hasselgren, Malin; Angerbjörn, Anders; Eide, Nina E; Erlandsson, Rasmus; Flagstad, Øystein; Landa, Arild; Wallén, Johan; Norén, Karin

    2018-03-28

    Isolation of small populations can reduce fitness through inbreeding depression and impede population growth. Outcrossing with only a few unrelated individuals can increase demographic and genetic viability substantially, but few studies have documented such genetic rescue in natural mammal populations. We investigate the effects of immigration in a subpopulation of the endangered Scandinavian arctic fox ( Vulpes lagopus ), founded by six individuals and isolated for 9 years at an extremely small population size. Based on a long-term pedigree (105 litters, 543 individuals) combined with individual fitness traits, we found evidence for genetic rescue. Natural immigration and gene flow of three outbred males in 2010 resulted in a reduction in population average inbreeding coefficient ( f ), from 0.14 to 0.08 within 5 years. Genetic rescue was further supported by 1.9 times higher juvenile survival and 1.3 times higher breeding success in immigrant first-generation offspring compared with inbred offspring. Five years after immigration, the population had more than doubled in size and allelic richness increased by 41%. This is one of few studies that has documented genetic rescue in a natural mammal population suffering from inbreeding depression and contributes to a growing body of data demonstrating the vital connection between genetics and individual fitness. © 2018 The Author(s).

  20. Oestrous synchronization, ovarian superovulation and intraspecific transfers from a closed breeding colony of inbred SLA miniature pigs.

    PubMed

    Arlaud, J J; Baker, L; Williams, R L; French, A J

    2010-12-01

    The inbred SLA miniature pig is a unique animal model developed for organ transplantation studies and pre-clinical experimental purposes. Reported oestrous synchronization and superovulation treatments were examined in two SLA haplotypes (AA and DD) to allow collection of embryos for both practical embryo transfer and experimental technologies from a closed breeding colony. Pre-puberal miniature pigs were poor responders to oestrous synchronization treatments, while post-puberal sows were equivalent to commercial sows. Following superovulation, the ovulation number (corpora .hemorrhagica) was higher (p < 0.05) in the cycling sows when compared with non-cycling sows. Ovulations were equivalent to commercial pre-puberal gilts and non-cycling sows (p > 0.05). No difference in ovulation number between haplotypes was observed, which differs from the previous report (DD>AA). Collection of zygotes for pronuclear injection was the highest in the non-cycling post-puberal miniature pig group (p < 0.05), although significantly lower when compared with the commercial pig treatment groups (p < 0.05). The incidence of cystic endometrial hyperplasia in our colony was equivalent to rates observed in commercial pigs. Pronuclear visualization following centrifugation was the highest in the non-cycling miniature sow group and approximates to about 25% of ovulations and about half the rate observed in the commercial pigs (50%). Miniature pig embryos transferred between SLA haplotypes and transfer of DD embryos to commercial pigs resulted in live births at a higher efficiency than previously reported. This study demonstrates the feasibility of undertaking assisted reproductive technologies in a closed breeding colony of inbred SLA miniature pigs without compromise to the breeding programmes. © 2009 Blackwell Verlag GmbH.

  1. A quantitative analysis of the effects of qualitatively different reinforcers on fixed ratio responding in inbred strains of mice

    PubMed Central

    Hutsell, Blake A.; Newland, M. Christopher

    2013-01-01

    Previous studies of inbred mouse strains have shown reinforcer-strain interactions that may potentially mask differences among strains in memory performance. The present research examined the effects of two qualitatively different reinforcers (heterogeneous mix of flavored pellets and sweetened-condensed milk) on responding maintained by fixed-ratio schedules of reinforcement in three inbred strains of mice (BALB/c, C57BL/6, & DBA/2). Responses rates for all strains were a bitonic (inverted U) function of the size of the fixed-ratio schedule and were generally higher when responding was maintained by milk. For the DBA/2 and C57BL/6 and to a lesser extent the BALB/c, milk primarily increased response rates at moderate fixed ratios, but not at the largest fixed ratios tested. A formal model of ratio-schedule performance, Mathematical Principles of Reinforcement (MPR), was applied to the response rate functions of individual mice. According to MPR, the differences in response rates maintained by pellets and milk were mostly due to changes in motoric processes as indicated by changes in the minimum response time (δ) produced by each reinforcer type and not specific activation (a), a model term that represents value and is correlated with reinforcer magnitude and the break point obtained under progressive ratio schedules. In addition, MPR also revealed that, although affected by reinforcer type, a parameter interpreted as the rate of saturation of working memory (λ), differed among the strains. PMID:23357283

  2. Introgression and pyramiding into common bean market class fabada of genes conferring resistance to anthracnose and potyvirus.

    PubMed

    Ferreira, Juan José; Campa, Ana; Pérez-Vega, Elena; Rodríguez-Suárez, Cristina; Giraldez, Ramón

    2012-03-01

    Anthracnose and bean common mosaic (BCM) are considered major diseases in common bean crop causing severe yield losses worldwide. This work describes the introgression and pyramiding of genes conferring genetic resistance to BCM and anthracnose local races into line A25, a bean genotype classified as market class fabada. Resistant plants were selected using resistance tests or combining resistance tests and marker-assisted selection. Lines A252, A321, A493, Sanilac BC6-Are, and BRB130 were used as resistance sources. Resistance genes to anthracnose (Co-2 ( C ), Co-2 ( A252 ) and Co-3/9) and/or BCM (I and bc-3) were introgressed in line A25 through six parallel backcrossing programs, and six breeding lines showing a fabada seed phenotype were obtained after six backcross generations: line A1258 from A252; A1231 from A321; A1220 from A493; A1183 and A1878 from Sanilac BC6-Are; and line A2418 from BRB130. Pyramiding of different genes were developed using the pedigree method from a single cross between lines obtained in the introgression step: line A1699 (derived from cross A1258 × A1220), A2438 (A1220 × A1183), A2806 (A1878 × A2418), and A3308 (A1699 × A2806). A characterization based on eight morpho-agronomic traits revealed a limited differentiation among the obtained breeding lines and the recurrent line A25. However, using a set of seven molecular markers linked to the loci used in the breeding programs it was possible to differentiate the 11 fabada lines. Considering the genetic control of the resistance in resistant donor lines, the observed segregations in the last backcrossing generation, the reaction against the pathogens, and the expression of the molecular markers it was also possible to infer the genotype conferring resistance in the ten fabada breeding lines obtained. As a result of these breeding programs, genetic resistance to three anthracnose races controlled by genes included in clusters Co-2 and Co-3/9, and genetic resistance to BCM controlled

  3. Novel Mechanisms Revealed in the Trachea Transcriptome of Resistant and Susceptible Chicken Lines following Infection with Newcastle Disease Virus.

    PubMed

    Deist, Melissa S; Gallardo, Rodrigo A; Bunn, David A; Kelly, Terra R; Dekkers, Jack C M; Zhou, Huaijun; Lamont, Susan J

    2017-05-01

    Newcastle disease virus (NDV) has a devastating impact on poultry production in developing countries. This study examined the transcriptome of tracheal epithelial cells from two inbred chicken lines that differ in NDV susceptibility after challenge with a high-titer inoculum of lentogenic NDV. The Fayoumi line had a significantly lower NDV load postchallenge than the Leghorn line, demonstrating the Fayoumi line's classification as a relatively NDV-resistant breed. Examination of the trachea transcriptome showed a large increase in immune cell infiltration in the trachea in both lines at all times postinfection. The pathways conserved across lines and at all three time points postinfection included iCOS-iCOSL signaling in T helper cells, NF-κB signaling, the role of nuclear factor of activated T cells in the regulation of the immune response, calcium-induced T lymphocyte apoptosis, phospholipase C signaling, and CD28 signaling in T helper cells. Although shared pathways were seen in the Fayoumi and Leghorn lines, each line showed unique responses as well. The downregulation of collagen and the activation of eukaryotic translation initiation factor 2 signaling in the Fayoumis relative to the Leghorns at 2 days postinfection may contribute to the resistance phenotype seen in the Fayoumis. This study provides a further understanding of host-pathogen interactions which could improve vaccine efficacy and, in combination with genome-wide association studies, has the potential to advance strategies for breeding chickens with enhanced resistance to NDV. Copyright © 2017 Deist et al.

  4. Novel Mechanisms Revealed in the Trachea Transcriptome of Resistant and Susceptible Chicken Lines following Infection with Newcastle Disease Virus

    PubMed Central

    Gallardo, Rodrigo A.; Bunn, David A.; Kelly, Terra R.; Dekkers, Jack C. M.; Zhou, Huaijun

    2017-01-01

    ABSTRACT Newcastle disease virus (NDV) has a devastating impact on poultry production in developing countries. This study examined the transcriptome of tracheal epithelial cells from two inbred chicken lines that differ in NDV susceptibility after challenge with a high-titer inoculum of lentogenic NDV. The Fayoumi line had a significantly lower NDV load postchallenge than the Leghorn line, demonstrating the Fayoumi line's classification as a relatively NDV-resistant breed. Examination of the trachea transcriptome showed a large increase in immune cell infiltration in the trachea in both lines at all times postinfection. The pathways conserved across lines and at all three time points postinfection included iCOS-iCOSL signaling in T helper cells, NF-κB signaling, the role of nuclear factor of activated T cells in the regulation of the immune response, calcium-induced T lymphocyte apoptosis, phospholipase C signaling, and CD28 signaling in T helper cells. Although shared pathways were seen in the Fayoumi and Leghorn lines, each line showed unique responses as well. The downregulation of collagen and the activation of eukaryotic translation initiation factor 2 signaling in the Fayoumis relative to the Leghorns at 2 days postinfection may contribute to the resistance phenotype seen in the Fayoumis. This study provides a further understanding of host-pathogen interactions which could improve vaccine efficacy and, in combination with genome-wide association studies, has the potential to advance strategies for breeding chickens with enhanced resistance to NDV. PMID:28331077

  5. Inbred or Outbred? Genetic Diversity in Laboratory Rodent Colonies

    PubMed Central

    Brekke, Thomas D.; Steele, Katherine A.; Mulley, John F.

    2017-01-01

    Nonmodel rodents are widely used as subjects for both basic and applied biological research, but the genetic diversity of the study individuals is rarely quantified. University-housed colonies tend to be small and subject to founder effects and genetic drift; so they may be highly inbred or show substantial genetic divergence from other colonies, even those derived from the same source. Disregard for the levels of genetic diversity in an animal colony may result in a failure to replicate results if a different colony is used to repeat an experiment, as different colonies may have fixed alternative variants. Here we use high throughput sequencing to demonstrate genetic divergence in three isolated colonies of Mongolian gerbil (Meriones unguiculatus) even though they were all established recently from the same source. We also show that genetic diversity in allegedly “outbred” colonies of nonmodel rodents (gerbils, hamsters, house mice, deer mice, and rats) varies considerably from nearly no segregating diversity to very high levels of polymorphism. We conclude that genetic divergence in isolated colonies may play an important role in the “replication crisis.” In a more positive light, divergent rodent colonies represent an opportunity to leverage genetically distinct individuals in genetic crossing experiments. In sum, awareness of the genetic diversity of an animal colony is paramount as it allows researchers to properly replicate experiments and also to capitalize on other genetically distinct individuals to explore the genetic basis of a trait. PMID:29242387

  6. Reward-Related Behavioral Paradigms for Addiction Research in the Mouse: Performance of Common Inbred Strains

    PubMed Central

    Feyder, Michael; Brigman, Jonathan L.; Crombag, Hans S.; Saksida, Lisa M.; Bussey, Timothy J.; Holmes, Andrew

    2011-01-01

    The mouse has emerged as a uniquely valuable species for studying the molecular and genetic basis of complex behaviors and modeling neuropsychiatric disease states. While valid and reliable preclinical assays for reward-related behaviors are critical to understanding addiction-related processes, and various behavioral procedures have been developed and characterized in rats and primates, there have been relatively few studies using operant-based addiction-relevant behavioral paradigms in the mouse. Here we describe the performance of the C57BL/6J inbred mouse strain on three major reward-related paradigms, and replicate the same procedures in two other commonly used inbred strains (DBA/2J, BALB/cJ). We examined Pavlovian-instrumental transfer (PIT) by measuring the ability of an auditory cue associated with food reward to promote an instrumental (lever press) response. In a separate experiment, we assessed the acquisition and extinction of a simple stimulus-reward instrumental behavior on a touchscreen-based task. Reinstatement of this behavior was then examined following either continuous exposure to cues (conditioned reinforcers, CRs) associated with reward, brief reward and CR exposure, or brief reward exposure followed by continuous CR exposure. The third paradigm examined sensitivity of an instrumental (lever press) response to devaluation of food reward (a probe for outcome insensitive, habitual behavior) by repeated pairing with malaise. Results showed that C57BL/6J mice displayed robust PIT, as well as clear extinction and reinstatement, but were insensitive to reinforcer devaluation. DBA/2J mice showed good PIT and (rewarded) reinstatement, but were slow to extinguish and did not show reinforcer devaluation or significant CR-reinstatement. BALB/cJ mice also displayed good PIT, extinction and reinstatement, and retained instrumental responding following devaluation, but, unlike the other strains, demonstrated reduced Pavlovian approach behavior (food

  7. Reward-related behavioral paradigms for addiction research in the mouse: performance of common inbred strains.

    PubMed

    Lederle, Lauren; Weber, Susanna; Wright, Tara; Feyder, Michael; Brigman, Jonathan L; Crombag, Hans S; Saksida, Lisa M; Bussey, Timothy J; Holmes, Andrew

    2011-01-10

    The mouse has emerged as a uniquely valuable species for studying the molecular and genetic basis of complex behaviors and modeling neuropsychiatric disease states. While valid and reliable preclinical assays for reward-related behaviors are critical to understanding addiction-related processes, and various behavioral procedures have been developed and characterized in rats and primates, there have been relatively few studies using operant-based addiction-relevant behavioral paradigms in the mouse. Here we describe the performance of the C57BL/6J inbred mouse strain on three major reward-related paradigms, and replicate the same procedures in two other commonly used inbred strains (DBA/2J, BALB/cJ). We examined Pavlovian-instrumental transfer (PIT) by measuring the ability of an auditory cue associated with food reward to promote an instrumental (lever press) response. In a separate experiment, we assessed the acquisition and extinction of a simple stimulus-reward instrumental behavior on a touch screen based task. Reinstatement of this behavior was then examined following either continuous exposure to cues (conditioned reinforcers, CRs) associated with reward, brief reward and CR exposure, or brief reward exposure followed by continuous CR exposure. The third paradigm examined sensitivity of an instrumental (lever press) response to devaluation of food reward (a probe for outcome insensitive, habitual behavior) by repeated pairing with malaise. Results showed that C57BL/6J mice displayed robust PIT, as well as clear extinction and reinstatement, but were insensitive to reinforcer devaluation. DBA/2J mice showed good PIT and (rewarded) reinstatement, but were slow to extinguish and did not show reinforcer devaluation or significant CR-reinstatement. BALB/cJ mice also displayed good PIT, extinction and reinstatement, and retained instrumental responding following devaluation, but, unlike the other strains, demonstrated reduced Pavlovian approach behavior (food

  8. Phenotypic integration among trabecular and cortical bone traits establishes mechanical functionality of inbred mouse vertebrae.

    PubMed

    Tommasini, Steven M; Hu, Bin; Nadeau, Joseph H; Jepsen, Karl J

    2009-04-01

    Conventional approaches to identifying quantitative trait loci (QTLs) regulating bone mass and fragility are limited because they examine cortical and trabecular traits independently. Prior work examining long bones from young adult mice and humans indicated that skeletal traits are functionally related and that compensatory interactions among morphological and compositional traits are critical for establishing mechanical function. However, it is not known whether trait covariation (i.e., phenotypic integration) also is important for establishing mechanical function in more complex, corticocancellous structures. Covariation among trabecular, cortical, and compositional bone traits was examined in the context of mechanical functionality for L(4) vertebral bodies across a panel of 16-wk-old female AXB/BXA recombinant inbred (RI) mouse strains. The unique pattern of randomization of the A/J and C57BL/6J (B6) genome among the RI panel provides a powerful tool that can be used to measure the tendency for different traits to covary and to study the biology of complex traits. We tested the hypothesis that genetic variants affecting vertebral size and mass are buffered by changes in the relative amounts of cortical and trabecular bone and overall mineralization. Despite inheriting random sets of A/J and B6 genomes, the RI strains inherited nonrandom sets of cortical and trabecular bone traits. Path analysis, which is a multivariate analysis that shows how multiple traits covary simultaneously when confounding variables like body size are taken into consideration, showed that RI strains that tended to have smaller vertebrae relative to body size achieved mechanical functionality by increasing mineralization and the relative amounts of cortical and trabecular bone. The interdependence among corticocancellous traits in the vertebral body indicated that variation in trabecular bone traits among inbred mouse strains, which is often thought to arise from genetic factors, is also

  9. Genetic analysis in a variant of limb girdle muscular dystrophy in an inbred aboriginal community

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Greenberg, C.R.; Nylen, E.G.; Halliday, W.

    1994-09-01

    Limb girdle muscular dystrophy (LGMD) is a heterogeneous group of disorders with variable inheritance patterns, age-of-onset, rates of progression and patterns of muscle involvement. To date, 4 different chromosomal assignments have been described; LGMD1 to chromosome 5q, LGMD2 to chromosome 15q, SCARMD to chromosome 13q and a fourth locus on chromosome 2p. Because of this genetic heterogeneity, only large unambiguous multiplex families which are clearly linked to a particular locus can be utilized in a genetic analysis. We now report preliminary findings in a large highly inbred aboriginal kindred with 8 probands (5 females, 3 males) from 6 nuclear familiesmore » with a progressive LMD. All presented in their mid- to late teens with gait disturbances. At time of presentation all except one had both proximal as well as distal muscle involvement, facial muscle sparing, CK levels 25 to 100 times normal (3762-20,400 U/l), dystrophic muscle biopsies and normal dystrophin and dystrophin-associated glycoprotein expression. We have studied the segregation of highly informative microsatellite markers for FBN1, D15S132 and the gene for thrombospondin on chromosome 15q and D2S134, D2S136, D2S147, and D2S166 on chromosome 2. Linkage to chromosome 15q has been excluded and two-point lod scores are not significant as yet to either confirm or exclude linkage to chromosome 2p. However, visual inspection reveals that affected individuals are not consistently homozygous for the chromosome 2p markers as would be predicted in such an inbred population. Clinically, SCARMD is unlikely and if the locus on chromosomes 2p and 5q can also be excluded, a genome-wide search using evenly spaced microsatellites will be initiated. A second geographically distinct aboriginal kindred with a similar clinical phenotype has now also been identified.« less

  10. Up-regulating the abscisic acid inactivation gene ZmABA8ox1b contributes to seed germination heterosis by promoting cell expansion.

    PubMed

    Li, Yangyang; Wang, Cheng; Liu, Xinye; Song, Jian; Li, Hongjian; Sui, Zhipeng; Zhang, Ming; Fang, Shuang; Chu, Jinfang; Xin, Mingming; Xie, Chaojie; Zhang, Yirong; Sun, Qixin; Ni, Zhongfu

    2016-04-01

    Heterosis has been widely used in agriculture, but the underlying molecular principles are still largely unknown. During seed germination, we observed that maize (Zea mays) hybrid B73/Mo17 was less sensitive than its parental inbred lines to exogenous abscisic acid (ABA), and endogenous ABA content in hybrid embryos decreased more rapidly than in the parental inbred lines. ZmABA8ox1b, an ABA inactivation gene, was consistently more highly up-regulated in hybrid B73/Mo17 than in its parental inbred lines at early stages of seed germination. Moreover, ectopic expression of ZmABA8ox1b obviously promoted seed germination in Arabidopsis Remarkably, microscopic observation revealed that cell expansion played a major role in the ABA-mediated maize seed germination heterosis, which could be attributed to the altered expression of cell wall-related genes. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  11. Linkage studies on 13 biochemical loci and 2 coat color loci in a [(BN x TM) x TM] backcross progeny of the rat (Rattus norvegicus).

    PubMed

    Yamada, J; Hamada, S; Bender, K; Adams, M

    1986-10-01

    In a [(BN X TM) X TM] backcross progeny of rats, nine significant linkage associations were found among 105 pairwise combinations of 15 loci. After comparing this with other published data and data of personal communications, we considered that the d gene we tentatively designated may be identical to the gene for pink-eyed dilution (p), and that the associations of Gc-Hbb, RT1-h, and Gc-Fh were due to chance rather than real linkage. The linkages obtained in this study, therefore, were Hbb-p (26.5 +/- 5.5) in LG I, Mup-1-Acon-1 (12.5 +/- 4.1) in LG II, Hao-1-Svp-1 (23.8 +/- 6.6) in LG IV, Es-1-Es-3 (17.2 +/- 4.7) in LG V, h-Gc (10.9 +/- 3.3) in LG VI, and Fh-Pep-3 (32.3 +/- 5.9) in LG X.

  12. Phenotypic characterization of the Komeda miniature rat Ishikawa, an animal model of dwarfism caused by a mutation in Prkg2.

    PubMed

    Tsuchida, Atsuko; Yokoi, Norihide; Namae, Misako; Fuse, Masanori; Masuyama, Taku; Sasaki, Masashi; Kawazu, Shoji; Komeda, Kajuro

    2008-12-01

    The Komeda miniature rat Ishikawa (KMI) is a spontaneous animal model of dwarfism caused by a mutation in Prkg2, which encodes cGMP-dependent protein kinase type II (cGKII). This strain has been maintained as a segregating inbred strain for the mutated allele mri. In this study, we characterized the phenotype of the KMI strain, particularly growth traits, craniofacial measurements, and organ weights. The homozygous mutant (mri/mri) animals were approximately 70% to 80% of the size of normal, heterozygous (mri/+) animals in regard to body length, weight, and naso-occipital length of the calvarium, and the retroperitoneal fat of mri/mri rats was reduced greatly. In addition, among progeny of the (BNxKMI-mri/mri)F1xKMI-mri/mri backcross, animals with the KMI phenotype (mri/mri) were easily distinguished from those showing the wild-type phenotype (mri/+) by using growth traits such as body length and weight. Genetic analysis revealed that all of the backcrossed progeny exhibiting the KMI phenotype were homozygous for the KMI allele in the 1.2-cM region between D14Rat5 and D14Rat80 on chromosome 14, suggesting strongly that mri acts in a completely recessive manner. The KMI strain is the first and only rat model with a confirmed mutation in Prkg2 and is a valuable model for studying dwarfism and longitudinal growth traits in humans and for functional studies of cGKII.

  13. Phenotypic Characterization of the Komeda Miniature Rat Ishikawa, an Animal Model of Dwarfism Caused by a Mutation in Prkg2

    PubMed Central

    Tsuchida, Atsuko; Yokoi, Norihide; Namae, Misako; Fuse, Masanori; Masuyama, Taku; Sasaki, Masashi; Kawazu, Shoji; Komeda, Kajuro

    2008-01-01

    The Komeda miniature rat Ishikawa (KMI) is a spontaneous animal model of dwarfism caused by a mutation in Prkg2, which encodes cGMP-dependent protein kinase type II (cGKII). This strain has been maintained as a segregating inbred strain for the mutated allele mri. In this study, we characterized the phenotype of the KMI strain, particularly growth traits, craniofacial measurements, and organ weights. The homozygous mutant (mri/mri) animals were approximately 70% to 80% of the size of normal, heterozygous (mri/+) animals in regard to body length, weight, and naso-occipital length of the calvarium, and the retroperitoneal fat of mri/mri rats was reduced greatly. In addition, among progeny of the (BN×KMI-mri/mri)F1×KMI-mri/mri backcross, animals with the KMI phenotype (mri/mri) were easily distinguished from those showing the wild-type phenotype (mri/+) by using growth traits such as body length and weight. Genetic analysis revealed that all of the backcrossed progeny exhibiting the KMI phenotype were homozygous for the KMI allele in the 1.2-cM region between D14Rat5 and D14Rat80 on chromosome 14, suggesting strongly that mri acts in a completely recessive manner. The KMI strain is the first and only rat model with a confirmed mutation in Prkg2 and is a valuable model for studying dwarfism and longitudinal growth traits in humans and for functional studies of cGKII. PMID:19149413

  14. Development and characterization of a complete set of Triticum aestivum-Roegneria ciliaris disomic addition lines.

    PubMed

    Kong, Lingna; Song, Xinying; Xiao, Jin; Sun, Haojie; Dai, Keli; Lan, Caixia; Singh, Pawan; Yuan, Chunxia; Zhang, Shouzhong; Singh, Ravi; Wang, Haiyan; Wang, Xiue

    2018-05-31

    A complete set wheat-R. ciliaris disomic addition lines (DALs) were characterized and the homoeologous groups and genome affinities of R. ciliaris chromosomes were determined. Wild relatives are rich gene resources for cultivated wheat. The development of alien addition chromosome lines not only greatly broadens the genetic diversity, but also provides genetic stocks for comparative genomics studies. Roegneria ciliaris (genome S c S c Y c Y c ), a tetraploid wild relative of wheat, is tolerant or resistant to many abiotic and biotic stresses. To develop a complete set of wheat-R. ciliaris disomic addition lines (DALs), we undertook a euplasmic backcrossing program to overcome allocytoplasmic effects and preferential chromosome transmission. To improve the efficiency of identifying chromosomes from S c and Y c , we established techniques including sequential genomic in situ hybridization/fluorescence in situ hybridization (FISH) and molecular marker analysis. Fourteen DALs of wheat, each containing one pair of R. ciliaris chromosomes pairs, were characterized by FISH using four repetitive sequences [pTa794, pTa71, RcAfa and (GAA) 10 ] as probes. One hundred and sixty-two R. ciliaris-specific markers were developed. FISH and marker analysis enabled us to assign the homoeologous groups and genome affinities of R. ciliaris chromosomes. FHB resistance evaluation in successive five growth seasons showed that the amphiploid, DA2Y c , DA5Y c and DA6S c had improved FHB resistance, indicating their potential value in wheat improvement. The 14 DALs are likely new gene resources and will be phenotyped for more agronomic performances traits.

  15. A Simple Sequence Repeat- and Single-Nucleotide Polymorphism-Based Genetic Linkage Map of the Brown Planthopper, Nilaparvata lugens

    PubMed Central

    Jairin, Jirapong; Kobayashi, Tetsuya; Yamagata, Yoshiyuki; Sanada-Morimura, Sachiyo; Mori, Kazuki; Tashiro, Kosuke; Kuhara, Satoru; Kuwazaki, Seigo; Urio, Masahiro; Suetsugu, Yoshitaka; Yamamoto, Kimiko; Matsumura, Masaya; Yasui, Hideshi

    2013-01-01

    In this study, we developed the first genetic linkage map for the major rice insect pest, the brown planthopper (BPH, Nilaparvata lugens). The linkage map was constructed by integrating linkage data from two backcross populations derived from three inbred BPH strains. The consensus map consists of 474 simple sequence repeats, 43 single-nucleotide polymorphisms, and 1 sequence-tagged site, for a total of 518 markers at 472 unique positions in 17 linkage groups. The linkage groups cover 1093.9 cM, with an average distance of 2.3 cM between loci. The average number of marker loci per linkage group was 27.8. The sex-linkage group was identified by exploiting X-linked and Y-specific markers. Our linkage map and the newly developed markers used to create it constitute an essential resource and a useful framework for future genetic analyses in BPH. PMID:23204257

  16. An improved procedure for integrated behavioral z-scoring illustrated with modified Hole Board behavior of male inbred laboratory mice.

    PubMed

    Labots, M Maaike; Laarakker, M C Marijke; Schetters, D Dustin; Arndt, S S Saskia; van Lith, H A Hein

    2018-01-01

    Guilloux et al. introduced: integrated behavioral z-scoring, a method for behavioral phenotyping of mice. Using this method multiple ethological variables can be combined to show an overall description of a certain behavioral dimension or motivational system. However, a problem may occur when the control group used for the calculation has a standard deviation of zero or when no control group is present to act as a reference group. In order to solve these problems, an improved procedure is suggested: taking the pooled data as reference. For this purpose a behavioral study with male mice from three inbred strains was carried out. The integrated behavioral z-scoring methodology was applied, thereby taking five different reference group options. The outcome regarding statistical significance and practical importance was compared. Significant effects and effect sizes were influenced by the choice of the reference group. In some cases it was impossible to use a certain population and condition, because one or more behavioral variables in question had a standard deviation of zero. Based on the improved method, male mice from the three inbred strains differed regarding activity and anxiety. Taking the method described by Guilloux et al. as basis, the present procedure improved the generalizability to all types of experimental designs in animal behavioral research. To solve the aforementioned problems and to avoid getting the diagnosis of data manipulation, the pooled data (combining the data from all experimental groups in a study) as reference option is recommended. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Analysis of the New Zealand Black contribution to lupus-like renal disease

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Drake, C.G.; Rozzo, S.J.; Hirschfeld, H.F.

    1995-03-01

    F{sub 1} progeny of New Zealand Black (NZB) and New Zealand White (NZW) mice spontaneously develop an autoimmune process remarkably similar to human systemic lupus erythematosus. Previous studies have implicated major genetic contributions from the NZW MHC and from a dominant NZB gene on chromosome 4. To identify additional NZB contributions to lupus-like disease, (NZB x SM/J)F{sub 1} x NZW backcross mice were followed for the development of severe renal disease and were comprehensively genotyped. Despite a 50% incidence of disease significant associations between the presence of the NZB genotype and disease were noted on chromosomes 1, 4, 7, 10,more » 13, and 19. The data indicated that multiple NZB genes, in different combinations, contribute to severe renal disease, and that no single gene is required. To further investigate this NZB contribution, NZB x SM/J (NXSM) recombinant inbred (RI) strains were crossed with NZW mice, and F{sub 1} progeny were analyzed for the presence of lupus-like renal disease. Interestingly, nearly all of the (RI x NZW)F{sub 1} cohorts studies expressed some level of disease. Five RI strains generated a high incidence of disease, similar to (NZB x NZW)F{sub 1} mice, and nearly one-half of the cohorts developed disease at intermediate levels. Only two cohorts demonstrated very little disease, supporting the conclusion that multiple genes are capable of disease induction. Experiments correlating the genotypes of these RI strains with their ability to generate disease revealed that none of the disease-associated loci defined by the backcross analysis were present in all five RI strains that generated disease at high levels. Overall, both the backcross data and RI analysis provide additional support for the genetic complexity of lupus nephritis and uphold the conclusion that heterogeneous combinations of contributing NZB genes seem to operate in a threshold manner to generate the disease phenotype. 31 refs., 3 figs., 2 tabs.« less

  18. Identification of genomic region controlling resistance to aflatoxin contamination in a peanut recombinant inbred line population (Tifrunner XGT-C20)

    USDA-ARS?s Scientific Manuscript database

    In peanut, limited genetic variation for disease resistance is available in breeding programs necessitating the identification of stable resistance sources for use in cultivar development. ‘Tifrunner’ is a runner cultivar while ‘GT-C20’ is a Spanish-type breeding line with resistance to aflatoxin co...

  19. [Testicular testosterone production in male mice of inbred strains PT and CBA/Lac after a long-term period of stable social hierarchy].

    PubMed

    Osadchuk, L V; Gutorova, N V; Kleshchev, M A

    2014-04-01

    Social dominance can alter testicular testosterone production, although there is pronounced variability in the relationship between social status and pattern of the testosterone response. The study designed to investigate how a long-term period of stable social hierarchy effects on testicular testosterone production in male mice of inbred strains PT and CBA/Lac. Paired males of different genotypes were housed together for 32 days beginning 38 day of age. Dyadic interactions of males generated dominance-subordination relationships during the first day after a social group has been produced and the social rank of each opponent was assessed by asymmetry in agonistic behaviour. Serum level of testosterone and its testicular content were evaluated in male mice of both inbred strains at 70 day of age after pair housing. Control animals were age- and genotype-matched single males that were housed in conventional cages. After a long-term period of pair housing, the serum testosterone level and its testicular content in males of both PT and CBA/Lac strains were not significantly different from the control. There were no significant differences in androgenic parameters between social ranks in male mice of both strains. The results indicate that in laboratory mice the pattern of testicular testosterone response to social hierarchy determined by a social situation, for example, a stability of social interactions, when the importance of aggressive competition for rank is minimal.

  20. Genotype Modulates Age-Related Alterations in Sensitivity to the Aversive Effects of Ethanol: An 8 Inbred Strain Analysis of Conditioned Taste Aversion

    PubMed Central

    Moore, Eileen M.; Forrest, Robert D.; Boehm, Stephen L.

    2012-01-01

    Adolescent individuals display altered behavioral sensitivity to ethanol, which may contribute to the increased ethanol consumption seen in this age-group. However, genetics also exert considerable influence on both ethanol intake and sensitivity. Thus far there is little research assessing the combined influence of developmental and genetic alcohol sensitivities. Sensitivity to the aversive effects of ethanol using a conditioned taste aversion (CTA) procedure was measured during both adolescence (P30) and adulthood (P75) in 8 inbred mouse strains (C57BL/6J, DBA/2J, 129S1/SvImJ, A/J, BALB/cByJ, BTBR T+tf/J, C3H/HeJ, and FVB/NJ). Adolescent and adult mice were water deprived, and subsequently provided with access to 0.9% (v/v) NaCl solution for 1h. Immediately following access mice were administered ethanol (0, 1.5, 2.25, 3g/kg, ip). This procedure was repeated in 72h intervals for a total of 5 CTA trials. Sensitivity to the aversive effects of ethanol was highly dependent upon both strain and age. Within an inbred strain, adolescent animals were consistently less sensitive to the aversive effects of ethanol than their adult counterparts. However, the dose of ethanol required to produce an aversion response differed as a function of both age and strain. PMID:23171343

  1. Quantitative trait loci for live animal and carcass composition traits in Jersey and Limousin back-cross cattle finished on pasture or feedlot.

    PubMed

    Morris, C A; Pitchford, W S; Cullen, N G; Esmailizadeh, A K; Hickey, S M; Hyndman, D; Dodds, K G; Afolayan, R A; Crawford, A M; Bottema, C D K

    2009-10-01

    A quantitative trait locus (QTL) study was carried out in two countries, recording live animal and carcass composition traits. Back-cross calves (385 heifers and 398 steers) were generated, with Jersey and Limousin breed backgrounds. The New Zealand cattle were reared on pasture to carcass weights averaging 229 kg, whilst the Australian cattle were reared on grass and finished on grain (for at least 180 days) to carcass weights averaging 335 kg. From 11 live animal traits and 31 carcass composition traits respectively, 5 and 22 QTL were detected in combined-sire analyses, which were significant (P < 0.05) on a genome-wise basis. Fourteen significant traits for carcass composition QTL were on chromosome 2 and these were traits associated with muscling and fatness. This chromosome carried a variant myostatin allele (F94L), segregating from the Limousin ancestry. Despite very different cattle management systems between the two countries, the two populations had a large number of QTL in common. Of the 18 traits which were common to both countries, and which had significant QTL at the genome-wise level, eight were significant in both countries.

  2. Systemic functional expression of N-acetyltransferase polymorphism in the F344 Nat2 congenic rat

    PubMed Central

    Hein, David W.; Bendaly, Jean; Neale, Jason R.; Doll, Mark A.

    2008-01-01

    Rat lines congenic for the rat N-acetyltransferase 2 [(RAT)Nat2] gene were constructed and characterized. F344 (homozygous Nat2 rapid) males were mated to WKY (homozygous Nat2 slow) females to produce heterozygous F1. F1 females were then backcrossed to F344 males. Heterozygous acetylator female progeny from this and each successive backcross were identified by rat Nat2 genotyping and mated with F344 rapid acetylator males. Following ten generations of backcross mating, heterozygous acetylator brother/sister progeny were mated to produce the homozgygous rapid and slow acetylator Nat2 congenic rat lines. p-Aminobenzoic acid (selective for rat NAT2) and 4-aminobiphenyl N-acetyltransferase activities were expressed in all tissues examined (liver, lung, esophagus, stomach, small intestine, colon, pancreas, kidney, skin, leukocytes, and urinary bladder in male and female rats and in breast of female and prostate of male rats). NAT2 expression in rat extrahepatic tissues was much higher than in liver. In each tissue, activities were Nat2-genotype dependent, with highest levels in homozygous rapid acetylators, intermediate levels in heterozygous acetylators, and lowest in homozygous slow acetylators. Sulfamethazine (selective for rat NAT1) N-acetyltransferase activities were observed in all tissues examined in both male and female rats except for breast (females), bladder and leukocytes. In each tissue, the activity was Nat2-genotype independent, with similar levels in homozygous rapid, heterozygous, and homozygous slow acetylators. These congenic rat lines are useful to investigate the role of NAT2 genetic polymorphism in susceptibility to cancers related to arylamine carcinogen exposures. PMID:18799801

  3. Forward genetics by sequencing EMS variation-induced inbred lines

    USDA-ARS?s Scientific Manuscript database

    The dramatic increase in throughput of sequencing techniques enables gene cloning through pre-existing forward genetics approaches. We show that it also brings with it the potential to change the crossing designs and approach of forward genetics. To achieve this for eukaryotic organisms with complex...

  4. Comparative Analysis of the Relationship between Trichloroethylene Metabolism and Tissue-Specific Toxicity among Inbred Mouse Strains: Kidney Effects

    PubMed Central

    Yoo, Hong Sik; Bradford, Blair U.; Kosyk, Oksana; Uehara, Takeki; Shymonyak, Svitlana; Collins, Leonard B.; Bodnar, Wanda M.; Ball, Louise M.; Gold, Avram; Rusyn, Ivan

    2014-01-01

    Trichloroethylene (TCE) is a well-known environmental and occupational toxicant that is classified as carcinogenic to humans based on the epidemiological evidence of an association with higher risk of renal cell carcinoma. A number of scientific issues critical for assessing human health risks from TCE remain unresolved, such as the amount of kidney-toxic glutathione conjugation metabolites formed, inter-species and -individual differences, and the mode of action for kidney carcinogenicity. We hypothesized that TCE metabolite levels in the kidney are associated with kidney-specific toxicity. Oral dosing with TCE was conducted in sub-acute (600 mg/kg/d; 5 days; 7 inbred mouse strains) and sub-chronic (100 or 400 mg/kg/d; 1, 2, or 4 weeks; 2 inbred mouse strains) designs. We evaluated the quantitative relationship between strain-, dose-, and time-dependent formation of TCE metabolites from cytochrome P450-mediated oxidation [trichloroacetic acid (TCA), dichloroacetic acid (DCA), and trichloroethanol] and glutathione conjugation [S-(1,2-dichlorovinyl)-L-cysteine and S-(1,2-dichlorovinyl)glutathione], and various kidney toxicity phenotypes. In sub-acute study, we observed inter-strain differences in TCE metabolite levels in the kidney. In addition, we found that in several strains kidney-specific effects of TCE included induction of peroxisome proliferator-marker genes Cyp4a10 and Acox1, increased cell proliferation, and expression of KIM-1, a marker of tubular damage and regeneration. In sub-chronic study, peroxisome proliferator-marker gene induction and kidney toxicity diminished while cell proliferative response was elevated in a dose-dependent manner in NZW/LacJ, but not C57BL/6J mice. Overall, we show that TCE metabolite levels in the kidney are associated with kidney-specific toxicity and that these effects are strain-dependent. PMID:25424545

  5. Comparative Analysis of the Relationship between Trichloroethylene Metabolism and Tissue-Specific Toxicity among Inbred Mouse Strains: Liver Effects

    PubMed Central

    Yoo, Hong Sik; Bradford, Blair U.; Kosyk, Oksana; Shymonyak, Svitlana; Uehara, Takeki; Collins, Leonard B.; Bodnar, Wanda M.; Ball, Louise M.; Gold, Avram; Rusyn, Ivan

    2014-01-01

    Trichloroethylene (TCE) is a widely used organic solvent. Although TCE is classified as carcinogenic to humans, substantial gaps remain in our understanding of inter-individual variability in TCE metabolism and toxicity, especially in the liver. We tested a hypothesis that amounts of oxidative metabolites of TCE in mouse liver are associated with liver-specific toxicity. Oral dosing with TCE was conducted in sub-acute (600 mg/kg/d; 5 days; 7 inbred mouse strains) and sub-chronic (100 or 400 mg/kg/d; 1, 2, or 4 weeks; 2 inbred mouse strains) designs. We evaluated the quantitative relationship between strain-, dose-, and time-dependent formation of TCE metabolites from cytochrome P450-mediated oxidation [trichloroacetic acid (TCA), dichloroacetic acid (DCA), and trichloroethanol] and glutathione conjugation [S-(1,2-dichlorovinyl)-L-cysteine and S-(1,2-dichlorovinyl)glutathione] in serum and liver, and various liver toxicity phenotypes. In sub-acute study, inter-strain variability in TCE metabolite amounts was observed in serum and liver. No induction of Cyp2e1 protein levels in liver was detected. Serum and liver levels of TCA and DCA were correlated with increased transcription of peroxisome proliferator-marker genes Cyp4a10 and Acox1, but not with degree of induction in hepatocellular proliferation. In sub-chronic study, serum and liver levels of oxidative metabolites gradually decreased over time despite continuous dosing. Liver protein levels of Cyp2e1, Adh and Aldh2 were unaffected by treatment with TCE. While the magnitude of induction of peroxisome proliferator-marker genes also declined, hepatocellular proliferation increased. This study offers a unique opportunity to provide a scientific data-driven rationale for some of the major assumptions in human health assessment of TCE. PMID:25424544

  6. Temporal factors in the extinction of fear in inbred mouse strains differing in extinction efficacy

    PubMed Central

    2013-01-01

    Background Various neuropsychiatric conditions, including posttraumatic stress disorder (PTSD), are characterized by deficient fear extinction, but individuals differ greatly in risk for these. While there is growing evidence that fear extinction is influenced by certain procedural variables, it is unclear how these influences might vary across individuals and subpopulations. To model individual differences in fear extinction, prior studies identified a strain of inbred mouse, 129S1/SvImJ (S1), which exhibits a profound deficit in fear extinction, as compared to other inbred strains, such as C57BL/6J (B6). Methods Here, we assessed the effects of procedural variables on the impaired extinction phenotype of the S1 strain and, by comparison, the extinction-intact B6 strain. The variables studied were 1) the interval between conditioning and extinction, 2) the interval between cues during extinction training, 3) single-cue exposure before extinction training, and 4) extinction of a second-order conditioned cue. Results Conducting extinction training soon after (‘immediately’) conditioning attenuated fear retrieval in S1 mice and impaired extinction in B6 mice. Spacing cue presentations with long inter-trial intervals during extinction training augmented fear in S1 and B6 mice. The effect of spacing was lost with one-trial fear conditioning in B6, but not S1 mice. A single exposure to a conditioned cue before extinction training did not alter extinction retrieval, either in B6 or S1 mice. Both the S1 and B6 strains exhibited robust second-order fear conditioning, in which a cue associated with footshock was sufficient to serve as a conditioned exciter to condition a fear association to a second cue. B6 mice extinguished the fear response to the second-order conditioned cue, but S1 mice failed to do so. Conclusions These data provide further evidence that fear extinction is strongly influenced by multiple procedural variables and is so in a highly strain

  7. Temporal factors in the extinction of fear in inbred mouse strains differing in extinction efficacy.

    PubMed

    MacPherson, Kathryn; Whittle, Nigel; Camp, Marguerite; Gunduz-Cinar, Ozge; Singewald, Nicolas; Holmes, Andrew

    2013-07-05

    Various neuropsychiatric conditions, including posttraumatic stress disorder (PTSD), are characterized by deficient fear extinction, but individuals differ greatly in risk for these. While there is growing evidence that fear extinction is influenced by certain procedural variables, it is unclear how these influences might vary across individuals and subpopulations. To model individual differences in fear extinction, prior studies identified a strain of inbred mouse, 129S1/SvImJ (S1), which exhibits a profound deficit in fear extinction, as compared to other inbred strains, such as C57BL/6J (B6). Here, we assessed the effects of procedural variables on the impaired extinction phenotype of the S1 strain and, by comparison, the extinction-intact B6 strain. The variables studied were 1) the interval between conditioning and extinction, 2) the interval between cues during extinction training, 3) single-cue exposure before extinction training, and 4) extinction of a second-order conditioned cue. Conducting extinction training soon after ('immediately') conditioning attenuated fear retrieval in S1 mice and impaired extinction in B6 mice. Spacing cue presentations with long inter-trial intervals during extinction training augmented fear in S1 and B6 mice. The effect of spacing was lost with one-trial fear conditioning in B6, but not S1 mice. A single exposure to a conditioned cue before extinction training did not alter extinction retrieval, either in B6 or S1 mice. Both the S1 and B6 strains exhibited robust second-order fear conditioning, in which a cue associated with footshock was sufficient to serve as a conditioned exciter to condition a fear association to a second cue. B6 mice extinguished the fear response to the second-order conditioned cue, but S1 mice failed to do so. These data provide further evidence that fear extinction is strongly influenced by multiple procedural variables and is so in a highly strain-dependent manner. This suggests that the efficacy of

  8. Oryza rufipogon introgressions improve yield in the U.S. cultivar Jefferson

    USDA-ARS?s Scientific Manuscript database

    An advanced backcross (BC2) population was developed to explore the breeding value of the wild ancestral species O. rufipogon (IRGC 105491) in a cross with the tropical japonica US variety, cv Jefferson. Early generation selection eliminated lines which possessed undesirable traits such as dormancy,...

  9. Comparative costs of programmes to conserve chicken genetic variation based on maintaining living populations or storing cryopreserved material

    USDA-ARS?s Scientific Manuscript database

    Consolidations in the poultry breeding industry and academic poultry departments have resulted in the loss of avian populations. The cost of maintaining living populations is high, but ex-situ alternatives are now available. Semen can be cryopreserved and lines can be recovered by backcrossing, or...

  10. Mapping of Powdery Mildew Resistance Gene pmCH89 in a Putative Wheat-Thinopyrum intermedium Introgression Line.

    PubMed

    Hou, Liyuan; Zhang, Xiaojun; Li, Xin; Jia, Juqing; Yang, Huizhen; Zhan, Haixian; Qiao, Linyi; Guo, Huijuan; Chang, Zhijian

    2015-07-28

    Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a globally serious disease adversely affecting wheat production. The Bgt-resistant wheat breeding line CH09W89 was derived after backcrossing a Bgt resistant wheat-Thinopyrum intermedium partial amphiploid TAI7045 with susceptible wheat cultivars. At the seedling stage, CH09W89 exhibited immunity or high resistance to Bgt pathotypes E09, E20, E21, E23, E26, Bg1, and Bg2, similar to its donor line TAI7045 and Th. intermedium. No Th. intermedium chromatin was detected based on genomic in situ hybridization of mitotic chromosomes. To determine the mode of inheritance of the Bgt resistance and the chromosomal location of the resistance gene, CH09W89 was crossed with two susceptible wheat cultivars. The results of the genetic analysis showed that the adult resistance to Bgt E09 in CH09W89 was controlled by a single recessive gene, which was tentatively designated as pmCH89. Two polymorphic SSR markers, Xwmc310 and Xwmc125, were linked to the resistance gene with genetic distances 3.1 and 2.7 cM, respectively. Using the Chinese Spring aneuploid and deletion lines, the resistance gene and its linked markers were assigned to chromosome arm 4BL in the bin 0.68-0.78. Due to its unique position on chromosome 4BL, pmCH89 appears to be a new locus for resistance to powdery mildew. These results will be of benefit for improving powdery mildew resistance in wheat breeding programs.

  11. Mapping of Powdery Mildew Resistance Gene pmCH89 in a Putative Wheat-Thinopyrum intermedium Introgression Line

    PubMed Central

    Hou, Liyuan; Zhang, Xiaojun; Li, Xin; Jia, Juqing; Yang, Huizhen; Zhan, Haixian; Qiao, Linyi; Guo, Huijuan; Chang, Zhijian

    2015-01-01

    Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a globally serious disease adversely affecting wheat production. The Bgt-resistant wheat breeding line CH09W89 was derived after backcrossing a Bgt resistant wheat-Thinopyrum intermedium partial amphiploid TAI7045 with susceptible wheat cultivars. At the seedling stage, CH09W89 exhibited immunity or high resistance to Bgt pathotypes E09, E20, E21, E23, E26, Bg1, and Bg2, similar to its donor line TAI7045 and Th. intermedium. No Th. intermedium chromatin was detected based on genomic in situ hybridization of mitotic chromosomes. To determine the mode of inheritance of the Bgt resistance and the chromosomal location of the resistance gene, CH09W89 was crossed with two susceptible wheat cultivars. The results of the genetic analysis showed that the adult resistance to Bgt E09 in CH09W89 was controlled by a single recessive gene, which was tentatively designated as pmCH89. Two polymorphic SSR markers, Xwmc310 and Xwmc125, were linked to the resistance gene with genetic distances 3.1 and 2.7 cM, respectively. Using the Chinese Spring aneuploid and deletion lines, the resistance gene and its linked markers were assigned to chromosome arm 4BL in the bin 0.68–0.78. Due to its unique position on chromosome 4BL, pmCH89 appears to be a new locus for resistance to powdery mildew. These results will be of benefit for improving powdery mildew resistance in wheat breeding programs. PMID:26225967

  12. Genotyping microsatellite DNA markers at putative disease loci in inbred/multiplex families with respiratory chain complex I deficiency allows rapid identification of a novel nonsense mutation (IVS1nt -1) in the NDUFS4 gene in Leigh syndrome.

    PubMed

    Bénit, Paule; Steffann, Julie; Lebon, Sophie; Chretien, Dominique; Kadhom, Noman; de Lonlay, Pascale; Goldenberg, Alice; Dumez, Yves; Dommergues, Marc; Rustin, Pierre; Munnich, Arnold; Rötig, Agnès

    2003-05-01

    Complex I deficiency, the most common cause of mitochondrial disorders, accounts for a variety of clinical symptoms and its genetic heterogeneity makes identification of the disease genes particularly tedious. Indeed, most of the 43 complex I subunits are encoded by nuclear genes, only seven of them being mitochondrially encoded. In order to offer urgent prenatal diagnosis, we have studied an inbred/multiplex family with complex I deficiency by using microsatellite DNA markers flanking the putative disease loci. Microsatellite DNA markers have allowed us to exclude the NDUFS7, NDUFS8, NDUFV1 and NDUFS1 genes and to find homozygosity at the NDUFS4 locus. Direct sequencing has led to identification of a homozygous splice acceptor site mutation in intron 1 of the NDUFS4 gene (IVS1nt -1, G-->A); this was not found in chorion villi of the ongoing pregnancy. We suggest that genotyping microsatellite DNA markers at putative disease loci in inbred/multiplex families helps to identify the disease-causing mutation. More generally, we suggest giving consideration to a more systematic microsatellite analysis of putative disease loci for identification of disease genes in inbred/multiplex families affected with genetically heterogeneous conditions.

  13. A genetic linkage map of the Durum x Triticum dicoccoides backcross population based on SSRs and AFLP markers, and QTL analysis for milling traits.

    PubMed

    Elouafi, I; Nachit, M M

    2004-02-01

    Durum wheat ( Triticum turgidum L. var durum) is mainly produced and consumed in the Mediterranean region; it is used to produce several specific end-products; such as local pasta, couscous and burghul. To study the genetics of grain-milling quality traits, chromosomal locations, and interaction with the environment, a genetic linkage map of durum was constructed and the quantitative trait loci QTLs for the milling-related traits, test weight (TW) and thousand-kernel weight (TKW), were identified. The population constituted 114 recombinant inbred lines derived from the cross: Omrabi 5 /Triticum dicoccoides 600545// Omrabi 5. TW and TKW were analyzed over 18 environments (sites x years). Single-sequence-repeat markers (SSRs), Amplified-fragment-length-polymorphism markers (AFLPs), and seed storage proteins (SSPs) showed a high level of polymorphism (>60%). The map was constructed with 124 SSRs, 149 AFLPs and 6 SSPs; its length covered 2,288.8 cM (8.2 cM/marker). The map showed high synteny with previous wheat maps, and both SSRs and AFLPs mapped evenly across the genome, with more markers in the B genome. However, some rearrangements were observed. For TW, a high genotypic effect was detected and two QTLs with epistasic effect were identified on 7AS and 6BS, explaining 30% of the total variation. The TKW showed a significant transgressive inheritance and five QTLs were identified, explaining 32% of the total variation, out of which 25% was of a genetic nature, and showing QTLxE interaction. The major TKW-QTLs were around the centromere region of 6B. For both traits, Omrabi 5 alleles had a significant positive effect. This population will be used to determine other QTLs of interest, as its parents are likely to harbor different genes for diseases and drought tolerance.

  14. Visualization of A- and B-genome chromosomes in wheat (Triticum aestivum L.) x jointed goatgrass (Aegilops cylindrica Host) backcross progenies.

    PubMed

    Wang, Z N; Hang, A; Hansen, J; Burton, C; Mallory-Smith, C A; Zemetra, R S

    2000-12-01

    Wheat (Triticum aestivum) and jointed goatgrass (Aegilops cylindrica) can cross with each other, and their self-fertile backcross progenies frequently have extra chromosomes and chromosome segments, presumably retained from wheat, raising the possibility that a herbicide resistance gene might transfer from wheat to jointed goatgrass. Genomic in situ hybridization (GISH) was used to clarify the origin of these extra chromosomes. By using T. durum DNA (AABB genome) as a probe and jointed goatgrass DNA (CCDD genome) as blocking DNA, one, two, and three A- or B-genome chromosomes were identified in three BC2S2 individuals where 2n = 29, 30, and 31 chromosomes, respectively. A translocation between wheat and jointed goatgrass chromosomes was also detected in an individual with 30 chromosomes. In pollen mother cells with meiotic configuration of 14 II + 2 I, the two univalents were identified as being retained from the A or B genome of wheat. By using Ae. markgrafii DNA (CC genome) as a probe and wheat DNA (AABBDD genome) as blocking DNA. 14 C-genome chromosomes were visualized in all BC2S2 individuals. The GISH procedure provides a powerful tool to detect the A or B-genome chromatin in a jointed goatgrass background, making it possible to assess the risk of transfer of herbicide resistance genes located on the A or B genome of wheat to jointed goatgrass.

  15. [Genetic improvement of breeding materials in tropical and sub- tropical maize].

    PubMed

    Sansern, Jampatong; Chaba, Jampatong

    2011-12-01

    In the present study, 122 maize local cultivars and adapted exotic germplasm from Thailand were used to develop open pollinate varieties (OPVs) using modified ear-to-row scheme, top-cross or test-cross programmes. Ten new maize OPVs with distinct characters were created based on the precise breeding objectives and directional design. The selection of breeding materials was based upon three factors: elite performance, broad adaptability, and genetic diversity. The synthesizing system provided four features: genetic mixing and recombination, equal comparable genetic contribution, mild selection pressure, and maximum intermating for genetic equilibrium (i.e., the female traits were close for the genetic com-positions). Subsequently, Suwan 1 composite and its deritives (Suwan 2, Suwan 3 composite, Suwan 5 and KS24 synthetics), KS6 and KS28 synthetics with the dent type of different origins, and Caripeno DMR composite, KS23, and KS27 synthetics with the dent type of Non-Suwan 1 origin were developed. These OPVs had been improved for 2~13 cycles using S1 recurrent selection method. About 50 inbred lines were developed from these OPVs, and 16 elite single (three-way) crosses were combined and released from these inbred lines. At present, at least one parental inbred line of all the tropical hybrids was derived from Suwan (KS) germplasm in Thailand. Based on the theory of the synthesizing OPVs and developing inbred lines, this paper discussed the genetic moderate diversity, relationship, heterotic group, and patterns for synthesizing OPVs, and inspiration for composed OPVs to heterosis breeding.

  16. Experimental strategies in carrying out VCU for tobacco crop I: plot design and size.

    PubMed

    Toledo, F H R B; Ramalho, M A P; Pulcinelli, C E; Bruzi, A T

    2013-09-19

    We aimed to establish standards for tobacco Valor de Cultivo e Uso (VCU) in Brazil. We obtained information regarding the size and design of plots of two varietal groups of tobacco (Virginia and Burley). Ten inbred lines of each varietal group were evaluated in a randomized complete block design with four replications. The plot contained 42 plants with six rows of seven columns each. For each experiment plant, considering the position of the respective plant in the plot (row and column) as a reference, cured leaf weight (g/plant), total sugar content (%), and total alkaloid content (%) were determined. The maximum curvature of the variations in coefficients was estimated. Trials with the number of plants per plot ranging from 2 to 41 were simulated. The use of a border was not justified because the interactions between inbred lines x position in the plots were never significant, showing that the behavior of the inbred lines coincided with the different positions. The plant performance varied according to the column position in the plot. To lessen the effect of this factor, the use of plots with more than one row is recommended. Experimental precision, evaluated by the CV%, increased with an increase in plot size; nevertheless, the maximum curvature of the variation coefficient method showed no expressive increase in precision if the number of plants was greater than seven. The result in identification of the best inbred line, in terms of the size of each plot, coincided with the maximum curvature method.

  17. MHC diversity in two Acrocephalus species: the outbred Great reed warbler and the inbred Seychelles warbler.

    PubMed

    Richardson, David S; Westerdahl, Helena

    2003-12-01

    The Great reed warbler (GRW) and the Seychelles warbler (SW) are congeners with markedly different demographic histories. The GRW is a normal outbred bird species while the SW population remains isolated and inbred after undergoing a severe population bottleneck. We examined variation at Major Histocompatibility Complex (MHC) class I exon 3 using restriction fragment length polymorphism, denaturing gradient gel electrophoresis and DNA sequencing. Although genetic variation was higher in the GRW, considerable variation has been maintained in the SW. The ten exon 3 sequences found in the SW were as diverged from each other as were a random sub-sample of the 67 sequences from the GRW. There was evidence for balancing selection in both species, and the phylogenetic analysis showing that the exon 3 sequences did not separate according to species, was consistent with transspecies evolution of the MHC.

  18. Genotype modulates age-related alterations in sensitivity to the aversive effects of ethanol: an eight inbred strain analysis of conditioned taste aversion.

    PubMed

    Moore, E M; Forrest, R D; Boehm, S L

    2013-02-01

    Adolescent individuals display altered behavioral sensitivity to ethanol, which may contribute to the increased ethanol consumption seen in this age-group. However, genetics also exert considerable influence on both ethanol intake and sensitivity. Currently there is little research assessing the combined influence of developmental and genetic alcohol sensitivities. Sensitivity to the aversive effects of ethanol using a conditioned taste aversion (CTA) procedure was measured during both adolescence (P30) and adulthood (P75) in eight inbred mouse strains (C57BL/6J, DBA/2J, 129S1/SvImJ, A/J, BALB/cByJ, BTBR T(+) tf/J, C3H/HeJ and FVB/NJ). Adolescent and adult mice were water deprived, and subsequently provided with access to 0.9% (v/v) NaCl solution for 1 h. Immediately following access mice were administered ethanol (0, 1.5, 2.25 and 3 g/kg, ip). This procedure was repeated in 72 h intervals for a total of five CTA trials. Sensitivity to the aversive effects of ethanol was highly dependent upon both strain and age. Within an inbred strain, adolescent animals were consistently less sensitive to the aversive effects of ethanol than their adult counterparts. However, the dose of ethanol required to produce an aversion response differed as a function of both age and strain. © 2012 Blackwell Publishing Ltd and International Behavioural and Neural Genetics Society.

  19. On the difficulties of discriminating between major and minor hybrid male sterility factors in Drosophila by examining the segregation ratio of sterile and fertile sons in backcrossing experiments.

    PubMed

    Maside, X R; Naveira, H F

    1996-10-01

    The observation of segregation ratios of sterile and fertile males in offspring samples from backcrossed hybrid females is, in principle, a valid method to unveil the genetic basis of hybrid male sterility in Drosophila. When the female parent is heterozygous (hybrid) for a sterility factor with major effects, equal proportions of fertile and sterile sons are expected in her offspring. However, intact (not recombined) chromosome segments of considerable length are expected to give segregation ratios that can not be easily differentiated from the 1:1 ratio expected from a single factor. When the phenotypic character under analysis can be determined by combinations of minor factors from the donor species spanning a certain chromosome length, very large offspring samples may be needed to test this alternative hypothesis against the null hypothesis of a single major factor. This is particularly the case of hybrid male sterility determinants in Drosophila.

  20. Evidence for Persistence of Ectromelia Virus in Inbred Mice, Recrudescence Following Immunosuppression and Transmission to Naïve Mice.

    PubMed

    Sakala, Isaac G; Chaudhri, Geeta; Scalzo, Anthony A; Eldi, Preethi; Newsome, Timothy P; Buller, Robert M; Karupiah, Gunasegaran

    2015-12-01

    Orthopoxviruses (OPV), including variola, vaccinia, monkeypox, cowpox and ectromelia viruses cause acute infections in their hosts. With the exception of variola virus (VARV), the etiological agent of smallpox, other OPV have been reported to persist in a variety of animal species following natural or experimental infection. Despite the implications and significance for the ecology and epidemiology of diseases these viruses cause, those reports have never been thoroughly investigated. We used the mouse pathogen ectromelia virus (ECTV), the agent of mousepox and a close relative of VARV to investigate virus persistence in inbred mice. We provide evidence that ECTV causes a persistent infection in some susceptible strains of mice in which low levels of virus genomes were detected in various tissues late in infection. The bone marrow (BM) and blood appeared to be key sites of persistence. Contemporaneous with virus persistence, antiviral CD8 T cell responses were demonstrable over the entire 25-week study period, with a change in the immunodominance hierarchy evident during the first 3 weeks. Some virus-encoded host response modifiers were found to modulate virus persistence whereas host genes encoded by the NKC and MHC class I reduced the potential for persistence. When susceptible strains of mice that had apparently recovered from infection were subjected to sustained immunosuppression with cyclophosphamide (CTX), animals succumbed to mousepox with high titers of infectious virus in various organs. CTX treated index mice transmitted virus to, and caused disease in, co-housed naïve mice. The most surprising but significant finding was that immunosuppression of disease-resistant C57BL/6 mice several weeks after recovery from primary infection generated high titers of virus in multiple tissues. Resistant mice showed no evidence of a persistent infection. This is the strongest evidence that ECTV can persist in inbred mice, regardless of their resistance status.

  1. Distinct Genetic Signatures for Variability in Total and Free Serum Thyroxine Levels in Four Sets of Recombinant Inbred Mice

    PubMed Central

    Lu, Lu; Aliesky, Holly A.; Williams, Robert W.; Rapoport, Basil

    2011-01-01

    C3H/He and BALB/c mice have elevated serum thyroxine levels associated with low deiodinase type-1 activity whereas C57BL/6 (B6) mice have low thyroxine levels and elevated deiodinase type-1 activity. High-resolution genetic maps are available for four sets of recombinant inbred (RI) mice derived from B6 parents bred to C3H/He, BALB/c, DBA/2, or A strains. Total and free T4 (T-T4 and F-T4) levels in females from these RI sets (BXH, CXB, BXD, and AXBXA) were analyzed to test two hypotheses: first, serum T4 variability is linked to the deiodinase type-1 gene; second, because of their shared B6 parent, the RI sets will share linkages responsible for T-T4 or F-T4 variability. A number of chromosomes (Chr) and loci were linked to T-T4 (Chr 1, 4, 13, 11) or F-T4 (Chr 1, 6, 13, 18, 19). Linkage between T-T4 and Chr 4 was limited to CXB and BXH strains, but the locus was distinct from the deiodinase type-1 gene. Surprisingly, many linkages were unique providing “genetic signatures” for T-T4 or F-T4 in each set of RI mice. Indeed, the strongest linkage between T-T4 (or F-T4) and a Chr 2 locus (logarithm of the odds scores >4.4) was only observed in AXBXA strains. Some loci corresponded to genes/Chr associated in humans with variable TSH or T-T4 levels. Unlike inbred mice, human populations are extremely diverse. Consequently, our data suggest that the contributions of unique chromosomes/loci controlling T-T4 and F-T4 in distinct human subgroups are likely to be “buried” in genetic analyses of heterogeneous human populations. PMID:21209025

  2. Selecting black-spot resistant papaya genotypes derived from backcrossing and hybrids.

    PubMed

    Poltronieri, T P S; Silveira, S F; Vivas, M; Santa Catarina, R; Cortes, D F M; Azevedo, A O N; Pereira, M G

    2017-02-23

    Papaya crop is important to Brazilian agribusiness. However, the expansion of papaya cultivation in the country is affected by the absence of commercial cultivars presenting good disease resistance. The black-spot caused by the fungus Asperisporium caricae is the most damaging foliar disease affecting Brazilian papaya crops. The use of genetically resistant cultivars is a promising strategy to reduce the dependence of papaya crops on fungicides. A field split-plot experiment was carried out in the municipality of Linhares, Espírito Santo State, and included 20 hybrids derived from the cross between 14 superior lines and four elite genotypes ('SS72/12', 'SEKATI', 'JS/12' and '41/7'), two commercial cultivars ('Golden' and 'Tainung 01'), and the superior line '36/7', which were evaluated for resistance to black-spot in the fruits and leaves. The treatments were arranged in a randomized block design with six repetitions of three plants per plot. The incidence and severity of black spot in the fruits and leaves were evaluated at three different times in the 2015-2016 crop season. Lines 4, 9, 21, and the parent SEKATI were notable for their capacity to reduce disease severity in the leaves and fruits. Lines 1, 2, 9, 16, and 19, and the parents 'SEKATI' and 'SS-72/12' had reduced disease incidence in their fruits. The most resistant hybrids 'SS-72/12 X 4', 'SS-72/12 X 6', 'SEKATI X 1', 'SEKATI X 2', 'SEKATI X 6', 'SEKATI X 9', and 'SEKATI X 20' presented negative heterosis values for improved black-spot resistance. The current study allowed the selection of black-spot resistant genotypes and hybrids, which presented a significantly reduced disease index in the field.

  3. Inbreeding and thermal adaptation in Drosophila subobscura.

    PubMed

    Zivanovic, Goran; Arenas, Conxita; Mestres, Francesc

    2014-09-01

    Using a well-adapted Drosophila subobscura population (Avala, Serbia), a drastic experiment of inbreeding was carried out to assess whether the expected level of homozygosity could be reached or if other evolutionary forces affected the process. In general, no significant changes of inversion (or arrangement) frequencies were detected after 12 brother-sister mating generations. Furthermore, no significant differences were obtained between observed and expected (under the inbreeding model) karyotypic frequencies. Thus, these results seemed to indicate that the main evolutionary factor in the experiment was inbreeding. However, in the G12 generation, complete chromosomal fixation was reached only in two out of the eight final inbred lines. In these lines, the chromosomal compositions were difficult to interpret, but they could be likely a consequence of adaptation to particular laboratory conditions (constant 18 °C, food, light period, etc.). Finally, in a second experiment, the inbred lines presented higher fertility at 18 °C than at 13 °C. Also, there was a significant line effect on fertility: inbred line number 6 (A1, J1, U1+2; U1+2+6, E8, and O3+4+7) presented the highest values, which maybe the result of an adaptation to laboratory conditions. Thus, the results obtained in our experiments reflect the adaptive potential of D. subobscura inversions.

  4. Fast-flowering mini-maize: seed to seed in 60 days

    USDA-ARS?s Scientific Manuscript database

    Two lines of Zea mays were developed as a short-generation model for maize. The Fast-Flowering Mini-Maize (FFMM) lines A and B are robust inbred lines with a significantly shorter generation time, much smaller stature, and better greenhouse adaptation than traditional maize varieties. Five generatio...

  5. The little women of Loja--growth hormone-receptor deficiency in an inbred population of southern Ecuador.

    PubMed

    Rosenbloom, A L; Guevara Aguirre, J; Rosenfeld, R G; Fielder, P J

    1990-11-15

    Laron-type dwarfism, which is characterized by the clinical appearance of isolated growth hormone deficiency with elevated serum levels of growth hormone and decreased serum levels of insulin-like growth factor I (IGF-I), has been described in approximately 50 patients. This condition is caused by a deficiency of the cellular receptor for growth hormone, and it is transmitted as an autosomal recessive trait, as indicated by an equal sex distribution and a high rate of consanguinity in affected families. We studied 20 patients (19 females and 1 male, 2 to 49 years of age), from an inbred Spanish population in southern Ecuador, who had the clinical features of Laron-type dwarfism. Seventeen patients were members of two large pedigrees. Among the 13 affected sibships, there were 19 affected and 24 unaffected female siblings and 1 affected and 21 unaffected male siblings. The patients' heights ranged from 10.0 to 6.7 SD below the normal mean height for age in the United States. In addition to the previously described features, 15 patients had limited elbow extensibility, all had blue scleras, affected adults had relatively short extremities, and all four affected women over 30 years of age had hip degeneration. Basal serum concentrations of growth hormone were elevated in all affected children (30 to 160 micrograms per liter) and normal to moderately elevated in the adults. The serum level of growth hormone-binding protein ranged from 1 to 30 percent of normal; IGF-I concentrations were low--less than or equal to 7 micrograms per liter in the children and less than or equal to 66 micrograms per liter in the adults (normal for Ecuadorean women, 98 to 238). Serum levels of IGF-II and growth hormone-dependent IGF-binding protein-3 were also low. We describe an inbred population with a high incidence of growth hormone-receptor deficiency resulting in a clinical picture resembling Laron-type dwarfism but differing principally in showing a marked predominance of affected

  6. Boron toxicity in rice (Oryza sativa L.). I. Quantitative trait locus (QTL) analysis of tolerance to boron toxicity.

    PubMed

    Ochiai, K; Uemura, S; Shimizu, A; Okumoto, Y; Matoh, T

    2008-06-01

    Boron toxicity tolerance of rice plants was studied. Modern japonica subspecies such as Koshihikari, Nipponbare, and Sasanishiki were tolerant, whereas indica subspecies such as Kasalath and IR36 were intolerant to excessive application of boron (B), even though their shoot B contents under B toxicity were not significantly different. Recombinant inbred lines (RILs) of japonica Nekken-1 and indica IR36 were used for quantitative trait locus (QTL) analysis to identify the gene responsible for B toxicity tolerance. A major QTL that could explain 45% of the phenotypic variation was detected in chromosome 4. The QTL was confirmed using a population derived from a recombinant inbred line which is heterogenic at the QTL region. The QTL was also confirmed in other chromosome segment substitution lines (CSSLs).

  7. A gene block causing cross-incompatibility hidden in wild and cultivated rice.

    PubMed Central

    Matsubara, Kazuki; Khin-Thidar; Sano, Yoshio

    2003-01-01

    Unidirectional cross-incompatibility was detected in advanced generations of backcrossing between wild (Oryza rufipogon) and cultivated (O. sativa) rice strains. The near-isogenic line (NIL) of T65wx (Japonica type) carrying an alien segment of chromosome 6 from a wild strain gave a reduced seed setting only when crossed with T65wx as the male. Cytological observations showed that abortion of hybrid seeds occurred as a consequence of a failure of early endosperm development followed by abnormalities in embryo development. The genetic basis of cross-incompatibility reactions in the female and male was investigated by testcrosses using recombinant inbred lines (RILs) that were established through dissecting the introgressed segments of wild and cultivated (Indica type) strains. The results revealed that the cross-incompatibility reaction was controlled by Cif in the female and by cim in the male. When the female plant with Cif was crossed with the male plant with cim, a failure of early endosperm development was observed in the hybrid zygotes. Among cultivars of O. sativa, cim was distributed predominantly in the Japonica type but not in the Indica type. In addition, a dominant suppressor, Su-Cif, which changes the reaction in the female from incompatible to compatible was proposed to present near the centromere of chromosome 6 of the Indica type. Further, the death of young F(1) zygotes was controlled by the parental genotypes rather than by the genotype of the hybrid zygote itself since all three genes acted sporophytically, which strongly suggests an involvement of parent-of-origin effects. We discuss the results in relation to the origin of a crossing barrier as well as their maintenance within the primary gene pool. PMID:14504241

  8. Joint Analysis of Strain and Parent-of-Origin Effects for Recombinant Inbred Intercrosses Generated from Multiparent Populations with the Collaborative Cross as an Example.

    PubMed

    Liu, Yanyan; Xiong, Sican; Sun, Wei; Zou, Fei

    2018-02-02

    Multiparent populations (MPP) have become popular resources for complex trait mapping because of their wider allelic diversity and larger population size compared with traditional two-way recombinant inbred (RI) strains. In mice, the collaborative cross (CC) is one of the most popular MPP and is derived from eight genetically diverse inbred founder strains. The strategy of generating RI intercrosses (RIX) from MPP in general and from the CC in particular can produce a large number of completely reproducible heterozygote genomes that better represent the (outbred) human population. Since both maternal and paternal haplotypes of each RIX are readily available, RIX is a powerful resource for studying both standing genetic and epigenetic variations of complex traits, in particular, the parent-of-origin (PoO) effects, which are important contributors to many complex traits. Furthermore, most complex traits are affected by >1 genes, where multiple quantitative trait locus mapping could be more advantageous. In this paper, for MPP-RIX data but taking CC-RIX as a working example, we propose a general Bayesian variable selection procedure to simultaneously search for multiple genes with founder allelic effects and PoO effects. The proposed model respects the complex relationship among RIX samples, and the performance of the proposed method is examined by extensive simulations. Copyright © 2018 Liu et al.

  9. Thermal Properties of Starch From New Corn Lines as Impacted by Environment and During Line Development

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lenihan, Elizabeth M

    The objectives of this research were to further characterize exotic by adapted corn inbreds by studying the impact of environment on their starch thermal properties, and investigating the development of starch thermal properties during kernel maturation by using differential scanning calorimetry (DSC). A method to expedite identification of unusual starch thermal traits was investigated by examining five corn kernels at a time, instead of one kernel, which the previous screening methods used. Corn lines with known thermal functions were blended with background starch (control) in ratios of unique starch to control starch, and analyzed by using DSC. Control starch wasmore » representative of typical corn starch. The values for each ratio within a mutant type were unique (α < 0.01) for most DSC measurements. These results supported the five-kernel method for rapidly screening large amounts of corn germplasm to identify unusual starch traits. The effects of 5 growing locations on starch thermal properties from exotic by adapted corn and Corn Belt lines were studied using DSC. The warmest location, Missouri, generally produced starch with greater gelatinization onset temperature (T oG), narrower range of gelatinization (R G), and greater enthalpy of gelatinization (ΔH G). The coolest location, Illinois, generally resulted in starch with lower T oG, wider R G, and lower ΔH G. Starch from the Ames 1 farm had thermal properties similar to those of Illinois, whereas starch from the Ames 2 farm had thermal properties similar to those of Missouri. The temperature at Ames 2 may have been warmer since it was located near a river; however, soil type and quality also were different. Final corn starch structure and function change during development and maturity. Thus, the changes in starch thermal properties during 5 stages of endosperm development from exotic by adapted corn and Corn Belt lines at two locations were studied by using DSC. The T oG tended to decrease during

  10. Are voluntary wheel running and open-field behavior correlated in mice? Different answers from comparative and artificial selection approaches.

    PubMed

    Careau, Vincent; Bininda-Emonds, Olaf R P; Ordonez, Genesis; Garland, Theodore

    2012-09-01

    Voluntary wheel running and open-field behavior are probably the two most widely used measures of locomotion in laboratory rodents. We tested whether these two behaviors are correlated in mice using two approaches: the phylogenetic comparative method using inbred strains of mice and an ongoing artificial selection experiment on voluntary wheel running. After taking into account the measurement error and phylogenetic relationships among inbred strains, we obtained a significant positive correlation between distance run on wheels and distance moved in the open-field for both sexes. Thigmotaxis was negatively correlated with distance run on wheels in females but not in males. By contrast, mice from four replicate lines bred for high wheel running did not differ in either distance covered or thigmotaxis in the open field as compared with mice from four non-selected control lines. Overall, results obtained in the selection experiment were generally opposite to those observed among inbred strains. Possible reasons for this discrepancy are discussed.

  11. Polyphenol oxidase activity and differential accumulation of polyphenolics in seed coats of pinto bean (Phaseolus vulgaris L.) characterize postharvest color changes.

    PubMed

    Marles, M A Susan; Vandenberg, Albert; Bett, Kirstin E

    2008-08-27

    Postharvest darkening of pinto bean (Phaseolus vulgaris L.) was evaluated in a population of recombinant inbred lines derived from a cross between CDC Pintium (a regular-darkening line) and 1533-15 (a slow-darkening line). Flavonoid metabolite concentrations, polyphenol oxidase activity, lignin concentration, and seed coat anatomy characteristics were assessed for cosegregation with the darkening phenotype. Significantly lower kaempferol concentrations (p = 0.00001) together with differences in polyphenol oxidase activity (p = 0.0045) were two of the key findings associated with these recombinant inbred lines. In addition, two different assays (thioglycolic acid and Klason lignin) to quantify lignin together with an assessment of extractable condensed tannin were used to estimate the contribution of these polymers to changes in the seed coat tissue. This is the first report of precise biochemical characterization of polyphenolics that associate with postharvest darkening in legumes.

  12. [The differences of the effects of Vrd1 and Ppd-D1 gene alleles on winterhardiness, frost resistance, and yield in winter wheat].

    PubMed

    Mokanu, N V; Faĭt, V I

    2008-01-01

    The influence of allelic differences of Vrd1 and Ppd-D1 genes on winterhardiness, frost resistance, yield and its components was studied in recombinant-inbred F5 lines of Odesskaya 16/Bezostaya 1. From 9 to 15% differences in the resistance of recombinant-inbred lines were determined by alternative alleles of Vrd1 gene and 10-16% of Ppd-D1 gene. Interaction of vrd1 and Ppd-D1a alleles led to the higher winterhardiness and frost resistance of tillered plants during the winter. At the same time the significant increase of the period to heading, plant height and the tendency of yield reduction were revealed for vrd1 vrd1 Ppd-D1a Ppd-D1a lines when compared to the lines of Vrd1 Vrd1 Ppd-D1a Ppd-D1a genotype.

  13. Genome sequence of M6, a diploid inbred clone of the high-glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity.

    PubMed

    Leisner, Courtney P; Hamilton, John P; Crisovan, Emily; Manrique-Carpintero, Norma C; Marand, Alexandre P; Newton, Linsey; Pham, Gina M; Jiang, Jiming; Douches, David S; Jansky, Shelley H; Buell, C Robin

    2018-05-01

    Cultivated potato (Solanum tuberosum L.) is a highly heterozygous autotetraploid that presents challenges in genome analyses and breeding. Wild potato species serve as a resource for the introgression of important agronomic traits into cultivated potato. One key species is Solanum chacoense and the diploid, inbred clone M6, which is self-compatible and has desirable tuber market quality and disease resistance traits. Sequencing and assembly of the genome of the M6 clone of S. chacoense generated an assembly of 825 767 562 bp in 8260 scaffolds with an N50 scaffold size of 713 602 bp. Pseudomolecule construction anchored 508 Mb of the genome assembly into 12 chromosomes. Genome annotation yielded 49 124 high-confidence gene models representing 37 740 genes. Comparative analyses of the M6 genome with six other Solanaceae species revealed a core set of 158 367 Solanaceae genes and 1897 genes unique to three potato species. Analysis of single nucleotide polymorphisms across the M6 genome revealed enhanced residual heterozygosity on chromosomes 4, 8 and 9 relative to the other chromosomes. Access to the M6 genome provides a resource for identification of key genes for important agronomic traits and aids in genome-enabled development of inbred diploid potatoes with the potential to accelerate potato breeding. © 2018 The Authors The Plant Journal © 2018 John Wiley & Sons Ltd.

  14. Genetic variation in the response of the weed Ruellia nudiflora (Acanthaceae) to arbuscular mycorrhizal fungi.

    PubMed

    Ramos-Zapata, José Alberto; Campos-Navarrete, María José; Parra-Tabla, Víctor; Abdala-Roberts, Luis; Navarro-Alberto, Jorge

    2010-04-01

    The main goal of this work was to test for plant genetic variation in the phenotypic plasticity response of the weed Ruellia nudiflora to arbuscular mycorrhizal (AM) fungi inoculation. We collected plants in the field, kept them under homogeneous conditions inside a nursery, and then collected seeds from these parent plants to generate five inbred lines (i.e., genetic families). Half of the plants of each inbred line were inoculated with AM fungi while the other half were not (controls); a fully crossed experimental design was then used to test for the effects of treatment (with or without AM fungi inoculation) and inbred line (genetic family). For each plant, we recorded the number of leaves produced and the number of days it survived during a 2-month period. Results showed a strong positive treatment effect (plastic response to AM fungi inoculation) for leaf production and survival. Moreover, in terms of survival, the treatment effect differed between genetic families (significant genetic family by treatment interaction). These findings indicate that the positive effect of AM fungi on plant survival (and potentially also growth) differs across plant genotypes and that such condition may contribute to R. nudiflora's capacity to colonize new environments.

  15. Characterization of swine leukocyte antigen alleles and haplotypes on a novel miniature pig line, Microminipig.

    PubMed

    Ando, A; Imaeda, N; Ohshima, S; Miyamoto, A; Kaneko, N; Takasu, M; Shiina, T; Kulski, J K; Inoko, H; Kitagawa, H

    2014-12-01

    Microminipigs are extremely small-sized, novel miniature pigs that were recently developed for medical research. The inbred Microminipigs with defined swine leukocyte antigen (SLA) haplotypes are expected to be useful for allo- and xenotransplantation studies and also for association analyses between SLA haplotypes and immunological traits. To establish SLA-defined Microminipig lines, we characterized the polymorphic SLA alleles for three class I (SLA-1, SLA-2 and SLA-3) and two class II (SLA-DRB1 and SLA-DQB1) genes of 14 parental Microminipigs using a high-resolution nucleotide sequence-based typing method. Eleven class I and II haplotypes, including three recombinant haplotypes, were found in the offspring of the parental Microminipigs. Two class I and class II haplotypes, Hp-31.0 (SLA-1*1502-SLA-3*070102-SLA-2*1601) and Hp-0.37 (SLA-DRB1*0701-SLA-DQB1*0502), are novel and have not so far been reported in other pig breeds. Crossover regions were defined by the analysis of 22 microsatellite markers within the SLA class III region of three recombinant haplotypes. The SLA allele and haplotype information of Microminipigs in this study will be useful to establish SLA homozygous lines including three recombinants for transplantation and immunological studies. © 2014 Stichting International Foundation for Animal Genetics.

  16. Inbred mouse strains C57BL/6J and DBA/2J vary in sensitivity to a subset of bitter stimuli

    PubMed Central

    Boughter, John D; Raghow, Sandeep; Nelson, Theodore M; Munger, Steven D

    2005-01-01

    Background Common inbred mouse strains are genotypically diverse, but it is still poorly understood how this diversity relates to specific differences in behavior. To identify quantitative trait genes that influence taste behavior differences, it is critical to utilize assays that exclusively measure the contribution of orosensory cues. With a few exceptions, previous characterizations of behavioral taste sensitivity in inbred mouse strains have generally measured consumption, which can be confounded by post-ingestive effects. Here, we used a taste-salient brief-access procedure to measure taste sensitivity to eight stimuli characterized as bitter or aversive in C57BL/6J (B6) and DBA/2J (D2) mice. Results B6 mice were more sensitive than D2 mice to a subset of bitter stimuli, including quinine hydrochloride (QHCl), 6-n-propylthiouracil (PROP), and MgCl2. D2 mice were more sensitive than B6 mice to the bitter stimulus raffinose undecaacetate (RUA). These strains did not differ in sensitivity to cycloheximide (CYX), denatonium benzoate (DB), KCl or HCl. Conclusion B6-D2 taste sensitivity differences indicate that differences in consumption of QHCl, PROP, MgCl2 and RUA are based on immediate orosensory cues, not post-ingestive effects. The absence of a strain difference for CYX suggests that polymorphisms in a T2R-type taste receptor shown to be differentially sensitive to CYX in vitro are unlikely to differentially contribute to the CYX behavioral response in vivo. The results of these studies point to the utility of these common mouse strains and their associated resources for investigation into the genetic mechanisms of taste. PMID:15967025

  17. A Congenic Line of the C57BL/6J Mouse Strain that is Proficient in Melatonin Synthesis.

    PubMed

    Zhang, Zhijing; Silveyra, Eduardo; Jin, Nange; Ribelayga, Christophe P

    2018-05-16

    The C57BL/6J (B6) is the most common inbred mouse strain used in biomedical research in the United States. Yet, this strain is notoriously known for being deficient in the biosynthesis of melatonin, an important effector of circadian clocks in the brain and in the retina. Melatonin deficiency in this strain results from non-functional alleles of the genes coding two key enzymes of the melatonin synthesis pathway: arylalkylamine-N-acetyltransferase (Aanat) and N-acetylserotonin-O-methyltransferase (Asmt). By introducing functional alleles of the Aanat and Asmt genes from the melatonin-proficient CBA/CaJ (CBA) mouse strain to B6, we have generated a B6 congenic line that has acquired the capacity of rhythmic melatonin synthesis. In addition, the melatonin-dependent rhythm of dopamine release in the retina is restored in the B6 congenic line. Finally, we have partially characterized the Aanat and Asmt genes of the CBA strain and have identified multiple differences between CBA and B6 alleles, including single nucleotide polymorphism and deletion/insertion of DNA segments of various sizes. As an improved model organism with functional components of the melatonin synthesis pathway and melatonin-dependent circadian regulations, the new line will be useful to researchers studying melatonin physiological functions in a variety of fields including, but not limited to, circadian biology and neuroscience. In particular, the congenic line will be useful to speed up introduction of melatonin production capacity into genetically-modified mouse lines of interest such as knockout lines, many of which are on B6 or mixed B6 backgrounds. The melatonin-proficient B6 congenic line will be widely distributed. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  18. A gene encoding an abscisic acid biosynthetic enzyme (LsNCED4) collocates with the high temperature germination locus Htg6.1 in lettuce (Lactuca sp.)

    PubMed Central

    Argyris, Jason; Truco, María José; Ochoa, Oswaldo; McHale, Leah; Dahal, Peetambar; Van Deynze, Allen; Michelmore, Richard W.

    2010-01-01

    Thermoinhibition, or failure of seeds to germinate when imbibed at warm temperatures, can be a significant problem in lettuce (Lactuca sativa L.) production. The reliability of stand establishment would be improved by increasing the ability of lettuce seeds to germinate at high temperatures. Genes encoding germination- or dormancy-related proteins were mapped in a recombinant inbred line population derived from a cross between L. sativa cv. Salinas and L. serriola accession UC96US23. This revealed several candidate genes that are located in the genomic regions containing quantitative trait loci (QTLs) associated with temperature and light requirements for germination. In particular, LsNCED4, a temperature-regulated gene in the biosynthetic pathway for abscisic acid (ABA), a germination inhibitor, mapped to the center of a previously detected QTL for high temperature germination (Htg6.1) from UC96US23. Three sets of sister BC3S2 near-isogenic lines (NILs) that were homozygous for the UC96US23 allele of LsNCED4 at Htg6.1 were developed by backcrossing to cv. Salinas and marker-assisted selection followed by selfing. The maximum temperature for germination of NIL seed lots with the UC96US23 allele at LsNCED4 was increased by 2–3°C when compared with sister NIL seed lots lacking the introgression. In addition, the expression of LsNCED4 was two- to threefold lower in the former NIL lines as compared to expression in the latter. Together, these data strongly implicate LsNCED4 as the candidate gene responsible for the Htg6.1 phenotype and indicate that decreased ABA biosynthesis at high imbibition temperatures is a major factor responsible for the increased germination thermotolerance of UC96US23 seeds. Electronic supplementary material The online version of this article (doi:10.1007/s00122-010-1425-3) contains supplementary material, which is available to authorized users. PMID:20703871

  19. Comparison of global brain gene expression profiles between inbred long-sleep and inbred short-sleep mice by high-density gene array hybridization.

    PubMed

    Xu, Y; Ehringer, M; Yang, F; Sikela, J M

    2001-06-01

    Inbred long-sleep (ILS) and short-sleep (ISS) mice show significant central nervous system-mediated differences in sleep time for sedative dose of ethanol and are frequently used as a rodent model for ethanol sensitivity. In this study, we have used complementary DNA (cDNA) array hybridization methodology to identify genes that are differentially expressed between the brains of ILS and ISS mice. To carry out this analysis, we used both the gene discovery array (GDA) and the Mouse GEM 1 Microarray. GDA consists of 18,378 nonredundant mouse cDNA clones on a single nylon filter. Complex probes were prepared from total brain mRNA of ILS or ISS mice by using reverse transcription and 33P labeling. The labeled probes were hybridized in parallel to the gene array filters. Data from GDA experiments were analyzed with SQL-Plus and Oracle 8. The GEM microarray includes 8,730 sequence-verified clones on a glass chip. Two fluorescently labeled probes were used to hybridize a microarray simultaneously. Data from GEM experiments were analyzed by using the GEMTools software package (Incyte). Differentially expressed genes identified from each method were confirmed by relative quantitative reverse transcription-polymerase chain reaction (RT-PCR). A total of 41 genes or expressed sequence tags (ESTs) display significant expression level differences between brains of ILS and ISS mice after GDA, GEM1 hybridization, and quantitative RT-PCR confirmation. Among them, 18 clones were expressed higher in ILS mice, and 23 clones were expressed higher in ISS mice. The individual gene or EST's function and mapping information have been analyzed. This study identified 41 genes that are differentially expressed between brains of ILS and ISS mice. Some of them may have biological relevance in mediation of phenotypic variation between ILS and ISS mice for ethanol sensitivity. This study also demonstrates that parallel gene expression comparison with high-density cDNA arrays is a rapid and

  20. Two genetic loci control syllable sequences of ultrasonic courtship vocalizations in inbred mice

    PubMed Central

    2011-01-01

    Background The ultrasonic vocalizations (USV) of courting male mice are known to possess a phonetic structure with a complex combination of several syllables. The genetic mechanisms underlying the syllable sequence organization were investigated. Results This study compared syllable sequence organization in two inbred strains of mice, 129S4/SvJae (129) and C57BL6J (B6), and demonstrated that they possessed two mutually exclusive phenotypes. The 129S4/SvJae (129) strain frequently exhibited a "chevron-wave" USV pattern, which was characterized by the repetition of chevron-type syllables. The C57BL/6J strain produced a "staccato" USV pattern, which was characterized by the repetition of short-type syllables. An F1 strain obtained by crossing the 129S4/SvJae and C57BL/6J strains produced only the staccato phenotype. The chevron-wave and staccato phenotypes reappeared in the F2 generations, following the Mendelian law of independent assortment. Conclusions These results suggest that two genetic loci control the organization of syllable sequences. These loci were occupied by the staccato and chevron-wave alleles in the B6 and 129 mouse strains, respectively. Recombination of these alleles might lead to the diversity of USV patterns produced by mice. PMID:22018021

  1. Ovariectomy results in inbred strain-specific increases in anxiety-like behavior in mice

    PubMed Central

    Schoenrock, Sarah Adams; Oreper, Daniel; Young, Nancy; Ervin, Robin Betsch; Bogue, Molly A.; Valdar, William; Tarantino, Lisa M.

    2017-01-01

    Women are at an increased risk for developing affective disorders during times of hormonal flux, including menopause when the ovaries cease production of estrogen. However, while all women undergo menopause, not all develop an affective disorder. Increased vulnerability can result from genetic predisposition, environmental factors and gene by environment interactions. In order to investigate interactions between genetic background and estrogen depletion, we performed bilateral ovariectomy, a surgical procedure that results in estrogen depletion and is thought to model the post-menopausal state, in a genetically defined panel of 37 inbred mouse strains. Seventeen days post-ovariectomy, we assessed behavior in two standard rodent assays of anxiety- and depressive-like behavior, the open field and forced swim tests. We detected a significant interaction between ovariectomy and genetic background on anxiety-like behavior in the open field. No strain specific effects of ovariectomy were observed in the forced swim assay. However, we did observe significant strain effects for all behaviors in both the open field and forced swim tests. This study is the largest to date to look at the effects of ovariectomy on behavior and provides evidence that ovariectomy interacts with genetic background to alter anxiety-like behavior in an animal model of menopause. PMID:27693591

  2. Quantitative genetic analysis of brain copper and zinc in BXD recombinant inbred mice.

    PubMed

    Jones, Leslie C; McCarthy, Kristin A; Beard, John L; Keen, Carl L; Jones, Byron C

    2006-01-01

    Copper and zinc are trace nutrients essential for normal brain function, yet an excess of these elements can be toxic. It is important therefore that these metals be closely regulated. We recently conducted a quantitative trait loci (QTL) analysis to identify chromosomal regions in the mouse containing possible regulatory genes. The animals came from 15 strains of the BXD/Ty recombinant inbred (RI) strain panel and the brain regions analyzed were frontal cortex, caudate-putamen, nucleus accumbens and ventral midbrain. Several QTL were identified for copper and/or zinc, most notably on chromosomes 1, 8, 16 and 17. Genetic correlational analysis also revealed associations between these metals and dopamine, cocaine responses, saccharine preference, immune response and seizure susceptibility. Notably, the QTL on chromosome 17 is also associated with seizure susceptibility and contains the histocompatibility H2 complex. This work shows that regulation of zinc and copper is under polygenic influence and is intimately related to CNS function. Future work will reveal genes underlying the QTL and how they interact with other genes and the environment. More importantly, revelation of the genetic underpinnings of copper and zinc brain homeostasis will aid our understanding of neurological diseases that are related to copper and zinc imbalance.

  3. Chemical and morphological characterization of Costa Rican papaya (Carica papaya L.) hybrids and lines with particular focus on their genuine carotenoid profiles.

    PubMed

    Schweiggert, Ralf M; Steingass, Christof B; Esquivel, Patricia; Carle, Reinhold

    2012-03-14

    Papaya (Carica papaya L.) F1 hybrids and inbred lines grown in Costa Rica were screened for morphological and nutritionally relevant fruit traits. The qualitative composition of carotenoids showed great similarity, being mostly composed of free and esterified β-cryptoxanthins accompanied by β-carotene, lycopene, and biosynthetic precursors. High levels of (all-E)-lycopene and its isomers were distinctive for red-fleshed hybrids, whereas yellow-fleshed fruits were virtually devoid of lycopenes. Because carotenoid levels among the investigated hybrids and lines differed significantly, this study supports the hypothesis of an exploitable genetic variability, and a potential heterotic effect regarding carotenoid expression may be instrumental in papaya-breeding programs. Due to significantly higher levels of provitamin A carotenoids and coinciding high levels of total lycopene, particularly red-fleshed hybrids might represent prospective sources of these compounds. Furthermore, the nutritional value of some genotypes was boosted by substantial amounts of ascorbic acid (up to 73 mg/100 g of fresh weight), which correlated to total soluble solids (R(2) = 0.86).

  4. Four chromosome-specific (Gossypium barbadense chromosome 5sh) Upland cotton RILs with improved elongation

    USDA-ARS?s Scientific Manuscript database

    A chromosome specific recombinant inbred line (CS-B05shRIL) population was created from a cross of TM-1, the genetic standard line of Gossypium hirsutum L. and CS-B05sh, a previously released interspecific chromosome substitution line in which all of the chromosome pairs are genetically similar to T...

  5. Development of breeding lines with three pyramided resistance genes that confer broad-spectrum bacterial blight resistance and their molecular analysis in rice.

    PubMed

    Suh, Jung-Pil; Jeung, Ji-Ung; Noh, Tae-Hwan; Cho, Young-Chan; Park, So-Hyun; Park, Hyun-Su; Shin, Mun-Sik; Kim, Chung-Kon; Jena, Kshirod K

    2013-02-08

    The development of resistant cultivars has been the most effective and economical strategy to control bacterial leaf blight (BB) disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo). Molecular markers have made it possible to identify and pyramid valuable genes of agronomic importance in resistance rice breeding. In this study, three resistance genes (Xa4 + xa5 + Xa21) were transferred from an indica donor (IRBB57), using a marker-assisted backcrossing (MAB) breeding strategy, into a BB-susceptible elite japonica rice cultivar, Mangeumbyeo, which is high yielding with good grain quality. Our analysis led to the development of three elite advanced backcross breeding lines (ABL) with three resistance genes by foreground and phenotypic selection in a japonica genetic background without linkage drag. The background genome recovery of the ABL expressed more than 92.1% using genome-wide SSR marker analysis. The pathogenicity assays of three resistance-gene-derived ABL were conducted under glasshouse conditions with the 18 isolates of Xoo prevalent in Korea. The ABL exhibited very small lesion lengths, indicating a hypersensitive reaction to all 18 isolates of Xoo, with agronomic and grain quality traits similar to those of the recurrent parent. Pyramiding the resistance genes Xa4, xa5 and Xa21 provided a higher resistance to Xoo than the introduction of the individual resistance genes. Additionally, the combination of two dominant and one recessive BB resistance gene did not express any negative effect on agronomic traits in the ABL. The strategy of simultaneous foreground and phenotypic selection to introduce multiple R genes is very useful to reduce the cost and the time required for the isolation of desirable recombinants with target resistance genes in rice. The resistance-gene-derived ABL have practical breeding value without a yield penalty by providing broad-spectrum resistance against most of the existing isolates of BB in South Korea and will

  6. Construction of a genome-anchored, high-density genetic map for melon (Cucumis melo L.) and identification of Fusarium oxysporum f. sp. melonis race 1 resistance QTL.

    PubMed

    Branham, Sandra E; Levi, Amnon; Katawczik, Melanie; Fei, Zhangjun; Wechter, W Patrick

    2018-04-01

    Four QTLs and an epistatic interaction were associated with disease severity in response to inoculation with Fusarium oxysporum f. sp. melonis race 1 in a recombinant inbred line population of melon. The USDA Cucumis melo inbred line, MR-1, harbors a wealth of alleles associated with resistance to several major diseases of melon, including powdery mildew, downy mildew, Alternaria leaf blight, and Fusarium wilt. MR-1 was crossed to an Israeli cultivar, Ananas Yok'neam, which is susceptible to all of these diseases, to generate a recombinant inbred line (RIL) population of 172 lines. In this study, the RIL population was genotyped to construct an ultra-dense genetic linkage map with 5663 binned SNPs anchored to the C. melo genome and exhibits the overall high quality of the assembly. The utility of the densely genotyped population was demonstrated through QTL mapping of a well-studied trait, resistance to Fusarium wilt caused by Fusarium oxysporum f. sp. melonis (Fom) race 1. A major QTL co-located with the previously validated resistance gene Fom-2. In addition, three minor QTLs and an epistatic interaction contributing to Fom race 1 resistance were identified. The MR-1 × AY RIL population provides a valuable resource for future QTL mapping studies and marker-assisted selection of disease resistance in melon.

  7. Genomic variants in an inbred mouse model predict mania-like behaviors.

    PubMed

    Saul, Michael C; Stevenson, Sharon A; Zhao, Changjiu; Driessen, Terri M; Eisinger, Brian E; Gammie, Stephen C

    2018-01-01

    Contemporary rodent models for bipolar disorders split the bipolar spectrum into complimentary behavioral endophenotypes representing mania and depression. Widely accepted mania models typically utilize single gene transgenics or pharmacological manipulations, but inbred rodent strains show great potential as mania models. Their acceptance is often limited by the lack of genotypic data needed to establish construct validity. In this study, we used a unique strategy to inexpensively explore and confirm population allele differences in naturally occurring candidate variants in a manic rodent strain, the Madison (MSN) mouse strain. Variants were identified using whole exome resequencing on a small population of animals. Interesting candidate variants were confirmed in a larger population with genotyping. We enriched these results with observations of locomotor behavior from a previous study. Resequencing identified 447 structural variants that are mostly fixed in the MSN strain relative to control strains. After filtering and annotation, we found 11 non-synonymous MSN variants that we believe alter protein function. The allele frequencies for 6 of these variants were consistent with explanatory variants for the Madison strain's phenotype. The variants are in the Npas2, Cp, Polr3c, Smarca4, Trpv1, and Slc5a7 genes, and many of these genes' products are in pathways implicated in human bipolar disorders. Variants in Smarca4 and Polr3c together explained over 40% of the variance in locomotor behavior in the Hsd:ICR founder strain. These results enhance the MSN strain's construct validity and implicate altered nucleosome structure and transcriptional regulation as a chief molecular system underpinning behavior.

  8. Heritability of articular cartilage regeneration and its association with ear wound healing in mice.

    PubMed

    Rai, Muhammad Farooq; Hashimoto, Shingo; Johnson, Eric E; Janiszak, Kara L; Fitzgerald, Jamie; Heber-Katz, Ellen; Cheverud, James M; Sandell, Linda J

    2012-07-01

    Emerging evidence suggests that genetic components contribute significantly to cartilage degeneration in osteoarthritis pathophysiology, but little information is available on the genetics of cartilage regeneration. Therefore, this study was undertaken to investigate cartilage regeneration in genetic murine models using common inbred strains and a set of recombinant inbred (RI) lines generated from LG/J (healer of ear wounds) and SM/J (nonhealer) inbred mouse strains. An acute full-thickness cartilage injury was introduced in the trochlear groove of 8-week-old mice (n=265) through microsurgery. Mouse knee joints were sagittally sectioned and stained with toluidine blue to evaluate regeneration. For the ear wound phenotype, a bilateral 2-mm through-and-through puncture was created in 6-week-old mice (n=229), and healing outcomes were measured after 30 days. Broad-sense heritability and genetic correlations were calculated for both phenotypes. Time-course analysis of the RI mouse lines showed no significant regeneration until 16 weeks after surgery; at that time, the strains could be segregated into 3 categories: good, intermediate, and poor healers. Analysis of heritability (H2) showed that both cartilage regeneration (H2=26%; P=0.006) and ear wound closure (H2=53%; P<0.00001) were significantly heritable. The genetic correlations between the two healing phenotypes for common inbred mouse strains (r=0.92) and RI mouse lines (r=0.86) were found to be extremely high. Our findings indicate that articular cartilage regeneration in mice is heritable, the differences between the mouse lines are due to genetic differences, and a strong genetic correlation between the two phenotypes exists, indicating that they plausibly share a common genetic basis. We therefore surmise that LG/J by SM/J intercross mice can be used to dissect the genetic basis of variation in cartilage regeneration. Copyright © 2012 by the American College of Rheumatology.

  9. Leaf physiology and biomass allocation of backcross hybrid American chestnut (Castanea dentata) seedlings in response to light and water availability.

    PubMed

    Brown, Caleb E; Mickelbart, Michael V; Jacobs, Douglass F

    2014-12-01

    Partial canopy cover promotes regeneration of many temperate forest trees, but the consequences of shading on seedling drought resistance are unclear. Reintroduction of blight-resistant American chestnut (Castanea dentata (Marsh.) Borkh.) into eastern North American forests will often occur on water-limited sites and under partial canopy cover. We measured leaf pre-dawn water potential (Ψpd), leaf gas exchange, and growth and biomass allocation of backcross hybrid American chestnut seedlings from three orchard sources grown under different light intensities (76, 26 and 8% full photosynthetically active radiation (PAR)) and subjected to well-watered or mid-season water-stressed conditions. Seedlings in the water-stress treatment were returned to well-watered conditions after wilting to examine recovery. Seedlings growing under medium- and high-light conditions wilted at lower leaf Ψpd than low-light seedlings. Recovery of net photosynthesis (Anet) and stomatal conductance (gs) was greater in low and medium light than in high light. Seed source did not affect the response to water stress or light level in most cases. Between 26 and 8% full PAR, light became limiting to the extent that the effects of water stress had no impact on some growth and morphological traits. We conclude that positive and negative aspects of shading on seedling drought tolerance and recovery are not mutually exclusive. Partial shade may help American chestnut tolerate drought during early establishment through effects on physiological conditioning. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  10. Regulation of Sex Determination in Mice by a Non-coding Genomic Region

    PubMed Central

    Arboleda, Valerie A.; Fleming, Alice; Barseghyan, Hayk; Délot, Emmanuèle; Sinsheimer, Janet S.; Vilain, Eric

    2014-01-01

    To identify novel genomic regions that regulate sex determination, we utilized the powerful C57BL/6J-YPOS (B6-YPOS) model of XY sex reversal where mice with autosomes from the B6 strain and a Y chromosome from a wild-derived strain, Mus domesticus poschiavinus (YPOS), show complete sex reversal. In B6-YPOS, the presence of a 55-Mb congenic region on chromosome 11 protects from sex reversal in a dose-dependent manner. Using mouse genetic backcross designs and high-density SNP arrays, we narrowed the congenic region to a 1.62-Mb genomic region on chromosome 11 that confers 80% protection from B6-YPOS sex reversal when one copy is present and complete protection when two copies are present. It was previously believed that the protective congenic region originated from the 129S1/SviMJ (129) strain. However, genomic analysis revealed that this region is not derived from 129 and most likely is derived from the semi-inbred strain POSA. We show that the small 1.62-Mb congenic region that protects against B6-YPOS sex reversal is located within the Sox9 promoter and promotes the expression of Sox9, thereby driving testis development within the B6-YPOS background. Through 30 years of backcrossing, this congenic region was maintained, as it promoted male sex determination and fertility despite the female-promoting B6-YPOS genetic background. Our findings demonstrate that long-range enhancer regions are critical to developmental processes and can be used to identify the complex interplay between genome variants, epigenetics, and developmental gene regulation. PMID:24793290

  11. Development and Evaluation of Glycine max Germplasm Lines with Quantitative Resistance to Sclerotinia sclerotiorum

    PubMed Central

    McCaghey, Megan; Willbur, Jaime; Ranjan, Ashish; Grau, Craig R.; Chapman, Scott; Diers, Brian; Groves, Carol; Kabbage, Mehdi; Smith, Damon L.

    2017-01-01

    Sclerotinia sclerotiorum, the causal agent of Sclerotinia stem rot, is a devastating fungal pathogen of soybean that can cause significant yield losses to growers when environmental conditions are favorable for the disease. The development of resistant varieties has proven difficult. However, poor resistance in commercial cultivars can be improved through additional breeding efforts and understanding the genetic basis of resistance. The objective of this project was to develop soybean germplasm lines that have a high level of Sclerotinia stem rot resistance to be used directly as cultivars or in breeding programs as a source of improved Sclerotinia stem rot resistance. Sclerotinia stem rot-resistant soybean germplasm was developed by crossing two sources of resistance, W04-1002 and AxN-1-55, with lines exhibiting resistance to Heterodera glycines and Cadophora gregata in addition to favorable agronomic traits. Following greenhouse evaluations of 1,076 inbred lines derived from these crosses, 31 lines were evaluated for resistance in field tests during the 2014 field season. Subsequently, 11 Sclerotinia stem rot resistant breeding lines were moved forward for field evaluation in 2015, and seven elite breeding lines were selected and evaluated in the 2016 field season. To better understand resistance mechanisms, a marker analysis was conducted to identify quantitative trait loci linked to resistance. Thirteen markers associated with Sclerotinia stem rot resistance were identified on chromosomes 15, 16, 17, 18, and 19. Our markers confirm previously reported chromosomal regions associated with Sclerotinia stem rot resistance as well as a novel region of chromosome 16. The seven elite germplasm lines were also re-evaluated within a greenhouse setting using a cut petiole technique with multiple S. sclerotiorum isolates to test the durability of physiological resistance of the lines in a controlled environment. This work presents a novel and comprehensive classical

  12. Meiotic behavior as a selection tool in silage corn breeding.

    PubMed

    Souza, V F; Pagliarini, M S; Scapim, C A; Rodovalho, M; Faria, M V

    2010-10-19

    In breeding programs, commercial hybrids are frequently used as a source of inbred lines to obtain new hybrids. Considering that maize production is dependent on viable gametes, the selection of populations to obtain inbred lines with high meiotic stability could contribute to the formation of new silage corn hybrids adapted to specific region. We evaluated the meiotic stability of five commercial hybrids of silage corn used in southern Brazil with conventional squashing methods. All of them showed meiotic abnormalities. Some abnormalities, such as abnormal chromosome segregation and absence of cytokinesis, occurred in all the genotypes, while others, including cytomixis and abnormal spindle orientation, were found only in some genotypes. The hybrid SG6010 had the lowest mean frequency of abnormal cells (21.27%); the highest frequency was found in the hybrid P30K64 (44.43%). However, the frequency of abnormal meiotic products was much lower in most genotypes, ranging from 7.63% in the hybrid CD304 to 43.86% in Garra. Taking into account the percentage of abnormal meiotic products and, hence, meiotic stability, only the hybrids CD304, P30K64, SG6010, and P30F53 are recommended to be retained in the breeding program to obtain inbred lines to create new hybrids.

  13. Evaluation of popcorn germplasm for resistance to Sesamia nonagrioides attack.

    PubMed

    Butrón, A; Sandoya, G; Revilla, P; Ordás, A; Malvar, R A

    2005-10-01

    Popcorn adapted to Spanish conditions could be an interesting and profitable alternative to field corn. However, little is known about breeding popcorn germplasm for adaptation to Spain. Sesamia nonagrioides Lefèvbre is the main insect pest affecting popcorn quality and yield under Spanish growing conditions. The objectives of the study were the search for sources of resistance to S. nonagrioides among popcorn germplasm and to study the genetics of the resistance to S. nonagrioides attack. Eight breeding populations along with a five-inbred line diallel and two popcorn commercial checks were evaluated under S. nonagrioides infestation in 2 yr. Significant differences were found among general combining ability (GCA) effects for days to silking, S. nonagrioides tunnel length, general appearance of the ear, kernel moisture, and yield. Specific combining ability (SCA) effects were found to be significant for yield and ear damage. Therefore, heterotic patterns among popcorn materials should be taken into account to generate new popcorn hybrids that are not only more productive but also have higher kernel quality. Breeding popcorn populations BSP4APC0 and PSPW1C1 could be base germplasms in a breeding program for obtaining parental inbreds of healthy kernel popcorn hybrids. New inbred lines could be generated from the cross BP1 x BP2 that would have improved GCA and SCA effects for S. nonagrioides resistance when crossed to South American inbreds.

  14. Restriction fragment length polymorphism and allozyme linkage map of Cuphea lanceolata.

    PubMed

    Webb, D M; Knapp, S J; Tagliani, L A

    1992-02-01

    Cuphea lanceolata Ait. has had a significant role in the domestication of Cuphea and is a useful experimental organism for investigating how medium-chain lipids are synthesized in developing seeds. To expand the genetics of this species, a linkage map of the C. lanceolata genome was constructed using five allozyme and 32 restriction-fragment-length-polymorphism (RFLP) marker loci. These loci were assigned to six linkage groups that correspond to the six chromosomes of this species. Map length is 288 cM. Levels of polymorphism were estimated for three inbred lines of C. lanceolata and an inbred line of C. viscosissima using 84 random genomic clones and two restriction enzymes, EcoRI and HindIII. Of the probes 29% detected RFLPs between C. lanceolata and C. viscosissima lines. Crosses between these species can be exploited to expand the map.

  15. Novel approach to the behavioural characterization of inbred mice: automated home cage observations.

    PubMed

    de Visser, L; van den Bos, R; Kuurman, W W; Kas, M J H; Spruijt, B M

    2006-08-01

    Here we present a newly developed tool for continuous recordings and analysis of novelty-induced and baseline behaviour of mice in a home cage-like environment. Aim of this study was to demonstrate the strength of this method by characterizing four inbred strains of mice, C57BL/6, DBA/2, C3H and 129S2/Sv, on locomotor activity. Strains differed in circadian rhythmicity, novelty-induced activity and the time-course of specific behavioural elements. For instance, C57BL/6 and DBA/2 mice showed a much faster decrease in activity over time than C3H and 129S2/Sv mice. Principal component analysis revealed two major factors within locomotor activity, which were defined as 'level of activity' and 'velocity/stops'. These factors were able to distinguish strains. Interestingly, mice that displayed high levels of activity in the initial phase of the home cage test were also highly active during an open-field test. Velocity and the number of stops during movement correlated positively with anxiety-related behaviour in the elevated plus maze. The use of an automated home cage observation system yields temporal changes in elements of locomotor activity with an advanced level of spatial resolution. Moreover, it avoids the confounding influence of human intervention and saves time-consuming human observations.

  16. Variation in Nicotine Consumption in Inbred Mice Is Not Linked to Orosensory Ability

    PubMed Central

    Glatt, A. Rebecca; Denton, Kelley

    2009-01-01

    Genetic studies of nicotine addiction in mice have utilized the oral self-administration model. However, it is unclear if strain differences in nicotine consumption are influenced by variation in bitter taste sensitivity. We measured both nicotine consumption and nicotine brief-access licking behavior in several commonly used inbred strains of mice that were previously shown to differ in nicotine consumption. A/J (A), C57BL/6J (B6), and DBA/2J (D2) mice were given a 2-bottle choice test with a single concentration of nicotine (75 μg/ml; nicotine vs. water). Mice of these strains were also tested with a range of nicotine concentrations (5–400 μg/ml) using a brief-access test, which measures orosensory response and minimizes postingestive effects. Although B6 mice consumed more 75-μg/ml nicotine than A or D2 mice in the 2-bottle test, these strains did not differ in level of aversion to nicotine when tested with the brief-access procedure. Strain differences in orosensory response to nicotine were not found; yet, differences emerged during the 2-bottle tests. This study provides evidence that variation in intake level of nicotine is likely not due to differences in taste or trigeminal sensitivity but likely due to postingestive factors. PMID:18775876

  17. Genetic Variation in an Inbred Plant: Variation in Tissue Cultures of Soybean [Glycine Max (L.) Merrill

    PubMed Central

    Roth, E. J.; Frazier, B. L.; Apuya, N. R.; Lark, K. G.

    1989-01-01

    Although soybean [Glycine max (L.) Merrill] grows as an inbreeding, generally homozygous, plant, the germplasm of the species contains large amounts of genetic variation. Analysis of soybean DNA has indicated that variation of RFLP (restriction fragment length polymorphism) markers within the species usually entails only two alleles at any one locus and that mixtures of such dimorphic loci account for virtually all of the restriction fragment variation seen in soybean (G. max), and in its ancestors, G. soja and G. gracilis. We report here that tissue cultures prepared from root tissue of individual soybean plants develop RFLP allelic differences at various loci. However, these newly generated alleles are almost always the same as ones previously found and characterized in other varieties of cultivated soybean (cultivars). This repeated generation of particular alleles suggests that much of the genetic variation seen in soybean could be the consequence of specific, relatively frequently employed, recombinational events. Such a mechanism would allow inbred cultivars to generate genetic variation (in the form of alternative alleles) in a controlled manner, perhaps in response to stress. PMID:2567263

  18. Genetic Regulation of Hypothalamic Cocaine and Amphetamine-Regulated Transcript (CART) in BxD Inbred Mice

    PubMed Central

    Hawks, Brian W.; Li, Wei; Garlow, Steven J.

    2009-01-01

    Cocaine-Amphetamine Regulated Transcript (CART) peptides are implicated in a wide range of behaviors including in the reinforcing properties of psychostimulants, feeding and energy balance and stress and anxiety responses. We conducted a complex trait analysis to examine natural variation in the regulation of CART transcript abundance (CARTta) in the hypothalamus. CART transcript abundance was measured in total hypothalamic RNA from 26 BxD recombinant inbred (RI) mouse strains and in the C57BL/6 (B6) and DBA/2J (D2) progenitor strains. The strain distribution pattern for CARTta was continuous across the RI panel, which is consistent with this being a quantitative trait. Marker regression and interval mapping revealed significant quantitative trait loci (QTL) on mouse chromosome 4 (around 58.2cM) and chromosome 11 (between 20–36cM) that influence CARTta and account for 31% of the between strain variance in this phenotype. There are numerous candidate genes and QTL in these chromosomal regions that may indicate shared genetic regulation between CART expression and other neurobiological processes referable to known actions of this neuropeptide. PMID:18199428

  19. Quantitative trait loci from two genotypes of oat (Avena sativa L.) conditioning resistance to Puccinia coronata

    USDA-ARS?s Scientific Manuscript database

    Developing oat cultivars with partial resistance to crown rust would be beneficial for disease management. Two recombinant inbred line (RIL) populations were derived by crossing the susceptible cultivar ‘Provena’ with two partially resistant sources, ‘CDC Boyer’ and breeding line 94197A1-9-2-2-2-5. ...

  20. Adult plant leaf rust resistance derived from the soft red winter wheat cultivar Caldwell maps to chromosome 3BS

    USDA-ARS?s Scientific Manuscript database

    'Caldwell' is a U.S. soft red winter wheat that has partial, adult plant resistance to the leaf rust pathogen Puccinia triticina. A line of 'Thatcher*2/Caldwell' with adult plant resistance derived from Caldwell was crossed with 'Thatcher' to develop a population of recombinant inbred lines (RILs). ...

  1. New QTL alleles for quality-related traits in spring wheat revealed by RIL population derived from supernumerary x non-supernumerary spikelet genotypes

    USDA-ARS?s Scientific Manuscript database

    Identifying new quantitative trait loci (QTLs) and alleles in exotic germplasm is paramount for further improvement of quality traits in wheat. In the present study, a population of recombinant inbred lines (RILs) developed from a cross between an elite wheat line (WCB414) and an exotic genotype wi...

  2. Note: implementation of a cold spot setup for controlled variation of vapor pressures and its application to an InBr containing discharge lamp.

    PubMed

    Briefi, S

    2013-02-01

    In order to allow for a systematic investigation of the plasma properties of discharges containing indium halides, which are proposed as an efficient alternative for mercury based low pressure discharge lamps, a controlled variation of the indium halide density is mandatory. This can be achieved by applying a newly designed setup in which a well-defined cold spot location is implemented and the cold spot temperature can be adjusted between 50 and 350 °C without influencing the gas temperature. The performance of the setup has been proved by comparing the calculated evaporated InBr density (using the vapor pressure curve) with the one measured via white light absorption spectroscopy.

  3. Variable phenotypic expressivity in inbred retinal degeneration mouse lines: A comparative study of C3H/HeOu and FVB/N rd1 mice.

    PubMed

    van Wyk, Michiel; Schneider, Sabine; Kleinlogel, Sonja

    2015-01-01

    Recent advances in optogenetics and gene therapy have led to promising new treatment strategies for blindness caused by retinal photoreceptor loss. Preclinical studies often rely on the retinal degeneration 1 (rd1 or Pde6b(rd1)) retinitis pigmentosa (RP) mouse model. The rd1 founder mutation is present in more than 100 actively used mouse lines. Since secondary genetic traits are well-known to modify the phenotypic progression of photoreceptor degeneration in animal models and human patients with RP, negligence of the genetic background in the rd1 mouse model is unwarranted. Moreover, the success of various potential therapies, including optogenetic gene therapy and prosthetic implants, depends on the progress of retinal degeneration, which might differ between rd1 mice. To examine the prospect of phenotypic expressivity in the rd1 mouse model, we compared the progress of retinal degeneration in two common rd1 lines, C3H/HeOu and FVB/N. We followed retinal degeneration over 24 weeks in FVB/N, C3H/HeOu, and congenic Pde6b(+) seeing mouse lines, using a range of experimental techniques including extracellular recordings from retinal ganglion cells, PCR quantification of cone opsin and Pde6b transcripts, in vivo flash electroretinogram (ERG), and behavioral optokinetic reflex (OKR) recordings. We demonstrated a substantial difference in the speed of retinal degeneration and accompanying loss of visual function between the two rd1 lines. Photoreceptor degeneration and loss of vision were faster with an earlier onset in the FVB/N mice compared to C3H/HeOu mice, whereas the performance of the Pde6b(+) mice did not differ significantly in any of the tests. By postnatal week 4, the FVB/N mice expressed significantly less cone opsin and Pde6b mRNA and had neither ERG nor OKR responses. At 12 weeks of age, the retinal ganglion cells of the FVB/N mice had lost all light responses. In contrast, 4-week-old C3H/HeOu mice still had ERG and OKR responses, and we still recorded

  4. Quantitative trait loci segregating in crosses between New Hampshire and White Leghorn chicken lines: III. Fat deposition and intramuscular fat content.

    PubMed

    Nassar, M K; Goraga, Z S; Brockmann, G A

    2013-02-01

    In this study, a genome scan was performed to detect genomic loci that affect fat deposition in white adipose tissues and muscles in 278 F (2) males of reciprocal crosses between the genetically and phenotypically extreme inbred chicken lines New Hampshire (NHI) and White Leghorn (WL77). Genome-wide highly significant quantitative trait loci (QTL) influencing fat deposition in white adipose tissues were found on GGA2 and 4. The peak QTL positions for different visceral and subcutaneous white adipose tissues were located between 41.4 and 112.4 Mb on GGA2 and between 76.2 and 78.7 Mb on GGA4, which explained 4.2-10.4% and 4.3-11.6% respectively of the phenotypic F (2) variances. Contrary to our expectations, the QTL allele descending from the lean line WL77 on GGA4 led to increased fat deposition. We suggest a transgressive action of the obesity allele only if it is not in the genetic background of the line WL77. Additional highly significant loci for subcutaneous adipose tissue mass were identified on GGA12 and 15. For intramuscular fat content, a suggestive QTL was located on GGA14. The analysed crosses provide a valuable resource for further fine mapping of fatness genes and subsequent gene discovery. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.

  5. Maximizing the reliability of genomic selection by optimizing the calibration set of reference individuals: comparison of methods in two diverse groups of maize inbreds (Zea mays L.).

    PubMed

    Rincent, R; Laloë, D; Nicolas, S; Altmann, T; Brunel, D; Revilla, P; Rodríguez, V M; Moreno-Gonzalez, J; Melchinger, A; Bauer, E; Schoen, C-C; Meyer, N; Giauffret, C; Bauland, C; Jamin, P; Laborde, J; Monod, H; Flament, P; Charcosset, A; Moreau, L

    2012-10-01

    Genomic selection refers to the use of genotypic information for predicting breeding values of selection candidates. A prediction formula is calibrated with the genotypes and phenotypes of reference individuals constituting the calibration set. The size and the composition of this set are essential parameters affecting the prediction reliabilities. The objective of this study was to maximize reliabilities by optimizing the calibration set. Different criteria based on the diversity or on the prediction error variance (PEV) derived from the realized additive relationship matrix-best linear unbiased predictions model (RA-BLUP) were used to select the reference individuals. For the latter, we considered the mean of the PEV of the contrasts between each selection candidate and the mean of the population (PEVmean) and the mean of the expected reliabilities of the same contrasts (CDmean). These criteria were tested with phenotypic data collected on two diversity panels of maize (Zea mays L.) genotyped with a 50k SNPs array. In the two panels, samples chosen based on CDmean gave higher reliabilities than random samples for various calibration set sizes. CDmean also appeared superior to PEVmean, which can be explained by the fact that it takes into account the reduction of variance due to the relatedness between individuals. Selected samples were close to optimality for a wide range of trait heritabilities, which suggests that the strategy presented here can efficiently sample subsets in panels of inbred lines. A script to optimize reference samples based on CDmean is available on request.

  6. Protein Profiles Reveal Diverse Responsive Signaling Pathways in Kernels of Two Maize Inbred Lines with Contrasting Drought Sensitivity

    PubMed Central

    Yang, Liming; Jiang, Tingbo; Fountain, Jake C.; Scully, Brian T.; Lee, Robert D.; Kemerait, Robert C.; Chen, Sixue; Guo, Baozhu

    2014-01-01

    Drought stress is a major factor that contributes to disease susceptibility and yield loss in agricultural crops. To identify drought responsive proteins and explore metabolic pathways involved in maize tolerance to drought stress, two maize lines (B73 and Lo964) with contrasting drought sensitivity were examined. The treatments of drought and well water were applied at 14 days after pollination (DAP), and protein profiles were investigated in developing kernels (35 DAP) using iTRAQ (isobaric tags for relative and absolute quantitation). Proteomic analysis showed that 70 and 36 proteins were significantly altered in their expression under drought treatments in B73 and Lo964, respectively. The numbers and levels of differentially expressed proteins were generally higher in the sensitive genotype, B73, implying an increased sensitivity to drought given the function of the observed differentially expressed proteins, such as redox homeostasis, cell rescue/defense, hormone regulation and protein biosynthesis and degradation. Lo964 possessed a more stable status with fewer differentially expressed proteins. However, B73 seems to rapidly initiate signaling pathways in response to drought through adjusting diverse defense pathways. These changes in protein expression allow for the production of a drought stress-responsive network in maize kernels. PMID:25334062

  7. Male Infertility Is Responsible for Nearly Half of the Extinction Observed in the Mouse Collaborative Cross

    PubMed Central

    Shorter, John R.; Odet, Fanny; Aylor, David L.; Pan, Wenqi; Kao, Chia-Yu; Fu, Chen-Ping; Morgan, Andrew P.; Greenstein, Seth; Bell, Timothy A.; Stevans, Alicia M.; Feathers, Ryan W.; Patel, Sunny; Cates, Sarah E.; Shaw, Ginger D.; Miller, Darla R.; Chesler, Elissa J.; McMillian, Leonard; O’Brien, Deborah A.; de Villena, Fernando Pardo-Manuel

    2017-01-01

    The goal of the Collaborative Cross (CC) project was to generate and distribute over 1000 independent mouse recombinant inbred strains derived from eight inbred founders. With inbreeding nearly complete, we estimated the extinction rate among CC lines at a remarkable 95%, which is substantially higher than in the derivation of other mouse recombinant inbred populations. Here, we report genome-wide allele frequencies in 347 extinct CC lines. Contrary to expectations, autosomes had equal allelic contributions from the eight founders, but chromosome X had significantly lower allelic contributions from the two inbred founders with underrepresented subspecific origins (PWK/PhJ and CAST/EiJ). By comparing extinct CC lines to living CC strains, we conclude that a complex genetic architecture is driving extinction, and selection pressures are different on the autosomes and chromosome X. Male infertility played a large role in extinction as 47% of extinct lines had males that were infertile. Males from extinct lines had high variability in reproductive organ size, low sperm counts, low sperm motility, and a high rate of vacuolization of seminiferous tubules. We performed QTL mapping and identified nine genomic regions associated with male fertility and reproductive phenotypes. Many of the allelic effects in the QTL were driven by the two founders with underrepresented subspecific origins, including a QTL on chromosome X for infertility that was driven by the PWK/PhJ haplotype. We also performed the first example of cross validation using complementary CC resources to verify the effect of sperm curvilinear velocity from the PWK/PhJ haplotype on chromosome 2 in an independent population across multiple generations. While selection typically constrains the examination of reproductive traits toward the more fertile alleles, the CC extinct lines provided a unique opportunity to study the genetic architecture of fertility in a widely genetically variable population. We

  8. Yield performance and stability of CMS-based triticale hybrids.

    PubMed

    Mühleisen, Jonathan; Piepho, Hans-Peter; Maurer, Hans Peter; Reif, Jochen Christoph

    2015-02-01

    CMS-based triticale hybrids showed only marginal midparent heterosis for grain yield and lower dynamic yield stability compared to inbred lines. Hybrids of triticale (×Triticosecale Wittmack) are expected to possess outstanding yield performance and increased dynamic yield stability. The objectives of the present study were to (1) examine the optimum choice of the biometrical model to compare yield stability of hybrids versus lines, (2) investigate whether hybrids exhibit a more pronounced grain yield performance and yield stability, and (3) study optimal strategies to predict yield stability of hybrids. Thirteen female and seven male parental lines and their 91 factorial hybrids as well as 30 commercial lines were evaluated for grain yield in up to 20 environments. Hybrids were produced using a cytoplasmic male sterility (CMS)-inducing cytoplasm that originated from Triticumtimopheevii Zhuk. We found that the choice of the biometrical model can cause contrasting results and concluded that a group-by-environment interaction term should be added to the model when estimating stability variance of hybrids and lines. midparent heterosis for grain yield was on average 3 % with a range from -15.0 to 11.5 %. No hybrid outperformed the best inbred line. Hybrids had, on average, lower dynamic yield stability compared to the inbred lines. Grain yield performance of hybrids could be predicted based on midparent values and general combining ability (GCA)-predicted values. In contrast, stability variance of hybrids could be predicted only based on GCA-predicted values. We speculated that negative effects of the used CMS cytoplasm might be the reason for the low performance and yield stability of the hybrids. For this purpose a detailed study on the reasons for the drawback of the currently existing CMS system in triticale is urgently required comprising also the search of potentially alternative hybridization systems.

  9. Mapping resistance to the Ug99 race group of the stem rust pathogen in a spring wheat landrace

    USDA-ARS?s Scientific Manuscript database

    Wheat landrace PI 374670 has seedling and field resistance to stem rust caused by Puccinia graminis f. sp tritici Eriks. & E. Henn (Pgt) race TTKSK. To elucidate the inheritance of resistance, 216 BC1F2 families, 192 double haploid (DH) lines, and 185 recombinant inbred lines (RILs) were developed b...

  10. Differential effects on nematode development of two QTLs for resistance to Meloidogyne incognita in cotton

    USDA-ARS?s Scientific Manuscript database

    QTLs qMi-C11 and qMi-C14 impart resistance to Meloidogyne incognita in cotton. Breeders had backcrossed both QTLs into Coker 201 (C201; susceptible) to create M-120 RNR (M-120; highly resistant), and we crossed C201 and M-120 to create near isogenic lines with either qMi-C11 or qMi-C14. Previous wor...

  11. Influence of simulated weightlessness on the rate of anomalies of the flour beetle Tribolium confusum.

    PubMed

    Briegleb, W; Neubert, J; Schatz, A; Sinapius, F

    1975-01-01

    Experiments with Tribolium confusum showed that the morphological characteristics of the beetles are modified by simulated weightlessness (fast running clinostat). Because of possible side effects due to differences in fertility of inbred lines, the first experiments were made with a genetically heterogeneous stock. Thereafter experiments were confirmed with inbred beetles. For both stocks a rise of mainly wing anomalies resulted from rotation of whole cultures of beetles within horizontal tubes. The extent to which these anomalies are teratogenetic or genetic has not yet been analysed in detail.

  12. Generation-based life table analysis reveals manifold effects of inbreeding on the population fitness in Plutella xylostella

    PubMed Central

    Peng, Lu; Zou, Mingmin; Ren, Nana; Xie, Miao; Vasseur, Liette; Yang, Yifan; He, Weiyi; Yang, Guang; Gurr, Geoff M.; Hou, Youming; You, Shijun; You, Minsheng

    2015-01-01

    Understanding how inbreeding affects fitness is biologically important for conservation and pest management. Despite being a worldwide pest of many economically important cruciferous crops, the influence of inbreeding on diamondback moth, Plutella xylostella (L.), populations is currently unknown. Using age-stage-specific life tables, we quantified the inbreeding effects on fitness-related traits and demographic parameters of P. xylostella. Egg hatching rate, survival and fecundity of the inbred line significantly declined compared to those of the outbred line over time. The inbred P. xylostella line showed significantly lower intrinsic rate of increase (r), net reproduction rate (R0), and finite increase rate (λ), and increasing generation time (T). Inbreeding effects vary with developmental stages and the fitness-related traits can be profoundly affected by the duration of inbreeding. Our work provides a foundation for further studies on molecular and genetic bases of the inbreeding depression for P. xylostella. PMID:26227337

  13. Development of Brassica oleracea-nigra monosomic alien addition lines: genotypic, cytological and morphological analyses.

    PubMed

    Tan, Chen; Cui, Cheng; Xiang, Yi; Ge, Xianhong; Li, Zaiyun

    2017-12-01

    We report the development and characterization of Brassica oleracea - nigra monosomic alien addition lines (MAALs) to dissect the Brassica B genome. Brassica nigra (2n = 16, BB) represents the diploid Brassica B genome which carries many useful genes and traits for breeding but received limited studies. To dissect the B genome from B. nigra, the triploid F 1 hybrid (2n = 26, CCB) obtained previously from the cross B. oleracea var. alboglabra (2n = 18, CC) × B. nigra was used as the maternal parent and backcrossed successively to parental B. oleracea. The progenies in BC 1 to BC 3 generations were analyzed by the methods of FISH and SSR markers to screen the monosomic alien addition lines (MAALs) with each of eight different B-genome chromosomes added to C genome (2n = 19, CC + 1B 1-8 ), and seven different MAALs were established, except for the one with chromosome B2 which existed in one triple addition. Most of these MAALs were distinguishable morphologically from each other, as they expressed the characters from B. nigra differently and at variable extents. The alien chromosome remained unpaired as a univalent in 86.24% pollen mother cells at diakinesis or metaphase I, and formed a trivalent with two C-genome chromosomes in 13.76% cells. Transmission frequency of all the added chromosomes was far higher through the ovules (averagely 14.40%) than the pollen (2.64%). The B1, B4 and B5 chromosomes were transmitted by female at much higher rates (22.38-30.00%) than the other four (B3, B6, B7, B8) (5.04-8.42%). The MAALs should be valuable for exploiting the genome structure and evolution of B. nigra.

  14. Resequencing of Capsicum annuum parental lines (YCM334 and Taean) for the genetic analysis of bacterial wilt resistance.

    PubMed

    Kang, Yang Jae; Ahn, Yul-Kyun; Kim, Ki-Taek; Jun, Tae-Hwan

    2016-10-28

    Bacterial wilt (BW) is a widespread plant disease that affects a broad range of dicot and monocot hosts and is particularly harmful for solanaceous plants, such as pepper, tomato, and eggplant. The pathogen responsible for BW is the soil-borne bacterium, Ralstonia solanacearum, which can adapt to diverse temperature conditions and is found in climates ranging from tropical to temperate. Resistance to BW has been detected in some pepper plant lines; however, the genomic loci and alleles that mediate this are poorly studied in this species. We resequenced the pepper cultivars YCM344 and Taean, which are parental recombinant inbred lines (RIL) that display differential resistance phenotypes against BW, with YCM344 being highly resistant to infection with this pathogen. We identified novel single nucleotide polymorphisms (SNPs) and insertions/deletions (Indels) that are only present in both parental lines, as compared to the reference genome and further determined variations that distinguish these two cultivars from one another. We then identified potentially informative SNPs that were found in genes related to those that have been previously associated with disease resistance, such as the R genes and stress response genes. Moreover, via comparative analysis, we identified SNPs located in genomic regions that have homology to known resistance genes in the tomato genomes. From our SNP profiling in both parental lines, we could identify SNPs that are potentially responsible for BW resistance, and practically, these may be used as markers for assisted breeding schemes using these populations. We predict that our analyses will be valuable for both better understanding the YCM334/Taean-derived populations, as well as for enhancing our knowledge of critical SNPs present in the pepper genome.

  15. Identification of salt-tolerant QTLs with strong genetic background effect using two sets of reciprocal introgression lines in rice.

    PubMed

    Cheng, Lirui; Wang, Yun; Meng, Lijun; Hu, Xia; Cui, Yanru; Sun, Yong; Zhu, Linghua; Ali, Jauhar; Xu, Jianlong; Li, Zhikang

    2012-01-01

    Effect of genetic background on detection of quantitative trait locus (QTL) governing salinity tolerance (ST) was studied using two sets of reciprocal introgression lines (ILs) derived from a cross between a moderately salinity tolerant japonica variety, Xiushui09 from China, and a drought tolerant but salinity susceptible indica breeding line, IR2061-520-6-9 from the Philippines. Salt toxicity symptoms (SST) on leaves, days to seedling survival (DSS), and sodium and potassium uptake by shoots were measured under salinity stress of 140 mmol/L of NaCl. A total of 47 QTLs, including 26 main-effect QTLs (M-QTLs) and 21 epistatic QTLs (E-QTLs), were identified from the two sets of reciprocal ILs. Among the 26 M-QTLs, only four (15.4%) were shared in the reciprocal backgrounds while no shared E-QTLs were detected, indicating that ST QTLs, especially E-QTLs, were very specific to the genetic background. Further, 78.6% of the M-QTLs for SST and DSS identified in the reciprocal ILs were also detected in the recombinant inbred lines (RILs) from the same cross, which clearly brings out the background effect on ST QTL detection and its utilization in ST breeding. The detection of ILs with various levels of pyramiding of nonallelic M-QTL alleles for ST from Xiushui09 into IR2061-520-6-9 allowed us to further improve the ST in rice.

  16. Growth, morphology, and developmental instability of rainbow trout, Yellowstone cutthroat trout, and four hybrid generations

    USGS Publications Warehouse

    Ostberg, C.O.; Duda, J.J.; Graham, J.H.; Zhang, S.; Haywood, K. P.; Miller, B.; Lerud, T.L.

    2011-01-01

    Hybridization of cutthroat trout Oncorhynchus clarkii with nonindigenous rainbow trout O. mykiss contributes to the decline of cutthroat trout subspecies throughout their native range. Introgression by rainbow trout can swamp the gene pools of cutthroat trout populations, especially if there is little selection against hybrids. We used rainbow trout, Yellowstone cutthroat trout O. clarkii bouvieri, and rainbow trout × Yellowstone cutthroat trout F1 hybrids as parents to construct seven different line crosses: F1 hybrids (both reciprocal crosses), F2 hybrids, first-generation backcrosses (both rainbow trout and Yellowstone cutthroat trout), and both parental taxa. We compared growth, morphology, and developmental instability among these seven crosses reared at two different temperatures. Growth was related to the proportion of rainbow trout genome present within the crosses. Meristic traits were influenced by maternal, additive, dominant, overdominant, and (probably) epistatic genetic effects. Developmental stability, however, was not disturbed in F1 hybrids, F2 hybrids, or backcrosses. Backcrosses were morphologically similar to their recurrent parent. The lack of developmental instability in hybrids suggests that there are few genetic incompatibilities preventing introgression. Our findings suggest that hybrids are not equal: that is, growth, development, character traits, and morphology differ depending on the genomic contribution from each parental species as well as the hybrid generation.

  17. GISH and AFLP analyses of novel Brassica napus lines derived from one hybrid between B. napus and Orychophragmus violaceus.

    PubMed

    Ma, Ni; Li, Zai-Yun; Cartagena, J A; Fukui, K

    2006-10-01

    New Brassica napus inbred lines with different petal colors and with canola quality and increased levels of oleic (approximately 70%, 10% higher than that of B. napus parent) and linoleic (28%) acids have been developed in the progenies of one B. napus cv. Oro x Orychophragmus violaceus F5 hybrid plant (2n = 31). Their genetic constituents were analyzed by using the methods of genomic in situ hybridization (GISH) and amplified fragments length polymorphism (AFLP). No intact chromosomes of O. violaceus origin were detected by GISH in their somatic cells of ovaries and root tips (2n = 38) and pollen mother cells (PMCs) with normal chromosome pairing (19 bivalents) and segregation (19:19), though signals of variable sizes and intensities were located mainly at terminal and centromeric parts of some mitotic chromosomes and meiotic bivalents at diakinesis or chromosomes in anaphase I groups and one large patch of chromatin was intensively labeled and separated spatially in some telophase I nuclei and metaphase II PMCs. AFLP analysis revealed that substantial genomic changes have occurred in these lines and O. violaceus-specific bands, deleted bands in 'Oro' and novel bands for two parents were detected. The possible mechanisms for these results were discussed.

  18. Mapping Genetic Variants Associated with Beta-Adrenergic Responses in Inbred Mice

    PubMed Central

    Hersch, Micha; Peter, Bastian; Kang, Hyun Min; Schüpfer, Fanny; Abriel, Hugues; Pedrazzini, Thierry; Eskin, Eleazar; Beckmann, Jacques S.

    2012-01-01

    β-blockers and β-agonists are primarily used to treat cardiovascular diseases. Inter-individual variability in response to both drug classes is well recognized, yet the identity and relative contribution of the genetic players involved are poorly understood. This work is the first genome-wide association study (GWAS) addressing the values and susceptibility of cardiovascular-related traits to a selective β 1-blocker, Atenolol (ate), and a β-agonist, Isoproterenol (iso). The phenotypic dataset consisted of 27 highly heritable traits, each measured across 22 inbred mouse strains and four pharmacological conditions. The genotypic panel comprised 79922 informative SNPs of the mouse HapMap resource. Associations were mapped by Efficient Mixed Model Association (EMMA), a method that corrects for the population structure and genetic relatedness of the various strains. A total of 205 separate genome-wide scans were analyzed. The most significant hits include three candidate loci related to cardiac and body weight, three loci for electrocardiographic (ECG) values, two loci for the susceptibility of atrial weight index to iso, four loci for the susceptibility of systolic blood pressure (SBP) to perturbations of the β-adrenergic system, and one locus for the responsiveness of QTc (p<10−8). An additional 60 loci were suggestive for one or the other of the 27 traits, while 46 others were suggestive for one or the other drug effects (p<10−6). Most hits tagged unexpected regions, yet at least two loci for the susceptibility of SBP to β-adrenergic drugs pointed at members of the hypothalamic-pituitary-thyroid axis. Loci for cardiac-related traits were preferentially enriched in genes expressed in the heart, while 23% of the testable loci were replicated with datasets of the Mouse Phenome Database (MPD). Altogether these data and validation tests indicate that the mapped loci are relevant to the traits and responses studied. PMID:22859963

  19. Detection of a new QTL/gene for growth habit in chickpea CaLG1 using wide and narrow crosses

    USDA-ARS?s Scientific Manuscript database

    A recombinant inbred line population (RIP-9) derived from an interspecific cross (ILC72 × Cr5-10) was evaluated for growth habit during two years (2003 and 2004). This RIP was used to develop a pair of near isogenic lines (NILs) for erect vs prostrate growth habit in chickpea. Molecular characteriza...

  20. Mapping QTLs for 100-seed weight in an interspecific soybean cross of Williams 82 (Glycine max) x PI 366121 (Glycine soja)

    USDA-ARS?s Scientific Manuscript database

    100-seed weight is a critical component for soybean quality and yield. The objective of the present study was to identify quantitative trait loci (QTLs) for 100-seed weight using 169 recombinant inbred lines (RILs) derived from the cross of Williams 82 x PI 366121. The parental lines and RILs were g...

  1. Genome-wide mapping of spike-related and agronomic traits in a common wheat population derived from a supernumerary parent and an elite parent

    USDA-ARS?s Scientific Manuscript database

    In wheat (Triticum aestivum L), exotic genotypes express a broad range of spike-related traits and could be used as a source of new genes to enrich the germplasm for wheat breeding programs. In the present study, a population of 163 recombinant inbred lines derived from a cross between an elite line...

  2. The Genetics of Leaf Flecking in Maize and Its Relationship to Plant Defense and Disease Resistance1[OPEN

    PubMed Central

    Bian, Yang; De Vries, Brian; Tracy, William F.

    2016-01-01

    Physiological leaf spotting, or flecking, is a mild-lesion phenotype observed on the leaves of several commonly used maize (Zea mays) inbred lines and has been anecdotally linked to enhanced broad-spectrum disease resistance. Flecking was assessed in the maize nested association mapping (NAM) population, comprising 4,998 recombinant inbred lines from 25 biparental families, and in an association population, comprising 279 diverse maize inbreds. Joint family linkage analysis was conducted with 7,386 markers in the NAM population. Genome-wide association tests were performed with 26.5 million single-nucleotide polymorphisms (SNPs) in the NAM population and with 246,497 SNPs in the association population, resulting in the identification of 18 and three loci associated with variation in flecking, respectively. Many of the candidate genes colocalizing with associated SNPs are similar to genes that function in plant defense response via cell wall modification, salicylic acid- and jasmonic acid-dependent pathways, redox homeostasis, stress response, and vesicle trafficking/remodeling. Significant positive correlations were found between increased flecking, stronger defense response, increased disease resistance, and increased pest resistance. A nonlinear relationship with total kernel weight also was observed whereby lines with relatively high levels of flecking had, on average, lower total kernel weight. We present evidence suggesting that mild flecking could be used as a selection criterion for breeding programs trying to incorporate broad-spectrum disease resistance. PMID:27670817

  3. The resistance of BALB/cJ mice to Yersinia pestis maps to the major histocompatibility complex of chromosome 17.

    PubMed

    Turner, Joshua K; McAllister, Milton M; Xu, John L; Tapping, Richard I

    2008-09-01

    Yersinia pestis, the causative agent of plague, has been well studied at the molecular and genetic levels, but little is known about the role that host genes play in combating this highly lethal pathogen. We challenged several inbred strains of mice with Y. pestis and found that BALB/cJ mice are highly resistant compared to susceptible strains such as C57BL/6J. This resistance was observed only in BALB/cJ mice and not in other BALB/c substrains. Compared to C57BL/6J mice, the BALB/cJ strain exhibited reduced bacterial burden in the spleen and liver early after infection as well as lower levels of serum interleukin-6. These differences were evident 24 h postinfection and became more pronounced with time. Although a significant influx of neutrophils in the spleen and liver was exhibited in both strains, occlusive fibrinous thrombi resulting in necrosis of the surrounding tissue was observed only in C57BL/6J mice. In an effort to identify the gene(s) responsible for resistance, we measured total splenic bacteria in 95 F(2) mice 48 h postinfection and performed quantitative trait locus mapping using 58 microsatellite markers spaced throughout the genome. This analysis revealed a single nonrecessive plague resistance locus, designated prl1 (plague resistance locus 1), which coincides with the major histocompatibility complex of chromosome 17. A second screen of 95 backcrossed mice verified that this locus confers resistance to Y. pestis early in infection. Finally, eighth generation backcrossed mice harboring prl1 were found to maintain resistance in the susceptible C57BL/6J background. These results identify a novel genetic locus in BALB/cJ mice that confers resistance to Y. pestis.

  4. The Resistance of BALB/cJ Mice to Yersinia pestis Maps to the Major Histocompatibility Complex of Chromosome 17▿

    PubMed Central

    Turner, Joshua K.; McAllister, Milton M.; Xu, John L.; Tapping, Richard I.

    2008-01-01

    Yersinia pestis, the causative agent of plague, has been well studied at the molecular and genetic levels, but little is known about the role that host genes play in combating this highly lethal pathogen. We challenged several inbred strains of mice with Y. pestis and found that BALB/cJ mice are highly resistant compared to susceptible strains such as C57BL/6J. This resistance was observed only in BALB/cJ mice and not in other BALB/c substrains. Compared to C57BL/6J mice, the BALB/cJ strain exhibited reduced bacterial burden in the spleen and liver early after infection as well as lower levels of serum interleukin-6. These differences were evident 24 h postinfection and became more pronounced with time. Although a significant influx of neutrophils in the spleen and liver was exhibited in both strains, occlusive fibrinous thrombi resulting in necrosis of the surrounding tissue was observed only in C57BL/6J mice. In an effort to identify the gene(s) responsible for resistance, we measured total splenic bacteria in 95 F2 mice 48 h postinfection and performed quantitative trait locus mapping using 58 microsatellite markers spaced throughout the genome. This analysis revealed a single nonrecessive plague resistance locus, designated prl1 (plague resistance locus 1), which coincides with the major histocompatibility complex of chromosome 17. A second screen of 95 backcrossed mice verified that this locus confers resistance to Y. pestis early in infection. Finally, eighth generation backcrossed mice harboring prl1 were found to maintain resistance in the susceptible C57BL/6J background. These results identify a novel genetic locus in BALB/cJ mice that confers resistance to Y. pestis. PMID:18573896

  5. Inbreeding depresses sperm competitiveness, but not fertilization or mating success in male Tribolium castaneum

    PubMed Central

    Michalczyk, Łukasz; Martin, Oliver Y.; Millard, Anna L.; Emerson, Brent C.; Gage, Matthew J. G.

    2010-01-01

    As populations decline to levels where reproduction among close genetic relatives becomes more probable, subsequent increases in homozygous recessive deleterious expression and/or loss of heterozygote advantage can lead to inbreeding depression. Here, we measure how inbreeding across replicate lines of the flour beetle Tribolium castaneum impacts on male reproductive fitness in the absence or presence of male–male competition. Effects on male evolution from mating pattern were removed by enforcing monogamous mating throughout. After inbreeding across eight generations, we found that male fertility in the absence of competition was unaffected. However, we found significant inbreeding depression of sperm competitiveness: non-inbred males won 57 per cent of fertilizations in competition, while inbred equivalents only sired 42 per cent. We also found that the P2 ‘offence’ role in sperm competition was significantly more depressed under inbreeding than sperm ‘defence’ (P1). Mating behaviour did not explain these differences, and there was no difference in the viability of offspring sired by inbred or non-inbred males. Sperm length variation was significantly greater in the ejaculates of inbred males. Our results show that male ability to achieve normal fertilization success was not depressed under strong inbreeding, but that inbreeding depression in these traits occurred when conditions of sperm competition were generated. PMID:20554548

  6. Inbreeding depresses sperm competitiveness, but not fertilization or mating success in male Tribolium castaneum.

    PubMed

    Michalczyk, Lukasz; Martin, Oliver Y; Millard, Anna L; Emerson, Brent C; Gage, Matthew J G

    2010-11-22

    As populations decline to levels where reproduction among close genetic relatives becomes more probable, subsequent increases in homozygous recessive deleterious expression and/or loss of heterozygote advantage can lead to inbreeding depression. Here, we measure how inbreeding across replicate lines of the flour beetle Tribolium castaneum impacts on male reproductive fitness in the absence or presence of male-male competition. Effects on male evolution from mating pattern were removed by enforcing monogamous mating throughout. After inbreeding across eight generations, we found that male fertility in the absence of competition was unaffected. However, we found significant inbreeding depression of sperm competitiveness: non-inbred males won 57 per cent of fertilizations in competition, while inbred equivalents only sired 42 per cent. We also found that the P(2) 'offence' role in sperm competition was significantly more depressed under inbreeding than sperm 'defence' (P(1)). Mating behaviour did not explain these differences, and there was no difference in the viability of offspring sired by inbred or non-inbred males. Sperm length variation was significantly greater in the ejaculates of inbred males. Our results show that male ability to achieve normal fertilization success was not depressed under strong inbreeding, but that inbreeding depression in these traits occurred when conditions of sperm competition were generated.

  7. Identification and characterization of contrasting sunflower genotypes to early leaf senescence process combining molecular and physiological studies (Helianthus annuus L.).

    PubMed

    López Gialdi, A I; Moschen, S; Villán, C S; López Fernández, M P; Maldonado, S; Paniego, N; Heinz, R A; Fernandez, P

    2016-09-01

    Leaf senescence is a complex mechanism ruled by multiple genetic and environmental variables that affect crop yields. It is the last stage in leaf development, is characterized by an active decline in photosynthetic rate, nutrients recycling and cell death. The aim of this work was to identify contrasting sunflower inbred lines differing in leaf senescence and to deepen the study of this process in sunflower. Ten sunflower genotypes, previously selected by physiological analysis from 150 inbred genotypes, were evaluated under field conditions through physiological, cytological and molecular analysis. The physiological measurement allowed the identification of two contrasting senescence inbred lines, R453 and B481-6, with an increase in yield in the senescence delayed genotype. These findings were confirmed by cytological and molecular analysis using TUNEL, genomic DNA gel electrophoresis, flow sorting and gene expression analysis by qPCR. These results allowed the selection of the two most promising contrasting genotypes, which enables future studies and the identification of new biomarkers associated to early senescence in sunflower. In addition, they allowed the tuning of cytological techniques for a non-model species and its integration with molecular variables. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  8. Quantitative trait loci for organ weights and adipose fat composition in Jersey and Limousin back-cross cattle finished on pasture or feedlot.

    PubMed

    Morris, C A; Bottema, C D K; Cullen, N G; Hickey, S M; Esmailizadeh, A K; Siebert, B D; Pitchford, W S

    2010-12-01

    A QTL study of live animal and carcass traits in beef cattle was carried out in New Zealand and Australia. Back-cross calves (385 heifers and 398 steers) were generated, with Jersey and Limousin backgrounds. This paper reports on weights of eight organs (heart, liver, lungs, kidneys, spleen, gastro-intestinal tract, fat, and rumen contents) and 12 fat composition traits (fatty acid (FA) percentages, saturated and monounsaturated FA subtotals, and fat melting point). The New Zealand cattle were reared and finished on pasture, whilst Australian cattle were reared on grass and finished on grain for at least 180 days. For organ weights and fat composition traits, 10 and 12 significant QTL locations (P<0.05), respectively, were detected on a genome-wide basis, in combined-sire or within-sire analyses. Seven QTL significant for organ weights were found at the proximal end of chromosome 2. This chromosome carries a variant myostatin allele (F94L), segregating from the Limousin ancestry, and this is a positional candidate for the QTL. Ten significant QTL for fat composition were found on chromosomes 19 and 26. Fatty acid synthase and stearoyl-CoA desaturase (SCD1), respectively, are positional candidate genes for these QTL. Two FA QTL found to be common to sire groups in both populations were for percentages of C14:0 and C14:1 (relative to all FAs) on chromosome 26, near the SCD1 candidate gene. © 2010 AgResearch Ltd, Animal Genetics © 2010 Stichting International Foundation for Animal Genetics.

  9. QTL analysis of cotton fiber length in advanced backcross populations derived from a cross between Gossypium hirsutum and G. mustelinum.

    PubMed

    Wang, Baohua; Draye, Xavier; Zhuang, Zhimin; Zhang, Zhengsheng; Liu, Min; Lubbers, Edward L; Jones, Don; May, O Lloyd; Paterson, Andrew H; Chee, Peng W

    2017-06-01

    QTLs for fiber length mapped in three generations of advanced backcross populations derived from crossing Gossypium hirsutum and Gossypium mustelinum showed opportunities to improve elite cottons by introgression from wild relatives. The molecular basis of cotton fiber length in crosses between Gossypium hirsutum and Gossypium mustelinum was dissected using 21 BC 3 F 2 and 12 corresponding BC 3 F 2:3 and BC 3 F 2:4 families. Sixty-five quantitative trait loci (QTLs) were detected by one-way analysis of variance. The QTL numbers detected for upper-half mean length (UHM), fiber uniformity index (UI), and short fiber content (SFC) were 19, 20, and 26 respectively. Twenty-three of the 65 QTLs could be detected at least twice near adjacent markers in the same family or near the same markers across different families/generations, and 32 QTLs were detected in both one-way variance analyses and mixed model-based composite interval mapping. G. mustelinum alleles increased UHM and UI and decreased SFC for five, one, and one QTLs, respectively. In addition to the main-effect QTLs, 17 epistatic QTLs were detected which helped to elucidate the genetic basis of cotton fiber length. Significant among-family genotypic effects were detected at 18, 16, and 16 loci for UHM, UI, and SFC, respectively. Six, two, and two loci showed genotype × family interaction for UHM, UI and SFC, respectively, illustrating complexities that might be faced in introgression of exotic germplasm into cultivated cotton. Co-location of many QTLs for UHM, UI, and SFC accounted for correlations among these traits, and selection of these QTLs may improve the three traits simultaneously. The simple sequence repeat (SSR) markers associated with G. mustelinum QTLs will assist breeders in transferring and maintaining valuable traits from this exotic source during cultivar development.

  10. Quantitative trait loci segregating in crosses between New Hampshire and White Leghorn chicken lines: II. Muscle weight and carcass composition.

    PubMed

    Nassar, M K; Goraga, Z S; Brockmann, G A

    2012-12-01

    In order to identify genetic factors influencing muscle weight and carcass composition in chicken, a linkage analysis was performed with 278 F(2) males of reciprocal crosses between the extremely different inbred lines New Hampshire (NHI) and White Leghorn (WL77). The NHI line had been selected for high meat yield and the WL77 for low egg weight before inbreeding. Highly significant quantitative trait loci (QTL) controlling body weight and the weights of carcass, breast muscle, drumsticks-thighs and wings were identified on GGA4 between 151.5 and 160.5 cM and on GGA27 between 4 and 52 cM. These genomic regions explained 13.7-40.2% and 5.3-13.8% of the phenotypic F(2) variances of the corresponding traits respectively. Additional genome-wide highly significant QTL for the weight of drumsticks-thighs were mapped on GGA1, 5 and 7. Moreover, significant QTL controlling body weight were found on GGA2 and 11. The data obtained in this study can be used for increasing the mapping resolution and subsequent gene targeting on GGA4 and 27 by combining data with other crosses where the same QTL were found. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.

  11. Molecular characterization of high performance inbred lines of Brazilian common beans.

    PubMed

    Cardoso, P C B; Veiga, M M; de Menezes, I P P; Valdisser, P A M R; Borba, T C O; Melo, L C; Del Peloso, M J; Brondani, C; Vianello, R P

    2013-02-06

    The identification of germplasm genetic variability in breeding programs of the common bean (Phaseolus vulgaris) is essential for determining the potential of each combination of parent plants to obtain superior genotypes. The present study aimed to estimated the extent of genetic diversity in 172 lineages and cultivars of the common bean by integrating five tests of value for cultivation and use (VCU) that were conducted over the last eight years by the breeding program of Embrapa Arroz e Feijão in Brazil. Nine multilocus genotyping systems composed of 36 fluorescent microsatellite markers distributed across 11 different chromosomes of the common bean were used, of which 24 were polymorphic in all trials. One hundred and eighty-seven alleles were identified, with an average of 7.79 alleles per locus and an average gene diversity of 0.65. The combined probability of identity for all loci was 1.32 x 10(-16). Lineages that are more genetically divergent between the selection cycles were identified, allowing the breeding program to develop a crossbreed between elite genotypes with a low degree of genetic relatedness. HE values ranged from 0.31 to 0.63, with a large reduction in the genetic base over successive selection cycles. The test showed a significant degree of differentiation (FST = 0.159). Private alleles (26%) were identified and can be directly incorporated into the gene pool of cultivated germplasm, thereby contributing effectively to the expansion of genetic diversity in this bean-breeding program.

  12. The development and phenotyping of diploid recombinant inbred lines of potato

    USDA-ARS?s Scientific Manuscript database

    Progress continues to be made in the effort to transform potato from a tetraploid outbreeding crop into a diploid inbreeding one. This transformation will ultimately lead to more efficient breeding and cultivar development. A variety of genetic resources will be required before a cultivated diploid ...

  13. Progress on genotyping and phenotyping recombinant inbred line populations of peanut

    USDA-ARS?s Scientific Manuscript database

    The biolistic method is reliable for delivering genes of interest into various species. Low transformation efficiency has been a limiting factor for its application. The DNA coating agent protamine was shown to improve transformation efficiency in rice, while a reduction of plasmid DNA in the bomb...

  14. A diploid inbred line strategy to accelerate genetic gain in potato

    USDA-ARS?s Scientific Manuscript database

    Breeding potato at the tetraploid level is inefficient and slow. Potato breeding has not kept pace with advances in breeding strategies and genomics tools. This project initiates our plan to convert potato into a diploid crop capable of self-pollination. This will allow breeders to realize the genet...

  15. An Analysis of the Mode of Gene Action Affecting Pupa Weight in TRIBOLIUM CASTANEUM

    PubMed Central

    Goodwill, R.

    1975-01-01

    Triple-testcross experiments (Kearsey and Jinks 1968) were employed to investigate the mode of gene action affecting pupa weight in Tribolium castaneum. Their experimental design involves two inbred lines, the F1 progeny and a segregating population derived from the cross of the inbred lines. In the present experiments, four segregating populations were used. These populations included the F2 generation, a select line (SEL) and two relaxed select lines (RSI and RSII). In addition, all possible reciprocal crosses were made among the RSI, RSII, and SEL populations. It was observed that: (1) additive, dominant and epistatic gene effects all made significant contributions to the pupa weight of the progeny from all four segregating populations; (2) there was no evidence of either accumulation of epistasis as a result of selection in the SEL population or decline in epistasis as a result of removing selection pressure from the RSI and RSII populations; and (3) significant negative heterosis and maternal effects contributed to the pupa weight of the crossbred progeny of the RSI, RSII and SEL populations. PMID:1132679

  16. Development of transgenic cotton lines expressing Allium sativum agglutinin (ASAL) for enhanced resistance against major sap-sucking pests.

    PubMed

    Vajhala, Chakravarthy S K; Sadumpati, Vijaya Kumar; Nunna, Hariprasad Rao; Puligundla, Sateesh Kumar; Vudem, Dashavantha Reddy; Khareedu, Venkateswara Rao

    2013-01-01

    Mannose-specific Allium sativum leaf agglutinin encoding gene (ASAL) and herbicide tolerance gene (BAR) were introduced into an elite cotton inbred line (NC-601) employing Agrobacterium-mediated genetic transformation. Cotton transformants were produced from the phosphinothricin (PPT)-resistant shoots obtained after co-cultivation of mature embryos with the Agrobacterium strain EHA105 harbouring recombinant binary vector pCAMBIA3300-ASAL-BAR. PCR and Southern blot analysis confirmed the presence and stable integration of ASAL and BAR genes in various transformants of cotton. Basta leaf-dip assay, northern blot, western blot and ELISA analyses disclosed variable expression of BAR and ASAL transgenes in different transformants. Transgenes, ASAL and BAR, were stably inherited and showed co-segregation in T1 generation in a Mendelian fashion for both PPT tolerance and insect resistance. In planta insect bioassays on T2 and T3 homozygous ASAL-transgenic lines revealed potent entomotoxic effects of ASAL on jassid and whitefly insects, as evidenced by significant decreases in the survival, development and fecundity of the insects when compared to the untransformed controls. Furthermore, the transgenic cotton lines conferred higher levels of resistance (1-2 score) with minimal plant damage against these major sucking pests when bioassays were carried out employing standard screening techniques. The developed transgenics could serve as a potential genetic resource in recombination breeding aimed at improving the pest resistance of cotton. This study represents the first report of its kind dealing with the development of transgenic cotton resistant to two major sap-sucking insects.

  17. Development of Transgenic Cotton Lines Expressing Allium sativum Agglutinin (ASAL) for Enhanced Resistance against Major Sap-Sucking Pests

    PubMed Central

    Nunna, Hariprasad Rao; Puligundla, Sateesh Kumar; Vudem, Dashavantha Reddy; Khareedu, Venkateswara Rao

    2013-01-01

    Mannose-specific Allium sativum leaf agglutinin encoding gene (ASAL) and herbicide tolerance gene (BAR) were introduced into an elite cotton inbred line (NC-601) employing Agrobacterium-mediated genetic transformation. Cotton transformants were produced from the phosphinothricin (PPT)-resistant shoots obtained after co-cultivation of mature embryos with the Agrobacterium strain EHA105 harbouring recombinant binary vector pCAMBIA3300-ASAL-BAR. PCR and Southern blot analysis confirmed the presence and stable integration of ASAL and BAR genes in various transformants of cotton. Basta leaf-dip assay, northern blot, western blot and ELISA analyses disclosed variable expression of BAR and ASAL transgenes in different transformants. Transgenes, ASAL and BAR, were stably inherited and showed co-segregation in T1 generation in a Mendelian fashion for both PPT tolerance and insect resistance. In planta insect bioassays on T2 and T3 homozygous ASAL-transgenic lines revealed potent entomotoxic effects of ASAL on jassid and whitefly insects, as evidenced by significant decreases in the survival, development and fecundity of the insects when compared to the untransformed controls. Furthermore, the transgenic cotton lines conferred higher levels of resistance (1–2 score) with minimal plant damage against these major sucking pests when bioassays were carried out employing standard screening techniques. The developed transgenics could serve as a potential genetic resource in recombination breeding aimed at improving the pest resistance of cotton. This study represents the first report of its kind dealing with the development of transgenic cotton resistant to two major sap-sucking insects. PMID:24023750

  18. Quantitative trait locus mapping of genes associated with vacuolation in the adrenal X-zone of the DDD/Sgn inbred mouse.

    PubMed

    Suto, Jun-Ichi

    2012-11-06

    Adrenal gland of mice contains a transient zone between the adrenal cortex and the adrenal medulla: the X-zone. There are clear strain differences in terms of X-zone morphology. Nulliparous females of the inbred mouse DDD strain develop adrenal X-zones containing exclusively vacuolated cells, whereas females of the inbred mouse B6 strain develop X-zones containing only non-vacuolated cells. The X-zone vacuolation is a physiologic process associated with the X-zone degeneration and is tightly regulated by genetic factors. Identification of the genetic factors controlling such strain differences should help analyze the X-zone function. In this study, a quantitative trait locus (QTL) analysis for the extent of X-zone vacuolation was performed for two types of F2 female mice: F2Ay mice (F2 mice with the Ay allele) and F2 non-Ay mice (F2 mice without the Ay allele). These were produced by crossing B6 females and DDD.Cg-Ay males. DDD.Cg-Ay is a congenic mouse strain for the Ay allele at the agouti locus and is used for this study because a close association between the X-zone morphology and the agouti locus genotype has been suggested. The Ay allele is dominant and homozygous lethal; therefore, living Ay mice are invariably heterozygotes. Single QTL scans identified significant QTLs on chromosomes 1, 2, 6, and X for F2 non-Ay mice, and on chromosomes 2, 6, and 12 for F2Ay mice. The QTL on chromosome 2 was considered to be because of the agouti locus, which has been suggested to be associated with X-zone vacuolation. A significant QTL that interacted with the agouti locus was identified on chromosome 8. The extent of X-zone vacuolation in DDD females was controlled by multiple genes with complex interactions. The murine X-zone is considered analogous structure to the human fetal zone. Therefore, the results of this study will aid in understanding function of not only of the X-zone but also of the human fetal zone. Identifying the genes responsible for the QTLs will be

  19. Quantitative trait locus mapping of genes associated with vacuolation in the adrenal X-zone of the DDD/Sgn inbred mouse

    PubMed Central

    2012-01-01

    Background Adrenal gland of mice contains a transient zone between the adrenal cortex and the adrenal medulla: the X-zone. There are clear strain differences in terms of X-zone morphology. Nulliparous females of the inbred mouse DDD strain develop adrenal X-zones containing exclusively vacuolated cells, whereas females of the inbred mouse B6 strain develop X-zones containing only non-vacuolated cells. The X-zone vacuolation is a physiologic process associated with the X-zone degeneration and is tightly regulated by genetic factors. Identification of the genetic factors controlling such strain differences should help analyze the X-zone function. In this study, a quantitative trait locus (QTL) analysis for the extent of X-zone vacuolation was performed for two types of F2 female mice: F2Ay mice (F2 mice with the Ay allele) and F2 non-Ay mice (F2 mice without the Ay allele). These were produced by crossing B6 females and DDD.Cg-Ay males. DDD.Cg-Ay is a congenic mouse strain for the Ay allele at the agouti locus and is used for this study because a close association between the X-zone morphology and the agouti locus genotype has been suggested. The Ay allele is dominant and homozygous lethal; therefore, living Ay mice are invariably heterozygotes. Results Single QTL scans identified significant QTLs on chromosomes 1, 2, 6, and X for F2 non-Ay mice, and on chromosomes 2, 6, and 12 for F2Ay mice. The QTL on chromosome 2 was considered to be because of the agouti locus, which has been suggested to be associated with X-zone vacuolation. A significant QTL that interacted with the agouti locus was identified on chromosome 8. Conclusions The extent of X-zone vacuolation in DDD females was controlled by multiple genes with complex interactions. The murine X-zone is considered analogous structure to the human fetal zone. Therefore, the results of this study will aid in understanding function of not only of the X-zone but also of the human fetal zone. Identifying the genes

  20. Strong conservation of inbred mouse strain microRNA loci but broad variation in brain microRNAs due to RNA editing and isomiR expression.

    PubMed

    Trontti, Kalevi; Väänänen, Juho; Sipilä, Tessa; Greco, Dario; Hovatta, Iiris

    2018-05-01

    Diversity in the structure and expression of microRNAs, important regulators of gene expression, arises from SNPs, duplications followed by divergence, production of isomiRs, and RNA editing. Inbred mouse strains and crosses using them are important reference populations for genetic mapping, and as models of human disease. We determined the nature and extent of interstrain miRNA variation by (i) identifying miRNA SNPs in whole-genome sequence data from 36 strains, and (ii) examining miRNA editing and expression in hippocampus (Hpc) and frontal cortex (FCx) of six strains, to facilitate the study of miRNAs in neurobehavioral phenotypes. miRNA loci were strongly conserved among the 36 strains, but even the highly conserved seed region contained 16 SNPs. In contrast, we identified RNA editing in 58.9% of miRNAs, including 11 consistent editing events in the seed region. We confirmed the functional significance of three conserved edits in the miR-379/410 cluster, demonstrating that edited miRNAs gained novel target mRNAs not recognized by the unedited miRNAs. We found significant interstrain differences in miRNA and isomiR expression: Of 779 miRNAs expressed in Hpc and 719 in FCx, 262 were differentially expressed (190 in Hpc, 126 in FCx, 54 in both). We also identified 32 novel miRNA candidates using miRNA prediction tools. Our studies provide the first comprehensive analysis of SNP, isomiR, and RNA editing variation in miRNA loci across inbred mouse strains, and a detailed catalog of expressed miRNAs in Hpc and FCx in six commonly used strains. These findings will facilitate the molecular analysis of neurological and behavioral phenotypes in this model organism. © 2018 Trontti et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.