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

Evaluation of resistance to aflatoxin contamination in kernels of maize genotypes using a GFP-expressing Aspergillus flavus strain

USDA-ARS?s Scientific Manuscript database

Evaluation of resistance or susceptibility of corn inbreds to infection by Aspergillus flavus was evaluated by a kernel screening assay. A GFP-expressing strain of A. flavus was used to accomplish this study to measure fungal spread and aflatoxin levels in real time. Among the four inbreds tested, ...

76 FR 37767 - Pioneer Hi-Bred International, Inc.; Determination of Nonregulated Status for Corn Genetically...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-28

... DEPARTMENT OF AGRICULTURE Animal and Plant Health Inspection Service [Docket No. APHIS-2010-0041] Pioneer Hi-Bred International, Inc.; Determination of Nonregulated Status for Corn Genetically Engineered To Produce Male Sterile/Female Inbred Plants AGENCY: Animal and Plant Health Inspection Service, USDA...

A maize inbred exhibits resistance against western corn root worm, Diabrotica vergifera vergifera.

USDA-ARS?s Scientific Manuscript database

Plants respond to insect infestations with a suite of natural defenses that vary depending on their genetic and phenotypic traits. Insect resistance traits against root herbivores like western corn rootworm (WCR, Diabrotica virgifera) are not well understood in non-transgenic maize. Using biomechani...

Accumulation of 5-hydroxynorvaline in maize (Zea mays) leaves is induced by insect feeding and abiotic stress.

PubMed

Yan, Jian; Lipka, Alexander E; Schmelz, Eric A; Buckler, Edward S; Jander, Georg

2015-02-01

Plants produce a wide variety of defensive metabolites to protect themselves against herbivores and pathogens. Non-protein amino acids, which are present in many plant species, can have a defensive function through their mis-incorporation during protein synthesis and/or inhibition of biosynthetic pathways in primary metabolism. 5-Hydroxynorvaline was identified in a targeted search for previously unknown non-protein amino acids in the leaves of maize (Zea mays) inbred line B73. Accumulation of this compound increases during herbivory by aphids (Rhopalosiphum maidis, corn leaf aphid) and caterpillars (Spodoptera exigua, beet armyworm), as well as in response to treatment with the plant signalling molecules methyl jasmonate, salicylic acid and abscisic acid. In contrast, ethylene signalling reduced 5-hydroxynorvaline abundance. Drought stress induced 5-hydroxynorvaline accumulation to a higher level than insect feeding or treatment with defence signalling molecules. In field-grown plants, the 5-hydroxynorvaline concentration was highest in above-ground vegetative tissue, but it was also detectable in roots and dry seeds. When 5-hydroxynorvaline was added to aphid artificial diet at concentrations similar to those found in maize leaves and stems, R. maidis reproduction was reduced, indicating that this maize metabolite may have a defensive function. Among 27 tested maize inbred lines there was a greater than 10-fold range in the accumulation of foliar 5-hydroxynorvaline. Genetic mapping populations derived from a subset of these inbred lines were used to map quantitative trait loci for 5-hydroxynorvaline accumulation to maize chromosomes 5 and 7. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Dynamic Maize Responses to Aphid Feeding Are Revealed by a Time Series of Transcriptomic and Metabolomic Assays1[OPEN

PubMed Central

Tzin, Vered; Fernandez-Pozo, Noe; Richter, Annett; Schmelz, Eric A.; Schoettner, Matthias; Schäfer, Martin; Ahern, Kevin R.; Meihls, Lisa N.; Kaur, Harleen; Huffaker, Alisa; Mori, Naoki; Degenhardt, Joerg; Mueller, Lukas A.; Jander, Georg

2015-01-01

As a response to insect attack, maize (Zea mays) has inducible defenses that involve large changes in gene expression and metabolism. Piercing/sucking insects such as corn leaf aphid (Rhopalosiphum maidis) cause direct damage by acquiring phloem nutrients as well as indirect damage through the transmission of plant viruses. To elucidate the metabolic processes and gene expression changes involved in maize responses to aphid attack, leaves of inbred line B73 were infested with corn leaf aphids for 2 to 96 h. Analysis of infested maize leaves showed two distinct response phases, with the most significant transcriptional and metabolic changes occurring in the first few hours after the initiation of aphid feeding. After 4 d, both gene expression and metabolite profiles of aphid-infested maize reverted to being more similar to those of control plants. Although there was a predominant effect of salicylic acid regulation, gene expression changes also indicated prolonged induction of oxylipins, although not necessarily jasmonic acid, in aphid-infested maize. The role of specific metabolic pathways was confirmed using Dissociator transposon insertions in maize inbred line W22. Mutations in three benzoxazinoid biosynthesis genes, Bx1, Bx2, and Bx6, increased aphid reproduction. In contrast, progeny production was greatly decreased by a transposon insertion in the single W22 homolog of the previously uncharacterized B73 terpene synthases TPS2 and TPS3. Together, these results show that maize leaves shift to implementation of physical and chemical defenses within hours after the initiation of aphid feeding and that the production of specific metabolites can have major effects in maize-aphid interactions. PMID:26378100

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

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.

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...

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...

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.

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.

Molecular mapping of QTLs for resistance to Gibberella ear rot, in corn, caused by Fusarium graminearum.

PubMed

Ali, M Liakat; Taylor, Jeff H; Jie, Liu; Sun, Genlou; William, Manilal; Kasha, Ken J; Reid, Lana M; Pauls, K Peter

2005-06-01

Gibberella ear rot, caused by the fungus Fusarium graminearum Schwabe, is a serious disease of corn (Zea mays) grown in northern climates. Infected corn is lower yielding and contains toxins that are dangerous to livestock and humans. Resistance to ear rot in corn is quantitative, specific to the mode of fungal entry (silk channels or kernel wounds), and highly influenced by the environment. Evaluations of ear rot resistance are complex and subjective; and they need to be repeated over several years. All of these factors have hampered attempts to develop F. graminearum resistant corn varieties. The aim of this study was to identify molecular markers linked to the genes for resistance to Gibberella ear rot. A recombinant inbred (RI) population, produced from a cross between a Gibberella ear rot resistant line (CO387) and a susceptible line (CG62), was field-inoculated and scored for Gibberella ear rot symptoms in the F4, F6, and F7 generations. The distributions of disease scores were continuous, indicating that resistance is probably conditioned by multiple loci. A molecular linkage map, based on segregation in the F5 RI population, contained 162 markers distributed over 10 linkage groups and had a total length of 2237 cM with an average distance between markers of 13.8 cM. Composite interval mapping identified 11 quantitative trait loci (QTLs) for Gibberella ear rot resistance following silk inoculation and 18 QTLs following kernel inoculation in 4 environments that accounted for 6.7%-35% of the total phenotypic variation. Only 2 QTLs (on linkage group 7) were detected in more than 1 test for silk resistance, and only 1 QTL (on linkage group 5) was detected in more than 1 test for kernel resistance, confirming the strong influence of the environment on these traits. The majority of the favorable alleles were derived from the resistant parent (CO387). The germplasm and markers for QTLs with significant phenotypic effects may be useful for marker-assisted selection to incorporate Gibberella ear rot resistance into commercial corn cultivars.

The Genomic Impacts of Drift and Selection for Hybrid Performance in Maize

PubMed Central

Gerke, Justin P.; Edwards, Jode W.; Guill, Katherine E.; Ross-Ibarra, Jeffrey; McMullen, Michael D.

2015-01-01

Although maize is naturally an outcrossing organism, modern breeding utilizes highly inbred lines in controlled crosses to produce hybrids. The U.S. Department of Agriculture’s reciprocal recurrent selection experiment between the Iowa Stiff Stalk Synthetic (BSSS) and the Iowa Corn Borer Synthetic No. 1 (BSCB1) populations represents one of the longest running experiments to understand the response to selection for hybrid performance. To investigate the genomic impact of this selection program, we genotyped the progenitor lines and >600 individuals across multiple cycles of selection using a genome-wide panel of ∼40,000 SNPs. We confirmed previous results showing a steady temporal decrease in genetic diversity within populations and a corresponding increase in differentiation between populations. Thanks to detailed historical information on experimental design, we were able to perform extensive simulations using founder haplotypes to replicate the experiment in the absence of selection. These simulations demonstrate that while most of the observed reduction in genetic diversity can be attributed to genetic drift, heterozygosity in each population has fallen more than expected. We then took advantage of our high-density genotype data to identify extensive regions of haplotype fixation and trace haplotype ancestry to single founder inbred lines. The vast majority of regions showing such evidence of selection differ between the two populations, providing evidence for the dominance model of heterosis. We discuss how this pattern is likely to occur during selection for hybrid performance and how it poses challenges for dissecting the impacts of modern breeding and selection on the maize genome. PMID:26385980

[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.

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.

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.

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

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...

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.

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 the present study facilitate the maize breeding work in Ethiopia and germplasm exchange among breeding programs in Africa. We suggest the incorporation of high density molecular marker information in future heterotic group assignments.

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

Inoculation Techniques in the Field Screening and Selection for Corn Inbred and Hybirds Resistance to Preharvest Aflatoxin Contamination

USDA-ARS?s Scientific Manuscript database

Preharvest aflatoxin contamination of grain grown on the U.S. Southeastern Coast Plain is provoked and aggravated by both biotic and abiotic stress factors that influence infection by Asperigillus flavus. An array of arthropod species contribute to the dispersal of this fungus as they attack and fee...

Relationship between aflatoxin contamination and physiological responses of corn plants under drought and heat stress.

PubMed

Kebede, Hirut; Abbas, Hamed K; Fisher, Daniel K; Bellaloui, Nacer

2012-11-20

Increased aflatoxin contamination in corn by the fungus Aspergillus flavus is associated with frequent periods of drought and heat stress during the reproductive stages of the plants. The objective of this study was to evaluate the relationship between aflatoxin contamination and physiological responses of corn plants under drought and heat stress. The study was conducted in Stoneville, MS, USA under irrigated and non-irrigated conditions. Five commercial hybrids, P31G70, P33F87, P32B34, P31B13 and DKC63-42 and two inbred germplasm lines, PI 639055 and PI 489361, were evaluated. The plants were inoculated with Aspergillus flavus (K-54) at mid-silk stage, and aflatoxin contamination was determined on the kernels at harvest. Several physiological measurements which are indicators of stress response were determined. The results suggested that PI 639055, PI 489361 and hybrid DKC63-42 were more sensitive to drought and high temperature stress in the non-irrigated plots and P31G70 was the most tolerant among all the genotypes. Aflatoxin contamination was the highest in DKC63-42 and PI 489361 but significantly lower in P31G70. However, PI 639055, which is an aflatoxin resistant germplasm, had the lowest aflatoxin contamination, even though it was one of the most stressed genotypes. Possible reasons for these differences are discussed. These results suggested that the physiological responses were associated with the level of aflatoxin contamination in all the genotypes, except PI 639055. These and other physiological responses related to stress may help examine differences among corn genotypes in aflatoxin contamination.

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...

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...

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 ...

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

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...

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...

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...

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 ...

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...

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...

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...

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.

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

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

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.

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

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...

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%...

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...

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...

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...

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 HD and biomass accumulation, vernalization was found to affect cell wall composition and free sugars accumulation in some Brachypodium inbred lines, suggesting genetic differences in how vernalization affects carbon flux to polysaccharides. Lastly, the availability of related RIL populations will allow for the genetic and molecular dissection of this natural variation, the knowledge of which may inform ways to genetically improve bioenergy crop grasses.« less

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 HD and biomass accumulation, vernalization was found to affect cell wall composition and free sugars accumulation in some Brachypodium inbred lines, suggesting genetic differences in how vernalization affects carbon flux to polysaccharides. Lastly, the availability of related RIL populations will allow for the genetic and molecular dissection of this natural variation, the knowledge of which may inform ways to genetically improve bioenergy crop grasses.« less

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 total amount extracted was observed, which reveals distinct in vivo associations and/or changes in binding strength between the inbred lines. Our approach produced information that relates protein content, relative protein content, and specific protein types to endosperm hardness and to the preferable use for "broa" bread-making.

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.

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...

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.

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 (...

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...

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

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

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.

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.

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.

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.

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

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

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.

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.

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...

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.

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...

Breeding maize for resistance to ear rot caused by Fusarium moniliforme.

PubMed

Hefny, M; Attaa, S; Bayoumi, T; Ammar, S; El-Bramawy, M

2012-01-15

Maize ear rots are among the most important impediments to increased maize production in Egypt. The present research was conducted to estimate combining abilities, heterosis and correlation coefficients for resistance to ear rot disease in seven corn inbred lines and their 21 crosses under field conditions. Results demonstrated that both additive and non-additive gene actions were responsible for the genetic expression of all characters with the preponderance of non-additive actions for days to 50% silking. The parental line L51 was the best combiner for earliness, low infection severity %, high phenols content, short plants and reasonable grain yield, while L101 was good combiner for low ear rot infection only. The cross: L122 x L84, L122 x L101, L51 x L101, L76 x L36, L76 x L84, L36 x L84, L36 x L81 and L36 x L101 which involved one or both parents with good General Combining Ability (GCA) effects expressed useful significant heterosis and Specific Combining Ability (SCA) effects for low infection severity %, high phenol contents, early silking, tall plants and high grain yield. Phenotypic and genotypic correlation coefficients suggest that selection for resistance to ear rot should identify lines with high yielding ability, early silking, tall plants, high phenols content and chitinase activity.

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.

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

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.

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.

[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.

A Foxtail mosaic virus Vector for Virus-Induced Gene Silencing in Maize.

PubMed

Mei, Yu; Zhang, Chunquan; Kernodle, Bliss M; Hill, John H; Whitham, Steven A

2016-06-01

Plant viruses have been widely used as vectors for foreign gene expression and virus-induced gene silencing (VIGS). A limited number of viruses have been developed into viral vectors for the purposes of gene expression or VIGS in monocotyledonous plants, and among these, the tripartite viruses Brome mosaic virus and Cucumber mosaic virus have been shown to induce VIGS in maize (Zea mays). We describe here a new DNA-based VIGS system derived from Foxtail mosaic virus (FoMV), a monopartite virus that is able to establish systemic infection and silencing of endogenous maize genes homologous to gene fragments inserted into the FoMV genome. To demonstrate VIGS applications of this FoMV vector system, four genes, phytoene desaturase (functions in carotenoid biosynthesis), lesion mimic22 (encodes a key enzyme of the porphyrin pathway), iojap (functions in plastid development), and brown midrib3 (caffeic acid O-methyltransferase), were silenced and characterized in the sweet corn line Golden × Bantam. Furthermore, we demonstrate that the FoMV infectious clone establishes systemic infection in maize inbred lines, sorghum (Sorghum bicolor), and green foxtail (Setaria viridis), indicating the potential wide applications of this viral vector system for functional genomics studies in maize and other monocots. © 2016 American Society of Plant Biologists. All Rights Reserved.

A Foxtail mosaic virus Vector for Virus-Induced Gene Silencing in Maize1[OPEN

PubMed Central

Mei, Yu; Kernodle, Bliss M.; Hill, John H.

2016-01-01

Plant viruses have been widely used as vectors for foreign gene expression and virus-induced gene silencing (VIGS). A limited number of viruses have been developed into viral vectors for the purposes of gene expression or VIGS in monocotyledonous plants, and among these, the tripartite viruses Brome mosaic virus and Cucumber mosaic virus have been shown to induce VIGS in maize (Zea mays). We describe here a new DNA-based VIGS system derived from Foxtail mosaic virus (FoMV), a monopartite virus that is able to establish systemic infection and silencing of endogenous maize genes homologous to gene fragments inserted into the FoMV genome. To demonstrate VIGS applications of this FoMV vector system, four genes, phytoene desaturase (functions in carotenoid biosynthesis), lesion mimic22 (encodes a key enzyme of the porphyrin pathway), iojap (functions in plastid development), and brown midrib3 (caffeic acid O-methyltransferase), were silenced and characterized in the sweet corn line Golden × Bantam. Furthermore, we demonstrate that the FoMV infectious clone establishes systemic infection in maize inbred lines, sorghum (Sorghum bicolor), and green foxtail (Setaria viridis), indicating the potential wide applications of this viral vector system for functional genomics studies in maize and other monocots. PMID:27208311

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.

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.

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...

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.

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

Genetic analysis of arsenic accumulation in maize using QTL mapping

NASA Astrophysics Data System (ADS)

Fu, Zhongjun; Li, Weihua; Xing, Xiaolong; Xu, Mengmeng; Liu, Xiaoyang; Li, Haochuan; Xue, Yadong; Liu, Zonghua; Tang, Jihua

2016-02-01

Arsenic (As) is a toxic heavy metal that can accumulate in crops and poses a threat to human health. The genetic mechanism of As accumulation is unclear. Herein, we used quantitative trait locus (QTL) mapping to unravel the genetic basis of As accumulation in a maize recombinant inbred line population derived from the Chinese crossbred variety Yuyu22. The kernels had the lowest As content among the different maize tissues, followed by the axes, stems, bracts and leaves. Fourteen QTLs were identified at each location. Some of these QTLs were identified in different environments and were also detected by joint analysis. Compared with the B73 RefGen v2 reference genome, the distributions and effects of some QTLs were closely linked to those of QTLs detected in a previous study; the QTLs were likely in strong linkage disequilibrium. Our findings could be used to help maintain maize production to satisfy the demand for edible corn and to decrease the As content in As-contaminated soil through the selection and breeding of As pollution-safe cultivars.

Genetic analysis of arsenic accumulation in maize using QTL mapping.

PubMed

Fu, Zhongjun; Li, Weihua; Xing, Xiaolong; Xu, Mengmeng; Liu, Xiaoyang; Li, Haochuan; Xue, Yadong; Liu, Zonghua; Tang, Jihua

2016-02-16

Arsenic (As) is a toxic heavy metal that can accumulate in crops and poses a threat to human health. The genetic mechanism of As accumulation is unclear. Herein, we used quantitative trait locus (QTL) mapping to unravel the genetic basis of As accumulation in a maize recombinant inbred line population derived from the Chinese crossbred variety Yuyu22. The kernels had the lowest As content among the different maize tissues, followed by the axes, stems, bracts and leaves. Fourteen QTLs were identified at each location. Some of these QTLs were identified in different environments and were also detected by joint analysis. Compared with the B73 RefGen v2 reference genome, the distributions and effects of some QTLs were closely linked to those of QTLs detected in a previous study; the QTLs were likely in strong linkage disequilibrium. Our findings could be used to help maintain maize production to satisfy the demand for edible corn and to decrease the As content in As-contaminated soil through the selection and breeding of As pollution-safe cultivars.

The Location of Genes Governing Long First Internode of Corn

PubMed Central

Troyer, A. F.

1997-01-01

Knowing breeding behavior and cytological location of traits helps breeders. My objective was to locate dominant genes for long first internode of corn (Zea mays L.). I determined that Hopi Indian corn PI213733 (variety Komona) displayed the trait and grew well in the U.S. Corn Belt. I crossed PI213733 to 26 translocation tester stocks in Minnesota inbred A188 background, backcrossed semi-sterile plants carrying the translocation to A188 the next generation, and grew the segregating generation planted in trenches 15 cm deep with ridges of dirt 10 cm high one year, in trenches 25 cm deep the other year and also at normal (6 cm) depth. Emerged plants were classified for semi-sterility or for normal pollen. I concluded from multiple testers for each chromosome arm that dominant genes for long first internode are located (chromosome and region) on 3S, on 6 near the centromere, and on 9S; spurious associations occurred for two testers. Measurement of cell lengths indicated that PI213733 had more cells than A188 both in upper and in lower mesocotyl sections and that lower, older cells elongated sooner. I found a normal-sized kernel with twin embryos that developed two long first internode seedlings indicating that the amount of endosperm did not limit mesocotyl growth. PMID:9093865

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

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.

Transgenic multivitamin corn through biofortification of endosperm with three vitamins representing three distinct metabolic pathways

PubMed Central

Naqvi, Shaista; Zhu, Changfu; Farre, Gemma; Ramessar, Koreen; Bassie, Ludovic; Breitenbach, Jürgen; Perez Conesa, Dario; Ros, Gaspar; Sandmann, Gerhard; Capell, Teresa; Christou, Paul

2009-01-01

Vitamin deficiency affects up to 50% of the world's population, disproportionately impacting on developing countries where populations endure monotonous, cereal-rich diets. Transgenic plants offer an effective way to increase the vitamin content of staple crops, but thus far it has only been possible to enhance individual vitamins. We created elite inbred South African transgenic corn plants in which the levels of 3 vitamins were increased specifically in the endosperm through the simultaneous modification of 3 separate metabolic pathways. The transgenic kernels contained 169-fold the normal amount of β-carotene, 6-fold the normal amount of ascorbate, and double the normal amount of folate. Levels of engineered vitamins remained stable at least through to the T3 homozygous generation. This achievement, which vastly exceeds any realized thus far by conventional breeding alone, opens the way for the development of nutritionally complete cereals to benefit the world's poorest people. PMID:19416835

Hydroxycinnamate Synthesis and Association with Mediterranean Corn Borer Resistance.

PubMed

Santiago, Rogelio; Malvar, Rosa Ana; Barros-Rios, Jaime; Samayoa, Luis Fernando; Butrón, Ana

2016-01-27

Previous results suggest a relationship between maize hydroxycinnamate concentration in the pith tissues and resistance to stem tunneling by Mediterranean corn borer (MCB, Sesamia nonagrioides Lef.) larvae. This study performs a more precise experiment, mapping an F2 derived from the cross between two inbreds with contrasting levels for hydroxycinnamates EP125 × PB130. We aimed to co-localize genomic regions involved in hydroxycinnamate synthesis and resistance to MCB and to highlight the particular route for each hydroxycinnamate component in relation to the better known phenylpropanoid pathway. Seven quantitative trait loci (QTLs) for p-coumarate, two QTLs for ferulate, and seven QTLs for total diferulates explained 81.7, 26.9, and 57.8% of the genotypic variance, respectively. In relation to borer resistance, alleles for increased hydroxycinnamate content (affecting one or more hydroxycinnamate compounds) could be associated with favorable effects on stem resistance to MCB, particularly the putative role of p-coumarate in borer resistance.

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

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.

Ethylene Contributes to maize insect resistance1-Mediated Maize Defense against the Phloem Sap-Sucking Corn Leaf Aphid1[OPEN

PubMed Central

Louis, Joe; Basu, Saumik; Varsani, Suresh; Castano-Duque, Lina; Jiang, Victoria; Williams, W. Paul; Felton, Gary W.; Luthe, Dawn S.

2015-01-01

Signaling networks among multiple phytohormones fine-tune plant defense responses to insect herbivore attack. Previously, it was reported that the synergistic combination of ethylene (ET) and jasmonic acid (JA) was required for accumulation of the maize insect resistance1 (mir1) gene product, a cysteine (Cys) proteinase that is a key defensive protein against chewing insect pests in maize (Zea mays). However, this study suggests that mir1-mediated resistance to corn leaf aphid (CLA; Rhopalosiphum maidis), a phloem sap-sucking insect pest, is independent of JA but regulated by the ET-signaling pathway. Feeding by CLA triggers the rapid accumulation of mir1 transcripts in the resistant maize genotype, Mp708. Furthermore, Mp708 provided elevated levels of antibiosis (limits aphid population)- and antixenosis (deters aphid settling)-mediated resistance to CLA compared with B73 and Tx601 maize susceptible inbred lines. Synthetic diet aphid feeding trial bioassays with recombinant Mir1-Cys Protease demonstrates that Mir1-Cys Protease provides direct toxicity to CLA. Furthermore, foliar feeding by CLA rapidly sends defensive signal(s) to the roots that trigger belowground accumulation of the mir1, signifying a potential role of long-distance signaling in maize defense against the phloem-feeding insects. Collectively, our data indicate that ET-regulated mir1 transcript accumulation, uncoupled from JA, contributed to heightened resistance to CLA in maize. In addition, our results underscore the significance of ET acting as a central node in regulating mir1 expression to different feeding guilds of insect herbivores. PMID:26253737

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.

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.

Development of Two Isogenic Sweet Corn Hybrids Differing for Glycinebetaine Content 1

PubMed Central

Rhodes, David; Rich, Patrick J.; Brunk, Dennis G.; Ju, Grace C.; Rhodes, Judith C.; Pauly, Michael H.; Hansen, Leon A.

1989-01-01

A hybrid of sweet corn, Zea mays L. (`1720'; Rogers Brothers Seed Co.), was found to be comprised of glycinebetaine-positive and glycinebetaine-deficient individuals in a 1:1 mixture. This phenomenon was traced to segregation for a single, nuclear, dominant gene determining leaf glycinebetaine content within the female inbred parent of this hybrid. Selection for homozygous recessive (glycinebetaine-deficient) and homozygous dominant (glycinebetaine-positive) genotypes of the female inbred parent enabled production of two isogenic versions of hybrid `1720' differing with respect to a single copy of the dominant allele, by mating these female parent selections with the common homozygous recessive (glycinebetaine-deficient) male parent. These two isogenic hybrids are shown to differ by a factor of 300- to 400-fold in glycinebetaine titer of young expanding leaves of salinized plants, but exhibit no striking differences in the levels of free amino acids or the level of N-methylnicotinic acid (nicotinic acid betaine; trigonelline). The only significant difference between the two hybrids in terms of amino acid composition was found to be in the level of alanine under nonsalinized conditions. The betaine-deficient hybrid exhibited a 14% lower alanine level than the betaine-positive hybrid. Betaine deficiency was not associated with altered stress-induced accumulation of amino acids such as proline, serine, and asparagine plus aspartate, attesting to the high specificity of the genetic difference between these isogenic hybrids with respect to betaine accumulation. This germplasm offers unique opportunities to test whether a single dominant allele determining stress-induced betaine accumulation capacity influences stress resistance in maize. PMID:16667120

Foliar resistance to fall armyworm in corn germplasm lines that confer resistance to root- and ear-feeding insects

USDA-ARS?s Scientific Manuscript database

A holistic approach to developing new corn germplasm that confers multiple insect resistance in various plant tissues at different growth stages was examined. Eight corn germplasm lines were examined for their foliage resistance to fall armyworm [Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noc...

Comprehensive field screenings for whorl- and ear-feeding insect resistance in corn germplasm lines

USDA-ARS?s Scientific Manuscript database

A holistic approach to developing new corn germplasm that confers multiple insect resistance in various plant tissues at different growth stages was examined in two separate studies. The first study was the screening of eight corn germplasm lines for resistance whorl damage to fall armyworm [Spodop...

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.

Aquatic degradation of Cry1Ab protein and decomposition dynamics of transgenic corn leaves under controlled conditions.

PubMed

Böttger, Rita; Schaller, Jörg; Lintow, Sven; Gert Dudel, E

2015-03-01

The increasing cultivation of genetically modified corn plants (Zea mays) during the last decades is suggested as a potential risk to the environment. One of these genetically modified variety expressed the insecticidal Cry1Ab protein originating from Bacillus thuringiensis (Bt), resulting in resistance against Ostrinia nubilalis, the European corn borer. Transgenic litter material is extensively studied regarding the decomposition in soils. However, only a few field studies analyzed the fate of the Cry1Ab protein and the impact of green and senescent leaf litter from corn on the decomposition rate and related ecosystem functions in aquatic environments. Consequently, a microbial litter decomposition experiment was conducted under controlled semi-natural conditions in batch culture using two maize varieties: one variety with Cry1Ab and another one with the appertaining Iso-line as control treatment. The results showed no significant differences between the treatment with Cry1Ab and the Iso-line regarding loss of total mass in dry weight of 43% for Iso-line and 45% for Bt-corn litter, lignin content increased to 137.5% (Iso-line) and 115.7% (Bt-corn), and phenol loss decreased by 53.6% (Iso-line), 62.2% (Bt-corn) during three weeks of the experiment. At the end of the experiment Cry1Ab protein was still detected with 6% of the initial concentration. A slightly but significant lower cellulose content was found for the Cry1Ab treatment compared to the Iso-line litter at the end of the experiment. The significant higher total protein (25%) and nitrogen (25%) content in Bt corn, most likely due to the additionally expression of the transgenic protein, may increase the microbial cellulose degradation and decrease microbial lignin degradation. In conclusion a relevant year by year input of protein and therefore nitrogen rich Bt corn litter into aquatic environments may affect the balanced nutrient turnover in aquatic ecosystems. Copyright © 2014 Elsevier Inc. All rights reserved.

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.

[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.

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.

Resistant Starch and Starch Thermal Characteristics in Exotic Corn Lines Grown in Temperate and Tropical Environments

USDA-ARS?s Scientific Manuscript database

Corn as a food that is heated and cooled to allow starch retrogradation has higher levels of resistant starch (RS). Increasing the amount of RS can make corn an even healthier food and may be accomplished by breeding and selection, especially by using exotic germplasm. Sixty breeding lines of introg...

Selection for Cry3Bb1 resistance in a genetically diverse population of non-diapausing western corn rootworm (Coleoptera: Chrysomelidae)

USDA-ARS?s Scientific Manuscript database

Five short-diapause laboratory lines of western corn rootworm (Diabrotica virgifera virgifera) were selected for resistance to MON863, a variety of corn genetically modified with the Bacillus thuringiensis (Bt) transgene that expresses the Cry3Bb1 d-endotoxin. Three of the selected lines were develo...

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...

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.

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 hypothesize that incompatibilities between alleles with different subspecific origins is a key driver of infertility. These results help clarify the factors that drove strain extinction in the CC, reveal the genetic regions associated with poor fertility in the CC, and serve as a resource to further study mammalian infertility. PMID:28592496

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.

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).

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.

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...

[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.

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.

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

Modulation of the Fecal Microbiota in Sprague-Dawley Rats Using Genetically Modified and Isogenic Corn Lines.

PubMed

Li, Penggao; Yang, Chun; Yue, Rong; Zhen, Yaping; Zhuo, Qin; Piao, Jianhua; Yang, Xiaoguang; Xiao, Rong

2018-01-17

This study investigated the composition and proportions of fecal microbiota in Sprague-Dawley rats after consuming two genetically modified (GM) corn lines in comparison with the isogenic corn and the AIN93G standard feed for 10 weeks using bar-coded 16S rRNA gene sequencing. As a result, GM corn did not significantly alter the overall health and alpha-diversity of fecal microbiota. Fecal microbiota structures could be separated into noncorn and corn but not non-GM and GM corn subgroups. Both non-GM and GM corn caused the increase in bacterial populations related to carbohydrates utilization, such as Lactobacillus, Barnesiella, and Bifidobacterium, and the reduction in potentially pathogenic populations, such as Tannerella and Moraxellaceae. In conclusion, similar effects on the fecal microbiota were observed after consuming a GM- and non-GM-corn-based diet for long periods. Further studies are warranted to elucidate the functional relevance of the changes in the proportions of bacterial populations in these diets.

[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.

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

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.

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...

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)...

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.

Evaluation of Bt Corn with Pyramided Genes on Efficacy and Insect Resistance Management for the Asian Corn Borer in China.

PubMed

Jiang, Fan; Zhang, Tiantao; Bai, Shuxiong; Wang, Zhenying; He, Kanglai

2016-01-01

A Bt corn hybrid (AcIe) with two Bt genes (cry1Ie and cry1Ac) was derived by breeding stack from line expressing Cry1Ie and a line expressing Cry1Ac. Efficacy of this pyramided Bt corn hybrid against the Asian corn borer (ACB), Ostrinia furnacalis, was evaluated. We conducted laboratory bioassays using susceptible and resistant ACB strains fed on artificial diet or fresh plant tissues. We also conducted field trials with artificial infestations of ACB neonates at the V6 and silk stages. The toxin-diet bioassay data indicated that mixtures of Cry1Ac and Cry1Ie proteins had synergistic insecticidal efficacy. The plant tissue bioassay data indicated that Bt corn hybrids expressing either a single toxin (Cry1Ac or Cry1Ie) or two toxins had high efficacy against susceptible ACB. Damage ratings in the field trials indicated that the Bt corn hybrids could effectively protect against 1st and the 2nd generation ACB in China. The hybrid line with two Bt genes showed a higher efficacy against ACB larvae resistant to Cry1Ac or CryIe than the hybrid containing one Bt gene, and the two gene hybrid would have increased potential for managing or delaying the evolution of ACB resistance to Bt corn plants.

Effect of reduced ferulate-mediated lignin/arabinoxylan cross-linking in corn silage on feed intake, digestibility, and milk production.

PubMed

Jung, H G; Mertens, D R; Phillips, R L

2011-10-01

Cross-linking of lignin to arabinoxylan by ferulates limits in vitro rumen digestibility of grass cell walls. The effect of ferulate cross-linking on dry matter intake (DMI), milk production, and in vivo digestibility was investigated in ad libitum and restricted-intake digestion trials with lambs, and in a dairy cow performance trial using the low-ferulate sfe corn mutant. Silages of 5 inbred corn lines were fed: W23, 2 W23sfe lines (M04-4 and M04-21), B73, and B73bm3. As expected, the W23sfe silages contained fewer ferulate ether cross-links and B73bm3 silage had a lower lignin concentration than the respective genetic controls. Silages were fed as the sole ingredient to 4 lambs per silage treatment. Lambs were confined to metabolism crates and fed ad libitum for a 12-d adaptation period followed by a 5-d collection period of feed refusals and feces. Immediately following the ad libitum feeding trial, silage offered was limited to 2% of body weight. After a 2-d adaptation to restricted feeding, feed refusals and feces were collected for 5 d. Seventy Holstein cows were blocked by lactation, days in milk, body weight, and milk production and assigned to total mixed ration diets based on the 5 corn silages. Diets were fed for 28 d and data were collected on weekly DMI and milk production and composition. Fecal grab samples were collected during the last week of the lactation trial for estimation of feed digestibility using acid-insoluble ash as a marker. Silage, total mixed ration, feed refusals, and fecal samples were analyzed for crude protein, starch, neutral detergent fiber (NDF), cell wall polysaccharides, and lignin. The W23sfe silages resulted in lower DMI in the ad libitum trial than the W23 silage, but DMI did not differ in the restricted trial. No differences were observed for NDF or cell wall polysaccharide digestibility by lambs with restricted feeding, but the amount of NDF digested daily increased for lambs fed the M04-21 W23sfe silage ad libitum. Lambs were less selective against NDF and lignin when offered W23sfe silages. The B73bm3 silage did not affect DMI or digestibility of cell walls at the restricted feeding level, but total daily NDF digested was greater at ad libitum intake. Intake, milk production, and cell wall digestibility were greater for cows fed diets containing W23sfe silages than for those fed W23 silage. Although milk production was greater for the B73bm3 diet, DMI and cell wall digestibility were not altered. Cows were less selective against cell wall material when fed both W23sfe and B73bm3 silages. Reduced ferulate cross-linking in sfe corn silage is a new genetic mechanism for improving milk production. Copyright © 2011 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

The genome architecture of the Collaborative Cross mouse genetic reference population.

PubMed

2012-02-01

The Collaborative Cross Consortium reports here on the development of a unique genetic resource population. The Collaborative Cross (CC) is a multiparental recombinant inbred panel derived from eight laboratory mouse inbred strains. Breeding of the CC lines was initiated at multiple international sites using mice from The Jackson Laboratory. Currently, this innovative project is breeding independent CC lines at the University of North Carolina (UNC), at Tel Aviv University (TAU), and at Geniad in Western Australia (GND). These institutions aim to make publicly available the completed CC lines and their genotypes and sequence information. We genotyped, and report here, results from 458 extant lines from UNC, TAU, and GND using a custom genotyping array with 7500 SNPs designed to be maximally informative in the CC and used a novel algorithm to infer inherited haplotypes directly from hybridization intensity patterns. We identified lines with breeding errors and cousin lines generated by splitting incipient lines into two or more cousin lines at early generations of inbreeding. We then characterized the genome architecture of 350 genetically independent CC lines. Results showed that founder haplotypes are inherited at the expected frequency, although we also consistently observed highly significant transmission ratio distortion at specific loci across all three populations. On chromosome 2, there is significant overrepresentation of WSB/EiJ alleles, and on chromosome X, there is a large deficit of CC lines with CAST/EiJ alleles. Linkage disequilibrium decays as expected and we saw no evidence of gametic disequilibrium in the CC population as a whole or in random subsets of the population. Gametic equilibrium in the CC population is in marked contrast to the gametic disequilibrium present in a large panel of classical inbred strains. Finally, we discuss access to the CC population and to the associated raw data describing the genetic structure of individual lines. Integration of rich phenotypic and genomic data over time and across a wide variety of fields will be vital to delivering on one of the key attributes of the CC, a common genetic reference platform for identifying causative variants and genetic networks determining traits in mammals.

Evaluation of corn germplasm lines for multiple ear-colonizing insect and disease resistance.

PubMed

Ni, Xinzhi; Xu, Wenwei; Blanco, Michael H; Wilson, Jeffrey P

2012-08-01

Ear-colonizing insects and diseases that reduce yield and impose health threats by mycotoxin contaminations in the grain, are critical impediments for corn (Zea mays L.) production in the southern United States. Ten germplasm lines from the Germplasm Enhancement of Maize (GEM) Program in Ames, IA, and Raleigh, NC, and 10 lines (derived from GEM germplasm) from the Texas Agricultural Experiment Station in Lubbock, TX, were examined in 2007 and 2008 with local resistant and susceptible controls. Four types of insect damage and smut disease (Ustilago maydis) infection, as well as gene X environment (G X E) interaction, was assessed on corn ears under field conditions. Insect damage on corn ears was further separated as cob and kernel damage. Cob penetration rating was used to assess corn earworm [Helicoverpa zea (Boddie)] and fall armyworm [Spodoptera frugiperda (J.E. Smith)] feeding on corn cobs, whereas kernel damage was assessed using three parameters: 1) percentage of kernels discolored by stink bugs (i.e., brown stink bug [Euschistus serous (Say)], southern green stink bug [Nezara viridula (L.)], and green stink bug [Chinavia (Acrosternum) hilare (Say)]; 2) percentage of maize weevil (Sitophilus zeamais Motschulsky)-damaged kernels; and 3) percentage of kernels damaged by sap beetle (Carpophilus spp.), "chocolate milkworm" (Moodna spp.), and pink scavenger caterpillar [Pyroderces (Anatrachyntis) rileyi (Walsingham)]. The smut infection rates on ears, tassels, and nodes also were assessed. Ear protection traits (i.e., husk tightness and extension) in relation to insect damage and smut infection also were examined. Significant differences in insect damage, smut infection, and husk protection traits were detected among the germplasm lines. Three of the 20 germplasm lines were identified as being multiple insect and smut resistant. Of the three lines, entries 5 and 7 were derived from DKXL370, which was developed using corn germplasm from Brazil, whereas entry 14 was derived from CUBA117.

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

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.

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

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 ...

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 ...

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

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.

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

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

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.

Liquid-liquid distribution of ion associates of tetrabromoindate(III) with quaternary ammonium counter ions.

PubMed

Yamamoto, K; Matsumoto, A

1997-11-01

The solvent extraction of an ion associate of tetrabromoindate(III) ion, InBr(-)(4), with quaternary ammonium cations (Q(+)) has been studied. The extraction constant (K(ex)) were determined for the ion associates of InBr(-)(4) with Q(+) between an aqueous phase and several organic phases (chloroform, chlorobenzene, benzene and toluene). A linear relationship was found between log K(ex) and the total number of carbon atoms in Q(+); from the slope of the lines, the contribution of a methylene group to log K(ex) was calculated to be 0.91 for the chloroform extraction system and 0.52 for the other extraction systems. The extractability with alkyltrimethylammonium cations was larger than that with symmetrical tetraalkylammonium cations and the mean difference in log K(ex) for two cations (one of each type) with the same number of carbon atoms was about 1.3. From the extraction constant obtained, the extractability of InBr(-)(4) among metal-halogeno complex anions was in the order TlBr(-)(4) > BiI(-)(4) > AuBr(-)(4) > AuCl(-)(4) > TlCl(-)(4) > InBr(-)(4) > CuCl(-)(2).

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...

[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 stimulant.

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...

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

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.

Breeding aflatoxin-resistant maize lines using recent advances in technologies - a review.

PubMed

Brown, Robert L; Menkir, Abebe; Chen, Zhi-Yuan; Bhatnagar, Deepak; Yu, Jiujiang; Yao, Haibo; Cleveland, Thomas E

2013-01-01

Aflatoxin contamination caused by Aspergillus flavus infection of corn is a significant and chronic threat to corn being used as food or feed. Contamination of crops at levels of 20 ng g(-1) or higher (as regulated by the USFDA) by this toxin and potent carcinogen makes the crop unsalable, resulting in a significant economic burden on the producer. This review focuses on elimination of this contamination in corn which is a major US crop and the basis of many products. Corn is also "nature's example" of a crop containing heritable resistance to aflatoxin contamination, thereby serving as a model for achieving resistance to aflatoxin contamination in other crops as well. This crop is the largest production grain crop worldwide, providing food for billions of people and livestock and critical feedstock for production of biofuels. In 2011, the economic value of the US corn crop was US$76 billion, with US growers producing an estimated 12 billion bushels, more than one-third of the world's supply. Thus, the economics and significance of corn as a food crop and the threat to food safety due to aflatoxin contamination of this major food crop have prompted the many research efforts in many parts of the world to identify resistance in corn to aflatoxin contamination. Plant breeding and varietal selection has been used as a tool to develop varieties resistance to disease. This methodology has been employed in defining a few corn lines that show resistance to A. flavus invasion; however, no commercial lines have been marketed. With the new tools of proteomics and genomics, identification of resistance mechanisms, and rapid resistance marker selection methodologies, there is an increasing possibility of finding significant resistance in corn, and in understanding the mechanism of this resistance.

Repression of P Element-Mediated Hybrid Dysgenesis in Drosophila Melanogaster

PubMed Central

Simmons, M. J.; Raymond, J. D.; Rasmusson, K. E.; Miller, L. M.; McLarnon, C. F.; Zunt, J. R.

1990-01-01

Inbred lines derived from a strain called Sexi were analyzed for their abilities to repress P element-mediated gonadal dysgenesis. One line had high repression ability, four had intermediate ability and two had very low ability. The four intermediate lines also exhibited considerable within-line variation for this trait; furthermore, in at least two cases, this variation could not be attributed to recurring P element movement. Repression of gonadal dysgenesis in the hybrid offspring of all seven lines was due primarily to a maternal effect; there was no evidence for repression arising de novo in the hybrids themselves. In one of the lines, repression ability was inherited maternally, indicating the involvement of cytoplasmic factors. In three other lines, repression ability appeared to be determined by partially dominant or additive chromosomal factors; however, there was also evidence for a maternal effect that reduced the expression of these factors in at least two of the lines. In another line, repression ability seemed to be due to recessive chromosomal factors. All seven lines possessed numerous copies of a particular P element, called KP, which has been hypothesized to produce a polypeptide repressor of gonadal dysgenesis. This hypothesis, however, does not explain why the inbred Sexi lines varied so much in their repression abilities. It is suggested that some of this variation may be due to differences in the chromosomal position of the KP elements, or that other nonautonomous P elements are involved in the repression of hybrid dysgenesis in these lines. PMID:2155854

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

Thc6 protein, isolated from Trichoderma harzianum, can induce maize defense response against Curvularia lunata.

PubMed

Fan, Lili; Fu, Kehe; Yu, Chuanjin; Li, Yingying; Li, Yaqian; Chen, Jie

2015-05-01

Mutant T66 was isolated from 450 mutants (constructed with Agrobacterium tumefaciens-mediated transformation method) of Trichoderma harzianum. Maize seeds coated with T66 were more susceptible to Curvularia lunata when compared with those coated with wild-type (WT) strain. The disease index of maize treated with T66 and WT were 62.5 and 42.1%, respectively. Further research showed T-DNA has inserted into the ORF of one gene, which resulted in the functional difference between WT and T66. The gene was cloned and named Thc6, which encodes a novel 327 amino acid protein. To investigate its function, we obtained knockout, complementation, and overexpression mutants of Thc6. Challenge inoculation studies suggested that the Thc6 overexpression mutant can reduce the disease index of maize inbred line Huangzao 4 against the leaf spot pathogen (C. lunata). Meanwhile, The Thc6 mutants were found to affect the resistance of maize inbred line Huangzao 4 against C. lunata by enhancing the activation of jasmonate-responsive genes expression. Liquid chromatography-mass spectrometry (LC-MS) data further confirmed that the concentration of jasmonate in the induced maize exhibits a parallel change tendency with the expression level of defense-related genes. Hence, the Thc6 gene could be participated in the induced resistance of maize inbred line Huangzao 4 against C. lunata infection through a jasmonic acid-dependent pathway. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A method for genotyping elite breeding stocks of leaf chicory (Cichorium intybus L.) by assaying mapped microsatellite marker loci.

PubMed

Ghedina, Andrea; Galla, Giulio; Cadalen, Thierry; Hilbert, Jean-Louis; Caenazzo, Silvano Tiozzo; Barcaccia, Gianni

2015-12-30

Leaf chicory (Cichorium intybus subsp. intybus var. foliosum L.) is a diploid plant species (2n = 18) of the Asteraceae family. The term "chicory" specifies at least two types of cultivated plants: a leafy vegetable, which is highly differentiated with respect to several cultural types, and a root crop, whose current industrial utilization primarily addresses the extraction of inulin or the production of a coffee substitute. The populations grown are generally represented by local varieties (i.e., landraces) with high variation and adaptation to the natural and anthropological environment where they originated, and have been yearly selected and multiplied by farmers. Currently, molecular genetics and biotechnology are widely utilized in marker-assisted breeding programs in this species. In particular, molecular markers are becoming essential tools for developing parental lines with traits of interest and for assessing the specific combining ability of these lines to breed F1 hybrids. The present research deals with the implementation of an efficient method for genotyping elite breeding stocks developed from old landraces of leaf chicory, Radicchio of Chioggia, which are locally dominant in the Veneto region, using 27 microsatellite (SSR) marker loci scattered throughout the linkage groups. Information on the genetic diversity across molecular markers and plant accessions was successfully assessed along with descriptive statistics over all marker loci and inbred lines. Our overall data support an efficient method for assessing a multi-locus genotype of plant individuals and lineages that is useful for the selection of new varieties and the certification of local products derived from Radicchio of Chioggia. This method proved to be useful for assessing the observed degree of homozygosity of the inbred lines as a measure of their genetic stability; plus it allowed an estimate of the specific combining ability (SCA) between maternal and paternal inbred lines on the basis of their genetic diversity and the predicted degree of heterozygosity of their F1 hybrids. This information could be exploited for planning crosses and predicting plant vigor traits (i.e., heterosis) of experimental F1 hybrids on the basis of the genetic distance and allelic divergence between parental inbred lines. Knowing the parental genotypes would allow us not only to protect newly registered varieties but also to assess the genetic purity and identity of the seed stocks of commercial F1 hybrids, and to certificate the origin of their food derivatives.

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

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.

Fitness of Bt-resistant Western Corn Rootworm on Mon863 and Isoline Corn

USDA-ARS?s Scientific Manuscript database

Abstract: To help ensure that insect resistance management plans mandated by the US Environmental Protection Agency are based on the best science available, we evaluated fitness costs associated with resistance development in artificially selected laboratory lines of the western corn rootworm, Diabr...

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.

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. ...

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...

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...

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). ...

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.

78 FR 13302 - Syngenta Biotechnology, Inc.; Determination of Nonregulated Status of Corn Genetically Engineered...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-27

...] Syngenta Biotechnology, Inc.; Determination of Nonregulated Status of Corn Genetically Engineered for... are advising the public of our determination that a corn line developed by the Syngenta Biotechnology... evaluation of data submitted by Syngenta Biotechnology, Inc., in its petition for a determination of...

75 FR 20560 - Syngenta Biotechnology, Inc.; Determination of Nonregulated Status for Corn Genetically...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-20

...] Syngenta Biotechnology, Inc.; Determination of Nonregulated Status for Corn Genetically Engineered for... are advising the public of our determination that a corn line developed by Syngenta Biotechnology, Inc... Biotechnology, Inc., in its petition for a determination of nonregulated status, our analysis of other...

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.

Selection for Cry3Bb1 resistance in a genetically diverse population of nondiapausing western corn rootworm (Coleoptera: Chrysomelidae).

PubMed

Oswald, Kenneth J; French, B Wade; Nielson, Chad; Bagley, Mark

2011-06-01

Five short-diapause laboratory lines of western corn rootworm, Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae), were selected for resistance to MON863, a variety of corn genetically modified with the Bacillus thuringiensis Berliner (Bt) transgene that expresses the Cry3Bb1 delta-endotoxin. Three of the selected lines were developed by incremental increase in the duration of exposure to MON863 over 11 generations (moderate selected lines). Two selected lines were developed from a control group by constant exposure to MON863 for at least 14 d posthatch over seven generations (intense selected lines). At the end of the experiment, survivorship, as measured by adult emergence, was approximately 4 times higher in each of the selected lines reared on MON863 compared with control lines. Estimates of realized heritabilities (h2) were 0.16 and 0.15 for the moderate and intense selected lines, respectively, and are consistent with h2 estimates reported previously from a variety of pest insects. These lines provide data necessary for evaluating the potential for Bt resistance within diabroticite beetles and will be useful for developing improved insect resistance management strategies.

Quantitative Trait Loci Mapping of Western Corn Rootworm (Coleoptera: Chrysomelidae) Host Plant Resistance in Two Populations of Doubled Haploid Lines in Maize (Zea mays L.).

PubMed

Bohn, Martin O; Marroquin, Juan J; Flint-Garcia, Sherry; Dashiell, Kenton; Willmot, David B; Hibbard, Bruce E

2018-02-09

Over the last 70 yr, more than 12,000 maize accessions have been screened for their level of resistance to western corn rootworm, Diabrotica virgifera virgifera (LeConte; Coleoptera: Chrysomelidae), larval feeding. Less than 1% of this germplasm was selected for initiating recurrent selection or other breeding programs. Selected genotypes were mostly characterized by large root systems and superior root regrowth after root damage caused by western corn rootworm larvae. However, no hybrids claiming native (i.e., host plant) resistance to western corn rootworm larval feeding are currently commercially available. We investigated the genetic basis of western corn rootworm resistance in maize materials with improved levels of resistance using linkage disequilibrium mapping approaches. Two populations of topcrossed doubled haploid maize lines (DHLs) derived from crosses between resistant and susceptible maize lines were evaluated for their level of resistance in three to four different environments. For each DHL topcross an average root damage score was estimated and used for quantitative trait loci (QTL) analysis. We found genomic regions contributing to western corn rootworm resistance on all maize chromosomes, except for chromosome 4. Models fitting all QTL simultaneously explained about 30 to 50% of the genotypic variance for root damage scores in both mapping populations. Our findings confirm the complex genetic structure of host plant resistance against western corn rootworm larval feeding in maize. Interestingly, three of these QTL regions also carry genes involved in ascorbate biosynthesis, a key compound we hypothesize is involved in the expression of western corn rootworm resistance. © The Author(s) 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Transient infrared spectroscopy for detection of toxigenic fungi in corn: potential for on-line evaluation.

PubMed

Gordon, S H; Jones, R W; McClelland, J F; Wicklow, D T; Greene, R V

1999-12-01

An urgent need for rapid sensors to detect contamination of food grains by toxigenic fungi such as Aspergillus flavus prompted research and development of Fourier transform infrared photoacoustic spectroscopy (FTIR-PAS) as a highly sensitive probe for fungi growing on the surfaces of individual corn kernels. However, the photoacoustic technique has limited potential for screening bulk corn because currently available photoacoustic detectors can accommodate only a single intact kernel at a time. Transient infrared spectroscopy (TIRS), on the other hand, is a promising new technique that can acquire analytically useful infrared spectra from a moving mass of solid materials. Therefore, the potential of TIRS for on-line, noncontact detection of A. flavus contamination in a moving bed of corn kernels was explored. Early test results based on visual inspection of TIRS spectral differences predict an 85% or 95% success rate in distinguishing healthy corn from grain infected with A. flavus. Four unique infrared spectral features which identified infected corn in FTIR-PAS were also found to be diagnostic in TIRS. Although the technology is still in its infancy, the preliminary results indicate that TIRS is a potentially effective screening method for bulk quantities of corn grain.

Permeability studies of redox-sensitive nitroxyl spin probes in corn oil using an L-band ESR spectrometer

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

Jebaraj, D. David; Utsumi, Hideo; Asath, R. Mohamed

Electron spin resonance (ESR) studies were carried out for 2mM {sup 14}N labeled {sup 2}H enriched 3-methoxycarbonyl-2,2,5,5-tetramethyl-pyrrolidine-1-oxyl (MC-PROXYL) and 3–carboxy-2,2,5,5,-tetramethyl-1-pyrrolidinyloxy (carboxy-PROXYL) in pure water and various concentrations of corn oil. The ESR parameters, such as the line width, hyperfine coupling constant, g-factor, rotational correlation time, partition parameter and permeability were reported for the samples. The line width broadening was observed for both nitroxyl radicals in corn oil solutions. The partition parameter for permeable MC-PROXYL in corn oil increases with increasing concentration of corn oil, which reveals that the nitroxyl spin probe permeates into the oil phase. From the results, themore » corn oil concentration was optimized as 50 % for phantom studies. The rotational correlation time also increases with increasing concentration of corn oil. The permeable and impermeable nature of nitroxyl spin probes was demonstrated. These results will be useful for the development of ESR/OMR imaging modalities in in vivo and in vitro studies.« less

[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.

Mapping QTL for popping expansion volume in popcorn with simple sequence repeat markers.

PubMed

Lu, H-J; Bernardo, R; Ohm, H W

2003-02-01

Popping expansion volume is the most important quality trait in popcorn ( Zea mays L.), but its genetics is not well understood. The objectives of this study were to map quantitative trait loci (QTLs) responsible for popping expansion volume in a popcorn x dent corn cross, and to compare the predicted efficiencies of phenotypic selection, marker-based selection, and marker-assisted selection for popping expansion volume. Of 259 simple sequence repeat (SSR) primer pairs screened, 83 pairs were polymorphic between the H123 (dent corn) and AG19 (popcorn) parental inbreds. Popping test data were obtained for 160 S(1) families developed from the [AG19(H123 x AG19)] BC(1) population. The heritability ( h(2)) for popping expansion volume on an S(1) family mean basis was 0.73. The presence of the gametophyte factor Ga1(s) in popcorn complicates the analysis of popcorn x dent corn crosses. But, from a practical perspective, the linkage between a favorable QTL allele and Ga1(s) in popcorn will lead to selection for the favorable QTL allele. Four QTLs, on chromosomes 1S, 3S, 5S and 5L, jointly explained 45% of the phenotypic variation. Marker-based selection for popping expansion volume would require less time and work than phenotypic selection. But due to the high h(2) of popping expansion volume, marker-based selection was predicted to be only 92% as efficient as phenotypic selection. Marker-assisted selection, which comprises index selection on phenotypic and marker scores, was predicted to be 106% as efficient as phenotypic selection. Overall, our results suggest that phenotypic selection will remain the preferred method for selection in popcorn x dent corn crosses.

Selection for Cry3Bb1 resistance in a genetically diverse population of nondiapausing Western Corn Rootworm (Coleoptera: Chrysomelidae)

EPA Science Inventory

Five short-diapause laboratory lines of western corn rootworm (Diabrotica virgifera virgifera) were selected for resistance to MON863, a variety of corn genetically modified with the Bacillus thuringiensis (Bt) transgene that expresses the Cry3Bb1 endotoxin. Three of the selecte...

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...

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...

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...

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...

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.

Growth and Reproduction of Glyphosate-Resistant and Susceptible Populations of Kochia scoparia

PubMed Central

Kumar, Vipan; Jha, Prashant

2015-01-01

Evolution of glyphosate-resistant kochia is a threat to no-till wheat-fallow and glyphosate-resistant (GR) cropping systems of the US Great Plains. The EPSPS (5-enol-pyruvylshikimate-3-phosphate synthase) gene amplification confers glyphosate resistance in the tested Kochia scoparia (L.) Schrad populations from Montana. Experiments were conducted in spring to fall 2014 (run 1) and summer 2014 to spring 2015 (run 2) to investigate the growth and reproductive traits of the GR vs. glyphosate-susceptible (SUS) populations of K. scoparia and to determine the relationship of EPSPS gene amplification with the level of glyphosate resistance. GR K. scoparia inbred lines (CHES01 and JOP01) exhibited 2 to 14 relative copies of the EPSPS gene compared with the SUS inbred line with only one copy. In the absence of glyphosate, no differences in growth and reproductive parameters were evident between the tested GR and SUS inbred lines, across an intraspecific competition gradient (1 to 170 plants m-2). GR K. scoparia plants with 2 to 4 copies of the EPSPS gene survived the field-use rate (870 g ha-1) of glyphosate, but failed to survive the 4,350 g ha-1 rate of glyphosate (five-times the field-use rate). In contrast, GR plants with 5 to 14 EPSPS gene copies survived the 4,350 g ha-1 of glyphosate. The results from this research indicate that GR K. scoparia with 5 or more EPSPS gene copies will most likely persist in field populations, irrespective of glyphosate selection pressure. PMID:26580558

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.

Development of CACTA transposon derived SCAR markers and their use in population structure analysis in Zea mays.

PubMed

Roy, Neha Samir; Park, Kyong-Cheul; Lee, Sung-Il; Im, Min-Ji; Ramekar, Rahul Vasudeo; Kim, Nam-Soo

2018-02-01

Molecular marker technologies have proven to be an important breakthrough for genetic studies, construction of linkage maps and population genetics analysis. Transposable elements (TEs) constitute major fractions of repetitive sequences in plants and offer a wide range of possible areas to be explored as molecular markers. Sequence characterized amplified region (SCAR) marker development provides us with a simple and time saving alternative approach for marker development. We employed the CACTA-TD to develop SCARs and then integrated them into linkage map and used them for population structure and genetic diversity analysis of corn inbred population. A total of 108 dominant SCAR markers were designed out of which, 32 were successfully integrated in to the linkage map of maize RIL population and the remaining were added to a physical map for references to check the distribution throughout all chromosomes. Moreover, 76 polymorphic SCARs were used for diversity analysis of corn accessions being used in Korean corn breeding program. The overall average polymorphic information content (PIC) was 0.34, expected heterozygosity was 0.324 and Shannon's information index was 0.491 with a percentage of polymorphism of 98.67%. Further analysis by associating with desirable traits may also provide some accurate trait specific tagged SCAR markers. TE linked SCARs can provide an added level of polymorphism as well as improved discriminating ability and therefore can be useful in further breeding programs to develop high yielding germplasm.

Analyzing Maize Anther Development Using Transposons

NASA Astrophysics Data System (ADS)

Han, S.

2011-12-01

Over the summer, we tackled two projects in studying more about transposons (moving/jumping genes) such as Mutator genes in corn for this project, and how the plants switch from the stages of mitosis to meiosis without a germ line. We use a transgenic corn line containing RescueMu (an artificial Mutator containing a plasmid in it), so we can keep track of the insertion events. This is a long term project so we haven't come to any final conclusions or results with tracking what happens in Mutator transposition during different stages of corn development but our process shows to work so we continue with what we've been doing.

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...

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...

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...

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.

Morphogenic Regulators Baby boom and Wuschel Improve Monocot Transformation.

PubMed

Lowe, Keith; Wu, Emily; Wang, Ning; Hoerster, George; Hastings, Craig; Cho, Myeong-Je; Scelonge, Chris; Lenderts, Brian; Chamberlin, Mark; Cushatt, Josh; Wang, Lijuan; Ryan, Larisa; Khan, Tanveer; Chow-Yiu, Julia; Hua, Wei; Yu, Maryanne; Banh, Jenny; Bao, Zhongmeng; Brink, Kent; Igo, Elizabeth; Rudrappa, Bhojaraja; Shamseer, P M; Bruce, Wes; Newman, Lisa; Shen, Bo; Zheng, Peizhong; Bidney, Dennis; Falco, S Carl; RegisterIII, James C; Zhao, Zuo-Yu; Xu, Deping; Jones, Todd J; Gordon-Kamm, William James

2016-09-06

While transformation of the major monocot crops is currently possible, the process typically remains confined to one or two genotypes per species, often with poor agronomics, and efficiencies that place these methods beyond the reach of most academic laboratories. Here, we report a transformation approach involving overexpression of the maize (Zea mays) Baby boom (Bbm) and maize Wuschel2 (Wus2) genes, which produced high transformation frequencies in numerous previously non-transformable maize inbred lines. For example, the Pioneer inbred PHH5G is recalcitrant to biolistic and Agrobacterium transformation. However, when Bbm and Wus2 were expressed, transgenic calli were recovered from over 40% of the starting explants, with most producing healthy, fertile plants. Another limitation for many monocots is the intensive labor and greenhouse space required to supply immature embryos for transformation. This problem could be alleviated by using alternative target tissues that could be supplied consistently with automated preparation. As a major step toward this objective, we transformed Bbm and Wus2 directly into either embryo slices from mature seed or leaf segments from seedlings in a variety of Pioneer inbred lines, routinely recovering healthy, fertile T0 plants. Finally, we demonstrated that the maize Bbm and Wus2 genes stimulate transformation in sorghum (Sorghum bicolor) immature embryos, sugarcane (Saccharum officinarum) callus, and indica rice (Oryza sativa var. indica) callus. {copyright, serif} 2016 American Society of Plant Biologists. All rights reserved.

Morphogenic Regulators Baby boom and Wuschel Improve Monocot Transformation[OPEN

PubMed Central

Lowe, Keith; Wu, Emily; Cho, Myeong-Je; Lenderts, Brian; Chamberlin, Mark; Cushatt, Josh; Ryan, Larisa; Khan, Tanveer; Chow-Yiu, Julia; Hua, Wei; Banh, Jenny; Bao, Zhongmeng; Brink, Kent; Igo, Elizabeth; Rudrappa, Bhojaraja; Shamseer, PM; Shen, Bo; Zheng, Peizhong; Bidney, Dennis; Falco, Carl; Zhao, Zuo-Yu; Xu, Deping

2016-01-01

While transformation of the major monocot crops is currently possible, the process typically remains confined to one or two genotypes per species, often with poor agronomics, and efficiencies that place these methods beyond the reach of most academic laboratories. Here, we report a transformation approach involving overexpression of the maize (Zea mays) Baby boom (Bbm) and maize Wuschel2 (Wus2) genes, which produced high transformation frequencies in numerous previously nontransformable maize inbred lines. For example, the Pioneer inbred PHH5G is recalcitrant to biolistic and Agrobacterium tumefaciens transformation. However, when Bbm and Wus2 were expressed, transgenic calli were recovered from over 40% of the starting explants, with most producing healthy, fertile plants. Another limitation for many monocots is the intensive labor and greenhouse space required to supply immature embryos for transformation. This problem could be alleviated using alternative target tissues that could be supplied consistently with automated preparation. As a major step toward this objective, we transformed Bbm and Wus2 directly into either embryo slices from mature seed or leaf segments from seedlings in a variety of Pioneer inbred lines, routinely recovering healthy, fertile T0 plants. Finally, we demonstrated that the maize Bbm and Wus2 genes stimulate transformation in sorghum (Sorghum bicolor) immature embryos, sugarcane (Saccharum officinarum) callus, and indica rice (Oryza sativa ssp indica) callus. PMID:27600536

Reinventing potato at the diploid level

USDA-ARS?s Scientific Manuscript database

We are positioned to revolutionize potato by reconstructing it as a diploid inbred-line based crop. Currently, potato is an asexually propagated cross-pollinated tetraploid crop, for which breeding methodologies have not changed substantially in 100 years. Current methods for creating new potato cul...

Maize cultivar performance under diverse organic production systems

USDA-ARS?s Scientific Manuscript database

Maize cultivar performance can vary widely among different production systems. The need for high-performing hybrids for organic systems with wide adaptation to various macroenvironments is becoming increasingly important. The goal of this study was to characterize inbred lines developed by distinc...

Antioxidant and antiproliferative activity of blue corn and tortilla from native maize.

PubMed

Herrera-Sotero, Mónica Y; Cruz-Hernández, Carlos D; Trujillo-Carretero, Carolina; Rodríguez-Dorantes, Mauricio; García-Galindo, Hugo S; Chávez-Servia, José L; Oliart-Ros, Rosa M; Guzmán-Gerónimo, Rosa I

2017-10-30

Blue corn is a cereal rich in phenolic compounds used to make blue tortillas. Tortillas are an important part of the Mexican diet. Blue corn and tortilla represent an important source of the natural antioxidants anthocyanins. However, studies on their biological activity on cancer cell lines are limited. The goal of this study was to evaluate the antioxidant and antiproliferative activity of blue corn and tortilla on different cancer cell lines. Total polyphenol content, monomeric anthocyanins, and antioxidant activity by the DPPH and TBARS methods of blue corn and tortilla were determined. The anthocyanin profile of tortilla was obtained by means of HPLC-ESI-MS. The antiproliferative activity of blue corn and tortilla extract on HepG2, H-460, Hela, MCF-7 and PC-3 was evaluated by the MTT assay. Blue corn had higher content of total polyphenols and monomeric anthocyanins as well as lower percentage of polymeric color than tortilla; however, both showed similar antioxidant activity by DPPH. In addition, although a higher degradation of anthocyanins was observed on tortilla extract, both extracts inhibited lipid peroxidation (IC50) at a similar concentration. The anthocyanin profile showed 28 compounds which are primarily derived from cyanidin, including acylated anthocyanins and proanthocyanidins. Blue corn and tortilla extracts showed antiproliferative effects against HepG2, H-460, MCF-7 and PC-3 cells at 1000 μg/mL, however Hela cells were more sensitive at this concentration. This is the first report to demonstrate anticancer properties in vitro of tortilla derived from blue corn, suggesting that this product has beneficial health effects. In addition, blue corn could be a potential source of nutraceuticals with anticancer activity.

Low-frequency ESR studies on permeable and impermeable deuterated nitroxyl radicals in corn oil solution.

PubMed

David Jebaraj, D; Utsumi, Hideo; Milton Franklin Benial, A

2018-04-01

Low-frequency electron spin resonance studies were performed for 2 mM concentration of deuterated permeable and impermeable nitroxyl spin probes, 3-methoxycarbonyl-2,2,5,5-tetramethyl-pyrrolidine-1-oxyl and 3-carboxy-2,2,5,5,-tetramethyl-1-pyrrolidinyloxy in pure water and various concentrations of corn oil solution. The electron spin resonance parameters such as the line width, hyperfine coupling constant, g factor, rotational correlation time, permeability, and partition parameter were estimated. The broadening of line width was observed for nitroxyl radicals in corn oil mixture. The rotational correlation time increases with increasing concentration of corn oil, which indicates the less mobile nature of spin probe in corn oil mixture. The membrane permeability and partition parameter values were estimated as a function of corn oil concentration, which reveals that the nitroxyl radicals permeate equally into the aqueous phase and oil phase at the corn oil concentration of 50%. The electron spin resonance spectra demonstrate the permeable and impermeable nature of nitroxyl spin probes. From these results, the corn oil concentration was optimized as 50% for phantom studies. In this work, the corn oil and pure water mixture phantom models with various viscosities correspond to plasma membrane, and whole blood membrane with different hematocrit levels was studied for monitoring the biological characteristics and their interactions with permeable nitroxyl spin probe. These results will be useful for the development of electron spin resonance and Overhauser-enhanced magnetic resonance imaging modalities in biomedical applications. Copyright © 2017 John Wiley & Sons, Ltd.

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.

Genome-Wide Association Study Identifies Candidate Genes for Starch Content Regulation in Maize Kernels

PubMed Central

Liu, Na; Xue, Yadong; Guo, Zhanyong; Li, Weihua; Tang, Jihua

2016-01-01

Kernel starch content is an important trait in maize (Zea mays L.) as it accounts for 65–75% of the dry kernel weight and positively correlates with seed yield. A number of starch synthesis-related genes have been identified in maize in recent years. However, many loci underlying variation in starch content among maize inbred lines still remain to be identified. The current study is a genome-wide association study that used a set of 263 maize inbred lines. In this panel, the average kernel starch content was 66.99%, ranging from 60.60 to 71.58% over the three study years. These inbred lines were genotyped with the SNP50 BeadChip maize array, which is comprised of 56,110 evenly spaced, random SNPs. Population structure was controlled by a mixed linear model (MLM) as implemented in the software package TASSEL. After the statistical analyses, four SNPs were identified as significantly associated with starch content (P ≤ 0.0001), among which one each are located on chromosomes 1 and 5 and two are on chromosome 2. Furthermore, 77 candidate genes associated with starch synthesis were found within the 100-kb intervals containing these four QTLs, and four highly associated genes were within 20-kb intervals of the associated SNPs. Among the four genes, Glucose-1-phosphate adenylyltransferase (APS1; Gene ID GRMZM2G163437) is known as an important regulator of kernel starch content. The identified SNPs, QTLs, and candidate genes may not only be readily used for germplasm improvement by marker-assisted selection in breeding, but can also elucidate the genetic basis of starch content. Further studies on these identified candidate genes may help determine the molecular mechanisms regulating kernel starch content in maize and other important cereal crops. PMID:27512395

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.

Identify and validate a quantitative trait locus underlying stearic acid on chromosome 14 in a soybean landrace using recombinant inbred lines and resident heterozygous lines

USDA-ARS?s Scientific Manuscript database

Stearic acid (ST) is one of the saturated fatty acids (FAs) in soybean oil and great efforts have been made to elevate ST content through plant breeding. Improving ST content will be helpful to reduce the health risk of coronary heart diseases and breast, colon and prostate cancer. In this study, re...

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.

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.

RADIATION-INDUCED GENETIC DAMAGE IN THE MEXICAN TOAD (BUFO VALLICEPS)

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

Blair, W.F.

1960-10-01

Lines of Mexican toads (Bufo valliceps) bearing x-ray induced genetic damage were established by mating normal females with males that had received gonadal x-ray doses ranging from 300 to 3000 r. Survival in the first generation was inversely proportional to dose,-as was expected. Toads of the 300-r and l000- r lines were inbred, and toads of these lines and of the 700-r line were outcrossed to normal ones. Two crosses were made between toads of the 500-r and 1000-r lines. Developmental abnormalities of various kinds appeared at life history stages rangthg from early embryonic development to post-metamorphic life in bothmore » inbred and outcross generations. These included abnormal gastrulation and neurulation, larval and post-metamorphic edema, abnormally positioned or missing limbs, optical deficiencies, prognathous jaw due to excessive elongation of the lower jaw, and melanin deficiency. The prognathous jaw, in its extreme expression, would probably be lethal in natural populations because of difficulty of feeding. The melanin deficiency, in its extreme expression, is lethal as metamorphosis fails to occur, and in lesser expression, it appears to be lethal or detrimental. The various abnormalities do not appear to be inherited in any simple way, but instead they vary in expression both within and between generations, possibly in relation to genotype and environment. (auth)« less

Effects of P Element Insertions on Quantitative Traits in Drosophila Melanogaster

PubMed Central

Mackay, TFC.; Lyman, R. F.; Jackson, M. S.

1992-01-01

P element mutagenesis was used to construct 94 third chromosome lines of Drosophila melanogaster which contained on average 3.1 stable P element inserts, in an inbred host strain background previously free of P elements. The homozygous and heterozygous effects of the inserts on viability and abdominal and sternopleural bristle number were ascertained by comparing the chromosome lines with inserts to insert-free control lines of the inbred host strain. P elements reduced average homozygous viability by 12.2% per insert and average heterozygous viability by 5.5% per insert, and induced recessive lethal mutations at a rate of 3.8% per insert. Mutational variation for the bristle traits averaged over both sexes was 0.03V(e) per homozygous P insert and 0.003V(e) per heterozygous P insert, where V(e) is the environmental variance. Mutational variation was greater for the sexes considered separately because inserts had large pleiotropic effects on sex dimorphism of bristle characters. The distributions of homozygous effects of inserts on the bristle traits were asymmetrical, with the largest effects in the direction of reducing bristle number; and highly leptokurtic, with most of the increase in variance contributed by a few lines with large effects. The inserts had partially recessive effects on the bristle traits. Insert lines with extreme bristle effects had on average greatly reduced viability. PMID:1311697

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

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.

Radiological study on newly developed composite corn advance lines in Malaysia

NASA Astrophysics Data System (ADS)

Adekunle Olatunji, Michael; Bemigho Uwatse, Onosohwo; Uddin Khandaker, Mayeen; Amin, Y. M.; Faruq, G.

2014-12-01

Owing to population growth, there has been high demand for food across the world, and hence, different agricultural activities such as use of phosphate fertilizers, recycling of organic matters, etc, have been deployed to increase crop yields. In Malaysia, a total of nine composite corn advance lines have been developed at the Institute of Biological Sciences, University of Malaya and are being grown under different conditions with a bid to meet the average daily human need for energy and fiber intake. To this end, the knowledge of radioactivity levels in these corn advance lines are of paramount importance for the estimation of possible radiological hazards due to its consumption. Hence, the radioactivity concentrations of 226Ra, 228Ra and 40K in the corn have been determined using HPGe γ-ray spectrometry. The activity concentrations in the corn ranged from 0.05 to 19.18 Bq kg-1 for 226Ra, from 0.10 to 3.22 Bq kg-1 for 228Ra and from 26.4 to 129 Bq kg-1 for 40K. In order to ascertain the radiological safety of the population regarding maize consumption, the daily intakes of these radionuclides as well as the annual effective dose were estimated. The total effective dose obtained due to the ingestion of radionuclides via maize consumption is 15.39 μSv y-1, which is less than the international recommendations.

A tonoplast sugar transporter underlies a sugar accumulation QTL in watermelon

USDA-ARS?s Scientific Manuscript database

The molecular mechanism controlling accumulation of soluble sugars in watermelon (Citrullus lanatus) fruit, a trait associated with sweet-dessert watermelon domestication, is still unknown. We re-sequenced 96 recombinant inbred lines, derived from a cross between sweet and unsweet watermelon accessi...

A high-resolution genetic map of yellow monkeyflower identifies chemical defense QTLs and recombination rate variation.

PubMed

Holeski, Liza M; Monnahan, Patrick; Koseva, Boryana; McCool, Nick; Lindroth, Richard L; Kelly, John K

2014-03-13

Genotyping-by-sequencing methods have vastly improved the resolution and accuracy of genetic linkage maps by increasing both the number of marker loci as well as the number of individuals genotyped at these loci. Using restriction-associated DNA sequencing, we construct a dense linkage map for a panel of recombinant inbred lines derived from a cross between divergent ecotypes of Mimulus guttatus. We used this map to estimate recombination rate across the genome and to identify quantitative trait loci for the production of several secondary compounds (PPGs) of the phenylpropanoid pathway implicated in defense against herbivores. Levels of different PPGs are correlated across recombinant inbred lines suggesting joint regulation of the phenylpropanoid pathway. However, the three quantitative trait loci identified in this study each act on a distinct PPG. Finally, we map three putative genomic inversions differentiating the two parental populations, including a previously characterized inversion that contributes to life-history differences between the annual/perennial ecotypes. Copyright © 2014 Holeski et al.

Give 'til it hurts: trade-offs between immunity and male reproductive effort in the decorated cricket, Gryllodes sigillatus.

PubMed

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

2010-04-01

Trade-offs between life-history variables can be manifested at either the phenotypic or genetic level, with vastly different evolutionary consequences. Here, we examined whether male decorated crickets (Gryllodes sigillatus) from eight inbred lines and the outbred founder population from which they were derived, trade-off immune effort [lytic activity, phenoloxidase (PO) activity or encapsulation] to produce spermatophylaxes: costly nuptial food gifts essential for successful sperm transfer. Canonical correlation analysis of the outbred population revealed a trade-off between spermatophylax mass and lytic activity. Analysis of our inbred lines, however, revealed that although PO activity, encapsulation, body mass, spermatophylax mass and ampulla (sperm capsule) mass were all highly heritable, lytic activity was not, and there was, therefore, no negative genetic correlation between lytic activity and spermatophylax mass. Thus, males showed a phenotypic but not a genetic trade-off between spermatophylax mass and lytic activity, suggesting that this trade-off is mediated largely by environmental factors.

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

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

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.

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.

Effects of corn oil administered orally on conspicuity of ultrasonographic small intestinal lesions in dogs with lymphangiectasia.

PubMed

Pollard, Rachel E; Johnson, Eric G; Pesavento, Patricia A; Baker, Tomas W; Cannon, Allison B; Kass, Philip H; Marks, Stanley L

2013-01-01

Lymphangiectasia is one of the causes of protein-losing enteropathy in dogs and characteristic ultrasonographic small intestinal lesions have been previously described. The purpose of this study was to determine whether corn oil administered orally (COAO) would result in increased conspicuity of these characteristic small intestinal ultrasonographic lesions in dogs with lymphangiectasia. Affected dogs were included if they underwent corn oil administered orally and had a surgical full-thickness intestinal biopsy diagnosis of lymphangiectasia. Control dogs had normal clinical examination and standard laboratory test findings. Ultrasound images of duodenum, jejunum, and ileum were obtained prior to and 30, 60, 90, and 120 min after corn oil administered orally for all dogs. Parameters recorded for each ultrasound study were intestinal wall thickness, mucosal echogenicity, and presence or absence of hyperechoic mucosal striations (HMS) and a parallel hyperechoic mucosal line (PHML). Nine affected and five controls dogs were included in the study. Seven of the nine dogs with lymphangiectasia had hyperechoic mucosal striations prior to corn oil administered orally. Jejunal hyperechoic mucosal striations were significantly associated with lymphangiectasia at multiple time points (P < 0.05) and were best identified in dogs with lymphangiectasia 60 or 90 min after corn oil administered orally. Increased mucosal echogenicity was observed in all dogs at multiple time points after corn oil administered orally. A parallel hyperechoic mucosal line was present in the jejunum in 4/5 healthy and 6/9 dogs with lymphangiectasia at one or more time points after corn oil administered orally. Findings indicated that corn oil administered orally improves conspicuity of characteristic ultrasonographic lesions in dogs with lymphangiectasia, however some of these lesions may also be present in healthy dogs that recently received a fatty meal. © 2013 Veterinary Radiology & Ultrasound.

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...

Epicuticular waxes and thrips resistance in onion

USDA-ARS?s Scientific Manuscript database

Next-generation sequencing of normalized cDNAs from two inbred lines of onion revealed over 3000 well supported single nucleotide polymorphisms (SNPs), of which over 800 have been mapped. This SNP-based map was used to identify quantitative trait loci (QTL) controlling the amounts and types of epicu...

Maize Genetic Resources Collections – Utilizing a Treasure Trove

USDA-ARS?s Scientific Manuscript database

The maize genetic resource collection managed by the USDA-ARS's National Plant Germplasm System is heavily utilized by researchers and educators. A collection of landraces, inbred lines from public and private sector sources, synthetics and key populations, it serves both as a living snapshot of th...

Cucumber as a model plant to study mitochondrial-nuclear interactions

USDA-ARS?s Scientific Manuscript database

The three genomes of cucumber (Cucumis sativus) show different modes of transmission: maternal for plastid, paternal for mitochondrial (mt), and biparental for nuclear DNA. When the highly inbred line ‘B’ is passed through cell cultures, paternally transmitted mosaic (MSC) phenotypes appear after re...

Colonization of wild potato plants by Streptomyces scabies

USDA-ARS?s Scientific Manuscript database

The bacterial pathogen Streptomyces scabies produces lesions on potato tubers, reducing their marketability and profitability. M6 and 524-8 are two closely related inbred diploid lines of the wild potato species Solanum chacoense. After testing in both field and greenhouse assays, it was found that ...

Genetic variation and differentiation in parent-descendant cattle and bison populations

USDA-ARS?s Scientific Manuscript database

Genetic variation and differentiation at 32 microsatellite DNA loci is quantified for parent-descendant cattle populations and parent-descendant bison (Bison bison) populations. Heterozygosity (Ho) and numbers of alleles/locus (AR) are less in the Line 1 Hereford inbred cattle population than in t...

Mapping quantitative trait loci of resistance to Tomato spotted wilt virus and leaf spots in a recombinant inbred line population of peanut (Arachis hypogae L.) from SunOleic 97R and NC94022

USDA-ARS?s Scientific Manuscript database

Peanut is vulnerable to a range of diseases, such as Tomato spotted wilt virus (TSWV) and leaf spots. The most sustainable and economical solution for managing peanut diseases is development of resistance cultivars. The new breeding line NC94022, high resistance to TSWV and moderate resistance to le...

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...

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.

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.

Top 5 exotic clones for potato breeding

USDA-ARS?s Scientific Manuscript database

Wild and cultivated relatives of potato feature prominently in breeding programs. In this short article, I describe five exotic clones that have promising traits for the future of the US potato industry. They include M6, an inbred line of S. chacoense that provides a source of genes for self-compati...

Field Performance of an Indica x Tropical Japonica Rice Mapping Population under AWD Stress

USDA-ARS?s Scientific Manuscript database

Alternating-wetting-drying (AWD) is an emerging rice irrigation management system that has the potential ability to reduce both irrigation water use and emissions of the greenhouse gas, methane. Based on preliminary experiments, 15 (F10) recombinant inbred lines (RILs) showing diversity for root an...

Cell wall composition and biomass recalcitrance differences within a set of Brachypodium distachyon inbred lines

USDA-ARS?s Scientific Manuscript database

Brachypodium distachyon (Brachypodium) has emerged as a useful model system for studying traits unique to graminaceous species, owing to its amenability to laboratory experimentation and the availability of extensive genetic and germplasm resources. We assessed the extent of natural variation for tr...

Effect of wild Helianthus cytoplasms on agronomic and oil characteristics of cultivated sunflower (H. annuus L.)

USDA-ARS?s Scientific Manuscript database

Sunflower (Helianthus annuus L.) productions reliance on a single source of cytoplasmic male-sterility, PET1, derived from H. petiolaris Nutt., makes the crop genetically vulnerable. Twenty diverse cytoplasmic substitution lines from annual and perennial wild species were compared with the inbred li...

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 ...

RILS: What are they, what are they good for, and do we have any?

USDA-ARS?s Scientific Manuscript database

RILs, or recombinant inbred lines, are a set of genetically related individuals that can simplify the gene discovery process. They are constructed using regular breeding processes rather than using tissue culture or other advanced biotechnology. Operationally, a hybrid is made, and this hybrid is se...

Multiple disease resistance to fungal and oomycete pathogens using a recombinant inbred line population in pepper

USDA-ARS?s Scientific Manuscript database

Incorporating disease resistance into cultivars is a primary focus of modern breeding programs. Resistance to pathogens is often introgressed from landrace or wild individuals with poor fruit quality into commercial-quality cultivars. Sites of multiple disease resistance (MDR) are regions or “hotspo...

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...

Evaluation of maize inbred lines for resistance to pre-harvest aflatoxin and fumonisin contamination in the field

USDA-ARS?s Scientific Manuscript database

Two important mycotoxins, aflatoxin and fumonisin, are among the most potent naturally occurring carcinogens, contaminating maize (Zea mays L.) and affecting the crop yield and quality. Resistance of maize to pre-harvest mycotoxin contamination, specifically aflatoxin produced by Aspergillus flavus ...

The genetic basis of flecking and its relationship to disease resistance in the IBM maize mapping population

USDA-ARS?s Scientific Manuscript database

Flecking is defined as a mild, often environmentally-dependent lesion phenotype observed on the leaves of several commonly used maize inbred lines. Anecdotal evidence suggests a link between flecking and enhanced broad-spectrum disease resistance. Neither the genetic basis underlying flecking nor ...

An Inter-varietal Cucumber Linkage Map with 133 New Microsatellite Markers

USDA-ARS?s Scientific Manuscript database

The cucumber (Cucumis sativus var. sativus L.) recombinant inbred line (RIL) population from inter-variety cross of G421 with H19 has been used extensively in genetic mapping of yield- and fruit quality-related QTLs with molecular markers. However, only ~200 molecular markers, mostly AFLPs and RPADs...

The mosaic mutants of cucumber: A system to produce mitochondrial knock-downs

USDA-ARS?s Scientific Manuscript database

The mitochondrial (mt) DNA of cucumber has several unique attributes, including paternal transmission and large size due in part to the accumulation of repetitive DNAs. Recombination among these repetitive motifs generates structural rearrangements in the mt DNAs. When the highly inbred line ‘B’ of ...

Field screening of sweet sorghum inbred lines for pest resistance and biomass production

USDA-ARS?s Scientific Manuscript database

Sweet sorghum [Sorghum bicolor (L.) Moench] is one of the favorable biofuel feedstocks for ethanol production. Fall armyworm [Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae)] is one of the most serious foliar-feeding insect pests in sorghum production in the southeastern US states. Sev...

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

USDA-ARS?s Scientific Manuscript database

Common bean (Phaseolus vulgaris L.) is able to fix atmospheric nitrogen (N2) through symbiotic nitrogen fixation (SNF). Effective utilization of existing variability for SNF in common bean for genetic improvement requires an understanding of underlying genes and molecular mechanisms. The utility of ...

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...

Effect of calcium on strawberry fruit flavonid gene expression and anthocyanins accumulation

USDA-ARS?s Scientific Manuscript database

Strawberry fruit contain phenolic compounds such as anthocyanins, which have beneficial effects against oxidative stress mediated diseases. Two diploid strawberry (Fragaria vesca) inbred lines, Ruegen F7-4 (red fruit) and YW5AF7 (yellow fruit) were used to study the regulation of anthocyanin biosynt...

Identification of Maize Breeding Markers through Investigations of Proteins Associated with Aflatoxin-Resistance

USDA-ARS?s Scientific Manuscript database

The goal of a collaborative research project between International Institute of Tropical Agriculture (IITA) in Nigeria and ARS-Southern Regional Research Center (SRRC) in New Orleans is to develop maize inbred lines with resistance against aflatoxin contamination by Aspergillus flavus. A second goal...

Genetic Variation in Taste Sensitivity to Sugars in Drosophila melanogaster.

PubMed

Uchizono, Shun; Tanimura, Teiichi

2017-05-01

Taste sensitivity plays a major role in controlling feeding behavior, and alterations in feeding habit induced by changes in taste sensitivity can drive speciation. We investigated variability in taste preferences in wild-derived inbred lines from the Drosophila melanogaster Genetic Reference Panel. Preferences for different sugars, which are essential nutrients for fruit flies, were assessed using two-choice preference tests that paired glucose with fructose, sucrose, or trehalose. The two-choice tests revealed that individual lines have differential and widely variable sugar preferences, and that sugar taste sensitivity is polygenic in the inbred population tested. We focused on 2 strains that exhibited opposing preferences for glucose and fructose, and performed proboscis extension reflex tests and electrophysiological recordings on taste sensilla upon exposure to fructose and glucose. The results indicated that taste sensitivity to fructose is dimorphic between the 2 lines. Genetic analysis showed that high sensitivity to fructose is autosomal dominant over low sensitivity, and that multiple loci on chromosomes 2 and 3 influence sensitivity. Further genetic complementation tests for fructose sensitivity on putative gustatory receptor (Gr) genes for sugars suggested that the Gr64a-Gr64f locus, not the fructose receptor gene Gr43a, might contribute to the dimorphic sensitivity to fructose between the 2 lines. © The Author 2017. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Transcriptomic analysis of inbreeding depression in cold-sensitive Drosophila melanogaster shows upregulation of the immune response.

PubMed

Vermeulen, C J; Sørensen, P; Kirilova Gagalova, K; Loeschcke, V

2013-09-01

In sexually reproducing species, increased homozygosity often causes a decline in fitness, called inbreeding depression. Recently, researchers started describing the functional genomic changes that occur during inbreeding, both in benign conditions and under environmental stress. To further this aim, we have performed a genome-wide gene expression study of inbreeding depression, manifesting as cold sensitivity and conditional lethality. Our focus was to describe general patterns of gene expression during inbreeding depression and to identify specific processes affected in our line. There was a clear difference in gene expression between the stressful restrictive environment and the benign permissive environment in both the affected inbred line and the inbred control line. We noted a strong inbreeding-by-environment interaction, whereby virtually all transcriptional differences between lines were found in the restrictive environment. Functional annotation showed enrichment of transcripts coding for serine proteases and their inhibitors (serpins and BPTI/Kunitz family), which indicates activation of the innate immune response. These genes have previously been shown to respond transcriptionally to cold stress, suggesting the conditional lethal effect is associated with an exaggerated cold stress response. The set of differentially expressed genes significantly overlapped with those found in three other studies of inbreeding depression, demonstrating that it is possible to detect a common signature across different genetic backgrounds. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

Dissection of genetic architecture of rice plant height and heading date by multiple-strategy-based association studies

PubMed Central

Zhou, Liyuan; Liu, Shouye; Wu, Weixun; Chen, Daibo; Zhan, Xiaodeng; Zhu, Aike; Zhang, Yingxin; Cheng, Shihua; Cao, Liyong; Lou, Xiangyang; Xu, Haiming

2016-01-01

Xieyou9308 is a certified super hybrid rice cultivar with a high grain yield. To investigate its underlying genetic basis of high yield potential, a recombinant inbred line (RIL) population derived from the cross between the maintainer line XieqingzaoB (XQZB) and the restorer line Zhonghui9308 (ZH9308) was constructed for identification of quantitative trait SNPs (QTSs) associated with two important agronomic traits, plant height (PH) and heading date (HD). By re-sequencing of 138 recombinant inbred lines (RILs), a total of ~0.7 million SNPs were identified for the association studies on the PH and HD. Three association mapping strategies (including hypothesis-free genome-wide association and its two complementary hypothesis-engaged ones, QTL-based association and gene-based association) were adopted for data analysis. Using a saturated mixed linear model including epistasis and environmental interaction, we identified a total of 31 QTSs associated with either the PH or the HD. The total estimated heritability across three analyses ranged from 37.22% to 45.63% and from 37.53% to 55.96% for the PH and HD, respectively. In this study we examined the feasibility of association studies in an experimental population (RIL) and identified several common loci through multiple strategies which could be preferred candidates for further research. PMID:27406081

Translations on North Korea No. 572 Kulloja, No. 11, 1977.

DTIC Science & Technology

1978-01-25

thoroughly carry through the chuche-oriented oil production line on obtaining edible oil from corn and industrial oils from rice bran , we will be...industrial oils with rice bran . The great leader Comrade Kim Il-song taught as follows: "The question of processing corn by industrial methods is...great leader on extracting oil from corn and rice bran makes it possible within a short period of time to produce oil in large quantities everywhere

Dietary cyanidin 3-glucoside from purple corn ameliorates doxorubicin-induced cardiotoxicity in mice.

PubMed

Petroni, K; Trinei, M; Fornari, M; Calvenzani, V; Marinelli, A; Micheli, L A; Pilu, R; Matros, A; Mock, H-P; Tonelli, C; Giorgio, M

2017-05-01

Anthracyclines are effective anticancer drugs that have improved prognosis of hundred thousand cancer patients worldwide and are currently the most common chemotherapeutic agents used for the treatment of blood, breast, ovarian and lung cancers. However, their use is limited because of a cumulative dose-dependent and irreversible cardiotoxicity that can cause progressive cardiomyopathy and congestive heart failure. Aim of the present study was to determine the cardioprotective activity of a dietary source of cyanidin 3-glucoside (C3G), such as purple corn, against doxorubicin (DOX)-induced cardiotoxicity in mice. In vitro studies on murine HL-1 cardiomyocytes showed that pretreatment with both pure C3G and purple corn extract improved survival upon DOX treatment. However, C3G and purple corn extract did not affect the cytotoxic effect of DOX on human cancer cell lines. We then validated in vivo the protective role of a C3G-enriched diet against DOX-induced cardiotoxicity by comparing the effect of dietary consumption of corn isogenic lines with high levels of anthocyanins (purple corn - Red diet - RD) or without anthocyanins (yellow corn - Yellow diet - YD) incorporated in standard rodent diets. Results showed that mice fed RD survived longer than mice fed YD upon injection of a toxic amount of DOX. In addition, ultrastructural analysis of hearts from mice fed RD showed reduced histopathological alterations. Dietary intake of C3G from purple corn protects mice against DOX-induced cardiotoxicity. Copyright © 2017 The Italian Society of Diabetology, the Italian Society for the Study of Atherosclerosis, the Italian Society of Human Nutrition, and the Department of Clinical Medicine and Surgery, Federico II University. Published by Elsevier B.V. All rights reserved.

Frost-Shielding Methodology and Demonstration for Shallow Burial of Water and Sewer Utility Lines.

DTIC Science & Technology

1998-06-01

Research and Engineering Laboratory (CRREL), and the Owens - Corning Specialty and Foam Products Division as partners. Test sites utilizing shielded pipes...predictions and provided valuable guidance for the frost shield design. The industry partner participant in the CPAR project, Owens - Corning Specialty and Foam

Oral toxicity of beta-N-acetyl hexosaminidase to insects.

PubMed

Dowd, Patrick F; Johnson, Eric T; Pinkerton, T Scott

2007-05-02

Insect chitin is a potential target for resistance plant proteins, but plant-derived chitin-degrading enzymes active against insects are virtually unknown. Commercial beta-N-acetylhexosaminidase (NAHA), a chitin-degrading enzyme from jack bean Canavalia ensiformis, caused significant mortality of fall armyworm Spodoptera frugiperda larvae at 75 microg/gm, but no significant mortality was noted with Aspergillus niger NAHA. Maize Zea mays callus transformed to express an Arabidopsis thaliana clone that putatively codes for NAHA caused significantly higher mortality of cigarette beetle Lasioderma serricorne larvae and significantly reduced growth rates (as reflected by survivor weights) of S. frugiperda as compared to callus that expressed control cDNAs. Tassels from model line Hi-II maize (Z. mays) plants transformed with the NAHA gene fed to S. frugiperda caused significantly higher mortality than tassels transformed to express glucuronidase; mortality was significantly correlated with NAHA expression levels detected histochemically. Leaf disks from inbred Oh43 maize plants transformed with the NAHA gene on average had significantly less feeding by caterpillars than null transformants. Leaf disks of Oh43 transformants caused significant mortality of both S. frugiperda and corn earworm Helicoverpa zea larvae, which was associated with higher expression levels of NAHA detected by isoelectric focusing, histochemically, or with antibody. Overall, these results suggest that plant NAHA has a role in insect resistance. Introduction of NAHA genes or enhancement of activity through breeding or genetic engineering has the potential to significantly reduce insect damage and thereby indirectly reduce mycotoxins that are harmful to animals and people.

Growth characteristics of a weed-suppressive indica x non-suppressive tropical japonica rice mapping population

USDA-ARS?s Scientific Manuscript database

The indica rice cultivar, PI 312777, can be highly productive as well as suppressive to C4 grass species such as barnyardgrass (Echinochloa crus-galli). A recombinant inbred line (RIL) mapping population was developed using single seed descent from a cross between ‘Katy’ (non-weed-suppressive) and ...

Identification of seedling vigor-associated quantitative trait loci in temperate japonica rice

USDA-ARS?s Scientific Manuscript database

A quantitative trait loci (QTL) analysis of seedling vigor traits was conducted under dry-seeded conditions using 176 recombinant inbred lines developed from a cross of two California temperate japonica rice varieties M-203 and M-206. Height at early seedling (HES) and late seedling (HLS) stage, gro...

A Dynamic Model of Heavy Ion 7Li Irradiation Mutagenesis Based on Maize Inbred Line Nutrition Difference

NASA Astrophysics Data System (ADS)

Hu, Jin-Shan; Geng, Jin-Peng; Li, Duo-Fang; Sui, Li; Zhan, Yong

2018-04-01

Not Available Supported by the National Natural Science Foundation of China under Grant No 11735006, the Hebei Natural Science Foundation of China under Grant No B2014209314, and the Hebei Science and Technology Research Project of Higher Education under Grant No ZD2017023.

Estimation methods and parameter assessment for ethanol yields from total soluble solids of sweet sorghum

USDA-ARS?s Scientific Manuscript database

Estimation methods and evaluation of ethanol yield from sweet sorghum (Sorghum bicolor (L.) Moench.) based on agronomic production traits and juice characteristics is important for developing parents and inbred lines of sweet sorghum that can be used by the bio-ethanol industry. The objectives of th...

Characterization of rice blast resistance gene Pi61(t) in rice germplasm

USDA-ARS?s Scientific Manuscript database

Identification of resistance (R) genes to races of Magnaporthe oryzae in rice germplasm is essential for the development of rice cultivars with long lasting blast resistance. In the present study, one major quantitative trait locus, qPi93-3, was fine mapped using a recombinant inbred line (RIL), F8 ...

Differential TCR Vbeta Usage in the Peripheral T Cells of Chickens Resistant and Susceptible to Marek’s Disease

USDA-ARS?s Scientific Manuscript database

Marek's disease (MD) is a herpesvirus-induced lymphoma in chickens with a significant economic impact to the poultry industry, costing the industry over $1 billion annually worldwide. MD is controllable by vaccination and improving genetic resistance in the host. Two inbred layer lines, matched at...

The genetics of leaf flecking in maize and its relationship to plant defense and disease resistance

USDA-ARS?s Scientific Manuscript database

Physiological/genetic leaf spotting, or flecking, is a mild lesion phenotype observed on the leaves of several commonly used maize inbred lines and has been anecdotally linked to enhanced broad-spectrum disease resistance. Flecking was assessed in the maize nested association mapping (NAM) populati...

The environment strongly affects estimates of heterosis in hybrid sweet sorghum

USDA-ARS?s Scientific Manuscript database

Sweet sorghum (Sorghum bicolor (L.) Moench) has potential as a biofuel feedstock but hybrid cultivars are needed to support an industry based on this crop. The purpose of this study was to compare five inbred sweet sorghum lines and 15 hybrids derived from them, and to determine the extent of envir...

The combined approach of strain discovery and the inbred line technique for improving control of Delia radicum with Heterorhabditis bacteriophora

USDA-ARS?s Scientific Manuscript database

Entomopathogenic nematodes are potent biocontrol agents but their efficacy can be compromised under unfavorable environmental conditions such as cold temperatures. Discovery of new nematode species or strains that are adapted to local conditions is one approach that can be used to enhance efficacy. ...

Contrasting insect attraction and herbivore-induced plant volatile production in maize

USDA-ARS?s Scientific Manuscript database

Maize inbred line W22 is an important resource for genetic studies due to the availability of the UniformMu mutant population and a complete genome sequence. In this study, we assessed the suitability of W22 as a model for tritrophic interactions between maize, Spodoptera frugiperda (fall armyworm) ...

Cytokinin-dependent secondary growth determines root biomass in radish (Raphanus sativus L.)

PubMed Central

Jang, Geupil; Lee, Jung-Hun; Rastogi, Khushboo; Park, Suhyoung; Oh, Sang-Hun; Lee, Ji-Young

2015-01-01

The root serves as an essential organ in plant growth by taking up nutrients and water from the soil and supporting the rest of the plant body. Some plant species utilize roots as storage organs. Sweet potatoes (Ipomoea batatas), cassava (Manihot esculenta), and radish (Raphanus sativus), for example, are important root crops. However, how their root growth is regulated remains unknown. In this study, we characterized the relationship between cambium and radial root growth in radish. Through a comparative analysis with Arabidopsis root expression data, we identified putative cambium-enriched transcription factors in radish and analysed their expression in representative inbred lines featuring distinctive radial growth. We found that cell proliferation activities in the cambium positively correlated with radial growth and final yields of radish roots. Expression analysis of candidate transcription factor genes revealed that some genes are differentially expressed between inbred lines and that the difference is due to the distinct cytokinin response. Taken together, we have demonstrated for the first time, to the best of our knowledge, that cytokinin-dependent radial growth plays a key role in the yields of root crops. PMID:25979997

Metabolic robustness in young roots underpins a predictive model of maize hybrid performance in the field.

PubMed

de Abreu E Lima, Francisco; Westhues, Matthias; Cuadros-Inostroza, Álvaro; Willmitzer, Lothar; Melchinger, Albrecht E; Nikoloski, Zoran

2017-04-01

Heterosis has been extensively exploited for yield gain in maize (Zea mays L.). Here we conducted a comparative metabolomics-based analysis of young roots from in vitro germinating seedlings and from leaves of field-grown plants in a panel of inbred lines from the Dent and Flint heterotic patterns as well as selected F 1 hybrids. We found that metabolite levels in hybrids were more robust than in inbred lines. Using state-of-the-art modeling techniques, the most robust metabolites from roots and leaves explained up to 37 and 44% of the variance in the biomass from plants grown in two distinct field trials. In addition, a correlation-based analysis highlighted the trade-off between defense-related metabolites and hybrid performance. Therefore, our findings demonstrated the potential of metabolic profiles from young maize roots grown under tightly controlled conditions to predict hybrid performance in multiple field trials, thus bridging the greenhouse-field gap. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce

PubMed Central

Truco, Maria José; Ashrafi, Hamid; Kozik, Alexander; van Leeuwen, Hans; Bowers, John; Wo, Sebastian Reyes Chin; Stoffel, Kevin; Xu, Huaqin; Hill, Theresa; Van Deynze, Allen; Michelmore, Richard W.

2013-01-01

We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa. The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species. PMID:23550116

An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce.

PubMed

Truco, Maria José; Ashrafi, Hamid; Kozik, Alexander; van Leeuwen, Hans; Bowers, John; Wo, Sebastian Reyes Chin; Stoffel, Kevin; Xu, Huaqin; Hill, Theresa; Van Deynze, Allen; Michelmore, Richard W

2013-04-09

We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F 7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species. Copyright © 2013 Truco et al.

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 a small genome, a seed to seed cycle of 3.0 - 3.5 months, and produce fruit in 7.5 cm pots in a growth chamber. YW5AF7 is runnerless and therefore easy to maintain in the greenhouse, forms abundant branch crowns for vegetative propagation, and produces highly aromatic yellow fruit throughout the year in the greenhouse. F. vesca can be transformed with Agrobacterium tumefaciens, making these plants suitable for insertional mutagenesis, RNAi and overexpression studies that can be compared against a stable baseline of phenotypic descriptors and can be readily genetically substantiated. PMID:19878589

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

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

Pro-apoptotic and anti-proliferative effects of corn silk extract on human colon cancer cell lines.

PubMed

Guo, Hao; Guan, Hong; Yang, Wenqin; Liu, Han; Hou, Huiling; Chen, Xue; Liu, Zhenyan; Zang, Chuangang; Liu, Yuchao; Liu, Jicheng

2017-02-01

Corn silk is an economically and nutritionally significant natural product as it represents a staple food for a large proportion of the world population. This study investigated the anticancer activity of corn silk extract in human colon cancer cells and human gastric cancer cells. Following treatment with corn silk extract, certain apoptosis-related events were observed, including inhibition of cell proliferation, loss of mitochondrial membrane potential (ΔΨm), release of Ca2+ and release of cytochrome c from the mitochondria into the cytosol. Our results revealed that corn silk extract inhibited the proliferation of cancer cells and increased the level of apoptosis in a concentration-dependent manner. Western blot analysis revealed that corn silk extract upregulated the levels of Bax, cytochrome c , caspase-3 and caspase-9, but downregulated the levels of B-cell lymphoma 2. These results suggest that corn silk extract may induce apoptosis through the mitochondria-mediated pathway.

Adaptation of LASCA method for diagnostics of malignant tumours in laboratory animals

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

Ul'yanov, S S; Laskavyi, V N; Glova, Alina B

The LASCA method is adapted for diagnostics of malignant neoplasms in laboratory animals. Tumours are studied in mice of Balb/c inbred line after inoculation of cells of syngeneic myeloma cell line Sp.2/0 Ag.8. The appropriateness of using the tLASCA method in tumour investigations is substantiated; its advantages in comparison with the sLASCA method are demonstrated. It is found that the most informative characteristic, indicating the presence of a tumour, is the fractal dimension of LASCA images.

A preliminary identification of Rf*-A619, a novel restorer gene for CMS-C in maize (Zea mays L.).

PubMed

Yongming, Liu; Zhuofan, Zhao; Yanli, Lu; Chuan, Li; Jing, Wang; Boxiao, Dong; Bing, Liang; Tao, Qiu; Wenbing, Zeng; Moju, Cao

2016-01-01

C-type cytoplasmic male sterility (CMS-C) is widely utilized for hybrid maize seed production. However, genetic mechanisms underlying the fertility restoration are very complicated. At present, there is a divergence on the number of fertility restorer genes in maize inbred line A619 for CMS-C. To further elucidate the restoring mechanism of A619, we used genetic analysis and molecular markers to confirm the restorer genes of maize inbred line A619 for C-type male sterile line C48-2 in this study. Firstly, the fertility segregations of (C48-2 × A619)F 2 populations were investigated under three environments during 2013-2015. The segregation ratio of fertile and sterile plants in the F 2 population fit to 15:1 via chi-square test and this result suggested that there are two dominant restorer genes in A619 for CMS-C, i.e., Rf4 and a novel gene named Rf*-A619 . Next, based on the sequence differences between Rf4 and its recessive allelic rf4 , a novel dominant marker F2/R2 was developed and validated to genotyping Rf4 in the F 2 population. Through genotypic analysis, we found that there were a certain amount of fertile individuals without Rf4 which accounted for 3/16 in the F 2 population via chi-square test at the 0.05 level. These results provided another proof to sustain that the inbred line A619 contains one additional restorer gene for CMS-C fertility restoration except Rf4 . At last, we used one SSR marker which is tightly linked with the dominant restorer gene Rf5 to analyze those fertile plants without Rf4 in the F 2 population. The PCR amplification results showed that Rf*-A619 is not allelic to Rf5 but a novel restorer gene for CMS-C. These results not only provide a basis for the mapping and characterization of a novel restorer gene but also give a new insight into the mechanism of CMS-C fertility restoration.

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.

Transcriptome profiling of pumpkin (Cucurbita moschata Duch.) leaves infected with powdery mildew

PubMed Central

Chen, Bi-Hua; Chen, Xue-Jin; Guo, Yan-Yan; Yang, He-Lian; Li, Xin-Zheng; Wang, Guang-Yin

2018-01-01

Cucurbit powdery mildew (PM) is one of the most severe fungal diseases, but the molecular mechanisms underlying PM resistance remain largely unknown, especially in pumpkin (Cucurbita moschata Duch.). The goal of this study was to identify gene expression differences in PM-treated plants (harvested at 24 h and 48 h after inoculation) and untreated (control) plants of inbred line “112–2” using RNA sequencing (RNA-Seq). The inbred line “112–2” has been purified over 8 consecutive generations of self-pollination and shows high resistance to PM. More than 7600 transcripts were examined in pumpkin leaves, and 3129 and 3080 differentially expressed genes (DEGs) were identified in inbred line “112–2” at 24 and 48 hours post inoculation (hpi), respectively. Based on the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway database and GO (Gene Ontology) database, a complex regulatory network for PM resistance that may involve hormone signal transduction pathways, transcription factors and defense responses was revealed at the transcription level. In addition, the expression profiles of 16 selected genes were analyzed using quantitative RT-PCR. Among these genes, the transcript levels of 6 DEGs, including bHLH87 (Basic Helix-loop-helix transcription factor), ERF014 (Ethylene response factor), WRKY21 (WRKY domain), HSF (heat stress transcription factor A), MLO3 (Mildew Locus O), and SGT1 (Suppressor of G-Two Allele of Skp1), in PM-resistant “112–2” were found to be significantly up- or down-regulated both before 9 hpi and at 24 hpi or 48 hpi; this behavior differed from that observed in the PM-susceptible material (cultivar “Jiujiangjiaoding”). The transcriptome data provide novel insights into the response of Cucurbita moschata to PM stress and are expected to be highly useful for dissecting PM defense mechanisms in this major vegetable and for improving pumpkin breeding with enhanced resistance to PM. PMID:29320569

Transcriptome profiling of pumpkin (Cucurbita moschata Duch.) leaves infected with powdery mildew.

PubMed

Guo, Wei-Li; Chen, Bi-Hua; Chen, Xue-Jin; Guo, Yan-Yan; Yang, He-Lian; Li, Xin-Zheng; Wang, Guang-Yin

2018-01-01

Cucurbit powdery mildew (PM) is one of the most severe fungal diseases, but the molecular mechanisms underlying PM resistance remain largely unknown, especially in pumpkin (Cucurbita moschata Duch.). The goal of this study was to identify gene expression differences in PM-treated plants (harvested at 24 h and 48 h after inoculation) and untreated (control) plants of inbred line "112-2" using RNA sequencing (RNA-Seq). The inbred line "112-2" has been purified over 8 consecutive generations of self-pollination and shows high resistance to PM. More than 7600 transcripts were examined in pumpkin leaves, and 3129 and 3080 differentially expressed genes (DEGs) were identified in inbred line "112-2" at 24 and 48 hours post inoculation (hpi), respectively. Based on the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway database and GO (Gene Ontology) database, a complex regulatory network for PM resistance that may involve hormone signal transduction pathways, transcription factors and defense responses was revealed at the transcription level. In addition, the expression profiles of 16 selected genes were analyzed using quantitative RT-PCR. Among these genes, the transcript levels of 6 DEGs, including bHLH87 (Basic Helix-loop-helix transcription factor), ERF014 (Ethylene response factor), WRKY21 (WRKY domain), HSF (heat stress transcription factor A), MLO3 (Mildew Locus O), and SGT1 (Suppressor of G-Two Allele of Skp1), in PM-resistant "112-2" were found to be significantly up- or down-regulated both before 9 hpi and at 24 hpi or 48 hpi; this behavior differed from that observed in the PM-susceptible material (cultivar "Jiujiangjiaoding"). The transcriptome data provide novel insights into the response of Cucurbita moschata to PM stress and are expected to be highly useful for dissecting PM defense mechanisms in this major vegetable and for improving pumpkin breeding with enhanced resistance to PM.

Dry In-Line Thermoplastic Matrix Impregnation. Phase 1

DTIC Science & Technology

1993-04-01

grades supplied by Hoechst Celanese under their designations Fortran 0203B6 and 0205B4. Fibers tested included Owens - Corning S Glass with an epoxy...it was found that it had a much greater tendency to shred and jam when fed through the tensioning pin system than did the Owens Corning s glass

Southern corn leaf blight a story worth retelling

USDA-ARS?s Scientific Manuscript database

The Southern Corn Leaf Blight Epidemic of 1970-1971 was one of the most costly disease outbreaks to affect North American agriculture, destroying 15% of the crop at a cost of $1.0 billion (US). It resulted from an over reliance on cytoplasmic Texas male sterile (cms-T) lines in hybrid seed producti...

Breeding aflatoxin resistant maize lines using recent advances in technologies-a review

USDA-ARS?s Scientific Manuscript database

Aflatoxin contamination caused by Aspergillus flavus infection of corn is a significant and chronic threat to corn being used as food or feed. Contamination of crops at levels of 20 ppb or higher (as regulated by the FDA) by this toxin and potent carcinogen makes the crop unsalable. This review focu...

The genetic basis of flecking and its relationship to disease resistance in the IBM maize mapping population.

PubMed

Vontimitta, Vijay; Olukolu, Bode A; Penning, Bryan W; Johal, Gurmukh; Balint-Kurti, P J

2015-11-01

In this paper, we determine the genetic architecture controlling leaf flecking in maize and investigate its relationship to disease resistance and the defense response. Flecking is defined as a mild, often environmentally dependent lesion phenotype observed on the leaves of several commonly used maize inbred lines. Anecdotal evidence suggests a link between flecking and enhanced broad-spectrum disease resistance. Neither the genetic basis underlying flecking nor its possible relationship to disease resistance has been systematically evaluated. The commonly used maize inbred Mo17 has a mild flecking phenotype. The IBM-advanced intercross mapping population, derived from a cross between Mo17 and another commonly used inbred B73, has been used for mapping a number of traits in maize including several related to disease resistance. In this study, flecking was assessed in the IBM population over 6 environments. Several quantitative trait loci for flecking were identified, with the strongest one located on chromosome 6. Low but moderately significant correlations were observed between stronger flecking and higher disease resistance with respect to two diseases, southern leaf blight and northern leaf blight and between stronger flecking and a stronger defense response.

Performance of laying hens fed diets containing DAS-59122-7 maize grain compared with diets containing nontransgenic maize grain.

PubMed

Jacobs, C M; Utterback, P L; Parsons, C M; Rice, D; Smith, B; Hinds, M; Liebergesell, M; Sauber, T

2008-03-01

An experiment using 216 Hy-Line W-36 pullets was conducted to evaluate transgenic maize grain containing the cry34Ab1 and cry35Ab1 genes from a Bacillus thuringiensis (Bt) strain and the phosphinothricin ace-tyltransferase (pat) gene from Streptomyces viridochromogenes. Expression of the cry34Ab1 and cry35Ab1 genes confers resistance to corn rootworms, and the pat gene confers tolerance to herbicides containing glufosinate-ammonium. Pullets (20 wk of age) were placed in cage lots (3 hens/cage, 2 cages/lot) and were randomly assigned to 1 of 3 corn-soybean meal dietary treatments (12 lots/treatment) formulated with the following maize grains: near-isogenic control (control), conventional maize, and transgenic test corn line 59122 containing event DAS-59122-7. Differences between 59122 and control group means were evaluated with statistical significance at P < 0.05. Body weight and gain, egg production, egg mass, and feed efficiency for hens fed the 59122 corn were not significantly different from the respective values for hens fed diets formulated with control maize grain. Egg component weights, Haugh unit measures, and egg weight class distribution were similar regardless of the corn source. This research indicates that performance of hens fed diets containing 59122 maize grain, as measured by egg production and egg quality, was similar to that of hens fed diets formulated with near-isogenic corn grain.

Breed effect between Mos rooster (Galician indigenous breed) and Sasso T-44 line and finishing feed effect of commercial fodder or corn.

PubMed

Franco, D; Rois, D; Vázquez, J A; Purriños, L; González, R; Lorenzo, J M

2012-02-01

The aim of this research was to study the Mos rooster breed growth performance, carcass, and meat quality. The breed effect (Mos vs. Sasso T-44) and finishing feed in the last month (fodder vs. corn) on animal growth, carcass characteristics, meat quality, and fatty and amino acid profiles were studied using a randomized block design with initial weight as covariance. In total, 80 roosters (n = 30 of Sasso T-44 line and n = 50 of Mos breed) were used. They were separated by breed and allocated to 2 feeding treatment groups (concentrate and corn). Each feeding treatment group consisted of 15 and 25 roosters, for Sasso T-44 line and Mos breed, respectively. Finishing feeding did not affect growth parameters in the 2 genotypes of rooster tested (P > 0.05). Nonetheless, the comparison between both types of roosters led to significant differences in growth parameters (P < 0.05). Regarding carcass characteristics, no significant influences of finishing feeding treatment (P > 0.05) were found, and as expected, carcass weight clearly differed between genotypes due to the lower growth rate of Mos roosters. However, drumstick, thigh, and wing percentages were greater in the Mos breed than in the hybrid line. In color instrumental traits, roosters feeding with corn showed breast meat with significantly (P < 0.001) higher a* and b* values than those of cocks feeding with commercial fodder. Values of shear force were less than 2 kg for both genotypes, thus it can be classified as very tender meat. Finishing with corn significantly increased (P < 0.001) the polyunsaturated fatty acid content in the breast; the Mos breed had a polyunsaturated to saturated fatty acid ratio of 0.73. The amino acid profile of the indigenous breed was not similar to that of the commercial strain. Finishing feeding treatment had a greater influence than breed effect on amino acid profile.

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

Hybrid wheat: quantitative genetic parameters and consequences for the design of breeding programs.

PubMed

Longin, Carl Friedrich Horst; Gowda, Manje; Mühleisen, Jonathan; Ebmeyer, Erhard; Kazman, Ebrahim; Schachschneider, Ralf; Schacht, Johannes; Kirchhoff, Martin; Zhao, Yusheng; Reif, Jochen Christoph

2013-11-01

Commercial heterosis for grain yield is present in hybrid wheat but long-term competiveness of hybrid versus line breeding depends on the development of heterotic groups to improve hybrid prediction. Detailed knowledge of the amount of heterosis and quantitative genetic parameters are of paramount importance to assess the potential of hybrid breeding. Our objectives were to (1) examine the extent of midparent, better-parent and commercial heterosis in a vast population of 1,604 wheat (Triticum aestivum L.) hybrids and their parental elite inbred lines and (2) discuss the consequences of relevant quantitative parameters for the design of hybrid wheat breeding programs. Fifteen male lines were crossed in a factorial mating design with 120 female lines, resulting in 1,604 of the 1,800 potential single-cross hybrid combinations. The hybrids, their parents, and ten commercial wheat varieties were evaluated in multi-location field experiments for grain yield, plant height, heading time and susceptibility to frost, lodging, septoria tritici blotch, yellow rust, leaf rust, and powdery mildew at up to five locations. We observed that hybrids were superior to the mean of their parents for grain yield (10.7 %) and susceptibility to frost (-7.2 %), leaf rust (-8.4 %) and septoria tritici blotch (-9.3 %). Moreover, 69 hybrids significantly (P < 0.05) outyielded the best commercial inbred line variety underlining the potential of hybrid wheat breeding. The estimated quantitative genetic parameters suggest that the establishment of reciprocal recurrent selection programs is pivotal for a successful long-term hybrid wheat breeding.

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.

Natural variation in maize aphid resistance is associated with 2,4-Dihydroxy-7-Methoxy-1,4-Benzoxazin-3-One Glucoside Methyltransferase activity

USDA-ARS?s Scientific Manuscript database

Plants differ greatly in their susceptibility to insect herbivory, suggesting both local adaptation and resistance tradeoffs. We used maize (Zea mays) recombinant inbred lines to map a quantitative trait locus (QTL) for the maize leaf aphid (Rhopalosiphum maidis) susceptibility to maize Chromosome 1...

Resistance to multiple soil-borne pathogens of the Pacific Northwest is co-located in a wheat recombinant inbred line population

USDA-ARS?s Scientific Manuscript database

Soil-borne pathogens of the Pacific Northwest decrease yields in both spring and winter wheat. Pathogens of economic importance include Fusarium culmorum, Pratylenchus neglectus, P. thornei, and Rhizoctonia solani AG8. Few options are available to growers to manage these pathogens and reduce yield l...

Phenotypic Evaluation of Weed-competitive Traits and Yield of Rice RILs from an Indica x Tropical Japonica Mapping Population

USDA-ARS?s Scientific Manuscript database

Indica rice cultivars can suppress weedy grasses. To better understand the important traits and genes underlying weed suppression and crop productivity, a recombinant inbred line (RIL) F8 population was developed by crossing non-suppressive ‘Katy’ and high-yielding, allelopathic ‘PI312777’. Three h...

Field evaluation of potential weed-suppressive traits in an indica x tropical japonica mapping population

USDA-ARS?s Scientific Manuscript database

The indica rice accession, PI 312777 (a.k.a. WC 4644), is highly productive and can suppress barnyardgrass (Echinochloa crus-galli) in reduced-input systems, but the genetic control of this weed suppression is unknown. A set of 330 recombinant inbred lines (RILs) was developed using single seed desc...

Response of sugar beet recombinant inbred lines to post-harvest rot fungi

USDA-ARS?s Scientific Manuscript database

Sugar beet is commonly stored in outdoor piles prior to processing. During this storage period the crop is subject to multiple post-harvest rots. Resistance to three post harvest rots was identified in two sugar beet germplasm in the 1970s, but there has been little work done on host resistance to p...

Response of sugar beet (Beta vulgaris) recombinant inbred lines to post-harvest rot fungi

USDA-ARS?s Scientific Manuscript database

Sugar beet (Beta vulgaris) is commonly stored in outdoor piles prior to processing for food and animal feed. During this storage period the crop is subject to multiple post-harvest rots. Resistance to three post harvest rots was identified in two sugar beet germplasm in the 1970s, but there has been...

Relocation of a rust resistance gene R2 and its marker-assisted gene pyramiding in confection sunflower (Helianthus annuus L.)

USDA-ARS?s Scientific Manuscript database

Rust (caused by Puccinia helianthi Schwein.) is a major disease of sunflower worldwide. Due to the frequent evolution of new pathogen races, the disease is a recurring threat to sunflower production especially in North America, Argentina, and Australia. The inbred line MC29 carries the rust resistan...

Crop characteristics and weed Interactions of diverse Rrecurrent Inbred Lines (RILs) from a weed-suppressive x non-suppressive rice mapping population

USDA-ARS?s Scientific Manuscript database

ndica rice genotypes with enhanced weed suppression traits have been previously identified as potentially useful in supplementing weed control efforts in drill-seeded systems in the southern USA. A particularly weed-suppressive indica genotype (PI 312777) that was also high tillering and high yield...

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...

Quantitative trait loci for non-race-specific, high-temperature adult-plant resistance to stripe rust in wheat cultivar Express

USDA-ARS?s Scientific Manuscript database

Wheat cultivar Express has durable, high-temperature adult-plant (HTAP) resistance to stripe rust (Puccinia striiformis f. sp. tritici). To elucidate the genetic basis of the resistance, Express was crossed with ‘Avocet Susceptible’ (AVS). A mapping population of 146 F5 recombinant inbred lines (R...

Growth Responses of Plantago major L. ssp. pleiosperma (Pilger) to Changes in Mineral Supply 1

PubMed Central

Kuiper, Daan

1988-01-01

Plants of an inbred line of Plantago major ssp. pleiosperma were subjected to an alteration in mineral supply. Observed responses of growth rate and shoot to root ratio are thought to be induced by changes in endogenous cytokinin concentration and not by mineral concentration in plant tissue. PMID:16666183

Genetic linkage maps of white birches (Betula platyphylla Suk. and B. pendula Roth) based on RAPD and AFLP markers

USDA-ARS?s Scientific Manuscript database

Genetic linkage maps in plants are usually constructed using segregating populations obtained from crosses between two inbred lines such as rice, maize, or soybean. Such populations are generally not available for forest trees because of time constraints. But tree species have the property of outcro...

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...

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...

Quantitative trait loci underlying seed sugars content in MD96-5722 by spencer recombinant inbred line population of soybean

USDA-ARS?s Scientific Manuscript database

Sucrose, raffinose, and stachyose are important soluble sugars in soybean [Glycine max (L.) Merr.] seeds, and soybean seeds with higher sucrose and lower raffinose and stachyose are desirable. Therefore, optimizing sugars biosynthesis is a major goal for soy food industry. The objective of this stud...

Barley 4H QTL confers NFNB resistance to a global set of P. teres f. teres isolates

USDA-ARS?s Scientific Manuscript database

Net form net blotch (NFNB), caused by Pyrenophora teres f. teres Drechs., is prevalent in barley-growing regions worldwide. A population of 132 recombinant inbred lines (RILs) developed from a cross of the barley varieties 'Falcon' and 'Azhul' were used to evaluate resistance to NFNB due to their di...

Quantitative trait loci for seed isoflavones contents in 'MD96-5722' by 'Spencer' recombinant inbred lines of soybean

USDA-ARS?s Scientific Manuscript database

Isoflavones from soybeans (Glycine max L. Merr.) have significant impact on human health in reducing the risk of several major diseases. Breeding soybean for high isoflavones content in the seed is possible through marker assisted selection (MAS), which can be based on quantitative trait loci (QTL)....

Biofortification of hard red winter wheat (Triticum aestivum L.) by genes conditioning low phytate and high grain protein concentration

USDA-ARS?s Scientific Manuscript database

Recombinant inbred lines (RILs) of winter wheat (Triticum aestivum L.) were used to determine whether the combination of low grain phytate (LPA) conditioned by lpa1-1, and Gpc-B1 (GPC- grain protein content) alleles would simultaneously increase beneficial mineral concentrations and grain protein wi...

Adult plant leaf rust resistance derived from Toropi wheat is conditioned by Lr78 and three minor QTL

USDA-ARS?s Scientific Manuscript database

Brazil, was noted to have long lasting leaf rust resistance that was effective only in adult plants. The objectives of this study were to determine the chromosome location of the leaf rust resistance genes derived from Toropi in two populations of recombinant inbred lines in a partial Thatcher wheat...

The use of disease severity variables in predicting efficacy of FOV4 resistance selection

USDA-ARS?s Scientific Manuscript database

In 2015, 85 Upland (Gossypium hirsutum L.) accessions from the USDA-ARS Cotton Collection and 126 F6 Pima-S6 x Pima-S7 (G. barbadense L.) recombinant inbred lines were evaluated for disease performance under pressure of Fusarium oxysporum f. sp. vasinfectum race 4 (FOV4) in a replicated field trial ...

Heterogeneous Stock Rat: A Unique Animal Model for Mapping Genes Influencing Bone Fragility

PubMed Central

Alam, Imranul; Koller, Daniel L.; Sun, Qiwei; Roeder, Ryan K.; Cañete, Toni; Blázquez, Gloria; López-Aumatell, Regina; Martínez-Membrives, Esther; Vicens-Costa, Elia; Mont, Carme; Díaz, Sira; Tobeña, Adolf; Fernández-Teruel, Alberto; Whitley, Adam; Strid, Pernilla; Diez, Margarita; Johannesson, Martina; Flint, Jonathan; Econs, Michael J.; Turner, Charles H.; Foroud, Tatiana

2011-01-01

Previously, we demonstrated that skeletal mass, structure and biomechanical properties vary considerably among 11 different inbred rat strains. Subsequently, we performed quantitative trait loci (QTL) analysis in 4 inbred rat strains (F344, LEW, COP and DA) for different bone phenotypes and identified several candidate genes influencing various bone traits. The standard approach to narrowing QTL intervals down to a few candidate genes typically employs the generation of congenic lines, which is time consuming and often not successful. A potential alternative approach is to use a highly genetically informative animal model resource capable of delivering very high-resolution gene mapping such as Heterogeneous stock (HS) rat. HS rat was derived from eight inbred progenitors: ACI/N, BN/SsN, BUF/N, F344/N, M520/N, MR/N, WKY/N and WN/N. The genetic recombination pattern generated across 50 generations in these rats has been shown to deliver ultra-high even gene-level resolution for complex genetic studies. The purpose of this study is to investigate the usefulness of the HS rat model for fine mapping and identification of genes underlying bone fragility phenotypes. We compared bone geometry, density and strength phenotypes at multiple skeletal sites in HS rats with those obtained from 5 of the 8 progenitor inbred strains. In addition, we estimated the heritability for different bone phenotypes in these rats and employed principal component analysis to explore relationships among bone phenotypes in the HS rats. Our study demonstrates that significant variability exists for different skeletal phenotypes in HS rats compared with their inbred progenitors. In addition, we estimated high heritability for several bone phenotypes and biologically interpretable factors explaining significant overall variability, suggesting that the HS rat model could be a unique genetic resource for rapid and efficient discovery of the genetic determinants of bone fragility. PMID:21334473

Heterogeneous stock rat: a unique animal model for mapping genes influencing bone fragility.

PubMed

Alam, Imranul; Koller, Daniel L; Sun, Qiwei; Roeder, Ryan K; Cañete, Toni; Blázquez, Gloria; López-Aumatell, Regina; Martínez-Membrives, Esther; Vicens-Costa, Elia; Mont, Carme; Díaz, Sira; Tobeña, Adolf; Fernández-Teruel, Alberto; Whitley, Adam; Strid, Pernilla; Diez, Margarita; Johannesson, Martina; Flint, Jonathan; Econs, Michael J; Turner, Charles H; Foroud, Tatiana

2011-05-01

Previously, we demonstrated that skeletal mass, structure and biomechanical properties vary considerably among 11 different inbred rat strains. Subsequently, we performed quantitative trait loci (QTL) analysis in four inbred rat strains (F344, LEW, COP and DA) for different bone phenotypes and identified several candidate genes influencing various bone traits. The standard approach to narrowing QTL intervals down to a few candidate genes typically employs the generation of congenic lines, which is time consuming and often not successful. A potential alternative approach is to use a highly genetically informative animal model resource capable of delivering very high resolution gene mapping such as Heterogeneous stock (HS) rat. HS rat was derived from eight inbred progenitors: ACI/N, BN/SsN, BUF/N, F344/N, M520/N, MR/N, WKY/N and WN/N. The genetic recombination pattern generated across 50 generations in these rats has been shown to deliver ultra-high even gene-level resolution for complex genetic studies. The purpose of this study is to investigate the usefulness of the HS rat model for fine mapping and identification of genes underlying bone fragility phenotypes. We compared bone geometry, density and strength phenotypes at multiple skeletal sites in HS rats with those obtained from five of the eight progenitor inbred strains. In addition, we estimated the heritability for different bone phenotypes in these rats and employed principal component analysis to explore relationships among bone phenotypes in the HS rats. Our study demonstrates that significant variability exists for different skeletal phenotypes in HS rats compared with their inbred progenitors. In addition, we estimated high heritability for several bone phenotypes and biologically interpretable factors explaining significant overall variability, suggesting that the HS rat model could be a unique genetic resource for rapid and efficient discovery of the genetic determinants of bone fragility. Copyright © 2010 Elsevier Inc. All rights reserved.

Impact of Bt-corn MON88017 in comparison to three conventional lines on Trigonotylus caelestialium (Kirkaldy) (Heteroptera: Miridae) field densities.

PubMed

Rauschen, Stefan; Schultheis, Eva; Pagel-Wieder, Sibylle; Schuphan, Ingolf; Eber, Sabine

2009-04-01

In Europe, Bt-corn resistant against the European Corn Borer has until now been the only genetically modified plant to be grown commercially. With the advent of the Western Corn Rootworm Bt-corn varieties with resistance against Coleoptera will become important. The cultivation of Bt-plants may have negative impacts on non-target organisms, i.e. all species not explicitly targeted by a given Bt-crop. One prominent non-target group in corn are the herbivorous plant bugs (Heteroptera: Miridae). They are common, abundant and exposed to the Cry-protein. We therefore assessed the potential impact of the cultivation of the Cry3Bb1-expressing Bt-corn variety MON88017 and three conventional varieties on this group. Trigonotylus caelestialium (Kirkaldy) was the most abundant plant bug at the experimental field. There was no evidence for a negative impact of MON88017 on this species, despite its considerable exposure to Cry3Bb1 demonstrated with ELISA. The conventional corn varieties, however, had a consistent and significant influence on the field densities of this species over all three growing seasons.

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.

Efficient analysis of mouse genome sequences reveal many nonsense variants

PubMed Central

Steeland, Sophie; Timmermans, Steven; Van Ryckeghem, Sara; Hulpiau, Paco; Saeys, Yvan; Van Montagu, Marc; Vandenbroucke, Roosmarijn E.; Libert, Claude

2016-01-01

Genetic polymorphisms in coding genes play an important role when using mouse inbred strains as research models. They have been shown to influence research results, explain phenotypical differences between inbred strains, and increase the amount of interesting gene variants present in the many available inbred lines. SPRET/Ei is an inbred strain derived from Mus spretus that has ∼1% sequence difference with the C57BL/6J reference genome. We obtained a listing of all SNPs and insertions/deletions (indels) present in SPRET/Ei from the Mouse Genomes Project (Wellcome Trust Sanger Institute) and processed these data to obtain an overview of all transcripts having nonsynonymous coding sequence variants. We identified 8,883 unique variants affecting 10,096 different transcripts from 6,328 protein-coding genes, which is about 28% of all coding genes. Because only a subset of these variants results in drastic changes in proteins, we focused on variations that are nonsense mutations that ultimately resulted in a gain of a stop codon. These genes were identified by in silico changing the C57BL/6J coding sequences to the SPRET/Ei sequences, converting them to amino acid (AA) sequences, and comparing the AA sequences. All variants and transcripts affected were also stored in a database, which can be browsed using a SPRET/Ei M. spretus variants web tool (www.spretus.org), including a manual. We validated the tool by demonstrating the loss of function of three proteins predicted to be severely truncated, namely Fas, IRAK2, and IFNγR1. PMID:27147605

Strain preservation of experimental animals: vitrification of two-cell stage embryos for multiple mouse strains.

PubMed

Eto, Tomoo; Takahashi, Riichi; Kamisako, Tsutomu

2015-04-01

Strain preservation of experimental animals is crucial for experimental reproducibility. Maintaining complete animal strains, however, is costly and there is a risk for genetic mutations as well as complete loss due to disasters or illness. Therefore, the development of effective vitrification techniques for cryopreservation of multiple experimental animal strains is important. We examined whether a vitrification method using cryoprotectant solutions, P10 and PEPeS, is suitable for preservation of multiple inbred and outbred mouse strains. First, we investigated whether our vitrification method using cryoprotectant solutions was suitable for two-cell stage mouse embryos. In vitro development of embryos exposed to the cryoprotectant solutions was similar to that of fresh controls. Further, the survival rate of the vitrified embryos was extremely high (98.1%). Next, we collected and vitrified two-cell stage embryos of 14 mouse strains. The average number of embryos obtained from one female was 7.3-33.3. The survival rate of vitrified embryos ranged from 92.8% to 99.1%, with no significant differences among mouse strains. In vivo development did not differ significantly between fresh controls and vitrified embryos of each strain. For strain preservation using cryopreserved embryos, two offspring for inbred lines and one offspring for outbred lines must be produced from two-cell stage embryos collected from one female. The expected number of surviving fetuses obtained from embryos collected from one female of either the inbred or outbred strains ranged from 2.9 to 19.5. The findings of the present study indicated that this vitrification method is suitable for strain preservation of multiple mouse strains. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

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. PMID:25352856

Manufacturing of Protected Lithium Electrodes for Advanced Lithium-Air, Lithium-Water & Lithium-Sulfur Batteries

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

Visco, Steven J

The global demand for rechargeable batteries is large and growing rapidly. Assuming the adoption of electric vehicles continues to increase, the need for smaller, lighter, and less expensive batteries will become even more pressing. In this vein, PolyPlus Battery Company has developed ultra-light high performance batteries based on its proprietary protected lithium electrode (PLE) technology. The Company’s Lithium-Air and Lithium-Seawater batteries have already demonstrated world record performance (verified by third party testing), and we are developing advanced lithium-sulfur batteries which have the potential deliver high performance at low cost. In this program PolyPlus Battery Company teamed with Corning Incorporated tomore » transition the PLE technology from bench top fabrication using manual tooling to a pre- commercial semi-automated pilot line. At the inception of this program PolyPlus worked with a Tier 1 battery manufacturing engineering firm to design and build the first-of-its-kind pilot line for PLE production. The pilot line was shipped and installed in Berkeley, California several months after the start of the program. PolyPlus spent the next two years working with and optimizing the pilot line and now produces all of its PLEs on this line. The optimization process successfully increased the yield, throughput, and quality of PLEs produced on the pilot line. The Corning team focused on fabrication and scale-up of the ceramic membranes that are key to the PLE technology. PolyPlus next demonstrated that it could take Corning membranes through the pilot line process to produce state-of-the-art protected lithium electrodes. In the latter part of the program the Corning team developed alternative membranes targeted for the large rechargeable battery market. PolyPlus is now in discussions with several potential customers for its advanced PLE-enabled batteries, and is building relationships and infrastructure for the transition into manufacturing. It is likely that the next step will be accomplished through a combination of joint venture partnering and licensing of the technology.« less

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.

Utilizing protein-lean coproducts from corn containing recombinant pharmaceutical proteins for ethanol production.

PubMed

Paraman, Ilankovan; Moeller, Lorena; Scott, M Paul; Wang, Kan; Glatz, Charles E; Johnson, Lawrence A

2010-10-13

Protein-lean fractions of corn (maize) containing recombinant (r) pharmaceutical proteins were evaluated as a potential feedstock to produce fuel ethanol. The levels of residual r-proteins in the coproduct, distillers dry grains with solubles (DDGS), were determined. Transgenic corn lines containing recombinant green fluorescence protein (r-GFP) and a recombinant subunit vaccine of Escherichia coli enterotoxin (r-LTB), primarily expressed in endosperm, and another two corn lines containing recombinant human collagen (r-CIα1) and r-GFP, primarily expressed in germ, were used as model systems. The kernels were either ground and used for fermentation or dry fractionated to recover germ-rich fractions prior to grinding for fermentation. The finished beers of whole ground kernels and r-protein-spent endosperm solids contained 127-139 and 138-155 g/L ethanol concentrations, respectively. The ethanol levels did not differ among transgenic and normal corn feedstocks, indicating the residual r-proteins did not negatively affect ethanol production. r-Protein extraction and germ removal also did not negatively affect fermentation of the remaining mass. Most r-proteins were inactivated during the mashing process used to prepare corn for fermentation. No functionally active r-GFP or r-LTB proteins were found after fermentation of the r-protein-spent solids; however, a small quantity of residual r-CIα1 was detected in DDGS, indicating that the safety of DDGS produced from transgenic grain for r-protein production needs to be evaluated for each event. Protease treatment during fermentation completely hydrolyzed the residual r-CIα1, and no residual r-proteins were detectable in DDGS.

Characterization of miRNAs in response to short-term waterlogging in three inbred lines of Zea mays

USDA-ARS?s Scientific Manuscript database

To characterize the involvement of miRNAs and their targets in response to short-term hypoxia conditions, a quantitative real time PCR (qRT-PCR) assay was used to quantify the expression of the 24 candidate mature miRNA signatures (22 known and 2 novel mature miRNAs, representing 66 miRNA loci) and ...

Identification of quantitative trait loci controlling root and shoot traits associated to drought tolerance in a lentil (Lens culinaris Medik.) recombinant inbred line population

USDA-ARS?s Scientific Manuscript database

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. In all, 252 co-dominant and dominant markers were used for genetic linkage map c...

Quantitative trait locus analysis of seed sulfur containing amino acids in two recombinant inbred line populations of soybean

USDA-ARS?s Scientific Manuscript database

Soybean (Glycine max (L.) Merr.) is a major source of plant protein for humans and livestock. Low levels of sulfur containing amino acids (cysteine and methionine) in soybean protein is the main limitation of soybean meal as animal food. The objectives of this study were to identify and validate Q...

Progress on genetic linkage maps, traits/QTLs, and utilization in two recombinant inbred line populations of peanuts (Arachis hypogaea L.)

USDA-ARS?s Scientific Manuscript database

Peanut, a highly nutritional crop, is used in edible products or crushed for cooking oil, and is susceptible to a range of diseases, including Tomato spotted wilt virus (TSWV), early and late leaf spot (ELS and LLS). Losses in productivity and quality are also attributable to environmental stresses ...

Quantitative trait locus mapping of drought and salt tolerance in as introgressed recombinant inbred line population of upland cotton under the greenhouse and feild conditions

USDA-ARS?s Scientific Manuscript database

Drought and salt tolerances are complex traits and controlled by multiple genes, environmental factors and their interactions. Drought and salt stresses can result in more than 50% yield loss in Upland cotton (Gossypium hirsutum L.). G. barbadense L. (the source of Pima cotton) carries desirable tra...

Dissection of genetic factors underlying wheat kernel shape and size in an elite x nonadapted cross using a high density SNP linkage map

USDA-ARS?s Scientific Manuscript database

Wheat kernel shape and size has been under selection since early domestication. Kernel morphology is a major consideration in wheat breeding, as it impacts grain yield and quality. A population of 160 recombinant inbred lines (RIL), developed using an elite (ND 705) and a nonadapted genotype (PI 414...

Quantitative trait loci affecting oil content, oil composition, and other agronomically important traits in Oat (Avena sativa L.)

USDA-ARS?s Scientific Manuscript database

Groat oil content and composition are important determinants of oat quality. We investigated these traits in a population of 146 recombinant inbred lines from a cross between 'Dal' (high oil) and 'Exeter' (low oil). A linkage map consisting of 475 DArT markers spanning 1271.8 cM across 40 linkage gr...

Identification of novel QTL for sawfly resistance in wheat

Treesearch

J. D. Sherman; D. K. Weaver; M. L. Hofland; S. E. Sing; M. Buteler; S. P. Lanning; Y. Naruoka; F. Crutcher; N. K. Blake; J. M. Martin; P. F. Lamb; G. R. Carlson; L. E. Talbert

2010-01-01

The wheat stem sawfly (WSS) (Cephus cinctus Nort.) is an important pest of wheat (Triticum aestivum L. em. Thell.) in the Northern Great Plains. This paper reports the genetic analysis of antixenosis for egg-laying WSS females in recombinant inbred lines (RIL) of hard red spring wheat. Female WSS preferentially choose certain wheat genotypes for egg-laying, with the...

Toward a better understanding of the genomic region harboring Fusarium head blight resistance QTL Qfhs.ndsu-3AS in durum wheat

USDA-ARS?s Scientific Manuscript database

The wild emmer wheat (Triticum dicoccoides)-derived Fusarium head blight (FHB) resistance quantitative trait locus (QTL) Qfhs.ndsu-3AS previously mapped to the short arm of chromosome 3A (3AS) in a population of recombinant inbred chromosome lines (RICLs). This study aimed to attain a better unders...

Use of diversity arrays technology markers for integration into a cotton reference map and anchoring to a recombinant inbred line map

USDA-ARS?s Scientific Manuscript database

A DArT marker platform is developed for the cotton genome to evaluate the use of DArT markers compared to AFLPs in mapping, and transferability across the mapping populations. We used a reference genetic map of tetraploid Gossypium that already contained ~5000 loci which coalesced into 26 chromosom...

Genetic Diversity and Molecular Evolution of Chinese Waxy Maize Germplasm

PubMed Central

Zheng, Hongjian; Wang, Hui; Yang, Hua; Wu, Jinhong; Shi, Biao; Cai, Run; Xu, Yunbi; Wu, Aizhong; Luo, Lijun

2013-01-01

Waxy maize (Zea mays L. var. certaina Kulesh), with many excellent characters in terms of starch composition and economic value, has grown in China for a long history and its production has increased dramatically in recent decades. However, the evolution and origin of waxy maize still remains unclear. We studied the genetic diversity of Chinese waxy maize including typical landraces and inbred lines by SSR analysis and the results showed a wide genetic diversity in the Chinese waxy maize germplasm. We analyzed the origin and evolution of waxy maize by sequencing 108 samples, and downloading 52 sequences from GenBank for the waxy locus in a number of accessions from genus Zea. A sharp reduction of nucleotide diversity and significant neutrality tests (Tajima’s D and Fu and Li’s F*) were observed at the waxy locus in Chinese waxy maize but not in nonglutinous maize. Phylogenetic analysis indicated that Chinese waxy maize originated from the cultivated flint maize and most of the modern waxy maize inbred lines showed a distinct independent origin and evolution process compared with the germplasm from Southwest China. The results indicated that an agronomic trait can be quickly improved to meet production demand by selection. PMID:23818949

High genetic load in the Pacific oyster Crassostrea gigas.

PubMed Central

Launey, S; Hedgecock, D

2001-01-01

The causes of inbreeding depression and the converse phenomenon of heterosis or hybrid vigor remain poorly understood despite their scientific and agricultural importance. In bivalve molluscs, related phenomena, marker-associated heterosis and distortion of marker segregation ratios, have been widely reported over the past 25 years. A large load of deleterious recessive mutations could explain both phenomena, according to the dominance hypothesis of heterosis. Using inbred lines derived from a natural population of Pacific oysters and classical crossbreeding experiments, we compare the segregation ratios of microsatellite DNA markers at 6 hr and 2-3 months postfertilization in F(2) or F(3) hybrid families. We find evidence for strong and widespread selection against identical-by-descent marker homozygotes. The marker segregation data, when fit to models of selection against linked deleterious recessive mutations and extrapolated to the whole genome, suggest that the wild founders of inbred lines carried a minimum of 8-14 highly deleterious recessive mutations. This evidence for a high genetic load strongly supports the dominance theory of heterosis and inbreeding depression and establishes the oyster as an animal model for understanding the genetic and physiological causes of these economically important phenomena. PMID:11560902

Rapid detection of fumonisin B1 using a colloidal gold immunoassay strip test in corn samples.

PubMed

Ling, Sumei; Wang, Rongzhi; Gu, Xiaosong; Wen, Can; Chen, Lingling; Chen, Zhibin; Chen, Qing-Ai; Xiao, Shiwei; Yang, Yanling; Zhuang, Zhenhong; Wang, Shihua

2015-12-15

Fumonisin B1 (FB1) is the most common and highest toxic of fumonisins species, exists frequently in corn and corn-based foods, leading to several animal and human diseases. Furthermore, FB1 was reported that it was associated with the human esophageal cancer. In view of the harmful of FB1, it is urgent to develop a feasible and accuracy method for rapid detection of FB1. In this study, a competitive immunoassay for FB1 detection was developed based on colloidal gold-antibody conjugate. The FB1-keyhole limpet hemoeyanin (FB1-KLH) conjugate was embedded in the test line, and goat anti-mouse IgG antibody embedded in the control line. The color density of the test line correlated with the concentration of FB1 in the range from 2.5 to 10 ng/mL, and the visual limit detection of test for FB1 was 2.5 ng/mL. The results indicated that the test strip is specific for FB1, and no cross-reactivity to other toxins. The quantitative detection for FB1 was simple, only needing one step without complicated assay performance and expensive equipment, and the total time of visual evaluation was less than 5 min. Hence, the developed colloidal gold-antibody assay can be used as a feasible method for FB1 rapid and quantitative detection in corn samples. Copyright © 2015 Elsevier Ltd. All rights reserved.

Surveying the Maize community for their diversity and pedigree visualization needs to prioritize tool development and curation

PubMed Central

Braun, Bremen L.; Schott, David A.; Portwood, II, John L.; Schaeffer, Mary L.; Harper, Lisa C.; Gardiner, Jack M.; Cannon, Ethalinda K.; Andorf, Carson M.

2017-01-01

Abstract The Maize Genetics and Genomics Database (MaizeGDB) team prepared a survey to identify breeders’ needs for visualizing pedigrees, diversity data and haplotypes in order to prioritize tool development and curation efforts at MaizeGDB. The survey was distributed to the maize research community on behalf of the Maize Genetics Executive Committee in Summer 2015. The survey garnered 48 responses from maize researchers, of which more than half were self-identified as breeders. The survey showed that the maize researchers considered their top priorities for visualization as: (i) displaying single nucleotide polymorphisms in a given region for a given list of lines, (ii) showing haplotypes for a given list of lines and (iii) presenting pedigree relationships visually. The survey also asked which populations would be most useful to display. The following two populations were on top of the list: (i) 3000 publicly available maize inbred lines used in Romay et al. (Comprehensive genotyping of the USA national maize inbred seed bank. Genome Biol, 2013;14:R55) and (ii) maize lines with expired Plant Variety Protection Act (ex-PVP) certificates. Driven by this strong stakeholder input, MaizeGDB staff are currently working in four areas to improve its interface and web-based tools: (i) presenting immediate progenies of currently available stocks at the MaizeGDB Stock pages, (ii) displaying the most recent ex-PVP lines described in the Germplasm Resources Information Network (GRIN) on the MaizeGDB Stock pages, (iii) developing network views of pedigree relationships and (iv) visualizing genotypes from SNP-based diversity datasets. These survey results can help other biological databases to direct their efforts according to user preferences as they serve similar types of data sets for their communities. Database URL: https://www.maizegdb.org PMID:28605768

Voluntary exercise and its effects on body composition depend on genetic selection history.

PubMed

Nehrenberg, Derrick L; Hua, Kunjie; Estrada-Smith, Daria; Garland, Theodore; Pomp, Daniel

2009-07-01

Little is known about how genetic variation affects the capacity for exercise to change body composition. We examined the extent to which voluntary exercise alters body composition in several lines of selectively bred mice compared to controls. Lines studied included high runner (HR) (selected for high wheel running), M16 (selected for rapid weight gain), Institute of Cancer Research (ICR) (randomly bred as control for M16), M16i (an inbred line derived from M16), HE (selected for high percentage of body fat while holding body weight constant), LF (selected for low percentage of body fat), C57BL/6J (common inbred line), and the F1 between HR and C57BL/6J. Body weight and body fat were recorded before and after 6 days of free access to running wheels in males and females that were individually caged. Total food intake was measured during this 6-day period. All pre- and postexercise measures showed significant strain effects. While HR mice predictably exercised at higher levels, all other selection lines had decreased levels of wheel running relative to ICR. The HR x B6 F1 ran at similar levels to HR demonstrating complete dominance for voluntary exercise. Also, all strains lost body fat after exercise, but the relationships between exercise and changes in percent body were not uniform across genotypes. These results indicate that there is significant genetic variation for voluntary exercise and its effects on body composition. It is important to carefully consider genetic background and/or selection history when using mice to model effects of exercise on body composition, and perhaps, other complex traits as well.

Validation of consensus quantitative trait loci associated with resistance to multiple foliar pathogens of maize.

PubMed

Asea, Godfrey; Vivek, Bindiganavile S; Bigirwa, George; Lipps, Patrick E; Pratt, Richard C

2009-05-01

Maize production in sub-Saharan Africa incurs serious losses to epiphytotics of foliar diseases. Quantitative trait loci conditioning partial resistance (rQTL) to infection by causal agents of gray leaf spot (GLS), northern corn leaf blight (NCLB), and maize streak have been reported. Our objectives were to identify simple-sequence repeat (SSR) molecular markers linked to consensus rQTL and one recently identified rQTL associated with GLS, and to determine their suitability as tools for selection of improved host resistance. We conducted evaluations of disease severity phenotypes in separate field nurseries, each containing 410 F2:3 families derived from a cross between maize inbred CML202 (NCLB and maize streak resistant) and VP31 (a GLS-resistant breeding line) that possess complimentary rQTL. F2:3 families were selected for resistance based on genotypic (SSR marker), phenotypic, or combined data and the selected F3:4 families were reevaluated. Phenotypic values associated with SSR markers for consensus rQTL in bins 4.08 for GLS, 5.04 for NCLB, and 1.04 for maize streak significantly reduced disease severity in both generations based on single-factor analysis of variance and marker-interval analysis. These results were consistent with the presence of homozygous resistant parent alleles, except in bin 8.06, where markers were contributed by the NCLB-susceptible parent. Only one marker associated with resistance could be confirmed in bins 2.09 (GLS) and 3.06 (NCLB), illustrating the need for more robust rQTL discovery, fine-mapping, and validation prior to undertaking marker-based selection.

Assessment of a Nutritional Rehabilitation Model in Two Modern Broilers and Their Jungle Fowl Ancestor: A Model for Better Understanding Childhood Undernutrition.

PubMed

Baxter, Mikayla F A; Latorre, Juan D; Koltes, Dawn A; Dridi, Sami; Greene, Elizabeth S; Bickler, Stephen W; Kim, Jae H; Merino-Guzman, Ruben; Hernandez-Velasco, Xochitl; Anthony, Nicholas B; Bottje, Walter G; Hargis, Billy M; Tellez, Guillermo

2018-01-01

This article is the first in a series of manuscripts to evaluate nutritional rehabilitation in chickens as a model to study interventions in children malnutrition (Part 1: Performance, Bone Mineralization, and Intestinal Morphometric Analysis). Inclusion of rye in poultry diets induces a nutritional deficit that leads to increased bacterial translocation, intestinal viscosity, and decreased bone mineralization. However, it is unclear the effect of diet on developmental stage or genetic strain. Therefore, the objective was to determine the effects of a rye diet during either the early or late phase of development on performance, bone mineralization, and intestinal morphology across three diverse genetic backgrounds. Modern 2015 (Cobb 500) broiler chicken, 1995 Cobb broiler chicken, and the Giant Jungle Fowl were randomly allocated into four different dietary treatments. Dietary treatments were (1) a control corn-based diet throughout the trial (corn-corn); (2) an early phase malnutrition diet where chicks received a rye-based diet for 10 days, and then switched to the control diet (rye-corn); (3) a malnutrition rye-diet that was fed throughout the trial (rye-rye); and (4) a late phase malnutrition diet where chicks received the control diet for 10 days, and then switched to the rye diet for the last phase (corn-rye). At 10 days of age, chicks were weighed and diets were switched in groups 2 and 4. At day 20 of age, all chickens were weighed and euthanized to collect bone and intestinal samples. Body weight, weight gain, and bone mineralization were different across diet, genetic line, age and all two- and three-way interactions ( P  < 0.05). Overall, Jungle Fowl were the most tolerant to a rye-based diet, and both the modern and 1995 broilers were significantly affected by the high rye-based diet. However, the 1995 broilers consuming the rye-based diet appeared to experience more permanent effects when compared with the modern broiler. The results of this study suggest that chickens have a great potential as a nutritional rehabilitation model in human trials. The 1995 broilers line was an intermediate genetic line between the fast growing modern line and the non-selected Jungle Fowl line, suggesting that it would be the most appropriate model to study for future studies.

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.

Quantitative trait loci mapping of western corn rootworm (Coleoptera: Chrysomelidae) host plant resistance in two populations of doubled haploid lines in maize (Zea mays L.)

USDA-ARS?s Scientific Manuscript database

Over the last 70 years, more than 12,000 maize accessions have been screened for their level of resistance to western corn rootworm, Diabrotica virgifera virgifera LeConte, larval feeding. Less than 1% of this germplasm was selected for initiating recurrent selection or other breeding programs. Sele...

Asian corn borer (ACB) and non-ACB pests in GM corn (Zea mays L.) in the Philippines.

PubMed

Afidchao, Miladis M; Musters, C J M; de Snoo, Geert R

2013-07-01

The Asian corn borer (ACB), Ostrinia furnacalis (Guenée), has become the most damaging pest in corn in south-east Asia. Corn farmers in the Philippines have incurred great yield losses in the past decades because of ACB infestation. Bacillus thuringiensis (Bt) and Bt herbicide-tolerant (BtHT) corns have been developed to reduce borer attacks worldwide. This study assessed the extent of ACB and non-ACB pest infestations in both GM and non-GM corn in Isabela Province, the Philippines. Specific aims were to reinvestigate the efficacy of Bt corn in controlling ACB, to evaluate what parts of Bt corn plants are susceptible to ACB, to monitor the potential development of ACB resistance and to evaluate whether secondary pests dominate in an ACB-free Bt corn environment. The study involved preparatory interviews with farmers, site selection, field scouting and visual inspection of 200 plants along 200 m transect lines through 198 cornfields. Bt corn can efficiently reduce the ACB pest problem and reduce borer damage by 44%, to damage levels in Bt and BtHT corn of 6.8 and 7% respectively. The leaves of Bt corn were more susceptible, while cobs of Bt corn were less affected by ACB. Non-ACB pests were common in Bt toxin-free cornfields and reduced in non-GM cornfields where ACB was abundant. No secondary pest outbreaks were found in ACB-free Bt cornfields. Bt and BtHT corn hybrids containing the Cry1Ab protein performed well in Isabela Province. Reduced cob damage by ACB on Bt fields could mean smaller economic losses even with ACB infestation. The occurrence of ACB in Bt and BtHT cornfields, although at a moderate and insignificant level, could imply the potential development of resistance to Bt toxin. © 2012 Society of Chemical Industry.

An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley

USDA-ARS?s Scientific Manuscript database

We explored the use of genotyping by sequencing (GBS) on a recombinant inbred line population (GPMx) derived from a cross between the two-rowed barley cultivar ‘Golden Promise’ (ari-e.GP/Vrs1) and the six-rowed cultivar ‘Morex’ (Ari-e/vrs1) to map plant height. We identified three Quantitative Trait...

Pl17 is a novel gene independent of known downy mildew resistance genes in the cultivated sunflower (Helianthus annuus L.)

USDA-ARS?s Scientific Manuscript database

Downy mildew (DM), caused by Plasmopara halstedii (Farl.) Berl. et de Toni, is one of the serious sunflower diseases in the world due to its high virulence and the variability of the pathogen. DM resistance in the USDA inbred line, HA 458, has been shown to be effective against all virulent races of...

Effects of peptides on generation of reactive oxygen species in subcellular fractions of Drosophila melanogaster.

PubMed

Khavinson, V K; Myl'nikov, S V; Oparina, T I; Arutyunyan, A V

2001-07-01

We studied the effects of Epithalon (Ala-Glu-Asp-Gly) and Vilon (Lys-Glu) on free radical processes in highly inbred HA(+)line of Drosophila melanogaster. Vilon inhibited generation of reactive oxygen species in mitochondria, but stimulated this process in the cytosol. We found sex- and age-related differences in the generation of reactive oxygen species and cytosol antioxidant activity.

Effect of pineal tetrapeptide on antioxidant defense in Drosophila melanogaster.

PubMed

Khavinson, V K; Myl'nikov, S V

2000-04-01

Effects of synthetic pineal tetrapeptide L-Ala-L-Glu-L-Asp-L-Glu (Epithalon) on specific catalase activity and the content of conjugated hydroperoxides in highly inbred Drosophila melanogaster lines differing in reproductive functions were studied. It was shown that Epithalon is a potent modulator of the antioxidant defense, whose biological activity 1000-fold surpasses that of the complex pineal peptide preparation Epithalamin.

Identification of quantitative trait loci (QTLs) responsible for sheath blight resistance in rice using recombinant inbred line population of Lemont X Jasmine 85

USDA-ARS?s Scientific Manuscript database

Rice sheath blight (RSB) caused by the soil borne pathogen Rhizoctonia solani, is one of the most destructive diseases of rice, causing severe losses in rice yield and quality annually. The major gene (s) governing the resistance to RSB have not been found in cultivated rice worldwide. However, ri...

Chromosomes 3B and 4D are associated with several milling and baking quality traits in a soft white spring wheat (Triticum aestivum L.) population

USDA-ARS?s Scientific Manuscript database

Wheat is marketed based on end-use quality characteristics and better knowledge of the underlying genetics of specific quality parameters is essential to enhance the breeding process. A set of 188 recombinant inbred lines from a ‘Louise’ by ‘Penawawa’ mapping population was grown in two crop years a...

Lost P1 allele in sh2 sweet corn: quantitative effects of p1 and a1 genes on concentrations of maysin, apimaysin, methoxymaysin, and chlorogenic acid in maize silk.

PubMed

Guo, B Z; Zhang, Z J; Butrón, A; Widstrom, N W; Snook, M E; Lynch, R E; Plaisted, D

2004-12-01

In the United States, insecticide is used extensively in the production of sweet corn due to consumer demand for zero damage to ears and to a sweet corn genetic base with little or no resistance to ear-feeding insects. Growers in the southern United States depend on scheduled pesticide applications to control ear-feeding insects. In a study of quantitative genetic control over silk maysin, AM-maysin (apimaysin and methoxymaysin), and chlorogenic acid contents in an F2 population derived from GE37 (dent corn, P1A1) and 565 (sh2 sweet corn, p1a1), we demonstrate that the P1 allele from field corn, which was selected against in the development of sweet corn, has a strong epistatic interaction with the a1 allele in sh2 sweet corn. We detected that the p1 gene has significant effects (P < 0.0001) not only on silk maysin concentrations but also on AM-maysin, and chlorogenic acid concentrations. The a1 gene also has significant (P < 0.0005) effects on these silk antibiotic chemicals. Successful selection from the fourth and fifth selfed backcrosses for high-maysin individuals of sweet corn homozygous for the recessive a1 allele (tightly linked to sh2) and the dominant P1 allele has been demonstrated. These selected lines have much higher (2 to 3 times) concentrations of silk maysin and other chemicals (AM-maysin and chlorogenic acid) than the donor parent GE37 and could enhance sweet corn resistance to corn earworm and reduce the number of applications of insecticide required to produce sweet corn.

Restriction fragment length polymorphism markers associated with silk maysin, antibiosis to corn earworm (Lepidoptera: Noctuidae) larvae, in a dent and sweet corn cross.

PubMed

Guo, B Z; Zhang, Z J; Li, R G; Widstrom, N W; Snook, M E; Lynch, R E; Plaisted, D

2001-04-01

Maysin, a C-glycosylflavone in maize silk, has insecticidal activity against corn earworm, Helicoverpa zea (Boddie), larvae. Sweet corn, Zea mays L., is a vulnerable crop to ear-feeding insects and requires pesticide protection from ear damage. This study was conducted to identify maize chromosome regions associated with silk maysin concentration and eventually to transfer and develop high silk maysin sweet corn lines with marker-assisted selection (MAS). Using an F2 population derived from SC102 (high maysin dent corn) and B31857 (low maysin sh2 sweet corn), we detected two major quantitative trait loci (QTL). It was estimated that 25.6% of the silk maysin variance was associated with segregation in the genomic region of npi286 (flanking to p1) on chromosome 1S. We also demonstrated that a1 on chromosome 3L had major contribution to silk maysin (accounted for 15.7% of the variance). Locus a1 has a recessive gene action for high maysin with the presence of functional p1 allele. Markers umc66a (near c2) and umc105a on chromosome 9S also were detected in this analysis with minor contribution. A multiple-locus model, which included npi286, a1, csu3 (Bin 1.05), umc245 (Bin 7.05), agrr21 (Bin 8.09), umc105a, and the epistatic interactions npi286 x a1, a1 x agrr21, csu3 x umc245, and umc105a x umc245, accounted for 76.3% of the total silk maysin variance. Tester crosses showed that at the a1 locus, SC102 has functional A1 alleles and B31857 has homozygous recessive a1 alleles. Individuals of (SC102 x B31857) x B31857 were examined with MAS and plants with p1 allele from SC102 and homozygous a1 alleles from B31857 had consistent high silk maysin. Marker-assisted selection seems to be a suitable method to transfer silk maysin to sweet corn lines to reduce pesticide application.

Recent Honey Bee Colony Declines

DTIC Science & Technology

2007-06-20

climate and temperature changes,38 the effects of feed supplements that are produced from transgenic or genetically modified crops, such as high - fructose ... corn syrup ,39 and also the effects of cell phone transmissions and radiation from power lines that may be interfering with a bee’s navigational...podcasts.psu.edu/taxonomy/term/62]. Staple crops such as wheat, corn , and rice do not rely on insect pollination and are mostly wind pollinated

Cytogenetic and Sequence Analyses of Mitochondrial DNA Insertions in Nuclear Chromosomes of Maize

PubMed Central

Lough, Ashley N.; Faries, Kaitlyn M.; Koo, Dal-Hoe; Hussain, Abid; Roark, Leah M.; Langewisch, Tiffany L.; Backes, Teresa; Kremling, Karl A. G.; Jiang, Jiming; Birchler, James A.; Newton, Kathleen J.

2015-01-01

The transfer of mitochondrial DNA (mtDNA) into nuclear genomes is a regularly occurring process that has been observed in many species. Few studies, however, have focused on the variation of nuclear-mtDNA sequences (NUMTs) within a species. This study examined mtDNA insertions within chromosomes of a diverse set of Zea mays ssp. mays (maize) inbred lines by the use of fluorescence in situ hybridization. A relatively large NUMT on the long arm of chromosome 9 (9L) was identified at approximately the same position in four inbred lines (B73, M825, HP301, and Oh7B). Further examination of the similarly positioned 9L NUMT in two lines, B73 and M825, indicated that the large size of these sites is due to the presence of a majority of the mitochondrial genome; however, only portions of this NUMT (∼252 kb total) were found in the publically available B73 nuclear sequence for chromosome 9. Fiber-fluorescence in situ hybridization analysis estimated the size of the B73 9L NUMT to be ∼1.8 Mb and revealed that the NUMT is methylated. Two regions of mtDNA (2.4 kb and 3.3 kb) within the 9L NUMT are not present in the B73 mitochondrial NB genome; however, these 2.4-kb and 3.3-kb segments are present in other Zea mitochondrial genomes, including that of Zea mays ssp. parviglumis, a progenitor of domesticated maize. PMID:26333837

Mapping quantitative trait loci affecting Arabidopsis thaliana seed morphology features extracted computationally from images.

PubMed

Moore, Candace R; Gronwall, David S; Miller, Nathan D; Spalding, Edgar P

2013-01-01

Seeds are studied to understand dispersal and establishment of the next generation, as units of agricultural yield, and for other important reasons. Thus, elucidating the genetic architecture of seed size and shape traits will benefit basic and applied plant biology research. This study sought quantitative trait loci (QTL) controlling the size and shape of Arabidopsis thaliana seeds by computational analysis of seed phenotypes in recombinant inbred lines derived from the small-seeded Landsberg erecta × large-seeded Cape Verde Islands accessions. On the order of 10(3) seeds from each recombinant inbred line were automatically measured with flatbed photo scanners and custom image analysis software. The eight significant QTL affecting seed area explained 63% of the variation, and overlapped with five of the six major-axis (length) QTL and three of the five minor-axis (width) QTL, which accounted for 57% and 38% of the variation in those traits, respectively. Because the Arabidopsis seed is exalbuminous, lacking an endosperm at maturity, the results are relatable to embryo length and width. The Cvi allele generally had a positive effect of 2.6-4.0%. Analysis of variance showed heritability of the three traits ranged between 60% and 73%. Repeating the experiment with 2.2 million seeds from a separate harvest of the RIL population and approximately 0.5 million seeds from 92 near-isogenic lines confirmed the aforementioned results. Structured for download are files containing phenotype measurements, all sets of seed images, and the seed trait measuring tool.

Genetic dissection of the maize (Zea mays L.) MAMP response.

PubMed

Zhang, Xinye; Valdés-López, Oswaldo; Arellano, Consuelo; Stacey, Gary; Balint-Kurti, Peter

2017-06-01

Loci associated with variation in maize responses to two microbe-associated molecular patterns (MAMPs) were identified. MAMP responses were correlated. No relationship between MAMP responses and quantitative disease resistance was identified. Microbe-associated molecular patterns (MAMPs) are highly conserved molecules commonly found in microbes which can be recognized by plant pattern recognition receptors. Recognition triggers a suite of responses including production of reactive oxygen species (ROS) and nitric oxide (NO) and expression changes of defense-related genes. In this study, we used two well-studied MAMPs (flg22 and chitooctaose) to challenge different maize lines to determine whether there was variation in the level of responses to these MAMPs, to dissect the genetic basis underlying that variation and to understand the relationship between MAMP response and quantitative disease resistance (QDR). Naturally occurring quantitative variation in ROS, NO production, and defense genes expression levels triggered by MAMPs was observed. A major quantitative traits locus (QTL) associated with variation in the ROS production response to both flg22 and chitooctaose was identified on chromosome 2 in a recombinant inbred line (RIL) population derived from the maize inbred lines B73 and CML228. Minor QTL associated with variation in the flg22 ROS response was identified on chromosomes 1 and 4. Comparison of these results with data previously obtained for variation in QDR and the defense response in the same RIL population did not provide any evidence for a common genetic basis controlling variation in these traits.

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.

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.

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

Aluminum tolerance in maize is associated with higher MATE1 gene copy number

PubMed Central

Maron, Lyza G.; Guimarães, Claudia T.; Kirst, Matias; Albert, Patrice S.; Birchler, James A.; Bradbury, Peter J.; Buckler, Edward S.; Coluccio, Alison E.; Danilova, Tatiana V.; Kudrna, David; Magalhaes, Jurandir V.; Piñeros, Miguel A.; Schatz, Michael C.; Wing, Rod A.; Kochian, Leon V.

2013-01-01

Genome structure variation, including copy number variation and presence/absence variation, comprises a large extent of maize genetic diversity; however, its effect on phenotypes remains largely unexplored. Here, we describe how copy number variation underlies a rare allele that contributes to maize aluminum (Al) tolerance. Al toxicity is the primary limitation for crop production on acid soils, which make up 50% of the world’s potentially arable lands. In a recombinant inbred line mapping population, copy number variation of the Al tolerance gene multidrug and toxic compound extrusion 1 (MATE1) is the basis for the quantitative trait locus of largest effect on phenotypic variation. This expansion in MATE1 copy number is associated with higher MATE1 expression, which in turn results in superior Al tolerance. The three MATE1 copies are identical and are part of a tandem triplication. Only three maize inbred lines carrying the three-copy allele were identified from maize and teosinte diversity panels, indicating that copy number variation for MATE1 is a rare, and quite likely recent, event. These maize lines with higher MATE1 copy number are also Al-tolerant, have high MATE1 expression, and originate from regions of highly acidic soils. Our findings show a role for copy number variation in the adaptation of maize to acidic soils in the tropics and suggest that genome structural changes may be a rapid evolutionary response to new environments. PMID:23479633

Nested Association Mapping of Stem Rust Resistance in Wheat Using Genotyping by Sequencing

PubMed Central

Rouse, Matthew N.; Tsilo, Toi J.; Macharia, Godwin K.; Bhavani, Sridhar; Jin, Yue; Anderson, James A.

2016-01-01

We combined the recently developed genotyping by sequencing (GBS) method with joint mapping (also known as nested association mapping) to dissect and understand the genetic architecture controlling stem rust resistance in wheat (Triticum aestivum). Ten stem rust resistant wheat varieties were crossed to the susceptible line LMPG-6 to generate F6 recombinant inbred lines. The recombinant inbred line populations were phenotyped in Kenya, South Africa, and St. Paul, Minnesota, USA. By joint mapping of the 10 populations, we identified 59 minor and medium-effect QTL (explained phenotypic variance range of 1% – 20%) on 20 chromosomes that contributed towards adult plant resistance to North American Pgt races as well as the highly virulent Ug99 race group. Fifteen of the 59 QTL were detected in multiple environments. No epistatic relationship was detected among the QTL. While these numerous small- to medium-effect QTL are shared among the families, the founder parents were found to have different allelic effects for the QTL. Fourteen QTL identified by joint mapping were also detected in single-population mapping. As these QTL were mapped using SNP markers with known locations on the physical chromosomes, the genomic regions identified with QTL could be explored more in depth to discover candidate genes for stem rust resistance. The use of GBS-derived de novo SNPs in mapping resistance to stem rust shown in this study could be used as a model to conduct similar marker-trait association studies in other plant species. PMID:27186883

Hyperspectral imaging system for whole corn ear surface inspection

NASA Astrophysics Data System (ADS)

Yao, Haibo; Kincaid, Russell; Hruska, Zuzana; Brown, Robert L.; Bhatnagar, Deepak; Cleveland, Thomas E.

2013-05-01

Aflatoxin is a mycotoxin produced mainly by Aspergillus flavus (A.flavus) and Aspergillus parasitiucus fungi that grow naturally in corn. Very serious health problems such as liver damage and lung cancer can result from exposure to high toxin levels in grain. Consequently, many countries have established strict guidelines for permissible levels in consumables. Conventional chemical-based analytical methods used to screen for aflatoxin such as thin-layer chromatography (TLC) and high performance liquid chromatography (HPLC) are time consuming, expensive, and require the destruction of samples as well as proper training for data interpretation. Thus, it has been a continuing effort within the research community to find a way to rapidly and non-destructively detect and possibly quantify aflatoxin contamination in corn. One of the more recent developments in this area is the use of spectral technology. Specifically, fluorescence hyperspectral imaging offers a potential rapid, and non-invasive method for contamination detection in corn infected with toxigenic A.flavus spores. The current hyperspectral image system is designed for scanning flat surfaces, which is suitable for imaging single or a group of corn kernels. In the case of a whole corn cob, it is preferred to be able to scan the circumference of the corn ear, appropriate for whole ear inspection. This paper discusses the development of a hyperspectral imaging system for whole corn ear imaging. The new instrument is based on a hyperspectral line scanner using a rotational stage to turn the corn ear.

Purple corn color inhibition of prostate carcinogenesis by targeting cell growth pathways.

PubMed

Long, Ne; Suzuki, Shugo; Sato, Shinya; Naiki-Ito, Aya; Sakatani, Keisuke; Shirai, Tomoyuki; Takahashi, Satoru

2013-03-01

Purple corn color is a widely used food colorant that was reported to have attenuating effects on hypertension, diabetes, and to have anti-cancer effects on colon and breast cancer. Our study is the first on its possible chemoprevention effects against prostate cancer. For this purpose an androgen-dependent prostate cancer cell line, LNCaP, was used to examine effects in vitro. Purple corn color inhibited the proliferation of LNCaP cells by decreasing the expression of Cyclin D1 and inhibiting the G1 stage of the cell cycle. Thirty-six male transgenic rats for adenocarcinoma of prostate were fed basic diet or diet with purple corn color for 8 weeks. Purple corn color decreased the incidence of adenocarcinoma in the lateral prostate and slowed down the progression of prostate cancer. A lower Ki67 positive rate, a decrease of the expression of Cyclin D1, and downregulation of the activation of Erk1/2 and p38 MAPK were observed in the group consuming purple corn color in the diet. Since purple corn color is a mixture, determining its active component should help in the understanding and usage of purple corn color for prostate cancer chemoprevention. Therefore, the three major anthocyanins in purple corn color, cyanidin-3-glucoside, pelargonidin-3-glucoside and peonidin-3-glucoside, were tested with LNCaP cells. The results suggested that cyanidin-3-glucoside and pelargonidin-3-glucoside are the active compounds. © 2012 Japanese Cancer Association.

Evaluation of limit feeding corn and distillers dried grains with solubles in non-feed-withdrawal molt programs for laying hens.

PubMed

Mejia, L; Meyer, E T; Utterback, P L; Utterback, C W; Parsons, C M; Koelkebeck, K W

2010-03-01

An experiment was conducted using 504 Hy-Line W-36 Single Comb White Leghorn hens (69 wk of age) randomly assigned to 1 of 7 treatments. These treatments consisted of a 47% corn:47% soy hulls diet (C:SH) fed ad libitum; a 94% corn diet fed at a rate of 36.3, 45.4, or 54.5 g/hen per day (CORN 36, CORN 45, and CORN 54, respectively); and a 94% corn distillers dried grains with solubles (DDGS) diet fed at the same rates as the previous corn diets (DDGS 36, DDGS 45, and DDGS 54, respectively) during the molt period of 28 d. The intent was to feed the DDGS diets for 28 d; however, all hens on these diets had very low feed intakes and greater than anticipated BW loss. Thus, they were switched to a 16% CP corn-soybean meal layer diet on d 19 of the molt period. At d 28, hens on all treatments were fed the same corn-soybean meal layer diet for 39 wk (73 to 112 wk of age). All DDGS diets and the CORN 36 diet resulted in total cessation of egg production during the molt period and egg production of hens fed the CORN 45, CORN 54, and C:SH diets had decreased to 3 and 4%, respectively, by d 28. Body weight loss during the 28-d molt period ranged from 14% for the CORN 54 diet to approximately 23% for the 3 DDGS diets. Postmolt egg production (5 to 43 wk) was higher for hens fed the DDGS molt diets than those fed the corn diets. There were no consistent differences in egg mass, egg-specific gravity, feed efficiency, or layer feed consumption among molt treatments for the postmolt period. These results indicate that limit feeding corn diet and DDGS diet in non-feed-withdrawal molt programs will yield long-term postmolt performance that is comparable to that observed by ad libitum feeding a C:SH diet.

QTL that underlie seed protein, oil, fatty and amino acids content in the ‘Hamilton’ by ‘Spencer’ recombinant inbred line population of soybean [Glycine max (L.) Merr.

USDA-ARS?s Scientific Manuscript database

Improving seed composition and quality, including protein, oil, fatty acids, and amino acids content is an important goal of soybean farmers and breeders. Our previous research identified novel QTLs associated with seed isoflavones. The aim of this study was to use the ‘Hamilton’ by ‘Spencer’ recomb...

Quantitative Trait Loci (QTL) that Underlie SCN Resistance in the Soybean [Glycine max (L.) Merr.] ‘PI438489B’ by ‘Hamilton’ Recombinant Inbred Line Population

USDA-ARS?s Scientific Manuscript database

Soybean cyst nematode caused by Heterodera glycines is the most devastating pest in soybean [Glycine max (L.) Merr.]. Resistance to SCN is complex, polygenic, race-cultivar specific, and controlled by several QTL. Our objective was to identify and map QTL for SCN resistance to races 3 and 5 using a ...

Fine mapping of the pleiotropic locus B for black spine and orange mature fruit color in cucumber identifies a 50 kb region containing a R2R3-MYB transcription factor

USDA-ARS?s Scientific Manuscript database

The spine and skin colors on fruits are two important fruit quality traits in cucumber for variety improvement. In this study, we investigated the inheritance of spine and mature fruit colors with segregation populations developed from the cross between two inbred lines WI7200 (black spine and orang...

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.

Effects of Varieties, Producing Areas, Ears, and Ear Positions of Single Maize Kernels on Near-Infrared Spectra for Identification and Traceability.

PubMed

An, Dong; Cui, Yongjin; Liu, Xu; Jia, Shiqiang; Zheng, Shuyun; Che, Xiaoping; Liu, Zhe; Zhang, Xiaodong; Zhu, Dehai; Li, Shaoming

2016-01-01

The effects of varieties, producing areas, ears, and ear positions of maize on near-infrared (NIR) spectra were investigated to determine the factors causing the differences in NIR fingerprints of maize varieties. A total of 130 inbred lines were grown in two regions in China, and 12,350 kernel samples were analyzed through NIR spectroscopy. Spectral differences among varieties, producing areas, ears, and ear positions were determined and compared on the basis of pretreated spectra. The bands at 1300-1470, 1768-1949, 2010-2064, and 2235-2311 nm were mainly affected by the producing area. Band selection and principal component analysis were applied to improve the influence of variety on NIR spectra by processing the pretreated spectra. The degrees of the influence of varieties, producing areas, ears, and ear positions were calculated, and the percentages of the influence of varieties, producing areas, ears, and ear positions were 45.40%, 42.66%, 8.22%, and 3.72%, respectively. Therefore, genetic differences among maize inbred lines are the main factors accounted for NIR spectral differences. Producing area is a secondary factor. These results could provide a reference for researchers who authenticate varieties, perform geographical origin traceabilities, and conduct maize seed breeding.

Genome-wide association analysis identifies loci governing mercury accumulation in maize.

PubMed

Zhao, Zhan; Fu, Zhongjun; Lin, Yanan; Chen, Hao; Liu, Kun; Xing, Xiaolong; Liu, Zonghua; Li, Weihua; Tang, Jihua

2017-03-21

Owing to the rapid development of urbanisation and industrialisation, heavy metal pollution has become a widespread environmental problem. Maize planted on mercury (Hg)-polluted soil can absorb and accumulate Hg in its edible parts, posing a potential threat to human health. To understand the genetic mechanism of Hg accumulation in maize, we performed a genome-wide association study using a mixed linear model on an association population consisting of 230 maize inbred lines with abundant genetic variation. The order of relative Hg concentrations in different maize tissues was as follows: leaves > bracts > stems > axes > kernels. Combined two locations, a total of 37 significant single-nucleotide polymorphisms (SNPs) associated with kernels, 12 with axes, 13 with stems, 27 with bracts and 23 with leaves were detected with p < 0.0001. Each significant SNP was calculated and the SNPs significant associated with kernels, axes, stems, bracts and leaves explained 6.96%-10.56%, 7.19%-15.87%, 7.11%-10.19%, 7.16%-8.71% and 6.91%-9.17% of the phenotypic variation, respectively. Among the significant SNPs, nine co-localised with previously detected quantitative trait loci. This study will aid in the selection of Hg-accumulation inbred lines that satisfy the needs for pollution-safe cultivars and maintaining maize production.

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.

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.

Transcriptomic and anatomical complexity of primary, seminal, and crown roots highlight root type-specific functional diversity in maize (Zea mays L.)

PubMed Central

Tai, Huanhuan; Lu, Xin; Opitz, Nina; Marcon, Caroline; Paschold, Anja; Lithio, Andrew; Nettleton, Dan; Hochholdinger, Frank

2016-01-01

Maize develops a complex root system composed of embryonic and post-embryonic roots. Spatio-temporal differences in the formation of these root types imply specific functions during maize development. A comparative transcriptomic study of embryonic primary and seminal, and post-embryonic crown roots of the maize inbred line B73 by RNA sequencing along with anatomical studies were conducted early in development. Seminal roots displayed unique anatomical features, whereas the organization of primary and crown roots was similar. For instance, seminal roots displayed fewer cortical cell files and their stele contained more meta-xylem vessels. Global expression profiling revealed diverse patterns of gene activity across all root types and highlighted the unique transcriptome of seminal roots. While functions in cell remodeling and cell wall formation were prominent in primary and crown roots, stress-related genes and transcriptional regulators were over-represented in seminal roots, suggesting functional specialization of the different root types. Dynamic expression of lignin biosynthesis genes and histochemical staining suggested diversification of cell wall lignification among the three root types. Our findings highlight a cost-efficient anatomical structure and a unique expression profile of seminal roots of the maize inbred line B73 different from primary and crown roots. PMID:26628518

Draft Sequences of the Radish (Raphanus sativus L.) Genome

PubMed Central

Kitashiba, Hiroyasu; Li, Feng; Hirakawa, Hideki; Kawanabe, Takahiro; Zou, Zhongwei; Hasegawa, Yoichi; Tonosaki, Kaoru; Shirasawa, Sachiko; Fukushima, Aki; Yokoi, Shuji; Takahata, Yoshihito; Kakizaki, Tomohiro; Ishida, Masahiko; Okamoto, Shunsuke; Sakamoto, Koji; Shirasawa, Kenta; Tabata, Satoshi; Nishio, Takeshi

2014-01-01

Radish (Raphanus sativus L., n = 9) is one of the major vegetables in Asia. Since the genomes of Brassica and related species including radish underwent genome rearrangement, it is quite difficult to perform functional analysis based on the reported genomic sequence of Brassica rapa. Therefore, we performed genome sequencing of radish. Short reads of genomic sequences of 191.1 Gb were obtained by next-generation sequencing (NGS) for a radish inbred line, and 76,592 scaffolds of ≥300 bp were constructed along with the bacterial artificial chromosome-end sequences. Finally, the whole draft genomic sequence of 402 Mb spanning 75.9% of the estimated genomic size and containing 61,572 predicted genes was obtained. Subsequently, 221 single nucleotide polymorphism markers and 768 PCR-RFLP markers were used together with the 746 markers produced in our previous study for the construction of a linkage map. The map was combined further with another radish linkage map constructed mainly with expressed sequence tag-simple sequence repeat markers into a high-density integrated map of 1,166 cM with 2,553 DNA markers. A total of 1,345 scaffolds were assigned to the linkage map, spanning 116.0 Mb. Bulked PCR products amplified by 2,880 primer pairs were sequenced by NGS, and SNPs in eight inbred lines were identified. PMID:24848699

Anatomic Characteristics Associated with Head Splitting in Cabbage (Brassica oleracea var. capitata L.)

PubMed Central

Li, Xiaonan; Choi, Su Ryun; Wang, Yunbo; Sung, Chang-keun; Im, Subin; Ramchiary, Nirala; Zhou, Guangsheng; Lim, Yong Pyo

2015-01-01

Cabbage belonging to Brassicaceae family is one of the most important vegetables cultivated worldwide. The economically important part of cabbage crop is head, formed by leaves which may be of splitting and non-splitting types. Cabbage varieties showing head splitting causes huge loss to the farmers and therefore finding the molecular and structural basis of splitting types would be helpful to breeders. To determine which anatomical characteristics were related to head-splitting in cabbage, we analyzed two contrasting cabbage lines and their offspring using a field emission scanning electron microscope. The inbred line “747” is an early head-splitting type, while the inbred line “748” is a head-splitting-resistant type. The petiole cells of “747” seems to be larger than those of “748” at maturity; however, there was no significant difference in petiole cell size at both pre-heading and maturity stages. The lower epidermis cells of “747” were larger than those of “748” at the pre-heading and maturity stages. “747” had thinner epidermis cell wall than “748” at maturity stage, however, there was no difference of the epidermis cell wall thickness in the two lines at the pre-heading stage. The head-splitting plants in the F1 and F2 population inherited the larger cell size and thinner cell walls of epidermis cells in the petiole. In the petiole cell walls of “747” and the F1 and F2 plants that formed splitting heads, the cellulose microfibrils were loose and had separated from each other. These findings verified that anomalous cellulose microfibrils, larger cell size and thinner-walled epidermis cells are important genetic factors that make cabbage heads prone to splitting. PMID:26536356

Mapping of new quantitative trait loci for sudden death syndrome and soybean cyst nematode resistance in two soybean populations.

PubMed

Swaminathan, Sivakumar; Abeysekara, Nilwala S; Knight, Joshua M; Liu, Min; Dong, Jia; Hudson, Matthew E; Bhattacharyya, Madan K; Cianzio, Silvia R

2018-05-01

Novel QTL conferring resistance to both the SDS and SCN was detected in two RIL populations. Dual resistant RILs could be used in breeding programs for developing resistant soybean cultivars. Soybean cultivars, susceptible to the fungus Fusarium virguliforme, which causes sudden death syndrome (SDS), and to the soybean cyst nematode (SCN) (Heterodera glycines), suffer yield losses valued over a billion dollars annually. Both pathogens may occur in the same production fields. Planting of cultivars genetically resistant to both pathogens is considered one of the most effective means to control the two pathogens. The objective of the study was to map quantitative trait loci (QTL) underlying SDS and SCN resistances. Two recombinant inbred line (RIL) populations were developed by crossing 'A95-684043', a high-yielding maturity group (MG) II line resistant to SCN, with 'LS94-3207' and 'LS98-0582' of MG IV, resistant to both F. virguliforme and SCN. Two hundred F 7 derived recombinant inbred lines from each population AX19286 (A95-684043 × LS94-3207) and AX19287 (A95-684043 × LS98-0582) were screened for resistance to each pathogen under greenhouse conditions. Five hundred and eighty and 371 SNP markers were used for mapping resistance QTL in each population. In AX19286, one novel SCN resistance QTL was mapped to chromosome 8. In AX19287, one novel SDS resistance QTL was mapped to chromosome 17 and one novel SCN resistance QTL was mapped to chromosome 11. Previously identified additional SDS and SCN resistance QTL were also detected in the study. Lines possessing superior resistance to both pathogens were also identified and could be used as germplasm sources for breeding SDS- and SCN-resistant soybean cultivars.

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.

QTL Mapping of Kernel Number-Related Traits and Validation of One Major QTL for Ear Length in Maize.

PubMed

Huo, Dongao; Ning, Qiang; Shen, Xiaomeng; Liu, Lei; Zhang, Zuxin

2016-01-01

The kernel number is a grain yield component and an important maize breeding goal. Ear length, kernel number per row and ear row number are highly correlated with the kernel number per ear, which eventually determines the ear weight and grain yield. In this study, two sets of F2:3 families developed from two bi-parental crosses sharing one inbred line were used to identify quantitative trait loci (QTL) for four kernel number-related traits: ear length, kernel number per row, ear row number and ear weight. A total of 39 QTLs for the four traits were identified in the two populations. The phenotypic variance explained by a single QTL ranged from 0.4% to 29.5%. Additionally, 14 overlapping QTLs formed 5 QTL clusters on chromosomes 1, 4, 5, 7, and 10. Intriguingly, six QTLs for ear length and kernel number per row overlapped in a region on chromosome 1. This region was designated qEL1.10 and was validated as being simultaneously responsible for ear length, kernel number per row and ear weight in a near isogenic line-derived population, suggesting that qEL1.10 was a pleiotropic QTL with large effects. Furthermore, the performance of hybrids generated by crossing 6 elite inbred lines with two near isogenic lines at qEL1.10 showed the breeding value of qEL1.10 for the improvement of the kernel number and grain yield of maize hybrids. This study provides a basis for further fine mapping, molecular marker-aided breeding and functional studies of kernel number-related traits in maize.

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.

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.

Fine mapping of the chromosome 5B region carrying closely linked rust resistance genes Yr47 and Lr52 in wheat

USDA-ARS?s Scientific Manuscript database

The widely effective and linked rust resistance genes Yr47 and Lr52 were previously mapped in the short arm of chromosome 5B in two F3 populations (Aus28183/Aus27229 and Aus28187/Aus27229). The Aus28183/Aus27229 F3 population was advanced to generate an F6 recombinant inbred line (RIL) population t...

Genetic Analysis of Seed Isoflavones, Protein, and Oil Contents in Soybean [Glycine max (L.) Merr.

DTIC Science & Technology

2014-09-13

high contents of protein , oil, isoflavones, and other bioactive compounds. However, it is susceptible to many biotic stresses such fungal, bacterial...for protein , oil, and isoflavones contents in three recombinant inbred line (RIL) populations of soybean. We have achieved 100% of the goals. We have...Jun-2011 31-May-2014 Approved for Public Release; Distribution Unlimited Final Report: Genetic Analysis of Seed Isoflavones, Protein , and Oil

The bottle gourd genome provides insights into Cucurbitaceae evolution and facilitates mapping of a Papaya ringspot virus resistance locus

USDA-ARS?s Scientific Manuscript database

Bottle gourd (Lagenaria siceraria) is an important vegetable crop as well as a rootstock for other cucurbit crops. In this study, we report a high-quality 313.4-Mb genome sequence of a bottle gourd inbred line, USVL1VR-Ls, with a scaffold N50 of 8.7 Mb and the longest of 19.0 Mb. About 98.3% of the ...

Corn silage from corn treated with foliar fungicide and performance of Holstein cows.

PubMed

Haerr, K J; Lopes, N M; Pereira, M N; Fellows, G M; Cardoso, F C

2015-12-01

Foliar fungicide application to corn plants is used in corn aimed for corn silage in the dairy industry, but questions regarding frequency of application and its effect on corn silage quality and feed conversion when fed to dairy cows remain prevalent. The objective of this study was to evaluate the effects of various foliar fungicide applications to corn on dry matter intake (DMI), milk production, and milk composition when fed to dairy cows. Sixty-four Holstein cows with parity 2.5±1.5, 653±80kg of body weight, and 161±51d in milk were blocked and randomly assigned to 1 of 4 corn silage treatments (total mixed ration with 35% of the dry matter as corn silage). Treatments were as follows: control (CON), corn silage with no applications of foliar fungicide; treatment 1 (1X), corn silage from corn that received 1 application of pyraclostrobin (PYR) foliar fungicide (Headline; BASF Corp.) at corn vegetative stage 5; treatment 2 (2X), corn silage from corn that received the same application as 1X plus another application of a mixture of PYR and metconazole (Headline AMP; BASF Corp.) at corn reproductive stage 1 ("silking"); and treatment 3 (3X), corn silage from corn that received the same applications as 2X as well as a third application of PYR and metconazole at reproductive stage 3 ("milky kernel"). Corn was harvested at about 32% dry matter and 3/4 milk line stage of kernel development and ensiled for 200d. Treatments were fed to cows for 5wk, with the last week being used for statistical inferences. Week -1 was used as a covariate in the statistical analysis. Dry matter intake tended to be lower for cows fed corn silage treated with fungicide than CON (23.8, 23.0, 19.5, and 21.3kg for CON, 1X, 2X, and 3X, respectively). A linear treatment effect for DMI was observed, with DMI decreasing as foliar fungicide applications increased. Treatments CON, 1X, 2X, and 3X did not differ for milk yield (34.5, 34.5, 34.2, and 34.4kg/d, respectively); however, a trend for increased feed conversion represented by fat-corrected milk/DMI (1.65 vs. 1.47) and energy-corrected milk/DMI (1.60 vs. 1.43) was noted for cows fed corn silage with fungicide compared with CON. In conclusion, cows receiving corn silage treated with foliar fungicide had better conversion of feed dry matter to milk than those receiving CON silage. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

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.

Widespread Gene Conversion in Centromere Cores

PubMed Central

Shi, Jinghua; Wolf, Sarah E.; Burke, John M.; Presting, Gernot G.; Ross-Ibarra, Jeffrey; Dawe, R. Kelly

2010-01-01

Centromeres are the most dynamic regions of the genome, yet they are typified by little or no crossing over, making it difficult to explain the origin of this diversity. To address this question, we developed a novel CENH3 ChIP display method that maps kinetochore footprints over transposon-rich areas of centromere cores. A high level of polymorphism made it possible to map a total of 238 within-centromere markers using maize recombinant inbred lines. Over half of the markers were shown to interact directly with kinetochores (CENH3) by chromatin immunoprecipitation. Although classical crossing over is fully suppressed across CENH3 domains, two gene conversion events (i.e., non-crossover marker exchanges) were identified in a mapping population. A population genetic analysis of 53 diverse inbreds suggests that historical gene conversion is widespread in maize centromeres, occurring at a rate >1×10−5/marker/generation. We conclude that gene conversion accelerates centromere evolution by facilitating sequence exchange among chromosomes. PMID:20231874

Performance of dairy cows fed silage and grain produced from second-generation insect-protected (Bacillus thuringiensis) corn (MON 89034), compared with parental line corn or reference corn.

PubMed

Castillo-Lopez, E; Clark, K J; Paz, H A; Ramirez Ramirez, H A; Klusmeyer, T H; Hartnell, G F; Kononoff, P J

2014-01-01

Corn grain and corn silage are major feed components in lactating dairy cow rations. Bacillus thuringiensis (B.t.) is a naturally occurring soil bacterium that produces a protein that is toxic to lepidopteran insects that may damage plant tissues and reduce corn quality and yields. During each of the four 28-d periods, cows were offered 1 of 4 rations in which the corn grain and silage originated from different corn hybrids: a nontransgenic corn control (from hybrid DKC63-78; Monsanto Co., St. Louis, MO), a B.t. test substance corn (MON 89034 in hybrid DKC63-78; Monsanto Co.), and 2 commercial nontransgenic reference (Ref) hybrids: DKC61-42 (Ref 1) and DKC62-30 (Ref 2; Monsanto Co.). Sixteen multiparous Holstein cows averaging 110 ± 21 d in milk and weighing 684 ± 62.3 kg were blocked by days in milk and milk yield and randomly assigned to one of four 4 × 4 Latin squares. Diets were formulated to contain 36.4% corn silage and 16.3% corn grain. Dry matter intake was greater for cows consuming B.t. corn (26.6 ± 0.59 kg/d) compared with the control, Ref 1, and Ref 2 corn diets (25.4, 25.0, and 25.6 ± 0.59 kg/d, respectively). Milk yield, fat yield, and percentage of fat (36.8 ± 0.98 kg/d, 1.22 ± 0.05 kg/d, and 3.3 ± 0.10%), milk protein yield and percentage of protein (1.11 ± 0.03 kg/d and 3.01 ± 0.05%), milk urea nitrogen concentration (14.01 ± 0.49 mg/dL), and 3.5% fat-corrected milk yield (35.7 ± 1.07 kg/d) were not different across treatments. The results from this study show that lactating dairy cows that consume B.t. corn (MON 89034) do not differ from lactating dairy cows that consume nontransgenic corn in milk yield, 3.5% fat-corrected milk per unit of dry matter intake, or milk components. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

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 the same time allowing flexible and realistic models to be explored. PMID:8005424

STAYGREEN (CsSGR) is a candidate for the anthracnose (Colletotrichum orbiculare) resistance locus cla in Gy14 cucumber.

PubMed

Pan, Junsong; Tan, Junyi; Wang, Yuhui; Zheng, Xiangyang; Owens, Ken; Li, Dawei; Li, Yuhong; Weng, Yiqun

2018-04-21

Map-based cloning identified a candidate gene for resistance to the anthracnose fungal pathogen Colletotrichum orbiculare in cucumber, which reveals a novel function for the highly conserved STAYGREEN family genes for host disease resistance in plants. Colletotrichum orbiculare is a hemibiotrophic fungal pathogen that causes anthracnose disease in cucumber and other cucurbit crops. No host resistance genes against the anthracnose pathogens have been cloned in crop plants. Here, we reported fine mapping and cloning of a resistance gene to the race 1 anthracnose pathogen in cucumber inbred lines Gy14 and WI 2757. Phenotypic and QTL analysis in multiple populations revealed that a single recessive gene, cla, was underlying anthracnose resistance in both lines, but WI2757 carried an additional minor-effect QTL. Fine mapping using 150 Gy14 × 9930 recombinant inbred lines and 1043 F 2 individuals delimited the cla locus into a 32 kb region in cucumber Chromosome 5 with three predicted genes. Multiple lines of evidence suggested that the cucumber STAYGREEN (CsSGR) gene is a candidate for the anthracnose resistance locus. A single nucleotide mutation in the third exon of CsSGR resulted in the substitution of Glutamine in 9930 to Arginine in Gy14 in CsSGR protein which seems responsible for the differential anthracnose inoculation responses between Gy14 and 9930. Quantitative real-time PCR analysis indicated that CsSGR was significantly upregulated upon anthracnose pathogen inoculation in the susceptible 9930, while its expression was much lower in the resistant Gy14. Investigation of allelic diversities in natural cucumber populations revealed that the resistance allele in almost all improved cultivars or breeding lines of the U.S. origin was derived from PI 197087. This work reveals an unknown function for the highly conserved STAYGREEN (SGR) family genes for host disease resistance in plants.

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

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 more G2 families representing this number of recombination points,. The TRP design can be an effective procedure for achieving high and ultra-high mapping resolution of a target QTN previously mapped to a known confidence interval (QTL).

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

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

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

Major quality trait analysis and QTL detection in hexaploid wheat in humid rain-fed agriculture.

PubMed

Li, H M; Tang, Z X; Zhang, H Q; Yan, B J; Ren, Z L

2013-05-21

Humid rain-fed agriculture is a special environment for wheat (Triticum aestivum) culture that tends to negatively affect wheat yield and quality. To identify quality characters of wheat in a humid environment, we conducted quality analysis and quantitative trait loci (QTL) detection in a recombinant inbred line whose parent had a high level of quality for several years. We found that high-quality wheat had less gluten content and lower protein content. Apparently, wheat quality and associated quantity traits were in a dynamic state of equilibrium. We detected 83 QTL for 10 wheat quality traits in this recombinant inbred line population. Nine QTL were detected in both evaluation years; Q.DT.scau-2A, linked to Xwmc522-2A, was detected at the same genetic location in both years. Other QTL for different traits were detected simultaneously in more than one location. Consequently, there appeared to be pleiotropic genes that control wheat quality. Based on previous studies and our research on QTL analysis of grain protein content, we conclude that there must be one or more genes for grain protein content on chromosome 6B, whose expression was little affected by environment. We constructed a consensus map and projected the QTL on it. It was useful for choosing optimal markers for marker-assisted breeding and map-based cloning.

Linkage Mapping of Stem Saccharification Digestibility in Rice

PubMed Central

Hua, Cangmei; Sun, Lili; Ali, Imran; Huang, Linli; Yu, Chunyan; Simister, Rachael; Steele-King, Clare; Gan, Yinbo; McQueen-Mason, Simon J.

2016-01-01

Rice is the staple food of almost half of the world population, and in excess 90% of it is grown and consumed in Asia, but the disposal of rice straw poses a problem for farmers, who often burn it in the fields, causing health and environmental problems. However, with increased focus on the development of sustainable biofuel production, rice straw has been recognized as a potential feedstock for non-food derived biofuel production. Currently, the commercial realization of rice as a biofuel feedstock is constrained by the high cost of industrial saccharification processes needed to release sugar for fermentation. This study is focused on the alteration of lignin content, and cell wall chemotypes and structures, and their effects on the saccharification potential of rice lignocellulosic biomass. A recombinant inbred lines (RILs) population derived from a cross between the lowland rice variety IR1552 and the upland rice variety Azucena with 271 molecular markers for quantitative trait SNP (QTS) analyses was used. After association analysis of 271 markers for saccharification potential, 1 locus and 4 pairs of epistatic loci were found to contribute to the enzymatic digestibility phenotype, and an inverse relationship between reducing sugar and lignin content in these recombinant inbred lines was identified. As a result of QTS analyses, several cell-wall associated candidate genes are proposed that may be useful for marker-assisted breeding and may aid breeders to produce potential high saccharification rice varieties. PMID:27415441

Restoring pollen fertility in transgenic male-sterile eggplant by Cre/loxp-mediated site-specific recombination system.

PubMed

Cao, Bihao; Huang, Zhiyin; Chen, Guoju; Lei, Jianjun

2010-04-01

This study was designed to control plant fertility by cell lethal gene Barnase expressing at specific developmental stage and in specific tissue of male organ under the control of Cre/loxP system, for heterosis breeding, producing hybrid seed of eggplant. The Barnase-coding region was flanked by loxP recognition sites for Cre-recombinase. The eggplant inbred/pure line ('E-38') was transformed with Cre gene and the inbred/pure line ('E-8') was transformed with the Barnase gene situated between loxp. The experiments were done separately, by means of Agrobacterium co-culture. Four T(0) -plants with the Barnase gene were obtained, all proved to be male-sterile and incapable of producing viable pollen. Flowers stamens were shorter, but the vegetative phenotype was similar to wild-type. Five T (0) -plants with the Cre gene developed well, blossomed out and set fruit normally. The crossing of male-sterile Barnase-plants with Cre expression transgenic eggplants resulted in site-specific excision with the male-sterile plants producing normal fruits. With the Barnase was excised, pollen fertility was fully restored in the hybrids. The phenotype of these restored plants was the same as that of the wild-type. Thus, the Barnase and Cre genes were capable of stable inheritance and expression in progenies of transgenic plants.

Transcriptomic and anatomical complexity of primary, seminal, and crown roots highlight root type-specific functional diversity in maize (Zea mays L.).

PubMed

Tai, Huanhuan; Lu, Xin; Opitz, Nina; Marcon, Caroline; Paschold, Anja; Lithio, Andrew; Nettleton, Dan; Hochholdinger, Frank

2016-02-01

Maize develops a complex root system composed of embryonic and post-embryonic roots. Spatio-temporal differences in the formation of these root types imply specific functions during maize development. A comparative transcriptomic study of embryonic primary and seminal, and post-embryonic crown roots of the maize inbred line B73 by RNA sequencing along with anatomical studies were conducted early in development. Seminal roots displayed unique anatomical features, whereas the organization of primary and crown roots was similar. For instance, seminal roots displayed fewer cortical cell files and their stele contained more meta-xylem vessels. Global expression profiling revealed diverse patterns of gene activity across all root types and highlighted the unique transcriptome of seminal roots. While functions in cell remodeling and cell wall formation were prominent in primary and crown roots, stress-related genes and transcriptional regulators were over-represented in seminal roots, suggesting functional specialization of the different root types. Dynamic expression of lignin biosynthesis genes and histochemical staining suggested diversification of cell wall lignification among the three root types. Our findings highlight a cost-efficient anatomical structure and a unique expression profile of seminal roots of the maize inbred line B73 different from primary and crown roots. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

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.

Nonadditive protein accumulation patterns in Maize (Zea mays L.) hybrids during embryo development.

PubMed

Marcon, Caroline; Schützenmeister, André; Schütz, Wolfgang; Madlung, Johannes; Piepho, Hans-Peter; Hochholdinger, Frank

2010-12-03

Heterosis describes the superior performance of heterozygous F(1)-hybrid plants compared to their homozygous parental inbred lines. In the present study, heterosis was detected for length, weight, and the time point of seminal root primordia initiation in maize (Zea mays L.) embryos of the reciprocal F(1)-hybrids UH005xUH250 and UH250xUH005. A two-dimensional gel electrophoresis (2-DE) proteome survey of the most abundant proteins of the reciprocal hybrids and their parental inbred lines 25 and 35 days after pollination revealed that 141 of 597 detected proteins (24%) exhibited nonadditive accumulation in at least one hybrid. Approximately 44% of all nonadditively accumulated proteins displayed an expression pattern that was not distinguishable from the low parent value. Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) analyses and subsequent functional classification of the 141 proteins revealed that development, protein metabolism, redox-regulation, glycolysis, and amino acid metabolism were the most prominent functional classes among nonadditively accumulated proteins. In 35-day-old embryos of the hybrid UH250xUH005, a significant up-regulation of enzymes related to glucose metabolism which often exceeded the best parent values was observed. A comparison of nonadditive protein accumulation between rice and maize embryo data sets revealed a significant overlap of nonadditively accumulated proteins suggesting conserved organ- or tissue-specific regulatory mechanisms in monocots related to heterosis.

Proteomic analysis of the maize rachis: potential roles of constitutive and induced proteins in resistance to Aspergillus flavus infection and aflatoxin accumulation.

PubMed

Pechanova, Olga; Pechan, Tibor; Williams, W Paul; Luthe, Dawn S

2011-01-01

Infection of the maize (Zea mays L.) with aflatoxigenic fungus Aspergillus flavus and consequent contamination with carcinogenic aflatoxin is a persistent and serious agricultural problem causing disease and significant crop losses worldwide. The rachis (cob) is an important structure of maize ear that delivers essential nutrients to the developing kernels and A. flavus spreads through the rachis to infect kernels within the ear. Therefore, rachis plays an important role in fungal proliferation and subsequent kernel contamination. We used proteomic approaches and investigated the rachis tissue from aflatoxin accumulation resistant (Mp313E and Mp420) and susceptible (B73 and SC212m) maize inbred lines. First, we compared rachis proteins from resistant and susceptible inbred lines, which revealed that the young resistant rachis contains higher levels of abiotic stress-related proteins and proteins from phenylpropanoid metabolism, whereas susceptible young rachis contains pathogenesis-related proteins, which are generally inducible upon biotic stress. Second, we identified A. flavus-responsive proteins in rachis of both resistant and susceptible genotypes after 10- and 35-day infection. Differential expression of many stress/defense proteins during rachis juvenility, maturation and after A. flavus challenge demonstrates that resistant rachis relies on constitutive defenses, while susceptible rachis is more dependent on inducible defenses. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genomic resources for gene discovery, functional genome annotation, and evolutionary studies of maize and its close relatives.

PubMed

Wang, Chao; Shi, Xue; Liu, Lin; Li, Haiyan; Ammiraju, Jetty S S; Kudrna, David A; Xiong, Wentao; Wang, Hao; Dai, Zhaozhao; Zheng, Yonglian; Lai, Jinsheng; Jin, Weiwei; Messing, Joachim; Bennetzen, Jeffrey L; Wing, Rod A; Luo, Meizhong

2013-11-01

Maize is one of the most important food crops and a key model for genetics and developmental biology. A genetically anchored and high-quality draft genome sequence of maize inbred B73 has been obtained to serve as a reference sequence. To facilitate evolutionary studies in maize and its close relatives, much like the Oryza Map Alignment Project (OMAP) (www.OMAP.org) bacterial artificial chromosome (BAC) resource did for the rice community, we constructed BAC libraries for maize inbred lines Zheng58, Chang7-2, and Mo17 and maize wild relatives Zea mays ssp. parviglumis and Tripsacum dactyloides. Furthermore, to extend functional genomic studies to maize and sorghum, we also constructed binary BAC (BIBAC) libraries for the maize inbred B73 and the sorghum landrace Nengsi-1. The BAC/BIBAC vectors facilitate transfer of large intact DNA inserts from BAC clones to the BIBAC vector and functional complementation of large DNA fragments. These seven Zea Map Alignment Project (ZMAP) BAC/BIBAC libraries have average insert sizes ranging from 92 to 148 kb, organellar DNA from 0.17 to 2.3%, empty vector rates between 0.35 and 5.56%, and genome equivalents of 4.7- to 8.4-fold. The usefulness of the Parviglumis and Tripsacum BAC libraries was demonstrated by mapping clones to the reference genome. Novel genes and alleles present in these ZMAP libraries can now be used for functional complementation studies and positional or homology-based cloning of genes for translational genomics.

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.

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.

Diversity of chromosomal karyotypes in maize and its relatives.

PubMed

Albert, P S; Gao, Z; Danilova, T V; Birchler, J A

2010-07-01

Maize is a highly diverse species on the gene sequence level. With the recent development of methods to distinguish each of the 10 pairs of homologues in somatic root tip spreads, a wide collection of maize lines was subjected to karyotype analysis to serve as a reference for the community and to examine the spectrum of chromosomal features in the species. The core nested association mapping progenitor collection and additional selections of diversity lines were examined. Commonly used inbred lines were included in the analysis. The centromere 4 specific repeat and ribosomal RNA loci were invariant. The CentC centromere repeat exhibited extensive differences in quantity on any particular chromosome across lines. Knob heterochromatin was highly variable with locations at many sites in the genome. Lastly, representative examples from other species in the genus Zea (teosintes) were examined, which provide information on the evolution of chromosomal features. Copyright 2010 S. Karger AG, Basel.

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.

Phosphorus bioavailability and digestibility of normal and genetically modified low-phytate corn for pigs.

PubMed

Spencer, J D; Allee, G L; Sauber, T E

2000-03-01

We conducted two studies to determine the bioavailability and apparent digestibility of P in a low-phytate corn hybrid (.28% total P, .10% phytate P) genetically modified to be homozygous for the 1pa1-1 allele and a nearly isogenic corn hybrid (normal) (.25% total P, .20% phytate P). Additionally, we conducted an in vitro assay involving a peptic and pancreatin digestion to estimate P availability. The first study used 50 individually penned pigs (initial body weight 9 kg) and 10 treatments in a randomized complete block design. A cornstarch-soybean meal basal diet (.6% Ca, .2% P) was used. Treatments consisted of the basal diet and the basal diet plus .05, .10, or .15% P from monosodium phosphate (MSP), low-phytate corn, or normal corn. After a 35-d feeding period, pigs were killed to collect the fourth metacarpal for measurements of ash and breaking load. Breaking load was regressed on added P intake, and the bioavailability of P was determined by the slope ratio method. The bioavailabilities of P (relative to MSP) for low-phytate and normal corn were 62 and 9%, respectively. These were similar to the determined in vitro values of 57 and 11% for low-phytate and normal corn, respectively. In the second study, 20 pigs (initial BW 20 kg) were used in a randomized complete block design with a 2 x 2 factorial arrangement of treatments. Two corn lines (low-phytate and normal) and two levels of supplemental P (0 and .2%) from dicalcium phosphate were used. Diets with no added P were formulated to contain .9% lysine, .6% Ca, and .34% P. Apparent nutrient digestibilities were calculated from total collection of urine and feces for 5 d. There were no differences among treatments for energy and nitrogen digestibility. Pigs fed low-phytate corn with no added P had increased digestibility and retention of P and reduced total P excretion (P < .05). We conclude that low-phytate corn contains at least five times as much available P as normal corn. The use oflow-phytate corn greatly reduced the amount of P excreted by the pig and increased the N:P ratio in the manure.

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.

[Virus resistance in transgenic watermelon plants containing a WMV-2 coat protein gene].

PubMed

Wang, Hui-Zhong; Zhao, Pei-Jie; Xu, Ji-Chen; Zhao, Huai; Zhang, Hong-Sheng

2003-01-01

Virus disease is a major cause that affects the quality and output of watermelon which is an important fruit in summer. So it is really urgent to develop disease resistance plants. But it takes a long time to breed such plants in conventional ways, and it is very difficult to get ideal result. With the development of plant genetic engineering, new ways have been found to breed plants with disease resistance. By using plant transgenic technique, much progress was been made in plant improvement. There are many successful cases of transgenic plants against corresponding virus disease through transferring coat protein gene. This paper reports the results of inheritance, segregation, expression of WMV-2 coat protein gene in inbred transgenic watermelon and its resistance to virus. Through PCR analysis of inbred plants, we found WMV-2 coat protein gene in the genome of progeny R1 separated with 3:1. After successive selection and identification of 4 generations, 8 transgenic pure lines with almost the same agronomic traits were obtained from 3 independent transformants of T7, T11 and T32. The result of Western blotting shows all 3 different transgenic lines of R4T7-1, R4T11-3 and R4T32-7 can produce coat protein. Disease resistance experiment on transgenic plants with WMV-2 shows that, compared with the control groups, transgenic plants can delay the disease infection and reduce the incidence and the symptoms of virus disease. And the transgenic line R4T32-7 expressed high resistance to infection by WMV-2, which lays a foundation for breeding of disease resistant varieties through plant transgenic technique.

Ethanol consumption in mice: relationships with circadian period and entrainment.

PubMed

Trujillo, Jennifer L; Do, David T; Grahame, Nicholas J; Roberts, Amanda J; Gorman, Michael R

2011-03-01

A functional connection between the circadian timing system and alcohol consumption is suggested by multiple lines of converging evidence. Ethanol consumption perturbs physiological rhythms in hormone secretion, sleep, and body temperature; and conversely, genetic and environmental perturbations of the circadian system can alter alcohol intake. A fundamental property of the circadian pacemaker, the endogenous period of its cycle under free-running conditions, was previously shown to differ between selectively bred high- (HAP) and low- (LAP) alcohol preferring replicate 1 mice. To test whether there is a causal relationship between circadian period and ethanol intake, we induced experimental, rather than genetic, variations in free-running period. Male inbred C57Bl/6J mice and replicate 2 male and female HAP2 and LAP2 mice were entrained to light:dark cycles of 26 or 22 h or remained in a standard 24 h cycle. On discontinuation of the light:dark cycle, experimental animals exhibited longer and shorter free-running periods, respectively. Despite robust effects on circadian period and clear circadian rhythms in drinking, these manipulations failed to alter the daily ethanol intake of the inbred strain or selected lines. Likewise, driving the circadian system at long and short periods produced no change in alcohol intake. In contrast with replicate 1 HAP and LAP lines, there was no difference in free-running period between ethanol naïve HAP2 and LAP2 mice. HAP2 mice, however, were significantly more active than LAP2 mice as measured by general home-cage movement and wheel running, a motivated behavior implicating a selection effect on reward systems. Despite a marked circadian regulation of drinking behavior, the free-running and entrained period of the circadian clock does not determine daily ethanol intake. Copyright © 2011 Elsevier Inc. All rights reserved.

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

Ethanol consumption in mice: relationships with circadian period and entrainment

PubMed Central

Trujillo, Jennifer L.; Do, David T.; Grahame, Nicholas J.; Roberts, Amanda J.; Gorman, Michael R.

2011-01-01

A functional connection between the circadian timing system and alcohol consumption is suggested by multiple lines of converging evidence. Ethanol consumption perturbs physiological rhythms in hormone secretion, sleep and body temperature, and conversely, genetic and environmental perturbations of the circadian system can alter alcohol intake. A fundamental property of the circadian pacemaker, the endogenous period of its cycle under free-running conditions, was previously shown to differ between selectively bred High- (HAP) and Low- (LAP) Alcohol Preferring replicate 1 mice. To test whether there is a causal relationship between circadian period and ethanol intake, we induced experimental, rather than genetic, variations in free-running period. Male inbred C57Bl/6J mice and replicate 2 male and female HAP2 and LAP2 mice were entrained to light:dark cycles of 26 h or 22 h or remained in a standard 24 h cycle. Upon discontinuation of the light:dark cycle, experimental animals exhibited longer and shorter free-running periods, respectively. Despite robust effects on circadian period and clear circadian rhythms in drinking, these manipulations failed to alter the daily ethanol intake of the inbred strain or selected lines. Likewise, driving the circadian system at long and short periods produced no change in alcohol intake. In contrast with replicate 1 HAP and LAP lines, there was no difference in free-running period between ethanol naïve HAP2 and LAP2 mice. HAP2 mice, however, were significantly more active than LAP2 mice as measured by general home-cage movement and wheel running, a motivated behavior implicating a selection effect on reward systems. Despite a marked circadian regulation of drinking behavior, the free-running and entrained period of the circadian clock does not determine daily ethanol intake. PMID:20880659

QTL analysis of fruit quality in fresh market tomato: a few chromosome regions control the variation of sensory and instrumental traits.

PubMed

Causse, M; Saliba-Colombani, V; Lecomte, L; Duffé, P; Rousselle, P; Buret, M

2002-10-01

The organoleptic quality of tomato fruit involves a set of attributes (flavour, aroma, texture) that can be evaluated either by sensory analyses or by instrumental measures. In order to study the genetic control of this characteristic, a recombinant inbred line (RIL) population was developed from an intraspecific cross between a cherry tomato line with a good overall aroma intensity and an inbred line with medium flavour but bigger fruits. A total of 38 traits involved in organoleptic quality were evaluated. Physical traits included fruit weight, diameter, colour, firmness, and elasticity. Chemical traits were dry matter weight, titratable acidity, pH, and the contents of soluble solids, sugars, lycopene, carotene, and 12 aroma volatiles. A panel of trained assessors quantified sensory attributes: flavour (sweetness and sourness), aroma (overall aroma intensity, together with candy, lemon, citrus fruit, and pharmaceutical aromas) and texture (firmness, meltiness, mealiness, juiciness, and skin difficult to swallow). RILs showed a large range of variation. Molecular markers were used to map a total of 130 quantitative trait loci (QTL) for the 38 traits. They were mainly distributed in a few chromosome regions. Major QTLs (R(2) >30%) were detected for fruit weight, diameter, colour, firmness, meltiness, and for six aroma volatiles. The relationships between instrumental measures and sensory traits were analysed with regard to the QTL map. A special insight was provided about the few regions where QTLs are related to multiple traits. A few examples are shown to illustrate how the simultaneous analysis of QTL segregation for related traits may aid in understanding the genetic control of quality traits and pave the way towards QTL characterization.

Genome Wide Association Study for Drought, Aflatoxin Resistance, and Important Agronomic Traits of Maize Hybrids in the Sub-Tropics

PubMed Central

Farfan, Ivan D. Barrero; De La Fuente, Gerald N.; Murray, Seth C.; Isakeit, Thomas; Huang, Pei-Cheng; Warburton, Marilyn; Williams, Paul; Windham, Gary L.; Kolomiets, Mike

2015-01-01

The primary maize (Zea mays L.) production areas are in temperate regions throughout the world and this is where most maize breeding is focused. Important but lower yielding maize growing regions such as the sub-tropics experience unique challenges, the greatest of which are drought stress and aflatoxin contamination. Here we used a diversity panel consisting of 346 maize inbred lines originating in temperate, sub-tropical and tropical areas testcrossed to stiff-stalk line Tx714 to investigate these traits. Testcross hybrids were evaluated under irrigated and non-irrigated trials for yield, plant height, ear height, days to anthesis, days to silking and other agronomic traits. Irrigated trials were also inoculated with Aspergillus flavus and evaluated for aflatoxin content. Diverse maize testcrosses out-yielded commercial checks in most trials, which indicated the potential for genetic diversity to improve sub-tropical breeding programs. To identify genomic regions associated with yield, aflatoxin resistance and other important agronomic traits, a genome wide association analysis was performed. Using 60,000 SNPs, this study found 10 quantitative trait variants for grain yield, plant and ear height, and flowering time after stringent multiple test corrections, and after fitting different models. Three of these variants explained 5–10% of the variation in grain yield under both water conditions. Multiple identified SNPs co-localized with previously reported QTL, which narrows the possible location of causal polymorphisms. Novel significant SNPs were also identified. This study demonstrated the potential to use genome wide association studies to identify major variants of quantitative and complex traits such as yield under drought that are still segregating between elite inbred lines. PMID:25714370

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 results suggest that different gene systems mediate blood cell responses to PHA as compared with Con A. The pattern of developmental differences between inbred lines indicates the existence of distinct or partly overlapping T cell subsets with different reactivities to PHA or Con A, and of higher suppressor activity of adherent cells in line 6(3) blood. Both these differences may be related to line 6(3) inherited resistance to Marek's disease.

Potential of four corn varieties at different harvest stages for tropical silage production in Malaysia.

PubMed

Nazli, Muhamad Hazim; Abdul Halim, Ridzwan; Abdullah, Amin Mahir; Husin, Ghazali; Samsudin, Anjas Asmara

2018-05-31

Apart from various climatic differences, corn harvest stage and varieties are two major factors that can influence the yield and quality of corn silage in the tropics. A study was conducted to determine the optimum harvest stage of four corn varieties for tropical silage production in Malaysia. Using a split plot design, corn was harvested at four growth stages; silking, milk, dough and dent stages using four varieties; Sweet Corn hybrid 926, Suwan, Breeding Test Line (BTL) 1 and BTL 2. The treatments were then analysed based on the plant growth performance, yield, nutritive and feeding values followed by a financial feasibility study for potential commercialization. Significant differences and interactions were detected across the parameters suggesting varying responses among the varieties towards the harvest stages. Sweet Corn was best harvested early in the dough stage due to high dry matter (DM) yield, digestible nutrient and energy content with low fibre portion. Suwan was recommended to be harvested at the dent stage when it gave the highest DM yield with optimum digestible nutrient and energy content with low acid detergent fibre (ADF). BTL 1 and BTL 2 varieties can either be harvested at dough or dent stages as the crude protein (CP), fibre, DM yield, DM content, digestible nutrient and energy were not significantly different at both stages. Further financial analysis showed that only Sweet Corn production was not financially feasible while Suwan had the best financial appraisal values among the grain varieties. In conclusion, only the grain varieties tested had the potential for silage making according to their optimum harvest stage but Suwan is highly recommended for commercialization as it was the most profitable.

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 rapid introgression of waterlogging tolerance in tropical maize breeding programs. PMID:25884393

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 rapid introgression of waterlogging tolerance in tropical maize breeding programs.

Identification of promoter motifs regulating ZmeIF4E expression level involved in maize rough dwarf disease resistance in maize (Zea Mays L.).

PubMed

Shi, Liyu; Weng, Jianfeng; Liu, Changlin; Song, Xinyuan; Miao, Hongqin; Hao, Zhuanfang; Xie, Chuanxiao; Li, Mingshun; Zhang, Degui; Bai, Li; Pan, Guangtang; Li, Xinhai; Zhang, Shihuang

2013-04-01

Maize rough dwarf disease (MRDD, a viral disease) results in significant grain yield losses, while genetic basis of which is largely unknown. Based on comparative genomics, eukaryotic translation initiation factor 4E (eIF4E) was considered as a candidate gene for MRDD resistance, validation of which will help to understand the possible genetic mechanism of this disease. ZmeIF4E (orthologs of eIF4E gene in maize) encodes a protein of 218 amino acids, harboring five exons and no variation in the cDNA sequence is identified between the resistant inbred line, X178 and susceptible one, Ye478. ZmeIF4E expression was different in the two lines plants treated with three plant hormones, ethylene, salicylic acid, and jasmonates at V3 developmental stage, suggesting that ZmeIF4E is more likely to be involved in the regulation of defense gene expression and induction of local and systemic resistance. Moreover, four cis-acting elements related to plant defense responses, including DOFCOREZM, EECCRCAH1, GT1GAMSCAM4, and GT1CONSENSUS were detected in ZmeIF4E promoter for harboring sequence variation in the two lines. Association analysis with 163 inbred lines revealed that one SNP in EECCRCAH1 is significantly associated with CSI of MRDD in two environments, which explained 3.33 and 9.04 % of phenotypic variation, respectively. Meanwhile, one SNP in GT-1 motif was found to affect MRDD resistance only in one of the two environments, which explained 5.17 % of phenotypic variation. Collectively, regulatory motifs respectively harboring the two significant SNPs in ZmeIF4E promoter could be involved in the defense process of maize after viral infection. These results contribute to understand maize defense mechanisms against maize rough dwarf virus.

Translational Genomics for the Improvement of Switchgrass

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

Carpita, Nicholas; McCann, Maureen

2014-05-07

Our objectives were to apply bioinformatics and high throughput sequencing technologies to identify and classify the genes involved in cell wall formation in maize and switchgrass. Targets for genetic modification were to be identified and cell wall materials isolated and assayed for enhanced performance in bioprocessing. We annotated and assembled over 750 maize genes into gene families predicted to function in cell wall biogenesis. Comparative genomics of maize, rice, and Arabidopsis sequences revealed differences in gene family structure. In addition, differences in expression between gene family members of Arabidopsis, maize and rice underscored the need for a grass-specific genetic modelmore » for functional analyses. A forward screen of mature leaves of field-grown maize lines by near-infrared spectroscopy yielded several dozen lines with heritable spectroscopic phenotypes, several of which near-infrared (nir) mutants had altered carbohydrate-lignin compositions. Our contributions to the maize genome sequencing effort built on knowledge of copy number variation showing that uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. For example, although about 25% of all duplicated genes remain genome-wide, all of the cellulose synthase (CesA) homologs were retained. We showed that guaiacyl and syringyl lignin in lignocellulosic cell-wall materials from stems demonstrate a two-fold natural variation in content across a population of maize Intermated B73 x Mo7 (IBM) recombinant inbred lines, a maize Association Panel of 282 inbreds and landraces, and three populations of the maize Nested Association Mapping (NAM) recombinant inbred lines grown in three years. We then defined quantitative trait loci (QTL) for stem lignin content measured using pyrolysis molecular-beam mass spectrometry, and glucose and xylose yield measured using an enzymatic hydrolysis assay. Among five multi-year QTL for lignin abundance, two for 4-vinylphenol abundance, and four for glucose and/or xylose yield, not a single QTL for aromatic abundance and sugar yield was shared. A genome-wide association study (GWAS) for lignin abundance and sugar yield of the 282-member maize Association Panel provided candidate genes in the eleven QTL and showed that many other alleles impacting these traits exist in the broader pool of maize genetic diversity. The maize B73 and Mo17 genotypes exhibited surprisingly large differences in gene expression in developing stem tissues, suggesting certain regulatory elements can significantly enhance activity of biomass synthesis pathways. Candidate genes, identified by GWAS or by differential expression, include genes of cell-wall metabolism, transcription factors associated with vascularization and fiber formation, and components of cellular signaling pathways. Our work provides new insights and strategies beyond modification of lignin to enhance yields of biofuels from genetically tailored biomass.« less

Improving seedless kelp (Saccharina japonica) during its domestication by hybridizing gametophytes and seedling-raising from sporophytes

PubMed Central

Li, Xiaojie; Zhang, Zhuangzhi; Qu, Shancun; Liang, Guangjin; Sun, Juan; Zhao, Nan; Cui, Cuiju; Cao, Zengmei; Li, Yan; Pan, Jinhua; Yu, Shenhui; Wang, Qingyan; Li, Xia; Luo, Shiju; Song, Shaofeng; Guo, Li; Yang, Guanpin

2016-01-01

Dongfang no.7 (Saccharina japonica) was bred and maintained by hybridizing gametophytes, self-crossing the best individuals, selecting the best self-crossing line and seedling-raising from yearly reconstructed sporophytes. It increased the air dry yield by 43.2% in average over 2 widely farmed controls. Dongfang no.7 was seedling-raised from bulked sporophytes reconstructed from its representative gametophyte clones. Such strategy ensured it against variety contamination due to possible cross fertilization and occasional mixing and inbred depletion due to self-crossing number-limited sporophytes year after year. It derived from an intraspecific hybrid through 4 rounds of self-crossing and selection and retained a certain degree of genetic heterozygosity, thus being immune to inbred depletion due to purification of unknown detrimental alleles. Most importantly, it can be farmed in currently available system as the seedlings for large scale culture can be raised from reconstructed Dongfang no.7 sporophytes. Breeding and maintaining Dongfang no.7 provided a model that other varieties of kelp (S. japonica) and brown algae may follow during their domestication. PMID:26887644

Differences in susceptibility of rat strains to experimental infection with Taenia teaniaeformis.

PubMed

Williams, J F; Shearer, A M; Ravitch, M M

1981-08-01

Age-matched, outbred, female, Sprague-Dawley-derived rats from different commercial suppliers were compared for their susceptibility to the establishment and growth of Taenia taeniaeformis. Two of the strains, Spb:[SD] and Kng:[SD], gave very similar results, but the third, Hap:[SD]f, was considerably less receptive. Approximately one in eight of the Hap:[SD]f rats proved refractory to infection, and worm growth was slower and more variable than in Spb:[SD] rats. Male Spb:[SD] rats were not detectably different from females in susceptibility or parasite growth rate. Female rats of four different inbred lines all accepted infection, though the proportion of infective eggs giving rise to hepatic cysts differed. These differences, however, were overshadowed by variations observed in susceptibility of inbred rats of the same strain (Wistar-Lewis) purchased from different commercial suppliers. The results emphasize the need for careful standardization of laboratory procedures and rat strains for experimentation with this host-parasite system. In addition, they illustrate the dangers of extrapolation from the extensive literature of the influence of rat strain and sex on susceptibility to infection with T. taeniaeformis.

Efficient generation of Rosa26 knock-in mice using CRISPR/Cas9 in C57BL/6 zygotes.

PubMed

Chu, Van Trung; Weber, Timm; Graf, Robin; Sommermann, Thomas; Petsch, Kerstin; Sack, Ulrike; Volchkov, Pavel; Rajewsky, Klaus; Kühn, Ralf

2016-01-16

The CRISPR/Cas9 system is increasingly used for gene inactivation in mouse zygotes, but homology-directed mutagenesis and use of inbred embryos are less established. In particular, Rosa26 knock-in alleles for the insertion of transgenes in a genomic 'safe harbor' site, have not been produced. Here we applied CRISPR/Cas9 for the knock-in of 8-11 kb inserts into Rosa26 of C57BL/6 zygotes. We found that 10-20 % of live pups derived from microinjected zygotes were founder mutants, without apparent off-target effects, and up to 50 % knock-in embryos were recovered upon coinjection of Cas9 mRNA and protein. Using this approach, we established a new mouse line for the Cre/loxP-dependent expression of Cas9. Altogether, our protocols and resources support the fast and direct generation of new Rosa26 knock-in alleles and of Cas9-mediated in vivo gene editing in the widely used C57BL/6 inbred strain.

MicroRNA genes are frequently located near mouse cancer susceptibility loci

PubMed Central

Sevignani, Cinzia; Calin, George A.; Nnadi, Stephanie C.; Shimizu, Masayoshi; Davuluri, Ramana V.; Hyslop, Terry; Demant, Peter; Croce, Carlo M.; Siracusa, Linda D.

2007-01-01

MicroRNAs (miRNAs) are short 19- to 24-nt RNA molecules that have been shown to regulate the expression of other genes in a variety of eukaryotic systems. Abnormal expression of miRNAs has been observed in several human cancers, and furthermore, germ-line and somatic mutations in human miRNAs were recently identified in patients with chronic lymphocytic leukemia. Thus, human miRNAs can act as tumor suppressor genes or oncogenes, where mutations, deletions, or amplifications can underlie the development of certain types of leukemia. In addition, previous studies have shown that miRNA expression profiles can distinguish among human solid tumors from different organs. Because a single miRNA can simultaneously influence the expression of two or more protein-coding genes, we hypothesized that miRNAs could be candidate genes for cancer risk. Research in complex trait genetics has demonstrated that genetic background determines cancer susceptibility or resistance in various tissues, such as colon and lung, of different inbred mouse strains. We compared the genome positions of mouse tumor susceptibility loci with those of mouse miRNAs. Here, we report a statistically significant association between the chromosomal location of miRNAs and those of mouse cancer susceptibility loci that influence the development of solid tumors. Furthermore, we identified distinct patterns of flanking DNA sequences for several miRNAs located at or near susceptibility loci in inbred strains with different tumor susceptibilities. These data provide a catalog of miRNA genes in inbred strains that could represent genes involved in the development and penetrance of solid tumors. PMID:17470785

Rodent model choice has major impact on variability of standard preclinical readouts associated with diabetes and obesity research

PubMed Central

Jensen, Victoria S; Porsgaard, Trine; Lykkesfeldt, Jens; Hvid, Henning

2016-01-01

Laboratory rodents are available as either genetically defined inbred strains or genetically undefined outbred stocks. As outbred rodents are generally thought to display a higher level of phenotypic variation compared to inbred strains, it has been argued that experimental studies should preferentially be performed by using inbred rodents. However, very few studies with adequate sample sizes have in fact compared phenotypic variation between inbred strains and outbred stocks of rodents and moreover, these studies have not reached consistent conclusions. The aim of the present study was to compare the phenotypic variation in commonly used experimental readouts within obesity and diabetes research, for four of the most frequently used mouse strains: inbred C57BL/6 and BALB/c and outbred NMRI and CD-1 mice. The variation for all readouts was examined by calculating the coefficient of variation (CV), i.e., the relative variation, including a 95% confidence interval for the CV. We observed that for the majority of the selected readouts, inbred and outbred mice showed comparable phenotypic variation. The observed variation appeared highly influenced by strain choice and type of readout, which suggests that these collectively would serve as more predictive of the phenotypic variation than the more general classification of mice as inbred or outbred based on genetic heterogeneity. PMID:27648148

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.

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

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

Genetic Analysis of Seed-Soluble Oligosaccharides in Relation to Seed Storability of Arabidopsis1

PubMed Central

Bentsink, Leónie; Alonso-Blanco, Carlos; Vreugdenhil, Dick; Tesnier, Karine; Groot, Steven P.C.; Koornneef, Maarten

2000-01-01

Seed oligosaccharides (OSs) and especially raffinose series OSs (RSOs) are hypothesized to play an important role in the acquisition of desiccation tolerance and consequently in seed storability. In the present work we analyzed the seed-soluble OS (sucrose, raffinose, and stachyose) content of several Arabidopsis accessions and thus identified the genotype Cape Verde Islands having a very low RSO content. By performing quantitative trait loci (QTL) mapping in a recombinant inbred line population, we found one major QTL responsible for the practically monogenic segregation of seed stachyose content. This locus also affected the content of the two other OSs, sucrose, and raffinose. Two candidate genes encoding respectively for galactinol synthase and raffinose synthase were located within the genomic region around this major QTL. In addition, three smaller-effect QTL were identified, each one specifically affecting the content of an individual OS. Seed storability was analyzed in the same recombinant inbred line population by measuring viability (germination) under two different seed aging assays: after natural aging during 4 years of dry storage at room temperature and after artificial aging induced by a controlled deterioration test. Thus, four QTL responsible for the variation of this trait were mapped. Comparison of the QTL genetic positions showed that the genomic region containing the major OS locus did not significantly affect the seed storability. We concluded that in the studied material neither RSOs nor sucrose content had a specific effect on seed storability. PMID:11115877

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 of metabolites exhibited a maize-genotype specific pattern of accumulation, suggesting that the highly diverse maize genetic resources could be further exploited in terms of beneficial plant-bacterial interactions for optimizing maize growth, with reduced N fertilization inputs. PMID:28362815

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 of metabolites exhibited a maize-genotype specific pattern of accumulation, suggesting that the highly diverse maize genetic resources could be further exploited in terms of beneficial plant-bacterial interactions for optimizing maize growth, with reduced N fertilization inputs.

Inbreeding effects on fertility in humans: evidence for reproductive compensation.

PubMed Central

Ober, C; Hyslop, T; Hauck, W W

1999-01-01

The effects of inbreeding on prereproductive mortality have been demonstrated in many natural populations, including humans. However, little is known about the effects in inbred individuals who survive to adulthood. We have investigated the effects of inbreeding on fertility among inbred adult Hutterites and demonstrate significantly reduced fecundity among the most inbred Hutterite women, as evidenced by longer interbirth intervals (P=.024) and longer intervals to a recognized pregnancy (P=.010) but not by increased rates of fetal loss (P>.50). These data suggest the presence of recessive alleles that adversely affect fecundity among the population. In contrast, completed family sizes do not differ among the more and the less-inbred Hutterite women who were born after 1920, suggesting that reproductive compensation is occurring among the more-inbred and less-fecund women. This recent reproductive strategy would facilitate the maintenance of recessive alleles and contribute to an overall decline in fertility in the population. PMID:9915962

A relative quantitative Methylation-Sensitive Amplified Polymorphism (MSAP) method for the analysis of abiotic stress.

PubMed

Bednarek, Piotr T; Orłowska, Renata; Niedziela, Agnieszka

2017-04-21

We present a new methylation-sensitive amplified polymorphism (MSAP) approach for the evaluation of relative quantitative characteristics such as demethylation, de novo methylation, and preservation of methylation status of CCGG sequences, which are recognized by the isoschizomers HpaII and MspI. We applied the technique to analyze aluminum (Al)-tolerant and non-tolerant control and Al-stressed inbred triticale lines. The approach is based on detailed analysis of events affecting HpaII and MspI restriction sites in control and stressed samples, and takes advantage of molecular marker profiles generated by EcoRI/HpaII and EcoRI/MspI MSAP platforms. Five Al-tolerant and five non-tolerant triticale lines were exposed to aluminum stress using the physiologicaltest. Total genomic DNA was isolated from root tips of all tolerant and non-tolerant lines before and after Al stress following metAFLP and MSAP approaches. Based on codes reflecting events affecting cytosines within a given restriction site recognized by HpaII and MspI in control and stressed samples demethylation (DM), de novo methylation (DNM), preservation of methylated sites (MSP), and preservation of nonmethylatedsites (NMSP) were evaluated. MSAP profiles were used for Agglomerative hierarchicalclustering (AHC) based on Squared Euclidean distance and Ward's Agglomeration method whereas MSAP characteristics for ANOVA. Relative quantitative MSAP analysis revealed that both Al-tolerant and non-tolerant triticale lines subjected to Al stress underwent demethylation, with demethylation of CG predominating over CHG. The rate of de novo methylation in the CG context was ~3-fold lower than demethylation, whereas de novo methylation of CHG was observed only in Al-tolerant lines. Our relative quantitative MSAP approach, based on methylation events affecting cytosines within HpaII-MspI recognition sequences, was capable of quantifying de novo methylation, demethylation, methylation, and non-methylated status in control and stressed Al-tolerant and non-tolerant triticale inbred lines. The method could also be used to analyze methylation events affecting CG and CHG contexts, which were differentially methylated under Al stress. We cannot exclude that the methylation changes revealed among lines as well as between Al-tolerant and non-tolerant groups of lines were due to some experimental errors or that the number of lines was too small for ANOVA to prove the influence of Al stress. Nevertheless, we suspect that Al tolerance in triticale could be partly regulated by epigenetic factors acting at the level of DNA methylation. This method provides a valuable tool for studies of abiotic stresses in plants.

A genetic variation map for chicken with 2.8 million single nucleotide polymorphisms

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

Wong, G K; Hillier, L; Brandstrom, M

2005-02-20

We describe a genetic variation map for the chicken genome containing 2.8 million single nucleotide polymorphisms (SNPs), based on a comparison of the sequences of 3 domestic chickens (broiler, layer, Silkie) to their wild ancestor Red Jungle Fowl (RJF). Subsequent experiments indicate that at least 90% are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about 5 SNP/kb for almost every possible comparison between RJF and domestic lines, between two different domestic lines, and within domestic lines--contrary to the idea that domestic animals are highly inbred relative to theirmore » wild ancestors. In fact, most of the SNPs originated prior to domestication, and there is little to no evidence of selective sweeps for adaptive alleles on length scales of greater than 100 kb.« less

Standardized ileal digestible tryptophan-to-lysine ratios in growing pigs fed corn-based and non-corn-based diets.

PubMed

Quant, A D; Lindemann, M D; Kerr, B J; Payne, R L; Cromwell, G L

2012-04-01

Two 21-d experiments were conducted to determine the optimum standardized ileal digestible (SID) Trp:Lys in growing pigs fed corn-based diets compared with non-corn-based diets. The primary response variables in both experiments were ADG and plasma urea N (PUN) concentrations with the optimum SID Trp:Lys determined using broken-line analysis. Experiment 1 evaluated the optimum SID Trp:Lys in growing pigs fed corn-based diets consisting primarily of corn with minor inclusion of Canadian field peas and corn gluten meal to keep the SID Trp:Lys low. This experiment used 120 crossbred pigs (initial BW: 25.73 ± 2.46 kg) that were blocked by sex and initial BW and allotted to 5 SID Trp:Lys with 5 pens each for the first 4 treatments and 4 pens for the last treatment and 5 pigs/pen. Diets were formulated by the addition of supplemental Trp to create various SID Trp:Lys (12.77, 14.07, 15.50, 16.91, and 17.94%) with a constant SID Lys of 0.66%, which was determined to be 83% of the Lys requirement for pigs at this location. As the SID Trp:Lys increased from 12.77 to 17.94%, ADG increased (0.562, 0.648, 0.788, 0.787, and 0.815 kg/d) linearly (P < 0.001) and quadratically (P = 0.009), resulting in an optimum SID Trp:Lys of 15.73% (P < 0.001). Plasma urea N decreased (10.43, 9.30, 8.21, 8.55, and 9.25 mg/dL) linearly (P = 0.069) and quadratically (P = 0.015), resulting in an optimum SID Trp:Lys of 15.83% (P = 0.007). Experiment 2 evaluated the optimum SID Trp:Lys in growing pigs fed non-corn-based diets consisting primarily of barley and Canadian field peas, with smaller proportions of corn and wheat. Experiment 2 used 120 crossbred pigs (initial BW: 28.49 ± 2.92 kg) that were allotted to 5 increasing SID Trp:Lys (13.05, 14.32, 15.59, 16.85, and 18.11%; 0.66% SID Lys) in the same manner as Exp. 1. As SID Trp:Lys increased in Exp. 2, ADG increased linearly (P = 0.007) with the optimum SID Trp:Lys of 15.99% (P = 0.048). Plasma urea N concentrations decreased linearly (P = 0.056) and quadratically (P = 0.067) as SID Trp:Lys increased, resulting in an optimum SID Trp:Lys of 15.29% (P = 0.009). Averaging the break point values for ADG and PUN obtained from broken-line analysis for Exp. 1 and 2 produced optimum SID Trp:Lys of 15.78 and 15.64%, respectively. Based on the results from these 2 experiments, it seems that the optimum SID Trp:Lys is virtually unaffected by the dietary feedstuffs used as long as the diets are formulated on an SID AA basis.

78 FR 25941 - Stine Seed Farm, Inc.; Extension of a Determination of Nonregulated Status of Corn Genetically...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-03

... Engineered for Herbicide Resistance AGENCY: Animal and Plant Health Inspection Service, USDA. ACTION: Notice... maize line HCEM485, which has been genetically engineered to be resistant to the herbicide glyphosate...

Fathead minnow genome sequencing and assembly

EPA Pesticide Factsheets

The dataset provides the URLs for accessing the genome sequence data and two draft assemblies as well as fathead minnow genotyping data associated with estimating the heterozygosity of the in-bred line.This dataset is associated with the following publication:Burns, F., L. Cogburn, G. Ankley , D. Villeneuve , E. Waits , Y. Chang, V. Llaca, S. Deschamps, R. Jackson, and R. Hoke. Sequencing and De novo Draft Assemblies of the Fathead Minnow (Pimphales promelas)Reference Genome. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 35(1): 212-217, (2016).

Fast-Flowering Mini-Maize: Seed to Seed in 60 Days

PubMed Central

McCaw, Morgan E.; Wallace, Jason G.; Albert, Patrice S.; Buckler, Edward S.; Birchler, James A.

2016-01-01

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 generations a year are typical. FFMM is the result of a modified double-cross hybrid between four fast-flowering lines: Neuffer’s Early ACR (full color), Alexander’s Early Early Synthetic, Tom Thumb Popcorn, and Gaspe Flint, followed by selection for early flowering and desirable morphology throughout an 11-generation selfing regime. Lines A and B were derived from different progeny of the initial hybrid, and crosses between Mini-Maize A and B exhibit heterosis. The ancestry of each genomic region of Mini-Maize A and B was inferred from the four founder populations using genotyping by sequencing. Other genetic and genomic tools for these lines include karyotypes for both lines A and B, kernel genetic markers y1 (white endosperm) and R1-scm2 (purple endosperm and embryo) introgressed into Mini-Maize A, and ∼24× whole-genome resequencing data for Mini-Maize A. PMID:27440866

Producing offspring in Armadillidium vulgare: Effects of genetic diversity and inbreeding.

PubMed

Durand, Sylvine; Loiseau, Vincent; Prigot, Cybèle; Braquart-Varnier, Christine; Beltran-Bech, Sophie

2018-03-01

Genetic diversity is known to be correlated to fitness traits, and inbred individuals often display lower values for life history traits. In this study, we attempt to quantify how inbreeding affects such traits in the terrestrial isopod Armadillidium vulgare by performing inbred and non-inbred crosses under laboratory conditions. We estimated genetic characteristics of parents and offspring, and related them to fecundity and fertility measures, as well as offspring growth and survival. Our study shows that a decrease in offspring number might result from mortality around birth, but not to changes in fecundity, fertilization rate, or developmental failure between inbred and non-inbred crosses. More heterozygous females tended to be bigger and had a higher fecundity, which could have implications in mate choice. No effect of inbreeding was detected on offspring growth and survival. These results can be related to previously observed effects of genetic characteristics on mating strategies in A. vulgare, and could shed light on mechanisms of inbreeding avoidance in this species. © 2018 Wiley Periodicals, Inc.

Natural antisense transcripts are significantly involved in regulation of drought stress in maize.

PubMed

Xu, Jie; Wang, Qi; Freeling, Micheal; Zhang, Xuecai; Xu, Yunbi; Mao, Yan; Tang, Xin; Wu, Fengkai; Lan, Hai; Cao, Moju; Rong, Tingzhao; Lisch, Damon; Lu, Yanli

2017-05-19

Natural antisense transcripts (NATs) are a prominent and complex class of regulatory RNAs. Using strand-specific RNA sequencing, we identified 1769 sense and antisense transcript pairs (NAT pairs) in two maize inbreds with different sensitivity to drought, as well as in two derivative recombination inbred lines (RILs). A significantly higher proportion of NATs relative to non-NATs are specifically expressed under water stress (WS). Surprisingly, expression of sense and antisense transcripts produced by NAT pairs is significantly correlated, particularly under WS. We found an unexpected large proportion of NATs with protein coding potential, as estimated by ribosome release scores. Small RNAs significantly accumulate within NAT pairs, with 21 nt smRNA particularly enriched in overlapping regions of these pairs of genes. The abundance of these smRNAs is significantly altered in the leafbladeless1 mutant, suggesting that these genes may be regulated by the tasiRNA pathway. Further, NATs are significantly hypomethylated and include fewer transposable element sequences relative to non-NAT genes. NAT gene regions also exhibit higher levels of H3K36me3, H3K9ac, and H3K4me3, but lower levels of H3K27me3, indicating that NAT gene pairs generally exhibit an open chromatin configuration. Finally, NAT pairs in 368 diverse maize inbreds and 19 segregating populations were specifically enriched for polymorphisms associated with drought tolerance. Taken together, the data highlight the potential impact of that small RNAs and histone modifications have in regulation of NAT expression, and the significance of NATs in response to WS. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

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

Cultivation and partial characterization of spiroplasmas in cell cultures.

PubMed Central

Steiner, T; McGarrity, G J; Phillips, D M

1982-01-01

Spiroplasmas were propagated in the Drosophila melanogaster cell line Dm-1. Spiroplasma citri and unidentified strains (corn shunt organism, 277F [tick isolate], powder puff, BNR-1, honey bee, and OBMG) grew to 10(8) to 10(9) colony-forming units per ml and could be passaged. Cytopathic effect (CPE) varied with the infecting spiroplasma. The honey bee isolate killed Dm-1 within 2 to 4 days and produced CPE in four mammalian cells tested. At 25 degrees C, suckling mouse cataract agent produced no CPE in Dm-1 cells. Dm-1 cells did not support growth of the spiroplasmal sex ratio organism. Spiroplasmas could be detected in the cell cultures by agar inoculation, dark-field microscopy, scanning electron microscopy, and DNA fluorescent staining. The uridine phosphorylase test showed significant levels of conversion of [14C]uridine to [14C]uracil for all but some plant isolates: S. citri, corn shunt organism, lettuce, cactus, and powder puff strains, the first mycoplasmas to lack the enzyme. Primary isolations of corn shunt organism from infected corn plants were made in Dm-1 and I-XII cultures. The course of corn stunt organism infection of Dm-1 was monitored for three passages. The use of agarose and Dienes staining of the colonies improved growth and colony counting of corn stunt organism. The number of viable infected DM-1 cells decreased from 1.2 x 10(7) at passage 1 to 7.0 x 10(6) at passage 2 and 3 x 10(5) at passage 3. Images PMID:6797950

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

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.

A Single Molecule Scaffold for the Maize Genome

PubMed Central

Zhou, Shiguo; Wei, Fusheng; Nguyen, John; Bechner, Mike; Potamousis, Konstantinos; Goldstein, Steve; Pape, Louise; Mehan, Michael R.; Churas, Chris; Pasternak, Shiran; Forrest, Dan K.; Wise, Roger; Ware, Doreen; Wing, Rod A.; Waterman, Michael S.; Livny, Miron; Schwartz, David C.

2009-01-01

About 85% of the maize genome consists of highly repetitive sequences that are interspersed by low-copy, gene-coding sequences. The maize community has dealt with this genomic complexity by the construction of an integrated genetic and physical map (iMap), but this resource alone was not sufficient for ensuring the quality of the current sequence build. For this purpose, we constructed a genome-wide, high-resolution optical map of the maize inbred line B73 genome containing >91,000 restriction sites (averaging 1 site/∼23 kb) accrued from mapping genomic DNA molecules. Our optical map comprises 66 contigs, averaging 31.88 Mb in size and spanning 91.5% (2,103.93 Mb/∼2,300 Mb) of the maize genome. A new algorithm was created that considered both optical map and unfinished BAC sequence data for placing 60/66 (2,032.42 Mb) optical map contigs onto the maize iMap. The alignment of optical maps against numerous data sources yielded comprehensive results that proved revealing and productive. For example, gaps were uncovered and characterized within the iMap, the FPC (fingerprinted contigs) map, and the chromosome-wide pseudomolecules. Such alignments also suggested amended placements of FPC contigs on the maize genetic map and proactively guided the assembly of chromosome-wide pseudomolecules, especially within complex genomic regions. Lastly, we think that the full integration of B73 optical maps with the maize iMap would greatly facilitate maize sequence finishing efforts that would make it a valuable reference for comparative studies among cereals, or other maize inbred lines and cultivars. PMID:19936062

Mapping QTL Associated with Photoperiod Sensitivity and Assessing the Importance of QTL×Environment Interaction for Flowering Time in Maize

PubMed Central

Wang, Cuiling; Chen, Yanhui; Ku, Lixia; Wang, Tiegu; Sun, Zhaohui; Cheng, Fangfang; Wu, Liancheng

2010-01-01

Background An understanding of the genetic determinism of photoperiod response of flowering is a prerequisite for the successful exchange of germplasm across different latitudes. In order to contribute to resolve the genetic basis of photoperiod sensitivity in maize, a set of 201 recombinant inbred lines (RIL), derived from a temperate and tropical inbred line cross were evaluated in 5 field trials spread in short- and long-day environments. Methodology/Principal Findings Firstly, QTL analyses for flowering time and photoperiod sensitivity in maize were conducted in individual photoperiod environments separately, and then, the total genetic effect was partitioned into additive effect (A) and additive-by-environment interaction effect (AE) by using a mixed-model-based composite interval mapping (MCIM) method. Conclusions/Significance Seven putative QTL were found associated with DPS thermal time based on the data estimated in individual environments. Nine putative QTL were found associated with DPS thermal time across environments and six of them showed significant QTL×enviroment (QE) interactions. Three QTL for photoperiod sensitivity were identified on chromosome 4, 9 and 10, which had the similar position to QTL for DPS thermal time in the two long-day environment. The major photoperiod sensitive loci qDPS10 responded to both short and long-day photoperiod environments and had opposite effects in different photoperiod environment. The QTL qDPS3, which had the greatest additive effect exclusively in the short-day environment, were photoperiod independent and should be classified in autonomous promotion pathway. PMID:21124912

Interchromosomal recombination in Zea mays.

PubMed Central

Hu, W; Timmermans, M C; Messing, J

1998-01-01

A new allele of the 27-kD zein locus in maize has been generated by interchromosomal recombination between chromosomes of two different inbred lines. A continuous patch of at least 11,817 bp of inbred W64A, containing the previously characterized Ra allele of the 27-kD zein gene, has been inserted into the genome of A188 by a single crossover. While both junction sequences are conserved, sequences of the two homologs between these junctions differ considerably. W64A contains the 7313-bp-long retrotransposon, Zeon-1. A188 contains a second copy of the 27-kD zein gene and a 2-kb repetitive element. Therefore, recombination results in a 7.3-kb insertion and a 14-kb deletion compared to the original S+A188 allele. If nonpairing sequences are looped out, 206 single base changes, frequently clustered, are present. The structure of this allele may explain how a recently discovered example of somatic recombination occurred in an A188/W64A hybrid. This would indicate that despite these sequence differences, pairing between these alleles could occur early during plant development. Therefore, such a somatically derived chimeric chromosome can also be heritable and give rise to new alleles. PMID:9799274

Standardizing practices: a socio-history of experimental systems in classical genetic and virological cancer research, ca. 1920-1978.

PubMed

Fujimura, J H

1996-01-01

This paper presents a narrative history of technologies in cancer research circa 1920-1978 and a theoretical perspective on the complex, intertwined relationships between scientific problems, material practices and technologies, concepts and theories, and other historical circumstances. The history presents several active lines of research and technology development in the genetics of cancer in the United States which were constitutive of proto-oncogene work in its current form. I write this history from the perspective of technology development. Scientists participating in cancer research created tools with which to study their problems of interest, but the development of the tools also influenced the questions asked and answered in the form of concepts and theories developed. These tools included genetic ideas of the 1920s, inbred mouse colonies, chemicals and antibiotics developed during World War Two, tissue cultures and their technical procedures, and viruses. I examine these tools as standardized experimental systems that standardized materials as well as practices in laboratories. Inbred animals, tissue culture materials and methods, and tumor viruses as experimental systems gave materiality to "genes' and "cancer'. They are technical-natural objects that stand-in for nature in the laboratory.

Metabolite profiling and quantitative genetics of natural variation for flavonoids in Arabidopsis

PubMed Central

Routaboul, Jean-Marc; Dubos, Christian; Beck, Gilles; Marquis, Catherine; Bidzinski, Przemyslaw; Loudet, Olivier; Lepiniec, Loïc

2012-01-01

Little is known about the range and the genetic bases of naturally occurring variation for flavonoids. Using Arabidopsis thaliana seed as a model, the flavonoid content of 41 accessions and two recombinant inbred line (RIL) sets derived from divergent accessions (Cvi-0×Col-0 and Bay-0×Shahdara) were analysed. These accessions and RILs showed mainly quantitative rather than qualitative changes. To dissect the genetic architecture underlying these differences, a quantitative trait locus (QTL) analysis was performed on the two segregating populations. Twenty-two flavonoid QTLs were detected that accounted for 11–64% of the observed trait variations, only one QTL being common to both RIL sets. Sixteen of these QTLs were confirmed and coarsely mapped using heterogeneous inbred families (HIFs). Three genes, namely TRANSPARENT TESTA (TT)7, TT15, and MYB12, were proposed to underlie their variations since the corresponding mutants and QTLs displayed similar specific flavonoid changes. Interestingly, most loci did not co-localize with any gene known to be involved in flavonoid metabolism. This latter result shows that novel functions have yet to be characterized and paves the way for their isolation. PMID:22442426

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

Outcrossing and crossbreeding recovers deteriorated traits in laboratory cultured Steinernema carpocapsae nematodes

PubMed Central

Chaston, John M.; Dillman, Adler R.; Shapiro-Ilan, David I.; Bilgrami, Anwar L.; Gaugler, Randy; Hopper, Keith R.; Adams, Byron J.

2011-01-01

The nematode Steinernema carpocapsae infects and kills many pest insects in agroecosystems and is commonly used in biocontrol of these pests. Growth of the nematodes prior to distribution for biocontrol commonly results in deterioration of traits that are essential for nematode persistence in field applications. To better understand the mechanisms underlying trait deterioration of the efficacy of natural parasitism in entomopathogenic nematodes, we explored the maintenance of fitness related traits including reproductive capacity, heat tolerance, virulence to insects and `tail standing' (formerly called nictation) among laboratory-cultured lines derived from natural, randomly mating populations of S. carpocapsae. Laboratory cultured nematode lines with fitness-related trait values below wild-type levels regained wild-type levels of reproductive and heat tolerance traits when outcrossed with a non-deteriorated line, while virulence and `tail standing' did not deteriorate in our experiments. Crossbreeding two trait-deteriorated lines with each other also resulted in restoration of trait means to wild-type levels in most crossbred lines. Our results implicate inbreeding depression as the primary cause of trait deterioration in the laboratory cultured S. carpocapsae. We further suggest the possibility of creating inbred lines purged of deleterious alleles as founders in commercial nematode growth. PMID:21447341

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.

Frequency of Cry1F Non-Recessive Resistance Alleles in North Carolina Field Populations of Spodoptera frugiperda (Lepidoptera: Noctuidae)

PubMed Central

Li, Guoping; Reisig, Dominic; Miao, Jin; Gould, Fred; Huang, Fangneng; Feng, Hongqiang

2016-01-01

Fall armyworm, Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), is a target species of transgenic corn (Zea mays L.) that expresses single and pyramided Bacillus thuringiensis (Bt) toxin. In 2014, S. frugiperda were collected from a light trap in North Carolina, and a total of 212 F1/F2 isofemale lines of S. frugiperda were screened for resistance to Bt and non-Bt corn. All of the 212 isolines were susceptible to corn tissue expressing Cry1A.105 + Cry2Ab, Cry1F + Cry1A.105 + Cry2Ab, and Cry1F + Cry1Ab + Vip3Aa20. Growth rate bioassays were performed to isolate non-recessive Bt resistance alleles. Seven individuals out of the 212 isofemale lines carried major non-recessive alleles conferring resistance to Cry1F. A pooled colony was created from the seven individuals. This colony was 151.21 times more resistant to Cry1F than a known-susceptible population and was also resistant to Cry1A.105, but was not resistant to Cry2Ab and Vip3Aa20. The results demonstrate that field populations of S. frugiperda collected from North Carolina are generally susceptible to Cry1F, but that some individuals carry resistant alleles. The data generated in this study can be used as baseline data for resistance monitoring. PMID:27119741

Frequency of Cry1F Non-Recessive Resistance Alleles in North Carolina Field Populations of Spodoptera frugiperda (Lepidoptera: Noctuidae).

PubMed

Li, Guoping; Reisig, Dominic; Miao, Jin; Gould, Fred; Huang, Fangneng; Feng, Hongqiang

2016-01-01

Fall armyworm, Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), is a target species of transgenic corn (Zea mays L.) that expresses single and pyramided Bacillus thuringiensis (Bt) toxin. In 2014, S. frugiperda were collected from a light trap in North Carolina, and a total of 212 F1/F2 isofemale lines of S. frugiperda were screened for resistance to Bt and non-Bt corn. All of the 212 isolines were susceptible to corn tissue expressing Cry1A.105 + Cry2Ab, Cry1F + Cry1A.105 + Cry2Ab, and Cry1F + Cry1Ab + Vip3Aa20. Growth rate bioassays were performed to isolate non-recessive Bt resistance alleles. Seven individuals out of the 212 isofemale lines carried major non-recessive alleles conferring resistance to Cry1F. A pooled colony was created from the seven individuals. This colony was 151.21 times more resistant to Cry1F than a known-susceptible population and was also resistant to Cry1A.105, but was not resistant to Cry2Ab and Vip3Aa20. The results demonstrate that field populations of S. frugiperda collected from North Carolina are generally susceptible to Cry1F, but that some individuals carry resistant alleles. The data generated in this study can be used as baseline data for resistance monitoring.

[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.

Genotypic and sex differences in anxiety-like behavior and alcohol-induced anxiolysis in High Drinking in the Dark selected mice.

PubMed

Barkley-Levenson, Amanda M; Crabbe, John C

2015-02-01

Alcohol use disorders and anxiety disorders are highly comorbid in humans. In rodent lines selected for alcohol drinking, differences in anxiety-like behavior are also seen. The High Drinking in the Dark (HDID) lines of mice are selectively bred for drinking to intoxication during limited access to alcohol, and these mice represent a genetic model of risk for binge-like drinking. The present studies investigated whether these selected lines differ from control (HS) mice in basal anxiety behavior or in anxiolytic response to alcohol. We also assessed the genetic correlation between alcohol drinking in the dark (DID) and basal anxiety-like behavior using existing inbred strain data. Mice of both sexes and HDID replicates (HDID-1 and HDID-2) were tested on an elevated zero maze immediately following a DID test. In general, HDID mice showed more time spent in the open arms after drinking alcohol than HS mice, and open-arm time was significantly correlated with blood alcohol concentration. HDID-1 male mice also showed less anxiety-like behavior at baseline (water-drinking controls). In a separate experiment, HDID-1 and HS mice were tested for anxiolytic dose-response to acute alcohol injections. Both genotypes showed increasing time spent in the open arms with increasing alcohol doses, and HDID-1 and female mice had greater open-arm time across all doses. HDID-1 control males showed lower anxiety-like behavior than the HS control males. Inbred strain data analysis also showed no significant genetic relationship between alcohol DID and anxiety. These findings suggest that HDID selection has not produced systematic changes in anxiety-like behavior or sensitivity to alcohol-induced anxiolysis, though there is a tendency in the male mice of the first replicate toward reduced basal anxiety-like behavior. Therefore, anxiety state and sensitivity to alcohol's anxiolytic effects do not appear to contribute significantly to the high drinking behavior of the HDID mice. Copyright © 2015 Elsevier Inc. All rights reserved.

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

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 this favorable allele for kernel weight could be used in molecular marker-assisted selection for improvement of grain yield components in Chinese maize breeding programs.

Breeding for Increased Water Use Efficiency in Corn (Maize) Using a Low-altitude Unmanned Aircraft System

NASA Astrophysics Data System (ADS)

Shi, Y.; Veeranampalayam-Sivakumar, A. N.; Li, J.; Ge, Y.; Schnable, J. C.; Rodriguez, O.; Liang, Z.; Miao, C.

2017-12-01

Low-altitude aerial imagery collected by unmanned aircraft systems (UAS) at centimeter-level spatial resolution provides great potential to collect high throughput plant phenotyping (HTP) data and accelerate plant breeding. This study is focused on UAS-based HTP for breeding increased water use efficiency in corn in eastern Nebraska. The field trail is part of an effort by the Genomes to Fields consortium effort to grow and phenotype many of the same corn (maize) hybrids at approximately 40 locations across the United States and Canada in order to stimulate new research in crop modeling, the development of new plant phenotyping technologies and the identification of genetic loci that control the adaptation of specific corn (maize) lines to specific environments. It included approximately 250 maize hybrids primary generated using recently off patent material from major seed companies. These lines are the closest material to what farmers are growing today which can be legally used for research purposes and genotyped by the public sector. During the growing season, a hexacopter equipped with a multispectral and a RGB cameras was flown and used to image this 1-hectare field trial near Mead, NE. Sensor data from the UAS were correlated directly with grain yield, measured at the end of the growing season, and were also be used to quantify other traits of interest to breeders including flowering date, plant height, leaf orientation, canopy spectral, and stand count. The existing challenges of field data acquisition (to ensure data quality) and development of effective image processing algorithms (such as detecting corn tassels) will be discussed. The success of this study and others like it will speed up the process of phenotypic data collection, and provide more accurate and detailed trait data for plant biologists, plant breeders, and other agricultural scientists. Employing advanced UAS-based machine vision technologies in agricultural applications have the potential to increase the rate of genetic gain in plant breeding applications, as well as guide the optimization of management practices in precision agriculture.

Evaluation of procoagulant tissue factor expression in canine hemangiosarcoma cell lines.

PubMed

Witter, Lauren E; Gruber, Erika J; Lean, Fabian Z X; Stokol, Tracy

2017-01-01

OBJECTIVE To evaluate expression of procoagulant tissue factor (TF) by canine hemangiosarcoma cells in vitro. SAMPLES 4 canine hemangiosarcoma cell lines (SB-HSA [mouse-passaged cutaneous tumor], Emma [primary metastatic brain tumor], and Frog and Dal-1 [primary splenic tumors]) and 1 nonneoplastic canine endothelial cell line (CnAoEC). PROCEDURES TF mRNA and TF antigen expression were evaluated by quantitative real-time PCR assay and flow cytometry, respectively. Thrombin generation was measured in canine plasma and in coagulation factor-replete or specific coagulation factor-deficient human plasma by calibrated automated thrombography. Corn trypsin inhibitor and annexin V were used to examine contributions of contact activation and membrane-bound phosphatidylserine, respectively, to thrombin generation. RESULTS All cell lines expressed TF mRNA and antigen, with significantly greater expression of both products in SB-HSA and Emma cells than in CnAoEC. A greater percentage of SB-HSA cells expressed TF antigen, compared with other hemangiosarcoma cell lines. All hemangiosarcoma cell lines generated significantly more thrombin than did CnAoEC in canine or factor-replete human plasma. Thrombin generation induced by SB-HSA cells was significantly lower in factor VII-deficient plasma than in factor-replete plasma and was abolished in factor X-deficient plasma; residual thrombin generation in factor VII-deficient plasma was abolished by incubation of cells with annexin V. Thrombin generation by SB-HSA cells was unaffected by the addition of corn trypsin inhibitor. CONCLUSIONS AND CLINICAL RELEVANCE Hemangiosarcoma cell lines expressed procoagulant TF in vitro. Further research is needed to determine whether TF can be used as a biomarker for hemostatic dysfunction in dogs with hemangiosarcoma.

Evaluation of procoagulant tissue factor expression in canine hemangiosarcoma cell lines

PubMed Central

Witter, Lauren E.; Gruber, Erika J.; Lean, Fabian Z. X.; Stokol, Tracy

2017-01-01

OBJECTIVE To evaluate expression of procoagulant tissue factor (TF) by canine hemangiosarcoma cells in vitro. SAMPLES 4 canine hemangiosarcoma cell lines (SB-HSA [mouse-passaged cutaneous tumor], Emma [primary metastatic brain tumor], and Frog and Dal-1 [primary splenic tumors]) and 1 nonneoplastic canine endothelial cell line (CnAoEC). PROCEDURES TF mRNA and TF antigen expression were evaluated by quantitative real-time PCR assay and flow cytometry, respectively. Thrombin generation was measured in canine plasma and in coagulation factor–replete or specific coagulation factor–deficient human plasma by calibrated automated thrombography. Corn trypsin inhibitor and annexin V were used to examine contributions of contact activation and membrane-bound phosphatidylserine, respectively, to thrombin generation. RESULTS All cell lines expressed TF mRNA and antigen, with significantly greater expression of both products in SB-HSA and Emma cells than in CnAoEC. A greater percentage of SB-HSA cells expressed TF antigen, compared with other hemangiosarcoma cell lines. All hemangiosarcoma cell lines generated significantly more thrombin than did CnAoEC in canine or factor-replete human plasma. Thrombin generation induced by SB-HSA cells was significantly lower in factor VII-deficient plasma than in factor-replete plasma and was abolished in factor X–deficient plasma; residual thrombin generation in FVII-deficient plasma was abolished by incubation of cells with annexin V. Thrombin generation by SB-HSA cells was unaffected by the addition of corn trypsin inhibitor. CONCLUSIONS AND CLINICAL RELEVANCE Hemangiosarcoma cell lines expressed procoagulant TF in vitro. Further research is needed to determine whether TF can be used as a biomarker for hemostatic dysfunction in dogs with hemangiosarcoma. PMID:28029283

Field tolerance to fungal pathogens of Brassica napus constitutively expressing a chimeric chitinase gene

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

Grison, R.; Grezes-Besset, B.; Lucante, N.

1996-05-01

Constitutive overexpression of a protein involved in plant defense mechanisms to disease is one of the strategies proposed to increase plant tolerance to fungal pathogens. A hybrid endochitinase gene under a constitutive promoter was introduced by Agrobacterium-mediated transformation into a winter-type oilseed rape (Brassica napus var. oleifera) inbred line. Progeny from transformed plants was challenged using three different fungal pathogens (Cylindrosporium concentricum, Phoma lingam, Sclerotinia sclerotiorum) in field trials at two different geographical locations. These plants exhibited an increased tolerance to disease as compared with the nontransgenic parental plants. 31 refs., 1 fig., 2 tabs.

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

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.

Low temperature caused modifications in the arrangement of cell wall pectins due to changes of osmotic potential of cells of maize leaves (Zea mays L.).

PubMed

Bilska-Kos, Anna; Solecka, Danuta; Dziewulska, Aleksandra; Ochodzki, Piotr; Jończyk, Maciej; Bilski, Henryk; Sowiński, Paweł

2017-03-01

The cell wall emerged as one of the important structures in plant stress responses. To investigate the effect of cold on the cell wall properties, the content and localization of pectins and pectin methylesterase (PME) activity, were studied in two maize inbred lines characterized by different sensitivity to cold. Low temperature (14/12 °C) caused a reduction of pectin content and PME activity in leaves of chilling-sensitive maize line, especially after prolonged treatment (28 h and 7 days). Furthermore, immunocytohistological studies, using JIM5 and JIM7 antibodies, revealed a decrease of labeling of both low- and high-methylesterified pectins in this maize line. The osmotic potential, quantified by means of incipient plasmolysis was lower in several types of cells of chilling-sensitive maize line which was correlated with the accumulation of sucrose. These studies present new finding on the effect of cold stress on the cell wall properties in conjunction with changes in the osmotic potential of maize leaf cells.

Multi-state trials of Bt sweet corn varieties for control of the corn earworm (Lepidoptera: Noctuidae).

PubMed

Shelton, A M; Olmstead, D L; Burkness, E C; Hutchison, W D; Dively, G; Welty, C; Sparks, A N

2013-10-01

Field tests in 2010-2011 were performed in New York, Minnesota, Maryland, Ohio, and Georgia to compare Bt sweet corn lines expressing Cry1A.105 + Cry2Ab2 and Cry1Ab with their non-Bt isolines, with and without the use of foliar insecticides. The primary insect pest in all locations during the trial years was Heliocoverpa zea (Boddie), which is becoming the most serious insect pest of sweet corn in the United States. At harvest, the ears were measured for marketability according to fresh market and processing standards. For fresh market and processing, least squares regression showed significant effects of protein expression, state, and insecticide frequency. There was a significant effect of year for fresh market but not for processing. The model also showed significant effects of H. zea per ear by protein expression. Sweet corn containing two genes (Cry1A.105 + Cry2Ab2) and a single gene (Cry1Ab) provided high marketability, and both Bt varieties significantly outperformed the traditional non-Bt isolines in nearly all cases regardless of insecticide application frequency. For pest suppression of H. zea, plants expressing Bt proteins consistently performed better than non-Bt isoline plants, even those sprayed at conventional insecticide frequencies. Where comparisons in the same state were made between Cry1A.105 + Cry2Ab2 and Cry1Ab plants for fresh market, the product expressing Cry1A.105 + Cry2Ab2 provided better protection and resulted in less variability in control. Overall, these results indicate Cry1A.105 + Cry2Ab2 and Cry1Ab plants are suitable for fresh market and processing corn production across a diversity of growing regions and years. Our results demonstrate that Bt sweet corn has the potential to significantly reduce the use of conventional insecticides against lepidopteran pests and, in turn, reduce occupational and environmental risks that arise from intensive insecticide use.

A role for 9-lipoxygenases in maize defense against insect herbivory.

PubMed

Woldemariam, Melkamu G; Ahern, Kevin; Jander, Georg; Tzin, Vered

2018-01-02

Feeding by Spodoptera exigua (beet armyworm) larvae on Zea mays (maize) induces expression of 9-lipoxygenases to a greater extent than 13-lipoxygenases. Whereas 13-lipoxygenases have an established role in the synthesis of jasmonates that serve as defense signaling molecules in many plant species, relatively little is known about the role of 9-lipoxygenases in herbivore defense. Phylogenetic analysis of lipoxygenases from maize inbred lines B73 and W22 shows that, although most Lox genes are present in both lines, Lox12, a 9-lipoxygenase that has been implicated in fungal defense, is truncated and unlikely to encode a functional protein in W22. Two independent Mutator transposon insertions in another 9-lipoxygenase, Lox4, caused improved S. exigua growth on the mutant lines relative to wildtype W22. This observation suggests a function in herbivore defense for metabolic products downstream of maize Lox4, either through direct toxicity or a perhaps an as yet unknown signaling function.

A pyramid breeding of eight grain-yield related quantitative trait loci based on marker-assistant and phenotype selection in rice (Oryza sativa L.).

PubMed

Zong, Guo; Wang, Ahong; Wang, Lu; Liang, Guohua; Gu, Minghong; Sang, Tao; Han, Bin

2012-07-20

1000-Grain weight and spikelet number per panicle are two important components for rice grain yield. In our previous study, eight quantitative trait loci (QTLs) conferring spikelet number per panicle and 1000-grain weight were mapped through sequencing-based genotyping of 150 rice recombinant inbred lines (RILs). In this study, we validated the effects of four QTLs from Nipponbare using chromosome segment substitution lines (CSSLs), and pyramided eight grain yield related QTLs. The new lines containing the eight QTLs with positive effects showed increased panicle and spikelet size as compared with the parent variety 93-11. We further proposed a novel pyramid breeding scheme based on marker-assistant and phenotype selection (MAPS). This scheme allowed pyramiding of as many as 24 QTLs at a single hybridization without massive cross work. This study provided insights into the molecular basis of rice grain yield for direct wealth for high-yielding rice breeding. Copyright © 2012. Published by Elsevier Ltd.

Environmental stress, inbreeding, and the nature of phenotypic and genetic variance in Drosophila melanogaster.

PubMed Central

Fowler, Kevin; Whitlock, Michael C

2002-01-01

Fifty-two lines of Drosophila melanogaster founded by single-pair population bottlenecks were used to study the effects of inbreeding and environmental stress on phenotypic variance, genetic variance and survivorship. Cold temperature and high density cause reduced survivorship, but these stresses do not cause repeatable changes in the phenotypic variance of most wing morphological traits. Wing area, however, does show increased phenotypic variance under both types of environmental stress. This increase is no greater in inbred than in outbred lines, showing that inbreeding does not increase the developmental effects of stress. Conversely, environmental stress does not increase the extent of inbreeding depression. Genetic variance is not correlated with environmental stress, although the amount of genetic variation varies significantly among environments and lines vary significantly in their response to environmental change. Drastic changes in the environment can cause changes in phenotypic and genetic variance, but not in a way reliably predicted by the notion of 'stress'. PMID:11934358

The correlation of chemical and physical corn kernel traits with production performance in broiler chickens and laying hens.

PubMed

Moore, S M; Stalder, K J; Beitz, D C; Stahl, C H; Fithian, W A; Bregendahl, K

2008-04-01

A study was conducted to determine the influence on broiler chicken growth and laying hen performance of chemical and physical traits of corn kernels from different hybrids. A total of 720 male 1-d-old Ross-308 broiler chicks were allotted to floor pens in 2 replicated experiments with a randomized complete block design. A total of 240 fifty-two-week-old Hy-Line W-36 laying hens were allotted to cages in a randomized complete block design. Corn-soybean meal diets were formulated for 3 broiler growth phases and one 14-wk-long laying hen phase to be marginally deficient in Lys and TSAA to allow for the detection of differences or correlations attributable to corn kernel chemical or physical traits. The broiler chicken diets were also marginally deficient in Ca and nonphytate P. Within a phase, corn- and soybean-based diets containing equal amounts of 1 of 6 different corn hybrids were formulated. The corn hybrids were selected to vary widely in chemical and physical traits. Feed consumption and BW were recorded for broiler chickens every 2 wk from 0 to 6 wk of age. Egg production was recorded daily, and feed consumption and egg weights were recorded weekly for laying hens between 53 and 67 wk of age. Physical and chemical composition of kernels was correlated with performance measures by multivariate ANOVA. Chemical and physical kernel traits were weakly correlated with performance in broiler chickens from 0 to 2 wk of age (P<0.05, | r |<0.42). However, from 4 to 6 wk of age and 0 to 6 wk of age, only kernel chemical traits were correlated with broiler chicken performance (P<0.05, | r |<0.29). From 53 to 67 wk of age, correlations were observed between both kernel physical and chemical traits and laying hen performance (P<0.05, | r |<0.34). In both experiments, the correlations of performance measures with individual kernel chemical and physical traits for any single kernel trait were not large enough to base corn hybrid selection on for feeding poultry.

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

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.

Genetic variation in food choice behaviour of amino acid-deprived Drosophila.

PubMed

Toshima, Naoko; Hara, Chieko; Scholz, Claus-Jürgen; Tanimura, Teiichi

2014-10-01

To understand homeostatic regulation in insects, we need to understand the mechanisms by which they respond to external stimuli to maintain the internal milieu. Our previous study showed that Drosophila melanogaster exhibit specific amino acid preferences. Here, we used the D.melanogaster Genetic Reference Panel (DGRP), which is comprised of multiple inbred lines derived from a natural population, to examine how amino acid preference changes depending on the internal nutritional state in different lines. We performed a two-choice preference test and observed genetic variations in the response to amino acid deprivation. For example, a high-responding line showed an enhanced preference for amino acids even after only 1day of deprivation and responded to a fairly low concentration of amino acids. Conversely, a low-responding line showed no increased preference for amino acids after deprivation. We compared the gene expression profiles between selected high- and the low-responding lines and performed SNP analyses. We found several groups of genes putatively involved in altering amino acid preference. These results will contribute to future studies designed to explore how the genetic architecture of an organism evolves to adapt to different nutritional environments. Copyright © 2014 Elsevier Ltd. All rights reserved.

Mouse genotypes drive the liver and adrenal gland clocks

NASA Astrophysics Data System (ADS)

Košir, Rok; Prosenc Zmrzljak, Uršula; Korenčič, Anja; Juvan, Peter; Ačimovič, Jure; Rozman, Damjana

2016-08-01

Circadian rhythms regulate a plethora of physiological processes. Perturbations of the rhythm can result in pathologies which are frequently studied in inbred mouse strains. We show that the genotype of mouse lines defines the circadian gene expression patterns. Expression of majority of core clock and output metabolic genes are phase delayed in the C56BL/6J line compared to 129S2 in the adrenal glands and the liver. Circadian amplitudes are generally higher in the 129S2 line. Experiments in dark - dark (DD) and light - dark conditions (LD), exome sequencing and data mining proposed that mouse lines differ in single nucleotide variants in the binding regions of clock related transcription factors in open chromatin regions. A possible mechanisms of differential circadian expression could be the entrainment and transmission of the light signal to peripheral organs. This is supported by the genotype effect in adrenal glands that is largest under LD, and by the high number of single nucleotide variants in the Receptor, Kinase and G-protein coupled receptor Panther molecular function categories. Different phenotypes of the two mouse lines and changed amino acid sequence of the Period 2 protein possibly contribute further to the observed differences in circadian gene expression.

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

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.

Water table management reduces tile nitrate loss in continuous corn and in a soybean-corn rotation.

PubMed

Drury, C F; Tan, C S; Gaynor, J D; Reynolds, W D; Welacky, T W; Oloya, T O

2001-10-25

Water table management systems can be designed to alleviate soil water excesses and deficits, as well as reduce nitrate leaching losses in tile discharge. With this in mind, a standard tile drainage (DR) system was compared over 8 years (1991 to 1999) to a controlled tile drainage/subirrigation (CDS) system on a low-slope (0.05 to 0.1%) Brookston clay loam soil (Typic Argiaquoll) in southwestern Ontario, Canada. In the CDS system, tile discharge was controlled to prevent excessive drainage, and water was pumped back up the tile lines (subirrigation) to replenish the crop root zone during water deficit periods. In the first phase of the study (1991 to 1994), continuous corn (Zea mays, L.) was grown with annual nitrogen (N) fertilizer inputs as per local soil test recommendations. In the second phase (1995 to 1999), a soybean (Glycine max L., Merr.)-corn rotation was used with N fertilizer added only during the two corn years. In Phase 1 when continuous corn was grown, CDS reduced total tile discharge by 26% and total nitrate loss in tile discharge by 55%, compared to DR. In addition, the 4-year flow weighted mean (FWM) nitrate concentration in tile discharge exceeded the Canadian drinking water guideline (10 mg N l(-1)) under DR (11.4 mg N l(-1)), but not under CDS (7.0 mg N l(-1)). In Phase 2 during the soybean-corn rotation, CDS reduced total tile discharge by 38% and total nitrate loss in tile discharge by 66%, relative to DR. The 4-year FWM nitrate concentration during Phase 2 in tile discharge was below the drinking water guideline for both DR (7.3 mg N l(-1)) and CDS (4.0 mg N l(-1)). During both phases of the experiment, the CDS treatment caused only minor increases in nitrate loss in surface runoff relative to DR. Hence CDS decreased FWM nitrate concentrations, total drainage water loss, and total nitrate loss in tile discharge relative to DR. In addition, soybean-corn rotation reduced FWM nitrate concentrations and total nitrate loss in tile discharge relative to continuous corn. CDS and crop rotations with reduced N fertilizer inputs can thus improve the quality of tile discharge water substantially.

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.

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.

The disadvantages of being a hybrid during drought: A combined analysis of plant morphology, physiology and leaf proteome in maize

PubMed Central

Benešová, Monika; Fischer, Lukáš; Haisel, Daniel; Hnilička, František; Hniličková, Helena; Jedelský, Petr L.; Kočová, Marie; Rothová, Olga; Tůmová, Lenka; Wilhelmová, Naďa

2017-01-01

A comparative analysis of various parameters that characterize plant morphology, growth, water status, photosynthesis, cell damage, and antioxidative and osmoprotective systems together with an iTRAQ analysis of the leaf proteome was performed in two inbred lines of maize (Zea mays L.) differing in drought susceptibility and their reciprocal F1 hybrids. The aim of this study was to dissect the parent-hybrid relationships to better understand the mechanisms of the heterotic effect and its potential association with the stress response. The results clearly showed that the four examined genotypes have completely different strategies for coping with limited water availability and that the inherent properties of the F1 hybrids, i.e. positive heterosis in morphological parameters (or, more generally, a larger plant body) becomes a distinct disadvantage when the water supply is limited. However, although a greater loss of photosynthetic efficiency was an inherent disadvantage, the precise causes and consequences of the original predisposition towards faster growth and biomass accumulation differed even between reciprocal hybrids. Both maternal and paternal parents could be imitated by their progeny in some aspects of the drought response (e.g., the absence of general protein down-regulation, changes in the levels of some carbon fixation or other photosynthetic proteins). Nevertheless, other features (e.g., dehydrin or light-harvesting protein contents, reduced chloroplast proteosynthesis) were quite unique to a particular hybrid. Our study also confirmed that the strategy for leaving stomata open even when the water supply is limited (coupled to a smaller body size and some other physiological properties), observed in one of our inbred lines, is associated with drought-resistance not only during mild drought (as we showed previously) but also during more severe drought conditions. PMID:28419152

Qualitative and quantitative trait loci conditioning resistance to Puccinia coronata pathotypes NQMG and LGCG in the oat (Avena sativa L.) cultivars Ogle and TAM O-301.

PubMed

Jackson, E W; Obert, D E; Menz, M; Hu, G; Bonman, J M

2008-02-01

Mapping disease resistance loci relies on the type and precision of phenotypic measurements. For crown rust of oat, disease severity is commonly assessed based on visual ratings of infection types (IT) and/or diseased leaf area (DLA) of infected plants in the greenhouse or field. These data can be affected by several variables including; (i) non-uniform disease development in the field; (ii) atypical symptom development in the greenhouse; (iii) the presence of multiple pathogenic races or pathotypes in the field, and (iv) rating bias. To overcome these limitations, we mapped crown rust resistance to single isolates in the Ogle/TAM O-301 (OT) recombinant inbred line (RIL) population using detailed measurements of IT, uredinia length (UL) and relative fungal DNA (FDNA) estimates determined by q-PCR. Measurements were taken on OT parents and recombinant inbred lines (RIL) inoculated with Puccinia coronata pathotypes NQMG and LGCG in separate greenhouse and field tests. Qualitative mapping identified an allele conferred by TAM O-301 on linkage group (LG) OT-11, which produced a bleached fleck phenotype to both NQMG and LGCG. Quantitative mapping identified two major quantitative trait loci (QTL) originating from TAM O-301 on LGs OT-11 and OT-32 which reduced UL and FDNA of both isolates in all experiments. Additionally, minor QTLs that reduced UL and FDNA were detected on LGs OT-15 and OT-8, originating from TAM O-301, and on LG OT-27, originating from Ogle. Detailed assessments of the OT population using two pathotypes in both the greenhouse and field provided comprehensive information to effectively map the genes responsible for crown rust resistance in Ogle and TAM O-301 to NQMG and LGCG.

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.

Heterosis-associated proteome analyses of maize (Zea mays L.) seminal roots by quantitative label-free LC-MS.

PubMed

Marcon, Caroline; Lamkemeyer, Tobias; Malik, Waqas Ahmed; Ungrue, Denise; Piepho, Hans-Peter; Hochholdinger, Frank

2013-11-20

Heterosis is the superior performance of heterozygous F1-hybrid plants compared to their homozygous genetically distinct parents. Seminal roots are embryonic roots that play an important role during early maize (Zea mays L.) seedling development. In the present study the most abundant soluble proteins of 2-4cm seminal roots of the reciprocal maize F1-hybrids B73×Mo17 and Mo17×B73 and their parental inbred lines B73 and Mo17 were quantified by label-free LC-MS/MS. In total, 1918 proteins were detected by this shot-gun approach. Among those, 970 were represented by at least two peptides and were further analyzed. Eighty-five proteins displayed non-additive accumulation in at least one hybrid. The functional category protein metabolism was the most abundant class of non-additive proteins represented by 27 proteins. Within this category 16 of 17 non-additively accumulated ribosomal proteins showed high or above high parent expression in seminal roots. These results imply that an increased protein synthesis rate in hybrids might be related to the early manifestation of hybrid vigor in seminal roots. In the present study a shot-gun proteomics approach allowed for the identification of 1917 proteins and analysis of 970 seminal root proteins of maize that were represented by at least 2 peptides. The comparison of proteome complexity of reciprocal hybrids and their parental inbred lines indicates an increased protein synthesis rate in hybrids that may contribute to the early manifestation of heterosis in seminal roots. This article is part of a Special Issue entitled: Translational Plant Proteomics. Copyright © 2013 Elsevier B.V. All rights reserved.

Genetic Dissection of Maize Embryonic Callus Regenerative Capacity Using Multi-Locus Genome-Wide Association Studies

PubMed Central

Ma, Langlang; Liu, Min; Yan, Yuanyuan; Qing, Chunyan; Zhang, Xiaoling; Zhang, Yanling; Long, Yun; Wang, Lei; Pan, Lang; Zou, Chaoying; Li, Zhaoling; Wang, Yanli; Peng, Huanwei; Pan, Guangtang; Jiang, Zhou; Shen, Yaou

2018-01-01

The regenerative capacity of the embryonic callus, a complex quantitative trait, is one of the main limiting factors for maize transformation. This trait was decomposed into five traits, namely, green callus rate (GCR), callus differentiating rate (CDR), callus plantlet number (CPN), callus rooting rate (CRR), and callus browning rate (CBR). To dissect the genetic foundation of maize transformation, in this study multi-locus genome-wide association studies (GWAS) for the five traits were performed in a population of 144 inbred lines genotyped with 43,427 SNPs. Using the phenotypic values in three environments and best linear unbiased prediction (BLUP) values, as a result, a total of 127, 56, 160, and 130 significant quantitative trait nucleotides (QTNs) were identified by mrMLM, FASTmrEMMA, ISIS EM-BLASSO, and pLARmEB, respectively. Of these QTNs, 63 QTNs were commonly detected, including 15 across multiple environments and 58 across multiple methods. Allele distribution analysis showed that the proportion of superior alleles for 36 QTNs was <50% in 31 elite inbred lines. Meanwhile, these superior alleles had obviously additive effect on the regenerative capacity. This indicates that the regenerative capacity-related traits can be improved by proper integration of the superior alleles using marker-assisted selection. Moreover, a total of 40 candidate genes were found based on these common QTNs. Some annotated genes were previously reported to relate with auxin transport, cell fate, seed germination, or embryo development, especially, GRMZM2G108933 (WOX2) was found to promote maize transgenic embryonic callus regeneration. These identified candidate genes will contribute to a further understanding of the genetic foundation of maize embryonic callus regeneration. PMID:29755499

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.

Quantitative trait loci mapping and gene network analysis implicate protocadherin-15 as a determinant of brain serotonin transporter expression.

PubMed

Ye, R; Carneiro, A M D; Han, Q; Airey, D; Sanders-Bush, E; Zhang, B; Lu, L; Williams, R; Blakely, R D

2014-03-01

Presynaptic serotonin (5-hydroxytryptamine, 5-HT) transporters (SERT) regulate 5-HT signaling via antidepressant-sensitive clearance of released neurotransmitter. Polymorphisms in the human SERT gene (SLC6A4) have been linked to risk for multiple neuropsychiatric disorders, including depression, obsessive-compulsive disorder and autism. Using BXD recombinant inbred mice, a genetic reference population that can support the discovery of novel determinants of complex traits, merging collective trait assessments with bioinformatics approaches, we examine phenotypic and molecular networks associated with SERT gene and protein expression. Correlational analyses revealed a network of genes that significantly associated with SERT mRNA levels. We quantified SERT protein expression levels and identified region- and gender-specific quantitative trait loci (QTLs), one of which associated with male midbrain SERT protein expression, centered on the protocadherin-15 gene (Pcdh15), overlapped with a QTL for midbrain 5-HT levels. Pcdh15 was also the only QTL-associated gene whose midbrain mRNA expression significantly associated with both SERT protein and 5-HT traits, suggesting an unrecognized role of the cell adhesion protein in the development or function of 5-HT neurons. To test this hypothesis, we assessed SERT protein and 5-HT traits in the Pcdh15 functional null line (Pcdh15(av-) (3J) ), studies that revealed a strong, negative influence of Pcdh15 on these phenotypes. Together, our findings illustrate the power of multidimensional profiling of recombinant inbred lines in the analysis of molecular networks that support synaptic signaling, and that, as in the case of Pcdh15, can reveal novel relationships that may underlie risk for mental illness. © 2014 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.

Natural variation for a hybrid incompatibility between two species of Mimulus.

PubMed

Sweigart, Andrea L; Mason, Amanda R; Willis, John H

2007-01-01

Understanding the process by which hybrid incompatibility alleles become established in natural populations remains a major challenge to evolutionary biology. Previously, we discovered a two-locus Dobzhansky-Muller incompatibility that causes severe hybrid male sterility between two inbred lines of the incompletely isolated wildflower species, Mimulus guttatus and M. nasutus. An interspecific cross between these two inbred lines revealed that the M. guttatus (IM62) allele at hybrid male sterility 1 (hms1) acts dominantly in combination with recessive M. nasutus (SF5) alleles at hybrid male sterility 2 (hms2) to cause nearly complete hybrid male sterility. In this report, we extend these genetic analyses to investigate intraspecific variation for the hms1-hms2 incompatibility in natural populations of M. nasutus and M. guttatus, performing a series of interspecific crosses between individuals collected from a variety of geographic locales. Our results suggest that hms2 incompatibility alleles are common and geographically widespread within M. nasutus, but absent or rare in M. guttatus. In contrast, the hms1 locus is polymorphic within M. guttatus and the incompatibility allele appears to be extremely geographically restricted. We found evidence for the presence of the hms1 incompatibility allele in only two M. guttatus populations that exist within a few kilometers of each other. The restricted distribution of the hms1 incompatibility allele might currently limit the potential for the hms1-hms2 incompatibility to act as a species barrier between sympatric populations of M. guttatus and M. nasutus. Extensive sampling within a single M. guttatus population revealed that the hms1 locus is polymorphic and that the incompatibility allele appears to segregate at intermediate frequency, a pattern that is consistent with either genetic drift or natural selection.

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

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.

The disadvantages of being a hybrid during drought: A combined analysis of plant morphology, physiology and leaf proteome in maize.

PubMed

Holá, Dana; Benešová, Monika; Fischer, Lukáš; Haisel, Daniel; Hnilička, František; Hniličková, Helena; Jedelský, Petr L; Kočová, Marie; Procházková, Dagmar; Rothová, Olga; Tůmová, Lenka; Wilhelmová, Naďa

2017-01-01

A comparative analysis of various parameters that characterize plant morphology, growth, water status, photosynthesis, cell damage, and antioxidative and osmoprotective systems together with an iTRAQ analysis of the leaf proteome was performed in two inbred lines of maize (Zea mays L.) differing in drought susceptibility and their reciprocal F1 hybrids. The aim of this study was to dissect the parent-hybrid relationships to better understand the mechanisms of the heterotic effect and its potential association with the stress response. The results clearly showed that the four examined genotypes have completely different strategies for coping with limited water availability and that the inherent properties of the F1 hybrids, i.e. positive heterosis in morphological parameters (or, more generally, a larger plant body) becomes a distinct disadvantage when the water supply is limited. However, although a greater loss of photosynthetic efficiency was an inherent disadvantage, the precise causes and consequences of the original predisposition towards faster growth and biomass accumulation differed even between reciprocal hybrids. Both maternal and paternal parents could be imitated by their progeny in some aspects of the drought response (e.g., the absence of general protein down-regulation, changes in the levels of some carbon fixation or other photosynthetic proteins). Nevertheless, other features (e.g., dehydrin or light-harvesting protein contents, reduced chloroplast proteosynthesis) were quite unique to a particular hybrid. Our study also confirmed that the strategy for leaving stomata open even when the water supply is limited (coupled to a smaller body size and some other physiological properties), observed in one of our inbred lines, is associated with drought-resistance not only during mild drought (as we showed previously) but also during more severe drought conditions.

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.

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

Towards a universal vaccine for avian influenza: Protective efficacy of modified Vaccinia virus Ankara and Adenovirus vaccines expressing conserved influenza antigens in chickens challenged with low pathogenic avian influenza virus

PubMed Central

Boyd, Amy C.; Ruiz-Hernandez, Raul; Peroval, Marylene Y.; Carson, Connor; Balkissoon, Devanand; Staines, Karen; Turner, Alison V.; Hill, Adrian V.S.; Gilbert, Sarah C.; Butter, Colin

2013-01-01

Current vaccines targeting surface proteins can drive antigenic variation resulting either in the emergence of more highly pathogenic viruses or of antigenically distinct viruses that escape control by vaccination and thereby persist in the host population. Influenza vaccines typically target the highly mutable surface proteins and do not provide protection against heterologous challenge. Vaccines which induce immune responses against conserved influenza epitopes may confer protection against heterologous challenge. We report here the results of vaccination with recombinant modified Vaccinia virus Ankara (MVA) and Adenovirus (Ad) expressing a fusion construct of nucleoprotein and matrix protein (NP + M1). Prime and boost vaccination regimes were trialled in different ages of chicken and were found to be safe and immunogenic. Interferon-γ (IFN-γ) ELISpot was used to assess the cellular immune response post secondary vaccination. In ovo Ad prime followed by a 4 week post hatch MVA boost was identified as the most immunogenic regime in one outbred and two inbred lines of chicken. Following vaccination, one inbred line (C15I) was challenged with low pathogenic avian influenza (LPAI) H7N7 (A/Turkey/England/1977). Birds receiving a primary vaccination with Ad-NP + M1 and a secondary vaccination with MVA-NP + M1 exhibited reduced cloacal shedding as measured by plaque assay at 7 days post infection compared with birds vaccinated with recombinant viruses containing irrelevant antigen. This preliminary indication of efficacy demonstrates proof of concept in birds; induction of T cell responses in chickens by viral vectors containing internal influenza antigens may be a productive strategy for the development of vaccines to induce heterologous protection against influenza in poultry. PMID:23200938

Biomass Allocation Patterns Are Linked to Genotypic Differences in Whole-Plant Transpiration Efficiency in Sunflower

PubMed Central

Velázquez, Luciano; Alberdi, Ignacio; Paz, Cosme; Aguirrezábal, Luis

2017-01-01

Increased transpiration efficiency (the ratio of biomass to water transpired, TE) could lead to increased drought tolerance under some water deficit scenarios. Intrinsic (i.e., leaf-level) TE is usually considered as the primary source of variation in whole-plant TE, but empirical data usually contradict this assumption. Sunflower has a significant variability in TE, but a better knowledge of the effect of leaf and plant-level traits could be helpful to obtain more efficient genotypes for water use. The objective of this study was, therefore, to assess if genotypic variation in whole-plant TE is better related to leaf- or plant-level traits. Three experiments were conducted, aimed at verifying the existence of variability in whole-plant TE and whole-plant and leaf-level traits, and to assess their correlation. Sunflower public inbred lines and a segregating population of recombinant inbred lines were grown under controlled conditions and subjected to well-watered and water-deficit treatments. Significant genotypic variation was found for TE and related traits. These differences in whole-plant transpiration efficiency, both between genotypes and between plants within each genotype, showed no association to leaf-level traits, but were significantly and negatively correlated to biomass allocation to leaves and to the ratio of leaf area to total biomass. These associations are likely of a physiological origin, and not only a consequence of genetic linkage in the studied population. These results suggest that genotypic variation for biomass allocation could be potentially exploited as a source for increased transpiration efficiency in sunflower breeding programmes. It is also suggested that phenotyping for TE in this species should not be restricted to leaf-level measurements, but also include measurements of plant-level traits, especially those related to biomass allocation between photosynthetic and non-photosynthetic organs. PMID:29204153

Biomass Allocation Patterns Are Linked to Genotypic Differences in Whole-Plant Transpiration Efficiency in Sunflower.

PubMed

Velázquez, Luciano; Alberdi, Ignacio; Paz, Cosme; Aguirrezábal, Luis; Pereyra Irujo, Gustavo

2017-01-01

Increased transpiration efficiency (the ratio of biomass to water transpired, TE) could lead to increased drought tolerance under some water deficit scenarios. Intrinsic (i.e., leaf-level) TE is usually considered as the primary source of variation in whole-plant TE, but empirical data usually contradict this assumption. Sunflower has a significant variability in TE, but a better knowledge of the effect of leaf and plant-level traits could be helpful to obtain more efficient genotypes for water use. The objective of this study was, therefore, to assess if genotypic variation in whole-plant TE is better related to leaf- or plant-level traits. Three experiments were conducted, aimed at verifying the existence of variability in whole-plant TE and whole-plant and leaf-level traits, and to assess their correlation. Sunflower public inbred lines and a segregating population of recombinant inbred lines were grown under controlled conditions and subjected to well-watered and water-deficit treatments. Significant genotypic variation was found for TE and related traits. These differences in whole-plant transpiration efficiency, both between genotypes and between plants within each genotype, showed no association to leaf-level traits, but were significantly and negatively correlated to biomass allocation to leaves and to the ratio of leaf area to total biomass. These associations are likely of a physiological origin, and not only a consequence of genetic linkage in the studied population. These results suggest that genotypic variation for biomass allocation could be potentially exploited as a source for increased transpiration efficiency in sunflower breeding programmes. It is also suggested that phenotyping for TE in this species should not be restricted to leaf-level measurements, but also include measurements of plant-level traits, especially those related to biomass allocation between photosynthetic and non-photosynthetic organs.

Outcrossing and crossbreeding recovers deteriorated traits in laboratory cultured Steinernema carpocapsae nematodes.

PubMed

Chaston, John M; Dillman, Adler R; Shapiro-Ilan, David I; Bilgrami, Anwar L; Gaugler, Randy; Hopper, Keith R; Adams, Byron J

2011-06-01

The nematode Steinernema carpocapsae infects and kills many pest insects in agro-ecosystems and is commonly used in biocontrol of these pests. Growth of the nematodes prior to distribution for biocontrol commonly results in deterioration of traits that are essential for nematode persistence in field applications. To better understand the mechanisms underlying trait deterioration of the efficacy of natural parasitism in entomopathogenic nematodes, we explored the maintenance of fitness related traits including reproductive capacity, heat tolerance, virulence to insects and 'tail standing' (formerly called nictation) among laboratory-cultured lines derived from natural, randomly mating populations of S. carpocapsae. Laboratory cultured nematode lines with fitness-related trait values below wild-type levels regained wild-type levels of reproductive and heat tolerance traits when outcrossed with a non-deteriorated line, while virulence and 'tail standing' did not deteriorate in our experiments. Crossbreeding two trait-deteriorated lines with each other also resulted in restoration of trait means to wild-type levels in most crossbred lines. Our results implicate inbreeding depression as the primary cause of trait deterioration in the laboratory cultured S. carpocapsae. We further suggest the possibility of creating inbred lines purged of deleterious alleles as founders in commercial nematode growth. Copyright © 2011 Australian Society for Parasitology Inc. All rights reserved.

Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

PubMed Central

Bushley, Kathryn E.; Ohm, Robin A.; Otillar, Robert; Martin, Joel; Schackwitz, Wendy; Grimwood, Jane; MohdZainudin, NurAinIzzati; Xue, Chunsheng; Wang, Rui; Manning, Viola A.; Dhillon, Braham; Tu, Zheng Jin; Steffenson, Brian J.; Salamov, Asaf; Sun, Hui; Lowry, Steve; LaButti, Kurt; Han, James; Copeland, Alex; Lindquist, Erika; Barry, Kerrie; Schmutz, Jeremy; Baker, Scott E.; Ciuffetti, Lynda M.; Grigoriev, Igor V.; Zhong, Shaobin; Turgeon, B. Gillian

2013-01-01

The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five percent of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25× higher than those between inbred lines and 50× lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP–encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence. PMID:23357949

Mouse Sperm Cryopreservation and Recovery using the I·Cryo Kit

PubMed Central

Liu, Ling; Sansing, Steven R.; Morse, Iva S.; Pritchett-Corning, Kathleen R.

2011-01-01

Thousands of new genetically modified (GM) strains of mice have been created since the advent of transgenesis and knockout technologies. Many of these valuable animals exist only as live animals, with no backup plan in case of emergency. Cryopreservation of embryos can provide this backup, but is costly, can be a lengthy procedure, and generally requires a large number of animals for success. Since the discovery that mouse sperm can be successfully cryopreserved with a basic cryoprotective agent (CPA) consisting of 18% raffinose and 3% skim milk, sperm cryopreservation has become an acceptable and cost-effective procedure for archiving, distributing and recovery of these valuable strains. Here we demonstrate a newly developed I•Cryo kit for mouse sperm cryopreservation. Sperm from five commonly-used strains of inbred mice were frozen using this kit and then recovered. Higher protection ratios of sperm motility (> 60%) and rapid progressive motility (> 45%) compared to the control (basic CPA) were seen for sperm frozen with this kit in 5 inbred mouse strains. Two cell stage embryo development after IVF with the recovered sperm was improved consistently in all 5 mouse strains examined. Over a 1.5 year period, 49 GM mouse lines were archived by sperm cryopreservation with the I•Cryo kit and later recovered by IVF. PMID:22214993

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

Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

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

Condon, Bradford J.; Leng, Yueqiang; Wu, Dongliang

The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five of each genome differs between strains of the same species,more » while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25 higher than those between inbred lines and 50 lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.« less

Assessment of a Nutritional Rehabilitation Model in Two Modern Broilers and Their Jungle Fowl Ancestor: A Model for Better Understanding Childhood Undernutrition

PubMed Central

Baxter, Mikayla F. A.; Latorre, Juan D.; Koltes, Dawn A.; Dridi, Sami; Greene, Elizabeth S.; Bickler, Stephen W.; Kim, Jae H.; Merino-Guzman, Ruben; Hernandez-Velasco, Xochitl; Anthony, Nicholas B.; Bottje, Walter G.; Hargis, Billy M.; Tellez, Guillermo

2018-01-01

This article is the first in a series of manuscripts to evaluate nutritional rehabilitation in chickens as a model to study interventions in children malnutrition (Part 1: Performance, Bone Mineralization, and Intestinal Morphometric Analysis). Inclusion of rye in poultry diets induces a nutritional deficit that leads to increased bacterial translocation, intestinal viscosity, and decreased bone mineralization. However, it is unclear the effect of diet on developmental stage or genetic strain. Therefore, the objective was to determine the effects of a rye diet during either the early or late phase of development on performance, bone mineralization, and intestinal morphology across three diverse genetic backgrounds. Modern 2015 (Cobb 500) broiler chicken, 1995 Cobb broiler chicken, and the Giant Jungle Fowl were randomly allocated into four different dietary treatments. Dietary treatments were (1) a control corn-based diet throughout the trial (corn–corn); (2) an early phase malnutrition diet where chicks received a rye-based diet for 10 days, and then switched to the control diet (rye–corn); (3) a malnutrition rye-diet that was fed throughout the trial (rye–rye); and (4) a late phase malnutrition diet where chicks received the control diet for 10 days, and then switched to the rye diet for the last phase (corn–rye). At 10 days of age, chicks were weighed and diets were switched in groups 2 and 4. At day 20 of age, all chickens were weighed and euthanized to collect bone and intestinal samples. Body weight, weight gain, and bone mineralization were different across diet, genetic line, age and all two- and three-way interactions (P < 0.05). Overall, Jungle Fowl were the most tolerant to a rye-based diet, and both the modern and 1995 broilers were significantly affected by the high rye-based diet. However, the 1995 broilers consuming the rye-based diet appeared to experience more permanent effects when compared with the modern broiler. The results of this study suggest that chickens have a great potential as a nutritional rehabilitation model in human trials. The 1995 broilers line was an intermediate genetic line between the fast growing modern line and the non-selected Jungle Fowl line, suggesting that it would be the most appropriate model to study for future studies. PMID:29629373

Strategies for mapping heterogeneous recessive traits by allele-sharing methods.

PubMed Central

Feingold, E; Siegmund, D O

1997-01-01

We investigate strategies for detecting linkage of recessive and partially recessive traits, using sibling pairs and inbred individuals. We assume that a genomewide search is being conducted and that locus heterogeneity of the trait is likely. For sibling pairs, we evaluate the efficiency of different statistics under the assumption that one does not know the true degree of recessiveness of the trait. We recommend a sibling-pair statistic that is a linear compromise between two previously suggested statistics. We also compare the power of sibling pairs to that of more distant relatives, such as cousins. For inbred individuals, we evaluate the power of offspring of different types of matings and compare them to sibling pairs. Over a broad range of trait etiologies, sibling pairs are more powerful than inbred individuals, but for traits caused by very rare alleles, particularly in the case of heterogeneity, inbred individuals can be much more powerful. The models we develop can also be used to examine specific situations other than those we look at. We present this analysis in the idealized context of a dense set of highly polymorphic markers. In general, incorporation of real-world complexities makes inbred individuals, particularly offspring of distant relatives, look slightly less useful than our results imply. PMID:9106544

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

Americo, Jeffrey L.; Sood, Cindy L.; Cotter, Catherine A.

Classical inbred mice are extensively used for virus research. However, we recently found that some wild-derived inbred mouse strains are more susceptible than classical strains to monkeypox virus. Experiments described here indicated that the 50% lethal dose of vaccinia virus (VACV) and cowpox virus (CPXV) were two logs lower in wild-derived inbred CAST/Ei mice than classical inbred BALB/c mice, whereas there was little difference in the susceptibility of the mouse strains to herpes simplex virus. Live bioluminescence imaging was used to follow spread of pathogenic and attenuated VACV strains and CPXV virus from nasal passages to organs in the chestmore » and abdomen of CAST/Ei mice. Luminescence increased first in the head and then simultaneously in the chest and abdomen in a dose-dependent manner. The spreading kinetics was more rapid with VACV than CPXV although the peak photon flux was similar. These data suggest advantages of CAST/Ei mice for orthopoxvirus studies. - Highlights: • Wild-derived inbred CAST/Ei mice are susceptible to vaccinia virus and cowpox virus. • Morbidity and mortality from orthopoxviruses are greater in CAST/Ei than BALB/c mice. • Morbidity and mortality from herpes simplex virus type 1 are similar in both mice. • Imaging shows virus spread from nose to lungs, abdominal organs and brain. • Vaccinia virus spreads more rapidly than cowpox virus.« less

New mouse tumor model system (RIF-1) for comparison of end-point studies

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

Twentyman, P.R.; Brown, J.M.; Gray, J.W.

1980-03-01

A new tumor model system (RIF-1) was developed that is very suitable for studies in which clonogenic survival is compared with growth delay and control probability following various forms of treatment. The tumor was a radiation-induced sarcoma in the inbred female C3H/Km mouse. It had a low median tumor dose, had a satisfactory plating efficiency direct from in vivo to in vitro, was nonimmunogenic or minimally immunogenic, and metastasized only at a relatively advanced stage of growth. The cell line grew either as a monolayer on plastic dishes, as tumor spheroids in spinner culture, as lung nodules following injection ofmore » a single-cell suspension into the tall veins of syngeneic mice, or as a solid tumor. Both diploid and tetraploid clonogenic cells were found in monolayer cultures of the RIF-1 line.« less

Cloning crops in a CELSS via tissue culture: Prospects and problems

NASA Technical Reports Server (NTRS)

Carman, John G.; Hess, J. Richard

1990-01-01

Micropropagation is currently used to clone fruits, nuts, and vegetables and involves controlling the outgrowth in vitro of basal, axillary, or adventitious buds. Following clonal multiplication, shoots are divided and rooted. This process has greatly reduced space and energy requirements in greenhouses and field nurseries and has increased multiplication rates by greater than 20 fold for some vegetatively propagated crops and breeding lines. Cereal and legume crops can also be cloned by tissue culture through somatic embryogenesis. Somatic embryos can be used to produce 'synthetic seed', which can tolerate desiccation and germinate upon rehydration. Synthetic seed of hybrid wheat, rice, soybean and other crops could be produced in a controlled ecological life support system. Thus, yield advantages of hybreds over inbreds (10 to 20 percent) could be exploited without having to provide additional facilities and energy for parental-line and hybrid seed nurseries.

The Big Deals in Biofuels

ERIC Educational Resources Information Center

Brainard, Jeffrey

2007-01-01

Plants that bear less familiar names such as switch grass, "Miscanthus," and kenaf, are not much to look at, having weathered Iowa's winter snows. But Iowa State researchers see these crops as seeds of change in alternative fuels. Rows of experimental crops line the test plots at Iowa State University's research farm. Although corn is…

Rapid assessment of corn seed viability using short wave infrared line-scan hyperspectral imaging and chemometrics

USDA-ARS?s Scientific Manuscript database

Knowledge of the viability status of seeds before sowing is important to farmers and seed suppliers. However, a myriad of factors can reduce viability of seeds or completely render seeds non-viable during pre- and post-harvest operations. Spectral imaging has shown potential for determining seed via...