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Sample records for aestivum genomes aabbdd

  1. The origin of the B-genome of bread wheat (Triticum aestivum L.).

    PubMed

    Haider, N

    2013-03-01

    Understanding the origin of cultivated wheats would further their genetic improvement. The hexaploid bread wheat (Triticum aestivum L., AABBDD) is believed to have originated through one or more rare hybridization events between Aegilops tauschii (DD) and the tetraploid T. turgidum (AABB). Progenitor of the A-genome of the tetraploid and hexaploid wheats has generally been accepted to be T. urartu. In spite of the large number of attempts and published reports about the origin of the B-genome in cultivated wheats, the donor of the B-genome is still relatively unknown and controversial and, hence, remains open. This genome has been found to be closely related to the S-genome of the Sitopsis section (Ae. speltoides, Ae. longissima, Ae. sharonensis, Ae. searsii, and Ae. bicornis) of the genus Aegilops L. Among Sitopsis species, the most positive evidence has been accumulated for Ae. speltoides as the progenitor of the B-genome. Therefore, one or more of the Sitopsis species were proposed frequently as the B-genome donor. Although several reviews have been written on the origin of the genomes of wheat over the years, this paper will attempt for the first time to review the immense literature on the subject, with a particular emphasis on the B-genome which has attracted a huge attention over some 100 years. The ambiguity and conflicting results in most of the methods employed in deducing the precise B-genome donor/s to bread wheat are also discussed. PMID:23755530

  2. Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In hexaploid wheat (Triticum aestivum L.) (AABBDD, C=17,000Mb), repeat DNA accounts for ~ 90% of the genome of which transposable elements (TEs) constitute 60-80 %. Despite the dynamic evolution of TEs, our previous study indicated that the majority of TEs between the homologous wheat genomes are co...

  3. Visualization of A- and B-genome chromosomes in wheat (Triticum aestivum L.) x jointed goatgrass (Aegilops cylindrica Host) backcross progenies.

    PubMed

    Wang, Z N; Hang, A; Hansen, J; Burton, C; Mallory-Smith, C A; Zemetra, R S

    2000-12-01

    Wheat (Triticum aestivum) and jointed goatgrass (Aegilops cylindrica) can cross with each other, and their self-fertile backcross progenies frequently have extra chromosomes and chromosome segments, presumably retained from wheat, raising the possibility that a herbicide resistance gene might transfer from wheat to jointed goatgrass. Genomic in situ hybridization (GISH) was used to clarify the origin of these extra chromosomes. By using T. durum DNA (AABB genome) as a probe and jointed goatgrass DNA (CCDD genome) as blocking DNA, one, two, and three A- or B-genome chromosomes were identified in three BC2S2 individuals where 2n = 29, 30, and 31 chromosomes, respectively. A translocation between wheat and jointed goatgrass chromosomes was also detected in an individual with 30 chromosomes. In pollen mother cells with meiotic configuration of 14 II + 2 I, the two univalents were identified as being retained from the A or B genome of wheat. By using Ae. markgrafii DNA (CC genome) as a probe and wheat DNA (AABBDD genome) as blocking DNA. 14 C-genome chromosomes were visualized in all BC2S2 individuals. The GISH procedure provides a powerful tool to detect the A or B-genome chromatin in a jointed goatgrass background, making it possible to assess the risk of transfer of herbicide resistance genes located on the A or B genome of wheat to jointed goatgrass. PMID:11195336

  4. Impact of the D genome and quantitative trait loci on quantitative traits in a spring durum by spring bread wheat cross

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Desirable agronomic traits are similar for common hexaploid (6X) bread wheat (Triticum aestivum, 2n = 6x = 42, genome, AABBDD) and tetraploid (4X) durum wheat (Triticum turgidum durum, 2n = 4x = 28, genome, AABB). However, they are genetically isolated from each other due to an unequal number of ge...

  5. Introgression of wheat DNA markers from A, B and D genomes in early generation progeny of Aegilops cylindrica Host x Triticum aestivum L. hybrids.

    PubMed

    Schoenenberger, N; Felber, F; Savova-Bianchi, D; Guadagnuolo, R

    2005-11-01

    Introgression from allohexaploid wheat (Triticum aestivum L., AABBDD) to allotetraploid jointed goatgrass (Aegilops cylindrica Host, CCDD) can take place in areas where the two species grow in sympatry and hybridize. Wheat and Ae. cylindrica share the D genome, issued from the common diploid ancestor Aegilops tauschii Coss. It has been proposed that the A and B genome of bread wheat are secure places to insert transgenes to avoid their introgression into Ae. cylindrica because during meiosis in pentaploid hybrids, A and B genome chromosomes form univalents and tend to be eliminated whereas recombination takes place only in D genome chromosomes. Wheat random amplified polymorphic DNA (RAPD) fragments, detected in intergeneric hybrids and introgressed to the first backcross generation with Ae. cylindrica as the recurrent parent and having a euploid Ae. cylindrica chromosome number or one supernumerary chromosome, were assigned to wheat chromosomes using Chinese Spring nulli-tetrasomic wheat lines. Introgressed fragments were not limited to the D genome of wheat, but specific fragments of A and B genomes were also present in the BC1. Their presence indicates that DNA from any of the wheat genomes can introgress into Ae. cylindrica. Successfully located RAPD fragments were then converted into highly specific and easy-to-use sequence characterised amplified regions (SCARs) through sequencing and primer design. Subsequently these markers were used to characterise introgression of wheat DNA into a BC1S1 family. Implications for risk assessment of genetically modified wheat are discussed. PMID:16133306

  6. Exploring the diploid wheat ancestral A genome through sequence comparison at the High-Molecular-Weight glutenin locus region

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The polyploid nature of hexaploid wheat (T. aestivum, AABBDD) often represents a great challenge in various aspects of research including genetic mapping, map-based cloning of important genes, and sequencing and accurate assembly of its genome. To explore the utility of ancestral diploid species o...

  7. Genome structure of introgressive lines Triticum aestivum/Aegilops sharonensis.

    PubMed

    Antonyuk, M Z; Bodylyova, M V; Ternovskaya, T K

    2009-01-01

    The lines Triticum aestivum/Aegilops sharonensis were explored in regard to the presence of introgressions in the line genomes, their amount and belonging to definite homoeologic group. The results of studying of chromosome associations in M1 of pollen mother celles in the hybrids between the lines with each other and with recurrent common wheat genotype Avrora were compared with the data of the line assessment for the chromosomal biochemical and morphological markers. 26 lines were distinguished between six groups with specific genome rearrangement regard to recurrent genotype. PMID:20458978

  8. [Detection of the introgression of genome elements of Aegilops cylindrica Host. into Triticum aestivum L. genome with ISSR-analysis].

    PubMed

    Galaev, A V; Babaiants, L T; Sivolap, Iu M

    2003-01-01

    Comparative analysis of introgressive and parental forms of wheat was carried out to reveal the sites of donor genome with new loci of resistance to fungal diseases. By ISSR-method 124 ISSR-loci were detected in the genomes of 18 individual plants of introgressive line 5/20-91; 17 of them have been related to introgressive fragments of Ae. cylindrica genome in T. aestivum. It was shown that ISSR-method is effective for detection of the variability caused by introgression of alien genetic material to T. aestivum genome. PMID:12945176

  9. [Evolution study of wheat (Tritium aestivum L.) A, B and D genome based on DNA sequence similarity].

    PubMed

    Yu, B L; Huang, Z F; Zhou, W J; Zhang, W J

    2001-01-01

    Tritium aestivum L., and its four potential origin species T. urartu T., T. monococcum L., Ae. squarrosa L. and T. dicoccum S., were amplified with MWG913, a STS marker located in 1H chromosome of barley. Those products are cloned and sequenced. By the discrepancies of these sequences, we have obtained some evidences about the origin of wheat A, B, D genomes at molecular level. The results showed that the studied sequence in A genomes of Tritium aestivum L. was identical with that of T. urartu T., T. monococcum L. and T. dicoccum S.; that in D genome of Tritium aestivum L. was as same as that of Ae. squarrosa L.; that in B genome of Tritium aestivum L. differed from that of T. dicoccum S. in 0.61%. The results also suggested that A, B and D genome have the different evolution speed. PMID:11480175

  10. Molecular and phylogenetic characterization of the homoeologous EPSP Synthase genes of allohexaploid wheat, Triticum aestivum (L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: 5-Enolpyruvylshikimate-3-phosphate synthase (EPSPS) is the sixth and penultimate enzyme in the shikimate biosynthesis pathway. The EPSPS genes of allohexaploid wheat (Triticum aestivum, AABBDD) have not been well characterized. Herein, the three homoeologous copies of the wheat EPSPS gen...

  11. Analysis of the allohexaploid bread wheat genome (Triticum aestivum) using comparative whole genome shotgun sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The large 17 Gb allopolyploid genome of bread wheat is a major challenge for genome analysis because it is composed of three closely- related and independently maintained genomes, with genes dispersed as small “islands” separated by vast tracts of repetitive DNA. We used a novel comparative genomi...

  12. Evaluation of genetic diversity and genome-wide linkage disequilibrium among US wheat (Triticum aestivum L.) germplasm representing different market classes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity and genome-wide linkage disequilibrium (LD) were investigated among forty-three U.S. wheat (Triticum aestivum L.) elite cultivars and breeding lines representing seven U.S. wheat market classes using 242 wheat genomic simple sequence repeat (SSR) markers distributed throughout the ...

  13. [Molecular-genetic analysis of wheat (T. aestivum L.) genome with introgression of Ae. cylindrica Host genetic elements].

    PubMed

    Galaev, A V; Sivolap, Iu M

    2005-01-01

    Wheat-aegilops hybrid plants Triticum aestivum L. (2n = 42) x Aegilops cylindrica Host (2n = 28) were investigated with using microsatellite markers. In two BC1F9 lines some genome modifications connected with losing DNA fragments of initial variety or appearing of Aegilops genome elements were detected. In some investigated hybrids new amplicons lacking in parental plants were found. Substitution of wheat chromosomes for aegilops chromosomes was not revealed. Analysis of microsatellite loci in BC2F5 plants showed stable introgression of aegilops genetic elements into wheat; elimination of some transferred aegilops DNA fragments in the course of backcrossing; decreasing size of introgressive elements after backcrossing. Introgressive lines were classified according to genome changes. PMID:16250247

  14. Sequence polymorphism in polyploid wheat and their d-genome diploid ancestor.

    PubMed

    Caldwell, Katherine S; Dvorak, Jan; Lagudah, Evans S; Akhunov, Eduard; Luo, Ming-Cheng; Wolters, Petra; Powell, Wayne

    2004-06-01

    Sequencing was used to investigate the origin of the D genome of the allopolyploid species Triticum aestivum and Aegilops cylindrica. A 247-bp region of the wheat D-genome Xwye838 locus, encoding ADP-glucopyrophosphorylase, and a 326-bp region of the wheat D-genome Gss locus, encoding granule-bound starch synthase, were sequenced in a total 564 lines of hexaploid wheat (T. aestivum, genome AABBDD) involving all its subspecies and 203 lines of Aegilops tauschii, the diploid source of the wheat D genome. In Ae. tauschii, two SNP variants were detected at the Xwye838 locus and 11 haplotypes at the Gss locus. Two haplotypes with contrasting frequencies were found at each locus in wheat. Both wheat Xwye838 variants, but only one of the Gss haplotypes seen in wheat, were found among the Ae. tauschii lines. The other wheat Gss haplotype was not found in either Ae. tauschii or 70 lines of tetraploid Ae. cylindrica (genomes CCDD), which is known to hybridize with wheat. It is concluded that both T. aestivum and Ae. cylindrica originated recurrently, with at least two genetically distinct progenitors contributing to the formation of the D genome in both species. PMID:15238542

  15. Exploring the diploid wheat ancestral A genome through sequence comparison at the high-molecular-weight glutenin locus region.

    PubMed

    Dong, Lingli; Huo, Naxin; Wang, Yi; Deal, Karin; Luo, Ming-Cheng; Wang, Daowen; Anderson, Olin D; Gu, Yong Qiang

    2012-12-01

    The polyploid nature of hexaploid wheat (T. aestivum, AABBDD) often represents a great challenge in various aspects of research including genetic mapping, map-based cloning of important genes, and sequencing and accurately assembly of its genome. To explore the utility of ancestral diploid species of polyploid wheat, sequence variation of T. urartu (A(u)A(u)) was analyzed by comparing its 277-kb large genomic region carrying the important Glu-1 locus with the homologous regions from the A genomes of the diploid T. monococcum (A(m)A(m)), tetraploid T. turgidum (AABB), and hexaploid T. aestivum (AABBDD). Our results revealed that in addition to a high degree of the gene collinearity, nested retroelement structures were also considerably conserved among the A(u) genome and the A genomes in polyploid wheats, suggesting that the majority of the repetitive sequences in the A genomes of polyploid wheats originated from the diploid A(u) genome. The difference in the compared region between A(u) and A is mainly caused by four differential TE insertion and two deletion events between these genomes. The estimated divergence time of A genomes calculated on nucleotide substitution rate in both shared TEs and collinear genes further supports the closer evolutionary relationship of A to A(u) than to A(m). The structure conservation in the repetitive regions promoted us to develop repeat junction markers based on the A(u) sequence for mapping the A genome in hexaploid wheat. Eighty percent of these repeat junction markers were successfully mapped to the corresponding region in hexaploid wheat, suggesting that T. urartu could serve as a useful resource for developing molecular markers for genetic and breeding studies in hexaploid wheat. PMID:23052831

  16. Organelle genome stability in anther-derived doubled haploids of wheat (Triticum aestivum L., cv. 'Moisson').

    PubMed

    Rode, A; Hartmann, C; Dron, M; Picard, E; Ouetier, F

    1985-12-01

    Chloroplast and mitochondrial compartments of a parental line of wheat (Triticum aestivum L., cv. 'Moisson') and its anther-derived doubled haploid lines have been analyzed and compared on the basis of their DNA restriction patterns. The results obtained show that no noticeable difference can be detected between doubled haploid lines and parental line at the level of ctDNA and mtDNA organization. It may be concluded that in vitro culture by itself does not systematically generate a cytoplasmic variation in germ cells. PMID:24247401

  17. Draft genome of the wheat A-genome progenitor Triticum urartu.

    PubMed

    Ling, Hong-Qing; Zhao, Shancen; Liu, Dongcheng; Wang, Junyi; Sun, Hua; Zhang, Chi; Fan, Huajie; Li, Dong; Dong, Lingli; Tao, Yong; Gao, Chuan; Wu, Huilan; Li, Yiwen; Cui, Yan; Guo, Xiaosen; Zheng, Shusong; Wang, Biao; Yu, Kang; Liang, Qinsi; Yang, Wenlong; Lou, Xueyuan; Chen, Jie; Feng, Mingji; Jian, Jianbo; Zhang, Xiaofei; Luo, Guangbin; Jiang, Ying; Liu, Junjie; Wang, Zhaobao; Sha, Yuhui; Zhang, Bairu; Wu, Huajun; Tang, Dingzhong; Shen, Qianhua; Xue, Pengya; Zou, Shenhao; Wang, Xiujie; Liu, Xin; Wang, Famin; Yang, Yanping; An, Xueli; Dong, Zhenying; Zhang, Kunpu; Zhang, Xiangqi; Luo, Ming-Cheng; Dvorak, Jan; Tong, Yiping; Wang, Jian; Yang, Huanming; Li, Zhensheng; Wang, Daowen; Zhang, Aimin; Wang, Jun

    2013-04-01

    Bread wheat (Triticum aestivum, AABBDD) is one of the most widely cultivated and consumed food crops in the world. However, the complex polyploid nature of its genome makes genetic and functional analyses extremely challenging. The A genome, as a basic genome of bread wheat and other polyploid wheats, for example, T. turgidum (AABB), T. timopheevii (AAGG) and T. zhukovskyi (AAGGA(m)A(m)), is central to wheat evolution, domestication and genetic improvement. The progenitor species of the A genome is the diploid wild einkorn wheat T. urartu, which resembles cultivated wheat more extensively than do Aegilops speltoides (the ancestor of the B genome) and Ae. tauschii (the donor of the D genome), especially in the morphology and development of spike and seed. Here we present the generation, assembly and analysis of a whole-genome shotgun draft sequence of the T. urartu genome. We identified protein-coding gene models, performed genome structure analyses and assessed its utility for analysing agronomically important genes and for developing molecular markers. Our T. urartu genome assembly provides a diploid reference for analysis of polyploid wheat genomes and is a valuable resource for the genetic improvement of wheat. PMID:23535596

  18. [Detection of the introgression of genome elements of the Aegilops cylindrica host. into the Triticum aestivum L. genome by ISSR and SSR analysis].

    PubMed

    Galaev, A V; Babaiants, L T; Sivolap, Iu M

    2004-12-01

    To reveal sites of the donor genome in wheat crossed with Aegilops cylindrica, which acquired conferred resistance to fungal diseases, a comparative analysis of introgressive and parental forms was conducted. Two systems of PCR analysis, ISSR and SSR-PCR, were employed. Upon use of 7 ISSR primers in genotypes of 30 individual plants BC1 F9 belonging to lines 5/55-91 and 5/20-91, 19 ISSR loci were revealed and assigned to introgressive fragments of Aegilops cylindrica genome in Triticum aestivum. The 40 pairs of SSR primers allowed the detection of seven introgressive alleles; three of these alleles were located on common wheat chromosomes in the B genome, while four alleles, in the D genome. Based on data of microsatellite analysis, it was assumed that the telomeric region of the long arm of common wheat chromosome 6A also changed. ISSR and SSR methods were shown to be effective for detecting variability caused by introgression of foreign genetic material into the genome of common wheat. PMID:15648148

  19. Comparison of genome-wide gene expression patterns in the seedlings of nascent allohexaploid wheats produced by two combinations of hybrids.

    PubMed

    Jung, Yeonju; Kawaura, Kanako; Kishii, Masahiro; Sakuma, Shun; Ogihara, Yasunari

    2015-01-01

    Allopolyploidization in plants is an important event that enhances heterosis and environmental adaptation. Common wheat, Triticum aestivum (AABBDD), which is an allohexaploid that evolved from an allopolyploidization event between T. turgidum (AABB) and Aegilops tauschii (DD), shows more growth vigor and wider adaptation than tetraploid wheats. To better understand the molecular basis for the heterosis of hexaploid wheat, we systematically analyzed the genome-wide gene expression patterns of two combinations of newly hybridized triploids (ABD), their chromosome-doubled hexaploids (AABBDD), stable synthetic hexaploids (AABBDD) and natural hexaploids, in addition to their parents, T. turgidum (AABB) and Ae. tauschii (DD), using a microarray to reconstruct the events of allopolyploidization and genome stabilization. Overall comparisons of gene expression profiles showed that the newly generated hexaploids exhibited gene expression patterns similar to those of their maternal tetraploids, irrespective of hybrid combination. With successive generations, the gene expression profiles of nascent hexaploids became less similar to the maternal profiles, and belonged to a separate cluster from the natural hexaploids. Triploids revealed characteristic expression patterns, suggesting endosperm effects. In the newly hybridized triploids (ABD) of two independent synthetic lines, approximately one-fifth of expressed genes displayed non-additive expression; the number of these genes decreased with polyploidization and genome stabilization. Approximately 20% of the non-additively expressed genes were transmitted across generations throughout allopolyploidization and successive self-pollinations, and 43 genes overlapped between the two combinations, indicating that shared gene expression patterns can be seen during allohexaploidization. Furthermore, four of these 43 genes were involved in starch and sucrose metabolism, suggesting that these metabolic events play key roles in the

  20. Genome-wide genetic dissection of supernumerary spikelet and related traits in common wheat (Triticum aestivum L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  1. Molecular evolution of Wcor15 gene enhanced our understanding of the origin of A, B and D genomes in Triticum aestivum

    PubMed Central

    Liu, Fangfang; Si, Hongqi; Wang, Chengcheng; Sun, Genlou; Zhou, Erting; Chen, Can; Ma, Chuanxi

    2016-01-01

    The allohexaploid bread wheat originally derived from three closely related species with A, B and D genome. Although numerous studies were performed to elucidate its origin and phylogeny, no consensus conclusion has reached. In this study, we cloned and sequenced the genes Wcor15-2A, Wcor15-2B and Wcor15-2D in 23 diploid, 10 tetraploid and 106 hexaploid wheat varieties and analyzed their molecular evolution to reveal the origin of the A, B and D genome in Triticum aestivum. Comparative analyses of sequences in diploid, tetraploid and hexaploid wheats suggest that T. urartu, Ae. speltoides and Ae. tauschii subsp. strangulata are most likely the donors of the Wcor15-2A, Wcor15-2B and Wcor15-2D locus in common wheat, respectively. The Wcor15 genes from subgenomes A and D were very conservative without insertion and deletion of bases during evolution of diploid, tetraploid and hexaploid. Non-coding region of Wcor15-2B gene from B genome might mutate during the first polyploidization from Ae. speltoides to tetraploid wheat, however, no change has occurred for this gene during the second allopolyploidization from tetraploid to hexaploid. Comparison of the Wcor15 gene shed light on understanding of the origin of the A, B and D genome of common wheat. PMID:27526862

  2. Molecular evolution of Wcor15 gene enhanced our understanding of the origin of A, B and D genomes in Triticum aestivum.

    PubMed

    Liu, Fangfang; Si, Hongqi; Wang, Chengcheng; Sun, Genlou; Zhou, Erting; Chen, Can; Ma, Chuanxi

    2016-01-01

    The allohexaploid bread wheat originally derived from three closely related species with A, B and D genome. Although numerous studies were performed to elucidate its origin and phylogeny, no consensus conclusion has reached. In this study, we cloned and sequenced the genes Wcor15-2A, Wcor15-2B and Wcor15-2D in 23 diploid, 10 tetraploid and 106 hexaploid wheat varieties and analyzed their molecular evolution to reveal the origin of the A, B and D genome in Triticum aestivum. Comparative analyses of sequences in diploid, tetraploid and hexaploid wheats suggest that T. urartu, Ae. speltoides and Ae. tauschii subsp. strangulata are most likely the donors of the Wcor15-2A, Wcor15-2B and Wcor15-2D locus in common wheat, respectively. The Wcor15 genes from subgenomes A and D were very conservative without insertion and deletion of bases during evolution of diploid, tetraploid and hexaploid. Non-coding region of Wcor15-2B gene from B genome might mutate during the first polyploidization from Ae. speltoides to tetraploid wheat, however, no change has occurred for this gene during the second allopolyploidization from tetraploid to hexaploid. Comparison of the Wcor15 gene shed light on understanding of the origin of the A, B and D genome of common wheat. PMID:27526862

  3. The tRNATyr multigene family of Triticum aestivum: genome organization, sequence analyses and maturation of intron-containing pre-tRNAs in wheat germ extract.

    PubMed

    Arends, S; Kraus, J; Beier, H

    1996-04-22

    Southern analysis of Triticum DNA has revealed that nuclear tRNATyr genes are dispersed at a minimum of 16 loci in the genome. We have isolated six independent tRNATyr genes from a Triticum aestivum library in addition to three known members of the Triticum tRNATyr family. Four of the sequenced tRNATyr genes code for Triticum tRNA Tyr and two code for tRNA2Tyr. Three genes encode tRNAsTyr which carry one or two nucleotide substitutions as compared to the conventional genes. The nine Triticum tRNATyr genes possess highly conserved intron sequences ranging in size from 12 to 14 nucleotides. A common secondary intron structure with the 5' and 3' splice site loops separated by five base pairs can be formed by all pre-tRNAs Tyr which are efficiently spliced in the homologous wheat germ extract. PMID:8617358

  4. A genome-wide analysis of the auxin/indole-3-acetic acid gene family in hexaploid bread wheat (Triticum aestivum L.)

    PubMed Central

    Qiao, Linyi; Zhang, Xiaojun; Han, Xiao; Zhang, Lei; Li, Xin; Zhan, Haixian; Ma, Jian; Luo, Peigao; Zhang, Wenping; Cui, Lei; Li, Xiaoyan; Chang, Zhijian

    2015-01-01

    The Auxin/indole-3-acetic acid (Aux/IAA) gene family plays key roles in the primary auxin-response process and controls a number of important traits in plants. However, the characteristics of the Aux/IAA gene family in hexaploid bread wheat (Triticum aestivum L.) have long been unknown. In this study, a comprehensive identification of the Aux/IAA gene family was performed using the latest draft genome sequence of the bread wheat “Chinese Spring.” Thirty-four Aux/IAA genes were identified, 30 of which have duplicated genes on the A, B or D sub-genome, with a total of 84 Aux/IAA sequences. These predicted Aux/IAA genes were non-randomly distributed in all the wheat chromosomes except for chromosome 2D. The information of wheat Aux/IAA proteins is also described. Based on an analysis of phylogeny, expression and adaptive evolution, we prove that the Aux/IAA family in wheat has been replicated twice in the two allopolyploidization events of bread wheat, when the tandem duplication also occurred. The duplicated genes have undergone an evolutionary process of purifying selection, resulting in the high conservation of copy genes among sub-genomes and functional redundancy among several members of the TaIAA family. However, functional divergence probably existed in most TaIAA members due to the diversity of the functional domain and expression pattern. Our research provides useful information for further research into the function of Aux/IAA genes in wheat. PMID:26483801

  5. Genome-Wide Analysis of Microsatellite Markers Based on Sequenced Database in Chinese Spring Wheat (Triticum aestivum L.)

    PubMed Central

    Tang, Zhaohui; Ren, Yongkang; Li, Yali; Zhang, Dayong; Dong, Yanhui; Zhao, Xinghua

    2015-01-01

    Microsatellites or simple sequence repeats (SSRs) are distributed across both prokaryotic and eukaryotic genomes and have been widely used for genetic studies and molecular marker-assisted breeding in crops. Though an ordered draft sequence of hexaploid bread wheat have been announced, the researches about systemic analysis of SSRs for wheat still have not been reported so far. In the present study, we identified 364,347 SSRs from among 10,603,760 sequences of the Chinese spring wheat (CSW) genome, which were present at a density of 36.68 SSR/Mb. In total, we detected 488 types of motifs ranging from di- to hexanucleotides, among which dinucleotide repeats dominated, accounting for approximately 42.52% of the genome. The density of tri- to hexanucleotide repeats was 24.97%, 4.62%, 3.25% and 24.65%, respectively. AG/CT, AAG/CTT, AGAT/ATCT, AAAAG/CTTTT and AAAATT/AATTTT were the most frequent repeats among di- to hexanucleotide repeats. Among the 21 chromosomes of CSW, the density of repeats was highest on chromosome 2D and lowest on chromosome 3A. The proportions of di-, tri-, tetra-, penta- and hexanucleotide repeats on each chromosome, and even on the whole genome, were almost identical. In addition, 295,267 SSR markers were successfully developed from the 21 chromosomes of CSW, which cover the entire genome at a density of 29.73 per Mb. All of the SSR markers were validated by reverse electronic-Polymerase Chain Reaction (re-PCR); 70,564 (23.9%) were found to be monomorphic and 224,703 (76.1%) were found to be polymorphic. A total of 45 monomorphic markers were selected randomly for validation purposes; 24 (53.3%) amplified one locus, 8 (17.8%) amplified multiple identical loci, and 13 (28.9%) did not amplify any fragments from the genomic DNA of CSW. Then a dendrogram was generated based on the 24 monomorphic SSR markers among 20 wheat cultivars and three species of its diploid ancestors showing that monomorphic SSR markers represented a promising source to

  6. Genome-Wide Analysis of Microsatellite Markers Based on Sequenced Database in Chinese Spring Wheat (Triticum aestivum L.).

    PubMed

    Han, Bin; Wang, Changbiao; Tang, Zhaohui; Ren, Yongkang; Li, Yali; Zhang, Dayong; Dong, Yanhui; Zhao, Xinghua

    2015-01-01

    Microsatellites or simple sequence repeats (SSRs) are distributed across both prokaryotic and eukaryotic genomes and have been widely used for genetic studies and molecular marker-assisted breeding in crops. Though an ordered draft sequence of hexaploid bread wheat have been announced, the researches about systemic analysis of SSRs for wheat still have not been reported so far. In the present study, we identified 364,347 SSRs from among 10,603,760 sequences of the Chinese spring wheat (CSW) genome, which were present at a density of 36.68 SSR/Mb. In total, we detected 488 types of motifs ranging from di- to hexanucleotides, among which dinucleotide repeats dominated, accounting for approximately 42.52% of the genome. The density of tri- to hexanucleotide repeats was 24.97%, 4.62%, 3.25% and 24.65%, respectively. AG/CT, AAG/CTT, AGAT/ATCT, AAAAG/CTTTT and AAAATT/AATTTT were the most frequent repeats among di- to hexanucleotide repeats. Among the 21 chromosomes of CSW, the density of repeats was highest on chromosome 2D and lowest on chromosome 3A. The proportions of di-, tri-, tetra-, penta- and hexanucleotide repeats on each chromosome, and even on the whole genome, were almost identical. In addition, 295,267 SSR markers were successfully developed from the 21 chromosomes of CSW, which cover the entire genome at a density of 29.73 per Mb. All of the SSR markers were validated by reverse electronic-Polymerase Chain Reaction (re-PCR); 70,564 (23.9%) were found to be monomorphic and 224,703 (76.1%) were found to be polymorphic. A total of 45 monomorphic markers were selected randomly for validation purposes; 24 (53.3%) amplified one locus, 8 (17.8%) amplified multiple identical loci, and 13 (28.9%) did not amplify any fragments from the genomic DNA of CSW. Then a dendrogram was generated based on the 24 monomorphic SSR markers among 20 wheat cultivars and three species of its diploid ancestors showing that monomorphic SSR markers represented a promising source to

  7. Genetic Basis for Spontaneous Hybrid Genome Doubling during Allopolyploid Speciation of Common Wheat Shown by Natural Variation Analyses of the Paternal Species

    PubMed Central

    Matsuoka, Yoshihiro; Nasuda, Shuhei; Ashida, Yasuyo; Nitta, Miyuki; Tsujimoto, Hisashi; Takumi, Shigeo; Kawahara, Taihachi

    2013-01-01

    The complex process of allopolyploid speciation includes various mechanisms ranging from species crosses and hybrid genome doubling to genome alterations and the establishment of new allopolyploids as persisting natural entities. Currently, little is known about the genetic mechanisms that underlie hybrid genome doubling, despite the fact that natural allopolyploid formation is highly dependent on this phenomenon. We examined the genetic basis for the spontaneous genome doubling of triploid F1 hybrids between the direct ancestors of allohexaploid common wheat (Triticum aestivum L., AABBDD genome), namely Triticumturgidum L. (AABB genome) and Aegilopstauschii Coss. (DD genome). An Ae. tauschii intraspecific lineage that is closely related to the D genome of common wheat was identified by population-based analysis. Two representative accessions, one that produces a high-genome-doubling-frequency hybrid when crossed with a T. turgidum cultivar and the other that produces a low-genome-doubling-frequency hybrid with the same cultivar, were chosen from that lineage for further analyses. A series of investigations including fertility analysis, immunostaining, and quantitative trait locus (QTL) analysis showed that (1) production of functional unreduced gametes through nonreductional meiosis is an early step key to successful hybrid genome doubling, (2) first division restitution is one of the cytological mechanisms that cause meiotic nonreduction during the production of functional male unreduced gametes, and (3) six QTLs in the Ae. tauschii genome, most of which likely regulate nonreductional meiosis and its subsequent gamete production processes, are involved in hybrid genome doubling. Interlineage comparisons of Ae. tauschii’s ability to cause hybrid genome doubling suggested an evolutionary model for the natural variation pattern of the trait in which non-deleterious mutations in six QTLs may have important roles. The findings of this study demonstrated that the

  8. Comparing genomic selection and marker-assisted selection for Fusarium head blight resistance in wheat (Triticum aestivum L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic selection (GS) and marker-assisted selection (MAS) rely on marker-trait associations and are both routinely used for breeding purposes. Although similar, these two approaches differ in their applications and how markers are used to estimate breeding values. In this study, GS and MAS were com...

  9. Genome-wide association mapping of fusarium head blight resistance in wheat (Triticum aestivum L.) using genotyping by sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fusarium head blight (FHB) is one of the most important wheat diseases worldwide and host resistance displays complex genetic control. A genome-wide association study (GWAS) was performed on 273 winter wheat breeding lines from the mid-western and eastern regions of the US to identify chromosomal re...

  10. Electrophoretic analysis of the high-molecular-weight glutenin subunits of Triticum monococcum, T. urartu, and the A genome of bread wheat (T. aestivum).

    PubMed

    Waines, J G; Payne, P I

    1987-05-01

    The high molecular weight (HMW) subunit composition of glutenin was analysed by sodium dodecyl sulphate, polyacrylamide gel electrophoresis (SDS-PAGE) in the A genome of 497 diploid wheats and in 851 landraces of bread wheat. The material comprised 209 accessions of wild Triticum monococcum ssp. boeoticum from Greece, Turkey, Lebanon, Armenia, Iraq, and Iran; 132 accessions of the primitive domesticate T. monococcum ssp. monococcum from many different germplasm collections; one accession of free-threshing T. monococcum ssp. sinskajae; 155 accessions of wild T. urartu from Lebanon, Turkey, Armenia, Iraq, and Iran; and landraces of T. aestivum, mainly from the Mediterranean area and countries bordering on the Himalayan Mountains. Four novel HMW glutenin sub-units were discovered in the landraces of bread wheat, and the alleles that control them were designated Glu-Ald through Glu-Alg, respectively. The HMW subunits of T. monococcum ssp. boeoticum have a major, "x" subunit of slow mobility and several, less prominent, "y" subunits of greater mobility, all of which fall within the mobility range of HMW subunits reported for bread wheat. In T. monococcum ssp. monococcum the range of the banding patterns for HMW subunits was similar to that of ssp. boeoticum. However, two accessions, while containing "y" subunits were null for "x" subunits. The single accession of Triticum monococcum ssp. sinskajae had a banding pattern similar to that of most ssp. boeoticum and ssp. monococcum accessions. The HMW subunit banding patterns of T. urartu accessions were distinct from those of T. monococcum. All of them contained one major "x" and most contained one major "y" subunit. In the other accessions a "y" subunit was not expressed. The active genes for "y" subunits, if transferred to bread wheat, may be useful in improving bread-making quality. PMID:24241459

  11. Genome-wide association mapping for stripe rust (Puccinia striiformis F. sp. tritici) in US Pacific Northwest winter wheat (Triticum aestivum L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Stripe rust (Puccinia striiformis F. sp. tritici; also known as yellow rust) is a globally devastating disease of wheat (Triticum aestivum L.) and a major threat to wheat production in the US Pacific Northwest (PNW), therefore both adult plant and all-stage resistance have been introduced into the w...

  12. THE EFFECT OF D-GENOME SUBSTITUTIONS ON AGRONOMIC PERFORMANCE AND END-USE QUALITY OF 'PRESTO' TRITICALE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Hexaploid triticale (2n = 6x = 42, AABBRR) and wheat (2n = 6x = 42, AABBDD) differ in their R and D genomes. An unanswered question is whether introgressions of the D-genome chromatin could improve triticale. For example, in hexaploid wheat, the endosperm storage proteins, which determine bread-maki...

  13. Simultaneous transfer, introgression, and genomic localization of genes for resistance to stem rust race TTKSK (Ug99) from Aegilops tauschii to wheat.

    PubMed

    Olson, Eric L; Rouse, Matthew N; Pumphrey, Michael O; Bowden, Robert L; Gill, Bikram S; Poland, Jesse A

    2013-05-01

    Wheat production is currently threatened by widely virulent races of the wheat stem rust fungus, Puccinia graminis f. sp. tritici, that are part of the TTKSK (also known as 'Ug99') race group. The diploid D genome donor species Aegilops tauschii (2n = 2x = 14, DD) is a readily accessible source of resistance to TTKSK and its derivatives that can be transferred to hexaploid wheat, Triticum aestivum (2n = 6x = 42, AABBDD). To expedite transfer of TTKSK resistance from Ae. tauschii, a direct hybridization approach was undertaken that integrates gene transfer, mapping, and introgression into one process. Direct crossing of Ae. tauschii accessions with an elite wheat breeding line combines the steps of gene transfer and introgression while development of mapping populations during gene transfer enables the identification of closely linked markers. Direct crosses were made using TTKSK-resistant Ae. tauschii accessions TA1662 and PI 603225 as males and a stem rust-susceptible T. aestivum breeding line, KS05HW14, as a female. Embryo rescue enabled recovery of F1 (ABDD) plants that were backcrossed as females to the hexaploid recurrent parent. Stem rust-resistant BC1F1 plants from each Ae. tauschii donor source were used as males to generate BC2F1 mapping populations. Bulked segregant analysis of BC2F1 genotypes was performed using 70 SSR loci distributed across the D genome. Using this approach, stem rust resistance genes from both accessions were located on chromosome arm 1DS and mapped using SSR and EST-STS markers. An allelism test indicated the stem rust resistance gene transferred from PI 603225 is Sr33. Race specificity suggests the stem rust resistance gene transferred from TA1662 is unique and this gene has been temporarily designated SrTA1662. Stem rust resistance genes derived from TA1662 and PI 603225 have been made available with selectable molecular markers in genetic backgrounds suitable for stem rust resistance breeding. PMID:23377571

  14. Development of genome-specific primers for homoeologous genes in allopolyploid species: the waxy and starch synthase II genes in allohexaploid wheat (Triticum aestivum L.) as examples

    PubMed Central

    2010-01-01

    Background In allopolypoid crops, homoeologous genes in different genomes exhibit a very high sequence similarity, especially in the coding regions of genes. This makes it difficult to design genome-specific primers to amplify individual genes from different genomes. Development of genome-specific primers for agronomically important genes in allopolypoid crops is very important and useful not only for the study of sequence diversity and association mapping of genes in natural populations, but also for the development of gene-based functional markers for marker-assisted breeding. Here we report on a useful approach for the development of genome-specific primers in allohexaploid wheat. Findings In the present study, three genome-specific primer sets for the waxy (Wx) genes and four genome-specific primer sets for the starch synthase II (SSII) genes were developed mainly from single nucleotide polymorphisms (SNPs) and/or insertions or deletions (Indels) in introns and intron-exon junctions. The size of a single PCR product ranged from 750 bp to 1657 bp. The total length of amplified PCR products by these genome-specific primer sets accounted for 72.6%-87.0% of the Wx genes and 59.5%-61.6% of the SSII genes. Five genome-specific primer sets for the Wx genes (one for Wx-7A, three for Wx-4A and one for Wx-7D) could distinguish the wild type wheat and partial waxy wheat lines. These genome-specific primer sets for the Wx and SSII genes produced amplifications in hexaploid wheat, cultivated durum wheat, and Aegilops tauschii accessions, but failed to generate amplification in the majority of wild diploid and tetraploid accessions. Conclusions For the first time, we report on the development of genome-specific primers from three homoeologous Wx and SSII genes covering the majority of the genes in allohexaploid wheat. These genome-specific primers are being used for the study of sequence diversity and association mapping of the three homoeologous Wx and SSII genes in natural

  15. Molecular characterization and genomic mapping of the pathogenesis-related protein 1 (PR-1) gene family in hexaploid wheat (Triticum aestivum L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The group 1 pathogenesis-related (PR-1) proteins, known as hallmarks of defense pathways, are encoded by multigene families in plants as evidenced by the presence of 22 and 32 PR-1 genes in the finished Arabidopsis and rice genomes, respectively. Here, we report the initial characterization and mapp...

  16. A genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in a worldwide collection of hexaploid spring wheat (Triticum aestivum L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    New races of Puccinia striiformis f. sp. tritici (Pst), the causal pathogen of wheat stripe rust, show high virulence to previously deployed resistance genes and are causing large yield losses worldwide. To identify new sources of resistance we performed a genome-wide association study (GWAS) using...

  17. Wheat - Aegilops introgressions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Aegilops is the most closely related genus to Triticum in the tribe Triticeae. Aegilops speltoides Tausch (B genome donor) and Ae. tauschii Coss. (D genome donor) contributed two of the three genomes present in common wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD genomes). The Aegilops genus c...

  18. Genome Wide Single Locus Single Trait, Multi-Locus and Multi-Trait Association Mapping for Some Important Agronomic Traits in Common Wheat (T. aestivum L.)

    PubMed Central

    Jaiswal, Vandana; Gahlaut, Vijay; Meher, Prabina Kumar; Mir, Reyazul Rouf; Jaiswal, Jai Prakash; Rao, Atmakuri Ramakrishna; Balyan, Harindra Singh; Gupta, Pushpendra Kumar

    2016-01-01

    Genome wide association study (GWAS) was conducted for 14 agronomic traits in wheat following widely used single locus single trait (SLST) approach, and two recent approaches viz. multi locus mixed model (MLMM), and multi-trait mixed model (MTMM). Association panel consisted of 230 diverse Indian bread wheat cultivars (released during 1910–2006 for commercial cultivation in different agro-climatic regions in India). Three years phenotypic data for 14 traits and genotyping data for 250 SSR markers (distributed across all the 21 wheat chromosomes) was utilized for GWAS. Using SLST, as many as 213 MTAs (p ≤ 0.05, 129 SSRs) were identified for 14 traits, however, only 10 MTAs (~9%; 10 out of 123 MTAs) qualified FDR criteria; these MTAs did not show any linkage drag. Interestingly, these genomic regions were coincident with the genomic regions that were already known to harbor QTLs for same or related agronomic traits. Using MLMM and MTMM, many more QTLs and markers were identified; 22 MTAs (19 QTLs, 21 markers) using MLMM, and 58 MTAs (29 QTLs, 40 markers) using MTMM were identified. In addition, 63 epistatic QTLs were also identified for 13 of the 14 traits, flag leaf length (FLL) being the only exception. Clearly, the power of association mapping improved due to MLMM and MTMM analyses. The epistatic interactions detected during the present study also provided better insight into genetic architecture of the 14 traits that were examined during the present study. Following eight wheat genotypes carried desirable alleles of QTLs for one or more traits, WH542, NI345, NI170, Sharbati Sonora, A90, HW1085, HYB11, and DWR39 (Pragati). These genotypes and the markers associated with important QTLs for major traits can be used in wheat improvement programs either using marker-assisted recurrent selection (MARS) or pseudo-backcrossing method. PMID:27441835

  19. Genome Wide Single Locus Single Trait, Multi-Locus and Multi-Trait Association Mapping for Some Important Agronomic Traits in Common Wheat (T. aestivum L.).

    PubMed

    Jaiswal, Vandana; Gahlaut, Vijay; Meher, Prabina Kumar; Mir, Reyazul Rouf; Jaiswal, Jai Prakash; Rao, Atmakuri Ramakrishna; Balyan, Harindra Singh; Gupta, Pushpendra Kumar

    2016-01-01

    Genome wide association study (GWAS) was conducted for 14 agronomic traits in wheat following widely used single locus single trait (SLST) approach, and two recent approaches viz. multi locus mixed model (MLMM), and multi-trait mixed model (MTMM). Association panel consisted of 230 diverse Indian bread wheat cultivars (released during 1910-2006 for commercial cultivation in different agro-climatic regions in India). Three years phenotypic data for 14 traits and genotyping data for 250 SSR markers (distributed across all the 21 wheat chromosomes) was utilized for GWAS. Using SLST, as many as 213 MTAs (p ≤ 0.05, 129 SSRs) were identified for 14 traits, however, only 10 MTAs (~9%; 10 out of 123 MTAs) qualified FDR criteria; these MTAs did not show any linkage drag. Interestingly, these genomic regions were coincident with the genomic regions that were already known to harbor QTLs for same or related agronomic traits. Using MLMM and MTMM, many more QTLs and markers were identified; 22 MTAs (19 QTLs, 21 markers) using MLMM, and 58 MTAs (29 QTLs, 40 markers) using MTMM were identified. In addition, 63 epistatic QTLs were also identified for 13 of the 14 traits, flag leaf length (FLL) being the only exception. Clearly, the power of association mapping improved due to MLMM and MTMM analyses. The epistatic interactions detected during the present study also provided better insight into genetic architecture of the 14 traits that were examined during the present study. Following eight wheat genotypes carried desirable alleles of QTLs for one or more traits, WH542, NI345, NI170, Sharbati Sonora, A90, HW1085, HYB11, and DWR39 (Pragati). These genotypes and the markers associated with important QTLs for major traits can be used in wheat improvement programs either using marker-assisted recurrent selection (MARS) or pseudo-backcrossing method. PMID:27441835

  20. A Genome-Wide Association Study of Resistance to Stripe Rust (Puccinia striiformis f. sp. tritici) in a Worldwide Collection of Hexaploid Spring Wheat (Triticum aestivum L.)

    PubMed Central

    Maccaferri, Marco; Zhang, Junli; Bulli, Peter; Abate, Zewdie; Chao, Shiaoman; Cantu, Dario; Bossolini, Eligio; Chen, Xianming; Pumphrey, Michael; Dubcovsky, Jorge

    2015-01-01

    New races of Puccinia striiformis f. sp. tritici (Pst), the causal pathogen of wheat stripe rust, show high virulence to previously deployed resistance genes and are responsible for large yield losses worldwide. To identify new sources of resistance we performed a genome-wide association study (GWAS) using a worldwide collection of 1000 spring wheat accessions. Adult plants were evaluated under field conditions in six environments in the western United States, and seedlings were tested with four Pst races. A single-nucleotide polymorphism (SNP) Infinium 9K-assay provided 4585 SNPs suitable for GWAS. High correlations among environments and high heritabilities were observed for stripe rust infection type and severity. Greater levels of Pst resistance were observed in a subpopulation from Southern Asia than in other groups. GWAS identified 97 loci that were significant for at least three environments, including 10 with an experiment-wise adjusted Bonferroni probability < 0.10. These 10 quantitative trait loci (QTL) explained 15% of the phenotypic variation in infection type, a percentage that increased to 45% when all QTL were considered. Three of these 10 QTL were mapped far from previously identified Pst resistance genes and QTL, and likely represent new resistance loci. The other seven QTL mapped close to known resistance genes and allelism tests will be required to test their relationships. In summary, this study provides an integrated view of stripe rust resistance resources in spring wheat and identifies new resistance loci that will be useful to diversify the current set of resistance genes deployed to control this devastating disease. PMID:25609748

  1. A genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in a worldwide collection of hexaploid spring wheat (Triticum aestivum L.).

    PubMed

    Maccaferri, Marco; Zhang, Junli; Bulli, Peter; Abate, Zewdie; Chao, Shiaoman; Cantu, Dario; Bossolini, Eligio; Chen, Xianming; Pumphrey, Michael; Dubcovsky, Jorge

    2015-03-01

    New races of Puccinia striiformis f. sp. tritici (Pst), the causal pathogen of wheat stripe rust, show high virulence to previously deployed resistance genes and are responsible for large yield losses worldwide. To identify new sources of resistance we performed a genome-wide association study (GWAS) using a worldwide collection of 1000 spring wheat accessions. Adult plants were evaluated under field conditions in six environments in the western United States, and seedlings were tested with four Pst races. A single-nucleotide polymorphism (SNP) Infinium 9K-assay provided 4585 SNPs suitable for GWAS. High correlations among environments and high heritabilities were observed for stripe rust infection type and severity. Greater levels of Pst resistance were observed in a subpopulation from Southern Asia than in other groups. GWAS identified 97 loci that were significant for at least three environments, including 10 with an experiment-wise adjusted Bonferroni probability < 0.10. These 10 quantitative trait loci (QTL) explained 15% of the phenotypic variation in infection type, a percentage that increased to 45% when all QTL were considered. Three of these 10 QTL were mapped far from previously identified Pst resistance genes and QTL, and likely represent new resistance loci. The other seven QTL mapped close to known resistance genes and allelism tests will be required to test their relationships. In summary, this study provides an integrated view of stripe rust resistance resources in spring wheat and identifies new resistance loci that will be useful to diversify the current set of resistance genes deployed to control this devastating disease. PMID:25609748

  2. Genome-wide gene expression analysis supports a developmental model of low temperature tolerance gene regulation in wheat (Triticum aestivum L.)

    PubMed Central

    2011-01-01

    Background To identify the genes involved in the development of low temperature (LT) tolerance in hexaploid wheat, we examined the global changes in expression in response to cold of the 55,052 potentially unique genes represented in the Affymetrix Wheat Genome microarray. We compared the expression of genes in winter-habit (winter Norstar and winter Manitou) and spring-habit (spring Manitou and spring Norstar)) cultivars, wherein the locus for the vernalization gene Vrn-A1 was swapped between the parental winter Norstar and spring Manitou in the derived near-isogenic lines winter Manitou and spring Norstar. Global expression of genes in the crowns of 3-leaf stage plants cold-acclimated at 6°C for 0, 2, 14, 21, 38, 42, 56 and 70 days was examined. Results Analysis of variance of gene expression separated the samples by genetic background and by the developmental stage before or after vernalization saturation was reached. Using gene-specific ANOVA we identified 12,901 genes (at p < 0.001) that change in expression with respect to both genotype and the duration of cold-treatment. We examined in more detail a subset of these genes (2,771) where expression was highly influenced by the interaction between these two main factors. Functional assignments using GO annotations showed that genes involved in transport, oxidation-reduction, and stress response were highly represented. Clustering based on the pattern of transcript accumulation identified genes that were up or down-regulated by cold-treatment. Our data indicate that the cold-sensitive lines can up-regulate known cold-responsive genes comparable to that of cold-hardy lines. The levels of expression of these genes were highly influenced by the initial rate and the duration of the gene's response to cold. We show that the Vrn-A1 locus controls the duration of gene expression but not its initial rate of response to cold treatment. Furthermore, we provide evidence that Ta.Vrn-A1 and Ta.Vrt1 originally hypothesized to

  3. Cytogenetic and molecular identification of three Triticum aestivum-Leymus racemosus translocation addition lines.

    PubMed

    Wang, Le; Yuan, Jianhua; Bie, Tongde; Zhou, Bo; Chen, Peidu

    2009-06-01

    Chromosome 2C from Aegilops cylindrica has the ability to induce chromosome breakage in common wheat (Tritivum aestivum). In the BC(1)F(3) generation of the T. aestivum cv. Chinese Spring and a hybrid between T. aestivum-Leymus racemosus Lr.7 addition line and T. aestivum-Ae. cylindrica 2C addition line, three disomic translocation addition lines (2n = 44) were selected by mitotic chromosome C-banding and genomic in situ hybridization. We further characterized these T. aestivum-L. racemosus translocation addition lines, NAU636, NAU637 and NAU638, by chromosome C-banding, in situ hybridization using the A- and D-genome-specific bacterial artificial chromosome (BAC) clones 676D4 and 9M13; plasmids pAs1 and pSc119.2, and 45S rDNA; as well as genomic DNA of L. racemosus as probes, in combination with double ditelosomic test cross and SSR marker analysis. The translocation chromosomes were designated as T3AS-Lr7S, T6BS-Lr7S, and T5DS-Lr7L. The translocation line T3AS-Lr7S was highly resistant to Fusarium head blight and will be useful germplasm for resistance breeding. PMID:19539248

  4. Genetic variation among laboratory accessions of Chinese spring wheat (Triticum aestivum L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Chinese Spring (CS) wheat (Triticum aestivum L.) is commonly used in genetic research including cytogenetic analysis, molecular mapping, and germplasm development. Aneuploid lines of alien chromosomes in CS background have been used in studies with diverse objectives. Thousands of genomic and cDNA...

  5. Genetic diversity among synthetic hexaploid wheat accessions with resistance to several fungal diseases

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Synthetic hexaploid wheat (SHW) is known to be an excellent vehicle for transferring large genetic variations especially the many useful traits present in the D genome of Aegilops tauschii Coss (2n=2x=14, DD) for improvement of cultivated wheat (Triticum aestivum L., 2n=6x=42, AABBDD). The objectiv...

  6. GENES ENCODING PLASTID ACETYL-COA CARBOXYLASE AND 3-PHOSPHOGLYCERATE KINASE OF THE TRITICUM/AEGILOPS COMPLEX AND THE EVOLUTIONARY HISTORY OF POLYPLOID WHEAT.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The classic wheat evolutionary history is one of adaptive radiation of the diploid Triticum/Aegilops species (A, S, D) , genome convergence and divergence of the tetraploid (T. turgidum AABB, and T. timopheevii AAAGG) and hexaploid (T. aestivum, AABBDD) species. The objective of this study was to a...

  7. Molecular Characterization and Global Expression Analysis of Lectin Receptor Kinases in Bread Wheat (Triticum aestivum)

    PubMed Central

    Pandey, Ajay K.; Singh, Kashmir; Upadhyay, Santosh Kumar

    2016-01-01

    Lectin receptor kinases (LRKs) play a critical role in plants during development and stress conditions, but a comprehensive analysis at genome level is still not carried out in Triticum aestivum. Herein, we performed the genome wide identification, characterization and expression analysis of these genes in T. aestivum (TaLRK). In-total 263 TaLRK genes were identified, which were further classified into three groups based on the nature of lectin domain. We identified, two TaLRKs consisted of calcium-dependent lectin (C-LRK), while 84 legume-lectin (L-LRK) and 177 bulb-lectin (B-LRK) domains. The L-LRK and B-LRK genes were distributed throughout the genome of T. aestivum. Most of the TaLRKs were clustered as homologs, which were distributed either in proximity on same chromosome or on homoeologous chromosomes of A, B and D sub-genomes. A total of 9 and 58 duplication events were also predicted in L-LRK and B-LRK, respectively. Phylogenetic analysis indicated conserved evolutionary relationship of homologous and orthologous genes from multiple plant species. Gene ontology analysis indicated TaLRKs role in binding, signaling and receptor activities. Most of the TaLRKs consisted of a trans-membrane domain and predicted to be localized in the plasma-membrane. A diverse expression pattern of TaLRK genes was found in various developmental stages and stress conditions. Some TaLRKs were found to be highly affected during a particular stress, which indicated a specialized role of each LRK gene in a specific stress condition. These results described various characteristic feature and expression pattern of TaLRK genes, which will pave the way for functional characterization in wheat. PMID:27111449

  8. PCR-based analysis of the intergenic spacers of the Nor loci on the A genomes of Triticum diploids and polyploids.

    PubMed

    Sallares, R; Brown, T A

    1999-02-01

    We present DNA sequence data showing population variation in the intergenic spacer (IGS) regions of the ribosomal DNAs (rDNAs) on the A genomes of 27 diploid and polyploid wheats. PCRs (polymerase chain reactions) specific for the A(m) genome gave products with five populations of Triticum monococcum but did not give products with AABB or AABBDD wheats. PCRs specific to the A(u) genome of T. urartu gave products with all the AABB and AABBDD polyploids that were tested, but not with T. monococcum. AAGG tetraploids gave products only with the A(u)-specific primers, but the AAAAGG hexaploid T. zhukovskyi gave products with both the A(u) and A(m) primers. Phylogenetic analysis showed a substantial degree of IGS divergence for both the A(m) and A(u) genomes in diploids and polyploids compared with other genomes of Triticum and Aegilops. The rate of evolution of the IGS is much greater than previously reported for the internal transcribed region of the rDNAs but the view that the IGS only gives random noise is rejected, the IGS sequences presented here reflecting the general evolutionary trends affecting the wheat genome as a whole. PMID:10208005

  9. [Influence of D genome of wheat on expression of novel type spike branching in hybrid populations of 171ACS line].

    PubMed

    Alieva, A J; Aminov, N Kh

    2013-11-01

    A 171ACS line (AABBDD, 2n = 6x = 42) has been crossed with the tetra- (AABB and AAGG, 2n = 4x = 28) and octoploid (AAAABBGG, 2n = 8x = 56) wheat species without the D genome, as well as with hexaploid (AABBDD and AAGGDD, 2n = 6x = 42) wheat species and tetra- (AADD, 2n = 4x = 28) and hexaploid (AADDSS, 2n = 6x = 42) amphidiploids that have the D genome. The inheritance of a novel type of spike branching in these obtained hybrid populations F1-F3 was studied. According to the results of a morphogenetic analysis of hybrid populations derived from crossings between 171ACS and wheat species without the D genome, the novel type of branching was found to be controlled by a single recessive gene (although a phenotype of the 171ACS line gives a handle for a doubt about occurrence of the second gene) and the 171ACS line is a source of gene of the novel type branching. However, not a single branched spike plant was observed in hybrid populations that were produced by crosses of the 171ACS line with wheat species, as well as with amphidiploids that have the D genome. This result also experimentally confirmed the inhibitor effect of chromosomes of the D genome on the expression of the spike-branching trait. The appearance of branched spike forms, together with normal spiked plants in hybrid populations of the 171ACS line and T. araraticum Jakubz. (AAGG) or T. fungicidum Zhuk. (AAAABBGG) confirmed that, as opposed to the D genome, neither genome G nor genome B demonstrated the inhibition of the expression of the spike-branching trait. In conclusion, keeping in mind that branching is exhibited in hybrid progenies obtained from crosses between the 171ACS line and wheat species with AABB and AAGG genomes, it can be said that this gene belongs to the A genome. PMID:25470929

  10. [Influence of D genome of wheat on expression of novel type spike branching in hybrid populations of 171ACS line].

    PubMed

    2013-11-01

    A 171ACS line (AABBDD, 2n = 6x = 42) has been crossed with the tetra- (AABB and AAGG, 2n = 4x = 28) and octoploid (AAAABBGG, 2n = 8x = 56) wheat species without the D genome, as well as with hexaploid (AABBDD and AAGGDD, 2n = 6x = 42) wheat species and tetra- (AADD, 2n = 4x = 28) and hexaploid (AADDSS, 2n = 6x = 42) amphidiploids that have the D genome. The inheritance of a novel type of spike branching in these obtained hybrid populations F1-F3 was studied. According to the results of a morphogenetic analysis of hybrid populations derived from crossings between 171ACS and wheat species without the D genome, the novel type of branching was found to be controlled by a single recessive gene (although a phenotype of the 171ACS line gives a handle for a doubt about occurrence of the second gene) and the 171ACS line is a source of gene of the novel type branching. However, not a single branched spike plant was observed in hybrid populations that were produced by crosses of the 171ACS line with wheat species, as well as with amphidiploids that have the D genome. This result also experimentally confirmed the inhibitor effect of chromosomes of the D genome on the expression of the spike-branching trait. The appearance of branched spike forms, together with normal spiked plants in hybrid populations of the 171ACS line and T. araraticum Jakubz. (AAGG) or T. fungicidum Zhuk. (AAAABBGG) confirmed that, as opposed to the D genome, neither genome G nor genome B demonstrated the inhibition of the expression of the spike-branching trait. In conclusion, keeping in mind that branching is exhibited in hybrid progenies obtained from crosses between the 171ACS line and wheat species with AABB and AAGG genomes, it can be said that this gene belongs to the A genome. PMID:25508556

  11. A whole-genome, radiation hybrid map of wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Generating a reference sequence of bread wheat (Triticum aestivum L.) is a challenging task because of its large, highly repetitive and allopolyploid genome. Ordering of BAC- and NGS-based contigs in ongoing wheat genome-sequencing projects primarily uses recombination and comparative genomics-base...

  12. Fertilizing wheat with dried sludge. [Triticum aestivum

    SciTech Connect

    Day, A.D.; Thompson, R.K.

    1986-09-01

    The purpose of a three-year experiment at the Mesa Agricultural Experiment Station in Arizona was to compare the performance of wheat (Triticum aestivum L.) cultivars grown on soils treated with dried sewage sludge with the growth and grain yield of the same cultivars fertilized with commercial inorganic fertilizers. Many researchers have obtained increased crop yields by using sludge as a fertilizer source (see Literature Cited). Some have shown that the growth rates of crops planted on a sandy soil were similar when soil was treated with either sludge or commercial fertilizer, while others reported that N, P and K released from sludge incorporated into a sandy loam soil increased grain yields of corn. A survey of various municipal sludges found a widespread range of trace metal elements. Plant availability of metals has been found to be influenced by the type and the rate of sludge applied but not directly to the concentrations of trace metals in the sludge.

  13. [Research advances in wheat (Triticum aestivum) allelopathy].

    PubMed

    Zhang, Xiaoke; Jiang, Yong; Liang, Wenju; Kong, Chuihua

    2004-10-01

    Wheat (Triticum aestivum) is the main food crop in the world, and plays an important role in agricultural production. In order to enhance wheat yield, herbicides and germicides were intensively applied and made negative effects on the environment. Wheat possesses allelopathic potential for weed suppression and disease control through the release of secondary metabolites from its living plants or residues, which could avoid the environment pollution brought by herbicides and germicides. This paper reviewed the research advances in wheat allelopathy. Hydroxamic acids and phenolic acids are the predominant allelochemicals frequently reported which could produce plant natural defense against weed, pest and disease. The allelopathic activity of allelochemicals is determined not only by the allelochemicals, but also by the factors of inheritance, environment and biology. The retention, transportation and transformation processes of allelochemicals, and the relationship between wheat allelopathy and soil biota and its mechanism were seldom studied and still needed to be researched profoundly. Utilizing wheat allelopathy in plant protection, environment protection and crop breeding would improve the stress-resistance, yield and quality of wheat in agricultural production. PMID:15624846

  14. [Cytogenetic analysis of alloplasmic recombinant lines (H. vulgare)-T. aestivum with unstable fertility and viability].

    PubMed

    Badaeva, E D; Pershina, L A; Bil'danova, L L

    2006-02-01

    Comparative cytogenetic analysis was performed with four alloplasmic recombinant (Hordeum vulgare)-Triticum aestivum lines differing in morphological traits, number of seeds per spike, and seed plumpness. None of the lines displayed introgression of the barley genetic material: the karyotypes included only common wheat chromosomes. Two lines, 79(B) and 79(D), were cytogenetically stable. Plants of lines 79(A) and 79(C) displayed a high frequency of unbalanced chromosome aberrations, including dicentric and polycentric chromosomes, terminal deletions varying in size, acentric fragments, and multiple unidentifiable translocations. Previous studies of the mitochondrial genome showed that the two cytologically unstable lines, which were also unstable in fertility and viability, are characterized by heteroplasmy at the mitochondrial 18S-5S locus (simultaneous presence of barley and wheat fragments). Stable lines 79(B) and 79(D) with normal fertility contained only wheat mitochondrial markers. It was assumed that the substantial instability of the nuclear genome in lines 79(C) and 79(A) was a result of nuclear-cytoplasmic incompatibility and was associated with heteroplasmy, while elimination or considerable reduction of barley material in the mitochondrial genome stabilized the nuclear genome of lines 79(B) and 79(D). In turn, the instability of the nuclear genome was responsible for a decrease in viability and fertility of plants. PMID:16583704

  15. Radiation hybrid maps of D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The large and complex genome of bread wheat (Triticum aestivum L., ~17 Gb) requires high-resolution genome maps saturated with ordered markers to assist in anchoring and orienting BAC contigs/ sequence scaffolds for whole genome sequence assembly. Radiation hybrid (RH) mapping has proven to be an e...

  16. Genetic Diversity, Population Structure, and Linkage Disequilibrium in Bread Wheat (Triticum aestivum L.).

    PubMed

    Tascioglu, Tulin; Metin, Ozge Karakas; Aydin, Yildiz; Sakiroglu, Muhammet; Akan, Kadir; Uncuoglu, Ahu Altinkut

    2016-08-01

    Bread wheat (Triticum aestivum L.) gene pool was analyzed with 117 microsatellite markers scattered throughout A, B, and D genomes. Ninety microsatellite markers were giving 1620 polymorphic alleles in 55 different bread wheat genotypes. These genotypes were found to be divided into three subgroups based on Bayesian model and Principal component analysis. The highest polymorphism information content value for the markers resides on A genome was estimated for wmc262 marker located on 4A chromosome with the polymorphism information content value of 0.960. The highest polymorphism information content value (0.954) among the markers known to be located on B genome was realized for wmc44 marker located on 1B chromosome. The highest polymorphism information content value for the markers specific to D genome was found in gwm174 marker located on 5D chromosome with the polymorphism information content value of 0.948. The presence of linkage disequilibrium between 81 pairwise SSR markers reside on the same chromosome was tested and very limited linkage disequilibrium was observed. The results confirmed that the most distant genotype pairs were as follows Ceyhan-99-Behoth 6, Gerek 79-Douma 40989, and Karahan-99-Douma 48114. PMID:27048293

  17. [Hybrids of Aegilops cylindrica Host with Triticum durum Desf. and T. aestivum L].

    PubMed

    Avsenin, V I; Motsnyĭ, A I; Rybalka, A I; Faĭt, V I

    2003-01-01

    The hybrids of durum and bread wheat with Ae. cylindrica have been obtained without using an embryo rescue technique. The hybrid output (of pollinated flower number) in the field conditions scored 1.0, 15.3 and 10.0% in the crosses T. durum x Ae. cylindrica, Ae. cylindrica x T. durum and T. aestivum x Ae. cylindrica, respectively. A high level of meiotic chromosome pairing between homologous D genomes of bread wheat and Aegilops has been revealed (c = 80.0-83.7%). The possibility of homoeological pairing between wheat and Ae. cylindrica chromosomes has been shown. Herewith, the correlation between the levels of homological and homoeological pairing is absent. The possibilities of genetic material interchange, including between the tetraploid species, as well as the using of Ae. cylindrica cytoplasm for durum wheat breeding are discussed. PMID:12741056

  18. Novel and conserved heat-responsive microRNAs in wheat (Triticum aestivum L.).

    PubMed

    Kumar, Ranjeet Ranjan; Pathak, Himanshu; Sharma, Sushil Kumar; Kala, Yugal Kishore; Nirjal, Mahesh Kumar; Singh, Gyanendra Pratap; Goswami, Suneha; Rai, Raj Deo

    2015-05-01

    MicroRNAs (miRNAs) are small endogenous RNAs of ~22 nucleotides that have been shown to play regulatory role by negatively affecting the expression of genes at the post-transcriptional level. Information of miRNAs on some important crops like soybean, Arabidopsis, and rice, etc. are available, but no study on heat-responsive novel miRNAs has yet been reported in wheat (Triticum aestivum L.). In the present investigation, a popular wheat cultivar HD2985 was used in small RNA library construction and Illumina HiSeq 2000 was used to perform high-throughput sequencing of the library after cluster generation; 110,896,604 and 87,743,861 reads were generated in the control (22 °C) and heat-treated (42 °C for 2 h) samples, respectively. Forty-four precursor and mature miRNAs were found in T. aestivum from miRBase v 19. The frequencies of the miRNA families varied from 2 (tae-miR1117) to 60,672 (tae-miR159b). We identify 1052 and 902 mature miRNA sequences in HD2985 control and HS-treated samples by mapping on reference draft genome of T. aestivum. Maximum identified miRNAs were located on IWGSC_CSS_3B_scaff (chromosome 3B). We could identify 53 and 46 mature miRNA in the control and HS samples and more than 516 target genes by mapping on the reference genome of Oryza sativa, Zea mays, and Sorghum bicolor. Using different pipelines and plant-specific criteria, 37 novel miRNAs were identified in the control and treated samples. Six novel miRNA were validated using qRT-PCR to be heat-responsive. A negative correlation was, however, observed between the expression of novel miRNAs and their targets. Target prediction and pathway analysis revealed their involvement in the heat stress tolerance. These novel miRNAs are new additions to miRNA database of wheat, and the regulatory network will be made use of in deciphering the mechanism of thermotolerance in wheat. PMID:25480755

  19. Novel nuclear-cytoplasmic interaction in wheat (Triticum aestivum) induces vigorous plants.

    PubMed

    Soltani, Ali; Kumar, Ajay; Mergoum, Mohamed; Pirseyedi, Seyed Mostafa; Hegstad, Justin B; Mazaheri, Mona; Kianian, Shahryar F

    2016-03-01

    Interspecific hybridization can be considered an accelerator of evolution, otherwise a slow process, solely dependent on mutation and recombination. Upon interspecific hybridization, several novel interactions between nuclear and cytoplasmic genomes emerge which provide additional sources of diversity. The magnitude and essence of intergenomic interactions between nuclear and cytoplasmic genomes remain unknown due to the direction of many crosses. This study was conducted to address the role of nuclear-cytoplasmic interactions as a source of variation upon hybridization. Wheat (Triticum aestivum) alloplasmic lines carrying the cytoplasm of Aegilops mutica along with an integrated approach utilizing comparative quantitative trait locus (QTL) and epigenome analysis were used to dissect this interaction. The results indicate that cytoplasmic genomes can modify the magnitude of QTL controlling certain physiological traits such as dry matter weight. Furthermore, methylation profiling analysis detected eight polymorphic regions affected by the cytoplasm type. In general, these results indicate that novel nuclear-cytoplasmic interactions can potentially trigger an epigenetic modification cascade in nuclear genes which eventually change the genetic network controlling physiological traits. These modified genetic networks can serve as new sources of variation to accelerate the evolutionary process. Furthermore, this variation can synthetically be produced by breeders in their programs to develop epigenomic-segregating lines. PMID:26860316

  20. Genomic selection for quantitative adult plant stem rust resistance in wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Quantitative adult plant resistance (APR) to stem rust (Puccinia graminis f. sp. tritici) is an important breeding target in wheat (Triticum aestivum L.) and a potential target for genomic selection (GS). To evaluate the relative importance of known APR loci in applying genomic selection, we charact...

  1. Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cycles of whole genome duplication (WGD) and diploidization are hallmarks of eukaryotic genome evolution and speciation. Polyploid wheat (Triticum aestivum) has had a massive increase in genome size largely due to recent WGDs. How these processes may impact the dynamics of gene evolution was studied...

  2. Nature's Anti-Alzheimer's Drug: Isolation and Structure Elucidation of Galantamine from "Leucojum Aestivum"

    ERIC Educational Resources Information Center

    Halpin, Catherine M.; Reilly, Ciara; Walsh, John J.

    2010-01-01

    The discovery that galantamine penetrates the blood-brain barrier has led to its clinical use in the treatment of choline-deficiency conditions in the brain, such as Alzheimer's disease. This experiment involves the isolation and structure elucidation of galantamine from "Leucojum aestivum". Isolation of the alkaloid constituents in "L. aestivum"…

  3. Genetic effect of the Aegilops caudata plasmon on the manifestation of the Ae. cylindrica genome.

    PubMed

    Tsunewaki, Koichiro; Mori, Naoki; Takumi, Shigeo

    2014-01-01

    In the course of reconstructing Aegilops caudata from its own genome (CC) and its plasmon, which had passed half a century in common wheat (genome AABBDD), we produced alloplasmic Ae. cylindrica (genome CCDD) with the plasmon of Ae. caudata. This line, designated (caudata)-CCDD, was found to express male sterility in its second substitution backcross generation (SB2) of (caudata)-AABBCCDD pollinated three times with the Ae. cylindrica pollen. We repeatedly backcrossed these SB2 plants with the Ae. cylindrica pollen until the SB5 generation, and SB5F2 progeny were produced by self-pollination of the SB5 plants. Thirteen morphological and physiological characters, including pollen and seed fertilities, of the (caudata)-CCDD SB5F2 were compared with those of the euplasmic Ae. cylindrica. The results indicated that the male sterility expressed by (caudata)-CCDD was due to genetic incompatibility between the Ae. cylindrica genome and Ae. caudata plasmon that did not affect any other characters of Ae. cylindrica. Also, we report that the genome integrity functions in keeping the univalent transmission rate high. PMID:25832746

  4. An intervarietal genetic linkage map of Indian bread wheat (Triticum aestivum L.) and QTL maps for some metric traits.

    PubMed

    Nalini, E; Bhagwat, S G; Jawali, N

    2007-06-01

    Bread wheat (Triticum aestivum L.) exhibits very narrow genetic diversity and hence there is high relatedness among cultivated varieties. However, a population generated from an intervarietal cross, with the parents differing in a large number of traits, could lead to the generation of QTL maps which will be useful in practice. In this report a genetic linkage map of wheat is constructed using a cross between two Indian bread wheat varieties: Sonalika and Kalyansona. The linkage map consisted of 236 markers and spanned a distance of 3639 cM, with 1211.2 cM for the A genome, 1669.2 cM for the B genome, 192.4 cM for the D genome and 566.2 cM for unassigned groups. Linkage analysis defined 37 linkage groups of which 24 were assigned to 17 chromosomes. The genetic map was used to identify QTLs by composite internal mapping (CIM) for three metric traits, viz. culm length (CL), flag leaf length (FLL) and flag leaf breadth (FLB). Of 25 QTLs identified in this study, 15 have not been reported previously. Multitrait CIM (MCIM) analysis was carried out for traits that were significantly correlated such as FLB-FLL and CL-FLB-FLL. Detection of a large number of QTLs for the three traits analysed suggests that in parent cultivars that are not too diverse, the differences at genetic level detected as polymorphisms may be mostly associated with QTLs for the observed differences. PMID:17894910

  5. Determination of flavonoids in Triticum aestivum L. treated with ampicillin

    NASA Astrophysics Data System (ADS)

    Soran, M. L.; Opriş, O.; Copaciu, F.; Varodi, C.

    2012-02-01

    Pharmaceutical residues in the environment, and their potential toxic effects, have been recognized as one of the emerging research area in the environmental chemistry. Antibiotics can reach plants from treated soil or due to irrigation. The flavonoids extraction from Triticum aestivum L. treated with ampicillin and separation of flavonoids are presented in this study. There were used classical and modern extraction techniques (maceration, microwave assisted solvents, etc). The efficiency of extraction process was spectrophotometricaly evaluated by determining the total flavonoids content and by HPTLC on silica gel plates using the mixture: carbon tetrachloride - acetone - formic acid (35:11:3, v/v) as mobile phase. The developed plates were inspected both in ultraviolet and visible after visualization with NTS reagent (diphenylboryloxyethylamin). The chromatographic plates were compared in respect to determine the changes in extract composition due to the different extraction techniques. Depending on the concentration of ampicillin administered to plants, comparative studies on flavonoids content were performed.

  6. New evidence for the symbiosis between Tuber aestivum and Picea abies.

    PubMed

    Stobbe, Ulrich; Stobbe, Annika; Sproll, Ludger; Tegel, Willy; Peter, Martina; Büntgen, Ulf; Egli, Simon

    2013-11-01

    The Burgundy truffle (Tuber aestivum Vittad.), an ectomycorrhizal fungus living in association with host plants, is one of the most exclusive delicacies. The symbiosis with deciduous oak, beech, and hazel dominates our concept of truffle ecophysiology, whereas potential conifer hosts have rarely been reported. Here, we present morphological and molecular evidence of a wildlife T. aestivum symbiosis with Norway spruce (Picea abies Karst.) and an independent greenhouse inoculation experiment, to confirm our field observation in southwest Germany. A total of 27 out of 50 P. abies seedlings developed T. aestivum ectomycorrhizae with a mean mycorrhization rate of 19.6 %. These findings not only suggest P. abies to be a productive host species under suitable biogeographic conditions but also emphasize the broad ecological amplitude and great symbiotic range of T. aestivum. While challenging common knowledge, this study demonstrates a significant expansion of the species' cultivation potential to the central European regions, where P. abies forests occur on calcareous soils. PMID:23674121

  7. Implication of Triticum searsii as the B-genome donor to wheat using DNA hybridizations.

    PubMed

    Nath, J; McNay, J W; Paroda, C M; Gulati, S C

    1983-08-01

    In vitro DNA:DNA hybridizations and hydroxyapatite thermal chromatography were employed to help identify the species ancestral to the B genome of the polyploid wheats. We hybridized 3H-Triticum aestivum DNA to the unlabeled DNAs of T. urartu, T. speltoides, T. sharonensis, T. bicorne, T. longissimum, and T. searsii, 3H-Labeled DNA of T. urartu was hybridized with the DNA of a synthetic tetraploid. AADD. The heteroduplex thermal stabilities indicated that T. searsii was most closely related to T. aestivum (ABD) and that the genome of T. urartu was more closely related to the A genome than the B genome. The degree of reassociation which may have occurred between the six diploid species and the D genome of T. aestivum was evaluated by hybridizing 3H-T. tauschii DNA with the DNAs of the diploids. The results indicated that T. urartu had the least sequence homology to T. tauschii, the D-genome donor lending additional support to the conclusion that T. urartu is related to the A genome. Thus, it is highly probable that T. searsii is the B-genome donor to the polyploid wheats or a major chromosome donor if the B genome is, in fact, polyphyletic in origin. PMID:6626143

  8. Competition increases sensitivity of wheat (Triticum aestivum) to biotic plant-soil feedback.

    PubMed

    Hol, W H Gera; de Boer, Wietse; ten Hooven, Freddy; van der Putten, Wim H

    2013-01-01

    Plant-soil feedback (PSF) and plant competition play an important role in structuring vegetation composition, but their interaction remains unclear. Recent studies suggest that competing plants could dilute pathogenic effects, whereas the standing view is that competition may increase the sensitivity of the focal plant to PSF. In agro-ecosystems each of these two options would yield contrasting outcomes: reduced versus enhanced effects of weeds on crop biomass production. To test the effect of competition on sensitivity to PSF, we grew Triticum aestivum (Common wheat) with and without competition from a weed community composed of Vicia villosa, Chenopodium album and Myosotis arvensis. Plants were grown in sterilized soil, with or without living field inoculum from 4 farms in the UK. In the conditioning phase, field inocula had both positive and negative effects on T. aestivum shoot biomass, depending on farm. In the feedback phase the differences between shoot biomass in T. aestivum monoculture on non-inoculated and inoculated soils had mostly disappeared. However, T. aestivum plants growing in mixtures in the feedback phase were larger on non-inoculated soil than on inoculated soil. Hence, T. aestivum was more sensitive to competition when the field soil biota was present. This was supported by the statistically significant negative correlation between shoot biomass of weeds and T. aestivum, which was absent on sterilized soil. In conclusion, competition in cereal crop-weed systems appears to increase cereal crop sensitivity to soil biota. PMID:23776610

  9. EVALUATION OF GENETIC DIVERSITY AND GENOME-WIDE LINKAGE DISEQUILIBRIUM AMOUNG US WHEAT (TRITICUM AETIVUM L.) GERMPLASM REPRESENTING DIFFERENT MARKET CLASSES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity and genome-wide linkage disequilibrium (LD) were investigated among forty-three US wheat (Triticum aestivum L.) elite cultivars and breeding lines representing seven US wheat market classes using 242 wheat genomic simple sequence repeat (SSR) markers distributed throughout the whea...

  10. Draft genome sequence of the phenazine-producing Pseudomonas fluorescens strain 2-79

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pseudomonas fluorescens strain 2-79, a natural isolate of the rhizosphere of wheat (Triticum aestivum L.), possesses antagonistic potential toward several fungal pathogens. We report the draft genome sequence of strain 2-79, which comprises 5,674 protein-coding sequences....

  11. Genetic gain from phenotypic and genomic selection for quantitative resistance to stem rust of wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Stem rust of wheat (Triticum aestivum L.), caused by Puccinia graminis f. sp. tritici, is a globally important disease that can cause severe yield loss. Breeding for quantitative stem rust resistance (QSRR) is important for developing cultivars with durable resistance. Genomic selection (GS) could i...

  12. Tuber aestivum Vittad. mycelium quantified: advantages and limitations of a qPCR approach.

    PubMed

    Gryndler, Milan; Trilčová, Jana; Hršelová, Hana; Streiblová, Eva; Gryndlerová, Hana; Jansa, Jan

    2013-07-01

    A quantitative real-time PCR (qPCR) marker Ta0 with hydrolysis probe ("TaqMan"), targeted to the internal transcribed spacer region of the ribosomal DNA, has been developed for quantification of summer truffle (Tuber aestivum) mycelium. Gene copy concentrations determined by the qPCR were calibrated against pure culture mycelium of T. aestivum, enabling quantification of the mycelium in soil and in host roots from the fields. Significant concentrations of the fungus were observed not only in the finest roots with ectomycorrhizae but also in other root types, indicating that the fungus is an important component of the microbial film at the root surface. The concentration of T. aestivum in soil is relatively high compared to other ectomycorrhizal fungi. To evaluate the reliability of the measurement of the soil mycelium density using qPCR, the steady basal extracellular concentration of the stabilized T. aestivum DNA should be known and taken into account. Therefore, we addressed the stability of the qPCR signal in soil subjected to different treatments. After the field soil was sieved, regardless of whether it was dried/rewetted or not, the T. aestivum DNA was quickly decomposed. It took just about 4 days to reach a steady concentration. This represents a conserved pool of T. aestivum DNA and determines detection limit of the qPCR quantification in our case. When the soil was autoclaved and recolonized by saprotrophic microorganisms, this conserved DNA pool was eliminated and the soil became free of T. aestivum DNA. PMID:23271632

  13. Transgenic approach to improve wheat (Triticum aestivum L.) nutritional quality.

    PubMed

    Tamás, Cecília; Kisgyörgy, Boglárka N; Rakszegi, Mariann; Wilkinson, Mark D; Yang, Moon-Sik; Láng, László; Tamás, László; Bedo, Zoltán

    2009-07-01

    An amaranth (Amaranthus hypochondriacus) albumin gene, encoding the 35-kDa AmA1 protein of the seed, with a high content of essential amino acids, was used in the biolistic transformation of bread wheat (Triticum aestivum L.) variety Cadenza. The transformation cassette carried the ama1 gene under the control of a powerful wheat endosperm-specific promoter (1Bx17 HMW-GS). Southern-blot analysis of T(1) lines confirmed the integration of the foreign gene, while RT-PCR and Western-blot analyses of the samples confirmed the transcription and translation of the transgene. The effects of the extra albumin protein on the properties of flour, produced from bulked T(2) seeds, were calculated using total protein and essential amino acid content analysis, polymeric/monomeric protein and HMW/LMW glutenin subunit ratio measurements. The results indicated that not only can essential amino acid content be increased, but some parameters associated with functional quality may also be improved because of the expression of the AmA1 protein. PMID:19466426

  14. Genetic diversity in bread wheat (Triticum aestivum L.) genotypes.

    PubMed

    Degewione, A; Alamerew, S

    2013-11-01

    Wheat is one most important cereal crops grown in Ethiopia. Yet, keeping in view insufficient information on exotic bread wheat genotypes is limiting the access to useful traits present among the genotypes in the Somali region of Ethiopia. The aim of the study was to assess the extent of genetic diversity among bread wheat genotypes. Twenty six bread wheat (Triticum aestivum L.) genotypes obtained from ICARDA-CIMMYT were tested at Gode and Kelafo research sites at three cropping seasons (2009/10, 2010/11 and 2011/12) under irrigation. The experiment was conducted in randomized complete block design with three replications. Ten agronomic traits were included in the study. The mean values, ranges and the coefficient of variation of the 10 characters indicated the existence of sufficient variability among genotypes. Multivariate techniques were used to classify 26 bread wheat genotypes. Principal component analysis showed that the first six principal components explained about 91.87% of the total variation. D2 analysis showed the 26 bread wheat genotypes grouped into six clusters. This made to become moderate diversity among the genotypes. The crosses between genotypes selected from cluster-III with cluster-VI and cluster V with cluster VI are expected to produce better genetic recombination and segregation in their progenies. Therefore, these bread wheat genotypes need to be crossed and selected to develop high yielding pure line variety. PMID:24511742

  15. From genome to gene: a new epoch for wheat research?

    PubMed

    Wang, Meng; Wang, Shubin; Xia, Guangmin

    2015-06-01

    Genetic research for bread wheat (Triticum aestivum), a staple crop around the world, has been impeded by its complex large hexaploid genome that contains a high proportion of repetitive DNA. Recent advances in sequencing technology have now overcome these challenges and led to genome drafts for bread wheat and its progenitors as well as high-resolution transcriptomes. However, the exploitation of these data for identifying agronomically important genes in wheat is lagging behind. We review recent wheat genome sequencing achievements and focus on four aspects of strategies and future hotspots for wheat improvement: positional cloning, 'omics approaches, combining forward and reverse genetics, and epigenetics. PMID:25887708

  16. Antidiabetic and Antioxidant Properties of Triticum aestivum in Streptozotocin-Induced Diabetic Rats.

    PubMed

    Mohan, Yogesha; Jesuthankaraj, Grace Nirmala; Ramasamy Thangavelu, Narendhirakannan

    2013-01-01

    The antidiabetic and antioxidant potential of Triticum aestivum were evaluated by using in vivo methods in normal and streptozotocin-induced diabetic rats. Diabetes was induced in the Wistar strain albino rats by injecting streptozotocin at a dose of 55 mg/kg body weight. Ethanolic extracts of Triticum aestivum at doses of 100 mg/kg body weight were administered orally for 30 days. Various parameters were studied and the treatment group with the extract showed a significant increase in the liver glycogen and a significant decrease in fasting blood glucose, glycosylated hemoglobin levels, and serum marker enzyme levels. The total cholesterol and serum triglycerides levels, low density lipoprotein, and very low density lipoprotein were also significantly reduced and the high density lipoprotein level was significantly increased upon treatment with the Triticum aestivum ethanol extract. A significant decrease in the levels of lipid peroxides, superoxide dismutase, and glutathione peroxidise and increase in the levels of vitamin E, catalase, and reduced glutathione were observed in Triticum aestivum treated diabetic rats. Thus, from this study we conclude that ethanolic extract of Triticum aestivum exhibited significant antihyperglycemic, hypolipidemic, and antioxidant activities in streptozotocin-induced diabetic rats. PMID:24416041

  17. [Development of Triticum aestivum-Haynaldia villosa 6VS ditelosomic substitution line via phlb mutant].

    PubMed

    Chen, J F; Ying, J; Wang, S L; Liu, Z H; Qi, L L; Chen, P D

    2001-01-01

    Chinese Spring phlb mutant (C S phlbphlb) was crossed to Triticum aestivum-Haynaldia villosa 6V (6A) alien substitution line and F1 back was crossed with C. S phlbphlb. One LV 02 with varied H. villosa 6V chromosome and one LV 02-01 with 40 T. aestivum chromosome, one H. villosa 6V and 6VS chromosome were screened in BC1F1 and BC1F2 respectively by C-banding and the fluorescence in situ hybridization (FISH). In segregated generation of LV 02-01, eight T. aestivum-H. villosa 6VS ditelosomic substitution lines were screened by FISH and C-banding. PMID:11209712

  18. Role of Triticum aestivum aqueous extract in glucocorticoid induced osteoporosis in rats.

    PubMed

    Banji, David; Banji, Otilia J F; Chiluka, Vijaya Laxmi; Abbagoni, Saidulu

    2014-02-01

    Administration of aqueous extract of T. aestivum (200 and 400 mg/kg/day, po, for 30 days) and risedronate (20 microg/kg, sc, five times a week for 30 days) following methyl prednisolone sodium succinate (10 mg/kg, sc, thrice a week for 4 weeks) induced osteoporosis in Wistar rats showed an increase in the serum levels of bone mineral content markers, decrease in the serum and urinary levels of bone resorption markers. An incline in strength of femur and tibia was seen particularly with 400 mg/kg of T. aestivum. Maintenance of calcium homeostasis, formation of collagen and scavenging of free radicals can plausibly be the mode of action of aqueous extract of T. aestivum thereby combating osteoporosis induced by glucocorticoids. PMID:24597148

  19. Metabolite profiling of wheat (Triticum aestivum L.) phloem exudate

    PubMed Central

    2014-01-01

    Background Biofortification of staple crops with essential micronutrients relies on the efficient, long distance transport of nutrients to the developing seed. The main route of this transport in common wheat (Triticum aestivum) is via the phloem, but due to the reactive nature of some essential micronutrients (specifically Fe and Zn), they need to form ligands with metabolites for transport within the phloem. Current methods available in collecting phloem exudate allows for small volumes (μL or nL) to be collected which limits the breadth of metabolite analysis. We present a technical advance in the measurement of 79 metabolites in as little as 19.5 nL of phloem exudate. This was achieved by using mass spectrometry based, metabolomic techniques. Results Using gas chromatography–mass spectrometry (GC-MS), 79 metabolites were detected in wheat phloem. Of these, 53 were identified with respect to their chemistry and 26 were classified as unknowns. Using the ratio of ion area for each metabolite to the total ion area for all metabolites, 39 showed significant changes in metabolite profile with a change in wheat reproductive maturity, from 8–12 to 17–21 days after anthesis. Of these, 21 were shown to increase and 18 decreased as the plant matured. An amine group derivitisation method coupled with liquid chromatography MS (LC-MS) based metabolomics was able to quantify 26 metabolites and semi-quantitative data was available for a further 3 metabolites. Conclusions This study demonstrates that it is possible to determine metabolite profiles from extremely small volumes of phloem exudate and that this method can be used to determine variability within the metabolite profile of phloem that has occurred with changes in maturity. This is also believed to be the first report of the presence of the important metal complexing metabolite, nicotianamine in the phloem of wheat. PMID:25143779

  20. Production of galanthamine by Leucojum aestivum shoots grown in different bioreactor systems.

    PubMed

    Schumann, Anika; Berkov, Strahil; Claus, Diana; Gerth, André; Bastida, Jaume; Codina, Carles

    2012-08-01

    The production of galanthamine by shoots of Leucojum aestivum grown in different bioreactor systems (shaking and nonshaking batch culture, temporary immersion system, bubble bioreactor, continuous and discontinuous gassing bioreactor) under different culture conditions was studied. The influence of the nutrient medium, weight of inoculum, and size of bioreactor on both growth and galanthamine production was studied. The maximal yield of galanthamine (19.416 mg) was achieved by cultivating the L. aestivum shoots (10 g of fresh inoculum) in a temporary immersion system in a 1-L bioreactor vessel which was used as an airlift culture vessel, gassing 12 times per day (5 min). PMID:22639366

  1. TYPES AND RATES OF SEQUENCE EVOLUTION AT HMW-GLUTENIN LOCUS IN HEXAPLOID WHEAT AND ITS ANCESTRAL GENOMES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Glu-1 locus, encoding the High Molecular Weight-glutenin protein subunits, controls bread-making quality in hexaploid wheat (Triticum aestivum) and represents a recently evolved region unique to Triticeae genomes. To understand the molecular evolution of this locus region, three orthologous Glu...

  2. Conserved globulin gene across eight grass genomes identify fundamental units of the loci encoding seed storage proteins

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The wheat high molecular weight (HMW)-glutenins are important seed storage proteins that determine bread-making quality in hexaploid wheat (Triticum aestivum). In this study, detailed comparative sequence analyses of large orthologous HMW-glutenin genomic regions from eight grass species, represent...

  3. DNA methylation pattern of Photoperiod-B1 is associated with photoperiod insensitivity in wheat (Triticum aestivum).

    PubMed

    Sun, Han; Guo, Zhiai; Gao, Lifeng; Zhao, Guangyao; Zhang, Wenping; Zhou, Ronghua; Wu, Yongzhen; Wang, Haiyang; An, Hailong; Jia, Jizeng

    2014-11-01

    As one of the three key components of the 'Green Revolution', photoperiod insensitivity is vital for improved adaptation of wheat (Triticum aestivum) cultivars to a wider geographical range. Photoperiod-B1a (Ppd-B1a) is one of the major genes that confers photoperiod insensitivity in 'Green Revolution' varieties, and has made a significant contribution to wheat yield improvement. In this study, we investigated the mechanisms underlying the photoperiod insensitivity of Ppd-B1a alleles from an epigenetic perspective using a combination of bisulfite genomic sequencing, orthologous comparative analysis, association analysis, linkage analysis and gene expression analysis. Based on the study of a large collection of wheat germplasm, we report two methylation haplotypes of Ppd-B1 and demonstrate that the higher methylation haplotype (haplotype a) was associated with increased copy numbers and higher expression levels of the Ppd-B1 gene, earlier heading and photoperiod insensitivity. Furthermore, assessment of the distribution frequency of the different methylation haplotypes suggested that the methylation patterns have undergone selection during the wheat breeding process. Our study suggests that DNA methylation in the regulatory region of the Ppd-B1 alleles, which is closely related to copy number variation, plays a significant role in wheat breeding, to confer photoperiod insensitivity and better adaptation to a wider geographical range. PMID:25078249

  4. Evaluation of assembly strategies using RNA-seq data associated with grain development of wheat (Triticum aestivum L.).

    PubMed

    Li, Huai-Zhu; Gao, Xiang; Li, Xiao-Yan; Chen, Qi-Jiao; Dong, Jian; Zhao, Wan-Chun

    2013-01-01

    Wheat (Triticum aestivum L.) is one of the most important crops cultivated worldwide. Identifying the complete transcriptome of wheat grain could serve as foundation for further study of wheat seed development. However, the relatively large size and the polyploid complexity of the genome have been substantial barriers to molecular genetics and transcriptome analysis of wheat. Alternatively, RNA sequencing has provided some useful information about wheat genes. However, because of the large number of short reads generated by RNA sequencing, factors that are crucial to transcriptome assembly, including software, candidate parameters and assembly strategies, need to be optimized and evaluated for wheat data. In the present study, four cDNA libraries associated with wheat grain development were constructed and sequenced. A total of 14.17 Gb of high-quality reads were obtained and used to assess different assembly strategies. The most successful approach was to filter the reads with Q30 prior to de novo assembly using Trinity, merge the assembled contigs with genes available in wheat cDNA reference data sets, and combine the resulting assembly with an assembly from a reference-based strategy. Using this approach, a relatively accurate and nearly complete transcriptome associated with wheat grain development was obtained, suggesting that this is an effective strategy for generation of a high-quality transcriptome from RNA sequencing data. PMID:24349528

  5. Development of a set of compensating Triticum aestivum-Dasypyrum villosum Robertsonian translocation lines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dasypyrum villosum (L.) Candargy, a wild relative of bread wheat (Triticum aestivum L.) is the source of agronomically important genes for wheat improvement. The first step in exploiting this variation is the production of compensating Robertsonian translocations (cRobTs) consisting of D. villosum c...

  6. Inheritance of grain polyphenol oxidase (PPO) activity in multiple wheat (Triticum aestivum L.) genetic backgrounds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Grain polyphenol oxidase (PPO) activity can cause discoloration of wheat (Triticum aestivum L.) food products. Five crosses (PI 117635/Antelope; Fielder/NW03681; Fielder/Antelope; NW07OR1070/Antelope; NW07OR1066/OR2050272H) were selected to study the genetic inheritance of PPO activity. STS marker...

  7. Distribution of cadmium, iron and zinc in millstreams of hard winter wheat (Triticum aestivum L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Hard winter wheat (Triticum aestivum L.) is a major crop in the Great Plains of the United 14 States, and our previous work demonstrated that wheat genotypes vary for grain cadmium 15 accumulation, with some exceeding the CODEX standard (0.2 mg kg-1). Previous reports of 16 cadmium distribution in ...

  8. Ractopamine uptake by alfalfa (Medicago sativa) and wheat (Triticum aestivum) from soil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ractopamine is a beta adrenergic agonist used as a growth promoter in swine, cattle and turkeys. To test whether ractopamine has the potential to accumulate in plants grown in contaminated soil, a greenhouse study was conducted with alfalfa (Medicago sativa) and wheat (Triticum aestivum) grown in t...

  9. A review of the occurrence of grain softness protein-1 genes in wheat (Triticum aestivum L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Grain softness protein-1 (Gsp-1) is a small, 495-bp intronless gene found throughout the Triticeae tribe at the distal end of group 5 chromosomes. With the Puroindolines, it constitutes a key component of the Hardness locus. In the polyploid wheats, Triticum aestivum and T. turgidum, the gene is pr...

  10. Did the house mouse (Mus musculus L.) shape the evolutionary trajectory of wheat (Triticum aestivum L.)?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Wheat (Triticum aestivum L.) is one of the most successful domesticated plant species in the world. The majority of wheat carries mutations in the Puroindoline genes that result in a hard kernel phenotype. An explanation as to the selection of these hard-kernel mutations has not been established. He...

  11. Nitrogen and Water Stress Impacts Hard Red Spring Wheat (Triticum aestivum) Canopy Reflectance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Remote sensing offers a simple, time efficient method for making in-season nitrogen (N) recommendations for spring wheat (Triticum aestivum). However, spectral crop reflectance can be confounded by water and N stress that simultaneously impact protein content and yields. The objective of this stu...

  12. In vitro effect of wheat bran (Triticum aestivum) extract on calcium oxalate urolithiasis crystallization.

    PubMed

    Sekkoum, Khaled; Cheriti, Abdelkrim; Taleb, Safia

    2011-10-01

    Urolithiasis can lead to the loss of renal function in some cases. In this study, we tested the inhibiting effect of wheat bran (Triticum aestivum L) extract on calcium oxalate crystallization in a turbidimetric model, by FTIR spectroscopy, and polarized microscopy. The results show that this plant extract has a major inhibitory effect on calcium oxalate crystallization. PMID:22164778

  13. Metabolic Pathways of the Wheat (Triticum aestivum)Endosperm Amyloplast Revealed by Proteomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    By definition, amyloplasts are plastids specialized for starch production. However, amyloplasts have a broader range of functions that are not widely recognized. A recent proteomic study of amyloplasts isolated from wheat (Triticum aestivum Butte 86) endosperm suggested that they share many of the ...

  14. Biochemical data bearing on the relationship between the genome of Triticum urartu and the A and B genomes of the polyploid wheats.

    PubMed

    Kerby, K; Kuspira, J; Jones, B L

    1988-08-01

    To determine whether the Triticum urartu genome is more closely related to the A or B genome of the polyploid wheats, the amino acid sequence of its purothionin was compared to the amino acid sequences of the purothionins in Triticum monococcum, Triticum turgidum, and Triticum aestivum. The residue sequence of the purothionin from T. urartu differs by five and six amino acid substitutions respectively from the alpha 1 and alpha 2 forms coded for by genes in the B and D genomes, and is identical to the beta form specified by a gene in the A genome. Therefore, the T. urartu purothionin is either coded by a gene in the A genome or a chromosome set highly homologous to it. The results demonstrate that at least a portion of the T. urartu and T. monococcum genomes is homologous and probably identical. A variety of other studies have also shown that T. urartu is very closely related to T. monococcum and, in all likelihood, also possesses the A genome. Therefore, it could be argued that either T. urartu and T. monococcum are the same species or that T. urartu rather than T. monococcum is the source of the A genome in T. turgidum and T. aestivum. Except for Johnson's results, our data and that of others suggest a revised origin of polyploid wheats. Specifically, the list of six putative B genome donor species is reduced to five, all members of the Sitopsis section of the genus Aegilops. PMID:3209062

  15. Introgression of an imidazolinone-resistance gene from winter wheat (Triticum aestivum L.) into jointed goatgrass (Aegilops cylindrica Host).

    PubMed

    Perez-Jones, Alejandro; Mallory-Smith, Carol A; Hansen, Jennifer L; Zemetra, Robert S

    2006-12-01

    Imidazolinone-resistant winter wheat (Triticum aestivum L.) is being commercialized in the USA. This technology allows wheat growers to selectively control jointed goatgrass (Aegilops cylindrica Host), a weed that is especially problematic because of its close genetic relationship with wheat. However, the potential movement of the imidazolinone-resistance gene from winter wheat to jointed goatgrass is a concern. Winter wheat and jointed goatgrass have the D genome in common and can hybridize and backcross under natural field conditions. Since the imidazolinone-resistance gene (Imi1) is located on the D genome, it is possible for resistance to be transferred to jointed goatgrass via hybridization and backcrossing. To study the potential for gene movement, BC(2)S(2) plants were produced artificially using imidazolinone-resistant winter wheat (cv. FS-4) as the female parent and a native jointed goatgrass collection as the male recurrent parent. FS-4, the jointed goatgrass collection, and 18 randomly selected BC(2)S(2) populations were treated with imazamox. The percentage of survival was 100% for the FS-4, 0% for the jointed goatgrass collection and 6 BC(2)S(2) populations, 40% or less for 2 BC(2)S(2) populations, and 50% or greater for the remaining 10 BC(2)S(2) populations. Chromosome counts in BC(2)S(3) plants showed a restoration of the chromosome number of jointed goatgrass, with four out of four plants examined having 28 chromosomes. Sequencing of AHASL1D in BC(2)S(3) plants derived from BC(2)S(2)-6 revealed the sexual transmission of Imi1 from FS-4 to jointed goatgrass. Imi1 conferred resistance to the imidazolinone herbicide imazamox, as shown by the in vitro assay for acetohydroxyacid synthase (AHAS) activity. PMID:17058103

  16. SSR-based identification of genetic groups within European populations of Tuber aestivum Vittad.

    PubMed

    Molinier, Virginie; Murat, Claude; Peter, Martina; Gollotte, Armelle; De la Varga, Herminia; Meier, Barbara; Egli, Simon; Belfiori, Beatrice; Paolocci, Francesco; Wipf, Daniel

    2016-02-01

    Tuber species are ectomycorrhizal ascomycetes establishing relationships with different host trees and forming hypogeous fruiting bodies known as truffles. Among Tuber species, Tuber aestivum Vittad. has a wide distributional range being found naturally all over Europe. Here, we performed large-scale population genetic analyses in T. aestivum to (i) investigate its genetic diversity at the European scale, (ii) characterize its genetic structure and test for the presence of ecotypes and (iii) shed light into its demographic history. To reach these goals, 230 ascocarps from different populations were genotyped using 15 polymorphic simple sequence repeat markers. We identified 181 multilocus genotypes and four genetic groups which did not show a clear geographical separation; although, one of them was present exclusively in Southeast France, Italy and Spain. Fixation index values between pairs of genetic groups were generally high and ranged from 0.29 to 0.45. A significant deficit of heterozygosity indicated a population expansion instead of a recent population bottleneck, suggesting that T. aestivum is not endangered in Europe, not even in Mediterranean regions. Our study based on a large-scale population genetic analysis suggests that genetically distinct populations and likely ecotypes within T. aestivum are present. In turn, this study paves the way to future investigations aimed at addressing the biological and/or ecological factors that have concurred in shaping the population genetic structure of this species. Present results should also have implications for the truffle market since defining genetic markers are now possible at least for some specific T. aestivum genetic groups. PMID:26070448

  17. Dynamics of rhizosphere properties and antioxidative responses in wheat (Triticum aestivum L.) under cadmium stress.

    PubMed

    Li, Yonghua; Wang, Li; Yang, Linsheng; Li, Hairong

    2014-04-01

    In this study, we performed a rhizobox experiment to examine the dynamic changes in the rhizosphere properties and antioxidant enzyme responses of Triticum aestivum L. under three levels of cadmium stress. A set of micro-techniques (i.e., Rhizobox and Rhizon SMS) were applied for the dynamically non-destructive collection of the rhizosphere soil solution to enable the observation at a high temporal resolution. The dynamics of soluble cadmium and dissolved organic carbon (DOC) in the rhizosphere soil solutions of the Triticum aestivum L. were characterised by the sequence week 0 after sowing (WAS0)<3 weeks after sowing (WAS3)<10 weeks after sowing (WAS10), whereas the soil solution pH was found to follow an opposite distribution pattern. Systematically, both superoxide dismutase (SOD) and catalase (CAT) activities in the leaves of the Triticum aestivum L. increased concomitantly with increasing cadmium levels (p>0.05) and growth duration (p<0.05), whilst ascorbate peroxidase (APX) activity was induced to an elevated level at moderate cadmium stress with a decrease at high cadmium stress (p>0.05). These results suggested the enhancement of DOC production and the greater antioxidant enzyme activities were two important protective mechanisms of Triticum aestivum L. under cadmium stress, whereas rhizosphere acidification might be an important mechanism for the mobilisation of soil cadmium. The results also revealed that plant-soil interactions strongly influence the soil solution chemistry in the rhizosphere of Triticum aestivum L., that, in turn, can stimulate chemical and biochemical responses in the plants. In most cases, these responses to cadmium stress were sensitive and might allow us to develop strategies for reducing the risks of the cadmium contamination to crop production. PMID:24580822

  18. An Efficient Approach for the Development of Locus Specific Primers in Bread Wheat (Triticum aestivum L.) and Its Application to Re-Sequencing of Genes Involved in Frost Tolerance

    PubMed Central

    Babben, Steve; Perovic, Dragan; Koch, Michael; Ordon, Frank

    2015-01-01

    Recent declines in costs accelerated sequencing of many species with large genomes, including hexaploid wheat (Triticum aestivum L.). Although the draft sequence of bread wheat is known, it is still one of the major challenges to developlocus specific primers suitable to be used in marker assisted selection procedures, due to the high homology of the three genomes. In this study we describe an efficient approach for the development of locus specific primers comprising four steps, i.e. (i) identification of genomic and coding sequences (CDS) of candidate genes, (ii) intron- and exon-structure reconstruction, (iii) identification of wheat A, B and D sub-genome sequences and primer development based on sequence differences between the three sub-genomes, and (iv); testing of primers for functionality, correct size and localisation. This approach was applied to single, low and high copy genes involved in frost tolerance in wheat. In summary for 27 of these genes for which sequences were derived from Triticum aestivum, Triticum monococcum and Hordeum vulgare, a set of 119 primer pairs was developed and after testing on Nulli-tetrasomic (NT) lines, a set of 65 primer pairs (54.6%), corresponding to 19 candidate genes, turned out to be specific. Out of these a set of 35 fragments was selected for validation via Sanger's amplicon re-sequencing. All fragments, with the exception of one, could be assigned to the original reference sequence. The approach presented here showed a much higher specificity in primer development in comparison to techniques used so far in bread wheat and can be applied to other polyploid species with a known draft sequence. PMID:26565976

  19. Assessment of genomic and species relationships in Triticum and Aegilops by PAGE and by differential staining of seed albumins and globulins.

    PubMed

    Caldwell, K A; Kasarda, D D

    1978-11-01

    Endosperm protein components from common bread wheats (Triticum aestivum L.) and related species were extracted with aluminum lactate, pH 3.2, and examined by electrophoresis in the same buffer. Electrophoretic patterns of the albumins and globulins were compared to evaluate the possibility that a particular species might have contributed its genome to tetraploid or hexaploid wheat. Together with protein component mobilities, differential band staining with Coomassie Brilliant Blue R250 was employed to test the identity or non-identity of bands. Eight species and 63 accessions, representative of Triticum and Aegilops were tested. Considerable intraspecific variation was observed for patterns of diploid but not for tetraploid or hexaploid species. Patterns of some accessions of Triticum urartu agreed closely with major parts of the patterns of Triticum dicoccoides and T. aestivum. A fast-moving, green band was found in all accessions of T. urartu and of Triticum boeoticum, however, that was not found in those of T. dicoccoides or T. aestivum. This band was present in all accessions of Triticum araraticum and Triticum zhukovskyi. Patterns of Aegilops longissima, which has been suggested as the donor of the B genome, differed substantially from those of T. dicoccoides and T. aestivum. Finally, two marker proteins of intermediate mobility were also observed and may be used to discriminate between accessions of T. araraticum/T. zhukovskyi and those of T. dicoccoides/T. aestivum. PMID:24317663

  20. Evolution of the tetraploid Anemone multifida (2n = 32) and hexaploid A. baldensis (2n = 48) (Ranunculaceae) was accompanied by rDNA loci loss and intergenomic translocation: evidence for their common genome origin

    PubMed Central

    Mlinarec, J.; Šatović, Z.; Malenica, N.; Ivančić-Baće, I.; Besendorfer, V.

    2012-01-01

    Background and Aims In the genus Anemone two small groups of taxa occur with the highest ploidy levels 2n = 6x = 48, belonging to the closely related clades: the montane/alpine Baldensis clade and the more temperate Multifida clade. To understand the formation of polyploids within these groups, the evolution of allohexaploid A. baldensis (AABBDD, 2n = 6x = 48) from Europe and allotetraploid Anemone multifida (BBDD, 2n = 4x = 32) from America was analysed. Methods Internal transcribed spacer and non-transcribed spacer sequences were used as molecular markers for phylogenetic analyses. Cytogenetic studies, including genomic in situ hybridization with genomic DNA of potential parental species as probe, fluorescence in situ hybridization with 5S and 18S rDNA as probes and 18S rDNA restriction analyses, were used to identify the parental origin of chromosomes and to study genomic changes following polyploidization. Key Results This study shows that A. multifida (BBDD, 2n= 4x = 32) and A. baldensis (AABBDD, 2n = 6x = 48) are allopolyploids originating from the crosses of diploid members of the Multifida (donor of the A and B subgenomes) and Baldensis groups (donor of the D subgenome). The A and B subgenomes are closely related to the genomes of A. sylvestris, A. virginiana and A. cylindrica, indicating that these species or their progeny might be the ancestral donors of the B subgenome of A. multifida and A and B subgenomes of A. baldensis. Both polyploids have undergone genomic changes such as interchromosomal translocation affecting B and D subgenomes and changes at rDNA sites. Anemone multifida has lost the 35S rDNA loci characteristic of the maternal donor (B subgenome) and maintained only the rDNA loci of the paternal donor (D subgenome). Conclusions It is proposed that A. multifida and A. baldensis probably had a common ancestor and their evolution was facilitated by vegetation changes during the Quaternary, resulting in their present disjunctive distribution. PMID

  1. EFFECTS OF SIMULATED ACIDIC RAIN ON YIELDS OF 'RAPHANUS SATIVUS', 'LACTUCA SATIVA', 'TRITICUM AESTIVUM' AND 'MEDICAGO SATIVA'

    EPA Science Inventory

    Experiments were performed to determine effects of simulated acidic rain on radishes (Raphanus sativus), wheat(Triticum aestivum) and alfalfa (Medicago sativa) grown under greenhouse conditions. Experimental designs allowed the detection of statistically significant differences a...

  2. The evolution of polyploid wheats: identification of the A genome donor species.

    PubMed

    Dvorák, J; Terlizzi, P; Zhang, H B; Resta, P

    1993-02-01

    Cytogenetic work has shown that the tetraploid wheats, Triticum turgidum and T. timopheevii, and the hexaploid wheat T. aestivum have one pair of A genomes, whereas hexaploid T. zhukovskyi has two. Variation in 16 repeated nucleotide sequences was used to identify sources of the A genomes. The A genomes of T. turgidum, T. timopheevii, and T. aestivum were shown to be contributed by T. urartu. Little divergence in the repeated nucleotide sequences was detected in the A genomes of these species from the genome of T. urartu. In T. zhukovskyi one A genome was contributed by T. urartu and the other was contributed by T. monococcum. It is concluded that T. zhukovskyi originated from hybridization of T. timopheevii with T. monococcum. The repeated nucleotide sequence profiles in the A genomes of T. zhukovskyi showed reduced correspondence with those in the genomes of both ancestral species, T. urartu and T. monococcum. This differentiation is attributed to heterogenetic chromosome pairing and segregation among chromosomes of the two A genomes in T. zhukovskyi. PMID:18469969

  3. Heavy metal uptake, translocation, and bioaccumulation studies of Triticum aestivum cultivated in contaminated dredged materials.

    PubMed

    Shumaker, Ketia L; Begonia, Gregorio

    2005-08-01

    Phytoremediation is a technology that uses vegetation to remediate contaminants from water, soil, and sediments. Unlike traditional remediation techniques such as soil washing or vitrification, phytoremediation offers a technology that is solar-driven, aesthetically pleasing, and cost effective. Recent studies indicate that winter wheat (Triticum aestivum L.) is a potential accumulator for heavy metals such as lead (Pb) and cadmium (Cd) in hydroponic systems. Based on these findings, a laboratory study was conducted with the primary objective of determining the phytoaccumulation capability of this plant species for heavy metals from contaminated dredged materials (DMs) originating from two confined disposal facilities (CDF). The United States Army Corps of Engineers (USACE) manages several hundred million cubic meters of DMs each year, and 5 to 10 % of these DMs require special handling because they are contaminated with hazardous substances that can move from the substrates into food webs causing unacceptable risk outside CDFs. Phytoremediation may offer an alternative to decrease this risk. Chemical analyses by USACE personnel identified 17 metals in various DMs, but in this present study, only zinc (Zn) and Cd were investigated. Pre-germinated seeds of the test plants were planted under laboratory conditions in pots containing the various DMs and reference soil. Four weeks after planting, plants were harvested and separated into roots and shoots for biomass production and tissue metal concentrations analyses. Results showed that T. aestivum plants have the capacity to tolerate and grow in multiple-metal contaminated DMs with the potential of accumulating various amounts of Zn and Cd. Root and shoot biomass of T. aestivum were not significantly affected by the DMs on which the plants were grown suggesting that this plant species can grow just as well on DMs contaminated by various metals as in the reference soil. No significant differences in the Zn tissue

  4. Heavy Metal Uptake, Translocation, and Bioaccumulation Studies of Triticum aestivum Cultivated in Contaminated Dredged Materials

    PubMed Central

    Shumaker, Ketia L.; Begonia, Gregorio

    2005-01-01

    Phytoremediation is a technology that uses vegetation to remediate contaminants from water, soil, and sediments. Unlike traditional remediation techniques such as soil washing or vitrification, phytoremediation offers a technology that is solar-driven, aesthetically pleasing, and cost effective. Recent studies indicate that winter wheat (Triticum aestivum L.) is a potential accumulator for heavy metals such as lead (Pb) and cadmium (Cd) in hydroponic systems. Based on these findings, a laboratory study was conducted with the primary objective of determining the phytoaccumulation capability of this plant species for heavy metals from contaminated dredged materials (DMs) originating from two confined disposal facilities (CDF). The United States Army Corps of Engineers (USACE) manages several hundred million cubic meters of DMs each year, and 5 to 10 % of these DMs require special handling because they are contaminated with hazardous substances that can move from the substrates into food webs causing unacceptable risk outside CDFs. Phytoremediation may offer an alternative to decrease this risk. Chemical analyses by USACE personnel identified 17 metals in various DMs, but in this present study, only zinc (Zn) and Cd were investigated. Pre-germinated seeds of the test plants were planted under laboratory conditions in pots containing the various DMs and reference soil. Four weeks after planting, plants were harvested and separated into roots and shoots for biomass production and tissue metal concentrations analyses. Results showed that T. aestivum plants have the capacity to tolerate and grow in multiple-metal contaminated DMs with the potential of accumulating various amounts of Zn and Cd. Root and shoot biomass of T. aestivum were not significantly affected by the DMs on which the plants were grown suggesting that this plant species can grow just as well on DMs contaminated by various metals as in the reference soil. No significant differences in the Zn tissue

  5. Wheat Genomics: Present Status and Future Prospects

    PubMed Central

    Gupta, P. K.; Mir, R. R.; Mohan, A.; Kumar, J.

    2008-01-01

    Wheat (Triticum aestivum L.), with a large genome (16000 Mb) and high proportion (∼80%) of repetitive sequences, has been a difficult crop for genomics research. However, the availability of extensive cytogenetics stocks has been an asset, which facilitated significant progress in wheat genomic research in recent years. For instance, fairly dense molecular maps (both genetic and physical maps) and a large set of ESTs allowed genome-wide identification of gene-rich and gene-poor regions as well as QTL including eQTL. The availability of markers associated with major economic traits also allowed development of major programs on marker-assisted selection (MAS) in some countries, and facilitated map-based cloning of a number of genes/QTL. Resources for functional genomics including TILLING and RNA interference (RNAi) along with some new approaches like epigenetics and association mapping are also being successfully used for wheat genomics research. BAC/BIBAC libraries for the subgenome D and some individual chromosomes have also been prepared to facilitate sequencing of gene space. In this brief review, we discuss all these advances in some detail, and also describe briefly the available resources, which can be used for future genomics research in this important crop. PMID:18528518

  6. Unlocking the Barley Genome by Chromosomal and Comparative Genomics[W][OA

    PubMed Central

    Mayer, Klaus F.X.; Martis, Mihaela; Hedley, Pete E.; Šimková, Hana; Liu, Hui; Morris, Jenny A.; Steuernagel, Burkhard; Taudien, Stefan; Roessner, Stephan; Gundlach, Heidrun; Kubaláková, Marie; Suchánková, Pavla; Murat, Florent; Felder, Marius; Nussbaumer, Thomas; Graner, Andreas; Salse, Jerome; Endo, Takashi; Sakai, Hiroaki; Tanaka, Tsuyoshi; Itoh, Takeshi; Sato, Kazuhiro; Platzer, Matthias; Matsumoto, Takashi; Scholz, Uwe; Doležel, Jaroslav; Waugh, Robbie; Stein, Nils

    2011-01-01

    We used a novel approach that incorporated chromosome sorting, next-generation sequencing, array hybridization, and systematic exploitation of conserved synteny with model grasses to assign ~86% of the estimated ~32,000 barley (Hordeum vulgare) genes to individual chromosome arms. Using a series of bioinformatically constructed genome zippers that integrate gene indices of rice (Oryza sativa), sorghum (Sorghum bicolor), and Brachypodium distachyon in a conserved synteny model, we were able to assemble 21,766 barley genes in a putative linear order. We show that the barley (H) genome displays a mosaic of structural similarity to hexaploid bread wheat (Triticum aestivum) A, B, and D subgenomes and that orthologous genes in different grasses exhibit signatures of positive selection in different lineages. We present an ordered, information-rich scaffold of the barley genome that provides a valuable and robust framework for the development of novel strategies in cereal breeding. PMID:21467582

  7. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome.

    PubMed

    Chapman, Jarrod A; Mascher, Martin; Buluç, Aydın; Barry, Kerrie; Georganas, Evangelos; Session, Adam; Strnadova, Veronika; Jenkins, Jerry; Sehgal, Sunish; Oliker, Leonid; Schmutz, Jeremy; Yelick, Katherine A; Scholz, Uwe; Waugh, Robbie; Poland, Jesse A; Muehlbauer, Gary J; Stein, Nils; Rokhsar, Daniel S

    2015-01-01

    Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population. PMID:25637298

  8. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

    SciTech Connect

    Chapman, Jarrod A.; Mascher, Martin; Buluc, Aydin; Barry, Kerrie; Georganas, Evangelos; Session, Adam; Strnadova, Veronika; Jenkins, Jerry; Sehgal, Sunish; Oliker, Leonid; Schmutz, Jeremy; Yelick, Katherine A.; Scholz, Uwe; Waugh, Robbie; Poland, Jesse A.; Muehlbauer, Gary J.; Stein, Nils; Rokhsar, Daniel S.

    2015-01-31

    We report that polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population.

  9. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

    DOE PAGESBeta

    Chapman, Jarrod A.; Mascher, Martin; Buluc, Aydin; Barry, Kerrie; Georganas, Evangelos; Session, Adam; Strnadova, Veronika; Jenkins, Jerry; Sehgal, Sunish; Oliker, Leonid; et al

    2015-01-31

    We report that polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible tomore » construct a mapping population.« less

  10. Delimitation of the Earliness per se D1 (Eps-D1) flowering gene to a subtelomeric chromosomal deletion in bread wheat (Triticum aestivum)

    PubMed Central

    Zikhali, Meluleki; Wingen, Luzie U.; Griffiths, Simon

    2016-01-01

    Earliness per se (Eps) genes account for the variation in flowering time when vernalization and photoperiod requirements are satisfied. Genomics and bioinformatics approaches were used to describe allelic variation for 40 Triticum aestivum genes predicted, by synteny with Brachypodium distachyon, to be in the 1DL Eps region. Re-sequencing 1DL genes revealed that varieties carrying early heading alleles at this locus, Spark and Cadenza, carry a subtelomeric deletion including several genes. The equivalent region in Rialto and Avalon is intact. A bimodal distribution in the segregating Spark X Rialto single seed descent (SSD) populations enabled the 1DL QTL to be defined as a discrete Mendelian factor, which we named Eps-D1. Near isogenic lines (NILs) and NIL derived key recombinants between markers flanking Eps-D1 suggest that the 1DL deletion contains the gene(s) underlying Eps-D1. The deletion spans the equivalent of the Triticum monoccocum Eps-A m 1 locus, and hence includes MODIFIER OF TRANSCRIPTION 1 (MOT1) and FTSH PROTEASE 4 (FTSH4), the candidates for Eps-A m 1. The deletion also contains T. aestivum EARLY FLOWERING 3-D1 (TaELF3-D1) a homologue of the Arabidopsis thaliana circadian clock gene EARLY FLOWERING 3. Eps-D1 is possibly a homologue of Eps-B1 on chromosome 1BL. NILs carrying the Eps-D1 deletion have significantly reduced total TaELF3 expression and altered TaGIGANTEA (TaGI) expression compared with wild type. Altered TaGI expression is consistent with an ELF3 mutant, hence we propose TaELF3-D1 as the more likely candidate for Eps-D1. This is the first direct fine mapping of Eps effect in bread wheat. PMID:26476691

  11. Extensive Pericentric Rearrangements in the Bread Wheat (Triticum aestivum L.) Genotype “Chinese Spring” Revealed from Chromosome Shotgun Sequence Data

    PubMed Central

    Ma, Jian; Stiller, Jiri; Wei, Yuming; Zheng, You-Liang; Devos, Katrien M.; Doležel, Jaroslav; Liu, Chunji

    2014-01-01

    The bread wheat (Triticum aestivum L.) genotype “Chinese Spring” (“CS”) is the reference base in wheat genetics and genomics. Pericentric rearrangements in this genotype were systematically assessed by analyzing homoeoloci for a set of nonredundant genes from Brachypodium distachyon, Triticum urartu, and Aegilops tauschii in the CS chromosome shotgun sequence obtained from individual chromosome arms flow-sorted from CS aneuploid lines. Based on patterns of their homoeologous arm locations, 551 genes indicated the presence of pericentric inversions in at least 10 of the 21 chromosomes. Available data from deletion bin-mapped expressed sequence tags and genetic mapping in wheat indicated that all inversions had breakpoints in the low-recombinant gene-poor pericentromeric regions. The large number of putative intrachromosomal rearrangements suggests the presence of extensive structural differences among the three subgenomes, at least some of which likely occurred during the production of the aneuploid lines of this hexaploid wheat genotype. These differences could have significant implications in wheat genome research where comparative approaches are used such as in ordering and orientating sequence contigs and in gene cloning. PMID:25349265

  12. Analysis of the bread wheat genome using whole-genome shotgun sequencing.

    PubMed

    Brenchley, Rachel; Spannagl, Manuel; Pfeifer, Matthias; Barker, Gary L A; D'Amore, Rosalinda; Allen, Alexandra M; McKenzie, Neil; Kramer, Melissa; Kerhornou, Arnaud; Bolser, Dan; Kay, Suzanne; Waite, Darren; Trick, Martin; Bancroft, Ian; Gu, Yong; Huo, Naxin; Luo, Ming-Cheng; Sehgal, Sunish; Gill, Bikram; Kianian, Sharyar; Anderson, Olin; Kersey, Paul; Dvorak, Jan; McCombie, W Richard; Hall, Anthony; Mayer, Klaus F X; Edwards, Keith J; Bevan, Michael W; Hall, Neil

    2012-11-29

    Bread wheat (Triticum aestivum) is a globally important crop, accounting for 20 per cent of the calories consumed by humans. Major efforts are underway worldwide to increase wheat production by extending genetic diversity and analysing key traits, and genomic resources can accelerate progress. But so far the very large size and polyploid complexity of the bread wheat genome have been substantial barriers to genome analysis. Here we report the sequencing of its large, 17-gigabase-pair, hexaploid genome using 454 pyrosequencing, and comparison of this with the sequences of diploid ancestral and progenitor genomes. We identified between 94,000 and 96,000 genes, and assigned two-thirds to the three component genomes (A, B and D) of hexaploid wheat. High-resolution synteny maps identified many small disruptions to conserved gene order. We show that the hexaploid genome is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded gene families that could be associated with crop productivity. Our analyses, coupled with the identification of extensive genetic variation, provide a resource for accelerating gene discovery and improving this major crop. PMID:23192148

  13. Pharmacognostic standardization, antioxidant and free radical scavenging activity of the seeds of Triticum aestivum L - A dietary staple

    PubMed Central

    Khan, Ghulam M.; Ansari, Shahid H.; Ahmad, Feroz

    2013-01-01

    Aims To establish the Quality standards of Triticum aestivum L, seeds as per WHO guidelines. To study the antioxidant and hepatoprotective profile of T. aestivum L. seeds. Methods Pharmacognostic studies like morphological, microscopical, physico-chemical, phytochemical evaluation, fluorescence analysis, TLC, HPTLC, phytochemical analysis etc. of various extracts of the seeds of T. aestivum were carried out as per established methods. The ethanolic extract was evaluated for antioxidant and hepatoprotective activity using rat model. Results Preliminary phytochemical analysis mainly revealed the presence of carbohydrates, phenolics, proteins, resins, lipids and flavonoids. T. aestivum at different doses, i.e. 5-45 μg/ml showed free radical scavenging activity in dose dependent manner. The amount of phenolic components was found to be 313.5 μg/mg indicating considerable antioxidant activity. The ethanolic extract of T. aestivum was administered at dose level of 100 mg/kg/day, every day for 21 days along with CCl4. Biochemical and histopathological results conclude that the seeds have hepatoprotective activity. PMID:24023455

  14. Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat.

    PubMed

    Huang, Shaoxing; Sirikhachornkit, Anchalee; Su, Xiujuan; Faris, Justin; Gill, Bikram; Haselkorn, Robert; Gornicki, Piotr

    2002-06-11

    The classic wheat evolutionary history is one of adaptive radiation of the diploid Triticum/Aegilops species (A, S, D), genome convergence and divergence of the tetraploid (Triticum turgidum AABB, and Triticum timopheevii AAGG) and hexaploid (Triticum aestivum, AABBDD) species. We analyzed Acc-1 (plastid acetyl-CoA carboxylase) and Pgk-1 (plastid 3-phosphoglycerate kinase) genes to determine phylogenetic relationships among Triticum and Aegilops species of the wheat lineage and to establish the timeline of wheat evolution based on gene sequence comparisons. Triticum urartu was confirmed as the A genome donor of tetraploid and hexaploid wheat. The A genome of polyploid wheat diverged from T. urartu less than half a million years ago (MYA), indicating a relatively recent origin of polyploid wheat. The D genome sequences of T. aestivum and Aegilops tauschii are identical, confirming that T. aestivum arose from hybridization of T. turgidum and Ae. tauschii only 8,000 years ago. The diploid Triticum and Aegilops progenitors of the A, B, D, G, and S genomes all radiated 2.5-4.5 MYA. Our data suggest that the Acc-1 and Pgk-1 loci have different histories in different lineages, indicating genome mosaicity and significant intraspecific differentiation. Some loci of the S genome of Aegilops speltoides and the G genome of T. timophevii are closely related, suggesting the same origin of some parts of their genomes. None of the Aegilops genomes analyzed is a close relative of the B genome, so the diploid progenitor of the B genome remains unknown. PMID:12060759

  15. Responses of alloplasmic (cytoplasm=Triticum timopheevii) and euplasmic wheats (Triticum aestivum) to photoperiod and vernalization.

    PubMed

    Ward, R W; Heyne, E G; Paulsen, G M

    1983-07-01

    Studies were conducted to determine the influence of the male sterility-inducing cytoplasm of Triticum timopheevii (Zhuk.) Zhuk. on response of several common winter wheat (T. aestivum L.) nuclear genotypes to photoperiod and vernalization. Comparative studies of cytoplasmic substitution lines provide information on the role of the cytoplasmic genetic mechanism in growth and development. In the case of cytoplasmic male sterility-based hybrid production systems, ubiquity of sterility-inducing cytoplasm in derived hybrids warrants thorough characterization of its influence on plant phenotype. Factorial combinations of cytoplasm (T. timopheevii and T. aestivum), nuclear genotype, and photoperiod or vernalization treatments were evaluated under hydroponic conditions in controlled environment chambers. Interaction of cytoplasm, photoperiod, and nuclear genotype was significant in one or more experiments for days to anthesis and potential spikelet number, and interaction of cytoplasm, vernalization, and nuclear genotype was significant for days to spike emergence. Long day length was associated with increased percentage seed set in one study, but interactions of photoperiod and cytoplasm were not detected for percentage seed set. Interactions involving cytoplasm and photoperiod or vernalization were interpreted as evidence of the existence of genetic factors in cytoplsam of T. timopheevii which alter photoperiod or vernalization responses of alloplasmic plants relative to responses exhibited by euplasmic plants. Since photoperiod and vernalization responses are critical to adaptation, T. timopheevii cytoplasm can alter adaptability of T. aestivum. The specific effect would be nuclear genotype dependent, and does not appear to be of a magnitude greater than that induced by nuclear genetic variability at loci conditioning photoperiod or vernalization responses or other adaptation-determining characteristics. Normal multilocation/year testing of alloplasmic hybrids should

  16. NIR FT-Raman study of biomass ( Triticum aestivum) treated with cellulase

    NASA Astrophysics Data System (ADS)

    Cao, Yu; Lu, Yonglai; Huang, Yong

    2004-05-01

    Multicomponent cellulase and purified endoglucanase were assayed and used to treat biomass ( Triticum aestivum). In this work we present FT-Raman spectra of enzymatic treated samples of biomass. Changes in structure and properties of the biomass caused by enzymatic treatment depend on the composition and the type of enzyme, as well as the treatment conditions. The lignin content of the biomass was most reduced in enzymatic treatment. Due to endoglucanase containing less xylanase activity than multicomponent cellulase, the samples modified with endoglucanase have a higher content of hemicellulose and lignin. The crystallinity of cellulose in the biomass increases during enzymatic treatment, as determined by FT-Raman analysis.

  17. LCMS and GCMS for the screening of alkaloids in natural and in vitro extracts of Leucojum aestivum.

    PubMed

    Ptak, Agata; El Tahchy, Anna; Dupire, François; Boisbrun, Michel; Henry, Max; Chapleur, Yves; Moś, Maria; Laurain-Mattar, Dominique

    2009-01-01

    HPLC coupled to a mass spectrometer (MS) was used for the analysis of galanthamine and lycorine in natural extracts of Leucojum aestivum and in their in vitro cultures grown with a precursor (ACC), inhibitors (AgNO(3), STS), or an absorber (KMnO(4)) of ethylene. The maximum galanthamine (0.002%) and lycorine (0.02%) concentrations in tissue cultures were obtained in the presence of KMnO(4). GCMS was used to investigate underivatized alkaloid mixtures from L. aestivum. Seven alkaloids were identified in in vivo bulbs. KMnO(4) led to the highest diversity of alkaloids in tissue culture extracts. PMID:19117485

  18. Phosphate depletion modulates auxin transport in Triticum aestivum leading to altered root branching

    PubMed Central

    Talboys, Peter J.; Healey, John R.; Withers, Paul J. A.; Jones, Davey L.

    2014-01-01

    Understanding the mechanisms by which nutritional signals impact upon root system architecture is a key facet in the drive for greater nutrient application efficiency in agricultural systems. Cereal plants reduce their rate of lateral root emergence under inorganic phosphate (Pi) shortage; this study uses molecular and pharmacological techniques to dissect this Pi response in Triticum aestivum. Plants were grown in coarse sand washed in high- or low-Pi nutrient solution before being assessed for their root branching density and expression of AUX/IAA and PIN genes. Seedlings were also grown on media containing [14C]indole acetic acid to measure basipetal auxin transport. Seedlings grown in low-Pi environments displayed less capacity to transport auxin basipetally from the seminal root apex, a reduction in root expression of PIN auxin transporter genes, and perturbed expression of a range of AUX/IAA auxin response genes. Given the known importance of basipetally transported auxin in stimulating lateral root initiation, it is proposed here that, in T. aestivum, Pi availability directly influences lateral root production through modulation of PIN expression. Understanding such processes is important in the drive for greater efficiency in crop use of Pi fertilizers in agricultural settings. PMID:25086590

  19. Phosphate depletion modulates auxin transport in Triticum aestivum leading to altered root branching.

    PubMed

    Talboys, Peter J; Healey, John R; Withers, Paul J A; Jones, Davey L

    2014-09-01

    Understanding the mechanisms by which nutritional signals impact upon root system architecture is a key facet in the drive for greater nutrient application efficiency in agricultural systems. Cereal plants reduce their rate of lateral root emergence under inorganic phosphate (Pi) shortage; this study uses molecular and pharmacological techniques to dissect this Pi response in Triticum aestivum. Plants were grown in coarse sand washed in high- or low-Pi nutrient solution before being assessed for their root branching density and expression of AUX/IAA and PIN genes. Seedlings were also grown on media containing [(14)C]indole acetic acid to measure basipetal auxin transport. Seedlings grown in low-Pi environments displayed less capacity to transport auxin basipetally from the seminal root apex, a reduction in root expression of PIN auxin transporter genes, and perturbed expression of a range of AUX/IAA auxin response genes. Given the known importance of basipetally transported auxin in stimulating lateral root initiation, it is proposed here that, in T. aestivum, Pi availability directly influences lateral root production through modulation of PIN expression. Understanding such processes is important in the drive for greater efficiency in crop use of Pi fertilizers in agricultural settings. PMID:25086590

  20. Production and cytogenetic analysis of BC1, BC 2, and BC 3 progenies of an intergeneric hybrid between Triticum aestivum (L.) Thell. and tetraploid Agropyron cristatum (L.) Gaertn.

    PubMed

    Chen, Q; Jahier, J; Cauderon, Y

    1992-08-01

    Intergeneric hybrids between Triticum aestivum cv 'Chinese Spring' and Agropyron cristatum 4x (2n= 5x=35, ABDPP genomes) with a high level of homoeologous meiotic pairing between the wheat chromosomes were backcrossed 3 times to wheat. Pollination of the F1 hybrid with 'Chinese Spring' resulted in 22 BC1 seeds with an average seed set of 1.52%. Five BC1 plants with 39-41 chromosomes were raised using embryo rescue techniques. Chromosome pairing in the BC1 was characterized by a high frequency of multivalent associations, but in spite of this there was no evidence of homoeologous pairing between chromosomes of wheat and those of Agropyron. All of the plants were self sterile. The embryo rescue technique was again essential to produce 39 BC2 plants with chromosome numbers ranging from 37 to 67. The phenomenon of meiotic non-reduction was also observed in the BC3 progenies. In this generation male and female fertility greatly increased, and meiotic pairing was fairly regular. Some monosomic (2n=43) and double monosomic (2n=44) lines were produced. Analysis of these progenies should permit the extraction of the seven possible wheat-Agropyron disomic addition lines including those with the added chromosomes carrying the genes involved in meiotic non-reduction and in suppression of Ph activity. PMID:24201360

  1. Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor Aegilops tauschii

    PubMed Central

    2012-01-01

    Background Development of a high quality reference sequence is a daunting task in crops like wheat with large (~17Gb), highly repetitive (>80%) and polyploid genome. To achieve complete sequence assembly of such genomes, development of a high quality physical map is a necessary first step. However, due to the lack of recombination in certain regions of the chromosomes, genetic mapping, which uses recombination frequency to map marker loci, alone is not sufficient to develop high quality marker scaffolds for a sequence ready physical map. Radiation hybrid (RH) mapping, which uses radiation induced chromosomal breaks, has proven to be a successful approach for developing marker scaffolds for sequence assembly in animal systems. Here, the development and characterization of a RH panel for the mapping of D-genome of wheat progenitor Aegilops tauschii is reported. Results Radiation dosages of 350 and 450 Gy were optimized for seed irradiation of a synthetic hexaploid (AABBDD) wheat with the D-genome of Ae. tauschii accession AL8/78. The surviving plants after irradiation were crossed to durum wheat (AABB), to produce pentaploid RH1s (AABBD), which allows the simultaneous mapping of the whole D-genome. A panel of 1,510 RH1 plants was obtained, of which 592 plants were generated from the mature RH1 seeds, and 918 plants were rescued through embryo culture due to poor germination (<3%) of mature RH1 seeds. This panel showed a homogenous marker loss (2.1%) after screening with SSR markers uniformly covering all the D-genome chromosomes. Different marker systems mostly detected different lines with deletions. Using markers covering known distances, the mapping resolution of this RH panel was estimated to be <140kb. Analysis of only 16 RH lines carrying deletions on chromosome 2D resulted in a physical map with cM/cR ratio of 1:5.2 and 15 distinct bins. Additionally, with this small set of lines, almost all the tested ESTs could be mapped. A set of 399 most informative RH

  2. Use of student’s t statistic as a phenotype of relative consumption preference of wheat (Triticum aestivum L.) grain

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Whole-grain wheat (Triticum aestivum L.) products provide essential nutrients to humans, but bran attributes may hinder consumption. Differences in grain attributes including flabor/aroma can be indentified using the house mouse (Mus musculus L.) as a model system. A potential application of this mo...

  3. Acute toxicity test of a natural iron chelator and an antioxidant, extracted from Triticum aestivum Linn. (wheat grass).

    PubMed

    Das, Priyabrata; Mukhopadhyay, Soma; Mandal, Suvra; Chakraborty, Abhijit; Pal, Amartya; Sarkar, Nirmal Kumar; Mukhopadhyay, Ashis

    2014-01-01

    Triticum aestivum (wheat grass) is widely used in traditional medicine to treat various diseases. Previously the purified compounds and crude extract of T. aestivum were established to have iron chelation potency and antioxidant activity. So it is necessary to evaluate the toxic properties of any compound isolated from plant extract to prevent any untoward side effects. The aim of this study was to determine the acute oral toxicity level of our purified compounds, i.e. mugineic acids and methylpheophorbide a., and crude extract of T. aestivum, on Swiss albino mice at dosage of 2000 mg/kg for a period of 14 days using the organisation for economic co-operation and development guidelines 423. There was no mortality. No change in behavioural pattern, clinical signs, body weight and blood biochemistry profile were observed. Kidney and liver showed normal histo-pathological architecture. Hence, the oral administration of compounds and extract of T. aestivum did not produce any significant toxic effect on mice. Thus we may conclude that the extract can be utilised for pharmaceutical formulations as iron chelator and antioxidant agent for various diseases. PMID:24697628

  4. Repeatability of mice consumption discrimination of wheat (Triticum aestivum L.) varieties across field experiments and mouse cohorts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Whole grain wheat (Triticum aestivum L.) foods can provide critical nutrients for health and nutrition in the human diet. However, undesirable flavors are often suggested as a barrier to increased whole-grain consumption, yet flavor differences among wheat varieties have not been widely studied. Pot...

  5. TOXICITY OF METHYL-TERT BYTYL ETHER (MTBE) TO PLANTS (AVENA SATIVA, ZEA MAYS, TRITICUM AESTIVUM, AND LACTUCA SATIVA)

    EPA Science Inventory

    Effects of Methyl tert-butyl ether (MTBE) on the germination of seeds and growth of the plant were studied in some laboratory experiments. Test plants were wild oat (Avena sative), sweet corn (Zea mays), wheat (Triticum aestivum), and lettuce (Lactuca sativa). Seed germination,...

  6. Wheat (Triticum aestivum) NAM proteins regulate the translocation of iron, zinc, and nitrogen compounds from vegetative tissues to grain

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The NAM-B1 gene is a NAC transcription factor that affects grain nutrient concentrations in wheat (Triticum aestivum). An RNAi line with reduced expression of NAM genes has lower grain protein, iron (Fe), and zinc (Zn) concentrations. To determine whether decreased remobilization, lower plant uptak...

  7. Heading date QTL in winter wheat (Triticum aestivum L.) coincide with major developmental genes Vernalization-1 and Photoperiod-1

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In wheat (Triticum aestivum L.), time from planting to spike emergence is influenced by genes controlling vernalization requirement and photoperiod response. Characterizing the available genetic diversity of known and novel alleles of Vernalization-1 (Vrn-1) and Photoperiod-1 (Ppd-1) in winter wheat...

  8. Effect of wheat (Triticum aestivum L.) grain color and hardness on the consumption preference of a mouse model system

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Wheat (Triticum aestivum L.) grain is a staple food and provides necessary nutrients for human health and nutrition. Yet, flavor differences among wheat varieties are not well understood. Grain flavor and consumption preference can be examined using the house mouse (Mus musculus L.) as a...

  9. Thinopyrum ponticum chromatin-integrated wheat genome shows salt-tolerance at germination stage.

    PubMed

    Yuan, Wen-Ye; Tomita, Motonori

    2015-01-01

    A wild wheatgrass, Thinopyrum ponticum (2n = 10x = 70), which exhibits substantially higher levels of salt tolerance than cultivated wheat, was employed to transfer its salt tolerance to common wheat by means of wide hybridization. A highly salt-tolerant wheat line S148 (2n = 42) was obtained from the BC3F2 progenies between Triticum aestivum (2n = 42) and Th. ponticum. In the cross of S148 × salt-sensitive wheat variety Chinese Spring, the BC4F2 seeds at germination stage segregated into a ratio of 3 salt tolerant to 1 salt sensitive, indicating that the salt tolerance was conferred by a dominant gene block. Genomic in situ hybridization analysis revealed that S148 had a single pair of Th. ponticum-T. aestivum translocated chromosomes bearing the salt-tolerance. This is an initial step of molecular breeding for salt-tolerant wheat. PMID:25809604

  10. Isolation of a wheat (Triticum aestivum L.) mutant in ABA 8'-hydroxylase gene: effect of reduced ABA catabolism on germination inhibition under field condition.

    PubMed

    Chono, Makiko; Matsunaka, Hitoshi; Seki, Masako; Fujita, Masaya; Kiribuchi-Otobe, Chikako; Oda, Shunsuke; Kojima, Hisayo; Kobayashi, Daisuke; Kawakami, Naoto

    2013-03-01

    Pre-harvest sprouting, the germination of mature seeds on the mother plant under moist condition, is a serious problem in cereals. To investigate the effect of reduced abscisic acid (ABA) catabolism on germination in hexaploid wheat (Triticum aestivum L.), we cloned the wheat ABA 8'-hydroxyase gene which was highly expressed during seed development (TaABA8'OH1) and screened for mutations that lead to reduced ABA catabolism. In a screen for natural variation, one insertion mutation in exon 5 of TaABA8'OH1 on the D genome (TaABA8'OH1-D) was identified in Japanese cultivars including 'Tamaizumi'. However, a single mutation in TaABA8'OH1-D had no clear effect on germination inhibition in double haploid lines. In a screen for a mutation, one deletion mutant lacking the entire TaABA8'OH1 on the A genome (TaABA8'OH1-A), TM1833, was identified from gamma-ray irradiation lines of 'Tamaizumi'. TM1833 (a double mutant in TaABA8'OH1-A and TaABA8'OH1-D) showed lower TaABA8'OH1 expression, higher ABA content in embryos during seed development under field condition and lower germination than those in 'Tamaizumi' (a single mutant in TaABA8'OH1-D). These results indicate that reduced ABA catabolism through mutations in TaABA8'OH1 may be effective in germination inhibition in field-grown wheat. PMID:23641187

  11. Distribution of Cadmium, Iron, and Zinc in Millstreams of Hard Winter Wheat (Triticum aestivum L.).

    PubMed

    Guttieri, Mary J; Seabourn, Bradford W; Liu, Caixia; Baenziger, P Stephen; Waters, Brian M

    2015-12-16

    Hard winter wheat (Triticum aestivum L.) is a major crop in the Great Plains of the United States, and our previous work demonstrated that wheat genotypes vary for grain cadmium accumulation with some exceeding the CODEX standard (0.2 mg kg(-1)). Previous reports of cadmium distribution in flour milling fractions have not included high cadmium grain. This study measured the distribution of cadmium, zinc, and iron in flour and bran streams from high cadmium (0.352 mg kg(-1)) grain on a pilot mill that produced 12 flour and four bran streams. Recovery in flour was substantially greater for cadmium (50%) than for zinc (31%) or iron (22%). Cadmium, zinc, and iron in the lowest mineral concentration flour stream, representing the purest endosperm fraction, were 52, 22, and 11%, respectively, of initial grain concentration. Our results indicate that, relative to zinc and iron, a greater proportion of cadmium is stored in the endosperm, the source of white flour. PMID:26568286

  12. [CdCl2-induced morphogenetic variation of Triticum aestivum cultivars].

    PubMed

    Chunetova, Zh Zh; Omirbekova, N Zh; Shulembaeva, K K

    2008-11-01

    The effect cadmium chloride on released local cultivars of soft spring wheat (Triticum aestivum) has been studied under laboratory and field conditions in order to widen the variation spectrum of this plant. It has been found that treatment of grains with a 0.01% aqueous solution of CdCl2 induces the appearance of tall, strong plants with productive bushiness in the M1 generation that are characterized by various morphological changes: elongated ears, scales, and grains; increased number of grains per ear and mass of 1000 grains; anthocyan pigmentation of the stem and leaf axil; etc. Study of meiosis showed chromosome aggregation, displacement of the mitotic spindle of the metaphase plate, and empty (sterile) cells in anaphases (AI and AII). The altered characters of M1 plants are preserved in the M2-M4 generations. PMID:19137733

  13. Gibberellic Acid Regulates Cell Wall Extensibility in Wheat (Triticum aestivum L.) 1

    PubMed Central

    Keyes, Geoff; Sorrells, Mark E.; Setter, Tim L.

    1990-01-01

    Mutations (Rht genes) blocking sensitivity to gibberellic acid (GA) were used to examine phytohormone mediated cell wall expansion in wheat (Triticum aestivum L.). Irreversible extensibility of immature leaf segments, as determined by stress/strain (instron) measurements, declined with Rht gene dose. Exogenous GA3 significantly increased wall extensibility in the nonmutant controls but had no effect on the near-isogenic GA-insensitive genotypes. Furthermore, ancymidol, an inhibitor of gibberellin biosynthesis, diminished wall extensibility in the nonmutant control. Extensibility of immature segments was highly correlated with mature leaf sheath length (R = +0.95). The results indicate that wall yielding properties of expanding wheat leaves are associated with leaf cell expansion potential and that GA is involved in the determination of those properties. PMID:16667254

  14. Characterization of hexokinase from wheat roots and its inhibition by aluminum. [Tritium aestivum

    SciTech Connect

    Whitman, C.E.; Caldwell, C.R.

    1986-04-01

    Hexokinase (HK) performs an important phosphate transfer function in the cell and may be a principal site of aluminum toxicity in plants. Therefore HK was partially purified from the roots of Al-tolerant and Al-sensitive wheat (Triticum aestivum) and its activity characterized. Double reciprocal plots of glucose phosphorylating activity were nonlinear. Localization of glucokinase activity in non-denaturing polyacrylamide gel electrophoresis (PAGE) confirmed the presence of two isozymes. Fructose phosphorylating activity exhibited simple linear kinetics, but non-denaturing PAGE resolved two isozymes. Aluminum had no effect on glucokinase at pH 7.9 but inhibited activity at pH 6.7; fructokinase was not inhibited at either pH. A comparison of the kinetic characteristics of HK from Al-tolerant and Al-sensitive wheat will be presented.

  15. Cellular and Subcellular Immunohistochemical Localization and Quantification of Cadmium Ions in Wheat (Triticum aestivum)

    PubMed Central

    Gao, Wei; Nan, Tiegui; Tan, Guiyu; Zhao, Hongwei; Tan, Weiming; Meng, Fanyun; Li, Zhaohu; Li, Qing X.; Wang, Baomin

    2015-01-01

    The distribution of metallic ions in plant tissues is associated with their toxicity and is important for understanding mechanisms of toxicity tolerance. A quantitative histochemical method can help advance knowledge of cellular and subcellular localization and distribution of heavy metals in plant tissues. An immunohistochemical (IHC) imaging method for cadmium ions (Cd2+) was developed for the first time for the wheat Triticum aestivum grown in Cd2+-fortified soils. Also, 1-(4-Isothiocyanobenzyl)-ethylenediamine-N,N,N,N-tetraacetic acid (ITCB-EDTA) was used to chelate the mobile Cd2+. The ITCB-EDTA/Cd2+ complex was fixed with proteins in situ via the isothiocyano group. A new Cd2+-EDTA specific monoclonal antibody, 4F3B6D9A1, was used to locate the Cd2+-EDTA protein complex. After staining, the fluorescence intensities of sections of Cd2+-positive roots were compared with those of Cd2+-negative roots under a laser confocal scanning microscope, and the location of colloidal gold particles was determined with a transmission electron microscope. The results enable quantification of the Cd2+ content in plant tissues and illustrate Cd2+ translocation and cellular and subcellular responses of T. aestivum to Cd2+ stress. Compared to the conventional metal-S coprecipitation histochemical method, this new IHC method is quantitative, more specific and has less background interference. The subcellular location of Cd2+ was also confirmed with energy-dispersive X-ray microanalysis. The IHC method is suitable for locating and quantifying Cd2+ in plant tissues and can be extended to other heavy metallic ions. PMID:25941807

  16. cis-Jasmone induces accumulation of defence compounds in wheat, Triticum aestivum.

    PubMed

    Moraes, Maria C Blassioli; Birkett, Michael A; Gordon-Weeks, Ruth; Smart, Lesley E; Martin, Janet L; Pye, Barry J; Bromilow, Richard; Pickett, John A

    2008-01-01

    Liquid phase extraction (LPE) and vapor phase extraction (VPE) methodologies were used to evaluate the impact of the plant activator, cis-jasmone, on the secondary metabolism of wheat, Triticum aestivum, var. Solstice. LPE allowed the measurement of benzoxazinoids, i.e. 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one (DIMBOA), 2-hydroxy-7-methoxy-1,4-benzoxazin-3-one (HMBOA) and 6-methoxy-benzoxazolin-2-one (MBOA), and phenolic acids such as trans-p-coumaric acid, syringic acid, p-hydroxybenzoic acid, vanillic acid and cis- and trans-ferulic acid. Using LPE, a significantly higher level of DIMBOA was found in aerial parts and roots of T. aestivum following treatment with cis-jasmone, when compared with untreated plants. Similar results were obtained for phenolic acids, such as trans-ferulic acid and vanillic acid in roots. Using VPE, it was possible to measure levels of 2-hydroxy-7-methoxy-(2H)-1,4-benzoxazin-3(4H)-one (HBOA), benzoxazolin-2(3H)-one (BOA), ferulic acid, syringic acid and coumaric acid. The levels of HBOA in aerial parts and roots were significantly greater in cis-jasmone treated plants compared to untreated plants. cis-Jasmone is known to be a plant activator in terms of production of defence-related volatile semiochemicals that repel aphids and increase the foraging activity of aphid parasitoids. These results show, for the first time, that cis-jasmone also induces selective production of secondary metabolites that are capable of directly reducing development of pests, diseases and weeds. PMID:17681563

  17. Analysis of Triticum aestivum seedling response to the excess of zinc.

    PubMed

    Glińska, Sława; Gapińska, Magdalena; Michlewska, Sylwia; Skiba, Elżbieta; Kubicki, Jakub

    2016-03-01

    The effects of 50 and 300 mg L(-1) Zn(2+) (50 Zn and 300 Zn) were investigated in Triticum aestivum (cv. Żura) grown hydroponically for 7 days. Although wheat treated with 50 Zn took up relatively high amount of the metal (8,943 and 1,503 mg kg(-1) DW in roots and shoots, respectively), none of the morphological and cytological parameters were changed. After 300 Zn, the metal concentration increased to 32,205 and 5,553 mg kg(-1) DW in roots and shoots, respectively. It was connected with the depletion of shoot and root growth, their fresh and dry weight, water content and mitotic index of root meristematic cells. Microelement contents (Cu, Mn and Fe) after 50 Zn were changed only in roots, while 300 Zn disturbed ion balance in whole plants. The most evident ultrastructural alterations of root meristematic cells caused by both tested Zn(2+) doses included increased vacuolization, accumulation of granular deposits inside vacuoles and cell wall thickening. The effect of 300 Zn on root cell ultrastructure was greater that of 50 Zn. The majority of mitochondria had condensed matrix and swollen cristae, plastids contained plastoglobuli, nucleoli were ring-shaped, thinned down cytoplasm with lipid droplets and swollen endoplasmic reticulum cisternae appeared. In mesophyll cells, 50 Zn caused slight reorganization of chloroplast thylakoids and formation of condensed mitochondria. Three hundred Zn triggered more extensive, but not degenerative, changes: plasmolysis of some cells; chloroplasts with protrusions, changed thylakoid organisation and often large starch grains; irregular, condensed mitochondria. The results indicate that T. aestivum cv. Żura is relatively tolerant to Zn stress. PMID:25902894

  18. Haplotype variation of Glu-D1 locus and the origin of Glu-D1d allele conferring superior end-use qualities in common wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In common wheat (Triticum aestivum, AABBDD), the Glu-D1 locus possesses multiple alleles, with Glu-D1a (coding for 1Dx2 and 1Dy12 subunits) and Glu-D1d (encoding 1Dx5 and 1Dy10 subunits) being intensively used in the genetic improvement of end-use qualities. Here, we studied the molecular variatio...

  19. TaXA21-A1 on chromosome 5AL is associated with resistance to multiple pests in wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A quantitative trait locus QYr.osu-5A on the long arm of chromosome 5A in bread wheat (Triticum aestivum L., 2n=6x=42; AABBDD) was previously reported to confer consistent resistance in adult plants to predominant stripe rust races, but the gene causing the quantitative trait locus (QTL) is not know...

  20. Genome walking.

    PubMed

    Shapter, Frances M; Waters, Daniel L E

    2014-01-01

    Genome walking is a method for determining the DNA sequence of unknown genomic regions flanking a region of known DNA sequence. The Genome walking has the potential to capture 6-7 kb of sequence in a single round. Ideal for identifying gene promoter regions where only the coding region. Genome walking also has significant utility for capturing homologous genes in new species when there are areas in the target gene with strong sequence conservation to the characterized species. The increasing use of next-generation sequencing technologies will see the principles of genome walking adapted to in silico methods. However, for smaller projects, PCR-based genome walking will remain an efficient method of characterizing unknown flanking sequence. PMID:24243201

  1. [Signal function of cytokinin 6-benzylaminopurine in the reaction of Triticum aestivum L. mesophyll cells to hyperthermia].

    PubMed

    Musiienko, M M; Zhuk, V V; Batsmanova, L M

    2014-01-01

    The signaling effect of 6-benzylaminopurine (BAP) on leaf mesophyll cells of Triticum aestivum L. under hyperthermic conditions was studied. It was found that BAP regulated photosynthetic pigment, hydrogen peroxide content and activity of antioxidant enzymes, namely superoxide dismutase, ascorbate peroxidase and catalase under high-temperature conditions. The additive effect of BAP and high temperature on the activation of cell antioxidant systems was demonstrated. BAP regulated reducing processes in mesophyll leaf cells under high-temperature conditions. PMID:25816607

  2. Genetic characterization and expression analysis of wheat (Triticum aestivum) line 07OR1074 exhibiting very low polyphenol oxidase (PPO) activity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Wheat (Triticum aestivum) polyphenol oxidase (PPO) contributes to the time dependent discoloration of Asian noodles. Wheat contains multiple paralogous and orthologous PPO genes , Ppo-A1, Ppo-D1, Ppo-A2, Ppo-D2, and Ppo-B2, expressed in wheat kernels, Ppo-A1, Ppo-D1, Ppo-A2, Ppo-D2, and Ppo-B2. To d...

  3. Effects of simulated acidic rain on yields of Raphanus sativus, Lactuca sativa, Triticum aestivum and Medicago sativa

    SciTech Connect

    Evans, L.S.; Gmur, N.F.; Mancini, D.

    1982-01-01

    Experiments were performed to determine effects of simulated acidic rain on radishes (Raphanus sativus), wheat(Triticum aestivum) and alfalfa (Medicago sativa) grown under greenhouse conditions. Experimental designs allowed the detection of statistically significant differences among means that differed by less than 10%. These results suggest that the efficiency of radish foliage in increasing; root mass decreases with increased rainfall acidity since only foliage was exposed to the treatments.

  4. Prophage Genomics

    PubMed Central

    Canchaya, Carlos; Proux, Caroline; Fournous, Ghislain; Bruttin, Anne; Brüssow, Harald

    2003-01-01

    The majority of the bacterial genome sequences deposited in the National Center for Biotechnology Information database contain prophage sequences. Analysis of the prophages suggested that after being integrated into bacterial genomes, they undergo a complex decay process consisting of inactivating point mutations, genome rearrangements, modular exchanges, invasion by further mobile DNA elements, and massive DNA deletion. We review the technical difficulties in defining such altered prophage sequences in bacterial genomes and discuss theoretical frameworks for the phage-bacterium interaction at the genomic level. The published genome sequences from three groups of eubacteria (low- and high-G+C gram-positive bacteria and γ-proteobacteria) were screened for prophage sequences. The prophages from Streptococcus pyogenes served as test case for theoretical predictions of the role of prophages in the evolution of pathogenic bacteria. The genomes from further human, animal, and plant pathogens, as well as commensal and free-living bacteria, were included in the analysis to see whether the same principles of prophage genomics apply for bacteria living in different ecological niches and coming from distinct phylogenetical affinities. The effect of selection pressure on the host bacterium is apparently an important force shaping the prophage genomes in low-G+C gram-positive bacteria and γ-proteobacteria. PMID:12794192

  5. Mycorrhization of pecan trees (Carya illinoinensis) with commercial truffle species: Tuber aestivum Vittad. and Tuber borchii Vittad.

    PubMed

    Benucci, Gian Maria Niccolò; Bonito, Gregory; Baciarelli Falini, Leonardo; Bencivenga, Mattia

    2012-07-01

    Pecan (Carya illinoinensis) is an economically important nut tree native to the Mississippi basin and cultivated worldwide. In North America, species of truffles are regularly found fruiting in productive pecan orchards and the truffle genus Tuber appears to be abundant in pecan ectomycorrhizal (EM) communities. As an initial step to determine the feasibility of co-cropping European truffle species with pecan, we evaluated whether mycorrhizae of highly esteemed European truffle species (Tuber aestivum Vittad. T. borchii and T. macrosporum) could be formed on pecan seedlings. Seedlings were inoculated with truffle spores and were grown in a greenhouse for 10 months. Levels of EM colonization were estimated visually and quantified by counting EM tips. Ectomycorrhizae were identified both morphologically and molecularly with species-specific amplification and by sequencing of the ITS region of the nuclear ribosomal DNA (nrDNA). Both T. borchii and T. aestivum spores produced well-formed ectomycorrhizae on pecan seedlings with average root colonization levels of about 62% and 42%, respectively, whereas no ectomycorrhizae of T. macrosporum were formed. The anatomy and morphology of these truffle ectomycorrhizae on pecan was characterized. The co-cropping of T. aestivum and T. borchii may hold promise as an additional stream of revenue to pecan growers, although, further studies are needed to assess whether this symbiosis is maintained after planting in the field and whether truffle production can be supported by this host species. PMID:21986799

  6. Molecular cloning and characterization of an up-regulated UDP-glucosyltransferase gene induced by DON from Triticum aestivum L. cv. Wangshuibai.

    PubMed

    Lulin, Ma; Yi, Shang; Aizhong, Cao; Zengjun, Qi; Liping, Xing; Peidu, Chen; Dajun, Liu; Xiu-E, Wang

    2010-02-01

    Fusarium head blight, also called scab, is a serious disease of small grain cereals and maize. Scab can not only cause yield loss, more seriously is that it can also deteriorate seed quality by contaminating the infected grains with trichothecenes toxins harmful to human and animal health. Deoxynivalenol (DON) is one of the most important toxin members. It was proposed that DON acted first as a virulence factor during fungal pathogenesis and then accumulated in grain to levels posing a threat to human and animal health. In the present research, by expression analysis of DON-induced samples using GeneChip Wheat Genome Array ( http://www.affymetrix.com/products/arrays/specific/wheat.affx ), a DON-resistance related gene TaUGT3 (GenBank accession FJ236328) was cloned and characterized from a scab resistant wheat (Triticum aestivum L.) variety Wangshuibai. The full-length cDNA of TaUGT3 was 1,755 bp and contained a putative open reading frame (ORF) with 496 amino acids encoding a UDP-glucosyltransferase (UGT). TaUGT3 showed high similarity in amino acid level with DOGT1 gene in Arabidopsis, which is able to detoxify DON. TaUGT3 was located on the group 3 chromosomes of wheat using nulli-tetrasomic lines and deletion lines of Chinese Spring. Co-transformed of TaUGT3 with GFP genes to onion epidermis cells using transient transformation technique by microprojectile bombardment indicated the subcellular location of the protein encoded by TaUGT3 was in the plasma membrane and nuclear. Transformation and overexpression of the TaUGT3 gene in Arabidopsis could enhance tolerance against DON. PMID:19585272

  7. Aquaculture Genomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genomics chapter covers the basics of genome mapping and sequencing and the current status of several relevant species. The chapter briefly describes the development and use of (cDNA, BAC, etc.) libraries for mapping and obtaining specific sequence information. Other topics include comparative ...

  8. Infrared microspectroscopic imaging of plant tissues: spectral visualization of Triticum aestivum kernel and Arabidopsis leaf microstructure

    PubMed Central

    Warren, Frederick J; Perston, Benjamin B; Galindez-Najera, Silvia P; Edwards, Cathrina H; Powell, Prudence O; Mandalari, Giusy; Campbell, Grant M; Butterworth, Peter J; Ellis, Peter R

    2015-01-01

    Infrared microspectroscopy is a tool with potential for studies of the microstructure, chemical composition and functionality of plants at a subcellular level. Here we present the use of high-resolution bench top-based infrared microspectroscopy to investigate the microstructure of Triticum aestivum L. (wheat) kernels and Arabidopsis leaves. Images of isolated wheat kernel tissues and whole wheat kernels following hydrothermal processing and simulated gastric and duodenal digestion were generated, as well as images of Arabidopsis leaves at different points during a diurnal cycle. Individual cells and cell walls were resolved, and large structures within cells, such as starch granules and protein bodies, were clearly identified. Contrast was provided by converting the hyperspectral image cubes into false-colour images using either principal component analysis (PCA) overlays or by correlation analysis. The unsupervised PCA approach provided a clear view of the sample microstructure, whereas the correlation analysis was used to confirm the identity of different anatomical structures using the spectra from isolated components. It was then demonstrated that gelatinized and native starch within cells could be distinguished, and that the loss of starch during wheat digestion could be observed, as well as the accumulation of starch in leaves during a diurnal period. PMID:26400058

  9. Toxic effect of perfluorooctanoic acid (PFOA) on germination and seedling growth of wheat (Triticum aestivum L.).

    PubMed

    Zhou, Lina; Xia, Mengjie; Wang, Li; Mao, Hui

    2016-09-01

    As a persistent organic pollutant in the environment, perfluorooctanoic acid (PFOA) has been extensively investigated. It can accumulate in food chains and in the human body. This work investigated the effect of PFOA on wheat (Triticum aestivum L.) germination and seedling growth by conducting a germination trial and a pot trial. A stimulatory effect of PFOA on seedling growth and root length of wheat was found at <0.2 mg kg(-1), while >800 mg kg(-1) PFOA inhibited germination rate, index, and root and shoot growth. In the pot trial, PFOA concentration in root was double that in the shoot. Soil and plant analyzer development (SPAD) and plant height of wheat seedling were inhibited by adding 200 mg kg(-1) PFOA. Proline content and POD activity in wheat seedlings increased as PFOA increased, while CAT activity decreased. Using logarithmic equations, proline content was selected as the most sensitive index by concentration for 50% of maximal effect (EC50). Hence, the tolerance of wheat seedlings to PFOA levels could be evaluated on the basis of the physiological index. PMID:27337433

  10. Proteomic Analysis Reveals Key Proteins and Phosphoproteins upon Seed Germination of Wheat (Triticum aestivum L.).

    PubMed

    Dong, Kun; Zhen, Shoumin; Cheng, Zhiwei; Cao, Hui; Ge, Pei; Yan, Yueming

    2015-01-01

    Wheat (Triticum aestivum L.) is one of the oldest cultivated crops and the second most important food crop in the world. Seed germination is the key developmental process in plant growth and development, and poor germination directly affects plant growth and subsequent grain yield. In this study, we performed the first dynamic proteome analysis of wheat seed germination using a two-dimensional differential gel electrophoresis (2D-DIGE)-based proteomic approach. A total of 166 differentially expressed protein (DEP) spots representing 73 unique proteins were identified, which are mainly involved in storage, stress/defense/detoxification, carbohydrate metabolism, photosynthesis, cell metabolism, and transcription/translation/transposition. The identified DEPs and their dynamic expression profiles generally correspond to three distinct seed germination phases after imbibition: storage degradation, physiological processes/morphogenesis, and photosynthesis. Some key DEPs involved in storage substance degradation and plant defense mechanisms, such as globulin 3, sucrose synthase type I, serpin, beta-amylase, and plastid ADP-glucose pyrophosphorylase (AGPase) small subunit, were found to be phosphorylated during seed germination. Particularly, the phosphorylation site Ser(355) was found to be located in the enzyme active region of beta-amylase, which promotes substrate binding. Phosphorylated modification of several proteins could promote storage substance degradation and environmental stress defense during seed germination. The central metabolic pathways involved in wheat seed germination are proposed herein, providing new insights into the molecular mechanisms of cereal seed germination. PMID:26635843

  11. Ractopamine up take by alfalfa (Medicago sativa) and wheat (Triticum aestivum) from soil.

    PubMed

    Shelver, Weilin L; DeSutter, Thomas M

    2015-08-01

    Ractopamine is a beta adrenergic agonist used as a growth promoter in swine, cattle and turkeys. To test whether ractopamine has the potential to accumulate in plants grown in contaminated soil, a greenhouse study was conducted with alfalfa (Medicago sativa) and wheat (Triticum aestivum) grown in two soils having different concentrations of organic matter (1.3% and 2.1%), amended with 0, 0.5, and 10 μg/g of ractopamine. Plant growth ranged from 2.7 to 8.8 g dry weight (dw) for alfalfa, and 8.7 to 40 g dw for wheat and was generally greater in the higher organic matter content soil. The uptake of ractopamine in plant tissues ranged from non-detectable to 897 ng/g and was strongly dependent on soil ractopamine concentration across soil and plant tissue. When adjusted to the total fortified quantities, the amount of ractopamine taken up by the plant tissue was low, <0.01% for either soil. PMID:26257350

  12. Functional study of a salt-inducible TaSR gene in Triticum aestivum.

    PubMed

    Ma, Xiao-Li; Cui, Wei-Na; Zhao, Qian; Zhao, Jing; Hou, Xiao-Na; Li, Dong-Yan; Chen, Zhao-Liang; Shen, Yin-Zhu; Huang, Zhan-Jing

    2016-01-01

    The gene expression chip of a salt-tolerant wheat mutant under salt stress was used to clone a salt-induced gene with unknown functions. This gene was designated as TaSR (Triticum aestivum salt-response gene) and submitted to GenBank under accession number EF580107. Quantitative polymerase chain reaction (PCR) analysis showed that gene expression was induced by salt stress. Arabidopsis and rice (Oryza sativa) plants expressing TaSR presented higher salt tolerance than the controls, whereas AtSR mutant and RNA interference rice plants were more sensitive to salt. Under salt stress, TaSR reduced Na(+) concentration and improved cellular K(+) and Ca(2+) concentrations; this gene was also localized on the cell membrane. β-Glucuronidase (GUS) staining and GUS fluorescence quantitative determination were conducted through fragmentation cloning of the TaSR promoter. Salt stress-responsive elements were detected at 588-1074 bp upstream of the start codon. GUS quantitative tests of the full-length promoter in different tissues indicated that promoter activity was highest in the leaf under salt stress. Bimolecular fluorescence complementation and yeast two-hybrid screening further showed the correlation of TaSR with TaPRK and TaKPP. In vitro phosphorylation of TaSR and TaPRK2697 showed that TaPRK2697 did not phosphorylate TaSR. This study revealed that the novel TaSR may be used to improve plant tolerance to salt stress. PMID:25855206

  13. Cerium oxide nanoparticles impact yield and modify nutritional parameters in wheat (Triticum aestivum L.).

    PubMed

    Rico, Cyren M; Lee, Sang Chul; Rubenecia, Rosnah; Mukherjee, Arnab; Hong, Jie; Peralta-Videa, Jose R; Gardea-Torresdey, Jorge L

    2014-10-01

    The implications of engineered nanomaterials on crop productivity and food quality are not yet well understood. The impact of cerium oxide nanoparticles (nCeO2) on growth and yield attributes and nutritional composition in wheat (Triticum aestivum L.) was examined. Wheat was cultivated to grain production in soil amended with 0, 125, 250, and 500 mg of nCeO2/kg (control, nCeO2-L, nCeO2-M, and nCeO2-H, respectively). At harvest, grains and tissues were analyzed for mineral, fatty acid, and amino acid content. Results showed that, relative to the control, nCeO2-H improved plant growth, shoot biomass, and grain yield by 9.0%, 12.7%, and 36.6%, respectively. Ce accumulation in roots increased at increased nCeO2 concentration but did not change across treatments in leaves, hull, and grains, indicating a lack of Ce transport to the above-ground tissues. nCeO2 modified S and Mn storage in grains. nCeO2-L modified the amino acid composition and increased linolenic acid by up to 6.17% but decreased linoleic acid by up to 1.63%, compared to the other treatments. The findings suggest the potential of nanoceria to modify crop physiology and food quality with unknown consequences for living organisms. PMID:25220448

  14. Infrared microspectroscopic imaging of plant tissues: spectral visualization of Triticum aestivum kernel and Arabidopsis leaf microstructure.

    PubMed

    Warren, Frederick J; Perston, Benjamin B; Galindez-Najera, Silvia P; Edwards, Cathrina H; Powell, Prudence O; Mandalari, Giusy; Campbell, Grant M; Butterworth, Peter J; Ellis, Peter R

    2015-11-01

    Infrared microspectroscopy is a tool with potential for studies of the microstructure, chemical composition and functionality of plants at a subcellular level. Here we present the use of high-resolution bench top-based infrared microspectroscopy to investigate the microstructure of Triticum aestivum L. (wheat) kernels and Arabidopsis leaves. Images of isolated wheat kernel tissues and whole wheat kernels following hydrothermal processing and simulated gastric and duodenal digestion were generated, as well as images of Arabidopsis leaves at different points during a diurnal cycle. Individual cells and cell walls were resolved, and large structures within cells, such as starch granules and protein bodies, were clearly identified. Contrast was provided by converting the hyperspectral image cubes into false-colour images using either principal component analysis (PCA) overlays or by correlation analysis. The unsupervised PCA approach provided a clear view of the sample microstructure, whereas the correlation analysis was used to confirm the identity of different anatomical structures using the spectra from isolated components. It was then demonstrated that gelatinized and native starch within cells could be distinguished, and that the loss of starch during wheat digestion could be observed, as well as the accumulation of starch in leaves during a diurnal period. PMID:26400058

  15. Movement of 14C-labeled Sugars into Kernels of Wheat (Triticum aestivum L.) 1

    PubMed Central

    Sakri, Faisal A. K.; Shannon, Jack C.

    1975-01-01

    An anatomical study of wheat (Triticum aestivum L.) kernels 14 days after anthesis revealed that the tracheary elements of the pericarp vascular bundle are not in direct continuity with those of the rachilla. The phloem was continuous from the rachilla into the crease of the pericarp. Shortly after exposure of the flag leaf to 14CO2, relatively high proportion of the 14C extracted from the pericarp and endosperm was found in glucose and fructose. With additional time, the percentage of 14C in the monosaccharides declined and that in sucrose increased to a maximum 3 hours after 14CO2 exposure. The monosaccharides comprised about one-half of the soluble sugars extracted from the pericarp. Based on these observations, it appeared that sucrose hydrolysis might be prerequisite to sugar movement from the terminal phloem elements in the pericarp and into the endosperm. However, when 14C-fructosyl-sucrose was injected into the peduncle, there was little additional randomization of the 14C between the glucose and fructose moieties of sucrose extracted from the pericarp and endosperm compared to the rachis sucrose. If we assume that injected sucose was transported to the kernels via the phloem, then either sucrose moves out of the terminal phloem elements in the pericarp and into the endosperm unaltered, or if hydrolysis and resynthesis are a prerequisite to transport into the endosperm, the products of hydrolysis are not freely available for isomerization. Images PMID:16659185

  16. Measurement of phloem transport rates by an indicator-dilution technique. [Triticum aestivum L

    SciTech Connect

    Fisher, D.B. )

    1990-10-01

    An indicator-dilution technique for the measurement of flow rates, commonly used by animal physiologists for circulation measurements, was adapted to the measurement of phloem translocation rates in the wheat (Triticum aestivum L.) peduncle. The approach is based on the observation that, during the transport of a given amount of solute, its mean concentration will be inversely proportional to flow rate. For phloem transport in the wheat peduncle, the necessary measurements are (a) the time course of tracer kinetics in the peduncle phloem, (b)the volume of sieve tubes and companion cells in the monitored segment of the peduncle, and (c) the amount of tracer transported past that point. The method was evaluated by in situ monitoring of {sup 32}PO{sub 4} transport in pulse-labeling experiments. Specific activities (i.e. {sup 32}P concentrations) of phloem exudate were in good agreement with those calculated from in situ count rates and measured phloem areas. Mass transport rates, calculated from volume flow rates and phloem exudate dry matter content, also agreed well with expected mass transport rates based on measurements of grain growth rate and net CO{sub 2} exchange by the ear. The indicator-dilution technique appears to offer good precision and accuracy for short-term measurements of phloem transport rates in the wheat peduncle and should be useful for other systems as well.

  17. Uptake of a cyanotoxin, β-N-methylamino-L-alanine, by wheat (Triticum aestivum).

    PubMed

    Contardo-Jara, Valeska; Schwanemann, Torsten; Pflugmacher, Stephan

    2014-06-01

    In order to study the uptake of the cyanobacterial neurotoxin β-N-methylamino-l-alanine (BMAA) into the crop plant Triticum aestivum during germination and primary growth imbibed grains and 7-day-old seedlings were irrigated with 100 and 1000µg l(-1) BMAA for 4 days and 100µg l(-1) BMAA for 28 days. Content of derivatized free and protein-associated BMAA in seedlings, root and shoot tissue, respectively, were analyzed by LC-MS/MS. Free BMAA was only detected in seedlings exposed to 1000µg l(-1) BMAA, whereas protein-associated BMAA was found at both exposure concentrations. Irrigation with 100µgl(-1) BMAA led to an uptake of the neurotoxin into roots and shoots and to immediate protein-association. In roots, protein-associated BMAA was detectable after 5 days with peaking amounts after 14 days. Longer exposure did not cause further accumulation in roots. In contrast, protein-associated BMAA was detected in shoot samples after only 1 day. In shoots the highest amounts of protein-associated BMAA were found after 28 days. In turn, in both plant compartments free BMAA was below the measurable concentration. PMID:24675440

  18. Effect of Lead stress on phosphatase activity and reducing power assay of Triticum aestivum.

    PubMed

    Gubrelay, U; Agnihotri, R K; Shrotriya, S; Sharma, R

    2015-01-01

    Lead (Pb) is a highly toxic heavy metal for both plants and animals; the environment is increasingly polluted with heavy metals and reduces crop productivity. Plants possess homeostatic mechanisms that allow them to keep correct concentrations of essential metal ions in cellular compartments and to minimize the damaging effects of an excess of nonessential ones. One of their adverse effects on plants are the generation of harmful active oxygen species, leading to oxidative stress and the antioxidative activity seems to be of fundamental importance for adaptive response of plant against environmental stress. The present study explores the effects of lead (soil treated twice/ week) with (10, 30 and 60 mM) on the specific activities of phosphatases which might lead to reducing power assay in (Triticum aestivum PBW344) seedling. A significant decrease in the redox potential of shoot compared to root was observed at the similar concentration of lead. A similar trend on leaves was also noted. Acid and alkaline phosphatase activities were significantly higher in roots than in shoot at all the three concentration of lead i.e. 10, 30 and 60 mM, compared to controls. The above mentioned changes were more pronounced at 60 mM concentration of lead than two other concentrations. These results lead us to suggest that increased lead concentration in soil might lead to adverse effects on plant growth and phosphatase activities. PMID:26107501

  19. Proteomic Analysis Reveals Key Proteins and Phosphoproteins upon Seed Germination of Wheat (Triticum aestivum L.)

    PubMed Central

    Dong, Kun; Zhen, Shoumin; Cheng, Zhiwei; Cao, Hui; Ge, Pei; Yan, Yueming

    2015-01-01

    Wheat (Triticum aestivum L.) is one of the oldest cultivated crops and the second most important food crop in the world. Seed germination is the key developmental process in plant growth and development, and poor germination directly affects plant growth and subsequent grain yield. In this study, we performed the first dynamic proteome analysis of wheat seed germination using a two-dimensional differential gel electrophoresis (2D-DIGE)-based proteomic approach. A total of 166 differentially expressed protein (DEP) spots representing 73 unique proteins were identified, which are mainly involved in storage, stress/defense/detoxification, carbohydrate metabolism, photosynthesis, cell metabolism, and transcription/translation/transposition. The identified DEPs and their dynamic expression profiles generally correspond to three distinct seed germination phases after imbibition: storage degradation, physiological processes/morphogenesis, and photosynthesis. Some key DEPs involved in storage substance degradation and plant defense mechanisms, such as globulin 3, sucrose synthase type I, serpin, beta-amylase, and plastid ADP-glucose pyrophosphorylase (AGPase) small subunit, were found to be phosphorylated during seed germination. Particularly, the phosphorylation site Ser355 was found to be located in the enzyme active region of beta-amylase, which promotes substrate binding. Phosphorylated modification of several proteins could promote storage substance degradation and environmental stress defense during seed germination. The central metabolic pathways involved in wheat seed germination are proposed herein, providing new insights into the molecular mechanisms of cereal seed germination. PMID:26635843

  20. Nitrogen Metabolism in Senescent Flag Leaves of Wheat (Triticum aestivum L.) in the Light

    PubMed Central

    Berger, Michael G.; Woo, K. C.; Wong, Suan-Chin; Fock, Heinrich P.

    1985-01-01

    Nitrogen metabolism was examined in senescent flag leaves of 90- to 93-day-old wheat (Triticum aestivum L. cv Yecora 70) plants. CO2 assimilation and the levels of protein, chlorophyll, and nitrogen in the leaves decreased with age. Glutamine synthetase activity decreased to one-eighth of the level in young flag leaves. Detached leaves were incubated (with the cut base) in 15N-labeled NH3, glutamate, or glycine in the light (1.8 millieinstein per square meter per second) at 25°C in an open gas exchange system under normal atmospheric conditions for up to 135 minutes. The 15N-enrichment of various amino acids derived from these 15N-substrates were examined. The amido-N of glutamine was the first 15N-labeled product in leaves incubated with 15NH4Cl whereas serine, closely followed by the amido- and amino-N of glutamine, were the most highly 15N-labeled products during incubation with [15N]glycine. In contrast, aspartate and alanine were the first 15N-labeled products when [15N] glutamate was used. These results indicate that NH3 was assimilated via glutamine synthetase and glutamate synthase activities and the photorespiratory nitrogen cycle remained functional in these senescent wheat flag leaves. In contrast, an involvement of glutamate dehydrogenase in the assimilation of ammonia could not be detected in these tissues. PMID:16664324

  1. Arsenate (As) uptake by and distribution in two cultivars of winter wheat (Triticum aestivum L.).

    PubMed

    Geng, Chun-Nu; Zhu, Yong-Guan; Tong, Yi-Ping; Smith, Sally E; Smith, F A

    2006-01-01

    Two cultivars of winter wheat (Triticum aestivum L.) (Jing 411 and Lovrin 10) were used to investigate arsenate (As) uptake and distribution in plants grown in hydroponic culture and in the soil. Results showed that without As addition, Lovrin 10 had higher biomass than Jing 411 in the soil pot experiment; in the hydroponic experiment Lovrin 10 had similar root biomass to and lower shoot biomass than Jing 411. Increasing P supply from 32 to 161 microM resulted in lower tissue As concentrations, and increasing As supply from 0 to 2,000 microM resulted in lower tissue P concentrations. Increasing P supply tended to increase shoot-to-root ratios of As concentrations, and increasing As supply tended to decrease shoot-to-root ratios of As concentrations. Both cultivars invested more in root production under P deficient conditions than under P sufficient conditions. Lovrin 10 invested more biomass production to roots than Jing 411, which might be partly responsible for higher shoot P and As concentrations and higher shoot-to-root ratios of As concentrations. Moreover, Lovrin 10 allocated less As to roots than Jing 411 and the difference disappeared with decreasing P supply. PMID:16081139

  2. Composition of cuticular waxes coating flag leaf blades and peduncles of Triticum aestivum cv. Bethlehem.

    PubMed

    Racovita, Radu C; Hen-Avivi, Shelly; Fernandez-Moreno, Josefina-Patricia; Granell, Antonio; Aharoni, Asaph; Jetter, Reinhard

    2016-10-01

    The work herein presents comprehensive analyses of the cuticular wax mixtures covering the flag leaf blade and peduncle of bread wheat (Triticum aestivum) cv. Bethlehem. Overall, Gas Chromatography-Mass Spectrometry and Flame Ionization Detection revealed a wax coverage of flag leaf blades (16 μg/cm(2)) a third that of peduncles (49 μg/cm(2)). Flag leaf blade wax was dominated by 1-alkanols, while peduncle wax contained primarily β-diketone and hydroxy-β-diketones, thus suggesting differential regulation of the acyl reduction and β-diketone biosynthetic pathways in the two analyzed organs. The characteristic chain length distributions of the various wax compound classes are discussed in light of their individual biosynthetic pathways and biosynthetic relationships between classes. Along with previously reported wheat wax compound classes (fatty acids, 1-alkanols, 1-alkanol esters, aldehydes, alkanes, β-diketone, hydroxy-β-diketones, alkylresorcinols and methyl alkylresorcinols), esters of 2-alkanols and three types of aromatic esters (benzyl, phenethyl and p-hydroxyphenethyl) are also reported. In particular, 2-heptanol esters were identified. Detailed analyses of the isomer distributions within 1-alkanol and 2-alkanol ester homologs revealed distinct patterns of esterified acids and alcohols, suggesting several wax ester synthases with very different substrate preferences in both wheat organs. Terpenoids, including two terpenoid esters, were present only in peduncle wax. PMID:27264640

  3. Overexpression of a Triticum aestivum Calreticulin gene (TaCRT1) Improves Salinity Tolerance in Tobacco

    PubMed Central

    Song, Min; Wang, Yun; Xu, Wenqi; Wu, Lintao; Wang, Hancheng; Ma, Zhengqiang

    2015-01-01

    Calreticulin (CRT) is a highly conserved and abundant multifunctional protein that is encoded by a small gene family and is often associated with abiotic/biotic stress responses in plants. However, the roles played by this protein in salt stress responses in wheat (Triticum aestivum) remain obscure. In this study, three TaCRT genes were identified in wheat and named TaCRT1, TaCRT2 and TaCRT3-1 based on their sequence characteristics and their high homology to other known CRT genes. Quantitative real-time PCR expression data revealed that these three genes exhibit different expression patterns in different tissues and are strongly induced under salt stress in wheat. The calcium-binding properties of the purified recombinant TaCRT1 protein were determined using a PIPES/Arsenazo III analysis. TaCRT1 gene overexpression in Nicotiana tabacum decreased salt stress damage in transgenic tobacco plants. Physiological measurements indicated that transgenic tobacco plants showed higher activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) than non-transgenic tobacco under normal growth conditions. Interestingly, overexpression of the entire TaCRT1 gene or of partial TaCRT1 segments resulted in significantly higher tolerance to salt stress in transgenic plants compared with their WT counterparts, thus revealing the essential role of the C-domain of TaCRT1 in countering salt stress in plants. PMID:26469859

  4. Neuroprotective effects of Triticum aestivum L. against beta-amyloid-induced cell death and memory impairments.

    PubMed

    Jang, Jung-Hee; Kim, Chang-Yul; Lim, Sun Ha; Yang, Chae Ha; Song, Kyung-Sik; Han, Hyung Soo; Lee, Hyeong-Kyu; Lee, Jongwon

    2010-01-01

    beta-Amyloid (A beta) is a key component of senile plaques, neuropathological hallmarks of Alzheimer's disease (AD) and has been reported to induce cell death via oxidative stress. This study investigated the protective effects of Triticum aestivum L. (TAL) on A beta-induced apoptosis in SH-SY5Y cells and cognitive dysfunctions in Sprague-Dawley (SD) rats. Cells treated with A beta exhibited decreased viability and apoptotic features, such as DNA fragmentation, alterations in mitochondria and an increased Bax/Bcl-2 ratio, which were attenuated by TAL extract (TALE) pretreatment. To elucidate the neuroprotective mechanisms of TALE, the study examined A beta-induced oxidative stress and cellular defense. TALE pretreatment suppressed A beta-increased intracellular accumulation of reactive oxygen species (ROS) via up-regulation of glutathione, an essential endogenous antioxidant. To further verify the effect of TALE on memory impairments, A beta or scopolamine was injected in SD rats and a water maze task conducted as a spatial memory test. A beta or scopolamine treatment increased the time taken to find the platform during training trials, which was decreased by TALE pretreatment. Furthermore, one of the active components of TALE, total dietary fiber also effectively inhibited A beta-induced cytotoxicity and scopolamine-caused memory deficits. These results suggest that TALE may have preventive and/or therapeutic potential in the management of AD. PMID:19441012

  5. Transcriptome Analysis of Purple Pericarps in Common Wheat (Triticum aestivum L.)

    PubMed Central

    Chen, Wenjie; Zhang, Bo; Liu, Dengcai; Liu, Baolong; Zhang, Huaigang

    2016-01-01

    Wheat (Triticum aestivum L.) cultivars possessing purple grain arethought to be more nutritious because of high anthocyanin contents in the pericarp. Comparative transcriptome analysis of purple (cv Gy115) and white pericarps was carried out using next-generation sequencing technology. There were 23,642 unigenes significantly differentially expressed in the purple and white pericarps, including 9945 up-regulated and 13,697 down-regulated. The differentially expressed unigenes were mainly involved in encoding components of metabolic pathways, The flavonoid biosynthesis pathway was the most represented in metabolic pathways. In the transcriptome of purple pericarp in Gy115, most structural and regulatory genes biosynthesizing anthocyanin were identified, and had higher expression levels than in white pericarp. The largestunigene of anthocyanin biosynthesis in Gy115 was longer than the reference genes, which implies that high-throughput sequencing could isolate the genes of anthocyanin biosynthesis in tissues or organs with high anthocyanin content. Based on present and previous results, three unigenes of MYB gene on chromosome 7BL and three unigenes of MYC on chromosome 2AL were predicted as candidate genes for the purple grain trait. This article was the first to provide a systematic overview comparing the transcriptomes of purple and white pericarps in common wheat, which should be very valuable for identifying the key genes for the purple pericarp trait. PMID:27171148

  6. Genetic Diversity and Population Structure Analysis of European Hexaploid Bread Wheat (Triticum aestivum L.) Varieties

    PubMed Central

    Nielsen, Nanna Hellum; Backes, Gunter; Stougaard, Jens; Andersen, Stig Uggerhøj; Jahoor, Ahmed

    2014-01-01

    Progress in plant breeding is facilitated by accurate information about genetic structure and diversity. Here, Diversity Array Technology (DArT) was used to characterize a population of 94 bread wheat (Triticum aestivum L.) varieties of mainly European origin. In total, 1,849 of 7,000 tested markers were polymorphic and could be used for population structure analysis. Two major subgroups of wheat varieties, GrI and GrII, were identified using the program STRUCTURE, and confirmed by principal component analysis (PCA). These subgroups were largely separated according to origin; GrI comprised varieties from Southern and Eastern Europe, whereas GrII contained mostly modern varieties from Western and Northern Europe. A large proportion of the markers contributing most to the genetic separation of the subgroups were located on chromosome 2D near the Reduced height 8 (Rht8) locus, and PCR-based genotyping suggested that breeding for the Rht8 allele had a major impact on subgroup separation. Consistently, analysis of linkage disequilibrium (LD) suggested that different selective pressures had acted on chromosome 2D in the two subgroups. Our data provides an overview of the allele composition of bread wheat varieties anchored to DArT markers, which will facilitate targeted combination of alleles following DArT-based QTL studies. In addition, the genetic diversity and distance data combined with specific Rht8 genotypes can now be used by breeders to guide selection of crossing parents. PMID:24718292

  7. Dissecting miRNAs in Wheat D Genome Progenitor, Aegilops tauschii.

    PubMed

    Akpinar, Bala A; Budak, Hikmet

    2016-01-01

    As the post-transcriptional regulators of gene expression, microRNAs or miRNAs comprise an integral part of understanding how genomes function. Although miRNAs have been a major focus of recent efforts, miRNA research is still in its infancy in most plant species. Aegilops tauschii, the D genome progenitor of bread wheat, is a wild diploid grass exhibiting remarkable population diversity. Due to the direct ancestry and the diverse gene pool, A. tauschii is a promising source for bread wheat improvement. In this study, a total of 87 Aegilops miRNA families, including 51 previously unknown, were computationally identified both at the subgenomic level, using flow-sorted A. tauschii 5D chromosome, and at the whole genome level. Predictions at the genomic and subgenomic levels suggested A. tauschii 5D chromosome as rich in pre-miRNAs that are highly associated with Class II DNA transposons. In order to gain insights into miRNA evolution, putative 5D chromosome miRNAs were compared to its modern ortholog, Triticum aestivum 5D chromosome, revealing that 48 of the 58 A. tauschii 5D miRNAs were conserved in orthologous T. aestivum 5D chromosome. The expression profiles of selected miRNAs (miR167, miR5205, miR5175, miR5523) provided the first experimental evidence for miR5175, miR5205 and miR5523, and revealed differential expressional changes in response to drought in different genetic backgrounds for miR167 and miR5175. Interestingly, while miR5523 coding regions were present and expressed as pre-miR5523 in both T. aestivum and A. tauschii, the expression of mature miR5523 was observed only in A. tauschii under normal conditions, pointing out to an interference at the downstream processing of pre-miR5523 in T. aestivum. Overall, this study expands our knowledge on the miRNA catalog of A. tauschii, locating a subset specifically to the 5D chromosome, with ample functional and comparative insight which should contribute to and complement efforts to develop drought tolerant

  8. Dissecting miRNAs in Wheat D Genome Progenitor, Aegilops tauschii

    PubMed Central

    Akpinar, Bala A.; Budak, Hikmet

    2016-01-01

    As the post-transcriptional regulators of gene expression, microRNAs or miRNAs comprise an integral part of understanding how genomes function. Although miRNAs have been a major focus of recent efforts, miRNA research is still in its infancy in most plant species. Aegilops tauschii, the D genome progenitor of bread wheat, is a wild diploid grass exhibiting remarkable population diversity. Due to the direct ancestry and the diverse gene pool, A. tauschii is a promising source for bread wheat improvement. In this study, a total of 87 Aegilops miRNA families, including 51 previously unknown, were computationally identified both at the subgenomic level, using flow-sorted A. tauschii 5D chromosome, and at the whole genome level. Predictions at the genomic and subgenomic levels suggested A. tauschii 5D chromosome as rich in pre-miRNAs that are highly associated with Class II DNA transposons. In order to gain insights into miRNA evolution, putative 5D chromosome miRNAs were compared to its modern ortholog, Triticum aestivum 5D chromosome, revealing that 48 of the 58 A. tauschii 5D miRNAs were conserved in orthologous T. aestivum 5D chromosome. The expression profiles of selected miRNAs (miR167, miR5205, miR5175, miR5523) provided the first experimental evidence for miR5175, miR5205 and miR5523, and revealed differential expressional changes in response to drought in different genetic backgrounds for miR167 and miR5175. Interestingly, while miR5523 coding regions were present and expressed as pre-miR5523 in both T. aestivum and A. tauschii, the expression of mature miR5523 was observed only in A. tauschii under normal conditions, pointing out to an interference at the downstream processing of pre-miR5523 in T. aestivum. Overall, this study expands our knowledge on the miRNA catalog of A. tauschii, locating a subset specifically to the 5D chromosome, with ample functional and comparative insight which should contribute to and complement efforts to develop drought tolerant

  9. Antarctic Genomics

    PubMed Central

    Clarke, Andrew; Cockell, Charles S.; Convey, Peter; Detrich III, H. William; Fraser, Keiron P. P.; Johnston, Ian A.; Methe, Barbara A.; Murray, Alison E.; Peck, Lloyd S.; Römisch, Karin; Rogers, Alex D.

    2004-01-01

    With the development of genomic science and its battery of technologies, polar biology stands on the threshold of a revolution, one that will enable the investigation of important questions of unprecedented scope and with extraordinary depth and precision. The exotic organisms of polar ecosystems are ideal candidates for genomic analysis. Through such analyses, it will be possible to learn not only the novel features that enable polar organisms to survive, and indeed thrive, in their extreme environments, but also fundamental biological principles that are common to most, if not all, organisms. This article aims to review recent developments in Antarctic genomics and to demonstrate the global context of such studies. PMID:18629155

  10. HANDS: a tool for genome-wide discovery of subgenome-specific base-identity in polyploids

    PubMed Central

    2013-01-01

    Background The analysis of polyploid genomes is problematic because homeologous subgenome sequences are closely related. This relatedness makes it difficult to assign individual sequences to the specific subgenome from which they are derived, and hinders the development of polyploid whole genome assemblies. Results We here present a next-generation sequencing (NGS)-based approach for assignment of subgenome-specific base-identity at sites containing homeolog-specific polymorphisms (HSPs): ‘HSP base Assignment using NGS data through Diploid Similarity’ (HANDS). We show that HANDS correctly predicts subgenome-specific base-identity at >90% of assayed HSPs in the hexaploid bread wheat (Triticum aestivum) transcriptome, thus providing a substantial increase in accuracy versus previous methods for homeolog-specific base assignment. Conclusion We conclude that HANDS enables rapid and accurate genome-wide discovery of homeolog-specific base-identity, a capability having multiple applications in polyploid genomics. PMID:24063258

  11. Genomic Testing

    MedlinePlus

    ... Working Group Independent Web site Informing the effective integration of genomics into health practice—Lynch syndrome ACCE Model for Evaluating Genetic Tests Recommendations by the EGAPP Working Group Top of ... ...

  12. Aluminum Tolerance in Wheat (Triticum aestivum L.) (I. Uptake and Distribution of Aluminum in Root Apices).

    PubMed Central

    Delhaize, E.; Craig, S.; Beaton, C. D.; Bennet, R. J.; Jagadish, V. C.; Randall, P. J.

    1993-01-01

    We investigated the uptake and distribution of Al in root apices of near-isogenic wheat (Triticum aestivum L.) lines differing in Al tolerance at a single locus (Alt1: aluminum tolerance). Seedlings were grown in nutrient solution that contained 100 [mu]M Al, and the roots were subsequently stained with hematoxylin, a compound that binds Al in vitro to form a colored complex. Root apices of Al-sensitive genotypes stained after short exposures to Al (10 min and 1 h), whereas apices of Al-tolerant seedlings showed less intense staining after equivalent exposures. Differential staining preceded differences observed in either root elongation or total Al concentrations of root apices (terminal 2-3 mm of root). After 4 h of exposure to 100 [mu]M Al in nutrient solution, Al-sensitive genotypes accumulated more total Al in root apices than Al-tolerant genotypes, and the differences became more marked with time. Analysis of freeze-dried root apices by x-ray microanalysis showed that Al entered root apices of Al-sensitive plants and accumulated in the epidermal layer and in the cortical layer immediately below the epidermis. Long-term exposure of sensitive apices to Al (24 h) resulted in a distribution of Al coinciding with the absence of K. Quantitation of Al in the cortical layer showed that sensitive apices accumulated 5- to 10-fold more Al than tolerant apices exposed to Al solutions for equivalent times. These data are consistent with the hypothesis that Alt1 encodes a mechanism that excludes Al from root apices. PMID:12231972

  13. Cultivar variations in cadmium and lead accumulation and distribution among 30 wheat (Triticum aestivum L.) cultivars.

    PubMed

    Liu, Weitao; Liang, Lichen; Zhang, Xue; Zhou, Qixing

    2015-06-01

    In recent years, heavy metal pollution in agricultural soil in China has received public concern. The concept of low-accumulation cultivars (LACs) was proposed to minimize the influx of pollutants to the human food chain. Variations in Cd and Pb accumulation, distribution, and tolerance among 30 wheat (Triticum aestivum L.) cultivars were studied in a hydroponic experiment to preliminary identify LACs of Cd or Pb for further field experiments. Of the 30 wheat cultivars tested, 27 and 26 wheat cultivars showed no effect of the Cd/Pb treatments on the shoot and root biomass, respectively. The results showed that the tested wheat cultivars had considerable tolerance to Cd and Pb toxicity. Significant (p < 0.05) differences in shoot Cd concentration were observed among the tested wheat cultivars under treatments Cd1.0 and Cd1.0Pb15, ranging from 0.91 to 6.74 and from 0.87 to 5.96, with the mean of 3.83 and 2.94 mg kg(-1) DW, respectively. Significant (p < 0.05) differences in shoot Pb concentration were also observed among the tested wheat cultivars under treatments Pb15 and Cd1.0Pb15, ranging from 22.18 to 94.03 and from 18.30 to 76.88, with the mean of 50.38 and 41.20 mg kg(-1) DW, respectively. Low accumulation and internal distribution may both affect the cultivar differences in Cd and Pb accumulation in wheat shoots. Overall, wheat cultivars LF-13, LF-16, and LF-21 had lower Cd-accumulating abilities in their shoots. Wheat cultivars LF-13, LF-23, LF-26, and LF-27 showed low Pb accumulation characteristics in their shoots. An antagonistic interaction occurred between Cd and Pb in accumulation in wheat roots and shoots, which will be further studied in field experiments. PMID:25548022

  14. Factors Affecting the Radiosensitivity of Hexaploid Wheat to -Irradiation: Radiosensitivity of Hexaploid Wheat (Triticum aestivum L.).

    PubMed

    Han, Bing; Gu, Jiayu; Zhao, Linshu; Guo, Huijun; Xie, Yongdun; Zhao, Shirong; Song, Xiyun; Han, Longzhi; Liu, Luxiang

    2016-01-01

    Understanding the radiosensitivity of plants, an important factor in crop mutation breeding programs, requires a thorough investigation of the factors that contribute to this trait. In this study, we used the highly radiosensitive wheat (Triticum aestivum L.) variety HY1 and J411, a γ-irradiation-insensitive control, which were screened from a natural population, to examine the factors affecting radiosensitivity, including free radical content and total antioxidant capacity, as well as the expression of TaKu70 and TaKu80 (DNA repair-related genes) as measured by real-time PCR. We also investigated the alternative splicing of this gene in the wild-type wheat ecotype by sequence analysis. Free radical contents and total antioxidant capacity significantly increased upon exposure of HY1 wheat to γ-irradiation in a dose-dependent manner. By contrast, in J411, the free radical contents exhibited a similar trend, but the total antioxidant capacity exhibited a downward trend upon increasing γ-irradiation. Additionally, we detected dose-dependent increases in TaKu70 and TaKu80 expression levels in γ-irradiated HY1, while in J411, TaKu70 expression levels increased, followed by a decline. We also detected alternative splicing of TaKu70 mRNA, namely, intron retention, in HY1 but not in J411. Our findings indicate that γ-irradiation induces oxidative stress and DNA damage in hexaploid wheat, resulting in growth retardation of seedlings, and they suggest that TaKu70 may play a causal role in radiosensitivity in HY1. Further studies are required to exploit these factors to improve radiosensitivity in other wheat varieties. PMID:27551965

  15. New isoforms and assembly of glutamine synthetase in the leaf of wheat (Triticum aestivum L.).

    PubMed

    Wang, Xiaochun; Wei, Yihao; Shi, Lanxin; Ma, Xinming; Theg, Steven M

    2015-11-01

    Glutamine synthetase (GS; EC 6.3.1.2) plays a crucial role in the assimilation and re-assimilation of ammonia derived from a wide variety of metabolic processes during plant growth and development. Here, three developmentally regulated isoforms of GS holoenzyme in the leaf of wheat (Triticum aestivum L.) seedlings are described using native-PAGE with a transferase activity assay. The isoforms showed different mobilities in gels, with GSII>GSIII>GSI. The cytosolic GSI was composed of three subunits, GS1, GSr1, and GSr2, with the same molecular weight (39.2kDa), but different pI values. GSI appeared at leaf emergence and was active throughout the leaf lifespan. GSII and GSIII, both located in the chloroplast, were each composed of a single 42.1kDa subunit with different pI values. GSII was active mainly in green leaves, while GSIII showed brief but higher activity in green leaves grown under field conditions. LC-MS/MS experiments revealed that GSII and GSIII have the same amino acid sequence, but GSII has more modification sites. With a modified blue native electrophoresis (BNE) technique and in-gel catalytic activity analysis, only two GS isoforms were observed: one cytosolic and one chloroplastic. Mass calibrations on BNE gels showed that the cytosolic GS1 holoenzyme was ~490kDa and likely a dodecamer, and the chloroplastic GS2 holoenzyme was ~240kDa and likely a hexamer. Our experimental data suggest that the activity of GS isoforms in wheat is regulated by subcellular localization, assembly, and modification to achieve their roles during plant development. PMID:26307137

  16. Aluminum Tolerance in Wheat (Triticum aestivum L.) (I. Uptake and Distribution of Aluminum in Root Apices).

    PubMed

    Delhaize, E.; Craig, S.; Beaton, C. D.; Bennet, R. J.; Jagadish, V. C.; Randall, P. J.

    1993-11-01

    We investigated the uptake and distribution of Al in root apices of near-isogenic wheat (Triticum aestivum L.) lines differing in Al tolerance at a single locus (Alt1: aluminum tolerance). Seedlings were grown in nutrient solution that contained 100 [mu]M Al, and the roots were subsequently stained with hematoxylin, a compound that binds Al in vitro to form a colored complex. Root apices of Al-sensitive genotypes stained after short exposures to Al (10 min and 1 h), whereas apices of Al-tolerant seedlings showed less intense staining after equivalent exposures. Differential staining preceded differences observed in either root elongation or total Al concentrations of root apices (terminal 2-3 mm of root). After 4 h of exposure to 100 [mu]M Al in nutrient solution, Al-sensitive genotypes accumulated more total Al in root apices than Al-tolerant genotypes, and the differences became more marked with time. Analysis of freeze-dried root apices by x-ray microanalysis showed that Al entered root apices of Al-sensitive plants and accumulated in the epidermal layer and in the cortical layer immediately below the epidermis. Long-term exposure of sensitive apices to Al (24 h) resulted in a distribution of Al coinciding with the absence of K. Quantitation of Al in the cortical layer showed that sensitive apices accumulated 5- to 10-fold more Al than tolerant apices exposed to Al solutions for equivalent times. These data are consistent with the hypothesis that Alt1 encodes a mechanism that excludes Al from root apices. PMID:12231972

  17. Silver nanoparticles disrupt wheat (Triticum aestivum L.) growth in a sand matrix.

    PubMed

    Dimkpa, Christian O; McLean, Joan E; Martineau, Nicole; Britt, David W; Haverkamp, Richard; Anderson, Anne J

    2013-01-15

    Hydroponic plant growth studies indicate that silver nanoparticles (Ag NPs) are phytotoxic. In this work, the phytotoxicity of commercial Ag NPs (10 nm) was evaluated in a sand growth matrix. Both NPs and soluble Ag were recovered from water extracts of the sand after growth of plants challenged with the commercial product; the surface charge of the Ag NPs in this extract was slightly reduced compared to the stock NPs. The Ag NPs reduced the length of shoots and roots of wheat in a dose-dependent manner. Furthermore, 2.5 mg/kg of the NPs increased branching in the roots of wheat (Triticum aestivum L.), thereby affecting plant biomass. Micron-sized (bulk) Ag particles (2.5 mg/kg) as well as Ag ions (63 μg Ag/kg) equivalent to the amount of soluble Ag in planted sand with Ag NPs (2.5 mg/kg) did not affect plant growth compared to control. In contrast, higher levels of Ag ions (2.5 mg/kg) reduced plant growth to a similar extent as the Ag NPs. Accumulation of Ag was detected in the shoots, indicating an uptake and transport of the metal from the Ag NPs in the sand. Transmision electron microscopy indicated that Ag NPs were present in shoots of plants with roots exposed to the Ag NPs or high levels of Ag ions. Both of these treatments caused oxidative stress in roots, as indicated by accumulation of oxidized glutathione, and induced expression of a gene encoding a metallothionein involved in detoxification by metal ion sequestration. Our findings demonstrate the potential effects of environmental contamination by Ag NPs on the metabolism and growth of food crops in a solid matrix. PMID:23259709

  18. Zinc and copper uptake by plants under two transpiration rates. Part I. Wheat (Triticum aestivum L.).

    PubMed

    Tani, F H; Barrington, S

    2005-12-01

    To evaluate the environmental risk of irrigating crops with treated wastewater, an experiment was conducted using two growth chambers, each offering a different vapour pressure deficit (VPD) for high and low transpiration rates (TR), respectively. One of the two sets of 24 pots planted with 6 week old wheat (Triticum aestivum L.), was placed in each growth chamber, and irrigated in triplicates for 20 days with 8 Zn and Cu solutions (0 and 25 mg Zn/L combined with 0, 5, 15 and 30 mg Cu/L). Water losses from planted and non-planted pots served to measure evapo-transpiration and evaporation, respectively. Pots were monitored for Cu and Zn uptake by collecting three plants (shoot and grain)/pots after 0, 10 and 20 days, and roots in each pot after 20 days, and analyzing these plant parts for dry mass, and Cu and Zn levels. Transpiration rate was not affected by any Cu/Zn treatment, but Cu and Zn uptake increase with the time, irrigation solution level and higher TR, with the roots retaining most Cu and Zn, compared to the shoot followed by the grain. For the shoot and grain, Cu had a significant synergetic effect on Zn uptake, when Zn had slight but insignificant antagonistic effects on Cu uptake. For the roots, Cu and Zn had significant synergetic effect on each other. Regression equations obtained from the data indicate that Cu and Zn levels normally found in treated wastewater (0.08 mg/L) are 300 times lower than those used for the most concentrated experimental solutions (30 and 25 mg/L, respectively) and may, on a long term basis, be beneficial rather than toxic to wheat plants and do not acidify soil pH. PMID:16043273

  19. Novel nuclear-cytoplasmic interaction in wheat (Triticum aestivum) induces vigorous plants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Interspecific hybridization can be considered an accelerator of evolution, otherwise a slow process, solely dependent on mutation and recombination. Upon interspecific hybridization, several novel interactions between nuclear and cytoplasmic genomes emerge which provide additional sources of diversi...

  20. Cytogenetics of Triticum x Dasypyrum hybrids and derived lines.

    PubMed

    Minelli, S; Ceccarelli, M; Mariani, M; De Pace, C; Cionini, P G

    2005-01-01

    Genomic in situ hybridization was used to study Triticum x Dasypyrum wide hybrids and derived lines. A cytogenetic investigation was carried out in progenies of (i) amphiploids derived from T. turgidum var. durum (T. durum; 2n = 14; genomes AABB) x D. villosum (2n = 14; genome VV), (ii) three-parental hybrids (T. durum x D. villosum) x T. aestivum (2n = 42, genomes A'A'B'B'D'D'), and (iii) T. aestivum aneuploid lines carrying D. villosum chromosomes or chromatin. The amphiploids derived from T. durum x D. villosum showed a stable chromosomal constitution, made up of 14 V chromosomes, 14 chromosomes carrying the wheat A genome and 14 chromosomes carrying the B genome. High karyological instability was observed in the progenies of three-parental hybrids ([T. durum x D. villosum] x T. aestivum). Plants having the expected 14 A chromosomes, 14 B chromosomes, 7 D chromosomes, and 7 V chromosomes were rather rare (4.5%). Many progeny plants (45.5%) had the hexaploid wheat genome with 42 chromosomes and lacked any detectable D. villosum chromatin. Other plants (50%) had 14 A chromosomes and 14 B chromosomes, plus variable numbers of D and V chromosomes, the former being better retained than the latter in most cases. Some T. aestivum lines carrying D. villosum chromosomes or chromatin, as the result of addition, substitution, or recombination events or even a combination of these karyological events, were found to be stable. Other lines were unstable, and these lines carried 1V, 3V, or 5V chromosomes or their portions. Substitution or recombination events where 1V chromosomes were involved could concern the homeologous counterparts in both the A and B and D genomes of wheat. No line could be recovered where the shorter arm of 3V chromosomes was present. Changes in the morphology and banding pattern of V chromosomes were observed in hybrids that did not carry the entire D. villosum complement. By comparing the results of our cytogenetic analyses with certain phenotypic

  1. Genome databases

    SciTech Connect

    Courteau, J.

    1991-10-11

    Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increasing number incorporate sophisticated search and analytical software, while others operate as little more than data lists. In consultation with numerous experts in the field, a list has been compiled of some key genome-related databases. The list was not limited to map and sequence databases but also included the tools investigators use to interpret and elucidate genetic data, such as protein sequence and protein structure databases. Because a major goal of the Genome Project is to map and sequence the genomes of several experimental animals, including E. coli, yeast, fruit fly, nematode, and mouse, the available databases for those organisms are listed as well. The author also includes several databases that are still under development - including some ambitious efforts that go beyond data compilation to create what are being called electronic research communities, enabling many users, rather than just one or a few curators, to add or edit the data and tag it as raw or confirmed.

  2. Acc homoeoloci and the evolution of wheat genomes

    PubMed Central

    Chalupska, D.; Lee, H. Y.; Faris, J. D.; Evrard, A.; Chalhoub, B.; Haselkorn, R.; Gornicki, P.

    2008-01-01

    The DNA sequences of wheat Acc-1 and Acc-2 loci, encoding the plastid and cytosolic forms of the enzyme acetyl-CoA carboxylase, were analyzed with a view to understanding the evolution of these genes and the origin of the three genomes in modern hexaploid wheat. Acc-1 and Acc-2 loci from each of the wheats Triticum urartu (A genome), Aegilops tauschii (D genome), Triticum turgidum (AB genome), and Triticum aestivum (ABD genome), as well as two Acc-2-related pseudogenes from T. urartu were sequenced. The 2.3–2.4 Mya divergence time calculated here for the three homoeologous chromosomes, on the basis of coding and intron sequences of the Acc-1 genes, is at the low end of other estimates. Our clock was calibrated by using 60 Mya for the divergence between wheat and maize. On the same time scale, wheat and barley diverged 11.6 Mya, based on sequences of Acc and other genes. The regions flanking the Acc genes are not conserved among the A, B, and D genomes. They are conserved when comparing homoeologous genomes of diploid, tetraploid, and hexaploid wheats. Substitution rates in intergenic regions consisting primarily of repetitive sequences vary substantially along the loci and on average are 3.5-fold higher than the Acc intron substitution rates. The composition of the Acc homoeoloci suggests haplotype divergence exceeding in some cases 0.5 Mya. Such variation might result in a significant overestimate of the time since tetraploid wheat formation, which occurred no more than 0.5 Mya. PMID:18599450

  3. Acc homoeoloci and the evolution of wheat genomes.

    PubMed

    Chalupska, D; Lee, H Y; Faris, J D; Evrard, A; Chalhoub, B; Haselkorn, R; Gornicki, P

    2008-07-15

    The DNA sequences of wheat Acc-1 and Acc-2 loci, encoding the plastid and cytosolic forms of the enzyme acetyl-CoA carboxylase, were analyzed with a view to understanding the evolution of these genes and the origin of the three genomes in modern hexaploid wheat. Acc-1 and Acc-2 loci from each of the wheats Triticum urartu (A genome), Aegilops tauschii (D genome), Triticum turgidum (AB genome), and Triticum aestivum (ABD genome), as well as two Acc-2-related pseudogenes from T. urartu were sequenced. The 2.3-2.4 Mya divergence time calculated here for the three homoeologous chromosomes, on the basis of coding and intron sequences of the Acc-1 genes, is at the low end of other estimates. Our clock was calibrated by using 60 Mya for the divergence between wheat and maize. On the same time scale, wheat and barley diverged 11.6 Mya, based on sequences of Acc and other genes. The regions flanking the Acc genes are not conserved among the A, B, and D genomes. They are conserved when comparing homoeologous genomes of diploid, tetraploid, and hexaploid wheats. Substitution rates in intergenic regions consisting primarily of repetitive sequences vary substantially along the loci and on average are 3.5-fold higher than the Acc intron substitution rates. The composition of the Acc homoeoloci suggests haplotype divergence exceeding in some cases 0.5 Mya. Such variation might result in a significant overestimate of the time since tetraploid wheat formation, which occurred no more than 0.5 Mya. PMID:18599450

  4. Molecular characterization of a diagnostic DNA marker for domesticated tetraploid wheat provides evidence for gene flow from wild tetraploid wheat to hexaploid wheat.

    PubMed

    Dvorak, Jan; Akhunov, Eduard D; Akhunov, Alina R; Deal, Karin R; Luo, Ming-Cheng

    2006-07-01

    All forms of domesticated tetraploid wheat (Triticum turgidum, genomes AABB) are nearly monomorphic for restriction fragment length polymorphism (RFLP) haplotype a at the Xpsr920 locus on chromosome 4A (Xpsr920-A1a), and wild tetraploid wheat is monomorphic for haplotype b. The Xpsr920-A1a/b dimorphism provides a molecular marker for domesticated and wild tetraploid wheat, respectively. Hexaploid wheat (Triticum aestivum, genomes AABBDD) is polymorphic for the 2 haplotypes. Bacterial artificial chromosome (BAC) clones hybridizing with PSR920 were isolated from Triticum urartu (genomes AA), Triticum monococcum (genomes AmAm), and T. turgidum ssp. durum (genomes AABB) and sequenced. PSR920 is a fragment of a putative ATP binding cassette (ABC) transporter gene (designated ABCT-1). The wheat ABCT-1 gene is more similar to the T. urartu gene than to the T. monococcum gene and diverged from the T. urartu gene about 0.7 MYA. The comparison of the sequence of the wheat A genome BAC clone with that of the T. urartu BAC clone provides the first insight into the microsynteny of the wheat A genome with that of T. urartu. Within 103 kb of orthologous intergenic space, 37 kb of new DNA has been inserted and 36 kb deleted leaving 49.7% of the region syntenic between the clones. The nucleotide substitution rate in the syntenic intergenic space has been 1.6 x 10(-8) nt(-1) year(-1), which is, respectively, 4 and 3 times as great as nucleotide substitution rates in the introns and the third codon positions of the juxtaposed gene. The RFLP is caused by a miniature inverted transposable element (MITE) insertion into intron 18 of the ABCT-A1 gene. Polymerase chain reaction primers were developed for the amplification of the MITE insertion site and its sequencing. The T. aestivum ABCT-A1a haplotype is identical to the haplotype of domesticated tetraploid wheat, and the ABCT-A1b haplotype is identical to that of wild tetraploid wheat. This finding shows for the first time that wild

  5. Listeria Genomics

    NASA Astrophysics Data System (ADS)

    Cabanes, Didier; Sousa, Sandra; Cossart, Pascale

    The opportunistic intracellular foodborne pathogen Listeria monocytogenes has become a paradigm for the study of host-pathogen interactions and bacterial adaptation to mammalian hosts. Analysis of L. monocytogenes infection has provided considerable insight into how bacteria invade cells, move intracellularly, and disseminate in tissues, as well as tools to address fundamental processes in cell biology. Moreover, the vast amount of knowledge that has been gathered through in-depth comparative genomic analyses and in vivo studies makes L. monocytogenes one of the most well-studied bacterial pathogens. This chapter provides an overview of progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism used by bacteria when growing in diverse environments, in particular in infected hosts.

  6. Genome Informatics

    PubMed Central

    Winslow, Raimond L.; Boguski, Mark S.

    2005-01-01

    This article reviews recent advances in genomics and informatics relevant to cardiovascular research. In particular, we review the status of (1) whole genome sequencing efforts in human, mouse, rat, zebrafish, and dog; (2) the development of data mining and analysis tools; (3) the launching of the National Heart, Lung, and Blood Institute Programs for Genomics Applications and Proteomics Initiative; (4) efforts to characterize the cardiac transcriptome and proteome; and (5) the current status of computational modeling of the cardiac myocyte. In each instance, we provide links to relevant sources of information on the World Wide Web and critical appraisals of the promises and the challenges of an expanding and diverse information landscape. PMID:12750305

  7. Gramene, a tool for grass genomics.

    PubMed

    Ware, Doreen H; Jaiswal, Pankaj; Ni, Junjian; Yap, Immanuel V; Pan, Xioakang; Clark, Ken Y; Teytelman, Leonid; Schmidt, Steven C; Zhao, Wei; Chang, Kuan; Cartinhour, Sam; Stein, Lincoln D; McCouch, Susan R

    2002-12-01

    Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses and a community resource for rice (Oryza sativa). It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, and publications, with a curated database of rice mutants (genes and alleles), molecular markers, and proteins. Gramene curators read and extract detailed information from published sources, summarize that information in a structured format, and establish links to related objects both inside and outside the database, providing seamless connections between independent sources of information. Genetic, physical, and sequence-based maps of rice serve as the fundamental organizing units and provide a common denominator for moving across species and genera within the grass family. Comparative maps of rice, maize (Zea mays), sorghum (Sorghum bicolor), barley (Hordeum vulgare), wheat (Triticum aestivum), and oat (Avena sativa) are anchored by a set of curated correspondences. In addition to sequence-based mappings found in comparative maps and rice genome displays, Gramene makes extensive use of controlled vocabularies to describe specific biological attributes in ways that permit users to query those domains and make comparisons across taxonomic groups. Proteins are annotated for functional significance using gene ontology terms that have been adopted by numerous model species databases. Genetic variants including phenotypes are annotated using plant ontology terms common to all plants and trait ontology terms that are specific to rice. In this paper, we present a brief overview of the search tools available to the plant research community in Gramene. PMID:12481044

  8. Triticum aestivum L. endoxylanase inhibitor (TAXI) consists of two inhibitors, TAXI I and TAXI II, with different specificities.

    PubMed Central

    Gebruers, K; Debyser, W; Goesaert, H; Proost, P; Van Damme J; Delcour, J A

    2001-01-01

    The Triticum aestivum L. endoxylanase inhibitor (TAXI) discovered by Debyser and Delcour [(1997) Eur. Pat. filed April 1997, published as WO 98/49278] and Debyser, Derdelinckx and Delcour [(1997) J. Am. Soc. Brew. Chem. 55, 153-156] seems to be a mixture of two different endoxylanase inhibitors, called TAXI I and TAXI II. By using Aspergillus niger as well as Bacillus subtilis endoxylanases for assaying inhibition activity, both inhibitors could be purified to homogeneity from wheat (Triticum aestivum L., var. Soissons). TAXI I and TAXI II have similar molecular structures. They both have a molecular mass of approx. 40.0 kDa, are not glycosylated and occur in two molecular forms, i.e. a non-proteolytically processed one and a proteolytically processed one. However, the pI of TAXI II (at least 9.3) is higher than that of TAXI I (8.8). TAXI I and TAXI II clearly show different inhibition activities towards different endoxylanases. The N-terminal amino acid sequences of both inhibitors show a high degree of identity, which might indicate that there is an evolutionary relationship between them. PMID:11139386

  9. Responses of wheat (Triticum aestivum) and turnip (Brassica rapa) to the combined exposure of carbaryl and ultraviolet radiation.

    PubMed

    Lima, Maria P R; Soares, Amadeu M V M; Loureiro, Susana

    2015-07-01

    The increase of ultraviolet (UV) radiation reaching the Earth's surface as a result of increased ozone layer depletion has affected crop production systems and, in combination with pesticides used in agricultural activities, can lead to greater risks to the environment. The impact of UV radiation and carbaryl singly and in combination on Triticum aestivum (wheat) and Brassica rapa (turnip) was studied. The combined exposure was analyzed using the MixTox tool and was based on the conceptual model of independent action, where possible deviations to synergism or antagonism and dose-ratio or dose-level response pattern were also considered. Compared with the control, carbaryl and UV radiation individually led to reductions in growth, fresh and dry weight, and water content for both species. Combined treatment of UV and carbaryl was more deleterious compared with single exposure. For T. aestivum length, no interaction between the 2 stressors was found (independent action), and a dose-level deviation was the best description for the weight parameters. For B. rapa, dose-ratio deviations from the conceptual model were found when length and dry weight were analyzed, and a higher than expected effect on the fresh weight (synergism) occurred with combined exposure. PMID:25754078

  10. Photosynthetic capacity and dry mass partitioning in dwarf and semi-dwarf wheat (Triticum aestivum L.)

    NASA Technical Reports Server (NTRS)

    Bishop, D. L.; Bugbee, B. G.

    1998-01-01

    Efficient use of space and high yields are critical for long-term food production aboard the International Space Station. The selection of a full dwarf wheat (less than 30 cm tall) with high photosynthetic and yield potential is a necessary prerequisite for growing wheat in the controlled, volume-limited environments available aboard long-term spaceflight missions. This study evaluated the photosynthetic capacity and carbon partitioning of a full-dwarf wheat cultivar, Super Dwarf, which is routinely used in spaceflight studies aboard U.S. space shuttle and NASA/Mir missions and made comparisons with other dwarf and semi-dwarf wheat cultivars utilized in other ground-based studies in plant space biology. Photosynthetic capacity of the flag leaf in two dwarf (Super Dwarf, BB-19), and three semi-dwarf (Veery-10, Yecora Rojo, IBWSN 199) wheat cultivars (Triticum aestivum L.) was assessed by measuring: net maximum photosynthetic rate, RuBP carboxylation efficiency, chlorophyll concentration and flag leaf area. Dry mass partitioning of carbohydrates to the leaves, sheaths, stems and ear was also assessed. Plants were grown under controlled environmental conditions in three replicate studies: slightly enriched CO2 (370 micromoles mol-1), high photosynthetic photon flux (1000 micromoles m-2 s-1; 58 mol m-2 d-1) for a 16 h photoperiod, 22/15 degrees C day/night temperatures, ample nutrients and water provided by one-half strength Hoagland's nutrient solution (Hoagland and Arnon, 1950). Photosynthetic capacity of the flag leaf was determined at anthesis using net CO2 exchange rate versus internal CO2 concentration curves measured under saturating light (2000 micromoles m-2 s-1) and CO2 (1000 micromoles mol-1). Dwarf wheat cultivars had greater photosynthetic capacities than the taller semi-dwarfs, they averaged 20% higher maximum net photosynthetic rates compared to the taller semi-dwarfs, but these higher rates occurred only at anthesis, had slightly greater carboxylation

  11. Potentially toxic elements in foodcrops: Triticum aestivum L., Zea mays L.

    NASA Astrophysics Data System (ADS)

    Bini, Claudio; Fontana, Silvia; Squizzato, Stefania; Minello, Fabiola; Fornasier, Flavio; Wahsha, Mohammad

    2013-04-01

    Soil is the basis of the ecosystems and of our system of food production. Crops can uptake heavy metals and potentially toxic elements from the soil and store them in the roots or translocate them to the aerial parts. Excessive content of these elements in edible parts can produce toxic effects and, through the food chain and food consumption, result in a potential hazard for human health. In this study soils and plants (spring wheat, Triticum aestivum L. and maize, Zea mays L.) from a tannery district in North-East Italy were analyzed to determine pedological characters, soil microbial indicators and the content of some major and micro-nutrients and potentially toxic elements (Al, Ca, Cd, Cr, Cu, Fe, K, Mg, Mn, Ni, P, Pb, S, Zn, V). The soils of the area are moderately polluted; Cr is the most important inorganic contaminant, followed by Ni, Cu and V. Factor analysis evidenced that the contaminants are in part anthropogenic and in part geogenic. Major anthropogenic origin was detected for Cr, Ni (from industrial activities), Zn, Cu, Cd (from agriculture practices). Biological Absorption Coefficient (BAC) from soil to plant roots and Translocation factor (TF) within the plant were calculated; major nutrients (K, P, S) and some micronutrients (Cu, Zn, Mg, Mn) are easily absorbed and translocated, whilst other nutrients (Ca, Fe) and potentially toxic elements or micronutrients (Al, Cd, Cr, Ni, Pb, V) are not accumulated in the seeds of the two considered species. However, the two edible species proved differently able to absorb and translocate elements, and this suggests to consider separately every species as potential PHEs transporter to the food chain and to humans. Cr concentrations in seeds and other aerial parts (stem and leaves) of the examined plants are higher than the values found for the same species and for other cereals grown on unpolluted soils. Comparing the Cr levels in edible parts with recommended dietary intake, besides other possible Cr sources

  12. Whither genomics?

    PubMed Central

    Murray, Andrew W

    2000-01-01

    The flood of data from genome-wide analysis is transforming biology. We need to develop new, interdisciplinary approaches to convert these data into information about the components and structures of individual biological pathways and to use the resulting information to yield knowledge about general principles that explain the functions and evolution of life. PMID:11104516

  13. The chloroplast view of the evolution of polyploid wheat.

    PubMed

    Gornicki, Piotr; Zhu, Huilan; Wang, Junwei; Challa, Ghana S; Zhang, Zhengzhi; Gill, Bikram S; Li, Wanlong

    2014-11-01

    Polyploid wheats comprise four species: Triticum turgidum (AABB genomes) and T. aestivum (AABBDD) in the Emmer lineage, and T. timopheevii (AAGG) and T. zhukovskyi (AAGGA(m) A(m) ) in the Timopheevi lineage. Genetic relationships between chloroplast genomes were studied to trace the evolutionary history of the species. Twenty-five chloroplast genomes were sequenced, and 1127 plant accessions were genotyped, representing 13 Triticum and Aegilops species. The A. speltoides (SS genome) diverged before the divergence of T. urartu (AA), A. tauschii (DD) and the Aegilops species of the Sitopsis section. Aegilops speltoides forms a monophyletic clade with the polyploid Emmer and Timopheevi wheats, which originated within the last 0.7 and 0.4 Myr, respectively. The geographic distribution of chloroplast haplotypes of the wild tetraploid wheats and A. speltoides illustrates the possible geographic origin of the Emmer lineage in the southern Levant and the Timopheevi lineage in northern Iraq. Aegilops speltoides is the closest relative of the diploid donor of the chloroplast (cytoplasm), as well as the B and G genomes to Timopheevi and Emmer lineages. Chloroplast haplotypes were often shared by species or subspecies within major lineages and between the lineages, indicating the contribution of introgression to the evolution and domestication of polyploid wheats. PMID:25059383

  14. High temperature during grain fill alters the morphology of protein and starch deposits in the starchy endosperm cells of the developing wheat (Triticum aestivum L.) grain

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High temperature during grain fill reduces wheat yield and alters flour quality. Starchy endosperm cell morphology was investigated in wheat (Triticum aestivum L. ‘Butte 86’) grain produced under a 24/17 °C or 37/28 °C day/night regimen imposed from anthesis to maturity to identify changes in cell s...

  15. Genetic mapping of quantitative trait loci associated with important agronomic traits in the spring wheat (Triticum aestivum L.) cross ‘Louise’ by ‘Penawawa’

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Understanding the genetic factors underlying agronomic traits in common wheat (Triticum aestivum L.) is essential to making gains from selection during the breeding process. A set of 188 recombinant inbred lines from a ‘Louise’ by ‘Penawawa’ mapping population was grown in two crop years at two loc...

  16. Starch granule formation and protein deposition in wheat (Triticum aestivum L.) starchy endosperm cells are altered by high temperature during grain fill

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High temperatures during wheat grain fill decrease starch and protein levels, adversely affecting wheat yield and flour quality. To determine the effect of high temperature on starchy endosperm cell development, grain (Triticum aestivum L. ‘Butte 86’) was produced under a 24/17°C or 37/28°C day/nigh...

  17. Molecular characterization of the Puroindolin a-D1b allele and develpment of an STS marker in wheat (Triticum aestivum L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Kernel texture (grain hardness) is a leading quality characteristic of bread wheat (Triticum aestivum L.) as it dramatically influences its milling and processing properties, and consequently is utilized in the classification and marketing of grain. According to many previous reports (reviewed in Bh...

  18. Effect of high temperature on cell structure and gluten protein accumulation in the endosperm of the developing wheat (Triticum aestivum L.) grain

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High temperature during grain fill is one of the more significant environmental factors that alters wheat yield and flour quality. To identify endosperm responses to high temperature, cell structure and gluten protein composition were investigated in developing wheat (Triticum aestivum L. cv. Butte ...

  19. The effect of high temperature on cell structure and gluten protein accumulation in the endosperm of the developing wheat (Triticum aestivum L.) grain

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High temperature during grain fill is one of the more significant environmental factors that alters wheat yield and flour quality. To identify endosperm responses to high temperature, cell structure and gluten protein composition were investigated in developing wheat (Triticum aestivum L. cv. Butte ...

  20. Isolation of ABA-responsive mutants in allohexaploid bread wheat (Triticum aestivum L.): Drawing connections to grain dormancy, preharvest sprouting, and drought tolerance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This paper describes the isolation of Wheat ABA-responsive mutants (Warm) in Chinese spring background of allohexaploid Triticum aestivum. The plant hormone abscisic acid (ABA) is required for the induction of seed dormancy, the induction of stomatal closure and drought tolerance, and is associated...

  1. Starch granule formation and protein deposition in wheat (Triticum aestivum L.) starchy endosperm cells is altered by high temperature during grain fill

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High temperatures during wheat grain fill decrease starch and protein levels, adversely affecting wheat yield and flour quality. To determine the effect of high temperature on starchy endosperm cell development, grain (Triticum aestivum L. "Butte 86") was produced under a 24/17°C or 37/28°C day/nigh...

  2. Omega Gliadin Genes Expressed in Triticum Aestivum cv Butte 86: Effects of Post-anthesis Fertilizer on Transcript Accumulation During Grain Development

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The partial coding sequences of omega gliadin genes expressed in developing wheat kernels Triticum aestivum cv Butte 86 were identified in EST databases. Three gene assemblies encode proteins with PQQPFP as the predominant repetitive motif. Of these, two encode proteins with at least one cysteine an...

  3. Comparative and evolutionary analysis of new variants of ω-gliadin genes from three A-genome diploid wheats.

    PubMed

    Zhuang, Qianqian; Zhang, Zhiguo; Chen, Fanguo; Xia, Guangmin

    2012-05-01

    A genomic polymerase chain reaction (PCR) cloning strategy was applied to isolate ω-gliadin sequences from three A-genome diploid wheats (Triticum monococcum, T. boeoticum and T. urartu). Amplicon lengths varied from 744 and 1,044 bp, and those of the corresponding deduced mature proteins from 248 to 348 residues. The primary structure of the deduced polypeptides comprised a short N- and C-terminal conserved domain, and a long, variable repetitive domain. A phylogenetic analysis recognised several clades: the first consisted of three T. aestivum sequences; the second and the third two T. boeoticum and six T. monococcum sequences; and the rest four T. urartu and three T. aestivum sequences. Among the functional (non-pseudogene) ARQ/E-type ω-gliadin sequences, two were derived from T. boeoticum and three from T. monococcum; one of the latter sequences appeared to be a chimera originating via illegitimate recombination between the other two T. monococcum sequences. None of the 12 intact ω-gliadin sequences contained any cysteine or methionine residues. We discussed the variation and evolution of A-genome ω-gliadin genes. PMID:22072274

  4. Molecular cloning and expression analysis of multiple polyphenol oxidase genes in developing wheat (Triticum aestivum) kernels

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Polyphenol oxidase (PPO, EC 1.10.31) is a major cause of discoloring in raw dough containing wheat flour. Minimization of PPO activity has proven difficult because bread wheat is genetically complex, composed of the genomes of three grass species. The PPO-A1 and PPO-D1 genes, on chromosomes 2A and...

  5. Citrus Genomics

    PubMed Central

    Talon, Manuel; Gmitter Jr., Fred G.

    2008-01-01

    Citrus is one of the most widespread fruit crops globally, with great economic and health value. It is among the most difficult plants to improve through traditional breeding approaches. Currently, there is risk of devastation by diseases threatening to limit production and future availability to the human population. As technologies rapidly advance in genomic science, they are quickly adapted to address the biological challenges of the citrus plant system and the world's industries. The historical developments of linkage mapping, markers and breeding, EST projects, physical mapping, an international citrus genome sequencing project, and critical functional analysis are described. Despite the challenges of working with citrus, there has been substantial progress. Citrus researchers engaged in international collaborations provide optimism about future productivity and contributions to the benefit of citrus industries worldwide and to the human population who can rely on future widespread availability of this health-promoting and aesthetically pleasing fruit crop. PMID:18509486

  6. Ancient genomics

    PubMed Central

    Der Sarkissian, Clio; Allentoft, Morten E.; Ávila-Arcos, María C.; Barnett, Ross; Campos, Paula F.; Cappellini, Enrico; Ermini, Luca; Fernández, Ruth; da Fonseca, Rute; Ginolhac, Aurélien; Hansen, Anders J.; Jónsson, Hákon; Korneliussen, Thorfinn; Margaryan, Ashot; Martin, Michael D.; Moreno-Mayar, J. Víctor; Raghavan, Maanasa; Rasmussen, Morten; Velasco, Marcela Sandoval; Schroeder, Hannes; Schubert, Mikkel; Seguin-Orlando, Andaine; Wales, Nathan; Gilbert, M. Thomas P.; Willerslev, Eske; Orlando, Ludovic

    2015-01-01

    The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past. PMID:25487338

  7. Genomic Imprinting

    PubMed Central

    Bajrami, Emirjeta; Spiroski, Mirko

    2016-01-01

    BACKGROUND: Genomic imprinting is the inheritance out of Mendelian borders. Many of inherited diseases and human development violates Mendelian law of inheritance, this way of inheriting is studied by epigenetics. AIM: The aim of this review is to analyze current opinions and options regarding to this way of inheriting. RESULTS: Epigenetics shows that gene expression undergoes changes more complex than modifications in the DNA sequence; it includes the environmental influence on the gametes before conception. Humans inherit two alleles from mother and father, both are functional for the majority of the genes, but sometimes one is turned off or “stamped” and doesn’t show in offspring, that gene is imprinted. Imprinting means that that gene is silenced, and gene from other parent is expressed. The mechanisms for imprinting are still incompletely defined, but they involve epigenetic modifications that are erased and then reset during the creation of eggs and sperm. Genomic imprinting is a process of silencing genes through DNA methylation. The repressed allele is methylated, while the active allele is unmethylated. The most well-known conditions include Prader-Willi syndrome, and Angelman syndrome. Both of these syndromes can be caused by imprinting or other errors involving genes on the long arm of chromosome 15. CONCLUSIONS: Genomic imprinting and other epigenetic mechanisms such as environment is shown that plays role in offspring neurodevelopment and autism spectrum disorder. PMID:27275355

  8. Evolution and Distribution of Hydrolytic Enzyme Activities during Preharvest Sprouting of Wheat (Triticum aestivum) in the Field.

    PubMed

    Olaerts, Heleen; Roye, Chiara; Derde, Liesbeth J; Sinnaeve, Georges; Meza, Walter R; Bodson, Bernard; Courtin, Christophe M

    2016-07-20

    To date, research on preharvest sprouted (PHS) wheat has mostly been conducted on kernels germinated under laboratory conditions, which differ widely from conditions in the field. To obtain detailed knowledge of the evolution of hydrolytic enzyme activities in PHS wheat (Triticum aestivum), a broad collection of samples from three varieties was obtained by harvesting before, at, and after maturity. Delaying harvest time coupled with periods of heavy rainfall caused sprouting in the kernels, observed as a drop in Falling Number and an increase in α-amylase activity. The appearance of α- and β-amylase, peptidase, and endoxylanase activity during field sprouting was independent from each other. Consequently, Falling Number could not be used to predict activity of other hydrolytic enzymes. When differentiating endogenous from kernel-associated microbial enzymes, results showed that α- and β-amylase and peptidase activity of PHS kernels were predominantly of endogenous origin, whereas endoxylanase activity was largely from microbial origin. PMID:27341479

  9. Growth responses of wheat (Triticum aestivum L. var. HD 2329) exposed to ambient air pollution under varying fertility regimes.

    PubMed

    Singh, Anoop; Agrawal, S B; Rathore, Dheeraj

    2003-08-20

    The problem of urban air pollution has attracted special attention in India due to a tremendous increase in the urban population; motor vehicles vis a vis the extent of energy utilization. Field studies were conducted on wheat crops (Triticum aestivum L. var. HD 2329) by keeping the pot-grown plants in similar edaphic conditions at nine different sites in Allahabad City to quantify the effects of ambient air pollution levels on selected growth and yield parameters. Air quality monitoring was done at all the sites for gaseous pollutants viz. SO2, NO2, and O3. Various growth parameters (plant height, biomass, leaf area, NPP, etc.) showed adverse effects at sites receiving higher pollution load. Reduction in test weight and harvest index was found to be directly correlated with the levels of pollutant concentrations. The study clearly showed the negative impact of air pollution on periurban agriculture. PMID:12941977

  10. Assessment of genotoxic effects of boron on wheat (Triticum aestivum L.) and bean (Phaseolus vulgaris L.) by using RAPD analysis.

    PubMed

    Kekec, Guzin; Sakcali, M Serdal; Uzonur, Irem

    2010-06-01

    In boron-rich soils of Turkey, boron tolerant wheat (Triticum aestivum L.) and sensitive bean (Phaseolus vulgaris L.) are most widely cultivated crops. In this study they have been studied to elucidate the probable genotoxic effects of boron by using RAPD analysis. During the study, root and stem lengths have been measured and inhibitory rates (%) of root growth have been found to be significant, starting from 10 (13%) and 5 ppm (19%) for wheat and bean, respectively, which is in strong correlation with the root DNA alterations; RAPD variations starting from 100 ppm for wheat and 25 ppm for bean. The preliminary findings encourage the use of these tools in investigation of genotoxic effects of boron on wheat, bean and the other crops. PMID:20467724

  11. Sampling system for wheat (Triticum aestivum L) area estimation using digital LANDSAT MSS data and aerial photographs. [Brazil

    NASA Technical Reports Server (NTRS)

    Parada, N. D. J. (Principal Investigator); Moreira, M. A.; Chen, S. C.; Batista, G. T.

    1984-01-01

    A procedure to estimate wheat (Triticum aestivum L) area using sampling technique based on aerial photographs and digital LANDSAT MSS data is developed. Aerial photographs covering 720 square km are visually analyzed. To estimate wheat area, a regression approach is applied using different sample sizes and various sampling units. As the size of sampling unit decreased, the percentage of sampled area required to obtain similar estimation performance also decreased. The lowest percentage of the area sampled for wheat estimation with relatively high precision and accuracy through regression estimation is 13.90% using 10 square km as the sampling unit. Wheat area estimation using only aerial photographs is less precise and accurate than those obtained by regression estimation.

  12. Comparative effects of glyphosate and atrazine in chloroplast ultrastructure of wheat and downy brome. [Triticum aestivum; Bromus tectorum

    SciTech Connect

    Auge, R.M.; Gealy, D.R.; Ogg, A.G.; Franceschi, V.R.

    1987-04-01

    Developing and mature leaves of winter wheat (Triticum aestivum L. var. Daws) and the weed species downy brome (Bromus tectorum L.) were subjected to 10 mM (foliar application) and 1 mM (root application) herbicide solutions. Glyphosate (N-(phosphonomethyl) glycine) and atrazine (2-chloro-4-(ethyl-amino)-6-(isopropylamino)-s-triazine) were prepared in a carrier composed of 5% soybean oil concentrate, 35% acetone and 60% water. Penetration experiments with /sup 3/H-labelled herbicides assessed what percentage of herbicide entered leaves, and microautoradiography was used to determine qualitatively how much herbicide was present in the sections viewed with TEM. Tissue was excised at 4, 18, 62 and 200 hours, and then either freeze-substituted or fixed chemically. Ultrastructural effects of each herbicide on chloroplasts from leaves of newly-germinated seedlings and of well-tillered plants are depicted and discussed. Temporal differences in response of chloroplasts to each herbicide are noted.

  13. Combined effects of elevated temperature and CO2 concentration on Cd and Zn accumulation dynamics in Triticum aestivum L.

    PubMed

    Wang, Xiaoheng; Li, Yu; Lu, Hong; Wang, Shigong

    2016-09-01

    A simulated climate warming experiment was conducted to evaluate the combined effects of elevated temperature and CO2 concentration on the bioaccumulation, translocation and subcellular distributions of Cd and Zn in wheat seedlings (Triticum aestivum L. cv. Xihan 1.) at Dingxi, Gansu Province, China. The objective was to find evidence that global climate change is affecting the bioaccumulation of Cd and Zn in T. aestivum L. cv. Xihan 1. The results showed that compared to control A, elevated temperature and CO2 increased Cd bioaccumulation in the shoots by 1.4-2.5 times, and increased that in the roots by 1.2-1.5 times, but decreased Zn levels in wheat shoots by 1.4-2.0 times, while decreased that in the roots by 1.6-1.9 times. Moreover, temperature and CO2 concentration increase also led to increased Cd concentration, and decreased Zn concentration in subcellular compartments of wheat seedlings. The largest Cd concentration increase (174.4%) was observed in the cell wall and debris fractions of shoots after they were subjected to the highest CO2 and temperature treatment (TC3). The largest Zn concentration decrease (53.1%) was observed in the soluble (F3) fractions of shoots after they were subjected to the medium CO2 and temperature treatment (TC2). The temperature and CO2 increase had no significant effect on the proportional distribution of Cd and Zn in the subcellular fractions. The root-to-shoot translocation of Cd increased with the increasing temperature and CO2 concentration. However, the Zn distributions only fluctuated within a small range. PMID:27593278

  14. Genetic and cytogenetic analyses of the A genome of Triticum monococcum. VIII. Localization of rDNAs and characterization of 5S rRNA genes.

    PubMed

    Kim, N S; Kuspira, J; Armstrong, K; Bhambhani, R

    1993-02-01

    In situ hybridization with [3H]dCTP labelled pScT7 (5S rDNA) and pTa80 (18S + 26S rDNA) indicated that both hybridized to the terminal regions of two pairs of chromosomes in Triticum monococcum. When the hybridization was performed with a mixture of both probes, only two pairs of chromosome arms were labelled, which suggested that the loci of both genes were located in juxtaposition to one another. Both probes labelled one pair of sites more heavily than the other. Southern analysis of 5S with BamHI-digested DNA from 12 accessions of T. monococcum (including T. urartu) produced two superimposed ladders of approximate sizes of 500 and 330 bp, which differ from T. aestivum in which 500- and 420-bp ladders were found. The 500-bp ladder is derived from chromosome 5A (5SDna-A2) and the 330-bp ladder from chromosome 1A (5SDna-A1). The recognition site for SstI was present in the long spacer region but absent in the short spacer as in T. aestivum; however, unlike T. aestivum, there were HaeIII (GGCC) and HindIII (AAGCTT) recognition sites in the short spacer region. The TaqI recognition sites (TCGA) in the long and short spacer regions are probably more highly methylated in T. monococcum than in T. aestivum. The results have implications regarding the evolutionary changes that occurred in the A genome of the hexaploid compared with the diploid. PMID:18469972

  15. Spontaneous and Divergent Hexaploid Triticales Derived from Common Wheat × Rye by Complete Elimination of D-Genome Chromosomes

    PubMed Central

    Wang, Changyou; Ji, Wanquan

    2015-01-01

    Background Hexaploid triticale could be either synthesized by crossing tetraploid wheat with rye, or developed by crossing hexaploid wheat with a hexaploid triticale or an octoploid triticale. Methodology/Principal Findings Here two hexaploid triticales with great morphologic divergence derived from common wheat cultivar M8003 (Triticum aestivum L.) × Austrian rye (Secale cereale L.) were reported, exhibiting high resistance for powdery mildew and stripe rust and potential for wheat improvement. Sequential fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH) karyotyping revealed that D-genome chromosomes were completely eliminated and the whole A-genome, B-genome and R-genome chromosomes were retained in both lines. Furthermore, plentiful alterations of wheat chromosomes including 5A and 7B were detected in both triticales and additionally altered 5B, 7A chromosome and restructured chromosome 2A was assayed in N9116H and N9116M, respectively, even after selfing for several decades. Besides, meiotic asynchrony was displayed and a variety of storage protein variations were assayed, especially in the HMW/LMW-GS region and secalins region in both triticales. Conclusion This study confirms that whole D-genome chromosomes could be preferentially eliminated in the hybrid of common wheat × rye, “genome shock” was accompanying the allopolyploidization of nascent triticales, and great morphologic divergence might result from the genetic variations. Moreover, new hexaploid triticale lines contributing potential resistance resources for wheat improvement were produced. PMID:25781330

  16. Genomes on ice.

    PubMed

    Parkhill, Julian

    2016-03-01

    This month's Genome Watch discusses the analysis of a Helicobacter pylori genome from the preserved Copper-Age mummy known as the Iceman and how ancient genomes shed light on the history of bacterial pathogens. PMID:26853114

  17. Whole Genome Sequencing

    MedlinePlus

    ... you want to learn. Search form Search Whole Genome Sequencing You are here Home Testing & Services Testing ... the full story, click here . What is whole genome sequencing? Whole genome sequencing is the mapping out ...

  18. Genome-wide characterization of microsatellites in Triticeae species: abundance, distribution and evolution.

    PubMed

    Deng, Pingchuan; Wang, Meng; Feng, Kewei; Cui, Licao; Tong, Wei; Song, Weining; Nie, Xiaojun

    2016-01-01

    Microsatellites are an important constituent of plant genome and distributed across entire genome. In this study, genome-wide analysis of microsatellites in 8 Triticeae species and 9 model plants revealed that microsatellite characteristics were similar among the Triticeae species. Furthermore, genome-wide microsatellite markers were designed in wheat and then used to analyze the evolutionary relationship of wheat and other Triticeae species. Results displayed that Aegilops tauschii was found to be the closest species to Triticum aestivum, followed by Triticum urartu, Triticum turgidum and Aegilops speltoides, while Triticum monococcum, Aegilops sharonensis and Hordeum vulgare showed a relatively lower PCR amplification effectivity. Additionally, a significantly higher PCR amplification effectivity was found in chromosomes at the same subgenome than its homoeologous when these markers were subjected to search against different chromosomes in wheat. After a rigorous screening process, a total of 20,666 markers showed high amplification and polymorphic potential in wheat and its relatives, which were integrated with the public available wheat markers and then anchored to the genome of wheat (CS). This study not only provided the useful resource for SSR markers development in Triticeae species, but also shed light on the evolution of polyploid wheat from the perspective of microsatellites. PMID:27561724

  19. Genome-wide characterization of microsatellites in Triticeae species: abundance, distribution and evolution

    PubMed Central

    Deng, Pingchuan; Wang, Meng; Feng, Kewei; Cui, Licao; Tong, Wei; Song, Weining; Nie, Xiaojun

    2016-01-01

    Microsatellites are an important constituent of plant genome and distributed across entire genome. In this study, genome-wide analysis of microsatellites in 8 Triticeae species and 9 model plants revealed that microsatellite characteristics were similar among the Triticeae species. Furthermore, genome-wide microsatellite markers were designed in wheat and then used to analyze the evolutionary relationship of wheat and other Triticeae species. Results displayed that Aegilops tauschii was found to be the closest species to Triticum aestivum, followed by Triticum urartu, Triticum turgidum and Aegilops speltoides, while Triticum monococcum, Aegilops sharonensis and Hordeum vulgare showed a relatively lower PCR amplification effectivity. Additionally, a significantly higher PCR amplification effectivity was found in chromosomes at the same subgenome than its homoeologous when these markers were subjected to search against different chromosomes in wheat. After a rigorous screening process, a total of 20,666 markers showed high amplification and polymorphic potential in wheat and its relatives, which were integrated with the public available wheat markers and then anchored to the genome of wheat (CS). This study not only provided the useful resource for SSR markers development in Triticeae species, but also shed light on the evolution of polyploid wheat from the perspective of microsatellites. PMID:27561724

  20. Genetic and epigenetic alterations induced by different levels of rye genome integration in wheat recipient.

    PubMed

    Zheng, X L; Zhou, J P; Zang, L L; Tang, A T; Liu, D Q; Deng, K J; Zhang, Y

    2016-01-01

    The narrow genetic variation present in common wheat (Triticum aestivum) varieties has greatly restricted the improvement of crop yield in modern breeding systems. Alien addition lines have proven to be an effective means to broaden the genetic diversity of common wheat. Wheat-rye addition lines, which are the direct bridge materials for wheat improvement, have been wildly used to produce new wheat cultivars carrying alien rye germplasm. In this study, we investigated the genetic and epigenetic alterations in two sets of wheat-rye disomic addition lines (1R-7R) and the corresponding triticales. We used expressed sequence tag-simple sequence repeat, amplified fragment length polymorphism, and methylation-sensitive amplification polymorphism analyses to analyze the effects of the introduction of alien chromosomes (either the entire genome or sub-genome) to wheat genetic background. We found obvious and diversiform variations in the genomic primary structure, as well as alterations in the extent and pattern of the genomic DNA methylation of the recipient. Meanwhile, these results also showed that introduction of different rye chromosomes could induce different genetic and epigenetic alterations in its recipient, and the genetic background of the parents is an important factor for genomic and epigenetic variation induced by alien chromosome addition. PMID:27323191

  1. Ensembl Genomes 2016: more genomes, more complexity.

    PubMed

    Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M

    2016-01-01

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. PMID:26578574

  2. Ensembl genomes 2016: more genomes, more complexity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent...

  3. Ensembl Genomes 2016: more genomes, more complexity

    PubMed Central

    Kersey, Paul Julian; Allen, James E.; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J.; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J.; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K.; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D.; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello–Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M.; Howe, Kevin L.; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M.

    2016-01-01

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. PMID:26578574

  4. Funding Opportunity: Genomic Data Centers

    Cancer.gov

    Funding Opportunity CCG, Funding Opportunity Center for Cancer Genomics, CCG, Center for Cancer Genomics, CCG RFA, Center for cancer genomics rfa, genomic data analysis network, genomic data analysis network centers,

  5. Asymmetric somatic hybridization between wheat (Triticum aestivum) and Avena sativa L.

    PubMed

    Xiang, Fengning; Xia, Guangmin; Chen, Huimin

    2003-06-01

    Protoplasts from cell suspensions ofyoung-embryo-derived calli, which were nonregenerable for long-term subculture and protoplasts from embryogenic calli with the regeneration capacity of 75% ofthe same wheat Jinan 177, were mixed as recipient. Protoplasts from embryogenic calli of Avena sativa (with the regeneration capacity ofless than 10%) irradiated with UV at an intensity of 300 muW/cm(2) for 30 s, 1 min, 2 min, 3 min, 5 min were used as the donor. Protoplasts ofthe recipient and the donor were fused by PEG method. Many calli and normal green plants were regenerated at high frequency, and were verified as somatic hybrids by chromosome counting, isozyme, 5S rDNA spacer sequence analysis and GISH (genomic in situ hybridization). Fusion combination between protoplasts either from the cell suspensions or from the calli and UV-treated Avena sativa protoplasts could not regenerate green plants. PMID:18763139

  6. The characteristics and functions of a miniature inverted-repeat transposable element TaMITE81 in the 5' UTR of TaCHS7BL from Triticum aestivum.

    PubMed

    Xi, Xinyuan; Li, Na; Li, Shiming; Chen, Wenjie; Zhang, Bo; Liu, Baolong; Zhang, Huaigang

    2016-10-01

    Miniature inverted-repeat transposable elements (MITEs) are truncated derivatives of autonomous DNA transposons, and are dispersed abundantly in eukaryotic and prokaryotic genomes. In this article, a MITE, TaMITE81, was isolated from the 5' untranslated region (UTR) of TaCHS7BL, chalcone synthase (CHS) catalyzing the first committed step of anthocyanin biosynthesis, in the wheat cultivar 'Opata' with white grain. TaMITE81 was only 81 nucleotides, including a terminal inverted repeat with 39 nucleotides and was flanked by two nucleotides, "TA", target site duplications that were typical features of stowaway-like MITEs. Compared with the wheat cultivar 'Gy115' with purple grain, which is without the insertion, the expression of TaCHS7BL was lower in several organs of 'Opata'. The insertion of TaMITE81 into the 5' UTR of the GUS gene also reduced the transient expression of GUS on the coleoptiles of 'Opata', which means the insertion of TaMITE81 was the reason for the low expression of TaCHS7BL in 'Opata'. But the genotype of TaCHS7BL was not linked to phenotype of grain color in the RILs derived from a cross 'Gy115' and 'Opata'. The TaMITE81 density of the hexaploid variety of T. aestivum was more than 10 times that of diploid relatives, which implies that polyploidization caused the amplification of TaMITE81 homologous sequences. Further research should be conducted on decoding the relationship between TaCHS7BL and other traits relative to anthocyanin biosynthesis in wheat, and discovering the mechanism of TaMITE81 transposon action. PMID:27481288

  7. Enabling functional genomics with genome engineering

    PubMed Central

    Hilton, Isaac B.; Gersbach, Charles A.

    2015-01-01

    Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances. PMID:26430154

  8. Increased Genomic Prediction Accuracy in Wheat Breeding Through Spatial Adjustment of Field Trial Data

    PubMed Central

    Lado, Bettina; Matus, Ivan; Rodríguez, Alejandra; Inostroza, Luis; Poland, Jesse; Belzile, François; del Pozo, Alejandro; Quincke, Martín; Castro, Marina; von Zitzewitz, Jarislav

    2013-01-01

    In crop breeding, the interest of predicting the performance of candidate cultivars in the field has increased due to recent advances in molecular breeding technologies. However, the complexity of the wheat genome presents some challenges for applying new technologies in molecular marker identification with next-generation sequencing. We applied genotyping-by-sequencing, a recently developed method to identify single-nucleotide polymorphisms, in the genomes of 384 wheat (Triticum aestivum) genotypes that were field tested under three different water regimes in Mediterranean climatic conditions: rain-fed only, mild water stress, and fully irrigated. We identified 102,324 single-nucleotide polymorphisms in these genotypes, and the phenotypic data were used to train and test genomic selection models intended to predict yield, thousand-kernel weight, number of kernels per spike, and heading date. Phenotypic data showed marked spatial variation. Therefore, different models were tested to correct the trends observed in the field. A mixed-model using moving-means as a covariate was found to best fit the data. When we applied the genomic selection models, the accuracy of predicted traits increased with spatial adjustment. Multiple genomic selection models were tested, and a Gaussian kernel model was determined to give the highest accuracy. The best predictions between environments were obtained when data from different years were used to train the model. Our results confirm that genotyping-by-sequencing is an effective tool to obtain genome-wide information for crops with complex genomes, that these data are efficient for predicting traits, and that correction of spatial variation is a crucial ingredient to increase prediction accuracy in genomic selection models. PMID:24082033

  9. Exploring Other Genomes: Bacteria.

    ERIC Educational Resources Information Center

    Flannery, Maura C.

    2001-01-01

    Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)

  10. Navigating yeast genome maintenance with functional genomics.

    PubMed

    Measday, Vivien; Stirling, Peter C

    2016-03-01

    Maintenance of genome integrity is a fundamental requirement of all organisms. To address this, organisms have evolved extremely faithful modes of replication, DNA repair and chromosome segregation to combat the deleterious effects of an unstable genome. Nonetheless, a small amount of genome instability is the driver of evolutionary change and adaptation, and thus a low level of instability is permitted in populations. While defects in genome maintenance almost invariably reduce fitness in the short term, they can create an environment where beneficial mutations are more likely to occur. The importance of this fact is clearest in the development of human cancer, where genome instability is a well-established enabling characteristic of carcinogenesis. This raises the crucial question: what are the cellular pathways that promote genome maintenance and what are their mechanisms? Work in model organisms, in particular the yeast Saccharomyces cerevisiae, has provided the global foundations of genome maintenance mechanisms in eukaryotes. The development of pioneering genomic tools inS. cerevisiae, such as the systematic creation of mutants in all nonessential and essential genes, has enabled whole-genome approaches to identifying genes with roles in genome maintenance. Here, we review the extensive whole-genome approaches taken in yeast, with an emphasis on functional genomic screens, to understand the genetic basis of genome instability, highlighting a range of genetic and cytological screening modalities. By revealing the biological pathways and processes regulating genome integrity, these analyses contribute to the systems-level map of the yeast cell and inform studies of human disease, especially cancer. PMID:26323482

  11. Conserved globulin gene across eight grass genomes identify fundamental units of the loci encoding seed storage proteins.

    PubMed

    Gu, Yong Qiang; Wanjugi, Humphrey; Coleman-Derr, Devin; Kong, Xiuying; Anderson, Olin D

    2010-03-01

    The wheat high molecular weight (HMW) glutenins are important seed storage proteins that determine bread-making quality in hexaploid wheat (Triticum aestivum). In this study, detailed comparative sequence analyses of large orthologous HMW glutenin genomic regions from eight grass species, representing a wide evolutionary history of grass genomes, reveal a number of lineage-specific sequence changes. These lineage-specific changes, which resulted in duplications, insertions, and deletions of genes, are the major forces disrupting gene colinearity among grass genomes. Our results indicate that the presence of the HMW glutenin gene in Triticeae genomes was caused by lineage-specific duplication of a globulin gene. This tandem duplication event is shared by Brachypodium and Triticeae genomes, but is absent in rice, maize, and sorghum, suggesting the duplication occurred after Brachypodium and Triticeae genomes diverged from the other grasses ~35 Ma ago. Aside from their physical location in tandem, the sequence similarity, expression pattern, and conserved cis-acting elements responsible for endosperm-specific expression further support the paralogous relationship between the HMW glutenin and globulin genes. While the duplicated copy in Brachypodium has apparently become nonfunctional, the duplicated copy in wheat has evolved to become the HMW glutenin gene by gaining a central prolamin repetitive domain. PMID:19707805

  12. Genome Maps, a new generation genome browser.

    PubMed

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

  13. Genome Maps, a new generation genome browser

    PubMed Central

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-01-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

  14. Leaf rust (Puccinia triticina) resistance in wheat (Triticum aestivum) cultivars grown in Northern Europe 1992-2002.

    PubMed

    Hysing, Shu-Chin; Singh, Ravi P; Huerta-Espino, Julio; Merker, Arnulf; Liljeroth, Erland; Diaz, Oscar

    2006-12-01

    Diversity of resistance to leaf rust caused by Puccinia triticina can be enhanced in wheat (Triticum aestivum) cultivars through a better knowledge of resistance genes that are present in important cultivars and germplasm. Multi-pathotype tests on 84 wheat cultivars grown in Denmark, Finland, Norway and Sweden during 1992-2002 and 39 differential testers enabled the postulation of nine known genes for seedling resistance to leaf rust. Genes Lr1, Lr2a, Lr3, Lr10, Lr13, Lr14a, Lr17, Lr23 and Lr26 were found singly or in combination in 47 of the cultivars (55.9%). The most frequently occurring genes in cultivars grown in Sweden were Lr13 (20.4%), Lr14a (14.8%) and Lr26 (14.8%). Lr14a was the most common gene in cultivars grown in Norway (18.7%), Lr13 in Denmark (35.5%) and Lr10 in Finland (20.0%). Although 28 cultivars (33.3%) exhibited a response pattern that could not be assigned to resistance genes or combinations present in the tester lines, several pathotypes carried virulence and hence these genes or combinations are of limited use. Nine cultivars (10.7%) lacked detectable seedling resistance. One cultivar was resistant to all pathotypes used in the study. PMID:17362328

  15. Low irradiances affect abscisic acid, indole-3-acidic acid, and cytokinin levels of wheat (Triticum aestivum L.) tissues

    NASA Technical Reports Server (NTRS)

    Nan, R.; Carman, J. G.; Salisbury, F. B.

    1999-01-01

    Wheat (Triticum aestivum L.) plants were grown under four irradiance levels: 1,400, 400, 200, and 100 micromol m-2 s-1. Leaves and roots were sampled before, during, and after the boot stage, and levels of abscisic acid (ABA), indole-3-acetic acid (IAA), zeatin, zeatin riboside, dihydrozeatin, dihydrozeatin riboside, isopentenyl adenine, and isopentenyl adenosine were quantified using noncompetitive indirect ELISA systems. Levels of IAA in leaves and roots of plants exposed to 100 micromol m-2 s-1 of irradiance were 0.7 and 2.9 micromol kg-1 dry mass (DM), respectively. These levels were 0.2 and 1.0 micromol kg-1 DM, respectively, when plants were exposed to 1,400 micromol m-2 s-1. Levels of ABA in leaves and roots of plants exposed to 100 micromol m-2 s-1 were 0.65 and 0.55 micromol kg-1 DM, respectively. They were 0.24 micromol kg-1 DM (both leaves and roots) when plants were exposed to 1,400 micromol m-2 s-1. Levels of isopentenyl adenosine in leaves (24.3 nmol kg-1 DM) and roots (29.9 nmol kg-1 DM) were not affected by differences in the irradiance regime. Similar values were obtained in a second experiment. Other cytokinins could not be detected (<10 nmol kg 1 DM) in either experiment with the sample sizes used (150-600 mg DM for roots and shoots, respectively).

  16. Nitrogen balance for wheat canopies (Triticum aestivum cv. Veery 10) grown under elevated and ambient CO2 concentrations

    NASA Technical Reports Server (NTRS)

    Smart, D. R.; Ritchie, K.; Bloom, A. J.; Bugbee, B. B.

    1998-01-01

    We examined the hypothesis that elevated CO2 concentration would increase NO3- absorption and assimilation using intact wheat canopies (Triticum aestivum cv. Veery 10). Nitrate consumption, the sum of plant absorption and nitrogen loss, was continuously monitored for 23 d following germination under two CO2 concentrations (360 and 1000 micromol mol-1 CO2) and two root zone NO3- concentrations (100 and 1000 mmol m3 NO3-). The plants were grown at high density (1780 m-2) in a 28 m3 controlled environment chamber using solution culture techniques. Wheat responded to 1000 micromol mol-1 CO2 by increasing carbon allocation to root biomass production. Elevated CO2 also increased root zone NO3- consumption, but most of this increase did not result in higher biomass nitrogen. Rather, nitrogen loss accounted for the greatest part of the difference in NO3- consumption between the elevated and ambient [CO2] treatments. The total amount of NO3(-)-N absorbed by roots or the amount of NO3(-)-N assimilated per unit area did not significantly differ between elevated and ambient [CO2] treatments. Instead, specific leaf organic nitrogen content declined, and NO3- accumulated in canopies growing under 1000 micromol mol-1 CO2. Our results indicated that 1000 micromol mol-1 CO2 diminished NO3- assimilation. If NO3- assimilation were impaired by high [CO2], then this offers an explanation for why organic nitrogen contents are often observed to decline in elevated [CO2] environments.

  17. Molecular cloning and characterization of cDNAs encoding hemoglobin from wheat (Triticum aestivum) and potato (Solanum tuberosum).

    PubMed

    Larsen, Knud

    2003-06-11

    Hemoglobins (Hbs) are heme proteins encountered in all five kingdoms of living organisms. In plants, two different classes of Hbs have been identified: nonsymbiotic (class I) from both monocot and dicot species and symbiotic (class II) Hbs from nitrogen-fixing plants. This work reports the cloning and analysis of three nonsymbiotic Hb genes from wheat (Triticum aestivum) and potato (Solanum tuberosum). The Hb cDNAs were amplified by reverse transcriptase polymerase chain reaction (RT-PCR) using consensus oligonucleotide primers for nonsymbiotic Hbs.A wheat Hb cDNA (TaHb1) was isolated and shows a very high similarity to nonsymbiotic Hbs from Hordeum vulgare (98%) and Zea mays (83%). Another wheat Hb cDNA, designated TaHb2, exhibited strong similarity to truncated bacterial Hbs, the so-called 2-on-2 Hbs. In addition, a third Hb was cloned from potato, StHb. Expression analysis by RT-PCR demonstrated a very high expression level of the TaHb1 gene only in wheat roots. In contrast, the other wheat hemoglobin gene, TaHb2, was demonstrated to be constitutively expressed although differences in expression level in different tissues were observed. The expression of the TaHb1 gene is induced in wheat roots exposed to microaerobic conditions. The potato Hb gene, StHb, was highly expressed in roots and also in tubers and stem tissue although at much reduced levels. PMID:12787929

  18. Fine-scale spatial genetic structure analysis of the black truffle Tuber aestivum and its link to aroma variability.

    PubMed

    Molinier, Virginie; Murat, Claude; Frochot, Henri; Wipf, Daniel; Splivallo, Richard

    2015-08-01

    Truffles are symbiotic fungi in high demand by food connoisseurs. Improving yield and product quality requires a better understanding of truffle genetics and aroma biosynthesis. One aim here was to investigate the diversity and fine-scale spatial genetic structure of the Burgundy truffle Tuber aestivum. The second aim was to assess how genetic structuring along with fruiting body maturation and geographical origin influenced single constituents of truffle aroma. A total of 39 Burgundy truffles collected in two orchards were characterized in terms of aroma profile (SPME-GC/MS) and genotype (microsatellites). A moderate genetic differentiation was observed between the populations of the two orchards. An important seasonal and spatial genetic structuring was detected. Within one orchard, individuals belonging to the same genet were generally collected during a single season and in the close vicinity from each other. Maximum genet size nevertheless ranged from 46 to 92 m. Geographical origin or maturity only had minor effects on aroma profiles but genetic structuring, specifically clonal identity, had a pronounced influence on the concentrations of C8 - and C4 -VOCs. Our results highlight a high seasonal genetic turnover and indicate that the aroma of Burgundy truffle is influenced by the identity of single clones/genets. PMID:26036799

  19. Enhancement of phototropic response to a range of light doses in Triticum aestivum coleoptiles in clinostat-simulated microgravity

    NASA Technical Reports Server (NTRS)

    Heathcote, D. G.; Bircher, B. W.; Brown, A. H. (Principal Investigator)

    1987-01-01

    The phototropic dose-response relationship has been determined for Triticum aestivum cv. Broom coleoptiles growing on a purpose-built clinostat apparatus providing gravity compensation by rotation about a horizontal axis at 2 rev min-1. These data are compared with data sets obtained with the clinostat axis vertical and stationary, as a 1 g control, and rotating vertically to examine clinostat effects other than gravity compensation. Triticum at 1 g follows the well-established pattern of other cereal coleoptiles with a first positive curvature at low doses, followed by an indifferent response region, and a second positive response at progressively increasing doses. However, these response regions lie at higher dose levels than reported for Avena. There is no significant difference between the responses observed with the clinostat axis vertical in the rotating and stationary modes, but gravity compensation by horizontal rotation increases the magnitude of first and second positive curvatures some threefold at 100 min after stimulation. The indifferent response is replaced by a significant curvature towards the light source, but remains apparent as a reduced curvature response at these dose levels.

  20. Spatial organization of the gravitropic response in plants: applicability of the revised local curvature distribution model to Triticum aestivum coleoptiles.

    PubMed

    Meskauskas, A; Jurkoniene, S; Moore, D

    1999-08-01

    The revised local curvature distribution model, which provides accurate computer simulations of the gravitropic response of mushroom stems, was found to produce accurate simulations of the gravitropic reaction of wheat (Triticum aestivum) coleoptiles. The key feature of the mathematical model that enables it to approach universality of application is the assumption that the stem has an autonomic straightening reaction (curvature compensation or 'autotropism'). In the model, the local bending rate for any segment of the organ is determined by the difference between the 'bending signal' (generated by the gravitropic signal perception system) and a 'straightening signal' (which is proportional to the local curvature of the segment). The model reveals three major differences between the gravitropic reactions of wheat coleoptiles and Coprinus mushroom stems. First, in Coprinus, the capacity for autonomic straightening is much more concentrated in the apical region of the stem. Second, local perception of the gravitropic signal, which is necessary for exact simulation in Coprinus, is not needed in wheat coleoptiles (the corresponding constant in the model can be set to zero). Third, the transmission rate of the gravitropic signal is about seven times faster in wheat coleoptiles than in the mushroom stem. Thus, we demonstrate that a single model, depending on the values given to its parameters, is able to simulate the spatial organization of the gravitropic reaction of wheat coleoptiles and Coprinus mushroom stems. The model promises to be a valuable predictive tool in guiding future research into the gravitropic reaction of axial organs of all types. PMID:11542912

  1. Effects of temperature - heavy metal interactions, antioxidant enzyme activity and gene expression in wheat (Triticum aestivum L.) seedlings.

    PubMed

    Ergün, N; Özçubukçu, S; Kolukirik, M; Temizkan, Ö

    2014-12-01

    In this study, the effect of heat and chromium (Cr) heavy metal interactions on wheat seedlings (Triticum aestivum L. cv. Ç-1252 and Gun91) was investigated by measuring total chlorophyll and carotenoid levels, catalase (CAT) and ascorbate peroxidase (APX) antioxidant enzyme activities, and MYB73, ERF1 and TaSRG gene expression. Examination of pigment levels demonstrated a decrease in total chlorophyll in both species of wheat under combined heat and heavy metal stress, while the carotenoid levels showed a slight increase. APX activity increased in both species in response to heavy metal stress, but the increase in APX activity in the Gun91 seedlings was higher than that in the Ç-1252 seedlings. CAT activity increased in Gun91 seedlings but decreased in Ç-1252 seedlings. These results showed that Gun91 seedling had higher resistance to Cr and Cr + heat stresses than the Ç-1252 seedling. The quantitative molecular analyses implied that the higher resistance was related to the overexpression of TaMYB73, TaERF1 and TaSRG transcription factors. The increase in the expression levels of these transcription factors was profound under combined Cr and heat stress. This study suggests that TaMYB73, TaERF1 and TaSRG transcription factors regulate Cr and heat stress responsive genes in wheat. PMID:25475983

  2. Comparative studies of mitochondrial proteomics reveal an intimate protein network of male sterility in wheat (Triticum aestivum L.)

    PubMed Central

    Wang, Shuping; Zhang, Gaisheng; Zhang, Yingxin; Song, Qilu; Chen, Zheng; Wang, Junsheng; Guo, Jialin; Niu, Na; Wang, Junwei; Ma, Shoucai

    2015-01-01

    Plant male sterility has often been associated with mitochondrial dysfunction; however, the mechanism in wheat (Triticum aestivum L.) has not been elucidated. This study set out to probe the mechanism of physiological male sterility (PHYMS) induced by the chemical hybridizing agent (CHA)-SQ-1, and cytoplasmic male sterility (CMS) of wheat at the proteomic level. A total of 71 differentially expressed mitochondrial proteins were found to be involved in pollen abortion and further identified by MALDI-TOF/TOF MS (matrix-assisted laser desorption/ionization-time of fight/time of flight mass spectrometry). These proteins were implicated in different cellular responses and metabolic processes, with obvious functional tendencies toward the tricarboxylic acid cycle, the mitochondrial electron transport chain, protein synthesis and degradation, oxidation stress, the cell division cycle, and epigenetics. Interactions between identified proteins were demonstrated by bioinformatics analysis, enabling a more complete insight into biological pathways involved in anther abortion and pollen defects. Accordingly, a mitochondria-mediated male sterility protein network in wheat is proposed; this network was further confirmed by physiological data, RT-PCR (real-time PCR), and TUNEL (terminal deoxynucleotidyl transferase-mediated dUTP nick end labelling) assay. The results provide intriguing insights into the metabolic pathway of anther abortion induced by CHA-SQ-1 and also give useful clues to identify the crucial proteins of PHYMS and CMS in wheat. PMID:26136264

  3. Effect of CO/sub 2/ enrichment on growth and reproduction of wheat grown under low oxygen. [Triticum aestivum

    SciTech Connect

    Musgrave, M.E.; Scheld, H.W.; Strain, B.R.

    1987-04-01

    Two cultivars of wheat (Triticum aestivum L. cvs Sonoita and Yecoro Rojo) were grown to maturity in a Phytotron B chamber within four sub-chambers which imposed two CO/sub 2/ levels (350 or 1000 ppm) at either ambient (21%) or low oxygen (5%). Techniques of growth analysis were used to characterize changes in plant carbon budgets imposed by the gas regimes. Large increases in leaf area were seen in the low oxygen treatments, due primarily to a stimulation of tillering. No necrosis was observed in roots developing at 5% oxygen but rather root development increased dramatically. Flowering was much delayed in the low oxygen, 350 ppm carbon dioxide regime and the spikes which did develop did not mature. While one cultivar (Sonoita) did not respond to CO/sub 2/ enrichment (1000 ppm) at ambient oxygen in terms of increases in leaf area and head number, carbon dioxide enrichment overcame the low oxygen effect on flowering in both cultivars. The results demonstrate a previously unknown interaction between carbon dioxide enrichment and low oxygen as they affect reproduction and may help elucidate the nature of low-oxygen-induced infertility.

  4. Auxin secretion by Bacillus amyloliquefaciens FZB42 both stimulates root exudation and limits phosphorus uptake in Triticum aestivum

    PubMed Central

    2014-01-01

    Background The use of auxin-producing rhizosphere bacteria as agricultural products promises increased root production and therefore greater phosphate (Pi) uptake. Whilst such bacteria promote root production in vitro, the nature of the bacteria-plant interaction in live soil, particularly concerning any effects on nutrient uptake, are not known. This study uses Bacillus amyloliquefaciens FZB42, an auxin-producing rhizobacterium, as a dressing on Triticum aestivum seeds. It then examines the effects on root production, Pi uptake, Pi-related gene expression and organic carbon (C) exudation. Results Seed treatment with B. amyloliquefaciens FZB42 increased root production at low environmental Pi concentrations, but significantly repressed root Pi uptake. This coincided with an auxin-mediated reduction in expression of the Pi transporters TaPHT1.8 and TaPHT1.10. Applied exogenous auxin also triggered an increase in root C exudation. At high external Pi concentrations, root production was promoted by B. amyloliquefaciens FZB42, but Pi uptake was unaffected. Conclusions We conclude that, alongside promoting root production, auxin biosynthesis by B. amyloliquefaciens FZB42 both re-models Pi transporter expression and elevates organic C exudation. This shows the potential importance of rhizobacterial-derived auxin following colonisation of root surfaces, and the nature of this bacteria-plant interaction in soil. PMID:24558978

  5. The Uptake of NO3−, NO2−, and NH4+ by Intact Wheat (Triticum aestivum) Seedlings 1

    PubMed Central

    Goyal, Sham S.; Huffaker, Ray C.

    1986-01-01

    The inducibility and kinetics of the NO3−, NO2−, and NH4+ transporters in roots of wheat seedlings (Triticum aestivum cv Yercora Rojo) were characterized using precise methods approaching constant analysis of the substrate solutions. A microcomputer-controlled automated high performance liquid chromatography system was used to determine the depletion of each N species (initially at 1 millimolar) from complete nutrient solutions. Uptake rate analyses were performed using computerized curve-fitting techniques. More precise estimates were obtained for the time required for and the extent of the induction of each transporter. Up to 10 and 6 hours, respectively, were required to achieve apparent full induction of the NO3− and NO2− transporters. Evidence for substrate inducibility of the NH4+ transporters requiring 5 hours is presented. The transport of NO3− was mediated by a dual system (or dual phasic), whereas only single systems were found for transport of NO2− and NH4+. The Km values for NO3−, NO2−, and NH4+ were, respectively, 0.027, 0.054, and 0.05 millimolar. The Km for mechanism II of NO3− transport could not be defined in this study as it exhibited only apparent first order kinetics up to 1 millimolar. PMID:11539085

  6. The Effects of N Nutrition on the Water Relations and Gas Exchange Characteristics of Wheat (Triticum aestivum L.) 1

    PubMed Central

    Morgan, Jack A.

    1986-01-01

    The purpose of this study was to characterize leaf photosynthetic and stomatal responses of wheat (Triticum aestivum L.) plants grown under two N-nutritional regimes. High- and low-N regimes were imposed on growth-chamber-grown plants by fertilizing with nutrient solutions containing 12 or 1 millimolar nitrogen, respectively. Gas-exchange measurements indicated not only greater photosynthetic capacity of high-N plants under well-watered conditions, but also a greater sensitivity of CO2 exchange rate and leaf conductance to CO2 and leaf water potential compared to low-N plants. Increased sensitivity of high-N plants was associated with greater tissue elasticity, lower values of leaf osmotic pressure and greater aboveground biomass. These N-nutritional-related changes resulted in greater desiccation (lowered relative water content) of high-N plants as leaf water potential fell, and were implicated as being important in causing greater sensitivity of high-N leaf gas exchange to reductions in water potential. Water use efficiency of leaves, calculated as CO2 exchange rate/transpiration, increased from 9.1 to 13 millimoles per mole and 7.9 to 9.1 millimoles per mole for high- and low-N plants as water became limiting. Stomatal oscillations were commonly observed in the low-N treatment at low leaf water potentials and ambient CO2 concentrations, but disappeared as CO2 was lowered and stomata opened. PMID:16664606

  7. Competition between plant and bacterial cells at the microscale regulates the dynamics of nitrogen acquisition in wheat (Triticum aestivum)

    PubMed Central

    Jones, David L; Clode, Peta L; Kilburn, Matt R; Stockdale, Elizabeth A; Murphy, Daniel V

    2013-01-01

    The ability of plants to compete effectively for nitrogen (N) resources is critical to plant survival. However, controversy surrounds the importance of organic and inorganic sources of N in plant nutrition because of our poor ability to visualize and understand processes happening at the root–microbial–soil interface. Using high-resolution nano-scale secondary ion mass spectrometry stable isotope imaging (NanoSIMS-SII), we quantified the fate of 15N over both space and time within the rhizosphere. We pulse-labelled the soil surrounding wheat (Triticum aestivum) roots with either or 15N-glutamate and traced the movement of 15N over 24 h. Imaging revealed that glutamate was rapidly depleted from the rhizosphere and that most 15N was captured by rhizobacteria, leading to very high 15N microbial enrichment. After microbial capture, approximately half of the 15N-glutamate was rapidly mineralized, leading to the excretion of , which became available for plant capture. Roots proved to be poor competitors for 15N-glutamate and took up N mainly as . Spatial mapping of 15N revealed differential patterns of 15N uptake within bacteria and the rapid uptake and redistribution of 15N within roots. In conclusion, we demonstrate the rapid cycling and transformation of N at the soil–root interface and that wheat capture of organic N is low in comparison to inorganic N under the conditions tested. PMID:23845035

  8. Wheat (Triticum aestivum) seedlings secrete proteases from the roots and, after protein addition, grow well on medium without inorganic nitrogen.

    PubMed

    Adamczyk, B; Godlewski, M; Zimny, J; Zimny, A

    2008-11-01

    This paper reports on the role of proteases secreted by roots in nitrogen capture by plants. The study was conducted on aseptically cultivated wheat seedlings (Triticum aestivum cv. Tacher) obtained from embryos isolated from grains. Seedlings were cultivated for 21 days on deionised water, Murashige Skoog medium (MS), MS without inorganic nitrogen (IN), and MS without IN, in which IN was replaced by casein (0.01%, 0.1% or 1%). Comparison of seedlings grown on these media showed that casein entirely compensated for the lack of inorganic nitrogen in the medium. Shoots and roots of seedlings cultivated on MS medium with this protein had higher fresh weight than those cultivated on MS medium without casein. The increase in fresh weight of seedlings was correlated with casein concentration and proteolytic activity in the medium. In conclusion, wheat that uses proteases secreted by the roots can directly utilise proteins in the medium as a source of nitrogen without prior digestion by microbial proteases and without protein mineralisation. These results suggest the important role of organic nitrogen fertilisers in increasing wheat yield. PMID:18950429

  9. Toxicity of methyl tert-butyl ether to plants (Avena sativa, Zea mays, Triticum aestivum, and Lactuca sativa).

    PubMed

    An, Youn-Joo; Kampbell, Donald H; McGill, Mary E

    2002-08-01

    Influence of methyl tert-butyl ether (MTBE) on the germination of seeds and growth of seedling plants were studied in laboratory experiments. Test plants were wild oats (Avena sativa), sweet corn (Zea mays), wheat (Triticum aestivum), and lettuce (Lactuca sativa). Seed germination, shoot growth, and root growth of plants exposed to different concentrations of MTBE in a moist soil were examined. Seed germination and seedling growth in MTBE-contaminated soil were markedly reduced in all test plants. The median lethal concentration values for seed germination tests and the median effective concentration values for shoot or root growth were calculated. The values for lettuce, wild oats, wheat, and sweet corn were in the range of 18 to 91, 362 to 459, 432 to 751, and 672 to 964 mg MTBE/kg soil as dry weight, respectively. Lettuce was most sensitive to MTBE, followed (in order of decreasing sensitivity) by wild oats, wheat, and sweet corn. Because MTBE can be readily absorbed by plants due to its high solubility in water, plant growth was a more sensitive endpoint than seed germination. Shoot length was more reduced in MTBE-contaminated soil than was the root length, which indicated that MTBE might be transported within the plant from the roots to the shoots. PMID:12152769

  10. The role of the F-box gene TaFBA1 from wheat (Triticum aestivum L.) in drought tolerance.

    PubMed

    Zhou, Shumei; Sun, Xiudong; Yin, Suhong; Kong, Xiangzhu; Zhou, Shan; Xu, Ying; Luo, Yin; Wang, Wei

    2014-11-01

    Drought is one of the most important factors limiting plant growth and development. We identified a gene in wheat (Triticum aestivum L.) under drought stress named TaFBA1. TaFBA1 encodes a putative 325-amino-acid F-box protein with a conserved N-terminal F-box domain and a C-terminal AMN1 domain. Real-time RT-PCR analysis revealed that TaFBA1 transcript accumulation was upregulated by high-salinity, water stress, and abscisic acid (ABA) treatment. To evaluate the functions of TaFBA1 in the regulation of drought stress responses, we produced transgenic tobacco lines overexpressing TaFBA1. Under water stress conditions, the transgenic tobacco plants had a higher germination rate, higher relative water content, net photosynthesis rate (Pn), less chlorophyll loss, and less growth inhibition than WT. These results demonstrate the high tolerance of the transgenic plants to drought stress compared to the WT. The enhanced oxidative stress tolerance of these plants, which may be involved in their drought tolerance, was indicated by their lower levels of reactive oxygen species (ROS) accumulation, MDA content, and cell membrane damage under drought stress compared to WT. The antioxidant enzyme activities were higher in the transgenic plants than in WT, which may be related to the upregulated expression of some antioxidant genes via overexpression of TaFBA1. PMID:25299612

  11. Near-isogenic lines of Triticum aestivum with distinct modes of resistance exhibit dissimilar transcriptional regulation during Diuraphis noxia feeding

    PubMed Central

    Botha, Anna-Maria; van Eck, Leon; Burger, N. Francois V.; Swanevelder, Zacharias H.

    2014-01-01

    ABSTRACT Russian wheat aphid (Diuraphis noxia, Kurdjumov) feeding on susceptible Triticum aestivum L. leads to leaf rolling, chlorosis and plant death – symptoms not present in resistant lines. Although the effects of several D. noxia (Dn) resistance genes are known, none have been isolated or characterized. Wheat varieties expressing different Dn genes exhibit distinct modes of D. noxia resistance, such as antibiosis (Dn1), tolerance (Dn2), and antixenosis (Dn5). However, the mechanism whereby feeding aphids are perceived, and how subsequent transcriptional responses are partitioned into resistance categories, remains unclear. Here we report on downstream events in near-isogenic wheat lines containing different Dn genes after D. noxia biotype SA1 feeding. Transcripts involved in stress, signal transduction, photosynthesis, metabolism and gene regulation were differentially regulated during D. noxia feeding. Expression analyses using RT-qPCR and RNA hybridization, as well as enzyme activity profiling, provide evidence that the timing and intensity of pathways induced are critical in the development of particular modes of resistance. Pathways involved include the generation of kinase signalling cascades that lead to a sustained oxidative burst, and a hypersensitive response that is active during antibiosis. Tolerance is a passive resistance mechanism that acts through repair or de novo synthesis of photosystem proteins. Results further suggest that ethylene-mediated pathways are possibly involved in generating volatile compounds and cell wall fortification during the antixenosic response. PMID:25361582

  12. Fluoranthene, a polycyclic aromatic hydrocarbon, inhibits light as well as dark reactions of photosynthesis in wheat (Triticum aestivum).

    PubMed

    Tomar, Rupal Singh; Jajoo, Anjana

    2014-11-01

    The toxic effect of fluoranthene (FLT) on seed germination, growth of seedling and photosynthesis processes of wheat (Triticum aestivum) was investigated. Wheat seeds were exposed to 5 µM and 25 µM FLT concentrations for 25 days and it was observed that FLT had inhibiting effect on rate of seed germination. The germination rate of wheat seeds decreased by 11% at 25 µM FLT concentration. Root/shoot growth and biomass production declined significantly even at low concentrations of FLT. Chlorophyll a fluorescence and gas exchange parameters were measured after 25 days to evaluate the effects of FLT on Photosystem II (PSII) activity and CO2 assimilation rate. The process of CO2 assimilation decreased more effectively by FLT as compared to the yield of PSII. A negative correlation was found between plant net photosynthesis, stomatal conductance, carboxylation capacity and biomass production with FLT. It is concluded that inhibiting effects of FLT on photosynthesis are contributed more by inhibition in the process of CO2 fixation rather than inhibition of photochemical events. PMID:25173746

  13. Cytological characteristics of F2 hybrids between Triticum aestivum L. and T. durum Desf. with reference to wheat breeding.

    PubMed

    Wang, Han-Yan; Liu, Deng-Cai; Yan, Ze-Hong; Wei, Yu-Ming; Zheng, You-Liang

    2005-01-01

    Cytological and agronomic characteristics of a F2 population from Triticum aestivum L. x T. durum Desf. hybrids were analyzed plant by plant. Means of morphologic traits in the F2 population were similar to those of the low-value parent. On average, F2 hybrids had 36.54 chromosomes per plant, indicating that each gamete lost 2.73 chromosomes at meiosis of the F1 generation. More than half of plants had 36-39 chromosomes, so male gametes with 19-21 chromosomes seemed to be superior to the others. The distribution frequency of chromosomes in this study differed from that in a previous report, where a different tetraploid wheat was used. This shows that a different breeding strategy may need to be taken when exploiting a different tetraploid wheat. According to our results, some plants with 42 chromosomes, having all the wheat A, B and D chromosomes, would appear in the F3 population, which provides a chance to obtain stable bread wheat lines from the self-pollinated progenies. Alternatively, the desirable individuals of the F2 population were backcrossed to bread wheat, which is very useful and efficient for the improvement of bread wheat by exploiting desirable genes in durum wheat. PMID:16278508

  14. Epiphytic pink-pigmented methylotrophic bacteria enhance germination and seedling growth of wheat (Triticum aestivum) by producing phytohormone.

    PubMed

    Meena, Kamlesh K; Kumar, Manish; Kalyuzhnaya, Marina G; Yandigeri, Mahesh S; Singh, Dhananjaya P; Saxena, Anil K; Arora, Dilip K

    2012-05-01

    Methylotrophic bacteria were isolated from the phyllosphere of different crop plants such as sugarcane, pigeonpea, mustard, potato and radish. The methylotrophic isolates were differentiated based on growth characteristics and colony morphology on methanol supplemented ammonium mineral salts medium. Amplification of the mxaF gene helped in the identification of the methylotrophic isolates as belonging to the genus Methylobacterium. Cell-free culture filtrates of these strains enhanced seed germination of wheat (Triticum aestivum) with highest values of 98.3% observed using Methylobacterium sp. (NC4). Highest values of seedling length and vigour were recorded with Methylobacterium sp. (NC28). HPLC analysis of production by bacterial strains ranged from 1.09 to 9.89 μg ml(-1) of cytokinins in the culture filtrate. Such cytokinin producing beneficial methylotrophs can be useful in developing bio-inoculants through co-inoculation of pink-pigmented facultative methylotrophs with other compatible bacterial strains, for improving plant growth and productivity, in an environment-friendly manner. PMID:22200783

  15. Interaction of Mg with heavy metals (Cu, Cd) in T. aestivum with special reference to oxidative and proline metabolism.

    PubMed

    Singh, Vijeta; Tripathi, Bhumi Nath; Sharma, Vinay

    2016-05-01

    Little effort has been made to understand the influence of Mg on cellular processes of plant cell during Cu and Cd toxicities. The present work demonstrates the influence of magnesium (Mg) on copper (Cu) and cadmium (Cd) toxicity on Triticum aestivum (Wheat). We measured a range of parameters related to oxidative stress in wheat exposed to Cu or Cd toxicity in media with different concentrations of Mg. Decreasing Mg concentration significantly exacerbated Cu and Cd toxicity and optimum supply of Mg improved the growth and decreased the toxicity-induced oxidative stress (a substantial decline in the amount of hydrogen peroxide (H2O2) and malondialdehyde (MDA) in root and shoot tissues). Activity of antioxidant enzymes-superoxide dismutase (SOD), ascorbae peroxidase (APX), catalase (CAT) was restored upon optimum Mg concentration in the presence of Cu and Cd toxicity. An increase in proline concentration in roots and shoots that was triggered by Cu and Cd exposure was partly reversed. This was due to decline in pyrroline-5-carboxylate synthetase (P5CS) and pyrroline-5-carboxylate reductase (P5CR) activity and enhanced proline dehydrogenase (PDH) activity. In conclusion, decreasing supply of Mg effectively exacerbated the toxicities of Cu and Cd in wheat. PMID:26547559

  16. Polysaccharide isolated from Triticum aestivum stimulates insulin release from pancreatic cells via the ATP-sensitive K+ channel.

    PubMed

    Lee, Sun-Hee; Lim, Sung-Won; Lee, Young-Mi; Lee, Hoi-Seon; Kim, Dae-Ki

    2012-05-01

    Traditional natural plants have been used throughout the world for their antidiabetic effects. The aim of the present study was to investigate the stimulating activity of a polysaccharide extract derived from T. aestivum sprout (TASP) on insulin secretion in vitro using the RIN-5F pancreatic β-cell line and rat pancreatic islets. In these experiments, TASP (0.1 to 2 mg/ml) augmented glucose-stimulated insulin secretion in a dose-dependent manner in the presence of a stimulatory glucose concentration (16.7 mM), but not of a basal concentration (1.1 mM). Although TASP failed to enhance the high K+-induced insulin secretion, the insulinotropic effect of TASP was significantly inhibited by diazoxide, an opener of ATP-sensitive K+ channel blocking insulin release. TASP potentiated the insulin secretion induced by other secretagogues, such as IBMX and tolbutamide. Moreover, glucose-derived blood insulin levels were significantly elevated by oral administration of TASP to mice, similarly to antidiabetic drugs. We also demonstrated that TASP significantly increased glucose-induced 45Ca2+ uptake and proinsulin mRNA expression in rat islets. Overall, our results suggest that TASP has a stimulating effect on insulin secretion and production in pancreatic β-cells via K+ channel closure and calcium influx. These results suggest that TASP may be useful as a candidate for the therapy of diabetes mellitus. PMID:22322245

  17. Anti-obesity effect of Triticum aestivum sprout extract in high-fat-diet-induced obese mice.

    PubMed

    Im, Ji-Young; Ki, Hyeon-Hui; Xin, Mingjie; Kwon, Se-Uk; Kim, Young Ho; Kim, Dae-Ki; Hong, Sun-Pyo; Jin, Jong-Sik; Lee, Young-Mi

    2015-01-01

    Obesity is a common disease worldwide that often results in serious conditions including hypertension, diabetes, and hyperlipidemia. Many herbal medicines have been examined with regard to ameliorating obesity. We investigated the anti-obesity effects of 50% EtOH extract of Triticum aestivum sprout (TAEE) in high-fat-diet (HFD)-induced obese mice. TAEE administration (10, 50, or 200 mg/kg) for 6 weeks significantly decreased the body weights, serum total cholesterol (TC), and low-density lipoprotein cholesterol levels in HFD-fed mice. TAEE treatment reduced lipid accumulation in epididymal white adipose tissue (EWAT) and liver. Moreover, TC and lipid levels were decreased by TAEE treatment in liver. Serum leptin and adiponectin concentrations were reduced by TAEE treatment. TAEE-treated mice showed decreases in peroxisome proliferator-activated receptor γ (PPARγ) and fatty acid synthase expression in EWAT. Furthermore, TAEE administration elevated levels of PPARα protein in the liver of HFD-induced obese mice. These results suggest that TAEE supplementation might be beneficial for the treatment and prevention of obesity and related diseases. PMID:25925980

  18. Microbial Diversity of Type I Sourdoughs Prepared and Back-Slopped with Wholemeal and Refined Soft (Triticum aestivum) Wheat Flours.

    PubMed

    Taccari, Manuela; Aquilanti, Lucia; Polverigiani, Serena; Osimani, Andrea; Garofalo, Cristiana; Milanović, Vesna; Clementi, Francesca

    2016-08-01

    The fermentation of type I sourdough was studied for 20 d with daily back-slopping under laboratory and artisan bakery conditions using 1 wholemeal and 2 refined soft wheat (Triticum aestivum) flours. The sourdough bacterial and yeast diversity and dynamics were investigated by plate counting and a combination of culture-dependent and culture-independent PCR-DGGE approach. The pH, total titrable acidity, and concentration of key organic acids (phytic, lactic, and acetic) were measured. Three flours differed for both chemical and rheological properties. A microbial succession was observed, with the atypical sourdough species detected at day 0 (i.e. Lactococcus lactis and Leuconostoc holzapfelii/citreum group for bacteria and Candida silvae and Wickerhamomyces anomalus for yeasts) being progressively replaced by taxa more adapted to the sourdough ecosystem (Lactobacillus brevis, Lactobacillus alimentarius/paralimentarius, Saccharomyces cerevisiae). In mature sourdoughs, a notably different species composition was observed. As sourdoughs propagated with the same flour at laboratory and artisan bakery level were compared, the influence of both the substrate and the propagation environment on microbial diversity was assumed. PMID:27332783

  19. Alleviation of salt stress by halotolerant and halophilic plant growth-promoting bacteria in wheat (Triticum aestivum).

    PubMed

    Orhan, Furkan

    2016-01-01

    In the current study, 18 halotolerant and halophilic bacteria have been investigated for their plant growth promoting abilities in vitro and in a hydroponic culture. The bacterial strains have been investigated for ammonia, indole-3-acetic acid and 1-aminocyclopropane-1-carboxylate-deaminase production, phosphate solubilisation and nitrogen fixation activities. Of the tested bacteria, eight were inoculated with Triticum aestivum in a hydroponic culture. The investigated bacterial strains were found to have different plant-growth promoting activities in vitro. Under salt stress (200mM NaCl), the investigated bacterial strains significantly increased the root and shoot length and total fresh weight of the plants. The growth rates of the plants inoculated with bacterial strains ranged from 62.2% to 78.1%. Identifying of novel halophilic and halotolerant bacteria that promote plant growth can be used as alternatives for salt sensitive plants. Extensive research has been conducted on several halophilic and halotolerant bacterial strains to investigate their plant growth promoting activities. However, to the best of my knowledge, this is the first study to inoculate these bacterial strains with wheat. PMID:27133557

  20. Wheat (Triticum aestivum) NAM proteins regulate the translocation of iron, zinc, and nitrogen compounds from vegetative tissues to grain.

    PubMed

    Waters, Brian M; Uauy, Cristobal; Dubcovsky, Jorge; Grusak, Michael A

    2009-01-01

    The NAM-B1 gene is a NAC transcription factor that affects grain nutrient concentrations in wheat (Triticum aestivum). An RNAi line with reduced expression of NAM genes has lower grain protein, iron (Fe), and zinc (Zn) concentrations. To determine whether decreased remobilization, lower plant uptake, or decreased partitioning to grain are responsible for this phenotype, mineral dynamics were quantified in wheat tissues throughout grain development. Control and RNAi wheat were grown in potting mix and hydroponics. Mineral (Ca, Cu, Fe, K, Mg, Mn, P, S, and Zn) and nitrogen (N) contents of organs were determined at regular intervals to quantify the net remobilization from vegetative tissues and the accumulation of nutrients in grain. Total nutrient accumulation was similar between lines, but grain Fe, Zn, and N were at lower concentrations in the NAM knockdown line. In potting mix, net remobilization of N, Fe, and Zn from vegetative tissues was impaired in the RNAi line. In hydroponics with ample nutrients, net remobilization was not observed, but grain Fe and Zn contents and concentrations remained lower in the RNAi line. When Fe or Zn was withheld post-anthesis, both lines demonstrated remobilization. These results suggest that a major effect of the NAM genes is an increased efflux of nutrients from the vegetative tissues and a higher partitioning of nutrients to grain. PMID:19858116

  1. Comparative studies of mitochondrial proteomics reveal an intimate protein network of male sterility in wheat (Triticum aestivum L.).

    PubMed

    Wang, Shuping; Zhang, Gaisheng; Zhang, Yingxin; Song, Qilu; Chen, Zheng; Wang, Junsheng; Guo, Jialin; Niu, Na; Wang, Junwei; Ma, Shoucai

    2015-10-01

    Plant male sterility has often been associated with mitochondrial dysfunction; however, the mechanism in wheat (Triticum aestivum L.) has not been elucidated. This study set out to probe the mechanism of physiological male sterility (PHYMS) induced by the chemical hybridizing agent (CHA)-SQ-1, and cytoplasmic male sterility (CMS) of wheat at the proteomic level. A total of 71 differentially expressed mitochondrial proteins were found to be involved in pollen abortion and further identified by MALDI-TOF/TOF MS (matrix-assisted laser desorption/ionization-time of fight/time of flight mass spectrometry). These proteins were implicated in different cellular responses and metabolic processes, with obvious functional tendencies toward the tricarboxylic acid cycle, the mitochondrial electron transport chain, protein synthesis and degradation, oxidation stress, the cell division cycle, and epigenetics. Interactions between identified proteins were demonstrated by bioinformatics analysis, enabling a more complete insight into biological pathways involved in anther abortion and pollen defects. Accordingly, a mitochondria-mediated male sterility protein network in wheat is proposed; this network was further confirmed by physiological data, RT-PCR (real-time PCR), and TUNEL (terminal deoxynucleotidyl transferase-mediated dUTP nick end labelling) assay. The results provide intriguing insights into the metabolic pathway of anther abortion induced by CHA-SQ-1 and also give useful clues to identify the crucial proteins of PHYMS and CMS in wheat. PMID:26136264

  2. Characterization of glutathione S-transferases from Sus scrofa, Cydia pomonella and Triticum aestivum: their responses to cantharidin.

    PubMed

    Yang, Xue-Qing; Zhang, Ya-Lin

    2015-02-01

    Glutathione S-transferases (GSTs) play a key role in detoxification of xenobiotics in organisms. However, their other functions, especially response to the natural toxin cantharidin produced by beetles in the Meloidae and Oedemeridae families, are less known. We obtained GST cDNAs from three sources: Cydia pomonella (CpGSTd1), Sus scrofa (SsGSTα1), and Triticum aestivum (TaGSTf3). The predicted molecular mass is 24.19, 25.28 and 24.49 kDa, respectively. These proteins contain typical N-terminal and C-terminal domains. Recombinant GSTs were heterologously expressed in Escherichia coli as soluble fusion proteins. Their optimal activities are exhibited at pH 7.0-7.5 at 30 °C. Activity of CpGSTd1 is strongly inhibited by cantharidin and cantharidic acid, but is only slightly suppressed by the demethylated analog of cantharidin and cantharidic acid. Enzymatic assays revealed that cantharidin has no effect on SsGSTα1 activity, while it significantly stimulates TaGSTf3 activity, with an EC50 value of 0.3852 mM. Activities of these proteins are potently inhibited by the known GST competitive inhibitor: S-hexylglutathione (GTX). Our results suggest that these GSTs from different sources share similar structural and biochemical characteristics. Our results also suggest that CpGSTd1 might act as a binding protein with cantharidin and its analogs. PMID:25640718

  3. Significant Changes in Cell and Chloroplast Development in Young Wheat Leaves (Triticum aestivum cv Hereward) Grown in Elevated CO2.

    PubMed Central

    Robertson, E. J.; Leech, R. M.

    1995-01-01

    Cell and chloroplast development were characterized in young Triticum aestivum cv Hereward leaves grown at ambient (350 [mu]L L-1) or at elevated (650 [mu]L L-1) CO2. In elevated CO2, cell and chloroplast expansion was accelerated by 10 and 25%, respectively, in the first leaf of 7-d-old wheat plants without disruption to the leaf developmental pattern. Elevated CO2 did not affect the number of chloroplasts in relation to mesophyll cell size or the linear relationship between chloroplast number or size and mesophyll cell size. No major changes in leaf anatomy or in chloroplast ultrastructure were detected as a result of growth in elevated CO2, but there was a marked reduction in starch accumulation. In leaf sections fluorescently tagged antisera were used to visualize and quantitate the amount of cytochrome f, the [alpha]- and [beta]-subunits of the coupling factor 1 in ATP synthase, D1 protein of the photosystem II reaction center, the 33-kD protein of the extrinsic oxygen-evolving complex, subunit II of photosystem I, and ribulose-1,5-bisphosphate carboxylase/oxygenase. A significant finding was that in 10 to 20% of the mesophyll cells grown in elevated CO2 the 33-kD protein of the extrinsic oxygen-evolving complex of photosystem II and cytochrome f were deficient by 75%, but the other proteins accumulated normally. PMID:12228342

  4. Seed coating with arbuscular mycorrhizal fungi as an ecotechnologicalapproach for sustainable agricultural production of common wheat (Triticum aestivum L.).

    PubMed

    Oliveira, Rui S; Rocha, Inês; Ma, Ying; Vosátka, Miroslav; Freitas, Helena

    2016-01-01

    The exploitation of arbuscular mycorrhizal (AM) fungi has become of great interest in agriculture due to their potential roles in reducing the need for agrochemicals, while improving plant growth and nutrition. Nevertheless, the application of AM fungi by dispersing inocula in granular form to open agricultural fields is not feasible because nontargeted spreading of inocula over large surface areas results in high cost per plant. Seed coating has the potential to significantly reduce the amount of inoculum needed, resulting in cost reduction and increased efficiency. The aim of this study was to assess whether seed coating with AM fungal inoculum is a feasible delivery system for production of common wheat (Triticum aestivum L.). Wheat seeds were coated with inoculum of Rhizophagus irregularis BEG140 and grown under different fertilization conditions: (1) none, (2) partial, or (3) complete. Data indicated that mycorrhizal inoculation via seed coating significantly increased the dry weight of shoot and seed spikes of wheat associated with reduced fertilization. Assessment of nutritional status of wheat showed that plants inoculated with R. irregularis via seed coating displayed enhanced stem concentrations of potassium (K), sulfur (S), and zinc (Zn). There were no significant differences in root colonization between plants conventionally inoculated with R. irregularis in soil and those inoculated via seed coating. Seed coating with AM fungi may be as effective as conventional soil inoculation and may contribute to reduce the utilization of chemical fertilizers. The application of AM via seed coating is proposed as an ecotechnological approach for sustainable agricultural wheat production. PMID:27077274

  5. Transcriptome profiling of the salt-stress response in Triticum aestivum cv. Kharchia Local

    PubMed Central

    Goyal, Etika; Amit, Singh K.; Singh, Ravi S.; Mahato, Ajay K.; Chand, Suresh; Kanika, Kumar

    2016-01-01

    Kharchia Local wheat variety is an Indian salt tolerant land race known for its tolerance to salinity. However, there is a lack of detailed information regarding molecular mechanism imparting tolerance to high salinity in this bread wheat. In the present study, differential root transcriptome analysis identifying salt stress responsive gene networks and functional annotation under salt stress in Kharchia Local was performed. A total of 453,882 reads were obtained after quality filtering, using Roche 454-GS FLX Titanium sequencing technology. From these reads 22,241 ESTs were generated out of which, 17,911 unigenes were obtained. A total of 14,898 unigenes were annotated against nr protein database. Seventy seven transcription factors families in 826 unigenes and 11,002 SSRs in 6,939 unigenes were identified. Kyoto Encyclopedia of Genes and Genomes database identified 310 metabolic pathways. The expression pattern of few selected genes was compared during the time course of salt stress treatment between salt-tolerant (Kharchia Local) and susceptible (HD2687). The transcriptome data is the first report, which offers an insight into the mechanisms and genes involved in salt tolerance. This information can be used to improve salt tolerance in elite wheat cultivars and to develop tolerant germplasm for other cereal crops. PMID:27293111

  6. An Assessment of Heavy Ion Irradiation Mutagenesis for Reverse Genetics in Wheat (Triticum aestivum L.)

    PubMed Central

    Fitzgerald, Timothy L.; Powell, Jonathan J.; Stiller, Jiri; Weese, Terri L.; Abe, Tomoko; Zhao, Guangyao; Jia, Jizeng; McIntyre, C. Lynne; Li, Zhongyi; Manners, John M.; Kazan, Kemal

    2015-01-01

    Reverse genetic techniques harnessing mutational approaches are powerful tools that can provide substantial insight into gene function in plants. However, as compared to diploid species, reverse genetic analyses in polyploid plants such as bread wheat can present substantial challenges associated with high levels of sequence and functional similarity amongst homoeologous loci. We previously developed a high-throughput method to identify deletions of genes within a physically mutagenized wheat population. Here we describe our efforts to combine multiple homoeologous deletions of three candidate disease susceptibility genes (TaWRKY11, TaPFT1 and TaPLDß1). We were able to produce lines featuring homozygous deletions at two of the three homoeoloci for all genes, but this was dependent on the individual mutants used in crossing. Intriguingly, despite extensive efforts, viable lines possessing homozygous deletions at all three homoeoloci could not be produced for any of the candidate genes. To investigate deletion size as a possible reason for this phenomenon, we developed an amplicon sequencing approach based on synteny to Brachypodium distachyon to assess the size of the deletions removing one candidate gene (TaPFT1) in our mutants. These analyses revealed that genomic deletions removing the locus are relatively large, resulting in the loss of multiple additional genes. The implications of this work for the use of heavy ion mutagenesis for reverse genetic analyses in wheat are discussed. PMID:25719507

  7. Transcriptome profiling of the salt-stress response in Triticum aestivum cv. Kharchia Local.

    PubMed

    Goyal, Etika; Amit, Singh K; Singh, Ravi S; Mahato, Ajay K; Chand, Suresh; Kanika, Kumar

    2016-01-01

    Kharchia Local wheat variety is an Indian salt tolerant land race known for its tolerance to salinity. However, there is a lack of detailed information regarding molecular mechanism imparting tolerance to high salinity in this bread wheat. In the present study, differential root transcriptome analysis identifying salt stress responsive gene networks and functional annotation under salt stress in Kharchia Local was performed. A total of 453,882 reads were obtained after quality filtering, using Roche 454-GS FLX Titanium sequencing technology. From these reads 22,241 ESTs were generated out of which, 17,911 unigenes were obtained. A total of 14,898 unigenes were annotated against nr protein database. Seventy seven transcription factors families in 826 unigenes and 11,002 SSRs in 6,939 unigenes were identified. Kyoto Encyclopedia of Genes and Genomes database identified 310 metabolic pathways. The expression pattern of few selected genes was compared during the time course of salt stress treatment between salt-tolerant (Kharchia Local) and susceptible (HD2687). The transcriptome data is the first report, which offers an insight into the mechanisms and genes involved in salt tolerance. This information can be used to improve salt tolerance in elite wheat cultivars and to develop tolerant germplasm for other cereal crops. PMID:27293111

  8. Synthetic hexaploids derived from under-exploited tetraploids as a new resource for disease resistance in wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Synthetic hexaploid wheat (SHW) (2n = 6x = 42, genome AABBDD), which is developed from the hybridization between tetraploid wheat (Triticum turgidum L., 2n = 4x = 28, genome AABB) and Aegilops tauschii Coss. (2n = 2x = 14, genome DD), is a useful bridging germplasm for the introgression of desirable...

  9. Genomic Encyclopedia of Fungi

    SciTech Connect

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  10. JGI Fungal Genomics Program

    SciTech Connect

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  11. Systematic Investigation of FLOWERING LOCUS T-Like Poaceae Gene Families Identifies the Short-Day Expressed Flowering Pathway Gene, TaFT3 in Wheat (Triticum aestivum L.)

    PubMed Central

    Halliwell, Joanna; Borrill, Philippa; Gordon, Anna; Kowalczyk, Radoslaw; Pagano, Marina L.; Saccomanno, Benedetta; Bentley, Alison R.; Uauy, Cristobal; Cockram, James

    2016-01-01

    To date, a small number of major flowering time loci have been identified in the related Triticeae crops, bread wheat (Triticum aestivum), durum wheat (T. durum), and barley (Hordeum vulgare). Natural genetic variants at these loci result in major phenotypic changes which have adapted crops to the novel environments encountered during the spread of agriculture. The polyploid nature of bread and durum wheat means that major flowering time loci in which recessive alleles confer adaptive advantage in related diploid species have not been readily identified. One such example is the PPD-H2 flowering time locus encoded by FLOWERING LOCUS T 3 (HvFT3) in the diploid crop barley, for which recessive mutant alleles confer delayed flowering under short day (SD) photoperiods. In autumn-sown barley, such alleles aid the repression of flowering over the winter, which help prevent the development of cold-sensitive floral organs until the onset of inductive long day (LD) photoperiods the following spring. While the identification of orthologous loci in wheat could provide breeders with alternative mechanisms to fine tune flowering time, systematic identification of wheat orthologs of HvFT3 has not been reported. Here, we characterize the FT gene families in six Poaceae species, identifying novel members in all taxa investigated, as well as FT3 homoeologs from the A, B and D genomes of hexaploid (TaFT3) and tetraploid wheat. Sequence analysis shows TaFT3 homoeologs display high similarity to the HvFT3 coding region (95–96%) and predicted protein (96–97%), with conservation of intron/exon structure across the five cereal species investigated. Genetic mapping and comparative analyses in hexaploid and tetraploid wheat find TaFT3 homoeologs map to the long arms of the group 1 chromosomes, collinear to HvFT3 in barley and FT3 orthologs in rice, foxtail millet and brachypodium. Genome-specific expression analyses show FT3 homoeologs in tetraploid and hexaploid wheat are upregulated

  12. Systematic Investigation of FLOWERING LOCUS T-Like Poaceae Gene Families Identifies the Short-Day Expressed Flowering Pathway Gene, TaFT3 in Wheat (Triticum aestivum L.).

    PubMed

    Halliwell, Joanna; Borrill, Philippa; Gordon, Anna; Kowalczyk, Radoslaw; Pagano, Marina L; Saccomanno, Benedetta; Bentley, Alison R; Uauy, Cristobal; Cockram, James

    2016-01-01

    To date, a small number of major flowering time loci have been identified in the related Triticeae crops, bread wheat (Triticum aestivum), durum wheat (T. durum), and barley (Hordeum vulgare). Natural genetic variants at these loci result in major phenotypic changes which have adapted crops to the novel environments encountered during the spread of agriculture. The polyploid nature of bread and durum wheat means that major flowering time loci in which recessive alleles confer adaptive advantage in related diploid species have not been readily identified. One such example is the PPD-H2 flowering time locus encoded by FLOWERING LOCUS T 3 (HvFT3) in the diploid crop barley, for which recessive mutant alleles confer delayed flowering under short day (SD) photoperiods. In autumn-sown barley, such alleles aid the repression of flowering over the winter, which help prevent the development of cold-sensitive floral organs until the onset of inductive long day (LD) photoperiods the following spring. While the identification of orthologous loci in wheat could provide breeders with alternative mechanisms to fine tune flowering time, systematic identification of wheat orthologs of HvFT3 has not been reported. Here, we characterize the FT gene families in six Poaceae species, identifying novel members in all taxa investigated, as well as FT3 homoeologs from the A, B and D genomes of hexaploid (TaFT3) and tetraploid wheat. Sequence analysis shows TaFT3 homoeologs display high similarity to the HvFT3 coding region (95-96%) and predicted protein (96-97%), with conservation of intron/exon structure across the five cereal species investigated. Genetic mapping and comparative analyses in hexaploid and tetraploid wheat find TaFT3 homoeologs map to the long arms of the group 1 chromosomes, collinear to HvFT3 in barley and FT3 orthologs in rice, foxtail millet and brachypodium. Genome-specific expression analyses show FT3 homoeologs in tetraploid and hexaploid wheat are upregulated under

  13. New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing

    PubMed Central

    Helguera, Marcelo; Rivarola, Máximo; Clavijo, Bernardo; Martis, Mihaela M.; Vanzetti, Leonardo S.; González, Sergio; Garbus, Ingrid; Leroy, Phillippe; Šimková, Hana; Valárik, Miroslav; Caccamo, Mario; Doležel, Jaroslav; Mayer, Klaus F.X.; Feuillet, Catherine; Tranquilli, Gabriela; Paniego, Norma; Echenique, Viviana

    2015-01-01

    Survey sequencing of the bread wheat (Triticum aestivum L.) genome (AABBDD) has been approached through different strategies delivering important information. However, the current wheat sequence knowledge is not complete. The aim of our study is to provide different and complementary set of data for chromosome 4D. A survey sequence was obtained by pyrosequencing of flow-sorted 4DS (7.2×) and 4DL (4.1×) arms. Single ends (SE) and long mate pairs (LMP) reads were assembled into contigs (223 Mb) and scaffolds (65 Mb) that were aligned to Aegilops tauschii draft genome (DD), anchoring 34 Mb to chromosome 4. Scaffolds annotation rendered 822 gene models. A virtual gene order comprising 1973 wheat orthologous gene loci and 381 wheat gene models was built. This order was largely consistent with the scaffold order determined based on a published high density map from the Ae. tauschii chromosome 4, using bin-mapped 4D ESTs as a common reference. The virtual order showed a higher collinearity with homeologous 4B compared to 4A. Additionally, a virtual map was constructed and ∼5700 genes (∼2200 on 4DS and ∼3500 on 4DL) predicted. The sequence and virtual order obtained here using the 454 platform were compared with the Illumina one used by the IWGSC, giving complementary information. PMID:25711827

  14. Similarities of omega gliadins from Triticum urartu to those encoded on chromosome 1A of hexaploid wheat and evidence for their post-translational processing.

    PubMed

    DuPont, F M; Vensel, W; Encarnacao, T; Chan, R; Kasarda, D D

    2004-05-01

    The omega-gliadins encoded on chromosome 1 of the A genome were purified from Triticum aestivum L. (2n=6 x=42, AABBDD) cv. Butte86, nullisomic 1D-tetrasomic 1A of cv. Chinese Spring (CS N1DT1A), and the diploid T. urartu (2n=2 x=14, AA ). Reverse-phase high-performance liquid chromatography combined with sodium dodecyl sulfate-polyacrylamide gel electrophoresis of gliadin extracts from CS nullisomic-tetrasomic (NT) lines confirmed the assignment to chromosome 1A. The purified omega-gliadins were characterized by mass spectrometry and N-terminal sequencing. The 1A-encoded omega-gliadins were smaller than 1B- or 1D-encoded omega-gliadins. The N-terminal amino acid sequences for 1A omega-gliadin mature peptides were nearly identical to those for the T. urartu omega-gliadins and were more similar to 1D omega-gliadin sequences than to sequences for T. monococum omega-gliadins, barley C-hordeins, or rye omega-secalins. They diverged greatly from the N-terminal sequences for the 1B omega-gliadins. The data suggest that T. urartu is the A-genome donor, and that post-translational cleavage by an asparaginyl endoprotease produces those omega-gliadins with N-terminal sequences beginning with KEL. PMID:14747918

  15. High Transferability of Homoeolog-Specific Markers between Bread Wheat and Newly Synthesized Hexaploid Wheat Lines.

    PubMed

    Zeng, Deying; Luo, Jiangtao; Li, Zenglin; Chen, Gang; Zhang, Lianquan; Ning, Shunzong; Yuan, Zhongwei; Zheng, Youliang; Hao, Ming; Liu, Dengcai

    2016-01-01

    Bread wheat (Triticum aestivum, 2n = 6x = 42, AABBDD) has a complex allohexaploid genome, which makes it difficult to differentiate between the homoeologous sequences and assign them to the chromosome A, B, or D subgenomes. The chromosome-based draft genome sequence of the 'Chinese Spring' common wheat cultivar enables the large-scale development of polymerase chain reaction (PCR)-based markers specific for homoeologs. Based on high-confidence 'Chinese Spring' genes with known functions, we developed 183 putative homoeolog-specific markers for chromosomes 4B and 7B. These markers were used in PCR assays for the 4B and 7B nullisomes and their euploid synthetic hexaploid wheat (SHW) line that was newly generated from a hybridization between Triticum turgidum (AABB) and the wild diploid species Aegilops tauschii (DD). Up to 64% of the markers for chromosomes 4B or 7B in the SHW background were confirmed to be homoeolog-specific. Thus, these markers were highly transferable between the 'Chinese Spring' bread wheat and SHW lines. Homoeolog-specific markers designed using genes with known functions may be useful for genetic investigations involving homoeologous chromosome tracking and homoeolog expression and interaction analyses. PMID:27611704

  16. Making the Bread: Insights from Newly Synthesized Allohexaploid Wheat.

    PubMed

    Li, Ai-li; Geng, Shuai-Feng; Zhang, Lian-quan; Liu, Deng-cai; Mao, Long

    2015-06-01

    Bread wheat (or common wheat, Triticum aestivum) is an allohexaploid (AABBDD, 2n = 6x = 42) that arose by hybridization between a cultivated tetraploid wheat T. turgidum (AABB, 2n = 4x = 28) and the wild goatgrass Aegilops tauschii (DD, 2n = 2x = 14). Polyploidization provided niches for rigorous genome modification at cytogenetic, genetic, and epigenetic levels, rendering a broader spread than its progenitors. This review summarizes the latest advances in understanding gene regulation mechanisms in newly synthesized allohexaploid wheat and possible correlation with polyploid growth vigor and adaptation. Cytogenetic studies reveal persistent association of whole-chromosome aneuploidy with nascent allopolyploids, in contrast to the genetic stability in common wheat. Transcriptome analysis of the euploid wheat shows that small RNAs are driving forces for homoeo-allele expression regulation via genetic and epigenetic mechanisms. The ensuing non-additively expressed genes and those with expression level dominance to the respective progenitor may play distinct functions in growth vigor and adaptation in nascent allohexaploid wheat. Further genetic diploidization of allohexaploid wheat is not random. Regional asymmetrical gene distribution, rather than subgenome dominance, is observed in both synthetic and natural allohexaploid wheats. The combinatorial effects of diverged genomes, subsequent selection of specific gene categories, and subgenome-specific traits are essential for the successful establishment of common wheat. PMID:25747845

  17. Genomics and Health Impact Update

    MedlinePlus

    ... Genomics in Practice Newborn Screening Pharmacogenomics Reproductive Health Tools and Databases About the Genomics & Health Impact Update The Office of Public Health Genomics provides updated and credible ...

  18. Integrating sequence, evolution and functional genomics in regulatory genomics

    PubMed Central

    Vingron, Martin; Brazma, Alvis; Coulson, Richard; van Helden, Jacques; Manke, Thomas; Palin, Kimmo; Sand, Olivier; Ukkonen, Esko

    2009-01-01

    With genome analysis expanding from the study of genes to the study of gene regulation, 'regulatory genomics' utilizes sequence information, evolution and functional genomics measurements to unravel how regulatory information is encoded in the genome. PMID:19226437

  19. Genomic Data Commons | Office of Cancer Genomics

    Cancer.gov

    The NCI’s Center for Cancer Genomics launches the Genomic Data Commons (GDC), a unified data sharing platform for the cancer research community. The mission of the GDC is to enable data sharing across the entire cancer research community, to ultimately support precision medicine in oncology.

  20. Harvesting rice's dispensable genome.

    PubMed

    Wing, Rod A

    2015-01-01

    A rapid and cost-effective approach has been developed to harvest and map the dispensable genome, that is, population-level natural sequence variation within a species that is not present in static genome assemblies. PMID:26429765

  1. Libraries for genomic SELEX.

    PubMed Central

    Singer, B S; Shtatland, T; Brown, D; Gold, L

    1997-01-01

    An increasing number of proteins are being identified that regulate gene expression by binding specific nucleic acidsin vivo. A method termed genomic SELEX facilitates the rapid identification of networks of protein-nucleic acid interactions by identifying within the genomic sequences of an organism the highest affinity sites for any protein of the organism. As with its progenitor, SELEX of random-sequence nucleic acids, genomic SELEX involves iterative binding, partitioning, and amplification of nucleic acids. The two methods differ in that the variable region of the nucleic acid library for genomic SELEX is derived from the genome of an organism. We have used a quick and simple method to construct Escherichia coli, Saccharomyces cerevisiae, and human genomic DNA PCR libraries that can be transcribed with T7 RNA polymerase. We present evidence that the libraries contain overlapping inserts starting at most of the positions within the genome, making these libraries suitable for genomic SELEX. PMID:9016629

  2. Genomic Data Commons launches

    Cancer.gov

    The Genomic Data Commons (GDC), a unified data system that promotes sharing of genomic and clinical data between researchers, launched today with a visit from Vice President Joe Biden to the operations center at the University of Chicago.

  3. GENOMICS AND ENVIRONMENTAL RESEARCH

    EPA Science Inventory

    The impact of recently developed and emerging genomics technologies on environmental sciences has significant implications for human and ecological risk assessment issues. The linkage of data generated from genomics, transcriptomics, proteomics, metabalomics, and ecology can be ...

  4. Structural analysis of xylanase inhibitor protein I (XIP-I), a proteinaceous xylanase inhibitor from wheat (Triticum aestivum, var. Soisson).

    PubMed Central

    Payan, Françoise; Flatman, Ruth; Porciero, Sophie; Williamson, Gary; Juge, Nathalie; Roussel, Alain

    2003-01-01

    A novel class of proteinaceous inhibitors exhibiting specificity towards microbial xylanases has recently been discovered in cereals. The three-dimensional structure of xylanase inhibitor protein I (XIP-I) from wheat (Triticum aestivum, var. Soisson) was determined by X-ray crystallography at 1.8 A (1 A=0.1 nm) resolution. The inhibitor possesses a (beta/alpha)(8) barrel fold and has structural features typical of glycoside hydrolase family 18, namely two consensus regions, approximately corresponding to the third and fourth barrel strands, and two non-proline cis -peptide bonds, Ser(36)-Phe and Trp(256)-Asp (in XIP-I numbering). However, detailed structural analysis of XIP-I revealed several differences in the region homologous with the active site of chitinases. The catalytic glutamic acid residue of family 18 chitinases [Glu(127) in hevamine, a chitinase/lysozyme from the rubber tree (Hevea brasiliensis)] is conserved in the structure of the inhibitor (Glu(128)), but its side chain is fully engaged in salt bridges with two neighbouring arginine residues. Gly(81), located in subsite -1 of hevamine, where the reaction intermediate is formed, is replaced by Tyr(80) in XIP-I. The tyrosine side chain fills the subsite area and makes a strong hydrogen bond with the side chain of Glu(190) located at the opposite side of the cleft, preventing access of the substrate to the catalytic glutamic acid. The structural differences in the inhibitor cleft structure probably account for the lack of activity of XIP-I towards chitin. PMID:12617724

  5. Activation of latent nucleolus organizers induced by experimental polyploidization in cells of hexaploid wheat Triticum aestivum L.

    PubMed

    Lazareva, E M; Khoudoleeva, O A; Chentsov YuS; Polyakov VYu

    2000-01-01

    The effect of prolonged colchicine-induced polyploidization on activation of latent nucleolus-organizing regions (NOR) of chromosomes was studied in diploid meristematic cells and polyploid root cells of Triticum aestivum L. It has been shown that control diploid and tetraploid cells have maximal number of nucleoli equal to four, which corresponds to the number of nucleolar chromosomes (NC) with active (visualized by staining with AgNO3) NOR (two pairs of homologous chromosomes 1B and 6B). Treatment of wheat seedlings with colchicine for 30 h results in following changes in polyploid cells: (1) impregnation of NOR with silver is observed on homologues of either chromosomes 1A or 5D in all tetraploid metaphase plates (4n, 2x, 4c), which is indicative of the NOR activation on this chromosome in pre-mitotic polyploid interphase; (2) In tetraploid metaphase, NOR in all four homologues of activated chromosomes or in only two of them may be stained; (3) maximal number of nucleoli in tetraploid nuclei is increased till 12, which confirms activation of transcription of additional rRNA gene clusters in polyploids; (4) activation of the rRNA gene expression is induced by the cell polyploidization rather than by colchicine, since in the colchicine-treated diploid cells both maximal number of nucleoli and the number of metaphase chromosomes with active NOR is not changed as compared with control. The obtained data allow us to suggest that structural "separation" of NC in polyploid nuclei stimulates activation of latent NOR. PMID:11093578

  6. Putative fasciclin-like arabinogalactan-proteins (FLA) in wheat (Triticum aestivum) and rice (Oryza sativa): identification and bioinformatic analyses.

    PubMed

    Faik, Ahmed; Abouzouhair, Jaouad; Sarhan, Fathey

    2006-11-01

    Putative plant adhesion molecules include arabinogalactan-proteins having fasciclin-like domains. In animal, fasciclin proteins participate in cell adhesion and communication. However, the molecular basis of interactions in plants is still unknown and none of these domains have been characterized in cereals. This work reports the characterization of 34 wheat (Triticum aestivum) and 24 rice (Oryza sativa) Fasciclin-Like Arabinogalactan-proteins (FLAs). Bioinformatics analyses show that cereal FLAs share structural characteristics with known Arabidopsis FLAs including arabinogalactan-protein and fasciclin conserved domains. At least 70% of the wheat and rice FLAs are predicted to be glycosylphosphatidylinositol-anchored to the plasma membranes. Expression analyses determined from the relative abundance of ESTs in the publicly available wheat EST databases and from RNA gel blots indicate that most of these genes are weakly expressed and found mainly in seeds and roots. Furthermore, most wheat genes were down regulated by abiotic stresses except for TaFLA9 and 12 where cold treatment induces their expression in roots. Plant fasciclin-like domains were predicted to have 3-D homology with FAS1 domain of the fasciclin I insect neural cell adhesion molecule with an estimated precision above 70%. The structural analysis shows that negatively charged amino acids are concentrated along the beta1-alpha3-alpha4-beta2 edges, while the positively charged amino acids are concentrated on the back side of the folds. This highly charged surface distribution could provide a way of mediating protein-protein interactions via electrostatic forces similar to many other adhesion molecules. The identification of wheat FLAs will facilitate studying their function in plant growth and development and their role in stress response. PMID:16944204

  7. Aluminum Partitioning in Intact Roots of Aluminum-Tolerant and Aluminum-Sensitive Wheat (Triticum aestivum L.) Cultivars

    PubMed Central

    Rincón, Magaly; Gonzales, Robert A.

    1992-01-01

    Aluminum (Al) partitioning in intact roots of wheat (Triticum aestivum L.) cultivars that differ in sensitivity to Al was investigated. Roots of intact seedlings were exposed to Al for up to 24 hours and distribution of Al was assessed visually by hematoxylin staining or by direct measurement of concentration of Al by atomic absorption spectrophotometry or ion chromatography. Major differences in Al accumulation between Al-tolerant (Atlas 66) and Al-sensitive (Tam 105) cultivars were found in the growing regions 0 to 2 and 2 to 5 millimeters from the root apex. Al content was 9 to 13 times greater in the 0 to 2 millimeters root tips of cv Tam 105 than in the tips of cv Atlas 66 when exposed to 50 micromolar Al for 19 to 24 hours. The oxidative phosphorylation inhibitor carbonyl cyanide m-chlorophenylhydrazone and the protein synthesis inhibitor cycloheximide increased Al uptake by intact root tips of cv Atlas 66. Also, loss of Al from the roots of both cultivars was measured after the roots were “pulsed” with 50 micromolar Al for 2 hours and then placed in an Al-free nutrient solution for 6 hours. The 0 to 2 millimeter root tips of cv Tam 105 lost 30% of the absorbed Al, whereas the tips of cv Atlas 66 lost 60%. In light of these results, we conclude that the differential Al sensitivity in wheat correlates with the concentration of Al in the root meristems. The data support the hypothesis that part of the mechanism for Al tolerance in wheat is based on a metabolism-dependent exclusion of Al from the sensitive meristems. ImagesFigure 1Figure 2 PMID:16668966

  8. Analysis of TaALMT1 traces the transmission of aluminum resistance in cultivated common wheat (Triticum aestivum L.).

    PubMed

    Raman, Harsh; Ryan, Peter R; Raman, Rosy; Stodart, Benjamin J; Zhang, Kerong; Martin, Peter; Wood, Rachel; Sasaki, Takayuki; Yamamoto, Yoko; Mackay, Michael; Hebb, Diane M; Delhaize, Emmanuel

    2008-02-01

    Allele diversities of four markers specific to intron three, exon four and promoter regions of the aluminum (Al) resistance gene of wheat (Triticum aestivum L.) TaALMT1 were compared in 179 common wheat cultivars used in international wheat breeding programs. In wheat cultivars released during the last 93 years, six different promoter types were identified on the basis of allele size. A previous study showed that Al resistance was not associated with a particular coding allele for TaALMT1 but was correlated with blocks of repeated sequence upstream of the coding sequence. We verified the linkage between these promoter alleles and Al resistance in three doubled haploid and one intercross populations segregating for Al resistance. Molecular and pedigree analysis suggest that Al resistance in modern wheat germplasm is derived from several independent sources. Analysis of a population of 278 landraces and subspecies of wheat showed that most of the promoter alleles associated with Al resistance pre-existed in Europe, the Middle East and Asia prior to dispersal of cultivated germplasm around the world. Furthermore, several new promoter alleles were identified among the landraces surveyed. The TaALMT1 promoter alleles found within the spelt wheats were consistent with the hypothesis that these spelts arose on several independent occasions from hybridisations between non-free-threshing tetraploid wheats and Al-resistant hexaploid bread wheats. The strong correlation between Al resistance and Al-stimulated malate efflux from the root apices of 49 diverse wheat genotypes examined was consistent with the previous finding that Al resistance in wheat is conditioned primarily by malate efflux. These results demonstrate that the markers based on intron, exon and promoter regions of TaALMT1 can trace the inheritance of the Al resistance locus within wheat pedigrees and track Al resistance in breeding programmes. PMID:18046532

  9. In vivo studies on artificial induction of thermotolerance to detached panicles of wheat (Triticum aestivum L) cultivars under heat stress.

    PubMed

    Asthir, Bavita; Bhatia, Surekha

    2014-01-01

    The mechanism imparting thermotolerance by gibberellic acid (GA3) and abscisic acid (ABA) is still unresolved using either spraying technique or in vitro conditions. Alternative way of studying these effects under near in vivo conditions is through the use of liquid culturing technique. Effects of GA3 and ABA (100 μM) on sucrose metabolism (invertase and sucrose synthase) and aminotransferases (GOT and GPT) in relation to starch and protein accumulation were studied in detached panicles of three wheat (Triticum aestivum L.) cultivars PBW 343, C 306 (heat tolerant) and WH 542 (heat susceptible) cultured in a liquid medium. Ears were subjected to heat shock treatment (45 °C for 2 h) and then maintained at 25 °C for 5 days. Heat shock treatment resulted in a significant decline in starch content but caused a marked build -up of total free sugars and protein content in grains of all cultivars. However, activities of acid and neutral invertases increased only in tolerant cultivars but reduced in susceptible cultivar. Following treatment with GA3 contents of starch and free sugars increased in grains maintained at 25 °C but free sugar content decreased in stressed grains compared to control. ABA application showed inhibitory effect on starch accumulation under normal temperature but was promotory under stress conditions. Concomitantly, soluble protein content also increased in conjunction with an increase in the activities of glutamate-oxaloacetate transaminase (GOT) and glutamate-pyruvate transaminase (GPT). Apparently, the wheat grain responds to heat shock mediated disruption of carbon metabolism by a compensatory effect on nitrogen metabolism. GA3 stimulated grain sink activity both under stress and non stress condition while ABA was promotory only under stress condition. PMID:24426056

  10. Identification of a MYB3R gene involved in drought, salt and cold stress in wheat (Triticum aestivum L.).

    PubMed

    Cai, Hongsheng; Tian, Shan; Liu, Changlai; Dong, Hansong

    2011-10-10

    Abiotic stress seriously affects crop growth and productivity. To better understand the mechanisms plant uses to cope with drought, cold and salt stress, it is necessary to isolate and characterize important regulators response to these stresses. In this study, we cloned a MYB gene from wheat (Triticum aestivum L.) and designated it as TaMYB3R1 based on its conserved three repeats in MYB domain. The sequence of TaMYB3R1 protein shares high identity to other plant MYB3R proteins. Subcellular localization experiment in onion epidermal cells proved that TaMYB3R1 localized in the nucleus. Trans-activation essays in yeast cells confirmed that TaMYB3R1 was a transcriptional activator, and only C-terminal region was able to activate the expression of β-galactosidase. DNA-binding test showed the MSA cis element-binding activity of TaMYB3R1. After exogenous application of phytohormone ABA, the expression of TaMYB3R1 was induced, and its transcripts accumulated up to 24h; this is also the case for MeJA treatment, but after it peaked at 4h, it decreased to low levels. However, either SA or ET had no obvious effect on the expression of TaMYB3R1. Furthermore, the TaMYB3R1 was initially expressed at low levels and was gradually induced following treatment with salt, and continued to increase up to 72 h. This was similar for the cold treatment. In contrast, the peak appeared at 6h of the PEG treatment, and then gradually decreased to low levels. Our results suggest that TaMYB3R1 is potentially involved in wheat response to drought, salt and cold stress. PMID:21763408

  11. Microsatellite mapping of a Triticum urartu Tum. derived powdery mildew resistance gene transferred to common wheat (Triticum aestivum L.).

    PubMed

    Qiu, Y C; Zhou, R H; Kong, X Y; Zhang, S S; Jia, J Z

    2005-11-01

    A powdery mildew resistance gene from Triticum urartu Tum. accession UR206 was successfully transferred into hexaploid wheat (Triticum aestivum L.) through crossing and backcrossing. The F1 plants, which had 28 chromosomes and an average of 5.32 bivalents and 17.36 univalents in meiotic pollen mother cells (PMC), were obtained through embryos rescued owing to shriveling of endosperm in hybrid seed of cross Chinese Spring (CS) x UR206. Hybrid seeds were produced through backcrossing F1 with common wheat parents. The derivative lines had normal chromosome numbers and powdery mildew resistance similar to the donor UR206, indicating that the powdery mildew resistance gene originating from T. urartu accession UR206 was successfully transferred and expressed in a hexaploid wheat background. Genetic analysis indicated that a single dominant gene controlled the powdery mildew resistance at the seedling stage. To map and tag the powdery mildew resistance gene, 143 F2 individuals derived from a cross UR206 x UR203 were used to construct a linkage map. The resistant gene was mapped on the chromosome 7AL based on the mapped microsatellite makers. The map spanned 52.1 cM and the order of these microsatellite loci agreed well with the established microsatellite map of chromosome arm 7AL. The resistance gene was flanked by the microsatellite loci Xwmc273 and Xpsp3003, with the genetic distances of 2.2 cM and 3.8 cM, respectively. On the basis of the origin and chromosomal location of the gene, it was temporarily designated PmU. PMID:16177900

  12. TLXI, a novel type of xylanase inhibitor from wheat (Triticum aestivum) belonging to the thaumatin family

    PubMed Central

    Fierens, Ellen; Rombouts, Sigrid; Gebruers, Kurt; Goesaert, Hans; Brijs, Kristof; Beaugrand, Johnny; Volckaert, Guido; Van Campenhout, Steven; Proost, Paul; Courtin, Christophe M.; Delcour, Jan A.

    2007-01-01

    Wheat (Triticum aestivum) contains a previously unknown type of xylanase (EC 3.2.1.8) inhibitor, which is described in the present paper for the first time. Based on its >60% similarity to TLPs (thaumatin-like proteins) and the fact that it contains the Prosite PS00316 thaumatin family signature, it is referred to as TLXI (thaumatin-like xylanase inhibitor). TLXI is a basic (pI≥9.3 in isoelectric focusing) protein with a molecular mass of approx. 18–kDa (determined by SDS/PAGE) and it occurs in wheat with varying extents of glycosylation. The TLXI gene sequence encodes a 26-amino-acid signal sequence followed by a 151-amino-acid mature protein with a calculated molecular mass of 15.6–kDa and pI of 8.38. The mature TLXI protein was expressed successfully in Pichia pastoris, resulting in a 21–kDa (determined by SDS/PAGE) recombinant protein (rTLXI). Polyclonal antibodies raised against TLXI purified from wheat react with epitopes of rTLXI as well as with those of thaumatin, demonstrating high structural similarity between these three proteins. TLXI has a unique inhibition specificity. It is a non-competitive inhibitor of a number of glycoside hydrolase family 11 xylanases, but it is inactive towards glycoside hydrolase family 10 xylanases. Progress curves show that TLXI is a slow tight-binding inhibitor, with a Ki of approx. 60–nM. Except for zeamatin, an α-amylase/trypsin inhibitor from maize (Zea mays), no other enzyme inhibitor is currently known among the TLPs. TLXI thus represents a novel type of inhibitor within this group of proteins. PMID:17269932

  13. Identification of kernel proteins associated with the resistance to fusarium head blight in winter wheat (Triticum aestivum L.).

    PubMed

    Perlikowski, Dawid; Wiśniewska, Halina; Góral, Tomasz; Kwiatek, Michał; Majka, Maciej; Kosmala, Arkadiusz

    2014-01-01

    Numerous potential components involved in the resistance to Fusarium head blight (FHB) in cereals have been indicated, however, our knowledge regarding this process is still limited and further work is required. Two winter wheat (Triticum aestivum L.) lines differing in their levels of resistance to FHB were analyzed to identify the most crucial proteins associated with resistance in this species. The presented work involved analysis of protein abundance in the kernel bulks of more resistant and more susceptible wheat lines using two-dimensional gel electrophoresis and mass spectrometry identification of proteins, which were differentially accumulated between the analyzed lines, after inoculation with F. culmorum under field conditions. All the obtained two-dimensional patterns were demonstrated to be well-resolved protein maps of kernel proteomes. Although, 11 proteins were shown to have significantly different abundance between these two groups of plants, only two are likely to be crucial and have a potential role in resistance to FHB. Monomeric alpha-amylase and dimeric alpha-amylase inhibitors, both highly accumulated in the more resistant line, after inoculation and in the control conditions. Fusarium pathogens can use hydrolytic enzymes, including amylases to colonize kernels and acquire nitrogen and carbon from the endosperm and we suggest that the inhibition of pathogen amylase activity could be one of the most crucial mechanisms to prevent infection progress in the analyzed wheat line with a higher resistance. Alpha-amylase activity assays confirmed this suggestion as it revealed the highest level of enzyme activity, after F. culmorum infection, in the line more susceptible to FHB. PMID:25340555

  14. A haplotype block associated with thousand-kernel weight on chromosome 5DS in common wheat (Triticum aestivum L.).

    PubMed

    Wang, Yuquan; Hao, Chenyang; Zheng, Jun; Ge, Hongmei; Zhou, Yang; Ma, Zhengqiang; Zhang, Xueyong

    2015-08-01

    Spike number per unit area, number of grains per spike, and thousand-kernel weight (TKW) are important yield components for wheat (Triticum aestivum L.). TKW has the highest heritability among the three components. We validated 27 simple sequence repeat (SSR) loci associated with TKW in an F(2:5) breeding population grown in four environments. A cfd7(8265bp) marker on chromosome 5DS showed the strongest association with TKW and had a significantly positive effect on TKW compared to allele cfd7(8259bp), with mean increases of 5.17, 3.63, 4.11, and 5.16 g in the four environments. Markers cfd67 and cfd40 flanking cfd78 also showed significantly positive associations with TKW with increases of 5.11, 3.29, 4.31, and 4.50 g for cfd67(205), and 4.98, 3.49, 4.06, and 4.84 g for cfd40(187) compared with cfd67(203) and cfd40(190) in the four environments, respectively. A major quantitative trait locus for TKW spanning 2.94 cM on chromosome 5DS was detected by association mapping. Strong linkage disequilibrium (LD) (r(2)  > 0.2) was detected among the three linked markers, which formed three haplotype blocks in the F(2:5) breeding population. Mean TKW differences between HapB-I and HapB-II were 5.80, 4.41, 4.02, and 5.06 g in the four environments, respectively. Moreover, significant LD was detected only between cfd78 and cfd67 and between cfd67 and cfd40 in a germplasm collection. This study provides a base for cloning genes related to TKW on chromosome 5DS. PMID:25318826

  15. Water extract of Triticum aestivum L. and its components demonstrate protective effect in a model of vascular dementia.

    PubMed

    Han, Hyung Soo; Jang, Jung-Hee; Jang, Jae Hee; Choi, Jung Sook; Kim, Yoon Jung; Lee, Chan; Lim, Sun Ha; Lee, Hyeong-Kyu; Lee, Jongwon

    2010-06-01

    Although vascular dementia is the second leading cause of dementia and often underdiagnosed, there are no drugs yet approved for the treatment of vascular dementia. In this study, it is demonstrated that water extract of Triticum aestivum L. (TALE) and some of its components have protective effects against vascular dementia-induced damage by preserving the myelin sheath and inhibiting astrocytic activation. The memory test used a vascular dementia model utilizing bilateral ligation of the carotid arteries of rats. TALE, some of its components, such as starch, total dietary fiber (TDF), arabinoxylan, beta-glucan, and degraded products of arabinoxylan, such as arabinose and xylose, were administered to the animals from day 8 to day 14, following the surgery. Twenty-one days after the surgery, the water maze test was performed for 5 days, and the time taken to find the platform during training trials (mean escape latency) was measured. The mean escape latency was decreased consistently in the TALE-, starch-, TDF-, arabinoxylan-, and arabinose-treated groups, compared with that in the vascular dementia group. To measure brain damage, Luxol fast blue staining and immunohistochemistry of myelin basic protein (MBP) were performed to observe myelin sheath in the white matter, and immunohistochemistry of glial fibrillary acidic protein (GFAP) was performed to observe the astrocytic reaction. Vascular dementia reduced the MBP level and increased the GFAP level. Arabinose effectively inhibited the MBP and GFAP change, whereas arabinoxylan inhibited the GFAP change only. These results suggest that TALE and some of its components can be used as a medicinal material for the development of neuroprotective agents against vascular dementia. PMID:20521983

  16. Exploiting the genome

    SciTech Connect

    Block, S.; Cornwall, J.; Dyson, F.; Koonin, S.; Lewis, N.; Schwitters, R.

    1998-09-11

    In 1997, JASON conducted a DOE-sponsored study of the human genome project with special emphasis on the areas of technology, quality assurance and quality control, and informatics. The present study has two aims: first, to update the 1997 Report in light of recent developments in genome sequencing technology, and second, to consider possible roles for the DOE in the ''post-genomic" era, following acquisition of the complete human genome sequence.

  17. NsLTP1 and NsLTP2 isoforms in soft wheat (Triticum aestivum Cv. Centauro) and farro (Triticum dicoccon Schrank) bran.

    PubMed

    Capocchi, Antonella; Fontanini, Debora; Muccilli, Vera; Cunsolo, Vincenzo; Saviozzi, Franco; Saletti, Rosaria; Lorenzi, Roberto; Foti, Salvatore; Galleschi, Luciano

    2005-10-01

    Isoforms of nonspecific lipid-transfer protein 1 (nsLTP1) and nonspecific lipid-transfer protein 2 (nsLTP2) were investigated in bran tissues isolated from caryopses of two cereal crops quite relevant for the Italian market, the cultivar Centauro of soft wheat (Triticum aestivum) and Italian emmer or farro (Triticum dicoccon Schrank). By sequential separation of the bran extracts on cation-exchange and gel filtration chromatographies, fractions containing only proteins belonging to the nsLTP1 and nsLTP2 classes were obtained. The proteins were roughly identified by SDS-PAGE and by immunoreactions in Western blotting experiments. By MALDI-MS and RP-HPLC/ESI-MS analyses we were able to show the presence of several LTP1 and LTP2 isoforms in the investigated species. Bioinformatic searches based on the determined Mr indicated that (i) two nsLTP1s already identified in T. aestivum have Mr and number of Cys residues identical to that of a 9.6 kDa protein present both in soft wheat cv. Centauro and in farro; (ii) two isoforms of nsLTP2 detected in T. aestivum have the same Mr and number of Cys residues of two 7 kDa proteins found in Centauro; and (iii) a nsLTP1 detected in Ambrosia artemisiifolia has Mr and number of Cys residues coincident to that of a 9.9 kDa protein found both in soft wheat cv. Centauro and in farro. PMID:16190659

  18. COMPARATIVE GENOMICS IN LEGUMES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The legume plant family will soon include three sequenced genomes. The majority of the gene-containing portions of the model legumes Medicago truncatula and Lotus japonicus have been sequenced in clone-by-clone projects, and the sequencing of the soybean genome is underway in a whole-genome shotgun ...

  19. Whole Genome Selection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Whole genome selection (WGS) is an approach to using DNA markers that are distributed throughout the entire genome. Genes affecting most economically-important traits are distributed throughout the genome and there are relatively few that have large effects with many more genes with progressively sm...

  20. Genome-Wide Association Mapping for Resistance to Leaf and Stripe Rust in Winter-Habit Hexaploid Wheat Landraces.

    PubMed

    Kertho, Albert; Mamidi, Sujan; Bonman, J Michael; McClean, Phillip E; Acevedo, Maricelis

    2015-01-01

    Leaf rust, caused by Puccinia triticina (Pt), and stripe rust, caused by P. striiformis f. sp. tritici (Pst), are destructive foliar diseases of wheat worldwide. Breeding for disease resistance is the preferred strategy of managing both diseases. The continued emergence of new races of Pt and Pst requires a constant search for new sources of resistance. Here we report a genome-wide association analysis of 567 winter wheat (Triticum aestivum) landrace accessions using the Infinium iSelect 9K wheat SNP array to identify loci associated with seedling resistance to five races of Pt (MDCL, MFPS, THBL, TDBG, and TBDJ) and one race of Pst (PSTv-37) frequently found in the Northern Great Plains of the United States. Mixed linear models identified 65 and eight significant markers associated with leaf rust and stripe rust, respectively. Further, we identified 31 and three QTL associated with resistance to Pt and Pst, respectively. Eleven QTL, identified on chromosomes 3A, 4A, 5A, and 6D, are previously unknown for leaf rust resistance in T. aestivum. PMID:26076040

  1. Genome-Wide Association Mapping for Resistance to Leaf and Stripe Rust in Winter-Habit Hexaploid Wheat Landraces

    PubMed Central

    Kertho, Albert; Mamidi, Sujan; Bonman, J. Michael; McClean, Phillip E.; Acevedo, Maricelis

    2015-01-01

    Leaf rust, caused by Puccinia triticina (Pt), and stripe rust, caused by P. striiformis f. sp. tritici (Pst), are destructive foliar diseases of wheat worldwide. Breeding for disease resistance is the preferred strategy of managing both diseases. The continued emergence of new races of Pt and Pst requires a constant search for new sources of resistance. Here we report a genome-wide association analysis of 567 winter wheat (Triticum aestivum) landrace accessions using the Infinium iSelect 9K wheat SNP array to identify loci associated with seedling resistance to five races of Pt (MDCL, MFPS, THBL, TDBG, and TBDJ) and one race of Pst (PSTv-37) frequently found in the Northern Great Plains of the United States. Mixed linear models identified 65 and eight significant markers associated with leaf rust and stripe rust, respectively. Further, we identified 31 and three QTL associated with resistance to Pt and Pst, respectively. Eleven QTL, identified on chromosomes 3A, 4A, 5A, and 6D, are previously unknown for leaf rust resistance in T. aestivum. PMID:26076040

  2. Homoeologous copy-specific expression patterns of MADS-box genes for floral formation in allopolyploid wheat.

    PubMed

    Tanaka, Miku; Tanaka, Hiroko; Shitsukawa, Naoki; Kitagawa, Satoshi; Takumi, Shigeo; Murai, Koji

    2016-01-01

    The consensus model for floral organ formation in higher plants, the so-called ABCDE model, proposes that floral whorl-specific combinations of class A, B, C, D, and E genes specify floral organ identity. Class A, B, C, D and E genes encode MADS-box transcription factors; the single exception being the class A gene APETALA2. Bread wheat (Triticum aestivum) is a hexaploid species with a genome constitution AABBDD; the hexaploid originated from a cross between tetraploid T. turgidum (AABB) and diploid Aegilops tauschii (DD). Tetraploid wheat is thought to have originated from a cross between the diploid species T. urartu (AA) and Ae. speltoides (BB). Consequently, the hexaploid wheat genome contains triplicated homoeologous copies (homoeologs) of each gene derived from the different ancestral diploid species. In this study, we examined the expression patterns of homoeologs of class B, C and D MADS-box genes during floral development. For the class B gene wheat PISTILLATA2 (WPI2), the homoeologs from the A and D genomes were expressed, while expression of the B genome homoeolog was suppressed. For the class C gene wheat AGAMOUS1 (WAG1), the homoeologs on the A and B genomes were expressed, while expression of the D genome homoeolog was suppressed. For the class D gene wheat SEEDSTICK (WSTK), the B genome homoeolog was preferentially expressed. These differential patterns of homoeolog expression were consistently observed among different hexaploid wheat varieties and synthetic hexaploid wheat lines developed by artificial crosses between tetraploid wheat and Ae. tauschii. These results suggest that homoeolog-specific regulation of the floral MADS-box genes occurs in allopolyploid wheat. PMID:26616759

  3. Genomics and functional genomics with haloarchaea.

    PubMed

    Soppa, J; Baumann, A; Brenneis, M; Dambeck, M; Hering, O; Lange, C

    2008-09-01

    The first haloarchaeal genome was published in 2000 and today five genome sequences are available. Transcriptome and proteome analyses have been established for two and three haloarchaeal species, respectively, and more than 20 studies using these functional genomic approaches have been published in the last two years. These studies gave global overviews of metabolic regulation (aerobic and anaerobic respiration, phototrophy, carbon source usage), stress response (UV, X-rays, transition metals, osmotic and temperature stress), cell cycle-dependent transcript level regulation, and transcript half-lives. The only translatome analysis available for any prokaryotic species revealed that 10 and 20% of all transcripts are translationally regulated in Haloferax volcanii and Halobacterium salinarum, respectively. Very effective methods for the construction of in frame deletion mutants have been established recently for haloarchaea and are intensively used to unravel the biological roles of genes in this group. Bioinformatic analyses include both cross-genome comparisons as well as integration of genomic data with experimental results. The first systems biology approaches have been performed that used experimental data to construct predictive models of gene expression and metabolism, respectively. In this contribution the current status of genomics, functional genomics, and molecular genetics of haloarchaea is summarized and selected examples are discussed. PMID:18493745

  4. Chromium and Genomic Stability

    PubMed Central

    Wise, Sandra S.; Wise, John Pierce

    2014-01-01

    Many metals serve as micronutrients which protect against genomic instability. Chromium is most abundant in its trivalent and hexavalent forms. Trivalent chromium has historically been considered an essential element, though recent data indicate that while it can have pharmacological effects and value, it is not essential. There are no data indicating that trivalent chromium promotes genomic stability and, instead may promote genomic instability. Hexavalent chromium is widely accepted as highly toxic and carcinogenic with no nutritional value. Recent data indicate that it causes genomic instability and also has no role in promoting genomic stability. PMID:22192535

  5. The Genomic Medicine Game.

    PubMed

    Tran, Elvis; de Andrés-Galiana, Enrique J; Benitez, Sonia; Martin-Sanchez, Fernando; Lopez-Campos, Guillermo H

    2016-01-01

    With advancements in genomics technology, health care has been improving and new paradigms of medicine such as genomic medicine have evolved. The education of clinicians, researchers and students to face the challenges posed by these new approaches, however, has been often lagging behind. From this the Genomic Medicine Game, an educational tool, was created for the purpose of conceptualizing the key components of Genomic Medicine. A number of phenotype-genotype associations were found through a literature review, which was used to be a base for the concepts the Genomic Medicine Game would focus on. Built in Java, the game was successfully tested with promising results. PMID:27577486

  6. Sequencing chromosome 5D of Aegilops tauschii and comparison with its allopolyploid descendant bread wheat (Triticum aestivum).

    PubMed

    Akpinar, Bala A; Lucas, Stuart J; Vrána, Jan; Doležel, Jaroslav; Budak, Hikmet

    2015-08-01

    Flow cytometric sorting of individual chromosomes and chromosome-based sequencing reduces the complexity of large, repetitive Triticeae genomes. We flow-sorted chromosome 5D of Aegilops tauschii, the D genome donor of bread wheat and sequenced it by Roche 454 GS FLX platform to approximately 2.2x coverage. Repetitive sequences represent 81.09% of the survey sequences of this chromosome, and Class I retroelements are the prominent type, with a particular abundance of LTR/Gypsy superfamily. Nonrepetitive sequences were assembled to cover 17.76% of the total chromosome regions. Up to 6188 nonrepetitive gene loci were predicted to be encoded by the 5D chromosome. The numbers and chromosomal distribution patterns of tRNA genes suggest abundance in tRNA(L) (ys) and tRNA(M) (et) species, while the nonrepetitive assembly reveals tRNA(A) (la) species as the most abundant type. A comparative analysis of the genomic sequences of bread wheat and Aegilops chromosome 5D indicates conservation of gene content. Orthologous unique genes, matching Aegilops 5D sequences, numbered 3730 in barley, 5063 in Brachypodium, 4872 in sorghum and 4209 in rice. In this study, we provide a chromosome-specific view into the structure and organization of the 5D chromosome of Ae. tauschii, the D genome ancestor of bread wheat. This study contributes to our understanding of the chromosome-level evolution of the wheat genome and presents a valuable resource in wheat genomics due to the recent hybridization of Ae. tauschii genome with its tetraploid ancestor. PMID:25516153

  7. Microbial genomic taxonomy.

    PubMed

    Thompson, Cristiane C; Chimetto, Luciane; Edwards, Robert A; Swings, Jean; Stackebrandt, Erko; Thompson, Fabiano L

    2013-01-01

    A need for a genomic species definition is emerging from several independent studies worldwide. In this commentary paper, we discuss recent studies on the genomic taxonomy of diverse microbial groups and a unified species definition based on genomics. Accordingly, strains from the same microbial species share >95% Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), >95% identity based on multiple alignment genes, <10 in Karlin genomic signature, and > 70% in silico Genome-to-Genome Hybridization similarity (GGDH). Species of the same genus will form monophyletic groups on the basis of 16S rRNA gene sequences, Multilocus Sequence Analysis (MLSA) and supertree analysis. In addition to the established requirements for species descriptions, we propose that new taxa descriptions should also include at least a draft genome sequence of the type strain in order to obtain a clear outlook on the genomic landscape of the novel microbe. The application of the new genomic species definition put forward here will allow researchers to use genome sequences to define simultaneously coherent phenotypic and genomic groups. PMID:24365132

  8. The Bluejay genome browser.

    PubMed

    Soh, Jung; Gordon, Paul M K; Sensen, Christoph W

    2012-03-01

    The Bluejay genome browser is a stand-alone visualization tool for the multi-scale viewing of annotated genomes and other genomic elements. Bluejay allows users to customize display features to suit their needs, and produces publication-quality graphics. Bluejay provides a multitude of ways to interrelate biological data at the genome scale. Users can load gene expression data into a genome display for expression visualization in context. Multiple genomes can be compared concurrently, including time series expression data, based on Gene Ontology labels. External, context-sensitive biological Web Services are linked to the displayed genomic elements ad hoc for in-depth genomic data analysis and interpretation. Users can mark multiple points of interest in a genome by creating waypoints, and exploit them for easy navigation of single or multiple genomes. Using this comprehensive visual environment, users can study a gene not just in relation to its genome, but also its transcriptome and evolutionary origins. Written in Java, Bluejay is platform-independent and is freely available from http://bluejay.ucalgary.ca. PMID:22389011

  9. Bacterial Genome Instability

    PubMed Central

    Darmon, Elise

    2014-01-01

    SUMMARY Bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile DNA elements. This implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. In this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. We then discuss the consequences of genome instability at the physiological level, where cells have harnessed instability to mediate phase and antigenic variation, and at the evolutionary level, where horizontal gene transfer has played an important role. Indeed, this ability to share DNA sequences has played a major part in the evolution of life on Earth. The evolutionary plasticity of bacterial genomes, coupled with the vast numbers of bacteria on the planet, substantially limits our ability to control disease. PMID:24600039

  10. UCSC genome browser tutorial.

    PubMed

    Zweig, Ann S; Karolchik, Donna; Kuhn, Robert M; Haussler, David; Kent, W James

    2008-08-01

    The University of California Santa Cruz (UCSC) Genome Bioinformatics website consists of a suite of free, open-source, on-line tools that can be used to browse, analyze, and query genomic data. These tools are available to anyone who has an Internet browser and an interest in genomics. The website provides a quick and easy-to-use visual display of genomic data. It places annotation tracks beneath genome coordinate positions, allowing rapid visual correlation of different types of information. Many of the annotation tracks are submitted by scientists worldwide; the others are computed by the UCSC Genome Bioinformatics group from publicly available sequence data. It also allows users to upload and display their own experimental results or annotation sets by creating a custom track. The suite of tools, downloadable data files, and links to documentation and other information can be found at http://genome.ucsc.edu/. PMID:18514479

  11. Variations in genome mass.

    PubMed

    Wachtel, S S; Tiersch, T R

    1993-02-01

    1. Genome size varies considerably among vertebrates, ranging from less than 1 pg to more than 200 pg; the amount of DNA differing among individuals in a population can equal the amount in the entire structural gene complement. 2. Recent technological advances permit evaluation of genome size variation at several levels including sub-chromosomal, chromosomal and cellular. 3. Genome size variation may also be viewed from taxonomic levels, and across evolutionary time frames. 4. As sources of genome size variation are identified and studied, the conundrum of the C-value paradox (lack of correlations among genome size, genomic complexity and phylogenetic status of organisms) may prove to be more apparent than real. 5. For example, the limited and relatively constant genome size of avians may be related to the physiological constraints of flight. PMID:8462275

  12. Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B.

    PubMed

    Paux, Etienne; Roger, Delphine; Badaeva, Ekatherina; Gay, Georges; Bernard, Michel; Sourdille, Pierre; Feuillet, Catherine

    2006-11-01

    Bread wheat (Triticum aestivum) is one of the most important crops worldwide. However, because of its large, hexaploid, highly repetitive genome it is a challenge to develop efficient means for molecular analysis and genetic improvement in wheat. To better understand the composition and molecular evolution of the hexaploid wheat homoeologous genomes and to evaluate the potential of BAC-end sequences (BES) for marker development, we have followed a chromosome-specific strategy and generated 11 Mb of random BES from chromosome 3B, the largest chromosome of bread wheat. The sequence consisted of about 86% of repetitive elements, 1.2% of coding regions, and 13% remained unknown. With 1.2% of the sequence length corresponding to coding sequences, 6000 genes were estimated for chromosome 3B. New repetitive sequences were identified, including a Triticineae-specific tandem repeat (Fat) that represents 0.6% of the B-genome and has been differentially amplified in the homoeologous genomes before polyploidization. About 10% of the BES contained junctions between nested transposable elements that were used to develop chromosome-specific markers for physical and genetic mapping. Finally, sequence comparison with 2.9 Mb of random sequences from the D-genome of Aegilops tauschii suggested that the larger size of the B-genome is due to a higher content in repetitive elements. It also indicated which families of transposable elements are mostly responsible for differential expansion of the homoeologous wheat genomes during evolution. Our data demonstrate that BAC-end sequencing from flow-sorted chromosomes is a powerful tool for analysing the structure and evolution of polyploid and highly repetitive genomes. PMID:17010109

  13. Genome-wide association study of drought-related resistance traits in Aegilops tauschii.

    PubMed

    Qin, Peng; Lin, Yu; Hu, Yaodong; Liu, Kun; Mao, Shuangshuang; Li, Zhanyi; Wang, Jirui; Liu, Yaxi; Wei, Yuming; Zheng, Youliang

    2016-07-01

    The D-genome progenitor of wheat (Triticum aestivum), Aegilops tauschii, possesses numerous genes for resistance to abiotic stresses, including drought. Therefore, information on the genetic architecture of A. tauschii can aid the development of drought-resistant wheat varieties. Here, we evaluated 13 traits in 373 A. tauschii accessions grown under normal and polyethylene glycol-simulated drought stress conditions and performed a genome-wide association study using 7,185 single nucleotide polymorphism (SNP) markers. We identified 208 and 28 SNPs associated with all traits using the general linear model and mixed linear model, respectively, while both models detected 25 significant SNPs with genome-wide distribution. Public database searches revealed several candidate/flanking genes related to drought resistance that were grouped into three categories according to the type of encoded protein (enzyme, storage protein, and drought-induced protein). This study provided essential information for SNPs and genes related to drought resistance in A. tauschii and wheat, and represents a foundation for breeding drought-resistant wheat cultivars using marker-assisted selection. PMID:27392238

  14. Genome-wide association study of drought-related resistance traits in Aegilops tauschii

    PubMed Central

    Qin, Peng; Lin, Yu; Hu, Yaodong; Liu, Kun; Mao, Shuangshuang; Li, Zhanyi; Wang, Jirui; Liu, Yaxi; Wei, Yuming; Zheng, Youliang

    2016-01-01

    Abstract The D-genome progenitor of wheat (Triticum aestivum), Aegilops tauschii, possesses numerous genes for resistance to abiotic stresses, including drought. Therefore, information on the genetic architecture of A. tauschii can aid the development of drought-resistant wheat varieties. Here, we evaluated 13 traits in 373 A. tauschii accessions grown under normal and polyethylene glycol-simulated drought stress conditions and performed a genome-wide association study using 7,185 single nucleotide polymorphism (SNP) markers. We identified 208 and 28 SNPs associated with all traits using the general linear model and mixed linear model, respectively, while both models detected 25 significant SNPs with genome-wide distribution. Public database searches revealed several candidate/flanking genes related to drought resistance that were grouped into three categories according to the type of encoded protein (enzyme, storage protein, and drought-induced protein). This study provided essential information for SNPs and genes related to drought resistance in A. tauschii and wheat, and represents a foundation for breeding drought-resistant wheat cultivars using marker-assisted selection. PMID:27560650

  15. Relationships among the A Genomes of Triticum L. species as evidenced by SSR markers, in Iran.

    PubMed

    Ehtemam, Mohammad Hosein; Rahiminejad, Mohammad Reza; Saeidi, Hojjatollah; Tabatabaei, Badraldin Ebrahim Sayed; Krattinger, Simon G; Keller, Beat

    2010-01-01

    The relationships among 55 wheat accessions (47 accessions collected from Iran and eight accessions provided by the Institute of Plant Biology of the University of Zurich, Switzerland) belonging to eight species carrying A genome (Triticum monococcum L., T. boeoticum Boiss., T. urartu Tumanian ex Gandilyan, T. durum Desf., T. turgidum L., T. dicoccum Schrank ex Schübler, T. dicoccoides (Körn. ex Asch. & Graebner) Schweinf. and T. aestivum L.) were evaluated using 31 A genome specific microsatellite markers. A high level of polymorphism was observed among the accessions studied (PIC = 0.77). The highest gene diversity was revealed among T. durum genotypes, while the lowest genetic variation was found in T. dicoccoides accessions. The analysis of molecular variance (AMOVA) showed a significant genetic variance (75.56%) among these accessions, representing a high intra-specific genetic diversity within Triticum taxa in Iran. However, such a variance was not observed among their ploidy levels. Based on the genetic similarity analysis, the accessions collected from Iran were divided into two main groups: diploids and polyploids. The genetic similarity among the diploid and polyploid species was 0.85 and 0.89 respectively. There were no significant differences in A genome diversity from different geographic regions. Based on the genetic diversity analyses, we consider there is value in a greater sampling of each species in Iran to discover useful genes for breeding purposes. PMID:21151440

  16. Relationships among the A Genomes of Triticum L. Species as Evidenced by SSR Markers, in Iran

    PubMed Central

    Ehtemam, Mohammad Hosein; Rahiminejad, Mohammad Reza; Saeidi, Hojjatollah; Tabatabaei, Badraldin Ebrahim Sayed; Krattinger, Simon G.; Keller, Beat

    2010-01-01

    The relationships among 55 wheat accessions (47 accessions collected from Iran and eight accessions provided by the Institute of Plant Biology of the University of Zurich, Switzerland) belonging to eight species carrying A genome (Triticum monococcum L., T. boeoticum Boiss., T. urartu Tumanian ex Gandilyan, T. durum Desf., T. turgidum L., T. dicoccum Schrank ex Schübler, T. dicoccoides (Körn. ex Asch. & Graebner) Schweinf. and T. aestivum L.) were evaluated using 31 A genome specific microsatellite markers. A high level of polymorphism was observed among the accessions studied (PIC = 0.77). The highest gene diversity was revealed among T. durum genotypes, while the lowest genetic variation was found in T. dicoccoides accessions. The analysis of molecular variance (AMOVA) showed a significant genetic variance (75.56%) among these accessions, representing a high intra-specific genetic diversity within Triticum taxa in Iran. However, such a variance was not observed among their ploidy levels. Based on the genetic similarity analysis, the accessions collected from Iran were divided into two main groups: diploids and polyploids. The genetic similarity among the diploid and polyploid species was 0.85 and 0.89 respectively. There were no significant differences in A genome diversity from different geographic regions. Based on the genetic diversity analyses, we consider there is value in a greater sampling of each species in Iran to discover useful genes for breeding purposes. PMID:21151440

  17. Genome-wide association study of drought-related resistance traits in Aegilops tauschii.

    PubMed

    Qin, Peng; Lin, Yu; Hu, Yaodong; Liu, Kun; Mao, Shuangshuang; Li, Zhanyi; Wang, Jirui; Liu, Yaxi; Wei, Yuming; Zheng, Youliang

    2016-01-01

    The D-genome progenitor of wheat (Triticum aestivum), Aegilops tauschii, possesses numerous genes for resistance to abiotic stresses, including drought. Therefore, information on the genetic architecture of A. tauschii can aid the development of drought-resistant wheat varieties. Here, we evaluated 13 traits in 373 A. tauschii accessions grown under normal and polyethylene glycol-simulated drought stress conditions and performed a genome-wide association study using 7,185 single nucleotide polymorphism (SNP) markers. We identified 208 and 28 SNPs associated with all traits using the general linear model and mixed linear model, respectively, while both models detected 25 significant SNPs with genome-wide distribution. Public database searches revealed several candidate/flanking genes related to drought resistance that were grouped into three categories according to the type of encoded protein (enzyme, storage protein, and drought-induced protein). This study provided essential information for SNPs and genes related to drought resistance in A. tauschii and wheat, and represents a foundation for breeding drought-resistant wheat cultivars using marker-assisted selection. PMID:27560650

  18. Effects on growth and physiological parameters in wheat (Triticum aestivum L.) grown in soil and irrigated with cyanobacterial toxin contaminated water.

    PubMed

    Pflugmacher, Stephan; Hofmann, Jeannette; Hübner, Bettina

    2007-12-01

    The present study investigates the germination and growth of Triticum aestivum exposed to two different microcystins (microcystin-LR [where the two variable places in the toxin molecule are leucine (L) and arginine (R) (MC-LR)] and microcystin-RR) and to cell-free cyanobacterial crude extract containing MC-LR. The concentration of the microcystins was set to 0.5 microg L(-1) and therefore is in the range of concentrations normally detected in the environment. In three experiments, the inhibition of germination, the inhibition of root and shoot development, photosynthesis, and activity of oxidative stress-response enzymes, such as glutathione-S-transferase, glutathione peroxidase, and glutathione reductase, were measured. All plants were placed in pots containing normal garden soil to investigate the effects of soil in the uptake of toxin by Triticum aestivum. The results showed clear effects on the morphology of roots and shoots, which were inhibited in exposures with cyanotoxins and crude extract. The inhibition of photosynthesis and the elevation of antioxidative-response enzymes indicate the generation of reactive oxygen species due to the exposure to the toxins resulting in oxidative stress for the plants. PMID:18020690

  19. Improving water use efficiency of wheat (triticum aestivum l. Giza 168) crop using 15N tracer technique under Egyptian environment

    NASA Astrophysics Data System (ADS)

    Refaie Emara, Eman Ibrahim; Hamed, Lamy Mamdoh Mohamed; Bocchi, Stefano; Galal, Yehia

    2015-04-01

    The Mediterranean environment is characterized by low and erratic rainfall amount which varies between (200-600 mm.year-1), and characterized also by high temperature which increase the rate of evapotranspiration from the cultivated soil. Under these conditions which have a great influence on crop production, there is a great needing to increase the crop water use efficiency. In this context, two field experiments were carried out in northern Cairo-Egypt, during November and December 2012 and April 2013, with two different textured soils. The soil in the first location (30° 16' N latitude, 30° 56' E longitude) is clay soil, while in the second one (30° 24' N latitude, 31° 35' E longitude) is sandy soil. The interaction effect of soil types, soil water regimes, nitrogen fertilizer application rates and timing on nitrogen balance of soil were studied, in terms of nitrogen gained by plant portions, remained in soil and losses through different ways for the wheat crop (Triticum aestivum L. Giza 168). The aim of this research is to increase the water use efficiency of wheat crop, in addition to identify the most proper and effective combinations of above-studied variables that provide a satisfactory grain wheat yield and finally to minimize the use of chemical nitrogen fertilizers. Three water regimes (100%, 75% and 50% of crop water requirements) using drip irrigation system and the application methods of Nitrogen rates, 100%, 80% and 60% of recommended rates, which are 178 Kg of Nitrogen for the clay soil and 238 Kg of Nitrogen for sandy soil, were applied to the two experimental fields. Ineed, two modes of agricultural management, mode A and B, were applied. Each mode is different than the other in terms of seedling and tillering practices, where mode A performed with 25% at seedling, 25% at tillering and 50% at jointing while mode B performed with 35% at seedling and 65% at tillering. The greatest limitation to growth and Nitrogen use efficiency was the amount

  20. Higher Ammonium Transamination Capacity Can Alleviate Glutamate Inhibition on Winter Wheat (Triticum aestivum L.) Root Growth under High Ammonium Stress

    PubMed Central

    Liu, Yang; Tian, Zhongwei; Muhammad, Abid; Zhang, Yixuan; Jiang, Dong; Cao, Weixing; Dai, Tingbo

    2016-01-01

    Most of the studies about NH4+ stress mechanism simply address the effects of free NH4+, failing to recognize the changed nitrogen assimilation products. The objective of this study was to elucidate the effects of glutamate on root growth under high ammonium (NH4+) conditions in winter wheat (Triticum aestivum L.). Hydroponic experiments were conducted using two wheat cultivars, AK58 (NH4+-sensitive) and Xumai25 (NH4+-tolerant) with either 5 mM NH4+ nitrogen (AN) as stress treatment or 5 mM nitrate (NO3-) nitrogen as control. To evaluate the effects of NH4+-assimilation products on plant growth, 1 μM L-methionine sulfoximine (MSO) (an inhibitor of glutamine synthetase (GS)) and 1 mM glutamates (a primary N assimilation product) were added to the solutions, respectively. The AN significantly reduced plant biomass, total root length, surface area and root volume in both cultivars, but less effect was observed in Xumai25. The inhibition effects were alleviated by the application of MSO but strengthened by the application of glutamate. The AN increased the activities of GS, glutamate dehydrogenase (GDH) in both cultivars, resulting in higher glutamate contents. However, its contents were decreased by the application of MSO. Compared to AK58, Xumai25 showed lower glutamate contents due to its higher activities of glutamic-oxaloacetic transaminase (GOT) and glutamic-pyruvic transaminase (GPT). With the indole-3-acetic acid (IAA) contents decreasing in roots, the ratio of shoot to root in IAA was increased, and further increased by the application of glutamate, and reduced by the application of MSO, but the ratio was lower in Xumai25. Meanwhile, the total soluble sugar contents and its root to shoot ratio also showed similar trends. These results indicate that the NH4+-tolerant cultivar has a greater transamination ability to prevent glutamate over-accumulation to maintain higher IAA transport ability, and consequently promoted soluble sugar transport to roots, further

  1. Heading Date QTL in Winter Wheat (Triticum aestivum L.) Coincide with Major Developmental Genes VERNALIZATION1 and PHOTOPERIOD1

    PubMed Central

    Hao, Yuan Feng; Johnson, Jerry; Harrison, Steve; Marshall, David

    2016-01-01

    In wheat (Triticum aestivum L.), time from planting to spike emergence is influenced by genes controlling vernalization requirement and photoperiod response. Characterizing the available genetic diversity of known and novel alleles of VERNALIZATION1 (VRN1) and PHOTOPERIOD1 (PPD1) in winter wheat can inform approaches for breeding climate resilient cultivars. This study identified QTL for heading date (HD) associated with multiple VRN1 and PPD1 loci in a population developed from a cross between two early flowering winter wheat cultivars. When the population was grown in the greenhouse after partial vernalization treatment, major heading date QTLs co-located with the VRN-A1 and VRN-B1 loci. Copy number variation at the VRN-A1 locus influenced HD such that RIL having three copies required longer cold exposure to transition to flowering than RIL having two VRN-A1 copies. Sequencing vrn-B1 winter alleles of the parents revealed multiple polymorphisms in the first intron that were the basis of mapping a major HD QTL coinciding with VRN-B1. A 36 bp deletion in the first intron of VRN-B1 was associated with earlier HD after partial vernalization in lines having either two or three haploid copies of VRN-A1. The VRN1 loci interacted significantly and influenced time to heading in field experiments in Louisiana, Georgia and North Carolina. The PPD1 loci were significant determinants of heading date in the fully vernalized treatment in the greenhouse and in all field environments. Heading date QTL were associated with alleles having large deletions in the upstream regions of PPD-A1 and PPD-D1 and with copy number variants at the PPD-B1 locus. The PPD-D1 locus was determined to have the largest genetic effect, followed by PPD-A1 and PPD-B1. Our results demonstrate that VRN1 and PPD1 alleles of varying strength allow fine tuning of flowering time in diverse winter wheat growing environments. PMID:27163605

  2. Higher Ammonium Transamination Capacity Can Alleviate Glutamate Inhibition on Winter Wheat (Triticum aestivum L.) Root Growth under High Ammonium Stress.

    PubMed

    Wang, Feng; Gao, Jingwen; Liu, Yang; Tian, Zhongwei; Muhammad, Abid; Zhang, Yixuan; Jiang, Dong; Cao, Weixing; Dai, Tingbo

    2016-01-01

    Most of the studies about NH4+ stress mechanism simply address the effects of free NH4+, failing to recognize the changed nitrogen assimilation products. The objective of this study was to elucidate the effects of glutamate on root growth under high ammonium (NH4+) conditions in winter wheat (Triticum aestivum L.). Hydroponic experiments were conducted using two wheat cultivars, AK58 (NH4+-sensitive) and Xumai25 (NH4+-tolerant) with either 5 mM NH4+ nitrogen (AN) as stress treatment or 5 mM nitrate (NO3-) nitrogen as control. To evaluate the effects of NH4+-assimilation products on plant growth, 1 μM L-methionine sulfoximine (MSO) (an inhibitor of glutamine synthetase (GS)) and 1 mM glutamates (a primary N assimilation product) were added to the solutions, respectively. The AN significantly reduced plant biomass, total root length, surface area and root volume in both cultivars, but less effect was observed in Xumai25. The inhibition effects were alleviated by the application of MSO but strengthened by the application of glutamate. The AN increased the activities of GS, glutamate dehydrogenase (GDH) in both cultivars, resulting in higher glutamate contents. However, its contents were decreased by the application of MSO. Compared to AK58, Xumai25 showed lower glutamate contents due to its higher activities of glutamic-oxaloacetic transaminase (GOT) and glutamic-pyruvic transaminase (GPT). With the indole-3-acetic acid (IAA) contents decreasing in roots, the ratio of shoot to root in IAA was increased, and further increased by the application of glutamate, and reduced by the application of MSO, but the ratio was lower in Xumai25. Meanwhile, the total soluble sugar contents and its root to shoot ratio also showed similar trends. These results indicate that the NH4+-tolerant cultivar has a greater transamination ability to prevent glutamate over-accumulation to maintain higher IAA transport ability, and consequently promoted soluble sugar transport to roots, further

  3. Molecular cytogenetic identification of a wheat-rye 1R addition line with multiple spikelets and resistance to powdery mildew.

    PubMed

    Yang, Wujuan; Wang, Changyou; Chen, Chunhuan; Wang, Yajuan; Zhang, Hong; Liu, Xinlun; Ji, Wanquan

    2016-04-01

    Alien addition lines are important for transferring useful genes from alien species into common wheat. Rye is an important and valuable gene resource for improving wheat disease resistance, yield, and environment adaptation. A new wheat-rye addition line, N9436B, was developed from the progeny of the cross of common wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) cultivar Shaanmai 611 and rye (Secale cereal L., 2n = 2x = 14, RR) accession Austrian rye. We characterized this new line by cytology, genomic in situ hybridization (GISH), fluorescence in situ hybridization (FISH), molecular markers, and disease resistance screening. N9436B was stable in morphology and cytology, with a chromosome composition of 2n = 42 + 2t = 22II. GISH investigations showed that this line contained two rye chromosomes. GISH, FISH, and molecular maker identification suggested that the introduced R chromosome and the missing wheat chromosome arms were 1R chromosome and 2DL chromosome arm, respectively. N9436B exhibited 30-37 spikelets per spike and a high level of resistance to powdery mildew (Blumeria graminis f. sp. tritici, Bgt) isolate E09 at the seedling stage. N9436B was cytologically stable, had the trait of multiple spikelets, and was resistant to powdery mildew; this line should thus be useful in wheat improvement. PMID:27021228

  4. Genomics of sorghum.

    PubMed

    Paterson, Andrew H

    2008-01-01

    Sorghum (Sorghum bicolor (L.) Moench) is a subject of plant genomics research based on its importance as one of the world's leading cereal crops, a biofuels crop of high and growing importance, a progenitor of one of the world's most noxious weeds, and a botanical model for many tropical grasses with complex genomes. A rich history of genome analysis, culminating in the recent complete sequencing of the genome of a leading inbred, provides a foundation for invigorating progress toward relating sorghum genes to their functions. Further characterization of the genomes other than Saccharinae cereals may shed light on mechanisms, levels, and patterns of evolution of genome size and structure, laying the foundation for further study of sugarcane and other economically important members of the group. PMID:18483564

  5. The tiniest tiny genomes.

    PubMed

    Moran, Nancy A; Bennett, Gordon M

    2014-01-01

    Starting in 2006, surprisingly tiny genomes have been discovered from numerous bacterial symbionts of insect hosts. Despite their size, each retains some genes that enable provisioning of limiting nutrients or other capabilities required by hosts. Genome sequence analyses show that genome reduction is an ongoing process, resulting in a continuum of sizes, with the smallest genome currently known at 112 kilobases. Genome reduction is typical in host-restricted symbionts and pathogens, but the tiniest genomes are restricted to symbionts required by hosts and restricted to specialized host cells, resulting from long coevolution with hosts. Genes are lost in all functional categories, but core genes for central informational processes, including genes encoding ribosomal proteins, are mostly retained, whereas genes underlying production of cell envelope components are especially depleted. Thus, these entities retain cell-like properties but are heavily dependent on coadaptation of hosts, which continuously evolve to support the symbionts upon which they depend. PMID:24995872

  6. Development and Characterization of Two New Triticum aestivum-Daspyrum villosum Robertsonian Translocation Lines T1DS.1V#3L and T1DL.1V#3S and Their Effect on Grain Quality

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dasypyrum villosum (L.) Candargy is a diploid, wild relative of bread wheat Triticum aestivum L. Previous studies showed that D. villosum chromosome 1V has genes that encode for seed storage proteins that may be used to enhance the grain quality of bread wheat. As a first step in genetic transfer, t...

  7. The house mouse (Mus musculus L.) exerts strong differential grain consumption preferences among hard red and white spring wheat (Triticum aestivum L.) varieties in a single-elimination tournament design

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Wheat (Triticum aestivum) plays a central role in the health and nutrition of humans. Yet, little is known about possible flavor differences among different varieties. We have developed a model system using the house mouse (Mus musculus) to determine feeding preferences as a prelude to extending res...

  8. Association of puroindoline b-2 variants with grain traits, yield components and flag leaf size in bread wheat (Triticum aestivum L.) varieties of Yellow and Huai Valley of China

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A total of 169 wheat (Triticum aestivum L.) varieties (landraces and cultivars) were used to asses the relationship between Puroindoline D1 alleles and Puroindoline b-B2 variants and grain hardness, other grain traits, grain yield components, and flag leaf size. Results indicated that the average SK...

  9. Segregation analysis indicates that Puroindoline b-2 variants 2 and 3 are allelic in Triticum aestivum L. and that a revision to Puroindoline b-2 gene symbolization is indicated

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Conclusive genetic and kernel texture phenotypic relationships between Puroindoline b 2 variant sequences 2 and 3 have not been fully established in wheat (Triticum aestivum L.). In the present study, a total of 480 F2 plants, derived from three hard spring wheat populations WSU.HRS1×WSU.HWS1 (abbre...

  10. Construction of Whole Genome Radiation Hybrid Panels and Map of Chromosome 5A of Wheat Using Asymmetric Somatic Hybridization

    PubMed Central

    Han, Lu; Wei, Jiajie; Jia, Li; Tan, Yang; Zhi, Daying; Wang, Zeng-Yu; Xia, Guangmin

    2012-01-01

    To explore the feasibility of constructing a whole genome radiation hybrid (WGRH) map in plant species with large genomes, asymmetric somatic hybridization between wheat (Triticum aestivum L.) and Bupleurum scorzonerifolium Willd. was performed. The protoplasts of wheat were irradiated with ultraviolet light (UV) and gamma-ray and rescued by protoplast fusion using B. scorzonerifolium as the recipient. Assessment of SSR markers showed that the radiation hybrids have the average marker retention frequency of 15.5%. Two RH panels (RHPWI and RHPWII) that contained 92 and 184 radiation hybrids, respectively, were developed and used for mapping of 68 SSR markers in chromosome 5A of wheat. A total of 1557 and 2034 breaks were detected in each panel. The RH map of chromosome 5A based on RHPWII was constructed. The distance of the comprehensive map was 2103 cR and the approximate resolution was estimated to be ∼501.6 kb/break. The RH panels evaluated in this study enabled us to order the ESTs in a single deletion bin or in the multiple bins cross the chromosome. These results demonstrated that RH mapping via protoplast fusion is feasible at the whole genome level for mapping purposes in wheat and the potential value of this mapping approach for the plant species with large genomes. PMID:22815731

  11. Querying genomic databases

    SciTech Connect

    Baehr, A.; Hagstrom, R.; Joerg, D.; Overbeek, R.

    1991-09-01

    A natural-language interface has been developed that retrieves genomic information by using a simple subset of English. The interface spares the biologist from the task of learning database-specific query languages and computer programming. Currently, the interface deals with the E. coli genome. It can, however, be readily extended and shows promise as a means of easy access to other sequenced genomic databases as well.

  12. Genome Aliquoting Revisited

    NASA Astrophysics Data System (ADS)

    Warren, Robert; Sankoff, David

    We prove that the genome aliquoting problem, the problem of finding a recent polyploid ancestor of a genome, with breakpoint distance can be solved in polynomial time. We propose an aliquoting algorithm that is a 2-approximation for the genome aliquoting problem with double cut and join distance, improving upon the previous best solution to this problem, Feijão and Meidanis' 4-approximation algorithm.

  13. Physician Assistant Genomic Competencies.

    PubMed

    Goldgar, Constance; Michaud, Ed; Park, Nguyen; Jenkins, Jean

    2016-09-01

    Genomic discoveries are increasingly being applied to the clinical care of patients. All physician assistants (PAs) need to acquire competency in genomics to provide the best possible care for patients within the scope of their practice. In this article, we present an updated version of PA genomic competencies and learning outcomes in a framework that is consistent with the current medical education guidelines and the collaborative nature of PAs in interprofessional health care teams. PMID:27490287

  14. Genetic Diversity, Population Structure and Linkage Disequilibrium in U.S. Elite Winter Wheat (Triticum Aestivum L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Information on genetic diversity and population structure of elite wheat breeding lines promotes effective use of genetic resources. We analyzed 205 elite wheat breeding lines from major winter wheat breeding programs in the U.S.A. using 245 markers across the wheat genomes. This collection showed a...

  15. Genotype dependent burst of transposable element expression in crowns of hexaploid wheat (Triticum aestivum L.) during cold acclimation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The expression of 1,613 transposable elements (TEs) represented in the Affymetix Wheat Genome Chip was examined during cold treatment in crowns of 4 hexaploid wheat genotypes that vary in tolerance to cold and in flowering time. The TE expression profiles showed a constant level of expression throug...

  16. Filarial and Wolbachia genomics.

    PubMed

    Scott, A L; Ghedin, E; Nutman, T B; McReynolds, L A; Poole, C B; Slatko, B E; Foster, J M

    2012-01-01

    Filarial nematode parasites, the causative agents for a spectrum of acute and chronic diseases including lymphatic filariasis and river blindness, threaten the well-being and livelihood of hundreds of millions of people in the developing regions of the world. The 2007 publication on a draft assembly of the 95-Mb genome of the human filarial parasite Brugia malayi- representing the first helminth parasite genome to be sequenced - has been followed in rapid succession by projects that have resulted in the genome sequencing of six additional filarial species, seven nonfilarial nematode parasites of animals and nearly 30 plant parasitic and free-living species. Parallel to the genomic sequencing, transcriptomic and proteomic projects have facilitated genome annotation, expanded our understanding of stage-associated gene expression and provided a first look at the role of epigenetic regulation of filarial genomes through microRNAs. The expansion in filarial genomics will also provide a significant enrichment in our knowledge of the diversity and variability in the genomes of the endosymbiotic bacterium Wolbachia leading to a better understanding of the genetic principles that govern filarial-Wolbachia mutualism. The goal here is to provide an overview of the trends and advances in filarial and Wolbachia genomics. PMID:22098559

  17. Fungal Genomics Program

    SciTech Connect

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  18. Genomics of Clostridium tetani.

    PubMed

    Brüggemann, Holger; Brzuszkiewicz, Elzbieta; Chapeton-Montes, Diana; Plourde, Lucile; Speck, Denis; Popoff, Michel R

    2015-05-01

    Genomic information about Clostridium tetani, the causative agent of the tetanus disease, is scarce. The genome of strain E88, a strain used in vaccine production, was sequenced about 10 years ago. One additional genome (strain 12124569) has recently been released. Here we report three new genomes of C. tetani and describe major differences among all five C. tetani genomes. They all harbor tetanus-toxin-encoding plasmids that contain highly conserved genes for TeNT (tetanus toxin), TetR (transcriptional regulator of TeNT) and ColT (collagenase), but substantially differ in other plasmid regions. The chromosomes share a large core genome that contains about 85% of all genes of a given chromosome. The non-core chromosome comprises mainly prophage-like genomic regions and genes encoding environmental interaction and defense functions (e.g. surface proteins, restriction-modification systems, toxin-antitoxin systems, CRISPR/Cas systems) and other fitness functions (e.g. transport systems, metabolic activities). This new genome information will help to assess the level of genome plasticity of the species C. tetani and provide the basis for detailed comparative studies. PMID:25638019

  19. Between two fern genomes.

    PubMed

    Sessa, Emily B; Banks, Jo Ann; Barker, Michael S; Der, Joshua P; Duffy, Aaron M; Graham, Sean W; Hasebe, Mitsuyasu; Langdale, Jane; Li, Fay-Wei; Marchant, D Blaine; Pryer, Kathleen M; Rothfels, Carl J; Roux, Stanley J; Salmi, Mari L; Sigel, Erin M; Soltis, Douglas E; Soltis, Pamela S; Stevenson, Dennis W; Wolf, Paul G

    2014-01-01

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves. PMID:25324969

  20. [Landscape and ecological genomics].

    PubMed

    2013-10-01

    Landscape genomics is the modern version of landscape genetics, a discipline that arose approximately 10 years ago as a combination of population genetics, landscape ecology, and spatial statistics. It studies the effects of environmental variables on gene flow and other microevolutionary processes that determine genetic connectivity and variations in populations. In contrast to population genetics, it operates at the level of individual specimens rather than at the level of population samples. Another important difference between landscape genetics and genomics and population genetics is that, in the former, the analysis of gene flow and local adaptations takes quantitative account of landforms and features of the matrix, i.e., hostile spaces that separate species habitats. Landscape genomics is a part of population ecogenomics, which, along with community genomics, is a major part of ecological genomics. One of the principal purposes of landscape genomics is the identification and differentiation of various genome-wide and locus-specific effects. The approaches and computation tools developed for combined analysis of genomic and landscape variables make it possible to detect adaptation-related genome fragments, which facilitates the planning of conservation efforts and the prediction of species' fate in response to expected changes in the environment. PMID:25508669

  1. [Landscape and ecological genomics].

    PubMed

    Tetushkin, E Ia

    2013-10-01

    Landscape genomics is the modern version of landscape genetics, a discipline that arose approximately 10 years ago as a combination of population genetics, landscape ecology, and spatial statistics. It studies the effects of environmental variables on gene flow and other microevolutionary processes that determine genetic connectivity and variations in populations. In contrast to population genetics, it operates at the level of individual specimens rather than at the level of population samples. Another important difference between landscape genetics and genomics and population genetics is that, in the former, the analysis of gene flow and local adaptations takes quantitative account of landforms and features of the matrix, i.e., hostile spaces that separate species habitats. Landscape genomics is a part of population ecogenomics, which, along with community genomics, is a major part of ecological genomics. One of the principal purposes of landscape genomics is the identification and differentiation of various genome-wide and locus-specific effects. The approaches and computation tools developed for combined analysis of genomic and landscape variables make it possible to detect adaptation-related genome fragments, which facilitates the planning of conservation efforts and the prediction of species' fate in response to expected changes in the environment. PMID:25474890

  2. Between Two Fern Genomes

    PubMed Central

    2014-01-01

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves. PMID:25324969

  3. Genomics of Disease

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This edited book represents the 23rd symposium in the Stadler Genetics Symposia series, and the general theme of this conference was "The Genomics of Disease." The 24 national and international speakers were invited to discuss their world-class research into the advances that genomics has made on c...

  4. Genomics for Weed Science

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Numerous genomic-based studies have provided insight to the physiological and evolutionary processes involved in developmental and environmental processes of model plants such as arabidopsis and rice. However, far fewer efforts have been attempted to use genomic resources to study physiological and ...

  5. Unlocking the bovine genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The draft genome sequence of cattle (Bos taurus) has now been analyzed by the Bovine Genome Sequencing and Analysis Consortium and the Bovine HapMap Consortium, which together represent an extensive collaboration involving more than 300 scientists from 25 different countries. ...

  6. Genetics and Genomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Good progress is being made on genetics and genomics of sugar beet, however it is in process and the tools are now being generated and some results are being analyzed. The GABI BeetSeq project released a first draft of the sugar beet genome of KWS2320, a dihaploid (see http://bvseq.molgen.mpg.de/Gen...

  7. Development of Genomic GMACE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The use of genomics to enhance national genetic evaluation systems of dairy cattle is quickly becoming standard practice. The current MACE procedure used by Interbull may not accommodate these new “genomically-enhanced” national evaluations. An important assumption in MACE may no longer be valid in ...

  8. GENOME OF HORSEPOX VIRUS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Here we present the genomic sequence of horsepox virus (HSPV) isolate MNR-76, an orthopoxvirus (OPV) isolated in 1976 from diseased Mongolian horses. The 212 kbp genome contained 7.5 kbp inverted terminal repeats (ITR) and lacked extensive terminal tandem repetition. HSPV contained 236 ORFs with sim...

  9. Genomic Instability and Cancer

    PubMed Central

    Yao, Yixin; Dai, Wei

    2014-01-01

    Genomic instability is a characteristic of most cancer cells. It is an increased tendency of genome alteration during cell division. Cancer frequently results from damage to multiple genes controlling cell division and tumor suppressors. It is known that genomic integrity is closely monitored by several surveillance mechanisms, DNA damage checkpoint, DNA repair machinery and mitotic checkpoint. A defect in the regulation of any of these mechanisms often results in genomic instability, which predisposes the cell to malignant transformation. Posttranslational modifications of the histone tails are closely associated with regulation of the cell cycle as well as chromatin structure. Nevertheless, DNA methylation status is also related to genomic integrity. We attempt to summarize recent developments in this field and discuss the debate of driving force of tumor initiation and progression. PMID:25541596

  10. Microbial Genomes Multiply

    NASA Technical Reports Server (NTRS)

    Doolittle, Russell F.

    2002-01-01

    The publication of the first complete sequence of a bacterial genome in 1995 was a signal event, underscored by the fact that the article has been cited more than 2,100 times during the intervening seven years. It was a marvelous technical achievement, made possible by automatic DNA-sequencing machines. The feat is the more impressive in that complete genome sequencing has now been adopted in many different laboratories around the world. Four years ago in these columns I examined the situation after a dozen microbial genomes had been completed. Now, with upwards of 60 microbial genome sequences determined and twice that many in progress, it seems reasonable to assess just what is being learned. Are new concepts emerging about how cells work? Have there been practical benefits in the fields of medicine and agriculture? Is it feasible to determine the genomic sequence of every bacterial species on Earth? The answers to these questions maybe Yes, Perhaps, and No, respectively.

  11. Intraspecific Polymorphisms of Cytogenetic Markers Mapped on Chromosomes of Triticum polonicum L.

    PubMed Central

    Majka, Maciej; Majka, Joanna; Belter, Jolanta; Suchowilska, Elżbieta; Wachowska, Urszula; Wiwart, Marian; Wiśniewska, Halina

    2016-01-01

    Triticum genus encloses several tetraploid species that are used as genetic stocks for expanding the genetic variability of wheat (Triticum aestivum L.). Although the T. aestivum (2n = 6x = 42, AABBDD) and T. durum (2n = 4x = 28, AABB) karyotypes were well examined by chromosome staining, Giemsa C-banding and FISH markers, other tetraploids are still poorly characterized. Here, we established and compared the fluorescence in situ hybridization (FISH) patterns on chromosomes of 20 accessions of T. polonicum species using different repetitive sequences from BAC library of wheat ‘Chinese Spring’. The chromosome patterns of Polish wheat were compared to tetraploid (2n = 4x = 28, AABB) Triticum species: T. durum, T. diccocon and T. turanicum, as well. A combination of pTa-86, pTa-535 and pTa-713 probes was the most informative among 6 DNA probes tested. Probe pTa-k374, which is similar to 28S rDNA sequence enabled to distinguish signal size and location differences, as well as rDNA loci elimination. Furthermore, pTa-465 and pTa-k566 probes are helpful for the detection of similar organized chromosomes. The polymorphisms of signals distribution were observed in 2A, 2B, 3B, 5B, 6A and 7B chromosomes. Telomeric region of the short arm of 6B chromosome was the most polymorphic. Our work is novel and contributes to the understanding of T. polonicum genome organization which is essential to develop successful advanced breeding strategies for wheat. Collection and characterization of this germplasm can contribute to the wheat biodiversity safeguard. PMID:27391447

  12. Phytozome Comparative Plant Genomics Portal

    SciTech Connect

    Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

    2014-09-09

    The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

  13. Using Transcriptomics to Understand the Wheat Genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Wheat (Triticum aestivum L.) is one of the most important food crops in the world, and transcriptomics studies of this crop promise to reveal the expression dynamics of genes that control many agriculturally important traits. In this review of wheat transcriptomics research, the current status of tr...

  14. Changes in host-mycorrhiza relationships revealed by stable isotopes after naturally-induced thinning of the stand: case study on Tuber aestivum.

    NASA Astrophysics Data System (ADS)

    Gavrichkova, Olga; Lauteri, Marco; Ciolfi, Marco; Chiocchini, Francesca; Paris, Pierluigi; Pisanelli, Andrea; Portarena, Silvia; Brugnoli, Enrico

    2016-04-01

    Terrestrial plants overcome nutrients and water limitations by forming mutualistic associations with mycorrhizal fungi. Fungi, in return, take advantage from the carbohydrates supplied by the host. Some mycorrhizal fruit bodies, like that of Tuber spp., have a peculiar gastronomic value with many efforts being undertaken to predict and enhance their productivity. However, many issues of truffle-producing mycorrhizal ecology are still poorly understood, in particular optimal conditions favoring fruit formation, potential host plants and host-mycorrhiza relationships. In this study, we tested the applicability of stable isotope measurements under natural abundance to identify the plants which likely host the mycorrhiza of Tuber aestivum and to characterize host-mycorrhizal nutrient, water and carbohydrate exchange under plant natural growing conditions and with the change of the forest cover after naturally occurred thinning. For these purposes, sampling of the fruit bodies of T. aestivum was performed during the growing season 2011 in a mixed broadleaved-coniferous forest in central Italy (initially the site was a manmade pine plantation). Nine truffle-producing parcels were identified with five being composed of the original Pinus pinaster -dominated vegetation and four in which pine was replaced by broadleaf species after both wind-induced thinning and natural dieback of pine trees. Seasonal variation of δ13C, δ15N and δ18O were analyzed in the fungal material, in the surrounding soil and in the plant material of the potential host species (xylem water in the trunk, branches and leaves, recently assimilated carbohydrates in phloem and leaves). The results showed a possibility of the identification of the mycorrhizal host species applying isotope analyses, with mycorrhiza receiving most part of the carbohydrates from the pine in pine-dominated parcels. Interestingly, in thinned parcels, the truffle bodies maintained isotope composition similar to bodies gathered

  15. Over-Expression of a Tobacco Nitrate Reductase Gene in Wheat (Triticum aestivum L.) Increases Seed Protein Content and Weight without Augmenting Nitrogen Supplying

    PubMed Central

    Zhao, Xiao-Qiang; Nie, Xuan-Li; Xiao, Xing-Guo

    2013-01-01

    Heavy nitrogen (N) application to gain higher yield of wheat (Triticum aestivum L.) resulted in increased production cost and environment pollution. How to diminish the N supply without losing yield and/or quality remains a challenge. To meet the challenge, we integrated and expressed a tobacco nitrate reductase gene (NR) in transgenic wheat. The 35S-NR gene was transferred into two winter cultivars, “Nongda146” and “Jimai6358”, by Agrobacterium-mediation. Over-expression of the transgene remarkably enhanced T1 foliar NR activity and significantly augmented T2 seed protein content and 1000-grain weight in 63.8% and 68.1% of T1 offspring (total 67 individuals analyzed), respectively. Our results suggest that constitutive expression of foreign nitrate reductase gene(s) in wheat might improve nitrogen use efficiency and thus make it possible to increase seed protein content and weight without augmenting N supplying. PMID:24040315

  16. Genome size evolution: sizing mammalian genomes.

    PubMed

    Redi, C A; Capanna, E

    2012-01-01

    The study of genome size (GS) and its variation is so fascinating to the scientific community because it constitutes the link between the present-day analytical and molecular studies of the genome and the old trunk of the holistic and synthetic view of the genome. The GS of several taxa vary over a broad range and do not correlate with the complexity of the organisms (the C-value paradox). However, the biology of transposable elements has let us reach a satisfactory view of the molecular mechanisms that give rise to GS variation and novelties, providing a less perplexing view of the significance of the GS (C-enigma). The knowledge of the composition and structure of a genome is a pre-requisite for trying to understand the evolution of the main genome signature: its size. The radiation of mammals provides an approximately 180-million-year test case for theories of how GS evolves. It has been found from data-mining GS databases that GS is a useful cyto-taxonomical instrument at the level of orders/superorders, providing genomic signatures characterizing Monotremata, Marsupialia, Afrotheria, Xenarthra, Laurasiatheria, and Euarchontoglires. A hypothetical ancestral mammalian-like GS of 2.9-3.7 pg has been suggested. This value appears compatible with the average values calculated for the high systematic levels of the extant Monotremata (∼2.97 pg) and Marsupialia (∼4.07 pg), suggesting invasion of mobile DNA elements concurrently with the separation of the older clades of Afrotheria (∼5.5 pg) and Xenarthra (∼4.5 pg) with larger GS, leaving the Euarchontoglires (∼3.4 pg) and Laurasiatheria (∼2.8 pg) genomes with fewer transposable elements. However, the paucity of GS data (546 mammalian species sized from 5,488 living species) for species, genera, and families calls for caution. Considering that mammalian species may be vanished even before they are known, GS data are sorely needed to phenotype the effects brought about by their variation and to validate any

  17. Evolution of genome architecture.

    PubMed

    Koonin, Eugene V

    2009-02-01

    Charles Darwin believed that all traits of organisms have been honed to near perfection by natural selection. The empirical basis underlying Darwin's conclusions consisted of numerous observations made by him and other naturalists on the exquisite adaptations of animals and plants to their natural habitats and on the impressive results of artificial selection. Darwin fully appreciated the importance of heredity but was unaware of the nature and, in fact, the very existence of genomes. A century and a half after the publication of the "Origin", we have the opportunity to draw conclusions from the comparisons of hundreds of genome sequences from all walks of life. These comparisons suggest that the dominant mode of genome evolution is quite different from that of the phenotypic evolution. The genomes of vertebrates, those purported paragons of biological perfection, turned out to be veritable junkyards of selfish genetic elements where only a small fraction of the genetic material is dedicated to encoding biologically relevant information. In sharp contrast, genomes of microbes and viruses are incomparably more compact, with most of the genetic material assigned to distinct biological functions. However, even in these genomes, the specific genome organization (gene order) is poorly conserved. The results of comparative genomics lead to the conclusion that the genome architecture is not a straightforward result of continuous adaptation but rather is determined by the balance between the selection pressure, that is itself dependent on the effective population size and mutation rate, the level of recombination, and the activity of selfish elements. Although genes and, in many cases, multigene regions of genomes possess elaborate architectures that ensure regulation of expression, these arrangements are evolutionarily volatile and typically change substantially even on short evolutionary scales when gene sequences diverge minimally. Thus, the observed genome

  18. The Banana Genome Hub

    PubMed Central

    Droc, Gaëtan; Larivière, Delphine; Guignon, Valentin; Yahiaoui, Nabila; This, Dominique; Garsmeur, Olivier; Dereeper, Alexis; Hamelin, Chantal; Argout, Xavier; Dufayard, Jean-François; Lengelle, Juliette; Baurens, Franc-Christophe; Cenci, Alberto; Pitollat, Bertrand; D’Hont, Angélique; Ruiz, Manuel; Rouard, Mathieu; Bocs, Stéphanie

    2013-01-01

    Banana is one of the world’s favorite fruits and one of the most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given the taxonomic position of Musa, the completed genomic sequence has particular comparative value to provide fresh insights about the evolution of the monocotyledons. The study of the banana genome has been enhanced by a number of tools and resources that allows harnessing its sequence. First, we set up essential tools such as a Community Annotation System, phylogenomics resources and metabolic pathways. Then, to support post-genomic efforts, we improved banana existing systems (e.g. web front end, query builder), we integrated available Musa data into generic systems (e.g. markers and genetic maps, synteny blocks), we have made interoperable with the banana hub, other existing systems containing Musa data (e.g. transcriptomics, rice reference genome, workflow manager) and finally, we generated new results from sequence analyses (e.g. SNP and polymorphism analysis). Several uses cases illustrate how the Banana Genome Hub can be used to study gene families. Overall, with this collaborative effort, we discuss the importance of the interoperability toward data integration between existing information systems. Database URL: http://banana-genome.cirad.fr/ PMID:23707967

  19. Genomic Insights into Bifidobacteria

    PubMed Central

    Lee, Ju-Hoon; O'Sullivan, Daniel J.

    2010-01-01

    Summary: Since the discovery in 1899 of bifidobacteria as numerically dominant microbes in the feces of breast-fed infants, there have been numerous studies addressing their role in modulating gut microflora as well as their other potential health benefits. Because of this, they are frequently incorporated into foods as probiotic cultures. An understanding of their full interactions with intestinal microbes and the host is needed to scientifically validate any health benefits they may afford. Recently, the genome sequences of nine strains representing four species of Bifidobacterium became available. A comparative genome analysis of these genomes reveals a likely efficient capacity to adapt to their habitats, with B. longum subsp. infantis exhibiting more genomic potential to utilize human milk oligosaccharides, consistent with its habitat in the infant gut. Conversely, B. longum subsp. longum exhibits a higher genomic potential for utilization of plant-derived complex carbohydrates and polyols, consistent with its habitat in an adult gut. An intriguing observation is the loss of much of this genome potential when strains are adapted to pure culture environments, as highlighted by the genomes of B. animalis subsp. lactis strains, which exhibit the least potential for a gut habitat and are believed to have evolved from the B. animalis species during adaptation to dairy fermentation environments. PMID:20805404

  20. Characterization of alien chromosomes in backcross derivatives of Triticum aestivum x Elymus rectisetus hybrids using molecular markers and sequential multi-color FISH/GISH

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Wild Triticeae grasses serve as important gene pools for forage and cereal crops. Based on DNA sequences of genome-specific RAPD markers, sequence tagged site (STS) markers specific for W and Y genomes have been obtained. Coupling with the use of genomic in situ hybridization (GISH), these STS mar...

  1. Ensembl comparative genomics resources

    PubMed Central

    Muffato, Matthieu; Beal, Kathryn; Fitzgerald, Stephen; Gordon, Leo; Pignatelli, Miguel; Vilella, Albert J.; Searle, Stephen M. J.; Amode, Ridwan; Brent, Simon; Spooner, William; Kulesha, Eugene; Yates, Andrew; Flicek, Paul

    2016-01-01

    Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and other relevant datasets in order to evaluate and answer evolutionary-related questions. However, the complexity and computational requirements of producing such data are substantial: this has led to only a small number of reference resources that are used for most comparative analyses. The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available. Database URL: http://www.ensembl.org. PMID:26896847

  2. Genome instability and aging.

    PubMed

    Vijg, Jan; Suh, Yousin

    2013-01-01

    Genome instability has long been implicated as the main causal factor in aging. Somatic cells are continuously exposed to various sources of DNA damage, from reactive oxygen species to UV radiation to environmental mutagens. To cope with the tens of thousands of chemical lesions introduced into the genome of a typical cell each day, a complex network of genome maintenance systems acts to remove damage and restore the correct base pair sequence. Occasionally, however, repair is erroneous, and such errors, as well as the occasional failure to correctly replicate the genome during cell division, are the basis for mutations and epimutations. There is now ample evidence that mutations accumulate in various organs and tissues of higher animals, including humans, mice, and flies. What is not known, however, is whether the frequency of these random changes is sufficient to cause the phenotypic effects generally associated with aging. The exception is cancer, an age-related disease caused by the accumulation of mutations and epimutations. Here, we first review current concepts regarding the relationship between DNA damage, repair, and mutation, as well as the data regarding genome alterations as a function of age. We then describe a model for how randomly induced DNA sequence and epigenomic variants in the somatic genomes of animals can result in functional decline and disease in old age. Finally, we discuss the genetics of genome instability in relation to longevity to address the importance of alterations in the somatic genome as a causal factor in aging and to underscore the opportunities provided by genetic approaches to develop interventions that attenuate genome instability, reduce disease risk, and increase life span. PMID:23398157

  3. Ensembl comparative genomics resources.

    PubMed

    Herrero, Javier; Muffato, Matthieu; Beal, Kathryn; Fitzgerald, Stephen; Gordon, Leo; Pignatelli, Miguel; Vilella, Albert J; Searle, Stephen M J; Amode, Ridwan; Brent, Simon; Spooner, William; Kulesha, Eugene; Yates, Andrew; Flicek, Paul

    2016-01-01

    Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and other relevant datasets in order to evaluate and answer evolutionary-related questions. However, the complexity and computational requirements of producing such data are substantial: this has led to only a small number of reference resources that are used for most comparative analyses. The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available. Database URL: http://www.ensembl.org. PMID:26896847

  4. Center for Cancer Genomics | Office of Cancer Genomics

    Cancer.gov

    The Center for Cancer Genomics (CCG) was established to unify the National Cancer Institute's activities in cancer genomics, with the goal of advancing genomics research and translating findings into the clinic to improve the precise diagnosis and treatment of cancers. In addition to promoting genomic sequencing approach

  5. Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley

    PubMed Central

    La Rota, Mauricio; Kantety, Ramesh V; Yu, Ju-Kyung; Sorrells, Mark E

    2005-01-01

    Background Earlier comparative maps between the genomes of rice (Oryza sativa L.), barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.) were linkage maps based on cDNA-RFLP markers. The low number of polymorphic RFLP markers has limited the development of dense genetic maps in wheat and the number of available anchor points in comparative maps. Higher density comparative maps using PCR-based anchor markers are necessary to better estimate the conservation of colinearity among cereal genomes. The purposes of this study were to characterize the proportion of transcribed DNA sequences containing simple sequence repeats (SSR or microsatellites) by length and motif for wheat, barley and rice and to determine in-silico rice genome locations for primer sets developed for wheat and barley Expressed Sequence Tags. Results The proportions of SSR types (di-, tri-, tetra-, and penta-nucleotide repeats) and motifs varied with the length of the SSRs within and among the three species, with trinucleotide SSRs being the most frequent. Distributions of genomic microsatellites (gSSRs), EST-derived microsatellites (EST-SSRs), and transcribed regions in the contiguous sequence of rice chromosome 1 were highly correlated. More than 13,000 primer pairs were developed for use by the cereal research community as potential markers in wheat, barley and rice. Conclusion Trinucleotide SSRs were the most common type in each of the species; however, the relative proportions of SSR types and motifs differed among rice, wheat, and barley. Genomic microsatellites were found to be primarily located in gene-rich regions of the rice genome. Microsatellite markers derived from the use of non-redundant EST-SSRs are an economic and efficient alternative to RFLP for comparative mapping in cereals. PMID:15720707

  6. Predicting Hybrid Performances for Quality Traits through Genomic-Assisted Approaches in Central European Wheat

    PubMed Central

    Liu, Guozheng; Zhao, Yusheng; Gowda, Manje; Longin, C. Friedrich H.; Reif, Jochen C.; Mette, Michael F.

    2016-01-01

    Bread-making quality traits are central targets for wheat breeding. The objectives of our study were to (1) examine the presence of major effect QTLs for quality traits in a Central European elite wheat population, (2) explore the optimal strategy for predicting the hybrid performance for wheat quality traits, and (3) investigate the effects of marker density and the composition and size of the training population on the accuracy of prediction of hybrid performance. In total 135 inbred lines of Central European bread wheat (Triticum aestivum L.) and 1,604 hybrids derived from them were evaluated for seven quality traits in up to six environments. The 135 parental lines were genotyped using a 90k single-nucleotide polymorphism array. Genome-wide association mapping initially suggested presence of several quantitative trait loci (QTLs), but cross-validation rather indicated the absence of major effect QTLs for all quality traits except of 1000-kernel weight. Genomic selection substantially outperformed marker-assisted selection in predicting hybrid performance. A resampling study revealed that increasing the effective population size in the estimation set of hybrids is relevant to boost the accuracy of prediction for an unrelated test population. PMID:27383841

  7. Predicting Hybrid Performances for Quality Traits through Genomic-Assisted Approaches in Central European Wheat.

    PubMed

    Liu, Guozheng; Zhao, Yusheng; Gowda, Manje; Longin, C Friedrich H; Reif, Jochen C; Mette, Michael F

    2016-01-01

    Bread-making quality traits are central targets for wheat breeding. The objectives of our study were to (1) examine the presence of major effect QTLs for quality traits in a Central European elite wheat population, (2) explore the optimal strategy for predicting the hybrid performance for wheat quality traits, and (3) investigate the effects of marker density and the composition and size of the training population on the accuracy of prediction of hybrid performance. In total 135 inbred lines of Central European bread wheat (Triticum aestivum L.) and 1,604 hybrids derived from them were evaluated for seven quality traits in up to six environments. The 135 parental lines were genotyped using a 90k single-nucleotide polymorphism array. Genome-wide association mapping initially suggested presence of several quantitative trait loci (QTLs), but cross-validation rather indicated the absence of major effect QTLs for all quality traits except of 1000-kernel weight. Genomic selection substantially outperformed marker-assisted selection in predicting hybrid performance. A resampling study revealed that increasing the effective population size in the estimation set of hybrids is relevant to boost the accuracy of prediction for an unrelated test population. PMID:27383841

  8. Human Genome Project

    SciTech Connect

    Block, S.; Cornwall, J.; Dally, W.; Dyson, F.; Fortson, N.; Joyce, G.; Kimble, H. J.; Lewis, N.; Max, C.; Prince, T.; Schwitters, R.; Weinberger, P.; Woodin, W. H.

    1998-01-04

    The study reviews Department of Energy supported aspects of the United States Human Genome Project, the joint National Institutes of Health/Department of Energy program to characterize all human genetic material, to discover the set of human genes, and to render them accessible for further biological study. The study concentrates on issues of technology, quality assurance/control, and informatics relevant to current effort on the genome project and needs beyond it. Recommendations are presented on areas of the genome program that are of particular interest to and supported by the Department of Energy.

  9. Genomic taxonomy of vibrios

    PubMed Central

    Thompson, Cristiane C; Vicente, Ana Carolina P; Souza, Rangel C; Vasconcelos, Ana Tereza R; Vesth, Tammi; Alves, Nelson; Ussery, David W; Iida, Tetsuya; Thompson, Fabiano L

    2009-01-01

    Background Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA), supertrees, Average Amino Acid Identity (AAI), genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.). A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in the birth of the online

  10. Human Genome Program

    SciTech Connect

    Not Available

    1993-01-01

    The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

  11. What Is a Genome?

    PubMed Central

    Goldman, Aaron David; Landweber, Laura F.

    2016-01-01

    The genome is often described as the information repository of an organism. Whether millions or billions of letters of DNA, its transmission across generations confers the principal medium for inheritance of organismal traits. Several emerging areas of research demonstrate that this definition is an oversimplification. Here, we explore ways in which a deeper understanding of genomic diversity and cell physiology is challenging the concepts of physical permanence attached to the genome as well as its role as the sole information source for an organism. PMID:27442251

  12. Comparative primate genomics: emerging patterns of genome content and dynamics

    PubMed Central

    Rogers, Jeffrey; Gibbs, Richard A.

    2014-01-01

    Preface Advances in genome sequencing technologies have created new opportunities for comparative primate genomics. Genome assemblies have been published for several primates, with analyses of several others underway. Whole genome assemblies for the great apes provide remarkable new information about the evolutionary origins of the human genome and the processes involved. Genomic data for macaques and other nonhuman primates provide valuable insight into genetic similarities and differences among species used as models for disease-related research. This review summarizes current knowledge regarding primate genome content and dynamics and offers a series of goals for the near future. PMID:24709753

  13. Comparative primate genomics: emerging patterns of genome content and dynamics.

    PubMed

    Rogers, Jeffrey; Gibbs, Richard A

    2014-05-01

    Advances in genome sequencing technologies have created new opportunities for comparative primate genomics. Genome assemblies have been published for various primate species, and analyses of several others are underway. Whole-genome assemblies for the great apes provide remarkable new information about the evolutionary origins of the human genome and the processes involved. Genomic data for macaques and other non-human primates offer valuable insights into genetic similarities and differences among species that are used as models for disease-related research. This Review summarizes current knowledge regarding primate genome content and dynamics, and proposes a series of goals for the near future. PMID:24709753

  14. GenomeView: a next-generation genome browser

    PubMed Central

    Abeel, Thomas; Van Parys, Thomas; Saeys, Yvan; Galagan, James; Van de Peer, Yves

    2012-01-01

    Due to ongoing advances in sequencing technologies, billions of nucleotide sequences are now produced on a daily basis. A major challenge is to visualize these data for further downstream analysis. To this end, we present GenomeView, a stand-alone genome browser specifically designed to visualize and manipulate a multitude of genomics data. GenomeView enables users to dynamically browse high volumes of aligned short-read data, with dynamic navigation and semantic zooming, from the whole genome level to the single nucleotide. At the same time, the tool enables visualization of whole genome alignments of dozens of genomes relative to a reference sequence. GenomeView is unique in its capability to interactively handle huge data sets consisting of tens of aligned genomes, thousands of annotation features and millions of mapped short reads both as viewer and editor. GenomeView is freely available as an open source software package. PMID:22102585

  15. Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine

    PubMed Central

    Elsik, Christine G.; Tayal, Aditi; Diesh, Colin M.; Unni, Deepak R.; Emery, Marianne L.; Nguyen, Hung N.; Hagen, Darren E.

    2016-01-01

    We report an update of the Hymenoptera Genome Database (HGD) (http://HymenopteraGenome.org), a model organism database for insect species of the order Hymenoptera (ants, bees and wasps). HGD maintains genomic data for 9 bee species, 10 ant species and 1 wasp, including the versions of genome and annotation data sets published by the genome sequencing consortiums and those provided by NCBI. A new data-mining warehouse, HymenopteraMine, based on the InterMine data warehousing system, integrates the genome data with data from external sources and facilitates cross-species analyses based on orthology. New genome browsers and annotation tools based on JBrowse/WebApollo provide easy genome navigation, and viewing of high throughput sequence data sets and can be used for collaborative genome annotation. All of the genomes and annotation data sets are combined into a single BLAST server that allows users to select and combine sequence data sets to search. PMID:26578564

  16. Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine.

    PubMed

    Elsik, Christine G; Tayal, Aditi; Diesh, Colin M; Unni, Deepak R; Emery, Marianne L; Nguyen, Hung N; Hagen, Darren E

    2016-01-01

    We report an update of the Hymenoptera Genome Database (HGD) (http://HymenopteraGenome.org), a model organism database for insect species of the order Hymenoptera (ants, bees and wasps). HGD maintains genomic data for 9 bee species, 10 ant species and 1 wasp, including the versions of genome and annotation data sets published by the genome sequencing consortiums and those provided by NCBI. A new data-mining warehouse, HymenopteraMine, based on the InterMine data warehousing system, integrates the genome data with data from external sources and facilitates cross-species analyses based on orthology. New genome browsers and annotation tools based on JBrowse/WebApollo provide easy genome navigation, and viewing of high throughput sequence data sets and can be used for collaborative genome annotation. All of the genomes and annotation data sets are combined into a single BLAST server that allows users to select and combine sequence data sets to search. PMID:26578564

  17. Comparative genome analysis between Agrostis stolonifera and members of the Pooideae subfamily, including Brachypodium distachyon.

    PubMed

    Araneda, Loreto; Sim, Sung-Chur; Bae, Jin-Joo; Chakraborty, Nanda; Curley, Joe; Chang, Taehyun; Inoue, Maiko; Warnke, Scott; Jung, Geunhwa

    2013-01-01

    Creeping bentgrass (Agrostis stolonifera, allotetraploid 2n = 4x = 28) is one of the major cool-season turfgrasses. It is widely used on golf courses due to its tolerance to low mowing and aggressive growth habit. In this study, we investigated genome relationships of creeping bentgrass relative to the Triticeae (a consensus map of Triticum aestivum, T. tauschii, Hordeum vulgare, and H. spontaneum), oat, rice, and ryegrass maps using a common set of 229 EST-RFLP markers. The genome comparisons based on the RFLP markers revealed large-scale chromosomal rearrangements on different numbers of linkage groups (LGs) of creeping bentgrass relative to the Triticeae (3 LGs), oat (4 LGs), and rice (8 LGs). However, we detected no chromosomal rearrangement between creeping bentgrass and ryegrass, suggesting that these recently domesticated species might be closely related, despite their memberships to different Pooideae tribes. In addition, the genome of creeping bentgrass was compared with the complete genome sequence of Brachypodium distachyon in Pooideae subfamily using both sequences of the above-mentioned mapped EST-RFLP markers and sequences of 8,470 publicly available A. stolonifera ESTs (AgEST). We discovered large-scale chromosomal rearrangements on six LGs of creeping bentgrass relative to B. distachyon. Also, a total of 24 syntenic blocks based on 678 orthologus loci were identified between these two grass species. The EST orthologs can be utilized in further comparative mapping of Pooideae species. These results will be useful for genetic improvement of Agrostis species and will provide a better understanding of evolution within Pooideae species. PMID:24244501

  18. Genetic analysis of the T. aestivum/Ae. sharonensis introgressive lines of common wheat for resistance to powdery mildew.

    PubMed

    Vdovychenko, Zh V; Antonyuk, M Z; Ternovskaya, T K

    2005-01-01

    Results of investigation of peculiarities of common wheat hybridological analysis for a discrete character, resistance for powdery mildew, governed by the alien gene from Ae. sharonensis are present. Relation between genome structure of crossed introgressive lines and deviation of empirical ratios of segregation in F2 from theoretical, based on the assumption about monogenic inheritance of considered character is established. The approach to the quantitative count of influence of such connection on distortion of actual segregation in comparison with theoretically expected ratio is developed. PMID:16250248

  19. Comparative genomic in situ hybridization (cGISH) analysis on plant chromosomes revealed by labelled Arabidopsis DNA.

    PubMed

    Zoller, J F; Yang, Y; Herrmann, R G; Hohmann, U

    2001-01-01

    A new approach for comparative cytogenetic banding analysis of plant chromosomes has been established. The comparative GISH (cGISH) technique is universally applicable to various complex genomes of Monocotyledonae (Triticum aestivum, Agropyron elongatum, Secale cereale, Hordeum vulgare, Allium cepa, Muscari armenaticum and Lilium longiflorum) and Dicotyledonae (Vicia faba, Beta vulgaris, Arabidopsis thaliana). Labelled total genomic DNA of A. thaliana generates signals at conserved chromosome regions. The nucleolus organizing regions (NORs) containing the majority of tandemly repeated rDNA sequences, N-band regions containing satellite DNA, conserved homologous sequences at telomeres and additional chromosome-characteristic markers were detected in heterologous FISH experiments. Multicolour FISH analysis with repetitive DNA probes simultaneously revealed the chromosome assignment of 56 cGISH signals in rye and 61 cGISH signals in barley. Further advantages of this technique are: (1) the fast and straightforward preparation of the probe; (2) the generation of signals with high intensity and reproducibility even without signal amplification; and (3) no requirement of species-specific sequences suitable for molecular karyotype analysis. Hybridization can be performed without competitive DNA. Signal detection without significant background is possible under low stringency conditions. The universal application of this fast and simple one-step fluorescence banding technique for plant cytogenetic and plant genome evolution is discussed. PMID:11448038

  20. Vita Genomics, Inc.

    PubMed

    Shih-Hsin Wu, Lawrence; Su, Chun-Lin; Chen, Ellson

    2007-06-01

    Vita Genomics, Inc., centered in Taiwan and China, aims to be a premier genomics-based biotechnological and biopharmaceutical company in the Asia-Pacific region. The company focuses on conducting pharmacogenomics research, in vitro diagnosis product development and specialty contract research services in both genomics and pharmacogenomics fields. We are now initiating a drug rescue program designed to resurrect drugs that have failed in the previous clinical trials owing to low efficacies. This program applies pharmacogenomics approaches using biomarkers to screen subsets of patients who may respond better or avoid adverse responses to the test drugs. Vita Genomics, Inc. has envisioned itself as an important player in the healthcare industry offering advanced molecular diagnostic products and services, revolutionizing thedrug-development process and providing pharmacogenomic solutions. PMID:17559355

  1. Lophotrochozoan mitochondrial genomes

    SciTech Connect

    Valles, Yvonne; Boore, Jeffrey L.

    2005-10-01

    Progress in both molecular techniques and phylogeneticmethods has challenged many of the interpretations of traditionaltaxonomy. One example is in the recognition of the animal superphylumLophotrochozoa (annelids, mollusks, echiurans, platyhelminthes,brachiopods, and other phyla), although the relationships within thisgroup and the inclusion of some phyla remain uncertain. While much ofthis progress in phylogenetic reconstruction has been based on comparingsingle gene sequences, we are beginning to see the potential of comparinglarge-scale features of genomes, such as the relative order of genes.Even though tremendous progress is being made on the sequencedetermination of whole nuclear genomes, the dataset of choice forgenome-level characters for many animals across a broad taxonomic rangeremains mitochondrial genomes. We review here what is known aboutmitochondrial genomes of the lophotrochozoans and discuss the promisethat this dataset will enable insight into theirrelationships.

  2. Androgen receptor genomic regulation

    PubMed Central

    Jin, Hong-Jian; Kim, Jung

    2013-01-01

    The transcriptional activity of the androgen receptor (AR) is not only critical for the normal development and function of the prostate but also pivotal to the onset and progression of prostate cancer (PCa). The studies of AR transcriptional regulation were previously limited to a handful of AR-target genes. Owing to the development of various high-throughput genomic technologies, significant advances have been made in recent years. Here we discuss the discoveries of genome-wide androgen-regulated genes in PCa cell lines, animal models and tissues using expression microarray and sequencing, the mapping of genomic landscapes of AR using Combining Chromatin Immunoprecipitation (ChIP)-on-chip and ChIP-seq assays, the interplay of transcriptional cofactors in defining AR binding profiles, and the genomic regulation and AR reprogramming in advanced PCa. PMID:25237629

  3. Mouse genome database 2016

    PubMed Central

    Bult, Carol J.; Eppig, Janan T.; Blake, Judith A.; Kadin, James A.; Richardson, Joel E.

    2016-01-01

    The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the primary community model organism database for the laboratory mouse and serves as the source for key biological reference data related to mouse genes, gene functions, phenotypes and disease models with a strong emphasis on the relationship of these data to human biology and disease. As the cost of genome-scale sequencing continues to decrease and new technologies for genome editing become widely adopted, the laboratory mouse is more important than ever as a model system for understanding the biological significance of human genetic variation and for advancing the basic research needed to support the emergence of genome-guided precision medicine. Recent enhancements to MGD include new graphical summaries of biological annotations for mouse genes, support for mobile access to the database, tools to support the annotation and analysis of sets of genes, and expanded support for comparative biology through the expansion of homology data. PMID:26578600

  4. The genomics of adaptation.

    PubMed

    Radwan, Jacek; Babik, Wiesław

    2012-12-22

    The amount and nature of genetic variation available to natural selection affect the rate, course and outcome of evolution. Consequently, the study of the genetic basis of adaptive evolutionary change has occupied biologists for decades, but progress has been hampered by the lack of resolution and the absence of a genome-level perspective. Technological advances in recent years should now allow us to answer many long-standing questions about the nature of adaptation. The data gathered so far are beginning to challenge some widespread views of the way in which natural selection operates at the genomic level. Papers in this Special Feature of Proceedings of the Royal Society B illustrate various aspects of the broad field of adaptation genomics. This introductory article sets up a context and, on the basis of a few selected examples, discusses how genomic data can advance our understanding of the process of adaptation. PMID:23097510

  5. Genomics and vaccine development

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic-based approaches are driving fundamental changes in our understanding of microbiology. Comparative analysis of microbial strain is providing new insights into pathogen evolution, virulence mechanisms, and host range specificity. Most importantly, gene discovery and genetic variations can now...

  6. Platyzoan mitochondrial genomes.

    PubMed

    Wey-Fabrizius, Alexandra R; Podsiadlowski, Lars; Herlyn, Holger; Hankeln, Thomas

    2013-11-01

    Platyzoa is a putative lophotrochozoan (spiralian) subtaxon within the protostome clade of Metazoa, comprising a range of biologically diverse, mostly small worm-shaped animals. The monophyly of Platyzoa, the relationships between the putative subgroups Platyhelminthes, Gastrotricha and Gnathifera (the latter comprising at least Gnathostomulida, "Rotifera" and Acanthocephala) as well as some aspects of the internal phylogenies of these subgroups are highly debated. Here we review how complete mitochondrial (mt) genome data contribute to these debates. We highlight special features of the mt genomes and discuss problems in mtDNA phylogenies of the clade. Mitochondrial genome data seem to be insufficient to resolve the position of the platyzoan clade within the Spiralia but can help to address internal phylogenetic questions. The present review includes a tabular survey of all published platyzoan mt genomes. PMID:23274056

  7. Mouse genome database 2016.

    PubMed

    Bult, Carol J; Eppig, Janan T; Blake, Judith A; Kadin, James A; Richardson, Joel E

    2016-01-01

    The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the primary community model organism database for the laboratory mouse and serves as the source for key biological reference data related to mouse genes, gene functions, phenotypes and disease models with a strong emphasis on the relationship of these data to human biology and disease. As the cost of genome-scale sequencing continues to decrease and new technologies for genome editing become widely adopted, the laboratory mouse is more important than ever as a model system for understanding the biological significance of human genetic variation and for advancing the basic research needed to support the emergence of genome-guided precision medicine. Recent enhancements to MGD include new graphical summaries of biological annotations for mouse genes, support for mobile access to the database, tools to support the annotation and analysis of sets of genes, and expanded support for comparative biology through the expansion of homology data. PMID:26578600

  8. The rise of genomics.

    PubMed

    Weissenbach, Jean

    2016-01-01

    A brief history of the development of genomics is provided. Complete sequencing of genomes of uni- and multicellular organisms is based on important progress in sequencing and bioinformatics. Evolution of these methods is ongoing and has triggered an explosion in data production and analysis. Initial analyses focused on the inventory of genes encoding proteins. Completeness and quality of gene prediction remains crucial. Genome analyses profoundly modified our views on evolution, biodiversity and contributed to the detection of new functions, yet to be fully elucidated, such as those fulfilled by non-coding RNAs. Genomics has become the basis for the study of biology and provides the molecular support for a bunch of large-scale studies, the omics. PMID:27263360

  9. Epidemiology & Genomics Research Program

    Cancer.gov

    The Epidemiology and Genomics Research Program, in the National Cancer Institute's Division of Cancer Control and Population Sciences, funds research in human populations to understand the determinants of cancer occurrence and outcomes.

  10. Genomic definition of species

    SciTech Connect

    Crkvenjakov, R.; Drmanac, R.

    1991-07-01

    The subject of this paper is the definition of species based on the assumption that genome is the fundamental level for the origin and maintenance of biological diversity. For this view to be logically consistent it is necessary to assume the existence and operation of the new law which we call genome law. For this reason the genome law is included in the explanation of species phenomenon presented here even if its precise formulation and elaboration are left for the future. The intellectual underpinnings of this definition can be traced to Goldschmidt. We wish to explore some philosophical aspects of the definition of species in terms of the genome. The point of proposing the definition on these grounds is that any real advance in evolutionary theory has to be correct in both its philosophy and its science.

  11. Molluscan Evolutionary Genomics

    SciTech Connect

    Simison, W. Brian; Boore, Jeffrey L.

    2005-12-01

    In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

  12. Biobanks for Genomics and Genomics for Biobanks

    PubMed Central

    Ducournau, Pascal; Gourraud, Pierre-Antoine; Pontille, David

    2003-01-01

    Biobanks include biological samples and attached databases. Human biobanks occur in research, technological development and medical activities. Population genomics is highly dependent on the availability of large biobanks. Ethical issues must be considered: protecting the rights of those people whose samples or data are in biobanks (information, autonomy, confidentiality, protection of private life), assuring the non-commercial use of human body elements and the optimal use of samples and data. They balance other issues, such as protecting the rights of researchers and companies, allowing long-term use of biobanks while detailed information on future uses is not available. At the level of populations, the traditional form of informed consent is challenged. Other dimensions relate to the rights of a group as such, in addition to individual rights. Conditions of return of results and/or benefit to a population need to be defined. With ‘large-scale biobanking’ a marked trend in genomics, new societal dimensions appear, regarding communication, debate, regulation, societal control and valorization of such large biobanks. Exploring how genomics can help health sector biobanks to become more rationally constituted and exploited is an interesting perspective. For example, evaluating how genomic approaches can help in optimizing haematopoietic stem cell donor registries using new markers and high-throughput techniques to increase immunogenetic variability in such registries is a challenge currently being addressed. Ethical issues in such contexts are important, as not only individual decisions or projects are concerned, but also national policies in the international arena and organization of democratic debate about science, medicine and society. PMID:18629026

  13. How the genome folds

    NASA Astrophysics Data System (ADS)

    Lieberman Aiden, Erez

    2012-02-01

    I describe Hi-C, a novel technology for probing the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. Working with collaborators at the Broad Institute and UMass Medical School, we used Hi-C to construct spatial proximity maps of the human genome at a resolution of 1Mb. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.

  14. Human Genome Annotation

    NASA Astrophysics Data System (ADS)

    Gerstein, Mark

    A central problem for 21st century science is annotating the human genome and making this annotation useful for the interpretation of personal genomes. My talk will focus on annotating the 99% of the genome that does not code for canonical genes, concentrating on intergenic features such as structural variants (SVs), pseudogenes (protein fossils), binding sites, and novel transcribed RNAs (ncRNAs). In particular, I will describe how we identify regulatory sites and variable blocks (SVs) based on processing next-generation sequencing experiments. I will further explain how we cluster together groups of sites to create larger annotations. Next, I will discuss a comprehensive pseudogene identification pipeline, which has enabled us to identify >10K pseudogenes in the genome and analyze their distribution with respect to age, protein family, and chromosomal location. Throughout, I will try to introduce some of the computational algorithms and approaches that are required for genome annotation. Much of this work has been carried out in the framework of the ENCODE, modENCODE, and 1000 genomes projects.

  15. An archaeal genomic signature

    NASA Technical Reports Server (NTRS)

    Graham, D. E.; Overbeek, R.; Olsen, G. J.; Woese, C. R.

    2000-01-01

    Comparisons of complete genome sequences allow the most objective and comprehensive descriptions possible of a lineage's evolution. This communication uses the completed genomes from four major euryarchaeal taxa to define a genomic signature for the Euryarchaeota and, by extension, the Archaea as a whole. The signature is defined in terms of the set of protein-encoding genes found in at least two diverse members of the euryarchaeal taxa that function uniquely within the Archaea; most signature proteins have no recognizable bacterial or eukaryal homologs. By this definition, 351 clusters of signature proteins have been identified. Functions of most proteins in this signature set are currently unknown. At least 70% of the clusters that contain proteins from all the euryarchaeal genomes also have crenarchaeal homologs. This conservative set, which appears refractory to horizontal gene transfer to the Bacteria or the Eukarya, would seem to reflect the significant innovations that were unique and fundamental to the archaeal "design fabric." Genomic protein signature analysis methods may be extended to characterize the evolution of any phylogenetically defined lineage. The complete set of protein clusters for the archaeal genomic signature is presented as supplementary material (see the PNAS web site, www.pnas.org).

  16. Ebolavirus comparative genomics

    DOE PAGESBeta

    Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat; Uberbacher, Edward C.; Land, Miriam; Zhang, Qian; Wanchai, Visanu; Chai, Juanjuan; Nielsen, Morten; Trolle, Thomas; et al

    2015-07-14

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. We examine the dynamics of this genome, comparing more than one hundred currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms a distinct group from all other sequenced viral genomes. All filovirus genomes sequenced to date encode proteins with similar functions and gene order, although there is considerable divergence in sequences between the three genera Ebolavirus, Cuevavirus, and Marburgvirus within the family Filoviridae. Whereas all ebolavirus genomes are quite similar (multiple sequences of themore » same strain are often identical), variation is most common in the intergenic regions and within specific areas of the genes encoding the glycoprotein (GP), nucleoprotein (NP), and polymerase (L). We predict regions that could contain epitope-binding sites, which might be good vaccine targets. In conclusion, this information, combined with glycosylation sites and experimentally determined epitopes, can identify the most promising regions for the development of therapeutic strategies.« less

  17. Barley Genomics: An Overview

    PubMed Central

    Sreenivasulu, Nese; Graner, Andreas; Wobus, Ulrich

    2008-01-01

    Barley (Hordeum vulgare), first domesticated in the Near East, is a well-studied crop in terms of genetics, genomics, and breeding and qualifies as a model plant for Triticeae research. Recent advances made in barley genomics mainly include the following: (i) rapid accumulation of EST sequence data, (ii) growing number of studies on transcriptome, proteome, and metabolome, (iii) new modeling techniques, (iv) availability of genome-wide knockout collections as well as efficient transformation techniques, and (v) the recently started genome sequencing effort. These developments pave the way for a comprehensive functional analysis and understanding of gene expression networks linked to agronomically important traits. Here, we selectively review important technological developments in barley genomics and related fields and discuss the relevance for understanding genotype-phenotype relationships by using approaches such as genetical genomics and association studies. High-throughput genotyping platforms that have recently become available will allow the construction of high-density genetic maps that will further promote marker-assisted selection as well as physical map construction. Systems biology approaches will further enhance our knowledge and largely increase our abilities to design refined breeding strategies on the basis of detailed molecular physiological knowledge. PMID:18382615

  18. Novel Structural and Functional Motifs in cellulose synthase (CesA) Genes of Bread Wheat (Triticum aestivum, L.).

    PubMed

    Kaur, Simerjeet; Dhugga, Kanwarpal S; Gill, Kulvinder; Singh, Jaswinder

    2016-01-01

    Cellulose is the primary determinant of mechanical strength in plant tissues. Late-season lodging is inversely related to the amount of cellulose in a unit length of the stem. Wheat is the most widely grown of all the crops globally, yet information on its CesA gene family is limited. We have identified 22 CesA genes from bread wheat, which include homoeologs from each of the three genomes, and named them as TaCesAXA, TaCesAXB or TaCesAXD, where X denotes the gene number and the last suffix stands for the respective genome. Sequence analyses of the CESA proteins from wheat and their orthologs from barley, maize, rice, and several dicot species (Arabidopsis, beet, cotton, poplar, potato, rose gum and soybean) revealed motifs unique to monocots (Poales) or dicots. Novel structural motifs CQIC and SVICEXWFA were identified, which distinguished the CESAs involved in the formation of primary and secondary cell wall (PCW and SCW) in all the species. We also identified several new motifs specific to monocots or dicots. The conserved motifs identified in this study possibly play functional roles specific to PCW or SCW formation. The new insights from this study advance our knowledge about the structure, function and evolution of the CesA family in plants in general and wheat in particular. This information will be useful in improving culm strength to reduce lodging or alter wall composition to improve biofuel production. PMID:26771740

  19. Novel Structural and Functional Motifs in cellulose synthase (CesA) Genes of Bread Wheat (Triticum aestivum, L.)

    PubMed Central

    Kaur, Simerjeet; Dhugga, Kanwarpal S.; Gill, Kulvinder; Singh, Jaswinder

    2016-01-01

    Cellulose is the primary determinant of mechanical strength in plant tissues. Late-season lodging is inversely related to the amount of cellulose in a unit length of the stem. Wheat is the most widely grown of all the crops globally, yet information on its CesA gene family is limited. We have identified 22 CesA genes from bread wheat, which include homoeologs from each of the three genomes, and named them as TaCesAXA, TaCesAXB or TaCesAXD, where X denotes the gene number and the last suffix stands for the respective genome. Sequence analyses of the CESA proteins from wheat and their orthologs from barley, maize, rice, and several dicot species (Arabidopsis, beet, cotton, poplar, potato, rose gum and soybean) revealed motifs unique to monocots (Poales) or dicots. Novel structural motifs CQIC and SVICEXWFA were identified, which distinguished the CESAs involved in the formation of primary and secondary cell wall (PCW and SCW) in all the species. We also identified several new motifs specific to monocots or dicots. The conserved motifs identified in this study possibly play functional roles specific to PCW or SCW formation. The new insights from this study advance our knowledge about the structure, function and evolution of the CesA family in plants in general and wheat in particular. This information will be useful in improving culm strength to reduce lodging or alter wall composition to improve biofuel production. PMID:26771740

  20. A Review on Genomics APIs

    PubMed Central

    Swaminathan, Rajeswari; Huang, Yungui; Moosavinasab, Soheil; Buckley, Ronald; Bartlett, Christopher W.; Lin, Simon M.

    2015-01-01

    The constant improvement and falling prices of whole human genome Next Generation Sequencing (NGS) has resulted in rapid adoption of genomic information at both clinics and research institutions. Considered together, the complexity of genomics data, due to its large volume and diversity along with the need for genomic data sharing, has resulted in the creation of Application Programming Interface (API) for secure, modular, interoperable access to genomic data from different applications, platforms, and even organizations. The Genomics APIs are a set of special protocols that assist software developers in dealing with multiple genomic data sources for building seamless, interoperable applications leading to the advancement of both genomic and clinical research. These APIs help define a standard for retrieval of genomic data from multiple sources as well as to better package genomic information for integration with Electronic Health Records. This review covers three currently available Genomics APIs: a) Google Genomics, b) SMART Genomics, and c) 23andMe. The functionalities, reference implementations (if available) and authentication protocols of each API are reviewed. A comparative analysis of the different features across the three APIs is provided in the Discussion section. Though Genomics APIs are still under active development and have yet to reach widespread adoption, they hold the promise to make building of complicated genomics applications easier with downstream constructive effects on healthcare. PMID:26702340

  1. WheatGenome.info: A Resource for Wheat Genomics Resource.

    PubMed

    Lai, Kaitao

    2016-01-01

    An integrated database with a variety of Web-based systems named WheatGenome.info hosting wheat genome and genomic data has been developed to support wheat research and crop improvement. The resource includes multiple Web-based applications, which are implemented as a variety of Web-based systems. These include a GBrowse2-based wheat genome viewer with BLAST search portal, TAGdb for searching wheat second generation genome sequence data, wheat autoSNPdb, links to wheat genetic maps using CMap and CMap3D, and a wheat genome Wiki to allow interaction between diverse wheat genome sequencing activities. This portal provides links to a variety of wheat genome resources hosted at other research organizations. This integrated database aims to accelerate wheat genome research and is freely accessible via the web interface at http://www.wheatgenome.info/ . PMID:26519407

  2. Pre-breeding for root rot resistance using root morphology and shoot length.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Our goal is to identify new wheat varieties that display field resistance/tolerance to root rot diseases, such as those caused by Rhizoctonia and Pythium. We are tapping into the genetic diversity of ‘synthetic’ hexaploid wheats (genome composition AABBDD), which were generated at CIMMYT by artifici...

  3. Characterization of chromosomal regions containing quantitive trait loci determining specificity towards bread and durum wheat cultivars in the fungal wheat pathogen Mycosphaerella graminicola

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Specificity of the haploid, plant-pathogenic fungus Mycosphaerella graminicola towards durum (tetraploid, genomes AABB) versus bread (AABBDD) wheat is well documented. To estimate the number of genes involved in host species specificity, we crossed an isolate of M. graminicola collected from bread w...

  4. GenomeVista

    SciTech Connect

    Poliakov, Alexander; Couronne, Olivier

    2002-11-04

    Aligning large vertebrate genomes that are structurally complex poses a variety of problems not encountered on smaller scales. Such genomes are rich in repetitive elements and contain multiple segmental duplications, which increases the difficulty of identifying true orthologous SNA segments in alignments. The sizes of the sequences make many alignment algorithms designed for comparing single proteins extremely inefficient when processing large genomic intervals. We integrated both local and global alignment tools and developed a suite of programs for automatically aligning large vertebrate genomes and identifying conserved non-coding regions in the alignments. Our method uses the BLAT local alignment program to find anchors on the base genome to identify regions of possible homology for a query sequence. These regions are postprocessed to find the best candidates which are then globally aligned using the AVID global alignment program. In the last step conserved non-coding segments are identified using VISTA. Our methods are fast and the resulting alignments exhibit a high degree of sensitivity, covering more than 90% of known coding exons in the human genome. The GenomeVISTA software is a suite of Perl programs that is built on a MySQL database platform. The scheduler gets control data from the database, builds a queve of jobs, and dispatches them to a PC cluster for execution. The main program, running on each node of the cluster, processes individual sequences. A Perl library acts as an interface between the database and the above programs. The use of a separate library allows the programs to function independently of the database schema. The library also improves on the standard Perl MySQL database interfere package by providing auto-reconnect functionality and improved error handling.

  5. GenomeVista

    2002-11-04

    Aligning large vertebrate genomes that are structurally complex poses a variety of problems not encountered on smaller scales. Such genomes are rich in repetitive elements and contain multiple segmental duplications, which increases the difficulty of identifying true orthologous SNA segments in alignments. The sizes of the sequences make many alignment algorithms designed for comparing single proteins extremely inefficient when processing large genomic intervals. We integrated both local and global alignment tools and developed a suitemore » of programs for automatically aligning large vertebrate genomes and identifying conserved non-coding regions in the alignments. Our method uses the BLAT local alignment program to find anchors on the base genome to identify regions of possible homology for a query sequence. These regions are postprocessed to find the best candidates which are then globally aligned using the AVID global alignment program. In the last step conserved non-coding segments are identified using VISTA. Our methods are fast and the resulting alignments exhibit a high degree of sensitivity, covering more than 90% of known coding exons in the human genome. The GenomeVISTA software is a suite of Perl programs that is built on a MySQL database platform. The scheduler gets control data from the database, builds a queve of jobs, and dispatches them to a PC cluster for execution. The main program, running on each node of the cluster, processes individual sequences. A Perl library acts as an interface between the database and the above programs. The use of a separate library allows the programs to function independently of the database schema. The library also improves on the standard Perl MySQL database interfere package by providing auto-reconnect functionality and improved error handling.« less

  6. New wheat microRNA using whole-genome sequence.

    PubMed

    Kurtoglu, Kuaybe Yucebilgili; Kantar, Melda; Budak, Hikmet

    2014-06-01

    MicroRNAs are post-transcriptional regulators of gene expression, taking roles in a variety of fundamental biological processes. Hence, their identification, annotation and characterization are of great significance, especially in bread wheat, one of the main food sources for humans. The recent availability of 5× coverage Triticum aestivum L. whole-genome sequence provided us with the opportunity to perform a systematic prediction of a complete catalogue of wheat microRNAs. Using an in silico homology-based approach, stem-loop coding regions were derived from two assemblies, constructed from wheat 454 reads. To avoid the presence of pseudo-microRNAs in the final data set, transposable element related stem-loops were eliminated by repeat analysis. Overall, 52 putative wheat microRNAs were predicted, including seven, which have not been previously published. Moreover, with distinct analysis of the two different assemblies, both variety and representation of putative microRNA-coding stem-loops were found to be predominant in the intergenic regions. By searching available expressed sequences and small RNA library databases, expression evidence for 39 (out of 52) putative wheat microRNAs was provided. Expression of three of the predicted microRNAs (miR166, miR396 and miR528) was also comparatively quantified with real-time quantitative reverse transcription PCR. This is the first report on in silico prediction of a whole repertoire of bread wheat microRNAs, supported by the wet-lab validation. PMID:24395439

  7. Genomes to Proteomes

    SciTech Connect

    Panisko, Ellen A.; Grigoriev, Igor; Daly, Don S.; Webb-Robertson, Bobbie-Jo; Baker, Scott E.

    2009-03-01

    Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

  8. Genome position specific priors for genomic prediction

    PubMed Central

    2012-01-01

    Background The accuracy of genomic prediction is highly dependent on the size of the reference population. For small populations, including information from other populations could improve this accuracy. The usual strategy is to pool data from different populations; however, this has not proven as successful as hoped for with distantly related breeds. BayesRS is a novel approach to share information across populations for genomic predictions. The approach allows information to be captured even where the phase of SNP alleles and casuative mutation alleles are reversed across populations, or the actual casuative mutation is different between the populations but affects the same gene. Proportions of a four-distribution mixture for SNP effects in segments of fixed size along the genome are derived from one population and set as location specific prior proportions of distributions of SNP effects for the target population. The model was tested using dairy cattle populations of different breeds: 540 Australian Jersey bulls, 2297 Australian Holstein bulls and 5214 Nordic Holstein bulls. The traits studied were protein-, fat- and milk yield. Genotypic data was Illumina 777K SNPs, real or imputed. Results Results showed an increase in accuracy of up to 3.5% for the Jersey population when using BayesRS with a prior derived from Australian Holstein compared to a model without location specific priors. The increase in accuracy was however lower than was achieved when reference populations were combined to estimate SNP effects, except in the case of fat yield. The small size of the Jersey validation set meant that these improvements in accuracy were not significant using a Hotelling-Williams t-test at the 5% level. An increase in accuracy of 1-2% for all traits was observed in the Australian Holstein population when using a prior derived from the Nordic Holstein population compared to using no prior information. These improvements were significant (P<0.05) using the Hotelling

  9. Sequencing of chloroplast genomes from wheat, barley, rye and their relatives provides a detailed insight into the evolution of the Triticeae tribe.

    PubMed

    Middleton, Christopher P; Senerchia, Natacha; Stein, Nils; Akhunov, Eduard D; Keller, Beat; Wicker, Thomas; Kilian, Benjamin

    2014-01-01

    Using Roche/454 technology, we sequenced the chloroplast genomes of 12 Triticeae species, including bread wheat, barley and rye, as well as the diploid progenitors and relatives of bread wheat Triticum urartu, Aegilops speltoides and Ae. tauschii. Two wild tetraploid taxa, Ae. cylindrica and Ae. geniculata, were also included. Additionally, we incorporated wild Einkorn wheat Triticum boeoticum and its domesticated form T. monococcum and two Hordeum spontaneum (wild barley) genotypes. Chloroplast genomes were used for overall sequence comparison, phylogenetic analysis and dating of divergence times. We estimate that barley diverged from rye and wheat approximately 8-9 million years ago (MYA). The genome donors of hexaploid wheat diverged between 2.1-2.9 MYA, while rye diverged from Triticum aestivum approximately 3-4 MYA, more recently than previously estimated. Interestingly, the A genome taxa T. boeoticum and T. urartu were estimated to have diverged approximately 570,000 years ago. As these two have a reproductive barrier, the divergence time estimate also provides an upper limit for the time required for the formation of a species boundary between the two. Furthermore, we conclusively show that the chloroplast genome of hexaploid wheat was contributed by the B genome donor and that this unknown species diverged from Ae. speltoides about 980,000 years ago. Additionally, sequence alignments identified a translocation of a chloroplast segment to the nuclear genome which is specific to the rye/wheat lineage. We propose the presented phylogeny and divergence time estimates as a reference framework for future studies on Triticeae. PMID:24614886

  10. Berkeley Quantitative Genome Browser

    SciTech Connect

    Hechmer, Aaron

    2008-02-29

    The Berkeley Quantitative Genome Browser provides graphical browsing functionality for genomic data organized, at a minimum, by sequence and position. While supporting the annotation browsing features typical of many other genomic browsers, additional emphasis is placed on viewing and utilizing quantitative data. Data may be read from GFF, SGR, FASTA or any column delimited format. Once the data has been read into the browser's buffer, it may be searched. filtered or subjected to mathematical transformation. The browser also supplies some graphical design manipulation functionality geared towards preparing figures for presentations or publication. A plug-in mechanism enables development outside the core functionality that adds more advanced or esoteric analysis capabilities. BBrowse's development and distribution is open-source and has been built to run on Linux, OSX and MS Windows operating systems.

  11. Genomics, health, and society.

    PubMed

    Chan, Chee Khoon

    2002-01-01

    On June 27, 2001, the World Health Organization conducted hearings in Geneva for a Special Report on Genomics & Health. Initially intended as a document to address the ethical, legal, and social implications of the gathering genomics resolution (ELSI), the terms of reference of the report were significantly modified to give primary emphasis to a scientific and technological assessment of the implications of genomics for human health. The Citizens' Health Initiative, one of two NGOs invited to make submissions at these consultations, suggested that no less important than the scientific and technical assessment was a perspective which gave due attention to the social context and political economy of scientific/technological development and its deployment. The article below touches upon neglected health priorities of poor countries, intellectual property rights and patents, risk management, insurance and discrimination, and predictive (prenatal) testing, reproductive choice, and eugenics. PMID:17208760

  12. Berkeley Quantitative Genome Browser

    2008-02-29

    The Berkeley Quantitative Genome Browser provides graphical browsing functionality for genomic data organized, at a minimum, by sequence and position. While supporting the annotation browsing features typical of many other genomic browsers, additional emphasis is placed on viewing and utilizing quantitative data. Data may be read from GFF, SGR, FASTA or any column delimited format. Once the data has been read into the browser's buffer, it may be searched. filtered or subjected to mathematical transformation.more » The browser also supplies some graphical design manipulation functionality geared towards preparing figures for presentations or publication. A plug-in mechanism enables development outside the core functionality that adds more advanced or esoteric analysis capabilities. BBrowse's development and distribution is open-source and has been built to run on Linux, OSX and MS Windows operating systems.« less

  13. Genomics for Weed Science

    PubMed Central

    Horvath, David

    2010-01-01

    Numerous genomic-based studies have provided insight to the physiological and evolutionary processes involved in developmental and environmental processes of model plants such as arabidopsis and rice. However, far fewer efforts have been attempted to use genomic resources to study physiological and evolutionary processes of weedy plants. Genomics-based tools such as extensive EST databases and microarrays have been developed for a limited number of weedy species, although application of information and resources developed for model plants and crops are possible and have been exploited. These tools have just begun to provide insights into the response of these weeds to herbivore and pathogen attack, survival of extreme environmental conditions, and interaction with crops. The potential of these tools to illuminate mechanisms controlling the traits that allow weeds to invade novel habitats, survive extreme environments, and that make weeds difficult to eradicate have potential for both improving crops and developing novel methods to control weeds. PMID:20808523

  14. SINGLE CELL GENOME SEQUENCING

    PubMed Central

    Yilmaz, Suzan; Singh, Anup K.

    2011-01-01

    Whole genome amplification and next-generation sequencing of single cells has become a powerful approach for studying uncultivated microorganisms that represent 90–99 % of all environmental microbes. Single cell sequencing enables not only the identification of microbes but also linking of functions to species, a feat not achievable by metagenomic techniques. Moreover, it allows the analysis of low abundance species that may be missed in community-based analyses. It has also proved very useful in complementing metagenomics in the assembly and binning of single genomes. With the advent of drastically cheaper and higher throughput sequencing technologies, it is expected that single cell sequencing will become a standard tool in studying the genome and transcriptome of microbial communities. PMID:22154471

  15. Genomic Southern blot analysis.

    PubMed

    Gebbie, Leigh

    2014-01-01

    This chapter describes a detailed protocol for genomic Southern blot analysis which can be used to detect transgene or endogenous gene sequences in cereal genomes. The protocol follows a standard approach that has been shown to generate high-quality results: size fractionation of genomic DNA; capillary transfer to a nylon membrane; hybridization with a digoxigenin-labelled probe; and detection using a chemiluminescent-based system. High sensitivity and limited background are key to successful Southern blots. The critical steps in this protocol are complete digestion of the right quantity of DNA, careful handling of the membrane to avoid unnecessary background, and optimization of probe concentration and temperatures during the hybridization step. Detailed instructions on how to successfully master these techniques are provided. PMID:24243203

  16. Genomics of Volvocine Algae

    PubMed Central

    Umen, James G.; Olson, Bradley J.S.C.

    2015-01-01

    Volvocine algae are a group of chlorophytes that together comprise a unique model for evolutionary and developmental biology. The species Chlamydomonas reinhardtii and Volvox carteri represent extremes in morphological diversity within the Volvocine clade. Chlamydomonas is unicellular and reflects the ancestral state of the group, while Volvox is multicellular and has evolved numerous innovations including germ-soma differentiation, sexual dimorphism, and complex morphogenetic patterning. The Chlamydomonas genome sequence has shed light on several areas of eukaryotic cell biology, metabolism and evolution, while the Volvox genome sequence has enabled a comparison with Chlamydomonas that reveals some of the underlying changes that enabled its transition to multicellularity, but also underscores the subtlety of this transition. Many of the tools and resources are in place to further develop Volvocine algae as a model for evolutionary genomics. PMID:25883411

  17. Genomic medicine and neurology.

    PubMed

    Vance, Jeffery M; Tekin, Demet

    2011-04-01

    The application of genetics to the understanding of neurology has been highly successful over the past several decades. During the past 10 years, tools were developed to begin genetic investigations into more common disorders such as Alzheimer disease, multiple sclerosis, autism, and Parkinson disease. The era of genomic medicine now has begun and will have an increasing effect on the daily care of common neurologic diseases. Thus it is important for neurologists to have a basic understanding of genomic medicine and how it differs from the traditional clinical genetics of the past. This article provides some basic information about genomic medicine and pharmacogenetics in neurology to help neurologists to begin to adopt these principles into their practice. PMID:22810818

  18. Genomic Imprinting in Mammals

    PubMed Central

    Barlow, Denise P.

    2014-01-01

    Genomic imprinting affects a subset of genes in mammals and results in a monoallelic, parental-specific expression pattern. Most of these genes are located in clusters that are regulated through the use of insulators or long noncoding RNAs (lncRNAs). To distinguish the parental alleles, imprinted genes are epigenetically marked in gametes at imprinting control elements through the use of DNA methylation at the very least. Imprinted gene expression is subsequently conferred through lncRNAs, histone modifications, insulators, and higher-order chromatin structure. Such imprints are maintained after fertilization through these mechanisms despite extensive reprogramming of the mammalian genome. Genomic imprinting is an excellent model for understanding mammalian epigenetic regulation. PMID:24492710

  19. Resequencing rice genomes: an emerging new era of rice genomics.

    PubMed

    Huang, Xuehui; Lu, Tingting; Han, Bin

    2013-04-01

    Rice is a model system for crop genomics studies. Much of the early work on rice genomics focused on analyzing genome-wide genetic variation to further understand rice gene functions in agronomic traits and to generate data and resources for rice research. The advent of next-generation high-throughput DNA sequencing technologies and the completion of high-quality reference genome sequences have enabled the development of sequencing-based genotyping and genome-wide association studies (GWAS) that have significantly advanced rice genetics research. This has led to the emergence of a new era of rice genomics aimed at bridging the knowledge gap between genotype and phenotype in rice. These technologies have also led to pyramid breeding through genomics-assisted selection, which will be useful in breeding elite varieties suitable for sustainable agriculture. Here, we review the recent advances in rice genomics and discuss the future of this line of research. PMID:23295340

  20. Brief Guide to Genomics: DNA, Genes and Genomes

    MedlinePlus

    ... guía de genómica A Brief Guide to Genomics DNA, Genes and Genomes Deoxyribonucleic acid (DNA) is the ... and lead to a disease such as cancer. DNA Sequencing Sequencing simply means determining the exact order ...

  1. Haemonchus contortus: Genome Structure, Organization and Comparative Genomics.

    PubMed

    Laing, R; Martinelli, A; Tracey, A; Holroyd, N; Gilleard, J S; Cotton, J A

    2016-01-01

    One of the first genome sequencing projects for a parasitic nematode was that for Haemonchus contortus. The open access data from the Wellcome Trust Sanger Institute provided a valuable early resource for the research community, particularly for the identification of specific genes and genetic markers. Later, a second sequencing project was initiated by the University of Melbourne, and the two draft genome sequences for H. contortus were published back-to-back in 2013. There is a pressing need for long-range genomic information for genetic mapping, population genetics and functional genomic studies, so we are continuing to improve the Wellcome Trust Sanger Institute assembly to provide a finished reference genome for H. contortus. This review describes this process, compares the H. contortus genome assemblies with draft genomes from other members of the strongylid group and discusses future directions for parasite genomics using the H. contortus model. PMID:27238013

  2. Ebolavirus comparative genomics

    PubMed Central

    Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat; Uberbacher, Edward C.; Land, Miriam; Zhang, Qian; Wanchai, Visanu; Chai, Juanjuan; Nielsen, Morten; Trolle, Thomas; Lund, Ole; Buzard, Gregory S.; Pedersen, Thomas D.; Wassenaar, Trudy M.; Ussery, David W.

    2015-01-01

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms a distinct group from all other sequenced viral genomes. All filovirus genomes sequenced to date encode proteins with similar functions and gene order, although there is considerable divergence in sequences between the three genera Ebolavirus, Cuevavirus and Marburgvirus within the family Filoviridae. Whereas all ebolavirus genomes are quite similar (multiple sequences of the same strain are often identical), variation is most common in the intergenic regions and within specific areas of the genes encoding the glycoprotein (GP), nucleoprotein (NP) and polymerase (L). We predict regions that could contain epitope-binding sites, which might be good vaccine targets. This information, combined with glycosylation sites and experimentally determined epitopes, can identify the most promising regions for the development of therapeutic strategies. This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan). PMID:26175035

  3. Ebolavirus comparative genomics.

    PubMed

    Jun, Se-Ran; Leuze, Michael R; Nookaew, Intawat; Uberbacher, Edward C; Land, Miriam; Zhang, Qian; Wanchai, Visanu; Chai, Juanjuan; Nielsen, Morten; Trolle, Thomas; Lund, Ole; Buzard, Gregory S; Pedersen, Thomas D; Wassenaar, Trudy M; Ussery, David W

    2015-09-01

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms a distinct group from all other sequenced viral genomes. All filovirus genomes sequenced to date encode proteins with similar functions and gene order, although there is considerable divergence in sequences between the three genera Ebolavirus, Cuevavirus and Marburgvirus within the family Filoviridae. Whereas all ebolavirus genomes are quite similar (multiple sequences of the same strain are often identical), variation is most common in the intergenic regions and within specific areas of the genes encoding the glycoprotein (GP), nucleoprotein (NP) and polymerase (L). We predict regions that could contain epitope-binding sites, which might be good vaccine targets. This information, combined with glycosylation sites and experimentally determined epitopes, can identify the most promising regions for the development of therapeutic strategies.This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan). PMID:26175035

  4. Genome Size and Species Diversification

    PubMed Central

    2010-01-01

    Theoretically, there are reasons to believe that large genome size should favour speciation. Several major factors contributing to genome size, such as duplications and transposable element activity have been proposed to facilitate the formation of new species. However, it is also possible that small genome size promotes speciation. For example, selection for genome reduction may be resolved in different ways in incipient species, leading to incompatibilities. Mutations and chromosomal rearrangements may also be more stably inherited in smaller genomes. Here I review the following lines of empirical evidence bearing on this question: (i) Correlations between genome size and species richness of taxa are often negative. (ii) Fossil evidence in lungfish shows that the accumulation of DNA in the genomes of this group coincided with a reduction in species diversity. (iii) Estimates of speciation interval in mammals correlate positively with genome size. (iv) Genome reductions are inferred at the base of particular species radiations and genome expansions at the base of others. (v) Insect clades that have been increasing in diversity up to the present have smaller genomes than clades that have remained stable or have decreased in diversity. The general pattern emerging from these observations is that higher diversification rates are generally found in small-genome taxa. Since diversification rates are the net effect of speciation and extinction, large genomes may thus either constrain speciation rate, increase extinction rate, or both. I argue that some of the cited examples are unlikely to be explained by extinction alone. PMID:22140283

  5. The cancer genome

    PubMed Central

    Stratton, Michael R.; Campbell, Peter J.; Futreal, P. Andrew

    2010-01-01

    All cancers arise as a result of changes that have occurred in the DNA sequence of the genomes of cancer cells. Over the past quarter of a century much has been learnt about these mutations and the abnormal genes that operate in human cancers. We are now, however, moving into an era in which it will be possible to obtain the complete DNA sequence of large numbers of cancer genomes. These studies will provide us with a detailed and comprehensive perspective on how individual cancers have developed. PMID:19360079

  6. Methanococcus jannaschii genome: revisited

    NASA Technical Reports Server (NTRS)

    Kyrpides, N. C.; Olsen, G. J.; Klenk, H. P.; White, O.; Woese, C. R.

    1996-01-01

    Analysis of genomic sequences is necessarily an ongoing process. Initial gene assignments tend (wisely) to be on the conservative side (Venter, 1996). The analysis of the genome then grows in an iterative fashion as additional data and more sophisticated algorithms are brought to bear on the data. The present report is an emendation of the original gene list of Methanococcus jannaschii (Bult et al., 1996). By using a somewhat more updated database and more relaxed (and operator-intensive) pattern matching methods, we were able to add significantly to, and in a few cases amend, the gene identification table originally published by Bult et al. (1996).

  7. Genomic standards consortium projects.

    PubMed

    Field, Dawn; Sterk, Peter; Kottmann, Renzo; De Smet, J Wim; Amaral-Zettler, Linda; Cochrane, Guy; Cole, James R; Davies, Neil; Dawyndt, Peter; Garrity, George M; Gilbert, Jack A; Glöckner, Frank Oliver; Hirschman, Lynette; Klenk, Hans-Peter; Knight, Rob; Kyrpides, Nikos; Meyer, Folker; Karsch-Mizrachi, Ilene; Morrison, Norman; Robbins, Robert; San Gil, Inigo; Sansone, Susanna; Schriml, Lynn; Tatusova, Tatiana; Ussery, Dave; Yilmaz, Pelin; White, Owen; Wooley, John; Caporaso, Gregory

    2014-06-15

    The Genomic Standards Consortium (GSC) is an open-membership community that was founded in 2005 to work towards the development, implementation and harmonization of standards in the field of genomics. Starting with the defined task of establishing a minimal set of descriptions the GSC has evolved into an active standards-setting body that currently has 18 ongoing projects, with additional projects regularly proposed from within and outside the GSC. Here we describe our recently enacted policy for proposing new activities that are intended to be taken on by the GSC, along with the template for proposing such new activities. PMID:25197446

  8. The Brachypodium genome sequence: a resource for oat genomics research

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Oat (Avena sativa) is an important cereal crop used as both an animal feed and for human consumption. Genetic and genomic research on oat is hindered because it is hexaploid and possesses a large (13 Gb) genome. Diploid Avena relatives have been employed for genetic and genomic studies, but only mod...

  9. Tick Genomics: The Ixodes genome project and beyond

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ticks and mites (subphylum Chelicerata; subclass Acari) are important pests of animals and plants worldwide. The Ixodes scapularis (black-legged tick) genome sequencing project marks the beginning of the genomics era for the field of acarology. This project is the first to sequence the genome of a...

  10. Multiplexed Fragaria Chloroplast Genome Sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A method to sequence multiple chloroplast genomes that uses the sequencing depth of ultra high throughput sequencing technologies was recently described. Sequencing complete chloroplast genomes can resolve phylogenetic relationships at low taxonomic levels and identify point mutations and indels tha...

  11. The diversity of fungal genome.

    PubMed

    Mohanta, Tapan Kumar; Bae, Hanhong

    2015-01-01

    The genome size of an organism varies from species to species. The C-value paradox enigma is a very complex puzzle with regards to vast diversity in genome sizes in eukaryotes. Here we reported the detailed genomic information of 172 fungal species among different fungal genomes and found that fungal genomes are very diverse in nature. In fungi, the diversity of genomes varies from 8.97 Mb to 177.57 Mb. The average genome sizes of Ascomycota and Basidiomycota fungi are 36.91 and 46.48 Mb respectively. But higher genome size is observed in Oomycota (74.85 Mb) species, a lineage of fungus-like eukaryotic microorganisms. The average coding genes of Oomycota species are almost doubled than that of Acomycota and Basidiomycota fungus. PMID:25866485

  12. Company profile: Complete Genomics Inc.

    PubMed

    Reid, Clifford

    2011-02-01

    Complete Genomics Inc. is a life sciences company that focuses on complete human genome sequencing. It is taking a completely different approach to DNA sequencing than other companies in the industry. Rather than building a general-purpose platform for sequencing all organisms and all applications, it has focused on a single application - complete human genome sequencing. The company's Complete Genomics Analysis Platform (CGA™ Platform) comprises an integrated package of biochemistry, instrumentation and software that sequences human genomes at the highest quality, lowest cost and largest scale available. Complete Genomics offers a turnkey service that enables customers to outsource their human genome sequencing to the company's genome sequencing center in Mountain View, CA, USA. Customers send in their DNA samples, the company does all the library preparation, DNA sequencing, assembly and variant analysis, and customers receive research-ready data that they can use for biological discovery. PMID:21345140

  13. On genomics, kin, and privacy

    PubMed Central

    Telenti, Amalio; Ayday, Erman; Hubaux, Jean Pierre

    2014-01-01

    The storage of greater numbers of exomes or genomes raises the question of loss of privacy for the individual and for families if genomic data are not properly protected. Access to genome data may result from a personal decision to disclose, or from gaps in protection. In either case, revealing genome data has consequences beyond the individual, as it compromises the privacy of family members. Increasing availability of genome data linked or linkable to metadata through online social networks and services adds one additional layer of complexity to the protection of genome privacy.  The field of computer science and information technology offers solutions to secure genomic data so that individuals, medical personnel or researchers can access only the subset of genomic information required for healthcare or dedicated studies. PMID:25254097

  14. National Human Genome Research Institute

    MedlinePlus

    ... for Patient Care Education All About the Human Genome Project Fact Sheets Genetic Education Resources for Teachers ... Education Kit Online Genetics Education Resources Smithsonian NHGRI Genome Exhibition Talking Glossary: English Talking Glossary: Español Issues ...

  15. Hormesis and Paradoxical Effects of Wheat Seedling (Triticum Aestivum L.) Parameters Upon Exposure to Different Pollutants in a Wide Range of Doses

    PubMed Central

    Erofeeva, Elena A.

    2014-01-01

    Chlorophyll and carotenoid content (ChCar), lipid peroxidation (LP) and growth parameters (GP) in plants are often used for environmental pollution estimation. However, the nonmonotonic dose–response dependences (hormesis and paradoxical effects) of these indices are insufficiently explored following exposure to different pollutants. In this experiment, we studied nonmonotonic changes in ChCar, LP, GP in wheat seedlings (Triticum aestivum L.) upon exposure to lead, cadmium, copper, manganese, formaldehyde, the herbicide glyphosate, and sodium chloride in a wide range from sublethal concentration to 102–105 times lower concentrations. 85.7% of dose–response dependences were nonmonotonic (of these, 5.5% were hormesis and paradoxical effects comprised 94.5%). Multiphasic dependences were the most widespread type of paradoxical effect. Hormesis was a part of some multiphasic responses (i.e. paradoxical effects), which indicates a relationship between these phenomena. Sublethal pollutant concentrations significantly increased LP (to 2.0–2.4 times, except for manganese and glyphosate) and decreased GP (to 2.1–36.6 times, except for glyphosate), while ChCar was reduced insignificantly, normalized or even increased. Lower pollutant concentrations caused a moderate deviation in all parameters from the control (not more than 62%) for hormesis and paradoxical effects. The seedling parameters could have different types of nonmonotonic responses upon exposure to the same pollutant. PMID:24659937

  16. Comparative phosphoproteome analysis of the developing grains in bread wheat (Triticum aestivum L.) under well-watered and water-deficit conditions.

    PubMed

    Zhang, Ming; Ma, Cao-Ying; Lv, Dong-Wen; Zhen, Shou-Min; Li, Xiao-Hui; Yan, Yue-Ming

    2014-10-01

    Wheat (Triticum aestivum), one of the most important cereal crops, is often threatened by drought. In this study, water deficit significantly reduced the height of plants and yield of grains. To explore further the effect of drought stress on the development and yield of grains, we first performed a large scale phosphoproteome analysis of developing grains in wheat. A total of 590 unique phosphopeptides, representing 471 phosphoproteins, were identified under well-watered conditions. Motif-X analysis showed that four motifs were enriched, including [sP], [Rxxs], [sDxE], and [sxD]. Through comparative phosphoproteome analysis between well-watered and water-deficit conditions, we found that 63 unique phosphopeptides, corresponding to 61 phosphoproteins, showed significant changes in phosphorylation level (≥2-fold intensities). Functional analysis suggested that some of these proteins may be involved in signal transduction, embryo and endosperm development of grains, and drought response and defense under water-deficit conditions. Moreover, we also found that some chaperones may play important roles in protein refolding or degradation when the plant is subjected to water stress. These results provide a detailed insight into the stress response and defense mechanisms of developmental grains at the phosphoproteome level. They also suggested some potential candidates for further study of transgenosis and drought stress as well as incorporation into molecular breeding for drought resistance. PMID:25145454

  17. Exogenous Nitric Oxide (NO) Interferes with Lead (Pb)-Induced Toxicity by Detoxifying Reactive Oxygen Species in Hydroponically Grown Wheat (Triticum aestivum) Roots.

    PubMed

    Kaur, Gurpreet; Singh, Harminder Pal; Batish, Daizy R; Mahajan, Priyanka; Kohli, Ravinder Kumar; Rishi, Valbha

    2015-01-01

    Nitric Oxide (NO) is a bioactive signaling molecule that mediates a variety of biotic and abiotic stresses. The present study investigated the role of NO (as SNP [sodium nitroprusside]) in ameliorating lead (Pb)-toxicity in Triticum aestivum (wheat) roots. Pb (50 and 250 μM) alone and in combination with SNP (100 μM) was given to hydroponically grown wheat roots for a period of 0-8 h. NO supplementation reduced the accumulation of oxidative stress markers (malondialdehyde, conjugated dienes, hydroxyl ions and superoxide anion) and decreased the antioxidant enzyme activity in wheat roots particularly up to 6 h, thereby suggesting its role as an antioxidant. NO ameliorated Pb-induced membrane damage in wheat roots as evidenced by decreased ion-leakage and in situ histochemical localization. Pb-exposure significantly decreased in vivo NO level. The study concludes that exogenous NO partially ameliorates Pb-toxicity, but could not restore the plant growth on prolonged Pb-exposure. PMID:26402793

  18. The uptake of NO3-, NO2-, and NH4+ by intact wheat (Triticum aestivum) seedlings. I. Induction and kinetics of transport systems

    NASA Technical Reports Server (NTRS)

    Goyal, S. S.; Huffaker, R. C.

    1986-01-01

    The inducibility and kinetics of the NO3-, NO2-, and NH4+ transporters in roots of wheat seedlings (Triticum aestivum cv Yercora Rojo) were characterized using precise methods approaching constant analysis of the substrate solutions. A microcomputer-controlled automated high performance liquid chromatography system was used to determine the depletion of each N species (initially at 1 millimolar) from complete nutrient solutions. Uptake rate analyses were performed using computerized curve-fitting techniques. More precise estimates were obtained for the time required for the extent of the induction of each transporter. Up to 10 and 6 hours, respectively, were required to achieve apparent full induction of the NO3- and NO2- transporters. Evidence for substrate inducibility of the NH4+ transporters requiring 5 hours is presented. The transport of NO3- was mediated by a dual system (or dual phasic), whereas only single systems were found for transport of NO2- and NH4+. The Km values for NO3-, NO2-, and NH4+ were, respectively, 0.027, 0.054, and 0.05 millimolar. The Km for mechanism II of NO3- transport could not be defined in this study as it exhibited only apparent first order kinetics up to 1 millimolar.

  19. The sequence of change within the photosynthetic apparatus of wheat following short-term exposure to ozone. [Triticum aestivum L. cv Avalon

    SciTech Connect

    Farage, P.K.; Long, S.P.; Baker, N.R. ); Lechner, E.G. )

    1991-02-01

    The basis of inhibition of photosynthesis by single acute O{sub 3} exposures was investigated in vivo using analyses based on leaf gas exchange measurements. The fully expanded second leaves of wheat plants (Triticum aestivum L. cv Avalon) were fumigated with either 200 or 400 nanomoles per mole O{sub 3} for between 4 and 16 hours. This reduced significantly the light-saturated rate of Co{sub 2} uptake and was accompanied by a parallel decrease in stomatal conductance. However, the stomatal limitation only increased significantly during the first 8 hours of exposure to 400 nanomoles per mole O{sub 3}; no significant increase occurred for any of the other treatments. Analysis of the response of CO{sub 2} uptake to the internal Co{sub 2} concentration implied that the predominant factor responsible for the reduction in light-saturated CO{sub 2} uptake was a decrease in the efficiency of carboxylation. At saturating concentrations of Co{sub 2}, photosynthesis was inhibited by no more than 22% after 16 hours, indicating that the capacity for regeneration of ribulose bisphosphate was less susceptible to O{sub 3}. Ozone fumigations also had a less pronounced effect on light-limited photosynthesis. The photochemical efficiency of photosystem II estimated from the ratio of variable to maximum chlorophyll fluorescence and the atrazine-binding capacity of isolated thylakoids demonstrated that photochemical reactions were not responsible for the initial inhibition of CO{sub 2} uptake.

  20. Low molecular weight glutenin subunit gene Glu-B3h confers superior dough strength and breadmaking quality in wheat (Triticum aestivum L.)

    PubMed Central

    Wang, Yaping; Zhen, Shoumin; Luo, Nana; Han, Caixia; Lu, Xiaobing; Li, Xiaohui; Xia, Xianchun; He, Zhonghu; Yan, Yueming

    2016-01-01

    Low molecular weight glutenin subunit is one of the important quality elements in wheat (Triticum aestivum L.). Although considerable allelic variation has been identified, the functional properties of individual alleles at Glu-3 loci are less studied. In this work, we performed the first comprehensive study on the molecular characteristics and functional properties of the Glu-B3h gene using the wheat cultivar CB037B and its Glu-B3 deletion line CB037C. The results showed that the Glu-B3h deletion had no significant effects on plant morphological or yield traits, but resulted in a clear reduction in protein body number and size and main quality parameters, including inferior mixing property, dough strength, loaf volume, and score. Molecular characterization showed that the Glu-B3h gene consists of 1179 bp, and its encoded B-subunit has a longer repetitive domain and an increased number of α-helices, as well as higher expression, which could contribute to superior flour quality. The SNP-based allele-specific PCR markers designed for the Glu-B3h gene were developed and validated with bread wheat holding various alleles at Glu-B3 locus, which could effectively distinguish the Glu-B3h gene from others at the Glu-B3 locus, and have potential applications for wheat quality improvement through marker-assisted selection. PMID:27273251

  1. Hybrid dwarfness in crosses between wheat (Triticum aestivum L.) and rye (Secale cereale L.): a new look at an old phenomenon.

    PubMed

    Tikhenko, N; Rutten, T; Tsvetkova, N; Voylokov, A; Börner, A

    2015-03-01

    The existence of hybrid dwarfs from intraspecific crosses in wheat (Triticum aestivum) was described 100 years ago, and the genetics underlying hybrid dwarfness are well understood. In this study, we report a dwarf phenotype in interspecific hybrids between wheat and rye (Secale cereale). We identified two rye lines that produce hybrid dwarfs with wheat and have none of the hitherto known hybrid dwarfing genes. Genetic analyses revealed that both rye lines carry a single allelic gene responsible for the dwarf phenotype. This gene was designated Hdw-R1 (Hybrid dwarf-R1). Application of gibberellic acid (GA3 ) to both intraspecific (wheat-wheat) and interspecific (wheat-rye) hybrids showed that hybrid dwarfness cannot be overcome by treatment with this phytohormone. Histological analysis of shoot apices showed that wheat-rye hybrids with the dwarf phenotype at 21 and 45 days after germination failed to develop further. Shoot apices of dwarf plants did not elongate, did not form new primordia and had a dome-shaped appearance in the seed. The possible relationship between hybrid dwarfness and the genes responsible for the transition from vegetative to generative growth stage is discussed. PMID:25251214

  2. The Dynamic Process of Interspecific Interactions of Competitive Nitrogen Capture between Intercropped Wheat (Triticum aestivum L.) and Faba Bean (Vicia faba L.)

    PubMed Central

    2014-01-01

    Wheat (Triticum aestivum L.)/faba bean (Vicia faba L.) intercropping shows significant overyielding and high nitrogen (N)-use efficiency, but the dynamics of plant interactions have rarely been estimated. The objective of the present study was to investigate the temporal dynamics of competitive N acquisition between intercropped wheat and faba bean with the logistic model. Wheat and faba bean were grown together or alone with limited N supply in pots. Data of shoot and root biomass and N content measured from 14 samplings were fitted to logistic models to determine instantaneous rates of growth and N uptake. The superiority of instantaneous biomass production and N uptake shifted from faba bean to wheat with their growth. Moreover, the shift of superiority on N uptake occurred 7–12 days earlier than that of biomass production. Interspecific competition stimulated intercropped wheat to have a much earlier and stronger superiority on instantaneous N uptake compared with isolated wheat. The modeling methodology characterized the temporal dynamics of biomass production and N uptake of intercropped wheat and faba bean in different planting systems, which helps to understand the underlying process of plant interaction for intercropping plants. PMID:25541699

  3. A sampling system for estimating the cultivation of wheat (Triticum aestivum L) from LANDSAT data. M.S. Thesis - 21 Jul. 1983

    NASA Technical Reports Server (NTRS)

    Parada, N. D. J. (Principal Investigator); Moreira, M. A.

    1983-01-01

    Using digitally processed MSS/LANDSAT data as auxiliary variable, a methodology to estimate wheat (Triticum aestivum L) area by means of sampling techniques was developed. To perform this research, aerial photographs covering 720 sq km in Cruz Alta test site at the NW of Rio Grande do Sul State, were visually analyzed. LANDSAT digital data were analyzed using non-supervised and supervised classification algorithms; as post-processing the classification was submitted to spatial filtering. To estimate wheat area, the regression estimation method was applied and different sample sizes and various sampling units (10, 20, 30, 40 and 60 sq km) were tested. Based on the four decision criteria established for this research, it was concluded that: (1) as the size of sampling units decreased the percentage of sampled area required to obtain similar estimation performance also decreased; (2) the lowest percentage of the area sampled for wheat estimation with relatively high precision and accuracy through regression estimation was 90% using 10 sq km s the sampling unit; and (3) wheat area estimation by direct expansion (using only aerial photographs) was less precise and accurate when compared to those obtained by means of regression estimation.

  4. Effects of chlorsulfuron on diclofop-methyl toxicity to Italian ryegrass (Lolium multiflorum) and Italian ryegrass interference in wheat (triticum aestivum)

    SciTech Connect

    Liebl, R.A.

    1985-01-01

    Chlorsulfuron )2-chloro-N-(((4-methoxy-6-methyl-1,3,5-triazin-2-yl)amino)carbonyl)benzenesulfonamide) and diclofop-methyl )methyl 2-(4-(2,4-dichlorophenoxy)phenoxy)propanoate) are herbicides used for the selective control of broadleaf and grassy weeds, respectively, in wheat (Triticum aestivum L.). The addition of chlorsulfuron (14.8 g ai/ha) to 0.90 kg ai/ha diclofop-methyl and applied postemergence reduced Italian ryegrass (Lolium multiflorum L.) control 27% and increased fresh weights over diclofop-methyl alone. Chlorsulfuron and diclofop-methyl were approximately 200 and 35%, respectively, more active on Italian ryegrass when applied pre-emergence compared to postemergence applications and responses of the combinations were additive. Although little movement of /sup 14/C-label occurred in either species, significantly more /sup 14/C-label translocated from the treated zone of Italian ryegrass. In metabolism studies, wheat was able to detoxify diclofop-methyl more rapidly than Italian ryegrass. In field interference studies, wheat grain yields were reduced an average of 4.2% for every 10 Italian ryegrass plants/m/sup 2/ because of decreased crop tillering. Italian ryegrass had net nitrate and potassium influx rates approximately 2-times greater than those for wheat when plants were growing in nutrient solution in the greenhouse.

  5. Accumulation and conversion of sugars by developing wheat grains. VII. Effect of changes in sieve tube and endosperm cavity sap concentrations on the grain filling rate. [Triticum aestivum

    SciTech Connect

    Fisher, D.B.; Gifford, R.M.

    1987-06-01

    The extent to which wheat grain growth is dependent on transport pool solute concentration was investigated by the use of illumination and partial grain removal to vary solute concentrations in the sieve tube and endosperm cavity saps of the wheat ear (Triticum aestivum L.). Short-term grain growth rates were estimated indirectly from the product of phloem area, sieve tube sap concentration, and /sup 32/P translocation velocity. On a per grain basis, calculated rates of mass transport through the peduncle were fairly constant over a substantial range in other transport parameters (i.e. velocity, concentration, phloem area, and grain number). The rates were about 40% higher than expected; this probably reflects some unavoidable bias on faster-moving tracer in the velocity estimates. Sieve tube sap concentration increased in all experiments (by 20 to 64%), with a concomitant decline in velocity (to as low as 8% of the initial value). Endosperm cavity sucrose concentration also increased in all experiments, but cavity sap osmolality and total amino acid concentration remained nearly constant. No evidence was found for an increase in the rate of mass transport per grain through the peduncle in response to the treatments. This apparent unresponsiveness of grain growth rate to increased cavity sap sucrose concentration conflicts with earlier in vitro endosperm studies showing that sucrose uptake increased with increasing external sucrose concentration up to 150 to 200 millimolar.

  6. Starch granule formation and protein deposition in wheat (Triticum aestivum L.) starchy endosperm cells is altered by high temperature during grain fill

    NASA Astrophysics Data System (ADS)

    Hurkman, William J.; Wood, Delilah F.

    2010-06-01

    High temperatures during wheat grain fill decrease starch and protein levels, adversely affecting wheat yield and flour quality. To determine the effect of high temperature on starchy endosperm cell development, grain (Triticum aestivum L. 'Butte 86') was produced under a 24/17°C or 37/28°C day/night regimen imposed from flowering to maturity and starch and protein deposition examined using scanning electron microscopy. The high temperature regimen shortened the duration of grain fill from 40 to 18 days. Under the 37/28°C regimen, A- and B-type starch granules decreased in size. A-type starch granules also exhibited pitting, suggesting enhanced action of starch degradative enzymes. Under both temperature regimens, protein bodies originated early in development and coalesced during mid to late development to form a continuous protein matrix surrounding the starch granules. Under the 37/28°C regimen, the proportion of protein matrix increased in endosperm cells of mature grain. Taken together, the changes in starch granule number and size and in protein matrix amount provide clues for understanding how high temperature during grain fill can affect end use properties of wheat flour.

  7. Nutrient variability in phloem: examining changes in K, Mg, Zn and Fe concentration during grain loading in common wheat (Triticum aestivum).

    PubMed

    Palmer, Lachlan J; Palmer, Lyndon T; Rutzke, Michael A; Graham, Robin D; Stangoulis, James C R

    2014-12-01

    In wheat, nutrients are transported to seeds via the phloem yet access to this vascular tissue for exudate collection and quantitative analysis of elemental composition is difficult. The purest phloem is collected through the use of aphid stylectomy with volumes of exudate collected normally in the range of 20-500 nl. In this work a new method using inductively coupled plasma mass spectroscopy (ICP-MS) was developed to measure the concentration of K, Mg, Zn and Fe in volumes of wheat (Triticum aestivum, genotype Samnyt 16) phloem as small as 15.5 nl. This improved method was used to observe changes in phloem nutrient concentration during the grain loading period. There were statistically significant increases in phloem Mg and Zn concentration and a significant decrease in K over the period from 1-2 days after anthesis (DAA) to 9-12 DAA. During this period, there was no statistically significant change in phloem Fe concentration. PMID:24735095

  8. TaSCL14, a novel wheat (Triticum aestivum L.) GRAS gene, regulates plant growth, photosynthesis, tolerance to photooxidative stress, and senescence.

    PubMed

    Chen, Kunmei; Li, Hongwei; Chen, Yaofeng; Zheng, Qi; Li, Bin; Li, Zhensheng

    2015-01-20

    Rates of photosynthesis, tolerance to photooxidative stress, and senescence are all important physiological factors that affect plant development and thus agricultural productivity. GRAS proteins play essential roles in plant growth and development as well as in plant responses to biotic and abiotic stresses. So far few GRAS genes in wheat (Triticum aestivum L.) have been characterized. A previous transcriptome analysis indicated that the expression of a GRAS gene (TaSCL14) was induced by high-light stress in Xiaoyan 54 (XY54), a common wheat cultivar with strong tolerance to high-light stress. In this study, TaSCL14 gene was isolated from XY54 and mapped on chromosome 4A. TaSCL14 was expressed in various wheat organs, with high levels in stems and roots. Our results confirmed that TaSCL14 expression was indeed responsive to high-light stress. Barley stripe mosaic virus (BSMV)-based virus-induced gene silencing (VIGS) of TaSCL14 in wheat was performed to help characterize its potential functions. Silencing of TaSCL14 resulted in inhibited plant growth, decreased photosynthetic capacity, and reduced tolerance to photooxidative stress. In addition, silencing of TaSCL14 in wheat promoted leaf senescence induced by darkness. These results suggest that TaSCL14 may act as a multifunctional regulator involved in plant growth, photosynthesis, tolerance to photooxidative stress, and senescence. PMID:25619599

  9. Variation of the phytotoxicity of municipal solid waste incinerator bottom ash on wheat (Triticum aestivum L.) seed germination with leaching conditions.

    PubMed

    Phoungthong, Khamphe; Zhang, Hua; Shao, Li-Ming; He, Pin-Jing

    2016-03-01

    Municipal solid waste incinerator bottom ash (MSWIBA) has long been regarded as an alternative building material in the construction industry. However, the pollutants contained in the bottom ash could potentially leach out and contaminate the local environment, which presents an obstacle to the reuse of the materials. To evaluate the environmental feasibility of using MSWIBA as a recycled material in construction, the leaching derived ecotoxicity was assessed. The leaching behavior of MSWIBA under various conditions, including the extractant type, leaching time, liquid-to-solid (L/S) ratio, and leachate pH were investigated, and the phytotoxicity of these leachates on wheat (Triticum aestivum L.) seed germination was determined. Moreover, the correlation between the germination index and the concentrations of various chemical constituents in the MSWIBA leachates was assessed using multivariate statistics with principal component analysis and Pearson's correlation analysis. It was found that, heavy metal concentrations in the leachate were pH and L/S ratio dependent, but were less affected by leaching time. Heavy metals were the main pollutants present in wheat seeds. Heavy metals (especially Ba, Cr, Cu and Pb) had a substantial inhibitory effect on wheat seed germination and root elongation. To safely use MSWIBA in construction, the potential risk and ecotoxicity of leached materials must be addressed. PMID:26745383

  10. Genetic variability in anthocyanin composition and nutritional properties of blue, purple, and red bread (Triticum aestivum L.) and durum (Triticum turgidum L. ssp. turgidum convar. durum) wheats.

    PubMed

    Ficco, Donatella B M; De Simone, Vanessa; Colecchia, Salvatore A; Pecorella, Ivano; Platani, Cristiano; Nigro, Franca; Finocchiaro, Franca; Papa, Roberto; De Vita, Pasquale

    2014-08-27

    Renewed interest in breeding for high anthocyanins in wheat (Triticum ssp.) is due to their antioxidant potential. A collection of different pigmented wheats was used to investigate the stability of anthocyanins over three crop years. The data show higher anthocyanins in blue-aleurone bread wheat (Triticum aestivum L.), followed by purple- and red-pericarp durum wheat (Triticum turgidum L. ssp. turgidum convar. durum), using cyanidin 3-O-glucoside as standard. HPLC of the anthocyanin components shows five to eight major anthocyanins for blue wheat extracts, compared to three anthocyanins for purple and red wheats. Delphinidin 3-O-rutinoside, delphinidin 3-O-glucoside, and malvidin 3-O-glucoside are predominant in blue wheat, with cyanidin 3-O-glucoside, peonidin 3-O-galactoside, and malvidin 3-O-glucoside in purple wheat. Of the total anthocyanins, 40-70% remain to be structurally identified. The findings confirm the high heritability for anthocyanins, with small genotype × year effects, which will be useful for breeding purposes, to improve the antioxidant potential of cereal-based foods. PMID:25130676

  11. Measurement of 2-carboxyarabinitol 1-phosphate in plant leaves by isotope dilution. [Spinacea oleracea; Triticum aestivum; Arabidopsis thaliana; Maize; Phaseolus vulgaris; Petunia hybrida

    SciTech Connect

    Moore, B.D.; Kobza, J.; Seemann, J.R. )

    1991-05-01

    The level of 2-carboxyarabinitol 1-phosphate (CA1P) in leaves of 12 species was determined by an isotope dilution assay. {sup 14}C-labeled standard was synthesized from (2-{sup 14}C)carboxyarabinitol 1,5-bisphosphate using acid phosphatase, and was added at the initial point of leaf extraction. Leaf CA1P was purified and its specific activity determined. CA1P was found in dark-treated leaves of all species examined, including spinach (Spinacea oleracea), wheat (Triticum aestivum), Arabidopsis thaliana, and maize (Zea mays). The highest amounts were found in bean (Phaseolus vulgaris) and petunia (Petunia hybrida), which had 1.5 to 1.8 moles CA1P per mole ribulose 1,5-bisphosphate carboxylase catalytic sites. Most species had intermediate amounts of CA1P (0.2 to 0.8 mole CA1P per mole catalytic sites). Such intermediate to high levels of CA1P support the hypothesis that CA1P functions in many species as a light-dependent regulator of ribulose 1,5-bisphosphate carboxylase activity and whole leaf photosynthetic CO{sub 2} assimilation. However, CA1P levels in spinach, wheat, and A. thaliana were particularly low (less than 0.09 mole CA1P per mole catalytic sites). In such species, CA1P does not likely have a significant role in regulating ribulose 1,5-bisphosphate carboxylase activity, but could have a different physiological role.

  12. Low molecular weight glutenin subunit gene Glu-B3h confers superior dough strength and breadmaking quality in wheat (Triticum aestivum L.).

    PubMed

    Wang, Yaping; Zhen, Shoumin; Luo, Nana; Han, Caixia; Lu, Xiaobing; Li, Xiaohui; Xia, Xianchun; He, Zhonghu; Yan, Yueming

    2016-01-01

    Low molecular weight glutenin subunit is one of the important quality elements in wheat (Triticum aestivum L.). Although considerable allelic variation has been identified, the functional properties of individual alleles at Glu-3 loci are less studied. In this work, we performed the first comprehensive study on the molecular characteristics and functional properties of the Glu-B3h gene using the wheat cultivar CB037B and its Glu-B3 deletion line CB037C. The results showed that the Glu-B3h deletion had no significant effects on plant morphological or yield traits, but resulted in a clear reduction in protein body number and size and main quality parameters, including inferior mixing property, dough strength, loaf volume, and score. Molecular characterization showed that the Glu-B3h gene consists of 1179 bp, and its encoded B-subunit has a longer repetitive domain and an increased number of α-helices, as well as higher expression, which could contribute to superior flour quality. The SNP-based allele-specific PCR markers designed for the Glu-B3h gene were developed and validated with bread wheat holding various alleles at Glu-B3 locus, which could effectively distinguish the Glu-B3h gene from others at the Glu-B3 locus, and have potential applications for wheat quality improvement through marker-assisted selection. PMID:27273251

  13. Exogenous Nitric Oxide (NO) Interferes with Lead (Pb)-Induced Toxicity by Detoxifying Reactive Oxygen Species in Hydroponically Grown Wheat (Triticum aestivum) Roots

    PubMed Central

    Kaur, Gurpreet; Singh, Harminder Pal; Batish, Daizy R.; Mahajan, Priyanka; Kohli, Ravinder Kumar; Rishi, Valbha

    2015-01-01

    Nitric Oxide (NO) is a bioactive signaling molecule that mediates a variety of biotic and abiotic stresses. The present study investigated the role of NO (as SNP [sodium nitroprusside]) in ameliorating lead (Pb)-toxicity in Triticum aestivum (wheat) roots. Pb (50 and 250 μM) alone and in combination with SNP (100 μM) was given to hydroponically grown wheat roots for a period of 0–8 h. NO supplementation reduced the accumulation of oxidative stress markers (malondialdehyde, conjugated dienes, hydroxyl ions and superoxide anion) and decreased the antioxidant enzyme activity in wheat roots particularly up to 6 h, thereby suggesting its role as an antioxidant. NO ameliorated Pb-induced membrane damage in wheat roots as evidenced by decreased ion-leakage and in situ histochemical localization. Pb-exposure significantly decreased in vivo NO level. The study concludes that exogenous NO partially ameliorates Pb-toxicity, but could not restore the plant growth on prolonged Pb-exposure. PMID:26402793

  14. Characterization of a wheat (Triticum aestivum L.) expansin gene, TaEXPB23, involved in the abiotic stress response and phytohormone regulation.

    PubMed

    Han, Yang yang; Li, Ai xiu; Li, Feng; Zhao, Mei rong; Wang, Wei

    2012-05-01

    Expansins are proteins that are generally accepted to be key regulators of cell wall extension and plant growth. We examined the expression pattern of TaEXPB23, a wheat (Triticum aestivum L.) expansin gene, under exogenous phytohormone and abiotic stress treatments. In addition, we evaluated its function in the tolerance to salt stress and high temperature (HT) by overexpressing it in transgenic tobacco plants. In subcellular localization assays, TaEXPB23 localized to the cell wall. Expression analysis demonstrated that the transcription pattern of TaEXPB23 corresponded to wheat coleoptile growth. Real-time RT-PCR analysis revealed that TaEXPB23 transcript expression was upregulated by exogenous methyl jasmonate (MeJA) and salt stress, but downregulated by exogenous gibberellins (GA₃), ethylene (ET), indole-3-acetic acid (IAA) and α-naphthlcetic acid (NAA). Overexpression of TaEXPB23 in tobacco (tabacum) conferred tolerance to salt stress by enhancing water retention ability (WRA) and decreasing osmotic potential (OP). However, transgenic plants overexpressing TaEXPB23 did not show any improvement in the tolerance to HT stress. These results suggested that TaEXPB23 is regulated by phytohormones and is involved in the regulation of salt stress tolerance. PMID:22381655

  15. Effects of elevated CO2 concentration on growth, photosynthetic characteristics and biomass of wheat (Triticum aestivum L.) in Lunar Palace 1

    NASA Astrophysics Data System (ADS)

    Dong, Chen; Liu, Hui; Liu, Hong; Wang, Minjuan; Fu, Yuming; Shao, Lingzhi; Liu, Guanghui; Yu, Juan

    Short- and long-term effects of elevated CO2 concentration on growth, photosynthetic characteristics and biomass of wheat (Triticum aestivum L.) are examined during 90 days in Lunar Palace 1. While a short-term exposure to elevated CO2 induces a large increase in photosynthesis in wheat plants, long-term growth in elevated CO2 often results in a smaller increase due to reduced photosynthetic capacity. In this study, it was also shown that, net photosynthesis per unit leaf area was raised at an increased CO2 concentration partly due to a decrease in photorespiration, partly due to an increased substrate supply. Transpiration was reduced due to a lower stomatal conductance. The growth response of whole plants to a high CO2 concentration will be the main subject of this paper. Firstly, an estimation is made to what extent a doubling in CO2 concentration affects wheat plant growth in Lunar Palace 1. Secondly, the mechanisms behind this growth stimulation will be assessed. Finally, in those cases where wheat plants are grown over a range of environmental conditions, we select that condition where control plants are growing fastest. Thus, this study may be a matter of interest for researchers in both space and unban agriculture fields.

  16. Spelt (Triticum spelta L.) and winter wheat (Triticum aestivum L.) wholemeals have similar sterol profiles, as determined by quantitative liquid chromatography and mass spectrometry analysis.

    PubMed

    Ruibal-Mendieta, Nike L; Rozenberg, Raoul; Delacroix, Dominique L; Petitjean, Géraldine; Dekeyser, Adrien; Baccelli, Chiara; Marques, Carole; Delzenne, Nathalie M; Meurens, Marc; Habib-Jiwan, Jean-Louis; Quetin-Leclercq, Joëlle

    2004-07-28

    From a nutritional point of view, cereal lipids include valuable molecules, such as essential fatty acids, phytosterols, and fat-soluble vitamins. Spelt (Triticum spelta L.) is an alternative hulled bread cereal mostly grown in Belgium, where it is mainly intended for animal feed but should increasingly be used for human consumption. The present research focused on phytosterol quantification by LC/APCI-MS2 in saponified wholemeal extracts of 16 dehulled spelt and 5 winter wheat (Triticum aestivum L.) varieties grown in Belgium during 2001-2002 at the same location. Glycosylated sterols and free and formerly esterified sterols could be determined in saponified extracts. Results show that the mean phytosterol content is comparable in both cereals (whereas other lipids, such as oleic and linoleic acids, are increased in spelt wholemeal): spelt extract has, on average, 527.7 microg of free and esterified sterols g(-1) of wholemeal and 123.8 microg of glycosylated sterols g(-1) of wholemeal versus 528.5 and 112.6 microg x g(-1) in winter wheat (values not corrected for recoveries). This is the first report on the application and validation of an LC/MS2 method for the quantification of phytosterols in spelt and winter wheat. PMID:15264918

  17. [Effects of soil pH value on the bioavailability and fractionation of rare earth elements in wheat seedling (Triticum aestivum L.)].

    PubMed

    Cao, Xinde; Ding, Zhuhong; Hu, Xin; Wang, Xiaorong

    2002-01-30

    The effect of soil pH value on the bioavailability and fractionation of rare earth elements (REEs) in wheat seedling (Triticum aestivum L.) were investigated. The results showed that the concentration of REEs in wheat decreased with increasing pH value, and their inter-relationship was best expressed as quadratic equation, with correlation coefficients from 0.6003 to 0.9572. The response of individual elements to pH value change tended to be Ce > La > Nd > Sm > Gd > Yb > Eu, with Ce most sensitive to changing pH conditions and Eu lest. Chemical fractionation indicated that the order of REEs concentration in three fractions could be as follows: B2(NH2OH.HCl extraction) > B3(H2O2-NH4Ac extract) > B1(HAc extract). The increase of pH value resulted in transformation from B1 to B2 and B3. Multiple regression analysis was utilized to obtain the regression equations for prediction plant uptake of REEs. B1 fraction was most available to wheat. Meanwhile, it was found that the fractionation factors of REEs in wheat were negatively correlated with the soil pH value. PMID:11987417

  18. When Isolated at Full Receptivity, in Vitro Fertilized Wheat (Triticum aestivum, L.) Egg Cells Reveal [Ca2+]cyt Oscillation of Intracellular Origin

    PubMed Central

    Pónya, Zsolt; Corsi, Ilaria; Hoffmann, Richárd; Kovács, Melinda; Dobosy, Anikó; Kovács, Attila Zoltán; Cresti, Mauro; Barnabás, Beáta

    2014-01-01

    During in vitro fertilization of wheat (Triticum aestivum, L.) in egg cells isolated at various developmental stages, changes in cytosolic free calcium ([Ca2+]cyt) were observed. The dynamics of [Ca2+]cyt elevation varied, reflecting the difference in the developmental stage of the eggs used. [Ca2+]cyt oscillation was exclusively observed in fertile, mature egg cells fused with the sperm cell. To determine how [Ca2+]cyt oscillation in mature egg cells is generated, egg cells were incubated in thapsigargin, which proved to be a specific inhibitor of the endoplasmic reticulum (ER) Ca2+-ATPase in wheat egg cells. In unfertilized egg cells, the addition of thapsigargin caused an abrupt transient increase in [Ca2+]cyt in the absence of extracellular Ca2+, suggesting that an influx pathway for Ca2+ is activated by thapsigargin. The [Ca2+]cyt oscillation seemed to require the filling of an intracellular calcium store for the onset of which, calcium influx through the plasma membrane appeared essential. This was demonstrated by omitting extracellular calcium from (or adding GdCl3 to) the fusion medium, which prevented [Ca2+]cyt oscillation in mature egg cells fused with the sperm. Combined, these data permit the hypothesis that the first sperm-induced transient increase in [Ca2+]cyt depletes an intracellular Ca2+ store, triggering an increase in plasma membrane Ca2+ permeability, and this enhanced Ca2+ influx results in [Ca2+]cyt oscillation. PMID:25535074

  19. When isolated at full receptivity, in vitro fertilized wheat (Triticum aestivum, L.) egg cells reveal [Ca2+]cyt oscillation of intracellular origin.

    PubMed

    Pónya, Zsolt; Corsi, Ilaria; Hoffmann, Richárd; Kovács, Melinda; Dobosy, Anikó; Kovács, Attila Zoltán; Cresti, Mauro; Barnabás, Beáta

    2014-01-01

    During in vitro fertilization of wheat (Triticum aestivum, L.) in egg cells isolated at various developmental stages, changes in cytosolic free calcium ([Ca2+]cyt) were observed. The dynamics of [Ca2+]cyt elevation varied, reflecting the difference in the developmental stage of the eggs used. [Ca2+]cyt oscillation was exclusively observed in fertile, mature egg cells fused with the sperm cell. To determine how [Ca2+]cyt oscillation in mature egg cells is generated, egg cells were incubated in thapsigargin, which proved to be a specific inhibitor of the endoplasmic reticulum (ER) Ca2+-ATPase in wheat egg cells. In unfertilized egg cells, the addition of thapsigargin caused an abrupt transient increase in [Ca2+]cyt in the absence of extracellular Ca2+, suggesting that an influx pathway for Ca2+ is activated by thapsigargin. The [Ca2+]cyt oscillation seemed to require the filling of an intracellular calcium store for the onset of which, calcium influx through the plasma membrane appeared essential. This was demonstrated by omitting extracellular calcium from (or adding GdCl3 to) the fusion medium, which prevented [Ca2+]cyt oscillation in mature egg cells fused with the sperm. Combined, these data permit the hypothesis that the first sperm-induced transient increase in [Ca2+]cyt depletes an intracellular Ca2+ store, triggering an increase in plasma membrane Ca2+ permeability, and this enhanced Ca2+ influx results in [Ca2+]cyt oscillation. PMID:25535074

  20. Importance of anchor genomes for any plant genome project

    PubMed Central

    Messing, Joachim; Llaca, Victor

    1998-01-01

    Progress in agricultural and environmental technologies is hampered by a slower rate of gene discovery in plants than animals. The vast pool of genes in plants, however, will be an important resource for insertion of genes, via biotechnological procedures, into an array of plants, generating unique germ plasms not achievable by conventional breeding. It just became clear that genomes of grasses have evolved in a manner analogous to Lego blocks. Large chromosome segments have been reshuffled and stuffer pieces added between genes. Although some genomes have become very large, the genome with the fewest stuffer pieces, the rice genome, is the Rosetta Stone of all the bigger grass genomes. This means that sequencing the rice genome as anchor genome of the grasses will provide instantaneous access to the same genes in the same relative physical position in other grasses (e.g., corn and wheat), without the need to sequence each of these genomes independently. (i) The sequencing of the entire genome of rice as anchor genome for the grasses will accelerate plant gene discovery in many important crops (e.g., corn, wheat, and rice) by several orders of magnitudes and reduce research and development costs for government and industry at a faster pace. (ii) Costs for sequencing entire genomes have come down significantly. Because of its size, rice is only 12% of the human or the corn genome, and technology improvements by the human genome project are completely transferable, translating in another 50% reduction of the costs. (iii) The physical mapping of the rice genome by a group of Japanese researchers provides a jump start for sequencing the genome and forming an international consortium. Otherwise, other countries would do it alone and own proprietary positions. PMID:9482827

  1. Characterization of a Putative New Semi-Dominant Reduced Height Gene, Rht_NM9, in Wheat (Triticum aestivum L.).

    PubMed

    Lu, Yuan; Xing, Liping; Xing, Shujuan; Hu, Ping; Cui, Chaofan; Zhang, Mingyi; Xiao, Jin; Wang, Haiyan; Zhang, Ruiqi; Wang, Xiue; Chen, Peidu; Cao, Aizhong

    2015-12-20

    Plant height is an important agronomic trait in cereal crops, and can affect both plant architecture and grain yield. New dwarfing genes are required for improving the genetic diversity of wheat. In this study, a novel dwarf mutant, NM9, was created by treating seeds of the wheat variety NAU9918 with ethyl methanesulfonate (EMS). NM9 showed obvious phenotypic changes, which were distinct from those caused by other dwarfing genes, especially the reduced plant height, increased effective tiller number, and elongated spike and grain length. The reduced plant height in NM9 was attributable to a semi-dominant dwarfing gene Rht_NM9, which was flanked by two closely linked SNP markers, SNP34 and SNP41, covering an 8.86-Mb region on the chromosome arm 2AS. The results of gibberellic acid (GA) sensitivity evaluation, comparative genomics analysis and allelism test indicated that Rht_NM9 was neither allelic to Rht7 and Rht21 nor homoeoallelic to Rht8, so Rht_NM9 was proposed to be a new dwarfing locus on the homoeologous group 2 chromosomes of wheat. Rht_NM9 has a negative effect on plant height and positive effects on effective tiller number and grain size, thus, Rht_NM9 could be used for elucidating the mechanisms underlying plant architecture and grain development. PMID:26743986

  2. Genomics in Cardiovascular Disease

    PubMed Central

    Roberts, Robert; Marian, A.J.; Dandona, Sonny; Stewart, Alexandre F.R.

    2013-01-01

    A paradigm shift towards biology occurred in the 1990’s subsequently catalyzed by the sequencing of the human genome in 2000. The cost of DNA sequencing has gone from millions to thousands of dollars with sequencing of one’s entire genome costing only $1,000. Rapid DNA sequencing is being embraced for single gene disorders, particularly for sporadic cases and those from small families. Transmission of lethal genes such as associated with Huntington’s disease can, through in-vitro fertilization, avoid passing it on to one’s offspring. DNA sequencing will meet the challenge of elucidating the genetic predisposition for common polygenic diseases, especially in determining the function of the novel common genetic risk variants and identifying the rare variants, which may also partially ascertain the source of the missing heritability. The challenge for DNA sequencing remains great, despite human genome sequences being 99.5% identical, the 3 million single nucleotide polymorphisms (SNPs) responsible for most of the unique features add up to 60 new mutations per person which, for 7 billion people, is 420 billion mutations. It is claimed that DNA sequencing has increased 10,000 fold while information storage and retrieval only 16 fold. The physician and health user will be challenged by the convergence of two major trends, whole genome sequencing and the storage/retrieval and integration of the data. PMID:23524054

  3. Poster: the macaque genome.

    PubMed

    2007-04-13

    The rhesus macaque (Macaca mulatta) facilitates an extraordinary range of biomedical and basic research, and the publication of the genome only makes it a more powerful model for studies of human disease; moreover, the macaque's position relative to humans and chimpanzees affords the opportunity to learn about the processes that have shaped the last 25 million years of primate evolution. To allow users to explore these themes of the macaque genome, Science has created a special interactive version of the poster published in the print edition of the 13 April 2007 issue. The interactive version includes additional text and exploration, as well as embedded video featuring seven scientists discussing the importance of the macaque and its genome sequence in studies of biomedicine and evolution. We have also created an accompanying teaching resource, including a lesson plan aimed at teachers of advanced high school life science students, for exploring what a comparison of the macaque and human genomes can tell us about human biology and evolution. These items are free to all site visitors. PMID:17431172

  4. (Genomic variation in maize)

    SciTech Connect

    Rivin, C.J.

    1991-01-01

    These studies have sought to learn how different DNA sequences and sequence arrangements contribute to genome plasticity in maize. We describe quantitative variation among maize inbred lines for tandemly arrayed and dispersed repeated DNA sequences and gene families, and qualitative variation for sequences homologous to the Mutator family of transposons. The potential of these sequences to undergo unequal crossing over, non-allelic (ectopic) recombination and transposition makes them a source of genome instability. We have found examples of rapid genomic change involving these sequences in Fl hybrids, tissue culture cells and regenerated plants. We describe the repetitive portion of the maize genome as composed primarily of sequences that vary markedly in copy number among different genetic stocks. The most highly variable is the 185 bp repeat associated with the heterochromatic chromosome knobs. Even in lines without visible knobs, there is a considerable quantity of tandemly arrayed repeats. We also found a high degree of variability for the tandemly arrayed 5S and ribosomal DNA repeats. While such variation might be expected as the result of unequal cross-over, we were surprised to find considerable variation among lower copy number, dispersed repeats as well. One highly repeated sequence that showed a complex tandem and dispersed arrangement stood out as showing no detectable variability among the maize lines. In striking contrast to the variability seen between the inbred stocks, individuals within a stock were indistinguishable with regard to their repeated sequence multiplicities.

  5. Better chocolate through genomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Theobroma cacao, the cacao or chocolate tree, is a tropical understory tree whose seeds are used to make chocolate. And like any important crop, cacao is the subject of much research. On September 15, 2010, scientists publicly released a preliminary sequence of the cacao genome--which contains all o...

  6. The Nostoc punctiforme Genome

    SciTech Connect

    John C. Meeks

    2001-12-31

    Nostoc punctiforme is a filamentous cyanobacterium with extensive phenotypic characteristics and a relatively large genome, approaching 10 Mb. The phenotypic characteristics include a photoautotrophic, diazotrophic mode of growth, but N. punctiforme is also facultatively heterotrophic; its vegetative cells have multiple development alternatives, including terminal differentiation into nitrogen-fixing heterocysts and transient differentiation into spore-like akinetes or motile filaments called hormogonia; and N. punctiforme has broad symbiotic competence with fungi and terrestrial plants, including bryophytes, gymnosperms and an angiosperm. The shotgun-sequencing phase of the N. punctiforme strain ATCC 29133 genome has been completed by the Joint Genome Institute. Annotation of an 8.9 Mb database yielded 7432 open reading frames, 45% of which encode proteins with known or probable known function and 29% of which are unique to N. punctiforme. Comparative analysis of the sequence indicates a genome that is highly plastic and in a state of flux, with numerous insertion sequences and multilocus repeats, as well as genes encoding transposases and DNA modification enzymes. The sequence also reveals the presence of genes encoding putative proteins that collectively define almost all characteristics of cyanobacteria as a group. N. punctiforme has an extensive potential to sense and respond to environmental signals as reflected by the presence of more than 400 genes encoding sensor protein kinases, response regulators and other transcriptional factors. The signal transduction systems and any of the large number of unique genes may play essential roles in the cell differentiation and symbiotic interaction properties of N. punctiforme.

  7. The human genome project.

    PubMed Central

    Olson, M V

    1993-01-01

    The Human Genome Project in the United States is now well underway. Its programmatic direction was largely set by a National Research Council report issued in 1988. The broad framework supplied by this report has survived almost unchanged despite an upheaval in the technology of genome analysis. This upheaval has primarily affected physical and genetic mapping, the two dominant activities in the present phase of the project. Advances in mapping techniques have allowed good progress toward the specific goals of the project and are also providing strong corollary benefits throughout biomedical research. Actual DNA sequencing of the genomes of the human and model organisms is still at an early stage. There has been little progress in the intrinsic efficiency of DNA-sequence determination. However, refinements in experimental protocols, instrumentation, and project management have made it practical to acquire sequence data on an enlarged scale. It is also increasingly apparent that DNA-sequence data provide a potent means of relating knowledge gained from the study of model organisms to human biology. There is as yet little indication that the infusion of technology from outside biology into the Human Genome Project has been effectively stimulated. Opportunities in this area remain large, posing substantial technical and policy challenges. PMID:8506271

  8. Genetics, genomics and fertility

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In order to enhance the sustainability of dairy businesses, new management tools are needed to increase the fertility of dairy cattle. Genomic selection has been successfully used by AI studs to screen potential sires and significantly decrease the generation interval of bulls. Buoyed by the success...

  9. Dairy genomics in application

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Implementation of genomic evaluation has caused profound changes in dairy cattle breeding. All young bulls bought by major artificial-insemination organizations now are selected based on these evaluation. Evaluation reliability can reach ~75% for yield traits, which is adequate for marketing semen o...

  10. Genomic selection in plant breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genomic selection (GS) is a method to predict the genetic value of selection candidates based on the genomic estimated breeding value (GEBV) predicted from high-density markers positioned throughout the genome. Unlike marker-assisted selection, the GEBV is based on all markers including both minor ...

  11. Plant functional genomics

    NASA Astrophysics Data System (ADS)

    Holtorf, Hauke; Guitton, Marie-Christine; Reski, Ralf

    2002-04-01

    Functional genome analysis of plants has entered the high-throughput stage. The complete genome information from key species such as Arabidopsis thaliana and rice is now available and will further boost the application of a range of new technologies to functional plant gene analysis. To broadly assign functions to unknown genes, different fast and multiparallel approaches are currently used and developed. These new technologies are based on known methods but are adapted and improved to accommodate for comprehensive, large-scale gene analysis, i.e. such techniques are novel in the sense that their design allows researchers to analyse many genes at the same time and at an unprecedented pace. Such methods allow analysis of the different constituents of the cell that help to deduce gene function, namely the transcripts, proteins and metabolites. Similarly the phenotypic variations of entire mutant collections can now be analysed in a much faster and more efficient way than before. The different methodologies have developed to form their own fields within the functional genomics technological platform and are termed transcriptomics, proteomics, metabolomics and phenomics. Gene function, however, cannot solely be inferred by using only one such approach. Rather, it is only by bringing together all the information collected by different functional genomic tools that one will be able to unequivocally assign functions to unknown plant genes. This review focuses on current technical developments and their impact on the field of plant functional genomics. The lower plant Physcomitrella is introduced as a new model system for gene function analysis, owing to its high rate of homologous recombination.

  12. Thinking laterally about genomes.

    PubMed

    Ragan, Mark A

    2009-10-01

    Perhaps the most-surprising discovery of the genome era has been the extent to which prokaryotic and many eukaryotic genomes incorporate genetic material from sources other than their parent(s). Lateral genetic transfer (LGT) among bacteria was first observed about 100 years ago, and is now accepted to underlie important phenomena including the spread of antibiotic resistance and ability to degrade xenobiotics. LGT is invoked, perhaps too readily, to explain a breadth of awkward data including compositional heterogeneity of genomes, disagreement among gene-sequence trees, and mismatch between physiology and systematics. At the same time many details of LGT remain unknown or controversial, and some key questions have scarcely been asked. Here I critically review what we think we know about the existence, extent, mechanism and impact of LGT; identify important open questions; and point to research directions that hold particular promise for elucidating the role of LGT in genome evolution. Evidence for LGT in nature is not only inferential but also direct, and potential vectors are ubiquitous. Genetic material can pass between diverse habitats and be significantly altered during residency in viruses, complicating the inference of donors, In prokaryotes about twice as many genes are interrupted by LGT as are transferred intact, and about 5Short protein domains can be privileged units of transfer. Unresolved phylogenetic issues include the correct null hypothesis, and genes as units of analysis. Themes are beginning to emerge regarding the effect of LGT on cellular networks, but I show why generalization is premature. LGT can associate with radical changes in physiology and ecological niche. Better quantitative models of genome evolution are needed, and theoretical frameworks remain to be developed for some observations including chromosome assembly by LGT. PMID:20180279

  13. TUTORIAL ON NETWORK GENOMICS.

    SciTech Connect

    Forst, C.

    2001-01-01

    With the ever-increasing genomic information pouring into the databases researchers start to look for pattern in genomes. Key questions are the identification of function. In the past function was mainly understood to be assigned to a single gene isolated from other cellular components or mechanisms. Sequence comparison fo single genes and their products (proteins) as well as of intergenic space are a consequence of a well established one-gene one-function interpretation. prediction of function solely by sequence similarity searches are powerful techniques that initiated the advent of bioinformatics and computational biology. Seminal work on sequence alignment by Temple Smith and Michael Waterman [33] and sequence searches with the BLAST algorithm by Altschul et al. [2] provide essential methods for sequence based determination of function. Similar outstanding contributions to determination of function have been archived in the area of structure prediction, molecular modeling and molecular dynamics. Techniques covering ab initio and homology modeling up to biophysical interpretation of long-run molecular dynamics simulations are mentioned ehre. With the ever-increasing number of information of different genetic/genomic origin, new aspect are looked for that deviate from the single gene at a time method. Especially with the identification of surprisingly few human genes the emerging perception in the scientific community that the concept of function has to be extended to include other sequence based as well as non-sequenced based information. A schema of determination of function by different concepts is shown in Figure 1. The tutorial is comprised of the following sections: The first two sections discuss the differences between genomic and non-genomic based context information, section three will cover combined methods. Finally, section four lsits web-resources and databases. All presented approaches extensively employ comparative methods.

  14. Genome size evolution in macroparasites.

    PubMed

    Sundberg, Lotta-Riina; Pulkkinen, Katja

    2015-04-01

    Reduction in genome size has been associated not only with a parasitic lifestyle in intracellular microparasites but also in some macroparasitic insects and nematodes. We collected the available data on genome size for flatworms, annelids, nematodes and arthropods, compared those with available data for the phylogenetically closest free-living taxa and found evidence of smaller genome sizes for parasites in six of nine comparisons. Our results suggest that despite great differences in evolutionary history and life cycles, parasitism as a lifestyle promotes convergent genome size reduction in macroparasites. We discuss factors that could be associated with small genome size in parasites which require further exploration in the future. PMID:25724591

  15. Professional medical education and genomics.

    PubMed

    Demmer, Laurie A; Waggoner, Darrel J

    2014-01-01

    Genomic medicine is a relatively new concept that involves using individual patients' genomic results in their clinical care. Genetic technology has advanced swiftly over the past decade, and most providers have been left behind without an understanding of this complex field. To realize its full potential, genomic medicine must be both understood and accepted by the greater medical community. The current state of professional medical education in genomics and genomic medicine is reviewed, including ongoing plans to expand educational efforts for medical students, clinical geneticists, and nongeneticist physicians. PMID:24635717

  16. Evolution of plant genome architecture.

    PubMed

    Wendel, Jonathan F; Jackson, Scott A; Meyers, Blake C; Wing, Rod A

    2016-01-01

    We have witnessed an explosion in our understanding of the evolution and structure of plant genomes in recent years. Here, we highlight three important emergent realizations: (1) that the evolutionary history of all plant genomes contains multiple, cyclical episodes of whole-genome doubling that were followed by myriad fractionation processes; (2) that the vast majority of the variation in genome size reflects the dynamics of proliferation and loss of lineage-specific transposable elements; and (3) that various classes of small RNAs help shape genomic architecture and function. We illustrate ways in which understanding these organism-level and molecular genetic processes can be used for crop plant improvement. PMID:26926526

  17. Rice: The First Crop Genome.

    PubMed

    Jackson, Scott A

    2016-12-01

    Rice was the first sequenced crop genome, paving the way for the sequencing of additional and more complicated crop genomes. The impact that the genome sequence made on rice genetics and breeding research was immediate, as evidence by citations and DNA marker use. The impact on other crop genomes was evident too, particularly for those within the grass family. As we celebrate 10 years since the completion of the rice genome sequence, we look forward to new empowering tool sets that will further revolutionize research in rice genetics and breeding and result in varieties that will continue to feed a growing population. PMID:27003180

  18. Nongenetic functions of the genome.

    PubMed

    Bustin, Michael; Misteli, Tom

    2016-05-01

    The primary function of the genome is to store, propagate, and express the genetic information that gives rise to a cell's architectural and functional machinery. However, the genome is also a major structural component of the cell. Besides its genetic roles, the genome affects cellular functions by nongenetic means through its physical and structural properties, particularly by exerting mechanical forces and by serving as a scaffold for binding of cellular components. Major cellular processes affected by nongenetic functions of the genome include establishment of nuclear structure, signal transduction, mechanoresponses, cell migration, and vision in nocturnal animals. We discuss the concept, mechanisms, and implications of nongenetic functions of the genome. PMID:27151873

  19. Genome of Crocodilepox Virus

    PubMed Central

    Afonso, C. L.; Tulman, E. R.; Delhon, G.; Lu, Z.; Viljoen, G. J.; Wallace, D. B.; Kutish, G. F.; Rock, D. L.

    2006-01-01

    Here, we present the genome sequence, with analysis, of a poxvirus infecting Nile crocodiles (Crocodylus niloticus) (crocodilepox virus; CRV). The genome is 190,054 bp (62% G+C) and predicted to contain 173 genes encoding proteins of 53 to 1,941 amino acids. The central genomic region contains genes conserved and generally colinear with those of other chordopoxviruses (ChPVs). CRV is distinct, as the terminal 33-kbp (left) and 13-kbp (right) genomic regions are largely CRV specific, containing 48 unique genes which lack similarity to other poxvirus genes. Notably, CRV also contains 14 unique genes which disrupt ChPV gene colinearity within the central genomic region, including 7 genes encoding GyrB-like ATPase domains similar to those in cellular type IIA DNA topoisomerases, suggestive of novel ATP-dependent functions. The presence of 10 CRV proteins with similarity to components of cellular multisubunit E3 ubiquitin-protein ligase complexes, including 9 proteins containing F-box motifs and F-box-associated regions and a homologue of cellular anaphase-promoting complex subunit 11 (Apc11), suggests that modification of host ubiquitination pathways may be significant for CRV-host cell interaction. CRV encodes a novel complement of proteins potentially involved in DNA replication, including a NAD+-dependent DNA ligase and a protein with similarity to both vaccinia virus F16L and prokaryotic serine site-specific resolvase-invertases. CRV lacks genes encoding proteins for nucleotide metabolism. CRV shares notable genomic similarities with molluscum contagiosum virus, including genes found only in these two viruses. Phylogenetic analysis indicates that CRV is quite distinct from other ChPVs, representing a new genus within the subfamily Chordopoxvirinae, and it lacks recognizable homologues of most ChPV genes involved in virulence and host range, including those involving interferon response, intracellular signaling, and host immune response modulation. These data reveal

  20. Genome of crocodilepox virus.

    PubMed

    Afonso, C L; Tulman, E R; Delhon, G; Lu, Z; Viljoen, G J; Wallace, D B; Kutish, G F; Rock, D L

    2006-05-01

    Here, we present the genome sequence, with analysis, of a poxvirus infecting Nile crocodiles (Crocodylus niloticus) (crocodilepox virus; CRV). The genome is 190,054 bp (62% G+C) and predicted to contain 173 genes encoding proteins of 53 to 1,941 amino acids. The central genomic region contains genes conserved and generally colinear with those of other chordopoxviruses (ChPVs). CRV is distinct, as the terminal 33-kbp (left) and 13-kbp (right) genomic regions are largely CRV specific, containing 48 unique genes which lack similarity to other poxvirus genes. Notably, CRV also contains 14 unique genes which disrupt ChPV gene colinearity within the central genomic region, including 7 genes encoding GyrB-like ATPase domains similar to those in cellular type IIA DNA topoisomerases, suggestive of novel ATP-dependent functions. The presence of 10 CRV proteins with similarity to components of cellular multisubunit E3 ubiquitin-protein ligase complexes, including 9 proteins containing F-box motifs and F-box-associated regions and a homologue of cellular anaphase-promoting complex subunit 11 (Apc11), suggests that modification of host ubiquitination pathways may be significant for CRV-host cell interaction. CRV encodes a novel complement of proteins potentially involved in DNA replication, including a NAD(+)-dependent DNA ligase and a protein with similarity to both vaccinia virus F16L and prokaryotic serine site-specific resolvase-invertases. CRV lacks genes encoding proteins for nucleotide metabolism. CRV shares notable genomic similarities with molluscum contagiosum virus, including genes found only in these two viruses. Phylogenetic analysis indicates that CRV is quite distinct from other ChPVs, representing a new genus within the subfamily Chordopoxvirinae, and it lacks recognizable homologues of most ChPV genes involved in virulence and host range, including those involving interferon response, intracellular signaling, and host immune response modulation. These data

  1. Evolution of small prokaryotic genomes

    PubMed Central

    Martínez-Cano, David J.; Reyes-Prieto, Mariana; Martínez-Romero, Esperanza; Partida-Martínez, Laila P.; Latorre, Amparo; Moya, Andrés; Delaye, Luis

    2015-01-01

    As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ∼800 genes as well as endosymbiotic bacteria with as few as ∼140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent role. However, new experimental data suggest that selective processes may be at operation as well for endosymbiotic prokaryotes at least during the first stages of genome reduction. Endosymbiotic prokaryotes have evolved diverse strategies for living with reduced gene sets inside a host-defined medium. These include utilization of host-encoded functions (some of them coded by genes acquired by gene transfer from the endosymbiont and/or other bacteria); metabolic complementation between co-symbionts; and forming consortiums with other bacteria within the host. Recent genome sequencing projects of intracellular mutualistic bacteria showed that previously believed universal evolutionary trends like reduced G+C content and conservation of genome synteny are not always present in highly reduced genomes. Finally, the simplified molecular machinery of some of these organisms with small genomes may be used to aid in the design of artificial minimal cells. Here we review recent genomic discoveries of the biology of prokaryotes endowed with small gene sets and discuss the evolutionary mechanisms that have been proposed to explain their peculiar nature. PMID:25610432

  2. Advances in plant chromosome genomics.

    PubMed

    Doležel, Jaroslav; Vrána, Jan; Cápal, Petr; Kubaláková, Marie; Burešová, Veronika; Simková, Hana

    2014-01-01

    Next generation sequencing (NGS) is revolutionizing genomics and is providing novel insights into genome organization, evolution and function. The number of plant genomes targeted for sequencing is rising. For the moment, however, the acquisition of full genome sequences in large genome species remains difficult, largely because the short reads produced by NGS platforms are inadequate to cope with repeat-rich DNA, which forms a large part of these genomes. The problem of sequence redundancy is compounded in polyploids, which dominate the plant kingdom. An approach to overcoming some of these difficulties is to reduce the full nuclear genome to its individual chromosomes using flow-sorting. The DNA acquired in this way has proven to be suitable for many applications, including PCR-based physical mapping, in situ hybridization, forming DNA arrays, the development of DNA markers, the construction of BAC libraries and positional cloning. Coupling chromosome sorting with NGS offers opportunities for the study of genome organization at the single chromosomal level, for comparative analyses between related species and for the validation of whole genome assemblies. Apart from the primary aim of reducing the complexity of the template, taking a chromosome-based approach enables independent teams to work in parallel, each tasked with the analysis of a different chromosome(s). Given that the number of plant species tractable for chromosome sorting is increasing, the likelihood is that chromosome genomics - the marriage of cytology and genomics - will make a significant contribution to the field of plant genetics. PMID:24406816

  3. Informational laws of genome structures

    PubMed Central

    Bonnici, Vincenzo; Manca, Vincenzo

    2016-01-01

    In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value of k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n is the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balances entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined. PMID:27354155

  4. Informational laws of genome structures.

    PubMed

    Bonnici, Vincenzo; Manca, Vincenzo

    2016-01-01

    In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value of k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n is the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balances entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined. PMID:27354155

  5. Informational laws of genome structures

    NASA Astrophysics Data System (ADS)

    Bonnici, Vincenzo; Manca, Vincenzo

    2016-06-01

    In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value of k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n is the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balances entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined.

  6. Dothideomycete–Plant Interactions Illuminated by Genome Sequencing and EST Analysis of the Wheat Pathogen Stagonospora nodorum[W][OA

    PubMed Central

    Hane, James K.; Lowe, Rohan G.T.; Solomon, Peter S.; Tan, Kar-Chun; Schoch, Conrad L.; Spatafora, Joseph W.; Crous, Pedro W.; Kodira, Chinappa; Birren, Bruce W.; Galagan, James E.; Torriani, Stefano F.F.; McDonald, Bruce A.; Oliver, Richard P.

    2007-01-01

    Stagonospora nodorum is a major necrotrophic fungal pathogen of wheat (Triticum aestivum) and a member of the Dothideomycetes, a large fungal taxon that includes many important plant pathogens affecting all major crop plant families. Here, we report the acquisition and initial analysis of a draft genome sequence for this fungus. The assembly comprises 37,164,227 bp of nuclear DNA contained in 107 scaffolds. The circular mitochondrial genome comprises 49,761 bp encoding 46 genes, including four that are intron encoded. The nuclear genome assembly contains 26 classes of repetitive DNA, comprising 4.5% of the genome. Some of the repeats show evidence of repeat-induced point mutations consistent with a frequent sexual cycle. ESTs and gene prediction models support a minimum of 10,762 nuclear genes. Extensive orthology was found between the polyketide synthase family in S. nodorum and Cochliobolus heterostrophus, suggesting an ancient origin and conserved functions for these genes. A striking feature of the gene catalog was the large number of genes predicted to encode secreted proteins; the majority has no meaningful similarity to any other known genes. It is likely that genes for host-specific toxins, in addition to ToxA, will be found among this group. ESTs obtained from axenic mycelium grown on oleate (chosen to mimic early infection) and late-stage lesions sporulating on wheat leaves were obtained. Statistical analysis shows that transcripts encoding proteins involved in protein synthesis and in the production of extracellular proteases, cellulases, and xylanases predominate in the infection library. This suggests that the fungus is dependant on the degradation of wheat macromolecular constituents to provide the carbon skeletons and energy for the synthesis of proteins and other components destined for the developing pycnidiospores. PMID:18024570

  7. Comparative genomics of Brassicaceae crops

    PubMed Central

    Sharma, Ashutosh; Li, Xiaonan; Lim, Yong Pyo

    2014-01-01

    The family Brassicaceae is one of the major groups of the plant kingdom and comprises diverse species of great economic, agronomic and scientific importance, including the model plant Arabidopsis. The sequencing of the Arabidopsis genome has revolutionized our knowledge in the field of plant biology and provides a foundation in genomics and comparative biology. Genomic resources have been utilized in Brassica for diversity analyses, construction of genetic maps and identification of agronomic traits. In Brassicaceae, comparative sequence analysis across the species has been utilized to understand genome structure, evolution and the detection of conserved genomic segments. In this review, we focus on the progress made in genetic resource development, genome sequencing and comparative mapping in Brassica and related species. The utilization of genomic resources and next-generation sequencing approaches in improvement of Brassica crops is also discussed. PMID:24987286

  8. Toward genome-enabled mycology.

    PubMed

    Hibbett, David S; Stajich, Jason E; Spatafora, Joseph W

    2013-01-01

    Genome-enabled mycology is a rapidly expanding field that is characterized by the pervasive use of genome-scale data and associated computational tools in all aspects of fungal biology. Genome-enabled mycology is integrative and often requires teams of researchers with diverse skills in organismal mycology, bioinformatics and molecular biology. This issue of Mycologia presents the first complete fungal genomes in the history of the journal, reflecting the ongoing transformation of mycology into a genome-enabled science. Here, we consider the prospects for genome-enabled mycology and the technical and social challenges that will need to be overcome to grow the database of complete fungal genomes and enable all fungal biologists to make use of the new data. PMID:23928422

  9. Comparative genomics of Brassicaceae crops.

    PubMed

    Sharma, Ashutosh; Li, Xiaonan; Lim, Yong Pyo

    2014-05-01

    The family Brassicaceae is one of the major groups of the plant kingdom and comprises diverse species of great economic, agronomic and scientific importance, including the model plant Arabidopsis. The sequencing of the Arabidopsis genome has revolutionized our knowledge in the field of plant biology and provides a foundation in genomics and comparative biology. Genomic resources have been utilized in Brassica for diversity analyses, construction of genetic maps and identification of agronomic traits. In Brassicaceae, comparative sequence analysis across the species has been utilized to understand genome structure, evolution and the detection of conserved genomic segments. In this review, we focus on the progress made in genetic resource development, genome sequencing and comparative mapping in Brassica and related species. The utilization of genomic resources and next-generation sequencing approaches in improvement of Brassica crops is also discussed. PMID:24987286

  10. eGenomics: Cataloguing Our Complete Genome Collection III

    PubMed Central

    Field, Dawn; Garrity, George; Gray, Tanya; Selengut, Jeremy; Sterk, Peter; Thomson, Nick; Tatusova, Tatiana; Cochrane, Guy; Glöckner, Frank Oliver; Kottmann, Renzo; Lister, Allyson L.; Tateno, Yoshio; Vaughan, Robert

    2007-01-01

    This meeting report summarizes the proceedings of the “eGenomics: Cataloguing our Complete Genome Collection III” workshop held September 11–13, 2006, at the National Institute for Environmental eScience (NIEeS), Cambridge, United Kingdom. This 3rd workshop of the Genomic Standards Consortium was divided into two parts. The first half of the three-day workshop was dedicated to reviewing the genomic diversity of our current and future genome and metagenome collection, and exploring linkages to a series of existing projects through formal presentations. The second half was dedicated to strategic discussions. Outcomes of the workshop include a revised “Minimum Information about a Genome Sequence” (MIGS) specification (v1.1), consensus on a variety of features to be added to the Genome Catalogue (GCat), agreement by several researchers to adopt MIGS for imminent genome publications, and an agreement by the EBI and NCBI to input their genome collections into GCat for the purpose of quantifying the amount of optional data already available (e.g., for geographic location coordinates) and working towards a single, global list of all public genomes and metagenomes.

  11. Genome-Wide Comparative Analysis of Flowering-Related Genes in Arabidopsis, Wheat, and Barley

    PubMed Central

    Peng, Fred Y.; Hu, Zhiqiu; Yang, Rong-Cai

    2015-01-01

    Early flowering is an important trait influencing grain yield and quality in wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) in short-season cropping regions. However, due to large and complex genomes of these species, direct identification of flowering genes and their molecular characterization remain challenging. Here, we used a bioinformatic approach to predict flowering-related genes in wheat and barley from 190 known Arabidopsis (Arabidopsis thaliana (L.) Heynh.) flowering genes. We identified 900 and 275 putative orthologs in wheat and barley, respectively. The annotated flowering-related genes were clustered into 144 orthologous groups with one-to-one, one-to-many, many-to-one, and many-to-many orthology relationships. Our approach was further validated by domain and phylogenetic analyses of flowering-related proteins and comparative analysis of publicly available microarray data sets for in silico expression profiling of flowering-related genes in 13 different developmental stages of wheat and barley. These further analyses showed that orthologous gene pairs in three critical flowering gene families (PEBP, MADS, and BBX) exhibited similar expression patterns among 13 developmental stages in wheat and barley, suggesting similar functions among the orthologous genes with sequence and expression similarities. The predicted candidate flowering genes can be confirmed and incorporated into molecular breeding for early flowering wheat and barley in short-season cropping regions. PMID:26435710

  12. Genomic regions associated with the nitrogen limitation response revealed in a global wheat core collection.

    PubMed

    Bordes, Jacques; Ravel, C; Jaubertie, J P; Duperrier, B; Gardet, O; Heumez, E; Pissavy, A L; Charmet, G; Le Gouis, J; Balfourier, F

    2013-03-01

    Modern wheat (Triticum aestivum L.) varieties in Western Europe have mainly been bred, and selected in conditions where high levels of nitrogen-rich fertilizer are applied. However, high input crop management has greatly increased the risk of nitrates leaching into groundwater with negative impacts on the environment. To investigate wheat nitrogen tolerance characteristics that could be adapted to low input crop management, we supplied 196 accessions of a wheat core collection of old and modern cultivars with high or moderate amounts of nitrogen fertilizer in an experimental network consisting of three sites and 2 years. The main breeding traits were assessed including grain yield and grain protein content. The response to nitrogen level was estimated for grain yield and grain number per m(2) using both the difference and the ratio between performance at the two input levels and the slope of joint regression. A large variability was observed for all the traits studied and the response to nitrogen level. Whole genome association mapping was carried out using 899 molecular markers taking into account the five ancestral group structure of the collection. We identified 54 main regions involving almost all chromosomes that influence yield and its components, plant height, heading date and grain protein concentration. Twenty-three regions, including several genes, spread over 16 chromosomes were involved in the response to nitrogen level. These chromosomal regions may be good candidates to be used in breeding programs to improve the performance of wheat varieties at moderate nitrogen input levels. PMID:23192671

  13. Genome-Wide Comparative Analysis of Flowering-Related Genes in Arabidopsis, Wheat, and Barley.

    PubMed

    Peng, Fred Y; Hu, Zhiqiu; Yang, Rong-Cai

    2015-01-01

    Early flowering is an important trait influencing grain yield and quality in wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) in short-season cropping regions. However, due to large and complex genomes of these species, direct identification of flowering genes and their molecular characterization remain challenging. Here, we used a bioinformatic approach to predict flowering-related genes in wheat and barley from 190 known Arabidopsis (Arabidopsis thaliana (L.) Heynh.) flowering genes. We identified 900 and 275 putative orthologs in wheat and barley, respectively. The annotated flowering-related genes were clustered into 144 orthologous groups with one-to-one, one-to-many, many-to-one, and many-to-many orthology relationships. Our approach was further validated by domain and phylogenetic analyses of flowering-related proteins and comparative analysis of publicly available microarray data sets for in silico expression profiling of flowering-related genes in 13 different developmental stages of wheat and barley. These further analyses showed that orthologous gene pairs in three critical flowering gene families (PEBP, MADS, and BBX) exhibited similar expression patterns among 13 developmental stages in wheat and barley, suggesting similar functions among the orthologous genes with sequence and expression similarities. The predicted candidate flowering genes can be confirmed and incorporated into molecular breeding for early flowering wheat and barley in short-season cropping regions. PMID:26435710

  14. The Genomic Standards Consortium

    PubMed Central

    Field, Dawn; Amaral-Zettler, Linda; Cochrane, Guy; Cole, James R.; Dawyndt, Peter; Garrity, George M.; Gilbert, Jack; Glöckner, Frank Oliver; Hirschman, Lynette; Karsch-Mizrachi, Ilene; Klenk, Hans-Peter; Knight, Rob; Kottmann, Renzo; Kyrpides, Nikos; Meyer, Folker; San Gil, Inigo; Sansone, Susanna-Assunta; Schriml, Lynn M.; Sterk, Peter; Tatusova, Tatiana; Ussery, David W.; White, Owen; Wooley, John

    2011-01-01

    A vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise its usefulness has become a major effort across the 'omics world. At the heart of this effort is the Genomic Standards Consortium (GSC), an open-membership organization that drives community-based standardization activities, Here we provide a short history of the GSC, provide an overview of its range of current activities, and make a call for the scientific community to join forces to improve the quality and quantity of contextual information about our public collections of genomes, metagenomes, and marker gene sequences. PMID:21713030

  15. The dog genome.

    PubMed

    Galibert, F; André, C

    2006-01-01

    Over the last few centuries, several hundred dog breeds have been artificially selected through intense breeding, resulting in the modern dog population having the widest polymorphism spectrum in terms of body shape, behavior and aptitude among mammals. Unfortunately, this diversification has predisposed most breeds to specific diseases of genetic origin. The highly fragmented nature of the dog population offers a great opportunity to track the genes and alleles responsible for these diseases as well as for the various phenotypic traits. This has led to a thorough analysis of the dog genome. Here, we report the main results obtained during the last ten years, culminating in the recent publication of a complete dog genome sequence. PMID:18753768

  16. Big cat genomics.

    PubMed

    O'Brien, Stephen J; Johnson, Warren E

    2005-01-01

    Advances in population and quantitative genomics, aided by the computational algorithms that employ genetic theory and practice, are now being applied to biological questions that surround free-ranging species not traditionally suitable for genetic enquiry. Here we review how applications of molecular genetic tools have been used to describe the natural history, present status, and future disposition of wild cat species. Insight into phylogenetic hierarchy, demographic contractions, geographic population substructure, behavioral ecology, and infectious diseases have revealed strategies for survival and adaptation of these fascinating predators. Conservation, stabilization, and management of the big cats are important areas that derive benefit from the genome resources expanded and applied to highly successful species, imperiled by an expanding human population. PMID:16124868

  17. Whole-genome profiling and shotgun sequencing delivers an anchored, gene-decorated, physical map assembly of bread wheat chromosome 6A.

    PubMed

    Poursarebani, Naser; Nussbaumer, Thomas; Simková, Hana; Safář, Jan; Witsenboer, Hanneke; van Oeveren, Jan; Doležel, Jaroslav; Mayer, Klaus F X; Stein, Nils; Schnurbusch, Thorsten

    2014-07-01

    Bread wheat (Triticum aestivum L.) is the most important staple food crop for 35% of the world's population. International efforts are underway to facilitate an increase in wheat production, of which the International Wheat Genome Sequencing Consortium (IWGSC) plays an important role. As part of this effort, we have developed a sequence-based physical map of wheat chromosome 6A using whole-genome profiling (WGP™). The bacterial artificial chromosome (BAC) contig assembly tools fingerprinted contig (fpc) and linear topological contig (ltc) were used and their contig assemblies were compared. A detailed investigation of the contigs structure revealed that ltc created a highly robust assembly compared with those formed by fpc. The ltc assemblies contained 1217 contigs for the short arm and 1113 contigs for the long arm, with an L50 of 1 Mb. To facilitate in silico anchoring, WGP™ tags underlying BAC contigs were extended by wheat and wheat progenitor genome sequence information. Sequence data were used for in silico anchoring against genetic markers with known sequences, of which almost 79% of the physical map could be anchored. Moreover, the assigned sequence information led to the 'decoration' of the respective physical map with 3359 anchored genes. Thus, this robust and genetically anchored physical map will serve as a framework for the sequencing of wheat chromosome 6A, and is of immediate use for map-based isolation of agronomically important genes/quantitative trait loci located on this chromosome. PMID:24813060

  18. Mapping the human genome

    SciTech Connect

    Annas, G.C.; Elias, S.

    1992-01-01

    This article is a review of the book Mapping the Human Genome: Using Law and Ethics as Guides, edited by George C. Annas and Sherman Elias. The book is a collection of essays on the subject of using ethics and laws as guides to justify human gene mapping. It addresses specific issues such problems related to eugenics, patents, insurance as well as broad issues such as the societal definitions of normality.

  19. Genomic landscape of liposarcoma

    PubMed Central

    Kanojia, Deepika; Nagata, Yasunobu; Garg, Manoj; Lee, Dhong Hyun; Sato, Aiko; Yoshida, Kenichi; Sato, Yusuke; Sanada, Masashi; Mayakonda, Anand; Bartenhagen, Christoph; Klein, Hans-Ulrich; Doan, Ngan B.; Said, Jonathan W.; Mohith, S.; Gunasekar, Swetha; Shiraishi, Yuichi; Chiba, Kenichi; Tanaka, Hiroko; Miyano, Satoru; Myklebost, Ola; Yang, Henry; Dugas, Martin; Meza-Zepeda, Leonardo A.; Silberman, Allan W.; Forscher, Charles; Tyner, Jeffrey W.; Ogawa, Seishi; Koeffler, H. Phillip

    2015-01-01

    Liposarcoma (LPS) is the most common type of soft tissue sarcoma accounting for 20% of all adult sarcomas. Due to absence of clinically effective treatment options in inoperable situations and resistance to chemotherapeutics, a critical need exists to identify novel therapeutic targets. We analyzed LPS genomic landscape using SNP arrays, whole exome sequencing and targeted exome sequencing to uncover the genomic information for development of specific anti-cancer targets. SNP array analysis indicated known amplified genes (MDM2, CDK4, HMGA2) and important novel genes (UAP1, MIR557, LAMA4, CPM, IGF2, ERBB3, IGF1R). Carboxypeptidase M (CPM), recurrently amplified gene in well-differentiated/de-differentiated LPS was noted as a putative oncogene involved in the EGFR pathway. Notable deletions were found at chromosome 1p (RUNX3, ARID1A), chromosome 11q (ATM, CHEK1) and chromosome 13q14.2 (MIR15A, MIR16-1). Significantly and recurrently mutated genes (false discovery rate < 0.05) included PLEC (27%), MXRA5 (21%), FAT3 (24%), NF1 (20%), MDC1 (10%), TP53 (7%) and CHEK2 (6%). Further, in vitro and in vivo functional studies provided evidence for the tumor suppressor role for Neurofibromin 1 (NF1) gene in different subtypes of LPS. Pathway analysis of recurrent mutations demonstrated signaling through MAPK, JAK-STAT, Wnt, ErbB, axon guidance, apoptosis, DNA damage repair and cell cycle pathways were involved in liposarcomagenesis. Interestingly, we also found mutational and copy number heterogeneity within a primary LPS tumor signifying the importance of multi-region sequencing for cancer-genome guided therapy. In summary, these findings provide insight into the genomic complexity of LPS and highlight potential druggable pathways for targeted therapeutic approach. PMID:26643872

  20. Bioinformatics and genomic medicine.

    PubMed

    Kim, Ju Han

    2002-01-01

    Bioinformatics is a rapidly emerging field of biomedical research. A flood of large-scale genomic and postgenomic data means that many of the challenges in biomedical research are now challenges in computational science. Clinical informatics has long developed methodologies to improve biomedical research and clinical care by integrating experimental and clinical information systems. The informatics revolution in both bioinformatics and clinical informatics will eventually change the current practice of medicine, including diagnostics, therapeutics, and prognostics. Postgenome informatics, powered by high-throughput technologies and genomic-scale databases, is likely to transform our biomedical understanding forever, in much the same way that biochemistry did a generation ago. This paper describes how these technologies will impact biomedical research and clinical care, emphasizing recent advances in biochip-based functional genomics and proteomics. Basic data preprocessing with normalization and filtering, primary pattern analysis, and machine-learning algorithms are discussed. Use of integrative biochip informatics technologies, including multivariate data projection, gene-metabolic pathway mapping, automated biomolecular annotation, text mining of factual and literature databases, and the integrated management of biomolecular databases, are also discussed. PMID:12544491