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Sample records for aestivum genomes aabbdd

  1. 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...

  2. 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...

  3. 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...

  4. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome.

    PubMed

    2014-07-18

    An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.

  5. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome.

    PubMed

    2014-07-18

    An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide. PMID:25035500

  6. 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...

  7. [Comparative Characteristic of Triticum aestivum/Triticum durum and Triticum aestivum/Triticum dicoccum hybrid lines by genomic composition and resistance to fungal diseases under different environmental conditions].

    PubMed

    Leonova, I N; Badaeva, E D; Orlovskaya, O A; Roder, M S; Khotyleva, L V; Salina, E A; Shumny, V K

    2013-11-01

    The genetic diversity of common wheat hybrid lines Triticum aestivum/Triticum durum and Triticum aestivum/Triticum dicoccum (2n = 42, F(6-7)) using chromosome-specific microsatellite (SSR) markers and C-staining of chromosomes was studied. Cluster analysis of data obtained by 42 SSR markers indicated that the hybrid lines can be broken into three groups according to their origin. There were two cases of complete genetic similarity between lines 183(2)-2/184(1)-6 and-208-3/213-1, which were obtained using common wheat as the parental plants. In cross combinations, when the stabilization of the nuclear genome of hexaploid lines occurred against a background of the cytoplasmic genome of tetraploid wheats, there was a high level of divergence between sister lines, in some cases exceeding 50%. The evaluation of the degree of susceptibility of the lines to powdery mildew, leaf and stem rust, and septoria leafblotch was performed under different environmental conditions. It was shown that resistance to powdery mildew and leaf rust significantly depended on the region where assays were conducted. An evaluation of the field data showed that he lines 195-3, 196-1, and 221-1 with T. durum genetic material displayed complex resistance to fungal pathogens in Western Siberia and the Republic of Belarus. For lines 195-3 and 196-1, one shows a possible contribution of chromosomes 4B and 5B in the formation of complex resistance to diseases. Hybrid lines with complex resistance can be used to expand the genetic diversity of modern common wheat cultivars for genes of immunity.

  8. 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.

  9. Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.)

    PubMed Central

    2010-01-01

    Background Single nucleotide polymorphisms (SNPs) are ideally suited for the construction of high-resolution genetic maps, studying population evolutionary history and performing genome-wide association mapping experiments. Here, we used a genome-wide set of 1536 SNPs to study linkage disequilibrium (LD) and population structure in a panel of 478 spring and winter wheat cultivars (Triticum aestivum) from 17 populations across the United States and Mexico. Results Most of the wheat oligo pool assay (OPA) SNPs that were polymorphic within the complete set of 478 cultivars were also polymorphic in all subpopulations. Higher levels of genetic differentiation were observed among wheat lines within populations than among populations. A total of nine genetically distinct clusters were identified, suggesting that some of the pre-defined populations shared significant proportion of genetic ancestry. Estimates of population structure (FST) at individual loci showed a high level of heterogeneity across the genome. In addition, seven genomic regions with elevated FST were detected between the spring and winter wheat populations. Some of these regions overlapped with previously mapped flowering time QTL. Across all populations, the highest extent of significant LD was observed in the wheat D-genome, followed by lower LD in the A- and B-genomes. The differences in the extent of LD among populations and genomes were mostly driven by differences in long-range LD ( > 10 cM). Conclusions Genome- and population-specific patterns of genetic differentiation and LD were discovered in the populations of wheat cultivars from different geographic regions. Our study demonstrated that the estimates of population structure between spring and winter wheat lines can identify genomic regions harboring candidate genes involved in the regulation of growth habit. Variation in LD suggests that breeding and selection had a different impact on each wheat genome both within and among populations. The

  10. Sorting the Wheat from the Chaff: Identifying miRNAs in Genomic Survey Sequences of Triticum aestivum Chromosome 1AL

    PubMed Central

    Lucas, Stuart J.; Budak, Hikmet

    2012-01-01

    Individual chromosome-based studies of bread wheat are beginning to provide valuable structural and functional information about one of the world’s most important crops. As new genome sequences become available, identifying miRNA coding sequences is arguably as important a task as annotating protein coding sequences, but one that is not as well developed. We compared conservation-based identification of conserved miRNAs in 1.5× coverage survey sequences of wheat chromosome 1AL with a predictive method based on pre-miRNA hairpin structure alone. In total, 42 sequences expected to encode conserved miRNAs were identified on chromosome 1AL, including members of several miRNA families that have not previously been reported to be expressed in T. aestivum. In addition, we demonstrate that a number of sequences previously annotated as novel wheat miRNAs are closely related to transposable elements, particularly Miniature Inverted Terminal repeat Elements (MITEs). Some of these TE-miRNAs may well have a functional role, but separating true miRNA coding sequences from TEs in genomic sequences is far from straightforward. We propose a strategy for annotation to minimize the risk of mis-identifying TE sequences as miRNAs. PMID:22815845

  11. Genomic Dissection and Expression Profiling Revealed Functional Divergence in Triticum aestivum Leucine Rich Repeat Receptor Like Kinases (TaLRRKs)

    PubMed Central

    Shumayla; Sharma, Shailesh; Kumar, Rohit; Mendu, Venugopal; Singh, Kashmir; Upadhyay, Santosh K.

    2016-01-01

    The leucine rich repeat receptor like kinases (LRRK) constitute the largest subfamily of receptor like kinases (RLK), which play critical roles in plant development and stress responses. Herein, we identified 531 TaLRRK genes in Triticum aestivum (bread wheat), which were distributed throughout the A, B, and D sub-genomes and chromosomes. These were clustered into 233 homologous groups, which were mostly located on either homeologous chromosomes from various sub-genomes or in proximity on the same chromosome. A total of 255 paralogous genes were predicted which depicted the role of duplication events in expansion of this gene family. Majority of TaLRRKs consisted of trans-membrane region and localized on plasma-membrane. The TaLRRKs were further categorized into eight phylogenetic groups with numerous subgroups on the basis of sequence homology. The gene and protein structure in terms of exon/intron ratio, domains, and motifs organization were found to be variably conserved across the different phylogenetic groups/subgroups, which indicated a potential divergence and neofunctionalization during evolution. High-throughput transcriptome data and quantitative real time PCR analyses in various developmental stages, and biotic and abiotic (heat, drought, and salt) stresses provided insight into modus operandi of TaLRRKs during these conditions. Distinct expression of majority of stress responsive TaLRRKs homologous genes suggested their specified role in a particular condition. These results provided a comprehensive analysis of various characteristic features including functional divergence, which may provide the way for future functional characterization of this important gene family in bread wheat. PMID:27713749

  12. Whole genome association mapping of plant height in winter wheat (Triticum aestivum L.).

    PubMed

    Zanke, Christine D; Ling, Jie; Plieske, Jörg; Kollers, Sonja; Ebmeyer, Erhard; Korzun, Viktor; Argillier, Odile; Stiewe, Gunther; Hinze, Maike; Neumann, Kerstin; Ganal, Martin W; Röder, Marion S

    2014-01-01

    The genetic architecture of plant height was investigated in a set of 358 recent European winter wheat varieties plus 14 spring wheat varieties based on field data in eight environments. Genotyping of diagnostic markers revealed the Rht-D1b mutant allele in 58% of the investigated varieties, while the Rht-B1b mutant was only present in 7% of the varieties. Rht-D1 was significantly associated with plant height by using a mixed linear model and employing a kinship matrix to correct for population stratification. Further genotyping data included 732 microsatellite markers, resulting in 770 loci, of which 635 markers were placed on the ITMI map plus a set of 7769 mapped SNP markers genotyped with the 90 k iSELECT chip. When Bonferroni correction was applied, a total of 153 significant marker-trait associations (MTAs) were observed for plant height and the SSR markers (-log10 (P-value) ≥ 4.82) and 280 (-log10 (P-value) ≥ 5.89) for the SNPs. Linear regression between the most effective markers and the BLUEs for plant height indicated additive effects for the MTAs of different chromosomal regions. Analysis of syntenic regions in the rice genome revealed closely linked rice genes related to gibberellin acid (GA) metabolism and perception, i.e. GA20 and GA2 oxidases orthologous to wheat chromosomes 1A, 2A, 3A, 3B, 5B, 5D and 7B, ent-kaurenoic acid oxidase orthologous to wheat chromosome 7A, ent-kaurene synthase on wheat chromosome 2B, as well as GA-receptors like DELLA genes orthologous to wheat chromosomes 4B, 4D and 7A and genes of the GID family orthologous to chromosomes 2B and 5B. The data indicated that besides the widely used GA-insensitive dwarfing genes Rht-B1 and Rht-D1 there is a wide spectrum of loci available that could be used for modulating plant height in variety development.

  13. Whole genome association mapping of plant height in winter wheat (Triticum aestivum L.).

    PubMed

    Zanke, Christine D; Ling, Jie; Plieske, Jörg; Kollers, Sonja; Ebmeyer, Erhard; Korzun, Viktor; Argillier, Odile; Stiewe, Gunther; Hinze, Maike; Neumann, Kerstin; Ganal, Martin W; Röder, Marion S

    2014-01-01

    The genetic architecture of plant height was investigated in a set of 358 recent European winter wheat varieties plus 14 spring wheat varieties based on field data in eight environments. Genotyping of diagnostic markers revealed the Rht-D1b mutant allele in 58% of the investigated varieties, while the Rht-B1b mutant was only present in 7% of the varieties. Rht-D1 was significantly associated with plant height by using a mixed linear model and employing a kinship matrix to correct for population stratification. Further genotyping data included 732 microsatellite markers, resulting in 770 loci, of which 635 markers were placed on the ITMI map plus a set of 7769 mapped SNP markers genotyped with the 90 k iSELECT chip. When Bonferroni correction was applied, a total of 153 significant marker-trait associations (MTAs) were observed for plant height and the SSR markers (-log10 (P-value) ≥ 4.82) and 280 (-log10 (P-value) ≥ 5.89) for the SNPs. Linear regression between the most effective markers and the BLUEs for plant height indicated additive effects for the MTAs of different chromosomal regions. Analysis of syntenic regions in the rice genome revealed closely linked rice genes related to gibberellin acid (GA) metabolism and perception, i.e. GA20 and GA2 oxidases orthologous to wheat chromosomes 1A, 2A, 3A, 3B, 5B, 5D and 7B, ent-kaurenoic acid oxidase orthologous to wheat chromosome 7A, ent-kaurene synthase on wheat chromosome 2B, as well as GA-receptors like DELLA genes orthologous to wheat chromosomes 4B, 4D and 7A and genes of the GID family orthologous to chromosomes 2B and 5B. The data indicated that besides the widely used GA-insensitive dwarfing genes Rht-B1 and Rht-D1 there is a wide spectrum of loci available that could be used for modulating plant height in variety development. PMID:25405621

  14. New insights into the origin of the B genome of hexaploid wheat: Evolutionary relationships at the SPA genomic region with the S genome of the diploid relative Aegilops speltoides

    PubMed Central

    Salse, Jérome; Chagué, Véronique; Bolot, Stéphanie; Magdelenat, Ghislaine; Huneau, Cécile; Pont, Caroline; Belcram, Harry; Couloux, Arnaud; Gardais, Soazic; Evrard, Aurélie; Segurens, Béatrice; Charles, Mathieu; Ravel, Catherine; Samain, Sylvie; Charmet, Gilles; Boudet, Nathalie; Chalhoub, Boulos

    2008-01-01

    Background Several studies suggested that the diploid ancestor of the B genome of tetraploid and hexaploid wheat species belongs to the Sitopsis section, having Aegilops speltoides (SS, 2n = 14) as the closest identified relative. However molecular relationships based on genomic sequence comparison, including both coding and non-coding DNA, have never been investigated. In an attempt to clarify these relationships, we compared, in this study, sequences of the Storage Protein Activator (SPA) locus region of the S genome of Ae. speltoides (2n = 14) to that of the A, B and D genomes co-resident in the hexaploid wheat species (Triticum aestivum, AABBDD, 2n = 42). Results Four BAC clones, spanning the SPA locus of respectively the A, B, D and S genomes, were isolated and sequenced. Orthologous genomic regions were identified as delimited by shared non-transposable elements and non-coding sequences surrounding the SPA gene and correspond to 35 268, 22 739, 43 397 and 53 919 bp for the A, B, D and S genomes, respectively. Sequence length discrepancies within and outside the SPA orthologous regions are the result of non-shared transposable elements (TE) insertions, all of which inserted after the progenitors of the four genomes divergence. Conclusion On the basis of conserved sequence length as well as identity of the shared non-TE regions and the SPA coding sequence, Ae speltoides appears to be more evolutionary related to the B genome of T. aestivum than the A and D genomes. However, the differential insertions of TEs, none of which are conserved between the two genomes led to the conclusion that the S genome of Ae. speltoides has diverged very early from the progenitor of the B genome which remains to be identified. PMID:19032732

  15. 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

    2016-08-16

    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.

  16. 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

  17. 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

  18. Genome-wide quantitative trait locus mapping identifies multiple major loci for brittle rachis and threshability in Tibetan semi-wild wheat (Triticum aestivum ssp. tibetanum Shao).

    PubMed

    Jiang, Yun-Feng; Lan, Xiu-Jin; Luo, Wei; Kong, Xing-Chen; Qi, Peng-Fei; Wang, Ji-Rui; Wei, Yu-Ming; Jiang, Qian-Tao; Liu, Ya-Xi; Peng, Yuan-Ying; Chen, Guo-Yue; Dai, Shou-Fen; Zheng, You-Liang

    2014-01-01

    Tibetan semi-wild wheat (Triticum aestivum ssp. tibetanum Shao) is a semi-wild hexaploid wheat resource that is only naturally distributed in the Qinghai-Tibet Plateau. Brittle rachis and hard threshing are two important characters of Tibetan semi-wild wheat. A whole-genome linkage map of T. aestivum ssp. tibetanum was constructed using a recombinant inbred line population (Q1028×ZM9023) with 186 lines, 564 diversity array technology markers, and 117 simple sequence repeat markers. Phenotypic data on brittle rachis and threshability, as two quantitative traits, were evaluated on the basis of the number of average spike rachis fragments per spike and percent threshability in 2012 and 2013, respectively. Quantitative trait locus (QTL) mapping performed using inclusive composite interval mapping analysis clearly identified four QTLs for brittle rachis and three QTLs for threshability. However, three loci on 2DS, 2DL, and 5AL showed pleiotropism for brittle rachis and threshability; they respectively explained 5.3%, 18.6%, and 18.6% of phenotypic variation for brittle rachis and 17.4%, 13.2%, and 35.2% of phenotypic variation for threshability. A locus on 3DS showed an independent effect on brittle rachis, which explained 38.7% of the phenotypic variation. The loci on 2DS and 3DS probably represented the effect of Tg and Br1, respectively. The locus on 5AL was in very close proximity to the Q gene, but was different from the predicted q in Tibetan semi-wild wheat. To our knowledge, the locus on 2DL has never been reported in common wheat but was prominent in T. aestivum ssp. tibetanum accession Q1028. It remarkably interacted with the locus on 5AL to affect brittle rachis. Several major loci for brittle rachis and threshability were identified in Tibetan semi-wild wheat, improving the understanding of these two characters and suggesting the occurrence of special evolution in Tibetan semi-wild wheat.

  19. 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

  20. 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

  1. 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...

  2. 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...

  3. Identification of differentially expressed proteins between hybrid and parents in wheat (Triticum aestivum L.) seedling leaves.

    PubMed

    Song, Xiao; Ni, Zhongfu; Yao, Yingyin; Zhang, Yinhong; Sun, Qixin

    2009-01-01

    In spite of commercial use of heterosis in agriculture, the molecular basis of heterosis is poorly understood. To gain a better understanding of the molecular basis of wheat heterosis, we carried out a comparative proteomic analysis in seedling leaves between wheat hybrid and parents. Common wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) Line 3338 and spelt wheat (Triticum spelta L., 2n = 6x = 42, AABBDD) Line 2463 were used to produce a heterotic F(1) hybrid. The expression patterns of the total proteins were compared in seedling leaves between hybrid and its parents by using two-dimensional gel electrophoresis with two pH ranges for the first dimension separation. Among ~900 protein spots reproducibly detected, 49 protein spots were identified as being differentially expressed between hybrid and its parental lines (P < 0.05) for more than 1.5-folds. Six possible modes of differential expression were observed, including high- and low-parent dominance, underdominance, and overdominance, uniparent silencing and uniparent dominance. Moreover, 30 of the 49 differentially expressed protein spots were identified, which were involved in metabolism, signal transduction, energy, cell growth and division, disease and defense, secondary metabolism. These results indicated that wheat hybridization can cause protein expression differences between hybrid and its parents; these proteins were involved in diverse physiological process pathways, which might be responsible for the observed heterosis.

  4. 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

  5. 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...

  6. 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.

  7. 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...

  8. 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...

  9. 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

  10. 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

  11. Identification of three wheat globulin genes by screening a Triticum aestivum BAC genomic library with cDNA from a diabetes-associated globulin

    PubMed Central

    Loit, Evelin; Melnyk, Charles W; MacFarlane, Amanda J; Scott, Fraser W; Altosaar, Illimar

    2009-01-01

    Background Exposure to dietary wheat proteins in genetically susceptible individuals has been associated with increased risk for the development of Type 1 diabetes (T1D). Recently, a wheat protein encoded by cDNA WP5212 has been shown to be antigenic in mice, rats and humans with autoimmune T1D. To investigate the genomic origin of the identified wheat protein cDNA, a hexaploid wheat genomic library from Glenlea cultivar was screened. Results Three unique wheat globulin genes, Glo-3A, Glo3-B and Glo-3C, were identified. We describe the genomic structure of these genes and their expression pattern in wheat seeds. The Glo-3A gene shared 99% identity with the cDNA of WP5212 at the nucleotide and deduced amino acid level, indicating that we have identified the gene(s) encoding wheat protein WP5212. Southern analysis revealed the presence of multiple copies of Glo-3-like sequences in all wheat samples, including hexaploid, tetraploid and diploid species wheat seed. Aleurone and embryo tissue specificity of WP5212 gene expression, suggested by promoter region analysis, which demonstrated an absence of endosperm specific cis elements, was confirmed by immunofluorescence microscopy using anti-WP5212 antibodies. Conclusion Taken together, the results indicate that a diverse group of globulins exists in wheat, some of which could be associated with the pathogenesis of T1D in some susceptible individuals. These data expand our knowledge of specific wheat globulins and will enable further elucidation of their role in wheat biology and human health. PMID:19615078

  12. 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.

  13. 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

    2015-01-20

    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.

  14. 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

  15. 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

  16. 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...

  17. 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...

  18. [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

  19. Sequence and tissue-specific expression of a putative peroxidase gene from wheat (Triticum aestivum L.).

    PubMed

    Hertig, C; Rebmann, G; Bull, J; Mauch, F; Dudler, R

    1991-01-01

    We have used a cDNA clone encoding a pathogen-induced putative wheat peroxidase to screen a genomic library of wheat (Triticum aestivum L. cv. Cheyenne) and isolated one positive clone, lambda POX1. Sequence analysis revealed that this clone contains a gene encoding a putative peroxidase with a calculated pI of 8.1 which exhibits 58% and 83% sequence identity to the amino acid sequence of the turnip (Brassica rapa) peroxidase and a pathogen-induced putative wheat peroxidase, respectively. The two introns in the wheat gene are at the same positions as introns in the peroxidase genes of tomato and horseradish. Results of S1-mapping experiments suggest that this gene is neither pathogen- nor wound-induced in leaves but is constitutively expressed in roots.

  20. Sequence and tissue-specific expression of a putative peroxidase gene from wheat (Triticum aestivum L.).

    PubMed

    Hertig, C; Rebmann, G; Bull, J; Mauch, F; Dudler, R

    1991-01-01

    We have used a cDNA clone encoding a pathogen-induced putative wheat peroxidase to screen a genomic library of wheat (Triticum aestivum L. cv. Cheyenne) and isolated one positive clone, lambda POX1. Sequence analysis revealed that this clone contains a gene encoding a putative peroxidase with a calculated pI of 8.1 which exhibits 58% and 83% sequence identity to the amino acid sequence of the turnip (Brassica rapa) peroxidase and a pathogen-induced putative wheat peroxidase, respectively. The two introns in the wheat gene are at the same positions as introns in the peroxidase genes of tomato and horseradish. Results of S1-mapping experiments suggest that this gene is neither pathogen- nor wound-induced in leaves but is constitutively expressed in roots. PMID:1653627

  1. 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.

  2. 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.

  3. 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...

  4. 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

  5. Optical Nano-mapping and Analysis of Plant Genomes.

    PubMed

    Luo, Ming-Cheng; Deal, Karin R; Murray, Armond; Zhu, Tingting; Hastie, Alex R; Stedman, Will; Sadowski, Henry; Saghbini, Michael

    2016-01-01

    Application of optical mapping based on BioNano Genomics Irys(®) technology ( http://www.bionanogenomics.com/ ) is growing rapidly since its debut in November 2012. The technology can be used to facilitate genome sequence assembly and analysis of genome structural variations. We describe here the detailed protocol that we used to generate a whole genome BioNano map for Aegilops tauschii, the D genome progenitor of hexaploid wheat (Triticum aestivum). We are using the whole genome BioNano map to validate sequence assembly based on the next-generation sequencing, order sequence scaffolds, and ultimately build pseudomolecules for the genome. PMID:27511170

  6. Identification and characterization of a subset of microRNAs in wheat (Triticum aestivum L.).

    PubMed

    Su, Chun; Yang, Xiaozeng; Gao, Shiqing; Tang, Yimiao; Zhao, Changping; Li, Lei

    2014-04-01

    MicroRNAs (miRNAs) represent a class of endogenous regulator for post-transcriptionally modulating gene expression. Elucidating complete miRNA repertoires for individual species is a long-desired goal in miRNA research. So far only 42 have been annotated for common wheat (Triticum aestivum) due to its large genome. Here, we employed miRDeep-P, a program developed previously for retrieving miRNAs from deep sequencing data in plants, to parse 14 sequenced small RNA libraries of wheat using expression sequence tags (ESTs) as the reference in lieu of a complete genome sequence. This effort identified 145 miRNAs along with the corresponding stem-looped precursors with many differentially expressed in development and associated with powdery mildew infection. Examination of the phylogenetic distribution of these miRNAs and their target genes revealed that many are conserved in monocots. The set of miRNAs identified in this study is thus useful to further miRNA research in wheat and other important cereal crop species.

  7. Development of an Expressed Sequence Tag (EST) Resource for Wheat (Triticum aestivum L.)

    PubMed Central

    Lazo, G. R.; Chao, S.; Hummel, D. D.; Edwards, H.; Crossman, C. C.; Lui, N.; Matthews, D. E.; Carollo, V. L.; Hane, D. L.; You, F. M.; Butler, G. E.; Miller, R. E.; Close, T. J.; Peng, J. H.; Lapitan, N. L. V.; Gustafson, J. P.; Qi, L. L.; Echalier, B.; Gill, B. S.; Dilbirligi, M.; Randhawa, H. S.; Gill, K. S.; Greene, R. A.; Sorrells, M. E.; Akhunov, E. D.; Dvořák, J.; Linkiewicz, A. M.; Dubcovsky, J.; Hossain, K. G.; Kalavacharla, V.; Kianian, S. F.; Mahmoud, A. A.; Miftahudin; Ma, X.-F.; Conley, E. J.; Anderson, J. A.; Pathan, M. S.; Nguyen, H. T.; McGuire, P. E.; Qualset, C. O.; Anderson, O. D.

    2004-01-01

    This report describes the rationale, approaches, organization, and resource development leading to a large-scale deletion bin map of the hexaploid (2n = 6x = 42) wheat genome (Triticum aestivum L.). Accompanying reports in this issue detail results from chromosome bin-mapping of expressed sequence tags (ESTs) representing genes onto the seven homoeologous chromosome groups and a global analysis of the entire mapped wheat EST data set. Among the resources developed were the first extensive public wheat EST collection (113,220 ESTs). Described are protocols for sequencing, sequence processing, EST nomenclature, and the assembly of ESTs into contigs. These contigs plus singletons (unassembled ESTs) were used for selection of distinct sequence motif unigenes. Selected ESTs were rearrayed, validated by 5′ and 3′ sequencing, and amplified for probing a series of wheat aneuploid and deletion stocks. Images and data for all Southern hybridizations were deposited in databases and were used by the coordinators for each of the seven homoeologous chromosome groups to validate the mapping results. Results from this project have established the foundation for future developments in wheat genomics. PMID:15514037

  8. 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"…

  9. 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...

  10. Comprehensive Functional Analyses of Expressed Sequence Tags in Common Wheat (Triticum aestivum)

    PubMed Central

    Manickavelu, Alagu; Kawaura, Kanako; Oishi, Kazuko; Shin-I, Tadasu; Kohara, Yuji; Yahiaoui, Nabila; Keller, Beat; Abe, Reina; Suzuki, Ayako; Nagayama, Taishi; Yano, Kentaro; Ogihara, Yasunari

    2012-01-01

    About 1 million expressed sequence tag (EST) sequences comprising 125.3 Mb nucleotides were accreted from 51 cDNA libraries constructed from a variety of tissues and organs under a range of conditions, including abiotic stresses and pathogen challenges in common wheat (Triticum aestivum). Expressed sequence tags were assembled with stringent parameters after processing with inbuild scripts, resulting in 37 138 contigs and 215 199 singlets. In the assembled sequences, 10.6% presented no matches with existing sequences in public databases. Functional characterization of wheat unigenes by gene ontology annotation, mining transcription factors, full-length cDNA, and miRNA targeting sites were carried out. A bioinformatics strategy was developed to discover single-nucleotide polymorphisms (SNPs) within our large EST resource and reported the SNPs between and within (homoeologous) cultivars. Digital gene expression was performed to find the tissue-specific gene expression, and correspondence analysis was executed to identify common and specific gene expression by selecting four biotic stress-related libraries. The assembly and associated information cater a framework for future investigation in functional genomics. PMID:22334568

  11. 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...

  12. 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.

  13. 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.

  14. 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

    2015-01-31

    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.

  15. Extensive pericentric rearrangements in the bread wheat (Triticum aestivum L.) genotype "Chinese Spring" revealed from chromosome shotgun sequence data.

    PubMed

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

    2014-10-27

    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.

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

    PubMed Central

    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. [Specific features of fertility restoration in alloplasmic lines obtained based on hybridization of self-fertilized offspring of barley-wheat (Hordeum vulgare L. x Triticum aestivum L.) amphiploid with common wheat varieties Saratovskaya 29 and Pyrotrix 28].

    PubMed

    Pershina, L A; Deviatkina, E P; Trubacheeva, N V; Kravtsova, L A; Dobrovol'skaia, O B

    2012-12-01

    The problems of fertility restoration in the progeny of barley-wheat hybrids (H. vulgare x T. aestivum) are explained by incompatibility between the cytoplasm of cultivated barley and the nuclear genome of common wheat. Suitable models for studying these problems are alloplasmic lines that combine the cytoplasm of barley and the nuclear genome of wheat. In this work, the specific features of fertility restoration in alloplasmic common wheat lines (H. vulgare)-T. aestivum were studied depending on the influence of wheat varieties Saratovskaya 29 (Sar29) and Pyrotrix 28 (Pyr28) used to produce these lines. The alloplasmic lines were created using hybrids between the 48-chromosome offspring (Amph1) of the barley-wheat amphiploid H. vulgare (ya-319) x T. aestivum (Sar29) and these wheat varieties. Backcrossing of the Amph1 (2n = 48) x Sar29 hybrid with the wheat variety Sar29 resulted in the complete sterility in the (H. vulgare)-Sar29 line, which suggests the incompatibility of the nuclear genome of the common wheat variety Sar29 with the cytoplasm of H. vulgare. Crossing of Amph1 (2n = 48) with Pyr28 resulted in the restoration of self-fertility in the hybrid with 2n = 44. In the alloplasmic lines (2n = 42) formed based on plants of the self-fertilized generations of this hybrid, the barley chromosomes were eliminated, and recombination between the nuclear genomes of the parental wheat varieties Sar29 and Pyr28 took place. Alloplasmic recombinant lines (H. vulgare)-T. aestivum with different levels of fertility were isolated. As was shown by the SSR analysis, differences in the fertility traits between these lines are determined by variations in the content of the genetic material from the wheat varieties Sar29 and Pyr28. The complete restoration of fertility in these alloplasmic recombinant lines is accompanied by the formation of a nuclear genome in which the genetic material of Pyr28 significantly prevails. The conclusion is made that the common wheat variety

  18. 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

  19. Fructan metabolism in developing wheat (Triticum aestivum L.) kernels.

    PubMed

    Verspreet, Joran; Cimini, Sara; Vergauwen, Rudy; Dornez, Emmie; Locato, Vittoria; Le Roy, Katrien; De Gara, Laura; Van den Ende, Wim; Delcour, Jan A; Courtin, Christophe M

    2013-12-01

    Although fructans play a crucial role in wheat kernel development, their metabolism during kernel maturation is far from being understood. In this study, all major fructan-metabolizing enzymes together with fructan content, fructan degree of polymerization and the presence of fructan oligosaccharides were examined in developing wheat kernels (Triticum aestivum L. var. Homeros) from anthesis until maturity. Fructan accumulation occurred mainly in the first 2 weeks after anthesis, and a maximal fructan concentration of 2.5 ± 0.3 mg fructan per kernel was reached at 16 days after anthesis (DAA). Fructan synthesis was catalyzed by 1-SST (sucrose:sucrose 1-fructosyltransferase) and 6-SFT (sucrose:fructan 6-fructosyltransferase), and to a lesser extent by 1-FFT (fructan:fructan 1-fructosyltransferase). Despite the presence of 6G-kestotriose in wheat kernel extracts, the measured 6G-FFT (fructan:fructan 6G-fructosyltransferase) activity levels were low. During kernel filling, which lasted from 2 to 6 weeks after anthesis, kernel fructan content decreased from 2.5 ± 0.3 to 1.31 ± 0.12 mg fructan per kernel (42 DAA) and the average fructan degree of polymerization decreased from 7.3 ± 0.4 (14 DAA) to 4.4 ± 0.1 (42 DAA). FEH (fructan exohydrolase) reached maximal activity between 20 and 28 DAA. No fructan-metabolizing enzyme activities were registered during the final phase of kernel maturation, and fructan content and structure remained unchanged. This study provides insight into the complex metabolism of fructans during wheat kernel development and relates fructan turnover to the general phases of kernel development.

  20. 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....

  1. Draft Genome Sequence of the Phenazine-Producing Pseudomonas fluorescens Strain 2-79.

    PubMed

    Nesemann, Kai; Braus-Stromeyer, Susanna A; Thuermer, Andrea; Daniel, Rolf; Mavrodi, Dmitri V; Thomashow, Linda S; Weller, David M; Braus, Gerhard H

    2015-03-26

    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.

  2. Reticulate evolution of the rye genome.

    PubMed

    Martis, Mihaela M; Zhou, Ruonan; Haseneyer, Grit; Schmutzer, Thomas; Vrána, Jan; Kubaláková, Marie; König, Susanne; Kugler, Karl G; Scholz, Uwe; Hackauf, Bernd; Korzun, Viktor; Schön, Chris-Carolin; Dolezel, Jaroslav; Bauer, Eva; Mayer, Klaus F X; Stein, Nils

    2013-10-01

    Rye (Secale cereale) is closely related to wheat (Triticum aestivum) and barley (Hordeum vulgare). Due to its large genome (~8 Gb) and its regional importance, genome analysis of rye has lagged behind other cereals. Here, we established a virtual linear gene order model (genome zipper) comprising 22,426 or 72% of the detected set of 31,008 rye genes. This was achieved by high-throughput transcript mapping, chromosome survey sequencing, and integration of conserved synteny information of three sequenced model grass genomes (Brachypodium distachyon, rice [Oryza sativa], and sorghum [Sorghum bicolor]). This enabled a genome-wide high-density comparative analysis of rye/barley/model grass genome synteny. Seventeen conserved syntenic linkage blocks making up the rye and barley genomes were defined in comparison to model grass genomes. Six major translocations shaped the modern rye genome in comparison to a putative Triticeae ancestral genome. Strikingly dissimilar conserved syntenic gene content, gene sequence diversity signatures, and phylogenetic networks were found for individual rye syntenic blocks. This indicates that introgressive hybridizations (diploid or polyploidy hybrid speciation) and/or a series of whole-genome or chromosome duplications played a role in rye speciation and genome evolution.

  3. 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.

  4. 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.

  5. The alpha-tubulin gene family in wheat (Triticum aestivum L.) and differential gene expression during cold acclimation.

    PubMed

    Ridha Farajalla, Mohammed; Gulick, Patrick J

    2007-05-01

    The alpha-tubulins and beta-tubulins are the major constituents of microtubules, which have been recognized as important structural elements in cell growth and morphogenesis, and, recently, for their role in regulation and signal transduction. We have identified 15 full-length cDNAs for the members of the alpha-tubulin gene family in hexaploid bread wheat (Triticum aestivum L.). The genes were clustered into 5 homeologous groups of 3 genes. Representatives of the 5 homeologous groups were mapped to different chromosome arms, and the genome of origin was determined for each gene. Changes in mRNA levels were observed for the paralogous members of the gene family during cold acclimation. Three members of the family had initial decreases in mRNA levels in response to cold treatment, which were followed by increases, each with a different pattern of reinduction. One gene-family member showed increased mRNA for up to 14 d during cold acclimation and had decreased levels after 36 d of cold treatment; a fifth paralogous member of the gene family had slowly declining mRNA levels up to 36 d. Subtle differences in the level of gene expression among homeologs and large differences among paralogs were detected by comparing the relative abundance of wheat alpha-tubulin expressed sequence tags (ESTs) in public databases. PMID:17612619

  6. Variability and genetics of spacer DNA sequences between the ribosomal-RNA genes of hexaploid wheat (Triticum aestivum).

    PubMed

    May, C E; Appels, R

    1987-09-01

    Using restriction enzyme digests of genomic DNA extracted from the leaves of 25 hexaploid wheat (Triticum aestivum L. em. Thell.) cultivars and their hybrids, restriction fragment length polymorphisms of the spacer DNA which separates the ribosomal-RNA genes have been examined. (From one to three thousand of these genes are borne on chromosomes 1B and 6B of hexaploid wheat). The data show that there are three distinct alleles of the 1B locus, designated Nor-B1a, Nor-B1b, and Nor-B1c, and at least five allelic variants of the 6B locus, designated Nor-B2a, Nor-B2b, Nor-B2c, Nor-B2d, and Nor-B2e. A further, previously reported allele on 6B has been named Nor-B2f. Chromosome 5D has only one allelic variant, Nor-D3. Whereas the major spacer variants of the 1B alleles apparently differ by the loss or gain of one or two of the 133 bp sub-repeat units within the spacer DNA, the 6B allelic variants show major differences in their compositions and lengths. This may be related to the greater number of rDNA repeat units at this locus. The practical implications of these differences and their application to wheat breeding are discussed.

  7. Genome interplay in the grain transcriptome of hexaploid bread wheat.

    PubMed

    Pfeifer, Matthias; Kugler, Karl G; Sandve, Simen R; Zhan, Bujie; Rudi, Heidi; Hvidsten, Torgeir R; Mayer, Klaus F X; Olsen, Odd-Arne

    2014-07-18

    Allohexaploid bread wheat (Triticum aestivum L.) provides approximately 20% of calories consumed by humans. Lack of genome sequence for the three homeologous and highly similar bread wheat genomes (A, B, and D) has impeded expression analysis of the grain transcriptome. We used previously unknown genome information to analyze the cell type-specific expression of homeologous genes in the developing wheat grain and identified distinct co-expression clusters reflecting the spatiotemporal progression during endosperm development. We observed no global but cell type- and stage-dependent genome dominance, organization of the wheat genome into transcriptionally active chromosomal regions, and asymmetric expression in gene families related to baking quality. Our findings give insight into the transcriptional dynamics and genome interplay among individual grain cell types in a polyploid cereal genome.

  8. 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...

  9. 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...

  10. 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 ...

  11. 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...

  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. 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...

  15. 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.

  16. 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

  17. 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

    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.

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

    PubMed

    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.

  20. 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

  1. About the origin of European spelt ( Triticum spelta L.): allelic differentiation of the HMW Glutenin B1-1 and A1-2 subunit genes.

    PubMed

    Blatter, R H E; Jacomet, S; Schlumbaum, A

    2004-01-01

    To investigate the origin of European spelt ( Triticum spelta L., genome AABBDD) and its relation to bread wheat ( Triticum aestivum L., AABBDD), we analysed an approximately 1-kb sequence, including a part of the promoter and the coding region, of the high-molecular-weight (HMW) glutenin B1-1 and A1-2 subunit genes in 58 accessions of hexa- and tetraploid wheat from different geographical regions. Six Glu-B1-1 and five Glu-A1-2 alleles were identified based on 21 and 19 informative sites, respectively, which suggests a polyphyletic origin of the A- and B-genomes of hexaploid wheat. In both genes, a group of alleles clustered in a distinct, so-called beta subclade. High frequencies of alleles from the Glu-B1-1 and Glu-A1-2 beta subclades differentiated European spelt from Asian spelt and bread wheat. This indicates different origins of European and Asian spelt, and that European spelt does not derive from the hulled progenitors of bread wheat. The conjoint differentiation of alleles of the A- and B-genome in European spelt suggests the introgression of a tetraploid wheat into free-threshing hexaploid wheat as the origin of European spelt.

  2. 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.

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

    DOE PAGES

    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

  4. Molecular characterization and sequence diversity of genes encoding the large subunit of the ADP-glucose pyrophosphorylase in wheat (Triticum aestivum L.).

    PubMed

    Rose, Meghan K; Huang, Xiu-Qiang; Brûlé-Babel, Anita

    2016-02-01

    The large subunit of ADP glucose pyrophosphorylase (AGPase), the rate limiting enzyme in starch biosynthesis in Triticum aestivum L., is encoded by the ADP glucose pyrophosphorylase large subunit (AGP-L) gene. This was the first report on the development of three genome-specific primer sets for isolating the complete genomic sequence of all three homoeologous AGP-L genes on group 1 chromosomes. All three AGP-L genes consisted of 15 introns and 15 exons. The lengths of the structural genes from start to stop codon were 3334 bp for AGP-L-A1, 3351 bp for AGP-L-B1, and 3340 bp for AGP-L-D1. The coding region was 1569 bases long in all three genomes. All three AGP-L genes encoded 522 amino acid residues including the transit peptide sequences with 62 amino acid residues and the mature protein with 460 amino acid residues. The mature protein of three AGP-L genes was highly conserved. Three AGP-L genes were sequenced in 47 diverse spring and winter wheat genotypes. One and two haplotypes were found for AGP-L-D1 and AGP-L-A1, respectively. In total, 67 SNPs (single nucleotide polymorphisms) and 13 indels (insertions or deletions) forming five haplotypes were identified for AGP-L-B1. All 13 indels and 58 of the 67 SNPs among the 47 genotypes were located in the non-coding regions, while the remaining nine SNPs were synonymous substitutions in the coding region. Significant LD was found among the 45 SNPs and ten indels located from intron 2 to intron 3. Association analysis indicated that four SNPs were strongly associated with seed number per spike and thousand kernel weight.

  5. Physiological and Antioxidant Responses in Wheat (Triticum aestivum) to HHCB in Soil.

    PubMed

    Chen, Cuihong; Cai, Zhang

    2015-08-01

    Seedlings of wheat (Triticum aestivum) were exposed in soil to the polycyclic musk chemical, 1,3,4,6,7,8-hexahydro-4,6,6,7,8,8-hexamethylcyclopenta[g]-2-benzopyran (HHCB) for 21 days, to evaluate its effect upon chlorophyll (CHL), lipid peroxidation and the antioxidant system. The content of CHL in leaves was inhibited significantly after 14- and 21-days exposures, whereas it was significantly induced by a low level of HHCB after a 7-days exposure. The content of malondialdehyde (MDA) in wheat leaves increased with an increase in the concentration of HHCB in soil, indicating that oxidative stress could be induced by HHCB. Moreover, HHCB exposure induced significant antioxidant responses in wheat. The activities of superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) in wheat leaves were induced by HHCB after 14 and 21 days of exposure. However, the changing trend of the antioxidant enzymes in wheat roots was different from that in leaves. The results suggested that the assayed parameters of T. aestivum could be used as responsive biomarkers for oxidative stress in the soil environment.

  6. 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

  7. 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...

  8. 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...

  9. Complementary epistasis involving Sr12 explains adult plant resistance to stem rust in Thatcher wheat (Triticum aestivum L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Adult plant resistance (APR) in wheat (Triticum aestivum L.) to stem rust, caused by Puccinia graminis f. sp. tritici, is desirable because this resistance can be race non-specific. Resistance derived from cultivar Thatcher can confer high levels of APR to the virulent P. graminis f. sp. tritici rac...

  10. 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...

  11. 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,...

  12. 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...

  13. Identification and characterization of the three homeologues of a new sucrose transporter in hexaploid wheat (Triticum aestivum L.)

    PubMed Central

    2013-01-01

    Background Sucrose transporters (SUTs) play important roles in regulating the translocation of assimilates from source to sink tissues. Identification and characterization of new SUTs in economically important crops such as wheat provide insights into their role in determining seed yield. To date, however, only one SUT of wheat has been reported and functionally characterized. The present study reports the isolation and characterization of a new SUT, designated as TaSUT2, and its homeologues (TaSUT2A, TaSUT2B and TaSUT2D) in hexaploid wheat (Triticum aestivum L.). Results TaSUT2A and TaSUT2B genes each encode a protein with 506 amino acids, whereas TaSUT2D encodes a protein of 508 amino acids. The molecular mass of these proteins is predicted to be ~ 54 kDA. Topological analysis of the amino acid sequences of the three homeologues revealed that they contain 12 transmembrane spanning helices, which are described as distinct characteristic features of glycoside-pentoside-hexuronide cation symporter family that includes all known plant SUTs, and a histidine residue that appears to be localized at and associated conformationally with the sucrose binding site. Yeast SUSY7/ura3 strain cells transformed with TaSUT2A, TaSUT2B and TaSUT2D were able to uptake sucrose and grow on a medium containing sucrose as a sole source of carbon; however, our subcellular localization study with plant cells revealed that TaSUT2 is localized to the tonoplast. The expression of TaSUT2 was detected in the source, including flag leaf blade, flag leaf sheath, peduncle, glumes, palea and lemma, and sink (seed) tissues. The relative contributions of the three genomes of wheat to the total expression of TaSUT2 appear to differ with tissues and developmental stages. At the cellular level, TaSUT2 is expressed mainly in the vein of developing seeds and subepidermal mesophyll cells of the leaf blade. Conclusion This study demonstrated that TaSUT2 is a new wheat SUT protein. Given that TaSUT2 is

  14. Development of T. aestivum L.-H. californicum alien chromosome lines and assignment of homoeologous groups of Hordeum californicum chromosomes.

    PubMed

    Fang, Yuhui; Yuan, Jingya; Wang, Zhangjun; Wang, Haiyan; Xiao, Jin; Yang, Zhixi; Zhang, Ruiqi; Qi, Zengjun; Xu, Weigang; Hu, Lin; Wang, Xiu-E

    2014-08-20

    Hordeum californicum (2n = 2x = 14, HH) is resistant to several wheat diseases and tolerant to lower nitrogen. In this study, a molecular karyotype of H. californicum chromosomes in the Triticum aestivum L. cv. Chinese Spring (CS)-H. californicum amphidiploid (2n = 6x = 56, AABBDDHH) was established. By genomic in situ hybridization (GISH) and multicolor fluorescent in situ hybridization (FISH) using repetitive DNA clones (pTa71, pTa794 and pSc119.2) as probes, the H. californicum chromosomes could be differentiated from each other and from the wheat chromosomes unequivocally. Based on molecular karyotype and marker analyses, 12 wheat-alien chromosome lines, including four disomic addition lines (DAH1, DAH3, DAH5 and DAH6), five telosomic addition lines (MtH7L, MtH1S, MtH1L, DtH6S and DtH6L), one multiple addition line involving H. californicum chromosome H2, one disomic substitution line (DSH4) and one translocation line (TH7S/1BL), were identified from the progenies derived from the crosses of CS-H. californicum amphidiploid with common wheat varieties. A total of 482 EST (expressed sequence tag) or SSR (simple sequence repeat) markers specific for individual H. californicum chromosomes were identified, and 47, 50, 45, 49, 21, 51 and 40 markers were assigned to chromosomes H1, H2, H3, H4, H5, H6 and H7, respectively. According to the chromosome allocation of these markers, chromosomes H2, H3, H4, H5, and H7 of H. californicum have relationship with wheat homoeologous groups 5, 2, 6, 3, and 1, and hence could be designated as 5H(c), 2H(c), 6H(c), 3H(c) and 1H(c), respectively. The chromosomes H1 and H6 were designated as 7H(c) and 4H(c), respectively, by referring to SSR markers located on rye chromosomes.

  15. 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.

  16. 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 Central

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

    2013-01-01

    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

  17. 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.

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

    PubMed Central

    Morris, C F; Fuerst, E P; Beecher, B S; Mclean, D J; James, C P; Geng, H W

    2013-01-01

    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 evolutionary explanation, or selective advantage, for the spread and persistence of these hard kernel mutations has yet to be established. Here, we demonstrate that the house mouse (Mus musculus L.) exerts a pronounced feeding preference for soft over hard kernels. When allele frequencies ranged from 0.5 to 0.009, mouse predation increased the hard allele frequency as much as 10-fold. Studies involving a single hard kernel mixed with ∼1000 soft kernels failed to recover the mutant kernel. Nevertheless, the study clearly demonstrates that the house mouse could have played a role in the evolution of wheat, and therefore the cultural trajectory of humankind. PMID:24223281

  19. 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

  20. 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

  1. 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.

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

    PubMed

    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.

  3. 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

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

    PubMed

    Yuan, Wen-Ye; Tomita, Motonori

    2015-02-26

    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.

  5. 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

  6. Assessment of candidate reference genes for the expression studies with brassinosteroids in Lolium perenne and Triticum aestivum.

    PubMed

    Jurczyk, Barbara; Pociecha, Ewa; Janeczko, Anna; Paczyński, Robert; Rapacz, Marcin

    2014-10-15

    Quantitative PCR studies need proper reference genes with expression stability exclusively validated under certain experimental conditions. The expression stability of several genes commonly used as references was tested under 24-epibrassinolide (EBR) and temperature treatment. Different statistical approaches (qBase(PLUS), BestKeeper, NormFinder) were used to prepare rankings of expression stability in two species of an economic importance: common wheat (Triticum aestivum) and perennial ryegrass (Lolium perenne). Candidate reference genes were shown to be regulated differentially in these two plant species. The maximum stability values indicated that the expression stability was higher in T. aestivum. Taking into account of all ranks it seems that TBP-1 and UBI in ryegrass and ACT, ADP and EF1A in wheat should be used as reference genes in the brassinosteroids and temperature involving studies.

  7. 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...

  8. 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.

  9. Ultrastructural studies on the sporogenous tissue and anther wall of Leucojum aestivum (amaryllidaceae) in different developmental stages.

    PubMed

    Ekici, Nuran; Dane, Feruzan

    2012-12-01

    In this study, ultrastructures of anther wall and sporogenous tissue of Leucojum aestivum were investigated during different developmental stages. Cytomictic channels were seen between pollen mother cells during prophase I. Polar distribution was described in the organelle content of pollen mother cells and microspores in early phases of microsporogenesis and also in pollen mitosis. Active secretion was observed in tapetal cells. Previous reports about developmental stages of male gametophyte were compared with the results of this study.

  10. [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

  11. Combined meta-genomics analyses unravel candidate genes for the grain dietary fiber content in bread wheat (Triticum aestivum L.).

    PubMed

    Quraishi, Umar Masood; Murat, Florent; Abrouk, Mickael; Pont, Caroline; Confolent, Carole; Oury, François Xavier; Ward, Jane; Boros, Danuta; Gebruers, Kurt; Delcour, Jan A; Courtin, Christophe M; Bedo, Zoltan; Saulnier, Luc; Guillon, Fabienne; Balzergue, Sandrine; Shewry, Peter R; Feuillet, Catherine; Charmet, Gilles; Salse, Jerome

    2011-03-01

    Grain dietary fiber content in wheat not only affects its end use and technological properties including milling, baking and animal feed but is also of great importance for health benefits. In this study, integration of association genetics (seven detected loci on chromosomes 1B, 3A, 3D, 5B, 6B, 7A, 7B) and meta-QTL (three consensus QTL on chromosomes 1B, 3D and 6B) analyses allowed the identification of seven chromosomal regions underlying grain dietary fiber content in bread wheat. Based either on a diversity panel or on bi-parental populations, we clearly demonstrate that this trait is mainly driven by a major locus located on chromosome 1B associated with a log of p value >13 and a LOD score >8, respectively. In parallel, we identified 73 genes differentially expressed during the grain development and between genotypes with contrasting grain fiber contents. Integration of quantitative genetics and transcriptomic data allowed us to propose a short list of candidate genes that are conserved in the rice, sorghum and Brachypodium chromosome regions orthologous to the seven wheat grain fiber content QTL and that can be considered as major candidate genes for future improvement of the grain dietary fiber content in bread wheat breeding programs.

  12. 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

  13. Heterologous expression of a plastid EF-Tu reduces protein thermal aggregation and enhances CO2 fixation in wheat (Triticum aestivum) following heat stress.

    PubMed

    Fu, Jianming; Momcilović, Ivana; Clemente, Thomas E; Nersesian, Natalya; Trick, Harold N; Ristic, Zoran

    2008-10-01

    Heat stress is a major constraint to wheat production and negatively impacts grain quality, causing tremendous economic losses, and may become a more troublesome factor due to global warming. At the cellular level, heat stress causes denaturation and aggregation of proteins and injury to membranes leading to alterations in metabolic fluxes. Protein aggregation is irreversible, and protection of proteins from thermal aggregation is a strategy a cell uses to tolerate heat stress. Here we report on the development of transgenic wheat (Triticum aestivum) events, expressing a maize gene coding for plastidal protein synthesis elongation factor (EF-Tu), which, compared to non-transgenic plants, display reduced thermal aggregation of leaf proteins, reduced heat injury to photosynthetic membranes (thylakoids), and enhanced rate of CO(2) fixation after exposure to heat stress. The results support the concept that EF-Tu ameliorates negative effects of heat stress by acting as a molecular chaperone. This is the first demonstration of the introduction of a plastidal EF-Tu in plants that leads to protection against heat injury and enhanced photosynthesis after heat stress. This is also the first demonstration that a gene other than HSP gene can be used for improvement of heat tolerance and that the improvement is possible in a species that has a complex genome, hexaploid wheat. The results strongly suggest that heat tolerance of wheat, and possibly other crop plants, can be improved by modulating expression of plastidal EF-Tu and/or by selection of genotypes with increased endogenous levels of this protein.

  14. Characterization of Triticum aestivum Abscisic Acid Receptors and a Possible Role for These in Mediating Fusairum Head Blight Susceptibility in Wheat

    PubMed Central

    Gordon, Cameron S.; Rajagopalan, Nandhakishore; Risseeuw, Eddy P.; Surpin, Marci; Ball, Fraser J.; Barber, Carla J.; Buhrow, Leann M.; Clark, Shawn M.; Page, Jonathan E.; Todd, Chris D.; Abrams, Suzanne R.; Loewen, Michele C.

    2016-01-01

    Abscisic acid (ABA) is a well-characterized plant hormone, known to mediate developmental aspects as well as both abiotic and biotic stress responses. Notably, the exogenous application of ABA has recently been shown to increase susceptibility to the fungal pathogen Fusarium graminearum, the causative agent of Fusarium head blight (FHB) in wheat and other cereals. However roles and mechanisms associated with ABA’s modulation of pathogen responses remain enigmatic. Here the identification of putative ABA receptors from available genomic databases for Triticum aestivum (bread wheat) and Brachypodium distachyon (a model cereal) are reported. A number of these were cloned for recombinant expression and their functionality as ABA receptors confirmed by in vitro assays against protein phosphatases Type 2Cs. Ligand selectivity profiling of one of the wheat receptors (Ta_PYL2DS_FL) highlighted unique activities compared to Arabidopsis AtPYL5. Mutagenic analysis showed Ta_PYL2DS_FL amino acid D180 as being a critical contributor to this selectivity. Subsequently, a virus induced gene silencing (VIGS) approach was used to knockdown wheat Ta_PYL4AS_A (and similar) in planta, yielding plants with increased early stage resistance to FHB progression and decreased mycotoxin accumulation. Together these results confirm the existence of a family of ABA receptors in wheat and Brachypodium and present insight into factors modulating receptor function at the molecular level. That knockdown of Ta_PYL4AS_A (and similar) leads to early stage FHB resistance highlights novel targets for investigation in the future development of disease resistant crops. PMID:27755583

  15. Molecular characterization and diversity of puroindoline b-2 variants in cultivated and wild diploid wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cloning and phylogenetic analysis of puroindoline b-2 variants in common wheat (Triticum aestivum L.) and its relatives would advance the understanding of the genetic diversity and evolution of puroindoline b-2 gene in common wheat and its related species. In the present study, common wheat (AABBDD)...

  16. 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...

  17. Evaluation of seedling resistance to tan spot and Stagonospora nodorum blotch in tetraploid wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tetraploid durum wheat (Triticum turgidum L. ssp. durum, 2n = 4x = 28, AABB) is an important cereal specifically used for making pasta products but its production is more vulnerable to various wheat diseases than hexaploid bread wheat (T. aestivum L., 2n = 6x = 42, AABBDD). In order to identify res...

  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. Structural and functional analysis of chitinase gene family in wheat (Triticum aestivum).

    PubMed

    Mishra, A K; Pandey, Bharati; Tyagi, Chetna; Chakraborty, Ohika; Kumar, Amrender; Jain, A K

    2015-04-01

    Chitinases are the hydrolytic enzymes which protect plants against pathogen attack. However, the precise role of chitinases in disease resistance has not been explored in wheat. In the present study, in silico approach, including secondary structure analysis, detailed signature pattern study, cis-acting regulatory elements survey, evolutionary trends and three-dimensional molecular modeling was used for different chitinase classes of wheat (Triticum aestivum). Homology modeling of class I, II, IV and 3 chitinase proteins was performed using the template crystal structure. The model structures were further refined by molecular mechanics methods using different tools, such as Procheck, ProSA and Verify3D. Secondary structure studies revealed greater percentage of residues forming a helix conformation with specific signature pattern, similar to casein kinase II phosphorylation site, amidation site, N-myristoylation (N-MYR) site and protein kinase C phoshorylation site. The expression profile suggested that wheat chitinase gene was highly expressed in cell culture and callus. We found that wheat chitinases showed more functional similarity with rice and barley. The results provide insight into the evolution of the chitinase family, constituting a diverse array of pathogenesis-related proteins. The study also provides insight into the possible binding sites of chitinase proteins and may further enhance our knowledge of fungal resistance mechanism in plants.

  20. 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

  1. Acid Carboxypeptidases in Grains and Leaves of Wheat, Triticum aestivum L.

    PubMed

    Mikola, L

    1986-07-01

    Extracts of resting and germinating (3 days at 20 degrees C) wheat (Triticum aestivum L. cv Ruso) grains rapidly hydrolyzed various benzyloxycarbonyldipeptides (Z-dipeptides) at pH 4 to 6. Similar activities were present in extracts of mature flag leaves. Fractionation by chromatography on CM-cellulose and on Sephadex G-200 showed that the activities in germinating grains were due to five acid carboxypeptidases with different and complementary substrate specificities. The wheat enzymes appeared to correspond to the five acid carboxypeptidases present in germinating barley (L Mikola 1983 Biochim Biophys Acta 747: 241-252). The enzymes were designated wheat carboxypeptidases I to V and their best or most characteristic substrates and approximate molecular weights were: I, Z-Phe-Ala, 120,000; II, Z-Ala-Arg, 120,000; III, Z-Ala-Phe, 40,000; IV, Z-Pro-Ala, 165,000; and V, Z-Pro-Ala, 150,000. Resting grains contained carboxypeptidase II as a series of three isoenzymes and low activities of carboxypeptidases IV and V. During germination the activity of carboxypeptidase II decreased, those of carboxypeptidases IV and V increased, and high activities of carboxypeptidases I and III appeared. The flag leaves contained high activity of carboxypeptidase I and lower activities of carboxypeptidases II, IV, and V, whereas carboxypeptidase III was absent.

  2. Acid Carboxypeptidases in Grains and Leaves of Wheat, Triticum aestivum L

    PubMed Central

    Mikola, Leena

    1986-01-01

    Extracts of resting and germinating (3 days at 20°C) wheat (Triticum aestivum L. cv Ruso) grains rapidly hydrolyzed various benzyloxycarbonyldipeptides (Z-dipeptides) at pH 4 to 6. Similar activities were present in extracts of mature flag leaves. Fractionation by chromatography on CM-cellulose and on Sephadex G-200 showed that the activities in germinating grains were due to five acid carboxypeptidases with different and complementary substrate specificities. The wheat enzymes appeared to correspond to the five acid carboxypeptidases present in germinating barley (L Mikola 1983 Biochim Biophys Acta 747: 241-252). The enzymes were designated wheat carboxypeptidases I to V and their best or most characteristic substrates and approximate molecular weights were: I, Z-Phe-Ala, 120,000; II, Z-Ala-Arg, 120,000; III, Z-Ala-Phe, 40,000; IV, Z-Pro-Ala, 165,000; and V, Z-Pro-Ala, 150,000. Resting grains contained carboxypeptidase II as a series of three isoenzymes and low activities of carboxypeptidases IV and V. During germination the activity of carboxypeptidase II decreased, those of carboxypeptidases IV and V increased, and high activities of carboxypeptidases I and III appeared. The flag leaves contained high activity of carboxypeptidase I and lower activities of carboxypeptidases II, IV, and V, whereas carboxypeptidase III was absent. PMID:16664910

  3. Determination of zinc oxide nanoparticles toxicity in root growth in wheat (Triticum aestivum L.) seedlings.

    PubMed

    Prakash, Meppaloor G; Chung, Ill Min

    2016-09-01

    The effect of zinc oxide nanoparticles (ZnONPs) was studied in wheat (Triticum aestivum L.) seedlings under in vitro exposure conditions. To avoid precipitation of nanoparticles, the seedlings were grown in half strength semisolid Murashige and Skoog medium containing 0, 50, 100, 200, 400 and 500 mg L(-1) of ZnONPs. Analysis of zinc (Zn) content showed significant increase in roots. In vivo detection using fluorescent probe Zynpyr-1 indicated accumulation of Zn in primary and lateral root tips. All concentrations of ZnONPs significantly reduced root growth. However, significant decrease in shoot growth was observed only after exposure to 400 and 500 mg L(-1) of ZnONPs. The reactive oxygen species and lipid peroxidation levels significantly increased in roots. Significant increase in cell-wall bound peroxidase activity was observed after exposure to 500 mg L(-1) of ZnONPs. Histochemical staining with phloroglucinol-HCl showed lignification of root cells upon exposure to 500 mg L(-1) of ZnONPs. Treatment with propidium iodide indicated loss of cell viability in root tips of wheat seedlings. These results suggest that redox imbalances, lignification and cell death has resulted in reduction of root growth in wheat seedlings exposed to ZnONPs nanoparticles. PMID:27630051

  4. 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.

  5. Diallel cross analysis of plesiomorphic traits in Triticum aestivum L. genotypes.

    PubMed

    Shehzad, M; Hussain, S B; Qureshi, M K; Akbar, M; Javed, M; Imran, H M; Manzoor, S A

    2015-10-28

    We conducted a 5 x 5 complete diallel cross experiment in bread wheat (Triticum aestivum) with the genotypes 6309, Chkwal-50, Dhrabi, Bhkhar-02, and FS-08. Our objective was to evaluate the type of gene action and the general and specific combining abilities required for various morphological traits in wheat. The results of analysis of variance revealed highly significant differences among genotypes for all the investigated traits. The results of joint regression analysis showed that the data for all the investigated traits fitted a simple additive dominance model. Graphical representation of variance and covariance suggested that most of the investigated traits were controlled by overdominance gene action. However, the peduncle length and plant height were controlled by additive gene action. Variety 6309 carried the highest number of dominant genes for the number of spikelets per spike, number of tillers per plant, plant height, number of fertile tillers per plant, and grain yield per plant. Chakwal-50 carried the highest number of recessive genes for grain yield per plant, number of tillers per plant, number of grains per spike, number of fertile tillers per plant, and plant height. Chakwal-50 and 6309 were the best general combiners for number of spikelets per spike, number of grains per spike, grain yield per plant, 1000-grain weight, number of fertile tillers per plant, and number of tillers per plant. On other hand, 6309 performed well in specific crosses with Chakwal-50, FS-08, and Bhakhar-02 for spike length and number of tillers per plant.

  6. 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.

  7. Hexaconazole-Cu complex improves the salt tolerance of Triticum aestivum seedlings.

    PubMed

    Li, Jie; Sun, Cuiyu; Yu, Nan; Wang, Chen; Zhang, Tongtong; Bu, Huaiyu

    2016-02-01

    Hexaconazole is one of the triazole complexes that are broadly used as systemic fungicides with non-traditional plant growth regulator properties. Hexaconazole-Cu complex (Hex-Cu) is a new triazole derivative, and the biological effect of Hex-Cu has been rarely studied. In this work, we investigated the functions of Hex-Cu in regulating growth and the response to salt stress in the seedlings of Triticum aestivum. Pretreated with 60μmolL(-1) Hex-Cu, the seedling plants got increased root/shoot ratio by 42.0%, and the contents of chlorophyll and soluble protein were also increased by 38.1% and 27.9%, respectively. Furthermore, Hex-Cu alleviated the growth inhibition caused by salt stress, enabled the seedlings to maintain a higher proline content and lower malondialdehyde accumulation. The functions of Hex-Cu in regulating the expression of proline synthetase (P5CS and P5CR) genes were investigated by quantitative real-time PCR (qPCR). Under 100mmolL(-1) NaCl stress, the expression of P5CS and P5CR in the seedlings by Hex-Cu pretreatment were significantly up-regulated. It attributed to the enhanced salt tolerance in plants.

  8. Nitric oxide mediates alginate oligosaccharides-induced root development in wheat (Triticum aestivum L.).

    PubMed

    Zhang, Yunhong; Liu, Hang; Yin, Heng; Wang, Wenxia; Zhao, Xiaoming; Du, Yuguang

    2013-10-01

    Alginate oligosaccharides (AOS), which are marine oligosaccharides, are involved in regulating plant root growth, but the promotion mechanism for AOS remains unclear. Here, AOS (10-80 mg L(-1)) were found to induce the generation of nitric oxide (NO) in the root system of wheat (Triticum aestivum L.), which promoted the formation and elongation of wheat roots in a dose-dependent manner. NO inhibitors suggested that nitrate reductase (NR), rather than nitric oxide synthase (NOS), was essential for AOS-induced root development. Further studies confirmed that AOS-induced NO generation in wheat roots by up-regulating the gene expression and enzyme activity of NR at the post-transcriptional level. The anatomy and RT-PCR results showed that AOS accelerated the division and growth of stele cells, leading to an increase in the ratio of stele area to root transverse area. This could be inhibited by the NR inhibitor, sodium tungstate, which indicated that NO catalyzed by the NR was involved in AOS regulation of root development. Taken together, in the early stage of AOS-induced root development, NO generation was a novel mechanism by which AOS regulated plant growth. The results also showed that this marine resource could be widely used for crop development.

  9. Proteomic analysis of peripheral layers during wheat (Triticum aestivum L.) grain development.

    PubMed

    Tasleem-Tahir, Ayesha; Nadaud, Isabelle; Girousse, Christine; Martre, Pierre; Marion, Didier; Branlard, Gérard

    2011-02-01

    Grains of hexaploid wheat, Triticum aestivum (cv. Récital), were collected at 15 stages of development, from anthesis to physiological maturity, 0-700°C days (degree days after anthesis). Two hundred and seven proteins of grain peripheral layers (inner pericarp, hyaline, testa and aleurone layer) were identified by 2-DE, MALDI-TOF MS and data mining, then were classified in 16 different functional categories. Study of the protein expression over time allowed identification of five main profiles and four distinct phases of development. Composite expression curves indicated that there was a shift from metabolic processes, translation, transcription and ATP interconversion towards storage and defence processes. Protein synthesis, protein turnover, signal transduction, membrane transport and biosynthesis of secondary metabolites were the mediating functions of this shift. A picture of the dynamic processes taking place in peripheral layers during grain development was obtained in this study. It should further help in the construction of proteome reference maps for the developing peripheral layers.

  10. Insights Into Triticum aestivum Seedling Root Rot Caused by Fusarium graminearum.

    PubMed

    Wang, Qing; Vera Buxa, Stefanie; Furch, Alexandra; Friedt, Wolfgang; Gottwald, Sven

    2015-12-01

    Fusarium graminearum is one of the most common and potent fungal pathogens of wheat (Triticum aestivum), known for causing devastating spike infections and grain yield damage. F. graminearum is a typical soil-borne pathogen that builds up during consecutive cereal cropping. Speculation on systemic colonization of cereals by F. graminearum root infection have long existed but have not been proven. We have assessed the Fusarium root rot disease macroscopically in a diverse set of 12 wheat genotypes and microscopically in a comparative study of two genotypes with diverging responses. Here, we show a 'new' aspect of the F. graminearum life cycle, i.e., the head blight fungus uses a unique root-infection strategy with an initial stage typical for root pathogens and a later stage typical for spike infection. Root colonization negatively affects seedling development and leads to systemic plant invasion by tissue-adapted fungal strategies. Another major outcome is the identification of partial resistance to root rot. Disease severity assessments and histological examinations both demonstrated three distinct disease phases that, however, proceeded differently in resistant and susceptible genotypes. Soil-borne inoculum and root infection are considered significant components of the F. graminearum life cycle with important implications for the development of new strategies of resistance breeding and disease control.

  11. Relevance for food sciences of quantitative spatially resolved element profile investigations in wheat (Triticum aestivum) grain.

    PubMed

    Pongrac, Paula; Kreft, Ivan; Vogel-Mikus, Katarina; Regvar, Marjana; Germ, Mateja; Vavpetic, Primoz; Grlj, Natasa; Jeromel, Luka; Eichert, Diane; Budic, Bojan; Pelicon, Primoz

    2013-07-01

    Bulk element concentrations of whole grain and element spatial distributions at the tissue level were investigated in wheat (Triticum aestivum) grain grown in Zn-enriched soil. Inductively coupled plasma mass spectrometry and inductively coupled plasma optical emission spectrometry were used for bulk analysis, whereas micro-proton-induced X-ray emission was used to resolve the two-dimensional localization of the elements. Soil Zn application did not significantly affect the grain yield, but did significantly increase the grain Ca, Fe and Zn concentrations, and decrease the grain Na, P and Mo concentrations; bulk Mg, S, K, Mn, Cu, Cd and Pb concentrations remained unchanged. These changes observed in bulk element concentrations are the reflection of tissue-specific variations within the grain, revealing that Zn application to soil can lead to considerable alterations in the element distributions within the grain, which might ultimately influence the quality of the milling fractions. Spatially resolved investigations into the partitioning of the element concentrations identified the tissues with the highest element concentrations, which is of utmost importance for accurate prediction of element losses during the grain milling and polishing processes.

  12. [Ecotoxicological effects of oxytetracycline on wheat (Triticum aestivum) based on seed germination and seedling development].

    PubMed

    An, Jing; Zhou, Qi-xing; Liu, Wei-tao

    2009-10-15

    The ecotoxicological effects of oxytetracycline (OTC) on the germination of wheat (Triticum aestivum) seeds and the early development of wheat seedlings were investigated. The results showed that the elongation of wheat shoots and roots was significantly (p < 0.05) inhibited by OTC, and there was a good dose-response relationship between the OTC concentration and inhibition rates. According to the linear regression equation, EC50 of OTC for inhibiting wheat shoot and root elongation was 65.5 mg/L and 34.7 mg/L, respectively. However, the germination of wheat seeds was not inhibited by OTC. Moreover, after a 21-day exposure to 0.15-2.40 mg/L OTC, the content of chlorophyll (CHL) decreased by 35.6%-47.3%, and the content of soluble protein (SP) in the leaves and roots of wheat plants decreased significantly. After a 7-day exposure, the activity of SOD and POD in wheat was not changed significantly. With the prolongation of exposure time, the activity of SOD and POD in wheat leaves and roots decreased significantly, the inhibition rate of SOD activity in roots increased up to 72.3% after a 21-day exposure to 2.4 mg/L OTC, which indicated that the antioxidant defense systems were damaged. The results above suggested that the low concentration OTC had ecotoxicological effects on wheat seedlings after chronic exposure.

  13. [Ecotoxicity of synthetical musks on wheat (Triticum aestivum) based on seed germination].

    PubMed

    Chen, Su; Sun, Li-na; Sun, Tie-heng; Chao, Lei; Sun, Wei-ke; Lou, Yang

    2011-05-01

    With soil culture the ecotoxicological effects of galaxolide (HHCB) and tonalide (AHTN) on the germination of wheat (Triticum aestivum) seeds were investigated. And the influence of these two synthetical musks on the wheat germination rate, inhibition rate of root elongation and inhibition rate of shoot elongation were studied. The results showed that there were no obvious dose-effect relationship between wheat germination rate and concentrations of these two synthetical musks. Lower dose (HHCB < or = 150 mg x kg(-1), AHTN < or = 200 mg x kg(-1)) could accelerate the germination of wheat. Under the test concentrations of synthetical musks, the wheat germination rates treated with HHCB and AHTN were 77.78%-95.56% and 84.44%-97.78%, respectively. There were good dose-effect relationship between inhibition rate of root elongation (or inhibition rate of shoot elongation) and synthetical musks concentrations. The EC50 of HHCB and AHTN based on shoot were 155.84 mg x kg(-1) and 290.58 mg x kg(-1), and were 215.66 mg x kg(-1) and 323.10 mg x kg(-1) based on root from linear model. The EC50 of wheat sensitive positions showed that the toxicity of HHCB was stronger than AHTN.

  14. 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

  15. Genetic diversity and population structure analysis of European hexaploid bread wheat (Triticum aestivum L.) varieties.

    PubMed

    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.

  16. 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

  17. 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

  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. 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.

  20. Nitrogen and Photosynthesis in the Flag Leaf of Wheat (Triticum aestivum L.).

    PubMed

    Evans, J R

    1983-06-01

    Wheat (Triticum aestivum L. cv Yecora 70) plants were grown with various concentrations of nitrate nitrogen available to the roots. Sampling of flag leaves began after they had reached full expansion and continued throughout senescence. Rates of gas exchange, ribulose-1,5-bisphosphate (RuP(2)) carboxylase activity, and the amounts of chlorophyll, soluble protein, nitrogen, and phosphorus were determined for each flag leaf. Rate of CO(2) assimilation was uniquely related to total leaf nitrogen irrespective of nutrient treatment, season, and leaf age. Assimilation rate increased with leaf nitrogen, but the slope of the relationship declined markedly when leaf nitrogen exceeded 125 millimoles nitrogen per square meter. Chlorophyll content and RuP(2) carboxylase activity were approximately proportional to leaf nitrogen content. As leaves aged, RuP(2) carboxylase activity and calculated Hill activity declined in parallel. With normal ambient partial pressure of CO(2), the intercellular partial pressure of CO(2) was always such that rate of assimilation appeared colimited by RuP(2) carboxylation and RuP(2) regeneration capacity.The initial slope of rate of CO(2) assimilation against intercellular partial pressure of CO(2) varied nonlinearly with carboxylase activity. It is suggested that this was due to a finite conductance to CO(2) diffusion in the wall and liquid phase which causes a drop in CO(2) partial pressure between the intercellular spaces and the site of carboxylation. A double reciprocal plot was used to obtain an estimate of the transfer conductance.

  1. Search for diagnostic proteins to prove authenticity of organic wheat grains (Triticum aestivum L.).

    PubMed

    Zörb, Christian; Betsche, Thomas; Langenkämper, Georg

    2009-04-01

    Research comparing the biochemical composition of wheat grains from organic or conventional agriculture has used the targeted analytical approach. To obtain a more comprehensive record of the food's composition, we employed protein profiling techniques. Levels of 1049 proteins were recorded in wheat grains (Triticum aestivum L., cv. Titlis) of two growing seasons from a rigorously controlled field trial in Switzerland, containing organic and conventional plots. Levels of 25 proteins were different between organic and conventional wheat in both years. Storage proteins, enzymes of carbohydrate metabolism, a peroxidase, and proteins of unknown function were affected by the agricultural regime. Total protein content was lower in organic wheat. We consider these differences negligible with regard to nutrition in an average diet and propose that food quality of conventional and organic wheat grown in the field trial was equal. Applying various filters and calculations, one of which takes seasonal influences into account, 16 of the 25 proteins with different levels in organic and conventional wheat were retained. These 16 "diagnostic" proteins have the potential to afford a signature to prove authenticity of organic wheat.

  2. Response of two cultivars of Triticum aestivum L. to simulated acid rain.

    PubMed

    Singh, A; Agrawal, M

    1996-01-01

    The present experiment was aimed at assessing the impact of simulated acidic precipitation (SAR) on growth, biomass accumulation and yield of two cultivars of wheat (Triticum aestivum L.), Malviya 206 and 234, varying in cuticular thickness and leaf area. Wheat cultivars were exposed to simulated rain acidified to pH 5.6 (control), 5.0, 4.5, 4.0 and 3.0 from 30 days of age, twice a week for five weeks. The plants received ambient precipitation of unknown acidity, as well as the acid rain treatments. Growth parameters such as shoot height, root length, and leaf area were reduced significantly in treated plants at different growth stages. Above and below-ground biomass also decreased significantly in the plants treated with acidic precipitation. Relative to control, the number of grains per plant and yield per m(2) declined significantly at all SAR treatments. The hypothesis that the variety with thinner cuticle and greater leaf area would be more susceptible to acidic precipitation was not supported by the present study.

  3. Cloning, characterization and functional analysis of novel 6-kestose exohydrolases (6-KEHs) from wheat (Triticum aestivum).

    PubMed

    Van den Ende, Wim; Yoshida, Midori; Clerens, Stefan; Vergauwen, Rudy; Kawakami, Akira

    2005-06-01

    Cereals accumulate graminan-type fructans which are subject to stress-related degradation by fructan 1-exohydrolases (1-FEHs) and fructan 6-exohydrolases (6-FEHs). To find new FEH genes related to freezing tolerance, a cold-hardened wheat crown cDNA library was screened. Here we report the cloning, purification and characterization of two novel 6-kestosidase (6-KEH) isoenzymes from wheat crowns (Triticum aestivum). Functional characterization in Pichia pastoris confirmed the extreme substrate selectivity for the fructan trisaccharide 6-kestose. Northern blotting showed that 6-KEH transcripts were constantly detected at the same level from autumn to winter in crown but not in leaf tissues. Apoplastic fluid isolations and activity measurements strongly suggest that 6-KEH is localized in the apoplast. It is proposed that 6-KEHs, together with other FEHs, might be involved in the breakdown of apoplastic fructans which may fulfil a role as membrane protectors under stress. Alternatively, a role in signalling processes, or in the degradation of exogenous 6-kestose from bacterial origin, cannot be excluded.

  4. 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

  5. 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

  6. 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

  7. Potential of antioxidant enzymes in depicting drought tolerance of wheat (Triticum aestivum L.).

    PubMed

    Devi, Rachana; Kaur, Narinder; Gupta, Anil Kumar

    2012-08-01

    In an effort to determine the biochemical markers for identifying genotypes before sowing for drought tolerance, changes in activities of antioxidant enzymes were determined in the seedlings of five drought-tolerant and five drought-sensitive wheat (Triticum aestivum L.) genotypes, each with different genetic background growing under normal and water deficit conditions induced by 6% mannitol. In comparison with non-stressed seedlings, the catalase (CAT) activity was upregulated by more than 50% in the roots of water-stressed seedlings in drought-tolerant genotypes. Water deficit stress also led to the upregulation of ascorbate peroxidase (APX) in the endosperms and glutathione reductase (GR), CAT and peroxidase (POD) in the shoots of stressed seedlings in drought-tolerant genotypes. Superoxide dismutase (SOD) activity was very low in roots and shoots and showed non-significant increase under water-stress in tolerant genotypes. Out of five specified enzyme activities (CAT in roots and shoots, APX in endosperms, GR and POD in shoots), if any three are upregulated in the specified tissues under water deficit conditions, the genotype is likely to be drought-tolerant. Wheat seedlings with low GR and APX activities and high POD activity in shoots with a low ratio of GR activity of shoot to root of non-stressed seedlings are likely to perform better under rainfed conditions. The observed data showed that status of antioxidant enzymes could provide a meaningful tool for depicting drought tolerance of a wheat genotype.

  8. 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

  9. Comparison of organic and inorganic amendments for enhancing soil lead phytoextraction by wheat (Triticum aestivum L.).

    PubMed

    Saifullah; Ghafoor, A; Zia, M H; Murtaza, G; Waraich, Ejaz Ahmad; Bibi, Sadia; Srivastava, P

    2010-09-01

    Phytoextraction has received increasing attention as a promising, cost-effective alternative to conventional engineering-based remediation methods for metal contaminated soils. In order to enhance the phytoremediative ability of green plants chelating agents are commonly used. Our study aims to evaluate whether, citric acid (CA) or elemental sulfur (S) should be used as an alternative to the ethylene diamine tetraacetic acid (EDTA)for chemically enhanced phytoextraction. Results showed that EDTA was more efficient than CA and S in solubilizing lead (Pb) from the soil. The application of EDTA and S increased the shoot biomass of wheat. However, application of CA at higher rates (30 mmol kg(-1)) resulted in significantly lower wheat biomass. Photosynthesis and transpiration rates increased with EDTA and S application, whereas these parameters were decreased with the application of CA. Elemental sulfur was ineffective for enhancing the concentration of Pb in wheat shoots. Although CA did not increase the Pb solubility measured at the end of experiment, however, it was more effective than EDTA in enhancing the concentration of Pb in the shoots of Triticum aestivum L. It was assumed that increase in Mn concentration to toxic levels in soil with CA addition might have resulted in unusual Pb concentration in wheat plants. The results of the present study suggest that under the conditions used in this experiment, CA at the highest dose was the best amendment for enhanced phytoextraction of Pb using wheat compared to either EDTA or S.

  10. Differential regulation of alanine aminotransferase homologues by abiotic stresses in wheat (Triticum aestivum L.) seedlings.

    PubMed

    Kendziorek, Maria; Paszkowski, Andrzej; Zagdańska, Barbara

    2012-06-01

    Wheat (Triticum aestivum L.) seedlings contain four alanine aminotransferase (AlaAT) homologues. Two of them encode AlaAT enzymes, whereas two homologues act as glumate:glyoxylate aminotransferase (GGAT). To address the function of the distinct AlaAT homologues a comparative examination of the changes in transcript level together with the enzyme activity and alanine and glutamate content in wheat seedlings subjected to low oxygen availability, nitrogen and light deficiency has been studied. Shoots of wheat seedlings were more tolerant to hypoxia than the roots as judging on the basis of enzyme activity and transcript level. Hypoxia induced AlaAT1 earlier in roots than in shoots, while AlaAT2 and GGAT were unaffected. The increase in AlaAT activity lagged behind the increase in alanine content. Nitrogen deficiency has little effect on the activity of GGAT. In contrast, lower activity of AlaAT and the level of mRNA for AlaAT1 and AlaAT2 in wheat seedlings growing on a nitrogen-free medium seems to indicate that AlaAT is regulated by the availability of nitrogen. Both AlaAT and GGAT activities were present in etiolated wheat seedlings but their activity was half of that observed in light-grown seedlings. Exposure of etiolated seedlings to light caused an increase in enzyme activities and up-regulated GGAT1. It is proposed that hypoxia-induced AlaAT1 and light-induced peroxisomal GGAT1 appears to be crucial for the regulation of energy availability in plants grown under unfavourable environmental conditions. Key message In young wheat seedlings, both AlaAT and GGAT are down-regulated by nitrogen deficiency, whereas AlaAT1 is upregulated by hypoxia and GGAT1 by light.

  11. 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.

  12. Characterization of a cysteine protease from wheat Triticum aestivum (cv. Giza 164).

    PubMed

    Fahmy, Afaf S; Ali, Ahmed A; Mohamed, Saleh A

    2004-02-01

    Enzymes, especially proteases, have become an important and indispensable part of the processes used by the modern food and feed industry to produce a large and diversified range of products for human and animal consumption. A cysteine protease, used extensively in the food industry, was purified from germinated wheat Triticum aestivum (cv. Giza 164) grains through a simple reproducible method consisting of extraction, ion exchange chromatography and gel filtration. The molecular weight of the enzyme was estimated to be 61000+/-1200-62000+/-1500 by SDS-PAGE and gel filtration. The cysteine protease had an isoelectric point and pH optimum at 4.4 and 4.0, respectively. The enzyme exhibited more activity toward azocasein than the other examined substrates with K(m) 2.8+/-0.15 mg azocasein/ml. In addition, it had a temperature optimum of 50 degrees C and based on a heat stability study 55% of its initial activity remained after preincubation of the enzyme at 50 degrees C for 30 min prior to substrate addition. All the examined metal cations inhibited the enzyme except Co(2+), Mg(2+), Mn(2+) and Li(+). The proteolytic activity of the enzyme was inhibited by thiol-specific inhibitors, whereas iodoacetate and p-hydroxymercuribenzoate caused a competitive inhibition with Ki values 6+/-0.3 mM and 21+/-1.2 microM, respectively. Soybean trypsin inhibitor had no effect on the enzyme. The enzyme activity remained almost constant for 150 days of storage at -20 degrees C. The properties of this enzyme, temperature and pH optima, substrate specificity, stability and sensitivity to inhibitors or activators, meet the prerequisites needed for food industries. PMID:14607490

  13. 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.

  14. Quantification of benzoxazinone derivatives in wheat (Triticum aestivum) varieties grown under contrasting conditions in Denmark.

    PubMed

    Mogensen, Betty B; Krongaard, Teddy; Mathiassen, Solvejg K; Kudsk, Per

    2006-02-22

    Three varieties of winter wheat (Triticum aestivum) were grown in both conventional and organic farming systems. The contents of the benzoxazinone derivatives 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA), 2-beta-d-glucopyranosyloxy-4-hydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA-Glc), 6-methoxybenzoxazolin-2-one (MBOA), 2-hydroxy-7-methoxy-1,4-benzoxazin-3-one (HMBOA), benzoxazolin-2-one (BOA), and 2-hydroxy-1,4-benzoxazin-3-one (HBOA) were analyzed at five growth stages (BBCH 9-10, 12, 21, 31, and 53). Major differences were found between the varieties, with Stakado exhibiting the highest contents. In contrast, only minor and erratic differences were found between the two farming systems, suggesting that the inherent differences in the content of benzoxazinone derivatives of the varieties were not significantly affected by the use of pesticides and synthetic fertilizers. The concentration of benzoxazinone derivatives in the foliage was considerably higher at the early growth stages than later in the growing season, with DIMBOA being the most abundant of the benzoxazinone derivatives. An increase in the concentration was observed in early spring compared to late autumn, suggesting that plants synthesized benzoxazinone derivatives at the commencement of growth in early spring. The concentrations in the roots were considerably lower than in the foliage at the early growth stages but remained relatively constant over time, resulting in a higher concentration than in the foliage at the late growth stages. The results are discussed in relation to previous findings that predominantly originate from experiments done under controlled conditions in either growth cabinets or greenhouses.

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

    PubMed Central

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

    2015-01-01

    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. Purification, cloning and functional characterization of a fructan 6-exohydrolase from wheat (Triticum aestivum L.).

    PubMed

    Van Riet, Liesbet; Nagaraj, Vinay; Van den Ende, Wim; Clerens, Stefan; Wiemken, Andres; Van Laere, André

    2006-01-01

    Fructans, beta2-1 and/or beta2-6 linked polymers of fructose, are produced by fructosyltransferases (FTs) from sucrose. They are important storage carbohydrates in many plants. Fructan reserves, widely distributed in plants, are believed to be mobilized via fructan exohydrolases (FEHs). The purification, cloning, and functional characterization of a 6-FEH from wheat (Triticum aestivum L.) are reported here. It is the first FEH shown to hydrolyse exclusively beta2-6 bonds found in a fructan-producing plant. The enzyme was purified to homogeneity using ammonium sulphate precipitation, ConA affinity-, ion exchange-, and size exclusion chromatography and yielded a single band of 70 kDa following SDS-PAGE. Sequence information obtained by mass spectrometry of in-gel trypsin digests demonstrated the presence of a single protein. Moreover, these unique peptide sequences, together with some ESTs coding for them, could be used in a RT-PCR based strategy to clone a 1.7 kb cDNA. Functionality tests of the cDNA performed after heterologous expression in the yeast Pichia pastoris showed--as did the native enzyme from wheat--a very high activity of the produced protein against bacterial levan, 6-kestose, and phlein whilst sucrose and inulin were not used as substrates. Therefore the enzyme is a genuine 6-FEH. In contrast to most FEHs from fructan-accumulating plants, this FEH is not inhibited by sucrose. The relative abundance of 6-FEH transcripts in various tissues of wheat was investigated using quantitative RT-PCR.

  17. 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.

  18. Characterization and Expression Analysis of Phytoene Synthase from Bread Wheat (Triticum aestivum L.)

    PubMed Central

    Flowerika; Alok, Anshu; Kumar, Jitesh; Thakur, Neha; Pandey, Ashutosh; Pandey, Ajay Kumar; Upadhyay, Santosh Kumar; Tiwari, Siddharth

    2016-01-01

    Phytoene synthase (PSY) regulates the first committed step of the carotenoid biosynthetic pathway in plants. The present work reports identification and characterization of the three PSY genes (TaPSY1, TaPSY2 and TaPSY3) in wheat (Triticum aestivum L.). The TaPSY1, TaPSY2, and TaPSY3 genes consisted of three homoeologs on the long arm of group 7 chromosome (7L), short arm of group 5 chromosome (5S), and long arm of group 5 chromosome (5L), respectively in each subgenomes (A, B, and D) with a similarity range from 89% to 97%. The protein sequence analysis demonstrated that TaPSY1 and TaPSY3 retain most of conserved motifs for enzyme activity. Phylogenetic analysis of all TaPSY revealed an evolutionary relationship among PSY proteins of various monocot species. TaPSY derived from A and D subgenomes shared proximity to the PSY of Triticum urartu and Aegilops tauschii, respectively. The differential expression of TaPSY1, TaPSY2, and TaPSY3 in the various tissues, seed development stages, and stress treatments suggested their role in plant development, and stress condition. TaPSY3 showed higher expression in all tissues, followed by TaPSY1. The presence of multiple stress responsive cis-regulatory elements in promoter region of TaPSY3 correlated with the higher expression during drought and heat stresses has suggested their role in these conditions. The expression pattern of TaPSY3 was correlated with the accumulation of β-carotene in the seed developmental stages. Bacterial complementation assay has validated the functional activity of each TaPSY protein. Hence, TaPSY can be explored in developing genetically improved wheat crop. PMID:27695116

  19. 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

  20. Cloning and sequencing of cDNAs encoding a pathogen-induced putative peroxidase of wheat (Triticum aestivum L.).

    PubMed

    Rebmann, G; Hertig, C; Bull, J; Mauch, F; Dudler, R

    1991-02-01

    We report here the complete amino acid sequence of a pathogen-induced putative peroxidase from wheat (Triticum aestivum L.) as deduced from cDNA clones representing mRNA from leaves infected with the powdery mildew fungus Erysiphe graminis. The protein consists of 312 amino acids, of which the first 22 form a putative signal sequence, and has a calculated pI of 5.7. Sequence comparison revealed that the putative wheat peroxidase is most similar to the turnip (Brassica rapa) peroxidase, with which it shares 57% identical and 13% conserved amino acids.

  1. Cloning and sequencing of cDNAs encoding a pathogen-induced putative peroxidase of wheat (Triticum aestivum L.).

    PubMed

    Rebmann, G; Hertig, C; Bull, J; Mauch, F; Dudler, R

    1991-02-01

    We report here the complete amino acid sequence of a pathogen-induced putative peroxidase from wheat (Triticum aestivum L.) as deduced from cDNA clones representing mRNA from leaves infected with the powdery mildew fungus Erysiphe graminis. The protein consists of 312 amino acids, of which the first 22 form a putative signal sequence, and has a calculated pI of 5.7. Sequence comparison revealed that the putative wheat peroxidase is most similar to the turnip (Brassica rapa) peroxidase, with which it shares 57% identical and 13% conserved amino acids. PMID:1893103

  2. Chromium uptake and toxicity effects on growth and metabolic activities in wheat, Triticum aestivum L. cv. UP 2003.

    PubMed

    Sharma, D C; Sharma, C P

    1996-07-01

    Chromium (Cr) at graded levels when added in sand culture of wheat (T. aestivum L. cv. UP2003) under glasshouse conditions resulted in reduction in biomass, chlorophyll and activities of catalase and peroxidase while enhanced acid phosphatase and ribonuclease activities. Elevated levels of Cr supply significantly reduced the concentration of inorganic phosphorus. With an increase in Cr supply the uptake of chromium also increased significantly in different plant parts especially in roots. Above metabolic lesions due to Cr in wheat provided evidence that the element in nutrient medium if present in excess may be inhibitory to plant growth and development.

  3. 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...

  4. 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

  5. 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

  6. 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

  7. Molecular Characterization and Expression Analysis of Triticum aestivum Squamosa-Promoter Binding Protein-Box Genes Involved in Ear Development

    PubMed Central

    Zhang, Bin; Liu, Xia; Zhao, Guangyao; Mao, Xinguo; Li, Ang; Jing, Ruilian

    2014-01-01

    Wheat (Triticum aestivum L.) is one of the most important crops in the world. Squamosa-promoter binding protein (SBP)-box genes play a critical role in regulating flower and fruit development. In this study, 10 novel SBP-box genes (TaSPL genes) were isolated from wheat ((Triticum aestivum L.) cultivar Yanzhan 4110). Phylogenetic analysis classified the TaSPL genes into five groups (G1–G5). The motif combinations and expression patterns of the TaSPL genes varied among the five groups with each having own distinctive characteristics: TaSPL20/21 in G1 and TaSPL17 in G2 mainly expressed in the shoot apical meristem and the young ear, and their expression levels responded to development of the ear; TaSPL6/15 belonging to G3 were upregulated and TaSPL1/23 in G4 were downregulated during grain development; the gene in G5 (TaSPL3) expressed constitutively. Thus, the consistency of the phylogenetic analysis, motif compositions, and expression patterns of the TaSPL genes revealed specific gene structures and functions. On the other hand, the diverse gene structures and different expression patterns suggested that wheat SBP-box genes have a wide range of functions. The results also suggest a potential role for wheat SBP-box genes in ear development. This study provides a significant beginning of functional analysis of SBP-box genes in wheat. PMID:24386921

  8. 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

  9. Molecular characterization and expression analysis of Triticum aestivum squamosa-promoter binding protein-box genes involved in ear development.

    PubMed

    Zhang, Bin; Liu, Xia; Zhao, Guangyao; Mao, Xinguo; Li, Ang; Jing, Ruilian

    2014-06-01

    Wheat (Triticum aestivum L.) is one of the most important crops in the world. Squamosa-promoter binding protein (SBP)-box genes play a critical role in regulating flower and fruit development. In this study, 10 novel SBP-box genes (TaSPL genes) were isolated from wheat ((Triticum aestivum L.) cultivar Yanzhan 4110). Phylogenetic analysis classified the TaSPL genes into five groups (G1-G5). The motif combinations and expression patterns of the TaSPL genes varied among the five groups with each having own distinctive characteristics: TaSPL20/21 in G1 and TaSPL17 in G2 mainly expressed in the shoot apical meristem and the young ear, and their expression levels responded to development of the ear; TaSPL6/15 belonging to G3 were upregulated and TaSPL1/23 in G4 were downregulated during grain development; the gene in G5 (TaSPL3) expressed constitutively. Thus, the consistency of the phylogenetic analysis, motif compositions, and expression patterns of the TaSPL genes revealed specific gene structures and functions. On the other hand, the diverse gene structures and different expression patterns suggested that wheat SBP-box genes have a wide range of functions. The results also suggest a potential role for wheat SBP-box genes in ear development. This study provides a significant beginning of functional analysis of SBP-box genes in wheat.

  10. Ecotoxicological effects of polycyclic musks and cadmium on seed germination and seedling growth of wheat (Triticum aestivum).

    PubMed

    Chen, Cuihong; Zhou, Qixing; Bao, Yanyu; Li, Yaning; Wang, Ping

    2010-01-01

    Single and joint toxic effects of polycyclic musks including 1,3,4,6,7,8-hexahydro-4,6,6,6,7,8,8-hexamethylcyclopenta[g]-2-benzopyran (HHCB) and 7-acetyl-1,1,3,4,4,6-hexamethyl-l,2,3,4-tetrahydronapthalene (AHTN) and cadmium (Cd) on seed germination and seedling growth of wheat (Triticum aestivum) were investigated. The results showed that the toxicity sequence of HHCB toxic to wheat seed germination and seedling growth was similar to that of AHTN, that is, germination rate > shoot elongation > root elongation, while the toxicity of Cd was in the sequence of root elongation > shoot elongation > germination rate, according to the LC50 and EC50 values. It is suggested that polycyclic musks and Cd had different toxicological mechanisms. Root and shoot elongation of wheat might be good bioindicators for the contamination of polycyclic musks and Cd in soil. The mixture of polycyclic musks and Cd had synergistic effects on T. aestivum according to the equi-toxic mixture approach when root elongation was selected as the toxicological endpoint. Thus, the joint toxicity of HHCB and Cd was significantly higher than the single toxicity of HHCB or Cd, which was also confirmed by the EC50 mix value of the mixture (EC50 mix = 0.530 TUmix). The EC(50mix) value of the mixture of AHTN and Cd was 0.614 TUmix, which indicated that the mixture toxicity was strengthened when AHTN coexisted with Cd.

  11. 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.

  12. 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

  13. 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

  14. Effect of dissolved organic matter on the toxicity of chlorotoluron to Triticum aestivum.

    PubMed

    Song, Ning-Hui; Yang, Zhi-Min; Zhou, Li-Xian; Wu, Xin; Yang, Hong

    2006-01-01

    Response of two wheat cultivars (Triticum aestivum cv. YM 158 and NM 9) to the herbicide chlorotoluron and the effect of two forms of dissolved organic matter on the chlorotoluron toxicity to the plants were characterized. Treatment with chlorotoluron at 10-50 microg/ml inhibited the seed germination and a dose-response was observed. The inhibition of seed germination was correlated to the depression of alpha-amylase activities. To identify whether chlorotoluron induced oxidative damage to wheat plants, the malondlaldehyde (MDA) content and electrolyte leakage were measured. Results showed that both MDA content and electrolyte leakage in the chlorotoluron-treated roots significantly increased. Activities of several key enzymes were measured that operate in citric acid cycle and carbohydrate metabolic pathway. Inhibited activities of citrate synthase and NADP-isocitrate dehydrogenase were observed in the chlorotoluron-treated roots as compared to control plants. We also examined malate dehydrogenase and phosphoenolpyruvate carboxylase in wheat roots exposed to 30 gg/ml chlorotoluron. However, none of the enzymes showed significant changes in activities. Application of 160 microg/ml dissolved organic matter (DOM) extracted from non-treated sludge (NTS) and heat-expanded sludge (HES) in the medium with 30 microg/ml chlorotoluron induced an additive inhibition of seed germination and plant growth. The inhibition of growth due to the DOM treatment was associated with the depression of activities of alpha-amylase, citrate synthase and NADP-isocitrate dehydrogenase, as well as the increase in malondlaldehyde content and electrolyte leakage. These results suggested that the presence of DOM might enhance the uptake and accumulation of chlorotoluron, and thus resulted in greater toxicity in wheat plants. The two forms of DOM exhibited differences in regulation of chlorotoluron toxicity to the wheat plants. Treatments with DOM-NTS induced greater toxicity to plants as

  15. 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 ...

  16. 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 ...

  17. 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 ...

  18. 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...

  19. 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...

  20. 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...

  1. 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...

  2. 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...

  3. Functional characterisation of wheat Pgip genes reveals their involvement in the local response to wounding.

    PubMed

    Janni, M; Bozzini, T; Moscetti, I; Volpi, C; D'Ovidio, R

    2013-11-01

    Polygalacturonase-inhibiting proteins (PGIPs) are cell wall leucine-rich repeat (LRR) proteins involved in plant defence. The hexaploid wheat (Triticum aestivum, genome AABBDD) genome contains one Pgip gene per genome. Tapgip1 (B genome) and Tapgip2 (D genome) are expressed in all tissues, whereas Tapgip3 (A genome) is inactive because of a long terminal repeat, Copia retrotransposon insertion within the coding region. To verify whether Tapgip1 and Tapgip2 encode active PGIPs and are involved in the wheat defence response, we expressed them transiently and analysed their expression under stress conditions. Neither TaPGIP1 nor TaPGIP2 showed inhibition activity in vitro against fungal polygalacturonases. Moreover, a wheat genotype (T. turgidum ssp. dicoccoides) lacking active homologues of Tapgip1 or Tapgip2 possesses PGIP activity. At transcript level, Tapgip1 and Tapgip2 were both up-regulated after fungal infection and strongly induced following wounding. This latter result has been confirmed in transgenic wheat plants expressing the β-glucuronidase (GUS) gene under control of the 5'-flanking region of Tdpgip1, a homologue of Tapgip1 with an identical sequence. Strong and transient GUS staining was mainly restricted to the damaged tissues and was not observed in adjacent tissues. Taken together, these results suggest that Tapgips and their homologues are involved in the wheat defence response by acting at the site of the lesion caused by pathogen infection.

  4. 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

  5. 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 ... ...

  6. Genetic variability of the low-molecular-weight glutenin subunits in spelt wheat (Triticum aestivum ssp. spelta L. em Thell.).

    PubMed

    Caballero, L; Martín, L M; Alvarez, J B

    2004-03-01

    The low-molecular-weight glutenin subunit composition of a collection of 403 accessions of spelt wheat ( Triticum aestivum ssp. spelta L. em. Thell) was analyzed by SDS-PAGE. Extensive variation was found, including 46 different patterns for zone B and 16 for zone C. Patterns within zone B exhibited from two to six bands and patterns in zone C had between four and six bands in SDS-PAGE gels. A higher number of bands was observed when urea was added to the gels. Zone B exhibited between six and 11 bands, and we identified 14 new patterns in this zone. For zone C, up to ten new patterns that comprised between five and nine bands were detected. For both zones, 86 patterns were found. The variability detected in this material is greater than that detected in other hulled wheats.

  7. 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

  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. 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.

  10. 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.

  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. 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.

  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. A Study of the Protective Effect of Triticum aestivum L. in an Experimental Animal Model of Chronic Fatigue Syndrome

    PubMed Central

    Borah, Mukundam; Sarma, Phulen; Das, Swarnamoni

    2014-01-01

    Background: Oxidative stress plays a major role in the pathogenesis of chronic fatigue syndrome (CFS). Keeping in view the proven antioxidant activity of Triticum aestivum L., this study has been undertaken to explore the potential therapeutic benefit of this plant in the treatment of CFS. Objective: To study the protective effect of the ethanolic extract of the leaves of Triticum aestivum (EETA) in an experimental mice model of CFS. Materials and Methods: Five groups of albino mice (20-25 g) were selected for the study, with five animals in each group. Group A served as the naïve control and Group B served as the stressed control. Groups C and D received EETA (100 mg/kg and 200 mg/kg b.w.). Group E received imipramine (20 mg/kg b.w.). Except for Group A, mice in each group were forced to swim 6 min each for 7 days to induce a state of chronic fatigue. Duration of immobility was measured on every alternate day. After 7 days, various behavioral tests (mirror chamber and elevated plus maize test for anxiety, open field test for locomotor activity) and biochemical estimations (malondialdehyde [MDA] and catalase activity) in mice brain were performed. Results: Forced swimming in the stressed group resulted in a significant increase in immobility period, decrease in locomotor activity and elevated anxiety level. The brain homogenate showed significantly increased MDA and decreased catalase levels. The extract-treated groups showed significantly (P < 0.05) improved locomotor activity, decreased anxiety level, elevated catalase levels and reduction of MDA. Conclusion: The study confirms the protective effects of EETA in CFS. PMID:25276064

  15. Identification and Characterization of Shared Duplications between Rice and Wheat Provide New Insight into Grass Genome Evolution[W

    PubMed Central

    Salse, Jérôme; Bolot, Stéphanie; Throude, Michaël; Jouffe, Vincent; Piegu, Benoît; Quraishi, Umar Masood; Calcagno, Thomas; Cooke, Richard; Delseny, Michel; Feuillet, Catherine

    2008-01-01

    The grass family comprises the most important cereal crops and is a good system for studying, with comparative genomics, mechanisms of evolution, speciation, and domestication. Here, we identified and characterized the evolution of shared duplications in the rice (Oryza sativa) and wheat (Triticum aestivum) genomes by comparing 42,654 rice gene sequences with 6426 mapped wheat ESTs using improved sequence alignment criteria and statistical analysis. Intraspecific comparisons identified 29 interchromosomal duplications covering 72% of the rice genome and 10 duplication blocks covering 67.5% of the wheat genome. Using the same methodology, we assessed orthologous relationships between the two genomes and detected 13 blocks of colinearity that represent 83.1 and 90.4% of the rice and wheat genomes, respectively. Integration of the intraspecific duplications data with colinearity relationships revealed seven duplicated segments conserved at orthologous positions. A detailed analysis of the length, composition, and divergence time of these duplications and comparisons with sorghum (Sorghum bicolor) and maize (Zea mays) indicated common and lineage-specific patterns of conservation between the different genomes. This allowed us to propose a model in which the grass genomes have evolved from a common ancestor with a basic number of five chromosomes through a series of whole genome and segmental duplications, chromosome fusions, and translocations. PMID:18178768

  16. Imaging genomics

    PubMed Central

    Thompson, Paul M.; Martin, Nicholas G.; Wright, Margaret J.

    2010-01-01

    Purpose of review Imaging genomics is an emerging field that is rapidly identifying genes that influence the brain, cognition, and risk for disease. Worldwide, thousands of individuals are being scanned with high-throughput genotyping (genome-wide scans), and new imaging techniques [high angular resolution diffusion imaging and resting state functional magnetic resonance imaging (MRI)] that provide fine-grained measures of the brain’s structural and functional connectivity. Along with clinical diagnosis and cognitive testing, brain imaging offers highly reproducible measures that can be subjected to genetic analysis. Recent findings Recent studies of twin, pedigree, and population-based datasets have discovered several candidate genes that consistently show small to moderate effects on brain measures. Many studies measure single phenotypes from the images, such as hippocampal volume, but voxel-wise genomic methods can plot the profile of genetic association at each 3D point in the brain. This exploits the full arsenal of imaging statistics to discover and replicate gene effects. Summary Imaging genomics efforts worldwide are now working together to discover and replicate many promising leads. By studying brain phenotypes closer to causative gene action, larger gene effects are detectable with realistic sample sizes obtainable from meta-analysis of smaller studies. Imaging genomics has broad applications to dementia, mental illness, and public health. PMID:20581684

  17. 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.

  18. 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.

  19. 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

  20. Dynamics and Differential Proliferation of Transposable Elements During the Evolution of the B and A Genomes of Wheat

    PubMed Central

    Charles, Mathieu; Belcram, Harry; Just, Jérémy; Huneau, Cécile; Viollet, Agnès; Couloux, Arnaud; Segurens, Béatrice; Carter, Meredith; Huteau, Virginie; Coriton, Olivier; Appels, Rudi; Samain, Sylvie; Chalhoub, Boulos

    2008-01-01

    Transposable elements (TEs) constitute >80% of the wheat genome but their dynamics and contribution to size variation and evolution of wheat genomes (Triticum and Aegilops species) remain unexplored. In this study, 10 genomic regions have been sequenced from wheat chromosome 3B and used to constitute, along with all publicly available genomic sequences of wheat, 1.98 Mb of sequence (from 13 BAC clones) of the wheat B genome and 3.63 Mb of sequence (from 19 BAC clones) of the wheat A genome. Analysis of TE sequence proportions (as percentages), ratios of complete to truncated copies, and estimation of insertion dates of class I retrotransposons showed that specific types of TEs have undergone waves of differential proliferation in the B and A genomes of wheat. While both genomes show similar rates and relatively ancient proliferation periods for the Athila retrotransposons, the Copia retrotransposons proliferated more recently in the A genome whereas Gypsy retrotransposon proliferation is more recent in the B genome. It was possible to estimate for the first time the proliferation periods of the abundant CACTA class II DNA transposons, relative to that of the three main retrotransposon superfamilies. Proliferation of these TEs started prior to and overlapped with that of the Athila retrotransposons in both genomes. However, they also proliferated during the same periods as Gypsy and Copia retrotransposons in the A genome, but not in the B genome. As estimated from their insertion dates and confirmed by PCR-based tracing analysis, the majority of differential proliferation of TEs in B and A genomes of wheat (87 and 83%, respectively), leading to rapid sequence divergence, occurred prior to the allotetraploidization event that brought them together in Triticum turgidum and Triticum aestivum, <0.5 million years ago. More importantly, the allotetraploidization event appears to have neither enhanced nor repressed retrotranspositions. We discuss the apparent proliferation

  1. Dynamics and differential proliferation of transposable elements during the evolution of the B and A genomes of wheat.

    PubMed

    Charles, Mathieu; Belcram, Harry; Just, Jérémy; Huneau, Cécile; Viollet, Agnès; Couloux, Arnaud; Segurens, Béatrice; Carter, Meredith; Huteau, Virginie; Coriton, Olivier; Appels, Rudi; Samain, Sylvie; Chalhoub, Boulos

    2008-10-01

    Transposable elements (TEs) constitute >80% of the wheat genome but their dynamics and contribution to size variation and evolution of wheat genomes (Triticum and Aegilops species) remain unexplored. In this study, 10 genomic regions have been sequenced from wheat chromosome 3B and used to constitute, along with all publicly available genomic sequences of wheat, 1.98 Mb of sequence (from 13 BAC clones) of the wheat B genome and 3.63 Mb of sequence (from 19 BAC clones) of the wheat A genome. Analysis of TE sequence proportions (as percentages), ratios of complete to truncated copies, and estimation of insertion dates of class I retrotransposons showed that specific types of TEs have undergone waves of differential proliferation in the B and A genomes of wheat. While both genomes show similar rates and relatively ancient proliferation periods for the Athila retrotransposons, the Copia retrotransposons proliferated more recently in the A genome whereas Gypsy retrotransposon proliferation is more recent in the B genome. It was possible to estimate for the first time the proliferation periods of the abundant CACTA class II DNA transposons, relative to that of the three main retrotransposon superfamilies. Proliferation of these TEs started prior to and overlapped with that of the Athila retrotransposons in both genomes. However, they also proliferated during the same periods as Gypsy and Copia retrotransposons in the A genome, but not in the B genome. As estimated from their insertion dates and confirmed by PCR-based tracing analysis, the majority of differential proliferation of TEs in B and A genomes of wheat (87 and 83%, respectively), leading to rapid sequence divergence, occurred prior to the allotetraploidization event that brought them together in Triticum turgidum and Triticum aestivum, <0.5 million years ago. More importantly, the allotetraploidization event appears to have neither enhanced nor repressed retrotranspositions. We discuss the apparent proliferation

  2. Toward a cytogenetically based physical map of the wheat genome.

    PubMed Central

    Werner, J E; Endo, T R; Gill, B S

    1992-01-01

    Bread wheat (Triticum aestivum L. em Thell) is well suited for cytogenetic analysis because the genome, buffered by polyploidy, can tolerate structurally and numerically engineered chromosomes for analysis over infinite generations. This feature of polyploidy can be used in developing a high-resolution, cytogenetically based physical map of the wheat genome. We show that numerous deletions, observed in the progeny of a monosomic addition of a chromosome from Triticum cylindricum in wheat, result from single breakpoints and a concomitant loss of distal fragments. Breakages occurred in euchromatic and heterochromatic regions. Forty-one deletions for chromosomes 7A, 7B, and 7D, and a set of genetically mapped DNA probes, were used to construct physical maps. Recombination was low in proximal chromosomal regions and very high toward the distal ends. Deletion mapping was more efficient than genetic mapping in resolving the order of proximal loci. Despite variation in size and arm ratio, relative gene position was largely conserved among chromosomes 7A, 7B, and 7D and a consensus group 7 physical map was constructed. Several molecularly tagged chromosome regions (MTCRs) of approximately one to a few million base pairs were identified that may be resolved by long-range mapping of DNA fragments. Thus, a cytogenetically based physical map may be used to integrate chromosome and DNA-based maps. The MTCRs may simplify strategies for cloning of agronomically useful genes despite the genetic complexity and the large genome size of wheat. Images PMID:1360666

  3. Comparative genomics - a perspective.

    PubMed

    Sivashankari, Selvarajan; Shanmughavel, Piramanayagam

    2007-03-27

    The rapidly emerging field of comparative genomics has yielded dramatic results. Comparative genome analysis has become feasible with the availability of a number of completely sequenced genomes. Comparison of complete genomes between organisms allow for global views on genome evolution and the availability of many completely sequenced genomes increases the predictive power in deciphering the hidden information in genome design, function and evolution. Thus, comparison of human genes with genes from other genomes in a genomic landscape could help assign novel functions for un-annotated genes. Here, we discuss the recently used techniques for comparative genomics and their derived inferences in genome biology.

  4. Comparative genomics - A perspective

    PubMed Central

    Sivashankari, Selvarajan; Shanmughavel, Piramanayagam

    2007-01-01

    The rapidly emerging field of comparative genomics has yielded dramatic results. Comparative genome analysis has become feasible with the availability of a number of completely sequenced genomes. Comparison of complete genomes between organisms allow for global views on genome evolution and the availability of many completely sequenced genomes increases the predictive power in deciphering the hidden information in genome design, function and evolution. Thus, comparison of human genes with genes from other genomes in a genomic landscape could help assign novel functions for un-annotated genes. Here, we discuss the recently used techniques for comparative genomics and their derived inferences in genome biology. PMID:17597925

  5. Genome cartography: charting the apicomplexan genome.

    PubMed

    Kissinger, Jessica C; DeBarry, Jeremy

    2011-08-01

    Genes reside in particular genomic contexts that can be mapped at many levels. Historically, 'genetic maps' were used primarily to locate genes. Recent technological advances in the determination of genome sequences have made the analysis and comparison of whole genomes possible and increasingly tractable. What do we see if we shift our focus from gene content (the 'inventory' of genes contained within a genome) to the composition and organization of a genome? This review examines what has been learned about the evolution of the apicomplexan genome as well as the significance and impact of genomic location on our understanding of the eukaryotic genome and parasite biology.

  6. Morphological, anatomical, and ultrastructural changes (visualized through scanning electron microscopy) induced in Triticum aestivum by Pb²⁺ treatment.

    PubMed

    Kaur, Gurpreet; Singh, Harminder Pal; Batish, Daizy Rani; Kohli, Ravinder Kumar

    2014-11-01

    Lead (Pb) causes severe damage to crops, ecosystems, and humans, and alters the physiology and biochemistry of various plant species. It is hypothesized that Pb-induced metabolic alterations could manifest as structural variations in the roots of plants. In light of this, the morphological, anatomical, and ultrastructural variations (through scanning electron microscopy, SEM) were studied in 4-day-old seedlings of Triticum aestivum grown under Pb stress (0, 8, 16, 40, and 80 mg Pb(2+) l(-1); mild to highly toxic). The toxic effect was more pronounced in radicle growth than on the plumule growth. The SEM of the root of T. aestivum depicted morphological alterations and surface ultrastructural changes. Compared to intact and uniform surface cells in the control roots, cells were irregular and desiccated in Pb(2+)-treated roots. In Pb(2+)-treated roots, the number of root hairs increased manifold, showing dense growth, and these were apparently longer. Apart from the deformity in surface morphology and anatomy of the roots in response to Pb(2+) toxicity, considerable anatomical alterations were also observed. Pb(2+)-treated root exhibited signs of injury in the form of cell distortion, particularly in the cortical cells. The endodermis and pericycle region showed loss of uniformity post Pb(2+) exposure (at 80 mg l(-1) Pb(2+)). The cells appeared to be squeezed with greater depositions observed all over the tissue. The study concludes that Pb(2+) treatment caused structural anomalies and induced anatomical and surface ultrastructural changes in T. aestivum.

  7. Triticum aestivum shows a greater biomass response to a supply of aluminium phosphate than Lupinus albus, despite releasing fewer carboxylates into the rhizosphere.

    PubMed

    Pearse, Stuart J; Veneklaas, Erik J; Cawthray, Greg; Bolland, Mike D A; Lambers, Hans

    2006-01-01

    The relationship between carboxylate release and the ability of plants to access phosphorus from AlPO4 and to detoxify aluminium was studied by comparing species with a low and high rate of carboxylate release, Triticum aestivum (wheat) and Lupinus albus (white lupin), respectively. Species were supplied with P at 10, 20, 40 or 100 mg P kg-1 sand in the form of sparingly soluble AlPO4 or soluble KH2PO4; control plants did not receive any P. Triticum aestivum was significantly better than L. albus at accessing P from AlPO4, despite accumulating fewer carboxylates in its rhizosphere. Rhizosphere pH of L. albus did not vary with form or level of P supply, while the rhizosphere pH of T. aestivum increased with the level of P supplied. Based on the evidence in the present study, a model is proposed to explain the poor performance of L. albus, whereby the release of carboxylates and associated protons reduces the chelating ability of exuded carboxylates, thus reducing P acquisition and increasing Al toxicity.

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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.

  13. Predictions of heading date in bread wheat (Triticum aestivum L.) using QTL-based parameters of an ecophysiological model.

    PubMed

    Bogard, Matthieu; Ravel, Catherine; Paux, Etienne; Bordes, Jacques; Balfourier, François; Chapman, Scott C; Le Gouis, Jacques; Allard, Vincent

    2014-11-01

    Prediction of wheat phenology facilitates the selection of cultivars with specific adaptations to a particular environment. However, while QTL analysis for heading date can identify major genes controlling phenology, the results are limited to the environments and genotypes tested. Moreover, while ecophysiological models allow accurate predictions in new environments, they may require substantial phenotypic data to parameterize each genotype. Also, the model parameters are rarely related to all underlying genes, and all the possible allelic combinations that could be obtained by breeding cannot be tested with models. In this study, a QTL-based model is proposed to predict heading date in bread wheat (Triticum aestivum L.). Two parameters of an ecophysiological model (V sat and P base , representing genotype vernalization requirements and photoperiod sensitivity, respectively) were optimized for 210 genotypes grown in 10 contrasting location × sowing date combinations. Multiple linear regression models predicting V sat and P base with 11 and 12 associated genetic markers accounted for 71 and 68% of the variance of these parameters, respectively. QTL-based V sat and P base estimates were able to predict heading date of an independent validation data set (88 genotypes in six location × sowing date combinations) with a root mean square error of prediction of 5 to 8.6 days, explaining 48 to 63% of the variation for heading date. The QTL-based model proposed in this study may be used for agronomic purposes and to assist breeders in suggesting locally adapted ideotypes for wheat phenology.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. PI3K is involved in nucleolar structure and function on root-tip meristematic cells of Triticum aestivum L.

    PubMed

    Ni, Xiaolin; Zhang, Feixiong

    2014-06-01

    In this study, wheat (Triticum aestivum L.) seeds were used to detect the effect of wortmannin, a specific inhibitor of PI3K, on the nucleolar structure and function. When the germinated seeds were treated with wortmannin, it was shown that the root growth was suppressed and the mitotic index was decreased. The inhibition effects were positively correlated with the concentrations of the drug. The observations of light and transmission electron microscopy revealed that the nucleolar morphology became irregular and their fine structure disappeared. Some granules with a size range of 0.05-0.30 μm diffused from the nucleoli and gradually moved to the nucleoplasm between or around the chromatin. Indirect immunofluorescence staining indicated that B23 shuttled from the nucleoli to the nucleoplasm, or even, to the cytoplasm. RT-PCR technique demonstrated that the expression of C23 was severely down-regulated. Our results suggest, for the first time, that wortmannin treatment can not only damage nucleolar structure, but also inhibit its function, implying that PI3K is involved in nucleolar structure and function.

  19. 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.

  20. Comprehensive analysis of the transcription of starch synthesis genes and the transcription factor RSR1 in wheat (Triticum aestivum) endosperm.

    PubMed

    Kang, Guo-Zhang; Xu, Wei; Liu, Guo-Qin; Peng, Xiao-Qi; Guo, Tian-Cai

    2013-02-01

    The cDNA sequences of 26 starch synthesis genes were identified in common wheat (Triticum aestivum L.), and their transcript levels were measured using quantitative real-time RT-PCR to assess the function of individual genes and the regulatory mechanism in wheat endosperm. The expression patterns of 26 genes in wheat endosperm were classified into three groups. The genes in group 1 were richly expressed in the early stage of grain development and may be involved in the construction of fundamental cell machinery, synthesis of glucan primers, and initiation of starch granules. The genes in group 2 were highly expressed during the middle and late stages of grain development, and their expression profiles were similar to the accumulation rate of endosperm starch; these genes are presumed to play a crucial role in starch production. The genes in group 3 were scantily expressed throughout the grain development period and might be associated with transitory starch synthesis. Transcripts of the negative transcription factor TaRSR1 were high at the early and late stages of grain development but low during the middle stage. The expression pattern of TaRSR1 was almost opposite to those of the group 2 starch synthesis genes, indicating that TaRSR1 might negatively regulate the expression of many endosperm starch synthesis genes during grain development.

  1. 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.

  2. 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

  3. Predictions of heading date in bread wheat (Triticum aestivum L.) using QTL-based parameters of an ecophysiological model

    PubMed Central

    Bogard, Matthieu; Ravel, Catherine; Paux, Etienne; Bordes, Jacques; Balfourier, François; Chapman, Scott C.; Le Gouis, Jacques; Allard, Vincent

    2014-01-01

    Prediction of wheat phenology facilitates the selection of cultivars with specific adaptations to a particular environment. However, while QTL analysis for heading date can identify major genes controlling phenology, the results are limited to the environments and genotypes tested. Moreover, while ecophysiological models allow accurate predictions in new environments, they may require substantial phenotypic data to parameterize each genotype. Also, the model parameters are rarely related to all underlying genes, and all the possible allelic combinations that could be obtained by breeding cannot be tested with models. In this study, a QTL-based model is proposed to predict heading date in bread wheat (Triticum aestivum L.). Two parameters of an ecophysiological model (V sat and P base, representing genotype vernalization requirements and photoperiod sensitivity, respectively) were optimized for 210 genotypes grown in 10 contrasting location × sowing date combinations. Multiple linear regression models predicting V sat and P base with 11 and 12 associated genetic markers accounted for 71 and 68% of the variance of these parameters, respectively. QTL-based V sat and P base estimates were able to predict heading date of an independent validation data set (88 genotypes in six location × sowing date combinations) with a root mean square error of prediction of 5 to 8.6 days, explaining 48 to 63% of the variation for heading date. The QTL-based model proposed in this study may be used for agronomic purposes and to assist breeders in suggesting locally adapted ideotypes for wheat phenology. PMID:25148833

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. Effects of As on As uptake, speciation, and nutrient uptake by winter wheat (Triticum aestivum L.) under hydroponic conditions.

    PubMed

    Liu, Quanji; Hu, Chengxiao; Tan, Qiling; Sun, Xuecheng; Su, Jingjun; Liang, Yuexiang

    2008-01-01

    A hydroponic experiment was conducted to investigate the effects of arsenic (As) stress on growth, nutrition and As uptake, and speciation in shoots and roots of winter wheat (Triticum aestivum L.). Winter wheat has high tolerance to As. Most As is accumulated in the roots, and an As concentration of 4,421 mg/kg was observed at a solution concentration of 20 mg/L As. Arsenic concentrations in roots were approximately 40-100 times greater than those in shoots. Arsenic in winter wheat roots and shoots occurred as both As3+ and As5+ species, although As3+ was the main species in winter wheat tissues. Arsenic significantly decreased the biomass of winter wheat shoots and roots and affected absorption and transport of micro- and macro-elements in winter wheat tissue. Arsenic treatment significantly increased the concentrations of total Magnesium (Mg) and calcium (Ca) in shoots and enhanced the transport of Mg and Ca from roots to shoots but decreased potassium (K), nitrogen (N), and phosphorus (P) concentrations in both shoots and roots, particularly the concentration of P. Concentrations of iron, copper, and zinc in winter wheat shoots were negatively related to As rates, with correlation coefficients (R2) of 0.93, 0.94, and 0.97, respectively.

  9. 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

  10. Cloning and Characterization of Low-Molecular-Weight Glutenin Subunit Alleles from Chinese Wheat Landraces (Triticum aestivum L.)

    PubMed Central

    Zhao, Manli; Zhang, Xin; Yao, Guoliang; Sun, Genlou

    2014-01-01

    Low-molecular-weight glutenin subunits (LMW-GS) are of great importance in processing quality and participate in the formation of polymers in wheat. In this study, eight new LMW-GS alleles were isolated from Chinese wheat landraces (Triticum aestivum L.) and designated as Glu-A3-1a, Glu-A3-1b, Glu-B3-1a, Glu-B3-1b, Glu-B3-1c, Glu-D3-1a, Glu-D3-1b, and Glu-D3-1c, which were located at the Glu-A3, Glu-B3, and Glu-D3 loci, respectively. Based on the proteins encoded, the number of deduced amino acids of Glu-B3 alleles was approximately 50 more than those of Glu-A3 and Glu-D3 alleles. The first cysteine of Glu-A3 and Glu-D3 alleles was located at the N-terminal domain, while that of Glu-B3 alleles was found in the repetitive domain, which may lead to the different functioning in forming disulfide bonds. All the eight genes were LMW-m types and the new allele of Glu-B3-1a which had nine cysteine residues may be the desirable LMW-GS gene for improving bread-making quality. PMID:24982945

  11. 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.

  12. 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).

  13. 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

  14. 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

  15. 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

  16. Effect of lead stress on mineral content and growth of wheat (Triticum aestivum) and spinach (Spinacia oleracea) seedlings.

    PubMed

    Lamhamdi, Mostafa; El Galiou, Ouiam; Bakrim, Ahmed; Nóvoa-Muñoz, Juan Carlos; Arias-Estévez, Manuel; Aarab, Ahmed; Lafont, René

    2013-01-01

    Lead (Pb) is the most common heavy metal contaminant in the environment. Pb is not an essential element for plants, but they absorb it when it is present in their environment, especially in rural areas when the soil is polluted by automotive exhaust and in fields contaminated with fertilizers containing heavy metal impurities. To investigate lead effects on nutrient uptake and metabolism, two plant species, spinach (Spinacia oleracea) and wheat (Triticum aestivum), were grown under hydroponic conditions and stressed with lead nitrate, Pb(NO3)2, at three concentrations (1.5, 3, and 15 mM). Lead is accumulated in a dose-dependent manner in both plant species, which results in reduced growth and lower uptake of all mineral ions tested. Total amounts and concentrations of most mineral ions (Na, K, Ca, P, Mg, Fe, Cu and Zn) are reduced, although Mn concentrations are increased, as its uptake is reduced less relative to the whole plant's growth. The deficiency of mineral nutrients correlates in a strong decrease in the contents of chlorophylls a and b and proline in both species, but these effects are less pronounced in spinach than in wheat. By contrast, the effects of lead on soluble proteins differ between species; they are reduced in wheat at all lead concentrations, whereas they are increased in spinach, where their value peaks at 3 mM Pb. The relative lead uptake by spinach and wheat, and the different susceptibility of these two species to lead treatment are discussed.

  17. 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.

  18. 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.

  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. 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

  1. 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

  2. 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

  3. 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

  4. 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

  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. Genome evolution of intermediate wheatgrass as revealed by EST-SSR markers developed from its three progenitor diploid species.

    PubMed

    Wang, Richard R-C; Larson, Steve R; Jensen, Kevin B; Bushman, B Shaun; DeHaan, Lee R; Wang, Shuwen; Yan, Xuebing

    2015-02-01

    Intermediate wheatgrass (Thinopyrum intermedium (Host) Barkworth & D.R. Dewey), a segmental autoallohexaploid (2n = 6x = 42), is not only an important forage crop but also a valuable gene reservoir for wheat (Triticum aestivum L.) improvement. Throughout the scientific literature, there continues to be disagreement as to the origin of the different genomes in intermediate wheatgrass. Genotypic data obtained from newly developed EST-SSR primers derived from the putative progenitor diploid species Pseudoroegneria spicata (Pursh) Á. Löve (St genome), Thinopyrum bessarabicum (Savul. & Rayss) Á. Löve (J = J(b) = E(b)), and Thinopyrum elongatum (Host) D. Dewey (E = J(e) = E(e)) indicate that the V genome of Dasypyrum (Coss. & Durieu) T. Durand is not one of the three genomes in intermediate wheatgrass. Based on all available information in the literature and findings in this study, the genomic designation of intermediate wheatgrass should be changed to J(vs)J(r)St, where J(vs) and J(r) represent ancestral genomes of present-day J(b) of Th. bessarabicum and J(e) of Th. elongatum, with J(vs) being more ancient. Furthermore, the information suggests that the St genome in intermediate wheatgrass is most similar to the present-day St found in diploid species of Pseudoroegneria from Eurasia.

  7. Genome evolution of intermediate wheatgrass as revealed by EST-SSR markers developed from its three progenitor diploid species.

    PubMed

    Wang, Richard R-C; Larson, Steve R; Jensen, Kevin B; Bushman, B Shaun; DeHaan, Lee R; Wang, Shuwen; Yan, Xuebing

    2015-02-01

    Intermediate wheatgrass (Thinopyrum intermedium (Host) Barkworth & D.R. Dewey), a segmental autoallohexaploid (2n = 6x = 42), is not only an important forage crop but also a valuable gene reservoir for wheat (Triticum aestivum L.) improvement. Throughout the scientific literature, there continues to be disagreement as to the origin of the different genomes in intermediate wheatgrass. Genotypic data obtained from newly developed EST-SSR primers derived from the putative progenitor diploid species Pseudoroegneria spicata (Pursh) Á. Löve (St genome), Thinopyrum bessarabicum (Savul. & Rayss) Á. Löve (J = J(b) = E(b)), and Thinopyrum elongatum (Host) D. Dewey (E = J(e) = E(e)) indicate that the V genome of Dasypyrum (Coss. & Durieu) T. Durand is not one of the three genomes in intermediate wheatgrass. Based on all available information in the literature and findings in this study, the genomic designation of intermediate wheatgrass should be changed to J(vs)J(r)St, where J(vs) and J(r) represent ancestral genomes of present-day J(b) of Th. bessarabicum and J(e) of Th. elongatum, with J(vs) being more ancient. Furthermore, the information suggests that the St genome in intermediate wheatgrass is most similar to the present-day St found in diploid species of Pseudoroegneria from Eurasia. PMID:26000870

  8. Lateral genomics.

    PubMed

    Doolittle, W F

    1999-12-01

    More than 20 complete prokaryotic genome sequences are now publicly available, each by itself an unparalleled resource for understanding organismal biology. Collectively, these data are even more powerful: they could force a dramatic reworking of the framework in which we understand biological evolution. It is possible that a single universal phylogenetic tree is not the best way to depict relationships between all living and extinct species. Instead a web- or net-like pattern, reflecting the importance of horizontal or lateral gene transfer between lineages of organisms, might provide a more appropriate visual metaphor. Here, I ask whether this way of thinking is really justified, and explore its implications.

  9. 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

    2016-06-17

    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.

  10. 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

  11. 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

  12. 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

  13. Molecular cytogenetic analysis of wheat - Elymus repens introgression lines with resistance to Fusarium head blight.

    PubMed

    Zeng, J; Cao, W; Hucl, P; Yang, Y; Xue, A; Chi, D; Fedak, G

    2013-01-01

    Elymus repens (L.) Gould (2n = 6x = 42, StStStStHH) is a hexaploid perennial wheatgrass species from the tribe Triticeae, distantly related to bread wheat Triticum aestivum L. (2n = 6x = 42, AABBDD). As a potential source of resistance to Fusarium head blight (FHB), E. repens was crossed to common wheat to transfer resistance genes. The progeny were advanced to homozygosity by single seed descent. A total of eight BC(1)F(9) progeny lines were selected and characterized in this study. The chromosome numbers of these derived lines ranged from 42 to 56, including lines with 44, 52, and 54 chromosomes. All of the lines were cytologically stable in terms of meiotic chromosome behavior. The univalent frequency in the lines varied between 0.34 and 2.36 per cell. Similarly, the multivalent frequency did not exceed 1% in any of the lines. GISH analysis revealed that the number of intact wheat chromosomes in the various lines varied between 40 and 44. Numerous translocated chromosomes were detected in all lines. The translocations involved chromosomal segments from wheat, and the St and H genomes of E. repens. Furthermore, trigenomic translocated chromosomes were detected in some of the lines. The introgression into wheat chromosomes included not only terminal types but also interstitial segments. The Fusarium head blight resistance of the eight lines, following point inoculation, varied from 5.65% infected florets to 11.46% compared with the check cultivars T. aestivum 'Roblin' and T. aestivum 'Crocus' at 100% and 85%, respectively.

  14. Molecular cytogenetic analysis of wheat - Elymus repens introgression lines with resistance to Fusarium head blight.

    PubMed

    Zeng, J; Cao, W; Hucl, P; Yang, Y; Xue, A; Chi, D; Fedak, G

    2013-01-01

    Elymus repens (L.) Gould (2n = 6x = 42, StStStStHH) is a hexaploid perennial wheatgrass species from the tribe Triticeae, distantly related to bread wheat Triticum aestivum L. (2n = 6x = 42, AABBDD). As a potential source of resistance to Fusarium head blight (FHB), E. repens was crossed to common wheat to transfer resistance genes. The progeny were advanced to homozygosity by single seed descent. A total of eight BC(1)F(9) progeny lines were selected and characterized in this study. The chromosome numbers of these derived lines ranged from 42 to 56, including lines with 44, 52, and 54 chromosomes. All of the lines were cytologically stable in terms of meiotic chromosome behavior. The univalent frequency in the lines varied between 0.34 and 2.36 per cell. Similarly, the multivalent frequency did not exceed 1% in any of the lines. GISH analysis revealed that the number of intact wheat chromosomes in the various lines varied between 40 and 44. Numerous translocated chromosomes were detected in all lines. The translocations involved chromosomal segments from wheat, and the St and H genomes of E. repens. Furthermore, trigenomic translocated chromosomes were detected in some of the lines. The introgression into wheat chromosomes included not only terminal types but also interstitial segments. The Fusarium head blight resistance of the eight lines, following point inoculation, varied from 5.65% infected florets to 11.46% compared with the check cultivars T. aestivum 'Roblin' and T. aestivum 'Crocus' at 100% and 85%, respectively. PMID:23379340

  15. 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

  16. 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

  17. 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

  18. 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.

  19. 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 ...

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

    PubMed Central

    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

  1. 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

  2. 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.

  3. 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

  4. Photosystem II thermostability in situ: environmentally induced acclimation and genotype-specific reactions in Triticum aestivum L.

    PubMed

    Brestic, Marian; Zivcak, Marek; Kalaji, Hazem M; Carpentier, Robert; Allakhverdiev, Suleyman I

    2012-08-01

    Photosystem II (PSII) thermostability and acclimation effects on PSII photochemical efficiency were analyzed in thirty field grown winter wheat (Triticum aestivum L.) genotypes using prompt chlorophyll a fluorescence kinetics before and after dark heat treatment. A gradual increase in temperature caused the appearance of K-bands at 300 μs on the chlorophyll fluorescence induction curve, indicating the impairment of the PSII donor side (even by heat treatment at 38 °C). An increase in basal fluorescence, commonly used as a criterion of PSII thermostability, was observed beyond a temperature threshold of 44 °C. Moreover, an acclimation shift (increase of critical temperature) was observed at the 3.5 °C identified for K-band appearance, but only by 1.1 °C for a steep increase in F(0). The single temperature approach with regular weekly observations completed within two months using dark heat treatment at 40 °C demonstrated that the acclimation effect is not gradual, but occurs immediately and is associated with an increase of daily temperature maxima over 30 °C. The acclimated heat treated samples had less effect on the donor side of PSII, the higher fraction of active Q(A)(-) reducing reaction centers and causing a much lower decrease of connectivity among PSII units compared to non-acclimated samples. In the non-treated plants the reduction of antennae size, increase of PSII connectivity and changes in the acceptor side occurred as a result of heat acclimation. The enhancement of PSII thermostability persisted over several weeks regardless of weather conditions. The genotype comparison identified three groups that differed either in initial PSII thermostability or in acclimation capacity; these groupings were clearly associated with the origin of the genotypes.

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

    PubMed

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

    2013-11-01

    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 ¹⁵NH₄⁺ 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 NH₄⁺, which became available for plant capture. Roots proved to be poor competitors for ¹⁵N-glutamate and took up N mainly as ¹⁵NH₄⁺. 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.

  6. 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

  7. 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

  8. Structural analysis of wheat wax (Triticum aestivum, c.v. 'Naturastar' L.): from the molecular level to three dimensional crystals.

    PubMed

    Koch, K; Barthlott, W; Koch, S; Hommes, A; Wandelt, K; Mamdouh, W; De-Feyter, S; Broekmann, P

    2006-01-01

    In order to elucidate the self assembly process of plant epicuticular waxes, and the molecular arrangement within the crystals, re-crystallisation of wax platelets was studied on biological and non-biological surfaces. Wax platelets were extracted from the leaf blades of wheat (Triticum aestivum L., c.v. 'Naturastar', Poaceae). Waxes were analysed by gas chromatography (GC) and mass spectrometry (MS). Octacosan-1-ol was found to be the most abundant chemical component of the wax mixture (66 m%) and also the determining compound for the shape of the wax platelets. The electron diffraction pattern showed that both the wax mixture and pure octacosan-1-ol are crystalline. The re-crystallisation of the natural wax mixture and the pure octacosan-1-ol were studied by scanning tunnelling microscopy (STM), atomic force microscopy (AFM), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). Crystallisation of wheat waxes and pure octacosano-1-ol on the non polar highly ordered pyrolytic graphite (HOPG) led to the formation of platelet structures similar to those found on the plant surface. In contrast, irregular wax morphologies and flat lying plates were formed on glass, silicon, salt crystals (NaCl) and mica surfaces. Movement of wheat wax through isolated Convallaria majalis cuticles led to typical wax platelets of wheat, arranged in the complex patterns typical for C. majalis. STM of pure octacosan-1-ol monolayers on HOPG showed that the arrangement of the molecules strictly followed the hexagonal structure of the substrate crystal. Re-crystallisation of wheat waxes on non-polar crystalline HOPG substrate showed that technical surfaces could be used to generate microstructured, biomimetic surfaces. AFM and SEM studies proved that a template effect of the substrate determined the orientation of the re-grown crystals. These effects of the structure and polarity of the substrate on the morphology of the epicuticular waxes are relevant for

  9. Identification of Kernel Proteins Associated with the Resistance to Fusarium Head Blight in Winter Wheat (Triticum aestivum L.)

    PubMed Central

    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

  10. 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...

  11. 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

  12. 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

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

    PubMed

    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

    2015-04-01

    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 (223Mb) and scaffolds (65Mb) that were aligned to Aegilops tauschii draft genome (DD), anchoring 34Mb 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.

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

    PubMed Central

    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

  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. 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,

  17. 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...

  18. Genome Mapping in Plant Comparative Genomics.

    PubMed

    Chaney, Lindsay; Sharp, Aaron R; Evans, Carrie R; Udall, Joshua A

    2016-09-01

    Genome mapping produces fingerprints of DNA sequences to construct a physical map of the whole genome. It provides contiguous, long-range information that complements and, in some cases, replaces sequencing data. Recent advances in genome-mapping technology will better allow researchers to detect large (>1kbp) structural variations between plant genomes. Some molecular and informatics complications need to be overcome for this novel technology to achieve its full utility. This technology will be useful for understanding phenotype responses due to DNA rearrangements and will yield insights into genome evolution, particularly in polyploids. In this review, we outline recent advances in genome-mapping technology, including the processes required for data collection and analysis, and applications in plant comparative genomics.

  19. Enabling functional genomics with genome engineering.

    PubMed

    Hilton, Isaac B; Gersbach, Charles A

    2015-10-01

    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.

  20. Enabling functional genomics with genome engineering.

    PubMed

    Hilton, Isaac B; Gersbach, Charles A

    2015-10-01

    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

  1. 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.

  2. 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

  3. 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)

  4. 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.

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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.

  10. 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

  11. 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

  12. 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.

  13. 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

  14. 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

  15. Identifying QTL for high-temperature adult-plant resistance to stripe rust (Puccinia striiformis f. sp. tritici) in the spring wheat (Triticum aestivum L.) cultivar ‘Louise’

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Over time, many single, all-stage resistance genes to stripe rust (Puccinia striiformis f. sp. tritici) in wheat (Triticum aestivum L.) are circumvented by race changes in the pathogen. In contrast, high-temperature, adult-plant resistance (HTAP), which only is expressed during the adult-plant stag...

  16. 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...

  17. 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

  18. 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.

  19. Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes

    PubMed Central

    Saski, Christopher; Lee, Seung-Bum; Fjellheim, Siri; Guda, Chittibabu; Jansen, Robert K.; Luo, Hong; Tomkins, Jeffrey; Rognli, Odd Arne; Clarke, Jihong Liu

    2009-01-01

    Comparisons of complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera to six published grass chloroplast genomes reveal that gene content and order are similar but two microstructural changes have occurred. First, the expansion of the IR at the SSC/IRa boundary that duplicates a portion of the 5′ end of ndhH is restricted to the three genera of the subfamily Pooideae (Agrostis, Hordeum and Triticum). Second, a 6 bp deletion in ndhK is shared by Agrostis, Hordeum, Oryza and Triticum, and this event supports the sister relationship between the subfamilies Erhartoideae and Pooideae. Repeat analysis identified 19–37 direct and inverted repeats 30 bp or longer with a sequence identity of at least 90%. Seventeen of the 26 shared repeats are found in all the grass chloroplast genomes examined and are located in the same genes or intergenic spacer (IGS) regions. Examination of simple sequence repeats (SSRs) identified 16–21 potential polymorphic SSRs. Five IGS regions have 100% sequence identity among Zea mays, Saccharum officinarum and Sorghum bicolor, whereas no spacer regions were identical among Oryza sativa, Triticum aestivum, H. vulgare and A. stolonifera despite their close phylogenetic relationship. Alignment of EST sequences and DNA coding sequences identified six C–U conversions in both Sorghum bicolor and H. vulgare but only one in A. stolonifera. Phylogenetic trees based on DNA sequences of 61 protein-coding genes of 38 taxa using both maximum parsimony and likelihood methods provide moderate support for a sister relationship between the subfamilies Erhartoideae and Pooideae. PMID:17534593

  20. 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 ...

  1. Plant genomics: an overview.

    PubMed

    Campos-de Quiroz, Hugo

    2002-01-01

    Recent technological advancements have substantially expanded our ability to analyze and understand plant genomes and to reduce the gap existing between genotype and phenotype. The fast evolving field of genomics allows scientists to analyze thousand of genes in parallel, to understand the genetic architecture of plant genomes and also to isolate the genes responsible for mutations. Furthermore, whole genomes can now be sequenced. This review addresses these issues and also discusses ways to extract biological meaning from DNA data. Although genomic issuesare addressed from a plant perspective, this review provides insights into the genomic analyses of other organisms. PMID:12462991

  2. 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.

  3. 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

  4. 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.

  5. 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 ...

  6. 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.

  7. Assessment of genomic diversity among wheat genotypes as determined by simple sequence repeats.

    PubMed

    Ahmad, M

    2002-08-01

    Simple sequence repeats (SSRs) have been used to examine the genomic diversity of wheat (Triticum aestivum L.) germplasm. Thirteen wheat genotypes of diverse origin were analyzed with 43 selected SSRs to provide uniform and maximum genome coverage. A total of 156 allelic variants were detected at 43 SSR loci, ranging from two to eight per locus with an average of 3.6. The polymorphic information content (PIC) values of the loci ranged from 0.10 (Xgwm264) to 0.89 (Xgwm471 and Xgwm577). Genetic similarities calculated from SSR data ranged from 30.1 ('Era' and 'Klasic') to 90.1 ('Neepawa' and 'Thatcher') between genotypes. UPGMA analysis based on genetic distance estimates produced three loose groupings that were generally consistent with available pedigree information. Cultivars 'Neepawa' and 'Thatcher' are closely related. Their genetic relationship was confirmed by the facts that they share a common ancestor and are clustered together. There were two different 'Era' genotypes, one used in the 'Otane' pedigree and one used in this study. None of the other genotypes had a close common ancestor indicating any close genetic relationships. Principal coordinate analysis also confirmed this pattern of genetic diversity. A wide range of genomic diversity was observed among all the genotypes, proving them to be prime candidates for selective breeding for specific traits and broadening the genetic base.

  8. 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

  9. 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

  10. 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.

  11. 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

  12. 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

  13. Confocal Raman microscopic characterization of the molecular species responsible for the grain cohesion of Triticum aestivum wheat: effect of chemical treatment

    NASA Astrophysics Data System (ADS)

    Piot, Olivier; Saadi, Abdelbasset; Autran, Jean-Claude; Manfait, Michel

    1999-04-01

    Raman microspectroscopy is a very well appropriate technique for the characterization of the molecules responsible of the wheat grain cohesion, since it is non-destructive and can be readily applied in-situ. The cohesion of the kernel or starchy endosperm depends on a protein content located at the interstices of starch granules. The separation between the kernel and the envelope depends on the composition of the aleurone cells layer, in phenolic acids and pentosans. Confocal Raman microscopy has been performed on kernel sections of various Triticum aestivum samples. Raman spectra recorded at different parts of such sections are very specific, such as spectra of the starchy endosperm protein. The technique has been also used to study the effect of chemical treatment on the binding of the constituents of the aleurone cells walls. In addition, certain marker bands of starch and proteins have been used to construct spectral images.

  14. Spelt (Triticum aestivum ssp. spelta) as a source of breadmaking flours and bran naturally enriched in oleic acid and minerals but not phytic acid.

    PubMed

    Ruibal-Mendieta, Nike L; Delacroix, Dominique L; Mignolet, Eric; Pycke, Jean-Marie; Marques, Carole; Rozenberg, Raoul; Petitjean, Géraldine; Habib-Jiwan, Jean-Louis; Meurens, Marc; Quetin-Leclercq, Joëlle; Delzenne, Nathalie M; Larondelle, Yvan

    2005-04-01

    The nutritional value of breadmaking cereal spelt (Triticum aestivum ssp. spelta) is said to be higher than that of common wheat (Triticum aestivum ssp. vulgare), but this traditional view is not substantiated by scientific evidence. In an attempt to clarify this issue, wholemeal and milling fractions (sieved flour, fine bran, and coarse bran) from nine dehulled spelt and five soft winter wheat samples were compared with regard to their lipid, fatty acid, and mineral contents. In addition, tocopherol (a biochemical marker of germ) was measured in all wholemeals, whereas phytic acid and phosphorus levels were determined in fine bran and coarse bran samples after 1 month of storage. Results showed that, on average, spelt wholemeals and milling fractions were higher in lipids and unsaturated fatty acids as compared to wheat, whereas tocopherol content was lower in spelt, suggesting that the higher lipid content of spelt may not be related to a higher germ proportion. Although milling fractionation produced similar proportions of flour and brans in spelt and wheat, it was found that ash, copper, iron, zinc, magnesium, and phosphorus contents were higher in spelt samples, especially in aleurone-rich fine bran and in coarse bran. Even though phosphorus content was higher in spelt than in wheat brans, phytic acid content showed the opposite trend and was 40% lower in spelt versus wheat fine bran, which may suggest that spelt has either a higher endogenous phytase activity or a lower phytic acid content than wheat. The results of this study give important indications on the real nutritional value of spelt compared to wheat. Moreover, they show that the Ca/Fe ratio, combined with that of oleate/palmitate, provides a highly discriminating tool to authenticate spelt from wheat flours and to face the growing issue of spelt flour adulteration. Finally, they suggest that aleurone differences, the nature of which still needs to be investigated, may account for the differential

  15. 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

  16. 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

  17. Enabling responsible public genomics.

    PubMed

    Conley, John M; Doerr, Adam K; Vorhaus, Daniel B

    2010-01-01

    As scientific understandings of genetics advance, researchers require increasingly rich datasets that combine genomic data from large numbers of individuals with medical and other personal information. Linking individuals' genetic data and personal information precludes anonymity and produces medically significant information--a result not contemplated by the established legal and ethical conventions governing human genomic research. To pursue the next generation of human genomic research and commerce in a responsible fashion, scientists, lawyers, and regulators must address substantial new issues, including researchers' duties with respect to clinically significant data, the challenges to privacy presented by genomic data, the boundary between genomic research and commerce, and the practice of medicine. This Article presents a new model for understanding and addressing these new challenges--a "public genomics" premised on the idea that ethically, legally, and socially responsible genomics research requires openness, not privacy, as its organizing principle. Responsible public genomics combines the data contributed by informed and fully consenting information altruists and the research potential of rich datasets in a genomic commons that is freely and globally available. This Article examines the risks and benefits of this public genomics model in the context of an ambitious genetic research project currently under way--the Personal Genome Project. This Article also (i) demonstrates that large-scale genomic projects are desirable, (ii) evaluates the risks and challenges presented by public genomics research, and (iii) determines that the current legal and regulatory regimes restrict beneficial and responsible scientific inquiry while failing to adequately protect participants. The Article concludes by proposing a modified normative and legal framework that embraces and enables a future of responsible public genomics.

  18. Whole-exome/genome sequencing and genomics.

    PubMed

    Grody, Wayne W; Thompson, Barry H; Hudgins, Louanne

    2013-12-01

    As medical genetics has progressed from a descriptive entity to one focused on the functional relationship between genes and clinical disorders, emphasis has been placed on genomics. Genomics, a subelement of genetics, is the study of the genome, the sum total of all the genes of an organism. The human genome, which is contained in the 23 pairs of nuclear chromosomes and in the mitochondrial DNA of each cell, comprises >6 billion nucleotides of genetic code. There are some 23,000 protein-coding genes, a surprisingly small fraction of the total genetic material, with the remainder composed of noncoding DNA, regulatory sequences, and introns. The Human Genome Project, launched in 1990, produced a draft of the genome in 2001 and then a finished sequence in 2003, on the 50th anniversary of the initial publication of Watson and Crick's paper on the double-helical structure of DNA. Since then, this mass of genetic information has been translated at an ever-increasing pace into useable knowledge applicable to clinical medicine. The recent advent of massively parallel DNA sequencing (also known as shotgun, high-throughput, and next-generation sequencing) has brought whole-genome analysis into the clinic for the first time, and most of the current applications are directed at children with congenital conditions that are undiagnosable by using standard genetic tests for single-gene disorders. Thus, pediatricians must become familiar with this technology, what it can and cannot offer, and its technical and ethical challenges. Here, we address the concepts of human genomic analysis and its clinical applicability for primary care providers.

  19. HeteroGenome: database of genome periodicity

    PubMed Central

    Chaley, Maria; Kutyrkin, Vladimir; Tulbasheva, Gayane; Teplukhina, Elena; Nazipova, Nafisa

    2014-01-01

    We present the first release of the HeteroGenome database collecting latent periodicity regions in genomes. Tandem repeats and highly divergent tandem repeats along with the regions of a new type of periodicity, known as profile periodicity, have been collected for the genomes of Saccharomyces cerevisiae, Arabidopsis thaliana, Caenorhabditis elegans and Drosophila melanogaster. We obtained data with the aid of a spectral-statistical approach to search for reliable latent periodicity regions (with periods up to 2000 bp) in DNA sequences. The original two-level mode of data presentation (a broad view of the region of latent periodicity and a second level indicating conservative fragments of its structure) was further developed to enable us to obtain the estimate, without redundancy, that latent periodicity regions make up ∼10% of the analyzed genomes. Analysis of the quantitative and qualitative content of located periodicity regions on all chromosomes of the analyzed organisms revealed dominant characteristic types of periodicity in the genomes. The pattern of density distribution of latent periodicity regions on chromosome unambiguously characterizes each chromosome in genome. Database URL: http://www.jcbi.ru/lp_baze/ PMID:24857969

  20. 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

  1. 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.

  2. State of cat genomics.

    PubMed

    O'Brien, Stephen J; Johnson, Warren; Driscoll, Carlos; Pontius, Joan; Pecon-Slattery, Jill; Menotti-Raymond, Marilyn

    2008-06-01

    Our knowledge of cat family biology was recently expanded to include a genomics perspective with the completion of a draft whole genome sequence of an Abyssinian cat. The utility of the new genome information has been demonstrated by applications ranging from disease gene discovery and comparative genomics to species conservation. Patterns of genomic organization among cats and inbred domestic cat breeds have illuminated our view of domestication, revealing linkage disequilibrium tracks consequent of breed formation, defining chromosome exchanges that punctuated major lineages of mammals and suggesting ancestral continental migration events that led to 37 modern species of Felidae. We review these recent advances here. As the genome resources develop, the cat is poised to make a major contribution to many areas in genetics and biology.

  3. 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

  4. 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.

  5. Identification of novel and useful EST-SSR markers from de novo transcriptome sequence of wheat (Triticum aestivum L.).

    PubMed

    Yang, Z J; Peng, Z S; Yang, H

    2016-01-01

    Simple sequence repeats (SSRs) are highly informative, polymorphic, and co-dominant Mendelian markers that provide an important genomic resource for genetic research. Recently, the use of large-scale transcriptome sequence has become a reliable and efficient approach for the identification and development of new EST-SSR markers. In this study, 8389 potential SSRs with a minimum of five repetitions for all motifs were identified from 121,210 unigenes. Gene ontology analysis indicated that the unigenes containing SSR loci participate in various biological processes of regulation, growth, development, metabolism, and apoptosis in wheat. As in many other plants, trinucleotide repeats were found to be the most abundant repeat units with a frequency of 62.33%. A subset of 300 EST-SSRs was randomly selected for the applicability of EST-SSRs to be evaluated. Of the 300 primer pairs tested, 177 (59%) yielded unambiguous PCR products among five wheat cultivars. Using the Chinese Spring nulli-tetrasomic line, 131 of the 177 EST-SSR primer pairs yielded products and 178 loci were found to be located on all the 21 wheat chromosomes. These findings suggest that the novel EST-SSR markers, as a basis for future genetic linkage and gene tagging analysis, are a valuable tool for genetic mapping, marker assisted selection, and comparative genome analysis. PMID:26909990

  6. Identification of novel and useful EST-SSR markers from de novo transcriptome sequence of wheat (Triticum aestivum L.).

    PubMed

    Yang, Z J; Peng, Z S; Yang, H

    2016-02-19

    Simple sequence repeats (SSRs) are highly informative, polymorphic, and co-dominant Mendelian markers that provide an important genomic resource for genetic research. Recently, the use of large-scale transcriptome sequence has become a reliable and efficient approach for the identification and development of new EST-SSR markers. In this study, 8389 potential SSRs with a minimum of five repetitions for all motifs were identified from 121,210 unigenes. Gene ontology analysis indicated that the unigenes containing SSR loci participate in various biological processes of regulation, growth, development, metabolism, and apoptosis in wheat. As in many other plants, trinucleotide repeats were found to be the most abundant repeat units with a frequency of 62.33%. A subset of 300 EST-SSRs was randomly selected for the applicability of EST-SSRs to be evaluated. Of the 300 primer pairs tested, 177 (59%) yielded unambiguous PCR products among five wheat cultivars. Using the Chinese Spring nulli-tetrasomic line, 131 of the 177 EST-SSR primer pairs yielded products and 178 loci were found to be located on all the 21 wheat chromosomes. These findings suggest that the novel EST-SSR markers, as a basis for future genetic linkage and gene tagging analysis, are a valuable tool for genetic mapping, marker assisted selection, and comparative genome analysis.

  7. 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

  8. Molecular cloning and characterization of a novel glyoxalase I gene TaGly I in wheat (Triticum aestivum L.).

    PubMed

    Lin, Fanyun; Xu, Jianhong; Shi, Jianrong; Li, Hongwei; Li, Bin

    2010-02-01

    Methylglyoxal is a kind of poisonous metabolite that can react with RNA, DNA and protein, which generally results in a number of side advert effects to cell. Glyoxalase I is a member of glyoxalase system that can detoxify methylglyoxal. An EST encoding a glyoxalase I was isolated from a SSH (suppression subtractive hybridization)-cDNA library of wheat spike inoculated by Fusarium graminearum. The corresponding full length gene, named TaGly I, was cloned, sequenced and characterized. Its genomic sequence consists of 2,719 bp, including seven exons and six introns, and its coding sequence is 929 bp with an open reading frame encoding 291 amino acids. Sequence alignment showed that there were two glyoxalase I domains in the deduced protein sequence. By using specific primers, TaGly I was mapped to chromosome 7D of wheat via a set of durum wheat 'Langdon' D-genome disomic-substitution lines. The result of Real-time quantitative polymerase chain reaction demonstrated that TaGly I was induced by the inoculation of Fusarium graminearum in wheat spikes. Additionally, it was also induced by high concentration of NaCl and ZnCl2. When TaGly I was overexpressed in tobacco leaves via Agrobacterium tumefaciens infection, the transgenic tobacco showed stronger tolerance to ZnCl2 stress relative to transgenic control with GFP. The above facts indicated that TaGly I might play a role in response to diverse stresses in plants.

  9. 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.

  10. 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.

  11. Genome packaging in viruses.

    PubMed

    Sun, Siyang; Rao, Venigalla B; Rossmann, Michael G

    2010-02-01

    Genome packaging is a fundamental process in a viral life cycle. Many viruses assemble preformed capsids into which the genomic material is subsequently packaged. These viruses use a packaging motor protein that is driven by the hydrolysis of ATP to condense the nucleic acids into a confined space. How these motor proteins package viral genomes had been poorly understood until recently, when a few X-ray crystal structures and cryo-electron microscopy (cryo-EM) structures became available. Here we discuss various aspects of genome packaging and compare the mechanisms proposed for packaging motors on the basis of structural information. PMID:20060706

  12. 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

  13. Disentangling associated genomes.

    PubMed

    Sloan, Daniel B; Bennett, Gordon M; Engel, Philipp; Williams, David; Ochman, Howard

    2013-01-01

    The recovery and assembly of genome sequences from samples containing communities of organisms pose several challenges. Because it is rarely possible to disassociate the resident organisms prior to sequencing, a major obstacle is the assignment of sequences to a single genome that can be fully assembled. This chapter delineates many of the decisions, methodologies, and approaches that can lead to the generation of complete or nearly complete microbial genome sequences from heterogeneous samples-that is, the procedures that allow us to turn metagenomes into genomes.

  14. 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.

  15. 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.

  16. [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

  17. [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

  18. 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

  19. Home - The Cancer Genome Atlas - Cancer Genome - TCGA

    Cancer.gov

    The Cancer Genome Atlas (TCGA) is a comprehensive and coordinated effort to accelerate our understanding of the molecular basis of cancer through the application of genome analysis technologies, including large-scale genome sequencing.

  20. 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

  1. 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

  2. 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...

  3. The UCSC Genome Browser

    PubMed Central

    Karolchik, Donna; Hinrichs, Angie S.; Kent, W. James

    2009-01-01

    The University of California Santa Cruz (UCSC) Genome Browser (genome.ucsc.edu) is a popular Web-based tool for quickly displaying a requested portion of a genome at any scale, accompanied by a series of aligned annotation “tracks”. The annotations—generated by the UCSC Genome Bioinformatics Group and external collaborators—display gene predictions, mRNA and expressed sequence tag alignments, simple nucleotide polymorphisms, expression and regulatory data, phenotype and variation data, and pairwise and multiple-species comparative genomics data. All information relevant to a region is presented in one window, facilitating biological analysis and interpretation. The database tables underlying the Genome Browser tracks can be viewed, downloaded, and manipulated using another Web-based application, the UCSC Table Browser. Users can upload data as custom annotation tracks in both browsers for research or educational use. This unit describes how to use the Genome Browser and Table Browser for genome analysis, download the underlying database tables, and create and display custom annotation tracks. PMID:19957273

  4. National Human Genome Research Institute

    MedlinePlus

    ... Director Organization Reports & Publications Español The National Human Genome Research Institute conducts genetic and genomic research, funds ... study, led by researchers at the National Human Genome Research Institute and the Eunice Kennedy Shriver National ...

  5. 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

  6. 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.

  7. The UCSC Genome Browser

    PubMed Central

    Karolchik, Donna; Hinrichs, Angie S.; Kent, W. James

    2011-01-01

    The University of California Santa Cruz (UCSC) Genome Browser is a popular Web-based tool for quickly displaying a requested portion of a genome at any scale, accompanied by a series of aligned annotation “tracks.” The annotations generated by the UCSC Genome Bioinformatics Group and external collaborators include gene predictions, mRNA and expressed sequence tag alignments, simple nucleotide polymorphisms, expression and regulatory data, phenotype and variation data, and pairwise and multiple-species comparative genomics data. All information relevant to a region is presented in one window, facilitating biological analysis and interpretation. The database tables underlying the Genome Browser tracks can be viewed, downloaded, and manipulated using another Web-based application, the UCSC Table Browser. Users can upload personal datasets in a wide variety of formats as custom annotation tracks in both browsers for research or educational purposes. PMID:21975940

  8. Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome.

    PubMed

    Akbari, Mona; Wenzl, Peter; Caig, Vanessa; Carling, Jason; Xia, Ling; Yang, Shiying; Uszynski, Grzegorz; Mohler, Volker; Lehmensiek, Anke; Kuchel, Haydn; Hayden, Mathew J; Howes, Neil; Sharp, Peter; Vaughan, Peter; Rathmell, Bill; Huttner, Eric; Kilian, Andrzej

    2006-11-01

    Despite a substantial investment in the development of panels of single nucleotide polymorphism (SNP) markers, the simple sequence repeat (SSR) technology with a limited multiplexing capability remains a standard, even for applications requiring whole-genome information. Diversity arrays technology (DArT) types hundreds to thousands of genomic loci in parallel, as previously demonstrated in a number diploid plant species. Here we show that DArT performs similarly well for the hexaploid genome of bread wheat (Triticum aestivum L.). The methodology previously used to generate DArT fingerprints of barley also generated a large number of high-quality markers in wheat (99.8% allele-calling concordance and approximately 95% call rate). The genetic relationships among bread wheat cultivars revealed by DArT coincided with knowledge generated with other methods, and even closely related cultivars could be distinguished. To verify the Mendelian behaviour of DArT markers, we typed a set of 90 Cranbrook x Halberd doubled haploid lines for which a framework (FW) map comprising a total of 339 SSR, restriction fragment length polymorphism (RFLP) and amplified fragment length polymorphism (AFLP) markers was available. We added an equal number of DArT markers to this data set and also incorporated 71 sequence tagged microsatellite (STM) markers. A comparison of logarithm of the odds (LOD) scores, call rates and the degree of genome coverage indicated that the quality and information content of the DArT data set was comparable to that of the combined SSR/RFLP/AFLP data set of the FW map. PMID:17033786

  9. 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

  10. Relationship between male sterility and β-1,3-glucanase activity and callose deposition-related gene expression in wheat (Triticum aestivum L.).

    PubMed

    Liu, H Z; Zhang, G S; Zhu, W W; Ba, Q S; Niu, N; Wang, J W; Ma, S C; Wang, J S

    2015-01-26

    In previous studies, we first isolated one different protein β-1,3-glucanase using two-dimensional electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry from normal wheat (Triticum aestivum L.) and chemical hybridization agent-induced male sterility (CIMS) wheat. In this experiment, β-1,3-glucanase activity and the expression of a callose deposition-related gene, UDP-glucose phosphorylase (UGPase), were determinate in normal, CIMS, and genetic male sterility (GS) wheat. β-1,3-glucanase activity was significantly different between the fertile and sterile lines during callose synthesis and degradation, but there was no difference between CIMS and GS wheat. The UGPase gene of callose deposition was highly expressed in the meiophase and sharply decreased in the tetrad stage. However, the expression of the UGPase gene was significantly different between the fertile and sterile lines. These data indicated that β-1,3-glucanase activity and the expression of the UGPase gene play important roles in the male sterility of wheat. Consequently, pollen mother cells (PMCs) might degenerate at the early meiosis stage, and differences in UGPase gene expression and β-1,3-glucanase activity might eventually result in complete pollen collapse. In addition, the critical period of anther abortion might be the meiosis stage to the tetrad stage rather than what we previously thought, the mononuclear period.

  11. Nitrate reductase-mediated early nitric oxide burst alleviates oxidative damage induced by aluminum through enhancement of antioxidant defenses in roots of wheat (Triticum aestivum).

    PubMed

    Sun, Chengliang; Lu, Lingli; Liu, Lijuan; Liu, Wenjing; Yu, Yan; Liu, Xiaoxia; Hu, Yan; Jin, Chongwei; Lin, Xianyong

    2014-03-01

    • Nitric oxide (NO) is an important signaling molecule involved in the physiological processes of plants. The role of NO release in the tolerance strategies of roots of wheat (Triticum aestivum) under aluminum (Al) stress was investigated using two genotypes with different Al resistances. • An early NO burst at 3 h was observed in the root tips of the Al-tolerant genotype Jian-864, whereas the Al-sensitive genotype Yang-5 showed no NO accumulation at 3 h but an extremely high NO concentration after 12 h. Stimulating NO production at 3 h in the root tips of Yang-5 with the NO donor relieved Al-induced root inhibition and callose production, as well as oxidative damage and ROS accumulation, while elimination of the early NO burst by NO scavenger aggravated root inhibition in Jian-864. • Synthesis of early NO in roots of Jian-864 was mediated through nitrate reductase (NR) but not through NO synthase. Elevated antioxidant enzyme activities were induced by Al stress in both wheat genotypes and significantly enhanced by NO donor, but suppressed by NO scavenger or NR inhibitor. • These results suggest that an NR-mediated early NO burst plays an important role in Al resistance of wheat through modulating enhanced antioxidant defense to adapt to Al stress.

  12. Dynamic changes of rhizosphere properties and antioxidant enzyme responses of wheat plants (Triticum aestivum L.) grown in mercury-contaminated soils.

    PubMed

    Li, Yonghua; Sun, Hongfei; Li, Hairong; Yang, Linsheng; Ye, Bixiong; Wang, Wuyi

    2013-10-01

    A pot experiment was conducted to investigate the dynamic changes in the rhizosphere properties and antioxidant enzyme responses of wheat plants (Triticum aestivum L.) grown in three levels of Hg-contaminated soils. The concentrations of soluble Hg and dissolved organic carbon (DOC) in the rhizosphere soil solutions of the wheat plants were characterised by the sequence before sowing>trefoil stage>stooling stage, whereas the soil solution pH was found to follow an opposite distribution pattern. The activities of antioxidant enzymes in wheat plants under Hg stress were substantially altered. Greater superoxide dismutase (SOD), catalase (CAT) and ascorbate peroxidase (APX) activities were observed in the wheat plants grown in a highly polluted soil than in a slightly polluted soil (with increases of 11-27% at the trefoil stage and 26-70% at the stooling stage); however, increasing concentrations of Hg up to seriously polluted level led to reduced enzyme activities. The present results suggest that wheat plants could positively adapt to environmental Hg stress, with rhizosphere acidification, the enhancement of DOC production and greater antioxidant enzyme activities perhaps being three important mechanisms involved in the metal uptake/tolerance in the rhizospheres of wheat plants grown in Hg-contaminated soils.

  13. 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.

  14. Identification of the TaBTF3 gene in wheat (Triticum aestivum L.) and the effect of its silencing on wheat chloroplast, mitochondria and mesophyll cell development.

    PubMed

    Ma, Hong-Zhen; Liu, Guo-Qin; Li, Cheng-Wei; Kang, Guo-Zhang; Guo, Tian-Cai

    2012-10-01

    The full-length cDNA (882bp) and DNA (1742bp) sequences encoding a basic transcription factor 3, designated as TaBTF3, were first isolated from common wheat (Triticum aestivum L.). Subcellular localization studies revealed that the TaBTF3 protein was mainly located in the cytoplasm and nucleus. In TaBTF3-silenced transgenic wheat seedlings obtained using the Virus-induced gene silencing (VIGS) method, the chlorophyll pigment content was markedly reduced. However, the malonaldehyde (MDA) and H(2)O(2) contents were enhanced, and the structure of the wheat mesophyll cell was seriously damaged. Furthermore, transcripts of the chloroplast- and mitochondrial-encoded genes were significantly reduced in TaBTF3-silenced transgenic wheat plants. These results suggest that the TaBTF3 gene might function in the development of the wheat chloroplast, mitochondria and mesophyll cell. This paper is the first report to describe the involvement of TaBTF3 in maintaining the normal plant mesophyll cell structure.

  15. 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.

  16. Alleviation of chromium toxicity by glycinebetaine is related to elevated antioxidant enzymes and suppressed chromium uptake and oxidative stress in wheat (Triticum aestivum L.).

    PubMed

    Ali, Shafaqat; Chaudhary, Aaifa; Rizwan, Muhammad; Anwar, Hafiza Tania; Adrees, Muhammad; Farid, Mujahid; Irshad, Muhammad Kashif; Hayat, Tahir; Anjum, Shakeel Ahmad

    2015-07-01

    Little information is available on the role of glycinebetaine (GB) in chromium (Cr) tolerance while Cr toxicity is widespread problem in crops grown on Cr-contaminated soils. In this study, we investigated the influence of GB on Cr tolerance in wheat (Triticum aestivum L.) grown in sand and soil mediums. Three concentrations of chromium (0, 0.25, and 0.5 mM) were tested with and without foliar application of GB (0.1 M). Chromium alone led to a significant growth inhibition and content of chlorophyll a, b, proteins and enhanced the activity of antioxidant enzymes. Glycinebetaine foliar application successfully alleviated the toxic effects of Cr on wheat plants and enhanced growth characteristics, biomass, proteins, and chlorophyll contents. Glycinebetaine also reduced Cr accumulation in wheat plants especially in grains and enhanced the activity of antioxidant enzymes in both shoots and roots. This study provides evidence that GB application contributes to decreased Cr concentrations in wheat plants and its importance in the detoxification of heavy metals.

  17. The dynamic process of interspecific interactions of competitive nitrogen capture between intercropped wheat (Triticum aestivum L.) and Faba Bean (Vicia faba L.).

    PubMed

    Li, Chunjie; Dong, Yan; Li, Haigang; Shen, Jianbo; Zhang, Fusuo

    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.

  18. 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.

  19. 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.

  20. Gluten of spelt wheat (Triticum aestivum subspecies spelta) as a source of peptides promoting viability and product yield of mouse hybridoma cell cultures.

    PubMed

    Franek, Frantisek

    2004-06-30

    The enzymic hydrolysate of gluten from spelt wheat (Triticum aestivum subsp. spelta), an ancient protein-rich wheat subspecies, was subjected to repeated chromatography runs on the small pore size exclusion chromatography matrix, Biogel P-2. Two small peptide fractions were purified by rechromatography. The amino acid analyses carried out upon total hydrolysis of these fractions have shown a very high proportion of glutamic acid/glutamine, leucine, and methionine. The biological activity of the peptide fractions was tested on a model hybridoma at a concentration range from 0.02 to 0.2%. The most striking effect of peptide fractions, apparent even at the lowest concentrations tested, was a significantly higher persistence of viable cells on day 6, i.e., at the decline phase of the cultures. Culture viability values in the presence of peptide fractions were 64-74%, in comparison with 56% in the control culture. The results of this work are consistent with the concept that peptide molecules may act as antiapoptotic agents, survival factors, rather than serving as metabolic substrates.

  1. Changes in the water status and osmotic solute contents in response to drought and salicylic acid treatments in four different cultivars of wheat (Triticum aestivum).

    PubMed

    Loutfy, Naglaa; El-Tayeb, Mohamed A; Hassanen, Ahmed M; Moustafa, Mahmoud F M; Sakuma, Yoh; Inouhe, Masahiro

    2012-01-01

    Salicylic acid (SA) controls growth and stress responses in plants. It also induces drought tolerance in plants. In this paper, four wheat (Triticum aestivum L.) cultivars with different drought responses were treated with SA in three levels of drain (90, 60, 30% of maximum field capacity) to examine its interactive effects on drought responses and contents of osmotic solutes that may be involved in growth and osmotic adjustment. Under drought condition, the cultivars Geza 164 and Sakha 69 had the plant biomass and leaf relative water content (LRWC) greater than the cultivars Gemaza 1 and Gemaza 3. In all cultivars, drought stress decreased the biomass, LRWC, and the contents of inorganic solutes (Ca, K, Mg) and largely increased the contents of organic solutes (soluble sugars and proline). By contrast, SA increased the biomass, LRWC and the inorganic and organic solute contents, except proline. Correlation analysis revealed that the LRWC correlated positively with the inorganic solute contents but negatively with proline in all cultivars. SA caused maximum accumulations of soluble sugars in roots under drought. These results indicated that SA-enhanced tolerance might involve solute accumulations but independently of proline biosynthesis. Drought-sensitive cultivars had a trait lowering Ca and K levels especially in shoots. Possible functions of the ions and different traits of cultivars were discussed.

  2. Construction and evaluation of cDNA libraries for large-scale expressed sequence tag sequencing in wheat (Triticum aestivum L.).

    PubMed

    Zhang, D; Choi, D W; Wanamaker, S; Fenton, R D; Chin, A; Malatrasi, M; Turuspekov, Y; Walia, H; Akhunov, E D; Kianian, P; Otto, C; Simons, K; Deal, K R; Echenique, V; Stamova, B; Ross, K; Butler, G E; Strader, L; Verhey, S D; Johnson, R; Altenbach, S; Kothari, K; Tanaka, C; Shah, M M; Laudencia-Chingcuanco, D; Han, P; Miller, R E; Crossman, C C; Chao, S; Lazo, G R; Klueva, N; Gustafson, J P; Kianian, S F; Dubcovsky, J; Walker-Simmons, M K; Gill, K S; Dvorák, J; Anderson, O D; Sorrells, M E; McGuire, P E; Qualset, C O; Nguyen, H T; Close, T J

    2004-10-01

    A total of 37 original cDNA libraries and 9 derivative libraries enriched for rare sequences were produced from Chinese Spring wheat (Triticum aestivum L.), five other hexaploid wheat genotypes (Cheyenne, Brevor, TAM W101, BH1146, Butte 86), tetraploid durum wheat (T. turgidum L.), diploid wheat (T. monococcum L.), and two other diploid members of the grass tribe Triticeae (Aegilops speltoides Tausch and Secale cereale L.). The emphasis in the choice of plant materials for library construction was reproductive development subjected to environmental factors that ultimately affect grain quality and yield, but roots and other tissues were also included. Partial cDNA expressed sequence tags (ESTs) were examined by various measures to assess the quality of these libraries. All ESTs were processed to remove cloning system sequences and contaminants and then assembled using CAP3. Following these processing steps, this assembly yielded 101,107 sequences derived from 89,043 clones, which defined 16,740 contigs and 33,213 singletons, a total of 49,953 "unigenes." Analysis of the distribution of these unigenes among the libraries led to the conclusion that the enrichment methods were effective in reducing the most abundant unigenes and to the observation that the most diverse libraries were from tissues exposed to environmental stresses including heat, drought, salinity, or low temperature. PMID:15514038

  3. Cloning of new members of heat shock protein HSP101 gene family in wheat (Triticum aestivum (L.) Moench) inducible by heat, dehydration, and ABA(1).

    PubMed

    Campbell, J L; Klueva, N Y; Zheng, H G; Nieto-Sotelo, J; Ho, T D; Nguyen, H T

    2001-01-26

    We have cloned two cDNAs, TaHSP101B and TaHSP101C, encoding two heat stress-inducible members of HSP101/ClpB family in bread wheat (Triticum aestivum (L.) Moench.). Proteins encoded by these cDNAs are highly similar at the primary sequence level and diverged from the previously reported TaHSP101 (designated TaHSP101A) both in the consensus ATP/GTP-binding region II and in the carboxy terminal region. The HSP101 gene was determined to be a single copy gene or a member of a small gene family in hexaploid wheat. Messages encoding HSP101 proteins were inducible by heat stress treatments in both wheat leaves and roots. Accumulation of the TaHSP101C mRNA was less abundant than that of TaHSP101B mRNA. We are showing for the first time that in addition to heat stress, expression of HSP101 mRNAs in wheat leaves was induced by a 2-h dehydration and a treatment with 5x10(-5)M ABA, but not affected by chilling or wounding, indicating that HSP101 proteins may be involved in both heat and drought responses in wheat. PMID:11342108

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. In Vivo Determination of Parameters of Nitrate Utilization in Wheat (Triticum aestivum L.) Seedlings Grown with Low Concentration of Nitrate in the Nutrient Solution 1

    PubMed Central

    Baer, Gianni R.; Collet, Gérald F.

    1981-01-01

    Six genotypes of winter wheat (Triticum aestivum L.) differing in grain protein concentration were grown on a nutrient solution containing low concentrations of NO3− (2 millimolar). Total NO3− uptake varied between genotypes but was not related to grain protein content. An in vivo nitrate reductase assay was used to determine the affinity of the enzyme for NO3−, and large phenotypic variations were observed. In vivo estimations of the concentration and size of the metabolic pool were variable. However, the three genotypes with the higher ratios of metabolic pool size to leaf total NO3− concentration were the high protein varieties. It is proposed that a high affinity of nitrate reductase for nitrate might be a biochemical marker for the capacity of the plant to continue assimilating NO3− for a longer period during the last stage of growth. The potential use of such physiological criteria as markers is discussed, in particular with respect to breeding programs for the development of plants with efficient nitrogen utilization. PMID:16662085

  11. Construction and Evaluation of cDNA Libraries for Large-Scale Expressed Sequence Tag Sequencing in Wheat (Triticum aestivum L.)

    PubMed Central

    Zhang, D.; Choi, D. W.; Wanamaker, S.; Fenton, R. D.; Chin, A.; Malatrasi, M.; Turuspekov, Y.; Walia, H.; Akhunov, E. D.; Kianian, P.; Otto, C.; Simons, K.; Deal, K. R.; Echenique, V.; Stamova, B.; Ross, K.; Butler, G. E.; Strader, L.; Verhey, S. D.; Johnson, R.; Altenbach, S.; Kothari, K.; Tanaka, C.; Shah, M. M.; Laudencia-Chingcuanco, D.; Han, P.; Miller, R. E.; Crossman, C. C.; Chao, S.; Lazo, G. R.; Klueva, N.; Gustafson, J. P.; Kianian, S. F.; Dubcovsky, J.; Walker-Simmons, M. K.; Gill, K. S.; Dvořák, J.; Anderson, O. D.; Sorrells, M. E.; McGuire, P. E.; Qualset, C. O.; Nguyen, H. T.; Close, T. J.

    2004-01-01

    A total of 37 original cDNA libraries and 9 derivative libraries enriched for rare sequences were produced from Chinese Spring wheat (Triticum aestivum L.), five other hexaploid wheat genotypes (Cheyenne, Brevor, TAM W101, BH1146, Butte 86), tetraploid durum wheat (T. turgidum L.), diploid wheat (T. monococcum L.), and two other diploid members of the grass tribe Triticeae (Aegilops speltoides Tausch and Secale cereale L.). The emphasis in the choice of plant materials for library construction was reproductive development subjected to environmental factors that ultimately affect grain quality and yield, but roots and other tissues were also included. Partial cDNA expressed sequence tags (ESTs) were examined by various measures to assess the quality of these libraries. All ESTs were processed to remove cloning system sequences and contaminants and then assembled using CAP3. Following these processing steps, this assembly yielded 101,107 sequences derived from 89,043 clones, which defined 16,740 contigs and 33,213 singletons, a total of 49,953 “unigenes.” Analysis of the distribution of these unigenes among the libraries led to the conclusion that the enrichment methods were effective in reducing the most abundant unigenes and to the observation that the most diverse libraries were from tissues exposed to environmental stresses including heat, drought, salinity, or low temperature. PMID:15514038

  12. 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.

  13. 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.

  14. Characterization of agronomic and quality traits and HSW-G5 compositions from the progenies of common wheat (Triticum aestivum L.) with different protein content.

    PubMed

    Bian, M; Sun, D K; Sun, D F; Sun, G L

    2015-01-01

    High molecular weight glutenin subunits (HMW-GS) play an essential role in wheat processing quality. In this study, we evaluated the genetic pattern with HMW-GS composition between generations and examined whether agronomic and quality traits were correlated with each other. A wheat (Triticum aestivum L.) cultivar with high protein content and 2 cultivars with low protein content were subjected to a reciprocal cross. Sixteen agronomic and 4 quality characteristics were investigated. A total of 216 seeds from each F2 generation were chosen randomly and analyzed for HMW-GS composition using sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Agronomic and quality characteristics were not significantly different between reciprocal crosses, indicating no cytoplasmic effect on the characteristics studied. The separation ratio of 2 HMW-GS loci was 9:3:3:1, indicating no linkage between any 2 loci. The novel HMW-GS N was detected in cultivar R145, which did not follow the Mendelian segregation ratio. A Glu-A1a(1) band was not detected in 1 individual from Tian8901xR145. Average grain weight per spike was significantly correlated with quality characteristics and may be a suitable criterion for selecting high protein content in wheat breeding programs. PMID:25867343

  15. 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.

  16. [Analysis of storage proteins (prolamines, puroindolines and waxy) in common wheat lines Triticum aestivum L. x (Triticum timopheevii Zhuk. x Triticum tauschii) with complex resistance to fungal infections].

    PubMed

    Obukhova, L V; Laĭkova, L I; Shumnyĭ, V K

    2010-06-01

    Storage proteins (prolamines, puroindolines, and Waxy) were studied in common wheat introgression lines obtained with the use of the Saratovskaya 29 (S29) cultivar line and synthetic hexaploid wheat (Triticum timopheevii Zhuk. x T. tauschii) (Sintetik, Sin.) and displaying complex resistance to fungal infections. Comparative analysis of storage proteins in the introgression lines of common wheat Triticum aestivum L. and in the parental forms revealed the only line (BC5) having a substitution at the Gli-B2 locus from Sintetik. Hybrid lines subjected to nine back crosses with the recurrent parental form S29 and selections for resistance to pathogens can be considered as nearly isogenic for the selected trait and retaining the allelic composition of (1) prolamines responsible for the bread-making qualitiy, (2) puroindolines associated with grain texture, and (3) Waxy proteins responsible for nutritive qualities. These lines are valuable as donors of immunity in breeding programs without the loss of the quality of flour and grain as compared to the S29 line and are also important in searching for genes determining resistance to leaf and stem rust and to powdery mildew. The amphiploid has a number of characters (silent Glu-A 1 locus and Ha genotype) that can negatively affect the quality of flour and grain and thus should be taken into account when choosing this donor.

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. A matrix attachment region is located upstream from the high-molecular-weight glutenin gene Bx7 in wheat (Triticum aestivum L.).

    PubMed

    Rampitsch, C; Jordan, M C; Cloutier, S

    2000-06-01

    A 2.2-kb nucleotide sequence rich in AT, located upstream from the Bx7 allele of the high-molecular-weight glutenin Glu-B1 locus in wheat (Triticum aestivum cv. Glenlea) was cloned following amplification by PCR. The 5' region of this sequence contains motifs typically found in matrix attachment regions (MARs) in other plants. We have shown that part of the 2.2-kb DNA binds to wheat nuclear matrix (NM) in vitro, at least as strongly as a known MAR (Adh1) from maize suggesting that there is a MAR upstream of Bx7. This MAR is approximately 800 bases in length running from -750 to -1560 bases, relative to the start codon. Although the MAR is associated with a tissue-specific gene and is beside a strong tissue-specific promoter, the MAR sequence did not lead to tissue-specific expression of the beta-glucuronidase marker gene under the control of the rice actin promoter in various tissues. Presence of the MAR was only slightly beneficial with respect to expression levels, which were not greatly altered in transient expression assays in various wheat tissues although a slight increase in the number of foci was observed in leaves, which have low transformation efficiencies.

  2. Chemically enhanced phytoextraction of risk elements from a contaminated agricultural soil using Zea mays and Triticum aestivum: performance and metal mobilization over a three year period.

    PubMed

    Neugschwandtner, Reinhard W; Tlustos, Pavel; Komárek, Michael; Száková, Jirina; Jakoubková, Lucie

    2012-09-01

    Enhanced phytoextraction using EDTA for the remediation of an agricultural soil contaminated with less mobile risk elements Cd and Pb originating from smelting activities in Príbram (Czech Republic) was assessed on the laboratory and the field scale. EDTA was applied to the first years crop Zea mays. Metal mobilization and metal uptake by the plants in the soil were monitored for two additional years when Triticum aestivum was planted. The application ofEDTA effectively increased water-soluble Cd and Pb concentrations in the soil. These concentrations decreased over time. Anyhow, increased concentrations could be still observed in the third experimental year indicating a low possibility of groundwater pollution after the addition of EDTA during and also after the enhanced phytoextraction process under prevailing climatic conditions. EDTA-applications caused phytotoxicity and thereby decreased biomass production and increased Cd and Pb uptake by the plants. Phytoextraction efficiency and phytoextraction potential were too low for Cd and Pb phytoextraction in the field in a reasonable time frame (as less than one-tenth of a percent of total Cd and Pb could be removed). This strongly indicates that EDTA-enhanced phytoextraction as implemented in this study is not a suitable remediation technique for risk metal contaminated soils.

  3. 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

  4. 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

  5. The UCSC Genome Browser.

    PubMed

    Karolchik, Donna; Hinrichs, Angie S; Kent, W James

    2012-12-01

    The University of California Santa Cruz (UCSC) Genome Browser is a popular Web-based tool for quickly displaying a requested portion of a genome at any scale, accompanied by a series of aligned annotation "tracks." The annotations generated by the UCSC Genome Bioinformatics Group and external collaborators include gene predictions, mRNA and expressed sequence tag alignments, simple nucleotide polymorphisms, expression and regulatory data, phenotype and variation data, and pairwise and multiple-species comparative genomics data. All information relevant to a region is presented in one window, facilitating biological analysis and interpretation. The database tables underlying the Genome Browser tracks can be viewed, downloaded, and manipulated using another Web-based application, the UCSC Table Browser. Users can upload personal datasets in a wide variety of formats as custom annotation tracks in both browsers for research or educational purposes. This unit describes how to use the Genome Browser and Table Browser for genome analysis, download the underlying database tables, and create and display custom annotation tracks.

  6. NCBI viral genomes resource.

    PubMed

    Brister, J Rodney; Ako-Adjei, Danso; Bao, Yiming; Blinkova, Olga

    2015-01-01

    Recent technological innovations have ignited an explosion in virus genome sequencing that promises to fundamentally alter our understanding of viral biology and profoundly impact public health policy. Yet, any potential benefits from the billowing cloud of next generation sequence data hinge upon well implemented reference resources that facilitate the identification of sequences, aid in the assembly of sequence reads and provide reference annotation sources. The NCBI Viral Genomes Resource is a reference resource designed to bring order to this sequence shockwave and improve usability of viral sequence data. The resource can be accessed at http://www.ncbi.nlm.nih.gov/genome/viruses/ and catalogs all publicly available virus genome sequences and curates reference genome sequences. As the number of genome sequences has grown, so too have the difficulties in annotating and maintaining reference sequences. The rapid expansion of the viral sequence universe has forced a recalibration of the data model to better provide extant sequence representation and enhanced reference sequence products to serve the needs of the various viral communities. This, in turn, has placed increased emphasis on leveraging the knowledge of individual scientific communities to identify important viral sequences and develop well annotated reference virus genome sets.

  7. 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

  8. The banana genome hub.

    PubMed

    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/

  9. 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.

  10. The 'Green Revolution' dwarfing genes play a role in disease resistance in Triticum aestivum and Hordeum vulgare.

    PubMed

    Saville, R J; Gosman, N; Burt, C J; Makepeace, J; Steed, A; Corbitt, M; Chandler, E; Brown, J K M; Boulton, M I; Nicholson, P

    2012-02-01

    The Green Revolution dwarfing genes, Rht-B1b and Rht-D1b, encode mutant forms of DELLA proteins and are present in most modern wheat varieties. DELLA proteins have been implicated in the response to biotic stress in the model plant, Arabidopsis thaliana. Using defined wheat Rht near-isogenic lines and barley Sln1 gain of function (GoF) and loss of function (LoF) lines, the role of DELLA in response to biotic stress was investigated in pathosystems representing contrasting trophic styles (biotrophic, hemibiotrophic, and necrotrophic). GoF mutant alleles in wheat and barley confer a resistance trade-off with increased susceptibility to biotrophic pathogens and increased resistance to necrotrophic pathogens whilst the converse was conferred by a LoF mutant allele. The polyploid nature of the wheat genome buffered the effect of single Rht GoF mutations relative to barley (diploid), particularly in respect of increased susceptibility to biotrophic pathogens. A role for DELLA in controlling cell death responses is proposed. Similar to Arabidopsis, a resistance trade-off to pathogens with contrasting pathogenic lifestyles has been identified in monocotyledonous cereal species. Appreciation of the pleiotropic role of DELLA in biotic stress responses in cereals has implications for plant breeding.

  11. 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

  12. 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

  13. 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.

  14. 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

  15. Genomics and plant breeding.

    PubMed

    Aljanabi, S

    2001-01-01

    Much of our most basic understanding of genetics has its roots in plant genetics and crop breeding. The study of plants has led to important insights into highly conserved biological process and a wealth of knowledge about development. Agriculture is now well positioned to take its share benefit from genomics. The primary sequences of most plant genes will be determined over the next few years. Informatics and functional genomics will help identify those genes that can be best utilized to crop production and quality through genetic engineering and plant breeding. Recent developments in plant genomics are reviewed.

  16. What Is a Genome?

    PubMed

    Goldman, Aaron David; Landweber, Laura F

    2016-07-01

    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

  17. Sampling in landscape genomics.

    PubMed

    Manel, Stéphanie; Albert, Cécile H; Yoccoz, Nigel G

    2012-01-01

    Landscape genomics, based on the sampling of individuals genotyped for a large number of markers, may lead to the identification of regions of the genome correlated to selection pressures caused by the environment. In this chapter, we discuss sampling strategies to be used in a landscape genomics approach. We suggest that designs based on model-based stratification using the climatic and/or biological spaces are in general more efficient than designs based on the geographic space. More work is needed to identify designs that allow disentangling environmental selection pressures versus other processes such as range expansions or hierarchical population structure.

  18. 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.

  19. 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.

  20. 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

  1. 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...

  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. 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.

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. Surveying genome replication

    PubMed Central

    Kearsey, Stephen

    2002-01-01

    Two recent studies have added microarrays to the toolkit used to analyze the origins of replication in yeast chromosomes, providing a fuller picture of how genomic DNA replication is organized. PMID:12093380

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. An Introduction to Genome Annotation.

    PubMed

    Campbell, Michael S; Yandell, Mark

    2015-12-17

    Genome projects have evolved from large international undertakings to tractable endeavors for a single lab. Accurate genome annotation is critical for successful genomic, genetic, and molecular biology experiments. These annotations can be generated using a number of approaches and available software tools. This unit describes methods for genome annotation and a number of software tools commonly used in gene annotation.

  3. 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

  4. 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.

  5. 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.

  6. 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).

  7. 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.

  8. Human Social Genomics

    PubMed Central

    Cole, Steven W.

    2014-01-01

    A growing literature in human social genomics has begun to analyze how everyday life circumstances influence human gene expression. Social-environmental conditions such as urbanity, low socioeconomic status, social isolation, social threat, and low or unstable social status have been found to associate with differential expression of hundreds of gene transcripts in leukocytes and diseased tissues such as metastatic cancers. In leukocytes, diverse types of social adversity evoke a common conserved transcriptional response to adversity (CTRA) characterized by increased expression of proinflammatory genes and decreased expression of genes involved in innate antiviral responses and antibody synthesis. Mechanistic analyses have mapped the neural “social signal transduction” pathways that stimulate CTRA gene expression in response to social threat and may contribute to social gradients in health. Research has also begun to analyze the functional genomics of optimal health and thriving. Two emerging opportunities now stand to revolutionize our understanding of the everyday life of the human genome: network genomics analyses examining how systems-level capabilities emerge from groups of individual socially sensitive genomes and near-real-time transcriptional biofeedback to empirically optimize individual well-being in the context of the unique genetic, geographic, historical, developmental, and social contexts that jointly shape the transcriptional realization of our innate human genomic potential for thriving. PMID:25166010

  9. Ebolavirus comparative genomics

    DOE PAGES

    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

  10. An archaeal genomic signature.

    PubMed

    Graham, D E; Overbeek, R; Olsen, G J; Woese, C R

    2000-03-28

    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).

  11. 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

  12. 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

  13. A Review on Genomics APIs.

    PubMed

    Swaminathan, Rajeswari; Huang, Yungui; Moosavinasab, Soheil; Buckley, Ronald; Bartlett, Christopher W; Lin, Simon M

    2016-01-01

    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

  14. 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/ .

  15. 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

  16. Detection of protein and DNA damage induced by elevated carbon dioxide and ozone in Triticum aestivum L. using biomarker and comet assay.

    PubMed

    Abdelhaliem, E; Al-Huqai, A A

    2016-01-01

    This study was designed to compare the genetic effects of elevated carbon dioxide (CO2) and ozone (O3), alone or in combination, under irrigated and non-irrigated conditions on proteins and DNA of wheat (Triticum aestivum L.). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), isozymes, random amplified polymorphic DNA (RAPD), and comet assays were used. SDS-PAGE analysis revealed distinctive polymorphisms (100%) based on the number of polypeptide bands (169) with molecular weights ranging from 300.0 to 24.00 kDa, band intensity, appearance, and loss of bands when compared with control samples. Six isozymes, malate dehydrogenase, amylase, leucine-aminopeptidase, esterase, peroxidase, and catalase, generated 100% polymorphism values based on zymogram number, relative front, and optical intensities. RAPD revealed 276 DNA bands with a distinctive polymorphism value of 92.31% based on the number of amplified DNA products, ranging from 45 to 1100 bp, and band intensity. In the comet assay, the highest extent of nuclear DNA damage was observed as tail length 8.70 μm, tailed DNA 8.01%, and tail moment unit 34.18 in non-irrigated O3-treated wheat nuclei. These results show that O3-treatment alone induced high levels of oxidative protein and DNA damage in wheat plant, especially in a non-irrigation system. Interestingly, CO2 in combination with O3 could ameliorate the negative impact of O3-oxidative stress. This study shows that protein and DNA biomarkers, and the comet assay, could be used for the reliable estimation of genotoxicity following the exposure of economic crop plants to air pollutants. PMID:27420988

  17. Integrated analysis of seed proteome and mRNA oxidation reveals distinct post-transcriptional features regulating dormancy in wheat (Triticum aestivum L.).

    PubMed

    Gao, Feng; Rampitsch, Christof; Chitnis, Vijaya R; Humphreys, Gavin D; Jordan, Mark C; Ayele, Belay T

    2013-10-01

    Wheat seeds can be released from a dormant state by after-ripening; however, the underlying molecular mechanisms are still mostly unknown. We previously identified transcriptional programmes involved in the regulation of after-ripening-mediated seed dormancy decay in wheat (Triticum aestivum L.). Here, we show that seed dormancy maintenance and its release by dry after-ripening in wheat is associated with oxidative modification of distinct seed-stored mRNAs that mainly correspond to oxidative phosphorylation, ribosome biogenesis, nutrient reservoir and α-amylase inhibitor activities, suggesting the significance of post-transcriptional repression of these biological processes in regulating seed dormancy. We further show that after-ripening induced seed dormancy release in wheat is mediated by differential expression of specific proteins in both dry and hydrated states, including those involved in proteolysis, cellular signalling, translation and energy metabolism. Among the genes corresponding to these proteins, the expression of those encoding α-amylase/trypsin inhibitor and starch synthase appears to be regulated by mRNA oxidation. Co-expression analysis of the probesets differentially expressed and oxidized during dry after-ripening along with those corresponding to proteins differentially regulated between dormant and after-ripened seeds produced three co-expressed gene clusters containing more candidate genes potentially involved in the regulation of seed dormancy in wheat. Two of the three clusters are enriched with elements that are either abscisic acid (ABA) responsive or recognized by ABA-regulated transcription factors, indicating the association between wheat seed dormancy and ABA sensitivity.

  18. Heavy metal and metalloid concentrations in components of 25 wheat (Triticum aestivum) varieties in the vicinity of lead smelters in Henan province, China.

    PubMed

    Xing, Weiqin; Zhang, Hongyi; Scheckel, Kirk G; Li, Liping

    2016-01-01

    Soil contamination and human impacts have been reported in the vicinity of lead (Pb) smelters in Henan, China. However, no information is available on crop uptake of soil contaminants near these smelters. Grains, glume, rachis, and stem/leaf samples of 25 wheat (Triticum aestivum) varieties were collected from a small, smelter-impacted agricultural area of Beishe Village, Henan Province, and were analyzed for arsenic (As), cadmium (Cd), copper (Cu), Pb, and zinc (Zn) concentrations. The study aim was to evaluate the level of contaminant uptake in wheat and ostensibly observe if specific varieties of wheat were more susceptible to uptake. The mean concentrations of As, Cd, Cu, Pb, and Zn in whole grain flour were 0.0915, 0.192, 3.22, 0.280, and 32.5 mg kg(-1), respectively. Grain concentrations of all 25 varieties for Cd as well as 16 varieties for Pb exceeded the maximum permissible concentrations (MPC) for consumption. Mean pollution indexes (MPI) (element concentration of wheat grain/MPC for As, Cd or Pb) of the grains varied 0.562-2.15. As, Pb, and Cd contributed 5.22, 40.0, and 54.8 % to the MPI for all 25 varieties, respectively. This survey highlights Cd and Pb contamination of wheat grains in the vicinity of lead smelters in Henan Province, and likely other farm villages in the area. Further work is needed to examine uptake and contamination of other crops and vegetables impacted from the lead smelters in Henan Province and the absorption of toxic elements from food sources by local inhabitants.

  19. FAR5, a fatty acyl-coenzyme A reductase, is involved in primary alcohol biosynthesis of the leaf blade cuticular wax in wheat (Triticum aestivum L.).

    PubMed

    Wang, Yong; Wang, Meiling; Sun, Yulin; Wang, Yanting; Li, Tingting; Chai, Guaiqiang; Jiang, Wenhui; Shan, Liwei; Li, Chunlian; Xiao, Enshi; Wang, Zhonghua

    2015-03-01

    A waxy cuticle that serves as a protective barrier against non-stomatal water loss and environmental damage coats the aerial surfaces of land plants. It comprises a cutin polymer matrix and waxes. Cuticular waxes are complex mixtures of very long chain fatty acids (VLCFAs) and their derivatives. Results show that primary alcohols are the major components of bread wheat (Triticum aestivum L.) leaf blade cuticular waxes. Here, the characterization of TaFAR5 from wheat cv Xinong 2718, which is allelic to TAA1b, an anther-specific gene, is reported. Evidence is presented for a new function for TaFAR5 in the biosynthesis of primary alcohols of leaf blade cuticular wax in wheat. Expression of TaFAR5 cDNA in yeast (Saccharomyces cerevisiae) led to production of C22:0 primary alcohol. The transgenic expression of TaFAR5 in tomato (Solanum lycopersicum) cv MicroTom leaves resulted in the accumulation of C26:0, C28:0, and C30:0 primary alcohols. TaFAR5 encodes an alcohol-forming fatty acyl-coenzyme A reductase (FAR). Expression analysis revealed that TaFAR5 was expressed at high levels in the leaf blades, anthers, pistils, and seeds. Fully functional green fluorescent protein-tagged TaFAR5 protein was localized to the endoplasmic reticulum (ER), the site of primary alcohol biosynthesis. SDS-PAGE analysis indicated that the TaFAR5 protein possessed a molecular mass of 58.4kDa, and it was also shown that TaFAR5 transcript levels were regulated in response to drought, cold, and abscisic acid (ABA). Overall, these data suggest that TaFAR5 plays an important role in the synthesis of primary alcohols in wheat leaf blade.

  20. Identification and Comparative Analysis of microRNA in Wheat (Triticum aestivum L.) Callus Derived from Mature and Immature Embryos during In vitro Culture

    PubMed Central

    Chu, Zongli; Chen, Junying; Xu, Haixia; Dong, Zhongdong; Chen, Feng; Cui, Dangqun

    2016-01-01

    Feasible and efficient tissue culture plays an important role in plant genetic engineering. Wheat (Triticum aestivum L.) immature embryos (IMEs) are preferred for tissue culture to mature embryos (MEs) because IMEs easily generate embryogenic callus, producing large number of plants. The molecular mechanisms of regulation and the biological pathways involved in embryogenic callus formation in wheat remain unclear. Here, microRNAs (miRNAs) potentially involved in embryogenic callus formation and somatic embryogenesis were identified through deep sequencing of small RNAs (sRNAs) and analyzed with bioinformatics tools. Six sRNA libraries derived from calli of IMEs and MEs after 3, 6, or 15 d of culture (DC) were constructed and sequenced. A total of 85 known miRNAs were identified, of which 30, 33, and 18 were differentially expressed (P < 0.05) between the IME and ME libraries at 3, 6, and 15 DC, respectively. Additionally, 171 novel and 41 candidate miRNAs were also identified, of the novel miRNA, 69, 67, and 37 were differentially expressed (P < 0.05) between the two types of libraries at 3, 6, and 15 DC, respectively. The expression patterns of eight known and eight novel miRNAs were validated using quantitative real-time polymerase chain reaction. Gene ontology annotation of differentially expressed miRNA targets provided information regarding the underlying molecular functions, biological processes, and cellular components involved in embryogenic callus development. Functional miRNAs, such as miR156, miR164, miR1432, miR398, and miR397, differentially expressed in IMEs and MEs might be related to embryogenic callus formation and somatic embryogenesis. This study suggests that miRNA plays an important role in embryogenic callus formation and somatic embryogenesis in wheat, and our data provide a useful resource for further research. PMID:27625667

  1. Heavy metal and metalloid concentrations in components of 25 wheat (Triticum aestivum) varieties in the vicinity of lead smelters in Henan province, China.

    PubMed

    Xing, Weiqin; Zhang, Hongyi; Scheckel, Kirk G; Li, Liping

    2016-01-01

    Soil contamination and human impacts have been reported in the vicinity of lead (Pb) smelters in Henan, China. However, no information is available on crop uptake of soil contaminants near these smelters. Grains, glume, rachis, and stem/leaf samples of 25 wheat (Triticum aestivum) varieties were collected from a small, smelter-impacted agricultural area of Beishe Village, Henan Province, and were analyzed for arsenic (As), cadmium (Cd), copper (Cu), Pb, and zinc (Zn) concentrations. The study aim was to evaluate the level of contaminant uptake in wheat and ostensibly observe if specific varieties of wheat were more susceptible to uptake. The mean concentrations of As, Cd, Cu, Pb, and Zn in whole grain flour were 0.0915, 0.192, 3.22, 0.280, and 32.5 mg kg(-1), respectively. Grain concentrations of all 25 varieties for Cd as well as 16 varieties for Pb exceeded the maximum permissible concentrations (MPC) for consumption. Mean pollution indexes (MPI) (element concentration of wheat grain/MPC for As, Cd or Pb) of the grains varied 0.562-2.15. As, Pb, and Cd contributed 5.22, 40.0, and 54.8 % to the MPI for all 25 varieties, respectively. This survey highlights Cd and Pb contamination of wheat grains in the vicinity of lead smelters in Henan Province, and likely other farm villages in the area. Further work is needed to examine uptake and contamination of other crops and vegetables impacted from the lead smelters in Henan Province and the absorption of toxic elements from food sources by local inhabitants. PMID:26661959

  2. Analysis of transgenic wheat (Triticum aestivum L.) harboring a maize (Zea mays L.) gene for plastid EF-Tu: segregation pattern, expression and effects of the transgene.

    PubMed

    Fu, Jianming; Ristic, Zoran

    2010-06-01

    We previously reported that transgenic wheat (Triticum aestivum L.) carrying a maize (Zea mays L.) gene (Zmeftu1) for chloroplast protein synthesis elongation factor, EF-Tu, displays reduced thermal aggregation of leaf proteins, reduced injury to photosynthetic membranes (thylakoids), and enhanced rate of CO(2) fixation following exposure to heat stress (18 h at 45 degrees C) [Fu et al. in Plant Mol Biol 68:277-288, 2008]. In the current study, we investigated the segregation pattern and expression of the transgene Zmeftu1 and determined the grain yield of transgenic plants after exposure to a brief heat stress (18 h at 45 degrees C). We also assessed thermal aggregation of soluble leaf proteins in transgenic plants, testing the hypothesis that increased levels of EF-Tu will lead to a non-specific protection of leaf proteins against thermal aggregation. The transgenic wheat displayed a single-gene pattern of segregation of Zmeftu1. Zmeftu1 was expressed, and the transgenic plants synthesized and accumulated three anti-EF-Tu cross-reacting polypeptides of similar molecular mass but different pI, suggesting the possibility of posttranslational modification of this protein. The transgenic plants also showed better grain yield after exposure to heat stress compared with their non-transgenic counterparts. Soluble leaf proteins of various molecular masses displayed lower thermal aggregation in transgenic than in non-transgenic wheat. The results suggest that overexpression of chloroplast EF-Tu can be beneficial to wheat tolerance to heat stress. Moreover, the results also support the hypothesis that EF-Tu contributes to heat tolerance by acting as a molecular chaperone and protecting heat-labile proteins from thermal aggregation in a non-specific manner.

  3. Kinetics of phosphorus and potassium release from rock phosphate and waste mica enriched compost and their effect on yield and nutrient uptake by wheat (Triticum aestivum).

    PubMed

    Nishanth, D; Biswas, D R

    2008-06-01

    An attempt was made to study the efficient use of rice straw and indigenous source of phosphorus and potassium in crop production through composting technology. Various enriched composts were prepared using rice straw, rock phosphate (RP), waste mica and bioinoculant (Aspergillus awamori) and kinetics of release of phosphorus and potassium from enriched composts and their effect on yield and nutrient uptake by wheat (Triticum aestivum) were carried out. Results showed sharp increases in release in water-soluble P and K from all the composts at 8th to 12th day of leaching, thereafter, it decreased gradually. Maximum release of water-soluble P and K were obtained in ordinary compost than enriched composts during the initial stages of leaching, but their differences narrowed down at latter stages. Data in pot experiments revealed that enriched composts performed poorly than diammonium phosphate during initial stages of crop growth, but they out yielded at the latter stages, particularly at maturity stage, as evident from their higher yield, uptake, nutrient recoveries and fertility status of P and K in soils. Moreover, enriched composts prepared with RP and waste mica along with A. awamori resulted in significantly higher biomass yield, uptake and recoveries of P and K as well as available P and K in soils than composts prepared without inoculant. Results indicated that enriched compost could be an alternate technology for the efficient management of rice straw, low-grade RP and waste mica in crop production, which could help to reduce the reliance on costly chemical fertilizers. PMID:17905580

  4. Quantitative Trait Loci Associated with Phenological Development, Low-Temperature Tolerance, Grain Quality, and Agronomic Characters in Wheat (Triticum aestivum L.).

    PubMed

    Fowler, D B; N'Diaye, A; Laudencia-Chingcuanco, D; Pozniak, C J

    2016-01-01

    Plants must respond to environmental cues and schedule their development in order to react to periods of abiotic stress and commit fully to growth and reproduction under favorable conditions. This study was initiated to identify SNP markers for characters expressed from the seedling stage to plant maturity in spring and winter wheat (Triticum aestivum L.) genotypes adapted to western Canada. Three doubled haploid populations with the winter cultivar 'Norstar' as a common parent were developed and genotyped with a 90K Illumina iSelect SNP assay and a 2,998.9 cM consensus map with 17,541 markers constructed. High heritability's reflected large differences among the parents and relatively low genotype by environment interactions for all characters considered. Significant QTL were detected for the 15 traits examined. However, different QTL for days to heading in controlled environments and the field provided a strong reminder that growth and development are being orchestrated by environmental cues and caution should be exercised when extrapolating conclusions from different experiments. A QTL on chromosome 6A for minimum final leaf number, which determines the rate of phenological development in the seedling stage, was closely linked to QTL for low-temperature tolerance, grain quality, and agronomic characters expressed up to the time of maturity. This suggests phenological development plays a critical role in programming subsequent outcomes for many traits. Transgressive segregation was observed for the lines in each population and QTL with additive effects were identified suggesting that genes for desirable traits could be stacked using Marker Assisted Selection. QTL were identified for characters that could be transferred between the largely isolated western Canadian spring and winter wheat gene pools demonstrating the opportunities offered by Marker Assisted Selection to act as bridges in the identification and transfer of useful genes among related genetic islands

  5. Genetic analysis and molecular mapping of a new fertility restorer gene Rf8 for Triticum timopheevi cytoplasm in wheat (Triticum aestivum L.) using SSR markers.

    PubMed

    Sinha, Pallavi; Tomar, S M S; Vinod; Singh, Vikas K; Balyan, H S

    2013-12-01

    A study on mode of inheritance and mapping of fertility restorer (Rf) gene(s) using simple sequence repeat (SSR) markers was conducted in a cross of male sterile line 2041A having Triticum timopheevi cytoplasm and a restorer line PWR4099 of common wheat (Triticum aestivum L.). The F1 hybrid was completely fertile indicating that fertility restoration is a dominant trait. Based on the pollen fertility and seed set of bagged spikes in F2 generation, the individual plants were classified into fertile and sterile groups. Out of 120 F2 plants, 97 were fertile and 23 sterile (based on pollen fertility) while 98 plants set ≥ 5 seeds/spike and 22 produced ≤ 4 or no seed. The observed frequency fits well into Mendelian ratio of 3 fertile: 1 sterile with χ(2) value of 2.84 for pollen fertility and 2.17 for seed setting indicating that the fertility restoration is governed by a single dominant gene in PWR4099. The three linked SSR markers, Xwmc503, Xgwm296 and Xwmc112 located on the chromosome 2DS were placed at a distance of 3.3, 5.8 and 6.7 cM, respectively, from the Rf gene. Since, no known Rf gene is located on the chromosome arm 2DS, the Rf gene in PWR4099 is a new gene and proposed as Rf8. The closest SSR marker, Xwmc503, linked to the Rf8 was validated in a set of Rf, maintainer and cytoplasmic male sterile lines. The closely linked SSR marker Xwmc503 may be used in marker-assisted backcross breeding facilitating the transfer of fertility restoration gene Rf8 into elite backgrounds with ease.

  6. Increase in growth, productivity and nutritional status of wheat (Triticum aestivum L. cv. WH-711) and enrichment in soil fertility applied with organic matrix entrapped urea.

    PubMed

    Kumar, Manoj; Bauddh, Kuldeep; Kumar, Sanjeev; Sainger, Manish; Sainger, Poonam A; Singh, Rana P

    2013-01-01

    Field experiments were conducted during two consequent years in semi-arid, subtropical climate of Rohtak district situated in North-West Indian state Haryana to evaluate the effects of eco-friendly organic matrix entrapped urea (OMEU) on wheat (Triticum aestivum L. cv. WH-711). The OMEU prepared in granular form contained cow dung, rice bran (grain cover of Oryza sativa), neem (Azadirachta indica) leaves and clay soil (diameter of particles < 0.002 mm) in 1:1:1:1 ratios and saresh (plant gum of Acacia sp.) as binder entrapping half of the recommended dose of urea. A basal application of organic matrix entrapped urea showed increase in plant growth in terms of fresh and dry weights, root length, root number, leaf number, tillers, plant height earlet number, earlet length and productivity in terms of grain yield and straw yield over free form of urea (FU) and no fertilizer (NF) application. The OMEU increased total soluble proteins, organic N and free ammonium content in the leaves at 45 and 60 days. The nutritional status of wheat grains in OMEU applied plants was almost similar to that observed for FU applied plants. An increase in organic carbon and available phosphorus (P) was observed in OMEU applied plots on harvest whereas pH was slightly decreased over FU applied plots. The microbial population and activity in terms of fungal and bacterial colony count and activities soil dehydrogenase and alkaline phosphatase were significantly higher in OMEU applied plots as compared to the FU applied plots. Our data indicate that OMEU which are low cost, biodegradable and non-toxic can be used to replace the expensive chemical fertilizers for wheat cultivation in semi-arid, subtropical climate. PMID:24006800

  7. Growth-suppressive effect of the α-amylase inhibitor of Triticum aestivum on stored-product mites varies by the species and type of diet.

    PubMed

    Hubert, Jan; Nesvorna, Marta; Erban, Tomas

    2014-01-01

    A naturally occurring α-amylase inhibitor (α-AI) of Triticum aestivum protects wheat grain from gramnivorous arthropod pests. The α-AI (Type-I) was incorporated into carbohydrate and protein diets to test its inhibitory activity on the stored-product mites Acarus siro, Lepidoglyphus destructor and Tyrophagus putrescentiae (Acari: Astigmata). Growth tests of mites fed the various diets were used to compare the suppressive effects. The final population size of mites attained from an initial population of 50 specimens maintained under controlled conditions (85 % relative humidity and 25 °C) was compared after 21 days of cultivation. The results showed that α-AI in the concentration in the range of 0.01-1 mg g(-1) did not suppress the growth of the tested stored-product mites. α-AI at a concentration of 10 mg g(-1) exerted a growth-suppressive effect that depended on the diet and species of the mites. The growth rate of A. siro was affected by the type of diet and was higher on carbohydrate diet than on the protein diet, the suppressive effect of α-AI was on the both diets. The growth-suppressive effect of α-AI on L. destructor and T. putrescentiae was significant when they were fed the protein diet but not when they were fed the carbohydrate diet. The higher resistance of tested mites to α-AI (proteinaceous) compared to non-proteinaceous acarbose corresponds to a powerful proteotolytic system in the mite gut. The results are discussed in terms of the adaptability of mites to utilize the starch from food sources.

  8. Significant changes in cell and chloroplast development in young wheat leaves (Triticum aestivum cv Hereward) grown in elevated CO{sub 2}

    SciTech Connect

    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{sup {minus}1}) or at elevated (650 {mu}L L{sup {minus}1}) CO{sub 2}. In elevated CO{sub 2}, 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 CO{sub 2} 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 CO{sub 2}, 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-biphosphate carboxylase/oxygenase. A significant finding was that in 10 to 20% of the mesophyll cells grown in elevated CO{sub 2} 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. 29 refs., 6 figs., 2 tabs.

  9. Molecular cloning and characterization of a proliferating cell nuclear antigen gene by chemically induced male sterility in wheat (Triticum aestivum L.).

    PubMed

    Yu, Y A; Zhang, G S; Zhang, J; Ju, L; Zhu, Q D; Song, Y L; Wang, J W; Niu, N; Ma, S C

    2015-10-05

    Although a number of studies have shown that chemical hybridizing agents (CHAs) affect anther growth and regulate cell-cycle progression, little is known about the molecular and cellular mechanisms involved. Proliferating cell nuclear antigen (PCNA) is an essential factor in DNA replication, and in many other processes in eukaryotic cells. In this study, the open reading frame of TaPCNA, the PCNA in wheat (Triticum aestivum L.), was cloned by reverse transcription polymerase chain reaction (RT-PCR). Sequence analysis revealed that this gene was 792-bp long and encoded a protein with 234 amino acids. Alignment of the TaPCNA-predicted sequence revealed a high degree of identity with PCNAs from other plant species. A subcellular localization assay indicated that TaPCNA was localized in the nucleus. The TaPCNA was cloned into the prokaryotic expression plasmid pET32a, and the recombinant plasmid was transformed into BL21 (DE3). TaPCNA expression was induced by 0.5 mM isopropyl-beta-D-thiogalactopyranoside and verified using sodium dodecyl sulfate polyacrylamide gel electrophoresis and western blot assays, which indicated that the fusion protein was successfully expressed. The gene involved in the G1-to-S transition, Histone H4, was downregulated by 1376- CIMS, which is a chemically induced male sterility line. However, a semi-quantitative RT-PCR revealed that TaPCNA expression was upregulated in 1376-CIMS. Our results suggest that CHAs (SQ-1) induce DNA damage in wheat anthers. DNA damage results in either the delay or arrest of cell-cycle progression, which affects anther development. This study will help to elucidate the mechanisms of SQ-1-induced male sterility.

  10. Kinetic properties of cell wall bound superoxide dismutase in leaves of wheat (Triticum aestivum L.) following stripe rust (Puccinia striiformis) infection.

    PubMed

    Asthir, Bavita; Koundal, A; Bains, N S

    2011-10-01

    Stripe rust (Puccinia striiformis f.sp. tritici) is the most devastating disease of wheat (Triticum aestivum L.) accounting huge economical losses to the industry worldwide. HD 2329 was a widely grown wheat cultivar which had become highly susceptible to stripe rust and was used to understand the biochemical aspects of the host pathogen interaction through characterization of superoxide dismutase (SOD). In the present study, two types of SOD, ionically or covalently bound to the particulate fraction were found in the stripe rust infected and uninfected wheat leaves of susceptible cultivar HD 2329. Cell walls of leaves contained a high level of SOD, of which 41-44% was extractable by 2 M NaCl and 10-13% by 0.5% EDTA in infected and uninfected leaves. The NaCl-released SOD constituted the predominant fraction. It exhibited maximum activity at pH 9.0, had a Km value of 1.82-2.51 for uninfected and 1.77-2.37 mM for infected, respectively with pyrogallol as the substrate, and a Vmax of 9.55-21.4 and 12.4-24.1 delta A min(-1)g(-1)FW. A temperature optimum of 20 degrees C was observed for SOD of both uninfected and infected leaves. SOD showed differential response to metal ions, suggesting their distinctive nature. Inhibition of wall bound SOD by iodine and its partial regeneration of activity by mercaptoethanol suggested the involvement of cysteine in active site of the enzyme. These two forms showed greater differences with respect to thermodynamic properties like energy of activation (Ea) and enthalpy change (delta H), while entropy change (delta S) and free energy change (delta G) were similar. The results further showed that pathogen infection of the leaves of susceptible wheat cultivar induced a decrease in the SOD activity and kinetics which might be critical during the response of plant cells to the infection. PMID:22165293

  11. Quantitative Trait Loci Associated with Phenological Development, Low-Temperature Tolerance, Grain Quality, and Agronomic Characters in Wheat (Triticum aestivum L.)

    PubMed Central

    Fowler, D. B.; N'Diaye, A.; Laudencia-Chingcuanco, D.; Pozniak, C. J.

    2016-01-01

    Plants must respond to environmental cues and schedule their development in order to react to periods of abiotic stress and commit fully to growth and reproduction under favorable conditions. This study was initiated to identify SNP markers for characters expressed from the seedling stage to plant maturity in spring and winter wheat (Triticum aestivum L.) genotypes adapted to western Canada. Three doubled haploid populations with the winter cultivar ‘Norstar’ as a common parent were developed and genotyped with a 90K Illumina iSelect SNP assay and a 2,998.9 cM consensus map with 17,541 markers constructed. High heritability’s reflected large differences among the parents and relatively low genotype by environment interactions for all characters considered. Significant QTL were detected for the 15 traits examined. However, different QTL for days to heading in controlled environments and the field provided a strong reminder that growth and development are being orchestrated by environmental cues and caution should be exercised when extrapolating conclusions from different experiments. A QTL on chromosome 6A for minimum final leaf number, which determines the rate of phenological development in the seedling stage, was closely linked to QTL for low-temperature tolerance, grain quality, and agronomic characters expressed up to the time of maturity. This suggests phenological development plays a critical role in programming subsequent outcomes for many traits. Transgressive segregation was observed for the lines in each population and QTL with additive effects were identified suggesting that genes for desirable traits could be stacked using Marker Assisted Selection. QTL were identified for characters that could be transferred between the largely isolated western Canadian spring and winter wheat gene pools demonstrating the opportunities offered by Marker Assisted Selection to act as bridges in the identification and transfer of useful genes among related genetic

  12. Kinetic properties of cell wall bound superoxide dismutase in leaves of wheat (Triticum aestivum L.) following stripe rust (Puccinia striiformis) infection.

    PubMed

    Asthir, Bavita; Koundal, A; Bains, N S

    2011-10-01

    Stripe rust (Puccinia striiformis f.sp. tritici) is the most devastating disease of wheat (Triticum aestivum L.) accounting huge economical losses to the industry worldwide. HD 2329 was a widely grown wheat cultivar which had become highly susceptible to stripe rust and was used to understand the biochemical aspects of the host pathogen interaction through characterization of superoxide dismutase (SOD). In the present study, two types of SOD, ionically or covalently bound to the particulate fraction were found in the stripe rust infected and uninfected wheat leaves of susceptible cultivar HD 2329. Cell walls of leaves contained a high level of SOD, of which 41-44% was extractable by 2 M NaCl and 10-13% by 0.5% EDTA in infected and uninfected leaves. The NaCl-released SOD constituted the predominant fraction. It exhibited maximum activity at pH 9.0, had a Km value of 1.82-2.51 for uninfected and 1.77-2.37 mM for infected, respectively with pyrogallol as the substrate, and a Vmax of 9.55-21.4 and 12.4-24.1 delta A min(-1)g(-1)FW. A temperature optimum of 20 degrees C was observed for SOD of both uninfected and infected leaves. SOD showed differential response to metal ions, suggesting their distinctive nature. Inhibition of wall bound SOD by iodine and its partial regeneration of activity by mercaptoethanol suggested the involvement of cysteine in active site of the enzyme. These two forms showed greater differences with respect to thermodynamic properties like energy of activation (Ea) and enthalpy change (delta H), while entropy change (delta S) and free energy change (delta G) were similar. The results further showed that pathogen infection of the leaves of susceptible wheat cultivar induced a decrease in the SOD activity and kinetics which might be critical during the response of plant cells to the infection.

  13. FAR5, a fatty acyl-coenzyme A reductase, is involved in primary alcohol biosynthesis of the leaf blade cuticular wax in wheat (Triticum aestivum L.)

    PubMed Central

    Wang, Yong; Wang, Meiling; Sun, Yulin; Wang, Yanting; Li, Tingting; Chai, Guaiqiang; Jiang, Wenhui; Shan, Liwei; Li, Chunlian; Xiao, Enshi; Wang, Zhonghua

    2015-01-01

    A waxy cuticle that serves as a protective barrier against non-stomatal water loss and environmental damage coats the aerial surfaces of land plants. It comprises a cutin polymer matrix and waxes. Cuticular waxes are complex mixtures of very long chain fatty acids (VLCFAs) and their derivatives. Results show that primary alcohols are the major components of bread wheat (Triticum aestivum L.) leaf blade cuticular waxes. Here, the characterization of TaFAR5 from wheat cv Xinong 2718, which is allelic to TAA1b, an anther-specific gene, is reported. Evidence is presented for a new function for TaFAR5 in the biosynthesis of primary alcohols of leaf blade cuticular wax in wheat. Expression of TaFAR5 cDNA in yeast (Saccharomyces cerevisiae) led to production of C22:0 primary alcohol. The transgenic expression of TaFAR5 in tomato (Solanum lycopersicum) cv MicroTom leaves resulted in the accumulation of C26:0, C28:0, and C30:0 primary alcohols. TaFAR5 encodes an alcohol-forming fatty acyl-coenzyme A reductase (FAR). Expression analysis revealed that TaFAR5 was expressed at high levels in the leaf blades, anthers, pistils, and seeds. Fully functional green fluorescent protein-tagged TaFAR5 protein was localized to the endoplasmic reticulum (ER), the site of primary alcohol biosynthesis. SDS–PAGE analysis indicated that the TaFAR5 protein possessed a molecular mass of 58.4kDa, and it was also shown that TaFAR5 transcript levels were regulated in response to drought, cold, and abscisic acid (ABA). Overall, these data suggest that TaFAR5 plays an important role in the synthesis of primary alcohols in wheat leaf blade. PMID:25468933

  14. Chemical, biochemical, and biological impact of untreated domestic sewage water use on Vertisol and its consequences on wheat (Triticum aestivum) productivity.

    PubMed

    Saha, J K; Panwar, N; Srivastava, Ajay; Biswas, A K; Kundu, S; Rao, A Subba

    2010-02-01

    In the peri-urban areas of central India, sewage water is a valuable resource for agricultural production. In this study, impact of domestic sewage water irrigation for 5 years on Vertisol with no previous history of sewage irrigation was investigated in an ongoing field experiment at Bhopal (India) under subtropical monsoon type climate. The wheat (Triticum aestivum) crop was grown during post-rainy winter season with 30 cm of irrigation (groundwater or sewage water) and four nutrient treatments (T(1), 0; T(2), 100%; T(3), 50%; and T(4), 50% of general recommended doses of NPK + FYM at 10 Mg/ha). Results showed that sewage irrigation of about 150 cm over a period of 5 years resulted significant increases in salinity as well as available fractions of N, P, K, and micronutrients, viz., Zn, Fe, and Mn in soils. Carbon and phosphorus applied through sewage water were accumulated more in subsoil layer compared to topmost plough layer. Soil microbiological activity, as indicated by soil respiration, microbial biomass C, as well as dehydrogenase enzyme activity was higher in sewage water-irrigated soils. There was also significant increase in fungal and actinomycetes as well as total coliform population in such soils. Nutrients supplied through sewage water were not able to raise the productivity of wheat to the level that obtained through fertilizers at the recommended level which indicated that additional nutrients through fertilizers are required to obtain higher productivity of wheat under sewage farming. Protein and Zn content in wheat grains were more when the crop was grown with sewage irrigation. Overall results show that except for increase in coliform population, short duration (5 years) of municipal sewage water irrigation did not have any appreciable harmful effect on soil quality as well as crop productivity; rather, it proved beneficial in improving soil fertility, wheat productivity, and produce quality. PMID:19219646

  15. Identification and Comparative Analysis of microRNA in Wheat (Triticum aestivum L.) Callus Derived from Mature and Immature Embryos during In vitro Culture.

    PubMed

    Chu, Zongli; Chen, Junying; Xu, Haixia; Dong, Zhongdong; Chen, Feng; Cui, Dangqun

    2016-01-01

    Feasible and efficient tissue culture plays an important role in plant genetic engineering. Wheat (Triticum aestivum L.) immature embryos (IMEs) are preferred for tissue culture to mature embryos (MEs) because IMEs easily generate embryogenic callus, producing large number of plants. The molecular mechanisms of regulation and the biological pathways involved in embryogenic callus formation in wheat remain unclear. Here, microRNAs (miRNAs) potentially involved in embryogenic callus formation and somatic embryogenesis were identified through deep sequencing of small RNAs (sRNAs) and analyzed with bioinformatics tools. Six sRNA libraries derived from calli of IMEs and MEs after 3, 6, or 15 d of culture (DC) were constructed and sequenced. A total of 85 known miRNAs were identified, of which 30, 33, and 18 were differentially expressed (P < 0.05) between the IME and ME libraries at 3, 6, and 15 DC, respectively. Additionally, 171 novel and 41 candidate miRNAs were also identified, of the novel miRNA, 69, 67, and 37 were differentially expressed (P < 0.05) between the two types of libraries at 3, 6, and 15 DC, respectively. The expression patterns of eight known and eight novel miRNAs were validated using quantitative real-time polymerase chain reaction. Gene ontology annotation of differentially expressed miRNA targets provided information regarding the underlying molecular functions, biological processes, and cellular components involved in embryogenic callus development. Functional miRNAs, such as miR156, miR164, miR1432, miR398, and miR397, differentially expressed in IMEs and MEs might be related to embryogenic callus formation and somatic embryogenesis. This study suggests that miRNA plays an important role in embryogenic callus formation and somatic embryogenesis in wheat, and our data provide a useful resource for further research. PMID:27625667

  16. The structural and photosynthetic characteristics of the exposed peduncle of wheat (Triticum aestivum L.): an important photosynthate source for grain-filling

    PubMed Central

    2010-01-01

    Background In wheat (Triticum aestivum L), the flag leaf has been thought of as the main source of assimilates for grain growth, whereas the peduncle has commonly been thought of as a transporting organ. The photosynthetic characteristics of the exposed peduncle have therefore been neglected. In this study, we investigated the anatomical traits of the exposed peduncle during wheat grain ontogenesis, and we compared the exposed peduncle to the flag leaf with respect to chloroplast ultrastructure, photosystem II (PSII) quantum yield, and phosphoenolpyruvate carboxylase (PEPCase; EC 4.1.1.31) activity. Results Transmission electron microscope observations showed well-developed chloroplasts with numerous granum stacks at grain-filling stages 1, 2 and 3 in both the flag leaf and the exposed peduncle. In the exposed peduncle, the membranes constituting the thylakoids were very distinct and plentiful, but in the flag leaf, there was a sharp breakdown at stage 4 and complete disintegration of the thylakoid membranes at stage 5. PSII quantum yield assays revealed that the photosynthetic efficiency remained constant at stages 1, 2 and 3 and then declined in both organs. However, the decline occurred more dramatically in the flag leaf than in the exposed peduncle. An enzyme assay showed that at stages 1 and 2 the PEPCase activity was lower in the exposed peduncle than in the flag leaf; but at stages 3, 4 and 5 the value was higher in the exposed peduncle, with a particularly significant difference observed at stage 5. Subjecting the exposed part of the peduncle to darkness following anthesis reduced the rate of grain growth. Conclusion Our results suggest that the exposed peduncle is a photosynthetically active organ that produces photosynthates and thereby makes a crucial contribution to grain growth, particularly during the late stages of grain-filling. PMID:20618993

  17. Heavy metal accumulation in soil amended with roadside pond sediment and uptake by winter wheat (Triticum aestivum L. cv. PBW 343).

    PubMed

    Karak, Tanmoy; Bhattacharyya, Pradip

    2010-01-01

    The risks of heavy metal accumulation and the dynamics related to roadside pond sediment application in comparison to control of winter wheat (Triticum aestivum L.) were investigated in field experiments. Selective sequential extraction procedures revealed that application of pond sediment in soil increases the labile pools of the studied heavy metals (Cd, Cr, Cu, Ni, Pb, and Zn). Risk assessment codes concluded that Cu and Pb were in the high-risk zone in both pond sediment and soil amended with pond sediment, whereas Zn and Cu were found in the medium-risk zone for control soil. Heavy metal accumulation by wheat straw and grain (39.38, 1.18, 23.73, 0.36, 0.18, and 16.8 mg kg⁻¹ for Zn, Cd, Cu, Cr, Ni, and Pb, respectively, for wheat grain) was significantly increased through application of pond sediment. However, metal accumulation did not thwart the enhancement of wheat yield when pond sediment was applied. Health risk indexes of analyzed heavy metals were found to be within the Indian permissible limit for foodstuffs. Pond sediments help to fortify wheat grain by increasing the concentration of Zn and Cu as a source of micronutrients in the diet. However, a significant increase of Pb in wheat grain through pond sediment could be a health concern for its long-term application. Therefore, pond sediment would be a valuable resource for agriculture as an alternative organic supplement, but long-term use may require the cessation of the excavated sediment as agricultural landfill in order to restrict heavy metal contamination through it.

  18. Increase in growth, productivity and nutritional status of wheat (Triticum aestivum L. cv. WH-711) and enrichment in soil fertility applied with organic matrix entrapped urea.

    PubMed

    Kumar, Manoj; Bauddh, Kuldeep; Kumar, Sanjeev; Sainger, Manish; Sainger, Poonam A; Singh, Rana P

    2013-01-01

    Field experiments were conducted during two consequent years in semi-arid, subtropical climate of Rohtak district situated in North-West Indian state Haryana to evaluate the effects of eco-friendly organic matrix entrapped urea (OMEU) on wheat (Triticum aestivum L. cv. WH-711). The OMEU prepared in granular form contained cow dung, rice bran (grain cover of Oryza sativa), neem (Azadirachta indica) leaves and clay soil (diameter of particles < 0.002 mm) in 1:1:1:1 ratios and saresh (plant gum of Acacia sp.) as binder entrapping half of the recommended dose of urea. A basal application of organic matrix entrapped urea showed increase in plant growth in terms of fresh and dry weights, root length, root number, leaf number, tillers, plant height earlet number, earlet length and productivity in terms of grain yield and straw yield over free form of urea (FU) and no fertilizer (NF) application. The OMEU increased total soluble proteins, organic N and free ammonium content in the leaves at 45 and 60 days. The nutritional status of wheat grains in OMEU applied plants was almost similar to that observed for FU applied plants. An increase in organic carbon and available phosphorus (P) was observed in OMEU applied plots on harvest whereas pH was slightly decreased over FU applied plots. The microbial population and activity in terms of fungal and bacterial colony count and activities soil dehydrogenase and alkaline phosphatase were significantly higher in OMEU applied plots as compared to the FU applied plots. Our data indicate that OMEU which are low cost, biodegradable and non-toxic can be used to replace the expensive chemical fertilizers for wheat cultivation in semi-arid, subtropical climate.

  19. Identification and mapping QTL for high-temperature adult-plant resistance to stripe rust in winter wheat (Triticum aestivum L.) cultivar 'Stephens'.

    PubMed

    Santra, D K; Chen, X M; Santra, M; Campbell, K G; Kidwell, K K

    2008-09-01

    High-temperature adult-plant (HTAP) resistance from the winter wheat (Triticum aestivum) cultivar 'Stephens' has protected wheat crops from stripe rust caused by Puccinia striiformis f. sp. tritici for 30 years. The objectives of this study were to identify quantitative trait loci (QTL) for HTAP resistance in Stephens through genetic linkage analysis and identify DNA markers linked to the QTL for use in marker-assisted breeding. Mapping populations consisted of 101 recombinant inbred lines (RILs) through single-seed descent from 'Stephens' (resistant) x 'Michigan Amber' (susceptible). F(5), F(6) and F(7) RILs were evaluated for stripe rust resistance at Pullman, WA in 1996, 1997 and 1998, respectively, whereas F(8) RILs were evaluated at Mt Vernon, WA, USA in 2005. The 101 F(8) RILs were evaluated with 250 resistance gene analog polymorphism (RGAP), 245 simple sequence repeat (SSR) and 1 sequence tagged site (STS) markers for genetic linkage map construction. Two QTL, which explained 48-61% of the total phenotypic variation of the HTAP resistance in Stephens, were identified. QYrst.wgp-6BS.1 was within a 3.9-cM region flanked by Xbarc101 and Xbarc136. QYrst.wgp-6BS.2 was mapped in a 17.5-cM region flanked by Xgwm132 and Xgdm113. Both two QTL were physically mapped to the short arm of chromosome 6B, but in different bins. Validation and polymorphism tests of the flanking markers in 43 wheat genotypes indicated that the molecular markers associated with these QTL should be useful in marker-assisted breeding programs to efficiently incorporate HTAP resistance into new wheat cultivars.

  20. Identification and Comparative Analysis of microRNA in Wheat (Triticum aestivum L.) Callus Derived from Mature and Immature Embryos during In vitro Culture

    PubMed Central

    Chu, Zongli; Chen, Junying; Xu, Haixia; Dong, Zhongdong; Chen, Feng; Cui, Dangqun

    2016-01-01

    Feasible and efficient tissue culture plays an important role in plant genetic engineering. Wheat (Triticum aestivum L.) immature embryos (IMEs) are preferred for tissue culture to mature embryos (MEs) because IMEs easily generate embryogenic callus, producing large number of plants. The molecular mechanisms of regulation and the biological pathways involved in embryogenic callus formation in wheat remain unclear. Here, microRNAs (miRNAs) potentially involved in embryogenic callus formation and somatic embryogenesis were identified through deep sequencing of small RNAs (sRNAs) and analyzed with bioinformatics tools. Six sRNA libraries derived from calli of IMEs and MEs after 3, 6, or 15 d of culture (DC) were constructed and sequenced. A total of 85 known miRNAs were identified, of which 30, 33, and 18 were differentially expressed (P < 0.05) between the IME and ME libraries at 3, 6, and 15 DC, respectively. Additionally, 171 novel and 41 candidate miRNAs were also identified, of the novel miRNA, 69, 67, and 37 were differentially expressed (P < 0.05) between the two types of libraries at 3, 6, and 15 DC, respectively. The expression patterns of eight known and eight novel miRNAs were validated using quantitative real-time polymerase chain reaction. Gene ontology annotation of differentially expressed miRNA targets provided information regarding the underlying molecular functions, biological processes, and cellular components involved in embryogenic callus development. Functional miRNAs, such as miR156, miR164, miR1432, miR398, and miR397, differentially expressed in IMEs and MEs might be related to embryogenic callus formation and somatic embryogenesis. This study suggests that miRNA plays an important role in embryogenic callus formation and somatic embryogenesis in wheat, and our data provide a useful resource for further research.

  1. Effects of electron-beam irradiation on the shelf life, microbial populations and sensory characteristics of summer truffles (Tuber aestivum) packaged under modified atmospheres.

    PubMed

    Rivera, Carmen Susana; Blanco, Domingo; Marco, Pedro; Oria, Rosa; Venturini, María Eugenia

    2011-02-01

    The effects of two doses of electron-beam irradiation (1.5 kGy and 2.5 kGy) on the microbial populations (total mesophilic aerobes, Pseudomonas genus, Enterobacteriaceae family, molds and yeasts) and sensory characteristics of Tuber aestivum packaged under modified atmospheres were monitored immediately after treatment, and weekly during 42 days of storage at 4 °C. Treatment with 1.5 and 2.5 kGy reduced the pseudomonads populations by 4.3 and 5.5 logs, respectively. Enterobacteriaceae counts decreased by 5.4 logs with the 1.5 kGy dose and counts below the detection limit (<1.0 log cfu/g) were obtained with the 2.5 kGy dose. Lactic acid bacteria and yeasts were less affected by the ionizing radiation treatments and they became the dominant microbial populations throughout storage with microbial counts up to 7.1 log cfu/g. The carbon dioxide levels inside the packages containing irradiated truffles were lower than those of the non-irradiated ones, suggesting a decrease in the respiration rate of the treated ascocarps. The treatments with 1.5 and 2.5 kGy e-beam did not negatively affect the sensory characteristics of truffles, but a visible superficial yeast growth was detected in truffles irradiated with 1.5 kGy at the end of their shelf life (day 28). Treatment with 2.5 kGy e-beam has prolonged the shelf life to 42 days, compared with 21 days for the untreated samples.

  2. Developmental Changes in Composition and Morphology of Cuticular Waxes on Leaves and Spikes of Glossy and Glaucous Wheat (Triticum aestivum L.)

    PubMed Central

    Chai, Guaiqiang; Li, Chunlian; Hu, Yingang; Chen, Xinhong; Wang, Zhonghua

    2015-01-01

    The glossy varieties (A14 and Jing 2001) and glaucous varieties (Fanmai 5 and Shanken 99) of wheat (Triticum aestivum L.) were selected for evaluation of developmental changes in the composition and morphology of cuticular waxes on leaves and spikes. The results provide us with two different wax development patterns between leaf and spike. The general accumulation trend of the total wax load on leaf and spike surfaces is first to increase and then decrease during the development growth period, but these changes were caused by different compound classes between leaf and spike. Developmental changes of leaf waxes were mainly the result of variations in composition of alcohols and alkanes. In addition, diketones were the third important contributor to the leaf wax changes in the glaucous varieties. Alkanes and diketones were the two major compound classes that caused the developmental changes of spike waxes. For leaf waxes, β- and OH-β-diketones were first detected in flag leaves from 200-day-old plants, and the amounts of β- and OH-β-diketones were significantly higher in glaucous varieties compared with glossy varieties. In spike waxes, β-diketone existed in all varieties, but OH-β-diketone was detectable only in the glaucous varieties. Unexpectedly, the glaucous variety Fanmai 5 yielded large amounts of OH-β-diketone. There was a significant shift in the chain length distribution of alkanes between early stage leaf and flag leaf. Unlike C28 alcohol being the dominant chain length in leaf waxes, the dominant alcohol chain length of spikes was C24 or C26 depending on varieties. Epicuticular wax crystals on wheat leaf and glume were comprised of platelets and tubules, and the crystal morphology changed constantly throughout plant growth, especially the abaxial leaf crystals. Moreover, our results suggested that platelets and tubules on glume surfaces could be formed rapidly within a few days. PMID:26506246

  3. Quantitative Trait Loci Associated with Phenological Development, Low-Temperature Tolerance, Grain Quality, and Agronomic Characters in Wheat (Triticum aestivum L.).

    PubMed

    Fowler, D B; N'Diaye, A; Laudencia-Chingcuanco, D; Pozniak, C J

    2016-01-01

    Plants must respond to environmental cues and schedule their development in order to react to periods of abiotic stress and commit fully to growth and reproduction under favorable conditions. This study was initiated to identify SNP markers for characters expressed from the seedling stage to plant maturity in spring and winter wheat (Triticum aestivum L.) genotypes adapted to western Canada. Three doubled haploid populations with the winter cultivar 'Norstar' as a common parent were developed and genotyped with a 90K Illumina iSelect SNP assay and a 2,998.9 cM consensus map with 17,541 markers constructed. High heritability's reflected large differences among the parents and relatively low genotype by environment interactions for all characters considered. Significant QTL were detected for the 15 traits examined. However, different QTL for days to heading in controlled environments and the field provided a strong reminder that growth and development are being orchestrated by environmental cues and caution should be exercised when extrapolating conclusions from different experiments. A QTL on chromosome 6A for minimum final leaf number, which determines the rate of phenological development in the seedling stage, was closely linked to QTL for low-temperature tolerance, grain quality, and agronomic characters expressed up to the time of maturity. This suggests phenological development plays a critical role in programming subsequent outcomes for many traits. Transgressive segregation was observed for the lines in each population and QTL with additive effects were identified suggesting that genes for desirable traits could be stacked using Marker Assisted Selection. QTL were identified for characters that could be transferred between the largely isolated western Canadian spring and winter wheat gene pools demonstrating the opportunities offered by Marker Assisted Selection to act as bridges in the identification and transfer of useful genes among related genetic islands

  4. Microbial activity and water-soluble trace element species in the rhizosphere of spring wheat (Triticum aestivum cv. USU-Perigee).

    PubMed

    Turmel, Marie-Claude; Courchesne, François; Cloutier-Hurteau, Benoît

    2011-04-01

    The influence of microbial activity on the concentration and speciation of trace elements (TEs) was assessed in a study on the bioavailability of TEs for edible plants. A growth chamber experiment with spring wheat (Triticum aestivum cv. USU-Perigee) was conducted and the bulk (Bk) and the rhizosphere (Rz) soil components were collected at maturity. A characterization of the microbial activity and population was made by measuring the microbial biomass, enzymes (acid phosphatase, arylsulfatase, dehydrogenase and urease) and 16S rDNA DGGE profiles. In soil water extracts, major solutes (H(+), Ca, Mg, Na, NH(4), K, Cl, NO(3), SO(4), total N, DON and DOC) and trace elements (Al, As, Cd, Ce, Cr, Cu, Fe, Pb, Tl, and Zn) including monomeric Al species, free Cu(2+) and labile Zn were determined. The partition of the variation indicated that 12.1% of the distribution of TEs in the Bk soil was significantly and exclusively explained by chemical properties while this value was less than 0.1% for the Rz soil. To the contrary, microbial properties contributed significantly to 12.3% of the distribution of TEs in the Rz soil whereas it explained less than 0.1% for the Bk soil. Detailed redundancy analyses identified several potential mechanisms (e.g. weathering of primary mineral, solubilisation of sesquioxides, bacterial effect on the redox status) explaining the fate of TEs in the Bk and Rz soils. This study revealed that microbial activity is strongly associated to the speciation of trace elements in the Rz of edible plants and points to some microbial processes influencing TE speciation.

  5. Liquid chromatography-diode array detection to study the metabolism of glufosinate in Triticum aestivum T-590 and influence of the genetic modification on its resistance.

    PubMed

    Rojano-Delgado, Antonia María; Priego-Capote, Feliciano; Barro, Francisco; de Castro, María Dolores Luque; De Prado, Rafael

    2013-12-01

    The resistance to glufosinate of two lines-genetically modified (GM) and unmodified (T-590 and T-549, respectively)-of Triticum aestivum has been studied. In the GM line, the bar gene was introduced to increase the resistance to glufosinate. Experiments in a controlled growth chamber showed that line T-590 presented a high resistance to glufosinate with an ED50 value of 478.59 g active ingredient per hectare (g ai ha(-1)) versus 32.65 g ai ha(-1) for line T-549. The activity of glutamine synthetase (GS) in leaf extracts from both lines was investigated. The I50 for line T-590 was 694.10 μM glufosinate versus 55.46 μM for line T-549, with a resistance factor of 12.51. Metabolism studies showed a higher and faster penetration of glufosinate in line T-549 than in line T-590. LC-TOF/MS analysis of glufosinate metabolism at 48 h after herbicide treatment (300 g ai ha(-1)) revealed an 83.4% conversion of the herbicide (66.5% in N-acetyl-glufosinate metabolite), while in line T-549 conversion of the herbicide was about 40% (0% to N-acetyl-glufosinate). These results suggest that metabolism of glufosinate by the bar gene is a key mechanism of resistance in line T-590 that explains such high levels of herbicide tolerated by the plant, together with other mechanisms due to unmodified pathway, absorption and loss of glufosinate affinity for its target site.

  6. 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

  7. Genome-Wide Prediction of Traits with Different Genetic Architecture Through Efficient Variable Selection

    PubMed Central

    Wimmer, Valentin; Lehermeier, Christina; Albrecht, Theresa; Auinger, Hans-Jürgen; Wang, Yu; Schön, Chris-Carolin

    2013-01-01

    In genome-based prediction there is considerable uncertainty about the statistical model and method required to maximize prediction accuracy. For traits influenced by a small number of quantitative trait loci (QTL), predictions are expected to benefit from methods performing variable selection [e.g., BayesB or the least absolute shrinkage and selection operator (LASSO)] compared to methods distributing effects across the genome [ridge regression best linear unbiased prediction (RR-BLUP)]. We investigate the assumptions underlying successful variable selection by combining computer simulations with large-scale experimental data sets from rice (Oryza sativa L.), wheat (Triticum aestivum L.), and Arabidopsis thaliana (L.). We demonstrate that variable selection can be successful when the number of phenotyped individuals is much larger than the number of causal mutations contributing to the trait. We show that the sample size required for efficient variable selection increases dramatically with decreasing trait heritabilities and increasing extent of linkage disequilibrium (LD). We contrast and discuss contradictory results from simulation and experimental studies with respect to superiority of variable selection methods over RR-BLUP. Our results demonstrate that due to long-range LD, medium heritabilities, and small sample sizes, superiority of variable selection methods cannot be expected in plant breeding populations even for traits like FRIGIDA gene expression in Arabidopsis and flowering time in rice, assumed to be influenced by a few major QTL. We extend our conclusions to the analysis of whole-genome sequence data and infer upper bounds for the number of causal mutations which can be identified by LASSO. Our results have major impact on the choice of statistical method needed to make credible inferences about genetic architecture and prediction accuracy of complex traits. PMID:23934883

  8. Using comparative genomics to reorder the human genome sequence into a virtual sheep genome

    PubMed Central

    Dalrymple, Brian P; Kirkness, Ewen F; Nefedov, Mikhail; McWilliam, Sean; Ratnakumar, Abhirami; Barris, Wes; Zhao, Shaying; Shetty, Jyoti; Maddox, Jillian F; O'Grady, Margaret; Nicholas, Frank; Crawford, Allan M; Smith, Tim; de Jong, Pieter J; McEwan, John; Oddy, V Hutton; Cockett, Noelle E

    2007-01-01

    Background Is it possible to construct an accurate and detailed subgene-level map of a genome using bacterial artificial chromosome (BAC) end sequences, a sparse marker map, and the sequences of other genomes? Results A sheep BAC library, CHORI-243, was constructed and the BAC end sequences were determined and mapped with high sensitivity and low specificity onto the frameworks of the human, dog, and cow genomes. To maximize genome coverage, the coordinates of all BAC end sequence hits to the cow and dog genomes were also converted to the equivalent human genome coordinates. The 84,624 sheep BACs (about 5.4-fold genome coverage) with paired ends in the correct orientation (tail-to-tail) and spacing, combined with information from sheep BAC comparative genome contigs (CGCs) built separately on the dog and cow genomes, were used to construct 1,172 sheep BAC-CGCs, covering 91.2% of the human genome. Clustered non-tail-to-tail and outsize BACs located close to the ends of many BAC-CGCs linked BAC-CGCs covering about 70% of the genome to at least one other BAC-CGC on the same chromosome. Using the BAC-CGCs, the intrachromosomal and interchromosomal BAC-CGC linkage information, human/cow and vertebrate synteny, and the sheep marker map, a virtual sheep genome was constructed. To identify BACs potentially located in gaps between BAC-CGCs, an additional set of 55,668 sheep BACs were positioned on the sheep genome with lower confidence. A coordinate conversion process allowed us to transfer human genes and other genome features to the virtual sheep genome to display on a sheep genome browser. Conclusion We demonstrate that limited sequencing of BACs combined with positioning on a well assembled genome and integrating locations from other less well assembled genomes can yield extensive, detailed subgene-level maps of mammalian genomes, for which genomic resources are currently limited. PMID:17663790

  9. Translational genomics for plant breeding with the genome sequence explosion.

    PubMed

    Kang, Yang Jae; Lee, Taeyoung; Lee, Jayern; Shim, Sangrea; Jeong, Haneul; Satyawan, Dani; Kim, Moon Young; Lee, Suk-Ha

    2016-04-01

    The use of next-generation sequencers and advanced genotyping technologies has propelled the field of plant genomics in model crops and plants and enhanced the discovery of hidden bridges between genotypes and phenotypes. The newly generated reference sequences of unstudied minor plants can be annotated by the knowledge of model plants via translational genomics approaches. Here, we reviewed the strategies of translational genomics and suggested perspectives on the current databases of genomic resources and the database structures of translated information on the new genome. As a draft picture of phenotypic annotation, translational genomics on newly sequenced plants will provide valuable assistance for breeders and researchers who are interested in genetic studies.

  10. 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

  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. Genomics of preterm birth.

    PubMed

    Swaggart, Kayleigh A; Pavlicev, Mihaela; Muglia, Louis J

    2015-02-02

    The molecular mechanisms controlling human birth timing at term, or resulting in preterm birth, have been the focus of considerable investigation, but limited insights have been gained over the past 50 years. In part, these processes have remained elusive because of divergence in reproductive strategies and physiology shown by model organisms, making extrapolation to humans uncertain. Here, we summarize the evolution of progesterone signaling and variation in pregnancy maintenance and termination. We use this comparative physiology to support the hypothesis that selective pressure on genomic loci involved in the timing of parturition have shaped human birth timing, and that these loci can be identified with comparative genomic strategies. Previous limitations imposed by divergence of mechanisms provide an important new opportunity to elucidate fundamental pathways of parturition control through increasing availability of sequenced genomes and associated reproductive physiology characteristics across diverse organisms.

  13. 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.

  14. Pancreatic cancer genomics.

    PubMed

    Chang, David K; Grimmond, Sean M; Biankin, Andrew V

    2014-02-01

    Pancreatic cancer is one of the most lethal malignancies. The overall median survival even with treatment is only 6-9 months, with almost 90% succumbing to the disease within a year of diagnosis. It is characterised by an intense desmoplastic stroma that may contribute to therapeutic resistance, and poses significant challenges for genomic sequencing studies. It is recalcitrant to almost all therapies and consequently remains the fourth leading cause of cancer death in Western societies. Genomic studies are unveiling a vast heterogeneity of mutated genes, and this diversity may explain why conventional clinical trial designs have mostly failed to demonstrate efficacy in unselected patients. Those that are available offer only marginal benefits overall, but are associated with clinically significant responses in as yet undefined subgroups. This chapter describes our current understanding of the genomics of pancreatic cancer and the potential impact of these findings on our approaches to treatment.

  15. Domestication and plant genomes.

    PubMed

    Tang, Haibao; Sezen, Uzay; Paterson, Andrew H

    2010-04-01

    The techniques of plant improvement have been evolving with the advancement of technology, progressing from crop domestication by Neolithic humans to scientific plant breeding, and now including DNA-based genotyping and genetic engineering. Archeological findings have shown that early human ancestors often unintentionally selected for and finally fixed a few major domestication traits over time. Recent advancement of molecular and genomic tools has enabled scientists to pinpoint changes to specific chromosomal regions and genetic loci that are responsible for dramatic morphological and other transitions that distinguish crops from their wild progenitors. Extensive studies in a multitude of additional crop species, facilitated by rapid progress in sequencing and resequencing(s) of crop genomes, will further our understanding of the genomic impact from both the unusual population history of cultivated plants and millennia of human selection.

  16. 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

  17. 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

  18. 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.

  19. Genomics of Salmonella Species

    NASA Astrophysics Data System (ADS)

    Canals, Rocio; McClelland, Michael; Santiviago, Carlos A.; Andrews-Polymenis, Helene

    Progress in the study of Salmonella survival, colonization, and virulence has increased rapidly with the advent of complete genome sequencing and higher capacity assays for transcriptomic and proteomic analysis. Although many of these techniques have yet to be used to directly assay Salmonella growth on foods, these assays are currently in use to determine Salmonella factors necessary for growth in animal models including livestock animals and in in vitro conditions that mimic many different environments. As sequencing of the Salmonella genome and microarray analysis have revolutionized genomics and transcriptomics of salmonellae over the last decade, so are new high-throughput sequencing technologies currently accelerating the pace of our studies and allowing us to approach complex problems that were not previously experimentally tractable.

  20. 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

  1. Genes, genome and Gestalt.

    PubMed

    Grisolia, Cesar Koppe

    2005-01-01

    According to Gestalt thinking, biological systems cannot be viewed as the sum of their elements, but as processes of the whole. To understand organisms we must start from the whole, observing how the various parts are related. In genetics, we must observe the genome over and above the sum of its genes. Either loss or addition of one gene in a genome can change the function of the organism. Genomes are organized in networks of genes, which need to be well integrated. In the case of genetically modified organisms (GMOs), for example, soybeans, rats, Anopheles mosquitoes, and pigs, the insertion of an exogenous gene into a receptive organism generally causes disturbance in the networks, resulting in the breakdown of gene interactions. In these cases, genetic modification increased the genetic load of the GMO and consequently decreased its adaptability (fitness). Therefore, it is hard to claim that the production of such organisms with an increased genetic load does not have ethical implications.

  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. 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 ...

  4. The genomics of mycobacteria.

    PubMed

    Viale, M N; Zumárraga, M J; Araújo, F R; Zarraga, A M; Cataldi, A A; Romano, M I; Bigi, F

    2016-04-01

    The species Mycobacterium bovis and Mycobacterium avium subspecies paratuberculosis are the causal agents, respectively, of tuberculosis and paratuberculosis in animals. Both mycobacteria, especially M. bovis, are also important to public health because they can infect humans. In recent years, this and the impact of tuberculosis and paratuberculosis on animal production have led to significant advances in knowledge about both pathogens and their host interactions. This article describes the contribution of genomics and functional genomics to studies of the evolution, virulence, epidemiology and diagnosis of both these pathogenic mycobacteria. PMID:27217180

  5. 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).

  6. The genomics of mycobacteria.

    PubMed

    Viale, M N; Zumárraga, M J; Araújo, F R; Zarraga, A M; Cataldi, A A; Romano, M I; Bigi, F

    2016-04-01

    The species Mycobacterium bovis and Mycobacterium avium subspecies paratuberculosis are the causal agents, respectively, of tuberculosis and paratuberculosis in animals. Both mycobacteria, especially M. bovis, are also important to public health because they can infect humans. In recent years, this and the impact of tuberculosis and paratuberculosis on animal production have led to significant advances in knowledge about both pathogens and their host interactions. This article describes the contribution of genomics and functional genomics to studies of the evolution, virulence, epidemiology and diagnosis of both these pathogenic mycobacteria.

  7. 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

  8. 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.

  9. Genomic Advances to Improve Biomass for Biofuels (Genomics and Bioenergy)

    SciTech Connect

    Rokhsar, Daniel

    2008-02-11

    Lawrence Berkeley National Lab bioscientist Daniel Rokhsar discusses genomic advances to improve biomass for biofuels. He presented his talk Feb. 11, 2008 in Berkeley, California as part of Berkeley Lab's community lecture series. Rokhsar works with the U.S. Department of Energy's Joint Genome Institute and Berkeley Lab's Genomics Division.

  10. 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...

  11. 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...

  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.

  13. 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

  14. Sixty years of genome biology

    PubMed Central

    2013-01-01

    Sixty years after Watson and Crick published the double helix model of DNA's structure, thirteen members of Genome Biology's Editorial Board select key advances in the field of genome biology subsequent to that discovery. PMID:23651518

  15. Genomic Data Commons launches - TCGA

    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.

  16. Recent Advances in Cotton Genomics

    PubMed Central

    Zhang, Hong-Bin; Li, Yaning; Wang, Baohua; Chee, Peng W.

    2008-01-01

    Genome research promises to promote continued and enhanced plant genetic improvement. As a world's leading crop and a model system for studies of many biological processes, genomics research of cottons has advanced rapidly in the past few years. This article presents a comprehensive review on the recent advances of cotton genomics research. The reviewed areas include DNA markers, genetic maps, mapped genes and QTLs, ESTs, microarrays, gene expression profiling, BAC and BIBAC libraries, physical mapping, genome sequencing, and applications of genomic tools in cotton breeding. Analysis of the current status of each of the genome research areas suggests that the areas of physical mapping, QTL fine mapping, genome sequencing, nonfiber and nonovule EST development, gene expression profiling, and association studies between gene expression and fiber trait performance should be emphasized currently and in near future to accelerate utilization of the genomics research achievements for enhancing cotton genetic improvement. PMID:18288253

  17. The tomato genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The tomato genome sequence was undertaken at a time when state-of-the-art sequencing methodologies were undergoing a transition to co-called next generation methodologies. The result was an international consortium undertaking a strategy merging both old and new approaches. Because biologists were...

  18. 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.

  19. 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...

  20. 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