Wheat Expressed Sequence Tags Research Articles

A High-Density Consensus Map of Common Wheat Integrating Four Mapping Populations Scanned by the 90K SNP Array.

A high-density consensus map is a powerful tool for gene mapping, cloning and molecular marker-assisted selection in wheat breeding. The objective of this study was to construct a high-density, single nucleotide polymorphism (SNP)-based consensus map of common wheat (Triticum aestivum L.) by integrating genetic maps from four recombinant inbred line populations. The populations were each genotyped using the wheat 90K Infinium iSelect SNP assay. A total of 29,692 SNP markers were mapped on 21 linkage groups corresponding to 21 hexaploid wheat chromosomes, covering 2,906.86 cM, with an overall marker density of 10.21 markers/cM. Compared with the previous maps based on the wheat 90K SNP chip detected 22,736 (76.6%) of the SNPs with consistent chromosomal locations, whereas 1,974 (6.7%) showed different chromosomal locations, and 4,982 (16.8%) were newly mapped. Alignment of the present consensus map and the wheat expressed sequence tags (ESTs) Chromosome Bin Map enabled assignment of 1,221 SNP markers to specific chromosome bins and 819 ESTs were integrated into the consensus map. The marker orders of the consensus map were validated based on physical positions on the wheat genome with Spearman rank correlation coefficients ranging from 0.69 (4D) to 0.97 (1A, 4B, 5B, and 6A), and were also confirmed by comparison with genetic position on the previously 40K SNP consensus map with Spearman rank correlation coefficients ranging from 0.84 (6D) to 0.99 (6A). Chromosomal rearrangements reported previously were confirmed in the present consensus map and new putative rearrangements were identified. In addition, an integrated consensus map was developed through the combination of five published maps with ours, containing 52,607 molecular markers. The consensus map described here provided a high-density SNP marker map and a reliable order of SNPs, representing a step forward in mapping and validation of chromosomal locations of SNPs on the wheat 90K array. Moreover, it can be used as a reference for quantitative trait loci (QTL) mapping to facilitate exploitation of genes and QTL in wheat breeding.

Construction of new EST-SSRs for Fusarium resistant wheat breeding

Surveying Fusarium resistance in wheat with easy applicable molecular markers such as simple sequence repeats (SSRs) is a prerequest for molecular breeding. Expressed sequence tags (ESTs) are one of the main sources for development of new SSR candidates. Therefore, 18.292 publicly available wheat ESTs were mined and genotyping of newly developed 55 EST-SSR derived primer pairs produced clear fragments in ten wheat cultivars carrying different levels of Fusarium resistance. Among the proved markers, 23 polymorphic EST-SSRs were obtained and related alleles were mostly found on B and D genome. Based on the fragment profiling and similarity analysis, a 327bp amplicon, which was a product of contig 1207 (chromosome 5BL), was detected only in Fusarium head blight (FHB) resistant cultivars (CM82036 and Sumai) and the amino acid sequences showed a similarity to pathogen related proteins. Another FHB resistance related EST-SSR, Contig 556 (chromosome 1BL) produced a 151bp fragment in Sumai and was associated to wax2-like protein. A polymorphic 204bp fragment, derived from Contig 578 (chromosome 1DL), was generated from root rot (FRR) resistant cultivars (2–49; Altay2000 and Sunco). A total of 98 alleles were displayed with an average of 1.8 alleles per locus and the polymorphic information content (PIC) ranged from 0.11 to 0.78. Dendrogram tree with two main and five sub-groups were displayed the highest genetic relationship between FRR resistant cultivars (2–49 and Altay2000), FRR sensitive cultivars (Seri82 and Scout66) and FHB resistant cultivars (CM82036 and Sumai). Thus, exploitation of these candidate EST-SSRs may help to genotype other wheat sources for Fusarium resistance.

Molecular and Functional Characterization of a Wheat B2 Protein Imparting Adverse Temperature Tolerance and Influencing Plant Growth

Genomic attempts were undertaken to elucidate the plant developmental responses to heat stress, and to characterize the roles of B2 protein in mediating those responses. A wheat expressed sequence tag for B2 protein was identified which was cloned and characterized to assess its functional relevance causing plant growth and development during stress adaptation. Here, we show that wheat B2 protein is highly expressed in root and shoot tissues as well as in developing seed tissues under high temperature stress conditions. Morphological studies of transgenic Arabidopsis overexpressing gene encoding wheat B2 protein and Δb2 mutant plants were studied at major developmental stages. The stunted growth phenotype of mutant plants, together with hypocotyl and root elongation analysis of transgenic plants showed that B2 protein exhibits a crucial role in plant growth and development. Additional physiological analyses highlights the role of B2 protein in increased tolerance to heat and cold stresses by maintaining high chlorophyll content, strong activity of photosystem II and less membrane damage of overexpression transgenics as compared with the wild-type. Furthermore, the constitutive overexpression of TaB2 in Arabidopsis resulted in ABA hypersensitivity. Taken together, these studies suggest a novel perspectives of B2 protein in plant development and in mediating the thermal stress tolerance.

Development of a diagnostic co-dominant marker for stem rust resistance gene Sr47 introgressed from Aegilops speltoides into durum wheat.

A robust and diagnostic STS marker for stem rust resistance gene Sr47 was developed and validated for marker-assisted selection. Stem rust (caused by Puccinia graminis f. sp. tritici, Pgt) resistance gene Sr47, originally transferred from Aegilops speltoides to durum wheat (Triticum turgidum subsp. durum) line DAS15, confers a high level of resistance to Pgt race TTKSK (Ug99). Recently, the durum Rusty 5D(5B) substitution line was used to reduce the Ae. speltoides segment, and the resulting lines had Sr47 on small Ae. speltoides segments on wheat chromosome arm 2BL. The objective of this study was to develop a robust marker for marker-assisted selection of Sr47. A 200-kb segment of the Brachypodium distachyon genome syntenic with the Sr47 region was used to identify wheat expressed sequence tags (ESTs) homologous to the B. distachyon genes. The wheat EST sequences were then used to develop sequence-tagged site (STS) markers. By analyzing the markers for polymorphism between Rusty and DAS15, we identified a co-dominant STS marker, designated as Xrwgs38, which amplified 175 and 187bp fragments from wheat chromosome 2B and Ae. speltoides chromosome 2S segments, respectively. The marker co-segregated with the Ae. speltoides segments carrying Sr47 in the families from four BC2F1 plants, including the parent plants for durum lines RWG35 and RWG36 with the pedigree of Rusty/3/Rusty 5D(5B)/DAS15//47-1 5D(5B). Analysis of 62 durum and common wheat cultivars/lines lacking the Sr47 segment indicated that they all possessed the 175-bp allele of Xrwgs38, indicating that it was diagnostic for the small Ae. speltoides segment carrying Sr47. This study demonstrated that Xrwgs38 will facilitate the selection of Sr47 in durum and common wheat breeding.

Chromosome mapping of four novel mutants in bread wheat (Triticum aestivum L.)

Induced mutants constitute an important resource for mapping and cloning of genes for specific traits. Five loci underlying four induced mutants in wheat were mapped using phenotypic data and simple sequence repeat (SSR) genotyping data collected on F2 and F3 populations. The four mutant traits included the following: (1) axillary branching, (2) early leaf senescence, (3) reduced plant height and (4) reduced number of nodes. The ‘axillary branching’ locus (Axb) was mapped near Xcfd152 at a distance of 7.5 cM on chromosome 3DS. The ‘early leaf senescence’ gene (els) was mapped on 2DL at a distance of 28.6 cM from the nearest marker Xgwm539. A wheat expressed sequence tag (EST) TaSAG1 representing a candidate for els gene for early leaf senescence was also identified. The ‘reduced plant height’ locus was mapped on chromosome 2BL close to Xwmc361, which is tightly linked with Xwmc317 associated with a ‘GA-responsive dwarfing gene’ Rht4; hence, the ‘dwarf mutant-3’ used in the present study may be a phenotypic manifestation of an another allele of the gene Rht4. The ‘reduced number of node’ mutant was mapped on two loci (rnd1 and rnd2) on chromosomes 2DS and 5AL. The marker locus Xgwm261-2D linked with rnd1 was earlier reported to be closely associated with Rht8 gene, suggesting that rnd1 may perhaps represent a mutation in Rht8 gene; the second locus rnd2 on 5AL represents a novel gene. These results may prove useful in explaining the genetics of four mutant traits and may later also facilitate cloning the genes for these traits.

Identification of the trehalose-6-phosphate synthase gene family in winter wheat and expression analysis under conditions of freezing stress.

Trehalose plays an important role in metabolic regulation and abiotic stress tolerance in plants. Trehalose contents are potentially modulated by trehalose-6-phosphate synthase (TPS), which is a key enzyme in the trehalose biosynthetic pathway. Using available wheat expressed sequence tag sequence information from NCBI and two wheat genome databases, we identified 12 wheat TPS genes and performed a comprehensive study on their structural, evolutionary and functional properties. The estimated divergence time of wheat TPS gene pairs and wheat-rice orthologues suggested that wheat and rice have a common ancestor. The number of TPS genes in the wheat genome was estimated to be at least 12, which is close to the number found in rice, Arabidopsis and soybean. Moreover, it has been reported earlier in other plants that TPS genes respond to abiotic stress, however, our study mainly analysed the TPS gene family under freezing conditions in winter wheat, and determined that most of the TPS gene expression in winter wheat was induced by freezing conditions, which further suggested that wheat TPS genes were involved in winter wheat freeze-resistance signal transduction pathways. Taken together, the current study represents the first comprehensive study of TPS genes in winter wheat and provides a foundation for future functional studies of this important gene family in Triticeae.

Genome-wide characterization of developmental stage- and tissue-specific transcription factors in wheat.

BackgroundWheat (Triticum aestivum) is one of the most important cereal crops, providing food for humans and feed for other animals. However, its productivity is challenged by various biotic and abiotic stresses such as fungal diseases, insects, drought, salinity, and cold. Transcription factors (TFs) regulate gene expression in different tissues and at various developmental stages in plants and animals, and they can be identified and classified into families according to their structural and specialized DNA-binding domains (DBDs). Transcription factors are important regulatory components of the genome, and are the main targets for engineering stress tolerance.ResultsIn total, 2407 putative TFs were identified from wheat expressed sequence tags, and then classified into 63 families by using Hmm searches against hidden Markov model (HMM) profiles. In this study, 2407 TFs represented approximately 2.22% of all genes in the wheat genome, a smaller proportion than those reported for other cereals in PlantTFDB V3.0 (3.33%–5.86%) and PlnTFDB (4.30%–6.46%). We assembled information from the various databases for individual TFs, including annotations and details of their developmental stage- and tissue-specific expression patterns. Based on this information, we identified 1257 developmental stage-specific TFs and 1104 tissue-specific TFs, accounting for 52.22% and 45.87% of the 2407 wheat TFs, respectively. We identified 338, 269, 262, 175, 49, and 18 tissue-specific TFs in the flower, seed, root, leaf, stem, and crown, respectively. There were 100, 6, 342, 141, 390, and 278 TFs specifically expressed at the dormant seed, germinating seed, reproductive, ripening, seedling, and vegetative stages, respectively. We constructed a comprehensive database of wheat TFs, designated as WheatTFDB (http://xms.sicau.edu.cn/wheatTFDB/).ConclusionsApproximately 2.22% (2407 genes) of all genes in the wheat genome were identified as TFs, and were clustered into 63 TF families. We identified 1257 developmental stage-specific TFs and 1104 tissue-specific TFs, based on information about their developmental- and tissue-specific expression patterns obtained from publicly available gene expression databases. The 2407 wheat TFs and their annotations are summarized in our database, WheatTFDB. These data will be useful identifying target TFs involved in the stress response at a particular stage of development.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1313-y) contains supplementary material, which is available to authorized users.

A simple approach based on intron length polymorphism (ILP) for chromosomal localization of GeneWAG-2

Intron polymorphism can be used to develop potential intron polymorphism (PIP) markers. Intron length polymorphism (ILP) is one of the most easily identified PIP markers. WAG-2, a class C MADS-box gene, had been isolated from the wheat expressed sequence tag (EST) database. Rich polymorphisms, such as intron allele variation, and length polymorphism occur in WAG-2 gene introns. Especially, a significant length polymorphism is shared by intron IV. In present study, based on intron IV length polymorphism, using wheat nullisomic-tetrasomic (NT) and ditelosomic (DT) lines, a pair of ILP primers were designed in exons flanking introns IV and the WAG-2 gene was located on the short arm of homologous group 3 chromosome in the wheat genome. The gene location approach by using ILP markers combining with aneuploidy is convenient, reliable, specific, codominant, and stable. It is expected that ILP markers will play important roles in the genetic studies and breeding of wheat.

Transcriptome-wide analysis of WRKY transcription factors in wheat and their leaf rust responsive expression profiling.

WRKY, a plant-specific transcription factor family, has important roles in pathogen defense, abiotic cues and phytohormone signaling, yet little is known about their roles and molecular mechanism of function in response to rust diseases in wheat. We identified 100 TaWRKY sequences using wheat Expressed Sequence Tag database of which 22 WRKY sequences were novel. Identified proteins were characterized based on their zinc finger motifs and phylogenetic analysis clustered them into six clades consisting of class IIc and class III WRKY proteins. Functional annotation revealed major functions in metabolic and cellular processes in control plants; whereas response to stimuli, signaling and defense in pathogen inoculated plants, their major molecular function being binding to DNA. Tag-based expression analysis of the identified genes revealed differential expression between mock and Puccinia triticina inoculated wheat near isogenic lines. Gene expression was also performed with six rust-related microarray experiments at Gene Expression Omnibus database. TaWRKY10, 15, 17 and 56 were common in both tag-based and microarray-based differential expression analysis and could be representing rust specific WRKY genes. The obtained results will bestow insight into the functional characterization of WRKY transcription factors responsive to leaf rust pathogenesis that can be used as candidate genes in molecular breeding programs to improve biotic stress tolerance in wheat.

Characterization of EST-SSR markers in durum wheat EST library and functional analysis of SSR-containing EST fragments

The goal of this study is to identify characterization of expressed sequence tag (EST)-simple sequence repeats (SSR) markers from EST library of durum wheat and functional analysis of SSR-containing EST sequences for application in comparative genomics and breeding. 19,141 sequences were analyzed among which 18,937 ESTs were selected. Consistent with MISA results, 313 EST-SSRs were yielded. The final EST-SSRs were compared to the GenBank non-redundant database using BLASTX and classified based on these functions. Results indicated that the perfect EST-SSRs are the most frequent. The TTG/CTG imperfect EST-SSR had gamma-gliadin putative function that can be appropriate for durum wheat. Also, the mononucleotides and trinucleotides were the most frequent. Findings suggested that the identified EST-SSRs could be categorized into 83 types. Motifs TTG in trinucleotides and TC in dinucleotides had the highest frequency. TTG is the new motif in durum wheat identified in this study. We identified new EST-SSRs with more than trinucleotide and detected motifs that have potential to code amino acids. Arginine was the most frequent amino acid. Enzymes had the highest frequency among predicted functions. EST-SSRs have been identified in this study can be used for developing ESS-SSR-based detection tool for durum wheat in future studies and will be a useful resource for molecular breeding, genetics, genomics, and environmental stress studies. Motifs coding amino acids could be used as a new source of functional markers and biological study. In addition to, designed new PCR primer pairs are new resources for to identify useful alleles in transcription factors, storage proteins, and enzymes which incorporated them again into the cultivated material.

Transference of Wheat Expressed Sequence Tag–Simple Sequence Repeats to Paspalum Species and Cross‐Species Amplification of Paspalum notatum Simple Sequence Repeats: Potential Use in Phylogenetic Analysis and Mapping

ABSTRACTThe genus Paspalum L. includes numerous species of agronomic importance. The objectives of this work were to evaluate the transferability and polymorphism of publicly available wheat (Triticum aestivum L.) expressed sequence tag (EST)–simple sequence repeat (SSR) (wEST‐SSR) markers to Paspalum spp., assess the cross‐species amplification of Paspalum notatum Flüggé genomic SSRs (PnSSRs) within the genus, and evaluate both types of markers for phylogenetic analyses and mapping. Thirty‐two accessions including 10 species were used. Moreover, 65 F1 hybrids of P. notatum were used for mapping. Transferability ratio of wEST‐SSRs was 72.72%. On average 19.25 bands per primer combination were obtained. Cross‐species amplification of PnSSRs was 55.37%, with an average of 9.45 fragments per primer pair. Both types of markers differed in the amplification capacity between primers pairs and species. Clustering analysis with wEST‐SSR data discriminated accessions by species and taxonomic groups. Genomic relationships were in agreement with previous works indicating that wEST‐SSRs are adequate for phylogenetic surveys in the genus. Mapping experiments showed that both wEST‐SSRs and PnSSRs mapped scattered in the genome. One hundred two new markers were added to the existent P. notatum linkage groups. Primer pairs ksum206, ksum219, and PN03 F2 generated markers linked to apospory. Sequences of EST‐SSRs experimentally mapped in P. notatum showed 46.23 to 55.27% similarity with the original wheat EST. A preliminary comparative mapping analysis was carried combining experimental and in silico mapping results.

Genetic mapping and marker development for resistance of wheat against the root lesion nematode Pratylenchus neglectus

BackgroundThe Rlnn1 locus, which resides on chromosome 7A of bread wheat (Triticum aestivum L.) confers moderate resistance against the root lesion nematode Pratylenchus neglectus. Prior to this research, the exact linkage relationships of Rlnn1 with other loci on chromosome 7A were not clear and there were no simple codominant markers available for selection of Rlnn1 in wheat breeding. The objectives of the research reported here were to (1) develop an improved genetic map of the Rlnn1 region of chromosome 7A and (2) develop molecular markers that could be used in marker-assisted selection to improve resistance of wheat against P. neglectus.ResultsA large-effect quantitative trait locus (QTL) for resistance against P. neglectus was genetically mapped using a population of Excalibur/Kukri doubled haploid lines. This QTL coincides in position with the rust resistance gene(s) Lr20/Sr15, the phytoene synthase gene Psy-A1 and 10 molecular markers, including five new markers designed using wheat-rice comparative genomics and wheat expressed sequence tags. Two of the new markers are suitable for use as molecular diagnostic tools to distinguish plants that carry Rlnn1 and Lr20/Sr15 from those that do not carry these resistance genes.ConclusionsThe genomic location of Rlnn1 was confirmed to be in the terminal region of the long arm of chromosome 7A. Molecular markers were developed that provide simple alternatives to costly phenotypic assessment of resistance against P. neglectus in wheat breeding. In Excalibur, genetic recombination seems to be completely suppressed in the Rlnn1 region.

Identification of Functional Genic Components of Major Fusarium Head Blight Resistance Quantitative Trait Loci in Wheat Cultivar Sumai 3

Fusarium head blight (FHB) is a devastating disease worldwide, affecting wheat and other small grains. To identify key wheat genes involved in FHB pathogenesis, 406 FHB-related wheat expressed sequence tags functionally identified in Sumai 3 were investigated for their association with FHB-resistance quantitative trait loci (QTL) Fhb1 and Fhb_6BL in 2010 and 2011. A total of 47 candidate genes were identified by bulk analysis, near-isogenic screening and expression QTL mapping, and were finally mapped to their carrier chromosomes with Chinese Spring nulli-tetra deficiency lines. One gene, designated WFhb1_c1 (wheat Fhb1 candidate gene 1), was both functionally associated with and physically located within Fhb1 and was found to be weakly similar (E = 5e+0) to an Arabidopsis gene encoding pectin methyl esterase inhibitor. Two other genes, designated WFI_6BL1 and WFI_6BL2 (wheat-Fusarium interaction genes 6BL1 and 6BL2), were functionally associated with Fhb_6BL but physically mapped on chromosomes 7D and 5A, respectively. WFI_6BL1 was annotated as a 13- lipoxygenase gene and WFI_6BL2 might encode a PR-4-like protein. Our data suggested that i) Fhb1 seems to contribute to FHB resistance by reducing susceptibility in the first 60 h, ii) Fhb_6BL makes its contribution via the jasmonate-mediated pathways, and iii) wheat seems to activate its defense mechanism in the biotrophic phase of FHB pathogenesis.

Fine Mapping of Wheat Stripe Rust Resistance Gene Yr26 Based on Collinearity of Wheat with Brachypodium distachyon and Rice

The Yr26 gene, conferring resistance to all currently important races of Puccinia striiformis f. sp. tritici (Pst) in China, was previously mapped to wheat chromosome deletion bin C-1BL-6-0.32 with low-density markers. In this study, collinearity of wheat to Brachypodium distachyon and rice was used to develop markers to saturate the chromosomal region containing the Yr26 locus, and a total of 2,341 F2 plants and 551 F2∶3 progenies derived from Avocet S×92R137 were used to develop a fine map of Yr26. Wheat expressed sequence tags (ESTs) located in deletion bin C-1BL-6-0.32 were used to develop sequence tagged site (STS) markers. The EST-STS markers flanking Yr26 were used to identify collinear regions of the rice and B. distachyon genomes. Wheat ESTs with significant similarities in the two collinear regions were selected to develop conserved markers for fine mapping of Yr26. Thirty-one markers were mapped to the Yr26 region, and six of them cosegregated with the resistance gene. Marker orders were highly conserved between rice and B. distachyon, but some rearrangements were observed between rice and wheat. Two flanking markers (CON-4 and CON-12) further narrowed the genomic region containing Yr26 to a 1.92 Mb region in B. distachyon chromosome 3 and a 1.17 Mb region in rice chromosome 10, and two putative resistance gene analogs were identified in the collinear region of B. distachyon. The markers developed in this study provide a potential target site for further map-based cloning of Yr26 and should be useful in marker assisted selection for pyramiding the gene with other resistance genes.

Identification of New Aquaporin Genes and Single Nucleotide Polymorphism in Bread Wheat

Major facilitators of water movement through plant cell membranes include aquaporin proteins. Wheat is among the largest and most important cereal crops worldwide; however, unlike other model plants such as rice, maize and Arabidopsis, little has been reported on wheat major intrinsic proteins (MIPs). This study presents a comprehensive computational identification of 349 new wheat expressed sequence tags (ESTs), encoding 13 wheat aquaporin genes. Identified aquaporins consist of 6 plasma membrane intrinsic proteins (PIP) and 1 TIP showing high sequence similarity with rice aquaporins. We also identified 4 NOD26-like intrinsic proteins (NIP) and 2 SIP members that showed more divergence. Further, expression analysis of the aquaporin genes using the available EST information in UniGene revealed their transcripts were differentially regulated in various stress- and tissue-specific libraries. Allele specific Polymerase chain reaction (PCR) primers based on single nucleotide polymorphism (SNP) were designed using PIP as the target gene and validated on a core set of Indian wheat genotypes. A 3D theoretical model of the wheat aquaporin protein was built by homology modeling and could prove to be useful in the further functional characterization of this protein. Collectively with expression and bioinformatics analysis, our results support the idea that the genes identified in this study signify an important genetic resource providing potential targets to modify the water use properties of wheat.

Identification of miRNAs and their targets in wheat (Triticum aestivum L.) by EST analysis

MicroRNAs (miRNAs) are a newly discovered class of noncoding small RNAs that regulate gene expression by directing target mRNA cleavage or translational inhibition. A large number of miRNAs have been identified in plants. Increasing evidence has shown that miRNAs play multiple roles in plant biological processes. So far, identification of miRNAs has been limited to a few model plant species, whose genomes have been sequenced. Wheat (Triticum aestivum L.) is one of the most important cereal crops worldwide. To date, only a few conserved miRNAs have been predicted in wheat. Here, we showed the conserved miRNAs identified in wheat by expressed sequence tag (EST) analysis. All previously known miRNAs from Arabidopsis, rice, and other plant species were used in a BLAST search against the wheat EST database to identify novel wheat miRNAs by a series of filtering criteria. By this strategy, we identified 62 conserved miRNAs, belonging to 30 miRNA families, 48 of which were newly discovered in wheat. These newly identified wheat miRNAs may regulate 287 potential targets, which are involved in development, signal transduction, metabolic pathways, disease resistance, ion transportation, and environmental stress response.

Phylogenetic Analysis and Expression Patterns of the MAPK Gene Family in Wheat (Triticum aestivum L.)

AbstractMitogen activated protein kinases (MAPK) cascades based on protein phosphorylation play an important role in plant growth and development. In this study, we have identified 15 putative members of the wheat MAPK gene (TaMPK) family through an in silico search of wheat expressed sequence tags (EST) databases based on the presence of amino acid sequence of Arabidopsis and rice MAPKs. Phylogenetic analyses of MAPKs from wheat, rice and Arabidopsis genomes have classified them into seven subgroups (A, B, C, D, E, F, and G). Using the available EST information as a source of expression data, the MAPK family genes from Triticum aestivum were detected in diverse tissues. Further expression analysis of the MAPKs in NCBI EST database revealed that their transcripts were most abundant in callus (20%), followed by leaf (12%) and inflorescence (12%). Most MAPK family genes showed some tissue specificity.

Ca2+ Induces Spontaneous Dephosphorylation of a Novel P5A-type ATPase

P5 ATPases constitute the least studied group of P-type ATPases, an essential family of ion pumps in all kingdoms of life. Although P5 ATPases are present in every eukaryotic genome analyzed so far, they have remained orphan pumps, and their biochemical function is obscure. We show that a P5A ATPase from barley, HvP5A1, locates to the endoplasmic reticulum and is able to rescue knock-out mutants of P5A genes in both Arabidopsis thaliana and Saccharomyces cerevisiae. HvP5A1 spontaneously forms a phosphorylated reaction cycle intermediate at the catalytic residue Asp-488, whereas, among all plant nutrients tested, only Ca(2+) triggers dephosphorylation. Remarkably, Ca(2+)-induced dephosphorylation occurs at high apparent [Ca(2+)] (K(i) = 0.25 mM) and is independent of the phosphatase motif of the pump and the putative binding site for transported ligands located in M4. Taken together, our results rule out that Ca(2+) is a transported substrate but indicate the presence of a cytosolic low affinity Ca(2+)-binding site, which is conserved among P-type pumps and could be involved in pump regulation. Our work constitutes the first characterization of a P5 ATPase phosphoenzyme and points to Ca(2+) as a modifier of its function.

Potential for detection of marker–trait associations in durum wheat using unbalanced, historical phenotypic datasets

Identification of marker–trait associations in germplasm relevant to a breeding program can be an effective way to identify quantitative trait loci (QTL) useful for selection and is critical to the success of genome-wide selection strategies. This approach is most cost-effective if phenotypic data routinely collected by breeding programs is used, necessitating only addition of genotypic data. The objective of this work was to evaluate such an approach using unbalanced phenotypic data from durum wheat (Triticum turgidum L. var. durum) registration trials genotyped with diversity arrays technology (DArT) markers. Plant height, grain cadmium concentration and yellow colour loss during pasta manufacture were chosen as example traits because all are influenced by major genes associated with known QTL. A further evaluation was performed on semolina yellow pigment concentration, a more complexly-inherited trait, but with numerous QTL identified. In total, 870 informative DArT markers were used to detect marker–trait associations. The genome coverage of markers was uneven, with low coverage of chromosomes 4B and 5A. The DArT coverage of chromosome 4B was too sparse to identify markers strongly associated with the semidwarf height locus Rht-B1 and the lipoxygenase locus Lpx-B1, both known to reside on 4B. The 20 DArT markers associated with pigment concentration localized to chromosomes 1B, 2A, 5B, 6A, 7A and 7B, linked to the trait in other studies. One DArT clone showed sequence identity to a single wheat expressed sequence tag that maps to the same deletion bin as Psy1-A1, a gene previously associated with yellow pigment concentration in durum wheat. Three markers were associated with grain cadmium and explained similar proportions of the phenotypic variance as the Xusw14 marker known to be physically linked to Cdu-B1, a major locus on 5B regulating cadmium accumulation. The sequences of these three DArT markers were 98 % identical, and were used to identify a single gene in rice that is physically linked to other rice genes that co-localize with Cdu-B1 in durum wheat. The results suggest that this historical phenotypic dataset is useful for QTL discovery and would potentially be a ‘training population’ for genomic selection when a high-density, low-cost marker platform becomes available.

Identification and Validation of a Major Quantitative Trait Locus for Slow‐rusting Resistance to Stripe Rust in WheatF

Stripe (yellow) rust, caused by Puccinia striiformis Westend. f. sp. tritici Eriks (Pst), is one of the most important wheat (Triticum aestivum L.) diseases and causes significant yield losses. A recombinant inbred (RI) population derived from a cross between Yanzhan 1 and Xichang 76-9 cultivars was evaluated for resistance to wheat stripe rust strain CYR32 at both the seedling and adult plant stages. Four resistance quantitative trait loci (QTLs) were detected in this population, in which the major one, designated as Yrq1, was mapped on chromosome 2DS. The strategy of using the Brachypodium distachyon genome, wheat expressed sequence tags and a draft DNA sequences (scaffolds) of the D-genome (Aegilops tauschii Coss.) for the development of simple sequence repeat (SSR) markers was successfully used to identify 147 SSRs in hexaploid wheat. Of the 19 polymorphic SSRs in the RI population, 17 SSRs were mapped in the homeologous group 2 chromosomes near Yrq1 region and eight SSRs were genetically mapped in the 2.7 cM region of Yrq1, providing abundant DNA markers for fine-mapping of Yrq1 and marker-assisted selection in wheat breeding program. The effectiveness of Yrq1 was validated in an independent population, indicating that this resistance QTL can be successfully transferred into a susceptible cultivar for improvement of stripe rust resistance.