wDBTF: an integrated database resource for studying wheat transcription factor families

<p>Abstract</p> <p>Background</p> <p>Transcription factors (TFs) regulate gene expression by interacting with promoters of their target genes and are classified into families based on their DNA-binding domains. Genes coding for TFs have been identified in the sequences of model plant genomes. The rice (<it>Oryza sativa </it>spp. <it>japonica</it>) genome contains 2,384 TF gene models, which represent the mRNA transcript of a locus, classed into 63 families.</p> <p>Results</p> <p>We have created an extensive list of wheat (<it>Triticum aestivum </it>L) TF sequences based on sequence homology with rice TFs identified and classified in the Database of Rice Transcription Factors (DRTF). We have identified 7,112 wheat sequences (contigs and singletons) from a dataset of 1,033,960 expressed sequence tag and mRNA (ET) sequences available. This number is about three times the number of TFs in rice so proportionally is very similar if allowance is made for the hexaploidy of wheat. Of these sequences 3,820 encode gene products with a DNA-binding domain and thus were confirmed as potential regulators. These 3,820 sequences were classified into 40 families and 84 subfamilies and some members defined orphan families. The results were compiled in the Database of Wheat Transcription Factor (wDBTF), an inventory available on the web <url>http://wwwappli.nantes.inra.fr:8180/wDBFT/</url>. For each accession, a link to its library source and its Affymetrix identification number is provided. The positions of Pfam (protein family database) motifs were given when known.</p> <p>Conclusions</p> <p>wDBTF collates 3,820 wheat TF sequences validated by the presence of a DNA-binding domain out of 7,112 potential TF sequences identified from publicly available gene expression data. We also incorporated <it>in silico </it>expression data on these TFs into the database. Thus this database provides a major resource for systematic studies of TF families and their expression in wheat as illustrated here in a study of DOF family members expressed during seed development.</p

High level of conservation between genes coding for the GAMYB transcription factor in barley (Hordeum vulgare L.) and bread wheat (Triticum aestivum L.) collections

The transcription factor GAMYB is involved in gibberellin signalling in cereal aleurone cells and in plant developmental processes. Nucleotide diversity of HvGAMYB and TaGAMYB was investigated in 155 barley (Hordeum vulgare) and 42 wheat (Triticum aestivum) accessions, respectively. Polymorphisms defined 18 haplotypes in the barley collection and 1, 7 and 3 haplotypes for the A, B, and D genomes of wheat, respectively. We found that (1) Hv- and TaGAMYB genes have identical structures. (2) Both genes show a high level of nucleotide identity (>95%) in the coding sequences and the distribution of polymorphisms is similar in both collections. At the protein level the functional domain is identical in both species. (3) GAMYB genes map to a syntenic position on chromosome 3. GAMYB genes are different in both collections with respect to the Tajima D statistic and linkage disequilibrium (LD). A moderate level of LD was observed in the barley collection. In wheat, LD is absolute between polymorphic sites, mostly located in the first intron, while it decays within the gene. Differences in Tajima D values might be due to a lower selection pressure on HvGAMYB, compared to its wheat orthologue. Altogether our results provide evidence that there have been only few evolutionary changes in Hv- and TaGAMYB. This confirms the close relationship between these species and also highlights the functional importance of this transcription factor

Wheat DOF transcription factor TaSAD and WPBF regulate glutenin gene expression in cooperation with SPA

International audienc

Wheat DOF transcription factors TaSAD and WPBF regulate glutenin gene expression in cooperation with SPA

International audienceGrain storage proteins (GSPs) quantity and composition determine the end-use value of wheat flour. GSPs consists of low-molecular-weight glutenins (LMW-GS), high-molecular-weight glutenins (HMW-GS) and gliadins. GSP gene expression is controlled by a complex network of DNA-protein and protein-protein interactions, which coordinate the tissue-specific protein expression during grain development. The regulatory network has been most extensively studied in barley, particularly the two transcription factors (TFs) of the DNA binding with One Finger (DOF) family, barley Prolamin-box Binding Factor (BPBF) and Scutellum and Aleurone-expressed DOF (SAD). They activate hordein synthesis by binding to the Prolamin box, a motif in the hordein promoter. The BPBF ortholog previously identified in wheat, WPBF, has a transcriptional activity in expression of some GSP genes. Here, the wheat ortholog of SAD, named TaSAD, was identified. The binding of TaSAD to GSP gene promoter sequences in vitro and its transcriptional activity in vivo were investigated. In electrophoretic mobility shift assays, recombinant TaSAD and WPBF proteins bound to cis-motifs like those located on HMW-GS and LMW-GS gene promoters known to bind DOF TFs. We showed by transient expression assays in wheat endosperms that TaSAD and WPBF activate GSP gene expression. Moreover, co-bombardment of Storage Protein Activator (SPA) with WPBF or TaSAD had an additive effect on the expression of GSP genes, possibly through conserved cooperative protein-protein interactions

Impacts de la surexpression du gène codant le facteur de transcription GAMYB sur la synthèse des protéines de réserve chez le blé tendre (Triticum aestivum)

Impacts de la surexpression du gène codant le facteur de transcription GAMYB sur la synthèse des protéines de réserve chez le blé tendre (Triticum aestivum). 5. Colloque du Réseau Français de Biologie des Graine

Effects of the replacement of Glu-A1 by Glu-D1 locus on agronomic performance and bread-making quality of the hexaploid wheat cv. Courtot

The aim of this study was to evaluate the cumulative and interactive effects on wheat (Triticum aestivum L.) gluten strength and mixing properties of dough associated with the duplication of the Glu-D1 locus. A partially isohomoeoallelic line RR240, in which a segment of the wheat chromosome 1D containing the Glu-D1 locus encoding the Dx2 + Dy12 subunits and translocated to the long arm of the chromosome 1A through homoeologous recombination, was assessed. Agronomic traits and yield components were studied in the translocated line RR240 and compared with the control line cv. Courtot. Both lines were evaluated under field conditions in two experimental years. Technological effects resulting from the duplication of HMW glutenin subunits Dx2 and Dy12 were evaluated using the Alveograph test, the Mixograph test and the baking test. The RR240 line was shown to have a lower agronomic performance for 1000-kernel weight and grain yield. However the duplication of the Glu-D1 allele was associated with a significant effect on dough strength and mixing resistance, and on the Zeleny sedimentation volume. Baking parameters were not significantly modified between both lines although the score values of the CNERNA test were observed to be slightly higher in RR240 than in Courtot

Recherche de protéines régulant le facteur de transcription SHP impliqué dans la synthèse des protéines de réserve chez le blé tendre

Recherche de protéines régulant le facteur de transcription SHP impliqué dans la synthèse des protéines de réserve chez le blé tendre. 6. Colloque du Réseau Français de Biologie des Graine

Régulation de la synthèse des protéines de réserve du grain de blé en réponse à la disponibilité en azote et soufre

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