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

Breeding schemes for the implementation of genomic selection in wheat (Triticum spp.)

In the last decade the breeding technology referred to as ‘genomic selection’ (GS) has been implemented in a variety of species, with particular success in animal breeding. Recent research shows the potential of GS to reshape wheat breeding. Many authors have concluded that the estimated genetic gain per year applying GS is several times that of conventional breeding. GS is, however, a new technology for wheat breeding and many programs worldwide are still struggling to identify the best strategy for its implementation. This article provides practical guidelines on the key considerations when implementing GS. A review of the existing GS literature for a range of species is provided and used to prime breeder-oriented considerations on the practical applications of GS. Furthermore, this article discusses potential breeding schemes for GS, genotyping considerations, and methods for effective training population design. The components of selection intensity, progress toward inbreeding in half- or full-sibs recurrent schemes, and the generation of selection are also presented

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

<p>Abstract</p> <p>Background</p> <p>Several studies suggested that the diploid ancestor of the B genome of tetraploid and hexaploid wheat species belongs to the <it>Sitopsis </it>section, having <it>Aegilops speltoides </it>(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 <it>Ae. speltoides </it>(2n = 14) to that of the A, B and D genomes co-resident in the hexaploid wheat species (<it>Triticum aestivum, AABBDD</it>, 2n = 42).</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>On the basis of conserved sequence length as well as identity of the shared non-TE regions and the SPA coding sequence, <it>Ae speltoides </it>appears to be more evolutionary related to the B genome of <it>T. aestivum </it>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 <it>Ae. speltoides </it>has diverged very early from the progenitor of the B genome which remains to be identified.</p

Diversité des agricultures – le cas des filières céréales, oléagineux et légumineuses à graines

L’objectif de cet article est de décrire, sans être exhaustif, la diversité des agricultures en mobilisant des exemples au niveau du système technique et des pratiques culturales, pour la France métropolitaine et pour trois filières : les céréales, les oléagineux et les légumineuses à graines. L’analyse de la diversité des agricultures montre que des voies de diversification des systèmes techniques et des pratiques culturales existent, mais que celles-ci sont fortement dépendantes de la diversité des voies de valorisation dans les filières. Au sein de ces dispositifs de valorisation, hormis quelques dispositifs spécifiques, les recommandations sur les pratiques sont suffisamment vastes pour permettre une diversité de systèmes de culture et de production, dès lors que les critères technologiques d’accès à la filière sont atteints. Il convient alors de s’interroger sur le poids de ces critères technologiques sur les choix techniques des agriculteurs. Il apparait également nécessaire de questionner la valeur donnée à la diversité par les différents acteurs des filières, de l’agriculteur au consommateur, en évaluant notamment la performance économique des systèmes agricoles les plus diversifiés ainsi que les leviers pour augmenter les performances d’une agriculture diversifiée. Il s’agit d’élargir le socle de connaissances sur lequel les acteurs pourront concevoir eux-mêmes de nouvelles formes de diversité et d’ouvrir le débat avec les acteurs des filières sur la préservation des formes de diversité des agricultures comme potentiel de résilience

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

Meeting the challenges facing wheat production: The strategic research agenda of the Global Wheat Initiative

Wheat occupies a special role in global food security since, in addition to providing 20% of our carbohydrates and protein, almost 25% of the global production is traded internationally. The importance of wheat for food security was recognised by the Chief Agricultural Scientists of the G20 group of countries when they endorsed the establishment of the Wheat Initiative in 2011. The Wheat Initiative was tasked with supporting the wheat research community by facilitating collaboration, information and resource sharing and helping to build the capacity to address challenges facing production in an increasingly variable environment. Many countries invest in wheat research. Innovations in wheat breeding and agronomy have delivered enormous gains over the past few decades, with the average global yield increasing from just over 1 tonne per hectare in the early 1960s to around 3.5 tonnes in the past decade. These gains are threatened by climate change, the rapidly rising financial and environmental costs of fertilizer, and pesticides, combined with declines in water availability for irrigation in many regions. The international wheat research community has worked to identify major opportunities to help ensure that global wheat production can meet demand. The outcomes of these discussions are presented in this paper

Power and accuracy of QTL detection: simulation studies of one-QTL models

Nonparametric selective resampling procedures were used to investigate the effect of several factors on the power of quantative trait loci (QTL) detection, the bias and confidence intervals of their position, effect and heritability. The factors studied were population size, QTL position, heritability of the QTL and marker coverage, i.e., marker density and their regular versus random spacing. Confidence intervals obtained using either Normal approximation, the bias corrected and accelerated (BC$_{\rm a}$) method and empirical bootstrap with 1 000 selected resamples were compared. The BC$_{\rm a}$ intervals were found to be very close to classic confidence intervals (CI) assuming normal distribution for sample sizes above 200, and to be slightly closer to empirical CI for small population sizes. The precision of the QTL position was found to be mostly affected by population size and heritability, and less by marker spacing, except in the case of sparse maps with irregular marker spacing. Bias in QTL position estimates can be high for small population sizes when QTL are located near the end of a chromosome, and, unexpectedly, selective bootstrap does not decrease this bias very much.La puissance et la précision de détection des QTL : études basées sur des méthodes de rééchantillonnage sélectif. On a utilisé des méthodes de rééchantillonnage sélectif pour étudier l'effet de plusieurs facteurs sur la puissance de détection des QTL (locus impliqué dans le déterminisme d'un caractère quantitatif), les biais et intervalles de confiances de leur position, effet et héritabilité (proportion de la variance du caractère expliquée par l'effet additif d'un QTL). Les facteurs étudiés étaient la taille de la population (haploïdes doublés), la position et l'héritabilité du QTL, la densité des marqueurs et leur espacement régulier ou au hasard. On a comparé les intervalles de confiance obtenus soit par l'approximation Normale, soit par la méthode BC$_{\rm a}$ (correction de biais et accélération), soit par bootstrap empirique avec $1 000$ échantillons sélectionnés. Les intervalles obtenus par la méthode BC$_{\rm a}$ sont très proches de ceux obtenus avec l'approximation Normale pour les tailles de population supérieures à 200, et sont légèrement plus proches des intervalles empiriques pour les petites populations. La précision de localisation du QTL est surtout affectée par son héritabilité et la taille de la population, et relativement peu par l'espacement des marqueurs, sauf dans les cas extrêmes de cartes lâches avec des marqueurs irrégulièrement espacés. Le biais dans l'estimation de la position d'un QTL peut être important quand celui-ci est proche de l'extrémité d'un chromosome et, de façon assez inattendue, le rééchantillonnage sélectif ne permet pas de réduire ce biais

Wheat domestication: Lessons for the future

Wheat was one of the first crops to be domesticated more than 10,000 years ago in the Middle East. Molecular genetics and archaeological data have allowed the reconstruction of plausible domestication scenarios leading to modern cultivars. For diploid einkorn and tetraploid durum wheat, a single domestication event has likely occurred in the Karacadag Mountains, Turkey. Following a cross between tetraploid durum and diploid T. tauschii, the resultant hexaploid bread wheat was domesticated and disseminated around the Caucasian region. These polyploidisation events facilitated wheat domestication and created genetic bottlenecks, which excluded potentially adaptive alleles. With the urgent need to accelerate genetic progress to confront the challenges of climate change and sustainable agriculture, wild ancestors and old landraces represent a reservoir of underexploited genetic diversity that may be utilized through modern breeding methods. Understanding domestication processes may thus help identifying new strategies. (C) 2011 Academie des sciences. Published by Elsevier Masson SAS. All rights reserved

Le poids de l'évolution du matériel vivant : l'exemple des céréales

National audienceLe paysage variétal du blé et du maïs a évolué en même temps que les itinéraires techniques et la structure des exploitations. Des fermes de subsistance de l’avant guerre (1940) qui cultivaient des variétés de pays, les exploitants ont adopté les variétés modernes issues de la génétique en même temps que la mécanisation, mais la polyculture-élevage a perduré en Limagne jusqu’aux années 1960. Les années suivantes ont alors connu une spécialisation en grandes cultures, avec un agrandissement des exploitations et l’adoption des hybrides de maïs, et pour le blé de variétés à haut rendement ou de haute qualité pour une valorisation du terroir. Cette spécialisation s’est encore accrue au 21° siècle avec le développement d’industries de transformation et l’intégration par un groupe coopératif de la filière depuis la production de semences jusqu’au produit fini, pain, biscuits ou semoules de maïs