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Aegilops tauschii is the diploid progenitor of the D genome of hexaploid wheat (Triticum aestivum, genomes AABBDD) and an important genetic resource for wheat. The large size and highly repetitive nature of the Ae. tauschii genome has until now precluded the development of a reference-quality genome sequence. Here we use an array of advanced technologies, including ordered-clone genome sequencing, whole-genome shotgun sequencing, and BioNano optical genome mapping, to generate a reference-quality genome sequence for Ae. tauschii ssp. strangulata accession AL8/78, which is closely related to the wheat D genome. We show that compared to other sequenced plant genomes, including a much larger conifer genome, the Ae. tauschii genome contains unprecedented amounts of very similar repeated sequences. Our genome comparisons reveal that the Ae. tauschii genome has a greater number of dispersed duplicated genes than other sequenced genomes and its chromosomes have been structurally evolving an order of magnitude faster than those of other grass genomes. The decay of colinearity with other grass genomes correlates with recombination rates along chromosomes. We propose that the vast amounts of very similar repeated sequences cause frequent errors in recombination and lead to gene duplications and structural chromosome changes that drive fast genome evolution.

Advances in genome sequencing and assembly technologies are generating many high-quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimized data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents >78% of the genome with a scaffold N50 of 88.8 kb that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNA-seq and Pacific Biosciences (PacBio) full-length cDNAs to identify 104,091 high-confidence protein-coding genes and 10,156 noncoding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop.

Crop production needs to increase to secure future food supplies, while reducing its impact on ecosystems. Detailed characterization of plant genomes and genetic diversity is crucial for meeting these challenges. Advances in genome sequencing and assembly are being used to access the large and complex genomes of crops and their wild relatives. These have helped to identify a wide spectrum of genetic variation and permitted the association of genetic diversity with diverse agronomic phenotypes. In combination with improved and automated phenotyping assays and functional genomic studies, genomics is providing new foundations for crop-breeding systems., Author(s): Michael W. Bevan (corresponding author) [1]; Cristobal Uauy [1]; Brande B. H. Wulff [1]; Ji Zhou [1, 2]; Ksenia Krasileva [2, 3]; Matthew D. Clark [2, 4] In the [...]

Bread wheat (Triticum aestivum) is a globally important crop, accounting for 20 per cent of the calories consumed by humans. Major efforts are underway worldwide to increase wheat production by extending genetic diversity and analysing key traits, and genomic resources can accelerate progress. But so far the very large size and polyploid complexity of the bread wheat genome have been substantial barriers to genome analysis. Here we report the sequencing of its large, 17-gigabase-pair, hexaploid genome using 454pyrosequencing, and comparison of this with the sequences of diploid ancestral and progenitor genomes. We identified between 94,000 and 96,000 genes, and assigned two-thirds to the three component genomes (A, B and D) of hexaploid wheat. High-resolution synteny maps identified many small disruptions to conserved gene order. We show that the hexaploid genome is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded gene families that could be associated with crop productivity. Our analyses, coupled with the identification of extensive genetic variation, provide a resource for accelerating gene discovery and improving this major crop., With a global output of 681 million tonnes in 2011 (1), bread wheat accounts for 20% of the calories consumed by humans (2) and is an important source of protein, [...]

The grass species Brachypodium distachyon (hereafter, Brachypodium) has been adopted as a model system for grasses. Here, we describe the development of a genetic linkage map of Brachypodium. The genetic linkage map was developed with an [F.sub.2] population from a cross between the diploid Brachypodium lines Bd3-1 and Bd21. The map was populated with polymorphic simple sequence repeat (SSR) markers from Brachypodium expressed sequence tag (EST) and bacterial artificial chromosome (BAC) end sequences and conserved orthologous sequence (COS) markers from other grass species. The map is 1386 cM in length and consists of 139 marker loci distributed across 20 linkage groups. Five of the linkage groups exceed 100 cM in length, with the largest being 231 cM long. Assessment of colinearity between the Brachypodium linkage map and the rice genome sequence revealed significant regions of macrosynteny between the two genomes, as well as rearrangements similar to those reported in other grass comparative structural genomics studies. The Brachypodium genetic linkage map described here will serve as a new tool to pursue a range of molecular genetic analyses and other applications in this new model plant system. Key words: Brachypodium, genetic analysis, molecular marker, SSR, linkage map, purple false brome. Le Brachypodium distachyon (Brachypodium) a ete adopte comme espece modele chez les graminees. Dans ce travail, les auteurs decrivent le developpement d'une carte genetique chez le Brachypodium. La carte a ete deeveloppeeea partir d'une population [F.sub.2] issue d'un croisement entre les ligneees diploldes Bd3-1 et Bd21 du Brachypodium. La carte est composee de marqueurs microsatellites (SSR) provenant de l'analyse d'eetiquettes de sequences exprimees (EST) et de sequences terminales de clones BAC (chromosomes bacteeriens artificiels) du Brachypodium ainsi que de marqueurs de sequences orthologues conservees (COS) provenant d'autres graminees. La carte mesure 1386 cM et compte 139 marqueurs distribues sur 20 groupes de liaison. Cinq des groupes de liaison mesurent plus de 100 cM, le plus long totalisant 231 cM. Une etude de la co-linearite entre la carte genetique du Brachypodium et la sequence genomique du riz a revele d'importantes regions de macrosynteenie entre les deux genomes, ainsi que des rearrangements semblables a ceux rapportees lors d'etudes similaires en genomique structurale chez d'autres graminees. La carte genetique du Brachypodium decrite dans ce travail servira de nouvel outil pour une gamme d'analyses moleculaires ainsi que d'autres applications chez ce nouveau modele chez les plantes. Mots-cles: Brachypodium, analyse genetique, marqueur moleeculaire, SSR, carte genetique, brachypode a deux epis. [Traduit par la Redaction], Introduction The majority of the domesticated grass crops are cool-season species belonging to one of the four core pooid tribes: the Triticeae, Aveneae, Bromeae, and Poeae (Davis and Soreng 1993). [...]

A high-throughput two-step PCR strategy for the identification of selected genes from a BAC library derived from hexaploid wheat (16974 Mbp) is described. The screen is based on the pooling of DNA from BAC clones into 675 'superpools' arrayed in a three-dimensional configuration. Each BAC clone is represented in three superpools to allow the identification of candidate 384-well plates of clones after the first round of PCR; identification is facilitated by an associated Perl script. A second round of PCR detects the specific BAC clone within the candidate plate that corresponds to the gene of interest. Thus, a single copy of the target gene can be identified from the library of over 700000 clones (approximately 5 genome equivalents) by assaying only three 384-well plates. The pooling strategy was validated by screening the library with primers specific for the reduced height (Rht-1a) gene. Using relatively stringent selection criteria, 13 Rht-containing clones were identified from 17 candidate plates, and sequence analysis of the amplified products showed that all three Rht homoeologues were represented. Furthermore, the method confirmed the estimated coverage of the BAC library. Thus, this methodology allows the rapid and cost-effective identification of genes, and their homoeologues, from large-insert libraries of complex genomes such as hexaploid wheat. Key words: hexaploid wheat, BAC library, Rht gene, library screening. Une strategie de criblage PCR a haut debit en deux etapes pour l'identification de genes cibles au sein d'une banque de clones BAC, issue du ble hexaploide (16974 Mb), est decrite. Le crible repose sur des ADN composites provenant de 675 << superpools >> de clones BAC disposes dans une configuration en trois dimensions. Chaque clone BAC est represente dans trois << superpools >>, ce qui permet d'identifier des plaques a 384 puns candidates apres une premiere amplification PCR. Cette identification est facilitee par l'emploi d'un script Perl. Une seconde ronde d'amplification PCR permet de detecter un clone BAC specifique qui contient le gene d'interet au sein de la plaque candidate. Ainsi, on peut identifier une copie unique du gene cible au sein dune banque de plus de 70 0000 clones (l'equivalent d'environ 5 genomes) en interrogeant seulement trois plaques a 384 puns. Cette strategie a ete validee en criblant la banque a l'aide d'amorces specifiques pour le gene reduced height (Rht-1a). A l'aide de criteres relativement stricts, 13 clones contenant Rht ont ete identifies parmi 17 plaques candidates et le sequencage des products amplifies a montre que les trois homeologues Rht etaient representes. De plus, la methode a permis de confirmer la couverture estimee de la banque de clones BAC. Ainsi, cette methodologie permet d'identifier rapidement et a peu de frais les genes et leurs homeologues au sein de banques d'inserts de grande taille pour des genomes complexes comme celui du ble hexaploide. Mots-cles : ble hexaploide, banque de clones BAC, gene Rht, criblage de banque. [Traduit par la Redaction], Introduction Producing sufficient healthy food and feed during a period of increasing population and the threat of global climate change is of paramount importance. Cereals such as rice, wheat, sorghum, [...]

The cleavage of intracellular domains of receptor-like kinases (RLKs) has an important functional role in the transduction of signals from the cell surface to the nucleus in many organisms. However, the peptidases that catalyze protein cleavage during signal transduction remain poorly understood despite their crucial roles in diverse signaling processes. Here, we report in the flowering plant Arabidopsis thaliana that members of the DA1 family of ubiquitin-regulated Zn metallopeptidases cleave the cytoplasmic kinase domain of transmembrane kinase 1 (TMK1), releasing it for nuclear localization where it represses auxin-responsive cell growth during apical hook formation by phosphorylation and stabilization of the transcriptional repressors IAA32 and IAA34. Mutations in DA1 family members exhibited reduced apical hook formation, and DA1 family-mediated cleavage of TMK1 was promoted by auxin treatment. Expression of the DA1 family-generated intracellular kinase domain of TMK1 by an auxin-responsive promoter fully restored apical hook formation in a tmk1 mutant, establishing the function of DA1 family peptidase activities in TMK1-mediated differential cell growth and apical hook formation. DA1 family peptidase activity therefore modulates TMK1 kinase activity between a membrane location where it stimulates acid cell growth and initiates an auxin-dependent kinase cascade controlling cell proliferation in lateral roots and a nuclear localization where it represses auxin-mediated gene expression and growth. [ABSTRACT FROM AUTHOR]