An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage–related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.

We produced a reference sequence of the 1-gigabase chromosome 3B of hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled a sequence of 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements. The distribution of structural and functional features along the chromosome revealed partitioning correlated with meiotic recombination. Comparative analyses indicated high wheat-specific inter- and intrachromosomal gene duplication activities that are potential sources of variability for adaption. In addition to providing a better understanding of the organization, function, and evolution of a large and polyploid genome, the availability of a high-quality sequence anchored to genetic maps will accelerate the identification of genes underlying important agronomic traits.

A molecular-marker linkage map has been constructed for perennial ryegrass (Lolium perenne L.) using a one-way pseudo-testcross population based on the mating of a multiple heterozygous individual with a doubled haploid genotype. RFLP, AFLP, isoenzyme, and EST data from four collaborating laboratories within the International Lolium Genome Initiative were combined to produce an integrated genetic map containing 240 loci covering 811 cM on seven linkage groups. The map contained 124 codominant markers, of which 109 were heterologous anchor RFLP probes from wheat, barley, oat, and rice, allowing comparative relationships between perennial ryegrass and other Poaceae species to be inferred. The genetic maps of perennial ryegrass and the Triticeae cereals are highly conserved in terms of synteny and colinearity. This observation was supported by the general agreement of the syntenic relationships between perennial ryegrass, oat, and rice and those between the Triticeae and these species. A lower level of synteny and colinearity was observed between perennial ryegrass and oat compared with the Triticeae, despite the closer taxonomic affinity between these species. It is proposed that the linkage groups of perennial ryegrass be numbered in accordance with these syntenic relationships, to correspond to the homoeologous groups of the Triticeae cereals.Key words: Lolium perenne, genetic linkage map, RFLP, AFLP, conserved synteny.Résumé : Une carte génétique composée de marqueurs moléculaires a été produite pour l'ivraie vivace (Lolium perenne L.) à l'aide d'une population issue d'un pseudo-testcross unidirectionnel. Les parents étaient, d'une part, un individu multiple hétérozygote et, d'autre part, un génotype haploïde doublé. Des données pour des marqueurs RFLP, AFLP, isoenzymatiques ainsi que des EST ont été contribuées par quatre laboratoires faisant partie du « International Lolium Genome Initiative (ILGI) ». Ces données ont été combinées pour produire une carte génétique intégrée comprenant 240 locus, formant sept groupes de liaison et s'étendant sur 811 cM. La carte compte 124 marqueurs codominants dont 169 sont des sondes-repères RFLP hétérologues provenant du blé, de l'orge, de l'avoine ou du riz. Ces sondes permettent d'examiner les relations entre l'ivraie vivace et d'autres espèces de graminées. Les cartes génétiques de l'ivraie vivace et des céréales de la tribu des hordées sont très conservées en termes de synténie et de colinéarité. Cette conclusion s'appuie sur une concordance générale au niveau des relations de synténie entre l'ivraie vivace, l'avoine et le riz ainsi qu'entre les hordées et ces espèces. Un plus faible niveau de synténie et de colinéarité a été observé entre l'ivraie vivace et l'avoine par rapport aux hordées, malgré la proximité taxinomique entre ces espèces. Il est suggéré que les groupes de liaison chez l'ivraie vivace soient numérotés en fonction des relations de synténie de façon à correspondre aux groupes d'homéologues chez les céréales.

For more than 10,000 years, the selection of plant and animal traits that are better tailored for human use has shaped the development of civilizations. During this period, bread wheat (Triticum aestivum) emerged as one of the world's most important crops. We used exome sequencing of a world-wide panel of almost 500 genotypes selected from across the geographical range of the wheat species complex to explore how 10,000 years of hybridization, selection, adaptation and plant breeding shaped the genetic makeup of modern bread wheats. We observed considerable genetic variations at the genic, chromosomal and subgenomic levels deciphering the likely origins of modern day wheats, the consequences of range expansion and allelic variants selected since its domestication. Our data supports a reconciled model of wheat evolution and provides novel avenues for future breeding improvement.