Analysis of the bread wheat genome using whole-genome shotgun sequencing

Abstract

SummaryBread wheat (Triticum aestivum) is a globally important crop, accounting for 20% of the calories consumed by mankind. We sequenced its large and challenging 17 Gb hexaploid genome using 454 pyrosequencing and compared this with the sequences of diploid ancestral and progenitor genomes. Between 94,000-96,000 genes were identified, and two-thirds were assigned to the A, B and D genomes. High-resolution synteny maps identified many small disruptions to conserved gene order. We show the hexaploid genome is highly dynamic, with significant loss of gene family members upon 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 new resource for accelerating gene discovery and improving this major crop.

Draft genome of the wheat A-genome progenitor Triticum urartu

“…The large set of gene models (34,879) and abundant genetic markers anchored in sequence scaffolds, together with the emerging genomic resources from bread wheat 8 , promise to accelerate deeper and more systematic genomic and breeding studies of bread wheat that are required to meet the future challenges of food security and sustainable agriculture.…”

“…7). More recently, a whole-genome shotgun sequence analysis of bread wheat and its diploid relatives 8 has allocated more than 60% of the genes to the A, B and D genomes with more than 70% confidence. The sequence of diploid progenitor genomes will allow the complete and unambiguous assignment of their homeologous relationships.…”

Mapping resistance to the bird cherry-oat aphid and the greenbug in wheat using sequence-based genotyping

“…Linkage groups having less than three markers or markers with no linkage where discarded from the analysis (altogether three out of 25). For assigning chromosome groups to the genomic regions of interests, 20% of the marker sequences in each LG were systematically searched with the Basic Local Alignment Search Tool (BLAST) in the wheat genome sequence published by Brenchley et al (2012) and available at EnsamblPlants (http://plants.ensembl.org/Triticum_aestivum/Info/Index).…”

Plant genomics: sowing the seeds of success

“…To apply effective genomics approaches to improve and breed new bread wheat varieties it will be essential to generate a complete genome sequence. Although whole genome shotgun sequencing allowed the recent assembly of the bread wheat gene set [3], a complete bread wheat genome will be necessary to determine the full effect of genomic variation on wheat phenotypes. Philippe et al [4] describe the application of BAC-by-BAC sequencing to generate a physical map of wheat chromosome 1BL, which has the highest marker density to-date with 11 markers per Mb, and also has high levels of anchoring and contig ordering.…”