title: Analysis of the bread wheat genome using whole-genome shotgun sequencing.
abstract: 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 454 pyrosequencing, 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.
authors.affiliation: Centre for Genome Research, University of Liverpool, Liverpool L69 7ZB, UK.
authors.forename: Rachel
authors.initials: R
authors.lastname: Brenchley
authors.forename: Manuel
authors.initials: M
authors.lastname: Spannagl
authors.forename: Matthias
authors.initials: M
authors.lastname: Pfeifer
authors.forename: Gary L A
authors.initials: GL
authors.lastname: Barker
authors.forename: Rosalinda
authors.initials: R
authors.lastname: D'Amore
authors.forename: Alexandra M
authors.initials: AM
authors.lastname: Allen
authors.forename: Neil
authors.initials: N
authors.lastname: McKenzie
authors.forename: Melissa
authors.initials: M
authors.lastname: Kramer
authors.forename: Arnaud
authors.initials: A
authors.lastname: Kerhornou
authors.forename: Dan
authors.initials: D
authors.lastname: Bolser
authors.forename: Suzanne
authors.initials: S
authors.lastname: Kay
authors.forename: Darren
authors.initials: D
authors.lastname: Waite
authors.forename: Martin
authors.initials: M
authors.lastname: Trick
authors.forename: Ian
authors.initials: I
authors.lastname: Bancroft
authors.forename: Yong
authors.initials: Y
authors.lastname: Gu
authors.forename: Naxin
authors.initials: N
authors.lastname: Huo
authors.forename: Ming-Cheng
authors.initials: MC
authors.lastname: Luo
authors.forename: Sunish
authors.initials: S
authors.lastname: Sehgal
authors.forename: Bikram
authors.initials: B
authors.lastname: Gill
authors.forename: Sharyar
authors.initials: S
authors.lastname: Kianian
authors.forename: Olin
authors.initials: O
authors.lastname: Anderson
authors.forename: Paul
authors.initials: P
authors.lastname: Kersey
authors.forename: Jan
authors.initials: J
authors.lastname: Dvorak
authors.forename: W Richard
authors.initials: WR
authors.lastname: McCombie
authors.forename: Anthony
authors.initials: A
authors.lastname: Hall
authors.forename: Klaus F X
authors.initials: KF
authors.lastname: Mayer
authors.forename: Keith J
authors.initials: KJ
authors.lastname: Edwards
authors.forename: Michael W
authors.initials: MW
authors.lastname: Bevan
authors.forename: Neil
authors.initials: N
authors.lastname: Hall
mesh_terms: D058431:Brachypodium / Q000235:genetics; D001939:Bread; D032461:Chromosomes, Plant / Q000235:genetics; D018556:Crops, Agricultural / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D005810:Multigene Family / Q000235:genetics; D012275:Oryza / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011123:Polyploidy; D011544:Pseudogenes / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D014908:Triticum / Q000145:classification / Q000235:genetics*; D003313:Zea mays / Q000235:genetics
chemical_list: D018076:DNA, Complementary; D018744:DNA, Plant