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Title: Analysis of the allohexaploid bread wheat genome (Triticum aestivum) using comparative whole genome shotgun sequencing

Author
item BRENCHLEY, RACHEL - University Of Liverpool
item SPANNAGL, MANUEL - Helmholtz Centre
item PFEIFER, MATTHIA - Helmholtz Centre
item BAKER, GARY - University Of Bristol
item D'AMORE, ROSALINDA - University Of Liverpool
item Gu, Yong
item LUO, MINGCHENG - University Of California
item HUO, NAXIN - University Of California
item Anderson, Olin
item DVORAK, JAN - University Of California
item HALL, ANTHONY - University Of Liverpool
item MAYER, KAUS - Helmholtz Centre
item EDWARD, KEITH - University Of Bristol
item HALL, NEIL - University Of Liverpool

Submitted to: Nature
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/1/2012
Publication Date: 11/29/2012
Citation: Brenchley, R., Spannagl, M., Pfeifer, M., Baker, G., D'Amore, R., Gu, Y.Q., Luo, M., Huo, N., Anderson, O.D., Dvorak, J., Hall, A., Mayer, K., Edward, K.J., Hall, N. 2012. Analysis of the allohexaploid bread wheat genome (Triticum aestivum) using comparative whole genome shotgun sequencing. Nature. 491:705-710.

Interpretive Summary: With a global output of 681 million tons in 2011, bread wheat accounts for 20% of human consumption of calories and protein and is an important source of vitamins and minerals. To maintain the agricultural food sustainability, wheat genomics research will play important role by providing invaluable genomics resources for developing molecule markers useful marker-assisted breeding program aiming at improving desirable traits for crop improvement. In this study, the bread wheat genome from cultivar Chinese Spring was sequenced using next generation Roche 454 sequencing technology. The sequence data generated represents 5x genome coverage, allowing for sequencing assembly of most genes present in bread wheat. This wheat genomics data have been widely used by wheat community for various research projects ranging from genetic mapping to wheat domestication and evolution study. The research project provided one of the largest and most important sequence data available to the community.

Technical Abstract: The large 17 Gb allopolyploid genome of bread wheat is a major challenge for genome analysis because it is composed of three closely- related and independently maintained genomes, with genes dispersed as small “islands” separated by vast tracts of repetitive DNA. We used a novel comparative genomics strategy to identify 88,854 wheat genes with associated sequence polymorphisms and assigned a significant proportion to the component A, B and D genomes. Our analysis reveals a highly dynamic genome, with rapid and extensive loss of gene family members upon polyploidization, and an abundance of gene fragments forming a potential reservoir for rapid gene evolution. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded Triticeae- specific gene families, consistent with the high productivity of the wheat crop. Our genome analysis, coupled with the identification of extensive genetic variation, provides an important new resource for accelerating gene discovery and improving this centrally important crop.