W090
The Pangenome of Brassica oleracea

Date: Saturday, January 14, 2017
Time: 11:55 AM
Room: Pacific Salon 2
Agnieszka Golicz , University of Queensland, Brisbane, Australia
Philipp E. Bayer , University of Western Australia, Perth, Australia
Guy Barker , University of Warwick, Warwks, United Kingdom
Patrick Edger , Department of Horticulture, Michigan State University, East Lansing, MI
Hye Ran Kim , KRIBB-Plant Systems Engineering Center, Daejeon, Korea, Republic of (South)
Paula Martinez , University of Queensland, St Lucia, Australia
Chon-Kit Kenneth Chan , University of Western Australia, Perth, Australia
Anita Severn-Ellis , University of Western Australia, Perth, Australia
W. Richard McCombie , Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
Isobel Parkin , Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
Andrew H. Paterson , Plant Genome Mapping Laboratory, University of Georgia, Athens, GA
J. Chris Pires , Division of Biological Sciences, University of Missouri, Columbia, MO
Andrew G. Sharpe , National Research Council Canada, Saskatoon, SK, Canada
Haibao Tang , Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fuzhou, AZ, China
Graham R. Teakle , University of Warwick, Warwick, United Kingdom
Christopher D. Town , J. Craig Venter Institute, Rockville, MD
Jacqueline Batley , University of Queensland, Brisbane, Australia
David Edwards , University of Western Australia, Perth, Australia
While two reference genomes of B. oleracea are available, they do not capture the entire gene content of the species owing to presence absence variants (PAV), genes which are present in one individual and not another. A reference which includes all genes for a species is termed the pangenome. We have constructed a draft pangenome using nine morphologically diverse B. oleracea varieties and a wild relative – Brassica macrocarpa. The pangenome comprises 61,379 genes, 18.7% of which demonstrate PAV in the varieties analysed. Several of the variable genes are annotated with functions related to major agronomic traits including disease resistance, flowering time, glucosinolate metabolism, and vitamin biosynthesis, suggesting that PAVs may be important for the breeding of improved Brassica crops. In addition to gene PAVs, a large number of allelic variants of genes were identified. A total of 4.8 million SNPs are present in the pangenome, 400,000 of which are in genomic regions not represented in the TO1000 reference. The pangenome provides the basis for comprehensive gene discovery and the association of variable genes and allelic variants with agronomic traits to support the breeding of improved Brassica crops.
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