Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus

• Published in: Plant biotechnology journal Vol. 16; no. 7; pp. 1265 - 1274
• Main Authors: Hurgobin, Bhavna, Golicz, Agnieszka A., Bayer, Philipp E., Chan, Chon‐Kit Kenneth, Tirnaz, Soodeh, Dolatabadian, Aria, Schiessl, Sarah V., Samans, Birgit, Montenegro, Juan D., Parkin, Isobel A. P., Pires, J. Chris, Chalhoub, Boulos, King, Graham J., Snowdon, Rod, Batley, Jacqueline, Edwards, David
• Format: Journal Article
• Language: English
• Published: England John Wiley & Sons, Inc 01.07.2018; Wiley; John Wiley and Sons Inc
• Subjects: agronomic traits; Agronomy; amphidiploidy; Brassica; Brassica napus; Brassica napus - genetics; canola; Diploidy; Disease resistance; Exchanging; Flow resistance; Flowering; flowering date; Gene Conversion - genetics; Gene Deletion; Gene Duplication; Genes; Genes, Plant - genetics; Genetic diversity; genetic variation; Genetic Variation - genetics; genome structure; Genome, Plant - genetics; glucosinolates; Life Sciences; Lipid metabolism; Metabolism; pangenome; phenotype; Phenotypes; Polyploidy; Quantitative Trait, Heritable; Rape plants; recombination; Vegetal Biology; Brassica napus; pangenome; recombination; genome structure; canola
• ISSN: 1467-7644; 1467-7652; 1467-7652
• DOI: 10.1111/pbi.12867

Summary Homoeologous exchanges (HEs) have been shown to generate novel gene combinations and phenotypes in a range of polyploid species. Gene presence/absence variation (PAV) is also a major contributor to genetic diversity. In this study, we show that there is an association between these two events, particularly in recent Brassica napus synthetic accessions, and that these represent a novel source of genetic diversity, which can be captured for the improvement of this important crop species. By assembling the pangenome of B. napus, we show that 38% of the genes display PAV behaviour, with some of these variable genes predicted to be involved in important agronomic traits including flowering time, disease resistance, acyl lipid metabolism and glucosinolate metabolism. This study is a first and provides a detailed characterization of the association between HEs and PAVs in B. napus at the pangenome level.