Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Hurgobin B

PROVIDER: S-EPMC5999312 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature

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

Hurgobin Bhavna B Golicz Agnieszka A AA Bayer Philipp E PE Chan Chon-Kit Kenneth CK Tirnaz Soodeh S Dolatabadian Aria A Schiessl Sarah V SV Samans Birgit B Montenegro Juan D JD Parkin Isobel A P IAP Pires J Chris JC Chalhoub Boulos B King Graham J GJ Snowdon Rod R Batley Jacqueline J Edwards David D

Plant biotechnology journal 20180110 7

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 assemb ...[more]

PMID: 29205771

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Project description:All crop species are current or ancient polyploids. Following whole genome duplication, structural and functional modifications result in differential gene content or regulation in the duplicated regions, which can play a fundamental role in the diversification of genes underlying complex traits. We have investigated this issue in Brassica napus, a species with a highly duplicated genome, with the aim of studying the structural and functional organization of duplicated regions involved in quantitative resistance to stem canker, a disease caused by the fungal pathogen Leptosphaeria maculans. Genome-wide association analysis on two oilseed rape panels confirmed that duplicated regions of ancestral blocks E, J, R, U, and W were involved in resistance to stem canker. The structural analysis of the duplicated genomic regions showed a higher gene density on the A genome than on the C genome and a better collinearity between homoeologous regions than paralogous regions, as overall in the whole B. napus genome. The three ancestral sub-genomes were involved in the resistance to stem canker and the fractionation profile of the duplicated regions corresponded to what was expected from results on the B. napus progenitors. About 60% of the genes identified in these duplicated regions were single-copy genes while less than 5% were retained in all the duplicated copies of a given ancestral block. Genes retained in several copies were mainly involved in response to stress, signaling, or transcription regulation. Genes with resistance-associated markers were mainly retained in more than two copies. These results suggested that some genes underlying quantitative resistance to stem canker might be duplicated genes. Genes with a hydrolase activity that were retained in one copy or R-like genes might also account for resistance in some regions. Further analyses need to be conducted to indicate to what extent duplicated genes contribute to the expression of the resistance phenotype.

Dataset Information

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

Publications

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

Similar Datasets

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