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Whole-genome resequencing reveals Brassica napus origin and genetic loci involved in its improvement.

ABSTRACT: Brassica napus (2n?=?4x?=?38, AACC) is an important allopolyploid crop derived from interspecific crosses between Brassica rapa (2n?=?2x?=?20, AA) and Brassica oleracea (2n?=?2x?=?18, CC). However, no truly wild B. napus populations are known; its origin and improvement processes remain unclear. Here, we resequence 588 B. napus accessions. We uncover that the A subgenome may evolve from the ancestor of European turnip and the C subgenome may evolve from the common ancestor of kohlrabi, cauliflower, broccoli, and Chinese kale. Additionally, winter oilseed may be the original form of B. napus. Subgenome-specific selection of defense-response genes has contributed to environmental adaptation after formation of the species, whereas asymmetrical subgenomic selection has led to ecotype change. By integrating genome-wide association studies, selection signals, and transcriptome analyses, we identify genes associated with improved stress tolerance, oil content, seed quality, and ecotype improvement. They are candidates for further functional characterization and genetic improvement of B. napus.

SUBMITTER: Lu K

PROVIDER: S-EPMC6411957 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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Whole-genome resequencing reveals Brassica napus origin and genetic loci involved in its improvement.

Lu Kun K Wei Lijuan L Li Xiaolong X Wang Yuntong Y Wu Jian J Liu Miao M Zhang Chao C Chen Zhiyou Z Xiao Zhongchun Z Jian Hongju H Cheng Feng F Zhang Kai K Du Hai H Cheng Xinchao X Qu Cunming C Qian Wei W Liu Liezhao L Wang Rui R Zou Qingyuan Q Ying Jiamin J Xu Xingfu X Mei Jiaqing J Liang Ying Y Chai You-Rong YR Tang Zhanglin Z Wan Huafang H Ni Yu Y He Yajun Y Lin Na N Fan Yonghai Y Sun Wei W Li Nan-Nan NN Zhou Gang G Zheng Hongkun H Wang Xiaowu X Paterson Andrew H AH Li Jiana J

Nature communications 20190311 1

Brassica napus (2n = 4x = 38, AACC) is an important allopolyploid crop derived from interspecific crosses between Brassica rapa (2n = 2x = 20, AA) and Brassica oleracea (2n = 2x = 18, CC). However, no truly wild B. napus populations are known; its origin and improvement processes remain unclear. Here, we resequence 588 B. napus accessions. We uncover that the A subgenome may evolve from the ancestor of European turnip and the C subgenome may evolve from the common ancestor of kohlrabi, cauliflow ...[more]

PMID: 30858362

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Project description:Sustainable canola production is essential to meet growing human demands for vegetable oil, biodiesel, and meal for stock feed markets. Blackleg, caused by the fungal pathogen, Leptosphaeria maculans is a devastating disease that can lead to significant yield loss in many canola production regions worldwide. Breakdown of race-specific resistance to L. maculans in commercial cultivars poses a constant threat to the canola industry. To identify new alleles, especially for quantitative resistance (QR), we analyzed 177 doubled haploid (DH) lines derived from an RP04/Ag-Outback cross. DH lines were evaluated for QR under field conditions in three experiments conducted at Wagga Wagga (2013, 2014) and Lake Green (2015), and under shade house conditions using the 'ascospore shower' test. DH lines were also characterized for qualitative R gene-mediated resistance via cotyledon tests with two differential single spore isolates, IBCN17 and IBCN76, under glasshouse conditions. Based on 18,851 DArTseq markers, a linkage map representing 2,019 unique marker bins was constructed and then utilized for QTL detection. Marker regression analysis identified 22 significant marker associations for resistance, allowing identification of two race-specific resistance R genes, Rlm3 and Rlm4, and 21 marker associations for QR loci. At least three SNP associations for QR were repeatedly detected on chromosomes A03, A07 and C04 across phenotyping environments. Physical mapping of markers linked with these consistent QR loci on the B. napus genome assembly revealed their localization in close proximity of the candidate genes of B. napus BnaA03g26760D (A03), BnaA07g20240D (A07) and BnaC04g02040D (C04). Annotation of these candidate genes revealed their association with protein kinase and jumonji proteins implicated in defense resistance. Both Rlm3 and Rlm4 genes identified in this DH population did not show any association with resistance loci detected under either field and/or shade house conditions (ascospore shower) suggesting that both genes are ineffective in conferring resistance to L. maculans in Australian field conditions. Taken together, our study identified sequence-based molecular markers for dissecting R and QR loci to L. maculans in a canola DH population from the RP04/Ag-Outback cross.

Dataset Information

Whole-genome resequencing reveals Brassica napus origin and genetic loci involved in its improvement.

Publications

Whole-genome resequencing reveals Brassica napus origin and genetic loci involved in its improvement.

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