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Plant J. 2017 Nov;92(3):452-468. doi: 10.1111/tpj.13669. Epub 2017 Oct 9.

The high-quality genome of Brassica napus cultivar 'ZS11' reveals the introgression history in semi-winter morphotype.

Author information

1
The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
2
Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China.
3
BGI-Qingdao, Qingdao, 266555, China.
4
State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China.
5
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
6
College of Agronomy, Hunan Agricultural University, Changsha, 410128, China.
7
College of Agronomy and Biotechnology, Southwest University, BeiBei District, Chongqing, 400715, China.
8
Qinghai Academy of Agricultural and Forestry, National Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Xining, 810016, China.
9
Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
10
Shichun Academy of Agricultural Sciences, Chengdu, 610066, China.
11
Institut National de Recherche Agronomique (INRA), Unité de Recherche en Génomique Végétale (URGV), UMR1165, Organization and Evolution of Plant Genomes (OEPG), 2 rue Gaston Crémieux, 91057, Evry, France.

Abstract

Allotetraploid oilseed rape (Brassica napus L.) is an agriculturally important crop. Cultivation and breeding of B. napus by humans has resulted in numerous genetically diverse morphotypes with optimized agronomic traits and ecophysiological adaptation. To further understand the genetic basis of diversification and adaptation, we report a draft genome of an Asian semi-winter oilseed rape cultivar 'ZS11' and its comprehensive genomic comparison with the genomes of the winter-type cultivar 'Darmor-bzh' as well as two progenitors. The integrated BAC-to-BAC and whole-genome shotgun sequencing strategies were effective in the assembly of repetitive regions (especially young long terminal repeats) and resulted in a high-quality genome assembly of B. napus 'ZS11'. Within a short evolutionary period (~6700 years ago), semi-winter-type 'ZS11' and the winter-type 'Darmor-bzh' maintained highly genomic collinearity. Even so, certain genetic differences were also detected in two morphotypes. Relative to 'Darmor-bzh', both two subgenomes of 'ZS11' are closely related to its progenitors, and the 'ZS11' genome harbored several specific segmental homoeologous exchanges (HEs). Furthermore, the semi-winter-type 'ZS11' underwent potential genomic introgressions with B. rapa (Ar ). Some of these genetic differences were associated with key agronomic traits. A key gene of A03.FLC3 regulating vernalization-responsive flowering time in 'ZS11' was first experienced HE, and then underwent genomic introgression event with Ar , which potentially has led to genetic differences in controlling vernalization in the semi-winter types. Our observations improved our understanding of the genetic diversity of different B. napus morphotypes and the cultivation history of semi-winter oilseed rape in Asia.

KEYWORDS:

Brassica napus ; ZS11; allotetraploid; genome; homoeolog; introgression; next-generation sequencing technologies; polyploid; subgenome

PMID:
28849613
DOI:
10.1111/tpj.13669
[Indexed for MEDLINE]
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