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Nature communications
03 11, 2019;10 (1): 1154.

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

Kun Lu, Lijuan Wei, Xiaolong Li, Yuntong Wang, Jian Wu, Miao Liu, Chao Zhang, Zhiyou Chen, Zhongchun Xiao, Hongju Jian, Feng Cheng, Kai Zhang, Hai Du, Xinchao Cheng, Cunming Qu, Wei Qian, Liezhao Liu, Rui Wang, Qingyuan Zou, Jiamin Ying, Xingfu Xu, Jiaqing Mei, Ying Liang, You-Rong Chai, Zhanglin Tang, Huafang Wan, Yu Ni, Yajun He, Na Lin, Yonghai Fan, Wei Sun, Nan-Nan Li, Gang Zhou, Hongkun Zheng, Xiaowu Wang, Andrew H Paterson, Jiana Li
Author Information
  1. Kun Lu: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China. ORCID
  2. Lijuan Wei: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.
  3. Xiaolong Li: Biomarker Technologies Corporation, 101300, Beijing, China.
  4. Yuntong Wang: Biomarker Technologies Corporation, 101300, Beijing, China.
  5. Jian Wu: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, 100081, Beijing, China.
  6. Miao Liu: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.
  7. Chao Zhang: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.
  8. Zhiyou Chen: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.
  9. Zhongchun Xiao: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.
  10. Hongju Jian: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.
  11. Feng Cheng: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, 100081, Beijing, China. ORCID
  12. Kai Zhang: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.
  13. Hai Du: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.
  14. Xinchao Cheng: State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Beibei, 400715, Chongqing, China.
  15. Cunming Qu: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.
  16. Wei Qian: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.
  17. Liezhao Liu: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.
  18. Rui Wang: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.
  19. Qingyuan Zou: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.
  20. Jiamin Ying: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.
  21. Xingfu Xu: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.
  22. Jiaqing Mei: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.
  23. Ying Liang: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.
  24. You-Rong Chai: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.
  25. Zhanglin Tang: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.
  26. Huafang Wan: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.
  27. Yu Ni: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.
  28. Yajun He: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.
  29. Na Lin: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.
  30. Yonghai Fan: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.
  31. Wei Sun: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China.
  32. Nan-Nan Li: Academy of Agricultural Sciences, Southwest University, Beibei, 400715, Chongqing, China.
  33. Gang Zhou: Biomarker Technologies Corporation, 101300, Beijing, China. ORCID
  34. Hongkun Zheng: Biomarker Technologies Corporation, 101300, Beijing, China. ORCID
  35. Xiaowu Wang: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, 100081, Beijing, China. wangxw@mail.caas.net.cn.
  36. Andrew H Paterson: Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, 30605, USA. paterson@uga.edu.
  37. Jiana Li: College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China. ljn1950@swu.edu.cn.
PMID: 30858362 DOI: 10.1038/s41467-019-09134-9

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.

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MeSH Term

Acclimatization
Brassica napus
Brassica rapa
Chromosomes, Plant
Ecotype
Gene Expression Profiling
Genetic Loci
Genetic Speciation
Genome, Plant
Plant Breeding
Seeds
Whole Genome Sequencing
Journal Article Research Support, Non-U.S. Gov't

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