Genomic insights into the origin, domestication and diversification of Brassica juncea
Lei Kang, Lunwen Qian, Ming Zheng, Liyang Chen, Hao Chen, Liu Yang, Liang You, Bin Yang, Mingli Yan, Yuanguo Gu, Tianyi Wang, Sarah Schießl, Hong An, Paul D. Blischak, Xianjun Liu, Hongfeng Lü, Dawei Zhang, Yong Rao, Donghai Jia, Dinggang Zhou, Huagui Xiao, Yonggang Wang, Xinghua Xiong, Annaliese S. Mason, J. Chris Pires, Rod J. Snowdon, Wei Hua, Zhongsong Liu
Abstract
Despite early domestication around 3000 BC, the evolutionary history of the ancient allotetraploid species Brassica juncea (L.) Czern & Coss remains uncertain. Here, we report a chromosome-scale de novo assembly of a yellow-seeded B. juncea genome by integrating long-read and short-read sequencing, optical mapping and Hi-C technologies. Nuclear and organelle phylogenies of 480 accessions worldwide supported that B. juncea is most likely a single origin in West Asia, 8,000-14,000 years ago, via natural interspecific hybridization. Subsequently, new crop types evolved through spontaneous gene mutations and introgressions along three independent routes of eastward expansion. Selective sweeps, genome-wide trait associations and tissue-specific RNA-sequencing analysis shed light on the domestication history of flowering time and seed weight, and on human selection for morphological diversification in this versatile species. Our data provide a comprehensive insight into the origin and domestication and a foundation for genomics-based breeding of B. juncea.