The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection.

Authors: Yang, Jinghua and Liu, Dongyuan and Wang, Xiaowu and Ji, Changmian and Cheng, Feng and Liu, Baoning and Hu, Zhongyuan and Chen, Sheng and Pental, Deepak and Ju, Youhui and Yao, Pu and Li, Xuming and Xie, Kun and Zhang, Jianhui and Wang, Jianlin and Liu, Fan and Ma, Weiwei and Shopan, Jannat and Zheng, Hongkun and Mackenzie, Sally A and Zhang, Mingfang

The Brassica genus encompasses three diploid and three allopolyploid genomes, but a clear understanding of the evolution of agriculturally important traits via polyploidy is lacking. We assembled an allopolyploid Brassica juncea genome by shotgun and single-molecule reads integrated to genomic and genetic maps. We discovered that the A subgenomes of B. juncea and Brassica napus each had independent origins. Results suggested that A subgenomes of B. juncea were of monophyletic origin and evolved into vegetable-use and oil-use subvarieties. Homoeolog expression dominance occurs between subgenomes of allopolyploid B. juncea, in which differentially expressed genes display more selection potential than neutral genes. Homoeolog expression dominance in B. juncea has facilitated selection of glucosinolate and lipid metabolism genes in subvarieties used as vegetables and for oil production. These homoeolog expression dominance relationships among Brassicaceae genomes have contributed to selection response, predicting the directional effects of selection in a polyploid crop genome.

Journal: Nature genetics
DOI: 10.1038/ng.3657
Year: 2016

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