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

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

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Abstract

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.

Original languageEnglish (US)
Pages (from-to)1225-1232
Number of pages8
JournalNature Genetics
Volume48
Issue number10
DOIs
StatePublished - Oct 1 2016

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ASJC Scopus subject areas

  • Genetics

Cite this

Yang, J., Liu, D., Wang, X., Ji, C., Cheng, F., Liu, B., Hu, Z., Chen, S., Pental, D., Ju, Y., Yao, P., Li, X., Xie, K., Zhang, J., Wang, J., Liu, F., Ma, W., Shopan, J., Zheng, H., ... Zhang, M. (2016). The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection. Nature Genetics, 48(10), 1225-1232. https://doi.org/10.1038/ng.3657