The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection.
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.
Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China.|Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China.|Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, China.
Jinghua
J
Yang
Biomarker Technologies Corporation, Beijing, China.
Dongyuan
D
Liu
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China.
Xiaowu
X
Wang
Biomarker Technologies Corporation, Beijing, China.
Changmian
C
Ji
Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing, China.
Feng
0000-0003-2982-9675
F
Cheng
Biomarker Technologies Corporation, Beijing, China.
Baoning
B
Liu
Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China.|Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China.|Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, China.
Zhongyuan
Z
Hu
School of Plant Biology (M084) and the UWA Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia.
Sheng
S
Chen
Center for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India.
Deepak
D
Pental
Biomarker Technologies Corporation, Beijing, China.
Youhui
Y
Ju
Biomarker Technologies Corporation, Beijing, China.
Pu
P
Yao
Biomarker Technologies Corporation, Beijing, China.
Xuming
X
Li
Biomarker Technologies Corporation, Beijing, China.
Kun
K
Xie
Biomarker Technologies Corporation, Beijing, China.
Jianhui
J
Zhang
College of Plant Science and Technology, Agricultural and Animal Husbandry College of Tibet University, Linzhi, China.
Jianlin
J
Wang
Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
Fan
F
Liu
Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China.
Weiwei
W
Ma
Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China.
Jannat
J
Shopan
Biomarker Technologies Corporation, Beijing, China.
Hongkun
0000-0002-9426-3615
H
Zheng
Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska, USA.
Sally A
SA
Mackenzie
Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou, China.|Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou, China.|Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, China.
Mingfang
M
Zhang
D018556:Crops, Agricultural / Q000235:genetics; D018744:DNA, Plant; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D009149:Mustard Plant / Q000145:classification / Q000235:genetics*; D011123:Polyploidy; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA
D018744:DNA, Plant