title: Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea.
abstract: Brassica species, including crops such as cabbage, turnip and oilseed, display enormous phenotypic variation. Brassica genomes have all undergone a whole-genome triplication (WGT) event with unknown effects on phenotype diversification. We resequenced 199 Brassica rapa and 119 Brassica oleracea accessions representing various morphotypes and identified signals of selection at the mesohexaploid subgenome level. For cabbage morphotypes with their typical leaf-heading trait, we identified four subgenome loci that show signs of parallel selection among subgenomes within B. rapa, as well as four such loci within B. oleracea. Fifteen subgenome loci are under selection and are shared by these two species. We also detected strong subgenome parallel selection linked to the domestication of the tuberous morphotypes, turnip (B. rapa) and kohlrabi (B. oleracea). Overall, we demonstrated that the mesohexaploidization of the two Brassica genomes contributed to their diversification into heading and tuber-forming morphotypes through convergent subgenome parallel selection of paralogous genes.
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Feng
authors.identifier: 0000-0003-2982-9675
authors.initials: F
authors.lastname: Cheng
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Rifei
authors.initials: R
authors.lastname: Sun
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Weigang, Nanjing, China.
authors.forename: Xilin
authors.initials: X
authors.lastname: Hou
authors.affiliation: Biomarker Technologies Corporation, Beijing, China.
authors.forename: Hongkun
authors.identifier: 0000-0002-9426-3615
authors.initials: H
authors.lastname: Zheng
authors.affiliation: Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing Vegetable Research Center (BVRC), Beijing, China.
authors.forename: Fenglan
authors.initials: F
authors.lastname: Zhang
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Yangyong
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Liu
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Jianli
authors.initials: J
authors.lastname: Liang
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Mu
authors.initials: M
authors.lastname: Zhuang
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Yunxia
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Biomarker Technologies Corporation, Beijing, China.
authors.forename: Dongyuan
authors.initials: D
authors.lastname: Liu
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Xiaobo
authors.initials: X
authors.lastname: Wang
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Pingxia
authors.initials: P
authors.lastname: Li
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Yumei
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands.
authors.forename: Ke
authors.initials: K
authors.lastname: Lin
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands.
authors.forename: Johan
authors.initials: J
authors.lastname: Bucher
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands.
authors.forename: Ningwen
authors.initials: N
authors.lastname: Zhang
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Yan
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Wang
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Deng
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Yongcui
authors.initials: Y
authors.lastname: Liao
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Keyun
authors.initials: K
authors.lastname: Wei
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Xueming
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Lixia
authors.initials: L
authors.lastname: Fu
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Yunyan
authors.initials: Y
authors.lastname: Hu
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Jisheng
authors.initials: J
authors.lastname: Liu
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Chengcheng
authors.initials: C
authors.lastname: Cai
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Shujiang
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Shifan
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Li
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Jifang
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Ning
authors.initials: N
authors.lastname: Guo
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Zhiyuan
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Jin
authors.initials: J
authors.lastname: Liu
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Sun
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Yuan
authors.initials: Y
authors.lastname: Ma
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Haijiao
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Cui
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, Berkley, California, USA.
authors.forename: Micheal R
authors.initials: MR
authors.lastname: Freeling
authors.affiliation: Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands.
authors.forename: Theo
authors.initials: T
authors.lastname: Borm
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.|Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, the Netherlands.
authors.forename: Guusje
authors.identifier: 0000-0002-2298-6849
authors.initials: G
authors.lastname: Bonnema
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Wu
authors.affiliation: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
authors.forename: Xiaowu
authors.initials: X
authors.lastname: Wang
mesh_terms: D001937:Brassica / Q000235:genetics*; D029741:Brassica rapa / Q000235:genetics*; D018556:Crops, Agricultural / Q000235:genetics; D018744:DNA, Plant; D014644:Genetic Variation; D018745:Genome, Plant; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D018744:DNA, Plant