Large-scale gene expression alterations introduced by structural variation drive morphotype diversification in Brassica oleracea

Xing Li; Yong Wang; Chengcheng Cai; Jialei Ji; Fengqing Han; Lei Zhang; Shumin Chen; Lingkui Zhang; Yinqing Yang; Qi Tang; Johan Bucher; Xuelin Wang; Limei Yang; Mu Zhuang; Kang Zhang; Honghao Lv; Guusje Bonnema; Yangyong Zhang; Feng Cheng

doi:10.1038/s41588-024-01655-4

Large-scale gene expression alterations introduced by structural variation drive morphotype diversification in Brassica oleracea

Xing Li(Institute of Vegetables and Flowers), Yong Wang(Institute of Vegetables and Flowers), Chengcheng Cai(Institute of Vegetables and Flowers), Jialei Ji(Institute of Vegetables and Flowers), Fengqing Han(Institute of Vegetables and Flowers), Lei Zhang(Institute of Vegetables and Flowers), Shumin Chen(Institute of Vegetables and Flowers), Lingkui Zhang(Institute of Vegetables and Flowers), Yinqing Yang(Institute of Vegetables and Flowers), Qi Tang(Institute of Vegetables and Flowers), Johan Bucher(Wageningen University & Research), Xuelin Wang(Institute of Vegetables and Flowers), Limei Yang(Institute of Vegetables and Flowers), Mu Zhuang(Institute of Vegetables and Flowers), Kang Zhang(Institute of Vegetables and Flowers), Honghao Lv(Institute of Vegetables and Flowers), Guusje Bonnema(Graduate School Experimental Plant Sciences), Yangyong Zhang(Institute of Vegetables and Flowers), Feng Cheng(Institute of Vegetables and Flowers)

Nature Genetics

February 13, 2024

10.1038/s41588-024-01655-4

Cited by 87Open Access

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Abstract

Brassica oleracea, globally cultivated for its vegetable crops, consists of very diverse morphotypes, characterized by specialized enlarged organs as harvested products. This makes B. oleracea an ideal model for studying rapid evolution and domestication. We constructed a B. oleracea pan-genome from 27 high-quality genomes representing all morphotypes and their wild relatives. We identified structural variations (SVs) among these genomes and characterized these in 704 B. oleracea accessions using graph-based genome tools. We show that SVs exert bidirectional effects on the expression of numerous genes, either suppressing through DNA methylation or promoting probably by harboring transcription factor-binding elements. The following examples illustrate the role of SVs modulating gene expression: SVs promoting BoPNY and suppressing BoCKX3 in cauliflower/broccoli, suppressing BoKAN1 and BoACS4 in cabbage and promoting BoMYBtf in ornamental kale. These results provide solid evidence for the role of SVs as dosage regulators of gene expression, driving B. oleracea domestication and diversification.

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