Impacts of reproductive systems on grapevine genome and breeding

Hua Xiao, Yue Wang, Wenwen Liu, Xiaoya Shi, Siyang Huang, Shuo Cao, Qiming Long, Xu Wang, Zhongjie Liu, Xiaodong Xu, Yanling Peng, Pengfei Wang, Zhonghao Jiang, Summaira Riaz, Andrew M. Walker, Brandon S. Gaut, Sanwen Huang and Yongfeng Zhou ()
Additional contact information
Hua Xiao: Chinese Academy of Agricultural Sciences
Yue Wang: Chinese Academy of Agricultural Sciences
Wenwen Liu: Chinese Academy of Agricultural Sciences
Xiaoya Shi: Chinese Academy of Agricultural Sciences
Siyang Huang: Chinese Academy of Agricultural Sciences
Shuo Cao: Chinese Academy of Agricultural Sciences
Qiming Long: Chinese Academy of Agricultural Sciences
Xu Wang: Chinese Academy of Agricultural Sciences
Zhongjie Liu: Chinese Academy of Agricultural Sciences
Xiaodong Xu: Chinese Academy of Agricultural Sciences
Yanling Peng: Chinese Academy of Agricultural Sciences
Pengfei Wang: Shandong Academy of Grape
Zhonghao Jiang: Shenzhen University
Summaira Riaz: San Joaquin Valley Agricultural Center, United States Department of Agriculture
Andrew M. Walker: San Joaquin Valley Agricultural Center, United States Department of Agriculture
Brandon S. Gaut: University of California
Sanwen Huang: Chinese Academy of Agricultural Sciences
Yongfeng Zhou: Chinese Academy of Agricultural Sciences

Nature Communications, 2025, vol. 16, issue 1, 1-15

Abstract: Abstract Diversified reproductive systems can be observed in the plant kingdom and applied in crop breeding; however, their impacts on crop genomic variation and breeding remain unclear. Grapevine (Vitis vinifera L.), a widely planted fruit tree, underwent a shift from dioecism to monoecism during domestication and involves crossing, self-pollination, and clonal propagation for its cultivation. In this study, we discover that the reproductive types, namely, crossing, selfing, and cloning, dramatically impact genomic landscapes and grapevine breeding based on comparative genomic and population genetics of wild grapevine and a complex pedigree of Pinot Noir. The impacts are widely divergent, which show interesting patterns of genomic purging and the Hill-Robertson interference. Selfing reduces genomic heterozygosity, while cloning increases it, resulting in a “double U-shaped” site frequency spectrum (SFS). Crossing and cloning conceal while selfing purges most deleterious and structural burdens. Moreover, the close leakage of large-effect deleterious and structural variations in repulsion phases maintains heterozygous genomic regions in 4.3% of the grapevine genome after successive selfing for nine generations. Our study provides new insights into the genetic basis of clonal propagation and genomic breeding of clonal crops by purging deleterious variants while integrating beneficial variants through various reproductive systems.

Date: 2025
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DOI: 10.1038/s41467-025-56817-7

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