Impacts of reproductive systems on grapevine genome and breeding

Authors: XIAO, HUA - Chinese Academy Of Agricultural Sciences; WANG, YUE - Chinese Academy Of Agricultural Sciences; LIU, WENWEN - Chinese Academy Of Agricultural Sciences; SHI, XIAOYA - Chinese Academy Of Agricultural Sciences; HUANG, SIYANG - Chinese Academy Of Agricultural Sciences; CAO, SHUO - Chinese Academy Of Agricultural Sciences; LONG, QIMING - Chinese Academy Of Agricultural Sciences; WANG, XU - Chinese Academy Of Agricultural Sciences; LIU, ZHONGJIE - Chinese Academy Of Agricultural Sciences; Riaz, Summaira

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/31/2025
Publication Date: 3/3/2025
Citation: Xiao, H., Wang, Y., Liu, W., Shi, X., Huang, S., Cao, S., Long, Q., Wang, X., Liu, Z., Riaz, S., et al. 2025. Impacts of reproductive systems on grapevine genome and breeding. Nature Communications. 16. Article 2031. https://doi.org/10.1038/s41467-025-56817-7.
DOI: https://doi.org/10.1038/s41467-025-56817-7

Interpretive Summary: Comparative genomic and population analysis of grapevine , Vitis vinifera cultivar Pinot Noir, were used to study the impact of different mating systems (i.e., crossing, cloning, and selfing) on the crop genome and breeding. Pinot Noir is one of the oldest wine grape cultivars with accumulated mutations that impact the phenotypic traits due to clonal propagation. For instance, occurrence of three different berry colors is one of the key examples that result in clonal somatic mutations. Results showed that clonal propagation increases genomic heterozygosity, whereas crossing and selfing removes deleterious genetic and structural burden. This information underscores the significance of mating systems in grapevine genomes, which is vital for grapevine breeding.

Technical Abstract: Crossing, cloning, and selfing are the primary plant mating systems, but their effects on crop genomes and breeding remain unclear. We employed grapevine (Vitis vinifera L.) cultivar Pinot Noir genome, along with its clonal, crossing, and selfing populations, and combined comparative genomics and population genetics to investigate the impact of these mating systems on genomic variation. Clonal propagation accumulated specific heterozygous mutations, which is pivotal for shaping the current texture of Pinot Noir, while TE-mediated structural variants profoundly change the phenotypic traits. Cloning increases genomic heterozygosity, while selfing reduces it tremendously. Cloning conceals, whereas crossing and selfing purge deleterious genetic and structural burden. Interestingly, close leakage of deleterious and structural variants in repulsion phases maintain heterozygous genomic regions after successive selfing. Our study underscores the significance of mating systems in crop genomes, vital for grapevine genomic breeding.