Restriction site-associated DNA sequencing reveals the molecular genetic diversity of grapevine and genes related to white rot disease

Abstract Grapevine (Vitis spp.) is an important crop worldwide, but its growth, fruit quality, and yield are frequently reduced by pathogens. Admixture of resistance genes is an effective method to breed new varieties. Wild grapevine populations are very important subjects for grapevine research, given their germplasmic resistance to various diseases, especially white rot disease caused by Coniella diplodiella. However, molecular and sequencing research is still required to fully understand the relationships among Vitis spp., particularly among Chinese Vitis species. We analyzed 88,877 single nucleotide polymorphisms (SNPs) from 386 grapevine genotypes through restriction site-associated DNA sequencing. Overall, Chinese Vitis spp. had considerably less linkage disequilibrium and exhibited stronger resistance to white rot disease than their European congeners. Association analysis revealed six SNPs associated with eight candidate genes linked to white rot resistance that were up-regulated by the pathogen. In resistant Vitis spp., genes XM_002272404.2 (WAT1-related protein At3g30340-like), XM_002278827.2 (receptor-like protein kinase HSL1), XM_002281911.3 (ethylene-responsive transcription factor ERF105-like), XM_002281568.4 (leucine rich repeat receptor-like serine/threonine-protein kinase At1g74360-like), and XM_003634259.2 (zinc finger RNA-binding protein) were more up-regulated by the pathogen than in susceptible Vitis species. The present results clarify the genetic basis of the geographical distribution, classification, and resistance traits of Chinese Vitis spp., thereby contributing to the use of wild Chinese Vitis spp. in breeding.