Whole-genome re-sequencing, diversity analysis, and stress-resistance analysis of 77 grape rootstock genotypes

Peipei Wang; Fanggui Zhao; Ting Zheng; Zhongjie Liu; Xinglong Ji; Zhichang Zhang; Tariq Pervaiz; Lingfei Shangguan; Jinggui Fang

doi:10.3389/fpls.2023.1102695

Whole-genome re-sequencing, diversity analysis, and stress-resistance analysis of 77 grape rootstock genotypes

Front Plant Sci. 2023 Feb 9:14:1102695. doi: 10.3389/fpls.2023.1102695. eCollection 2023.

Authors

Peipei Wang¹, Fanggui Zhao^{1

2}, Ting Zheng², Zhongjie Liu², Xinglong Ji¹, Zhichang Zhang³, Tariq Pervaiz⁴, Lingfei Shangguan², Jinggui Fang^{1

2}

Affiliations

¹ College of Horticulture, Qingdao Agricultural University, Qingdao, China.
² College of Horticulture, Nanjing Agricultural University, Nanjing, China.
³ Shandong Zhichang Agricultural Science and Technology Development Co. LTD, Rizhao, China.
⁴ Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, United States.

Abstract

Introduction: Grape rootstocks play critical role in the development of the grape industry over the globe for their higher adaptability to various environments, and the evaluation of their genetic diversity among grape genotypes is necessary to the conservation and utility of genotypes.

Methods: To analyze the genetic diversity of grape rootstocks for a better understanding multiple resistance traits, whole-genome re-sequencing of 77 common grape rootstock germplasms was conducted in the present study.

Results: About 645 billion genome sequencing data were generated from the 77 grape rootstocks at an average depth of ~15.5×, based on which the phylogenic clusters were generated and the domestication of grapevine rootstocks was explored. The results indicated that the 77 rootstocks originated from five ancestral components. Through phylogenetic, principal components, and identity-by-descent (IBD) analyses, these 77 grape rootstocks were assembled into ten groups. It is noticed that the wild resources of V. amurensis and V. davidii, originating from China and being generally considered to have stronger resistance against biotic and abiotic stresses, were sub-divided from the other populations. Further analysis indicated that a high level of linkage disequilibrium was found among the 77 rootstock genotypes, and a total of 2,805,889 single nucleotide polymorphisms (SNPs) were excavated, GWAS analysis among the grape rootstocks located 631, 13, 9, 2, 810, and 44 SNP loci that were responsible to resistances to phylloxera, root-knot nematodes, salt, drought, cold and waterlogging traits.

Discussion: This study generated a significant amount of genomic data from grape rootstocks, thus providing a theoretical basis for further research on the resistance mechanism of grape rootstocks and the breeding of resistant varieties. These findings also reveal that China originated V. amurensis and V. davidii could broaden the genetic background of grapevine rootstocks and be important germplasm used in breeding high stress-resistant grapevine rootstocks.

Keywords: genetic diversity; grapevine; resequencing; rootstocks; stress-resistance.

Grants and funding

This work was supported by the High-level Scientific Research Foundation of Qingdao Agricultural University (665/1119002) and the National Key Research and Development Project (2019YFD1000101). The funding agency provided financial support to this study, including experimental implementation, data analysis, and the publication fee.