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

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.

Figure 1

Phylogenetic analysis of 77 rootstocks samples. (A) Neighbor-joining (NJ) phylogenetic tree of grapevine accessions inferred from the whole-genome SNPs with 100 nonparametric bootstraps. (B) Five populations of 77 rootstock samples belonging to 10 groups.

Figure 2

PCA plots of the first three components of 77 grape rootstocks using whole-genome SNP data.

Figure 3

First-degree relationship network of 74 rootstock accessions. A dashed line represents an identity-by-descent (IBD) value between 0.45 and 0.50 ( Figure S2 ). A solid line represents an IBD value equal to or greater than 0.50. The thickness of the line is proportional to the calculated IBD value.

Figure 4

Decay of linkage disequilibrium of the rootstocks of different grape varieties. The abscissa represents the distance of linkage disequilibrium (LD), and the ordinate is the correlation coefficient of linkage disequilibrium.

Figure 5

Selective sweep regions and gene enrichment analysis of major groups. (A) group3 vs. group4; (B) group4 vs. group6; (C) group2 vs. group5; and (D) group5 vs. group6. Each group includes the Fst distribution map (X-axis represents different chromosomes, Y-axis represents the Fst value in the corresponding chromosome window, and the dotted line represents the selection threshold top 5%); overlap number (X-axis represents different chromosomes, and Y-axis represents the number of corresponding overlaps); and GO term and KEGG pathway enrichment of the candidate selective sweep genes. The size of the bubble represents the number of genes in the corresponding GO category. The color of the bubble shows the corresponding P-value. Rich factor shows the percentage of enriched genes out of the total number in the GO category.

Figure 6

Selection elimination and gene enrichment analysis of the Chinese population and other groups. (A) Overlap Number (the x-axis represents different chromosomes, and the y-axis represents the number of corresponding overlaps). (B, C) group9 vs group2, group9 vs group5, Fst distribution map of eight groups (the x-axis represents different chromosomes, the y-axis represents the Fst value in the corresponding chromosome window, and the dotted line represents the selection threshold top 5%); and GO term and KEGG pathway enrichment of the candidate selective sweep genes (the size of the bubble represents the number of genes in the corresponding GO category, the color of the bubble shows the corresponding P-value, and the rich factor shows the percentage of enriched genes out of the total number in the GO category).

Figure 7

Comparison of the results of the association analysis of six resistance traits. Comparison of the number of associated SNPs and genes; QQ-plot based on the MLM model shows the distribution of actual P-values and the expected P-values of the non-relevant null hypothesis.

Figure 8

Genome-wide association analysis of six resistance traits. (A) The distribution of the P-values of the whole genome on the chromosome. The genetic marker effect value is the P-value of the whole genome after the F-test is sorted according to the physical location on the chromosome. The X-axis represents the genome coordinates, and the Y-axis represents log₁₀P. The smaller the P-value, the stronger the correlation, which is expressed as a larger ordinate. (B) The distribution of the located genes on the chromosomes, P: phylloxera, R: root-knot nematode, S: salt, D, drought, C: cold, W: waterlogging.