Genetic Diversity and Population Structure in a Vitis spp. Core Collection Investigated by SNP Markers

Abstract

Single nucleotide polymorphism (SNP) genotyping arrays are powerful tools to measure the level of genetic polymorphism within a population. The coming of next-generation sequencing technologies led to identifying thousands and millions of SNP loci useful in assessing the genetic diversity. The Vitis genotyping array, containing 18k SNP loci, has been developed and used to detect genetic diversity of Vitis vinifera germplasm. So far, this array was not validated on non-vinifera genotypes used as grapevine rootstocks. In this work, a core collection of 70 grapevine rootstocks, composed of individuals belonging to Vitis species not commonly used in the breeding programs, was genotyped using the 18k SNP genotyping array. SNP results were compared to the established SSR (Simple Sequence Repeat) markers in terms of heterozygosity and genetic structure of the core collection. Genotyping array has proved to be a valuable tool for genotyping of grapevine rootstocks, with more than 90% of SNPs successfully amplified. Structure analysis detected a high degree of admixed genotypes, supported by the complex genetic background of non-vinifera germplasm. Moreover, SNPs clearly differentiated non-vinifera and vinifera germplasm. These results represent a first step in studying the genetic diversity of non-conventional breeding material that will be used to select rootstocks with high tolerance to limiting environmental conditions.

DNA-based genealogy reconstruction of Nebbiolo, Barbera and other ancient grapevine cultivars from northwestern Italy

“… 29 – 31 . Their use is increasing, taking advantage of automated processing, high repeatability, and the richness of information they provide, depending on the number of SNPs scored 14 , 16 , 22 , 32 , 33 .…”

Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops

“…Following several updates of the genome sequence and creation of the GrapeReSeq consortium, an 18K SNP array was presented for cultivar identification, parental and population structure clarification, genetic diversity assessment, and applicability for GWAS [ 25 ]. The 18K SNP array has been used in many instances; analysis of 279 accessions in the French germplasm repository demonstrated the suitability for identification of associations with highly precise phenotyping data [ 94 ], while analysis of a core collection of rootstock accessions (including different Vitis species and interspecific hybrids) demonstrated great marker transferability [ 95 ]. Analysis of 150 wild V. vinifera subsp.…”

Genome-wide DNA Variants Identify Genetic Diversity and Population Structure of Leptosphaeria maculans in Western Canada

“…The remaining 158 isolates showed breadth of coverage of >80% (S Fig. 2 A), and ve SCs (SC 27,28,33,34,36) had lower breadth of coverage ranging from 49.6 to 73.8% (S Fig. 2 B).…”

“…Initially, the popular Bayesian-based STRUCTURE software was tested for population structure analysis; it imposed tremendous computational burden due to the large number of variants involved, making implementation extremely ine cient. Landscape and ecological association (LEA), an R package [22], was used to perform STRUCTURE-like analysis and estimate admixture coe cients e ciently with improved algorithms [21,34]. LEA was run rst to establish a curve of cross-entropy versus number of ancestral populations, the optimal number K=3 indicated three ancestral populations in western Canada (Fig.…”