Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape

Abstract

BackgroundThe economic importance of grapevine has driven significant efforts in genomics to accelerate the exploitation of Vitis resources for development of new cultivars. However, although a large number of clonally propagated accessions are maintained in grape germplasm collections worldwide, their use for crop improvement is limited by the scarcity of information on genetic diversity, population structure and proper phenotypic assessment. The identification of representative and manageable subset of accessions would facilitate access to the diversity available in large collections. A genome-wide germplasm characterization using molecular markers can offer reliable tools for adjusting the quality and representativeness of such core samples.ResultsWe investigated patterns of molecular diversity at 22 common microsatellite loci and 384 single nucleotide polymorphisms (SNPs) in 2273 accessions of domesticated grapevine V. vinifera ssp. sativa, its wild relative V. vinifera ssp. sylvestris, interspecific hybrid cultivars and rootstocks. Despite the large number of putative duplicates and extensive clonal relationships among the accessions, we observed high level of genetic variation. In the total germplasm collection the average genetic diversity, as quantified by the expected heterozygosity, was higher for SSR loci (0.81) than for SNPs (0.34). The analysis of the genetic structure in the grape germplasm collection revealed several levels of stratification. The primary division was between accessions of V. vinifera and non-vinifera, followed by the distinction between wild and domesticated grapevine. Intra-specific subgroups were detected within cultivated grapevine representing different eco-geographic groups. The comparison of a phenological core collection and genetic core collections showed that the latter retained more genetic diversity, while maintaining a similar phenotypic variability.ConclusionsThe comprehensive molecular characterization of our grape germplasm collection contributes to the knowledge about levels and distribution of genetic diversity in the existing resources of Vitis and provides insights into genetic subdivision within the European germplasm. Genotypic and phenotypic information compared in this study may efficiently guide further exploration of this diversity for facilitating its practical use.

GENETIC DIVERSITY AND GENETIC RELATIONSHIP OF SENGON (Falcataria moluccana) REVEALED USING SINGLE NUCLEOTIDE POLYMORPHISM (SNP) MARKERS

“…A population structure and genetic diversity based on 1,537 elite maize inbred lines using 359 SSR and 8,8244 SNP markers found the total gene diversity was 0.69 for the SSRs and half as much (0.32) for the SNPs (Inghelandt et al, 2010). A similar result was found in 2273 accessions of domesticated grapevine analyzed using 22 common SSR and 384 SNP markers, the average genetic diversity was higher for SSR loci (0.81) than for SNPs (0.34) (Emanuelli et al, 2013).…”

Genetic Diversity, Population Structure, Parentage Analysis, and Construction of Core Collections in the French Apple Germplasm Based on SSR Markers

“…Additional phenotypic information was not enough available to help building the core collections despite it can help to optimize further screening and analyses of agronomical traits (Nicolaï et al 2013). In grapevine, Emanuelli et al (2013) compared a phenotypic and a genetic core collection. They showed that the latter retained more genetic diversity while maintaining a similar phenotypic variability.…”

Assessing the Genetic Diversity and Genealogical Reconstruction of Cypress (Cupressus funebris Endl.) Breeding Parents Using SSR Markers

“…The ∆K statistics provided the highest value at K = 2 (∆K = 82.59). As the ad hoc statistic ∆K preferentially detects the uppermost level of structure [47,48], K = 2 was considered as the starting point for the first ground clustering in all 343 individuals. Structure analysis identified two subgroups among the breeding parents.…”