Single nucleotide polymorphism profiles reveal an admixture genetic structure of grapevine germplasm from Calabria, Italy, uncovering its key role for the diversification of cultivars in the Mediterranean Basin

Abstract

Background and Aims: Grapevine (Vitis vinifera L.) is one of the earliest domesticated crops, dating back 6000 years ago in the Near East before spreading into Europe. Despite the abundance of historical, archaeological and genetic records, until now secondary domestication events in European regions are not well demonstrated. Here, a genetic characterisation of grape germplasm from Calabria in Southern Italy, a crucial area of the Mediterranean Basin, aims to validate this area as a secondary centre of crop domestication. Methods and Results: True-to-type cultivar classification of 72 accessions was carried out by using microsatellite loci (simple sequence repeat) along with the main Organisation Internationale de la Vigne et du Vin ampelographic descriptors. The classification highlighted a high level of genetic diversity (H e = 0.83) among native cultivars from Calabria. A decay of genetic diversity moving from southern Italy to north-western Mediterranean regions was observed, probably because of repeated founder effects during the grapevine expansion from the Mediterranean Basin to Europe. Single nucleotide polymorphism analysis showed an admixture genetic structure at K = 7, clarifying a complex network of pedigree relationships generated by crosses among cultivars. Parentage analysis underlined a high proportion of parent-offspring relationships (76%) in Mantonico Bianco and Pecorello, hypothesising their key role in the pedigree of many native cultivars from the southern Mediterranean area. Conclusion: Overall, our results appear to indicate a pivotal role of cultivars from Calabria in the grape genetic diversity of southern Italy. Furthermore, genetic analysis of grape wild accessions from Calabria should be of value in a discussion of a secondary centre of grape domestication. Significance of the Study: A large grape collection from Calabria was for the first time characterised through ampelographic and genetic analysis.

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

“…In this work, the array was validated on 70 genotypes of a grapevine rootstock core collection, obtaining a final dataset of 14,180 SNP loci. This number of SNP loci was in line with the ones reported for V. vinifera germplasm, ranging from 10,041 to 16,501 SNPs [23,24,26,31,[33][34][35], resulting in an informative tool for grapevine rootstock genetic characterization. Among the core collection genotypes with a known pedigree [19], the species mostly represented are V. riparia (29 genotypes), V. berlandieri (16), V. rupestris (11), and V. vinifera (10).…”

“…SNPs are widely used to genotype crops [57][58][59][60][61] and are markers of choice for QTL and GWAS [24,29,30,[62][63][64] due to their number, distribution, and density along the genome. In V. vinifera, the genotyping SNP array has been used successfully to investigate the genetic diversity of grapevine, to discriminate among the wild and cultivated compartments, to infer population structure, and to reconstruct the pedigree of cultivars [23,24,26,31,[33][34][35]. Its attractiveness is due to a number of advantages, such as their high reproducibility among the laboratories, transferability, throughput, automatization, and inexpensiveness.…”

“…In this project, a total of 18,071 SNPs were selected, a third of which (4510 SNPs) identified in the Northern American species genome [24]. Several studies validated the 18k SNP set for the evaluation of genetic diversity in V. vinifera [19,23,24,26,[31][32][33][34], but the Vitis18kSNP array could also represent a potentially effective tool for rootstock characterization, due to the consistent number of SNPs detected in the Northern American species genome.…”

A transcriptomic variation map provides insights into the genetic basis of Pinus massoniana Lamb. evolution and the association with oleoresin yield

“…Taking advantage of next generation sequencing (NGS) technologies, millions of SNPs for crops can be rapidly developed at low cost [9]. These high-throughput SNPs have been successfully used to evaluate genetic diversity and to deduce population structure [15,16] and kinships [17]. As an important forest tree in southern China, a high-density SNP map is essential for genetic innovation and improving the traits of masson pine in future breeding programs.…”

A Transcriptomic Variation Map Provides Insights into The Genetic Basis of Pinus massoniana Evolution and Association of Oleoresin Yield

“…Taking advantage of next generation sequencing (NGS) technologies, we could rapidly develop millions of SNPs for crops with low cost [9]. The high-throughput SNPs have been successfully used to evaluate genetic diversity, to infer population structure [15,16] and kinships [17]. As an important forest tree in South China, high density SNPs map is essential for genetic innovation and traits improvements in masson pine's future breeding.…”