Grapevine Non-vinifera Genetic Diversity Assessed by Simple Sequence Repeat Markers as a Starting Point for New Rootstock Breeding Programs

Abstract

20Microsatellite markers are valuable tool to facilitate management of germplasm 21 collections and to access the genetic diversity. In this study, the genetic characterization 22 of a large collection of 379 rootstocks and other non-vinifera accessions maintained at 23 the University of Milan (Italy) has been reported. Accessions were genotyped with 22 24 2 highly polymorphic microsatellite markers (including the nine 'international' loci used 25 for grapevine identification, three VMC, three VrZAG and seven VChr loci), but only 26 17 loci were retained for cultivar identification, to investigate genetic diversity, for 27 pedigree analysis, to infer population structure and to design a core collection. Two 28 hundred thirty-two unique genotypes were identified. The allelic profiles of sixty-nine 29 rootstocks were confirmed according to literature and databases, while the profiles of 44 30 rootstocks were proposed for the first time. Pedigree analysis highlighted 77 parent-31 offspring (PO) trios and XX PO relationships, some of them already known and some 32 other new. Analysis of the genetic structure showed a more likely number of three 33 ancestral groups, with a high percentage of admixed samples. A structure based on the 34 genetic background of genotypes was not observed. A core collection of seventy 35 genotypes captured 100% of the entire number (373) of detected alleles. Most of these 36 genotypes were unidentified or poorly characterized genotypes. The information 37 provided in this paper could assist breeders in better addressing their efforts in the 38 exploitation of still unexplored individuals useful for long-term breeding plans. 39 40 population structure, VVMD25 and VVMD32. 42 43 1855), a phytophage that attacks V. vinifera roots, by importing American vines, nearly 47 cultivar identification (Migliaro et al. 2013); iii) the three VrZAG loci are obtained from 132 V. riparia (Sefc et al. 1999); iv) the seven VChr loci are suggested for an easier 133 genotyping in V. vinifera (Cipriani et al. 2008) and not yet tested on non-vinifera 134 varieties. 135 PCR reactions were performed using forward primers labeled with fluorescent dyes (6-136 FAM, PET, VIC, or NED); three multiplex panels of fluorescent-labeled microsatellite 137 loci were used. Simultaneous PCR amplifications were conducted in a final volume of 138 595

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

“…Seventy Vitis ssp. genotypes belonging to a core collection identified in Migliaro et al [19] were genotyped using 18k SNP. The pedigree of 31 genotypes is unknown, and the others are 31 hybrids genotypes and 8 traced to pure Vitis species ( Table 1).…”

“…Recently, the grapevine rootstock collection of the University of Milan (Italy), composed of 379 accessions and including the largest part of the rootstock germplasm currently available worldwide, has been genotyped by SSR (Simple Sequence Repeats) to investigate genetic diversity, infer population structure, analyze pedigrees, and design a core collection. [19]. Molecular analysis identified 232 unique genotypes with a high level of admixture and a narrow genetic background.…”

“…So far, SSR markers were one of the most reliable and robust tool used for the genetic characterization of vinifera and non-vinifera germplasm, widely adopted for their high degree of information provided by the large number of detected alleles per locus [8][9][10][11][12][13][14][15][16][17][18][19][20]. Recently, SNP (Single Nucleotide Polymorphism) markers have rapidly gained high popularity in the scene of V. vinifera molecular genetics [10,[21][22][23][24][25][26].…”

“…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.…”

“…The aim of this study was to validated the Vitis18kSNP genotyping array on non-vinifera germplasm core collection [19], representing the whole genetic diversity of grapevine rootstock collection housed at the University of Milan, and to evaluate the goodness of this new plant material. SNP and SSR profiles have been compared for their usefulness to detect genetic diversity and population structure.…”