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.
Highlights
Vitis vinifera cultivars, the most important economic fruit species in the modern world, is usually grown on rootstocks due to its susceptibility to phylloxera attack, a homopteran insect (Daktulosphaira vitifoliae Fitch) that feeds on the V. vinifera roots [1]
V. riparia and V. ruprestris, two species worldwide used in the breeding programs of grapevine rootstocks for their resistance trait to phylloxera [7], were not included in the panel of species used to identify and select the Single nucleotide polymorphism (SNP) [24], genotypes having in their pedigree the genetic background of these two species were successfully analyzed
The genetic base of available Vitis rootstocks derived from a restricted number of genotypes, selected among North American Vitis species at the end of the XIX century
Summary
The most important economic fruit species in the modern world, is usually grown on rootstocks (a mixture of non-vinifera grapevine species and hybrids) due to its susceptibility to phylloxera attack, a homopteran insect (Daktulosphaira vitifoliae Fitch) that feeds on the V. vinifera roots [1]. Several studies report an effect of rootstocks on limestone tolerance [2,3], nutrients uptake [4], and water stress tolerance [5]. Relevant efforts in grapevine rootstock selection were made on the turn of the 20th century, only a few genotypes found a large spread in vineyards and nowadays more than the 90% of V. vinifera varieties are grown grafted onto less than 10 rootstocks [6], with negative consequences on the tolerance to biotic and abiotic stresses [3] and on genetic diversity.
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