Isolation of (AC)n-microsatellites in Vitis vinifera L. and analysis of genetic background in grapevines under marker assisted selection

Abstract

Primers were developed for 118 microsatellites isolated from grape (Vitis vinifera) genomic libraries enriched for (AC)n repeats. Only one microsatellite sequence matched other grape SSR-sequences in the GeneBank database. Genotyping was carried out in the parental lines and four offspring of two pseudo-test-cross populations, ‘Cabernet Sauvignon’ x ‘Seyval’ and ‘Chardonnay’ x ‘Bianca’, and a further six other grape genotypes (V. vinifera ‘Sultanina’, ‘Merlot’, ‘Syrah’, ‘Muller-Thurgau’, Vitis ‘Regent’ and V. riparia ‘Gloire de Montpellier’). A total of 108 microsatellites showed easily scorable alleles and 100 of them segregated according to a configuration suitable for mapping in either cross. A further 8 SSRs, although unsuitable for mapping in those crosses, showed polymorphism in the other genotypes tested. This set of markers was used, along with 75 microsatellites of other repeat-types, to fingerprint 46 offspring of the cross ‘Chardonnay’ x ‘Bianca’. For each full-sib, individual heterozygosity and distance in repeat units between pairs of alleles at each locus (mean d2) were calculated as a tool for predicting ‘highly outbred’ recombinant individuals. Six microsatellites with segregation ratios significantly distorted towards the lack of homozygous sibs were identified and mapped to linkage groups LG 3 and LG 5. Estimation of heterozygosity at genome-wide level and genotyping at loci for which homozygous sibs are discriminated against are discussed for marker-assisted background selection in outcrossing grapevines.