Assessment of two highly polymorphic microsatellite loci in 103 accessions of Vitis species

Abstract

We assessed the discriminative power of two nuclear microsatellite (nSSR, nuclear simple sequence repeated) loci, ssrVvUCH12 and ssrVvUCH29, which had been suspected to be highly polymorphic and to display specific alleles in the frame of a previous characterization work. As more genotyping of more plant material at a higher number of nSSR loci was needed for an extensive comparison, one hundred and three accessions of Vitis vinifera, other Vitis species, and 3 related genera were submitted to microsatellite profiling at fourteen nuclear nSSR loci, including ssrVvUCH12 and vsrVvUCH29. The loci ssrVvUCH12 and ssrVvUCH29 loci displayed each 30 alleles found in 103 accessions while the most polymorphic loci among the 12 other nSSR loci tested, were ssrVrZAG93 and VMc8a7, which displayed 31 and 23 alleles respectively. These 2 last loci had however the disadvantage to display a three banded pattern in some individuals, probably due to chimerism. Most interestingly average similarity found in this pool of 103 accessions was also lower with the combination ssrVvUCH12-ssrVvUCH29 than with the combination ssrVrZAG-VMC8a7, while observed heterozygocity was higher with the combination ssrVvUCH12-ssrVvUCH29. Comparisons were made easily visible under the form of UPGMA phenograms for each combination of loci and plant sets and the most resolutive combination was always the combination ssrVvUCH12- ssrVvUCH29.

At last, numerous specific alleles were found for rootstocks and Vitis species at loci ssrVvUCH12 and ssrVvUCH29, while the other combination did not show many specific alleles. These features allow to think that this 2-loci combination could be considered for managing collections of Vitis species in addition of previously evaluated highly polymorphic microsatellite markers. It could also be useful as a quality control tool for rootstock material in nurseries or trade.