Development and characterization of a large set of microsatellite markers for grape phylloxera (Daktulosphaira vitifoliae Fitch)

This study describes novel simple sequence repeat (SSR) primers from a genomic DNA sequence of the grape phylloxera. A total of 130 SSR primers were designed from 145 unique sequences with di, tri, tetra and penta simple sequence repeats. The SSR primers were tested on DNA from 10 grape phylloxera strains chosen for their behavioral and geographic diversity. Eightynine primers generated easy to score alleles with standardized conditions of amplification. Twenty-eight new and four previously published markers were selected to genotype 32 root and leaf phylloxera samples in order to identify reliable markers for future genetic diversity and phylloxera population studies. SSR data from these samples was also used to determine the frequency of null alleles, and locus specific estimates of population differentiation and clustering. Up to six alleles were detected with a mean expected heterozygosity (He) of 0.51. The observed heterozygosity (Ho) was 0.73 and the majority of markers had higher Ho values. Null allees for four markers were considered to be the result of homozygous genotypes. The 89 SSR loci developed in this study represent a new and informative set of markers that are easy to combine for multi-loading and suitable for large-scale genetic analyses of population structure, genetic diversity, and the origin of host specific strains in grape phylloxera.