Tropical fruits in Asia - diversity, maintenance, conservation and use

This study describes novel simple sequence repeat (SSR) primers designed from a genomic DNA sequence of 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 phylloxera strains chosen for behavioral and geographic diversity. Eighty-nine 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 to validate markers. SSR data from these samples also was used to determine frequency of null alleles, locus specific estimates of population differentiation, and genotype 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 alleles 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 origin of host specific strains in grape phylloxera