Identification of full-sibling families from natural single-tree ash progenies based on SSR markers and genome-wide SNPs

Abstract

Common ash, Fraxinus excelsior, is threatened by the invasive pathogen Hymenoscyphus fraxineus, which causes ash dieback. The pathogen is rapidly spreading throughout Europe with severe ecological and economic consequences. Multiple studies have presented evidence for the existence of a small fraction of genotypes with low susceptibility. Such genotypes can be targets for natural and artificial selection to conserve F. excelsior and associated ecosystems. To resolve the genetic architecture of variation in susceptibility it is necessary to analyze segregating populations. Here we employed about 1,000 individuals of each of four single-tree progenies from potentially tolerant mother trees to identify full-sibling (full-sib) families. To this end, we first genotyped all 4,000 individuals and the four mothers with eight SSR markers. We then used the program Colony to predict full-sibs without knowledge of the paternal genotypes. For each single-tree progeny, Colony predicted dozens of full-sib families, ranging from 3-165 individuals. In a next step, 910 individuals assigned to full-sib families with more than 30 individuals were subjected to high-resolution genotyping using over one million genome-wide SNPs which were identified with Illumina low-coverage resequencing. Using these SNP genotyping data in principal component analyses we were able to assign individuals to full-sib families with high confidence. Together the analyses revealed five large families with 80-212 individuals. These can be used to generate genetic linkage maps and to perform quantitative trait locus analyses for ash dieback susceptibility or other traits to H. fraxineus or other traits. The elucidation of the genetic basis of natural variation in ash may support breeding and conservation efforts and may contribute to more robust forest ecosystems.