Genotyping-by-sequencing of pear (Pyrus spp.) accessions unravels novel patterns of genetic diversity and selection footprints

Understanding of genetic diversity and marker-trait relationships in pears ( Pyrus spp.) forms an important part of gene conservation and cultivar breeding. Accessions of Asian and European pear species, and interspecific hybrids were planted in a common garden experiment. Genotyping-by-sequencing (GBS) was used to genotype 214 accessions, which were also phenotyped for fruit quality traits. A combination of selection scans and association analyses were used to identify signatures of selection. Patterns of genetic diversity, population structure and introgression were also investigated. About 15 000 high-quality SNP markers were identified from the GBS data, of which 25% and 11% harboured private alleles for European and Asian species, respectively. Bayesian clustering analysis suggested negligible gene flow, resulting in highly significant population differentiation (F st =0.45) between Asian and European pears. Interspecific hybrids displayed an average of 55% and 45% introgression from their Asian and European ancestors, respectively. Phenotypic (firmness, acidity, shape and so on) variation between accessions was significantly associated with genetic differentiation. Allele frequencies at large-effect SNP loci were significantly different between genetic groups, suggesting footprints of directional selection. Selection scan analyses identified over 20 outlier SNP loci with substantial statistical support, likely to be subject to directional selection or closely linked to loci under selection. Crop breeding: Probing pear diversity Researchers have characterized the genetic differences between European and Asian varieties of pears. Satish Kumar and colleagues at the New Zealand Institute for Plant and Food Research used a high-throughput sequencing technique to genotype more than 200 varieties in the Institute’s collection. Studies using a small number of genetic markers had already shown that European and Asian varieties are genetically distinct, but analysis of the entire pear genome revealed a larger gap than reported previously. Combining the genomic data with characterization of the fruit identified several genomic regions that are linked to desirable traits. However, genetic variation accounted for only a small fraction of the variation in fruit characteristics, which suggests a complex link between genotype and phenotype. These findings clarify the history of European and Asian pears and have implications for breeding efforts.