Using genotyping-by-sequencing derived SNPs to examine the genetic structure and identify a core set of Corylus americana germplasm

Abstract

The American hazelnut (Corylus americana) is native to a broad range of the eastern United States and southern Canada. It is the endemic host of the fungus Anisogramma anomala, which causes eastern filbert blight (EFB) disease and limits European hazelnut (C. avellana) production in eastern North America. While C. americana has thick-shelled, tiny nuts not suited for commercial production, it is cold hardy, highly tolerant of EFB, and phenotypically diverse. Previous studies with simple sequence repeat markers show that it is also genetically diverse. Further, the species is cross-compatible with C. avellana and is thus a valuable donor of EFB resistance and climate adaptability traits. However, only a narrow set of C. americana parents has been used in interspecific hybridizations, and current germplasm availability likely does not fully represent the species’ genetic diversity, given its vast range. A new collection of open-pollinated C. americana seed was assembled at Rutgers University to broaden available genetic resources. Here, we study the genetic diversity and population structure of 272 of these individuals, which represent 55 seedlots from across 15 states of the species’ native range. We use multivariate analyses to examine the distribution of genetic variation within the collection and to support the identification of a core set. A genotyping-by-sequencing (GBS) approach yielded 2653 single nucleotide polymorphisms and subsequent analyses revealed a collection with high estimates of heterozygosity (HE = 0.276, HO = 0.280), moderate differentiation (FST = 0.108) and low inbreeding (FIS = −0.136). Bayesian model-based and neighbor-joining (NJ) clustering corroborate an uppermost grouping of K = 3, with the NJ dendrogram depicting many small subgroups equally distant from common ancestry. Discriminant analysis of principal components (DAPC) reveals between-subgroup variation (K = 15) within the NJ dendrogram and allows the identification of 19 consensus subgroups. In general, our results support the assembly of a genetically diverse collection where a majority of the variation is explained at the genotype and subgroup levels, which aligns with previous studies of C. americana. Fifty-one accessions were identified that represent 95% of the observed allelic variation. These genotypes are suggested for inclusion in a core collection, which, when coupled to concurrent phenotypic evaluations, will aid in genetic resource assembly that preserves unique phenotypes and retains genetic variation.