Composite interval mapping and genomic prediction of nut quality traits in American and American–European interspecific hybrid hazelnuts

Abstract The native, perennial shrub American hazelnut ( Corylus americana ) is cultivated in the US Midwest for its significant ecological benefits, as well as its high‐value nut crop. Genetic improvement of perennial crops involves long‐term breeding efforts, and benefits from the use of genetic data in selection to reduce breeding cycle time. In addition, high‐throughput phenotyping methods are essential to the efficient and accurate screening of large breeding populations. This study reports novel advances in both of these domains, for American ( C. americana ) and interspecific hybrids between European ( Corylus avellana ) and American hazelnuts. Two populations of hazelnuts, one composed of C. americana and one composed of C. americana × C. avellana hybrids, were phenotyped over the course of 2 years in two locations using a digital imagery‐based method for quantifying morphological nut and kernel traits. These data were used to perform composite interval mapping using a recently released genetic map, and genomic prediction using a newly available chromosome‐scale reference genome for C. americana . Multiple quantitative trait loci were detected for all traits analyzed, with an average total R 2 of 52%. Genomic prediction exhibited high accuracy, with an average correlation coefficient between genotypic values and phenotypic observations of 0.78 across both environments. These results suggest that incorporating genetic data in selection is a tenable method for improving genetic gain for highly polygenic traits in hazelnut breeding programs.