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

The native, perennial shrub American hazelnut (Corylus americana) is cultivated in the Midwestern U.S. 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 (C. avellana) and American hazelnuts. Two populations of hazelnuts, one composed of C. americana and one composed of C. americana x C. avellana hybrids, were phenotyped over the course of two years in two locations using a digital imagery-based method for quantifying morphological nut and kernel traits. This data was used to perform composite interval mapping (CIM) using a recently released genetic map, and genomic prediction using a newly-available chromosome-scale reference genome for C. americana. Multiple QTL were detected for all traits analyzed, with an average total R2 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. Core ideasO_LIMorphological nut characteristics are under polygenic control in American and American- European interspecific hazelnuts. C_LIO_LIBest linear unbiased predictors allow for accurate prediction of morphological nut characteristics. C_LIO_LIMarker density and training population design must be tailored to the sample population for which predictions are being made. C_LI