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

ABSTRACT 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 ideas Morphological nut characteristics are under polygenic control in American and American- European interspecific hazelnuts. Best linear unbiased predictors allow for accurate prediction of morphological nut characteristics. Marker density and training population design must be tailored to the sample population for which predictions are being made. Competing Interest Statement The authors have declared no competing interest. Footnotes Minor edits received from reviewers & edits to text size in figures made during review of proofs. Abbreviations - EFB - Eastern Filbert Blight, Anisogramma anomala - UMHDI - Upper Midwest Hazelnut Development Initiative - Eric\Jeff - Eric4-21 x Jefferson - Gibs\OSU - Gibs5-15 x OSU-919-031 - Gibs\York - Gibs5-15 x York - LD - linkage disequilibrium - RSS - residual sums of squares - BLUPs - best linear unbiased predictors - BLUEs - best linear unbiased estimators - PVE - percent variance explained - Stagewise- r2 - mean r2 returned by StageWise - Pearson-r2 - correlation coefficients between the predicted genotypic values and BLUEs for each genotype calculated on the basis of the observed phenotypes - QTL - quantitative trait loci - LG - linkage group - SNP - single nucleotide polymorphism