Improving selection efficiency in C. americana × C. avellana interspecific hybrids through the development of an indel-based genetic map

This study reports a genetic map created using a progeny family from the interspecific hazelnut cross Corylus avellana × Corylus americana. This research represents a critical step in the development of genomic tools that enable the deployment of next-generation sequencing methods in the breeding of hazelnut, specifically the improvement of well-adapted Midwestern hazelnut cultivars. To produce this map, we first developed high-density molecular markers using short-read Illumina sequencing of genotype-by-sequencing libraries. By aligning reads to a newly assembled reference genome for C. americana, we were able to identify over 75,000 high-quality indel polymorphisms across the F1 experimental population. These markers exhibited both high allele depth coverage, and low linkage disequilibrium, making them well-suited to genetic map development. We constructed such a map using 95 individuals from a single F1 family, demonstrating the utility of next-generation sequencing to efficiently and accurately generate high-density genetic maps. This research will improve the efficiency of breeding efforts through the validation of specific molecular markers that are associated with agronomically-relevant traits in breeding populations of interest.