A fascinating region of the apple genome is the proximal third of chromosome 16. Features detected in breeding germplasm using resources generated by the RosBREED project include a hotspot for heterozygosity, a hotspot for recombination, an introgressed segment from an enigmatic crab apple source, and a hotspot for QTLs covering all major categories of fruit quality: flavor via acidity and sweetness, texture via firmness and crispness, appearance via fruit size and bitter pit incidence, and even nutritional composition via phenolics content! The region was genetically dissected into several haplotype blocks (“haploblocks”). Focusing on U.S. apple breeding germplasm, breeding utility was assigned to each haploblock. Breeding utility was primarily characterized by effects on trait levels and the relative economic value of trait levels differentiated and the allele frequencies and sources in breeding germplasm. Often, alleles associated with desirable levels of one trait are linked in repulsion phase with those of another trait (e.g., acidity and phenolics; crispness and bitter pit incidence). However, most such linkages can be broken. Ideally, breeding parents contain the most valuable haploblocks in coupling phase and in homozygosity for use in efficiently enriching subsequent breeding families with alleles for superior performance in multiple traits. The best haploblock combinations identified within rare individuals of RosBREED’s reference U.S. germplasm represent valuable parents for imparting superior genetic potential. As collaborative research efforts rapidly accumulate DNA information across the genome for apple and related rosaceous crops, useful genetic stocks can be developed by targeted haploblock assembly into desired configurations.
