Genetic mapping and haploblock characterization of two novel major dwarfing loci in reciprocal Pyrus rootstock seedling families

US pear production is constrained by the lack of dwarfing and precocious rootstocks that revolutionized other fruit crops, such as apple. While quince is used as a rootstock in global pear production, concerns about potential graft incompatibility and lack of cold hardiness limit its adoption in the US. This work was aimed at identifying genetic determinants of dwarfing in Pyrus backgrounds to inform future breeding for dwarfing Pyrus rootstocks. In 2018, 145 rootstock seedlings of two reciprocal crosses were budded with a standard scion variety. Rootstock seedlings were also genotyped with the 70 K Pyrus SNP array. Based on two-year orchard architectural phenotypes, quantitative trait loci (QTLs) were consistently mapped on both chromosomes 5 and 15 for dwarfing traits, namely scion trunk cross-sectional area (TCA), total scion annual growth, and central leader annual growth. QTLs for rootstock TCA were also detected on both chromosomes 5 and 15; however, the chromosome 15 QTL did not co-localize with the scion trait locus. Each dwarfing haplotype accounted for 30% to 50% reduction in vigor (p < 0.05). Combined haplotype analysis showed that one dwarfing locus was sufficient to significantly reduce vigor. Presence of two dwarfing haplotypes further reduced vigor by a total of 50% to 70% (p < 0.05), but their combinatory effects were not purely additive due to epistasis. Discovery of these novel dwarfing loci (named P×Dwg1 and P×Dwg2) in Pyrus facilitates future DNA test development to enable informed parental and seedling selection for dwarfing potential.