Multi-parental cross design-based QTL mapping approach elucidates fruit firmness and softening genetic control in European pears (Pyrus communis)

Fruit firmness and softening rate are two key quality parameters defined by the enzymatic disassembly of the polysaccharide architecture of the primary cell wall and middle lamella. Technological control of fruit ripening in pear, while extending shelf-life, can negatively affect general fruit quality. Therefore, genetic improvement of these properties can represent a valuable alternative. Two bi-parental populations were employed to dissect the genetic control of static and dynamic firmness traits, considering fruit firmness assessed at both harvest and after storage, by defining softening and storage index-derived parameters. Integrated QTL analysis was performed through a multi-parental cross design based on a Pedigree Based Analysis approach. This allowed the identification of specific QTL signatures distinguished by an increasing cumulative percentage of variability expressed from the harvest to the post-harvest stage and highlighted the presence of a major QTL on linkage group 3. The QTL intervals were distinguished by the presence of several classes of genes involved in the degradation of the cell wall, such as expansins, polygalacturonases, and pectate lyase. Haploblocks (HBs) derived by single SNPs also elucidated the role of HB-alleles as potential marker tools to assist in breeding programmes aimed at improving fruit firmness and softening, especially during post- harvest.