Region-wide association analysis and high-throughput resequencing strategies in peach to develop molecular markers for flat fruit marker-assisted selection

Commercial interest in flat-fruit peaches is increasing. Many genetic studies have aimed to unravel the genetic basis of fruit shape, especially in model species. However, no candidate genes have been reported to date for peach. This trait in peach is determined by a single dominant gene S mapped on chromosome 6. The allele conferring the flat appearance is partly dominant: s/s fruits are round and S/s flat, while S/S fruits abort a few weeks after anthesis. Several markers have been identified around the S locus through the analysis of mapping populations and germplasm, and one of them works efficiently in marker-assisted selection (MAS). By conducting an association analysis of the flat shape candidate region and by resequencing five flat and five round peach cultivars, we have identified size polymorphisms as well as single nucleotide polymorphisms (SNPs) that co-segregate with the trait. These polymorphisms affect coding regions of an LRR-RL kinase. Associated polymorphisms have been evaluated in a panel of peach commercial cultivars (including flat and round fruits) demonstrating their efficiency for MAS.