Combining genome-wide association analyses and QTL detection to identify loci controlling phenology-related and fruit quality traits in sweet cherry

In perennial fruit species, phenology and fruit quality traits are highly dependent on environmental conditions. In the context of climate change, a rise of fall and winter temperatures leads to a slowing down of the dormancy release which may result in a dramatic decrease of the production. Also, a rise of spring temperatures induces a significant advance of blooming date, increasing risks of damages by the frost. Moreover, the higher frequency of spring rainy periods has serious consequences for fruit quality, particularly on fruit cracking. The objective of our study is to identify the genetic determinism of the cherry tree response to the climate change. Several F1 sweet cherry progenies and a germplasm collection were evaluated for phenological traits and fruit quality. One of the mapping progenies, Regina × Lapins, was evaluated in five sites in order to study the genotype × environment interactions. The progenies were genotyped with the SNP RosBREED arrays and the collection using a genotyping-by-sequencing (GBS) approach. QTL detection and GWAS were performed allowing the identification of the genomic regions associated with the phenological and the fruit quality traits. The comparison of the genomic regions identified by the two analyses was achieved. For both datasets, we revealed that a genomic region at the end of Chromosome 1 controls both flowering and chilling requirements in sweet cherry, consistent with the observed strong phenotypical correlation between these traits. For the first time, marker-trait associations on several chromosomes were found for traits related to sweet cherry fruit quality.