New sweet cherry genomic tools and their use in marker-assisted breeding

Thanks to the new sequencing technologies, a vast amount of genomic data such as genome sequences, high density genetic maps and transcriptomic data, have become available for genetic studies in sweet cherries. Using all these resources, it is possible to detect QTLs covering a very small chromosomic region and to find molecular markers tightly linked to traits of interest. Moreover, based on fine mapping and RNASeq analyses, candidate genes can be easily identified with a higher accuracy. Hence, marker-assisted breeding (MAB) has now become a reality for this species. Given that sweet cherry has a long period of juvenility and that large areas are needed to evaluate thousands of new hybrids, MAB will allow breeders to increase the efficiency of their programs and plant only those hybrids with favorable allelic combinations for the most critical agronomic traits. The main goal of our team is to understand sweet cherry adaptive responses to climate change in order to create sweet cherry cultivars well adapted to the global warming, with a good yield and good fruit quality. We focus on complex traits such as chilling and heat requirements for flowering as well as fruit weight, firmness and additional fruit quality traits in order to meet farmer's needs. In this study, we will present the new 'Regina' genome sequence using a combination of sequencing strategies (PacBio RSII sequencing and BioNano optical mapping). The efficiency of the two genotyping technologies, 15K SNP arrays and genotyping by sequencing (GBS) will be compared for the construction of high density linkage maps. Moreover, new prospects offered by genomic selection approaches, aiming at selecting hybrids for difficult and expensive traits to phenotype, will be presented. These genomics tools will considerably decrease the cost and the duration of our sweet cherry breeding program