Construction and comparative analyses of highly dense linkage maps of two sweet cherry intra-specific progenies of commercial cultivars

Despite the agronomical importance and high synteny with other Prunus species, breeding improvements for cherry have been slow compared to other temperate fruits, such as apple or peach. However, the recent release of the peach genome v1.0 by the International Peach Genome Initiative and the sequencing of cherry accessions to identify Single Nucleotide Polymorphisms (SNPs) provide an excellent basis for the advancement of cherry genetic and genomic studies. The availability of dense genetic linkage maps in phenotyped segregating progenies would be a valuable tool for breeders and geneticists. Using two sweet cherry (Prunus avium L.) intra-specific progenies derived from crosses between 'Black Tartarian' * 'Kordia' (BT*K) and 'Regina' * 'Lapins'(R*L), high-density genetic maps of the four parental lines and the two segregating populations were constructed. For BT*K and R*L, 89 and 121 F(1) plants were used for linkage mapping, respectively. A total of 5,696 SNP markers were tested in each progeny. As a result of these analyses, 723 and 687 markers were mapped into eight linkage groups (LGs) in BT*K and R*L, respectively. The resulting maps spanned 752.9 and 639.9 cM with an average distance of 1.1 and 0.9 cM between adjacent markers in BT*K and R*L, respectively. The maps displayed high synteny and co-linearity between each other, with the Prunus bin map, and with the peach genome v1.0 for all eight LGs (LG1-LG8). These maps provide a useful tool for investigating traits of interest in sweet cherry and represent a qualitative advance in the understanding of the cherry genome and its synteny with other members of the Rosaceae family

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

International audienceThanks 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

The Sweet Cherry Genome: A New Sequencing Project

The Sweet Cherry Genome: A New Sequencing Project. Plant and Animal Genomes XX