Abstract
Linkage maps are valuable tools in genetic and genomic studies. For sweet cherry, linkage maps have been constructed using mainly microsatellite markers (SSRs) and, recently, using single nucleotide polymorphism markers (SNPs) from a cherry 6K SNP array. Genotyping-by-sequencing (GBS), a new methodology based on high-throughput sequencing, holds great promise for identification of high number of SNPs and construction of high density linkage maps. In this study, GBS was used to identify SNPs from an intra-specific sweet cherry cross. A total of 8,476 high quality SNPs were selected for mapping. The physical position for each SNP was determined using the peach genome, Peach v1.0, as reference, and a homogeneous distribution of markers along the eight peach scaffolds was obtained. On average, 65.6% of the SNPs were present in genic regions and 49.8% were located in exonic regions. In addition to the SNPs, a group of SSRs was also used for construction of linkage maps. Parental and consensus high density maps were constructed by genotyping 166 siblings from a ‘Rainier’ x ‘Rivedel’ (Ra x Ri) cross. Using Ra x Ri population, 462, 489 and 985 markers were mapped into eight linkage groups in ‘Rainier’, ‘Rivedel’ and the Ra x Ri map, respectively, with 80% of mapped SNPs located in genic regions. Obtained maps spanned 549.5, 582.6 and 731.3 cM for ‘Rainier’, ‘Rivedel’ and consensus maps, respectively, with an average distance of 1.2 cM between adjacent markers for both ‘Rainier’ and ‘Rivedel’ maps and of 0.7 cM for Ra x Ri map. High synteny and co-linearity was observed between obtained maps and with Peach v1.0. These new high density linkage maps provide valuable information on the sweet cherry genome, and serve as the basis for identification of QTLs and genes relevant for the breeding of the species.
Highlights
IntroductionKlagges et al [7] published high density linkage maps using the RosBREED cherry 6K single nucleotide polymorphisms (SNPs) array v1.0 [9]
Sweet cherry (Prunus avium L., 2n = 2x = 16) belonging to the Prunus genus, a member of Rosaceae family, is an important tree fruit in Chile
From a total of 11,854 single nucleotide polymorphisms (SNPs) obtained in the progeny (MAF > 0.05), markers that represented more than 10% of missing data in the population and markers with incorrect genotypes were eliminated
Summary
Klagges et al [7] published high density linkage maps using the RosBREED cherry 6K SNP array v1.0 [9]. This array contains 5,696 SNPs obtained from re-sequencing of 16 sweet and eight sour cherry accessions, with physical position of each SNP based on the peach reference genome (Peach v1.0) as reference. SNP markers included in the SNP chips are carefully chosen and present potentially a high number of markers, informativeness of those markers is not ensured for all genetic backgrounds and can hamper the construction of saturated linkage maps
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have