Construction of High Density Sweet Cherry (Prunus avium L.) Linkage Maps Using Microsatellite Markers and SNPs Detected by Genotyping-by-Sequencing (GBS)

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.

Whole-genome single-nucleotide polymorphism (SNP) marker discovery and association analysis with the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content inLarimichthys crocea

“…More than half (∼53%) of those detected quality SNP markers resided in genic regions, enabling us to probe the possible association of trait with the nearby functional genes. We noticed that the percentage of markers in genic regions was higher than that of previous reports in soybean (39.5%) (Sonah et al, 2013) but lower than that of sweat cherry (65.6%) (Guajardo et al, 2015). Those SNP markers generated from the reduced representation library, especially those in genic regions, provided us an easy and efficient manner to detect genomic small variants and to identify genomic regions related to important traits of large yellow croaker at genomic scale.…”

Genotyping‐by‐sequencing approaches to characterize crop genomes: choosing the right tool for the right application

“…The GBS method was originally tested with 276 RILs from a maize mapping population, which led to the identification of 200 000 markers (Elshire et al ., ). This method has seen wide use for linkage mapping and QTL analysis in diverse crops including rice (Spindel et al ., , ) and sweet cherry (Guajardo et al ., ). The ddRAD method has been employed, for instance, to genotype canola (Chen et al ., ) and for genetic linkage mapping in cultivated peanut (Zhou et al ., ) and kiwifruit (Scaglione et al ., ).…”

Evaluation of multiple approaches to identify genome-wide polymorphisms in closely related genotypes of sweet cherry ( Prunus avium L.)

“…Despite an estimated genome size of 225–330 Mb [8], [9], sweet cherry is lacking in genomic information in comparison with other prominent Rosaceae members, including peach and apple [10], [11]. Linkage maps and molecular markers have been developed for sweet cherry [12] as well as peach and almond, two other members of the sub-family Prunoideae [13], [14], [15], and a comprehensive and advanced draft of the peach genome serves as the foundation for several comparative studies [10]. Recently, a draft genome of sweet cherry cultivar ‘Stella’ was released [16].…”