Construction of high density sweet cherry (Prunus avium L.) linkage maps using microsatellite markers and SNPs detected by genotyping-by-sequencing (GBS).

Publication Overview
TitleConstruction of high density sweet cherry (Prunus avium L.) linkage maps using microsatellite markers and SNPs detected by genotyping-by-sequencing (GBS).
AuthorsGuajardo V, Solís S, Sagredo B, Gainza F, Muñoz C, Gasic K, Hinrichsen P. Construction of high density sweet cherry (Prunus avium L.) linkage maps using microsatellite markers and SNPs detected by genotyping-by-sequencing (GBS). PLoS ONE 2015.
TypeJournal Article
Journal NamePLoS ONE
Volume10
Issue5
Year2015
Page(s)e0127750
CitationGuajardo V, Solís S, Sagredo B, Gainza F, Muñoz C, Gasic K, Hinrichsen P. Construction of high density sweet cherry (Prunus avium L.) linkage maps using microsatellite markers and SNPs detected by genotyping-by-sequencing (GBS). PLoS ONE 2015.

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.
Features
This publication contains information about 8,477 features:
Feature NameUniquenameType
s1_12181482s1_12181482genetic_marker
s1_12254982s1_12254982genetic_marker
s1_12255020s1_12255020genetic_marker
s1_12256939s1_12256939genetic_marker
s1_12257390s1_12257390genetic_marker
s1_12281523s1_12281523genetic_marker
s1_12284952s1_12284952genetic_marker
s1_1238635s1_1238635genetic_marker
s1_1238680s1_1238680genetic_marker
s1_1270204s1_1270204genetic_marker
s1_12959899s1_12959899genetic_marker
s1_13363295s1_13363295genetic_marker
s1_13493935s1_13493935genetic_marker
s1_13493994s1_13493994genetic_marker
s1_13494039s1_13494039genetic_marker
s1_13495868s1_13495868genetic_marker
s1_13495951s1_13495951genetic_marker
s1_1429658s1_1429658genetic_marker
s1_1429677s1_1429677genetic_marker
s1_15071820s1_15071820genetic_marker
s1_15086404s1_15086404genetic_marker
s1_1541669s1_1541669genetic_marker
s1_1761297s1_1761297genetic_marker
s1_1761660s1_1761660genetic_marker
s1_1839844s1_1839844genetic_marker

Pages

Featuremaps
This publication contains information about 4 maps:
Map Name
Sweet Cherry-Ra-F1
Sweet Cherry-Ri-F1
Sweet Cherry-RaxRi-F1
Sweet_cherry_RaxRi_F1-physical-Prunus-persicaV1.0