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_8027649s1_8027649genetic_marker
s1_8514165s1_8514165genetic_marker
s1_8760055s1_8760055genetic_marker
s1_8782297s1_8782297genetic_marker
s1_8813976s1_8813976genetic_marker
s1_8870536s1_8870536genetic_marker
s1_9196124s1_9196124genetic_marker
s1_9209151s1_9209151genetic_marker
s1_9622900s1_9622900genetic_marker
s2_10147949s2_10147949genetic_marker
s2_10147955s2_10147955genetic_marker
s2_10147988s2_10147988genetic_marker
s2_10147990s2_10147990genetic_marker
s2_10147991s2_10147991genetic_marker
s2_10223139s2_10223139genetic_marker
s2_10223150s2_10223150genetic_marker
s2_10223626s2_10223626genetic_marker
s2_10258716s2_10258716genetic_marker
s2_11354990s2_11354990genetic_marker
s2_11355024s2_11355024genetic_marker
s2_11355040s2_11355040genetic_marker
s2_11564418s2_11564418genetic_marker
s2_12441799s2_12441799genetic_marker
s2_12447854s2_12447854genetic_marker
s2_12752388s2_12752388genetic_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