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
s8_20261549s8_20261549genetic_marker
s8_20261554s8_20261554genetic_marker
s8_20261576s8_20261576genetic_marker
s8_20262178s8_20262178genetic_marker
s8_20262179s8_20262179genetic_marker
s8_20262232s8_20262232genetic_marker
s8_20270509s8_20270509genetic_marker
s8_20376775s8_20376775genetic_marker
s8_20450196s8_20450196genetic_marker
s8_20450275s8_20450275genetic_marker
s8_20495674s8_20495674genetic_marker
s8_20495711s8_20495711genetic_marker
s8_20495801s8_20495801genetic_marker
s8_20495808s8_20495808genetic_marker
s8_20521380s8_20521380genetic_marker
s8_20521492s8_20521492genetic_marker
s8_20549886s8_20549886genetic_marker
s8_20549895s8_20549895genetic_marker
s8_20549902s8_20549902genetic_marker
s8_20549906s8_20549906genetic_marker
s8_20677056s8_20677056genetic_marker
s8_20677079s8_20677079genetic_marker
s8_20677081s8_20677081genetic_marker
s8_20677761s8_20677761genetic_marker
s8_20677811s8_20677811genetic_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