High density SNP mapping and QTL analysis for fruit quality characteristics in peach (Prunus persica L.)

Publication Overview
TitleHigh density SNP mapping and QTL analysis for fruit quality characteristics in peach (Prunus persica L.)
AuthorsMartínez-García PJ, Parfitt DE, Ogundiwin EA, Fass J, Chan HM, Ahmad R, Lurie S, Dandekar A, Gradziel TM, Crisosto CH
TypeJournal Article
Journal NameTree Genetics and Genomes
Volume9
Issue1
Year2013
Page(s)19-36
CitationMartínez-García PJ, Parfitt DE, Ogundiwin EA, Fass J, Chan HM, Ahmad R, Lurie S, Dandekar A, Gradziel TM, Crisosto CH. High density SNP mapping and QTL analysis for fruit quality characteristics in peach (Prunus persica L.). Tree Genetics and Genomes. 2013; 9(1):19-36.

Abstract

Single nucleotide polymorphisms (SNPs) were used to construct an integrated SNP linkage map of peach (Prunus persica (L.) Batsch). A set of 1,536 SNPs were evaluated with the GoldenGate Genotyping assay in two mapping populations, Pop-DF, and Pop-DG. After genotyping and filtering, a final set of 1,400 high quality SNPs in Pop-DF and 962 in Pop-DG with full map coverage were selected and used to construct two linkage maps with JoinMapÂ4.0. The Pop-DF map covered 422 cM of the peach genome and included 1,037 SNP markers, and Pop-DG map covered 369 cM and included 738 SNPs. A consensus map was constructed with 588 SNP markers placed in eight linkage groups (n = 8 for peach), with map coverage of 454 cM and an average distance of 0.81 cM/marker site. Placements of SNPs on the “peach v1.0” physical map were compared to placement on the linkage maps and several differences were observed. Using the SNP linkage map of Pop-DG and phenotypic data collected for three harvest seasons, a QTL analysis for fruit quality traits and chilling injury symptoms was carried out with the mapped SNPs. Significant QTL effects were detected for mealiness (M) and flesh bleeding (FBL) QTLs on linkage group 4 and flesh browning (FBr) on linkage group 5. This study represents one of the first examples of QTL detection for quality traits and chilling injury symptoms using a high-density SNP map in a single peach F1 family.
Projects
This publication contains information about 1 projects:
Project NameDescription
Peach-Fruit_quality_characteristics-Crisosto-2013
Features
This publication contains information about 1,594 features:
Feature NameUniquenameType
chilling injury resistanceqCI.DG-G1QTL
chilling injury resistanceqCI.DG-G4QTL
chilling injury resistanceqCI.DG-G4.1QTL
chilling injury resistanceqCI.DG-G5QTL
flesh color around the stoneqFCLST.DG-G1QTL
flesh adhesionqFSHA.DG-G4QTL
flesh adhesionqFSHA.DG-G4.2QTL
flesh adhesionqFSHA.DG-G4.3QTL
flesh adhesionqFSHA.DG-G4.4QTL
flesh adhesionqFSHA.DG-G4.5QTL
flesh adhesionqFSHA.DG-G4.6QTL
mesocarp colorqMCCL.DG-G1.1QTL
mesocarp colorqMCCL.DG-G1.10QTL
mesocarp colorqMCCL.DG-G1.11QTL
mesocarp colorqMCCL.DG-G1.12QTL
mesocarp colorqMCCL.DG-G1.13QTL
mesocarp colorqMCCL.DG-G1.14QTL
mesocarp colorqMCCL.DG-G1.15QTL
mesocarp colorqMCCL.DG-G1.16QTL
mesocarp colorqMCCL.DG-G1.8QTL
mesocarp colorqMCCL.DG-G1.9QTL
rs159240266rs159240266genetic_marker
rs159238552rs159238552genetic_marker
rs159240150rs159240150genetic_marker
rs159235684rs159235684genetic_marker

Pages

Featuremaps
This publication contains information about 3 maps:
Map Name
Peach-DF-F1-2013
Peach-DG-F1-2013
Peach_DGxDF_Consensus-2013
Properties
Additional details for this publication include:
Property NameValue
URLhttp://dx.doi.org/10.1007/s11295-012-0522-7
Language Abbreng
Publication Date2013
Publication Model[electronic resource].
Publication TypeJournal Article
URLhttps://link.springer.com/article/10.1007/s11295-012-0522-7
KeywordsPrunus persica, chilling injury, chromosome mapping, fruit quality, genotyping, linkage groups, peaches, quantitative trait loci, single nucleotide polymorphism
Cross References
This publication is also available in the following databases:
DatabaseAccession
AGL: USDA National Agricultural LibraryAGL:4786098