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
rs159235969rs159235969genetic_marker
rs159238417rs159238417genetic_marker
rs159236617rs159236617genetic_marker
rs159235540rs159235540genetic_marker
rs159240518rs159240518genetic_marker
rs159236463rs159236463genetic_marker
rs159237446rs159237446genetic_marker
rs159239892rs159239892genetic_marker
rs159237833rs159237833genetic_marker
rs159238109rs159238109genetic_marker
rs159238738rs159238738genetic_marker
rs159237984rs159237984genetic_marker
rs159236507rs159236507genetic_marker
rs159235807rs159235807genetic_marker
rs159238251rs159238251genetic_marker
rs159238315rs159238315genetic_marker
rs159235770rs159235770genetic_marker
rs159237513rs159237513genetic_marker
rs159237843rs159237843genetic_marker
rs159235881rs159235881genetic_marker
rs159236632rs159236632genetic_marker
rs159241537rs159241537genetic_marker
rs159240606rs159240606genetic_marker
rs159238103rs159238103genetic_marker
rs159239831rs159239831genetic_marker

Pages

Featuremaps
This publication contains information about 3 maps:
Map Name
Peach-DF-F1-2013
Peach-DG-F1-2013
Peach_DGxDF_Consensus-2013
Cross References
This publication is also available in the following databases:
DatabaseAccession
AGL: USDA National Agricultural LibraryAGL:4786098