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
rs159238859rs159238859genetic_marker
rs159237563rs159237563genetic_marker
rs159241105rs159241105genetic_marker
rs159235727rs159235727genetic_marker
rs159236447rs159236447genetic_marker
rs159239402rs159239402genetic_marker
rs159237069rs159237069genetic_marker
rs159236647rs159236647genetic_marker
rs159238107rs159238107genetic_marker
rs159238129rs159238129genetic_marker
rs159237250rs159237250genetic_marker
rs159236109rs159236109genetic_marker
rs159240568rs159240568genetic_marker
rs159237648rs159237648genetic_marker
rs159238486rs159238486genetic_marker
rs159239760rs159239760genetic_marker
rs159239354rs159239354genetic_marker
rs159242112rs159242112genetic_marker
rs159240678rs159240678genetic_marker
rs159236576rs159236576genetic_marker
rs159237329rs159237329genetic_marker
rs159240691rs159240691genetic_marker
rs159236473rs159236473genetic_marker
rs159241154rs159241154genetic_marker
rs159240442rs159240442genetic_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