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.
Features
This publication contains information about 1,594 features:
Feature NameUniquenameType
rs159236499rs159236499genetic_marker
rs159239647rs159239647genetic_marker
rs159236563rs159236563genetic_marker
rs159240930rs159240930genetic_marker
rs159239219rs159239219genetic_marker
rs159237519rs159237519genetic_marker
rs159237262rs159237262genetic_marker
rs159237485rs159237485genetic_marker
rs159237616rs159237616genetic_marker
rs159237091rs159237091genetic_marker
rs159238456rs159238456genetic_marker
rs159241459rs159241459genetic_marker
rs159237073rs159237073genetic_marker
rs159241582rs159241582genetic_marker
rs159240376rs159240376genetic_marker
rs159238972rs159238972genetic_marker
rs159236371rs159236371genetic_marker
rs159240986rs159240986genetic_marker
rs159239557rs159239557genetic_marker
rs159236450rs159236450genetic_marker
rs159240072rs159240072genetic_marker
rs159240013rs159240013genetic_marker
rs159238100rs159238100genetic_marker
rs159241220rs159241220genetic_marker
rs159238835rs159238835genetic_marker

Pages

Projects
This publication contains information about 1 projects:
Project NameDescription
Peach-Fruit_quality_characteristics-Crisosto-2013
Featuremaps
This publication contains information about 3 maps:
Map Name
Peach-DF-F1-2013
Peach-DG-F1-2013
Peach_DGxDF_Consensus-2013