Identification and characterization of QTLs for fruit quality traits in peach through a multi-family approach.

Publication Overview
TitleIdentification and characterization of QTLs for fruit quality traits in peach through a multi-family approach.
AuthorsRawandoozi ZJ, Hartmann TP, Carpenedo S, Gasic K, da Silva Linge C, Cai L, Van de Weg E, Byrne DH
TypeJournal Article
Journal NameBMC genomics
Volume21
Issue1
Year2020
Page(s)522
CitationRawandoozi ZJ, Hartmann TP, Carpenedo S, Gasic K, da Silva Linge C, Cai L, Van de Weg E, Byrne DH. Identification and characterization of QTLs for fruit quality traits in peach through a multi-family approach.. BMC genomics. 2020 Jul 29; 21(1):522.

Abstract

BACKGROUND
Fruit quality traits have a significant effect on consumer acceptance and subsequently on peach (Prunus persica (L.) Batsch) consumption. Determining the genetic bases of key fruit quality traits is essential for the industry to improve fruit quality and increase consumption. Pedigree-based analysis across multiple peach pedigrees can identify the genomic basis of complex traits for direct implementation in marker-assisted selection. This strategy provides breeders with better-informed decisions and improves selection efficiency and, subsequently, saves resources and time.

RESULTS
Phenotypic data of seven F1 low to medium chill full-sib families were collected over 2 years at two locations and genotyped using the 9 K SNP Illumina array. One major QTL for fruit blush was found on linkage group 4 (LG4) at 40-46 cM that explained from 20 to 32% of the total phenotypic variance and showed three QTL alleles of different effects. For soluble solids concentration (SSC), one QTL was mapped on LG5 at 60-72 cM and explained from 17 to 39% of the phenotypic variance. A major QTL for titratable acidity (TA) co-localized with the major locus for low-acid fruit (D-locus). It was mapped at the proximal end of LG5 and explained 35 to 80% of the phenotypic variance. The new QTL for TA on the distal end of LG5 explained 14 to 22% of the phenotypic variance. This QTL co-localized with the QTL for SSC and affected TA only when the first QTL is homozygous for high acidity (epistasis). Haplotype analyses revealed SNP haplotypes and predictive SNP marker(s) associated with desired QTL alleles.

CONCLUSIONS
A multi-family-based QTL discovery approach enhanced the ability to discover a new TA QTL at the distal end of LG5 and validated other QTLs which were reported in previous studies. Haplotype characterization of the mapped QTLs distinguishes this work from the previous QTL studies. Identified predictive SNPs and their original sources will facilitate the selection of parents and/or seedlings that have desired QTL alleles. Our findings will help peach breeders develop new predictive, DNA-based molecular marker tests for routine use in marker-assisted breeding.

Projects
This publication contains information about 2 projects:
Project NameDescription
Peach-fruit_quality-Rawandoozi-2020
Peach-fruit_quality-Rawandoozi-Haplotype-2020Peach-fruit_quality-Rawandoozi-Haplotype-2020
Features
This publication contains information about 18 features:
Feature NameUniquenameType
red skin pigmentationqRSP.RB-4K-2019-LG4-CA12QTL
red skin pigmentationqRSP.RB-4K-2019-LG4-TX12QTL
red skin pigmentationqRSP.RB-4K-2019-LG4-TX13QTL
red skin pigmentationqRSP.RB-4K-2019-LG4-meanQTL
total water soluble contentqSSC.RB-4K-2019-LG5-CA11QTL
total water soluble contentqSSC.RB-4K-2019-LG5-CA12QTL
total water soluble contentqSSC.RB-4K-2019-LG5-TX13QTL
total water soluble contentqSSC.RB-4K-2019-LG5-meanQTL
titratable acidityqTITA.RB-4K-2019-LG5a-CA11QTL
titratable acidityqTITA.RB-4K-2019-LG5a-CA12QTL
titratable acidityqTITA.RB-4K-2019-LG5b-CA12QTL
titratable acidityqTITA.RB-4K-2019-LG5-TX12QTL
titratable acidityqTITA.RB-4K-2019-LG5a-meanQTL
titratable acidityqTITA.RB-4K-2019-LG5b-meanQTL
Ppe-HB-qBlush4Ppe-HB-qBlush4haplotype_block
Ppe-HB-qSSC5Ppe-HB-qSSC5haplotype_block
Ppe-HB-qTA5aPpe-HB-qTA5ahaplotype_block
Ppe-HB-qTA5bPpe-HB-qTA5bhaplotype_block
Featuremaps
This publication contains information about 1 maps:
Map Name
Peach-RosBREED-4K-2019
Stocks
This publication contains information about 3 stocks:
Stock NameUniquenameType
Y426–371Y426–371cultivar
Y434–40Y434–40cultivar
Y435–246Y435–246cultivar
Cross References
This publication is also available in the following databases:
DatabaseAccession
PMID: PubMedPMID:32727362