Fine mapping and identification of a candidate gene for a major locus controlling maturity date in peach

Publication Overview
TitleFine mapping and identification of a candidate gene for a major locus controlling maturity date in peach
AuthorsPirona R, Eduardo I, Pacheco I, Da Silva Linge C, Miculan M, Verde I, Tartarini S, Dondini L, Pea G, Bassi D, Rossini L
TypeJournal Article
Journal NameBMC plant biology
Volume13
Issue1
Year2013
Page(s)166
CitationPirona R, Eduardo I, Pacheco I, Da Silva Linge C, Miculan M, Verde I, Tartarini S, Dondini L, Pea G, Bassi D, Rossini L. Fine mapping and identification of a candidate gene for a major locus controlling maturity date in peach. BMC plant biology. 2013 Oct 22; 13(1):166.

Abstract

BACKGROUND
Maturity date is a crucial factor for marketing of fresh fruit, especially those with limited shelf-life such as peach (Prunus persica L. Batsch): selection of several cultivars with differing MD would be advantageous to cover and extend the marketing season. Aims of this work were the fine mapping and identification of candidate genes for the major maturity date locus previously identified on peach linkage group 4. To improve genetic resolution of the target locus two F2 populations derived from the crosses Contender x Ambra (CxA, 306 individuals) and PI91459 (NJ Weeping) x Bounty (WxBy, 103 individuals) were genotyped with the Sequenom and 9K Illumina Peach Chip SNP platforms, respectively.

RESULTS
Recombinant individuals from the WxBy F2 population allowed the localisation of maturity date locus to a 220 kb region of the peach genome. Among the 25 annotated genes within this interval, functional classification identified ppa007577m and ppa008301m as the most likely candidates, both encoding transcription factors of the NAC (NAM/ATAF1, 2/CUC2) family. Re-sequencing of the four parents and comparison with the reference genome sequence uncovered a deletion of 232 bp in the upstream region of ppa007577m that is homozygous in NJ Weeping and heterozygous in Ambra, Bounty and the WxBy F1 parent. However, this variation did not segregate in the CxA F2 population being the CxA F1 parent homozygous for the reference allele. The second gene was thus examined as a candidate for maturity date. Re-sequencing of ppa008301m, showed an in-frame insertion of 9 bp in the last exon that co-segregated with the maturity date locus in both CxA and WxBy F2 populations.

CONCLUSIONS
Using two different segregating populations, the map position of the maturity date locus was refined from 3.56 Mb to 220 kb. A sequence variant in the NAC gene ppa008301m was shown to co-segregate with the maturity date locus, suggesting this gene as a candidate controlling ripening time in peach. If confirmed on other genetic materials, this variant may be used for marker-assisted breeding of new cultivars with differing maturity date.

Features
This publication contains information about 11 features:
Feature NameUniquenameType
PTP_11PTP_11genetic_marker
PTP_SNP353PTP_SNP353genetic_marker
PTP_10PTP_10genetic_marker
PTP_4PTP_4genetic_marker
PTP_8PTP_8genetic_marker
PTP_SNP40PTP_SNP40genetic_marker
PTP_SNP82PTP_SNP82genetic_marker
PTP_SNP618PTP_SNP618genetic_marker
PTP_SNP930PTP_SNP930genetic_marker
PTP_SNP1149PTP_SNP1149genetic_marker
PTP_SNP1320PTP_SNP1320genetic_marker