Open Access Highly Accessed Research article

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

Raul Pirona1, Iban Eduardo1, Igor Pacheco2, Cassia Da Silva Linge2, Mara Miculan34, Ignazio Verde5, Stefano Tartarini6, Luca Dondini6, Giorgio Pea1, Daniele Bassi2 and Laura Rossini12*

Author Affiliations

1 Plant Genomics Section, Parco Tecnologico Padano, Lodi 26900, Italy

2 Università degli Studi di Milano, DiSAA, Via Celoria 2, Milan 20133, Italy

3 Istituto di Genomica Applicata, Via Linussio 51, Udine 33100, Italy

4 Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Udine, Via delle Scienze 206, Udine 33100, Italy

5 Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Frutticoltura, Via Fioranello 52, 00134 Roma, Italy

6 DCA, Department of Fruit Tree and Woody Plant Science, University of Bologna, Bologna 40126, Italy

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BMC Plant Biology 2013, 13:166  doi:10.1186/1471-2229-13-166

Published: 22 October 2013

Abstract

Background

Maturity date (MD) 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 (

    N
AM/
    A
TAF1, 2/
    C
UC2) 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.

Keywords:
Maturity date; Prunus persica; QTL; Candidate gene