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

Abstract

BackgroundMaturity 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.ResultsRecombinant 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.ConclusionsUsing 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.

QTL mapping for brown rot (Monilinia fructigena) resistance in an intraspecific peach (Prunus persica L. Batsch) F1 progeny

“…3). MD_2009.4 and MD_2010.4 QTLs coincide with the position of a major MD locus previously found in a related progeny (Eduardo et al 2010b;Pirona et al 2013), as well as others from Prunus genetic backgrounds (Quilot et al 2004) and in apple (Kenis et al 2008), this latter associated with loci in Malus LG3 and LG10, previously described as syntenic with LG4 of Prunus (Dirlewanger et al 2004b;Illa et al 2011). In addition to its strong effect in MD phenotype, in this study, MD QTLs of LG4 positively correlated in both years to most of the traits in at least one season ( Table 2).…”

“…However, further dissection of these chromosomal regions is required to obtain tightly linked markers, and F2 populations need to be studied to evaluate with more precision the additive, dominance effects and/or epistatic interactions of these QTLs, as well as to detect new regions contributing to the phenotypic variation on the studied populations. The recent publication of the peach genome (Verde et al 2013) and the previously released SNP platforms, allowing simultaneous analysis in thousands of SNPs (Ahmad et al 2011;Verde et al 2012), offer unprecedented opportunities to find polymorphic markers in order to saturate these regions. grant RBIP06CTBR.…”

“…An inversion was observed in the top of group C×EL-6, between markers SNP_IGA_615381 and SNP_IGA_604703; also, SNP_IGA_460591, expected to be on Scaffold_4, was mapped in C×EL-2. These results could be explained by a misassembly in this region of peach genome (Verde et al 2013). Similar results have been obtained in other works of peach linkage mapping using SNP markers (Eduardo et al 2012;Martinez-Garcia et al 2013b).…”

“…The availability of thousands of molecular markers (Jung et al 2008) has allowed the construction of multiple genetic maps and the development of synteny studies (Dirlewanger et al 2004b;Illa et al 2009). Moreover, the peach genome sequence Verde et al 2013) and re-sequencing of many Prunus cultivars have led to the generation of thousands of singlenucleotide polymorphism (SNP) markers (Sosinski et al 2009;Ahmad et al 2011;Verde et al 2012), whose efficiency is being tested and validated in marker-assisted breeding programs.…”

Breeding rootstocks for Prunus species: Advances in genetic and genomics of peach and cherry as a model

“…The International Peach SNP Consortium (IPSC) developed a chip for this species consisting of 8144 SNPs, which was validated by 709 peach accessions and identified 6869 polymorphisms (Verde et al, 2012). Pirona et al (2013) used this chip to analyze the F 2 PI91459 ('NJ Weeping' × 'Bounty') population (W×By, 103 individuals), which led to the identification of a candidate gene that appears to control maturation date in peach, while Eduardo et al (2013) and Sánchez et al (2014) used the chip to identify QTLs for fruit volatile organic compounds in peach. A chip is also available for cherry with 5696 SNPs, which was validated by evaluating 269 cherry and 330 sour cherry accessions (Peace et al, 2012).…”