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Identification of candidate genes associated with mealiness and maturity date in peach [Prunus persica (L.) Batsch] using QTL analysis and deep sequencing

Abstract

Peach and nectarine quality traits such as flavor, texture, and juiciness are important for consumer acceptance. Maturity date (MD) also plays a role in the fruit-ripening process and is an important factor for marketing fresh fruit. On the other hand, cold storage produces a physiological disorder known as chilling injury where the most important symptom is a lack of juice in the flesh or mealiness (M). In this study, we analyzed an F2 population obtained from a self-pollination of “Venus” nectarine that segregates for MD and M. We built a linkage map with 1,830 SNPs, 7 SSRs and two slow-ripening (SR) morphological markers, spanning 389.2 cM distributed over eight linkage groups (LGs). The SR trait was mapped to LG4 and we compared the whole genome sequences of a SR individual and “Venus” and identified a deletion of 26.6 kb containing ppa008301m (ANAC072) co-localized with the SR trait. Three Quantitative Trait Loci (QTL) for MD were detected; they all co-localize on LG4 between 31.0 and 42.0 cM. Four co-localizing QTLs on LG4 between 33.3 and 40.3 cM were detected for M, explaining 34 % of the phenotypic variation. We identified five and nine candidate genes (CGs) for MD and M from the QTL regions, respectively. Our results suggest that the transcription factors (TFs) ANAC072 and ppa010982m (ERF4) are CGs for both traits. LG4 contains a cluster for genetic factors that possibly regulate M and MD, but functional validation is necessary to unravel the complexity of genetic control responsible for fruit traits.

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Acknowledgments

This research was supported by Conicyt-Fondecyt 11121396, Conicyt-FONDEF G13i10005 (RCV and CM), Corfo-Innova 09PMG-7240 (CM), Fondo de Areas Prioritarias Centro de Regulación del Genoma 15090007 (AO), PFB-16 (AO), and UNAB internal project DI-489-14R (CM) grants. This work was also supported by CONICYT fellowships D-21090737 (GNL) and (ACE) grants. There are no conflicts of interest to declare.

Authors’ contributions

GNL carried out the experimental design, DNA extraction of the siblings of the F2 population, phenotypic data analysis, SSR genotyping, genetic map construction, QTL analysis, mapping of reads against the reference genome and SNP detection using the “Venus” sequence. ACE carried out the sibling phenotyping of the F2 population, phenotypic data analysis and structural variants genotyped. MT carried out the SNP genotyping with the Infinium bead array for peach, the SNP data analysis, drafted the manuscript and made substantive intellectual contributions to the manuscript. DM carried out the SNP genotyping with the Infinium bead array for peach, the SNP data analysis and drafted the manuscript. RI supported the phenotypic evaluation of fruit quality traits and made substantive intellectual contributions to the manuscript. RCV carried out the experimental design, the phenotypic data analysis and made substantive intellectual contributions to the manuscript. AO carried out the experimental design and made substantive intellectual contributions to the manuscript. FBH carried out the experimental design, CG selection, drafted the manuscript and made substantive intellectual contributions to the manuscript. CM carried out the experimental design, the data analysis, drafted the manuscript and made substantive intellectual contributions to the manuscript. All authors read, revised the manuscript critically and approved the final version of the manuscript.

Data archiving statement

The data reported here are archived and publicly available at the National Center for Biotechnology Information (NCBI; https://www.ncbi.nlm.nih.gov/) and Genome Database for Rosaceae (GDR; http://www.rosaceae.org/). Sequence raw data of “Venus” in fastaq format (accession numbers SRR1867740, SRR1867794 and SRR1867795) and sequence raw data of slow ripening sibling p152-sr in fastaq format (accession number SRR1867806) are available at the NCBI. The mapped markers were submitted to GDR (tfGDR1015).

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Correspondence to Claudio Meneses.

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Communicated by C. Dardick

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Fig. S1

Genotyping of 151 siblings from F2 population for the dominant molecular marker of the SR phenotype. Each lane corresponds to the siblings of the “Venus” × “Venus” F2 population. The amplifications of PCR products of 892 bp correspond to the siblings with melting flesh (Mf) and the absence of PCR products correspond to the slow ripening siblings (SR). Lanes “C-” are negative controls and “V,” “F,” and “S” correspond to “Venus”, “Flamekist,” and “Stark Red  Gold,” respectively. The first lane corresponds to the ladder (bp) (DOCX 1.24 mb)

Fig. S2

Genotyping of structural variant of the ERF4 promoter region in the F2 population by capillary electrophoresis. Each lane corresponds to one individual of the F2 population. On the top of each lane, the letter “Es” corresponds to the early-season siblings, “Ms” corresponds to the mid-season siblings, and “SR” corresponds to the slow ripening siblings. On the bottom of the each lane, the letter “A” represents two alleles from a female parent, “B” represents two alleles from a male parent, and “H” represents one allele from each parent. “C-” are the negative controls. The first and last lanes are the ladders (bp) (DOCX 215 kb)

Fig. S3

MD haplotype analysis in LG4. Genotypes of 10 early-season siblings, 10 mid-season siblings, and 10 Sr siblings for all mapped markers on LG4. On the left, LG4 of the genetic linkage map is shown. On the right, the genotype of each marker is coded as A, H, B, C, or D. The homozygous genotypes (A) are shown in red, the heterozygous genotypes are shown in yellow (H), and the homozygous genotypes (B) are shown in blue. “C” stands for either homozygous “B” or heterozygous “H.” “D” stands for either homozygous “A” or heterozygous “H.” Missing data are shown in white. The black box indicates the regions of the LG where the MD QTL are co-localized with the Sr marker. In this region, genotype A is associated with the early-season siblings, genotype H is associated with mid-season siblings, and genotype B is associated with Sr siblings (DOCX 441 kb)

Table S1

Physiological parameters of progeny during three seasons at harvest stage (DOCX 32 kb)

Table S2

Sequencing metrics of the genomes of the parent “Venus” and the sibling of the F2 population p152-sr (DOCX 27 kb)

Table S3

List of the SSR primers using for “Venus” × “Venus” map construction (DOCX 35 kb)

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Nuñez-Lillo, G., Cifuentes-Esquivel, A., Troggio, M. et al. Identification of candidate genes associated with mealiness and maturity date in peach [Prunus persica (L.) Batsch] using QTL analysis and deep sequencing. Tree Genetics & Genomes 11, 86 (2015). https://doi.org/10.1007/s11295-015-0911-9

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  • DOI: https://doi.org/10.1007/s11295-015-0911-9

Keywords

  • Genetic linkage map
  • Slow ripening
  • ANAC072
  • ERF4