Genome-wide Association Analysis of Red Flesh Character Based on Resequencing Approach in Peach

in Journal of the American Society for Horticultural Science

Anthocyanins are important molecules that are responsible for fruit color formation and are also beneficial to human health. To date, numerous structural and regulatory genes associated with anthocyanin biosynthesis in peach (Prunus persica) have been reported based on linkage analysis. In this study, we sought to identify further genes associated with anthocyanin content in peach by conducting a genome-wide association analysis of 129 peach accessions to detect markers associated with the trait. Significant association signals were detected when anthocyanin content was considered a qualitative character but not when it was considered a quantitative trait. We detected an association region located between 11.7 and 13.1 Mb in chromosome 1, a region in which only 133 of 146 genes have previously been functionally annotated. Gene ontology annotation of the genes in this region showed that membrane-associated genes (including one gene encoding a chloride channel protein and 17 sugar transport/carrier-associated genes) were significantly enriched, and we focused on these in subsequent analyses. Based on in vitro induction of anthocyanins in fruit flesh using different exogenously applied sugars and subsequent culture, we found that the expression level of 3 of the 18 membrane-associated genes, Prupe.1G156300, Prupe.1G156900, and Prupe.1G157000, increased during induction treatment. Furthermore, during the fruit development period of a white-fleshed and a red-fleshed peach cultivar, the expression of one gene encoding a transmembrane sugar transport protein was observed to be positively correlated with anthocyanin biosynthesis. These results will facilitate understanding of the molecular mechanism of anthocyanin biosynthesis in peach.

Contributor Notes

This work was supported by the National Natural Science Foundation of China (grant no. 31672130) and the Agricultural Science and Technology Innovation Program (grant CAAS-ASTIP-2017-ZFRI-01). We thank Central Public-interest Scientific Institution Basal Research Fund the Preliminary Establishment and Capacity Improvements of the Molecular Breeding Platform for Fruit Trees (Y2019PT19-02).

The authors declare that they have no competing interests.

The RNA-sequencing data of two cultivars (Tianjin Shui Mi and Hakuho peach) have been deposited into the Figshare database (https://doi.org/10.6084/m9.figshare.5576368.v1).

Corresponding authors. Email: wyandck@126.com or wanglirong@caas.cn.

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Article Figures

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    Anthocyanin quantification in fruit of 129 peach accessions in (A and B) 2014, (C) in 2015, and (D) classification. FW = fresh weight.

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    Manhattan and quantile-quantile plots of estimated −log10 P from association analysis of anthocyanin absent/present in fruit of 129 peach accessions using (A) general linear model (GLM)–no principal components analysis (PCA), (B) GLM-PCA, and (C) mixed linear model (MLM). Negative log10 P values from the genome-wide scan were plotted against single-nucleotide polymorphism position on each of the eight chromosomes. The dotted horizontal line indicates the genome-wide significance threshold (−log10 P = 8.49).

  • View in gallery

    The cellular component of gene ontology annotation of the 133 target genes and in comparison of all genes annotated in the genome (designated as background genes). The left and right y-axes present the proportion and number of genes among of different categories.

  • View in gallery

    (A) Anthocyanin content and (B) gene expression profile using RNA-seq in the fruit flesh of a red-fleshed peach ‘Tianjin Shui Mi’ induced by different sugar, including glucose, sucrose, fructose, and sorbitol, at 0, 12, and 24 h, compared with the control (mannitol treatment). The anthocyanin content is expressed as the mean ± sd of triplicates in each sample. Asterisks indicate significant differences between the sugar and the control in 12- or 24-h treatment (** P < 0.01, one-way analysis of variance). FW = fresh weight.

  • View in gallery

    The relative expression of different genes using quantitative real-time polymerase chain reaction and anthocyanin content in the fruit flesh during the development period of white-flesh [(A) ‘Hakuho’] and red flesh [(B) ‘Tianjin Shui Mi’] peach fruit. FW = fresh weight.

  • View in gallery

    Manhattan and quantile-quantile plots of estimated ·log10 P from association analysis of cyanidin-3-glucoside content in 2014 (A) and 2015 (B) in fruit of 129 accessions using mixed linear model. Negative log10 P values from the genome-wide scan were plotted against single-nucleotide polymorphism position on each of the eight chromosomes. The dotted line indicates the genome-wide significance threshold (·log10 P = 8.49).

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