Dataset Information

Copy number variation of a gene cluster encoding endopolygalacturonase mediates flesh texture and stone adhesion in peach.

ABSTRACT: Texture is an important attribute affecting consumer perception of fruit quality. Peach melting flesh and flesh adhesion to stone (endocarp) are simply inherited and controlled by the F-M locus on linkage group (LG) 4. Here, we report that two genes encoding endopolygalacturonase (endoPG) in the F-M locus, designated PpendoPGF and PpendoPGM, are associated with the melting flesh and stone adhesion traits. PpendoPGM controls melting flesh while PpendoPGF has pleiotropic effects on both melting flesh and stone adhesion. The F-M locus has three allelic copy number variants of endoPG, H1 (PpendoPGF and PpendoPGM), H2 (PpendoPGM), and H3 (null). The H2 haplotype represents the ancestral one while the H1 and H3 haplotypes are two variants due to duplication and deletion of PpendoPGM, respectively. Accessions with H1H1, H1H2, or H1H3 genotypes show the freestone or semi-freestone and melting flesh phenotype, while both H2H2 and H2H3 accessions have the clingstone and melting flesh phenotype. The H3H3 accessions have the clingstone and non-melting flesh phenotype. Our study not only demonstrates a driving role of gene copy number variations in flesh texture diversification in fruit trees, but also provides a useful diagnostic tool for early seedling selection in peach breeding programmes.

SUBMITTER: Gu C

PROVIDER: S-EPMC4783375 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature

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Copy number variation of a gene cluster encoding endopolygalacturonase mediates flesh texture and stone adhesion in peach.

Gu Chao C Wang Lu L Wang Wei W Zhou Hui H Ma Baiquan B Zheng Hongyu H Fang Ting T Ogutu Collins C Vimolmangkang Sornkanok S Han Yuepeng Y

Journal of experimental botany 20160205 6

Texture is an important attribute affecting consumer perception of fruit quality. Peach melting flesh and flesh adhesion to stone (endocarp) are simply inherited and controlled by the F-M locus on linkage group (LG) 4. Here, we report that two genes encoding endopolygalacturonase (endoPG) in the F-M locus, designated PpendoPGF and PpendoPGM, are associated with the melting flesh and stone adhesion traits. PpendoPGM controls melting flesh while PpendoPGF has pleiotropic effects on both melting fl ...[more]

PMID: 26850878

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Project description:The postharvest properties of two ultra-late maturing peach cultivars, "Tobihaku" (TH) and "Daijumitsuto" (DJ), were investigated. Fruit were harvested at commercial maturity and held at 25°C. TH exhibited the characteristics of normal melting flesh (MF) peach, including rapid fruit softening associated with appropriate level of endogenous ethylene production In contrast, DJ did not soften at all during 3 weeks experimental period even though considerable ethylene production was observed. Fruit of TH and DJ were treated with 5,000 ppm of propylene, an ethylene analog, continuously for 7 days. TH softened rapidly whereas DJ maintained high flesh firmness in spite of an increase in endogenous ethylene production, suggesting that DJ but not TH lacked the ability to be softened in response to endogenous and exogenous ethylene/propylene. DNA-seq analysis showed that tandem endo-polygalacturonase (endoPG) genes located at melting flesh (M) locus, Pp-endoPGM (PGM), and Pp-endoPGF (PGF), were deleted in DJ. The endoPG genes at M locus are known to control flesh texture of peach fruit, and it was suggested that the non-softening property of DJ is due to the lack of endoPG genes. On the other hand, TH possessed an unidentified M haplotype that is involved in determination of MF phenotype. Structural identification of the unknown M haplotype, designated as M 0, through comparison with previously reported M haplotypes revealed distinct differences between PGM on M 0 haplotype (PGM-M0 ) and PGM on other haplotypes (PGM-M1 ). Peach M haplotypes were classified into four main haplotypes: M 0 with PGM-M0 ; M 1 with both PGM-M1 and PGF; M 2 with PGM-M1 ; and M 3 lacking both PGM and PGF. Re-evaluation of M locus in association with MF/non-melting flesh (NMF) phenotypes in more than 400 accessions by using whole genome shotgun sequencing data on database and/or by PCR genotyping demonstrated that M 0 haplotype was the common haplotype in MF accessions, and M 0 and M 1 haplotypes were dominant over M 2 and M 3 haplotypes and co-dominantly determined the MF trait. It was also assumed on the basis of structural comparison of M haplotypes among Prunus species that the ancestral haplotype of M 0 diverged from those of the other haplotypes before the speciation of Prunus persica.

Dataset Information

Copy number variation of a gene cluster encoding endopolygalacturonase mediates flesh texture and stone adhesion in peach.

Publications

Copy number variation of a gene cluster encoding endopolygalacturonase mediates flesh texture and stone adhesion in peach.

Similar Datasets

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