Mapping and validation of the epistatic D and P genes controlling anthocyanin biosynthesis in the peel of eggplant (Solanum melongena L.) fruit

Abstract

Fruit color is an important trait influencing the commercial value of eggplant fruits. Three dominant genes (D, P and Y) cooperatively control the anthocyanin coloration in eggplant fruits, but none has been mapped. In this study, two white-fruit accessions (19 141 and 19 147) and their F₂ progeny, with 9:7 segregation ratio of anthocyanin pigmented versus non-pigmented fruits, were used for mapping the D and P genes. A high-density genetic map was constructed with 5270 SNPs spanning 1997.98 cM. Three QTLs were identified, including two genes on chromosome 8 and one on chromosome 10. Gene expression analyses suggested that the SmANS on chromosome 8 and SmMYB1 on chromosome 10 were the putative candidate genes for P and D, respectively. We further identified (1) a SNP leading to a premature stop codon within the conserved PLN03176 domain of SmANS in 19 141, (2) a G base InDel in the promoter region leading to an additional cis-regulatory element and (3) a 6-bp InDel within the R2-MYB DNA binding domain of SmMYB1, in 19 147. Subsequently, these three variations were validated by PARMS technology as related to phenotypes in the F₂ population. Moreover, silencing of SmANS or SmMYB1 in the purple red fruits of F₁ (E3316) led to inhibition of anthocyanin biosynthesis in the peels. Conversely, overexpression of SmANS or SmMYB1 restored anthocyanin biosynthesis in the calli of 19 141 and 19 147 respectively. Our findings demonstrated the epistatic interactions underlying the white color of eggplant fruits, which can be potentially applied to breeding of eggplant fruit peel color.

Acknowledgements

The present study was financially supported by the National Natural Science Foundation of China (Grant No. 31501755), the Guangdong Provincial Natural Science Foundation (Grant No. 2021A1515012490), Major special projects of Guangxi science and technology program (AA22068088), the Department of agriculture and rural areas of Guangdong province of China, grant No. 2022KJ110 and 2022KJ106, and the Special fund for scientific innovation strategy-construction of high level Academy of Agriculture Science, grant number R2019PY-JX003, R2019PY-QF009, 202114TD, R2021YJ-YB3019. The authors would like to express their gratitude to EditSprings (https://www.editsprings.cn) for the expert linguistic services provided.

Author contributions

S.B.J., L.Z.L., and S.G.W. conceived and designed the experiment. Y.Q. analyzed the data and wrote the manuscript. W.J., L.H.M and L.T conducted experiments, including sample collection, DNA and RNA extraction, qRT-PCR analysis, VIGS and overexpression. W.Y.K shared the GUIQIE1–1 reference genome and annotation files with us for this project. All authors read and approved the final manuscript.

Data availability

All the raw sequencing data have been deposited at China National GeneBank (CNGB) database under Project accession number CNP0003597, Sample accession number CNS0623704-CNS0623905, and Experiment/Run accession number CNR0637917-CNR0638118.

Conflict of interest

The authors declare no competing interests.

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