Open Access

ARTICLE

Mapping of the Pepper Purple Fruit Gene and Development of Molecular Markers Based on BSA-Seq

Xinxin Liu^1,#, Yueyue Zhang^1,#, Rahat Sharif¹, Weiqin Mo², Zhenrong Li¹, Guiling Yang¹, Chao Song¹, Ting Ye^2,*, Changming Chen^1,*

1 Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
2 Dongguan Agricultural Scientific Research Center, Dongguan, 523086, China

* Corresponding Authors: Ting Ye. Email: ; Changming Chen. Email:
# These authors contributed equally to this work

(This article belongs to the Special Issue: Plant Genetic Diversity and Evolution)

Phyton-International Journal of Experimental Botany 2025, 94(6), 1695-1709. https://doi.org/10.32604/phyton.2025.063349

Received 12 January 2025; Accepted 06 May 2025; Issue published 27 June 2025

Abstract

The color difference of capsicum fruit is closely related to the type and content of pigment in the peel, which is mainly determined by anthocyanins, chlorophyll, and carotenoids. This study used green “CA59” and purple “Z81” pepper fruits as parents to create the F₂ generation. The fruit color of 466 F₂ population was identified, and the extreme individuals from this population were selected for Bulked Segregant Analysis (BSA) using resequencing. Genetic analysis revealed that a pair of genes controls the expression of the purple fruit trait in capsicum. Using functional annotation, expression analysis, and sequencing analysis of candidate genes, it was determined that there were four genes in the region between InDel 67 and InDel 75 (185,664,068 BP-186,514,350 bp) on chromosome 10, that is the linkage interval for pepper purple fruit. There are 7 SNPs in the CaMYB1 gene (Capann_59V1aChr10g016200) in the pepper variety “Z81”. Of these, 4 SNPs are located in the gene’s coding region. These 4 SNPs lead to 2 mutations that do not change the amino acid sequence (synonymous mutations) and 2 mutations that do change the amino acid sequence (non-synonymous mutations). Additionally, the expression level of the CaMYB1 gene in the purple fruit of “Z81” is significantly higher than that in the green fruit of “CA59”. CaMYB1 is believed to be a crucial candidate gene in regulating anthocyanin production in purple capsicum fruit. A molecular marker, InDel 67, was successfully developed, with a total separation rate of 92.4%.

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Supplementary Material

Supplementary Material File

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