ORIGINAL RESEARCH article
Front. Genet.
Sec. Evolutionary, Population, and Conservation Genetics
QTL mapping for young leaf color trait in Eggplant (Solanum melongena L.) using BSA-seq
Provisionally accepted
- 1Shaoguan University, Shaoguan, China
- 2South China Agricultural University College of Horticulture, Guangzhou, China
- 3Guangdong Academy of Agricultural Sciences, Guangzhou, China
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Young leaf color is a crucial agronomic trait in eggplant (Solanum melongena L.) significantly influencing photosynthetic efficiency, stress resistance, fruit quality, and ornamental value. However, research focusing on this trait remains relatively scarce. In this study, an F₂ (EP02×EP01) segregating population (n=646) was developed from a cross between the purple young-leaved line EP02 and green young-leaved line EP01. Phenotypic characterization of the F₂ population revealed that the segregation ratio of green, purple-green, and purple phenotypes conformed to the expected 1:2:1 Mendelian ratio (χ² = 3.40, P > 0.05), indicating that the young leaf color trait in eggplant is controlled by a single incompletely dominant gene. To identify candidate loci associated with young leaf color, 30 individuals with extreme purple phenotypes and 30 individuals with extreme green phenotypes were selected from the F₂ population to establish two DNA bulks, namely the purple trait bulk (ZS-pool) and the green trait bulk (LS-pool), respectively. Bulked Segregant Analysis (BSA) combined with whole-genome resequencing was performed on the two parental lines (EP02 and EP01) and the two bulks (ZS-pool and LS-pool). A total of 1,416,609 high-quality single nucleotide polymorphisms (SNPs) were generated and used for quantitative trait locus (QTL) mapping. Using the SNP-index method and Euclidean Distance (ED) analysis, a single QTL associated with young leaf color was identified on chromosome 10, covering a physical interval of 17.49 Mb (59,315,357-76,806,837 bp). Integrated analysis of SNP indices, ED values, and gene functional annotations suggested that Smechr1002213, Smechr1001752, and Smechr1001815 might be the candidate gene regulating young leaf color formation in eggplant. The findings of this study will lay a foundation for gene isolation and the elucidation of the genetic mechanisms underlying young leaf coloration in eggplant.
Keywords: BSA-seq, eggplant, genetic analysis, QTL, Young leaf color
Received: 12 Dec 2025; Accepted: 09 Feb 2026.
Copyright: © 2026 Hu, Zhang, Li, Yuan, Song, Hu and Cheng. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Fang Hu
Jiaowen Cheng
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