# QTL mapping for young leaf color trait in eggplant (Solanum melongena L.) using BSA-seq

## TL;DR

This study identifies a genetic region linked to young leaf color in eggplants, which could help improve breeding for better photosynthesis and plant resilience.

## Contribution

The study maps a QTL for young leaf color in eggplant using BSA-seq, identifying candidate genes for this trait.

## Key findings

- Young leaf color in eggplant is controlled by a single incompletely dominant gene.
- A QTL on chromosome 10 was identified as associated with young leaf color.
- Three candidate genes (Smechr1002213, Smechr1001752, Smechr1001815) were suggested to regulate leaf color formation.

## Abstract

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.