# Rapid Identification of Candidate SNPs and QTLs for Capsicum annuum Chili Fruit Size and Capsaicin Content Using ddRAD-Sequencing and Bulk Segregant Analysis

## TL;DR

This study identifies genetic markers linked to chili fruit size and pungency using sequencing and genetic analysis, offering targets for breeding.

## Contribution

The study combines ddRAD-sequencing and bulk segregant analysis to identify SNPs and QTLs influencing multiple chili traits.

## Key findings

- BSA identified SNPs associated with pungency, fruit length, and fruit weight.
- Genetic mapping revealed overlapping QTL regions on chromosome 6 influencing multiple traits.
- The findings suggest potential pleiotropy and provide targets for multi-trait breeding.

## Abstract

Fruit size and pungency are key yield and quality traits in chili. This study combines high-throughput genotyping with bulk segregant analysis (BSA) to identify candidate SNPs and quantitative trait loci (QTLs) by analyzing extreme phenotypes from a Ghotki × Chakwal-4 F2 population. The traits were fruit length, diameter, length-to-diameter ratio, and weight, along with capsaicin content. Significant correlations were observed among length, diameter, and length-to-diameter ratio. A total of 534 single nucleotide polymorphisms (SNP) markers were used to develop genetic maps from 4315 to 6607 cM long. The SNP frequency data was pooled for the 25% of individuals showing extreme values for each measured trait, and bulk segregant analysis (BSA) was performed. BSA identified high-scoring SNPs associated with pungency (SNP 1_41308232; SNP 12_104377148), fruit length (SNP 1_92509300; SNP 6_218780813), and fruit weight (SNP 6_100989762 and SNP 6_138660974). Genetic mapping identified twelve pungency QTLs, three for fruit length, two for fruit diameter, two for the length-to-diameter ratio, and thirteen for fruit weight. Overlapping QTL regions on chromosome 6 influence fruit length, fruit width, and capsaicin content, indicating potential pleiotropy and offering promising targets for multi-trait selection in chili breeding. The study identifies key SNPs and QTLs that simultaneously influence chili fruit size and pungency, providing valuable targets for multi-trait breeding.