Capsicum annuum Raw sequence reads

Capsicum is a highly valued crop for fresh as well as industrial applications, which faces problems of yield, quality, and biotic and abiotic stress tolerance. Hence, this study aimed to unravel the genetic loci linked with 11 agronomic traits in Capsicum species through genome wide association studies by genotyping-by-sequencing. A diverse set of 100 Capsicum genotypes was evaluated under field conditions for two years. Further, genotyping was performed through GBS using Illumina platform to detect single nucleotide polymorphism (SNP) markers linked to these traits. The GBS data analysis resulted into a high-quality 16,745 SNPs. The linkage disequilibrium was assessed in 16,745 SNPs across the 12 chromosomes of Capsicum, as a result 835 LD blocks were determined. GWAS analysis was performed with 16,745 SNPs using Generalized Linear Model (GLM), Mixed Linear Model (MLM), and Fixed and random model Circulating Probability Unification (FarmCPU) models. As a result, 34 SNPs significantly associated within 28 QTL regions were identified. Few of the putatively identified candidate genes were functionally validated by qRT-PCR using contrasting genotypes for these traits. Overall, our study generates genomics resources and reveals candidate genes associated with key traits in Capsicum, which will accelerate genomics-assisted breeding for high genetic gain.