Molecular dissection of heat stress tolerance in chilli (Capsicum annuum L.) through GBS approach
the research farm of the Division of Vegetable Science, ICAR-IARI, New Delhi, India. The F1 was developed by crossing DLS-161-1 (heat tolerant) and PBC-345 (heat susceptible) and subsequently selfed to generate the F2 population. Phenotypic evaluation of the parental lines revealed that DLS-161-1 performed significantly better for key morphological, physiological, and biochemical traits affected by heat stress, including plant height, number of fruits per plant, average fruit length, canopy temperature depression, membrane stability index, pollen viability, photosynthetic rate, and antioxidant enzyme activities. These results indicate that DLS-161-1 possesses superior adaptability to high-temperature conditions through efficient regulation of multiple morphological, physiological, and biochemical mechanisms.A wide range of variation observed in the F2 population under high-temperature conditions confirmed the quantitative nature of heat tolerance. Genotyping of the F2 population was performed using double digest restriction-site associated DNA (ddRAD) sequencing on the Illumina NovaSeq 6000 platform, generating 121.85 Gb of raw sequencing data. Alignment with the reference genome of Capsicum annuum followed by variant calling using the UGBS-GATK pipeline resulted in the identification of 8,766,819 polymorphic SNP markers, which were grouped into 12 linkage groups. QTL analysis using composite interval mapping identified 161 QTLs associated with 22 traits; however, after eliminating those with low LOD scores and minimal phenotypic variance, 7 major QTLs were retained. The LOD values of these QTLs ranged from 2.57 to 7.48, while the phenotypic variance explained (PVE) ranged from 10.00% to 15.21%, highlighting their significance for heat stress tolerance and their potential utility in marker-assisted breeding of chilli.