Morpho-molecular diversity analysis of chilli (Capsicum sp.) genotypes using quantitative traits and SSR markers

The processing industry increasingly demands high-quality chilli, yet quality has declined due to yield-oriented genotype selection and intermixing of local cultivars. To address this, 46 genotypes belonging to Capsicum annuum, C. chinense, and C. frutescens were evaluated for yield, biochemical traits, and molecular diversity at Tamil Nadu Agricultural University, Coimbatore, during Kharif 2023. Analysis of variance revealed significant differences across 15 traits. High GCV and PCV were recorded for plant height, fruit length, fruit girth, fresh and dry fruit weight, number of fruits per plant, number of seeds per fruit, capsaicin, capsanthin, ascorbic acid, and titratable acidity. Mahalanobis D2 analysis grouped the genotypes into seven clusters, while PCA explained 75.88% of total variation. Among 25 SSR markers screened, 16 (64%) were polymorphic, with PIC values ranging from 0.112 to 0.851 (mean 0.543). Molecular clustering using SSRs separated the genotypes into five major groups. Genetic similarity ranged from 0.06 to 0.97, and markers AVRDC PP 67, EPMS 376, and CAMS 647 were identified as the most informative for diversity assessment. AMOVA indicated that 57% of the variation occurred among individuals, while PCoA revealed that the first three coordinates accounted for 35.01% of cumulative variation. The genotypes CC-CBE-003, CC-CBE-004, and CC-CBE-017 showed superior yield and biochemical attributes, highlighting their potential as high-value raw materials for pharmaceutical and processing industries. The comprehensive morphological and molecular information generated will aid future crop improvement and germplasm conservation efforts.