Morpho-phytochemical and molecular diversity in cherry tomato (Solanum lycopersicum var. cerasiforme) germplasm

Cherry tomatoes (Solanum lycopersicum var. cerasiforme) have emerged as one of the most sought-after exotic crops in Bangladesh, necessitating genetic diversity assessment for effective breeding programs. This study evaluated 36 cherry tomato genotypes at Hajee Mohammad Danesh Science and Technology University, Dinajpur, Bangladesh, from September 2021 to March 2022, using a Randomized Complete Block Design with three replications. Analysis of variance revealed significant differences among the genotypes. Red0107 (3.74 kg plant–1), Red02 (3.34 kg plant–1), and Red001 (3.27 kg plant–1) were identified as high-yielding genotypes. Meanwhile, TM-02 recorded the highest total carotenoid content, TM-03 had the highest total sugar content, and Cherry tomato-4 exhibited the highest total lycopene content. Morphological clustering grouped the genotypes into five clusters, with the highest inter-cluster distance observed between Cluster III and Cluster V. Principal component analysis explained 82.03% of total variation, and biplot analysis identified several promising genotypes for total lycopene content and fruit set. Molecular analysis using 14 SSR markers revealed allelic variation (3–8 alleles per marker), with SSR63 exhibiting the highest polymorphism. Population structure analysis identified three groups. Morphological and molecular clustering showed alignment, confirming genetic diversity. Based on the combined analyses, TM-01, TM-02, Orange, CTOM-1208, TM-06, Cherry tomato-5, Red03, Red007, TM-23, Cherry tomato-2, Cherry tomato-3, BU cherry tomato-2, TM-07, and Red04 are recommended as potential parents for future hybridization programs.