Morphological and molecular characterization of Cucurbita moschata genotypes: insights from RAPD and SSR marker analyses across Indian agro-climatic zones

Cucurbita moschata (pumpkin) is the most important vegetable crop that belongs to the Cucurbitaceae family and is widely cultivated in India. The present study explores both morphological traits and molecular markers (RAPD and SSR) to assess the germplasm diversity within the species and their relationship. The study consisting of 34 pumpkin genotypes collected from different agro-climatic zones in India. Morphological data reveals significant variation in quantitative traits, such as flowering time (42–60 days) for male flowering and (48–61 days) for female flowering, number of primary branches (3–4), node for first flower (12–17), vine length (3.15–6.55 m), fruit weight (1.55–8.98 kg), polar and equatorial diameter (38.34–90 and 40–96.75 cm), and yield per plant (3.1–17.96 kg). The RAPD analysis, employing 25 primers, exhibited high polymorphism (76.4%) among the amplified DNA segments while the polymorphism information content (PIC) varied from 0.4 to 0.95. Similarly, the study employed eight polymorphic SSR primers to analyze microsatellite markers, revealing a more moderate polymorphism level (5.36%). The percentage of polymorphic products in the case of RAPD and SSR markers was 76.4 and 58.9, respectively. The study provides detailed information on broader as well precise allelic genetic diversity by using RAPD and SSR markers respectively, which is crucial for targeted breeding and conservation of important genetic traits in C. moschata germplasm. RAPD and SSR markers revealed significant polymorphism (76.4% RAPD), with consistent clustering patterns observed across molecular and morphological data. These findings underscore the utility of integrating molecular markers in breeding strategies for C. moschata.