Integrated analysis of morphological and molecular diversity in tomato (Solanum lycopersicum L.) cultivated under protected environment

The continuous use of a narrow genetic base in tomato ( Solanum lycopersicum L.) breeding programmes has constrained the development of high-yielding cultivars with superior fruit quality and broader adaptability. The present investigation was undertaken to assess the agro-morphological and molecular diversity among tomato genotypes and to identify genetically diverse parental lines for utilization in breeding programmes under protected cultivation. Thirty-six tomato genotypes, selected from an initial set of fifty-eight genotypes based on growth and yield performance, were evaluated using fourteen quantitative and qualitative traits during two growing seasons, viz., spring-summer and autumn-winter. Significant differences among the genotypes for all the studied traits indicated the presence of substantial genetic variability. Principal component analysis explained 72.94 and 75.56 per cent of the total variation during the spring-summer and autumn-winter seasons, respectively. Morphological diversity analysis grouped the genotypes into fifteen clusters during spring-summer and eight clusters during autumn-winter season, reflecting considerable genetic divergence. Out of eighty-two SSR primers screened, forty-one were polymorphic, of which twenty-five informative primers were selected for molecular characterization, generating a total of sixty-two alleles. Molecular analyses, including UPGMA clustering, neighbour-joining analysis, principal coordinate analysis (PCoA), population structure analysis and analysis of molecular variance (AMOVA), consistently revealed substantial genetic diversity and distinct genetic groupings among the evaluated genotypes. By integrating agro-morphological performance with molecular diversity analyses, genotypes PTH-1, Palam Pride, BT-20-3, CLN-1314-G and Naveen 2000 + were identified as promising donor parents because of their superior agronomic performance and distinct genetic backgrounds. These genotypes provide valuable parental resources for heterosis breeding and the development of high-yielding, superior-quality and genetically diverse tomato cultivars suitable for protected cultivation.