Elucidating Morpho-Molecular Diversity and Population Structure of Elite Tomato (Solanum lycopersicum L.) Germplasm

Abstract Background Tomato (Solanum lycopersicum L.) crop is well known for its versatility worldwide and recognized as model species used extensively for various genetic studies. This study was carried out to evaluate some indigenous and exotic tomato genotypes for divergence studies using a combined multidisciplinary approach. Regardless of its significant contributions to nutritional and economic status globally, lack of diversity among the cultivated species has been witnessed extensively due to the intensive selection of genotypes with respect to specific traits and severe genetic bottlenecks. Methods and Results As a part of the countermeasure to restore the genetic diversity in tomato, the incorporation of wild varieties, landraces, and traditional varieties in the crop-breeding scheme is highly acknowledged. On these grounds, inter and intra-genetic diversity was assessed among 51 tomato genotypes morphologically, biochemically, and by using DNA-based marker SSR markers. A total of 15 discrete agro-morphological traits and 6 biochemical traits were undertaken in the current study for evaluating the analysis of variance, genetic parameters, and correlation. Morphological clustering divided the genotypes into 2 clusters and the genotype-wise distance matrix was obtained to identify the most diverse genotypes. PCA analysis was conducted to understand the directive relation of traits and the magnitude of variability contributed by them. SSR profiling with 24 primers identified 44 alleles with 1.83 as a mean number of alleles/SSR with an average PIC value of 0.31. Structure analysis revealed two sub-populations (K = 2). The AMOVA indicated that 98% of the total variation was present within the populations. This study presents a roadmap for composing future breeding strategies for integrating desirable traits in novel tomato lines that combine robustness and nutritive value. Conclusion The tomato genotypes were found to be a rich resource of germplasm with respect to genetic variation and needs to be preserved and utilized efficiently in breeding programs to rescue the gene pool wealth. The clustering patterns revealed the distinctiveness and relatedness of the panel under study. A substantial degree of morphological and molecular diversity was attained within and among the genotypes and populations. The efficiency of the SSR marker technique used in the current study can be considered for future breeding programs.