Genome-Wide InDel Marker Development and Genetic Diversity Analysis of 52 Tomato Germplasm Accessions

To address the challenges of narrow genetic backgrounds and low phenotypic selection efficiency in tomato breeding, comparative genomics was applied. Based on the genomic sequences of five tomato varieties (‘Micro-Tom’, ‘Moneymaker’, ‘M82’, ‘Heinz 1706’, and ‘LA2093’), a total of 285,796 InDel loci were preliminarily identified. Based on these loci, a total of 255 pairs of molecular markers were developed. Subsequently, based on InDel length, polymorphism, and electrophoretic performance, 63 InDel markers with stable amplification, clear polymorphic bands, and coverage across all 12 chromosomes were rigorously selected. These markers were subsequently used to analyze the genetic diversity of 52 tomato germplasm resources. The polymorphism information content (PIC) values of the markers ranged from 0.074 to 0.402, with an average of 0.2804. Cluster analysis based on InDel genotyping data divided the 52 germplasm samples into four distinct groups with significant genetic differentiation, which was validated in conjunction with previously collected phenotypic data from the 52 tomato germplasm resources. Furthermore, a set of core InDel primer combinations (24 pairs) was selected to construct unique DNA fingerprint profiles for each germplasm group. Overall, the InDel markers developed in this study provide an efficient tool for evaluating genetic diversity in tomato germplasm and offer a reliable molecular basis for germplasm identification, heterosis prediction, and marker-assisted breeding, thereby facilitating the development of improved tomato cultivars.