Genetic diversity and population structure assessment of Iraqi tomato accessions using fruit characteristics and molecular markers

Accessions are a prospective source of genetic variability, as well as valuable genetic resources for crop improvement. Assessing the population structure and genetic diversity of Iraqi tomato accessions is therefore critical in breeding programs for the production of high-yielding cultivars, as well as widening the genetic base of tomato. Using fruit quality indices and molecular markers, a panel of 64 tomato accessions taken from six northern provinces of Iraq were analyzed for genetic diversity and population structure. In the analysis of variance, the fruit phenotypic data revealed a high level of significant variability (p ≤ 0.01) among tomato accessions. The most important characteristics for explaining fruit morphological variability, according to principal component analysis (PCA), were fruit weight, fruit size, fruit diameter, total soluble solids, and moisture content. Seven clades with different fruit characteristics were revealed in the cluster analysis. Genetic diversity and relationships among accessions were analyzed using thirteen inter simple sequence repeat (ISSR), twenty-six start codon-targeted (SCoT) polymorphisms, and fifteen conserved DNA-derived polymorphisms (CDDP). The ISSR, SCoT, and CDDP markers generated 121, 294, and 170 polymorphic bands, respectively, showing a high prevalence of polymorphism. The average polymorphism information content (PIC) values for ISSR, SCoT, and CDDP were 0.81, 0.84, and 0.84, respectively. The accessions were divided into two groups based on the cluster and STRUCTURE analysis results. The Mantel test revealed that three sets of markers had a positive and significant relationship. The increased genetic variation within the populations was found by the analysis of molecular variance (AMOVA), indicating considerable gene exchange between populations. To the best of our knowledge, this is the first extensive report on the use of gene-targeted molecular markers for genetic diversity analysis of tomato accessions in Iraq. Our findings demonstrated the utility of these markers for genetic diversity study in tomato accessions, as well as their potential for genome diversity and germplasm conservation.