Genetic diversity of 324 cultivated tomato germplasm resources using agronomic traits and InDel markers

The study of morphological and molecular diversity and grouping analysis for cultivated inbred tomato lines is very important to help breeders in selecting parental lines for hybrid breeding and developing heterotic groups. In this study, a total of 324 cultivated inbred tomato lines collected from various sources were investigated for the presence of 17 agronomic traits and subsequently genotyped with a 56- (insertion–deletion) InDel assay. The phenotypic coefficient of variation ranged from 5 to 108% with an average of 36%, and the range of phenotypic diversity index was 0.41– 2.06, with an average of 1.59. The outstanding traits in terms of causing phenotypic diversity of the inbred tomato lines are resistance to gray leaf spot, hypocotyl colour, growth habit, fruit shape, plant height, days to 30% first flower, weight per fruit, hardness, brix, acid, number of locules and transverse diameter of fruit by principal component analyses (PCA). The values of Shannon’s information index, polymorphic information content and heterozygosity are 0.61, 0.33 and 0.06 respectively. The PCA and Ward’s method for cluster multivariate analysis based on 17 agronomic traits revealed that there are four major groups with rich genetic diversity within groups. Model-based population structure analysis indicated that the 324 cultivated inbred tomato lines were separated into two main groups that were different from the results of the three main groups and five subgroups by Nei’s (Am Nat 106:283–292, 1973) cluster analysis based on InDel markers. The Mantel test correlation coefficient of the matrices of morphological and InDel distances was 0.229. Overall, this study reveals that 324 cultivated inbred tomato lines are diverse with high homozygosity and a rich genetic background. Nei’s (1973) cluster analysis can serve as an effective approach for assigning germplasm into groups and for providing guidelines for parental selection in hybrid tomato breeding.