Assessment of genetic diversity and population structure among some tomato (Solanum lycopersicum) genotypes using ISSR markers

Document Type : Research Paper

Authors

1 PhD student, Department of Plant Production and Genetics, Faculty of Agriculture, Shahid Bahonar University, Kerman, Iran

2 Assistant Professor, Research and Technology Institute of Plant Production, Afzalipour Research Institute, Shahid Bahonar University of Kerman, Kerman, Iran

3 Department of Plant Production and Genetics, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran

4 Assistant Professor, Department of Plant Production and Genetics, Faculty of Agriculture, Shahid Bahonar University, Kerman, Iran

5 Assistant Professor, Research and Technology Institute of Plant Production, Afzalipour Research Institute, Shahid Bahonar University of Kerman, Kerman, Iran.

Abstract

Objective
The aim of this study was assessment of the population structure and genetic diversity among 33 tomato genotypes including standard-fruit and cherry types, using ten ISSR markers through AMOVA, PCoA and STRUCTURE analysis in order to finding the best genetic materials for the future breeding program.
Materials and methods
DNA extraction was preformed from young leaves at first fruit set growth stage via CTAB method and genetic diversity of 33 genotypes in this study were assessed using 10 ISSR markers. PCR products of each ISSR marker were separated by agarose gel electrophoresis and presence/absence of the electrophoresis bands were scored. Afterward, different parameters including number and percentage of polymorphic bands, PIC and MI were calculated. The population diversity and structure were analyzed using UPGMA clustering method, STRUCTURE (admixture model), AMOVA and principal coordinates analysis (PCoA). PCoA data validation was performed using discriminant function analysis (DFA) method.
Results
A total number of 10 ISSR anchored primers produced 130 bands of which 71 bands (more than 54.5%) were polymorphic. The highest polymorphic content was observed in markers (GA)₈C, (AC)₈G and (AG)₈YC with 76.47, 75 and 68.42 percent respectively and the lowest polymorphic percentage was observed in marker (AGG)₆ with 23.07 percent. Based on the results of this study, markers with the highest polymorphic percentage were selected as suitable markers for studying the genetic diversity of tomato. STRUCTURE analysis K = 3 showed the proportion of shared genetic groups among three populations of tomato. Analysis of molecular variance study revealed that 91% of the total variance was within groups groups and 9% among group. Analyzing by PCoA reproduced a three cluster pattern in which Maya (T12) and Lucid Gem American (T16) appeared as distant branches. DFA also confirmed clear group separation.
Conclusions
ISSR markers particularly (GA)₈C and (AC)₈G effectively discriminated tomato genotypes. The identification of distinct accessions such as T12 and T16 provides valuable parents for wide crosses to broaden allelic diversity. The observed partial overlap between standard-fruit and cherry types is consistent with a shared breeding history and supports crossing across market classes to expand variation.

Keywords

References

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Agricultural Biotechnology Journal
Volume 18, Issue 1
January 2026
Pages 139-162

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