Molecular characterization and construction of population structure of selected tomato genotypes (Solanum lycopersicum L.) under high temperature stress condition

Abstract

The study entitled "Molecular characterization and construction of population structure of selected tomato genotypes (Solanum lycopersicum L.) under high-temperature stress conditions” was undertaken during 2019-20 at the Department of Plant Physiology, College of Agriculture, Vellayani. The study was undertaken to evaluate the molecular variation between different tomato genotypes using simple sequence repeat (SSR) markers and the construction of the population structure of tomato genotypes. Tomato (Solanum lycopersicum) is the second most important vegetable crop, cultivated worldwide in both temperate and tropical regions. High-temperature stress is one of the major abiotic stress affecting tomatoes and significantly reducing their fruit yield and quality. Molecular markers linked to high temperature can be used for marker-assisted selection for high-temperature tolerance in tomato genotypes. Hence the present study was focused on the identification of molecular markers linked to high-temperature tolerance in tomato. The study included an experiment, in which twenty two tomato genotypes (KAU released varieties, NBPGR accessions including wild relatives of tomato) were raised in pot trays and the genomic DNA from one-month-old leaf samples was isolated by CTAB method. The quality and quantity of the isolated DNA from the twenty-two genotypes were analyzed. After checking the quality and quantity of DNA samples, they were screened using twenty-five microsatellite primers. PCR reaction was carried out using 25 selected primers of which 3 primers SSR 80, SSR 331, SSR 341 did not show any amplification and hence they were not used for further analysis. Out of the twenty-two; fifteen SSR markers viz., SSR450, SSR 602, SSR20, SSR111, SSR70, SSR 124, SSR 293, SSR 19, SSR115, SSR 304, SSR 276, SSR 47, SSR 75, SSR 134 and SSR 4 amplified monomorphic banding patterns, hence they were not considered for further analysis. Seven markers were thus selected for final analysis. The polymorphic 114 markers for temperature tolerance were SSR 96, SSR 63, SSR 13, SSR 270, SSR 356, SSR 605, and SSR 248. Among the 7 SSR markers, distinct polymorphic bands for temperature tolerance was shown by markers SSR 63 and SSR 96. The value of polymorphic information content (PIC) is commonly used in genetics, which provides an estimate of the discriminatory power of a locus or loci, taking into account not only the number of alleles expressed but also the relative frequencies of those alleles, and is a measure of polymorphism for the locus marker used in linkage analysis. The PIC values for polymorphic markers ranged from 0 to 0.65. The primers which showed the highest PIC values were SSR96 (0.65) followed by SSR63 and SSR 248 (0.612). The population structure of the 22 genotypes was performed using the Bayesian model-based scoring software STRUCTURE v2.3.4. Structure analysis divided the 22 genotypes into four subpopulations, in which tolerant genotypes were grouped into one sub-population, whereas the moderately tolerant, susceptible genotypes, genotypes which showed mixed characteristics were grouped into separate sub-populations. The presence of a band was scored as 1 and absence was scored as 0. In the NTedit program of NTSYSpc (Numerical Taxonomy SYStem) version 2.10 software, binary data generated for all varieties for the polymorphic markers were entered. The phylogenetic tree was constructed using UPGMA (Un-weighted pair group method with arithmetic mean) using NTSYSpc cluster analysis software, resulted in the dendrogram and divided the 22 tomato genotypes into four major clusters. The pattern of grouping genotypes into the clusters was similar to that in the study of the population structure. Phenotypic data of the same genotypes were collected from the Department of Plant Physiology, College of Agriculture, Vellayani was utilized for the interpretation of molecular data, the grouping of genotypes obtained from population structure and cluster analysis. Based on the interpretation of all the data obtained, among the 22 tomato genotypes; Kashi Vishesh, Anagha, Vellayani Vijay 115 were grouped as tolerant varieties. IIHR-2200, Manuprabha, Akshaya were categorized as moderately tolerant varieties. Varieties that showed mixed characteristics were Nandi, Vaibhav, Pusa Ruby, Manulakshmi, Arka Alok, Sakthi, IIHR-26372, Arka Vikas, Arka Abha, IC-45, Arka Samrat and PKM-1. Genotypes that were categorized as susceptible varieties were Arka Saurabh, Pusa Rohini, Palam Pride, and Arka Rakshak. Among the markers, distinct polymorphism for temperature tolerance between temperature tolerant (Kashi Vishesh, Anagha, and Vellayani Vijay) and susceptible varieties (Arka Saurabh, Pusa Rohini, Palam Pride, and Arka Rakshak) was shown by SSR 63 and SSR 96.