Development of indel markers in eggplant using new generation sequencing data

Genetic diversity is very important for the sustainability of breeding programs and the transfer of new traits to cultivars. Due to the inadequacy of morphological markers in determining genetic diversity, molecular markers are preferred. Among molecular marker systems, markers such as SSR (Simple Sequence Repeat), AFLP (Amplified Fragment Length Polymorphism), ISSR (Inter Simple Sequence Repeat) and SNP (Single Nucleotide Polymorphism) are used to determine genetic diversity, to create genetic linkage maps and to examine genome structure in many plant species. SSR and AFLP can be separated by Polyacrylamide Gel Electrophoresis. However, SNP (Single Nucleotide Polymorphism) markers are obtained using next generation sequencing data and require high cost. The products of InDel primers designed from both sides of the insertion-deletion sequence region are suitable to separate in agarose gel with high polymorphism rate. Various studies have been carried out in many plant species by developing InDel markers. However, studies to develop InDel markers in eggplant (Solanum melongena L) are limited and no eggplant InDel markers suitable to agarose gel electrophoresis have been found in the literature. The aim of this study was to develop InDel markers for different eggplant genotypes using next generation sequencing data. InDel regions were identified using Dindel software program and primers associated with the identified InDel regions were designed using Primer3 program. The newly designed InDel markers are aimed to contribute to future genetic mapping and breeding studies by identifying eggplant genetic resources and determining their polymorphism level.