Genetic diversity analysis with the development of new SSR markers in Cucurbita pepo L. population

Abstract

Cucurbitaceae family, contain lots of important species in terms of worldwide nutritional and economical value. Despite the molecular genetic researches conducted in recent years, genome data is quite limited for C. pepo which is agriculturally important. The main motivation of this work is to develop new and numerous SSR markers (Simple Sequence Repetitions) that is unique to Cucurbita genome which has extremely small number of genome-specific markers. The reference genome was scanned with bioinformatic tools in terms of repetitive motifs and 76744 genome-specific SSR loci were found. In this scope, 52303 SSR markers were developed for the first time by containing 20 chromosomes in C. pepo L. genotype and the data that belongs to the developed markers is saved in a database. The majority of the most common SSR motifs were detected as di-nucleotide repeats which was rich in terms of AT/AT. To evaluate the amplification efficiency and polymorphic band producing capability of newly developed SSR markers, a collection which contains 39 Cucurbita pepo L. genotypes is characterized and the SSR alleles are scored as 0/1, so that the data file was subjected to the analysis of genetic diversity in DARwin6 software program. The results of this study were evaluated as obtaining important molecular genetic markers of the pumpkin and using them in the future studies of molecular breeding and mapping to obtain important information.