Agarose-Resolvable SSR Markers Based on ddRADSeq in Chickpea

Abstract

Exploitation of genetic diversity is essential for sustainable crop production. Molecular markers have potential to reach these goals in more rapid and efficient manner. Simple sequence repeats (SSRs) are one of the most popular molecular markers in breeding studies due to their co-dominant inheritance, abundance in the genome, multi-allelic and reproducible nature. Here, we developed genomic SSR markers from chickpea with the use of ddRADSeq data. 1,396 SSR regions with an average of 530 SSR/Mb in the whole genome were successfully identified. Considering different types of repeats, dinucleotides were the most frequent type accounting for 62.03% of the total SSR regions identified, followed by trinucleotides (25.50%) and tetranucleotides (4.58%). The AT/TA motif was greatly characterized among dinucleotide repeats, and it was also the most common type in the chickpea genome accounting for 36.5% of the total SSR regions identified, followed by AG/GA (139) and TC/CT (135) among dinucleotide motifs. Considering their genomic distribution and simple visualization on agarose gels, we examined SSR regions of 10 bp and longer for identification of SSR markers. A total of 10 SSR markers were successfully designed and resulted in successful polymorphic bands among chickpea genotypes. Consequently, the results show that ddRADSeq is effective for marker development and these markers might be valuable for biodiversity studies, marker-assisted selection (MAS) and linkage map construction in chickpea.