Characterization of EST‑SSR markers in bread wheat EST related to drought tolerance and functional analysis of SSR‑containing unigenes

Abstract

Bread wheat (Triticum aestivum) is an important staple food around the world. The enormous volume of the genome of wheat makes it quite slow to progress in traditional scientific research. On the other hand, incessant databases and suitable tools on web sites make progress in wheat research quicker and easier. Drought is a major abiotic stress in accordance with weather changes and accelerated increase in drylands. In this study, 9077 ESTs related to drought tolerance in hexaploid wheat were downloaded from NCBI and assembled into 12062 contigs and 4141 singletons. It was found that trinucleotide had the highest frequency 64.71%. Moreover, 53.80% of SSRs found in coding regions in respect of ORFs. The highest amino acids found for tri-and hexanucleotides were Arginine. In addition, 81% of SSR-containing unigenes had one chromosome location and the highest number of loci was found in chromosomes 1B (69). The distribution of genic SSR loci among the 21 wheat chromosomes, the three subgenomes, and the seven homoeologous groups of wheat chromosomes was significant, with P<0.01 indicating a non-random distribution. Functional annotation and characterization of SSR-containing unigenes have been performed. Eighty-six sequences were identified and sorted into 25 putative TF families and establish 166 pathways using KEGG. Primer-BLAST was used to predict the polymorphism, which was 39% of the 63 primer pairs of SSR markers. Our current study attempts to help farmers in wheat breeding programs to have drought-tolerant accessions, particularly in developing countries.