Common wheat (Triticum aestivum) is the most widely grown cereal crop and is cultivated extensively in dry regions. Water shortage, resulting from either drought or salinity, leads to slow growth and loss of wheat yield. In order to predict new genes responsive to the drought and salt stresses in wheat, 6,717 expressed sequence tags (ESTs), expressed in drought and salinity stress conditions were collected from the National Center for Biotechnology Information (NCBI). The downloaded ESTs were clustered and assembled into 354 contigs; 14 transcription factor families in 29 contigs were identified. In addition, 119 contigs were organized in five enzyme classes. Biological functions were obtained for only 324 of the 354 contigs using gene ontology. In addition, using Kyoto Encyclopedia of Genes and Genomes database, 191 metabolic pathways were identified. The remaining contigs were used for further analysis and the search for new genes responsive to drought and salt stresses. These contigs were mapped on the International Wheat Genome Sequencing Consortium RefSeq v1.0 assembly, the most complete version of the reference sequence of the bread wheat variety Chinese Spring. They were found to have from one to three locations on the subgenomes A, B, and D. Full-length gene sequences were designed for these contigs, which were further validated using promoter analysis. These predicted genes may have applications in molecular breeding programs and wheat drought and salinity research.
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
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