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Isolation and sequence analysis of DREB2A homologs in five crop species

Nayak, S., Balaji, J., Chattopadhyay, D., Upadhyaya, H.D., Hash, T., Polavarapu, K.K.B., Baum, M., McNally, K., Rodriguez, L.M., Blair, M.W., This, D., Hoisington, D.A. and Varshney, R.ORCID: 0000-0002-4562-9131 (2008) Isolation and sequence analysis of DREB2A homologs in five crop species. In: Plant & Animal Genomes XVI Conference, 12 - 16 January 2008, Town & Country Convention Center. San Diego, CA.


The transcriptional factor, DREB2A, is one of the promising candidate genes involved in drought tolerance in crop plants. In order to explore the possibilities of candidate gene-based association mapping across cereals (rice, barley and sorghum), legumes (common bean and chickpea) and root/tuber crops (potato and cassava) under ADOC project of Generation Challenge Programme, DREB2A was isolated using either specific or degenerate primers. After retrieving the sequences for DREB2A, a reconciled phylogenetic tree was constructed combining the gene-tree with the species-tree and degenerate primers designed for each clade of the phylogenetic tree. Gene-specific primers amplified putative DREB2A homologs in rice (AF300971), barley (AF521307), common bean (CV535836, BQ481823) and chickpea CAP2 (DQ321719), while degenerate primers amplified the corresponding gene in sorghum. The amplicons were generated and sequenced in 7-8 diverse genotypes from each species. The sequence information was used to construct a phylogenetic tree using the parsimony algorithm. The phylogenetic tree reveals distinct separation of the cereals and legumes. Crop-wise grouping of the putative DREB2A homologs was also evident. The sequences from all the species were checked for the presence of SNPs. A maximum of eight SNPs were found in the common bean DREB2A, indicating two distinct haplotypes, whereas a single SNP was observed in case of rice, sorghum and chickpea promoter and no SNPs were found in barley. As expected, the AP2 domain in DREB2A homologs is conserved across the species. Further sequence analysis is in progress to understand sequence diversity and effect of SNPs on gene function in these species.

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