In silico characterization and expression analysis of SnRK2 family in barley

Panahi Fakoor, Yaser; Shobbar, Zahra-Sadat; Pourabed, Ehsan; Ghane Golmohamadi, Farzan; Razavi, Seyed Morteza

In silico characterization and expression analysis of SnRK2 family in barley

Document Type : Research Paper

Authors

¹ M.Sc., Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran

² Assistant Professor, Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Education and Extension Organization (AREEO), Karaj, Iran

Abstract

Abiotic stresses are among major factors limiting crop yields, and SnRK2 protein kinases are one of the key regulators of plant response to abiotic stresses. Due to the economic importance, cultivation area, and tolerance of barley to the abiotic stresses, identification and characterization of SnRK2 family members in barley is performed in present research. SnRK2 conserved sequences were used as a query for tBLASTn analysis in different databases such as NCBI and international barley sequencing consortium against all of the reported barley sequences. As a result, 10 members were identified (HvSnRK2.1 to HvSnRK2.10) which 8 of them were not yet reported. These HvSnRK2 members were aligned with AtSnRK2s and OsSnRK2s and a phylogenetic tree was constructed. Detection of chromosomal localization, promoter analysis and gene structure determination was also performed. Half of the family members were located on chromosome 2 and the rest on chromosomes 1, 4, 5 and 6. Number of introns in the gene family members varied from 0 to 8. Totally, 19 sorts of cis elements including abiotic stress responsive elements were found in HvSnRK2s promoter sequences. Expression pattern of the family members were evaluated in different tissues, treatments and genotypes, based on the microarray data. Expression of HvSnRK2.6 was up-regulated by drought, salt and cold stresses implementing its important role in signal transduction of these stresses and tolerance induction to them. It is expected that this gene could be used in plant manipulation and breeding programs aimed for tolerance enhancement to abiotic stresses especially drought.

Keywords

20.1001.1.22520783.1394.5.12.3.6

Main Subjects

Bioinformatics

Full Text

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