Cilt:28 Sayı:01 (2019)

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https://dspace.ankara.edu.tr/handle/20.500.12575/76462

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Browsing Cilt:28 Sayı:01 (2019) by Subject "Bioinformatics"

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    Common bean (phaseolus vulgaris l.) dof transcrıptıon factors dıfferentıally expressed under salt stress
    (Ankara Üniversitesi Fen Fakültesi, 2019) Büyük, İlker; Biyoloji; Fen Fakültesi
    DNA-binding with one finger (DOF) transcription factor family has found to be playing important roles for seed germination, photosynthesis, plant development and stress responses in several plant species. Hence, this study aimed to characterize the DOF genes in common bean at the genome-scale level. The various bioinformatics tools were used and the results were confirmed through bench-work studies. Expression levels of putative PvDOF genes were analyzed using publicly available RNA-seq data and the expression levels of five selected PvDOF genes were further analyzed through qPCR in tolerant cv. ‘Yakutiye’ and sensitive cv. ‘Zulbiye’ subjected to salt stress. As a result, 42 candidate PvDOF genes were defined. The length of PvDOF proteins ranged from 181 (PvDOF-41) to 503 (PvDOF-35) amino acids (aa). pIs of PvDOF proteins were between 5.03 (PvDOF-21) and 8.92 (PvDOF-6) ranging from acidic to alkaline, and the molecular weight of PvDOFs were between 21944.3 Da (PvDOF-14) and 54786.5 Da (PvDOF-35). While the highest number of PvDOFs was found on chromosome 2 (eight genes), the lowest number of PvDOF genes was identified on chromosomes 4 and 7 (one gene). Two segmentally duplicated gene couple were detected. A total of 21 PvDOF genes were targeted by miRNAs of 20 plant species. According to the normalized RPKM (Read Per Kilobase Million) values which were obtained from the RNAseq analysis, PvDOF-6, 8, 9, 17, 27, 28, 30, 35 and 39 genes were found up- or down-regulated after salt stress treatment in the leaf and root tissues of common bean. Additionally, the most of the qPCR data were found to be consistent with the RNAseq data and the PvDOF17 gene was found as being the most expressional divergent gene between cv. ‘Zulbiye and cv. ‘Yakutiye’. In conclusion, the results of this study might help understanding the biological roles of PvDOF TF family under salt stress and can be used for the improving of common bean through biotechnological approaches.