COMMON BEAN (Phaseolus vulgaris L.) DOF TRANSCRIPTION FACTORS DIFFERENTIALLY EXPRESSED UNDER SALT STRESS

Year 2019, Volume: 28 Issue: 1, 43 - 66, 30.06.2019

İlker Buyuk , Behcet Inal , Emre Ilhan , Sumer Aras

Abstract

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.

Keywords

Bioinformatics, DOF, RNAseq, qPCR, Phaseolus vulgaris, salinity

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