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Genome-wide analysis of Phaseolus vulgaris C2C2-YABBY transcription factors under salt stress conditions

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Abstract

The aim of this study was to identify and characterize the C2C2-YABBY family of genes by a genome-wide scale in common bean. Various in silico approaches were used for the study and the results were confirmed through common molecular biology techniques. Quantitative real-time PCR (qPCR) analysis was performed for identified putative PvulYABBY genes in leaf and root tissues of two common bean cultivars, namely Yakutiye and Zulbiye under salt stress condition. Eight candidate PvulYABBY proteins were discovered and the length of these proteins ranged from 173 to 256 amino acids. The isoelectric points (pIs) of YABBY proteins were between 5.18 and 9.34 and ranged from acidic to alkaline, and the molecular weight of PvulYABBYs were between 18978.4 and 28916.8 Da. Three segmentally duplicated gene couples among the identified eight PvulYABBY genes were detected. These segmentally duplicated gene couples were PvulYABBY-1/PvulYABBY-3, PvulYABBY-5/PvulYABBY-7 and PvulYABBY-6/PvulYABBY-8. The predicted number of exons among the PvulYABBY genes varied from 6 to 8 exons. Additionally, all genes found included introns within ORFs. PvulYABBY-2, -4, -5 and -7 genes were targeted by miRNAs of five plant species and a total of five miRNA families (miR5660, miR1157, miR5769, miR5286 and miR8120) were detected. According to RNA-seq analysis, all genes were up- or down-regulated except for PvulYABBY-1 and PvulYABBY-6 after salt stress treatment in leaf and root tissues of common bean. According to the qPCR analysis, six out of eight genes were expressed in the leaves but only four out of eight genes were expressed in the roots and these genes exhibited tissue- and cultivar-specific expression patterns.

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Acknowledgements

Ilker Buyuk received financial support from TUBITAK-BIDEB 2219- International Postdoctoral Research Fellowship Programme (Grant no: 1059B191600028) for his studies at Michigan State University in USA.

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Authors and Affiliations

  1. Department of Agricultural Biotechnology, Faculty of Agriculture, Siirt University, Siirt, Turkey

    Behcet İnal

  2. Department of Biology, Faculty of Science, Ankara University, Ankara, Turkey

    İlker Büyük & Sümer Aras

  3. Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA

    İlker Büyük

  4. Faculty of Science, Department of Molecular Biology and Genetics, Erzurum Technical University, Erzurum, Turkey

    Emre İlhan

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  1. Behcet İnal
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  2. İlker Büyük
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Correspondence to İlker Büyük.

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İnal, B., Büyük, İ., İlhan, E. et al. Genome-wide analysis of Phaseolus vulgaris C2C2-YABBY transcription factors under salt stress conditions. 3 Biotech 7, 302 (2017). https://doi.org/10.1007/s13205-017-0933-0

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