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Genome-wide identification and co-expression network analysis of nuclear factor-Y in barley revealed potential functions in salt stress

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Abstract

Nuclear factor-Ys (NF-Ys) were previously shown to have important regulatory impacts in different developmental and physiological process. However, in barley the function of the NF-Y genes at system levels is not well known. To identify barley NF-Ys, Arabidopsis and wheat NF-Y protein sequences were retrieved and the BLAST program along with the hidden Markov model were used. Multiple sequence alignments of identified NF-Ys were constructed using ClustalW. Expression patterns of the NF-Ys at different physiological and developmental conditions were also surveyed based on microarray datasets in public databases and subsequently co-expression network were constructed. Validation of in silico expression analysis was performed by real-time qPCR under salt stress condition. In total, 23 barley NF-Ys (8 NF-YA, 11 NF-YB and 4 NF-YC) were identified. Based on the sequence homology, the subunits of the NF-Y complex were divided into three to five groups. Structural analysis highlighted the conserved domains of HvNF-YA, HvNF-YB and HvNF-YC. Co-expression network analysis indicated the potential functions of HvNF-Ys in photosynthesis, starch biosynthesis and osmotic stress tolerance. The results of qRT-PCR also confirmed the HvNF-Ys roles in adaptation responses of barley to salt stress. We identified some potential candidate genes which could be used for improvements of cereals tolerance to salinity stress.

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Acknowledgements

We thanks of Dr Jalil Fallah (Lister Institute of Microbiology) for providing the Real time PCR reagants.

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Authors and Affiliations

  1. Department of Genomics, Branch for Northwest and West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran

    Bahman Panahi

  2. Department of Plant Breeding and Biotechnology, University of Tabriz, Tabriz, Iran

    Seyyed Abolghasem Mohammadi & Hossein Abbasi Holaso

  3. Center of Excellence in Cereal Molecular Breeding, University of Tabriz, Tabriz, Iran

    Seyyed Abolghasem Mohammadi

  4. Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, Prague 6, Czech Republic

    Kamil Ruzicka

  5. Higher Education Complex of Shirvan, Shirvan, Iran

    Mohammad Zare Mehrjerdi

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  1. Bahman Panahi
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Contributions

Conceived and designed the experiments: BP, SAM. Performed the experiments: BP, HAH,SAM, Analyzed the data: BP, SAM, HAH, MZM, KR. Wrote the paper: BP, SAM, KR, HAH, MZM.

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Correspondence to Bahman Panahi or Seyyed Abolghasem Mohammadi.

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Panahi, B., Mohammadi, S.A., Ruzicka, K. et al. Genome-wide identification and co-expression network analysis of nuclear factor-Y in barley revealed potential functions in salt stress. Physiol Mol Biol Plants 25, 485–495 (2019). https://doi.org/10.1007/s12298-018-00637-1

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