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

  • Bahman PanahiEmail author
  • Seyyed Abolghasem MohammadiEmail author
  • Kamil Ruzicka
  • Hossein Abbasi Holaso
  • Mohammad Zare Mehrjerdi
Research Article


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.


Nuclear factor Y Phylogeny Co-expression network qRT-PCR Salt stress 



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

Authors’ 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.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

12298_2018_637_MOESM1_ESM.docx (17 kb)
Supplementary material 1 (DOCX 16 kb)


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Copyright information

© Prof. H.S. Srivastava Foundation for Science and Society 2019

Authors and Affiliations

  • Bahman Panahi
    • 1
    Email author
  • Seyyed Abolghasem Mohammadi
    • 2
    • 3
    Email author
  • Kamil Ruzicka
    • 4
  • Hossein Abbasi Holaso
    • 2
  • Mohammad Zare Mehrjerdi
    • 5
  1. 1.Department of Genomics, Branch for Northwest and West Region, Agricultural Biotechnology Research Institute of Iran (ABRII)Agricultural Research, Education and Extension Organization (AREEO)TabrizIran
  2. 2.Department of Plant Breeding and BiotechnologyUniversity of TabrizTabrizIran
  3. 3.Center of Excellence in Cereal Molecular BreedingUniversity of TabrizTabrizIran
  4. 4.Laboratory of Hormonal Regulations in Plants, Institute of Experimental BotanyCzech Academy of SciencesPrague 6Czech Republic
  5. 5.Higher Education Complex of ShirvanShirvanIran

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