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

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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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.

Corresponding authors

Correspondence to Bahman Panahi or Seyyed Abolghasem Mohammadi.

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The authors declare that they have no conflict of interest.

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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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Keywords

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