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Genome-wide identification and expression analysis of the NF-Y family of transcription factors in Triticum aestivum

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Abstract

Nuclear Factor Y (NF-Y) is a trimeric complex that binds to the CCAAT box, a ubiquitous eukaryotic promoter element. The three subunits NF-YA, NF-YB and NF-YC are represented by single genes in yeast and mammals. However, in model plant species (Arabidopsis and rice) multiple genes encode each subunit providing the impetus for the investigation of the NF-Y transcription factor family in wheat. A total of 37 NF-Y and Dr1 genes (10 NF-YA, 11 NF-YB, 14 NF-YC and 2 Dr1) in Triticum aestivum were identified in the global DNA databases by computational analysis in this study. Each of the wheat NF-Y subunit families could be further divided into 4–5 clades based on their conserved core region sequences. Several conserved motifs outside of the NF-Y core regions were also identified by comparison of NF-Y members from wheat, rice and Arabidopsis. Quantitative RT-PCR analysis revealed that some of the wheat NF-Y genes were expressed ubiquitously, while others were expressed in an organ-specific manner. In particular, each TaNF-Y subunit family had members that were expressed predominantly in the endosperm. The expression of nine NF-Y and two Dr1 genes in wheat leaves appeared to be responsive to drought stress. Three of these genes were up-regulated under drought conditions, indicating that these members of the NF-Y and Dr1 families are potentially involved in plant drought adaptation. The combined expression and phylogenetic analyses revealed that members within the same phylogenetic clade generally shared a similar expression profile. Organ-specific expression and differential response to drought indicate a plant-specific biological role for various members of this transcription factor family.

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Abbreviations

AEL:

Apparent expression level

CBF:

CAAT-binding factor

CYC1:

Cytochrome c, isoform 1

EST:

Expressed sequence tag

HFM:

Histone-fold motif

LEC1:

LEAFY COTYLEDON1

NC2:

Negative Cofactor 2

NJ:

Neighbor-joining

NF-Y:

Nuclear Factor Y

TBP:

TATA-binding protein

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Acknowledgements

The authors are grateful to Jason Kam and Lindsay Shaw for providing RNA samples. The laboratory expense for this study was supported by a grant from the Australian Grains Research & Development Corporation.

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Authors and Affiliations

  1. CSIRO Plant Industry, 306 Carmody Road, St Lucia, QLD, 4067, Australia

    Troy J. Stephenson, C. Lynne McIntyre & Gang-Ping Xue

  2. School of Life Sciences, Queensland University of Technology, GPO Box 2434, Brisbane, QLD, 4001, Australia

    Troy J. Stephenson & Christopher Collet

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  1. Troy J. Stephenson
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  2. C. Lynne McIntyre
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  3. Christopher Collet
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  4. Gang-Ping Xue
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Correspondence to Gang-Ping Xue.

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Stephenson, T.J., McIntyre, C.L., Collet, C. et al. Genome-wide identification and expression analysis of the NF-Y family of transcription factors in Triticum aestivum . Plant Mol Biol 65, 77–92 (2007). https://doi.org/10.1007/s11103-007-9200-9

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