BACKGROUND: Pearl millet (Pennisetum glaucum) is a cereal crop that possesses the ability to withstand drought, salinity and high temperature stresses. The NAC [NAM (No Apical Meristem), ATAF1 (Arabidopsis thaliana Activation Factor 1), and CUC2 (Cup-shaped Cotyledon)] transcription factor family is one of the largest transcription factor families in plants. NAC family members are known to regulate plant growth and abiotic stress response. Currently, no reports are available on the functions of the NAC family in pearl millet.
RESULTS: Our genome-wide analysis found 151 NAC transcription factor genes (PgNACs) in the pearl millet genome. Thirty-eight and 76 PgNACs were found to be segmental and dispersed duplicated respectively. Phylogenetic analysis divided these NAC transcription factors into 11 groups (A-K). Three PgNACs (− 073, − 29, and − 151) were found to be membrane-associated transcription factors. Seventeen other conserved motifs were found in PgNACs. Based on the similarity of PgNACs to NAC proteins in other species, the functions of PgNACs were predicted. In total, 88 microRNA target sites were predicted in 59 PgNACs. A previously performed transcriptome analysis suggests that the expression of 30 and 42 PgNACs are affected by salinity stress and drought stress, respectively. The expression of 36 randomly selected PgNACs were examined by quantitative reverse transcription-PCR. Many of these genes showed diverse salt- and drought-responsive expression patterns in roots and leaves. These results confirm that PgNACs are potentially involved in regulating abiotic stress tolerance in pearl millet.
CONCLUSION: The pearl millet genome contains 151 NAC transcription factor genes that can be classified into 11 groups. Many of these genes are either upregulated or downregulated by either salinity or drought stress and may therefore contribute to establishing stress tolerance in pearl millet.
Digital Object Identifier (DOI)
Dudhate, Ambika; Shinde, Harshraj; Yu, Pei; Tsugama, Daisuke; Gupta, Shashi Kumar; Liu, Shenkui; and Takano, Tetsuo, "Comprehensive Analysis of NAC Transcription Factor Family Uncovers Drought and Salinity Stress Response in Pearl Millet (Pennisetum glaucum)" (2021). Pharmaceutical Sciences Faculty Publications. 154.
Additional file 1. List of primers used in quantitative real time-PCR expression analysis of PgNAC genes.
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Additional file 2. Detail catalogue of NAC in pearl millet.
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Additional file 3. Gene structure of PgNACs. Image was created by submitting the sequences to the gene structure display 2.0 online tool. Red boxes denote the exon/coding region, black lines are intron and blue boxes defines.
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Additional file 4. Location of 17 Motifs on the PgNACs. The location of motifs were derived by the multiple alignment of the motifs by online tool MAST. Each of the following 152 sequences has an E-value less than 10. The motif matches shown here have a position p-value less than 0.0001. Colored boxes represent the respective motif.
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Additional file 5. Analyzing pearl millet miRNAs targeting PgNACs.