Comprehensive analysis of NAC transcription factor family uncovers drought and salinity stress response in pearl millet (Pennisetum glaucum)

Abstract 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.

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Comprehensive analysis of NAC transcription factor family uncovers drought and salinity stress response in pearl millet (Pennisetum glaucum)

10.21203/rs.3.rs-37445/v2 ◽

2020 ◽

Author(s):

Ambika Dudhate ◽

Harshraj Shinde ◽

Pei Yu ◽

Daisuke Tsugama ◽

Shashi Kumar Gupta ◽

...

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Abiotic Stress ◽

Drought Stress ◽

Pearl Millet ◽

Pennisetum Glaucum ◽

Nac Transcription Factor ◽

Transcription Factor Family ◽

Transcription Factor Genes ◽

Nac Family

Abstract 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.

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Comprehensive Analysis of NAC Transcription Factor Family in Pearl Millet Uncovers Drought and Salinity Stress Responsive NAC in Pearl Millet (Pennisetum Glaucum)

10.21203/rs.3.rs-37445/v1 ◽

2020 ◽

Author(s):

Ambika Dudhate ◽

Harshraj Shinde ◽

Pei Yu ◽

Daisuke Tsugama ◽

Shashi Kumar Gupta ◽

...

Keyword(s):

Transcription Factor ◽

Abiotic Stress ◽

Stress Tolerance ◽

Pearl Millet ◽

Pennisetum Glaucum ◽

Abiotic Stress Tolerance ◽

Nac Transcription Factor ◽

Transcription Factor Family ◽

Transcription Factor Genes ◽

Nac Family

Abstract 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 and (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 tolerance. 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. 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 (MTF). 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 was 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.

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Transcription factors involved in abiotic stress responses in maize (Zea mays L.) and their roles in enhanced productivity in the post genomics era

10.7287/peerj.preprints.27549v1 ◽

2019 ◽

Author(s):

Roy Njoroge Kimotho ◽

Elamin Hafiz Baillo ◽

Zhengbin Zhang

Keyword(s):

Zea Mays ◽

Transcription Factor ◽

Transcription Factors ◽

Abiotic Stress ◽

Stress Responses ◽

Abiotic Stresses ◽

Target Genes ◽

Animal Feed ◽

Specific Transcription Factor ◽

Transcription Factor Genes

Background: Maize (Zea mays L.) is a principal cereal crop cultivated worldwide for human food, animal feed, and more recently as a source of biofuel. However, as a direct consequence of water insufficiency and climate change, frequent occurrences of both biotic and abiotic stresses have been reported in different regions around the world, and recently, this has become a major threat in increasing global maize yields. Plants respond to abiotic stresses by utilizing the activity of transcription factors, which are families of genes coding for specific transcription factor proteins whose target genes form a regulon which is involved in the repression/ activation of genes associated with abiotic stress responses. Therefore, it is of uttermost importance to have a systematic study on each family of the transcription factors, the downstream target genes they regulate, and the specific transcription factor genes which are involved in multiple abiotic stress responses in maize and other main crops. Method: In this review, the main transcription factor families, the specific transcription factor genes and their regulons which are involved in abiotic stress regulation will be momentarily discussed. Great emphasis will be given on maize abiotic stress improvement throughout this review, although other examples from other plants like rice, Arabidopsis, wheat, and barley will be used. Results: We have described in detail the main transcription factor families in maize which take part in abiotic stress responses together with their regulons. Furthermore, we have also briefly described the utilization of high-efficiency technologies in the study and characterization of TFs involved in the abiotic stress regulatory networks in plants with an emphasis on increasing maize production. Examples of these technologies include next-generation sequencing, microarray analysis, machine learning and RNA-Seq technology. Conclusion: In conclusion, it is hoped that all the information provided in this review may in time contribute to the use of TF genes in the research, breeding, and development of new abiotic stress tolerant maize cultivars.

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Transcription factors involved in abiotic stress responses in maize (Zea mays L.) and their roles in enhanced productivity in the post genomics era

10.7287/peerj.preprints.27549 ◽

2019 ◽

Cited By ~ 1

Author(s):

Roy Njoroge Kimotho ◽

Elamin Hafiz Baillo ◽

Zhengbin Zhang

Keyword(s):

Zea Mays ◽

Transcription Factor ◽

Transcription Factors ◽

Abiotic Stress ◽

Stress Responses ◽

Abiotic Stresses ◽

Target Genes ◽

Animal Feed ◽

Specific Transcription Factor ◽

Transcription Factor Genes

Background: Maize (Zea mays L.) is a principal cereal crop cultivated worldwide for human food, animal feed, and more recently as a source of biofuel. However, as a direct consequence of water insufficiency and climate change, frequent occurrences of both biotic and abiotic stresses have been reported in different regions around the world, and recently, this has become a major threat in increasing global maize yields. Plants respond to abiotic stresses by utilizing the activity of transcription factors, which are families of genes coding for specific transcription factor proteins whose target genes form a regulon which is involved in the repression/ activation of genes associated with abiotic stress responses. Therefore, it is of uttermost importance to have a systematic study on each family of the transcription factors, the downstream target genes they regulate, and the specific transcription factor genes which are involved in multiple abiotic stress responses in maize and other main crops. Method: In this review, the main transcription factor families, the specific transcription factor genes and their regulons which are involved in abiotic stress regulation will be momentarily discussed. Great emphasis will be given on maize abiotic stress improvement throughout this review, although other examples from other plants like rice, Arabidopsis, wheat, and barley will be used. Results: We have described in detail the main transcription factor families in maize which take part in abiotic stress responses together with their regulons. Furthermore, we have also briefly described the utilization of high-efficiency technologies in the study and characterization of TFs involved in the abiotic stress regulatory networks in plants with an emphasis on increasing maize production. Examples of these technologies include next-generation sequencing, microarray analysis, machine learning and RNA-Seq technology. Conclusion: In conclusion, it is hoped that all the information provided in this review may in time contribute to the use of TF genes in the research, breeding, and development of new abiotic stress tolerant maize cultivars.

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Evolution and functional diversity of abiotic stress-responsive NAC transcription factor genes in Linum usitatissimum L

Environmental and Experimental Botany ◽

10.1016/j.envexpbot.2021.104512 ◽

2021 ◽

pp. 104512

Author(s):

Dipnarayan Saha ◽

Arun Kumar Shaw ◽

Subhojit Datta ◽

Jiban Mitra

Keyword(s):

Transcription Factor ◽

Abiotic Stress ◽

Functional Diversity ◽

Linum Usitatissimum ◽

Nac Transcription Factor ◽

Linum Usitatissimum L ◽

Transcription Factor Genes

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Transcriptome-wide and expression analysis of the NAC gene family in pepino (Solanum muricatum) during drought stress

PeerJ ◽

10.7717/peerj.10966 ◽

2021 ◽

Vol 9 ◽

pp. e10966

Author(s):

Shipeng Yang ◽

Haodong Zhu ◽

Liping Huang ◽

Guangnan Zhang ◽

Lihui Wang ◽

...

Keyword(s):

Transcription Factor ◽

Amino Acid ◽

Drought Stress ◽

Gene Family ◽

Nac Transcription Factor ◽

Sequence Length ◽

Transcription Factor Family ◽

Expression Levels ◽

Solanum Muricatum ◽

Nac Gene Family

Solanum muricatum (Pepino) is an increasingly popular solanaceous crop and is tolerant of drought conditions. In this study, 71 NAC transcription factor family genes of S. muricatum were selected to provide a theoretical basis for subsequent in-depth study of their regulatory roles in the response to biological and abiotic stresses, and were subjected to whole-genome analysis. The NAC sequences obtained by transcriptome sequencing were subjected to bioinformatics prediction and analysis. Three concentration gradient drought stresses were applied to the plants, and the target gene sequences were analyzed by qPCR to determine their expression under drought stress. The results showed that the S. muricatum NAC family contains 71 genes, 47 of which have conserved domains. The protein sequence length, molecular weight, hydrophilicity, aliphatic index and isoelectric point of these transcription factors were predicted and analyzed. Phylogenetic analysis showed that the S. muricatum NAC gene family is divided into seven subfamilies. Some NAC genes of S. muricatum are closely related to the NAC genes of Solanaceae crops such as tomato, pepper and potato. The seedlings of S. muricatum were grown under different gradients of drought stress conditions and qPCR was used to analyze the NAC expression in roots, stems, leaves and flowers. The results showed that 13 genes did not respond to drought stress while 58 NAC genes of S. muricatum that responded to drought stress had obvious tissue expression specificity. The overall expression levels in the root were found to be high. The number of genes at extremely significant expression levels was very large, with significant polarization. Seven NAC genes with significant responses were selected to analyze their expression trend in the different drought stress gradients. It was found that genes with the same expression trend also had the same or part of the same conserved domain. Seven SmNACs that may play an important role in drought stress were selected for NAC amino acid sequence alignment of Solanaceae crops. Four had strong similarity to other Solanaceae NAC amino acid sequences, and SmNAC has high homology with the Solanum pennellii. The NAC transcription factor family genes of S. muricatum showed strong structural conservation. Under drought stress, the expression of NAC transcription factor family genes of S. muricatum changed significantly, which actively responded to and participated in the regulation process of drought stress, thereby laying foundations for subsequent in-depth research of the specific functions of NAC transcription factor family genes of S. muricatum.

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