Shivhare R, Lata C. Exploration of Genetic and Genomic Resources for Abiotic and Biotic Stress Tolerance in Pearl Millet. Front Plant Sci. 2017;7. https://doi.org/10.3389/fpls.2016.02069.
Dudhate A, Shinde H, Tsugama D, Liu S, Takano T. Transcriptomic analysis reveals the differentially expressed genes and pathways involved in drought tolerance in pearl millet [Pennisetum glaucum (l.) r. Br]. PLoS One. 2018;13:e0195908. https://doi.org/10.1371/journal.pone.01.
Jaiswal S, Antala TJ, Mandavia MK, Chopra M, Jasrotia RS, Tomar RS, et al. Transcriptomic signature of drought response in pearl millet (Pennisetum glaucum L.) and development of web-genomic resources. Sci Rep. 2018;8:3382.
Shinde H, Tanaka K, Dudhate A, Tsugama D, Mine Y, Kamiya T, et al. Comparative de novo transcriptomic profiling of the salinity stress responsiveness in contrasting pearl millet lines. Environ Exp Bot. 2018;155:619–27.
Shivhare R, Asif MH, Lata C. Comparative transcriptome analysis reveals the genes and pathways involved in terminal drought tolerance in pearl millet. Plant Mol Biol. 2020;103:639–52.
Varshney RK, Shi C, Thudi M, Mariac C, Wallace J, Qi P, et al. Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nat Biotechnol. 2017;35:969.
Shrivastava P, Kumar R. Soil salinity: a serious environmental issue and plant growth promoting bacteria as one of the tools for its alleviation. Saudi J Biol Sci. 2015;22:123–31.
Daryanto S, Wang L, Jacinthe PA. Global synthesis of drought effects on maize and wheat production. PLoS One. 2016;11:1–16.
Nelson GC, Valin H, Sands RD, Havlík P, Ahammad H, Deryng D, et al. Climate change effects on agriculture: economic responses to biophysical shocks. Proc Natl Acad Sci. 2014;111:3274–9.
Shinozaki K, Yamaguchi-Shinozaki K, Seki M. Regulatory network of gene expression in the drought and cold stress responses. Curr Opin Plant Biol. 2003;6:410–7.
Jin J, Tian F, Yang DC, Meng YQ, Kong L, Luo J, et al. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res. 2017;45:D1040–5.
Nuruzzaman M, Sharoni AM, Kikuchi S. Roles of NAC transcription factors in the regulation of biotic and abiotic stress responses in plants. Front Microbiol. 2013;4:1–16.
Aida M. Genes involved in organ separation in Arabidopsis: an analysis of the cup-shaped cotyledon mutant. Plant Cell Online. 1997;9:841–57.
Kikuchi K, Ueguchi-Tanaka M, Yoshida KT, Nagato Y, Matsusoka M, Hirano HY. Molecular analysis of the NAC gene family in rice. Mol Gen Genet. 2000;262:1047–51.
Liu G, Li X, Jin S, Liu X, Zhu L, Nie Y, et al. Overexpression of rice NAC gene SNAC1 improves drought and salt tolerance by enhancing root development and reducing transpiration rate in transgenic cotton. PLoS One. 2014;9:e86895. https://doi.org/10.1371/journal.pone.0086895.
Rachmat A, Nugroho S, Sukma D, Aswidinnoor H. Sudarsono. Overexpression of OsNAC6 transcription factor from Indonesia rice cultivar enhances drought and salt tolerance. Emirates J Food Agric. 2014;26:519–27.
Mao X, Zhang H, Qian X, Li A, Zhao G, Jing R. TaNAC2, a NAC-type wheat transcription factor conferring enhanced multiple abiotic stress tolerances in Arabidopsis. J Exp Bot. 2012;63:2933–46.
Xue GP, Way HM, Richardson T, Drenth J, Joyce PA, McIntyre CL. Overexpression of TaNAC69 leads to enhanced transcript levels of stress up-regulated genes and dehydration tolerance in bread wheat. Mol Plant. 2011;4:697–712. https://doi.org/10.1093/mp/ssr013.
Li X, Li X, Li M, Yan Y, Liu X, Li L. Dual function of NAC072 in ABF3-mediated ABA-responsive gene regulation in Arabidopsis. Front Plant Sci. 2016;7:1–9.
Shiriga K, Sharma R, Kumar K, Yadav SK, Hossain F, Thirunavukkarasu N. Genome-wide identification and expression pattern of drought-responsive members of the NAC family in maize. Meta Gene. 2014;2:407–17.
Jiang D, Zhou L, Chen W, Ye N, Xia J, Zhuang C. Overexpression of a microRNA-targeted NAC transcription factor improves drought and salt tolerance in Rice via ABA-mediated pathways. Rice. 2019;12. https://doi.org/10.1186/s12284-019-0334-6.
Jeong JS, Kim YS, Redillas MCFR, Jang G, Jung H, Bang SW, et al. OsNAC5 overexpression enlarges root diameter in rice plants leading to enhanced drought tolerance and increased grain yield in the field. Plant Biotechnol J. 2013;11:101–14.
Ooka H, Satoh K, Doi K, Nagata T, Otomo Y, Murakami K, et al. Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana. DNA Res. 2003;10:239–47.
Puranik S, Sahu PP, Mandal SN, Suresh BV, Parida SK, Prasad M. Comprehensive genome-wide survey, genomic constitution and expression profiling of the NAC transcription factor family in foxtail millet (Setaria italica L.). PLoS One. 2013;8:1–16.
Yue E, Liu Z, Li C, Li Y, Liu Q, Xu JH. Overexpression of miR529a confers enhanced resistance to oxidative stress in rice (Oryza sativa L.). Plant Cell Rep. 2017;36:1171–82.
Nuruzzaman M, Manimekalai R, Sharoni AM, Satoh K, Kondoh H, Ooka H, et al. Genome-wide analysis of NAC transcription factor family in rice. Gene. 2010;465:30–44.
Singh A, Sharma V, Pal A. Genome-wide organization and expression profiling of the NAC transcription factor family in potato (Solanum tuberosum L.). DNA Res. 2013;20:403–23.
You J, Zhang L, Song B, Qi X, Chan Z. Systematic analysis and identification of stress-responsive genes of the NAC gene family in Brachypodium distachyon. PLoS One. 2015;10:1–20.
Shang H, Li W, Zou C, Yuan Y. Analyses of the NAC transcription factor gene family in gossypium raimondii Ulbr.: chromosomal location, structure, phylogeny, and expression patterns. J Integr Plant Biol. 2013;55:663–76.
Cenci A, Guignon V, Roux N, Rouard M. Genomic analysis of NAC transcription factors in banana (Musa acuminata) and definition of NAC orthologous groups for monocots and dicots. Plant Mol Biol. 2014;85:63–80.
Hu W, Wei Y, Xia Z, Yan Y, Hou X, Zou M, et al. Genome-wide identification and expression analysis of the NAC transcription factor family in cassava. PLoS One. 2015;10:1–25.
Panchy N, Lehti-Shiu M, Shiu SH. Evolution of gene duplication in plants. Plant Physiol. 2016;171:2294–316.
AFA S, Sajad M, Nazaruddin N, Fauzi IA, AMA M, Zainal Z, et al. MicroRNA and transcription factor: Key players in plant regulatory network. Front Plant Sci. 2017;8:1–18.
Hernández Y, Sanan-Mishra N. miRNA mediated regulation of NAC transcription factors in plant development and environment stress response. Plant Gene. 2017;11:190–8.
Zhu G, Chen G, Zhu J, Zhu Y, Lu X, Li X, et al. Molecular characterization and expression profiling of NAC transcription factors in Brachypodium distachyon L. PLoS One. 2015;10:e0139794. https://doi.org/10.1371/journal.pone.0139794.
Wu J, Wang L, Wang S. Comprehensive analysis and discovery of drought-related NAC transcription factors in common bean. BMC Plant Biol. 2016;16:10.1186/s12870-016-0882–5.
Thirumalaikumar VP, Devkar V, Mehterov N, Ali S, Ozgur R, Turkan I, et al. NAC transcription factor JUNGBRUNNEN1 enhances drought tolerance in tomato. Plant Biotechnol J. 2018;16:354–66. https://doi.org/10.1111/pbi.12776.
Balazadeh S, Siddiqui H, Allu AD, Matallana-Ramirez LP, Caldana C, Mehrnia M, et al. A gene regulatory network controlled by the NAC transcription factor ANAC092/AtNAC2/ORE1 during salt-promoted senescence. Plant J. 2010;62:250–64.
Nakashima K, Tran LSP, Van Nguyen D, Fujita M, Maruyama K, Todaka D, et al. Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice. Plant J. 2007;51:617–30.
Ohnishi T, Sugahara S, Yamada T, Kikuchi K, Yoshiba Y, Hirano H-Y, et al. OsNAC6, a member of the NAC gene family, is induced by various stresses in rice. Genes Genet Syst. 2005;80:135–9.
Ooka H, Satoh K, Doi K, Nagata T, Otomo Y, Murakami K, et al. Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana. DNA Res. 2003;239–47.
Shinde H, Dudhate A, Tsugama D, Gupta SK, Liu S, Takano T. Pearl millet stress-responsive NAC transcription factor PgNAC21 enhances salinity stress tolerance in Arabidopsis. Plant Physiol Biochem. 2019;135:546–53.
Rice P, Longden L, Bleasby A. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 2000;16:276–87.
Carver T, Bleasby A. The design of Jemboss: a graphical user interface to EMBOSS. Bioinformatics. 2003;19:1837–43.
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, et al. Pfam: The protein families database. Nucleic Acids Res. 2014;1:222–30.
Sonnhammer ELL, Eddy SR, Birney E, Bateman A, Durbin R. Pfam: Multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res. 1998.
Coggill P, Finn RD, Bateman A. Identifying protein domains with the Pfam database. Curr Protoc Bioinformatics. 2008;1:512–9.
Finn RD, Clements J, Arndt W, Miller BL, Wheeler TJ, Schreiber F, et al. HMMER web server: 2015 Update. Nucleic Acids Res. 2015;43:W30–8.
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:10.1186/1471-2105-10–421.
Voorrips RE. MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered. 2002;93:77–8.
Hu B, Jin J, Guo AY, Zhang H, Luo J, Gao G. GSDS 2.0: An upgraded gene feature visualization server. Bioinformatics. 2015;31:1296–7.
Huala E, Dickerman AW, Garcia-Hernandez M, Weems D, Reiser L, LaFond F, et al. The Arabidopsis information resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res. 2001;29:102–5.
Wang Y, Tang H, Debarry JD, Tan X, Li J, Wang X, et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012;40:1–14.
Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33:1870–4.
Buske FA, Bodén M, Bauer DC, Bailey TL. Assigning roles to DNA regulatory motifs using comparative genomics. Bioinformatics. 2010;26:860–6.
Shinde H, Dudhate A, Anand L, Tsugama D, Gupta SK, Liu S, et al. Small RNA sequencing reveals the role of pearl millet miRNAs and their targets in salinity stress responses. South African J Bot. 2020;132:395–402.
Voinnet O. Origin, biogenesis, and activity of plant MicroRNAs. Cell. 2009;136:669–87.
Dai X, Zhuang Z, Zhao PX. PsRNATarget: a plant small RNA target analysis server (2017 release). Nucleic Acids Res. 2018;46:49–54.
Conesa A, Götz S. Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics. 2007;2008:1–12.
Shivhare R, Lata C. Selection of suitable reference genes for assessing gene expression in pearl millet under different abiotic stresses and their combinations. Sci Rep. 2016;14:23036. https://doi.org/10.1038/srep23036.
Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods. 2001;25:402–8.