Skip to main content
SpringerLink
Log in

Identification, phylogeny and transcript profiling of ERF family genes during temperature stress treatment in Pea (Pisum sativum L.)

  • Original Article
  • Published:
Journal of Plant Biochemistry and Biotechnology Aims and scope Submit manuscript

Abstract

Ethylene responsive transcription factors is a superfamily of transcription factors, regulates various developmental, defense and stress responses, and their use in plant improvement require to have better understanding of these proteins. In the present study, 68 ERF genes have been selected from Pea EST raw data from various publically available databases. Phylogenetic analysis with pea ERF domain shows its close relatedness to ERF60 and ERF92. Transcriptomic analysis revealed that ERF60 and ERF92 are more specific to temperature stress tolerance. Broad phenotypic variability among the temperature stress treated and control of pea varieties, i.e. P-89, Arkel, and Azad Pea-1 were detected by using morphological descriptors. A set of seven gene-specific primers were developed based on ERF unigenes which gave 100% polymorphism. The results from present study reveal that the genes of ERF family play various roles in plants life and generated comprehensive data will be useful in conducting functional genomics. Physiological and molecular analyses of stress treated pea varieties showed that low temperature Arkel variety performed best under low temperature stress condition and could be used for crop breeding programs.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

Abbreviations

ERF:

Ethylene responsive transcription factor

TF:

Transcription factor

NCBI:

National Centre for Biotechnology Information

HMM:

Hidden Markov model

EST-SSR:

Expressed sequence tags-simple sequence repeat

UPGMA:

Unweighted pair group method with arithmetic mean

TSS:

Total soluble solid

CTAB:

Cetyl tri-methyl ammonium bromide

EDTA:

Ethylene diamine tetra acetic acid

PVP:

Poly vinyl pyrrolidone

DNA:

Deoxyribonucleic acid

RNA:

Ribonucleic acid

SAHN:

Sequential Agglomerative Hierarchical Nesting

PIC:

Polymorphism information content

References

  • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Arora R, Agarwal P, Ray S, Singh AK, Singh VP, Tyagi AK, Kapoor S (2007) MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress. BMC Genomics 8:242. https://doi.org/10.1186/1471-2164-8-242

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bozoglu HE, Peksen A, Gulumser A (2007) Determination of the yield performance and harvesting periods of fifteen pea (Pea L.) cultivars sown in autumn and spring. Pak J Bot 39(6):2017–2025

    Google Scholar 

  • Brown RL, Kazan K, McGrath KC, Maclean DJ, Manners JM (2003) A role for the GCC-box in jasmonate-mediated activation of the PDF1.2 gene of Arabidopsis. Plant Physiol 132:1020–1032

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bueckert RA, Wagenhoffer S, Hnatowich G, Warkentin TD (2015) Effect of heat and precipitation on pea yield and reproductive performance in the field. Can J Plant Sci 95:629–639

    Article  Google Scholar 

  • Cao Y, Song F, Goodman RM, Zheng Z (2006) Molecular characterization of four rice genes encoding ethylene-responsive transcriptional factors and their expressions in response to biotic and abiotic stress. J Plant Physiol 163:1167–1178

    Article  CAS  PubMed  Google Scholar 

  • Chakraborty D, Mandal SM (2008) Fractional changes in phenolic acids composition in root nodules of Arachis hypogaea L. Plant Growth Regul 55(3):159–163

    Article  CAS  Google Scholar 

  • Chen G, Hu Z, Grierson D (2008) Differential regulation of tomato ethylene responsive factor LeERF3b, a putative repressor, and the activator Pti4 in ripening mutants and in response to environmental stresses. J Plant Physiol 165:662–670

    Article  CAS  PubMed  Google Scholar 

  • Chen M, Wang QY, Cheng XG, Xu ZS, Li LC, Ye XG, Xia LQ, Ma YZ (2007) GmDREB2, a soybean DRE-binding transcription factor, conferred drought and high-salt tolerance in transgenic plants. Biochem Biophys Res Commun 353:299–305

    Article  CAS  PubMed  Google Scholar 

  • Das A, Kumar S, Nandeesha P, Yadav IS, Saini J, Chaturvedi SK, Datta S (2013) An efficient in vitro regeneration system of field pea (Pea L.) via shoot organogenesis. J Plant Biochem Biotechnol 23(2):184–189

    Article  CAS  Google Scholar 

  • Fujimoto SY, Ohta M, Usui A, Shinshi H, Takagi M (2000) Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression. Plant Cell 12:393–404

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ghafoor A, Ahmad Z, Anwar R (2005) Genetic diversity in Pisum sativum and a strategy for indigenous biodiversity conservation. Pak J Bot 37:71–77

    Google Scholar 

  • Gu YQ, Wildermuth MC, Chakravarthy S, Loh YT, Yang C, He X, Han Y, Martin GB (2002) Tomato transcription factors pti4, pti5, and pti6 activate defense responses when expressed in Arabidopsis. Plant Cell 14:817–831

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Grotewolda E (2008) Transcription factors for predictive plant metabolic engineering: are we there yet? Curr Opin Biotechnol 19:138–144

    Article  CAS  Google Scholar 

  • Goremykin V, Moser C (2009) Classification of the Arabidopsis ERF gene family based on Bayesian analysis. Mol Biol 43:789–794

    Article  CAS  Google Scholar 

  • Haake V, Cook D, Riechmann JL, Pineda O, Thomashow MF, Zhang JZ (2002) Transcription factor CBF4 is a regulator of drought adaptation in Arabidopsis. Plant Physiol 130:639–648

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang X, Madan A (1999) CAP3: A DNA sequence assembly program. Genome Res 9:868–877

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Iida K, Seki M, Sakurai T, Satou M, Akiyama K, Toyoda T, Konagaya A, Shinozaki K (2005) RARTF: database and tools for complete sets of Arabidopsis transcription factors. DNA Res 12:247–256

    Article  CAS  PubMed  Google Scholar 

  • Iqbal A, Shah S, Nisar M, Ghafoor A (2017) Morphological characterization and selection for high yielding and powdery mildew resistant pea (Pisum sativum) lines. Sains Malaysiana 46:1727–1734

    Article  CAS  Google Scholar 

  • Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol 138–148

  • Jaccard P (1908) Nouvelles Recherches sur la distribution florale. Bull Soc Vaud Sci Nat 44:223–270

    Google Scholar 

  • Komatsu M, Chujo A, Nagato Y, Shimamoto K, Kyozuka J (2003) FRIZZY PANICLE is required to prevent the formation of axillary meristems and to establish floral meristem identity in rice spikelets. Development 130:3841–3850

    Article  CAS  PubMed  Google Scholar 

  • Kumar S, Pandey G (2020) Biofortification of pulses and legumes to enhance nutrition. Heliyon 6(3):e03682

    Article  PubMed  PubMed Central  Google Scholar 

  • Liu Q, Kasuga M, Sakuma Y, Abe H, Miura S, Yamaguchi-Shinozaki K, Shinozaki K (1998) Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought- and low-temperature-responsive gene expression, respectively, in Arabidopsis. Plant Cell 10:1391–1406

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu Y, Zhao TJ, Liu JM, Liu WQ, Liu Q, Yan YB, Zhou HM (2006) The conserved Ala37 in the ERF/AP2 domain is essential for binding with the DRE element and the GCC box. FEBS Lett 580:1303–1308

    Article  CAS  PubMed  Google Scholar 

  • Madera M, Gough J (2002) A comparison of profile hidden Markov model procedures for remote homology detection. Nucleic Acids Res 30:4321–4328

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Marsch-Martinez N, Greco R, Becker JD, Dixit S, Bergervoet JH, Karaba A, de Folter S, Pereira A (2006) BOLITA, an Arabidopsis AP2/ERF-like transcription factor that affects cell expansion and proliferation/differentiation pathways. Plant Mol Biol 62:825–843

    Article  CAS  PubMed  Google Scholar 

  • Mysore KS, Tuori RP, Martin GB (2001) Arabidopsis genome sequence as a tool for functional genomics in tomato. Genome Biol. https://doi.org/10.1186/gb-2001-2-1

    Article  PubMed  PubMed Central  Google Scholar 

  • Nakano T, Suzuki K, Fujimura T, Shinshi H (2006) Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiol 140:411–432

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nijhawan A, Jain M, Tyagi AK, Khurana JP (2008) Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice. Plant Physiol 146:333–350

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nisar M, Khan A, Wadood SF, Shah AA, Hanci F (2017) Molecular characterization of edible pea through EST-SSR markers. Turk J Bot 41:338–346

    Article  CAS  Google Scholar 

  • Ofga B, Petros Y (2017) Genetic variability and association among agronomic characters in selected field pea (Pea L.) genotypes at Bale zone, Sinana Research Center, Oromia Region, Ethopia. Int J Genet Genom 5(6):63–75

    Article  Google Scholar 

  • Page RD (1996) TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358

    CAS  PubMed  Google Scholar 

  • Park JM, Park CJ, Lee SB, Ham BK, Shin R, Paek KH (2001) Overexpression of the tobacco Tsi1 gene encoding an EREBP/ AP2-type transcription factor enhances resistance against pathogen attack and osmotic stress in tobacco. Plant Cell 13:1035–1046

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ribalta FM, Navarro MP, Edwards K, Ross JJ, Croser JS, Ochatt SJ (2019) Expression patterns of key hormones related to Pea (Pea L.) embryo physiological maturity shift in response to accelerated growth conditions. Front Plant Sci. https://doi.org/10.3389/fpls.2019.01154

    Article  PubMed  PubMed Central  Google Scholar 

  • Rohlf FJ (2000) NTSYSpc numerical taxonomy and multivariate analysis version 2.0.h. Applied Biostatics Inc, New York, p 25

    Google Scholar 

  • Rozen S, Skaletsky HJ (2000) Primer 3 on the www for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386

    Google Scholar 

  • Samriti KR, Shilpa MEV, Poonam TD, Kumar K (2017) Assessment of genetic diversity in Rubus ellipticus (Smith) Using molecular markers. Proc Indian Natl Sci Acad 83(3):669–679

    Google Scholar 

  • Shah BH, Hamid FS, Islam SU, Fayaz A, Sohail A, Khan N (2016) Evaluation of different pea (Pea L.) genotypes for yield and other attributes at Shinkiari. Mansehra. Pak J Agri Res 29(4):323–330

    Google Scholar 

  • Sharma MK, Kumar R, Solanke AKU, Sharma R, Tyagi AK, Sharma AK (2010) Identification, phylogeny, and transcript profiling of ERF family genes during development and abiotic stress treatments in tomato. Mol Genet Genomics 284:455–475

    Article  CAS  PubMed  Google Scholar 

  • Sharma D, Chauhan A, Jarial K (2020) Performance of pea varieties in different altitude ranges under North-Western Himalayan Region. Int J Curr Microbiol Appl Sci 9(06):3292–3302

    Article  Google Scholar 

  • Sharma R, Yeh KC (2020) The dual benefit of a dominant mutation in Arabidopsis IRON DEFICIENCY TOLERANT1 for iron biofortification and heavy metal phytoremediation. Plant Biotechnol J 18:1200–1210

    Article  CAS  PubMed  Google Scholar 

  • Sharma S, Dobbal S, Thakur KR, S, (2019a) Morphological, physiological and molecular analysis of Line 3 Tester in Populus deltoides Bartr. Indian J Plant Physiol 25:87–106. https://doi.org/10.1007/s40502-019-00479-3

    Article  CAS  Google Scholar 

  • Sharma S, Dobhal S, Thakur S (2018) Analysis of genetic diversity in parents and hybrids of Populus deltoids Bartr. using microsatellite markers. Appl Biol Res 20(3):262–270

    Article  Google Scholar 

  • Sharma S, Kaur R, Kumar K (2019b) Studies on genetic fidelity of long term micropropagated culture derived plants of Ofra strawberry using molecular markers. Indian J Hortic 76(4):596–603

    Article  Google Scholar 

  • Sharma S, Kaur R, Kumar K, Kumar D, Solanke AKU (2021) Genetic diversity in Rubus ellipticus collections assessed by morphological traits and EST-SSR markers. J Plant Biochem Biotechnol 30:37–55

    Article  CAS  Google Scholar 

  • Sharma S, Kaur R, Solanke AKU, Dubey H, Tiwari S, Kumar K (2019) Transcriptome sequencing of Himalayan Raspberry (Rubus ellipticus) and development of simple sequence repeat markers. 3 Biotech. https://doi.org/10.1007/s13205-019-1685-9

  • Sharma S, Sharma A (2018) Molecular markers based plant breeding. Adv Res 16(1):1–15

    Article  Google Scholar 

  • Singh TJ, Gupta T, Sharma S (2019) Development and purity identification of hybrids by using molecular marker in wild pomegranate (Punica granatum L.). Sci Hortic 247:436–448

    Article  CAS  Google Scholar 

  • Sneath PHA, Sokal RR (1973) NumericalTaxonomy. WH Freeman and Company, San Francisco

  • Talalaiev O, Korduym E (2014) Expression of small heat shock protein (sHSP) genes in the garden pea (Pea) under slow horizontal clinorotation. Plant Signal Behav 9(e29035):1–5

    Google Scholar 

  • Van de Wouw M, van Hintum T, Kik C, van Treuren R, Visser B (2010) Genetic diversity trends in twentieth century crop cultivars: a meta analysis. Theor Appl Genet 120:1241–1252

    Article  PubMed  PubMed Central  Google Scholar 

  • Xie M, Chung CY-L, Li M-W et al (2019) A reference-grade wild soybean genome. Nat Commun 10(1):12–16

    Article  CAS  Google Scholar 

  • Xiao G, Zhang Q, Wang R, Yao Y, Zhao H, Bai H, Youcai X (2009) Effects of Temperature Increase on Pea Production in a Semiarid Region of China. Air, Soil and Water Research 2. https://doi.org/10.4137/ASWR.S2488

  • Zhu QH, Hoque MS, Dennis ES, Upadhyaya NM (2003) Ds tagging of BRANCHED FLORETLESS 1 (BFL1) that mediates the transition from spikelet to floret meristem in rice (Oryza sativa L). BMC Plant Biol 3:1–13

    Article  Google Scholar 

  • Zhuang J, Cai B, Peng RH, Zhu B, Jin XF, Xue Y, Gao F, Fu XY, Tian YS, Zhao W, Qiao YS, Zhang Z, Xiong AS, Yao QH (2008) Genome-wide analysis of the AP2/ERF gene family in Populus trichocarpa. Biochem Biophys Res Commun 371:468–474

    Article  CAS  PubMed  Google Scholar 

  • Zong X, Redden RJ, Liu Q, Wang S, Guan J, Liu J, Xu Y, Liu X, Gu J, Yan L, Ades P, Ford R (2009) Analysis of a diverse global Pisum sp. collections and comparison to a Chinese local Pisum sativum L. collection with microsatellite markers. Theor Appl Genet 118:193–204

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biotechnology Chandigarh Group of Colleges, Landran, Mohali, India

    Samriti Sharma & Anuraj Chahal

  2. Department of Fruit Science, DrYashwant Singh Parmar University of Horticulture and Forestry, Nauni, Solan, India

    Heerendra Prasad

  3. Department of Microbiology, College of Basic Sciences, CSKHPKV, Palampur, HP, India

    Abhishek Walia

  4. ICAR-Central Soil Salinity Research Institute, Zarifa Farm, Karnal, India

    Raj Kumar

  5. Uttarakhand University of Horticulture and Forestry, Ranichauri, Uttarakhand, India

    Sneha Dobhal

Authors
  1. Samriti Sharma
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Anuraj Chahal
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Heerendra Prasad
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Abhishek Walia
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Raj Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Sneha Dobhal
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Samriti Sharma.

Ethics declarations

Conflict of interest

I certify that there is no actual or potential conflict of interest in relation to this article. All authors have participated in (a) conception and design, or analysis and interpretation of the data; (b) drafting the article or revising it critically for important intellectual content; and (c) approval of the final version. This manuscript has not been submitted to, nor is under review at, another journal or other publishing venue.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Sharma, S., Chahal, A., Prasad, H. et al. Identification, phylogeny and transcript profiling of ERF family genes during temperature stress treatment in Pea (Pisum sativum L.). J. Plant Biochem. Biotechnol. 31, 561–572 (2022). https://doi.org/10.1007/s13562-021-00709-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13562-021-00709-6

Keywords

Search

Navigation