Document Type : Research Paper
Author
Assistant Professor, Department of Agriculture, Lahijan Branch, Islamic Azad University, Lahijan, Iran.
Abstract
Growth regulating factors (Growth Regulatory Factors) are plant-specific transcription factors which contain two conserved domains, QLQ and WRC. Members of this family are involved in diverse biological and physiological processes, such as growth, development and stress and hormone responses. In this study, wheat GRF genes were identified and analysis by bioinformatics methods. GRF genes identification was performed by blastP. Then evolutionary relationships, gene structure, promoter, miRNA, gene ontology and expression of identified genes were analyzed. 30 TaGRFs (TaGRF1–30) distributed on 12 chromosomes were identified by searching wheat genome database and were clustered into six subgroups according to their phylogenetic relationships. TaGRFs belonging to the same subgroup shared a similar motif composition and gene structure. They all contain two conserved motifs (QLQ and WRC) and have 2–5 exons. Due to the identification of stresses, hormones and tissue specific cis elements in the TaGRFs promoter, these genes are involved in many biological processes of wheat. MiR396 target analysis indicated that 26 GRFs mRNA contained miRNA396 target position in wheat. RNA-seq data from the expVip database showed that TaGRF1, TaGRF4 and TaGRF7 were strongly expressed in root, shoot, leave, spike and grain in vegetative and reproductive stages. This data also indicated that all TaGRF genes except TaGRF16 were expressed in vegetative stage of spike. The results of this study provide the evolutionary and functional information needed for Design of functional studies of this gene family.
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Amberg A. (2013) In Silico Methods. In: Vogel HG, Maas J, Hock FJ, Mayer D. (eds) Drug Discovery and Evaluation: Safety and Pharmacokinetic Assays. Springer, Berlin, Heidelberg.
Bing J, Xiao E, Li C, Wang Z (2019) Genome-Wide Identification and Expression Analysis of Growth-Regulating Factor Family Genes in Sunflower (Helianthus annuus L.). Preprints:2019120151.
Bolduc N, Hake S (2009) The maize transcription factor KNOTTED1 directly regulates the gibberellin catabolism gene ga2ox1. The Plant Cell 21 (6):1647-1658.
Cao JF, Huang JQ, Liu, X, Huang, CC, Zheng, ZS, Zhang, XF, Shangguan, XX, Wang LJ, Zhang YG, Wendel JF, Grover, CE. (2020). Genome-wide characterization of the GRF family and their roles in response to salt stress in Gossypium. BMC genomics.21(1):1-16.
Cao Y, Han Y, Jin Q, Lin Y, Cai Y (2016) Comparative genomic analysis of the GRF genes in Chinese pear (Pyrus bretschneideri Rehd), poplar (Populous), grape (Vitis vinifera), Arabidopsis and rice (Oryza sativa). Frontiers in plant science. 7: 1750.
Chen F, Yang Y, Luo X, Zhou W, Dai Y, Zheng C, Liu W, Yang W, Shu K (2019) Genome-wide identification of GRF transcription factors in soybean and expression analysis of GmGRF family under shade stress. BMC plant biology. 19 (1): 269.
Choi D, Kim JH, Kende H (2004) Whole genome analysis of the OsGRF gene family encoding plant-specific putative transcription activators in rice (Oryza sativa L.). Plant Cell Physiology. 45 (7): 897-904.
Hewezi T, Maier TR, Nettleton D, Baum TJ (2012) The Arabidopsis microRNA396-GRF1/GRF3 regulatory module acts as a developmental regulator in the reprogramming of root cells during cyst nematode infection. Plant physiology. 159 (1): 321-335.
Hu Z, Ban Q, Hao J, Zhu X, Cheng Y, Mao J, Lin M, Xia E, Li Y. (2020). Genome-wide characterization of the C-repeat binding factor (CBF) gene family involved in the response to abiotic stresses in tea plant (Camellia sinensis). Frontiers in plant science. 11: 921.
Hughes TR (2011) A handbook of transcription factors, vol 52. Springer Science & Business Media,
Jin J, Tian F, Yang D-C, Meng Y-Q, Kong L, Luo J, Gao G (2016) PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic acids research. gkw982.
Kaur S, Dhugga KS, Gill K, Singh J (2016) Novel structural and functional motifs in cellulose synthase (CesA) genes of bread wheat (Triticum aestivum L.). PLoS One. 11 (1).
Khatun K, Robin AHK, Park J-I, Nath UK, Kim CK, Lim KB, Nou IS, Chung M-Y (2017) Molecular characterization and expression profiling of tomato GRF transcription factor family genes in response to abiotic stresses and phytohormones. International journal of molecular sciences. 18 (5): 1056.
Kim JH, Choi D, Kende H (2003) The AtGRF family of putative transcription factors is involved in leaf and cotyledon growth in Arabidopsis. The Plant Journal. 36 (1): 94-104.
Kim JH, Tsukaya H (2015) Regulation of plant growth and development by the GROWTH-REGULATING FACTOR and GRF-INTERACTING FACTOR duo. Journal of experimental botany 66 (20): 6093-6107.
Koul A, Sharma D, Kaul S, Dhar MK (2019) Identification and in silico characterization of cis-acting elements of genes involved in carotenoid biosynthesis in tomato. 3 Biotech. 9 (7): 287.
Kuijt SJ, Greco R, Agalou A, Shao J, CJ‘t Hoen C, Övernäs E, Osnato M, Curiale S, Meynard D, van Gulik R (2014) Interaction between the growth-regulating factor and knotted1-like homeobox families of transcription factors. Plant Physiology. 164 (4): 1952-1966.
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular biology evolution. 33 (7): 1870-1874.
Li S-B, OuYang W-Z, Hou X-J, Xie L-L, Hu C-G, Zhang J-Z (2015) Genome-wide identification, isolation and expression analysis of auxin response factor (ARF) gene family in sweet orange (Citrus sinensis). Frontiers in Plant Science. 6: 119.
Liu X, Guo L-X, Jin L-F, Liu Y-Z, Liu T, Fan Y-H, Peng S-A (2016) Identification and transcript profiles of citrus growth-regulating factor genes involved in the regulation of leaf and fruit development. Molecular biology reports. 43 (10): 1059-1067.
Ma JQ, Jian H-J, Yang B, Lu K, Zhang A-X, Liu P, Li J-N (2017) Genome-wide analysis and expression profiling of the GRF gene family in oilseed rape (Brassica napus L.). Gene. 620: 36-45.
Mathur S, Priyadarshini SS, Singh V, Vashisht I, Jung KH, Sharma R, Sharma MK. (2020). Comprehensive phylogenomic analysis of ERF genes in sorghum provides clues to the evolution of gene functions and redundancy among gene family members. 3 Biotech. 10 (3): 1-16.
Mirzaei K, Bahramnejad B, Fatemi S. (2020). Genome-wide identification and characterization of the bZIP gene family in potato (Solanum tuberosum). Plant Gene, p.100257.
Moore RC, Purugganan MD (2003) The early stages of duplicate gene evolution. Proceedings of the National Academy of Sciences. 100 (26): 15682-15687.
Nair MM, Krishna T, Alagu M (2020) Bioinformatics insights into microRNA mediated gene regulation in Triticum aestivum during multiple fungal diseases. Plant Gene. 21: 100219.
Omidbakhshfard MA, Proost S, Fujikura U, Mueller-Roeber B (2015) Growth-regulating factors (GRFs): a small transcription factor family with important functions in plant biology. Molecular plant. 8 (7): 998-1010.
Rosin FM, Hart JK, Horner HT, Davies PJ, Hannapel D (2003) Overexpression of a knotted-like homeobox gene of potato alters vegetative development by decreasing gibberellin accumulation. Plant Physiology. 132 (1): 106-117.
Sanjari S, Shirzadian-Khorramabad R, Shobbar ZS, Shahbazi M. (2019). Systematic analysis of NAC transcription factors’ gene family and identification of post-flowering drought stress responsive members in sorghum. Plant cell reports. 38 (3): 361-376.
Sun T-P, Gubler F (2004) Molecular mechanism of gibberellin signaling in plants.Annu Rev Plant Biol.55:197-223.
Van Daele I, Gonzalez N, Vercauteren I, de Smet L, Inzé D, Roldán‐Ruiz I, Vuylsteke M (2012) A comparative study of seed yield parameters in Arabidopsis thaliana mutants and transgenics. Plant biotechnology journal. 10 (4): 488-500.
van der Knaap E, Kim JH, Kende H (2000) A novel gibberellin-induced gene from rice and its potential regulatory role in stem growth. Plant physiology. 122 (3): 695-704.
Wang D, Ling L, Zhang W, Bai Y, Shu Y, Guo C (2018) Uncovering key small RNAs associated with gametocidal action in wheat. Journal of experimental botany. 69 (20): 4739-4756.
Wang F, Qiu N, Ding Q, Li J, Zhang Y, Li H, Gao J (2014) Genome-wide identification and analysis of the growth-regulating factor family in Chinese cabbage (Brassica rapa L. ssp. pekinensis). BMC genomics. 15 (1): 807.
Wang M, Yue H, Feng K, Deng P, Song W, Nie X (2016) Genome-wide identification, phylogeny and expressional profiles of mitogen activated protein kinase kinase kinase (MAPKKK) gene family in bread wheat (Triticum aestivum L.). BMC genomics. 17 (1): 668.
Wu L, Zhang D, Xue M, Qian J, He Y, Wang S (2014) Overexpression of the maize GRF10, an endogenous truncated growth‐regulating factor protein, leads to reduction in leaf size and plant height. Journal of integrative plant biology. 56 (11): 1053-1063.
Wu Z-J, Wang W-L, Zhuang JJF, genomics i (2017) Developmental processes and responses to hormonal stimuli in tea plant (Camellia sinensis) leaves are controlled by GRF and GIF gene families. Functional integrative genomics. 17 (5): 503-512.
Xiao J, Hu R, Gu T, Han J, Qiu D, Su P, Feng J, Chang J, Yang G, He G (2019) Genome-wide identification and expression profiling of trihelix gene family under abiotic stresses in wheat. BMC genomics. 20 (1): 287.
Yan F, Zhou H, Yue M, Yang G, Li H, Zhang S, Zhao P (2019) Genome-wide identification and transcriptional expression profiles of the f-box gene family in common walnut (Juglans regia L.). Forests. 10 (3): 275.
Yang F, Liang G, Liu D, Yu D (2009) Arabidopsis miR396 mediates the development of leaves and flowers in transgenic tobacco. Journal of Plant Biology. 52 (5): 475-481.
Yu X, Han J, Wang E, Xiao J, Hu R, Yang G, He G (2019) Genome-wide identification and homoeologous expression analysis of PP2C genes in wheat (Triticum aestivum L.). Frontiers in genetics. 10: 561.
Zhang D, Han Z, Li J, Qin H, Zhou L, Wang Y, Zhu X, Ma Y, Fang W. (2020). Genome-wide analysis of the SBP-box gene family transcription factors and their responses to abiotic stresses in tea (Camellia sinensis). Genomics. 112 (3): 2194-2202.
Zhang J, Li Z, Jin J, Xie X, Zhang H, Chen Q, Luo Z, Yang J (2018) Genome-wide identification and analysis of the growth-regulating factor family in tobacco (Nicotiana tabacum). Gene. 639: 117-127.
Zhao J, Zhang X, Wan W, Zhang H, Liu J, Li M, Wang H, Xiao J, Wang X (2019a) Identification and characterization of the EXO70 gene family in polyploid wheat and related species. International Journal of Molecular Sciences. 20 (1): 60.
Zhao K, Li K, Ning L, He J, Ma X, Li Z, Zhang X, Yin D (2019b) Genome-Wide Analysis of the Growth-Regulating Factor Family in Peanut (Arachis hypogaea L.). International journal of molecular sciences. 20 (17): 4120.
Zheng J, Liu F, Zhu C, Li X, Dai X, Yang B, Zou X, Ma Y. (2019). Identification, expression, alternative splicing and functional analysis of pepper WRKY gene family in response to biotic and abiotic stresses. PloS one. 14 (7): p.e0219775.
Zhou Y, Ge L, Li G, Jiang L, Yang YJAoBS (2018) Characterization and expression analysis of growth regulating factor (GRF) family genes in cucumber. Archives of Biological Sciences. 70 (4): 629-637.
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