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Nazir N, Iqbal A, Hussain H, Ali F, Almaary KS, Aktar MN, Sajid M, Bourhia M, Salamatullah AM. In silico genome-wide analysis of the growth-regulating factor gene family and their expression profiling in Vitis vinifera under biotic stress. Cell Biochem Biophys 2025; 83:1207-1221. [PMID: 39485599 DOI: 10.1007/s12013-024-01554-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2024] [Indexed: 11/03/2024]
Abstract
Growth regulatory factors (GRFs) are transcription factors that encode the proteins involved in plant growth and development. However, no comprehensive analysis of Vitis vinifera GRF genes has yet been conducted. In the current study, we performed a genome-wide analysis of the GRF gene family to explore the VvGRF gene's role in Vitis vinifera. We identified 30 VvGRF genes in the Vitis vinifera genome, localized over 20 chromosomes. Based on evolutionary analysis, 49 GRF genes (nine AtGRF, ten FvGRF, and 30 VvGRF) were clustered into six groups. Many cis-elements involved in light control, defense, and plant growth have been identified in the promoter region of VvGRF genes, and multiple miRNAs have been predicted to be involved in regulating VvGRF gene expression. Protein-protein interaction analysis showed that nine VvGRF proteins formed a complex protein interaction network. Furthermore, the gene expression analysis of VvGRF revealed that VvGRF-5 and VvGRF-6 were highly upregulated suggesting that these genes are involved in biotic responses. This study provides comprehensive insights into the functional characteristics and occurrence of the VvGRF gene family in Vitis vinifera, which may be applied in breeding programs to enhance the growth of Vitis vinifera varieties under stress and growth changes.
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Affiliation(s)
- Nimra Nazir
- Department of Biotechnology, Faculty of Life Sciences, University of Okara, Okara, Punjab, 56300, Pakistan
| | - Azhar Iqbal
- Department of Biotechnology, Faculty of Life Sciences, University of Okara, Okara, Punjab, 56300, Pakistan
| | - Hadia Hussain
- Department of Biotechnology, Faculty of Life Sciences, University of Okara, Okara, Punjab, 56300, Pakistan
| | - Faisal Ali
- Department of Biotechnology, Faculty of Life Sciences, University of Okara, Okara, Punjab, 56300, Pakistan
| | - Khalid S Almaary
- Department of Botany and Microbiology, College of Science, King Saud University, P. O. BOX 2455, Riyadh, 11451, Saudi Arabia.
| | - Most Nazmin Aktar
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Muhammad Sajid
- Department of Biotechnology, Faculty of Life Sciences, University of Okara, Okara, Punjab, 56300, Pakistan.
| | - Mohammed Bourhia
- Laboratory of Biotechnology and Natural Resources Valorization, Faculty of Sciences, Ibn Zohr University, 80060, Agadir, Morocco
| | - Ahmad Mohammad Salamatullah
- Department of Food Science & Nutrition, College of Food and Agricultural Sciences, King Saud University, 11 P.O. Box 2460, Riyadh, 11451, Saudi Arabia
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Omondi E, Barchi L, Gaccione L, Portis E, Toppino L, Tassone MR, Alonso D, Prohens J, Rotino GL, Schafleitner R, van Zonneveld M, Giuliano G. Association analyses reveal both anthropic and environmental selective events during eggplant domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2025; 121:e17229. [PMID: 39918113 PMCID: PMC11803709 DOI: 10.1111/tpj.17229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 11/25/2024] [Accepted: 12/16/2024] [Indexed: 02/11/2025]
Abstract
Eggplant (Solanum melongena) is one of the four most important Solanaceous crops, widely cultivated and consumed in Asia, the Mediterranean basin, and Southeast Europe. We studied the genome-wide association of historical genebank phenotypic data on a genotyped worldwide collection of 3449 eggplant accessions. Overall, 334 significant associations for key agronomic traits were detected. Significant correlations were obtained between different types of phenotypic data, some of which were not obvious, such as between fruit size/yield and fruit color components, suggesting simultaneous anthropic selection for genetically unrelated traits. Anthropic selection of traits like leaf prickles, fruit color, and yield, acted on distinct genomic regions in the two domestication centers (India and Southeast Asia), further confirming the multiple domestication of eggplant. To discriminate anthropic from environmental selection in domestication centers, we conducted a genotype-environment association (GEA) on a subset of georeferenced accessions from the Indian subcontinent. The population structure in this area revealed four genetic clusters, corresponding to a latitudinal gradient, and environmental factors explained 31% of the population structure when the effect of spatial distances was removed. GEA and outlier association identified 305 candidate regions under environmental selection, containing genes for abiotic stress responses, plant development, and flowering transition. Finally, in the Indian domestication center anthropic and environmental selection acted largely independently, and on different genomic regions. These data allow a better understanding of the different effects of environmental and anthropic selection during domestication of a crop, and the different world regions where some traits were initially selected by humans.
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Affiliation(s)
| | - Lorenzo Barchi
- DISAFA – Plant GeneticsUniversity of TurinGrugliascoTO10095Italy
| | - Luciana Gaccione
- DISAFA – Plant GeneticsUniversity of TurinGrugliascoTO10095Italy
| | - Ezio Portis
- DISAFA – Plant GeneticsUniversity of TurinGrugliascoTO10095Italy
| | - Laura Toppino
- CREA Research Centre for Genomics and BioinformaticsVia Paullese 28Montanaso LombardoLO26836Italy
| | - Maria Rosaria Tassone
- CREA Research Centre for Genomics and BioinformaticsVia Paullese 28Montanaso LombardoLO26836Italy
| | - David Alonso
- Universitat Politècnica de ValènciaCamino de Vera 1446022ValenciaSpain
| | - Jaime Prohens
- Universitat Politècnica de ValènciaCamino de Vera 1446022ValenciaSpain
| | - Giuseppe Leonardo Rotino
- CREA Research Centre for Genomics and BioinformaticsVia Paullese 28Montanaso LombardoLO26836Italy
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Wang L, Qian Y, Wu L, Wei K, Wang L. The MADS-box transcription factor CsAGL9 plays essential roles in seed setting in Camellia sinensis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108301. [PMID: 38232497 DOI: 10.1016/j.plaphy.2023.108301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 01/19/2024]
Abstract
The number of seed setting (NSS) is an important biological trait that affects tea propagation and yield. In this study, the NSS of an F1 tea population (n = 324) generated via a cross between 'Longjing 43' and 'Baihaozao' was investigated at two locations in two consecutive years. Quantitative trait locus (QTL) mapping of the NSS was performed, and 10 major QTLs were identified. In total, 318 genes were found in these 10 QTLs intervals, and 11 key candidate genes were preliminarily identified. Among them, the MADS-box transcription factor AGAMOUS LIKE 9 (CsAGL9, CSS0037962) located in the most stable QTL (qNSS2) was identified as a key gene affecting the NSS. CsAGL9 overexpression in Arabidopsis promoted early flowering and significantly decreased the length and number of pods and number of seeds per pod. Transcriptome analysis demonstrated that the auxin pathway, a key hormone pathway regulating plant reproduction, was highly affected in the transgenic lines. The auxin pathway was likewise the most prominent in the gene co-expression network study of CsAGL9 in tea plants. In summary, we identified CsAGL9 is essential for seed setting using QTL mapping integrated with RNA-seq, which shed a new light on the mechanism NSS of seed setting in tea plants.
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Affiliation(s)
- Liubin Wang
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, 310008, China; Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yinhong Qian
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, 310008, China; Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Liyun Wu
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, 310008, China
| | - Kang Wei
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, 310008, China.
| | - Liyuan Wang
- Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou, 310008, China.
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Lv Z, Zhao W, Kong S, Li L, Lin S. Overview of molecular mechanisms of plant leaf development: a systematic review. FRONTIERS IN PLANT SCIENCE 2023; 14:1293424. [PMID: 38146273 PMCID: PMC10749370 DOI: 10.3389/fpls.2023.1293424] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/22/2023] [Indexed: 12/27/2023]
Abstract
Leaf growth initiates in the peripheral region of the meristem at the apex of the stem, eventually forming flat structures. Leaves are pivotal organs in plants, serving as the primary sites for photosynthesis, respiration, and transpiration. Their development is intricately governed by complex regulatory networks. Leaf development encompasses five processes: the leaf primordium initiation, the leaf polarity establishment, leaf size expansion, shaping of leaf, and leaf senescence. The leaf primordia starts from the side of the growth cone at the apex of the stem. Under the precise regulation of a series of genes, the leaf primordia establishes adaxial-abaxial axes, proximal-distal axes and medio-lateral axes polarity, guides the primordia cells to divide and differentiate in a specific direction, and finally develops into leaves of a certain shape and size. Leaf senescence is a kind of programmed cell death that occurs in plants, and as it is the last stage of leaf development. Each of these processes is meticulously coordinated through the intricate interplay among transcriptional regulatory factors, microRNAs, and plant hormones. This review is dedicated to examining the regulatory influences of major regulatory factors and plant hormones on these five developmental aspects of leaves.
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Affiliation(s)
- Zhuo Lv
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, China
- College of Life Science, Nanjing Forestry University, Nanjing, China
| | - Wanqi Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, China
- College of Life Science, Nanjing Forestry University, Nanjing, China
| | - Shuxin Kong
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, China
- College of Life Science, Nanjing Forestry University, Nanjing, China
| | - Long Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, China
- College of Life Science, Nanjing Forestry University, Nanjing, China
| | - Shuyan Lin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, China
- College of Life Science, Nanjing Forestry University, Nanjing, China
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Lu J, Wang Z, Li J, Zhao Q, Qi F, Wang F, Xiaoyang C, Tan G, Wu H, Deyholos MK, Wang N, Liu Y, Zhang J. Genome-Wide Analysis of Flax ( Linum usitatissimum L.) Growth-Regulating Factor (GRF) Transcription Factors. Int J Mol Sci 2023; 24:17107. [PMID: 38069430 PMCID: PMC10707037 DOI: 10.3390/ijms242317107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Flax is an important cash crop globally with a variety of commercial uses. It has been widely used for fiber, oil, nutrition, feed and in composite materials. Growth regulatory factor (GRF) is a transcription factor family unique to plants, and is involved in regulating many processes of growth and development. Bioinformatics analysis of the GRF family in flax predicted 17 LuGRF genes, which all contained the characteristic QLQ and WRC domains. Equally, 15 of 17 LuGRFs (88%) are predicted to be regulated by lus-miR396 miRNA. Phylogenetic analysis of GRFs from flax and several other well-characterized species defined five clades; LuGRF genes were found in four clades. Most LuGRF gene promoters contained cis-regulatory elements known to be responsive to hormones and stress. The chromosomal locations and collinearity of LuGRF genes were also analyzed. The three-dimensional structure of LuGRF proteins was predicted using homology modeling. The transcript expression data indicated that most LuGRF family members were highly expressed in flax fruit and embryos, whereas LuGRF3, LuGRF12 and LuGRF16 were enriched in response to salt stress. Real-time quantitative fluorescent PCR (qRT-PCR) showed that both LuGRF1 and LuGRF11 were up-regulated under ABA and MeJA stimuli, indicating that these genes were involved in defense. LuGRF1 was demonstrated to be localized to the nucleus as expected for a transcription factor. These results provide a basis for further exploration of the molecular mechanism of LuGRF gene function and obtaining improved flax breeding lines.
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Affiliation(s)
- Jianyu Lu
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Zhenhui Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Jinxi Li
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Qian Zhao
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Fan Qi
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Fu Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Chunxiao Xiaoyang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Guofei Tan
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Hanlu Wu
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Michael K. Deyholos
- Department of Biology, University of British Columbia, Okanagan, Kelowna, BC V5K1K5, Canada;
| | - Ningning Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Yingnan Liu
- Institute of Natural Resources and Ecology, Heilongjiang Academy of Science, Harbin 150040, China
| | - Jian Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
- Department of Biology, University of British Columbia, Okanagan, Kelowna, BC V5K1K5, Canada;
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Huang J, Chen GZ, Ahmad S, Hao Y, Chen JL, Zhou YZ, Lan SR, Liu ZJ, Peng DH. Genome-Wide Identification and Characterization of the GRF Gene Family in Melastoma dodecandrum. Int J Mol Sci 2023; 24:ijms24021261. [PMID: 36674776 PMCID: PMC9863823 DOI: 10.3390/ijms24021261] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/30/2022] [Accepted: 01/06/2023] [Indexed: 01/10/2023] Open
Abstract
Growth-regulating factor (GRF) is a kind of transcription factor unique to plants, playing an important role in the flowering regulation, growth, and development of plants. Melastoma dodecandrum is an important member of Melastomataceae, with ornamental, medicinal, and edible benefits. The identification of the GRF gene family in M. dodecandrum can help to improve their character of flavor and continuous flowering. The members of the GRF gene family were identified from the M. dodecandrum genome, and their bioinformatics, selective pressure, and expression patterns were analyzed. The results showed that there were 20 GRF genes in M. dodecandrum. Phylogenetic analysis showed that the 71 GRF genes from M. dodecandrum, Arabidopsis thaliana, Camellia sinensis, and Oryza sativa can be divided into three clades and six subclades. The 20 GRF genes of M. dodecandrum were distributed in twelve chromosomes and one contig. Furthermore, the gene structure and motif analysis showed that the intron and motif within each clade were very similar, but there were great differences among different clades. The promoter contained cis-acting elements related to hormone induction, stress, and growth and development. Different transcriptomic expression of MdGRFs indicated that MdGRFs may be involved in regulating the growth and development of M. dodecandrum. The results laid a foundation for further study on the function and molecular mechanism of the M. dodecandrum GRF gene family.
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Comprehensive Analysis for GRF Transcription Factors in Sacred Lotus ( Nelumbo nucifera). Int J Mol Sci 2022; 23:ijms23126673. [PMID: 35743113 PMCID: PMC9224289 DOI: 10.3390/ijms23126673] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/09/2022] [Accepted: 06/13/2022] [Indexed: 12/10/2022] Open
Abstract
Sacred lotus (Nelumbo nucifera) is an aquatic perennial plant with essential food, ornamental, and pharmacological value. Growth-regulating factor (GRF) is a transcription factor (TF) family that plays an important role in regulating the growth and development of plants. In this study, a comprehensive analysis of the GRF family in N. nucifera was performed, and its role in N. nucifera development was studied. A total of eight GRF genes were identified in the N. nucifera genome. Phylogenetic analysis divided the 38 GRF genes into six clades, while the NuGRFs only contained five clades. The analyses of gene structures, motifs, and cis-acting regulatory elements of the GRF gene family were performed. In addition, the chromosome location and collinearity were analyzed. The expression pattern based on transcriptomic data and real-time reverse transcription-quantitative PCR (qRT-PCR) revealed that the GRF genes were expressed in multiple organs and were abundant in actively growing tissues, and the expression levels decreased as the age of N. nucifera increased. Then, 3D structures of the NuGRF proteins were predicted by homology modeling. Finally, the subcellular localization of GRF1 was ascertained in the tobacco leaf through a vector. Therefore, this study provides a comprehensive overview of the GRF TF family in N. nucifera.
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Devi TR, Dasgupta M, Sahoo MR, Kole PC, Prakash N. High efficient de novo root-to-shoot organogenesis in Citrus jambhiri Lush.: Gene expression, genetic stability and virus indexing. PLoS One 2021; 16:e0246971. [PMID: 33606806 PMCID: PMC7894961 DOI: 10.1371/journal.pone.0246971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 01/28/2021] [Indexed: 11/19/2022] Open
Abstract
A protocol for high-frequency direct organogenesis from root explants of Kachai lemon (Citrus jambhiri Lush.) was developed. Full-length roots (~3 cm) were isolated from the in vitro grown seedlings and cultured on Murashige and Skoog basal medium supplemented with Nitsch vitamin (MSN) with different concentrations of cytokinin [6-benzylaminopurine, (BAP)] and gibberellic acid (GA3). The frequency of multiple shoot proliferation was very high, with an average of 34.3 shoots per root explant when inoculated on the MSN medium supplemented with BAP (1.0 mg L–1) and GA3 (1.0 mg L–1). Optimal rooting was induced in the plantlets under half strength MSN medium supplemented with indole-3-acetic acid (IAA, 0.5–1.0 mg L–1). IAA induced better root structure than 1-naphthaleneacetic acid (NAA), which was evident from the scanning electron microscopy (SEM). The expressions of growth regulating factor genes (GRF1 and GRF5) and GA3 signaling genes (GA2OX1 and KO1) were elevated in the regenerants obtained from MSN+BAP (1.0 mg L-1)+GA3 (1.0 mg L-1). The expressions of auxin regulating genes were high in roots obtained in ½ MSN+IAA 1.0 mg L-1. Furthermore, indexing of the regenerants confirmed that there was no amplicons detected for Huanglongbing bacterium and Citrus tristeza virus. Random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) markers detected no polymorphic bands amongst the regenerated plants. This is the first report that describes direct organogenesis from the root explant of Citrus jambhiri Lush. The high-frequency direct regeneration protocol in the present study provides an enormous significance in Citrus organogenesis, its commercial cultivation and genetic conservation.
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Affiliation(s)
| | - Madhumita Dasgupta
- ICAR Research Complex for North Eastern Hill Region, Imphal, Manipur, India
| | - Manas Ranjan Sahoo
- ICAR Research Complex for North Eastern Hill Region, Imphal, Manipur, India
- * E-mail:
| | | | - Narendra Prakash
- ICAR Research Complex for North Eastern Hill Region, Imphal, Manipur, India
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Huang W, He Y, Yang L, Lu C, Zhu Y, Sun C, Ma D, Yin J. Genome-wide analysis of growth-regulating factors (GRFs) in Triticum aestivum. PeerJ 2021; 9:e10701. [PMID: 33552727 PMCID: PMC7821759 DOI: 10.7717/peerj.10701] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 12/14/2020] [Indexed: 12/15/2022] Open
Abstract
The Growth-Regulating Factor (GRF) family encodes a type of plant-specific transcription factor (TF). GRF members play vital roles in plant development and stress response. Although GRF family genes have been investigated in a variety of plants, they remain largely unstudied in bread wheat (Triticum aestivum L.). The present study was conducted to comprehensively identify and characterize the T. aestivum GRF (TaGRF) gene family members. We identified 30 TaGRF genes, which were divided into four groups based on phylogenetic relationship. TaGRF members within the same subgroup shared similar motif composition and gene structure. Synteny analysis suggested that duplication was the dominant reason for family member expansion. Expression pattern profiling showed that most TaGRF genes were highly expressed in growing tissues, including shoot tip meristems, stigmas and ovaries, suggesting their key roles in wheat growth and development. Further qRT-PCR analysis revealed that all 14 tested TaGRFs were significantly differentially expressed in responding to drought or salt stresses, implying their additional involvement in stress tolerance of wheat. Our research lays a foundation for functional determination of TaGRFs, and will help to promote further scrutiny of their regulatory network in wheat development and stress response.
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Affiliation(s)
- Wendi Huang
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innocation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Yiqin He
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innocation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Lei Yang
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innocation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Chen Lu
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innocation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Yongxing Zhu
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innocation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, Hubei, China
| | - Cai Sun
- Plant Protection and Fruiter Technical Extension Station, Wanzhou District, Chongqing, China
| | - Dongfang Ma
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innocation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, Hubei, China.,Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central China, Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Junliang Yin
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/Hubei Collaborative Innocation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, Hubei, China.,Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central China, Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, China
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Wang J, Zhou H, Zhao Y, Sun P, Tang F, Song X, Lu MZ. Characterization of poplar growth-regulating factors and analysis of their function in leaf size control. BMC PLANT BIOLOGY 2020; 20:509. [PMID: 33153427 PMCID: PMC7643314 DOI: 10.1186/s12870-020-02699-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 10/13/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Growth-regulating factors (GRFs) are plant-specific transcription factors that control organ size. Nineteen GRF genes were identified in the Populus trichocarpa genome and one was reported to control leaf size mainly by regulating cell expansion. In this study, we further characterize the roles of the other poplar GRFs in leaf size control in a similar manner. RESULTS The 19 poplar GRF genes were clustered into six groups according to their phylogenetic relationship with Arabidopsis GRFs. Bioinformatic analysis, degradome, and transient transcription assays showed that 18 poplar GRFs were regulated by miR396, with GRF12b the only exception. The functions of PagGRF6b (Pag, Populus alba × P. glandulosa), PagGRF7a, PagGRF12a, and PagGRF12b, representing three different groups, were investigated. The results show that PagGRF6b may have no function on leaf size control, while PagGRF7a functions as a negative regulator of leaf size by regulating cell expansion. By contrast, PagGRF12a and PagGRF12b may function as positive regulators of leaf size control by regulating both cell proliferation and expansion, primarily cell proliferation. CONCLUSIONS The diversity of poplar GRFs in leaf size control may facilitate the specific, coordinated regulation of poplar leaf development through fine adjustment of cell proliferation and expansion.
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Affiliation(s)
- Jinnan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Houjun Zhou
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Ludong University, Yantai, 264025, China
| | - Yanqiu Zhao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Pengbo Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Fang Tang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Xueqin Song
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
| | - Meng-Zhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
- Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China.
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11
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Chen F, Yang Y, Luo X, Zhou W, Dai Y, Zheng C, Liu W, Yang W, Shu K. Genome-wide identification of GRF transcription factors in soybean and expression analysis of GmGRF family under shade stress. BMC PLANT BIOLOGY 2019; 19:269. [PMID: 31226949 PMCID: PMC6588917 DOI: 10.1186/s12870-019-1861-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/31/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND The Growth-regulating factor (GRF) family encodes plant-specific transcription factors which contain two conserved domains, QLQ and WRC. Members of this family play vital roles in plant development and stress response processes. Although GRFs have been identified in various plant species, we still know little about the GRF family in soybean (Glycine max). RESULTS In the present study, 22 GmGRFs distributed on 14 chromosomes and one scaffold were identified by searching soybean genome database and were clustered into five subgroups according to their phylogenetic relationships. GmGRFs belonging to the same subgroup shared a similar motif composition and gene structure. Synteny analysis revealed that large-scale duplications played key roles in the expansion of the GmGRF family. Tissue-specific expression data showed that GmGRFs were strongly expressed in growing tissues, including the shoot apical meristems, developing seeds and flowers, indicating that GmGRFs play critical roles in plant growth and development. On the basis of expression analysis of GmGRFs under shade conditions, we found that all GmGRFs responded to shade stress. Most GmGRFs were down-regulated in soybean leaves after shade treatment. CONCLUSIONS Taken together, this research systematically analyzed the characterization of the GmGRF family and its primary roles in soybean development and shade stress response. Further studies of the function of the GmGRFs in the growth, development and stress tolerance of soybean, especially under shade stress, will be valuable.
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Affiliation(s)
- Feng Chen
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, 710129 China
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Yingzeng Yang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, 710129 China
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Xiaofeng Luo
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, 710129 China
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Wenguan Zhou
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, 710129 China
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Yujia Dai
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, 710129 China
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Chuan Zheng
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, 710129 China
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Weiguo Liu
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Wenyu Yang
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Kai Shu
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an, 710129 China
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130 China
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12
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Wang P, Shi S, Ma J, Song H, Zhang Y, Gao C, Zhao C, Zhao S, Hou L, Lopez-Baltazar J, Fan S, Xia H, Wang X. Global Methylome and gene expression analysis during early Peanut pod development. BMC PLANT BIOLOGY 2018; 18:352. [PMID: 30545288 PMCID: PMC6293580 DOI: 10.1186/s12870-018-1546-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 11/20/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Early peanut pod development is an important process of peanut reproductive development. Modes of DNA methylation during early peanut pod development are still unclear, possibly because its allotetraploid genome may cause difficulty for the methylome analysis. RESULTS To investigate the functions of the dynamic DNA methylation during the early development of the peanut pod, global methylome and gene expression analyses were carried out by Illumina high throughput sequencing. A novel mapping strategy of reads was developed and used for methylome and gene expression analysis. Differentially methylated genes, such as nodulin, cell number regulator-like protein, and senescence-associated genes, were identified during the early developmental stages of the peanut pod. The expression levels of gibberellin-related genes changed during this period of pod development. From the stage one (S1) gynophore to the stage two (S2) gynophore, the expression levels of two key methyltransferase genes, DRM2 and MET1, were up-regulated, which may lead to global DNA methylation changes between these two stages. The differentially methylated and expressed genes identified in the S1, S2, and stage 3 (S3) gynophore are involved in different biological processes such as stem cell fate determination, response to red, blue, and UV light, post-embryonic morphogenesis, and auxin biosynthesis. The expression levels of many genes were co-related by their DNA methylation levels. In addition, our results showed that the abundance of some 24-nucleotide siRNAs and miRNAs were positively associated with DNA methylation levels of their target loci in peanut pods. CONCLUSION A novel mapping strategy of reads was described and verified in this study. Our results suggest that the methylated modes of the S1, S2, and S3 gynophore are different. The methylation changes that were identified during early peanut pod development provide useful information for understanding the roles of epigenetic regulation in peanut pod development.
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Affiliation(s)
- Pengfei Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
- Shandong Academy of Grape, Jinan, 250100 People’s Republic of China
| | - Suhua Shi
- Life Science College of Shandong Normal University, Jinan, 250014 People’s Republic of China
| | - Junjie Ma
- Life Science College of Shandong University, Jinan, 250100 People’s Republic of China
| | - Hui Song
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
| | - Ye Zhang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
| | - Chao Gao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
| | - Chuanzhi Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
- Life Science College of Shandong Normal University, Jinan, 250014 People’s Republic of China
| | - Shuzhen Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
- Life Science College of Shandong Normal University, Jinan, 250014 People’s Republic of China
| | - Lei Hou
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
| | | | - Shoujin Fan
- Life Science College of Shandong Normal University, Jinan, 250014 People’s Republic of China
| | - Han Xia
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
- Life Science College of Shandong Normal University, Jinan, 250014 People’s Republic of China
| | - Xingjun Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
- Life Science College of Shandong Normal University, Jinan, 250014 People’s Republic of China
- Life Science College of Shandong University, Jinan, 250100 People’s Republic of China
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Hou Y, Zhai L, Li X, Xue Y, Wang J, Yang P, Cao C, Li H, Cui Y, Bian S. Comparative Analysis of Fruit Ripening-Related miRNAs and Their Targets in Blueberry Using Small RNA and Degradome Sequencing. Int J Mol Sci 2017; 18:ijms18122767. [PMID: 29257112 PMCID: PMC5751366 DOI: 10.3390/ijms18122767] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 12/11/2017] [Accepted: 12/18/2017] [Indexed: 01/12/2023] Open
Abstract
MicroRNAs (miRNAs) play vital roles in the regulation of fruit development and ripening. Blueberry is an important small berry fruit crop with economical and nutritional value. However, nothing is known about the miRNAs and their targets involved in blueberry fruit ripening. In this study, using high-throughput sequencing of small RNAs, 84 known miRNAs belonging to 28 families and 16 novel miRNAs were identified in white fruit (WF) and blue fruit (BF) libraries, which represent fruit ripening onset and in progress, respectively. Among them, 41 miRNAs were shown to be differentially expressed during fruit maturation, and 16 miRNAs representing 16 families were further chosen to validate the sRNA sequencing data by stem-loop qRT-PCR. Meanwhile, 178 targets were identified for 41 known and 7 novel miRNAs in WF and BF libraries using degradome sequencing, and targets of miR160 were validated using RLM-RACE (RNA Ligase-Mediated (RLM)-Rapid Amplification of cDNA Ends) approach. Moreover, the expression patterns of 6 miRNAs and their targets were examined during fruit development and ripening. Finally, integrative analysis of miRNAs and their targets revealed a complex miRNA-mRNA regulatory network involving a wide variety of biological processes. The findings will facilitate future investigations of the miRNA-mediated mechanisms that regulate fruit development and ripening in blueberry.
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Affiliation(s)
- Yanming Hou
- College of Plant Science, Jilin University, Changchun 130062, China.
| | - Lulu Zhai
- College of Plant Science, Jilin University, Changchun 130062, China.
| | - Xuyan Li
- College of Plant Science, Jilin University, Changchun 130062, China.
| | - Yu Xue
- College of Life Sciences, Jilin University, Changchun 130012, China.
| | - Jingjing Wang
- College of Plant Science, Jilin University, Changchun 130062, China.
| | - Pengjie Yang
- College of Plant Science, Jilin University, Changchun 130062, China.
| | - Chunmei Cao
- College of Plant Science, Jilin University, Changchun 130062, China.
| | - Hongxue Li
- College of Plant Science, Jilin University, Changchun 130062, China.
| | - Yuhai Cui
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON N5V 4T3, Canada.
| | - Shaomin Bian
- College of Plant Science, Jilin University, Changchun 130062, China.
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Li M, Liang Z, He S, Zeng Y, Jing Y, Fang W, Wu K, Wang G, Ning X, Wang L, Li S, Tan H, Tan F. Genome-wide identification of leaf abscission associated microRNAs in sugarcane (Saccharum officinarum L.). BMC Genomics 2017; 18:754. [PMID: 28946845 PMCID: PMC5613641 DOI: 10.1186/s12864-017-4053-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/11/2017] [Indexed: 11/16/2022] Open
Abstract
Background Sugarcane (Saccharum officinarum L.) is an economically important crop, mainly due to the production of sugar and biofuel (Azevedo RA, Carvalho RF, Cia MC, & Gratão PL, Trop Plant Biol 4:42-51, 2011). Grown mainly in tropical and subtropical countries, sugarcane is a highly polyploid plant with up to ten copies of each chromosome, which increases the difficulties of genome assembly and genetic, physiologic and biochemical analyses. The increasing demands of sugar and the increasing cost of sugarcane harvest require sugarcane varieties which can shed their leaves during the maturity time, so it is important to study the mechanism of leaf abscission in sugarcane. Results To improve the understanding of miRNA roles in sugarcane leaf abscission, we reported the genome-wide characterization of miRNAs and their putative targets in sugarcane using deep sequencing for six small RNA libraries. In total, 93 conserved miRNAs and 454 novel miRNAs were identified in sugarcane using previously reported transcriptome as reference. Among them, 25 up-regulated and 13 down-regulated miRNAs were identified in leaf abscission sugarcane plants (LASP) compared to leaf packaging sugarcane plants (LPSP). Target prediction revealed several miRNA-mRNA modules including miR156-SPL, miR319-TPR2, miR396-GRF and miR408-LAC3 might be involved in the sugarcane leaf abscission. KEGG pathway enrichment analysis showed differentially expressed miRNAs may regulate pathways like “plant hormone signal transduction” and “plant-pathogen interaction”, which is consistent with previous transcriptome study. In addition, we identified 96 variant miRNAs with 135 single nucleotide polymorphisms (SNPs). The expression of sugarcane miRNAs and variant miRNAs were confirmed by qRT-PCR. We identified a possible poaceae specific miRNA called miR5384 for the first time in sugarcane. Conclusions We not only reported miR5384, a possible poaceae specific miRNA, for the first time in sugarcane but also presented some miRNA-mRNA modules including miR156-SPL, miR319-TPR2, miR396-GRF and miR408-LAC in sugarcane. These modules might be involved in the regulation of sugarcane leaf abscission during the maturity time. All of these findings may lay ground work for future application of sugarcane breeding program and benefit research studies of sugarcane miRNAs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4053-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ming Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China.
| | - Zhaoxu Liang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Shanshan He
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Yuan Zeng
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Yan Jing
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Weikuan Fang
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Kaichao Wu
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Guanyu Wang
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Xia Ning
- Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Lunwang Wang
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Song Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Hongwei Tan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
| | - Fang Tan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, People's Republic of China
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15
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Khatun K, Robin AHK, Park JI, Nath UK, Kim CK, Lim KB, Nou IS, Chung MY. Molecular Characterization and Expression Profiling of Tomato GRF Transcription Factor Family Genes in Response to Abiotic Stresses and Phytohormones. Int J Mol Sci 2017; 18:ijms18051056. [PMID: 28505092 PMCID: PMC5454968 DOI: 10.3390/ijms18051056] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/07/2017] [Accepted: 05/09/2017] [Indexed: 12/22/2022] Open
Abstract
Growth regulating factors (GRFs) are plant-specific transcription factors that are involved in diverse biological and physiological processes, such as growth, development and stress and hormone responses. However, the roles of GRFs in vegetative and reproductive growth, development and stress responses in tomato (Solanum lycopersicum) have not been extensively explored. In this study, we characterized the 13 SlGRF genes. In silico analysis of protein motif organization, intron–exon distribution, and phylogenetic classification confirmed the presence of GRF proteins in tomato. The tissue-specific expression analysis revealed that most of the SlGRF genes were preferentially expressed in young and growing tissues such as flower buds and meristems, suggesting that SlGRFs are important during growth and development of these tissues. Some of the SlGRF genes were preferentially expressed in fruits at distinct developmental stages suggesting their involvement in fruit development and the ripening process. The strong and differential expression of different SlGRFs under NaCl, drought, heat, cold, abscisic acid (ABA), and jasmonic acid (JA) treatment, predict possible functions for these genes in stress responses in addition to their growth regulatory functions. Further, differential expression of SlGRF genes upon gibberellic acid (GA3) treatment indicates their probable function in flower development and stress responses through a gibberellic acid (GA)-mediated pathway. The results of this study provide a basis for further functional analysis and characterization of this important gene family in tomato.
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Affiliation(s)
- Khadiza Khatun
- Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950, Korea.
| | - Arif Hasan Khan Robin
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950, Korea.
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950, Korea.
| | - Ujjal Kumar Nath
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950, Korea.
| | - Chang Kil Kim
- Department of Horticultural Science, Kyungpook National University, Daegu 702-701, Korea.
| | - Ki-Byung Lim
- Department of Horticultural Science, Kyungpook National University, Daegu 702-701, Korea.
| | - Ill Sup Nou
- Department of Horticulture, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950, Korea.
| | - Mi-Young Chung
- Department of Agricultural Industry Economy and Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950, Korea.
- Department of Agricultural Education, Sunchon National University, 413 Jungangno, Suncheon, Jeonnam 540-950, Korea.
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Khodadadi E, Mehrabi AA, Najafi A, Rastad S, Masoudi-Nejad A. Systems biology study of transcriptional and post-transcriptional co-regulatory network sheds light on key regulators involved in important biological processes in Citrus sinensis. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:331-342. [PMID: 28461722 PMCID: PMC5391350 DOI: 10.1007/s12298-017-0416-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 12/25/2016] [Accepted: 01/17/2017] [Indexed: 05/08/2023]
Abstract
Transcriptional and post-transcriptional regulators including transcription regulator, transcription factor and miRNA are the main endogenous molecular elements which control complex cellular mechanisms such as development, growth and response to biotic and abiotic stresses in a coordinated manner in plants. Utilizing the most recent information on such relationships in a plant species, obtained from high-throughput experimental technologies and advanced computational tools, we can reconstruct its co-regulatory network which consequently sheds light on key regulators involved in its important biological processes. In this article, combined systems biology approaches such as mining the literatures, various databases and network reconstruction, analysis, and visualization tools were employed to infer and visualize the coregulatory relationships between miRNAs and transcriptional regulators in Citrus sinensis. Using computationally and experimentally verified miRNA-target interactions and constructed co-expression networks on array-based data, 10 coregulatory networks and 10 corresponding subgraphs include FFL motifs were obtained for 10 distinct tissues/conditions. Then PPI subnetworks were extracted for transcripts/genes included in mentioned subgraphs in order to the functional analysis of extracted coregulatory circuits. These proposed coregulatory connections shed light on precisely identifying C. sinensis metabolic pathways key switches, which are demanded for ultimate goals such as genome editing.
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Affiliation(s)
- Ehsan Khodadadi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Ilam, Ilam, Iran
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Ali Ashraf Mehrabi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Ilam, Ilam, Iran
| | - Ali Najafi
- Department of Molecular Biology, Medical University of Baqiyatalah, Tehran, Iran
| | - Saber Rastad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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