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Li L, Xu JB, Zhu ZW, Ma R, Wu XZ, Geng YK. Genome-wide identification and expression analysis of the SPL transcription factor family and its response to abiotic stress in Pisum sativum L. BMC Genomics 2024; 25:539. [PMID: 38822248 PMCID: PMC11140923 DOI: 10.1186/s12864-024-10262-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/27/2024] [Indexed: 06/02/2024] Open
Abstract
Squamous promoter binding protein-like (SPL) genes encode plant-specific transcription factors (TFs) that play essential roles in modulating plant growth, development, and stress response. Pea (Pisum sativum L.) is a coarse grain crop of great importance in food production, biodiversity conservation and molecular genetic research, providing genetic information and nutritional resources for improving agricultural production and promoting human health. However, only limited researches on the structure and functions of SPL genes exist in pea (PsSPLs). In this study, we identified 22 PsSPLs and conducted a genome-wide analysis of their physical characteristics, chromosome distribution, gene structure, phylogenetic evolution and gene expression patterns. As a result, the PsSPLs were unevenly distributed on the seven chromosomes of pea and harbored the SBP domain, which is composed of approximately 76 amino acid residues. The phylogenetic analysis revealed that the PsSPLs clustered into eight subfamilies and showed high homology with SPL genes in soybean. Further analysis showed the presence of segmental duplications in the PsSPLs. The expression patterns of 22 PsSPLs at different tissues, developmental stages and under various stimulus conditions were evaluated by qRT-PCR method. It was found that the expression patterns of PsSPLs from the same subfamily were similar in different tissues, the transcripts of most PsSPLs reached the maximum peak value at 14 days after anthesis in the pod. Abiotic stresses can cause significantly up-regulated PsSPL19 expression with spatiotemporal specificity, in addition, four plant hormones can cause the up-regulated expression of most PsSPLs including PsSPL19 in a time-dependent manner. Therefore, PsSPL19 could be a key candidate gene for signal transduction during pea growth and development, pod formation, abiotic stress and plant hormone response. Our findings should provide insights for the elucidating of development regulation mechanism and breeding for resistance to abiotic stress pea.
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Affiliation(s)
- Long Li
- Minzu University of China, 100010, Beijing, P.R. China
- College of Agronomy, Hebei Agricultural University, 071001, Baoding, P.R. China
| | - Jian Bo Xu
- School of Food and Biological engineering, Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China
| | - Zhi Wen Zhu
- School of Food and Biological engineering, Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China
| | - Rui Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 712100, Yangling, Shaanxi, P.R. China
| | - Xiao Zong Wu
- School of Food and Biological engineering, Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China.
- Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China.
| | - Yu Ke Geng
- Minzu University of China, 100010, Beijing, P.R. China.
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Ledford WC, Silvestri A, Fiorilli V, Roth R, Rubio-Somoza I, Lanfranco L. A journey into the world of small RNAs in the arbuscular mycorrhizal symbiosis. THE NEW PHYTOLOGIST 2024; 242:1534-1544. [PMID: 37985403 DOI: 10.1111/nph.19394] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/15/2023] [Indexed: 11/22/2023]
Abstract
Arbuscular mycorrhizal (AM) symbiosis is a mutualistic interaction between fungi and most land plants that is underpinned by a bidirectional exchange of nutrients. AM development is a tightly regulated process that encompasses molecular communication for reciprocal recognition, fungal accommodation in root tissues and activation of symbiotic function. As such, a complex network of transcriptional regulation and molecular signaling underlies the cellular and metabolic reprogramming of host cells upon AM fungal colonization. In addition to transcription factors, small RNAs (sRNAs) are emerging as important regulators embedded in the gene network that orchestrates AM development. In addition to controlling cell-autonomous processes, plant sRNAs also function as mobile signals capable of moving to different organs and even to different plants or organisms that interact with plants. AM fungi also produce sRNAs; however, their function in the AM symbiosis remains largely unknown. Here, we discuss the contribution of host sRNAs in the development of AM symbiosis by considering their role in the transcriptional reprogramming of AM fungal colonized cells. We also describe the characteristics of AM fungal-derived sRNAs and emerging evidence for the bidirectional transfer of functional sRNAs between the two partners to mutually modulate gene expression and control the symbiosis.
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Affiliation(s)
- William Conrad Ledford
- Department of Life Sciences and Systems Biology, University of Turin, Turin, 10125, Italy
- Molecular Reprogramming and Evolution (MoRE) Lab, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, 08193, Spain
| | - Alessandro Silvestri
- Molecular Reprogramming and Evolution (MoRE) Lab, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, 08193, Spain
| | - Valentina Fiorilli
- Department of Life Sciences and Systems Biology, University of Turin, Turin, 10125, Italy
| | - Ronelle Roth
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Ignacio Rubio-Somoza
- Molecular Reprogramming and Evolution (MoRE) Lab, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, 08193, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, 08001, Spain
| | - Luisa Lanfranco
- Department of Life Sciences and Systems Biology, University of Turin, Turin, 10125, Italy
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Fan Y, Wan X, Zhang X, Zhang J, Zheng C, Yang Q, Yang L, Li X, Feng L, Zou L, Xiang D. GRAS gene family in rye (Secale cereale L.): genome-wide identification, phylogeny, evolutionary expansion and expression analyses. BMC PLANT BIOLOGY 2024; 24:46. [PMID: 38216860 PMCID: PMC10787399 DOI: 10.1186/s12870-023-04674-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 12/08/2023] [Indexed: 01/14/2024]
Abstract
BACKGROUND The GRAS transcription factor family plays a crucial role in various biological processes in different plants, such as tissue development, fruit maturation, and environmental stress. However, the GRAS family in rye has not been systematically analyzed yet. RESULTS In this study, 67 GRAS genes in S. cereale were identified and named based on the chromosomal location. The gene structures, conserved motifs, cis-acting elements, gene replications, and expression patterns were further analyzed. These 67 ScGRAS members are divided into 13 subfamilies. All members include the LHR I, VHIID, LHR II, PFYRE, and SAW domains, and some nonpolar hydrophobic amino acid residues may undergo cross-substitution in the VHIID region. Interested, tandem duplications may have a more important contribution, which distinguishes them from other monocotyledonous plants. To further investigate the evolutionary relationship of the GRAS family, we constructed six comparative genomic maps of homologous genes between rye and different representative monocotyledonous and dicotyledonous plants. The response characteristics of 19 ScGRAS members from different subfamilies to different tissues, grains at filling stages, and different abiotic stresses of rye were systematically analyzed. Paclobutrazol, a triazole-based plant growth regulator, controls plant tissue and grain development by inhibiting gibberellic acid (GA) biosynthesis through the regulation of DELLA proteins. Exogenous spraying of paclobutrazol significantly reduced the plant height but was beneficial for increasing the weight of 1000 grains of rye. Treatment with paclobutrazol, significantly reduced gibberellin levels in grain in the filling period, caused significant alteration in the expression of the DELLA subfamily gene members. Furthermore, our findings with respect to genes, ScGRAS46 and ScGRAS60, suggest that these two family members could be further used for functional characterization studies in basic research and in breeding programmes for crop improvement. CONCLUSIONS We identified 67 ScGRAS genes in rye and further analysed the evolution and expression patterns of the encoded proteins. This study will be helpful for further analysing the functional characteristics of ScGRAS genes.
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Affiliation(s)
- Yu Fan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, P.R. China
| | - Xianqi Wan
- Sichuan Academy of Agricultural Machinery Science, Chengdu, 610011, P.R. China
| | - Xin Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, P.R. China
| | - Jieyu Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, P.R. China
| | - Chunyu Zheng
- College of Food Science and Engineering, Xinjiang Institute of Technology, Aksu, 843100, P.R. China
| | - Qiaohui Yang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, P.R. China
| | - Li Yang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, P.R. China
| | - Xiaolong Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, P.R. China
| | - Liang Feng
- Chengdu Institute of Food Inspection, Chengdu, 610000, P.R. China
| | - Liang Zou
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, P.R. China.
| | - Dabing Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, P.R. China.
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Reinprecht Y, Schram L, Perry GE, Morneau E, Smith TH, Pauls KP. Mapping yield and yield-related traits using diverse common bean germplasm. Front Genet 2024; 14:1246904. [PMID: 38234999 PMCID: PMC10791882 DOI: 10.3389/fgene.2023.1246904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 11/29/2023] [Indexed: 01/19/2024] Open
Abstract
Common bean (bean) is one of the most important legume crops, and mapping genes for yield and yield-related traits is essential for its improvement. However, yield is a complex trait that is typically controlled by many loci in crop genomes. The objective of this research was to identify regions in the bean genome associated with yield and a number of yield-related traits using a collection of 121 diverse bean genotypes with different yields. The beans were evaluated in replicated trials at two locations, over two years. Significant variation among genotypes was identified for all traits analyzed in the four environments. The collection was genotyped with the BARCBean6K_3 chip (5,398 SNPs), two yield/antiyield gene-based markers, and seven markers previously associated with resistance to common bacterial blight (CBB), including a Niemann-Pick polymorphism (NPP) gene-based marker. Over 90% of the single-nucleotide polymorphisms (SNPs) were polymorphic and separated the panel into two main groups of small-seeded and large-seeded beans, reflecting their Mesoamerican and Andean origins. Thirty-nine significant marker-trait associations (MTAs) were identified between 31 SNPs and 15 analyzed traits on all 11 bean chromosomes. Some of these MTAs confirmed genome regions previously associated with the yield and yield-related traits in bean, but a number of associations were not reported previously, especially those with derived traits. Over 600 candidate genes with different functional annotations were identified for the analyzed traits in the 200-Kb region centered on significant SNPs. Fourteen SNPs were identified within the gene model sequences, and five additional SNPs significantly associated with five different traits were located at less than 0.6 Kb from the candidate genes. The work confirmed associations between two yield/antiyield gene-based markers (AYD1m and AYD2m) on chromosome Pv09 with yield and identified their association with a number of yield-related traits, including seed weight. The results also confirmed the usefulness of the NPP marker in screening for CBB resistance. Since disease resistance and yield measurements are environmentally dependent and labor-intensive, the three gene-based markers (CBB- and two yield-related) and quantitative trait loci (QTL) that were validated in this work may be useful tools for simplifying and accelerating the selection of high-yielding and CBB-resistant bean cultivars.
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Affiliation(s)
| | - Lyndsay Schram
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Gregory E. Perry
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Emily Morneau
- Harrow Research and Development Centre, Agriculture and Agri-Food Canada, Harrow, ON, Canada
| | - Thomas H. Smith
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - K. Peter Pauls
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
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Zou T, Zhang K, Zhang J, Liu S, Liang J, Liu J, Zhu J, Liang Y, Wang S, Deng Q, Liu H, Jin J, Li P, Li S. DWARF AND LOW-TILLERING 2 functions in brassinosteroid signaling and controls plant architecture and grain size in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1766-1783. [PMID: 37699038 DOI: 10.1111/tpj.16464] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/22/2023] [Accepted: 09/01/2023] [Indexed: 09/14/2023]
Abstract
Brassinosteroids (BRs) are a class of steroid phytohormones that control various aspects of plant growth and development. Several transcriptional factors (TFs) have been suggested to play roles in BR signaling. However, their possible relationship remains largely unknown. Here, we identified a rice mutant dwarf and low-tillering 2 (dlt2) with altered plant architecture, increased grain width, and reduced BR sensitivity. DLT2 encodes a GIBBERELLIN INSENSITIVE (GAI)-REPRESSOR OF GAI (RGA)-SCARECROW (GRAS) TF that is mainly localized in the nucleus and has weak transcriptional activity. Our further genetic and biochemical analyses indicate that DLT2 interacts with two BR-signaling-related TFs, DLT and BRASSINAZOLE-RESISTANT 1, and probably modulates their transcriptional activity. These findings imply that DLT2 is implicated in a potentially transcriptional complex that mediates BR signaling and rice development and suggests that DLT2 could be a potential target for improving rice architecture and grain morphology. This work also sheds light on the role of rice GRAS members in regulating numerous developmental processes.
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Affiliation(s)
- Ting Zou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Kaixuan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jing Zhang
- Technical Center of Chengdu Customs, Chengdu, 610041, Sichuan, China
| | - Sijing Liu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jing Liang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jiaxu Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jun Zhu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yueyang Liang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Shiquan Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qiming Deng
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Huainian Liu
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jinghua Jin
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ping Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Shuangcheng Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
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Wu X, Cheng C, Ma R, Xu J, Ma C, Zhu Y, Ren Y. Genome-wide identification, expression analysis, and functional study of the bZIP transcription factor family and its response to hormone treatments in pea (Pisum sativum L.). BMC Genomics 2023; 24:705. [PMID: 37993794 PMCID: PMC10666455 DOI: 10.1186/s12864-023-09793-5] [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] [Received: 08/04/2023] [Accepted: 11/08/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Basic leucine zipper (bZIP) protein is a plant-specific transcription factor involved in various biological processes, including light signaling, seed maturation, flower development, cell elongation, seed accumulation protein, and abiotic and biological stress responses. However, little is known about the pea bZIP family. RESULTS In this study, we identified 87 bZIP genes in pea, named PsbZIP1 ~ PsbZIP87, via homology analysis using Arabidopsis. The genes were divided into 12 subfamilies and distributed unevenly in 7 pea chromosomes. PsbZIPs in the same subfamily contained similar intron/exon organization and motif composition. 1 tandem repeat event and 12 segmental duplication events regulated the expansion of the PsbZIP gene family. To better understand the evolution of the PsbZIP gene family, we conducted collinearity analysis using Arabidopsis thaliana, Oryza sativa Japonica, Fagopyrum tataricum, Solanum lycopersicum, Vitis vinifera, and Brachypodium distachyon as the related species of pea. In addition, interactions between PsbZIP proteins and promoters containing hormone- and stress-responsive cis-acting elements suggest that the regulation of PsbZIP expression was complex. We also evaluated the expression patterns of bZIP genes in different tissues and at different fruit development stages, all while subjecting them to five hormonal treatments. CONCLUSION These results provide a deeper understanding of PsbZIP gene family evolution and resources for the molecular breeding of pea. The findings suggested that PsbZIP genes, specifically PSbZIP49, play key roles in the development of peas and their response to various hormones.
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Affiliation(s)
- Xiaozong Wu
- Zhengzhou University of Light Industry, Zhengzhou, 450002, People's Republic of China
| | - Changhe Cheng
- China Tobacco Zhejiang Industrial Co., LTD, Hangzhou, 310000, People's Republic of China
| | - Rui Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Jianbo Xu
- Zhengzhou University of Light Industry, Zhengzhou, 450002, People's Republic of China
| | - Congcong Ma
- College of Medical Technology, Luoyang Polytechnic, Luoyang, 471000, China
| | - Yutao Zhu
- College of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, 462500, China.
- Henan University of Urban Construction, Pingdingshan, 467036, Henan, China.
| | - Yanyan Ren
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
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Rana D, Sharma P, Arpita K, Srivastava H, Sharma S, Gaikwad K. Genome-wide identification and characterization of GRAS gene family in pigeonpea ( Cajanus cajan (L.) Millspaugh). 3 Biotech 2023; 13:363. [PMID: 37840881 PMCID: PMC10570252 DOI: 10.1007/s13205-023-03782-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023] Open
Abstract
The GRAS proteins are plant-specific transcription factors (TFs) that play a crucial role in various plant physiological processes, including tissue development and stress responses. To date, GRAS family has been comprehensively characterized in Arabidopsis, soybean, rice, chickpea and other plant species. To understand the structural and functional aspects of pigeonpea (C. cajan), we identified 60 putative GRAS (CcGRAS) genes from pigeonpea genome and further analysed their physicochemical properties, subcellular locations, evolutionary classification, exon-intron structures, conserved domains, gene duplication events and cis-promoter regions. Based on the sequence similarity, CcGRAS family was clustered into 9 subfamilies and the genes with a similar structure and motif distribution were clustered in the same group. The gene duplication studies revealed that these genes were derived from tandem and dispersed duplication events. The cis-promoter regulatory analysis of CcGRAS genes indicated the presence of three types of cis-acting elements including light-responsive, hormone-responsive and plant growth and development related. The expression profiling of CcGRAS genes revealed their tissue-specific functions and differential nature. Collectively, this study highlights relevant functional and regulatory elements of GRAS family in pigeonpea creating a significant resource for future functional studies. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03782-x.
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Affiliation(s)
- Divyansh Rana
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313 India
| | - Priya Sharma
- Department of Biotechnology, Jamia Hamdard, New Delhi, Delhi 110062 India
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
| | - Kumari Arpita
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
| | - Harsha Srivastava
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
| | - Sandhya Sharma
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
| | - Kishor Gaikwad
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
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Weng Y, Chen X, Hao Z, Lu L, Wu X, Zhang J, Wu J, Shi J, Chen J. Genome-wide analysis of the GRAS gene family in Liriodendron chinense reveals the putative function in abiotic stress and plant development. FRONTIERS IN PLANT SCIENCE 2023; 14:1211853. [PMID: 37810392 PMCID: PMC10551155 DOI: 10.3389/fpls.2023.1211853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/22/2023] [Indexed: 10/10/2023]
Abstract
Introduction GRAS genes encode plant-specific transcription factors that play essential roles in plant growth and development. However, the members and the function of the GRAS gene family have not been reported in Liriodendron chinense. L. chinense, a tree species in the Magnolia family that produces excellent timber for daily life and industry. In addition, it is a good relict species for plant evolution research. Methods Therefore, we conducted a genome-wide study of the LcGRAS gene family and identified 49 LcGRAS genes in L. chinense. Results We found that LcGRAS could be divided into 13 sub-groups, among which there is a unique branch named HAM-t. We carried out RNA sequencing analysis of the somatic embryos from L. chinense and found that LcGRAS genes are mainly expressed after heart-stage embryo development, suggesting that LcGRAS may have a function during somatic embryogenesis. We also investigated whether GRAS genes are responsive to stress by carrying out RNA sequencing (RNA-seq) analysis, and we found that the genes in the PAT subfamily were activated upon stress treatment, suggesting that these genes may help plants survive stressful environments. We found that PIF was downregulated and COR was upregulated after the transient overexpression of PATs, suggesting that PAT may be upstream regulators of cold stress. Discussion Collectively, LcGRAS genes are conserved and play essential roles in plant development and adaptation to abiotic stress.
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Affiliation(s)
- Yuhao Weng
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Xinying Chen
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Zhaodong Hao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Lu Lu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Xinru Wu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Jiaji Zhang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Jingxiang Wu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Jisen Shi
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Jinhui Chen
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
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Ren Y, Ma R, Xie M, Fan Y, Feng L, Chen L, Yang H, Wei X, Wang X, Liu K, Cheng P, Wang B. Genome-wide identification, phylogenetic and expression pattern analysis of HSF family genes in the Rye (Secale cereale L.). BMC PLANT BIOLOGY 2023; 23:441. [PMID: 37726665 PMCID: PMC10510194 DOI: 10.1186/s12870-023-04418-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/24/2023] [Indexed: 09/21/2023]
Abstract
BACKGROUND Heat shock factor (HSF), a typical class of transcription factors in plants, has played an essential role in plant growth and developmental stages, signal transduction, and response to biotic and abiotic stresses. The HSF genes families has been identified and characterized in many species through leveraging whole genome sequencing (WGS). However, the identification and systematic analysis of HSF family genes in Rye is limited. RESULTS In this study, 31 HSF genes were identified in Rye, which were unevenly distributed on seven chromosomes. Based on the homology of A. thaliana, we analyzed the number of conserved domains and gene structures of ScHSF genes that were classified into seven subfamilies. To better understand the developmental mechanisms of ScHSF family during evolution, we selected one monocotyledon (Arabidopsis thaliana) and five (Triticum aestivum L., Hordeum vulgare L., Oryza sativa L., Zea mays L., and Aegilops tauschii Coss.) specific representative dicotyledons associated with Rye for comparative homology mapping. The results showed that fragment replication events modulated the expansion of the ScHSF genes family. In addition, interactions between ScHSF proteins and promoters containing hormone- and stress-responsive cis-acting elements suggest that the regulation of ScHSF expression was complex. A total of 15 representative genes were targeted from seven subfamilies to characterize their gene expression responses in different tissues, fruit developmental stages, three hormones, and six different abiotic stresses. CONCLUSIONS This study demonstrated that ScHSF genes, especially ScHSF1 and ScHSF3, played a key role in Rye development and its response to various hormones and abiotic stresses. These results provided new insights into the evolution of HSF genes in Rye, which could help the success of molecular breeding in Rye.
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Affiliation(s)
- Yanyan Ren
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Rui Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Muhua Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yue Fan
- College of Food Science and Engineering, Xinjiang Institute of Technology, Aksu, 843100, People's Republic of China
| | - Liang Feng
- Chengdu Institute of Food Inspection, Chengdu, 610000, People's Republic of China
| | - Long Chen
- Tianfu New Area General Aviation Profession Academy, Meishan, 620564, China
| | - Hao Yang
- Agricultural Service Center of Langde Town of Leishan County, Qiandongnan Miao and Dong Autonomous Prefecture, 556019, China
| | - Xiaobao Wei
- Guizhou Provincial Center For Disease Control And Prevention, Guiyang, 550025, People's Republic of China
| | - Xintong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Kouhan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Peng Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - Baotong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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Chang J, Fan D, Lan S, Cheng S, Chen S, Lin Y, Cao S. Genome-Wide Identification, Expression and Stress Analysis of the GRAS Gene Family in Phoebe bournei. PLANTS (BASEL, SWITZERLAND) 2023; 12:2048. [PMID: 37653964 PMCID: PMC10222183 DOI: 10.3390/plants12102048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 09/02/2023]
Abstract
GRAS genes are important transcriptional regulators in plants that govern plant growth and development through enhancing plant hormones, biosynthesis, and signaling pathways. Drought and other abiotic factors may influence the defenses and growth of Phoebe bournei, which is a superb timber source for the construction industry and building exquisite furniture. Although genome-wide identification of the GRAS gene family has been completed in many species, that of most woody plants, particularly P. bournei, has not yet begun. We performed a genome-wide investigation of 56 PbGRAS genes, which are unequally distributed across 12 chromosomes. They are divided into nine subclades. Furthermore, these 56 PbGRAS genes have a substantial number of components related to abiotic stress responses or phytohormone transmission. Analysis using qRT-PCR showed that the expression of four PbGRAS genes, namely PbGRAS7, PbGRAS10, PbGRAS14 and PbGRAS16, was differentially increased in response to drought, salt and temperature stresses, respectively. We hypothesize that they may help P. bournei to successfully resist harsh environmental disturbances. In this work, we conducted a comprehensive survey of the GRAS gene family in P. bournei plants, and the results provide an extensive and preliminary resource for further clarification of the molecular mechanisms of the GRAS gene family in P. bournei in response to abiotic stresses and forestry improvement.
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Affiliation(s)
- Jiarui Chang
- International College, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Dunjin Fan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (D.F.); (S.C.); (S.C.)
| | - Shuoxian Lan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shengze Cheng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (D.F.); (S.C.); (S.C.)
| | - Shipin Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (D.F.); (S.C.); (S.C.)
| | - Yuling Lin
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shijiang Cao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (D.F.); (S.C.); (S.C.)
- Key Laboratory of Fujian Universities for Stress Physiology Ecology and Molecular Biology of Forest, Fuzhou 350002, China
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11
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Liu C, Wang K, Yun Z, Liu W, Zhao M, Wang Y, Hu J, Liu T, Wang N, Wang Y, Zhang M. Functional Study of PgGRAS68-01 Gene Involved in the Regulation of Ginsenoside Biosynthesis in Panax ginseng. Int J Mol Sci 2023; 24:ijms24043347. [PMID: 36834759 PMCID: PMC9961673 DOI: 10.3390/ijms24043347] [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: 10/22/2022] [Revised: 12/11/2022] [Accepted: 01/28/2023] [Indexed: 02/11/2023] Open
Abstract
Ginseng (Panax ginseng C. A. Meyer) is a perennial herb from the genus Panax in the family Araliaceae. It is famous in China and abroad. The biosynthesis of ginsenosides is controlled by structural genes and regulated by transcription factors. GRAS transcription factors are widely found in plants. They can be used as tools to modify plant metabolic pathways by interacting with promoters or regulatory elements of target genes to regulate the expression of target genes, thereby activating the synergistic interaction of multiple genes in metabolic pathways and effectively improving the accumulation of secondary metabolites. However, there are no reports on the involvement of the GRAS gene family in ginsenoside biosynthesis. In this study, the GRAS gene family was located on chromosome 24 pairs in ginseng. Tandem replication and fragment replication also played a key role in the expansion of the GRAS gene family. The PgGRAS68-01 gene closely related to ginsenoside biosynthesis was screened out, and the sequence and expression pattern of the gene were analyzed. The results showed that the expression of PgGRAS68-01 gene was spatio-temporal specific. The full-length sequence of PgGRAS68-01 gene was cloned, and the overexpression vector pBI121-PgGRAS68-01 was constructed. The ginseng seedlings were transformed by Agrobacterium rhifaciens-mediated method. The saponin content in the single root of positive hair root was detected, and the inhibitory role of PgGRAS68-01 in ginsenoside synthesis is reported.
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Affiliation(s)
- Chang Liu
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
| | - Kangyu Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (K.W.); (M.Z.)
| | - Ziyi Yun
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
| | - Wenbo Liu
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
| | - Mingzhu Zhao
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
| | - Yanfang Wang
- Laboratory for Cultivation and Breeding of Medicinal Plants of National Administration of Traditional Chinese Medicine, Jilin Agricultural University, Changchun 130118, China
| | - Jian Hu
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
| | - Tao Liu
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
| | - Nan Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
| | - Yi Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
| | - Meiping Zhang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (K.W.); (M.Z.)
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12
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Yu L, Hui C, Huang R, Wang D, Fei C, Guo C, Zhang J. Genome-wide identification, evolution and transcriptome analysis of GRAS gene family in Chinese chestnut ( Castanea mollissima). Front Genet 2023; 13:1080759. [PMID: 36685835 PMCID: PMC9845266 DOI: 10.3389/fgene.2022.1080759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/06/2022] [Indexed: 01/05/2023] Open
Abstract
GRAS transcription factors play an important role in regulating various biological processes in plant growth and development. However, their characterization and potential function are still vague in Chinese chestnut (Castanea mollissima), an important nut with rich nutrition and high economic value. In this study, 48 CmGRAS genes were identified in Chinese chestnut genome and phylogenetic analysis divided CmGRAS genes into nine subfamilies, and each of them has distinct conserved structure domain and features. Genomic organization revealed that CmGRAS tend to have a representative GRAS domain and fewer introns. Tandem duplication had the greatest contribution for the CmGRAS expansion based on the comparative genome analysis, and CmGRAS genes experienced strong purifying selection pressure based on the Ka/Ks. Gene expression analysis revealed some CmGRAS members with potential functions in bud development and ovule fertility. CmGRAS genes with more homologous relationships with reference species had more cis-acting elements and higher expression levels. Notably, the lack of DELLA domain in members of the DELLA subfamily may cause de functionalization, and the differences between the three-dimensional structures of them were exhibited. This comprehensive study provides theoretical and practical basis for future research on the evolution and function of GRAS gene family.
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Affiliation(s)
- Liyang Yu
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China,Hebei Collaborative Innovation Center of Chestnut Industry, Qinhuangdao, Hebei, China
| | - Cai Hui
- The Office of Scientific Research, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Ruimin Huang
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China,Hebei Collaborative Innovation Center of Chestnut Industry, Qinhuangdao, Hebei, China
| | - Dongsheng Wang
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China,Hebei Collaborative Innovation Center of Chestnut Industry, Qinhuangdao, Hebei, China
| | - Cao Fei
- Hebei Collaborative Innovation Center of Chestnut Industry, Qinhuangdao, Hebei, China,Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, Qinhuangdao, Hebei, China
| | - Chunlei Guo
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China,Hebei Collaborative Innovation Center of Chestnut Industry, Qinhuangdao, Hebei, China
| | - Jingzheng Zhang
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China,Hebei Collaborative Innovation Center of Chestnut Industry, Qinhuangdao, Hebei, China,Hebei Key Laboratory of Horticultural Germplasm Excavation and Innovative Utilization, Qinhuangdao, Hebei, China,*Correspondence: Jingzheng Zhang,
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13
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Pan J, Zhou Q, Wang H, Chen Y, Wang Z, Zhang J. Genome-wide identification and characterization of abiotic stress responsive GRAS family genes in oat ( Avena sativa). PeerJ 2023; 11:e15370. [PMID: 37187518 PMCID: PMC10178225 DOI: 10.7717/peerj.15370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Abstract
Background GRAS transcription factors play a variety of functions in plant growth and development and are named after the first three transcription factors GAI (GIBBERRELLICACIDINSENSITIVE), RGA (REPRESSOROFGAI), and SCR (SCARECROW) found in this family. Oat (Avena sativa) is one of the most important forage grasses in the world. However, there are few reports on the GRAS gene family in oat. Methods In order to understand the information and expression pattern of oat GRAS family members, we identified the GRAS members and analyzed their phylogenetic relationship, gene structure, and expression pattern in oat by bioinformatics technology. Results The results showed that the oat GRAS family consists of 30 members, and most of the AsGRAS proteins were neutral or acidic proteins. The phylogenetic tree divided the oat GRAS members into four subfamilies, and each subfamily has different conservative domains and functions. Chromosome location analysis suggested that 30 GRAS genes were unevenly distributed on five chromosomes of oat. The results of real-time quantitative reverse transcription-PCR (qRT-PCR) showed that some AsGRAS genes (AsGRAS12, AsGRAS14, AsGRAS21, and AsGRAS24) were all up-regulated with increasing stress treatment time.The results of this study provide a theoretical basis for further research into the corresponding stress of oat. Therefore, further studies concentrating on these AsGRAS genes might reveal the many roles played by GRAS genes in oat.
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Affiliation(s)
- Jing Pan
- Southwest Minzu University, Institute of Qinghai-Tibetan Plateau, Chengdu, Sichuan Province, China
- Southwest Minzu University, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Chengdu, Sichuan Province, China
| | - Qingping Zhou
- Southwest Minzu University, Institute of Qinghai-Tibetan Plateau, Chengdu, Sichuan Province, China
- Southwest Minzu University, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Chengdu, Sichuan Province, China
| | - Hui Wang
- Southwest Minzu University, Institute of Qinghai-Tibetan Plateau, Chengdu, Sichuan Province, China
- Southwest Minzu University, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Chengdu, Sichuan Province, China
| | - Youjun Chen
- Southwest Minzu University, Institute of Qinghai-Tibetan Plateau, Chengdu, Sichuan Province, China
- Southwest Minzu University, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Chengdu, Sichuan Province, China
| | - Zhiqiang Wang
- Southwest Minzu University, Institute of Qinghai-Tibetan Plateau, Chengdu, Sichuan Province, China
- Southwest Minzu University, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Chengdu, Sichuan Province, China
| | - Junchao Zhang
- Southwest Minzu University, Institute of Qinghai-Tibetan Plateau, Chengdu, Sichuan Province, China
- Southwest Minzu University, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Chengdu, Sichuan Province, China
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14
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Tian S, Wan Y, Jiang D, Gong M, Lin J, Xia M, Shi C, Xing H, Li HL. Genome-Wide Identification, Characterization, and Expression Analysis of GRAS Gene Family in Ginger ( Zingiber officinale Roscoe). Genes (Basel) 2022; 14:96. [PMID: 36672837 PMCID: PMC9859583 DOI: 10.3390/genes14010096] [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: 11/30/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/30/2022] Open
Abstract
GRAS family proteins are one of the most abundant transcription factors in plants; they play crucial roles in plant development, metabolism, and biotic- and abiotic-stress responses. The GRAS family has been identified and functionally characterized in some plant species. However, this family in ginger (Zingiber officinale Roscoe), a medicinal crop and non-prescription drug, remains unknown to date. In the present study, 66 GRAS genes were identified by searching the complete genome sequence of ginger. The GRAS family is divided into nine subfamilies based on the phylogenetic analyses. The GRAS genes are distributed unevenly across 11 chromosomes. By analyzing the gene structure and motif distribution of GRAS members in ginger, we found that the GRAS genes have more than one cis-acting element. Chromosomal location and duplication analysis indicated that whole-genome duplication, tandem duplication, and segmental duplication may be responsible for the expansion of the GRAS family in ginger. The expression levels of GRAS family genes are different in ginger roots and stems, indicating that these genes may have an impact on ginger development. In addition, the GRAS genes in ginger showed extensive expression patterns under different abiotic stresses, suggesting that they may play important roles in the stress response. Our study provides a comprehensive analysis of GRAS members in ginger for the first time, which will help to better explore the function of GRAS genes in the regulation of tissue development and response to stress in ginger.
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Affiliation(s)
- Shuming Tian
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404020, China
| | - Yuepeng Wan
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
| | - Dongzhu Jiang
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
| | - Min Gong
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404020, China
| | - Junyao Lin
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
| | - Maoqin Xia
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
| | - Cuiping Shi
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
| | - Haitao Xing
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing 402160, China
| | - Hong-Lei Li
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
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Zhao X, Liu DK, Wang QQ, Ke S, Li Y, Zhang D, Zheng Q, Zhang C, Liu ZJ, Lan S. Genome-wide identification and expression analysis of the GRAS gene family in Dendrobium chrysotoxum. FRONTIERS IN PLANT SCIENCE 2022; 13:1058287. [PMID: 36518517 PMCID: PMC9742484 DOI: 10.3389/fpls.2022.1058287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/11/2022] [Indexed: 06/17/2023]
Abstract
The GRAS gene family encodes transcription factors that participate in plant growth and development phases. They are crucial in regulating light signal transduction, plant hormone (e.g. gibberellin) signaling, meristem growth, root radial development, response to abiotic stress, etc. However, little is known about the features and functions of GRAS genes in Orchidaceae, the largest and most diverse angiosperm lineage. In this study, genome-wide analysis of the GRAS gene family was conducted in Dendrobium chrysotoxum (Epidendroideae, Orchidaceae) to investigate its physicochemical properties, phylogenetic relationships, gene structure, and expression patterns under abiotic stress in orchids. Forty-six DchGRAS genes were identified from the D. chrysotoxum genome and divided into ten subfamilies according to their phylogenetic relationships. Sequence analysis showed that most DchGRAS proteins contained conserved VHIID and SAW domains. Gene structure analysis showed that intronless genes accounted for approximately 70% of the DchGRAS genes, the gene structures of the same subfamily were the same, and the conserved motifs were also similar. The Ka/Ks ratios of 12 pairs of DchGRAS genes were all less than 1, indicating that DchGRAS genes underwent negative selection. The results of cis-acting element analysis showed that the 46 DchGRAS genes contained a large number of hormone-regulated and light-responsive elements as well as environmental stress-related elements. In addition, the real-time reverse transcription quantitative PCR (RT-qPCR) experimental results showed significant differences in the expression levels of 12 genes under high temperature, drought and salt treatment, among which two members of the LISCL subfamily (DchGRAS13 and DchGRAS15) were most sensitive to stress. Taken together, this paper provides insights into the regulatory roles of the GRAS gene family in orchids.
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Affiliation(s)
- Xuewei Zhao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ding-Kun Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qian-Qian Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shijie Ke
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuanyuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qinyao Zheng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Cuili Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhong-Jian Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Siren Lan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
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He Z, Tian Z, Zhang Q, Wang Z, Huang R, Xu X, Wang Y, Ji X. Genome-wide identification, expression and salt stress tolerance analysis of the GRAS transcription factor family in Betula platyphylla. FRONTIERS IN PLANT SCIENCE 2022; 13:1022076. [PMID: 36352865 PMCID: PMC9638169 DOI: 10.3389/fpls.2022.1022076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
The GRAS gene family is a plant-specific family of transcription factors and play a vital role in many plant growth processes and abiotic stress responses. Nevertheless, the functions of the GRAS gene family in woody plants, especially in Betula platyphylla (birch), are hardly known. In this study, we performed a genome-wide analysis of 40 BpGRAS genes (BpGRASs) and identified typical GRAS domains of most BpGRASs. The BpGRASs were unevenly distributed on 14 chromosomes of birch and the phylogenetic analysis of six species facilitated the clustering of 265 GRAS proteins into 17 subfamilies. We observed that closely related GRAS homologs had similar conserved motifs according to motif analysis. Besides, an analysis of the expression patterns of 26 BpGRASs showed that most BpGRASs were highly expressed in the leaves and responded to salt stress. Six BpGRASs were selected for cis-acting element analysis because of their significant upregulation under salt treatment, indicating that many elements were involved in the response to abiotic stress. This result further confirmed that these BpGRASs might participate in response to abiotic stress. Transiently transfected birch plants with transiently overexpressed 6 BpGRASs and RNAi-silenced 6 BpGRASs were generated for gain- and loss-of-function analysis, respectively. In addition, overexpression of BpGRAS34 showed phenotype resistant to salt stress, decreased the cell death and enhanced the reactive oxygen species (ROS) scavenging capabilities and proline content under salt treatment, consistent with the results in transiently transformed birch plants. This study is a systematic analysis of the GRAS gene family in birch plants, and the results provide insight into the molecular mechanism of the GRAS gene family responding to abiotic stress in birch plants.
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Affiliation(s)
- Zihang He
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
- The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Zengzhi Tian
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Qun Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Zhibo Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ruikun Huang
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
- The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Xin Xu
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Yucheng Wang
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
- The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xiaoyu Ji
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
- The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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Cenci A, Concepción-Hernández M, Guignon V, Angenon G, Rouard M. Genome-Wide Classification and Phylogenetic Analyses of the GDSL-Type Esterase/Lipase (GELP) Family in Flowering Plants. Int J Mol Sci 2022; 23:ijms232012114. [PMID: 36292971 PMCID: PMC9602515 DOI: 10.3390/ijms232012114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 11/16/2022] Open
Abstract
GDSL-type esterase/lipase (GELP) enzymes have key functions in plants, such as developmental processes, anther and pollen development, and responses to biotic and abiotic stresses. Genes that encode GELP belong to a complex and large gene family, ranging from tens to more than hundreds of members per plant species. To facilitate functional transfer between them, we conducted a genome-wide classification of GELP in 46 plant species. First, we applied an iterative phylogenetic method using a selected set of representative angiosperm genomes (three monocots and five dicots) and identified 10 main clusters, subdivided into 44 orthogroups (OGs). An expert curation for gene structures, orthogroup composition, and functional annotation was made based on a literature review. Then, using the HMM profiles as seeds, we expanded the classification to 46 plant species. Our results revealed the variable evolutionary dynamics between OGs in which some expanded, mostly through tandem duplications, while others were maintained as single copies. Among these, dicot-specific clusters and specific amplifications in monocots and wheat were characterized. This approach, by combining manual curation and automatic identification, was effective in characterizing a large gene family, allowing the establishment of a classification framework for gene function transfer and a better understanding of the evolutionary history of GELP.
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Affiliation(s)
- Alberto Cenci
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
- Correspondence: (A.C.); (M.R.)
| | - Mairenys Concepción-Hernández
- Instituto de Biotecnología de las Plantas, Universidad Central “Marta Abreu” de Las Villas (UCLV), Carretera a Camajuaní km 5.5, Santa Clara C.P. 54830, Villa Clara, Cuba
- Research Group Plant Genetics, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium
| | - Valentin Guignon
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
| | - Geert Angenon
- Research Group Plant Genetics, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
- Correspondence: (A.C.); (M.R.)
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18
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Jaiswal V, Kakkar M, Kumari P, Zinta G, Gahlaut V, Kumar S. Multifaceted Roles of GRAS Transcription Factors in Growth and Stress Responses in Plants. iScience 2022; 25:105026. [PMID: 36117995 PMCID: PMC9474926 DOI: 10.1016/j.isci.2022.105026] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Vandana Jaiswal
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Mrinalini Kakkar
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi 110021, India
| | - Priya Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Gaurav Zinta
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
- Corresponding author
| | - Vijay Gahlaut
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi 110021, India
- Corresponding author
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
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Waseem M, Nkurikiyimfura O, Niyitanga S, Jakada BH, Shaheen I, Aslam MM. GRAS transcription factors emerging regulator in plants growth, development, and multiple stresses. Mol Biol Rep 2022; 49:9673-9685. [PMID: 35713799 DOI: 10.1007/s11033-022-07425-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 02/23/2022] [Accepted: 03/24/2022] [Indexed: 10/18/2022]
Abstract
GRAS transcription factors play multifunctional roles in plant growth, development, and resistance to various biotic and abiotic stresses. The structural and functional features of GRAS TFs have been unveiled in the last two decades. A typical GRAS protein contained a C-terminal GRAS domain with a highly variable N-terminal region. Studies on these TFs increase in numbers and are reported to be involved in various important developmental processes such as flowering, root formation, and stress responses. The GRAS TFs and hormone signaling crosstalk can be implicated in plant development and to stress responses. There are relatively few reports about GRAS TFs roles in plants, and no related reviews have been published. In this review, we summarized the features of GRAS TFs, their targets, and the roles these GRAS TFs playing in plant development and multiple stresses.
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Affiliation(s)
- Muhammad Waseem
- Department of Botany, University of Narowal, Narowal, Punjab, Pakistan. .,College of Life Science, Hainan University, Hainan, P.R. China.
| | - Oswald Nkurikiyimfura
- Key Lab for Bio-Pesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, 350002, Fuzhou, Fujian, China
| | - Sylvain Niyitanga
- Department of Plant Pathology, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Bello Hassan Jakada
- College of Life Science, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, 350002, Fuzhou, Fujian, China
| | - Iffat Shaheen
- Faculty of Agriculture Science and Technology, Bahauddin Zakariya University, Multan, Pakistan
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20
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Zhang X, Yang X, He Q, Wang Y, Liang G, Liu T. Genome-wide Identification and Characterization of the GRAS Transcription Factors in Garlic ( Allium sativum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:890052. [PMID: 35498719 PMCID: PMC9039536 DOI: 10.3389/fpls.2022.890052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
GRAS transcription factors play crucial roles in plant growth and development and have been widely explored in many plant species. Garlic (Allium sativum L.) is an important crop owing to its edible and medicinal properties. However, no GRAS transcription factors have been identified in this crop. In this study, 46 garlic GRAS genes were identified and assigned to 16 subfamilies using the GRAS members of Arabidopsis thaliana, Oryza sativa, and Amborella trichopoda as reference queries. Expression analysis revealed that garlic GRAS genes showed distinct differences in various garlic tissues, as well as during different growth stages of the bulbs. Five of these 46 genes were identified as DELLA-like protein-encoding genes and three of which, Asa2G00237.1/Asa2G00240.1 and Asa4G02090.1, responded to exogenous GA3 treatment, and showed a significant association between their transcription abundance and bulb traits in 102 garlic accessions, thereby indicating their role in regulating the growth of garlic bulbs. These results will lay a useful foundation for further investigation of the biological functions of GRAS genes and guiding the genetic breeding of garlic in the future.
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Affiliation(s)
- Xueyu Zhang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Xiai Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Qiaoyun He
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Yanzhou Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Guolu Liang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
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21
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Khan Y, Xiong Z, Zhang H, Liu S, Yaseen T, Hui T. Expression and roles of GRAS gene family in plant growth, signal transduction, biotic and abiotic stress resistance and symbiosis formation-a review. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:404-416. [PMID: 34854195 DOI: 10.1111/plb.13364] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/15/2021] [Indexed: 06/13/2023]
Abstract
The GRAS (derived from GAI, RGA and SCR) gene family consists of plant-specific genes, works as a transcriptional regulator and plays a key part in the regulation of plant growth and development. The past decade has witnessed significant progress in understanding and advances on GRAS transcription factors in various plants. A notable concern is to what extent the mechanisms found in plants, particularly crops, are shared by other species, and what other characteristics are dependent on GRAS transcription factor (TFS)-mediated gene expression. GRAS are involved in many processes that are intimately linked to plant growth regulation. However, GRAS also perform additional roles against environmental stresses, allowing plants to function more efficiently. GRAS increase plant growth and development by improving several physiological processes, such as phytohormone, biosynthetic and signalling pathways. Furthermore, the GRAS gene family plays an important role in response to abiotic stresses, e.g. photooxidative stress. Moreover, evidence shows the involvement of GRAS in arbuscule development during plant-mycorrhiza associations. In this review, the diverse roles of GRAS in plant systems are highlighted that could be useful in enhancing crop productivity through genetic modification, especially of crops. This is the first review to report the role and function of the GRAS gene family in plant systems. Furthermore, a large number of studies are reviewed, and several limitations and research gaps identified that must be addressed in future studies.
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Affiliation(s)
- Y Khan
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resource and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - Z Xiong
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resource and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - H Zhang
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resource and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - S Liu
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resource and Environment, Northwest A&F University, Yangling, Shaanxi, China
| | - T Yaseen
- Department of Botany, Bacha Khan University, Charsadda, Khyber Pakhtunkhwa, Pakistan
| | - T Hui
- Key Laboratory of Plant Nutrition and Agri-environment in Northwest China, Ministry of Agriculture, College of Natural Resource and Environment, Northwest A&F University, Yangling, Shaanxi, China
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22
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Shi X, Yang H, Chen C, Hou J, Ji T, Cheng J, Birchler JA. Effect of aneuploidy of a non-essential chromosome on gene expression in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:193-211. [PMID: 34997647 PMCID: PMC9310612 DOI: 10.1111/tpj.15665] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 05/20/2023]
Abstract
The non-essential supernumerary maize (Zea mays) B chromosome (B) has recently been shown to contain active genes and to be capable of impacting gene expression of the A chromosomes. However, the effect of the B chromosome on gene expression is still unclear. In addition, it is unknown whether the accumulation of the B chromosome has a cumulative effect on gene expression. To examine these questions, the global expression of genes, microRNAs (miRNAs), and transposable elements (TEs) of leaf tissue of maize W22 plants with 0-7 copies of the B chromosome was studied. All experimental genotypes with B chromosomes displayed a trend of upregulated gene expression for a subset of A-located genes compared to the control. Over 3000 A-located genes are significantly differentially expressed in all experimental genotypes with the B chromosome relative to the control. Modulations of these genes are largely determined by the presence rather than the copy number of the B chromosome. By contrast, the expression of most B-located genes is positively correlated with B copy number, showing a proportional gene dosage effect. The B chromosome also causes increased expression of A-located miRNAs. Differentially expressed miRNAs potentially regulate their targets in a cascade of effects. Furthermore, the varied copy number of the B chromosome leads to the differential expression of A-located and B-located TEs. The findings provide novel insights into the function and properties of the B chromosome.
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Affiliation(s)
- Xiaowen Shi
- Division of Biological SciencesUniversity of MissouriColumbiaMissouri65211USA
- Present address:
College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Hua Yang
- Division of Biological SciencesUniversity of MissouriColumbiaMissouri65211USA
| | - Chen Chen
- Department of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaMissouri65211USA
| | - Jie Hou
- Department of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaMissouri65211USA
| | - Tieming Ji
- Department of StatisticsUniversity of MissouriColumbiaMissouri65211USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer ScienceUniversity of MissouriColumbiaMissouri65211USA
| | - James A. Birchler
- Division of Biological SciencesUniversity of MissouriColumbiaMissouri65211USA
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Ho-Plágaro T, García-Garrido JM. Multifarious and Interactive Roles of GRAS Transcription Factors During Arbuscular Mycorrhiza Development. FRONTIERS IN PLANT SCIENCE 2022; 13:836213. [PMID: 35419017 PMCID: PMC8996055 DOI: 10.3389/fpls.2022.836213] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/10/2022] [Indexed: 06/01/2023]
Abstract
Arbuscular mycorrhiza (AM) is a mutualistic symbiotic interaction between plant roots and AM fungi (AMF). This interaction is highly beneficial for plant growth, development and fitness, which has made AM symbiosis the focus of basic and applied research aimed at increasing plant productivity through sustainable agricultural practices. The creation of AM requires host root cells to undergo significant structural and functional modifications. Numerous studies of mycorrhizal plants have shown that extensive transcriptional changes are induced in the host during all stages of colonization. Advances have recently been made in identifying several plant transcription factors (TFs) that play a pivotal role in the transcriptional regulation of AM development, particularly those belonging to the GRAS TF family. There is now sufficient experimental evidence to suggest that GRAS TFs are capable to establish intra and interspecific interactions, forming a transcriptional regulatory complex that controls essential processes in the AM symbiosis. In this minireview, we discuss the integrative role of GRAS TFs in the regulation of the complex genetic re-programming determining AM symbiotic interactions. Particularly, research being done shows the relevance of GRAS TFs in the morphological and developmental changes required for the formation and turnover of arbuscules, the fungal structures where the bidirectional nutrient translocation occurs.
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24
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Wu Y, Wen J, Xia Y, Zhang L, Du H. Evolution and functional diversification of R2R3-MYB transcription factors in plants. HORTICULTURE RESEARCH 2022; 9:uhac058. [PMID: 35591925 PMCID: PMC9113232 DOI: 10.1093/hr/uhac058] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 02/24/2022] [Indexed: 05/31/2023]
Abstract
R2R3-MYB genes (R2R3-MYBs) form one of the largest transcription factor gene families in the plant kingdom, with substantial structural and functional diversity. However, the evolutionary processes leading to this amazing functional diversity have not yet been clearly established. Recently developed genomic and classical molecular technologies have provided detailed insights into the evolutionary relationships and functions of plant R2R3-MYBs. Here, we review recent genome-level and functional analyses of plant R2R3-MYBs, with an emphasis on their evolution and functional diversification. In land plants, this gene family underwent a large expansion by whole genome duplications and small-scale duplications. Along with this population explosion, a series of functionally conserved or lineage-specific subfamilies/groups arose with roles in three major plant-specific biological processes: development and cell differentiation, specialized metabolism, and biotic and abiotic stresses. The rapid expansion and functional diversification of plant R2R3-MYBs are highly consistent with the increasing complexity of angiosperms. In particular, recently derived R2R3-MYBs with three highly homologous intron patterns (a, b, and c) are disproportionately related to specialized metabolism and have become the predominant subfamilies in land plant genomes. The evolution of plant R2R3-MYBs is an active area of research, and further studies are expected to improve our understanding of the evolution and functional diversification of this gene family.
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Affiliation(s)
- Yun Wu
- Department of Landscape Architecture, School of Civil Engineering and Architecture, Zhejiang Sci-Tech University, Hangzhou, 310018, China
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jing Wen
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Yiping Xia
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Liangsheng Zhang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Hai Du
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
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Genome-wide identification and expression analysis of the GRAS gene family in response to drought stress in chickpea ( Cicer arietinum L.). 3 Biotech 2022; 12:64. [PMID: 35186661 PMCID: PMC8828820 DOI: 10.1007/s13205-021-03104-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 12/28/2021] [Indexed: 11/01/2022] Open
Abstract
The GRAS (gibberellic acid insensitive, repressor of GAI and scarecrow) transcription factors (TFs) regulate diverse biological processes involved in plant growth and development. These TFs are also known to regulate gene expression in response to various abiotic stress factors like cold, drought, etc. In chickpea one of the most devastating abiotic stress factors is terminal drought. The GRAS TF family has not been characterized in chickpea (Cicer arietinum L.) until now. In this study, we report 46 GRAS TF genes (CaGRAS genes) in the chickpea genome. The CaGRAS proteins were categorized into nine subfamilies based on their phylogenetic relationship with known GRAS members of Arabidopsis and soybean. The PAT subfamily was the largest consisting of ten CaGRAS members whereas the LAS subfamily was the smallest with only one member. Gene duplication analysis revealed that segmental duplication was the primary reason for the expansion of this gene family within the chickpea genome. The gene expression levels of CaGRAS genes were analysed using two different chickpea varieties contrasting for drought tolerance trait, i.e., ICC 4958 (drought tolerant) and ICC 1882 (drought sensitive). On exposure to drought stress, the two chickpea genotypes, exhibited differential drought response, which was quantified and estimated in terms of differences in leaf relative water content (RWC). The well-watered or control plants of the drought tolerant variety were able to maintain a higher leaf RWC by the end of the drought stress period, whereas the control plants of the drought sensitive variety continued to show a decline in leaf RWC. The two genotypes also differed in their root morphologies, under well-watered and drought stress conditions. The gene expression analysis revealed a potential role of PAT, SCR, SCL3 and SHR GRAS members in the regulation of differential response to drought, in the root tissues, for both the genotypes. CaGRAS 12 (SCR) was identified as a drought-responsive GRAS TF gene, which could serve as a potential candidate gene for utilization in developing chickpea varieties with improved drought tolerance. This study demonstrates the drought-responsive expression of CaGRAS genes in chickpea and also describes the morpho-physiological response of chickpea plants to drought stress conditions. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03104-z.
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Xu Y, Liu F, Wu F, Zhao M, Zou R, Wu J, Li X. A novel SCARECROW-LIKE3 transcription factor LjGRAS36 in Lotus japonicus regulates the development of arbuscular mycorrhizal symbiosis. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:573-583. [PMID: 35465207 PMCID: PMC8986927 DOI: 10.1007/s12298-022-01161-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 02/11/2022] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
UNLABELLED The symbiosis with arbuscular mycorrhizal (AM) fungi improves plants' nutrient uptake. During this process, transcription factors have been highlighted to play crucial roles. Members of the GRAS transcription factor gene family have been reported involved in AM symbiosis, but little is known about SCARECROW-LIKE3 (SCL3) genes belonging to this family in Lotus japonicus. In this study, 67 LjGRAS genes were identified from the L. japonicus genome, seven of which were clustered in the SCL3 group. Three of the seven LjGRAS genes expression levels were upregulated by AM fungal inoculation, and our biochemical results showed that the expression of LjGRAS36 was specifically induced by AM colonization. Functional loss of LjGRAS36 in mutant ljgras36 plants exhibited a significantly reduced mycorrhizal colonization rate and arbuscular size. Transcriptome analysis showed a deficiency of LjGRAS36 led to the dysregulation of the gibberellic acid signal pathway associated with AM symbiosis. Together, this study provides important insights for understanding the important potential function of SCL3 genes in regulating AM symbiotic development. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01161-z.
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Affiliation(s)
- Yunjian Xu
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, 650500 Kunming, China
- Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, 230036 Hefei, China
| | - Fang Liu
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, 230036 Hefei, China
- School of Agriculture, Yunnan University, 650500 Kunming, China
| | - Fulang Wu
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, 230036 Hefei, China
| | - Manli Zhao
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, 230036 Hefei, China
| | - Ruifan Zou
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, 230036 Hefei, China
| | - Jianping Wu
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, 650500 Kunming, China
- Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China
| | - Xiaoyu Li
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, 230036 Hefei, China
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Bengoa Luoni SA, Cenci A, Moschen S, Nicosia S, Radonic LM, Sabio J, Garcia, Langlade NB, Vile D, Rovere CV, Fernandez P. Genome-wide and comparative phylogenetic analysis of senescence-associated NAC transcription factors in sunflower (Helianthus annuus). BMC Genomics 2021; 22:893. [PMID: 34906091 PMCID: PMC8670195 DOI: 10.1186/s12864-021-08199-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/19/2021] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Leaf senescence delay impacts positively in grain yield by maintaining the photosynthetic area during the reproductive stage and during grain filling. Therefore a comprehensive understanding of the gene families associated with leaf senescence is essential. NAC transcription factors (TF) form a large plant-specific gene family involved in regulating development, senescence, and responses to biotic and abiotic stresses. The main goal of this work was to identify sunflower NAC TF (HaNAC) and their association with senescence, studying their orthologous to understand possible functional relationships between genes of different species. RESULTS To clarify the orthologous relationships, we used an in-depth comparative study of four divergent taxa, in dicots and monocots, with completely sequenced genomes (Arabidopsis thaliana, Vitis vinifera, Musa acuminata and Oryza sativa). These orthologous groups provide a curated resource for large scale protein sequence annotation of NAC TF. From the 151 HaNAC genes detected in the latest version of the sunflower genome, 50 genes were associated with senescence traits. These genes showed significant differential expression in two contrasting lines according to an RNAseq assay. An assessment of overexpressing the Arabidopsis line for HaNAC001 (a gene of the same orthologous group of Arabidopsis thaliana ORE1) revealed that this line displayed a significantly higher number of senescent leaves and a pronounced change in development rate. CONCLUSIONS This finding suggests HaNAC001 as an interesting candidate to explore the molecular regulation of senescence in sunflower.
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Affiliation(s)
- Sofia A Bengoa Luoni
- Instituto de Agrobiotecnología y Biología Molecular, INTA-Castelar, Buenos Aires, Argentina
| | | | - Sebastian Moschen
- Estación Experimental Agropecuaria Famaillá, INTA-Famaillá, Tucumán, Argentina
| | - Salvador Nicosia
- Instituto de Agrobiotecnología y Biología Molecular, INTA-Castelar, Buenos Aires, Argentina
| | - Laura M Radonic
- Instituto de Agrobiotecnología y Biología Molecular, INTA-Castelar, Buenos Aires, Argentina
| | | | - Garcia
- Instituto de Agrobiotecnología y Biología Molecular, INTA-Castelar, Buenos Aires, Argentina
| | | | - Denis Vile
- LEPSE, Université de Montpellier, INRAE, Montpellier, France
| | - Cecilia Vazquez Rovere
- Instituto de Agrobiotecnología y Biología Molecular, INTA-Castelar, Buenos Aires, Argentina
| | - Paula Fernandez
- Instituto de Agrobiotecnología y Biología Molecular, INTA-Castelar, Buenos Aires, Argentina.
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Dutta M, Saha A, Moin M, Kirti PB. Genome-Wide Identification, Transcript Profiling and Bioinformatic Analyses of GRAS Transcription Factor Genes in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:777285. [PMID: 34899804 PMCID: PMC8660974 DOI: 10.3389/fpls.2021.777285] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/26/2021] [Indexed: 05/28/2023]
Abstract
Our group has previously identified the activation of a GRAS transcription factor (TF) gene in the gain-of-function mutant population developed through activation tagging in rice (in an indica rice variety, BPT 5204) that was screened for water use efficiency. This family of GRAS transcription factors has been well known for their diverse roles in gibberellin signaling, light responses, root development, gametogenesis etc. Recent studies indicated their role in biotic and abiotic responses as well. Although this family of TFs received significant attention, not many genes were identified specifically for their roles in mediating stress tolerance in rice. Only OsGRAS23 (here named as OsGRAS22) was reported to code for a TF that induced drought tolerance in rice. In the present study, we have analyzed the expression patterns of rice GRAS TF genes under abiotic (NaCl and ABA treatments) and biotic (leaf samples infected with pathogens, Xanthomonas oryzae pv. oryzae that causes bacterial leaf blight and Rhizoctonia solani that causes sheath blight) stress conditions. In addition, their expression patterns were also analyzed in 13 different developmental stages. We studied their spatio-temporal regulation and correlated them with the in-silico studies. Fully annotated genomic sequences available in rice database have enabled us to study the protein properties, ligand interactions, domain analysis and presence of cis-regulatory elements through the bioinformatic approach. Most of the genes were induced immediately after the onset of stress particularly in the roots of ABA treated plants. OsGRAS39 was found to be a highly expressive gene under sheath blight infection and both abiotic stress treatments while OsGRAS8, OsSHR1 and OsSLR1 were also responsive. Our earlier activation tagging based functional characterization followed by the genome-wide characterization of the GRAS gene family members in the present study clearly show that they are highly appropriate candidate genes for manipulating stress tolerance in rice and other crop plants.
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Affiliation(s)
- Mouboni Dutta
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Anusree Saha
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Mazahar Moin
- Department of Biotechnology, Indian Institute of Rice Research, Hyderabad, India
| | - Pulugurtha Bharadwaja Kirti
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
- Agri Biotech Foundation, PJTS Agricultural University Campus, Hyderabad, India
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Fan Y, Wei X, Lai D, Yang H, Feng L, Li L, Niu K, Chen L, Xiang D, Ruan J, Yan J, Cheng J. Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.). BMC PLANT BIOLOGY 2021; 21:508. [PMID: 34732123 PMCID: PMC8565077 DOI: 10.1186/s12870-021-03277-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/18/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND GRAS transcription factors perform indispensable functions in various biological processes, such as plant growth, fruit development, and biotic and abiotic stress responses. The development of whole-genome sequencing has allowed the GRAS gene family to be identified and characterized in many species. However, thorough in-depth identification or systematic analysis of GRAS family genes in foxtail millet has not been conducted. RESULTS In this study, 57 GRAS genes of foxtail millet (SiGRASs) were identified and renamed according to the chromosomal distribution of the SiGRAS genes. Based on the number of conserved domains and gene structure, the SiGRAS genes were divided into 13 subfamilies via phylogenetic tree analysis. The GRAS genes were unevenly distributed on nine chromosomes, and members of the same subfamily had similar gene structures and motif compositions. Genetic structure analysis showed that most SiGRAS genes lacked introns. Some SiGRAS genes were derived from gene duplication events, and segmental duplications may have contributed more to GRAS gene family expansion than tandem duplications. Quantitative polymerase chain reaction showed significant differences in the expression of SiGRAS genes in different tissues and stages of fruits development, which indicated the complexity of the physiological functions of SiGRAS. In addition, exogenous paclobutrazol treatment significantly altered the transcription levels of DELLA subfamily members, downregulated the gibberellin content, and decreased the plant height of foxtail millet, while it increased the fruit weight. In addition, SiGRAS13 and SiGRAS25 may have the potential for genetic improvement and functional gene research in foxtail millet. CONCLUSIONS Collectively, this study will be helpful for further analysing the biological function of SiGRAS. Our results may contribute to improving the genetic breeding of foxtail millet.
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Affiliation(s)
- Yu Fan
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
- School of Food and Biological engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Xiaobao Wei
- Guizhou provincial Center For Disease Control And Prevention, Guiyang, 550025, People's Republic of China
| | - Dili Lai
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Hao Yang
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Liang Feng
- Chengdu Institute of Food Inspection, Chengdu, 610030, People's Republic of China
| | - Long Li
- Henan university of technology, Zhengzhou, 450001, People's Republic of China
| | - Kexin Niu
- Henan university of technology, Zhengzhou, 450001, People's Republic of China
| | - Long Chen
- Department of Nursing, Sichuan Tianyi College, Mianzhu, 618200, People's Republic of China
| | - Dabing Xiang
- School of Food and Biological engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Jun Yan
- School of Food and Biological engineering, Chengdu University, Chengdu, 610106, People's Republic of China.
| | - Jianping Cheng
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China.
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Laskar P, Bhattacharya S, Chaudhuri A, Kundu A. Exploring the GRAS gene family in common bean (Phaseolus vulgaris L.): characterization, evolutionary relationships, and expression analyses in response to abiotic stresses. PLANTA 2021; 254:84. [PMID: 34561734 DOI: 10.1007/s00425-021-03725-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/05/2021] [Indexed: 06/13/2023]
Abstract
Genome-wide identification reveals 55 PvuGRAS genes belonging to 16 subfamilies and their gene structures and evolutionary relationships were characterized. Expression analyses highlight their prominence in plant growth, development and abiotic stress responses. GRAS proteins comprise a plant-specific transcription factor family involved in multiple growth regulatory pathways and environmental cues including abiotic/biotic stresses. Despite its crucial importance, characterization of this gene family is still elusive in common bean. A systematic genome-wide scan identified 55 PvuGRAS genes unevenly anchored to the 11 common bean chromosomes. Segmental duplication appeared to be the key driving force behind expansion of this gene family that underwent purifying selection during evolution. Computational investigation unraveled their intronless organization and identified similar motif composition within the same subfamily. Phylogenetic analyses clustered the PvuGRAS proteins into 16 phylogenetic clades and established extensive orthologous relationships with Arabidopsis and rice. Analysis of the upstream promoter region uncovered cis-elements responsive to growth, development, and abiotic stresses that may account for their differential expression. The identified SSRs could serve as putative molecular markers facilitating future breeding programs. 37 PvuGRAS transcripts were post-transcriptionally regulated by different miRNA families, miR171 being the major player preferentially targeting members of the HAM subfamily. Global expression profile based on RNA-seq data indicates a clade specific expression pattern in various tissues and developmental stages. Additionally, nine PvuGRAS genes were chosen for further qPCR analyses under drought, salt, and cold stress suggesting their involvement in acclimation to environmental stimuli. Combined, the present results significantly contribute to the current understanding of the complexity and biological function of the PvuGRAS gene family. The resources generated will provide a solid foundation in future endeavors for genetic improvement in common bean.
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Affiliation(s)
- Parbej Laskar
- Plant Genomics and Bioinformatics Laboratory, P.G. Department of Botany, Ramakrishna Mission Vivekananda Centenary College (Autonomous), Rahara, Kolkata, 700118, India
| | - Saswati Bhattacharya
- Department of Botany, Dr. A.P.J. Abdul Kalam Government College, New Town, Rajarhat, India
| | - Atreyee Chaudhuri
- Aquatic Bioresource Research Laboratory, Department of Zoology , University of Calcutta, Kolkata, India
| | - Anirban Kundu
- Plant Genomics and Bioinformatics Laboratory, P.G. Department of Botany, Ramakrishna Mission Vivekananda Centenary College (Autonomous), Rahara, Kolkata, 700118, India.
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Yang C, Marillonnet S, Tissier A. The scarecrow-like transcription factor SlSCL3 regulates volatile terpene biosynthesis and glandular trichome size in tomato (Solanum lycopersicum). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1102-1118. [PMID: 34143914 DOI: 10.1111/tpj.15371] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 05/20/2023]
Abstract
Tomato (Solanum lycopersicum L.) type VI glandular trichomes that occur on the surface of leaves, stems, young fruits and flowers produce and store a blend of volatile monoterpenes and sesquiterpenes. These compounds play important roles in the interaction with pathogens and herbivorous insects. Although the function of terpene synthases in the biosynthesis of volatile terpenes in tomato has been comprehensively investigated, the deciphering of their transcriptional regulation is only just emerging. We selected transcription factors that are over-expressed in trichomes based on existing transcriptome data and silenced them individually by virus-induced gene silencing. Of these, SlSCL3, a scarecrow-like (SCL) subfamily transcription factor, led to a significant decrease in volatile terpene content and expression of the corresponding terpene synthase genes when its transcription level was downregulated. Overexpression of SlSCL3 dramatically increased both the volatile terpene content and glandular trichome size, whereas its homozygous mutants showed reduced terpene biosynthesis. However, its heterozygous mutants also showed a significantly elevated volatile terpene content and enlarged glandular trichomes, similar to the overexpression plants. SlSCL3 modulates the expression of terpene biosynthetic pathway genes by transcriptional activation, but neither direct protein-DNA binding nor interaction with known regulators was observed. Moreover, transcript levels of the endogenous copy of SlSCL3 were decreased in the overexpression plants but increased in the heterozygous and homozygous mutants, suggesting feedback repression of its own promoter. Taken together, our results provide new insights into the role of SlSCL3 in the complex regulation of volatile terpene biosynthesis and glandular trichome development in tomato.
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Affiliation(s)
- Changqing Yang
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), 06120, Germany
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong, 266100, China
| | - Sylvestre Marillonnet
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), 06120, Germany
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), 06120, Germany
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Zhu X, Wang B, Wei X. Genome wide identification and expression pattern analysis of the GRAS family in quinoa. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:948-962. [PMID: 34092279 DOI: 10.1071/fp21017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/13/2021] [Indexed: 06/12/2023]
Abstract
GRAS, a key transcription factor in plant growth and development, has not yet been reported in quinoa. Therefore, this study used the latest quinoa genomic data to identify and analyse GRAS genes in quinoa: 52 GRAS genes were identified in quinoa, these being unevenly distributed on 19 chromosomes. Fragment duplication and tandem duplication events were the main reasons for the expansion of the GRAS gene family in quinoa. Protein sequence analysis showed that there were some differences in amino acid numbers and isoelectric points amongst different subfamilies, and the main secondary structures were α-helix and random coil. The CqGRAS gene was divided into 14 subfamilies based on results from phylogenetic analysis. The genes located in the same subfamily had similar gene structures, conserved motifs, and three-level models. Promoter region analysis showed that the GRAS family genes contained multiple homeostasis elements that responded to hormones and adversity. GO enrichment indicated that CqGRAS genes were involved in biological processes, cell components, and molecular functions. By analysing the expression of CqGRAS genes in different tissues and different treatments, it was found that GRAS genes had obvious differential expression in different tissues and stress, which indicates that GRAS genes had tissue or organ expression specificity and thus might play an important role in response to stress. These results laid a foundation for further functional research on the GRAS gene family in quinoa.
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Affiliation(s)
- Xiaolin Zhu
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; and Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Baoqiang Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaohong Wei
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; and Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China; and College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; and Corresponding author.
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33
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Fan Y, Yan J, Lai D, Yang H, Xue G, He A, Guo T, Chen L, Cheng XB, Xiang DB, Ruan J, Cheng J. Genome-wide identification, expression analysis, and functional study of the GRAS transcription factor family and its response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]. BMC Genomics 2021; 22:509. [PMID: 34229611 PMCID: PMC8259154 DOI: 10.1186/s12864-021-07848-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/24/2021] [Indexed: 11/10/2022] Open
Abstract
Background GRAS, an important family of transcription factors, have played pivotal roles in regulating numerous intriguing biological processes in plant development and abiotic stress responses. Since the sequencing of the sorghum genome, a plethora of genetic studies were mainly focused on the genomic information. The indepth identification or genome-wide analysis of GRAS family genes, especially in Sorghum bicolor, have rarely been studied. Results A total of 81 SbGRAS genes were identified based on the S. bicolor genome. They were named SbGRAS01 to SbGRAS81 and grouped into 13 subfamilies (LISCL, DLT, OS19, SCL4/7, PAT1, SHR, SCL3, HAM-1, SCR, DELLA, HAM-2, LAS and OS4). SbGRAS genes are not evenly distributed on the chromosomes. According to the results of the gene and motif composition, SbGRAS members located in the same group contained analogous intron/exon and motif organizations. We found that the contribution of tandem repeats to the increase in sorghum GRAS members was slightly greater than that of fragment repeats. By quantitative (q) RT-PCR, the expression of 13 SbGRAS members in different plant tissues and in plants exposed to six abiotic stresses at the seedling stage were quantified. We further investigated the relationship between DELLA genes, GAs and grain development in S. bicolor. The paclobutrazol treatment significantly increased grain weight, and affected the expression levels of all DELLA subfamily genes. SbGRAS03 is the most sensitive to paclobutrazol treatment, but also has a high response to abiotic stresses. Conclusions Collectively, SbGRAs play an important role in plant development and response to abiotic stress. This systematic analysis lays the foundation for further study of the functional characteristics of GRAS genes of S. bicolor. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07848-z.
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Affiliation(s)
- Yu Fan
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China
| | - Jun Yan
- School of Food and Biological engineering, Chengdu University, 610106, Chengdu, People's Republic of China
| | - Dili Lai
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China
| | - Hao Yang
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China
| | - Guoxing Xue
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China
| | - Ailing He
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China
| | - Tianrong Guo
- Chengdu Institute of Food Inspection, 610030, Chengdu, People's Republic of China
| | - Long Chen
- Department of Nursing, Sichuan Tianyi College, 618200, Mianzhu, People's Republic of China
| | - Xiao-Bin Cheng
- Department of Environmental and Life Sciences, Sichuan MinZu College, 626001, Kangding, People's Republic of China
| | - Da-Bing Xiang
- School of Food and Biological engineering, Chengdu University, 610106, Chengdu, People's Republic of China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China
| | - Jianping Cheng
- College of Agriculture, Guizhou University, Huaxi District, 550025, Guiyang, People's Republic of China.
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Molecular Cloning, Transcriptional Profiling, Subcellular Localization, and miRNA-Binding Site Analysis of Six SCL9 Genes in Poplar. PLANTS 2021; 10:plants10071338. [PMID: 34208997 PMCID: PMC8309000 DOI: 10.3390/plants10071338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/25/2021] [Accepted: 06/27/2021] [Indexed: 11/16/2022]
Abstract
The SCL9 subfamily is a key member of the GRAS family that regulates plant development and stress responses. Nevertheless, the functional role of these genes in the growth and development of poplar still unclear. Here, we reported the six SCL9 genes, which were found to be differentially expressed during poplar adventitious root formation. The full-length sequences of PeSCL9 genes of ‘Nanlin895’ poplar (Populus deltoids × Populus euramericana) were cloned by the RACE technique All PeSCL9 genes lacked introns. RT-qPCR revealed that PeSCL9 genes displayed a dynamic expression pattern in the adventitious root of poplar, according to RT-qPCR data. A series of comprehensive genes characteristics analysis were carried out for six genes by bioinformation. Meanwhile, transient expression analysis of the Populus protoplasts showed that all the PeSCL9 proteins were localized in the nucleus. In addition, the degradome and sRNA of ‘Nanlin895’ poplar in combination were used to predict miRNAs that regulate PeSCL9. It was found that miR396a and miR396c may affect PeSCL9 expression via cleavage, which was further verified by a transient expression experiment in Populus protoplasts. Overall, the development of poplar adventitious root and other tissues was closely related to these six SCL9 genes, and they serve as a starting point for further research into the mechanisms regulating poplar growth and development.
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Kumar B, Bhalothia P. Evolutionary analysis of GRAS gene family for functional and structural insights into hexaploid bread wheat (Triticum aestivum). J Biosci 2021. [DOI: 10.1007/s12038-021-00163-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Sarfraz Z, Iqbal MS, Geng X, Iqbal MS, Nazir MF, Ahmed H, He S, Jia Y, Pan Z, Sun G, Ahmad S, Wang Q, Qin H, Liu J, Liu H, Yang J, Ma Z, Xu D, Yang J, Zhang J, Li Z, Cai Z, Zhang X, Zhang X, Huang A, Yi X, Zhou G, Li L, Zhu H, Pang B, Wang L, Sun J, Du X. GWAS Mediated Elucidation of Heterosis for Metric Traits in Cotton ( Gossypium hirsutum L.) Across Multiple Environments. FRONTIERS IN PLANT SCIENCE 2021; 12:565552. [PMID: 34093598 PMCID: PMC8173050 DOI: 10.3389/fpls.2021.565552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
For about a century, plant breeding has widely exploited the heterosis phenomenon-often considered as hybrid vigor-to increase agricultural productivity. The ensuing F1 hybrids can substantially outperform their progenitors due to heterozygous combinations that mitigate deleterious mutations occurring in each genome. However, only fragmented knowledge is available concerning the underlying genes and processes that foster heterosis. Although cotton is among the highly valued crops, its improvement programs that involve the exploitation of heterosis are still limited in terms of significant accomplishments to make it broadly applicable in different agro-ecological zones. Here, F1 hybrids were derived from mating a diverse Upland Cotton germplasm with commercially valuable cultivars in the Line × Tester fashion and evaluated across multiple environments for 10 measurable traits. These traits were dissected into five different heterosis types and specific combining ability (SCA). Subsequent genome-wide predictions along-with association analyses uncovered a set of 298 highly significant key single nucleotide polymorphisms (SNPs)/Quantitative Trait Nucleotides (QTNs) and 271 heterotic Quantitative Trait Nucleotides (hQTNs) related to agronomic and fiber quality traits. The integration of a genome wide association study with RNA-sequence analysis yielded 275 candidate genes in the vicinity of key SNPs/QTNs. Fiber micronaire (MIC) and lint percentage (LP) had the maximum number of associated genes, i.e., each with 45 related to QTNs/hQTNs. A total of 54 putative candidate genes were identified in association with HETEROSIS of quoted traits. The novel players in the heterosis mechanism highlighted in this study may prove to be scientifically and biologically important for cotton biologists, and for those breeders engaged in cotton fiber and yield improvement programs.
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Affiliation(s)
- Zareen Sarfraz
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Muhammad Shahid Iqbal
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
- Cotton Research Institute, Ayub Agricultural Research Institute, Multan, Pakistan
| | - Xiaoli Geng
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Muhammad Sajid Iqbal
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
- Cotton Research Institute, Ayub Agricultural Research Institute, Multan, Pakistan
| | - Mian Faisal Nazir
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Haris Ahmed
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Yinhua Jia
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Zhaoe Pan
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Gaofei Sun
- Anyang Institute of Technology, Anyang, China
| | - Saghir Ahmad
- Cotton Research Institute, Ayub Agricultural Research Institute, Multan, Pakistan
| | - Qinglian Wang
- Henan Institute of Science and Technology, Xinxiang, China
| | - Hongde Qin
- Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Jinhai Liu
- Zhongmian Seed Technologies Co., Ltd., Zhengzhou, China
| | - Hui Liu
- Jing Hua Seed Industry Technologies Inc., Jingzhou, China
| | - Jun Yang
- Cotton Research Institute of Jiangxi Province, Jiujiang, China
| | - Zhiying Ma
- Key Laboratory for Crop Germplasm Resources of Hebei, Agricultural University of Hebei, Baoding, China
| | - Dongyong Xu
- Guoxin Rural Technical Service Association, Hebei, China
| | - Jinlong Yang
- Zhongmian Seed Technologies Co., Ltd., Zhengzhou, China
| | | | - Zhikun Li
- Key Laboratory for Crop Germplasm Resources of Hebei, Agricultural University of Hebei, Baoding, China
| | - Zhongmin Cai
- Zhongmian Seed Technologies Co., Ltd., Zhengzhou, China
| | | | - Xin Zhang
- Henan Institute of Science and Technology, Xinxiang, China
| | - Aifen Huang
- Sanyi Seed Industry of Changde in Hunan Inc., Changde, China
| | - Xianda Yi
- Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Guanyin Zhou
- Zhongmian Seed Technologies Co., Ltd., Zhengzhou, China
| | - Lin Li
- Zhongli Company of Shandong, Shandong, China
| | - Haiyong Zhu
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Baoyin Pang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Liru Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Junling Sun
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Xiongming Du
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
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Geng Y, Cai C, McAdam SAM, Banks JA, Wisecaver JH, Zhou Y. A De Novo Transcriptome Assembly of Ceratopteris richardii Provides Insights into the Evolutionary Dynamics of Complex Gene Families in Land Plants. Genome Biol Evol 2021; 13:6157829. [PMID: 33681974 PMCID: PMC7975763 DOI: 10.1093/gbe/evab042] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2021] [Indexed: 01/26/2023] Open
Abstract
As the closest extant sister group to seed plants, ferns are an important reference point to study the origin and evolution of plant genes and traits. One bottleneck to the use of ferns in phylogenetic and genetic studies is the fact that genome-level sequence information of this group is limited, due to the extreme genome sizes of most ferns. Ceratopteris richardii (hereafter Ceratopteris) has been widely used as a model system for ferns. In this study, we generated a transcriptome of Ceratopteris, through the de novo assembly of the RNA-seq data from 17 sequencing libraries that are derived from two sexual types of gametophytes and five different sporophyte tissues. The Ceratopteris transcriptome, together with 38 genomes and transcriptomes from other species across the Viridiplantae, were used to uncover the evolutionary dynamics of orthogroups (predicted gene families using OrthoFinder) within the euphyllophytes and identify proteins associated with the major shifts in plant morphology and physiology that occurred in the last common ancestors of euphyllophytes, ferns, and seed plants. Furthermore, this resource was used to identify and classify the GRAS domain transcriptional regulators of many developmental processes in plants. Through the phylogenetic analysis within each of the 15 GRAS orthogroups, we uncovered which GRAS family members are conserved or have diversified in ferns and seed plants. Taken together, the transcriptome database and analyses reported here provide an important platform for exploring the evolution of gene families in land plants and for studying gene function in seed-free vascular plants.
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Affiliation(s)
- Yuan Geng
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | - Chao Cai
- Purdue University Libraries and School of Information Studies, Purdue University, West Lafayette, Indiana, USA
| | - Scott A M McAdam
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | - Jo Ann Banks
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | - Jennifer H Wisecaver
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA.,Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Yun Zhou
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
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Liu M, Sun W, Li C, Yu G, Li J, Wang Y, Wang X. A multilayered cross-species analysis of GRAS transcription factors uncovered their functional networks in plant adaptation to the environment. J Adv Res 2021; 29:191-205. [PMID: 33842016 PMCID: PMC8020295 DOI: 10.1016/j.jare.2020.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/07/2020] [Accepted: 10/24/2020] [Indexed: 11/16/2022] Open
Abstract
Introduction Environmental stress is both a major force of natural selection and a prime factor affecting crop qualities and yields. The impact of the GRAS [gibberellic acid-insensitive (GAI), repressor of GA1-3 mutant (RGA), and scarecrow (SCR)] family on plant development and the potential to resist environmental stress needs much emphasis. Objectives This study aims to investigate the evolution, expansion, and adaptive mechanisms of GRASs of important representative plants during polyploidization. Methods We explored the evolutionary characteristics of GRASs in 15 representative plant species by systematic biological analysis of the genome, transcriptome, metabolite, protein complex map and phenotype. Results The GRAS family was systematically identified from 15 representative plant species of scientific and agricultural importance. The detection of gene duplication types of GRASs in all species showed that the widespread expansion of GRASs in these species was mainly contributed by polyploidization events. Evolutionary analysis reveals that most species experience independent genome-wide duplication (WGD) events and that interspecies GRAS functions may be broadly conserved. Polyploidy-related Chenopodium quinoa GRASs (CqGRASs) and Arabidopsis thaliana GRASs (AtGRASs) formed robust networks with flavonoid pathways by crosstalk with auxin and photosynthetic pathways. Furthermore, Arabidopsis thaliana population transcriptomes and the 1000 Plants (OneKP) project confirmed that GRASs are components of flavonoid biosynthesis, which enables plants to adapt to the environment by promoting flavonoid accumulation. More importantly, the GRASs of important species that may potentially improve important agronomic traits were mapped through TAIR and RARGE-II publicly available phenotypic data. Determining protein interactions and target genes contributes to determining GRAS functions. Conclusion The results of this study suggest that polyploidy-related GRASs in multiple species may be a target for improving plant growth, development, and environmental adaptation.
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Affiliation(s)
- Moyang Liu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- College of Life Science, Sichuan Agricultural University, Ya’an 625014, China
| | - Wenjun Sun
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- College of Life Science, Sichuan Agricultural University, Ya’an 625014, China
| | - Chaorui Li
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guolong Yu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiahao Li
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yudong Wang
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xu Wang
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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Fenn MA, Giovannoni JJ. Phytohormones in fruit development and maturation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:446-458. [PMID: 33274492 DOI: 10.1111/tpj.15112] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 05/21/2023]
Abstract
Phytohormones are integral to the regulation of fruit development and maturation. This review expands upon current understanding of the relationship between hormone signaling and fruit development, emphasizing fleshy fruit and highlighting recent work in the model crop tomato (Solanum lycopersicum) and additional species. Fruit development comprises fruit set initiation, growth, and maturation and ripening. Fruit set transpires after fertilization and is associated with auxin and gibberellic acid (GA) signaling. Interaction between auxin and GAs, as well as other phytohormones, is mediated by auxin-responsive Aux/IAA and ARF proteins. Fruit growth consists of cell division and expansion, the former shown to be influenced by auxin signaling. While regulation of cell expansion is less thoroughly understood, evidence indicates synergistic regulation via both auxin and GAs, with input from additional hormones. Fruit maturation, a transitional phase that precipitates ripening, occurs when auxin and GA levels subside with a concurrent rise in abscisic acid (ABA) and ethylene. During fruit ripening, ethylene plays a clear role in climacteric fruits, whereas non-climacteric ripening is generally associated with ABA. Recent evidence indicates varying requirements for both hormones within both ripening physiologies, suggesting rebalancing and specification of roles for common regulators rather than reliance upon one. Numerous recent discoveries pertaining to the molecular basis of hormonal activity and crosstalk are discussed, while we also note that many questions remain such as the molecular basis of additional hormonal activities, the role of epigenome changes, and how prior discoveries translate to the plethora of angiosperm species.
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Affiliation(s)
- Matthew A Fenn
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - James J Giovannoni
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
- United States Department of Agriculture - Agricultural Research Service and Boyce Thompson Institute for Plant Research, Cornell University campus, Ithaca, NY, 14853, USA
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Genome-Wide Characterization of Cucumber (Cucumis sativus L.) GRAS Genes and Their Response to Various Abiotic Stresses. HORTICULTURAE 2020. [DOI: 10.3390/horticulturae6040110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The GRAS (gibberellic acid insensitive, repressor of GAI, and scarecrow) proteins are a family of plant-specific transcription factors that regulate plant growth, development, and stress response. Currently, the role of GRAS transcription factors in various abiotic stress responses has not been systematically studied in cucumber (Cucumis sativus L.), a popular vegetable crop. Here, we provide a comprehensive bioinformatics analysis of the 35 GRAS genes identified in the cucumber genome. In this study, cucumber genotypes, i.e., “CG104”, which is stress-tolerant, and genotype “CG37”, which is stress-sensitive, were examined to provide insight on potential differences in the GRAS-regulated abiotic stress pathways. Transcriptional analysis by RNA-seq or qRT-PCR of these two genotypes revealed common and divergent functions of CsGRAS genes regulated by low and high temperatures, salinity, and by exposure to the phytohormones gibberellin (GA) and abscisic acid (ABA). Notably, CsGRAS2 (DELLA) and CsGRAS26 (LISCL) were regulated by all abiotic stresses and hormone treatments, suggesting that they may function in the biological cross-talk between multiple signaling pathways. This study provides candidate genes for improving cucumber tolerance to various environmental stresses.
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Müller LM, Campos-Soriano L, Levesque-Tremblay V, Bravo A, Daniels DA, Pathak S, Park HJ, Harrison MJ. Constitutive Overexpression of RAM1 Leads to an Increase in Arbuscule Density in Brachypodium distachyon. PLANT PHYSIOLOGY 2020; 184:1263-1272. [PMID: 32873628 PMCID: PMC7608154 DOI: 10.1104/pp.20.00997] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 08/20/2020] [Indexed: 05/27/2023]
Abstract
Arbuscular mycorrhizal (AM) symbiosis is a mutually beneficial association of plants and fungi of the subphylum Glomeromycotina. Endosymbiotic AM fungi colonize the inner cortical cells of the roots, where they form branched hyphae called arbuscules that function in nutrient exchange with the plant. To support arbuscule development and subsequent bidirectional nutrient exchange, the root cortical cells undergo substantial transcriptional reprogramming. REDUCED ARBUSCULAR MYCORRHIZA1 (RAM1), previously studied in several dicot plant species, is a major regulator of this cortical cell transcriptional program. Here, we generated ram1 mutants and RAM1 overexpressors in a monocot, Brachypodium distachyon. The AM phenotypes of two ram1 lines revealed that RAM1 is only partly required to enable arbuscule development in B. distachyon Transgenic lines constitutively overexpressing BdRAM1 showed constitutive expression of AM-inducible genes even in the shoots. Following inoculation with AM fungi, BdRAM1-overexpressing plants showed higher arbuscule densities relative to controls, indicating the potential to manipulate the relative proportion of symbiotic interfaces via modulation of RAM1 However, the overexpressors also show altered expression of hormone biosynthesis genes and aberrant growth patterns, including stunted bushy shoots and poor seed set. While these phenotypes possibly provide additional clues about the scope of influence of BdRAM1, they also indicate that directed approaches to increase the density of symbiotic interfaces will require a more focused, potentially cell type specific manipulation of transcription factor gene expression.
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Affiliation(s)
| | | | | | | | | | | | - Hee-Jin Park
- Boyce Thompson Institute, Ithaca, New York 14853
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Keller J, Delcros P, Libourel C, Cabello-Hurtado F, Aïnouche A. DELLA family duplication events lead to different selective constraints in angiosperms. Genetica 2020; 148:243-251. [PMID: 32862323 DOI: 10.1007/s10709-020-00102-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 08/14/2020] [Indexed: 11/29/2022]
Abstract
Gibberellic acid (GA) is a major plant hormone involved in several biological processes from the flowering to the symbiosis with microorganisms. Thus, the GA regulation is crucial for plant biology. This regulation occurs via the DELLA proteins that belong to the GRAS transcription factor family. DELLA proteins are characterised by a DELLA N-terminal and a GRAS C-terminal domains. It is well known that DELLA activity appears after the bryophytes divergence and then evolved in the vascular plant lineages. Here we present the phylogeny of DELLA across 75 species belonging to various lineages from algae, liverworts and angiosperms. Our study confirmed two main duplication events, the first occurring before the angiosperms divergence and the other specific to the eudicots lineage. Comparative analysis of DELLA subclades in angiosperms revealed the loss in Poaceae and strong alteration in other species of the DELLA functional domain in the DELLA2 clade. In addition, molecular evolution analysis suggests that each of the clades (named DELLA1.1, DELLA1.2 and DELLA2) evolved differently but copies of each subclade are under strong purifying selection. This also suggests that, although the DELLA functional domain is altered in DELLA2, DELLA2 orthologs are still functional and operate in a different way compared to DELLA1 copies. In angiosperms, additional duplication events occurred and led to duplicate copies in species, genus or family such as in the Fabaceae subfamily Papilionoideae. This duplication led to the formation of additional paralogs in the DELLA1.2 subclade (DELLA1.2.1 and DELLA1.2.2). Interestingly, both copies appeared to be under relaxing selection revealing different evolutionary fate of the DELLA duplicated copies.
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Affiliation(s)
- J Keller
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042, Rennes, France.,LRSV, Université de Toulouse, CNRS, UPS, Castanet-Tolosan, France
| | - P Delcros
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042, Rennes, France
| | - C Libourel
- LRSV, Université de Toulouse, CNRS, UPS, Castanet-Tolosan, France
| | - F Cabello-Hurtado
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042, Rennes, France
| | - A Aïnouche
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042, Rennes, France.
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Genome-wide identification and analysis of GRAS transcription factors in the bottle gourd genome. Sci Rep 2020; 10:14338. [PMID: 32868844 PMCID: PMC7459283 DOI: 10.1038/s41598-020-71240-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/06/2020] [Indexed: 12/01/2022] Open
Abstract
GRAS genes belong to the plant-specific transcription factors (TF’s) family that are known to be involved in plant growth and development. In this study, we have identified 37 genes from the bottle gourd genome that encodes for GRAS TF’s. Except for the SCLA, we were able to identify at least one gene from each of the 17 subfamilies. Gene structure and chromosomal analysis showed that maximum seven genes are present on Chr7 followed by six genes on Chr1. The subcellular location analysis revealed that most of the genes were localized in the nucleus, except for a few in chloroplast and mitochondria. Additionally, we have identified one tandem gene duplication event on Chr7 and three major motifs that were present in all the GRAS genes. Furthermore, the protein–protein interaction prediction and gene expression analysis showed five candidate hub-genes interact with various other genes and thus probably control the expression of interacting partners in different plant tissues. Overall, this study provides a comprehensive analysis of GRAS transcription factors in bottle gourd genome which could be further extended to other vegetable crops.
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Prochetto S, Reinheimer R. Step by step evolution of Indeterminate Domain (IDD) transcriptional regulators: from algae to angiosperms. ANNALS OF BOTANY 2020; 126:85-101. [PMID: 32206771 PMCID: PMC7304464 DOI: 10.1093/aob/mcaa052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 03/19/2020] [Indexed: 06/10/2023]
Abstract
INTRODUCTION The Indeterminate Domain (IDD) proteins are a plant-specific subclass of C2H2 Zinc Finger transcription factors. Some of these transcription factors play roles in diverse aspects of plant metabolism and development, but the function of most of IDD genes is unknown and the molecular evolution of the subfamily has not been explored in detail. METHODS In this study, we mined available genome sequences of green plants (Viridiplantae) to reconstruct the phylogeny and then described the motifs/expression patterns of IDD genes. KEY RESULTS We identified the complete set of IDD genes of 16 Streptophyta genomes. We found that IDD and its sister clade STOP arose by a duplication at the base of Streptophyta. Once on land, the IDD genes duplicated extensively, giving rise to at least ten lineages. Some of these lineages were lost in extant non-vascular plants and gymnosperms, but all of them were retained in angiosperms, duplicating profoundly in dicots and monocots and acquiring, at the same time, surprising heterogeneity in their C-terminal regions and expression patterns. CONCLUSIONS IDDs were present in the last common ancestor of Streptophyta. On land, IDDs duplicated extensively, leading to ten lineages. Later, IDDs were recruited by angiosperms where they diversified greatly in number, C-terminal and expression patterns. Interestingly, such diversification occurred during the evolution of novel traits of the plant body. This study provides a solid framework of the orthology relationships of green land plant IDD transcription factors, thus increasing the accuracy of orthologue identification in model and non-model species and facilitating the identification of agronomically important genes related to plant metabolism and development.
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Affiliation(s)
- Santiago Prochetto
- Fellow of Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina (CONICET), FBCB, Santa Fe, Argentina
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB, Santa Fe, Argentina
| | - Renata Reinheimer
- Member of Consejo Nacional de Investigaciones Científicas y Técnicas de la República Argentina (CONICET), FBCB, Santa Fe, Argentinaand
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB, Santa Fe, Argentina
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Wang N, Wang K, Li S, Jiang Y, Li L, Zhao M, Jiang Y, Zhu L, Wang Y, Su Y, Wang Y, Zhang M. Transcriptome-Wide Identification, Evolutionary Analysis, and GA Stress Response of the GRAS Gene Family in Panax ginseng C. A. Meyer. PLANTS 2020; 9:plants9020190. [PMID: 32033157 PMCID: PMC7076401 DOI: 10.3390/plants9020190] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/22/2020] [Accepted: 01/24/2020] [Indexed: 11/22/2022]
Abstract
GRAS transcription factors are a kind of plant-specific transcription factor that have been found in a variety of plants. According to previous studies, GRAS proteins are widely involved in the physiological processes of plant signal transduction, stress, growth and development. The Jilin ginseng (Panax ginseng C.A. Meyer) is a heterogeneous tetraploid perennial herb of the Araliaceae family, ginseng genus. Important information regarding the GRAS transcription factors has not been reported in ginseng. In this study, 59 Panax ginseng GRAS (PgGRAS) genes were obtained from the Jilin ginseng transcriptome data and divided into 13 sub-families according to the classification of Arabidopsis thaliana. Through systematic evolution, structural variation, function and gene expression analysis, we further reveal GRAS’s potential function in plant growth processes and its stress response. The expression of PgGRAS genes responding to gibberellin acids (GAs) suggests that these genes could be activated after application concentration of GA. The qPCR analysis result shows that four PgGRAS genes belonging to the DELLA sub-family potentially have important roles in the GA stress response of ginseng hairy roots. This study provides not only a preliminary exploration of the potential functions of the GRAS genes in ginseng, but also valuable data for further exploration of the candidate PgGRAS genes of GA signaling in Jilin ginseng, especially their roles in ginseng hairy root development and GA stress response.
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Affiliation(s)
- Nan Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, Jilin, China; (N.W.); (K.W.); (S.L.); (Y.J.); (L.L.); (M.Z.); (Y.J.); (L.Z.); (Y.S.)
- Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, Jilin, China;
| | - Kangyu Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, Jilin, China; (N.W.); (K.W.); (S.L.); (Y.J.); (L.L.); (M.Z.); (Y.J.); (L.Z.); (Y.S.)
- Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, Jilin, China;
| | - Shaokun Li
- College of Life Science, Jilin Agricultural University, Changchun 130118, Jilin, China; (N.W.); (K.W.); (S.L.); (Y.J.); (L.L.); (M.Z.); (Y.J.); (L.Z.); (Y.S.)
- Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, Jilin, China;
| | - Yang Jiang
- College of Life Science, Jilin Agricultural University, Changchun 130118, Jilin, China; (N.W.); (K.W.); (S.L.); (Y.J.); (L.L.); (M.Z.); (Y.J.); (L.Z.); (Y.S.)
- Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, Jilin, China;
| | - Li Li
- College of Life Science, Jilin Agricultural University, Changchun 130118, Jilin, China; (N.W.); (K.W.); (S.L.); (Y.J.); (L.L.); (M.Z.); (Y.J.); (L.Z.); (Y.S.)
- Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, Jilin, China;
| | - Mingzhu Zhao
- College of Life Science, Jilin Agricultural University, Changchun 130118, Jilin, China; (N.W.); (K.W.); (S.L.); (Y.J.); (L.L.); (M.Z.); (Y.J.); (L.Z.); (Y.S.)
- Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, Jilin, China;
| | - Yue Jiang
- College of Life Science, Jilin Agricultural University, Changchun 130118, Jilin, China; (N.W.); (K.W.); (S.L.); (Y.J.); (L.L.); (M.Z.); (Y.J.); (L.Z.); (Y.S.)
- Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, Jilin, China;
| | - Lei Zhu
- College of Life Science, Jilin Agricultural University, Changchun 130118, Jilin, China; (N.W.); (K.W.); (S.L.); (Y.J.); (L.L.); (M.Z.); (Y.J.); (L.Z.); (Y.S.)
- Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, Jilin, China;
| | - Yanfang Wang
- Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, Jilin, China;
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Yingjie Su
- College of Life Science, Jilin Agricultural University, Changchun 130118, Jilin, China; (N.W.); (K.W.); (S.L.); (Y.J.); (L.L.); (M.Z.); (Y.J.); (L.Z.); (Y.S.)
| | - Yi Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, Jilin, China; (N.W.); (K.W.); (S.L.); (Y.J.); (L.L.); (M.Z.); (Y.J.); (L.Z.); (Y.S.)
- Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, Jilin, China;
- Correspondence: (Y.W.); (M.Z.)
| | - Meiping Zhang
- College of Life Science, Jilin Agricultural University, Changchun 130118, Jilin, China; (N.W.); (K.W.); (S.L.); (Y.J.); (L.L.); (M.Z.); (Y.J.); (L.Z.); (Y.S.)
- Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, Jilin, China;
- Correspondence: (Y.W.); (M.Z.)
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Zhang J, Fu XX, Li RQ, Zhao X, Liu Y, Li MH, Zwaenepoel A, Ma H, Goffinet B, Guan YL, Xue JY, Liao YY, Wang QF, Wang QH, Wang JY, Zhang GQ, Wang ZW, Jia Y, Wang MZ, Dong SS, Yang JF, Jiao YN, Guo YL, Kong HZ, Lu AM, Yang HM, Zhang SZ, Van de Peer Y, Liu ZJ, Chen ZD. The hornwort genome and early land plant evolution. NATURE PLANTS 2020; 6:107-118. [PMID: 32042158 PMCID: PMC7027989 DOI: 10.1038/s41477-019-0588-4] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 12/20/2019] [Indexed: 05/10/2023]
Abstract
Hornworts, liverworts and mosses are three early diverging clades of land plants, and together comprise the bryophytes. Here, we report the draft genome sequence of the hornwort Anthoceros angustus. Phylogenomic inferences confirm the monophyly of bryophytes, with hornworts sister to liverworts and mosses. The simple morphology of hornworts correlates with low genetic redundancy in plant body plan, while the basic transcriptional regulation toolkit for plant development has already been established in this early land plant lineage. Although the Anthoceros genome is small and characterized by minimal redundancy, expansions are observed in gene families related to RNA editing, UV protection and desiccation tolerance. The genome of A. angustus bears the signatures of horizontally transferred genes from bacteria and fungi, in particular of genes operating in stress-response and metabolic pathways. Our study provides insight into the unique features of hornworts and their molecular adaptations to live on land.
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Affiliation(s)
- Jian Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xin-Xing Fu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rui-Qi Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiang Zhao
- PubBio-Tech Services Corporation, Wuhan, China
| | - Yang Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
| | - Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Arthur Zwaenepoel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Yan-Long Guan
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jia-Yu Xue
- Center for Plant Diversity and Systematics, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yi-Ying Liao
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Qing-Feng Wang
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Qing-Hua Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jie-Yu Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Guo-Qiang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | - Yu Jia
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Mei-Zhi Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Shan-Shan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Jian-Fen Yang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Yuan-Nian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hong-Zhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - An-Ming Lu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | | | - Shou-Zhou Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, Pretoria, South Africa.
- College of Horticulture, Nanjing Agricultural University, Nanjing, China.
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China.
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Zhi-Duan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.
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Cheng S, Xian W, Fu Y, Marin B, Keller J, Wu T, Sun W, Li X, Xu Y, Zhang Y, Wittek S, Reder T, Günther G, Gontcharov A, Wang S, Li L, Liu X, Wang J, Yang H, Xu X, Delaux PM, Melkonian B, Wong GKS, Melkonian M. Genomes of Subaerial Zygnematophyceae Provide Insights into Land Plant Evolution. Cell 2019; 179:1057-1067.e14. [DOI: 10.1016/j.cell.2019.10.019] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/27/2019] [Accepted: 10/21/2019] [Indexed: 01/11/2023]
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48
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Guo P, Wen J, Yang J, Ke Y, Wang M, Liu M, Ran F, Wu Y, Li P, Li J, Du H. Genome-wide survey and expression analyses of the GRAS gene family in Brassica napus reveals their roles in root development and stress response. PLANTA 2019; 250:1051-1072. [PMID: 31161396 DOI: 10.1007/s00425-019-03199-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/25/2019] [Indexed: 06/09/2023]
Abstract
Genome-wide identification, classification, expression analyses, and functional characterization of GRAS genes in oil crop, Brassica napus, indicate their importance in root development and stress response. GRAS proteins are a plant-specific transcription factor gene family involved in tissues development and stress response. We classified 87 putative GRAS genes in the Brassica napus genome (BnGRASs) into 13 subfamilies by phylogenetic analysis. The C-terminal GRAS domains of Brassica napus (B. napus) proteins were less conserved among subfamilies, but were conserved within each subfamily. A series of analyses revealed that 89.7% of the BnGRASs did not have intron insertions, and 24 specific-motifs were found at the N-terminal. A highly conserved microRNA 171 (miRNA171) target was observed specifically in the HAM subfamily across land plants. A total of 868 pairs of interaction proteins were predicted, the primary of which were transcription factors involved in transcriptional regulation and signal transduction. Integrated comparative analysis of GRAS genes across 26 species of algae, mosses, ferns, gymnosperms, and angiosperms revealed that this gene family originated in early mosses and was classified into 19 subfamilies, 14 of which may have originated prior to bryophyte evolution. RNA-Seq analysis demonstrated that most BnGRASs were widely expressed in different tissues/organs at different stages in B. napus, and 24 BnGRASs were highly/specifically expressed in roots. Results from a qRT-PCR analysis suggested that two BnGRASs belonging to SCR and LISCL subfamilies potentially have important roles in the stress response of roots.
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Affiliation(s)
- Pengcheng Guo
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Jing Wen
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Jin Yang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yunzhuo Ke
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Mangmang Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Mingming Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Feng Ran
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Yunwen Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Pengfeng Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China
| | - Hai Du
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.
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49
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Baison J, Vidalis A, Zhou L, Chen Z, Li Z, Sillanpää MJ, Bernhardsson C, Scofield D, Forsberg N, Grahn T, Olsson L, Karlsson B, Wu H, Ingvarsson PK, Lundqvist S, Niittylä T, García‐Gil MR. Genome-wide association study identified novel candidate loci affecting wood formation in Norway spruce. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:83-100. [PMID: 31166032 PMCID: PMC6852177 DOI: 10.1111/tpj.14429] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/16/2019] [Accepted: 05/20/2019] [Indexed: 05/26/2023]
Abstract
Norway spruce is a boreal forest tree species of significant ecological and economic importance. Hence there is a strong imperative to dissect the genetics underlying important wood quality traits in the species. We performed a functional genome-wide association study (GWAS) of 17 wood traits in Norway spruce using 178 101 single nucleotide polymorphisms (SNPs) generated from exome genotyping of 517 mother trees. The wood traits were defined using functional modelling of wood properties across annual growth rings. We applied a Least Absolute Shrinkage and Selection Operator (LASSO-based) association mapping method using a functional multilocus mapping approach that utilizes latent traits, with a stability selection probability method as the hypothesis testing approach to determine a significant quantitative trait locus. The analysis provided 52 significant SNPs from 39 candidate genes, including genes previously implicated in wood formation and tree growth in spruce and other species. Our study represents a multilocus GWAS for complex wood traits in Norway spruce. The results advance our understanding of the genetics influencing wood traits and identifies candidate genes for future functional studies.
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Affiliation(s)
- John Baison
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural ScienceParallellvägen 21Umeå907 36Sweden
| | - Amaryllis Vidalis
- Section of Population Epigenetics and EpigenomicsCentre of Life and Food Sciences WeihenstephanTechnische Universität MünchenLichtenbergstr. 2aMünchen85748Germany
| | - Linghua Zhou
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural ScienceParallellvägen 21Umeå907 36Sweden
| | - Zhi‐Qiang Chen
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural ScienceParallellvägen 21Umeå907 36Sweden
| | - Zitong Li
- Ecological Genetics Research UnitDepartment of BiosciencesUniversity of HelsinkiP.O. Box 65FI‐00014HelsinkiFinland
| | - Mikko J. Sillanpää
- Department of Mathematical SciencesBiocenter OuluUniversity of OuluPentti Kaiteran katu 1OuluFinland
| | - Carolina Bernhardsson
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural ScienceParallellvägen 21Umeå907 36Sweden
- Department of Ecology and Environmental ScienceUmeå UniversityLinnaeus väg 4-6Umeå907 36Sweden
| | - Douglas Scofield
- Uppsala Multidisciplinary Centre for Advanced Computational ScienceUppsala UniversityLägerhyddsvägen 2Uppsala752 37Sweden
| | - Nils Forsberg
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural ScienceParallellvägen 21Umeå907 36Sweden
| | - Thomas Grahn
- RISE BioeconomyDrottning Kristinas väg 61SE‐114 86StockholmSweden
| | - Lars Olsson
- RISE BioeconomyDrottning Kristinas väg 61SE‐114 86StockholmSweden
| | | | - Harry Wu
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural ScienceParallellvägen 21Umeå907 36Sweden
| | - Pär K. Ingvarsson
- Department of Ecology and Environmental ScienceUmeå UniversityLinnaeus väg 4-6Umeå907 36Sweden
- Department of Ecology and Genetics: Evolutionary BiologyUppsala UniversityKåbovägen 4Uppsala752 36Sweden
| | - Sven‐Olof Lundqvist
- RISE BioeconomyDrottning Kristinas väg 61SE‐114 86StockholmSweden
- IICRosenlundsgatan 48BSE‐118 63StockholmSweden
| | - Totte Niittylä
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural ScienceParallellvägen 21Umeå907 36Sweden
| | - M Rosario García‐Gil
- Department of Forest Genetics and Plant PhysiologyUmeå Plant Science CentreSwedish University of Agricultural ScienceParallellvägen 21Umeå907 36Sweden
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50
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Identification and Expression Analysis of GRAS Transcription Factors to Elucidate Candidate Genes Related to Stolons, Fruit Ripening and Abiotic Stresses in Woodland Strawberry ( Fragaria vesca). Int J Mol Sci 2019; 20:ijms20184593. [PMID: 31533278 PMCID: PMC6770801 DOI: 10.3390/ijms20184593] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 09/12/2019] [Accepted: 09/14/2019] [Indexed: 12/17/2022] Open
Abstract
The cultivated strawberry (Fragaria × ananassa), an allo-octoploid with non-climacteric fleshy fruits, is a popular Rosaceae horticultural crop worldwide that is mainly propagated via stolons during cultivation. Woodland strawberry (Fragaria vesca), one of the four diploid progenitor species of cultivated strawberry, is widely used as a model plant in the study of Rosaceae fruit trees, non-climacteric fruits and stolons. One GRAS transcription factor has been shown to regulate stolon formation; the other GRAS proteins in woodland strawberry remain unknown. In this study, we identified 54 FveGRAS proteins in woodland strawberry, and divided them into 14 subfamilies. Conserved motif analysis revealed that the motif composition of FveGRAS proteins was conserved within each subfamily, but diverged widely among subfamilies. We found 56 orthologous pairs of GRAS proteins between woodland strawberry and Arabidopsis thaliana, 47 orthologous pairs between woodland strawberry and rice and 92 paralogous pairs within woodland strawberry. The expression patterns of FveGRAS genes in various organs and tissues, and changes therein under cold, heat and GA3 treatments, were characterized using transcriptomic analysis. The results showed that 34 FveGRAS genes were expressed with different degrees in at least four organs, including stolons; only a few genes displayed organ-specific expression. The expression levels of 16 genes decreased, while that of four genes increased during fruit ripening; FveGRAS54 showed the largest increase in expression. Under cold, heat and GA3 treatments, around half of the FveGRAS genes displayed increased or decreased expression to some extent, suggesting differing functions of these FveGRAS genes in the responses to cold, heat and GAs. This study provides insight into the potential functions of FveGRAS genes in woodland strawberry. A few FveGRAS genes were identified as candidate genes for further study, in terms of their functions in stolon formation, fruit ripening and abiotic stresses.
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