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Hao X, Gong Y, Chen S, Ma C, Duanmu H. Genome-Wide Identification of GRAS Transcription Factors and Their Functional Analysis in Salt Stress Response in Sugar Beet. Int J Mol Sci 2024; 25:7132. [PMID: 39000240 PMCID: PMC11241673 DOI: 10.3390/ijms25137132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/08/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024] Open
Abstract
GAI-RGA-and-SCR (GRAS) transcription factors can regulate many biological processes such as plant growth and development and stress defense, but there are few related studies in sugar beet. Salt stress can seriously affect the yield and quality of sugar beet (Beta vulgaris). Therefore, this study used bioinformatics methods to identify GRAS transcription factors in sugar beet and analyzed their structural characteristics, evolutionary relationships, regulatory networks and salt stress response patterns. A total of 28 BvGRAS genes were identified in the whole genome of sugar beet, and the sequence composition was relatively conservative. According to the topology of the phylogenetic tree, BvGRAS can be divided into nine subfamilies: LISCL, SHR, PAT1, SCR, SCL3, LAS, SCL4/7, HAM and DELLA. Synteny analysis showed that there were two pairs of fragment replication genes in the BvGRAS gene, indicating that gene replication was not the main source of BvGRAS family members. Regulatory network analysis showed that BvGRAS could participate in the regulation of protein interaction, material transport, redox balance, ion homeostasis, osmotic substance accumulation and plant morphological structure to affect the tolerance of sugar beet to salt stress. Under salt stress, BvGRAS and its target genes showed an up-regulated expression trend. Among them, BvGRAS-15, BvGRAS-19, BvGRAS-20, BvGRAS-21, LOC104892636 and LOC104893770 may be the key genes for sugar beet's salt stress response. In this study, the structural characteristics and biological functions of BvGRAS transcription factors were analyzed, which provided data for the further study of the molecular mechanisms of salt stress and molecular breeding of sugar beet.
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Affiliation(s)
- Xiaolin Hao
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150080, China; (X.H.); (Y.G.); (C.M.)
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Yongyong Gong
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150080, China; (X.H.); (Y.G.); (C.M.)
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Sixue Chen
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA;
| | - Chunquan Ma
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150080, China; (X.H.); (Y.G.); (C.M.)
- Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region, School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Huizi Duanmu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150080, China; (X.H.); (Y.G.); (C.M.)
- Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin 150080, China
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Wang W, Huang S, Wang Z, Cao P, Luo M, Wang F. Unraveling wheat's response to salt stress during early growth stages through transcriptomic analysis and co-expression network profiling. BMC Genom Data 2024; 25:36. [PMID: 38609855 PMCID: PMC11015659 DOI: 10.1186/s12863-024-01221-1] [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: 08/15/2023] [Accepted: 03/14/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Soil salinization is one of the vital factors threatening the world's food security. To reveal the biological mechanism of response to salt stress in wheat, this study was conducted to resolve the transcription level difference to salt stress between CM6005 (salt-tolerant) and KN9204 (salt-sensitive) at the germination and seedling stage. RESULTS To investigate the molecular mechanism underlying salt tolerance in wheat, we conducted comprehensive transcriptome analyses at the seedling and germination stages. Two wheat cultivars, CM6005 (salt-tolerant) and KN9204 (salt-sensitive) were subjected to salt treatment, resulting in a total of 24 transcriptomes. Through expression-network analysis, we identified 17 modules, 16 and 13 of which highly correlate with salt tolerance-related phenotypes in the germination and seedling stages, respectively. Moreover, we identified candidate Hub genes associated with specific modules and explored their regulatory relationships using co-expression data. Enrichment analysis revealed specific enrichment of gibberellin-related terms and pathways in CM6005, highlighting the potential importance of gibberellin regulation in enhancing salt tolerance. In contrast, KN9204 exhibited specific enrichment in glutathione-related terms and activities, suggesting the involvement of glutathione-mediated antioxidant mechanisms in conferring resistance to salt stress. Additionally, glucose transport was found to be a fundamental mechanism for salt tolerance during wheat seedling and germination stages, indicating its potential universality in wheat. Wheat plants improve their resilience and productivity by utilizing adaptive mechanisms like adjusting osmotic balance, bolstering antioxidant defenses, accumulating compatible solutes, altering root morphology, and regulating hormones, enabling them to better withstand extended periods of salt stress. CONCLUSION Through utilizing transcriptome-level analysis employing WGCNA, we have revealed a potential regulatory mechanism that governs the response to salt stress and recovery in wheat cultivars. Furthermore, we have identified key candidate central genes that play a crucial role in this mechanism. These central genes are likely to be vital components within the gene expression network associated with salt tolerance. The findings of this study strongly support the molecular breeding of salt-tolerant wheat, particularly by utilizing the genetic advancements based on CM6005 and KN9204.
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Affiliation(s)
- Wei Wang
- Cangzhou Academy of Agriculture and Forestry Sciences, 061001, Cangzhou, Hebei, China.
- Hebei Key Laboratory of Drought-Alkali Tolerance in Wheat, 061001, Cangzhou, Hebei, China.
| | - Sufang Huang
- Cangzhou Academy of Agriculture and Forestry Sciences, 061001, Cangzhou, Hebei, China
- Hebei Key Laboratory of Drought-Alkali Tolerance in Wheat, 061001, Cangzhou, Hebei, China
| | - Zhi Wang
- Cangzhou Academy of Agriculture and Forestry Sciences, 061001, Cangzhou, Hebei, China
- Hebei Key Laboratory of Drought-Alkali Tolerance in Wheat, 061001, Cangzhou, Hebei, China
| | - Pingping Cao
- Cangzhou Academy of Agriculture and Forestry Sciences, 061001, Cangzhou, Hebei, China
- Hebei Key Laboratory of Drought-Alkali Tolerance in Wheat, 061001, Cangzhou, Hebei, China
| | - Meng Luo
- Shanghai Majorbio Bio-pharm Technology Co., Ltd, 200120, Shanghai, China
| | - Fengzhi Wang
- Cangzhou Academy of Agriculture and Forestry Sciences, 061001, Cangzhou, Hebei, China.
- Hebei Key Laboratory of Drought-Alkali Tolerance in Wheat, 061001, Cangzhou, Hebei, China.
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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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Zhu L, Yin T, Zhang M, Yang X, Wu J, Cai H, Yang N, Li X, Wen K, Chen D, Zhang H, Liu X. Genome-wide identification and expression pattern analysis of the kiwifruit GRAS transcription factor family in response to salt stress. BMC Genomics 2024; 25:12. [PMID: 38166720 PMCID: PMC10759511 DOI: 10.1186/s12864-023-09915-z] [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: 04/25/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND GRAS is a family of plant-specific transcription factors (TFs) that play a vital role in plant growth and development and response to adversity stress. However, systematic studies of the GRAS TF family in kiwifruit have not been reported. RESULTS In this study, we used a bioinformatics approach to identify eighty-six AcGRAS TFs located on twenty-six chromosomes and phylogenetic analysis classified them into ten subfamilies. It was found that the gene structure is relatively conserved for these genes and that fragmental duplication is the prime force for the evolution of AcGRAS genes. However, the promoter region of the AcGRAS genes mainly contains cis-acting elements related to hormones and environmental stresses, similar to the results of GO and KEGG enrichment analysis, suggesting that hormone signaling pathways of the AcGRAS family play a vital role in regulating plant growth and development and adversity stress. Protein interaction network analysis showed that the AcGRAS51 protein is a relational protein linking DELLA, SCR, and SHR subfamily proteins. The results demonstrated that 81 genes were expressed in kiwifruit AcGRAS under salt stress, including 17 differentially expressed genes, 13 upregulated, and four downregulated. This indicates that the upregulated AcGRAS55, AcGRAS69, AcGRAS86 and other GRAS genes can reduce the salt damage caused by kiwifruit plants by positively regulating salt stress, thus improving the salt tolerance of the plants. CONCLUSIONS These results provide a theoretical basis for future exploration of the characteristics and functions of more AcGRAS genes. This study provides a basis for further research on kiwifruit breeding for resistance to salt stress. RT-qPCR analysis showed that the expression of 3 AcGRAS genes was elevated under salt stress, indicating that AcGRAS exhibited a specific expression pattern under salt stress conditions.
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Affiliation(s)
- Ling Zhu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Tuo Yin
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Mengjie Zhang
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China
| | - Xiuyao Yang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Jiexin Wu
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China
| | - Hanbing Cai
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Na Yang
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China
| | - Xulin Li
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China
| | - Ke Wen
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China
| | - Daming Chen
- Research Institute of Agriculture Ecological in Hot Areas, Yunnan Academy of Agricultural Science, Yuan Mou, Yunnan, 651300, China
| | - Hanyao Zhang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China.
| | - Xiaozhen Liu
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming, 650224, Yunnan Province, China.
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Neves C, Ribeiro B, Amaro R, Expósito J, Grimplet J, Fortes AM. Network of GRAS transcription factors in plant development, fruit ripening and stress responses. HORTICULTURE RESEARCH 2023; 10:uhad220. [PMID: 38077496 PMCID: PMC10699852 DOI: 10.1093/hr/uhad220] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 10/20/2023] [Indexed: 06/23/2024]
Abstract
The plant-specific family of GRAS transcription factors has been wide implicated in the regulation of transcriptional reprogramming associated with a diversity of biological functions ranging from plant development processes to stress responses. Functional analyses of GRAS transcription factors supported by in silico structural and comparative analyses are emerging and clarifying the regulatory networks associated with their biological roles. In this review, a detailed analysis of GRAS proteins' structure and biochemical features as revealed by recent discoveries indicated how these characteristics may impact subcellular location, molecular mechanisms, and function. Nomenclature issues associated with GRAS classification into different subfamilies in diverse plant species even in the presence of robust genomic resources are discussed, in particular how it affects assumptions of biological function. Insights into the mechanisms driving evolution of this gene family and how genetic and epigenetic regulation of GRAS contributes to subfunctionalization are provided. Finally, this review debates challenges and future perspectives on the application of this complex but promising gene family for crop improvement to cope with challenges of environmental transition.
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Affiliation(s)
- Catarina Neves
- BioISI–Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| | - Beatriz Ribeiro
- BioISI–Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| | - Rute Amaro
- BioISI–Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| | - Jesús Expósito
- BioISI–Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| | - Jérôme Grimplet
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Departamento de Ciencia Vegetal, Gobierno de Aragón, Avda. Montañana 930, 50059 Zaragoza, Spain
- Instituto Agroalimentario de Aragón—IA2 (CITA-Universidad de Zaragoza), Calle Miguel Servet 177, 50013 Zaragoza, Spain
| | - Ana Margarida Fortes
- BioISI–Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
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Aslam MM, Fritschi FB, Di Z, Wang G, Li H, Lam HM, Waseem M, Weifeng X, Zhang J. Overexpression of LaGRAS enhances phosphorus acquisition via increased root growth of phosphorus-deficient white lupin. PHYSIOLOGIA PLANTARUM 2023; 175:e13962. [PMID: 37343119 DOI: 10.1111/ppl.13962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/01/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023]
Abstract
The GRAS transcription factors play an indispensable role in plant growth and responses to environmental stresses. The GRAS gene family has extensively been explored in various plant species; however, the comprehensive investigation of GRAS genes in white lupin remains insufficient. In this study, bioinformatics analysis of white lupin genome revealed 51 LaGRAS genes distributed into 10 distinct phylogenetic clades. Gene structure analyses revealed that LaGRAS proteins were considerably conserved among the same subfamilies. Notably, 25 segmental duplications and a single tandem duplication showed that segmental duplication was the major driving force for the expansion of GRAS genes in white lupin. Moreover, LaGRAS genes exhibited preferential expression in young cluster root and mature cluster roots and may play key roles in nutrient acquisition, particularly phosphorus (P). To validate this, RT-qPCR analysis of white lupin plants grown under +P (normal P) and -P (P deficiency) conditions elucidated significant differences in the transcript level of GRAS genes. Among them, LaGRAS38 and LaGRAS39 were identified as potential candidates with induced expression in MCR under -P. Additionally, white lupin transgenic hairy root overexpressing OE-LaGRAS38 and OE-LaGRAS39 showed increased root growth, and P concentration in root and leaf compared to those with empty vector control, suggesting their role in P acquisition. We believe this comprehensive analysis of GRAS members in white lupin is a first step in exploring their role in the regulation of root growth, tissue development, and ultimately improving P use efficiency in legume crops under natural environments.
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Affiliation(s)
- Mehtab Muhammad Aslam
- College of Agriculture, Yangzhou University, Yangzhou, China
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- College of Agriculture, Food and Natural Resources (CAFNR), Division of Plant Sciences & Technology, University of Missouri, Columbia, Missouri, USA
| | - Felix B Fritschi
- College of Agriculture, Food and Natural Resources (CAFNR), Division of Plant Sciences & Technology, University of Missouri, Columbia, Missouri, USA
| | - Zhang Di
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Guanqun Wang
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Haoxuan Li
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Hon-Ming Lam
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Muhammad Waseem
- College of Horticulture, Hainan University, Haikou, China
- Department of Botany, University of Narowal, Narowal, Pakistan
| | - Xu Weifeng
- College of Agriculture, Yangzhou University, Yangzhou, China
- Center for Plant Water-Use and Nutrition Regulation and College of Resource and Environment, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
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Dong X, Liu Z, Wei J, Zheng G, Li H, Wang Y, Tian H, Cui J, Wu Z, Cao X, Xu C. The BrAFP1 promoter drives gene-specific expression in leaves and stems of winter rapeseed (Brassica rapa L.) under cold induction. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 331:111669. [PMID: 36870371 DOI: 10.1016/j.plantsci.2023.111669] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
BrAFP1(antifreeze protein in winter turnip rape) effectively limits recrystallization and growth of ice crystals. The BrAFP1 expression level determines whether the freezing-induced damage to winter turnip rape plants is avoided. This study analyzed the activity of the BrAFP1 promoters of several varieties at various cold tolerance levels. We cloned the BrAFP1 promoters from five winter rapeseed cultivars. The multiple sequence alignment revealed the presence of one inDel and eight single-nucleotide mutations (SNMs) in the promoters. One of these SNMs (base mutation from C to T) at the -836 site away from the transcription start site (TSS) enhanced the transcriptional activity of the promoter at low temperature. The promoter activity was specific in cotyledons and hypocotyls during the seedling stage and was referential in stems, leaves, and flowers but not the calyx. This consequently drove the downstream gene to be specifically expressed in leaves and stems, but not in roots at low temperature. The truncated fragment GUS staining assays revealed that the core region of the BrAFP1 promoter was included in the 98 bp fragment from the -933 to -836 site away from the TSS, which was necessary for transcriptional activity. The LTR element of the promoter significantly enhanced expression at low temperatures and suppressed expression at moderate temperatures. Moreover, the BrAFP1 5'-UTR intron bound the scarecrow-like transcription factor and enhanced expression at low temperature.
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Affiliation(s)
- Xiaoyun Dong
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Zigang Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
| | - Jiaping Wei
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Guoqiang Zheng
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Hui Li
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Ying Wang
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Haiyan Tian
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Junmei Cui
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Zefeng Wu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaodong Cao
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Chunmei Xu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
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Jagram N, Dasgupta I. Principles and practice of virus induced gene silencing for functional genomics in plants. Virus Genes 2023; 59:173-187. [PMID: 36266497 DOI: 10.1007/s11262-022-01941-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 10/05/2022] [Indexed: 10/24/2022]
Abstract
Virus induced gene silencing (VIGS) has, of late, emerged as an important tool for transient silencing of genes in plants. This is now being increasingly used to determine functions of novel genes in a wide variety of plants, many of which are important crops yielding food and fiber or are sources of products having pharmaceutical uses. The technology for VIGS comprises the development of vectors derived from viruses, choosing the optimal orientation and size of the gene to be targeted and adopting the most suitable method of inoculation. This review gives a brief overview of the main aspects of VIGS technology as is being practiced. It also discusses the challenges the technology faces and the possible way ahead to improve its robustness, so that the technology finds wider applications.
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Affiliation(s)
- Neelam Jagram
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Indranil Dasgupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
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Zhou X, Li X, Zhang X, Yin D, Wang J, Zhao Y. Construction of a high-density genetic map and localization of grazing-tolerant QTLs in Medicago falcata L. FRONTIERS IN PLANT SCIENCE 2022; 13:985603. [PMID: 36262664 PMCID: PMC9574245 DOI: 10.3389/fpls.2022.985603] [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: 07/04/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Using genomic DNA from 79 F1 plants resulted from a crossing between parents with strong and weak grazing tolerance in Medicago falcata L., we generated an EcoRI restriction site-associated DNA (RAD) sequencing library. After sequencing and assembly, a high-density genetic map with high-quality SNP markers was constructed, with a total length of 1312.238 cM and an average density of 0.844 SNP/cM. METHODS The phenotypic traits of 79 F1 families were observed and the QTLS of 6 traits were analyzed by interval mapping. RESULTS Sixty three QTLs were identified for seven traits with LOD values from 3 to 6 and the contribution rates from 15% to 30%. Among the 63 QTLs, 17 were for natural shoot height, 12 for rhizome Length, 10 for Shoot canopy diameter, 9 for Basal plant diameter, 6 for stem number, 5 for absolute shoot height, and 4 for rhizome width. These QTLs were concentrated on LG2, LG4, LG5, LG7, and LG8. LG6 had only 6 QTLs. According to the results of QTL mapping, comparison of reference genomes, and functional annotation, 10 candidate genes that may be related to grazing tolerance were screened. qRT-PCR analysis showed that two candidate genes (LOC11412291 and LOC11440209) may be the key genes related to grazing tolerance of M. falcata. CONCLUSION The identified trait-associated QTLs and candidate genes in this study will provide a solid foundation for future molecular breeding for enhanced grazing-tolerance in M. falcata.
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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: 15] [Impact Index Per Article: 7.5] [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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Genome–Wide Identification of the GRAS Family Genes in Melilotus albus and Expression Analysis under Various Tissues and Abiotic Stresses. Int J Mol Sci 2022; 23:ijms23137403. [PMID: 35806414 PMCID: PMC9267034 DOI: 10.3390/ijms23137403] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/27/2022] [Accepted: 07/01/2022] [Indexed: 12/12/2022] Open
Abstract
The GRAS gene family is a plant–specific family of transcription factors, which play an important role in many metabolic pathways, such as plant growth and development and stress response. However, there is no report on the comprehensive study of the GRAS gene family of Melilotus albus. Here, we identified 55 MaGRAS genes, which were classified into 8 subfamilies by phylogenetic analysis, and unevenly distributed on 8 chromosomes. The structural analysis indicated that 87% of MaGRAS genes have no intron, which is highly conservative in different species. MaGRAS proteins of the same subfamily have similar protein motifs, which are the source of functional differences of different genomes. Transcriptome and qRT–PCR data were combined to determine the expression of 12 MaGRAS genes in 6 tissues, including flower, seed, leaf, stem, root and nodule, which indicated the possible roles in plant growth and development. Five and seven MaGRAS genes were upregulated under ABA, drought, and salt stress treatments in the roots and shoots, respectively, indicating that they play vital roles in the response to ABA and abiotic stresses in M. albus. Furthermore, in yeast heterologous expression, MaGRAS12, MaGRAS34 and MaGRAS33 can enhance the drought or salt tolerance of yeast cells. Taken together, these results provide basic information for understanding the underlying molecular mechanisms of GRAS proteins and valuable information for further studies on the growth, development and stress responses of GRAS proteins in M. albus.
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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: 20] [Impact Index Per Article: 10.0] [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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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: 19] [Impact Index Per Article: 9.5] [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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14
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Nutrient Deficiency Affects the Growth and Nitrate Concentration of Hydroponic Radish. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7120525] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In hydroponics, a continuous supply of mineral nutrients is essential for plant growth. However, constitutive nutrient-rich conditions also increase the nitrate content in the plants, which can be harmful to human health. Here, we investigated the effect of nutrient deficiency on the growth and component composition of hydroponic radish by changing the timing of nutrient removal from the hydroponic solution. Radish plants that were 14 days old were transferred to four different nutrient conditions for 14 days: nutrient deficiency for 14 days (WW), full nutrient for 14 days (NN), nutrient deficiency for the last 7 days (NW), and nutrient deficiency for the first 7 days (WN). After the treatments, the NW plants had similar taproot growth to NN plants. In contrast, the WN plants significantly reduced taproot growth. The WW plants reduced the shoot and taproot weight and their water contents. The nitrate content in the taproots was reduced in the NW and WW plants. The WW plants contained lower total phenol and higher ascorbic acid and sugar contents. These results suggest that the uptake of nutrient minerals at the young growth stage is important for the growth of radish taproot. Nutrient deficiency management can be one of the most effective tools for regulating radish growth and composition.
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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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Qiao H, Liu Y, Cheng L, Gu X, Yin P, Li K, Zhou S, Wang G, Zhou C. TaWRKY13-A Serves as a Mediator of Jasmonic Acid-Related Leaf Senescence by Modulating Jasmonic Acid Biosynthesis. FRONTIERS IN PLANT SCIENCE 2021; 12:717233. [PMID: 34539711 PMCID: PMC8442999 DOI: 10.3389/fpls.2021.717233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
Leaf senescence is crucial for crop yield and quality. Transcriptional regulation is a key step for integrating various senescence-related signals into the nucleus. However, few regulators of senescence implicating transcriptional events have been functionally characterized in wheat. Based on our RNA-seq data, we identified a WRKY transcription factor, TaWRKY13-A, that predominately expresses at senescent stages. By using the virus-induced gene silencing (VIGS) method, we manifested impaired transcription of TaWRKY13-A leading to a delayed leaf senescence phenotype in wheat. Moreover, the overexpression (OE) of TaWRKY13-A accelerated the onset of leaf senescence under both natural growth condition and darkness in Brachypodium distachyon and Arabidopsis thaliana. Furthermore, by physiological and molecular investigations, we verified that TaWRKY13-A participates in the regulation of leaf senescence via jasmonic acid (JA) pathway. The expression of JA biosynthetic genes, including AtLOX6, was altered in TaWRKY13-A-overexpressing Arabidopsis. We also demonstrated that TaWRKY13-A can interact with the promoter of AtLOX6 and TaLOX6 by using the electrophoretic mobility shift assay (EMSA) and luciferase reporter system. Consistently, we detected a higher JA level in TaWRKY13-A-overexpressing lines than that in Col-0. Moreover, our data suggested that TaWRKY13-A is partially functional conserved with AtWRKY53 in age-dependent leaf senescence. Collectively, this study manifests TaWRKY13-A as a positive regulator of JA-related leaf senescence, which could be a new clue for molecular breeding in wheat.
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Affiliation(s)
- Hualiang Qiao
- Ministry of Education Key Laboratory of Molecular and Cell Biology, Hebei Innovation Center for Cell Signaling, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang, China
| | - Yongwei Liu
- Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang, China
| | - Lingling Cheng
- Ministry of Education Key Laboratory of Molecular and Cell Biology, Hebei Innovation Center for Cell Signaling, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Xuelin Gu
- Ministry of Education Key Laboratory of Molecular and Cell Biology, Hebei Innovation Center for Cell Signaling, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Pengcheng Yin
- Ministry of Education Key Laboratory of Molecular and Cell Biology, Hebei Innovation Center for Cell Signaling, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Ke Li
- Ministry of Education Key Laboratory of Molecular and Cell Biology, Hebei Innovation Center for Cell Signaling, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Shuo Zhou
- Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang, China
| | - Geng Wang
- Ministry of Education Key Laboratory of Molecular and Cell Biology, Hebei Innovation Center for Cell Signaling, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Chunjiang Zhou
- Ministry of Education Key Laboratory of Molecular and Cell Biology, Hebei Innovation Center for Cell Signaling, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
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Malik P, Kumar J, Sharma S, Sharma R, Sharma S. Multi-locus genome-wide association mapping for spike-related traits in bread wheat (Triticum aestivum L.). BMC Genomics 2021; 22:597. [PMID: 34353288 PMCID: PMC8340506 DOI: 10.1186/s12864-021-07834-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 06/23/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Bread wheat (Triticum aestivum L.) is one of the most important cereal food crops for the global population. Spike-layer uniformity (the consistency of the spike distribution in the vertical space)-related traits (SLURTs) are quantitative and have been shown to directly affect yield potential by modifying the plant architecture. Therefore, these parameters are important breeding targets for wheat improvement. The present study is the first genome-wide association study (GWAS) targeting SLURTs in wheat. In this study, a set of 225 diverse spring wheat accessions were used for multi-locus GWAS to evaluate SLURTs, including the number of spikes per plant (NSPP), spike length (SL), number of spikelets per spike (NSPS), grain weight per spike (GWPS), lowest tiller height (LTH), spike-layer thickness (SLT), spike-layer number (SLN) and spike-layer uniformity (SLU). RESULTS In total, 136 significant marker trait associations (MTAs) were identified when the analysis was both performed individually and combined for two environments. Twenty-nine MTAs were detected in environment one, 48 MTAs were discovered in environment two and 59 MTAs were detected using combined data from the two environments. Altogether, 15 significant MTAs were found for five traits in one of the two environments, and four significant MTAs were detected for the two traits, LTH and SLU, in both environments i.e. E1, E2 and also in combined data from the two environments. In total, 279 candidate genes (CGs) were identified, including Chaperone DnaJ, ABC transporter-like, AP2/ERF, SWEET sugar transporter, as well as genes that have previously been associated with wheat spike development, seed development and grain yield. CONCLUSIONS The MTAs detected through multi-locus GWAS will be useful for improving SLURTs and thus yield in wheat production through marker-assisted and genomic selection.
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Affiliation(s)
- Parveen Malik
- Department of Genetics and Plant Breeding, ChaudharyCharan Singh University (CCSU), Meerut, 250 004, India
| | - Jitendra Kumar
- Department of Genetics and Plant Breeding, ChaudharyCharan Singh University (CCSU), Meerut, 250 004, India.,National Agri-Food Biotechnology Institute (NABI), Sector 81(Knowledge City), SahibzadaAjit Singh Nagar, Punjab, 140306, India
| | - Shiveta Sharma
- Department of Genetics and Plant Breeding, ChaudharyCharan Singh University (CCSU), Meerut, 250 004, India
| | - Rajiv Sharma
- Scotland's Rural College (SRUC), Peter Wilson Building, West Mains Road, Edinburgh, EH9 3JG, UK
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, ChaudharyCharan Singh University (CCSU), Meerut, 250 004, India.
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Malik P, Kumar J, Singh S, Sharma S, Meher PK, Sharma MK, Roy JK, Sharma PK, Balyan HS, Gupta PK, Sharma S. Single-trait, multi-locus and multi-trait GWAS using four different models for yield traits in bread wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:46. [PMID: 37309385 PMCID: PMC10236106 DOI: 10.1007/s11032-021-01240-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/30/2021] [Indexed: 06/14/2023]
Abstract
A genome-wide association study (GWAS) for 10 yield and yield component traits was conducted using an association panel comprising 225 diverse spring wheat genotypes. The panel was genotyped using 10,904 SNPs and evaluated for three years (2016-2019), which constituted three environments (E1, E2 and E3). Heritability for different traits ranged from 29.21 to 97.69%. Marker-trait associations (MTAs) were identified for each trait using data from each environment separately and also using BLUP values. Four different models were used, which included three single trait models (CMLM, FarmCPU, SUPER) and one multi-trait model (mvLMM). Hundreds of MTAs were obtained using each model, but after Bonferroni correction, only 6 MTAs for 3 traits were available using CMLM, and 21 MTAs for 4 traits were available using FarmCPU; none of the 525 MTAs obtained using SUPER could qualify after Bonferroni correction. Using BLUP, 20 MTAs were available, five of which also figured among MTAs identified for individual environments. Using mvLMM model, after Bonferroni correction, 38 multi-trait MTAs, for 15 different trait combinations were available. Epistatic interactions involving 28 pairs of MTAs were also available for seven of the 10 traits; no epistatic interactions were available for GNPS, PH, and BYPP. As many as 164 putative candidate genes (CGs) were identified using all the 50 MTAs (CMLM, 3; FarmCPU, 9; mvLMM, 6, epistasis, 21 and BLUP, 11 MTAs), which ranged from 20 (CMLM) to 66 (epistasis) CGs. In-silico expression analysis of CGs was also conducted in different tissues at different developmental stages. The information generated through the present study proved useful for developing a better understanding of the genetics of each of the 10 traits; the study also provided novel markers for marker-assisted selection (MAS) to be utilized for the development of wheat cultivars with improved agronomic traits. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01240-1.
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Affiliation(s)
- Parveen Malik
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India
| | - Jitendra Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India
- National Agri-Food Biotechnology Institute (NABI), Sector 81, Sahibzada Ajit Singh Nagar, 140306 Punjab India
| | - Sahadev Singh
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India
| | - Shiveta Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India
| | - Prabina Kumar Meher
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Mukesh Kumar Sharma
- Department of Mathematics, Chaudhary Charan Singh University, Meerut 250004, India
| | - Joy Kumar Roy
- National Agri-Food Biotechnology Institute (NABI), Sector 81, Sahibzada Ajit Singh Nagar, 140306 Punjab India
| | - Pradeep Kumar Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India
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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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20
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Liu Y, Wang W. Characterization of the GRAS gene family reveals their contribution to the high adaptability of wheat. PeerJ 2021; 9:e10811. [PMID: 33665016 PMCID: PMC7908883 DOI: 10.7717/peerj.10811] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/30/2020] [Indexed: 01/18/2023] Open
Abstract
GRAS transcription factors play important roles in many processes of plant development as well as abiotic and biotic stress responses. However, little is known about this gene family in bread wheat (Triticum aestivum), one of the most important crops worldwide. The completion of a quality draft genome allows genome-wide detection and evolutionary analysis of the GRAS gene family in wheat. In this study, 188 TaGRAS genes were detected and divided into 12 subfamilies based on phylogenetic analyses: DELLA, DLT, HAM, LISCL, SCL3, SCL4/7, SCR, SHR, PAT1, Os19, Os4 and LAS. Tandem and segmental duplications are the main contributors to the expansion of TaGRAS, which may contribute to the adaptation of wheat to various environmental conditions. A high rate of homoeolog retention during hexaploidization was detected, suggesting the nonredundancy and biological importance of TaGRAS homoeologs. Systematic analyses of TaGRAS indicated the conserved expression pattern and function of the same subfamily during evolution. In addition, we detected five genes belonging to the LISCL subfamily induced by both biotic and abiotic stresses and they may be potential targets for further research through gene editing. Using degradome and ChIP-seq data, we identified the targets of miR171 and histone modifications and further analyzed the contribution of epigenetic modification to the subfunctionalization of TaGRAS. This study laid a foundation for further functional elucidation of TaGRAS genes.
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Affiliation(s)
- Yanfeng Liu
- School of Resources and Environmental Engineering, Ludong University, Yantai, Shandong, China
| | - Wei Wang
- School of Resources and Environmental Engineering, Ludong University, Yantai, Shandong, China
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21
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Yang S, Ma S, Qiu R, Guang Q, Lv Y, Dong Y, Wu J, Song L. Comparative analysis of RNA-Seq data reveals adventitious root development is mediated by ChIFNα in lotus japonicus. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1859946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Shimei Yang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou Key Lab of Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, People’s Republic of China
| | - Siyu Ma
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou Key Lab of Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, People’s Republic of China
| | - Riguang Qiu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou Key Lab of Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, People’s Republic of China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, Guangdong, People’s Republic of China
| | - Qiao Guang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou Key Lab of Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, People’s Republic of China
| | - Yun Lv
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou Key Lab of Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, People’s Republic of China
| | - Yaping Dong
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou Key Lab of Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, People’s Republic of China
| | - Jiahai Wu
- Institute of Fruit Research, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, People’s Republic of China
| | - Li Song
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou Key Lab of Agro-Bioengineering, College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, People’s Republic of China
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Yang Z, Wang K, Aziz U, Zhao C, Zhang M. Evaluation of duplicated reference genes for quantitative real-time PCR analysis in genome unknown hexaploid oat ( Avena sativa L.). PLANT METHODS 2020; 16:138. [PMID: 33072174 PMCID: PMC7560290 DOI: 10.1186/s13007-020-00679-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/05/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Oat (Avena sativa L.), a hexaploid crop with unknown genome, has valuable nutritional, medicinal and pharmaceutical uses. However, no suitable RGs (reference genes) for qPCR (quantitative real-time PCR) has been documented for oat yet. Single-copy gene is often selected as RG, which is challengeable or impactable in unexplored polyploids. RESULTS In this study, eleven candidate RGs, including four duplicated genes, were selected from oat transcriptome. The stability and the optimal combination of these candidate RGs were assessed in 18 oat samples by using four statistical algorithms including the ΔCt method, geNorm, NormFinder and BestKeeper. The most stable RGs for "all samples", "shoots and roots of seedlings", "developing seeds" and "developing endosperms" were EIF4A (Eukaryotic initiation factor 4A-3), UBC21 (Ubiquitin-Conjugating Enzyme 21), EP (Expressed protein) and EIF4A respectively. Among these RGs, UBC21 was a four-copy duplicated gene. The reliability was validated by the expression patterns of four various genes normalized to the most and the least stable RGs in different sample sets. CONCLUSIONS Results provide a proof of concept that the duplicated RG is feasible for qPCR in polyploids. To our knowledge, this study is the first systematic research on the optimal RGs for accurate qPCR normalization of gene expression in different organs and tissues of oat.
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Affiliation(s)
- Zheng Yang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Kai Wang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Usman Aziz
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Cuizhu Zhao
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Meng Zhang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
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Dong J, Zheng Y, Fu Y, Wang J, Yuan S, Wang Y, Zhu Q, Ou X, Li G, Kang G. PDIL1-2 can indirectly and negatively regulate expression of the AGPL1 gene in bread wheat. Biol Res 2019; 52:56. [PMID: 31699158 PMCID: PMC6839113 DOI: 10.1186/s40659-019-0263-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 10/25/2019] [Indexed: 12/02/2022] Open
Abstract
Background ADP-glucose pyrophosphorylase (AGPase), the key enzyme in plant starch biosynthesis, is a heterotetramer composed of two identical large subunits and two identical small subunits. AGPase has plastidial and cytosolic isoforms in higher plants, whereas it is mainly detected in the cytosol of grain endosperms in cereal crops. Our previous results have shown that the expression of the TaAGPL1 gene, encoding the cytosolic large subunit of wheat AGPase, temporally coincides with the rate of starch accumulation and that its overexpression dramatically increases wheat AGPase activity and the rate of starch accumulation, suggesting an important role. Methods In this study, we performed yeast one-hybrid screening using the promoter of the TaAGPL1 gene as bait and a wheat grain cDNA library as prey to screen out the upstream regulators of TaAGPL1 gene. And the barley stripe mosaic virus-induced gene-silencing (BSMV-VIGS) method was used to verify the functional characterization of the identified regulators in starch biosynthesis. Results Disulfide isomerase 1-2 protein (TaPDIL1-2) was screened out, and its binding to the TaAGPL1-1D promoter was further verified using another yeast one-hybrid screen. Transiently silenced wheat plants of the TaPDIL1-2 gene were obtained by using BSMV-VIGS method under field conditions. In grains of BSMV-VIGS-TaPDIL1-2-silenced wheat plants, the TaAGPL1 gene transcription levels, grain starch contents, and 1000-kernel weight also significantly increased. Conclusions As important chaperones involved in oxidative protein folding, PDIL proteins have been reported to form hetero-dimers with some transcription factors, and thus, our results suggested that TaPDIL1-2 protein could indirectly and negatively regulate the expression of the TaAGPL1 gene and function in starch biosynthesis.
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Affiliation(s)
- Jie Dong
- The National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzihu College District, Zhengzhou, 450046, China
| | - Yongxing Zheng
- The National Engineering Research Center for Wheat, Henan Agricultural University, #63 Nongye Road, Zhengzhou, 450046, Henan, China
| | - Yihan Fu
- The National Engineering Research Center for Wheat, Henan Agricultural University, #63 Nongye Road, Zhengzhou, 450046, Henan, China
| | - Jinxi Wang
- The National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzihu College District, Zhengzhou, 450046, China
| | - Shasha Yuan
- The National Engineering Research Center for Wheat, Henan Agricultural University, #63 Nongye Road, Zhengzhou, 450046, Henan, China
| | - Yonghua Wang
- The National Engineering Research Center for Wheat, Henan Agricultural University, #63 Nongye Road, Zhengzhou, 450046, Henan, China
| | - Qidi Zhu
- The School of Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Xingqi Ou
- The School of Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Gezi Li
- The National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzihu College District, Zhengzhou, 450046, China.
| | - Guozhang Kang
- The National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzihu College District, Zhengzhou, 450046, China. .,The National Engineering Research Center for Wheat, Henan Agricultural University, #63 Nongye Road, Zhengzhou, 450046, Henan, China.
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Niu X, Chen S, Li J, Liu Y, Ji W, Li H. Genome-wide identification of GRAS genes in Brachypodium distachyon and functional characterization of BdSLR1 and BdSLRL1. BMC Genomics 2019; 20:635. [PMID: 31387534 PMCID: PMC6683515 DOI: 10.1186/s12864-019-5985-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 07/19/2019] [Indexed: 12/02/2022] Open
Abstract
Background As one of the most important transcription factor families, GRAS proteins are involved in numerous regulatory processes, especially plant growth and development. However, they have not been systematically analyzed in Brachypodium distachyon, a new model grass. Results In this study, 48 BdGRAS genes were identified. Duplicated genes account for 41.7% of them and contribute to the expansion of this gene family. 33, 39, 35 and 35 BdGRAS genes were identified by synteny with their orthologs in rice, sorghum, maize and wheat genome, respectively, indicating close relationships among these species. Based on their phylogenic relationships to GRAS genes in rice and maize, BdGRAS genes can be divided into ten subfamilies in which members of the same subfamily showed similar protein sequences, conserved motifs and gene structures, suggesting possible conserved functions. Although expression variation is high, some BdGRAS genes are tissue-specific, phytohormones- or abiotic stresses-responsive, and they may play key roles in development, signal transduction pathways and stress responses. In addition, DELLA genes BdSLR1 and BdSLRL1 were functionally characterized to play a role in plant growth via the GA signal pathway, consistent with GO annotations and KEGG pathway analyses. Conclusions Systematic analyses of BdGRAS genes indicated that members of the same subfamily may play similar roles. This was supported by the conserved functions of BdSLR1 and BdSLRL1 in GA pathway. These results laid a foundation for further functional elucidation of BdGRAS genes, especially, BdSLR1 and BdSLRL1. Electronic supplementary material The online version of this article (10.1186/s12864-019-5985-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xin Niu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Shoukun Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Jiawei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Yue Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China.
| | - Haifeng Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China.
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Tavakol E. Virus-Induced Gene Silencing (VIGS) in Aegilops tauschii and Its Use in Functional Analysis of AetDREB2. Mol Biotechnol 2017; 60:41-48. [PMID: 29196985 DOI: 10.1007/s12033-017-0042-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Among the available reverse genetic approaches for studying gene function, virus-induced gene silencing (VIGS) has several advantages. It allows rapid characterization of gene function independent of stable transformation, which is basically difficult to achieve in monocots, and offers the potential to silence individual or multiple genes of a gene family. In order to establish a VIGS system in Aegilops tauschii, modified vectors derived from Barley stripe mosaic virus (BSMV) were used for silencing a phytoene desaturase gene that provides a convenient visual reporter for silencing. The results demonstrated a high efficiency of BSMV-VIGS in A. tauschii. Moreover, the BSMV-VIGS system was used to target a 354 bp specific region of the Dehydration-responsive element-binding (AetDreb2) gene, resulting in successful silencing of the gene in A. tauschii plants, as verified by real-time qRT-PCR. Indeed, in comparison with plants that were inoculated with an empty vector (BSMV:00), a faster rate of wilting and a lower relative water content were observed in plants inoculated with BSMV:AetDreb2 when they were exposed to drought stress. Therefore, BSMV-VIGS can be efficiently employed as a novel tool for reverse genetics in A. tauschii. It can also be used to study the effects of polyploidization on the gene function by a comparative analysis between bread wheat and its diploid progenitor.
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Affiliation(s)
- Elahe Tavakol
- Department of Crop Production and Plant Breeding, College of Agriculture, Shiraz University, 7144165186, Shiraz, Iran.
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Liu H, Qin J, Fan H, Cheng J, Li L, Liu Z. Genome-wide identification, phylogeny and expression analyses of SCARECROW- LIKE( SCL) genes in millet ( Setaria italica). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:629-640. [PMID: 28878501 PMCID: PMC5567716 DOI: 10.1007/s12298-017-0455-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 05/13/2017] [Accepted: 05/29/2017] [Indexed: 06/04/2023]
Abstract
As a member of the GRAS gene family, SCARECROW-LIKE (SCL) genes encode transcriptional regulators that are involved in plant information transmission and signal transduction. In this study, 44 SCL genes including two SCARECROW genes in millet were identified to be distributed on eight chromosomes, except chromosome 6. All the millet genes contain motifs 6-8, indicating that these motifs are conserved during the evolution. SCL genes of millet were divided into eight groups based on the phylogenetic relationship and classification of Arabidopsis SCL genes. Several putative millet orthologous genes in Arabidopsis, maize and rice were identified. High throughput RNA sequencing revealed that the expressions of millet SCL genes in root, stem, leaf, spica, and along leaf gradient varied greatly. Analyses combining the gene expression patterns, gene structures, motif compositions, promoter cis-elements identification, alternative splicing of transcripts and phylogenetic relationship of SCL genes indicate that the these genes may play diverse functions. Functionally characterized SCL genes in maize, rice and Arabidopsis would provide us some clues for future characterization of their homologues in millet. To the best of our knowledge, this is the first study of millet SCL genes at the genome wide level. Our work provides a useful platform for functional analysis of SCL genes in millet, a model crop for C4 photosynthesis and bioenergy studies.
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Affiliation(s)
- Hongyun Liu
- College of Life Sciences, Hebei University, Baoding, 071002 People’s Republic of China
| | - Jiajia Qin
- School of Physical Sciences, University of the Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Hui Fan
- College of Life Sciences, Hebei University, Baoding, 071002 People’s Republic of China
| | - Jinjin Cheng
- College of Life Sciences, Hebei University, Baoding, 071002 People’s Republic of China
| | - Lin Li
- College of Biology, Hunan University, Changsha, 410082 People’s Republic of China
| | - Zheng Liu
- College of Life Sciences, Hebei University, Baoding, 071002 People’s Republic of China
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Zhang J, Yu D, Zhang Y, Liu K, Xu K, Zhang F, Wang J, Tan G, Nie X, Ji Q, Zhao L, Li C. Vacuum and Co-cultivation Agroinfiltration of (Germinated) Seeds Results in Tobacco Rattle Virus (TRV) Mediated Whole-Plant Virus-Induced Gene Silencing (VIGS) in Wheat and Maize. FRONTIERS IN PLANT SCIENCE 2017; 8:393. [PMID: 28382049 PMCID: PMC5360694 DOI: 10.3389/fpls.2017.00393] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/07/2017] [Indexed: 05/06/2023]
Abstract
Tobacco rattle virus (TRV)-mediated virus-induced gene silencing (VIGS) has been frequently used in dicots. Here we show that it can also be used in monocots, by presenting a system involving use of a novel infiltration solution (containing acetosyringone, cysteine, and Tween 20) that enables whole-plant level VIGS of (germinated) seeds in wheat and maize. Using the established system, phytoene desaturase (PDS) genes were successfully silenced, resulting in typical photo-bleaching symptoms in the leaves of treated wheat and maize. In addition, three wheat homoeoalleles of MLO, a key gene repressing defense responses to powdery mildew in wheat, were simultaneously silenced in susceptible wheat with this system, resulting in it becoming resistant to powdery mildew. The system has the advantages generally associated with TRV-mediated VIGS systems (e.g., high-efficiency, mild virus infection symptoms, and effectiveness in different organs). However, it also has the following further advantages: (germinated) seed-stage agroinfiltration; greater rapidity and convenience; whole-plant level gene silencing; adequately stable transformation; and suitability for studying functions of genes involved in seed germination and early plant development stages.
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Affiliation(s)
- Ju Zhang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
| | - Deshui Yu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
| | - Yi Zhang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
- College of Agronomy, Henan Agricultural University, ZhengzhouChina
| | - Kun Liu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
| | - Kedong Xu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
| | - Fuli Zhang
- College of Life Science and Agronomy, Zhoukou Normal University, ZhoukouChina
| | - Jian Wang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
| | - Guangxuan Tan
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
| | - Xianhui Nie
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
- College of Life Science and Agronomy, Zhoukou Normal University, ZhoukouChina
| | - Qiaohua Ji
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
- College of Life Science and Agronomy, Zhoukou Normal University, ZhoukouChina
| | - Lu Zhao
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
- College of Life Science and Agronomy, Zhoukou Normal University, ZhoukouChina
| | - Chengwei Li
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, ZhoukouChina
- Henan Key Laboratory of Crop Molecular Breeding and Bioreactor, ZhoukouChina
- College of Life Science and Technology, Henan Institute of Science and Technology, XinxiangChina
- *Correspondence: Chengwei Li,
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Abstract
In the past two decades, Chinese scientists have achieved significant progress on three aspects of wheat genetic transformation. First, the wheat transformation platform has been established and optimized to improve the transformation efficiency, shorten the time required from starting of transformation procedure to the fertile transgenic wheat plants obtained as well as to overcome the problem of genotype-dependent for wheat genetic transformation in wide range of wheat elite varieties. Second, with the help of many emerging techniques such as CRISPR/cas9 function of over 100 wheat genes has been investigated. Finally, modern technology has been combined with the traditional breeding technique such as crossing to accelerate the application of wheat transformation. Overall, the wheat end-use quality and the characteristics of wheat stress tolerance have been improved by wheat genetic engineering technique. So far, wheat transgenic lines integrated with quality-improved genes and stress tolerant genes have been on the way of Production Test stage in the field. The debates and the future studies on wheat transformation have been discussed, and the brief summary of Chinese wheat breeding research history has also been provided in this review.
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Liu G, Wu Y, Xu M, Gao T, Wang P, Wang L, Guo T, Kang G. Virus-Induced Gene Silencing Identifies an Important Role of the TaRSR1 Transcription Factor in Starch Synthesis in Bread Wheat. Int J Mol Sci 2016; 17:E1557. [PMID: 27669224 PMCID: PMC5085620 DOI: 10.3390/ijms17101557] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/28/2016] [Accepted: 09/07/2016] [Indexed: 12/16/2022] Open
Abstract
The function of a wheat starch regulator 1 (TaRSR1) in regulating the synthesis of grain storage starch was determined using the barley stripe mosaic virus-virus induced gene-silencing (BSMV-VIGS) method in field experiments. Chlorotic stripes appeared on the wheat spikes infected with barley stripe mosaic virus-virus induced gene-silencing- wheat starch regulator 1 (BSMV-VIGS-TaRSR1) at 15 days after anthesis, at which time the transcription levels of the TaRSR1 gene significantly decreased. Quantitative real-time PCR was also used to measure the transcription levels of 26 starch synthesis-related enzyme genes in the grains of BSMV-VIGS-TaRSR1-silenced wheat plants at 20, 27, and 31 days after anthesis. The results showed that the transcription levels of some starch synthesis-related enzyme genes were markedly induced at different sampling time points: TaSSI, TaSSIV, TaBEIII, TaISA1, TaISA3, TaPHOL, and TaDPE1 genes were induced at each of the three sampling time points and TaAGPS1-b, TaAGPL1, TaAGPL2, TaSSIIb, TaSSIIc, TaSSIIIb, TaBEI, TaBEIIa, TaBEIIb, TaISA2, TaPHOH, and TaDPE2 genes were induced at one sampling time point. Moreover, both the grain starch contents, one thousand kernel weights, grain length and width of BSMV-VIGS-TaRSR1-infected wheat plants significantly increased. These results suggest that TaRSR1 acts as a negative regulator and plays an important role in starch synthesis in wheat grains by temporally regulating the expression of specific starch synthesis-related enzyme genes.
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Affiliation(s)
- Guoyu Liu
- The Collaborative Innovation Center of Henan Food Crops, Henan Agricultural University, Zhengzhou 450002, China.
| | - Yufang Wu
- The Collaborative Innovation Center of Henan Food Crops, Henan Agricultural University, Zhengzhou 450002, China.
- The National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China.
| | - Mengjun Xu
- The National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China.
- The National Engineering Research Centre for Wheat, Henan Agricultural University, Zhengzhou 450002, China.
| | - Tian Gao
- The National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China.
- The National Engineering Research Centre for Wheat, Henan Agricultural University, Zhengzhou 450002, China.
| | - Pengfei Wang
- The Collaborative Innovation Center of Henan Food Crops, Henan Agricultural University, Zhengzhou 450002, China.
- The National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China.
| | - Lina Wang
- The Collaborative Innovation Center of Henan Food Crops, Henan Agricultural University, Zhengzhou 450002, China.
- The National Engineering Research Centre for Wheat, Henan Agricultural University, Zhengzhou 450002, China.
| | - Tiancai Guo
- The Collaborative Innovation Center of Henan Food Crops, Henan Agricultural University, Zhengzhou 450002, China.
- The National Engineering Research Centre for Wheat, Henan Agricultural University, Zhengzhou 450002, China.
| | - Guozhang Kang
- The Collaborative Innovation Center of Henan Food Crops, Henan Agricultural University, Zhengzhou 450002, China.
- The National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China.
- The National Engineering Research Centre for Wheat, Henan Agricultural University, Zhengzhou 450002, China.
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30
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Feller U. Drought stress and carbon assimilation in a warming climate: Reversible and irreversible impacts. JOURNAL OF PLANT PHYSIOLOGY 2016; 203:84-94. [PMID: 27083537 DOI: 10.1016/j.jplph.2016.04.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 04/01/2016] [Accepted: 04/04/2016] [Indexed: 06/05/2023]
Abstract
Global change is characterized by increased CO2 concentration in the atmosphere, increasing average temperature and more frequent extreme events including drought periods, heat waves and flooding. Especially the impacts of drought and of elevated temperature on carbon assimilation are considered in this review. Effects of extreme events on the subcellular level as well as on the whole plant level may be reversible, partially reversible or irreversible. The photosynthetically active biomass depends on the number and the size of mature leaves and the photosynthetic activity in this biomass during stress and subsequent recovery phases. The total area of active leaves is determined by leaf expansion and senescence, while net photosynthesis per leaf area is primarily influenced by stomatal opening (stomatal conductance), mesophyll conductance, activity of the photosynthetic apparatus (light absorption and electron transport, activity of the Calvin cycle) and CO2 release by decarboxylation reactions (photorespiration, dark respiration). Water status, stomatal opening and leaf temperature represent a "magic triangle" of three strongly interacting parameters. The response of stomata to altered environmental conditions is important for stomatal limitations. Rubisco protein is quite thermotolerant, but the enzyme becomes at elevated temperature more rapidly inactivated (decarbamylation, reversible effect) and must be reactivated by Rubisco activase (carbamylation of a lysine residue). Rubisco activase is present under two forms (encoded by separate genes or products of alternative splicing of the pre-mRNA from one gene) and is very thermosensitive. Rubisco activase was identified as a key protein for photosynthesis at elevated temperature (non-stomatal limitation). During a moderate heat stress Rubisco activase is reversibly inactivated, but during a more severe stress (higher temperature and/or longer exposure) the protein is irreversibly inactivated, insolubilized and finally degraded. On the level of the leaf, this loss of photosynthetic activity may still be reversible when new Rubisco activase is produced by protein synthesis. Rubisco activase as well as enzymes involved in the detoxification of reactive oxygen species or in osmoregulation are considered as important targets for breeding crop plants which are still productive under drought and/or at elevated leaf temperature in a changing climate.
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Affiliation(s)
- Urs Feller
- Institute of Plant Sciences and Oeschger Centre for Climate Change Research (OCCR), University of Bern, Altenbergrain 21, CH-3013 Bern, Switzerland.
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Grimplet J, Agudelo-Romero P, Teixeira RT, Martinez-Zapater JM, Fortes AM. Structural and Functional Analysis of the GRAS Gene Family in Grapevine Indicates a Role of GRAS Proteins in the Control of Development and Stress Responses. FRONTIERS IN PLANT SCIENCE 2016; 7:353. [PMID: 27065316 PMCID: PMC4811876 DOI: 10.3389/fpls.2016.00353] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/07/2016] [Indexed: 05/18/2023]
Abstract
GRAS transcription factors are involved in many processes of plant growth and development (e.g., axillary shoot meristem formation, root radial patterning, nodule morphogenesis, arbuscular development) as well as in plant disease resistance and abiotic stress responses. However, little information is available concerning this gene family in grapevine (Vitis vinifera L.), an economically important woody crop. We performed a model curation of GRAS genes identified in the latest genome annotation leading to the identification of 52 genes. Gene models were improved and three new genes were identified that could be grapevine- or woody-plant specific. Phylogenetic analysis showed that GRAS genes could be classified into 13 groups that mapped on the 19 V. vinifera chromosomes. Five new subfamilies, previously not characterized in other species, were identified. Multiple sequence alignment showed typical GRAS domain in the proteins and new motifs were also described. As observed in other species, both segmental and tandem duplications contributed significantly to the expansion and evolution of the GRAS gene family in grapevine. Expression patterns across a variety of tissues and upon abiotic and biotic conditions revealed possible divergent functions of GRAS genes in grapevine development and stress responses. By comparing the information available for tomato and grapevine GRAS genes, we identified candidate genes that might constitute conserved transcriptional regulators of both climacteric and non-climacteric fruit ripening. Altogether this study provides valuable information and robust candidate genes for future functional analysis aiming at improving the quality of fleshy fruits.
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Affiliation(s)
- Jérôme Grimplet
- Instituto de Ciencias de la Vid y del Vino (Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja)Logroño, Spain
| | | | - Rita T. Teixeira
- Faculdade de Ciências de Lisboa, BioISI, Universidade de LisboaLisboa, Portugal
| | - Jose M. Martinez-Zapater
- Instituto de Ciencias de la Vid y del Vino (Consejo Superior de Investigaciones Científicas-Universidad de La Rioja-Gobierno de La Rioja)Logroño, Spain
| | - Ana M. Fortes
- Faculdade de Ciências de Lisboa, BioISI, Universidade de LisboaLisboa, Portugal
- Instituto de Tecnologia de Química Biológica, Biotecnologia de Células VegetaisOeiras, Portugal
- *Correspondence: Ana M. Fortes
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Borah L, Baruah KK. Nitrous oxide emission and mitigation from wheat agriculture: association of physiological and anatomical characteristics of wheat genotypes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:709-721. [PMID: 26335526 DOI: 10.1007/s11356-015-5299-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 08/21/2015] [Indexed: 06/05/2023]
Abstract
Agriculture is an important source of emission of the greenhouse gas nitrous oxide (N2O). The observed differences in N2O emission among different varieties of agricultural crops can be a key factor for developing N2O emission reduction strategies. N2O emissions were estimated from three varieties of wheat viz. Sonalika, DBW 39, and K 0307 during 2010-2011 in an attempt to identify plant physiological and anatomical factors contributing to differences in gas emissions within the varieties. Sonalika was identified as a low N2O emitting variety and DBW 39 as high emitting when grown in a uniform field condition. The experiment was repeated in 2011-2012 selecting low emitting Sonalika and high emitting variety DBW 39 for further confirmation of the results obtained during the first year of experimentation. Important plant factors namely rate of photosynthesis and transpiration in flag leaf, stomatal frequency of adaxial flag leaf surface, and size of the xylem vessels (mean vessel size of node, stem, and root) were studied, and their relationship with N2O flux was worked out. A good correlation between transpiration and N2O flux was observed in this study. Scanning electron microscopic investigation revealed strong association of flag leaf stomatal frequency and xylem size with N2O emission. Sonalika, identified as low N2O emitting variety during both the years of study, also recorded higher grain yield due to its higher efficiency of photosynthate allocation toward the developing grains. The observed differences in N2O emission are considered to be due largely to genetic differences in the wheat genotypes.
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Affiliation(s)
- Leena Borah
- Department of Environmental Science, Tezpur Central University, Tezpur, 784028, Assam, India
| | - Kushal Kumar Baruah
- Department of Environmental Science, Tezpur Central University, Tezpur, 784028, Assam, India.
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