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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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Hu Y, Dai Z, Huang J, Han M, Wang Z, Jiao W, Gao Z, Liu X, Liu L, Ma Z. Genome-wide identification and expression analysis of the glutamate receptor gene family in sweet potato and its two diploid relatives. FRONTIERS IN PLANT SCIENCE 2023; 14:1255805. [PMID: 38179475 PMCID: PMC10764598 DOI: 10.3389/fpls.2023.1255805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 11/06/2023] [Indexed: 01/06/2024]
Abstract
Plant glutamate receptor (GLR) homologs are crucial calcium channels that play an important role in plant development, signal transduction, and response to biotic and abiotic stresses. However, the GLR gene family has not yet been thoroughly and systematically studied in sweet potato. In this study, a total of 37 GLR genes were identified in the cultivated hexaploid sweet potato (Ipomoea batatas), and 32 GLR genes were discovered in each of the two diploid relatives (Ipomoea trifida and Ipomoea triloba) for the first time. Based on their evolutionary relationships to those of Arabidopsis, these GLRs were split into five subgroups. We then conducted comprehensive analysis to explore their physiological properties, protein interaction networks, promoter cis-elements, chromosomal placement, gene structure, and expression patterns. The results indicate that the homologous GLRs of the cultivated hexaploid sweet potato and its two relatives are different. These variations are reflected in their functions related to plant growth, hormonal crosstalk, development of tuberous roots, resistance to root rot, and responses to abiotic stress factors, all of which are governed by specific individual GLR genes. This study offers a comprehensive analysis of GLR genes in sweet potato and its two diploid relatives. It also provides a theoretical basis for future research into their regulatory mechanisms, significantly influencing the field of molecular breeding in sweet potatoes.
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Affiliation(s)
- Yaya Hu
- Hebei Key Laboratory of Crop Genetics and Breeding, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Zhuoru Dai
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, College of Agronomy & Biotechnology, China Agricultural University, Beijing, China
| | - Jinan Huang
- Hebei Key Laboratory of Crop Genetics and Breeding, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Meikun Han
- Hebei Key Laboratory of Crop Genetics and Breeding, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Zhiwei Wang
- Department of Agriculture Forestry and Biological Engineering, Baoding Vocational and Technical College, Baoding, Hebei, China
| | - Weijing Jiao
- Hebei Key Laboratory of Crop Genetics and Breeding, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Zhiyuan Gao
- Hebei Key Laboratory of Crop Genetics and Breeding, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Xinliang Liu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China
| | - Lanfu Liu
- Hebei Key Laboratory of Crop Genetics and Breeding, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Zhimin Ma
- Hebei Key Laboratory of Crop Genetics and Breeding, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, 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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Rana D, Sharma P, Arpita K, Srivastava H, Sharma S, Gaikwad K. Genome-wide identification and characterization of GRAS gene family in pigeonpea ( Cajanus cajan (L.) Millspaugh). 3 Biotech 2023; 13:363. [PMID: 37840881 PMCID: PMC10570252 DOI: 10.1007/s13205-023-03782-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023] Open
Abstract
The GRAS proteins are plant-specific transcription factors (TFs) that play a crucial role in various plant physiological processes, including tissue development and stress responses. To date, GRAS family has been comprehensively characterized in Arabidopsis, soybean, rice, chickpea and other plant species. To understand the structural and functional aspects of pigeonpea (C. cajan), we identified 60 putative GRAS (CcGRAS) genes from pigeonpea genome and further analysed their physicochemical properties, subcellular locations, evolutionary classification, exon-intron structures, conserved domains, gene duplication events and cis-promoter regions. Based on the sequence similarity, CcGRAS family was clustered into 9 subfamilies and the genes with a similar structure and motif distribution were clustered in the same group. The gene duplication studies revealed that these genes were derived from tandem and dispersed duplication events. The cis-promoter regulatory analysis of CcGRAS genes indicated the presence of three types of cis-acting elements including light-responsive, hormone-responsive and plant growth and development related. The expression profiling of CcGRAS genes revealed their tissue-specific functions and differential nature. Collectively, this study highlights relevant functional and regulatory elements of GRAS family in pigeonpea creating a significant resource for future functional studies. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03782-x.
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Affiliation(s)
- Divyansh Rana
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313 India
| | - Priya Sharma
- Department of Biotechnology, Jamia Hamdard, New Delhi, Delhi 110062 India
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
| | - Kumari Arpita
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
| | - Harsha Srivastava
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
| | - Sandhya Sharma
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
| | - Kishor Gaikwad
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
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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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Xia S, Zhang H, He S. Genome-Wide Identification and Expression Analysis of ACTIN Family Genes in the Sweet Potato and Its Two Diploid Relatives. Int J Mol Sci 2023; 24:10930. [PMID: 37446107 DOI: 10.3390/ijms241310930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
ACTINs are structural proteins widely distributed in plants. They are the main components of microfilaments and participate in many crucial physiological activities, including the maintenance of cell shape and cytoplasmic streaming. Meanwhile, ACTIN, as a housekeeping gene, is widely used in qRT-PCR analyses of plants. However, ACTIN family genes have not been explored in the sweet potato. In this study, we identified 30, 39, and 44 ACTINs in the cultivated hexaploid sweet potato (Ipomoea batatas, 2n = 6x = 90) and its two diploid relatives, Ipomoea trifida (2n = 2x = 30) and Ipomoea triloba (2n = 2x = 30), respectively, via analysis of their genome structure and by phylogenetic characterization. These ACTINs were divided into six subgroups according to their phylogenetic relationships with Arabidopsis thaliana. The physiological properties of the protein, chromosome localization, phylogenetic relationship, gene structure, promoter cis-elements, protein interaction networks, and expression patterns of these 113 ACTINs were systematically investigated. The results suggested that homologous ACTINs are differentiated in the sweet potato and its two diploid relatives, and play various vital roles in plant growth, tuberous root development, hormone crosstalk, and abiotic stress responses. Some stable ACTINs that could be used as internal reference genes were found in the sweet potato and its two diploid relatives, e.g., IbACTIN18, -20, and -16.2; ItfACTIN2.2, -16, and -10; ItbACTIN18 and -19.1. This work provides a comprehensive comparison and furthers our understanding of the ACTIN genes in the sweet potato and its two diploid relatives, thereby supplying a theoretical foundation for their functional study and further facilitating the molecular breeding of sweet potatoes.
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Affiliation(s)
- Shuanghong Xia
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
| | - Huan Zhang
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Shaozhen He
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis & Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing 100193, China
- Sanya Institute of China Agricultural University, Sanya 572025, China
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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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Chang J, Fan D, Lan S, Cheng S, Chen S, Lin Y, Cao S. Genome-Wide Identification, Expression and Stress Analysis of the GRAS Gene Family in Phoebe bournei. PLANTS (BASEL, SWITZERLAND) 2023; 12:2048. [PMID: 37653964 PMCID: PMC10222183 DOI: 10.3390/plants12102048] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 09/02/2023]
Abstract
GRAS genes are important transcriptional regulators in plants that govern plant growth and development through enhancing plant hormones, biosynthesis, and signaling pathways. Drought and other abiotic factors may influence the defenses and growth of Phoebe bournei, which is a superb timber source for the construction industry and building exquisite furniture. Although genome-wide identification of the GRAS gene family has been completed in many species, that of most woody plants, particularly P. bournei, has not yet begun. We performed a genome-wide investigation of 56 PbGRAS genes, which are unequally distributed across 12 chromosomes. They are divided into nine subclades. Furthermore, these 56 PbGRAS genes have a substantial number of components related to abiotic stress responses or phytohormone transmission. Analysis using qRT-PCR showed that the expression of four PbGRAS genes, namely PbGRAS7, PbGRAS10, PbGRAS14 and PbGRAS16, was differentially increased in response to drought, salt and temperature stresses, respectively. We hypothesize that they may help P. bournei to successfully resist harsh environmental disturbances. In this work, we conducted a comprehensive survey of the GRAS gene family in P. bournei plants, and the results provide an extensive and preliminary resource for further clarification of the molecular mechanisms of the GRAS gene family in P. bournei in response to abiotic stresses and forestry improvement.
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Affiliation(s)
- Jiarui Chang
- International College, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Dunjin Fan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (D.F.); (S.C.); (S.C.)
| | - Shuoxian Lan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shengze Cheng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (D.F.); (S.C.); (S.C.)
| | - Shipin Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (D.F.); (S.C.); (S.C.)
| | - Yuling Lin
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shijiang Cao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (D.F.); (S.C.); (S.C.)
- Key Laboratory of Fujian Universities for Stress Physiology Ecology and Molecular Biology of Forest, Fuzhou 350002, China
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9
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Li M, Zhou Y, Li K, Guo H. Genome-Wide Comparative Analysis of the R2R3-MYB Gene Family in Six Ipomoea Species and the Identification of Anthocyanin-Related Members in Sweet Potatoes. PLANTS (BASEL, SWITZERLAND) 2023; 12:1731. [PMID: 37111954 PMCID: PMC10140993 DOI: 10.3390/plants12081731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 06/19/2023]
Abstract
Sweet potatoes (Ipomoea batatas) are one of the important tuberous root crops cultivated worldwide, and thier storage roots are rich in antioxidants, such as anthocyanins. R2R3-MYB is a large gene family involved in various biological processes, including anthocyanin biosynthesis. However, few reports about the R2R3-MYB gene family of sweet potatoes have been released to date. In the present study, a total of 695 typical R2R3-MYB genes were identified in six Ipomoea species, including 131 R2R3-MYB genes in sweet potatoes. A maximum likelihood phylogenetic analysis divided these genes into 36 clades, referring to the classification of 126 R2R3-MYB proteins of Arabidopsis. Clade C25(S12) has no members in six Ipomoea species, whereas four clades (i.e., clade C21, C26, C30, and C36), including 102 members, had no members in Arabidopsis, and they were identified as Ipomoea-specific clades. The identified R2R3-MYB genes were unevenly distributed on all chromosomes in six Ipomoea species genomes, and the collinearity analysis among hexaploid I. batatas and another five diploid Ipomoea species suggested that the sweet potato genome might have undergone a larger chromosome rearrangement during the evolution process. Further analyses of gene duplication events showed that whole-genome duplication, transposed duplication, and dispersed duplication events were the primary forces driving the R2R3-MYB gene family expansion of Ipomoea plants, and these duplicated genes experienced strong purifying selection because of their Ka/Ks ratio, which is less than 1. Additionally, the genomic sequence length of 131 IbR2R3-MYBs varied from 923 bp to ~12.9 kb with a mean of ~2.6 kb, and most of them had more than three exons. The Motif 1, 2, 3, and 4 formed typical R2 and R3 domains and were identified in all IbR2R3-MYB proteins. Finally, based on multiple RNA-seq datasets, two IbR2R3-MYB genes (IbMYB1/g17138.t1 and IbMYB113/g17108.t1) were relatively highly expressed in pigmented leaves and tuberous root flesh and skin, respectively; thus, they were identified to regulate tissue-specific anthocyanin accumulation in sweet potato. This study provides a basis for the evolution and function of the R2R3-MYB gene family in sweet potatoes and five other Ipomoea species.
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Affiliation(s)
- Maoxing Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.Z.); (K.L.)
- Yunnan Engineering Research Center of Tuber and Root Crop Bio-Breeding and Healthy Seed Propagation, Yunnan Agricultural University, Kunming 650201, China
| | - Yuanping Zhou
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.Z.); (K.L.)
- Yunnan Engineering Research Center of Tuber and Root Crop Bio-Breeding and Healthy Seed Propagation, Yunnan Agricultural University, Kunming 650201, China
| | - Kaifeng Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.Z.); (K.L.)
- Yunnan Engineering Research Center of Tuber and Root Crop Bio-Breeding and Healthy Seed Propagation, Yunnan Agricultural University, Kunming 650201, China
| | - Huachun Guo
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (M.L.); (Y.Z.); (K.L.)
- Yunnan Engineering Research Center of Tuber and Root Crop Bio-Breeding and Healthy Seed Propagation, Yunnan Agricultural University, Kunming 650201, China
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Identification of Small RNAs Associated with Salt Stress in Chrysanthemums through High-Throughput Sequencing and Bioinformatics Analysis. Genes (Basel) 2023; 14:genes14030561. [PMID: 36980835 PMCID: PMC10048073 DOI: 10.3390/genes14030561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/12/2023] [Accepted: 02/20/2023] [Indexed: 02/27/2023] Open
Abstract
The Chrysanthemum variety “Niu 9717” exhibits excellent characteristics as an ornamental plant and has good salt resistance. In this study, this plant was treated with 200 mM NaCl for 12 h followed by high-throughput sequencing of miRNA and degradome. Subsequently, the regulatory patterns of potential miRNAs and their target genes were searched to elucidate how Chrysanthemum miRNAs respond to salt. From the root and leaf samples, we identified a total of 201 known miRNAs belonging to 40 families; furthermore, we identified 79 new miRNAs, of which 18 were significantly differentially expressed (p < 0.05). The expressed miRNAs, which targeted a total of 144 mRNAs in the leaf and 215 mRNAs in the root, formed 144 and 226 miRNA–target pairs in roots and leaves, respectively. Combined with the miRNA expression profile, degradome and transcriptome data were then analyzed to understand the possible effects of the miRNA target genes and their pathways on salt stress. The identified genes were mostly located in pathways related to hormone signaling during plant growth and development. Overall, these findings suggest that conserved and novel miRNAs may improve salt tolerance through the regulation of hormone signal synthesis or expression of genes involved in hormone synthesis.
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11
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Tian S, Wan Y, Jiang D, Gong M, Lin J, Xia M, Shi C, Xing H, Li HL. Genome-Wide Identification, Characterization, and Expression Analysis of GRAS Gene Family in Ginger ( Zingiber officinale Roscoe). Genes (Basel) 2022; 14:96. [PMID: 36672837 PMCID: PMC9859583 DOI: 10.3390/genes14010096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/30/2022] Open
Abstract
GRAS family proteins are one of the most abundant transcription factors in plants; they play crucial roles in plant development, metabolism, and biotic- and abiotic-stress responses. The GRAS family has been identified and functionally characterized in some plant species. However, this family in ginger (Zingiber officinale Roscoe), a medicinal crop and non-prescription drug, remains unknown to date. In the present study, 66 GRAS genes were identified by searching the complete genome sequence of ginger. The GRAS family is divided into nine subfamilies based on the phylogenetic analyses. The GRAS genes are distributed unevenly across 11 chromosomes. By analyzing the gene structure and motif distribution of GRAS members in ginger, we found that the GRAS genes have more than one cis-acting element. Chromosomal location and duplication analysis indicated that whole-genome duplication, tandem duplication, and segmental duplication may be responsible for the expansion of the GRAS family in ginger. The expression levels of GRAS family genes are different in ginger roots and stems, indicating that these genes may have an impact on ginger development. In addition, the GRAS genes in ginger showed extensive expression patterns under different abiotic stresses, suggesting that they may play important roles in the stress response. Our study provides a comprehensive analysis of GRAS members in ginger for the first time, which will help to better explore the function of GRAS genes in the regulation of tissue development and response to stress in ginger.
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Affiliation(s)
- Shuming Tian
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404020, China
| | - Yuepeng Wan
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
| | - Dongzhu Jiang
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
| | - Min Gong
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing 404020, China
| | - Junyao Lin
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
| | - Maoqin Xia
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
| | - Cuiping Shi
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
| | - Haitao Xing
- Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing University of Arts and Sciences, Chongqing 402160, China
| | - Hong-Lei Li
- College of Landscape Architecture and life Science/Institute of special Plants, Chongqing University of Arts and Sciences, Chongqing 402168, China
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12
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He Z, Tian Z, Zhang Q, Wang Z, Huang R, Xu X, Wang Y, Ji X. Genome-wide identification, expression and salt stress tolerance analysis of the GRAS transcription factor family in Betula platyphylla. FRONTIERS IN PLANT SCIENCE 2022; 13:1022076. [PMID: 36352865 PMCID: PMC9638169 DOI: 10.3389/fpls.2022.1022076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
The GRAS gene family is a plant-specific family of transcription factors and play a vital role in many plant growth processes and abiotic stress responses. Nevertheless, the functions of the GRAS gene family in woody plants, especially in Betula platyphylla (birch), are hardly known. In this study, we performed a genome-wide analysis of 40 BpGRAS genes (BpGRASs) and identified typical GRAS domains of most BpGRASs. The BpGRASs were unevenly distributed on 14 chromosomes of birch and the phylogenetic analysis of six species facilitated the clustering of 265 GRAS proteins into 17 subfamilies. We observed that closely related GRAS homologs had similar conserved motifs according to motif analysis. Besides, an analysis of the expression patterns of 26 BpGRASs showed that most BpGRASs were highly expressed in the leaves and responded to salt stress. Six BpGRASs were selected for cis-acting element analysis because of their significant upregulation under salt treatment, indicating that many elements were involved in the response to abiotic stress. This result further confirmed that these BpGRASs might participate in response to abiotic stress. Transiently transfected birch plants with transiently overexpressed 6 BpGRASs and RNAi-silenced 6 BpGRASs were generated for gain- and loss-of-function analysis, respectively. In addition, overexpression of BpGRAS34 showed phenotype resistant to salt stress, decreased the cell death and enhanced the reactive oxygen species (ROS) scavenging capabilities and proline content under salt treatment, consistent with the results in transiently transformed birch plants. This study is a systematic analysis of the GRAS gene family in birch plants, and the results provide insight into the molecular mechanism of the GRAS gene family responding to abiotic stress in birch plants.
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Affiliation(s)
- Zihang He
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
- The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Zengzhi Tian
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Qun Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Zhibo Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ruikun Huang
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
- The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Xin Xu
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Yucheng Wang
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
- The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xiaoyu Ji
- College of Forestry, Shenyang Agricultural University, Shenyang, Liaoning, China
- The Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, Shenyang Agricultural University, Shenyang, Liaoning, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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13
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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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14
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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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15
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Zhang C, Liu S, Liu D, Guo F, Yang Y, Dong T, Zhang Y, Ma C, Tang Z, Li F, Meng X, Zhu M. Genome-wide survey and expression analysis of GRAS transcription factor family in sweetpotato provides insights into their potential roles in stress response. BMC PLANT BIOLOGY 2022; 22:232. [PMID: 35524176 PMCID: PMC9074257 DOI: 10.1186/s12870-022-03618-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/27/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The plant-specific GRAS transcription factors play pivotal roles in various adverse environmental conditions. Numerous GRAS genes have been explored and characterized in different plants, however, comprehensive survey on GRASs in sweetpotato is lagging. RESULTS In this study, 72 putative sweetpotato IbGRAS genes with uneven distribution were isolated on 15 chromosomes and classified into 12 subfamilies supported by gene structures and motif compositions. Moreover, both tandem duplication and segmental duplication events played critical roles in the expansion of sweetpotato GRAS genes, and the collinearity between IbGRAS genes and the related orthologs from nine other plants further depicted evolutionary insights into GRAS gene family. RNA-seq analysis under salt stress and qRT-PCR detection of 12 selected IbGRAS genes demonstrated their significant and varying inductions under multiple abiotic stresses (salt, drought, heat and cold) and hormone treatments (ABA, ACC and JA). Consistently, the promoter regions of IbGRAS genes harbored a series of stress- and hormone-associated cis-acting elements. Among them, IbGRAS71, the potential candidate for breeding tolerant plants, was characterized as having transactivation activity in yeasts, while IbGRAS-2/-4/-9 did not. Moreover, a complex interaction relationship between IbGRASs was observed through the interaction network analysis and yeast two-hybrid assays. CONCLUSIONS Our results laid a foundation for further functional identifications of IbGRAS genes, and multiple members may serve as potential regulators for molecular breeding of tolerant sweetpotato.
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Affiliation(s)
- Chengbin Zhang
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Siyuan Liu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Delong Liu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Fen Guo
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Yiyu Yang
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Tingting Dong
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Yi Zhang
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Chen Ma
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Zixuan Tang
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Feifan Li
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China
| | - Xiaoqing Meng
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China.
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China.
| | - Mingku Zhu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China.
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu Province, China.
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16
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Beheshti H, Strotbek C, Arif MA, Klingl A, Top O, Frank W. PpGRAS12 acts as a positive regulator of meristem formation in Physcomitrium patens. PLANT MOLECULAR BIOLOGY 2021; 107:293-305. [PMID: 33598827 PMCID: PMC8648639 DOI: 10.1007/s11103-021-01125-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/01/2021] [Indexed: 05/29/2023]
Abstract
This study focused on the key regulatory function of Physcomitrium patens GRAS12 gene underlying an increasing plant complexity, an important step in plant terrestrialization and the evolutionary history of life. The miR171-GRAS module has been identified as a key player in meristem maintenance in angiosperms. PpGRAS12 is a member of the GRAS family and a validated target for miR171 in Physcomitrium (Physcomitrella) patens. Here we show a regulatory function of miR171 at the gametophytic vegetative growth stage and targeted deletion of the PpGRAS12 gene adversely affects sporophyte production since fewer sporophytes were produced in ΔPpGRAS12 knockout lines compared to wild type moss. Furthermore, highly specific and distinct growth arrests were observed in inducible PpGRAS12 overexpression lines at the protonema stage. Prominent phenotypic aberrations including the formation of multiple apical meristems at the gametophytic vegetative stage in response to elevated PpGRAS12 transcript levels were discovered via scanning electron microscopy. The production of multiple buds in the PpGRAS12 overexpression lines similar to ΔPpCLV1a/1b disruption mutants is accompanied by an upregulation of PpCLE and downregulation of PpCLV1, PpAPB, PpNOG1, PpDEK1, PpRPK2 suggesting that PpGRAS12 acts upstream of these genes and negatively regulates the proposed pathway to specify simplex meristem formation. As CLV signaling pathway components are not present in the chlorophytic or charophytic algae and arose with the earliest land plants, we identified a key regulatory function of PpGRAS12 underlying an increasing plant complexity, an important step in plant terrestrialization and the evolutionary history of life.
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Affiliation(s)
- Hossein Beheshti
- Plant Molecular Cell Biology, Department Biology I, LMU Biocenter, Ludwig-Maximilians-University Munich, Großhardener Straße 2-4, Planegg-Martinsried, Germany
| | - Christoph Strotbek
- Plant Molecular Cell Biology, Department Biology I, LMU Biocenter, Ludwig-Maximilians-University Munich, Großhardener Straße 2-4, Planegg-Martinsried, Germany
| | - M Asif Arif
- Plant Molecular Cell Biology, Department Biology I, LMU Biocenter, Ludwig-Maximilians-University Munich, Großhardener Straße 2-4, Planegg-Martinsried, Germany
| | - Andreas Klingl
- Plant Developmental Biology, Department Biology I, LMU Biocenter, Ludwig-Maximilians-University Munich, Großhardener Straße 2-4, Planegg-Martinsried, Germany
| | - Oguz Top
- Plant Molecular Cell Biology, Department Biology I, LMU Biocenter, Ludwig-Maximilians-University Munich, Großhardener Straße 2-4, Planegg-Martinsried, Germany
| | - Wolfgang Frank
- Plant Molecular Cell Biology, Department Biology I, LMU Biocenter, Ludwig-Maximilians-University Munich, Großhardener Straße 2-4, Planegg-Martinsried, Germany.
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17
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Huang Z, Wang Z, Li X, He S, Liu Q, Zhai H, Zhao N, Gao S, Zhang H. Genome-Wide Identification and Expression Analysis of JAZ Family Involved in Hormone and Abiotic Stress in Sweet Potato and Its Two Diploid Relatives. Int J Mol Sci 2021; 22:ijms22189786. [PMID: 34575953 PMCID: PMC8468994 DOI: 10.3390/ijms22189786] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/06/2021] [Accepted: 09/06/2021] [Indexed: 01/03/2023] Open
Abstract
Jasmonate ZIM-domain (JAZ) proteins are key repressors of a jasmonic acid signaling pathway. They play essential roles in the regulation of plant growth and development, as well as environmental stress responses. However, this gene family has not been explored in sweet potato. In this study, we identified 14, 15, and 14 JAZs in cultivated hexaploid sweet potato (Ipomoea batatas, 2n = 6x = 90), and its two diploid relatives Ipomoea trifida (2n = 2x = 30) and Ipomoea triloba (2n = 2x = 30), respectively. These JAZs were divided into five subgroups according to their phylogenetic relationships with Arabidopsis. The protein physiological properties, chromosome localization, phylogenetic relationship, gene structure, promoter cis-elements, protein interaction network, and expression pattern of these 43 JAZs were systematically investigated. The results suggested that there was a differentiation between homologous JAZs, and each JAZ gene played different vital roles in growth and development, hormone crosstalk, and abiotic stress response between sweet potato and its two diploid relatives. Our work provided comprehensive comparison and understanding of the JAZ genes in sweet potato and its two diploid relatives, supplied a theoretical foundation for their functional study, and further facilitated the molecular breeding of sweet potato.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Huan Zhang
- Correspondence: ; Tel./Fax: +86-010-6273-2559
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18
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Wang X, Li G, Sun Y, Qin Z, Feng P. Genome-wide analysis and characterization of GRAS family in switchgrass. Bioengineered 2021; 12:6096-6114. [PMID: 34477486 PMCID: PMC8806906 DOI: 10.1080/21655979.2021.1972606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Panicum virgatum, a model plant of cellulosic ethanol conversion, not only has high large biomass and strong adaptability to soil, but also grows well in marginal soil and has the advantage of improving saline-alkali soil. GRAS transcription factor gene family play important roles in individual environment adaption, and these vital functions has been proved in several plants, however, the research of GRAS in the development of switchgrass (Panicum virgatum) were limited. A comprehensive study was investigated to explore the relationship between GRAS gene family and resistance. According to the phylogenetic analysis, a total of 144 GRAS genes were identified and renamed which were classified into eight subfamilies. Chromosome distribution, tandem and segmental repeats analysis indicated that gene duplication events contributed a lot to the expansion of GRAS genes in the switchgrass genome. Sixty-six GRAS genes in switchgrass were identified as having orthologous genes with rice through gene duplication analysis. Most of these GRAS genes contained zero or one intron, and closely related genes in evolution shared similar motif composition. Interaction networks were analyzed including DELLA and ten interaction proteins that were primarily involved in gibberellin acid mediated signaling. Notably, online analysis indicated that the promoter regions of the identified PvGRAS genes contained many cis-elements including light responsive elements, suggesting that PvGRAS might involve in light signal cross-talking. This work provides key insights into resistance and bioavailability in switchgrass and would be helpful to further study the function of GRAS and GRAS-mediated signal transduction pathways.
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Affiliation(s)
- Xiaoqin Wang
- Department of Anesthesiology, Changzhi Medical College, Changzhi, Shanxi, China
| | - Guixia Li
- Department of Basic Medicine, Changzhi Medical College, Changzhi, Shanxi, China
| | - Yajing Sun
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Zhongyu Qin
- Department of Basic Medicine, Changzhi Medical College, Changzhi, Shanxi, China
| | - Pengcheng Feng
- Department of Basic Medicine, Changzhi Medical College, Changzhi, Shanxi, China
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Sun H, Mei J, Zhao W, Hou W, Zhang Y, Xu T, Wu S, Zhang L. Phylogenetic Analysis of the SQUAMOSA Promoter-Binding Protein-Like Genes in Four Ipomoea Species and Expression Profiling of the IbSPLs During Storage Root Development in Sweet Potato ( Ipomoea batatas). FRONTIERS IN PLANT SCIENCE 2021; 12:801061. [PMID: 35126426 PMCID: PMC8815303 DOI: 10.3389/fpls.2021.801061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 12/17/2021] [Indexed: 05/11/2023]
Abstract
As a major plant-specific transcription factor family, SPL genes play a crucial role in plant growth, development, and stress tolerance. The SPL transcription factor family has been widely studied in various plant species; however, systematic studies on SPL genes in the genus Ipomoea are lacking. Here, we identified a total of 29, 27, 26, and 23 SPLs in Ipomoea batatas, Ipomoea trifida, Ipomoea triloba, and Ipomoea nil, respectively. Based on the phylogenetic analysis of SPL proteins from model plants, the Ipomoea SPLs were classified into eight clades, which included conserved gene structures, domain organizations and motif compositions. Moreover, segmental duplication, which is derived from the Ipomoea lineage-specific whole-genome triplication event, was speculated to have a predominant role in Ipomoea SPL expansion. Particularly, tandem duplication was primarily responsible for the expansion of SPL subclades IV-b and IV-c. Furthermore, 25 interspecific orthologous groups were identified in Ipomoea, rice, Arabidopsis, and tomato. These findings support the expansion of SPLs in Ipomoea genus, with most of the SPLs being evolutionarily conserved. Of the 105 Ipomoea SPLs, 69 were predicted to be the targets of miR156, with seven IbSPLs being further verified as targets using degradome-seq data. Using transcriptomic data from aboveground and underground sweet potato tissues, IbSPLs showed diverse expression patterns, including seven highly expressed IbSPLs in the underground tissues. Furthermore, the expression of 11 IbSPLs was validated using qRT-PCR, and two (IbSPL17/IbSPL28) showed significantly increased expression during root development. Additionally, the qRT-PCR analysis revealed that six IbSPLs were strongly induced in the roots under phytohormone treatments, particularly zeatin and abscisic acid. Finally, the transcriptomic data of storage roots from 88 sweet potato accessions were used for weighted gene co-expression network analysis, which revealed four IbSPLs (IbSPL16/IbSPL17/IbSPL21/IbSPL28) clusters with genes involved in "regulation of root morphogenesis," "cell division," "cytoskeleton organization," and "plant-type cell wall organization or biogenesis," indicating their potential role in storage root development. This study not only provides novel insights into the evolutionary and functional divergence of the SPLs in the genus Ipomoea but also lays a foundation for further elucidation of the potential functional roles of IbSPLs on storage root development.
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Affiliation(s)
- Haoyun Sun
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jingzhao Mei
- Department of Biochemistry and Molecular Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Weiwei Zhao
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Wenqian Hou
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yang Zhang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Tao Xu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Tao Xu,
| | - Shaoyuan Wu
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Department of Biochemistry and Molecular Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Shaoyuan Wu,
| | - Lei Zhang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- *Correspondence: Lei Zhang,
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Wang L, Ding X, Gao Y, Yang S. Genome-wide identification and characterization of GRAS genes in soybean (Glycine max). BMC PLANT BIOLOGY 2020; 20:415. [PMID: 32891114 PMCID: PMC7487615 DOI: 10.1186/s12870-020-02636-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/30/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND GRAS proteins are crucial transcription factors, which are plant-specific and participate in various plant biological processes. Thanks to the rapid progress of the whole genome sequencing technologies, the GRAS gene families in different plants have been broadly explored and studied. However, comprehensive research on the soybean (Glycine max) GRAS gene family is relatively lagging. RESULTS In this study, 117 Glycine max GRAS genes (GmGRAS) were identified. Further phylogenetic analyses showed that the GmGRAS genes could be categorized into nine gene subfamilies: DELLA, HAM, LAS, LISCL, PAT1, SCL3, SCL4/7, SCR and SHR. Gene structure analyses turned out that the GmGRAS genes lacked introns and were relatively conserved. Conserved domains and motif patterns of the GmGRAS members in the same subfamily or clade exhibited similarities. Notably, the expansion of the GmGRAS gene family was driven both by gene tandem and segmental duplication events. Whereas, segmental duplications took the major role in generating new GmGRAS genes. Moreover, the synteny and evolutionary constraints analyses of the GRAS proteins among soybean and distinct species (two monocots and four dicots) provided more detailed evidence for GmGRAS gene evolution. Cis-element analyses indicated that the GmGRAS genes may be responsive to diverse environmental stresses and regulate distinct biological processes. Besides, the expression patterns of the GmGRAS genes were varied in various tissues, during saline and dehydration stresses and during seed germination processes. CONCLUSIONS We conducted a systematic investigation of the GRAS genes in soybean, which may be valuable in paving the way for future GmGRAS gene studies and soybean breeding.
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Affiliation(s)
- Liang Wang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xianlong Ding
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yingqi Gao
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shouping Yang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
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Genome-wide identification and analysis of GRAS transcription factors in the bottle gourd genome. Sci Rep 2020; 10:14338. [PMID: 32868844 PMCID: PMC7459283 DOI: 10.1038/s41598-020-71240-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/06/2020] [Indexed: 12/01/2022] Open
Abstract
GRAS genes belong to the plant-specific transcription factors (TF’s) family that are known to be involved in plant growth and development. In this study, we have identified 37 genes from the bottle gourd genome that encodes for GRAS TF’s. Except for the SCLA, we were able to identify at least one gene from each of the 17 subfamilies. Gene structure and chromosomal analysis showed that maximum seven genes are present on Chr7 followed by six genes on Chr1. The subcellular location analysis revealed that most of the genes were localized in the nucleus, except for a few in chloroplast and mitochondria. Additionally, we have identified one tandem gene duplication event on Chr7 and three major motifs that were present in all the GRAS genes. Furthermore, the protein–protein interaction prediction and gene expression analysis showed five candidate hub-genes interact with various other genes and thus probably control the expression of interacting partners in different plant tissues. Overall, this study provides a comprehensive analysis of GRAS transcription factors in bottle gourd genome which could be further extended to other vegetable crops.
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Tang C, Han R, Zhou Z, Yang Y, Zhu M, Xu T, Wang A, Li Z, Dong T. Identification of candidate miRNAs related in storage root development of sweet potato by high throughput sequencing. JOURNAL OF PLANT PHYSIOLOGY 2020; 251:153224. [PMID: 32634748 DOI: 10.1016/j.jplph.2020.153224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 06/17/2020] [Accepted: 06/24/2020] [Indexed: 05/16/2023]
Abstract
Sweet potato (Ipomoea batatas L.) is a food consumed worldwide, an industrial raw material and new energy crop. The storage root is the most economical part of the crop. However, the mechanism of storage root initiation and development is still unclear. In this study, conserved and novel miRNAs during storage root development were identified by high-throughput sequencing technology by constructing small RNA libraries from sweet potato fibrous roots (F) and storage roots at four different developmental stages (storage roots with different diameters: 1 cm, D1; 3 cm, D3; 5 cm, D5 and 10 cm, D10). A total of 61 known miRNAs and 471 novel miRNAs were identified. In addition, 145 differentially expressed miRNAs were identified in the F library compared with the four storage root libraries, with 30 known miRNAs and 115 novel miRNAs. Moreover, the targets of the differentially expressed miRNAs were predicted and their network was further investigated by GO analysis using our previous transcriptome data. The GO analysis revealed that antioxidant activity and binding process were the most enriched terms of the target genes. The secondary structure and expression of six candidate miRNAs including three conserved miRNAs and three novel miRNAs were investigated and their predicted targets were validated by qRT-PCR. The results showed that the expression levels of the miRNAs were all consistent with the sequencing data. Most of the miRNAs and their corresponding targets had obvious negative correlations. This study contributed to elucidating the potential miRNA mediated regulatory mechanism of storage root development in sweet potato. The specific differentially expressed miRNAs in sweet potato storage roots can be used to breed high-yield sweet potatoes and other tuberous root crops.
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Affiliation(s)
- Cheng Tang
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Rongpeng Han
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Zhengkun Zhou
- College of Health Sciences, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Yiyu Yang
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Mingku Zhu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Tao Xu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Aimin Wang
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Zongyun Li
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
| | - Tingting Dong
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu Province, People's Republic of China.
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23
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Wan R, Liu J, Yang Z, Zhu P, Cao Q, Xu T. Genome-wide identification, characterisation and expression profile analysis of DEAD-box family genes in sweet potato wild ancestor Ipomoea trifida under abiotic stresses. Genes Genomics 2020; 42:325-335. [DOI: 10.1007/s13258-019-00910-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/18/2019] [Indexed: 12/18/2022]
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