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Li H, Liang Z, Chao Y, Wei X, Zou Y, Qu H, Wang J, Li M, Huang W, Luo J, Peng X. Exploring the GRAS gene family in Taraxacum kok-saghyz Rodin:characterization, evolutionary relationships, and expression analyses in response to abiotic stresses. Biochem Biophys Res Commun 2024; 733:150693. [PMID: 39326257 DOI: 10.1016/j.bbrc.2024.150693] [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: 06/10/2024] [Revised: 09/03/2024] [Accepted: 09/11/2024] [Indexed: 09/28/2024]
Abstract
The GRAS gene is an important specific transcription factor in plants, which has multiple functions such as signal transduction, cell morphogenesis and stress response. Although it is widely distributed in plants and has been characterized in several species, however, information about the GRAS family in Taraxacum kok-saghyz Rodin remains unknown. Here, TkGRAS family members were identified and analyzed for molecular characterization, tissue expression patterns and induced expression patterns. A total of 64 GRAS family members were identified at the genome-wide level, which could be categorized into 14 subfamilies by phylogenetic analysis. Most TkGRASs were intronless and had essentially the same gene structure in the same subfamily. Meanwhile, there were multiple response elements found in the promoters of TkGRASs. Tissue expression patterns and induced expression patterns showed that TkGRASs were expressed in different tissues and induced by abiotic stresses. Notably, the expression level of TkGRAS20 was up-regulated under different stresses, suggesting that this gene plays a pivotal role in the stress response. TkGRAS20 showed transcriptional activity in yeast cells and localized in the nucleus and plasma membrane. In conclusion, our study provided valuable insights into the genetic mechanisms underlying stress tolerance in TKS, and several key genes may be used for genetic breeding to improve stress tolerance.
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Affiliation(s)
- Hao Li
- Anhui Agricultural University, School of Life Sciences, Hefei, Anhui, China
| | - Zeyuan Liang
- Anhui Agricultural University, School of Life Sciences, Hefei, Anhui, China
| | - Yunhan Chao
- Anhui Agricultural University, School of Life Sciences, Hefei, Anhui, China
| | - Xiao Wei
- Anhui Agricultural University, School of Life Sciences, Hefei, Anhui, China
| | - Yan Zou
- Anhui Agricultural University, School of Life Sciences, Hefei, Anhui, China
| | - Haibo Qu
- Anhui Agricultural University, School of Life Sciences, Hefei, Anhui, China
| | - Jiahua Wang
- Anhui Agricultural University, School of Life Sciences, Hefei, Anhui, China
| | - Menglong Li
- Anhui Agricultural University, School of Life Sciences, Hefei, Anhui, China
| | - Wanchang Huang
- Anhui Agricultural University, School of Life Sciences, Hefei, Anhui, China
| | - Jinxue Luo
- Anhui Agricultural University, School of Life Sciences, Hefei, Anhui, China; Guangdong ZhongXun Agri-science Corporation, Huizhou, Guangdong, China.
| | - Xiaojian Peng
- Anhui Agricultural University, School of Life Sciences, Hefei, Anhui, China.
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Duan L, Mo Z, Li K, Pi K, Luo J, Que Y, Zhang Q, Zhang J, Wu G, Liu R. Non-additive expression genes play a critical role in leaf vein ratio heterosis in Nicotiana tabacum L. BMC Genomics 2024; 25:924. [PMID: 39363277 PMCID: PMC11451143 DOI: 10.1186/s12864-024-10821-1] [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: 12/22/2023] [Accepted: 09/20/2024] [Indexed: 10/05/2024] Open
Abstract
Heterosis, recognized for improving crop performance, especially in the first filial (F1) generation, remains an area of significant study in the tobacco industry. The low utilization of leaf veins in tobacco contributes to economic inefficiency and resource waste. Despite the positive impacts of heterosis on crop genetics, investigations into leaf-vein ratio heterosis in tobacco have been lacking. Understanding the mechanisms underlying negative heterosis in leaf vein ratio at the molecular level is crucial for advancing low vein ratio leaf breeding research. This study involved 12 hybrid combinations and their parental lines to explore heterosis associated with leaf vein ratios. The hybrids displayed diverse patterns of positive or negative leaf vein ratio heterosis across different developmental stages. Notably, the F1 hybrid (G70 × Qinggeng) consistently exhibited substantial negative heterosis, reaching a maximum of -19.79% 80 days after transplanting. A comparative transcriptome analysis revealed that a significant proportion of differentially expressed genes (DEGs), approximately 39.04% and 23.73%, exhibited dominant and over-dominant expression patterns, respectively. These findings highlight the critical role of non-additive gene expression, particularly the dominance pattern, in governing leaf vein ratio heterosis. The non-additive genes, largely associated with various GO terms such as response to abiotic stimuli, galactose metabolic process, plant-type cell wall organization, auxin-activated signaling pathway, hydrolase activity, and UDP-glycosyltransferase activity, were identified. Furthermore, KEGG enrichment analysis unveiled their involvement in phenylpropanoid biosynthesis, galactose metabolism, plant hormone signal transduction, glutathione metabolism, MAPK signaling pathway, starch, and sucrose metabolism. Among the non-additive genes, we identified some genes related to leaf development, leaf size, leaf senescence, and cell wall extensibility that showed significantly lower expression in F1 than in its parents. These results indicate that the non-additive expression of genes plays a key role in the heterosis of the leaf vein ratio in tobacco. This study marks the first exploration into the molecular mechanisms governing leaf vein ratio heterosis at the transcriptome level. These findings significantly contribute to understanding leaf vein ratios in tobacco breeding strategies.
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Affiliation(s)
- Lili Duan
- College of Tobacco, Guizhou University, Guiyang, 550025, China
- Key Laboratory for Tobacco Quality Research Guizhou Province, Guizhou University, Guiyang, 550025, China
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Zejun Mo
- College of Tobacco, Guizhou University, Guiyang, 550025, China
- Key Laboratory for Tobacco Quality Research Guizhou Province, Guizhou University, Guiyang, 550025, China
| | - Kuiyin Li
- Anshun University, Anshun, 561099, China
| | - Kai Pi
- College of Tobacco, Guizhou University, Guiyang, 550025, China
- Key Laboratory for Tobacco Quality Research Guizhou Province, Guizhou University, Guiyang, 550025, China
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Jiajun Luo
- College of Tobacco, Guizhou University, Guiyang, 550025, China
- Key Laboratory for Tobacco Quality Research Guizhou Province, Guizhou University, Guiyang, 550025, China
| | - Yuanhui Que
- College of Tobacco, Guizhou University, Guiyang, 550025, China
| | - Qian Zhang
- College of Tobacco, Guizhou University, Guiyang, 550025, China
- Key Laboratory for Tobacco Quality Research Guizhou Province, Guizhou University, Guiyang, 550025, China
| | - Jingyao Zhang
- College of Tobacco, Guizhou University, Guiyang, 550025, China
| | - Guizhi Wu
- College of Tobacco, Guizhou University, Guiyang, 550025, China
| | - Renxiang Liu
- College of Tobacco, Guizhou University, Guiyang, 550025, China.
- Key Laboratory for Tobacco Quality Research Guizhou Province, Guizhou University, Guiyang, 550025, China.
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Wang A, Guo W, Wang S, Wang Y, Kong D, Li W. Transcriptome analysis unveiled the genetic basis of rapid seed germination strategies in alpine plant Rheum pumilum. Sci Rep 2024; 14:19194. [PMID: 39160287 PMCID: PMC11333768 DOI: 10.1038/s41598-024-70320-x] [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: 04/30/2024] [Accepted: 08/14/2024] [Indexed: 08/21/2024] Open
Abstract
Rheum pumilum stands as both a quintessential alpine plant and a significant traditional Chinese and Tibetan medicinal herb. Unraveling the molecular intricacies of seed germination in Rh. pumilum not only unveils the genetic foundations of plant seed germination strategies in high-altitude environments but also offers insights for cultivating Rh. pumilum medicinal materials. Employing transcriptome sequencing and the Weighted Gene Co-expression Network Analysis, this study delved into the shifts in gene expression levels across various stages of seed germination in Rh. pumilum. The process of seed germination in Rh. pumilum entails a cascade of complex physiological events. Six hormones (ABA, IAA, ETH, GA, BR, CK) emerged as pivotal players in seeds breaking in shells and the facilitation of rapid seed germination in Rh. pumilum. Fourteen transcription factor families (LOB, GRAS, B3, bHLH, bZIP, EIL, MYB, MYB related, NAC, TCP, WRKY, HSF, PLATZ, and SBP) along with four key genes (E2.4.1.13, EIN3, BZR, and BIN2) were identified that may be associated with both biotic and abiotic environmental stress. The ETR, ACACA and ATPeV0C genes were linked with energy accumulation during the initial stages of seed germination, CYP707A may play an important role in breaking seed dormancy, while the BRI1 gene may be correlated with swift seed germination. Additionally, several unidentified genes were recognized to play key roles in seed germination of Rh. pumilum, warranting further investigation. Moreover, Rh. pumilum demonstrates full activation of crucial physiological functions such as energy metabolism, signal transduction, and responses to biological and abiotic stresses during the seed breaking in shells. This study provides molecular evidence elucidating the swift seed germination strategies adopted by alpine plants to thrive in high-altitude environments. Furthermore, it serves as a foundational reference for enhancing seed germination rates and breeding practices to promote the sustainable development of Rh. pumilum medicinal materials.
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Affiliation(s)
- Ailan Wang
- School of Life Sciences, Ludong University, Yantai, Shandong, China
| | - Wenjie Guo
- School of Life Sciences, Ludong University, Yantai, Shandong, China
| | - Shimeng Wang
- School of Life Sciences, Ludong University, Yantai, Shandong, China
| | - Yanfang Wang
- School of Life Sciences, Ludong University, Yantai, Shandong, China
| | - Dongrui Kong
- School of Life Sciences, Ludong University, Yantai, Shandong, China
| | - Weiwei Li
- School of Life Sciences, Ludong University, Yantai, Shandong, China.
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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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Liao TJ, Huang T, Xiong HY, Duo JC, Ma JZ, Du MY, Duan RJ. Genome-wide identification, characterization, and evolutionary analysis of the barley TALE gene family and its expression profiles in response to exogenous hormones. FRONTIERS IN PLANT SCIENCE 2024; 15:1421702. [PMID: 38993938 PMCID: PMC11236544 DOI: 10.3389/fpls.2024.1421702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 06/07/2024] [Indexed: 07/13/2024]
Abstract
Three-amino-loop-extension (TALE) family belongs to the homeobox gene superfamily and occurs widely in plants, playing a crucial role in regulating their growth and development. Currently, genome-wide analysis of the TALE family has been completed in many plants. However, the systematic identification and hormone response analysis of the TALE gene family in barley are still lacking. In this study, 21 TALE candidate genes were identified in barley, which can be divided into KNOX and BELL subfamilies. Barley TALE members in the same subfamily of the phylogenetic tree have analogically conserved motifs and gene structures, and segmental duplications are largely responsible for the expansion of the HvTALE family. Analysis of TALE orthologous and homologous gene pairs indicated that the HvTALE family has mainly undergone purifying selective pressure. Through spatial structure simulation, HvKNOX5-HvKNOX6 and HvKNOX5-HvBELL11 complexes are all formed through hydrogen bonding sites on both the KNOX2 and homeodomain (HD) domains of HvKNOX5, which may be essential for protein interactions among the HvTALE family members. Expression pattern analyses reveal the potential involvement of most HvTALE genes in responses to exogenous hormones. These results will lay the foundation for regulation and function analyses of the barley TALE gene family in plant growth and development by hormone regulation.
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Affiliation(s)
- Tian-jiang Liao
- College of Eco-environmental Engineering, Qinghai University, Xining, Qinghai, China
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai, China
| | - Tao Huang
- College of Eco-environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Hui-yan Xiong
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai, China
| | - Jie-cuo Duo
- College of Eco-environmental Engineering, Qinghai University, Xining, Qinghai, China
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai, China
| | - Jian-zhi Ma
- College of Eco-environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Ming-yang Du
- College of Eco-environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Rui-jun Duan
- College of Eco-environmental Engineering, Qinghai University, Xining, Qinghai, China
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, Qinghai, China
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Huang Y, Zheng Q, Zhang MM, He X, Zhao X, Wang L, Lan S, Liu ZJ. Genome-Wide Identification and Expression Analysis of the GRAS Gene Family and Their Responses to Heat Stress in Cymbidium goeringii. Int J Mol Sci 2024; 25:6363. [PMID: 38928070 PMCID: PMC11204107 DOI: 10.3390/ijms25126363] [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: 05/16/2024] [Revised: 05/29/2024] [Accepted: 06/01/2024] [Indexed: 06/28/2024] Open
Abstract
The GRAS gene family, responsible for encoding transcription factors, serves pivotal functions in plant development, growth, and responses to stress. The exploration of the GRAS gene family within the Orchidaceae has been comparatively limited, despite its identification and functional description in various plant species. This study aimed to conduct a thorough examination of the GRAS gene family in Cymbidum goeringii, focusing on its physicochemical attributes, phylogenetic associations, gene structure, cis-acting elements, and expression profiles under heat stress. The results show that a total of 54 CgGRASs were pinpointed from the genome repository and categorized into ten subfamilies via phylogenetic associations. Assessment of gene sequence and structure disclosed the prevalent existence of the VHIID domain in most CgGRASs, with around 57.41% (31/54) CgGRASs lacking introns. The Ka/Ks ratios of all CgGRASs were below one, indicating purifying selection across all CgGRASs. Examination of cis-acting elements unveiled the presence of numerous elements linked to light response, plant hormone signaling, and stress responsiveness. Furthermore, CgGRAS5 contained the highest quantity of cis-acting elements linked to stress response. Experimental results from RT-qPCR demonstrated notable variations in the expression levels of eight CgGRASs after heat stress conditions, particularly within the LAS, HAM, and SCL4/7 subfamilies. In conclusion, this study revealed the expression pattern of CgGRASs under heat stress, providing reference for further exploration into the roles of CgGRAS transcription factors in stress adaptation.
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Affiliation(s)
- Ye Huang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (Q.Z.); (L.W.)
| | - Qinyao Zheng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (Q.Z.); (L.W.)
| | - Meng-Meng Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-M.Z.); (X.H.); (X.Z.)
| | - Xin He
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-M.Z.); (X.H.); (X.Z.)
| | - Xuewei Zhao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-M.Z.); (X.H.); (X.Z.)
| | - Linying Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (Q.Z.); (L.W.)
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (Q.Z.); (L.W.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-M.Z.); (X.H.); (X.Z.)
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (Q.Z.); (L.W.)
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.-M.Z.); (X.H.); (X.Z.)
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Chen L, Qin Y, Fan S. Genome-Wide Identification and Characterization of the GRAS Gene Family in Lettuce Revealed That Silencing LsGRAS13 Delayed Bolting. PLANTS (BASEL, SWITZERLAND) 2024; 13:1360. [PMID: 38794431 PMCID: PMC11124801 DOI: 10.3390/plants13101360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024]
Abstract
Lettuce is susceptible to high-temperature stress during cultivation, leading to bolting and affecting yield. Plant-specific transcription factors, known as GRAS proteins, play a crucial role in regulating plant growth, development, and abiotic stress responses. In this study, the entire lettuce LsGRAS gene family was identified. The results show that 59 LsGRAS genes are unevenly distributed across the nine chromosomes. Additionally, all LsGRAS proteins showed 100% nuclear localization based on the predicted subcellular localization and were phylogenetically classified into nine conserved subfamilies. To investigate the expression profiles of these genes in lettuce, we analyzed the transcription levels of all 59 LsGRAS genes in the publicly available RNA-seq data under the high-temperature treatment conducted in the presence of exogenous melatonin. The findings indicate that the transcript levels of the LsGRAS13 gene were higher on days 6, 9, 15, 18, and 27 under the high-temperature (35/30 °C) treatment with melatonin than on the same treatment days without melatonin. The functional studies demonstrate that silencing LsGRAS13 accelerated bolting in lettuce. Furthermore, the paraffin sectioning results showed that flower bud differentiation in LsGRAS13-silenced plants occurred significantly faster than in control plants. In this study, the LsGRAS genes were annotated and analyzed, and the expression pattern of the LsGRAS gene following melatonin treatment under high-temperature conditions was explored. This exploration provides valuable information and identifies candidate genes associated with the response mechanism of lettuce plants high-temperature stress.
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Affiliation(s)
- Li Chen
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China; (L.C.); (Y.Q.)
| | - Yong Qin
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China; (L.C.); (Y.Q.)
| | - Shuangxi Fan
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China; (L.C.); (Y.Q.)
- Plant Science and Technology College, Beijing Vocational College of Agriculture, Beijing 102442, China
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8
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Li Y, Cao Y, Fan Y, Fan G. Comprehensive Analysis of the GRAS Gene Family in Paulownia fortunei and the Response of DELLA Proteins to Paulownia Witches' Broom. Int J Mol Sci 2024; 25:2425. [PMID: 38397102 PMCID: PMC10888722 DOI: 10.3390/ijms25042425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/10/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
The GRAS (GAI\RGA\SCL) gene family encodes plant-specific transcription factors that play crucial roles in plant growth and development, stress tolerance, and hormone network regulation. Plant dwarfing symptom is mainly regulated by DELLA proteins of the GRAS gene subfamily. In this study, the association between the GRAS gene family and Paulownia witches' broom (PaWB) was investigated. A total of 79 PfGRAS genes were identified using bioinformatics methods and categorized into 11 groups based on amino acid sequences. Tandem duplication and fragment duplication were found to be the main modes of amplification of the PfGRAS gene family. Gene structure analysis showed that more than 72.1% of the PfGRASs had no introns. The genes PfGRAS12/18/58 also contained unique DELLA structural domains; only PfGRAS12, which showed significant response to PaWB phytoplasma infection in stems, showed significant tissue specificity and responded to gibberellin (GA3) in PaWB-infected plants. We found that the internodes were significantly elongated under 100 µmol·L-1 GA3 treatment for 30 days. The subcellular localization analysis indicated that PfGRAS12 is located in the nucleus and cell membrane. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays confirmed that PfGRAS12 interacted with PfJAZ3 in the nucleus. Our results will lay a foundation for further research on the functions of the PfGRAS gene family and for genetic improvement and breeding of PaWB-resistant trees.
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Affiliation(s)
- Yixiao Li
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (Y.L.); (Y.C.); (Y.F.)
- Institute of Paulownia, Henan Agricultural University, Zhengzhou 450002, China
| | - Yabing Cao
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (Y.L.); (Y.C.); (Y.F.)
- Institute of Paulownia, Henan Agricultural University, Zhengzhou 450002, China
| | - Yujie Fan
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (Y.L.); (Y.C.); (Y.F.)
- Institute of Paulownia, Henan Agricultural University, Zhengzhou 450002, China
| | - Guoqiang Fan
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (Y.L.); (Y.C.); (Y.F.)
- Institute of Paulownia, Henan Agricultural University, Zhengzhou 450002, China
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9
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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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10
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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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11
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Chen B, Liu T, Yang Z, Yang S, Chen J. PacBio Full-Length Transcriptome Sequencing Reveals the Mechanism of Salt Stress Response in Sonneratia apetala. PLANTS (BASEL, SWITZERLAND) 2023; 12:3849. [PMID: 38005746 PMCID: PMC10675792 DOI: 10.3390/plants12223849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023]
Abstract
Sonneratia apetala is an essential mangrove wetland restoration tree species. Studying its molecular mechanism for salt tolerance could lay a foundation for further cultivating excellent resistant germplasm. This study used a combination of PacBio isoform sequencing (Iso-seq) and BGISEQ RNA sequencing (RNA-seq) to analyze the molecular mechanism to salt stress response of one-year-old S. apetala leaves. The growth and physiological analysis showed that physiological indexes such as growth rate, net photosynthetic rate and antioxidant enzyme activity all exhibit significant changes under salt stress. From Iso-seq, a total of 295,501 full-length transcripts, with an average length of 1418 bp, were obtained. RNA-seq produced 4712 differentially expressed genes (DEGs) as compared to a control group. Of these, 930 were identified to be co-expressed during the STEM time sequence analysis. Further, 715 and 444 co-expressed DEGs were annotated by GO and KEGG analyses, respectively. Moreover, 318 of the co-expressed DEGs were annotated as essential genes that were implicated in salt stress response of S. apetala, which were involved in transcription factors, signal transduction, hormone response, ROS homeostasis, osmotic balance, cell wall synthesis or modification. These results provide candidate targets for further characterization and offer insights into the salt-tolerant mechanism of S. apetala.
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Affiliation(s)
- Beibei Chen
- Mangrove Research Center of Guangdong Ocean University, College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (B.C.); (T.L.); (Z.Y.); (S.Y.)
| | - Tingting Liu
- Mangrove Research Center of Guangdong Ocean University, College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (B.C.); (T.L.); (Z.Y.); (S.Y.)
| | - Zhuanying Yang
- Mangrove Research Center of Guangdong Ocean University, College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (B.C.); (T.L.); (Z.Y.); (S.Y.)
| | - Shaoxia Yang
- Mangrove Research Center of Guangdong Ocean University, College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (B.C.); (T.L.); (Z.Y.); (S.Y.)
| | - Jinhui Chen
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572019, China
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12
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Rana D, Sharma P, Arpita K, Srivastava H, Sharma S, Gaikwad K. Genome-wide identification and characterization of GRAS gene family in pigeonpea ( Cajanus cajan (L.) Millspaugh). 3 Biotech 2023; 13:363. [PMID: 37840881 PMCID: PMC10570252 DOI: 10.1007/s13205-023-03782-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023] Open
Abstract
The GRAS proteins are plant-specific transcription factors (TFs) that play a crucial role in various plant physiological processes, including tissue development and stress responses. To date, GRAS family has been comprehensively characterized in Arabidopsis, soybean, rice, chickpea and other plant species. To understand the structural and functional aspects of pigeonpea (C. cajan), we identified 60 putative GRAS (CcGRAS) genes from pigeonpea genome and further analysed their physicochemical properties, subcellular locations, evolutionary classification, exon-intron structures, conserved domains, gene duplication events and cis-promoter regions. Based on the sequence similarity, CcGRAS family was clustered into 9 subfamilies and the genes with a similar structure and motif distribution were clustered in the same group. The gene duplication studies revealed that these genes were derived from tandem and dispersed duplication events. The cis-promoter regulatory analysis of CcGRAS genes indicated the presence of three types of cis-acting elements including light-responsive, hormone-responsive and plant growth and development related. The expression profiling of CcGRAS genes revealed their tissue-specific functions and differential nature. Collectively, this study highlights relevant functional and regulatory elements of GRAS family in pigeonpea creating a significant resource for future functional studies. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03782-x.
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Affiliation(s)
- Divyansh Rana
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313 India
| | - Priya Sharma
- Department of Biotechnology, Jamia Hamdard, New Delhi, Delhi 110062 India
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
| | - Kumari Arpita
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
| | - Harsha Srivastava
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
| | - Sandhya Sharma
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
| | - Kishor Gaikwad
- ICAR National Institute for Plant Biotechnology, ICAR, New Delhi, Delhi 110012 India
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Weng Y, Chen X, Hao Z, Lu L, Wu X, Zhang J, Wu J, Shi J, Chen J. Genome-wide analysis of the GRAS gene family in Liriodendron chinense reveals the putative function in abiotic stress and plant development. FRONTIERS IN PLANT SCIENCE 2023; 14:1211853. [PMID: 37810392 PMCID: PMC10551155 DOI: 10.3389/fpls.2023.1211853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/22/2023] [Indexed: 10/10/2023]
Abstract
Introduction GRAS genes encode plant-specific transcription factors that play essential roles in plant growth and development. However, the members and the function of the GRAS gene family have not been reported in Liriodendron chinense. L. chinense, a tree species in the Magnolia family that produces excellent timber for daily life and industry. In addition, it is a good relict species for plant evolution research. Methods Therefore, we conducted a genome-wide study of the LcGRAS gene family and identified 49 LcGRAS genes in L. chinense. Results We found that LcGRAS could be divided into 13 sub-groups, among which there is a unique branch named HAM-t. We carried out RNA sequencing analysis of the somatic embryos from L. chinense and found that LcGRAS genes are mainly expressed after heart-stage embryo development, suggesting that LcGRAS may have a function during somatic embryogenesis. We also investigated whether GRAS genes are responsive to stress by carrying out RNA sequencing (RNA-seq) analysis, and we found that the genes in the PAT subfamily were activated upon stress treatment, suggesting that these genes may help plants survive stressful environments. We found that PIF was downregulated and COR was upregulated after the transient overexpression of PATs, suggesting that PAT may be upstream regulators of cold stress. Discussion Collectively, LcGRAS genes are conserved and play essential roles in plant development and adaptation to abiotic stress.
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Affiliation(s)
- Yuhao Weng
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Xinying Chen
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Zhaodong Hao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Lu Lu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Xinru Wu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Jiaji Zhang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Jingxiang Wu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Jisen Shi
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Jinhui Chen
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
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14
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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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15
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Samarina L, Wang S, Malyukova L, Bobrovskikh A, Doroshkov A, Koninskaya N, Shkhalakhova R, Matskiv A, Fedorina J, Fizikova A, Manakhova K, Loshkaryova S, Tutberidze T, Ryndin A, Khlestkina E. Long-term cold, freezing and drought: overlapping and specific regulatory mechanisms and signal transduction in tea plant ( Camellia sinensis (L.) Kuntze). FRONTIERS IN PLANT SCIENCE 2023; 14:1145793. [PMID: 37235017 PMCID: PMC10206121 DOI: 10.3389/fpls.2023.1145793] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/11/2023] [Indexed: 05/28/2023]
Abstract
Introduction Low temperatures and drought are two main environmental constraints reducing the yield and geographical distribution of horticultural crops worldwide. Understanding the genetic crosstalk between stress responses has potential importance for crop improvement. Methods In this study, Illumina RNA-seq and Pac-Bio genome resequencing were used to annotate genes and analyze transcriptome dynamics in tea plants under long-term cold, freezing, and drought. Results The highest number of differentially expressed genes (DEGs) was identified under long-term cold (7,896) and freezing (7,915), with 3,532 and 3,780 upregulated genes, respectively. The lowest number of DEGs was observed under 3-day drought (47) and 9-day drought (220), with five and 112 genes upregulated, respectively. The recovery after the cold had 6.5 times greater DEG numbers as compared to the drought recovery. Only 17.9% of cold-induced genes were upregulated by drought. In total, 1,492 transcription factor genes related to 57 families were identified. However, only 20 transcription factor genes were commonly upregulated by cold, freezing, and drought. Among the 232 common upregulated DEGs, most were related to signal transduction, cell wall remodeling, and lipid metabolism. Co-expression analysis and network reconstruction showed 19 genes with the highest co-expression connectivity: seven genes are related to cell wall remodeling (GATL7, UXS4, PRP-F1, 4CL, UEL-1, UDP-Arap, and TBL32), four genes are related to calcium-signaling (PXL1, Strap, CRT, and CIPK6), three genes are related to photo-perception (GIL1, CHUP1, and DnaJ11), two genes are related to hormone signaling (TTL3 and GID1C-like), two genes are involved in ROS signaling (ERO1 and CXE11), and one gene is related to the phenylpropanoid pathway (GALT6). Discussion Based on our results, several important overlapping mechanisms of long-term stress responses include cell wall remodeling through lignin biosynthesis, o-acetylation of polysaccharides, pectin biosynthesis and branching, and xyloglucan and arabinogalactan biosynthesis. This study provides new insight into long-term stress responses in woody crops, and a set of new target candidate genes were identified for molecular breeding aimed at tolerance to abiotic stresses.
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Affiliation(s)
- Lidiia Samarina
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia
| | - Songbo Wang
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Lyudmila Malyukova
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Alexandr Bobrovskikh
- Institute of Cytology and Genetics Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexey Doroshkov
- Institute of Cytology and Genetics Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Natalia Koninskaya
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Ruset Shkhalakhova
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Alexandra Matskiv
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Jaroslava Fedorina
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia
| | - Anastasia Fizikova
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia
| | - Karina Manakhova
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia
| | - Svetlana Loshkaryova
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Tsiala Tutberidze
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Alexey Ryndin
- Federal Research Centre the Subtropical Scientific Centre, Russian Academy of Sciences, Sochi, Russia
| | - Elena Khlestkina
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius, Russia
- Federal Research Center, N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), Saint Petersburg, Russia
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16
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Chen C, Lu LL, Ma SY, Zhao YP, Wu N, Li WJ, Ma L, Kong XH, Xie ZM, Hou YX. Analysis of PAT1 subfamily members in the GRAS family of upland cotton and functional characterization of GhSCL13-2A in Verticillium dahliae resistance. PLANT CELL REPORTS 2023; 42:487-504. [PMID: 36680639 DOI: 10.1007/s00299-022-02971-x] [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: 09/08/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
GhSCL13-2A, a member of the PAT1 subfamily in the GRAS family, positively regulates cotton resistance to Verticillium dahliae by mediating the jasmonic acid and salicylic acid signaling pathways and accumulation of reactive oxygen species. Verticillium wilt (VW) is a devastating disease of upland cotton (Gossypium hirsutum) that is primarily caused by the soil-borne fungus Verticillium dahliae. Scarecrow-like (SCL) proteins are known to be involved in plant abiotic and biotic stress responses, but their roles in cotton defense responses are still unclear. In this study, a total of 25 GhPAT1 subfamily members in the GRAS family were identified in upland cotton. Gene organization and protein domain analysis showed that GhPAT1 members were highly conserved. GhPAT1 genes were widely expressed in various tissues and at multiple developmental stages, and they were responsive to jasmonic acid (JA), salicylic acid (SA), and ethylene (ET) signals. Furthermore, GhSCL13-2A was induced by V. dahliae infection. V. dahliae resistance was enhanced in Arabidopsis thaliana by ectopic overexpression of GhSCL13-2A, whereas cotton GhSCL13-2A knockdowns showed increased susceptibility. Levels of reactive oxygen species (ROS) and JA were also increased and SA content was decreased in GhSCL13-2A knockdowns. At the gene expression level, PR genes and SA signaling marker genes were down-regulated and JA signaling marker genes were upregulated in GhSCL13-2A knockdowns. GhSCL13-2A was shown to be localized to the cell membrane and the nucleus. Yeast two-hybrid and luciferase complementation assays indicated that GhSCL13-2A interacted with GhERF5. In Arabidopsis, V. dahliae resistance was enhanced by GhERF5 overexpression; in cotton, resistance was reduced in GhERF5 knockdowns. This study revealed a positive role of GhSCL13-2A in V. dahliae resistance, establishing it as a strong candidate gene for future breeding of V. dahliae-resistant cotton cultivars.
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Affiliation(s)
- Chen Chen
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Li-Li Lu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- National NanfanResearch Institute (Sanya), Chinese Academy ofAgricultural Sciences, Sanya, 572024, Hainan, China
| | - Shu-Ya Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yan-Peng Zhao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Na Wu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wen-Jie Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Li Ma
- Agricultural Science Institute of the Third Division of Xinjiang Production and Construction Corps, Tumushuke, 843901, Xinjiang, China
| | - Xian-Hui Kong
- Agricultural Science Institute of the Third Division of Xinjiang Production and Construction Corps, Tumushuke, 843901, Xinjiang, China
- Xinjiang Production & Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China
| | - Zong-Ming Xie
- Xinjiang Production & Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Xinjiang Academy of Agricultural and Reclamation Science, Shehezi, 832000, Xinjiang, China.
| | - Yu-Xia Hou
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
- College of Science, China Agricultural University, Beijing, 100193, China.
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Aycan M, Nahar L, Baslam M, Mitsui T. B-type response regulator hst1 controls salinity tolerance in rice by regulating transcription factors and antioxidant mechanisms. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:542-555. [PMID: 36774910 DOI: 10.1016/j.plaphy.2023.02.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/19/2023] [Accepted: 02/04/2023] [Indexed: 06/18/2023]
Abstract
Salinity is a serious environmental problem that limits plant yield in almost half of the agricultural fields. The hitomebore salt tolerant 1(hst1) is a mutant B-type response regulator gene that was reported to improve salinity tolerance in the 'YNU31-2-4' (YNU) genotype. The sister line (SL) is salt-sensitive, and the nearest genomic relative of the YNU plant has the OsRR22 gene, which is the non-mutant form of the hst1 gene. Biochemical and comprehensive transcriptome analysis of SL and YNU plants was performed to clarify the salinity tolerance mechanism(s) mediated by the hst1 gene. The hst1 gene reduced Na+ ions, lipid peroxidation, and H2O2 content, and improve proline and antioxidant enzymes activities under salt stress. Various transporter and gene-specific transcriptional regulator genes up-regulated in presence of the hst1 gene under saline conditions, identifying that post-stress transcription factors (OsbHLH056, OsH43, OsGRAS29, and OsMADS1) contributed to improved salinity tolerance in YNU plants. Specifically, OsSalT, miR156, and OsLPT1.16 genes were up-regulated, while upstream (OsHKs and OsHPs) and downstream regulators of the OsRR22 gene were down-regulated in YNU plants under saline conditions. Notably, the transcription factors reprogramming, upstream and downstream genes, indicate that these pathways are transcriptionally regulated by the hst1 gene. The findings of the regulatory role of the hst1 gene on plant transcriptome provide a greater understanding of hst1-mediated salt tolerance in rice plants. This knowledge will contribute to understanding the salinity tolerance mechanisms in rice and the evolution of salt-tolerant crops with the ability to withstand higher salinity to ensure food security during climate change.
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Affiliation(s)
- Murat Aycan
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata, 950-2181, Japan.
| | - Lutfun Nahar
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata, 950-2181, Japan; Department of Agricultural Botany, Sher-e-Bangla Agricultural University, Dhaka, 1207, Bangladesh
| | - Marouane Baslam
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata, 950-2181, Japan
| | - Toshiaki Mitsui
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata, 950-2181, Japan.
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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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Cheng Y, Liang C, Qiu Z, Zhou S, Liu J, Yang Y, Wang R, Yin J, Ma C, Cui Z, Song J, Li D. Jasmonic acid negatively regulates branch growth in pear. FRONTIERS IN PLANT SCIENCE 2023; 14:1105521. [PMID: 36824194 PMCID: PMC9941643 DOI: 10.3389/fpls.2023.1105521] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
The quality of seedlings is an important factor for development of the pear industry. A strong seedling with few branches and suitable internodes is ideal material as a rootstock for grafting and breeding. Several branching mutants of pear rootstocks were identified previously. In the present study, 'QAU-D03' (Pyrus communis L.) and it's mutants were used to explore the mechanism that affects branch formation by conducting phenotypic trait assessment, hormone content analysis, and transcriptome analysis. The mutant plant (MP) showed fewer branches, shorter 1-year-old shoots, and longer petiole length, compared to original plants (OP), i.e., wild type. Endogenous hormone analysis revealed that auxin, cytokinin, and jasmonic acid contents in the stem tips of MP were significantly higher than those of the original plants. In particular, the jasmonic acid content of the MP was 1.8 times higher than that of the original plants. Transcriptome analysis revealed that PcCOI1, which is a transcriptional regulatory gene downstream of the jasmonic acid signaling pathway, was expressed more highly in the MP than in the original plants, whereas the expression levels of PcJAZ and PcMYC were reduced in the MP compared with that of the original plants. In response to treatment with exogenous methyl jasmonate, the original plants phenotype was consistent with that of the MP in developing less branches. These results indicate that jasmonic acid negatively regulates branch growth of pear trees and that jasmonic acid downstream regulatory genes play a crucial role in regulating branching.
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Affiliation(s)
- Yuanyuan Cheng
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticultural Plants, Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Chenglin Liang
- Haidu College, Qingdao Agricultural University, Laiyang, China
| | - Zhiyun Qiu
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticultural Plants, Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Siqi Zhou
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticultural Plants, Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Jianlong Liu
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticultural Plants, Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Yingjie Yang
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticultural Plants, Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Ran Wang
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticultural Plants, Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Jie Yin
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticultural Plants, Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Chunhui Ma
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticultural Plants, Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Zhenhua Cui
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticultural Plants, Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Jiankun Song
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticultural Plants, Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Dingli Li
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticultural Plants, Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, China
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Zhao H, Gao Y, Du Y, Du J, Han Y. Genome-wide analysis of the CML gene family and its response to melatonin in common bean (Phaseolus vulgaris L.). Sci Rep 2023; 13:1196. [PMID: 36681714 PMCID: PMC9867747 DOI: 10.1038/s41598-023-28445-y] [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: 05/22/2022] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
Calmodulin-like proteins (CML) are important calcium signal transduction proteins in plants. CML genes have been analyzed in several plants. However, little information on CML in Phaseolus vulgare is available. In this study, we identified 111 PvCMLs distributed on eleven chromosomes. Phylogenetic analysis classified them into seven subfamilies. Cis-acting element prediction showed that PvCML contained elements related to growth and development, response to abiotic stress and hormones. Moreover, the majority of PvCMLs showed different expression patterns in most of the nine tissues and developmental stages which indicated the role of PvCML in the growth and development of common bean. Additionally, the common bean was treated with melatonin by seed soaking, and root transcriptome at the 5th day and qRT-PCR of different tissue at several stages were performed to reveal the response of PvCML to the hormone. Interestingly, 9 PvCML genes of subfamily VI were detected responsive to exogenous melatonin, and the expression dynamics of nine melatonin response PvCML genes after seed soaking with melatonin were revealed. Finally, the protein interaction network analysis of nine melatonin responsive PvCMLs was constructed. The systematic analysis of the PvCML gene family provides theoretical support for the further elucidation of their functions, and melatonin response molecular mechanism of the CML family in P. vulgaris.
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Affiliation(s)
- Hongyan Zhao
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, People's Republic of China
- National Coarse Cereals Engineering Research Center, Daqing, 163319, Heilongjiang, People's Republic of China
| | - Yamei Gao
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in the Cold Region, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Yanli Du
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, People's Republic of China
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, People's Republic of China
| | - Jidao Du
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, People's Republic of China
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, People's Republic of China
| | - Yiqiang Han
- College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, People's Republic of China.
- National Coarse Cereals Engineering Research Center, Daqing, 163319, Heilongjiang, People's Republic of China.
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21
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Ling L, Li M, Chen N, Ren G, Qu L, Yue H, Wu X, Zhao J. Genome-Wide Analysis and Expression of the GRAS Transcription Factor Family in Avena sativa. Genes (Basel) 2023; 14:genes14010164. [PMID: 36672905 PMCID: PMC9858933 DOI: 10.3390/genes14010164] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The GRAS transcription factor is an important transcription factor in plants. In recent years, more GRAS genes have been identified in many plant species. However, the GRAS gene family has not yet been studied in Avena sativa. We identified 100 members of the GRAS gene family in A. sativa (Avena sativa), named them AsGRAS1~AsGRAS100 according to the positions of 21 chromosomes, and classified them into 9 subfamilies. In this study, the motif and gene structures were also relatively conserved in the same subfamilies. At the same time, we found a great deal related to the stress of cis-acting promoter regulatory elements (MBS, ABRE, and TC-rich repeat elements). qRT-PCR suggested that the AsGRAS gene family (GRAS gene family in A. sativa) can regulate the response to salt, saline-alkali, and cold and freezing abiotic stresses. The current study provides original and detailed information about the AsGRAS gene family, which contributes to the functional characterization of GRAS proteins in other plants.
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22
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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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Genome-Wide Identification and Expression Pattern of the GRAS Gene Family in Pitaya ( Selenicereus undatus L.). BIOLOGY 2022; 12:biology12010011. [PMID: 36671704 PMCID: PMC9854919 DOI: 10.3390/biology12010011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
The GRAS gene family is one of the most important families of transcriptional factors that have diverse functions in plant growth and developmental processes including axillary meristem patterning, signal-transduction, cell maintenance, phytohormone and light signaling. Despite their importance, the function of GRAS genes in pitaya fruit (Selenicereus undatus L.) remains unknown. Here, 45 members of the HuGRAS gene family were identified in the pitaya genome, which was distributed on 11 chromosomes. All 45 members of HuGRAS were grouped into nine subfamilies using phylogenetic analysis with six other species: maize, rice, soybeans, tomatoes, Medicago truncatula and Arabidopsis. Among the 45 genes, 12 genes were selected from RNA-Seq data due to their higher expression in different plant tissues of pitaya. In order to verify the RNA-Seq data, these 12 HuGRAS genes were subjected for qRT-PCR validation. Nine HuGRAS genes exhibited higher relative expression in different tissues of the plant. These nine genes which were categorized into six subfamilies inlcuding DELLA (HuGRAS-1), SCL-3 (HuGRAS-7), PAT1 (HuGRAS-34, HuGRAS-35, HuGRAS-41), HAM (HuGRAS-37), SCR (HuGRAS-12) and LISCL (HuGRAS-18, HuGRAS-25) might regulate growth and development in the pitaya plant. The results of the present study provide valuable information to improve tropical pitaya through a molecular and conventional breeding program.
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Bai Y, Liu H, Zhu K, Cheng ZM. Evolution and functional analysis of the GRAS family genes in six Rosaceae species. BMC PLANT BIOLOGY 2022; 22:569. [PMID: 36471247 PMCID: PMC9724429 DOI: 10.1186/s12870-022-03925-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND GRAS genes formed one of the important transcription factor gene families in plants, had been identified in several plant species. The family genes were involved in plant growth, development, and stress resistance. However, the comparative analysis of GRAS genes in Rosaceae species was insufficient. RESULTS In this study, a total of 333 GRAS genes were identified in six Rosaceae species, including 51 in strawberry (Fragaria vesca), 78 in apple (Malus domestica), 41 in black raspberry (Rubus occidentalis), 59 in European pear (Pyrus communis), 56 in Chinese rose (Rosa chinensis), and 48 in peach (Prunus persica). Motif analysis showed the VHIID domain, SAW motif, LR I region, and PFYRE motif were considerably conserved in the six Rosaceae species. All GRAS genes were divided into 10 subgroups according to phylogenetic analysis. A total of 15 species-specific duplicated clades and 3 lineage-specific duplicated clades were identified in six Rosaceae species. Chromosomal localization presented the uneven distribution of GRAS genes in six Rosaceae species. Duplication events contributed to the expression of the GRAS genes, and Ka/Ks analysis suggested the purification selection as a major force during the evolution process in six Rosaceae species. Cis-acting elements and GO analysis revealed that most of the GRAS genes were associated with various environmental stress in six Rosaceae species. Coexpression network analysis showed the mutual regulatory relationship between GRAS and bZIP genes, suggesting the ability of the GRAS gene to regulate abiotic stress in woodland strawberry. The expression pattern elucidated the transcriptional levels of FvGRAS genes in various tissues and the drought and salt stress in woodland strawberry, which were verified by RT-qPCR analysis. CONCLUSIONS The evolution and functional analysis of GRAS genes provided insights into the further understanding of GRAS genes on the abiotic stress of Rosaceae species.
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Affiliation(s)
- Yibo Bai
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Hui Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Kaikai Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Zong-Ming Cheng
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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25
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Genome-Wide Characterization and Expression Profiling of the GRAS Gene Family in Salt and Alkali Stresses in Miscanthus sinensis. Int J Mol Sci 2022; 23:ijms232314521. [PMID: 36498850 PMCID: PMC9737823 DOI: 10.3390/ijms232314521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/10/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
The GRAS family genes encode plant-specific transcription factors that play important roles in a diverse range of developmental processes and abiotic stress responses. However, the information of GRAS gene family in the bioenergy crop Miscanthus has not been available. Here, we report the genome-wide identification of GRAS gene family in Micanthus sinensis. A total of 123 MsGRAS genes were identified, which were divided into ten subfamilies based on the phylogenetic analysis. The co-linearity analysis revealed that 59 MsGRAS genes experienced segmental duplication, forming 35 paralogous pairs. The expression of six MsGRAS genes in responding to salt, alkali, and mixed salt-alkali stresses was analyzed by transcriptome and real-time quantitative PCR (RT-qPCR) assays. Furthermore, the role of MsGRAS60 in salt and alkali stress response was characterized in transgenic Arabidopsis. The MsGRAS60 overexpression lines exhibited hyposensitivity to abscisic acid (ABA) treatment and resulted in compromised tolerance to salt and alkali stresses, suggesting that MsGRAS60 is a negative regulator of salt and alkali tolerance via an ABA-dependent signaling pathway. The salt and alkali stress-inducible MsGRAS genes identified serve as candidates for the improvement of abiotic stress tolerance in Miscanthus.
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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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A Comparative Transcriptome Analysis Reveals the Molecular Mechanisms That Underlie Somatic Embryogenesis in Peaonia ostii ‘Fengdan’. Int J Mol Sci 2022; 23:ijms231810595. [PMID: 36142512 PMCID: PMC9505998 DOI: 10.3390/ijms231810595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 11/20/2022] Open
Abstract
Low propagation rate is the primary problem that limits industry development of tree peony. In this study, a highly efficient regeneration system for tree peony using somatic embryogenesis (SE) was established. The transcriptomes of zygotic embryo explants (S0), non-embryonic callus (S1), embryonic callus (S2), somatic embryos (S3), and regenerated shoots (S4) were analyzed to determine the regulatory mechanisms that underlie SE in tree peony. The differentially expressed genes (DEGs) were identified in the pairwise comparisons of S1-vs-S2 and S1-vs-S3, respectively. The enriched DEGs were primarily involved in hormone signal transduction, stress response and the nucleus (epigenetic modifications). The results indicated that cell division, particularly asymmetric cell division, was enhanced in S3. Moreover, the genes implicated in cell fate determination played central roles in S3. Hormone signal pathways work in concert with epigenetic modifications and stress responses to regulate SE. SERK, WOX9, BBM, FUS3, CUC, and WUS were characterized as the molecular markers for tree peony SE. To our knowledge, this is the first study of the SE of tree peony using transcriptome sequencing. These results will improve our understanding of the molecular mechanisms that underly SE in tree peony and will benefit the propagation and genetic engineering of this plant.
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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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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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Duan L, Mo Z, Fan Y, Li K, Yang M, Li D, Ke Y, Zhang Q, Wang F, Fan Y, Liu R. Genome-wide identification and expression analysis of the bZIP transcription factor family genes in response to abiotic stress in Nicotiana tabacum L. BMC Genomics 2022; 23:318. [PMID: 35448973 PMCID: PMC9027840 DOI: 10.1186/s12864-022-08547-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 04/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The basic leucine zipper (bZIP) transcription factor (TF) is one of the largest families of transcription factors (TFs). It is widely distributed and highly conserved in animals, plants, and microorganisms. Previous studies have shown that the bZIP TF family is involved in plant growth, development, and stress responses. The bZIP family has been studied in many plants; however, there is little research on the bZIP gene family in tobacco. RESULTS In this study, 77 bZIPs were identified in tobacco and named NtbZIP01 through to NtbZIP77. These 77 genes were then divided into eleven subfamilies according to their homology with Arabidopsis thaliana. NtbZIPs were unevenly distributed across twenty-two tobacco chromosomes, and we found sixteen pairs of segmental duplication. We further studied the collinearity between these genes and related genes of six other species. Quantitative real-time polymerase chain reaction analysis identified that expression patterns of bZIPs differed, including in different organs and under various abiotic stresses. NtbZIP49 might be important in the development of flowers and fruits; NtbZIP18 might be an important regulator in abiotic stress. CONCLUSIONS In this study, the structures and functions of the bZIP family in tobacco were systematically explored. Many bZIPs may play vital roles in the regulation of organ development, growth, and responses to abiotic stresses. This research has great significance for the functional characterisation of the tobacco bZIP family and our understanding of the bZIP family in higher plants.
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Affiliation(s)
- Lili Duan
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
- Guizhou Key Laboratory for Tobacco Quality Research, Guizhou University, Guiyang, 550025, People's Republic of China
- College of Tobacco, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Zejun Mo
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
- Guizhou Key Laboratory for Tobacco Quality Research, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Yue Fan
- College of Food Science and Engineering, Xinjiang Institute of Technology, Aksu, 843100, People's Republic of China
| | - Kuiyin Li
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Mingfang Yang
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Dongcheng Li
- Guizhou Key Laboratory for Tobacco Quality Research, Guizhou University, Guiyang, 550025, People's Republic of China
- College of Tobacco, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Yuzhou Ke
- Guizhou Key Laboratory for Tobacco Quality Research, Guizhou University, Guiyang, 550025, People's Republic of China
- College of Tobacco, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Qian Zhang
- Guizhou Key Laboratory for Tobacco Quality Research, Guizhou University, Guiyang, 550025, People's Republic of China
- College of Tobacco, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Feiyan Wang
- Guizhou Key Laboratory for Tobacco Quality Research, Guizhou University, Guiyang, 550025, People's Republic of China
- College of Tobacco, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Yu Fan
- School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, People's Republic of China.
| | - Renxiang Liu
- Guizhou Key Laboratory for Tobacco Quality Research, Guizhou University, Guiyang, 550025, People's Republic of China.
- College of Tobacco, Guizhou University, Guiyang, 550025, People's Republic of China.
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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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Lu L, Diao Z, Yang D, Wang X, Zheng X, Xiang X, Xiao Y, Chen Z, Wang W, Wu Y, Tang D, Li S. The 14-3-3 protein GF14c positively regulates immunity by modulating the protein homoeostasis of the GRAS protein OsSCL7 in rice. PLANT, CELL & ENVIRONMENT 2022; 45:1065-1081. [PMID: 35129212 DOI: 10.1111/pce.14278] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 01/07/2022] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
Various types of transcription factors have been reported to be involved in plant-pathogen interactions by regulating defence-related genes. GRAS proteins, plant- specific transcription factors, have been shown to play essential roles in plant growth, development and stress responses. By performing a transcriptome study on rice early defence responses to Magnaporthe oryzae, we identified a GRAS protein, OsSCL7, which was induced by M. oryzae infection. We characterized the function of OsSCL7 in rice disease resistance. OsSCL7 was upregulated upon exposure to M. oryzae and pathogen-associated molecular pattern treatments, and knocking out OsSCL7 resulted in decreased disease resistance of rice to M. oryzae. In contrast, overexpression of OsSCL7 could improve rice disease resistance to M. oryzae. OsSCL7 was mainly localized in the nucleus and showed transcriptional activity. OsSCL7 can interact with GF14c, a 14-3-3 protein, and loss-of-function GF14c leads to enhanced susceptibility to M. oryzae. Additionally, OsSCL7 protein levels were reduced in the gf14c mutant and knocking out OsSCL7 affected the expression of a series of defence-related genes. Taken together, these findings uncover the important roles of OsSCL7 and GF14c in plant immunity and a potential mechanism by which plants fine-tune immunity by regulating the protein stability of a GRAS protein via a 14-3-3 protein.
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Affiliation(s)
- Ling Lu
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding, and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhijuan Diao
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding, and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dewei Yang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding, and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Xun Wang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding, and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xingxing Zheng
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding, and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xinquan Xiang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding, and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yueping Xiao
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding, and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhiwei Chen
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding, and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei Wang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding, and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yunkun Wu
- College of Life Science, Fujian Normal University, Fuzhou, China
| | - Dingzhong Tang
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding, and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shengping Li
- State Key Laboratory of Ecological Control of Fujian-Taiwan Crop Pests, Key Laboratory of Ministry of Education for Genetics, Breeding, and Multiple Utilization of Crops, Plant Immunity Center, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China
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Kesawat MS, Kherawat BS, Singh A, Dey P, Routray S, Mohapatra C, Saha D, Ram C, Siddique KHM, Kumar A, Gupta R, Chung SM, Kumar M. Genome-Wide Analysis and Characterization of the Proline-Rich Extensin-like Receptor Kinases (PERKs) Gene Family Reveals Their Role in Different Developmental Stages and Stress Conditions in Wheat ( Triticum aestivum L.). PLANTS (BASEL, SWITZERLAND) 2022; 11:496. [PMID: 35214830 PMCID: PMC8880425 DOI: 10.3390/plants11040496] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 05/19/2023]
Abstract
Proline-rich extensin-like receptor kinases (PERKs) are a class of receptor kinases implicated in multiple cellular processes in plants. However, there is a lack of information on the PERK gene family in wheat. Therefore, we identified 37 PERK genes in wheat to understand their role in various developmental processes and stress conditions. Phylogenetic analysis of PERK genes from Arabidopsis thaliana, Oryza sativa, Glycine max, and T. aestivum grouped them into eight well-defined classes. Furthermore, synteny analysis revealed 275 orthologous gene pairs in B. distachyon, Ae. tauschii, T. dicoccoides, O. sativa and A. thaliana. Ka/Ks values showed that most TaPERK genes, except TaPERK1, TaPERK2, TaPERK17, and TaPERK26, underwent strong purifying selection during evolutionary processes. Several cis-acting regulatory elements, essential for plant growth and development and the response to light, phytohormones, and diverse biotic and abiotic stresses, were predicted in the promoter regions of TaPERK genes. In addition, the expression profile of the TaPERK gene family revealed differential expression of TaPERK genes in various tissues and developmental stages. Furthermore, TaPERK gene expression was induced by various biotic and abiotic stresses. The RT-qPCR analysis also revealed similar results with slight variation. Therefore, this study's outcome provides valuable information for elucidating the precise functions of TaPERK in developmental processes and diverse stress conditions in wheat.
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Affiliation(s)
- Mahipal Singh Kesawat
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sri Sri University, Cuttack 754006, Odisha, India; (M.S.K.); (A.S.); (P.D.)
- School of Biological Sciences and Institute for Molecular Biology and Genetics, Seoul National University, Seoul 08826, Korea
| | - Bhagwat Singh Kherawat
- Krishi Vigyan Kendra, Bikaner II, Swami Keshwanand Rajasthan Agricultural University, Bikaner 334603, Rajasthan, India;
| | - Anupama Singh
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sri Sri University, Cuttack 754006, Odisha, India; (M.S.K.); (A.S.); (P.D.)
| | - Prajjal Dey
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sri Sri University, Cuttack 754006, Odisha, India; (M.S.K.); (A.S.); (P.D.)
| | - Snehasish Routray
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Sri Sri University, Cuttack 754006, Odisha, India; (S.R.); (C.M.)
| | - Chinmayee Mohapatra
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Sri Sri University, Cuttack 754006, Odisha, India; (S.R.); (C.M.)
| | - Debanjana Saha
- Department of Biotechnology, Centurion University of Technology and Management, Bhubaneshwar 752050, Odisha, India;
| | - Chet Ram
- ICAR-Central Institute for Arid Horticulture, Bikaner 334006, Rajasthan, India;
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia;
| | - Ajay Kumar
- Agriculture Research Organization, Volcani Center, Department of Postharvest Science, Rishon Lezzion 50250, Israel;
| | - Ravi Gupta
- College of General Education, Kookmin University, Seoul 02707, Korea;
| | - Sang-Min Chung
- Department of Life Science, Dongguk University, Dong-gu, Ilsan, Seoul 10326, Korea;
| | - Manu Kumar
- Department of Life Science, Dongguk University, Dong-gu, Ilsan, Seoul 10326, Korea;
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Shuai Y, Feng G, Yang Z, Liu Q, Han J, Xu X, Nie G, Huang L, Zhang X. Genome-wide identification of C2H2-type zinc finger gene family members and their expression during abiotic stress responses in orchardgrass ( Dactylis glomerata). Genome 2022; 65:189-203. [PMID: 35104149 DOI: 10.1139/gen-2020-0201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The C2H2-type zinc finger protein (ZFP) family is one of the largest transcription factor families in the plant kingdom and its members are involved in plant growth, development, and stress responses. As an economically valuable perennial graminaceous forage crop, orchardgrass (Dactylis glomerata) is an important feedstuff resource owing to its high yield and quality. In this study, 125 C2H2-type ZFPs in orchardgrass (Dg-ZFPs) were identified and further classified by phylogenetic analysis. The members with similar gene structures were generally clustered into the same groups, with proteins containing the conserved QALGGH motif being concentrated in groups VIII and IX. Gene ontology and miRNA target analyses indicated that Dg-ZFPs likely perform diverse biological functions through their gene interactions. The RNA-seq data revealed differentially expressed genes across tissues and development phases, suggesting that some Dg-ZFPs might participate in growth and development regulation. Abiotic stress responses of Dg-ZFP genes were verified by qPCR and Saccharomyces cerevisiae transformation, revealing that Dg-ZFP125 could enhance the tolerance of yeasts to osmotic and salt stresses. Our study performed a novel systematic analysis of Dg-ZFPs in orchardgrass, providing a reference for this gene family in other grasses and revealing new insights for enhancing gene utilization.
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Affiliation(s)
- Yang Shuai
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhongfu Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiuxu Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiating Han
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaoheng Xu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
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Bano N, Fakhrah S, Nayak SP, Bag SK, Mohanty CS. Identification of miRNA and their target genes in Cestrum nocturnum L. and Cestrum diurnum L. in stress responses. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:31-49. [PMID: 35221570 PMCID: PMC8847519 DOI: 10.1007/s12298-022-01127-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 12/14/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
UNLABELLED MicroRNAs (miRNAs) are small, highly conserved non-coding RNA molecules and products of primary miRNAs that regulate the target gene expression. Homology-based approaches were employed to identify miRNAs and their targets in Cestrum nocturnum L. and Cestrum diurnum L. A total of 32 and 12 miRNA candidates were identified in C. nocturnum and C. diurnum. These miRNAs belong to 26 and 10 miRNA families and regulate 1024 and 1007 target genes in C. nocturnum, and C. diurnum, respectively. The functional roles of these miRNAs have not been earlier elucidated in Cestrum. MiR815a, miR849, miR1089 and miR172 have a strong propensity to target genes controlling phytochrome-interacting factor 1 (PIF1), ubiquitin-specific protease 12 (UBP12), leucine-rich repeat (LRR) protein kinase and GAI, RGA, SCR (GRAS) family transcription factor in C. nocturnum. While miR5205a, miR1436 and miR530 regulate PATATIN-like protein 6 (PLP6), PHD finger transcription factor and myb domain protein 48 (MYB48) in C. diurnum. Overall, these miRNAs have regulatory responses in biotic and abiotic stresses in both plant species. Eight putative miRNAs and their target genes were selected for qRT-PCR validation. The validated results suggested the importance of miR815a, miR849, miR5205a, miR1089, miR172, miR1436, and miR530 in exerting control over stress responses in C. nocturnum and C. diurnum. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01127-1.
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Affiliation(s)
- Nasreen Bano
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Shafquat Fakhrah
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Department of Botany, University of Lucknow, Lucknow, Uttar Pradesh 226007 India
| | - Sagar Prasad Nayak
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Sumit Kumar Bag
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Lucknow, India
| | - Chandra Sekhar Mohanty
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
- Plant Genetic Resources and Improvement Division, CSIR-National Botanical Research Institute, Lucknow, India
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Ali F, Li Y, Li F, Wang Z. Genome-wide characterization and expression analysis of cystathionine β-synthase genes in plant development and abiotic stresses of cotton (Gossypium spp.). Int J Biol Macromol 2021; 193:823-837. [PMID: 34687765 DOI: 10.1016/j.ijbiomac.2021.10.079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 10/09/2021] [Accepted: 10/11/2021] [Indexed: 11/20/2022]
Abstract
Cystathionine β-synthase (CBS) domains containing proteins (CDCPs) form a large family and play roles in development via regulation of the thioredoxin system as well as abiotic and biotic stress responses of plant. However, the comprehensive study of CBS genes remained elusive in cotton. Here, we identified 237 CBS genes in 11 plant species and the phylogenetic analysis categorized CBS genes into four groups. Whole-genome or segmental with dispersed duplication events contributed to GhCBS gene family expansion. Moreover, orthologous/paralogous genes among three cotton species (G. hirsutum, G. arboreum, and G. raimondii) were detected from the syntenic map among eight plant species. Strong purifying selection for dicotyledonous and monocotyledonous CBS genes, and cis-elements related to plant growth and development, abiotic and hormonal response were observed. Transcriptomic data and qRT-PCR validation of 12 GhCBS genes indicated their critical role in ovule development as most of the genes showed high enrichment. Further, some of GhCBS (GhCBS5, GhCBS16, GhCBS17, GhCBS24, GhCBS25, GhCBS26, and GhCBS52) genes were regulated under various abiotic and hormonal treatments for different time points and involve in ovule and fiber development which provided key genes for future cotton breeding programs. In addition, transgenic tobacco plants overexpressing GhCBS4 transiently exhibited higher water and chlorophyll content indicating improved tolerance toward drought stress. Overall, this study provides the characterization of GhCBS genes for plant growth, abiotic and hormonal stresses, thereby, intimating their significance in cotton molecular breeding for resistant cultivars.
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Affiliation(s)
- Faiza Ali
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450001 Zhengzhou, China
| | - Yonghui Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450001 Zhengzhou, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450001 Zhengzhou, China; State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Zhi Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, 450001 Zhengzhou, China; State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
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Frosi G, Ferreira-Neto JRC, Bezerra-Neto JP, Pandolfi V, da Silva MD, de Lima Morais DA, Benko-Iseppon AM, Santos MG. Transcriptome of Cenostigma pyramidale roots, a woody legume, under different salt stress times. PHYSIOLOGIA PLANTARUM 2021; 173:1463-1480. [PMID: 33973275 DOI: 10.1111/ppl.13456] [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: 02/26/2021] [Revised: 04/24/2021] [Accepted: 05/04/2021] [Indexed: 05/20/2023]
Abstract
Salinity stress has a significant impact on the gain of plant biomass. Our study provides the first root transcriptome of Cenostigma pyramidale, a tolerant woody legume from a tropical dry forest, under three different salt stress times (30 min, 2 h, and 11 days). The transcriptome was assembled using the RNA sequencing (RNA-Seq) de novo pipeline from GenPipes. We observed 932, 804, and 3157 upregulated differentially expressed genes (DEGs) and 164, 273, and 1332 downregulated DEGs for salt over 30 min, 2 h, and 11 days, respectively. For DEGs annotated with the Viridiplantae clade in the early stress periods, the response to salt stress was mainly achieved by stabilizing homeostasis of such ions like Na+ and K+ , signaling by Ca2+ , transcription factor modulation, water transport, and oxidative stress. For salt stress at 11 days, we observed a higher modulation of transcription factors including the WRKY, MYB, bHLH, NAC, HSF, and AP2-EREBP families, as well as DEGs involved in hormonal responses, water transport, sugar metabolism, proline, and reactive oxygen scavenging mechanisms. Five selected DEGs (K+ transporter, aquaporin, glutathione S-transferase, cyclic nucleotide-gated channel, and superoxide dismutase) were validated by qPCR. Our results indicated that C. pyramidale had an early perception of salt stress modulating ionic channels and transporters, and as the stress progressed, the focus turned to the antioxidant system, aquaporins, and complex hormone responses. The results of this first root transcriptome provide clues on how this native species modulate gene expression to achieve salt stress tolerance.
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Affiliation(s)
- Gabriella Frosi
- Departamento de Botânica, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
- Faculté des Sciences, Départament de Biologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | | | | | - Valesca Pandolfi
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | | | | | | | - Mauro Guida Santos
- Departamento de Botânica, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
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Liu X, Yang X, Zhang B. Transcriptome analysis and functional identification of GmMYB46 in soybean seedlings under salt stress. PeerJ 2021; 9:e12492. [PMID: 34824922 PMCID: PMC8590805 DOI: 10.7717/peerj.12492] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/25/2021] [Indexed: 01/19/2023] Open
Abstract
Salinity is one of the major abiotic stress that limits crop growth and productivity. We investigated the transcriptomes of salt-treated soybean seedlings versus a control using RNA-seq to better understand the molecular mechanisms of the soybean (Glycine max L.) response to salt stress. Transcriptome analysis revealed 1,235 differentially expressed genes (DEGs) under salt stress. Several important pathways and key candidate genes were identified by KEGG enrichment. A total of 116 differentially expressed transcription factors (TFs) were identified, and 17 TFs were found to belong to MYB families. Phylogenetic analysis revealed that these TFs may be involved in salt stress adaptation. Further analysis revealed that GmMYB46 was up-regulated by salt and mannitol and was localized in the nucleus. The salt tolerance of transgenic Arabidopsis overexpressing GmMYB46 was significantly enhanced compared to wild-type (WT). GmMYB46 activates the expression of salt stress response genes (P5CS1, SOD, POD, NCED3) in Arabidopsis under salt stress, indicating that the GmMYB46 protein mediates the salt stress response through complex regulatory mechanisms. This study provides information with which to better understand the molecular mechanism of salt tolerance in soybeans and to genetically improve the crop.
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Affiliation(s)
- Xun Liu
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, China.,College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xinxia Yang
- Department of Logistics, Hunan University of Science and Engineering, Yongzhou, China
| | - Bin Zhang
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, China
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Dutta M, Saha A, Moin M, Kirti PB. Genome-Wide Identification, Transcript Profiling and Bioinformatic Analyses of GRAS Transcription Factor Genes in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:777285. [PMID: 34899804 PMCID: PMC8660974 DOI: 10.3389/fpls.2021.777285] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/26/2021] [Indexed: 05/28/2023]
Abstract
Our group has previously identified the activation of a GRAS transcription factor (TF) gene in the gain-of-function mutant population developed through activation tagging in rice (in an indica rice variety, BPT 5204) that was screened for water use efficiency. This family of GRAS transcription factors has been well known for their diverse roles in gibberellin signaling, light responses, root development, gametogenesis etc. Recent studies indicated their role in biotic and abiotic responses as well. Although this family of TFs received significant attention, not many genes were identified specifically for their roles in mediating stress tolerance in rice. Only OsGRAS23 (here named as OsGRAS22) was reported to code for a TF that induced drought tolerance in rice. In the present study, we have analyzed the expression patterns of rice GRAS TF genes under abiotic (NaCl and ABA treatments) and biotic (leaf samples infected with pathogens, Xanthomonas oryzae pv. oryzae that causes bacterial leaf blight and Rhizoctonia solani that causes sheath blight) stress conditions. In addition, their expression patterns were also analyzed in 13 different developmental stages. We studied their spatio-temporal regulation and correlated them with the in-silico studies. Fully annotated genomic sequences available in rice database have enabled us to study the protein properties, ligand interactions, domain analysis and presence of cis-regulatory elements through the bioinformatic approach. Most of the genes were induced immediately after the onset of stress particularly in the roots of ABA treated plants. OsGRAS39 was found to be a highly expressive gene under sheath blight infection and both abiotic stress treatments while OsGRAS8, OsSHR1 and OsSLR1 were also responsive. Our earlier activation tagging based functional characterization followed by the genome-wide characterization of the GRAS gene family members in the present study clearly show that they are highly appropriate candidate genes for manipulating stress tolerance in rice and other crop plants.
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Affiliation(s)
- Mouboni Dutta
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Anusree Saha
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Mazahar Moin
- Department of Biotechnology, Indian Institute of Rice Research, Hyderabad, India
| | - Pulugurtha Bharadwaja Kirti
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
- Agri Biotech Foundation, PJTS Agricultural University Campus, Hyderabad, India
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Zhao Z, Shuang J, Li Z, Xiao H, Liu Y, Wang T, Wei Y, Hu S, Wan S, Peng R. Identification of the Golden-2-like transcription factors gene family in Gossypium hirsutum. PeerJ 2021; 9:e12484. [PMID: 34820202 PMCID: PMC8603818 DOI: 10.7717/peerj.12484] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 10/22/2021] [Indexed: 01/19/2023] Open
Abstract
Background Golden2-Like (GLK) transcription factors are a type of transcriptional regulator in plants. They play a pivotal role in the plant physiological activity process and abiotic stress response. Methods In this study, the potential function of GLK family genes in Gossypium hirsutum was studied based on genomic identification, phylogenetic analysis, chromosome mapping and cis-regulatory elements prediction. Gene expression of nine key genes were analyzed by qRT-PCR experiments. Results Herein, we identified a total of 146 GhGLK genes in Gossypium hirsutum, which were unevenly distributed on each of the chromosomes. There were significant differences in the number and location of genes between the At sub-genome and the Dt sub-genome. According to the phylogenetic analysis, they were divided into ten subgroups, each of which had very similar number and structure of exons and introns. Some cis-regulatory elements were identified through promoter analysis, including five types of elements related to abiotic stress response, five types of elements related to phytohormone and five types of elements involved in growth and development. Based on public transcriptome data analysis, we identified nine key GhGLKs involved in salt, cold, and drought stress. The qRT-PCR results showed that these genes had different expression patterns under these stress conditions, suggesting that GhGLK genes played an important role in abiotic stress response. This study laid a theoretical foundation for the screening and functional verification of genes related to stress resistance of GLK gene family in cotton.
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Affiliation(s)
- Zilin Zhao
- College of Plant Science, Tarim University, Alar, Xinjiang, China.,Anyang Institute of Technology, Anyang, Henan, China
| | - Jiaran Shuang
- Anyang Institute of Technology, Anyang, Henan, China
| | - Zhaoguo Li
- Anyang Institute of Technology, Anyang, Henan, China
| | - Huimin Xiao
- Anyang Institute of Technology, Anyang, Henan, China
| | - Yuling Liu
- Anyang Institute of Technology, Anyang, Henan, China
| | - Tao Wang
- Anyang Institute of Technology, Anyang, Henan, China
| | - Yangyang Wei
- Anyang Institute of Technology, Anyang, Henan, China
| | - Shoulin Hu
- College of Plant Science, Tarim University, Alar, Xinjiang, China
| | - Sumei Wan
- College of Plant Science, Tarim University, Alar, Xinjiang, China
| | - Renhai Peng
- College of Plant Science, Tarim University, Alar, Xinjiang, China.,Anyang Institute of Technology, Anyang, Henan, China
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Fan Y, Wei X, Lai D, Yang H, Feng L, Li L, Niu K, Chen L, Xiang D, Ruan J, Yan J, Cheng J. Genome-wide investigation of the GRAS transcription factor family in foxtail millet (Setaria italica L.). BMC PLANT BIOLOGY 2021; 21:508. [PMID: 34732123 PMCID: PMC8565077 DOI: 10.1186/s12870-021-03277-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/18/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND GRAS transcription factors perform indispensable functions in various biological processes, such as plant growth, fruit development, and biotic and abiotic stress responses. The development of whole-genome sequencing has allowed the GRAS gene family to be identified and characterized in many species. However, thorough in-depth identification or systematic analysis of GRAS family genes in foxtail millet has not been conducted. RESULTS In this study, 57 GRAS genes of foxtail millet (SiGRASs) were identified and renamed according to the chromosomal distribution of the SiGRAS genes. Based on the number of conserved domains and gene structure, the SiGRAS genes were divided into 13 subfamilies via phylogenetic tree analysis. The GRAS genes were unevenly distributed on nine chromosomes, and members of the same subfamily had similar gene structures and motif compositions. Genetic structure analysis showed that most SiGRAS genes lacked introns. Some SiGRAS genes were derived from gene duplication events, and segmental duplications may have contributed more to GRAS gene family expansion than tandem duplications. Quantitative polymerase chain reaction showed significant differences in the expression of SiGRAS genes in different tissues and stages of fruits development, which indicated the complexity of the physiological functions of SiGRAS. In addition, exogenous paclobutrazol treatment significantly altered the transcription levels of DELLA subfamily members, downregulated the gibberellin content, and decreased the plant height of foxtail millet, while it increased the fruit weight. In addition, SiGRAS13 and SiGRAS25 may have the potential for genetic improvement and functional gene research in foxtail millet. CONCLUSIONS Collectively, this study will be helpful for further analysing the biological function of SiGRAS. Our results may contribute to improving the genetic breeding of foxtail millet.
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Affiliation(s)
- Yu Fan
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
- School of Food and Biological engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Xiaobao Wei
- Guizhou provincial Center For Disease Control And Prevention, Guiyang, 550025, People's Republic of China
| | - Dili Lai
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Hao Yang
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Liang Feng
- Chengdu Institute of Food Inspection, Chengdu, 610030, People's Republic of China
| | - Long Li
- Henan university of technology, Zhengzhou, 450001, People's Republic of China
| | - Kexin Niu
- Henan university of technology, Zhengzhou, 450001, People's Republic of China
| | - Long Chen
- Department of Nursing, Sichuan Tianyi College, Mianzhu, 618200, People's Republic of China
| | - Dabing Xiang
- School of Food and Biological engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China
| | - Jun Yan
- School of Food and Biological engineering, Chengdu University, Chengdu, 610106, People's Republic of China.
| | - Jianping Cheng
- College of Agriculture, Guizhou University, Guiyang, 550025, People's Republic of China.
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Laskar P, Bhattacharya S, Chaudhuri A, Kundu A. Exploring the GRAS gene family in common bean (Phaseolus vulgaris L.): characterization, evolutionary relationships, and expression analyses in response to abiotic stresses. PLANTA 2021; 254:84. [PMID: 34561734 DOI: 10.1007/s00425-021-03725-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/05/2021] [Indexed: 06/13/2023]
Abstract
Genome-wide identification reveals 55 PvuGRAS genes belonging to 16 subfamilies and their gene structures and evolutionary relationships were characterized. Expression analyses highlight their prominence in plant growth, development and abiotic stress responses. GRAS proteins comprise a plant-specific transcription factor family involved in multiple growth regulatory pathways and environmental cues including abiotic/biotic stresses. Despite its crucial importance, characterization of this gene family is still elusive in common bean. A systematic genome-wide scan identified 55 PvuGRAS genes unevenly anchored to the 11 common bean chromosomes. Segmental duplication appeared to be the key driving force behind expansion of this gene family that underwent purifying selection during evolution. Computational investigation unraveled their intronless organization and identified similar motif composition within the same subfamily. Phylogenetic analyses clustered the PvuGRAS proteins into 16 phylogenetic clades and established extensive orthologous relationships with Arabidopsis and rice. Analysis of the upstream promoter region uncovered cis-elements responsive to growth, development, and abiotic stresses that may account for their differential expression. The identified SSRs could serve as putative molecular markers facilitating future breeding programs. 37 PvuGRAS transcripts were post-transcriptionally regulated by different miRNA families, miR171 being the major player preferentially targeting members of the HAM subfamily. Global expression profile based on RNA-seq data indicates a clade specific expression pattern in various tissues and developmental stages. Additionally, nine PvuGRAS genes were chosen for further qPCR analyses under drought, salt, and cold stress suggesting their involvement in acclimation to environmental stimuli. Combined, the present results significantly contribute to the current understanding of the complexity and biological function of the PvuGRAS gene family. The resources generated will provide a solid foundation in future endeavors for genetic improvement in common bean.
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Affiliation(s)
- Parbej Laskar
- Plant Genomics and Bioinformatics Laboratory, P.G. Department of Botany, Ramakrishna Mission Vivekananda Centenary College (Autonomous), Rahara, Kolkata, 700118, India
| | - Saswati Bhattacharya
- Department of Botany, Dr. A.P.J. Abdul Kalam Government College, New Town, Rajarhat, India
| | - Atreyee Chaudhuri
- Aquatic Bioresource Research Laboratory, Department of Zoology , University of Calcutta, Kolkata, India
| | - Anirban Kundu
- Plant Genomics and Bioinformatics Laboratory, P.G. Department of Botany, Ramakrishna Mission Vivekananda Centenary College (Autonomous), Rahara, Kolkata, 700118, India.
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Chen J, Yan Q, Li J, Feng L, Zhang Y, Xu J, Xia R, Zeng Z, Liu Y. The GRAS gene family and its roles in seed development in litchi (Litchi chinensis Sonn). BMC PLANT BIOLOGY 2021; 21:423. [PMID: 34535087 PMCID: PMC8447652 DOI: 10.1186/s12870-021-03193-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/25/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The GRAS gene family plays crucial roles in multiple biological processes of plant growth, including seed development, which is related to seedless traits of litchi (Litchi chinensis Sonn.). However, it hasn't been fully identified and analyzed in litchi, an economic fruit tree cultivated in subtropical regions. RESULTS In this study, 48 LcGRAS proteins were identified and termed according to their chromosomal location. LcGRAS proteins can be categorized into 14 subfamilies through phylogenetic analysis. Gene structure and conserved domain analysis revealed that different subfamilies harbored various motif patterns, suggesting their functional diversity. Synteny analysis revealed that the expansion of the GRAS family in litchi may be driven by their tandem and segmental duplication. After comprehensively analysing degradome data, we found that four LcGRAS genes belong to HAM subfamily were regulated via miR171-mediated degradation. The various expression patterns of LcGRAS genes in different tissues uncovered they were involved in different biological processes. Moreover, the different temporal expression profiles of LcGRAS genes between abortive and bold seed indicated some of them were involved in maintaining the normal development of the seed. CONCLUSION Our study provides comprehensive analyses on GRAS family members in litchi, insight into a better understanding of the roles of GRAS in litchi development, and lays the foundation for further investigations on litchi seed development.
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Affiliation(s)
- Jingwen Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 483 Wushan Road, Tianhe, Guangzhou, 510642, Guangdong Province, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Qian Yan
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture / Guangdong ProvinceKey Laboratary of Tropical and Subtropical Fruit Tree Research / Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jiawei Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 483 Wushan Road, Tianhe, Guangzhou, 510642, Guangdong Province, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Lei Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 483 Wushan Road, Tianhe, Guangzhou, 510642, Guangdong Province, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Yi Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 483 Wushan Road, Tianhe, Guangzhou, 510642, Guangdong Province, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jing Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 483 Wushan Road, Tianhe, Guangzhou, 510642, Guangdong Province, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, China
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 483 Wushan Road, Tianhe, Guangzhou, 510642, Guangdong Province, China.
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, China.
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China.
| | - Zaohai Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 483 Wushan Road, Tianhe, Guangzhou, 510642, Guangdong Province, China.
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, China.
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China.
| | - Yuanlong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 483 Wushan Road, Tianhe, Guangzhou, 510642, Guangdong Province, China.
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, South China Agricultural University, Guangzhou, China.
- Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China.
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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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Fang T, Motte H, Parizot B, Beeckman T. Early "Rootprints" of Plant Terrestrialization: Selaginella Root Development Sheds Light on Root Evolution in Vascular Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:735514. [PMID: 34671375 PMCID: PMC8521068 DOI: 10.3389/fpls.2021.735514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
Roots provide multiple key functions for plants, including anchorage and capturing of water and nutrients. Evolutionarily, roots represent a crucial innovation that enabled plants to migrate from aquatic to terrestrial environment and to grow in height. Based on fossil evidence, roots evolved at least twice independently, once in the lycophyte clade and once in the euphyllophyte (ferns and seed plants) clade. In lycophytes, roots originated in a stepwise manner. Despite their pivotal position in root evolution, it remains unclear how root development is controlled in lycophytes. Getting more insight into lycophyte root development might shed light on how genetic players controlling the root meristem and root developmental processes have evolved. Unfortunately, genetic studies in lycophytes are lagging behind, lacking advanced biotechnological tools, partially caused by the limited economic value of this clade. The technology of RNA sequencing (RNA-seq) at least enabled transcriptome studies, which could enhance the understanding or discovery of genes involved in the root development of this sister group of euphyllophytes. Here, we provide an overview of the current knowledge on root evolution followed by a survey of root developmental events and how these are genetically and hormonally controlled, starting from insights obtained in the model seed plant Arabidopsis and where possible making a comparison with lycophyte root development. Second, we suggest possible key genetic regulators in root development of lycophytes mainly based on their expression profiles in Selaginella moellendorffii and phylogenetics. Finally, we point out challenges and possible future directions for research on root evolution.
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Affiliation(s)
- Tao Fang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hans Motte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Boris Parizot
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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48
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Dong Y, Ye X, Xiong A, Zhu N, Jiang L, Qu S. The regulatory role of gibberellin related genes DKGA2ox1 and MIR171f_3 in persimmon dwarfism. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 310:110958. [PMID: 34315584 DOI: 10.1016/j.plantsci.2021.110958] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/17/2021] [Accepted: 05/26/2021] [Indexed: 06/13/2023]
Abstract
'Nantongxiaofangshi' (Diospyros kaki Thunb., D. kaki Thunb.) is a local cultivar of persimmon with dwarf-like traits in Jiangsu, China. Closely spaced planting afforded by dwarfism is usually one of the most important ways to promote fruit cultivation and production. However, the understanding of dwarfism in D. kaki Thunb. is very limited at the molecular level, which hinders the further increase of the fruit production. In this work, a persimmon transgenic system was successfully established, and the field experiments of grafting phenotype were carried out. The results showed that D. kaki Thunb. could be used as an interstock to induce dwarfing in grafted scions, and the dwarf character was better when interstock lengths were between 20 and 25 cm. Furthermore, the key genes related to dwarfism in D. kaki Thunb. were screened and verified, and subsequently, the regulatory role of related genes in persimmon dwarfism was figured out. It was found that the gene encoding gibberellin 2-oxidase-1 (DkGA2ox1) involved in GA biosynthesis was associated with the dwarfing in D. kaki Thunb. Overexpression of DkGA2ox1 in Diospyros lotus resulted in a typical dwarf phenotype. Meanwhile, the microRNA data showed that the miR171f_3 demonstrated the active involvement in GA pathway response in persimmon dwarfism. DkGA2ox1 and MIR171f_3, as two highly expressed genes in D. kaki Thunb. interstock, could be used as stimulus signals to affect the content of GA in scion, however, the specific transmission mechanism still needs to be further explored. Ultimately, the bioactive GA level was decreased, resulting in the scion dwarfism.
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Affiliation(s)
- Yuhan Dong
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Xialin Ye
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Aisheng Xiong
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Ning Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Luping Jiang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Shenchun Qu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, PR China.
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Jha DK, Chanwala J, Sandeep IS, Dey N. Comprehensive identification and expression analysis of GRAS gene family under abiotic stress and phytohormone treatments in Pearl millet. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:1039-1052. [PMID: 34266539 DOI: 10.1071/fp21051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 06/15/2021] [Indexed: 06/13/2023]
Abstract
Pearl millet is an important C4 cereal plant that possesses enormous capacity to survive under extreme climatic conditions. It serves as a major food source for people in arid and semiarid regions of south-east Asia and Africa. GRAS is an important transcription factor gene family of plant that play a critical role in regulating developmental processes, stress responses and phytohormonal signalling. In the present study, we have identified a total number of 57 GRAS members in pearl millet. Phylogenetic analysis clustered all the PgGRAS genes into eight groups (GroupI-GroupVIII). Motif analysis has shown that all the PgGRAS proteins had conserved GRAS domains and gene structure analysis revealed a high structural diversity among PgGRAS genes. Expression patterns of PgGRAS genes in different tissues (leaf, stem and root) and under various abiotic stress (drought, heat and salinity) were determined. Further, expression analysis was also carried out in response to various hormones (SA, MeJA, GA and ABA). The results provide a clear understanding of GRAS transcription factor family in pearl millet, and lay a good foundation for the functional characterisation of GRAS genes in pearl millet.
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Affiliation(s)
- Deepak Kumar Jha
- Department of Gene Function and Regulation, Institute of Life Sciences, Chandrasekharpur,Bhubaneswar, Odisha, India
| | - Jeky Chanwala
- Department of Gene Function and Regulation, Institute of Life Sciences, Chandrasekharpur,Bhubaneswar, Odisha, India; and Regional Centre for Biotechnology, Faridabad, 121001 Haryana, India
| | - I Sriram Sandeep
- Department of Gene Function and Regulation, Institute of Life Sciences, Chandrasekharpur,Bhubaneswar, Odisha, India
| | - Nrisingha Dey
- Department of Gene Function and Regulation, Institute of Life Sciences, Chandrasekharpur,Bhubaneswar, Odisha, India; and Corresponding author. ,
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50
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Wang J, Zhang Y, Xu N, Zhang H, Fan Y, Rui C, Han M, Malik WA, Wang Q, Sun L, Chen X, Lu X, Wang D, Zhao L, Wang J, Wang S, Chen C, Guo L, Ye W. Genome-wide identification of CK gene family suggests functional expression pattern against Cd 2+ stress in Gossypium hirsutum L. Int J Biol Macromol 2021; 188:272-282. [PMID: 34364943 DOI: 10.1016/j.ijbiomac.2021.07.190] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 11/29/2022]
Abstract
Choline kinase (CK) gene plays an important role in plants growth, development and resistance to stress. It mainly regulates the biosynthesis of phosphatidylcholine. This study aims to explore the structure-function relationship, and to provide a framework for functional validation and biochemical characterization of various CK genes. Our analysis showed that 87 CK genes were identified in cotton and 7 diploid plants, of which 43 genes encode CK proteins in 4 cotton species, and 13 genes were identified in Gossypium hirsutum. Most of GhCK genes are affected by the abiotic stress conditions, indicating the importance of CK proteins for plant development and response to abiotic stress. RT-qPCR analysis showed the tissue specificity of GhCK genes in response to Cd2+ and other abiotic stresses. Under Cd2+ stress, the expression level of GhCK gene family members has undergone different changes. The expression level of GhCK5 was enhanced, indicating that Cd2+ stress caused the increase of phosphatidylcholine content, which in turn reacted on the plant cell membrane, finally reached the absorption of Cd2+ into plant cells to repair Cd2+ the purpose of contaminated soil. This study will further broaden our understanding of the association between evolution and function of the GhCK gene family.
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Affiliation(s)
- Jing Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Yuexin Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Nan Xu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Hong Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Yapeng Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Cun Rui
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Mingge Han
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Waqar Afzal Malik
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Qinqin Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Liangqing Sun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Xiugui Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Xuke Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Delong Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Lanjie Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Junjuan Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Shuai Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Chao Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Lixue Guo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China
| | - Wuwei Ye
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Zhengzhou University, Key Laboratory for Cotton Genetic Improvement, MOA, Anyang, Henan 455000, China.
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