1
|
Shi Y, Ding G, Shen H, Li Z, Li H, Xiao G. Genome-wide identification and expression profiles analysis of the authentic response regulator gene family in licorice. FRONTIERS IN PLANT SCIENCE 2024; 14:1309802. [PMID: 38273943 PMCID: PMC10809405 DOI: 10.3389/fpls.2023.1309802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024]
Abstract
Introduction As one of the traditional Chinese medicinal herbs that were most generally used, licorice attracts lots of interest due to its therapeutic potential. Authentic response regulators (ARRs) are key factors in cytokinin signal transduction and crucial for plant growth and stress response processes. Nevertheless, the characteristics and functions of the licorice ARR genes are still unknown. Results In present study, a systematic genome-wide identification and expression analysis of the licorice ARR gene family were conducted and 51 ARR members were identified. Collinearity analysis revealed the significant roles of segmental duplications in the expansion of licorice ARR genes. The cis-acting elements associated with development, stress and phytohormone responses were identified, implying their pivotal roles in diverse regulatory processes. RNA-seq and qRT-PCR results suggested that A-type, but not B-type ARRs were induced by zeatin. Additionally, ARRs participated in diverse abiotic stresses and phytohormones responses. Yeast one-hybrid assay demonstrated that GuARR1, GuARR2, GuARR11, GuARR12, GuARR10-1, GuARR10-2 and GuARR14 were able to bind to the promoter of GuARR8-3, and GuARR1, GuARR12 bound to the GuARR8-1 promoter. GuARR1, GuARR2, GuARR11 and GuARR10-2 bound to the GuARR6-2 promoter as well as GuARR12 and GuARR10-2 bound to the GuARR6-1 promoter. Discussion Collectively, these findings provide a basis for future ARR genes function investigations, shedding light on the potential medicinal properties and agricultural applications of licorice.
Collapse
Affiliation(s)
- Yanping Shi
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, China
| | - Guohua Ding
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Haitao Shen
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, China
| | - Zihan Li
- Geosystems Research Institute, Mississippi State University, Starkville, MS, United States
| | - Hongbin Li
- College of Life Sciences, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, China
| | - Guanghui Xiao
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| |
Collapse
|
2
|
Akram J, Siddique R, Shafiq M, Tabassum B, Manzoor MT, Javed MA, Anwar S, Nisa BU, Saleem MH, Javed B, Malik T, Mustafa AEZMA, Ali B. Genome-wide identification of CCO gene family in cucumber (Cucumis sativus) and its comparative analysis with A. thaliana. BMC PLANT BIOLOGY 2023; 23:640. [PMID: 38082240 PMCID: PMC10712067 DOI: 10.1186/s12870-023-04647-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023]
Abstract
Carotenoid cleavage oxygenase (CCO) is an enzyme capable of converting carotenoids into volatile, aromatic compounds and it plays an important role in the production of two significant plant hormones, i.e., abscisic acid (ABA) and strigolactone (SL). The cucumber plant genome has not been mined for genomewide identification of the CCO gene family. In the present study, we conducted a comprehensive genome-wide analysis to identify and thoroughly examine the CCO gene family within the genomic sequence of Cucumis sativus L. A Total of 10 CCO genes were identified and mostly localized in the cytoplasm and chloroplast. The CCO gene is divided into seven subfamilies i.e. 3 NCED, 3 CCD, and 1 CCD-like (CCDL) subfamily according to phylogenetic analysis. Cis-regulatory elements (CREs) analysis revealed the elements associated with growth and development as well as reactions to phytohormonal, biotic, and abiotic stress conditions. CCOs were involved in a variety of physiological and metabolic processes, according to Gene Ontology annotation. Additionally, 10 CCO genes were regulated by 84 miRNA. The CsCCO genes had substantial purifying selection acting upon them, according to the synteny block. In addition, RNAseq analysis indicated that CsCCO genes were expressed in response to phloem transportation and treatment of chitosan oligosaccharides. CsCCD7 and CsNCED2 showed the highest gene expression in response to the exogenous application of chitosan oligosaccharides to improve cold stress in cucumbers. We also found that these genes CsCCD4a and CsCCDL-a showed the highest expression in different plant organs with respect to phloem content. The cucumber CCO gene family was the subject of the first genome-wide report in this study, which may help us better understand cucumber CCO proteins and lay the groundwork for the gene family's future cloning and functional investigations.
Collapse
Affiliation(s)
- Jannat Akram
- Department of Botany, Lahore College for Women University, Lahore, 54000, Pakistan
| | - Riffat Siddique
- Department of Botany, Lahore College for Women University, Lahore, 54000, Pakistan
| | - Muhammad Shafiq
- Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Bushra Tabassum
- School of Biological Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Muhammad Tariq Manzoor
- Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Muhammad Arshad Javed
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Samia Anwar
- Department of Botany, Lahore College for Women University, Lahore, 54000, Pakistan
| | - Bader Un Nisa
- Department of Botany, Lahore College for Women University, Lahore, 54000, Pakistan
| | - Muhammad Hamzah Saleem
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bilal Javed
- Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore, 54590, Pakistan
| | - Tabarak Malik
- Department of Biomedical Sciences, Institute of Health, Jimma University, 378, Jimma, Ethiopia.
| | - Abd El-Zaher M A Mustafa
- Department of Botany and Microbiology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Baber Ali
- Department of Plant Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan.
| |
Collapse
|
3
|
Alshegaihi RM, Alshamrani SM. Genome-wide identification of CaARR-Bs transcription factor gene family in pepper and their expression patterns under salinity stress. PeerJ 2023; 11:e16332. [PMID: 37927789 PMCID: PMC10625354 DOI: 10.7717/peerj.16332] [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: 03/30/2023] [Accepted: 09/30/2023] [Indexed: 11/07/2023] Open
Abstract
In plants, ARRs-B transcription factors play a crucial role in regulating cytokinin signal transduction, abiotic stress resistance, and plant development. A number of adverse environmental conditions have caused severe losses for the pepper (Capsicum annuum L.)-a significant and economically important vegetable. Among the transcription factors of the type B-ARRs family, multiple members have different functions. In pepper, only a few members of the ARRs-B family have been reported and characterized. The current study aimed to characterize ARRs-B transcription factors in C. annuum, including phylogenetic relationships, gene structures, protein motif arrangement, and RT-qPCR expression analyses and their role in salinity stress. In total, ten genes encode CaARRs-B transcription factors (CaARR1 to CaARR10) from the largest subfamily of type-B ARRs were identified in C. annum. The genome-wide analyses of the CaARRs-B family in C. annuum were performed based on the reported ARRs-B genes in Arabidopsis. An analysis of homologous alignments of candidate genes, including their phylogenetic relationships, gene structures, conserved domains, and qPCR expression profiles, was conducted. In comparison with other plant ARRs-B proteins, CaARRs-B proteins showed gene conservation and potentially specialized functions. In addition, tissue-specific expression profiles showed that CaARRs-B genes were differentially expressed, suggesting functionally divergent. CaARRs-B proteins had a typical conserved domain, including AAR-like (pfam: PF00072) and Myb DNA binding (pfam: PF00249) domains. Ten of the CaARRs-B genes were asymmetrically mapped on seven chromosomes in Pepper. Additionally, the phylogenetic tree of CaARRs-B genes from C. annuum and other plant species revealed that CaARRs-B genes were classified into four clusters, which may have evolved conservatively. Further, using quantitative real-time qRT-PCR, the study assessed the expression patterns of CaARRs-B genes in Capsicum annuum seedlings subjected to salt stress. The study used quantitative real-time qRT-PCR to examine CaARRs-B gene expression in Capsicum annuum seedlings under salt stress. Roots exhibited elevated expression of CaARR2 and CaARR9, while leaves showed decreased expression for CaARR3, CaARR4, CaARR7, and CaARR8. Notably, no amplification was observed for CaARR10. This research sheds light on the roles of CaARRs-B genes in pepper's response to salinity stress. These findings enrich our comprehension of the functional implications of CaARRs-B genes in pepper, especially in responding to salinity stress, laying a solid groundwork for subsequent in-depth studies and applications in the growth and development of Capsicum annuum.
Collapse
Affiliation(s)
- Rana M. Alshegaihi
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | | |
Collapse
|
4
|
Bae Y, Song SJ, Lim CW, Kim CM, Lee SC. Tomato salt-responsive pseudo-response regulator 1, SlSRP1, negatively regulates the high-salt and dehydration stress responses. PHYSIOLOGIA PLANTARUM 2023; 175:e14082. [PMID: 38148202 DOI: 10.1111/ppl.14082] [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: 08/06/2023] [Revised: 10/29/2023] [Accepted: 10/31/2023] [Indexed: 12/28/2023]
Abstract
Under severe environmental stress conditions, plants inhibit their growth and development and initiate various defense mechanisms to survive. The pseudo-response regulator (PRRs) genes have been known to be involved in fruit ripening and plant immunity in various plant species, but their role in responses to environmental stresses, especially high salinity and dehydration, remains unclear. Here, we focused on PRRs in tomato plants and identified two PRR2-like genes, SlSRP1 and SlSRP1H, from the leaves of salt-treated tomato plants. After exposure to dehydration and high-salt stresses, expression of SISRP1, but not SlSRP1H, was significantly induced in tomato leaves. Subcellular localization analysis showed that SlSRP1 was predominantly located in the nucleus, while SlSRP1H was equally distributed in the nucleus and cytoplasm. To further investigate the potential role of SlSRP1 in the osmotic stress response, we generated SISRP1-silenced tomato plants. Compared to control plants, SISRP1-silenced tomato plants exhibited enhanced tolerance to high salinity, as evidenced by a high accumulation of proline and reduced chlorosis, ion leakage, and lipid peroxidation. Moreover, SISRP1-silenced tomato plants showed dehydration-tolerant phenotypes with enhanced abscisic acid sensitivity and increased expression of stress-related genes, including SlRD29, SlAREB, and SlDREB2. Overall, our findings suggest that SlSRP1 negatively regulates the osmotic stress response.
Collapse
Affiliation(s)
- Yeongil Bae
- Department of Life Science (BK21 program), Chung-Ang University, Seoul, Korea
| | - Se Jin Song
- Department of Horticulture Industry, Wonkwang University, Iksan, Jeonbuk, Korea
| | - Chae Woo Lim
- Department of Life Science (BK21 program), Chung-Ang University, Seoul, Korea
| | - Chul Min Kim
- Department of Horticulture Industry, Wonkwang University, Iksan, Jeonbuk, Korea
| | - Sung Chul Lee
- Department of Life Science (BK21 program), Chung-Ang University, Seoul, Korea
| |
Collapse
|
5
|
Haider MZ, Sami A, Shafiq M, Anwar W, Ali S, Ali Q, Muhammad S, Manzoor I, Shahid MA, Ali D, Alarifi S. Genome-wide identification and in-silico expression analysis of carotenoid cleavage oxygenases gene family in Oryza sativa (rice) in response to abiotic stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1269995. [PMID: 37954992 PMCID: PMC10634354 DOI: 10.3389/fpls.2023.1269995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/06/2023] [Indexed: 11/14/2023]
Abstract
Rice constitutes a foundational cereal and plays a vital role in the culinary sector. However, the detriments of abiotic stress on rice quality and productivity are noteworthy. Carotenoid cleavage oxygenases (CCO) hold vital importance as they enable the particular breakdown of carotenoids and significantly contribute towards the growth and response to abiotic stress in rice. Due to the insufficient information regarding rice CCOs and their potential role in abiotic stress, their utilization in stress-resistant genetic breeding remains limited. The current research identified 16 CCO genes within the Oryza sativa japonica group. These OsCCO genes can be bifurcated into three categories based on their conserved sequences: NCEDs (9-Cis-epoxycarotenoid dioxygenases), CCDs (Carotenoid cleavage dioxygenases) and CCD-like (Carotenoid cleavage dioxygenases-like). Conserved motifs were found in the OsCCO gene sequence via MEME analysis and multiple sequence alignment. Stress-related cis-elements were detected in the promoter regions of OsCCOs genes, indicating their involvement in stress response. Additionally, the promoters of these genes had various components related to plant light, development, and hormone responsiveness, suggesting they may be responsive to plant hormones and involved in developmental processes. MicroRNAs play a pivotal role in the regulation of these 16 genes, underscoring their significance in rice gene regulation. Transcriptome data analysis suggests a tissue-specific expression pattern for rice CCOs. Only OsNCED6 and OsNCED10 significantly up-regulated during salt stress, as per RNA seq analyses. CCD7 and CCD8 levels were also higher in the CCD group during the inflorescence growth stage. This provides insight into the function of rice CCOs in abiotic stress response and identifies possible genes that could be beneficial for stress-resistant breeding.
Collapse
Affiliation(s)
- Muhammad Zeshan Haider
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Adnan Sami
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad Shafiq
- Department of Horticulture, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Waheed Anwar
- Department of Plant Pathology, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Sajid Ali
- Department of Agronomy, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Qurban Ali
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Sher Muhammad
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Irfan Manzoor
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Adnan Shahid
- Horticultural Sciences Department, University of Florida/Institute of Food and Agricultural Sciences (IFAS), North Florida Research and Education Center, Quincy, FL, United States
| | - Daoud Ali
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saud Alarifi
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| |
Collapse
|
6
|
Qiao H, Jiao B, Wang J, Yang Y, Yang F, Geng Z, Zhao G, Liu Y, Dong F, Wang Y, Zhou S. Comparative Analysis of miRNA Expression Profiles under Salt Stress in Wheat. Genes (Basel) 2023; 14:1586. [PMID: 37628637 PMCID: PMC10454085 DOI: 10.3390/genes14081586] [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: 06/30/2023] [Revised: 07/26/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
Salt stress is one of the important environmental factors that inhibit the normal growth and development of plants. Plants have evolved various mechanisms, including signal transduction regulation, physiological regulation, and gene transcription regulation, to adapt to environmental stress. MicroRNAs (miRNAs) play a role in regulating mRNA expression. Nevertheless, miRNAs related to salt stress are rarely reported in bread wheat (Triticum aestivum L.). In this study, using high-throughput sequencing, we analyzed the miRNA expression profile of wheat under salt stress. We identified 360 conserved and 859 novel miRNAs, of which 49 showed considerable changes in transcription levels after salt treatment. Among them, 25 were dramatically upregulated and 24 were downregulated. Using real-time quantitative PCR, we detected significant changes in the relative expression of miRNAs, and the results showed the same trend as the sequencing data. In the salt-treated group, miR109 had a higher expression level, while miR60 and miR202 had lower expression levels. Furthermore, 21 miRNAs with significant changes were selected from the differentially expressed miRNAs, and 1023 candidate target genes were obtained through the prediction of the website psRNATarget. Gene ontology (GO) analysis of the candidate target genes showed that the expressed miRNA may be involved in the response to biological processes, molecular functions, and cellular components. In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis confirmed their important functions in RNA degradation, metabolic pathways, synthesis pathways, peroxisome, environmental adaptation, global and overview maps, and stress adaptation and the MAPK signal pathway. These findings provide a basis for further exploring the function of miRNA in wheat salt tolerance.
Collapse
Affiliation(s)
- Hualiang Qiao
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Bo Jiao
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Jiao Wang
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Yang Yang
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Fan Yang
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Zhao Geng
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Guiyuan Zhao
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Yongwei Liu
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Fushuang Dong
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| | - Yongqiang Wang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Shuo Zhou
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China; (H.Q.); (B.J.)
| |
Collapse
|
7
|
Abbas F, Yu Y, Bendahmane M, Wang HC. Plant volatiles and color compounds: From biosynthesis to function. PHYSIOLOGIA PLANTARUM 2023; 175:e13947. [PMID: 37357979 DOI: 10.1111/ppl.13947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 06/27/2023]
Affiliation(s)
- Farhat Abbas
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China/Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Yixun Yu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China/Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Mohammed Bendahmane
- Laboratoire Reproduction et Development des Plantes, INRA-CNRS-Lyon1-ENS, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Hui-Cong Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China/Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China
| |
Collapse
|
8
|
Qiang Y, He X, Li Z, Li S, Zhang J, Liu T, Tursunniyaz M, Wang X, Liu Z, Fang L. Genome-wide identification and expression analysis of the response regulator gene family in alfalfa ( Medicago sativa L.) reveals their multifarious roles in stress response. FRONTIERS IN PLANT SCIENCE 2023; 14:1149880. [PMID: 36998691 PMCID: PMC10043395 DOI: 10.3389/fpls.2023.1149880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/23/2023] [Indexed: 06/19/2023]
Abstract
As important components of the two-component regulatory system, response regulatory proteins (RRPs) play a crucial role in histidine phosphorylation-mediated signal transduction in response to environmental fluctuations. Accumulating evidence has revealed that RRPs play important roles in plant growth and stress response. However, the specific functions of RR genes (RRs) in cultivated alfalfa remain ambiguous. Therefore, in this study, we identified and characterized the RR family genes in the alfalfa genome using bioinformatics methods. Our analysis revealed 37 RRs in the alfalfa genome of Zhongmu No.1 that were unevenly distributed on the chromosomes. Cis-elements analysis revealed the involvement of RRs in responses to light, stress, and various plant hormones. Expression analysis of RRs in different tissues revealed their distinct tissue expression patterns. These findings provide preliminary insights into the roles of RRs in plant responses to abiotic stress, which can be used to improve the stress tolerance of autotetraploid-cultivated alfalfa plants via genetic engineering.
Collapse
Affiliation(s)
- Yuqin Qiang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaojuan He
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhen Li
- National Engineering Laboratory for Volatile Organic Compounds Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Siqi Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Jia Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Tao Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Mamateliy Tursunniyaz
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xinyu Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhipeng Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Longfa Fang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| |
Collapse
|
9
|
Liu H, Chen R, Li H, Lin J, Wang Y, Han M, Wang T, Wang H, Chen Q, Chen F, Chu P, Liang C, Ren C, Zhang Y, Yang F, Sheng Y, Wei J, Wu X, Yu G. Genome-wide identification and expression analysis of SlRR genes in response to abiotic stress in tomato. PLANT BIOLOGY (STUTTGART, GERMANY) 2023; 25:322-333. [PMID: 36457231 DOI: 10.1111/plb.13494] [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: 04/30/2022] [Accepted: 11/15/2022] [Indexed: 06/17/2023]
Abstract
The cytokinin two-component signal transduction system (TCS) is involved in many biological processes, including hormone signal transduction and plant growth regulation. Although cytokinin TCS has been well characterized in Arabidopsis thaliana, its role in tomato remains elusive. In this study, we characterized the diversity and function of response regulator (RR) genes, a critical component of TCS, in tomato. In total, we identified 31 RR genes in the tomato genome. These SlRR genes were classified into three subgroups (type-A, type-B and type-C). Various stress-responsive cis-elements were present in the tomato RR gene promoters. Their expression responses under pesticide treatment were evaluated by transcriptome analysis. Their expression under heat, cold, ABA, salinity and NaHCO3 treatments was further investigated by qRT-PCR and complemented with the available transcription data under these treatments. Specifically, SlRR13 expression was significantly upregulated under salinity, drought, cold and pesticide stress and was downregulated under ABA treatment. SlRR23 expression was induced under salt treatment, while the transcription level of SlRR1 was increased under cold and decreased under salt stress. We also found that GATA transcription factors played a significant role in the regulation of SlRR genes. Based on our results, tomato SlRR genes are involved in responses to abiotic stress in tomato and could be implemented in molecular breeding approaches to increase resistance of tomato to environmental stresses.
Collapse
Affiliation(s)
- H Liu
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - R Chen
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - H Li
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - J Lin
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - Y Wang
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - M Han
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - T Wang
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - H Wang
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - Q Chen
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - F Chen
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - P Chu
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - C Liang
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - C Ren
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - Y Zhang
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - F Yang
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - Y Sheng
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - J Wei
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - X Wu
- Heilongjiang Bayi Agricultural University, Daqing, China
| | - G Yu
- Heilongjiang Bayi Agricultural University, Daqing, China
| |
Collapse
|
10
|
Rao Y, Peng T, Xue S. Mechanisms of plant saline-alkaline tolerance. JOURNAL OF PLANT PHYSIOLOGY 2023; 281:153916. [PMID: 36645936 DOI: 10.1016/j.jplph.2023.153916] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/28/2022] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Saline-alkaline soil affects crop growth and development, thereby suppressing the yields. Human activities and climate changes are putting arable land under the threat of saline-alkalization. To feed a growing global population in limited arable land, it is of great urgence to breed saline-alkaline tolerant crops to cope with food security. Plant salt-tolerance mechanisms have already been explored for decades. However, to date, the molecular mechanisms underlying plants responses to saline-alkaline stress have remained largely elusive. Here, we summarize recent advances in plant response to saline-alkaline stress and propose some points deserving of further exploration.
Collapse
Affiliation(s)
- Ying Rao
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Ting Peng
- College of Agriculture, Guizhou University, Guiyang, 550025, China.
| | - Shaowu Xue
- College of Life Science and Technology, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
| |
Collapse
|
11
|
Saleem B, Farooq U, Rehman OU, Aqeel M, Farooq MS, Naeem MK, Inam S, Ajmal W, Rahim AA, Chen M, Kalsoom R, Uzair M, Fiaz S, Attia K, Alafari HA, Khan MR, Yu G. Genome-wide and molecular characterization of the DNA replication helicase 2 ( DNA2) gene family in rice under drought and salt stress. Front Genet 2022; 13:1039548. [PMID: 36506305 PMCID: PMC9728955 DOI: 10.3389/fgene.2022.1039548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022] Open
Abstract
Rice plants experience various biotic (such as insect and pest attack) and abiotic (such as drought, salt, heat, and cold etc.) stresses during the growing season, resulting in DNA damage and the subsequent losses in rice production. DNA Replication Helicase/Nuclease2 (DNA2) is known to be involved in DNA replication and repair. In animals and yeast DNA2 are well characterized because it has the abilities of both helicase and nuclease, it plays a crucial role in DNA replication in the nucleus and mitochondrial genomes. However; they are not fully examined in plants due to less focused on plants damage repair. To fill this research gap, the current study focused on the genome-wide identification and characterization of OsDNA2 genes, along with analyses of their transcriptional expression, duplication, and phylogeny in rice. Overall, 17 OsDNA2 members were reported to be found on eight different chromosomes (2, 3, 4, 6, 7, 9, 10, and 11). Among these chromosomes (Chr), Chr4 contained a maximum of six OsDNA2 genes. Based on phylogenetic analysis, the OsDNA2 gene members were clustered into three different groups. Furthermore, the conserved domains, gene structures, and cis-regulatory elements were systematically investigated. Gene duplication analysis revealed that OsDNA2_2 had an evolutionary relationship with OsDNA2_14, OsDNA2_5 with OsDNA2_6, and OsDNA2_1 with OsDNA2_8. Moreover, results showed that the conserved domain (AAA_11 superfamily) were present in the OsDNA2 genes, which belongs to the DEAD-like helicase superfamily. In addition, to understand the post-transcriptional modification of OsDNA2 genes, miRNAs were predicted, where 653 miRNAs were reported to target 17 OsDNA2 genes. The results indicated that at the maximum, OsDNA2_1 and OsDNA2_4 were targeted by 74 miRNAs each, and OsDNA2_9 was less targeted (20 miRNAs). The three-dimensional (3D) structures of 17 OsDNA2 proteins were also predicted. Expression of OsDNA2 members was also carried out under drought and salt stresses, and conclusively their induction indicated the possible involvement of OsDNA2 in DNA repair under stress when compared with the control. Further studies are recommended to confirm where this study will offer valuable basic data on the functioning of DNA2 genes in rice and other crop plants.
Collapse
Affiliation(s)
- Bilal Saleem
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Umer Farooq
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Obaid Ur Rehman
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan,Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Muhammad Aqeel
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Muhammad Shahbaz Farooq
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Muhammad Kashif Naeem
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Safeena Inam
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Wajya Ajmal
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Amna Abdul Rahim
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Rabia Kalsoom
- School of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan,National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China,*Correspondence: Muhammad Uzair, ; Muhammad Ramzan Khan, ; Guoping Yu,
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Kotb Attia
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Hayat Ali Alafari
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan,*Correspondence: Muhammad Uzair, ; Muhammad Ramzan Khan, ; Guoping Yu,
| | - Guoping Yu
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China,China National Rice Research Institute, Hangzhou, China,Hainan Yazhou Bay Seed Lab, Sanya, China,*Correspondence: Muhammad Uzair, ; Muhammad Ramzan Khan, ; Guoping Yu,
| |
Collapse
|
12
|
Hua YP, Wu PJ, Zhang TY, Song HL, Zhang YF, Chen JF, Yue CP, Huang JY, Sun T, Zhou T. Genome-Scale Investigation of GARP Family Genes Reveals Their Pivotal Roles in Nutrient Stress Resistance in Allotetraploid Rapeseed. Int J Mol Sci 2022; 23:ijms232214484. [PMID: 36430962 PMCID: PMC9698747 DOI: 10.3390/ijms232214484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/14/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
The GARP genes are plant-specific transcription factors (TFs) and play key roles in regulating plant development and abiotic stress resistance. However, few systematic analyses of GARPs have been reported in allotetraploid rapeseed (Brassica napus L.) yet. In the present study, a total of 146 BnaGARP members were identified from the rapeseed genome based on the sequence signature. The BnaGARP TFs were divided into five subfamilies: ARR, GLK, NIGT1/HRS1/HHO, KAN, and PHL subfamilies, and the members within the same subfamilies shared similar exon-intron structures and conserved motif configuration. Analyses of the Ka/Ks ratios indicated that the GARP family principally underwent purifying selection. Several cis-acting regulatory elements, essential for plant growth and diverse biotic and abiotic stresses, were identified in the promoter regions of BnaGARPs. Further, 29 putative miRNAs were identified to be targeting BnaGARPs. Differential expression of BnaGARPs under low nitrate, ammonium toxicity, limited phosphate, deficient boron, salt stress, and cadmium toxicity conditions indicated their potential involvement in diverse nutrient stress responses. Notably, BnaA9.HHO1 and BnaA1.HHO5 were simultaneously transcriptionally responsive to these nutrient stresses in both hoots and roots, which indicated that BnaA9.HHO1 and BnaA1.HHO5 might play a core role in regulating rapeseed resistance to nutrient stresses. Therefore, this study would enrich our understanding of molecular characteristics of the rapeseed GARPs and will provide valuable candidate genes for further in-depth study of the GARP-mediated nutrient stress resistance in rapeseed.
Collapse
Affiliation(s)
- Ying-Peng Hua
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Peng-Jia Wu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Tian-Yu Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Hai-Li Song
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yi-Fan Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Jun-Fan Chen
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Cai-Peng Yue
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Jin-Yong Huang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Tao Sun
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- Correspondence: (T.S.); (T.Z.); Tel.: +86-187-0271-0749 (T.Z.)
| | - Ting Zhou
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- Correspondence: (T.S.); (T.Z.); Tel.: +86-187-0271-0749 (T.Z.)
| |
Collapse
|
13
|
Genome-Wide Analysis of the Type-B Authentic Response Regulator Gene Family in Brassica napus. Genes (Basel) 2022; 13:genes13081449. [PMID: 36011360 PMCID: PMC9408017 DOI: 10.3390/genes13081449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/07/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
The type-B authentic response regulators (type-B ARRs) are positive regulators of cytokinin signaling and involved in plant growth and stress responses. In this study, we used bioinformatics, RNA-seq, and qPCR to study the phylogenetic and expression pattern of 35 type-B ARRs in Brassica napus. The BnARRs experienced gene expansion and loss during genome polyploidization and were classified into seven groups. Whole-genome duplication (WGD) and segmental duplication were the main forces driving type-B ARR expansion in B. napus. Several BnARRs with specific expression patterns during rapeseed development were identified, including BnARR12/14/18/23/33. Moreover, we found the type-B BnARRs were involved in rapeseed development and stress responses, through participating in cytokinin and ABA signaling pathways. This study revealed the origin, evolutionary history, and expression pattern of type-B ARRs in B. napus and will be helpful to the functional characterization of BnARRs.
Collapse
|
14
|
Rahim AA, Uzair M, Rehman N, Rehman OU, Zahra N, Khan MR. Genome-Wide Identification and Characterization of Receptor-Like Protein Kinase 1 (RPK1) Gene Family in Triticum aestivum Under Drought Stress. Front Genet 2022; 13:912251. [PMID: 35860467 PMCID: PMC9289140 DOI: 10.3389/fgene.2022.912251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/24/2022] [Indexed: 01/08/2023] Open
Abstract
Receptor-like protein kinase1 (RPK1) genes play crucial roles in plant growth and development processes, root architecture, and abiotic stress regulation. A comprehensive study of the RPK1 gene family has not been reported in bread wheat (Triticum aestivum). Here, we reported the genome-wide identification, characterization, and expression patterns of the RPK1 gene family in wheat. Results confirmed 15 TaRPK1 genes, classified mainly into three sub-clades based on a phylogenetic tree. The TaRPK1 genes were mapped on chromosomes 1–3 in the respective A, B, and D genomes. Gene structure, motif conservation, collinearity prediction, and synteny analysis were carried out systematically. A Gene ontology study revealed that TaRPK1 genes play a vital role during molecular and biological processes. We also identified 18 putative miRNAs targeting TaRPK1 genes, suggesting their roles in growth, development, and stress responses. Cis-Regulatory elements interpreted the presence of light-related elements, hormone responsiveness, and abiotic stress-related motifs in the promoter regions. The SWISS_MODEL predicted the successful models of TaRPK1 proteins with at least 30% identity to the template, a widely accepted threshold for successful modeling. In silico expression analysis in different tissues and stages suggested that TaRPK1 genes exhibited the highest expression in root tissues. Moreover, qRT-PCR further validated the higher expression of TaRPK1 genes in roots of drought-tolerant varieties compared to the drought-susceptible variety. Collectively, the present study renders valuable information on the functioning of TaRPK1 genes in wheat that will be useful in further functional validation of these genes in future studies.
Collapse
Affiliation(s)
- Amna Abdul Rahim
- National Centre for Bioinformatics (NCB), Quaid-e-Azam University, Islamabad, Pakistan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Islamabad, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Islamabad, Pakistan
| | - Nazia Rehman
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Islamabad, Pakistan
| | - Obaid Ur Rehman
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Islamabad, Pakistan
| | - Nageen Zahra
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Islamabad, Pakistan
| | - Muhammad Ramzan Khan
- National Centre for Bioinformatics (NCB), Quaid-e-Azam University, Islamabad, Pakistan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Islamabad, Pakistan
- *Correspondence: Muhammad Ramzan Khan,
| |
Collapse
|
15
|
Evaluation of Green Super Rice Lines for Agronomic and Physiological Traits under Salinity Stress. PLANTS 2022; 11:plants11111461. [PMID: 35684234 PMCID: PMC9182741 DOI: 10.3390/plants11111461] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 11/17/2022]
Abstract
Rice (Oryza sativa) is an important staple food crop worldwide, especially in east and southeast Asia. About one-third of rice cultivated area is under saline soil, either natural saline soils or irrigation with brackish water. Salinity stress is among the devastating abiotic stresses that not only affect rice growth and crop productivity but also limit its cultivation area globally. Plants adopt multiple tolerance mechanisms at the morphological, physiological, and biochemical levels to tackle salinity stress. To identify these tolerance mechanisms, this study was carried out under both a controlled glass house as well as natural saline field conditions using 22 green super rice (GSR) lines along with two local varieties (“IRRI 6 and Kissan Basmati”). Several morpho-physiological and biochemical parameters along with stress-responsive genes were used as evaluation criteria under normal and salinity stress conditions. Correlation and Principal Component Analysis (PCA) suggested that shoot-related parameters and the salt susceptible index (SSI) can be used for the identification of salt-tolerant genotypes. Based on Agglomerative Hierarchical Cluster (AHC) analysis, two saline-tolerant (“S19 and S20”) and saline-susceptible (“S3 and S24”) lines were selected for further molecular evaluation. Quantitative RT-PCR was performed, and results showed that expression of 1-5-phosphoribosyl -5-5-phosphoribosyl amino methylidene amino imidazole-4-carboxamide isomerase, DNA repair protein recA, and peptide transporter PTR2 related genes were upregulated in salt-tolerant genotypes, suggesting their potential role in salinity tolerance. However, additional validation using reverse genetics approaches will further confirm their specific role in salt tolerance. Identified saline-tolerant lines in this study will be useful genetic resources for future salinity breeding programs.
Collapse
|