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Kumar RR, Niraj RK, Goswami S, Thimmegowda V, Mishra GP, Mishra D, Rai GK, Kumar SN, Viswanathan C, Tyagi A, Singh GP, Rai AK. Characterization of putative calcium-dependent protein kinase-1 ( TaCPK-1) gene: hubs in signalling and tolerance network of wheat under terminal heat. 3 Biotech 2024; 14:150. [PMID: 38725866 PMCID: PMC11076446 DOI: 10.1007/s13205-024-03989-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
Calcium-dependent protein kinase (CDPK) is member of one of the most important signalling cascades operating inside the plant system due to its peculiar role as thermo-sensor. Here, we identified 28 full length putative CDPKs from wheat designated as TaCDPK (1-28). Based on digital gene expression, we cloned full length TaCPK-1 gene of 1691 nucleotides with open reading frame (ORF) of 548 amino acids (accession number OP125853). The expression of TaCPK-1 was observed maximum (3.1-fold) in leaf of wheat cv. HD2985 (thermotolerant) under T2 (38 ± 3 °C, 2 h), as compared to control. A positive correlation was observed between the expression of TaCPK-1 and other stress-associated genes (MAPK6, CDPK4, HSFA6e, HSF3, HSP17, HSP70, SOD and CAT) involved in thermotolerance. Global protein kinase assay showed maximum activity in leaves, as compared to root, stem and spike under heat stress. Immunoblot analysis showed abundance of CDPK protein in wheat cv. HD2985 (thermotolerant) in response to T2 (38 ± 3 °C, 2 h), as compared to HD2329 (thermosusceptible). Calcium ion (Ca2+), being inducer of CDPK, showed strong Ca-signature in the leaf tissue (Ca-622 ppm) of thermotolerant wheat cv. under heat stress, whereas it was minimum (Ca-201 ppm) in spike tissue. We observed significant variations in the ionome of wheat under HS. To conclude, TaCPK-1 plays important role in triggering signaling network and in modulation of HS-tolerance in wheat. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03989-6.
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Affiliation(s)
- Ranjeet R. Kumar
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Ravi K. Niraj
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Suneha Goswami
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Vinutha Thimmegowda
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Gyan P. Mishra
- Division of Seed Technology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Dwijesh Mishra
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
| | - Gyanendra K. Rai
- Sher-E-Kashmir University of Agricultural Science and Technology, Chatta, Jammu, 180009 India
| | | | - Chinnusamy Viswanathan
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Aruna Tyagi
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Gyanendra P. Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012 India
| | - Anil K. Rai
- Centre for Agricultural Bioinformatics (CABin), ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012 India
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Chen X, Li H, Dong Y, Xu Y, Xu K, Zhang Q, Yao Z, Yu Q, Zhang H, Zhang Z. A wild melon reference genome provides novel insights into the domestication of a key gene responsible for melon fruit acidity. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:144. [PMID: 38809285 DOI: 10.1007/s00122-024-04647-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024]
Abstract
KEY MESSAGE A wild melon reference genome elucidates the genomic basis of fruit acidity domestication. Structural variants (SVs) have been reported to impose major effects on agronomic traits, representing a significant contributor to crop domestication. However, the landscape of SVs between wild and cultivated melons is elusive and how SVs have contributed to melon domestication remains largely unexplored. Here, we report a 379-Mb chromosome-scale genome of a wild progenitor melon accession "P84", with a contig N50 of 14.9 Mb. Genome comparison identifies 10,589 SVs between P84 and four cultivated melons with 6937 not characterized in previously analysis of 25 melon genome sequences. Furthermore, the population-scale genotyping of these SVs was determined in 1175 accessions, and 18 GWAS signals including fruit acidity, fruit length, fruit weight, fruit color and sex determination were detected. Based on these genotyped SVs, we identified 3317 highly diverged SVs between wild and cultivated melons, which could be the potential SVs associated with domestication-related traits. Furthermore, we identify novel SVs affecting fruit acidity and proposed the diverged evolutionary trajectories of CmPH, a key regulator of melon fruit acidity, during domestication and selection of different populations. These results will offer valuable resources for genomic studies and genetic improvement in melon.
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Affiliation(s)
- Xinxiu Chen
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Hongbo Li
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Shenzhen Branch, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, Guangdong, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Yuanhua Dong
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Yuanchao Xu
- Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Shenzhen Branch, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, Guangdong, China
| | - Kuipeng Xu
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qiqi Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Zhiwang Yao
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qing Yu
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Huimin Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Zhonghua Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.
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Fatima K, Sadaqat M, Azeem F, Rao MJ, Albekairi NA, Alshammari A, Tahir ul Qamar M. Integrated omics and machine learning-assisted profiling of cysteine-rich-receptor-like kinases from three peanut spp . revealed their role in multiple stresses. Front Genet 2023; 14:1252020. [PMID: 37799143 PMCID: PMC10547876 DOI: 10.3389/fgene.2023.1252020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/05/2023] [Indexed: 10/07/2023] Open
Abstract
Arachis hypogaea (peanut) is a leading oil and protein-providing crop with a major food source in many countries. It is mostly grown in tropical regions and is largely affected by abiotic and biotic stresses. Cysteine-rich receptor-like kinases (CRKs) is a family of transmembrane proteins that play important roles in regulating stress-signaling and defense mechanisms, enabling plants to tolerate stress conditions. However, almost no information is available regarding this gene family in Arachis hypogaea and its progenitors. This study conducts a pangenome-wide investigation of A. hypogaea and its two progenitors, A. duranensis and A. ipaensis CRK genes (AhCRKs, AdCRKs, and AiCRKs). The gene structure, conserved motif patterns, phylogenetic history, chromosomal distribution, and duplication were studied in detail, showing the intraspecies structural conservation and evolutionary patterns. Promoter cis-elements, protein-protein interactions, GO enrichment, and miRNA targets were also predicted, showing their potential functional conservation. Their expression in salt and drought stresses was also comprehensively studied. The CRKs identified were divided into three groups, phylogenetically. The expansion of this gene family in peanuts was caused by both types of duplication: tandem and segmental. Furthermore, positive as well as negative selection pressure directed the duplication process. The peanut CRK genes were also enriched in hormones, light, development, and stress-related elements. MicroRNA (miRNA) also targeted the AhCRK genes, which suggests the regulatory association of miRNAs in the expression of these genes. Transcriptome datasets showed that AhCRKs have varying expression levels under different abiotic stress conditions. Furthermore, the multi-stress responsiveness of the AhCRK genes was evaluated using a machine learning-based method, Random Forest (RF) classifier. The 3D structures of AhCRKs were also predicted. Our study can be utilized in developing a detailed understanding of the stress regulatory mechanisms of the CRK gene family in peanuts and its further studies to improve the genetic makeup of peanuts to thrive better under stress conditions.
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Affiliation(s)
- Kinza Fatima
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Muhammad Sadaqat
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Farrukh Azeem
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Muhammad Junaid Rao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Norah A. Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Tahir ul Qamar
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
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Liu G, Liu D, Zhang A, Liu H, Mia MS, Mullan D, Yan G. Identification of KASP markers and candidate genes for drought tolerance in wheat using 90K SNP array genotyping of near-isogenic lines targeting a 4BS quantitative trait locus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:190. [PMID: 37584740 PMCID: PMC10432333 DOI: 10.1007/s00122-023-04438-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023]
Abstract
KEY MESSAGE This study identified a novel SNP and developed a highly efficient KASP marker for drought tolerance in wheat by genotyping NILs targeting a major QTL for drought tolerance using an SNP array and validation with commercial varieties. Common wheat (Triticum aestivum L.) is an important winter crop worldwide and a typical allopolyploid with a large and complex genome. With global warming, the environmental volatility and incidence of drought in wheat-producing areas will increase. Molecular markers for drought tolerance are urgently needed to enhance drought tolerance breeding. Here, we genotyped four near-isogenic line (NIL) pairs targeting a major QTL qDSI.4B.1 on wheat chromosome arm 4BS for drought tolerance using the 90K SNP Illumina iSelect array and discovered a single nucleotide polymorphism (SNP) (Excalibur_c100336_106) with consistent genotype-phenotype associations among all four NIL pairs and their parents. Then, we converted the SNP into a Kompetitive Allele-Specific PCR (KASP) marker, with an accuracy of 100% for the four NIL pairs and their parents and as high as 81.8% for the 44 tested wheat lines with known phenotypes collected from Australia and China. Two genes near this SNP were suggested as candidate genes for drought tolerance in wheat after checking the Chinese Spring reference genome annotation version 1.1. One gene, TraesCS4B02G085300, encodes an F-box protein reportedly related to the ABA network, a main pathway for drought tolerance, and another gene, TraesCS4B02G085400, encodes a calcineurin-like metallophos-phoesterase transmembrane protein, which participates in Ca2+-dependent phosphorylation regulatory system. Based on this work and previous research on pre-harvest sprouting, we established a quick and efficient general SQV-based approach for KASP marker development, integrating genotyping by SNP arrays (S) using NILs targeting major QTL for a specific trait (Q) and validating them with commercial varieties (V). The identified SNP and developed KASP marker could be applied to marker-assisted selection in drought breeding, and further study of the candidate genes may improve our understanding of drought tolerance in wheat.
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Affiliation(s)
- Guannan Liu
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
| | - Dongcheng Liu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agriculture University, Baoding, 071000 Hebei China
| | - Aimin Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agriculture University, Baoding, 071000 Hebei China
| | - Hui Liu
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
| | - Md Sultan Mia
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
| | - Daniel Mullan
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
- InterGrain Pty. Ltd., 19 Ambitious Link, Bibra Lake, WA 6163 Australia
| | - Guijun Yan
- UWA School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
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Miao R, Li M, Wen Z, Meng J, Liu X, Fan D, Lv W, Cheng T, Zhang Q, Sun L. Whole-Genome Identification of Regulatory Function of CDPK Gene Families in Cold Stress Response for Prunus mume and Prunus mume var. Tortuosa. PLANTS (BASEL, SWITZERLAND) 2023; 12:2548. [PMID: 37447109 DOI: 10.3390/plants12132548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/16/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023]
Abstract
Calcium-dependent protein kinases (CDPK) are known to mediate plant growth and development and respond to various environmental changes. Here, we performed whole-genome identification of CDPK families in cultivated and wild mei (Prunus mume). We identified 14 and 17 CDPK genes in P. mume and P. mume var. Tortuosa genomes, respectively. All 270 CPDK proteins were classified into four clade, displaying frequent homologies between these two genomes and those of other Rosaceae species. Exon/intron structure, motif and synteny blocks were conserved between P. mume and P. mume var. Tortuosa. The interaction network revealed all PmCDPK and PmvCDPK proteins is interacted with respiratory burst oxidase homologs (RBOHs) and mitogen-activated protein kinase (MAPK). RNA-seq data analysis of cold experiments show that cis-acting elements in the PmCDPK genes, especially PmCDPK14, are associated with cold hardiness. Our results provide and broad insights into CDPK gene families in mei and their role in modulating cold stress response in plants.
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Affiliation(s)
- Runtian Miao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Mingyu Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Zhenying Wen
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Juan Meng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Xu Liu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Dongqing Fan
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Wenjuan Lv
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Lidan Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
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Kajla M, Roy A, Singh IK, Singh A. Regulation of the regulators: Transcription factors controlling biosynthesis of plant secondary metabolites during biotic stresses and their regulation by miRNAs. FRONTIERS IN PLANT SCIENCE 2023; 14:1126567. [PMID: 36938003 PMCID: PMC10017880 DOI: 10.3389/fpls.2023.1126567] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Biotic stresses threaten to destabilize global food security and cause major losses to crop yield worldwide. In response to pest and pathogen attacks, plants trigger many adaptive cellular, morphological, physiological, and metabolic changes. One of the crucial stress-induced adaptive responses is the synthesis and accumulation of plant secondary metabolites (PSMs). PSMs mitigate the adverse effects of stress by maintaining the normal physiological and metabolic functioning of the plants, thereby providing stress tolerance. This differential production of PSMs is tightly orchestrated by master regulatory elements, Transcription factors (TFs) express differentially or undergo transcriptional and translational modifications during stress conditions and influence the production of PSMs. Amongst others, microRNAs, a class of small, non-coding RNA molecules that regulate gene expression post-transcriptionally, also play a vital role in controlling the expression of many such TFs. The present review summarizes the role of stress-inducible TFs in synthesizing and accumulating secondary metabolites and also highlights how miRNAs fine-tune the differential expression of various stress-responsive transcription factors during biotic stress.
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Affiliation(s)
- Mohini Kajla
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Amit Roy
- Excellent Team for Mitigation (ETM), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Indrakant K. Singh
- Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- Jagdish Chandra Bose Center for Plant Genomics, Hansraj College, University of Delhi, Delhi, India
- Delhi School of Climate Change and Sustainability, Institution of Eminence, Maharishi Karnad Bhawan, University of Delhi, Delhi, India
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7
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Sarwar R, Li L, Yu J, Zhang Y, Geng R, Meng Q, Zhu K, Tan XL. Functional Characterization of the Cystine-Rich-Receptor-like Kinases ( CRKs) and Their Expression Response to Sclerotinia sclerotiorum and Abiotic Stresses in Brassica napus. Int J Mol Sci 2022; 24:ijms24010511. [PMID: 36613954 PMCID: PMC9820174 DOI: 10.3390/ijms24010511] [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: 12/01/2022] [Revised: 12/24/2022] [Accepted: 12/24/2022] [Indexed: 12/29/2022] Open
Abstract
Cysteine-rich receptor-like kinases (CRKs) are transmembrane proteins that bind to the calcium ion to regulate stress-signaling and plant development-related pathways, as indicated by several pieces of evidence. However, the CRK gene family hasn’t been inadequately examined in Brassica napus. In our study, 27 members of the CRK gene family were identified in Brassica napus, which are categorized into three phylogenetic groups and display synteny relationship to the Arabidopsis thaliana orthologs. All the CRK genes contain highly conserved N-terminal PKINASE domain; however, the distribution of motifs and gene structure were variable conserved. The functional divergence analysis between BnaCRK groups indicates a shift in evolutionary rate after duplication events, demonstrating that BnaCRKs might direct a specific function. RNA-Seq datasets and quantitative real-time PCR (qRT-PCR) exhibit the complex expression profile of the BnaCRKs in plant tissues under multiple stresses. Nevertheless, BnaA06CRK6-1 and BnaA08CRK8 from group B were perceived to play a predominant role in the Brassica napus stress signaling pathway in response to drought, salinity, and Sclerotinia sclerotiorum infection. Insights gained from this study improve our knowledge about the Brassica napus CRK gene family and provide a basis for enhancing the quality of rapeseed.
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Affiliation(s)
- Rehman Sarwar
- School of Food Science and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Lei Li
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Jiang Yu
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Yijie Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Rui Geng
- School of Food Science and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Qingfeng Meng
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Keming Zhu
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Xiao-Li Tan
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
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8
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Li T, Wei Q, Sun W, Tan H, Cui Y, Han C, Zhang H, Zeng F, Huang M, Yan D. Spraying sorbitol-chelated calcium affected foliar calcium absorption and promoted the yield of peanut ( Arachis hypogaea L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1075488. [PMID: 36518507 PMCID: PMC9742265 DOI: 10.3389/fpls.2022.1075488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
The prevalent use of foliar calcium fertilizers in peanut production is inorganic, but calcium absorbed from the foliar has poor availability. Sorbitol-chelated calcium is a novel organic foliar calcium fertilizer that has rarely been studied for application in peanut production. To explore whether calcium absorption and peanut yields can be affected by foliar application of sorbitol-chelated calcium, this study conducted two field experiments using Virginia peanut (Huayu-22) in 2020 and 2021. The five spray treatments included: deionized water (CK), sorbitol (Sor), calcium nitrate (CaN), a mixture of sorbitol and calcium nitrate (SN), and sorbitol-chelated calcium (SC). The yield of peanuts treated with sorbitol-chelated calcium was increased by 12.31-16.63%, 10.22-11.83%, 6.31-9.69%, and 4.18-6.99% compared to the CK, Sor, CaN, and SN treatments, respectively. Sorbitol-chelated calcium had the lowest contact angle due to the wetting effect of sorbitol, which promoted calcium absorption by leaves. Sorbitol-chelated calcium improved the leaf calcium concentration by 13.12-19.32% and kernel calcium concentration by 6.49-8.15% compared to the CK treatment. Foliar fertilization increased the calcium concentration of each subcellular fraction of leaves and changed the distribution of calcium in mesophyll cells. This change was directly observed by transmission electron microscopy. Additionally, spraying sorbitol alone obtained similar effects to spraying calcium nitrate alone, indicating that the benefits of sorbitol itself were not negligible. The results of the principal component and correlation analysis showed that the increase in calcium concentrations and the change in calcium distribution improved the pod traits of the peanut, thus affecting the peanut yield. The above results showed that from the perspective of calcium absorption and distribution, sorbitol-chelated calcium is a more effective foliar calcium fortifier for peanuts and effectively improves peanut yields.
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9
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Dekomah SD, Bi Z, Dormatey R, Wang Y, Haider FU, Sun C, Yao P, Bai J. The role of CDPKs in plant development, nutrient and stress signaling. Front Genet 2022; 13:996203. [PMID: 36246614 PMCID: PMC9561101 DOI: 10.3389/fgene.2022.996203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 09/14/2022] [Indexed: 11/13/2022] Open
Abstract
The second messenger calcium (Ca2+) is a ubiquitous intracellular signaling molecule found in eukaryotic cells. In plants, the multigene family of calcium-dependent protein kinases (CDPKs) plays an important role in regulating plant growth, development, and stress tolerance. CDPKs sense changes in intracellular Ca2+ concentration and translate them into phosphorylation events that initiate downstream signaling processes. Several functional and expression studies on different CDPKs and their encoding genes have confirmed their multifunctional role in stress. Here, we provide an overview of the signal transduction mechanisms and functional roles of CDPKs. This review includes details on the regulation of secondary metabolites, nutrient uptake, regulation of flower development, hormonal regulation, and biotic and abiotic stress responses.
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Affiliation(s)
- Simon Dontoro Dekomah
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Zhenzhen Bi
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Richard Dormatey
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Yihao Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Fasih Ullah Haider
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou, China
| | - Chao Sun
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Panfeng Yao
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
| | - Jiangping Bai
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Jiangping Bai,
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Dekomah SD, Wang Y, Qin T, Xu D, Sun C, Yao P, Liu Y, Bi Z, Bai J. Identification and Expression Analysis of Calcium-Dependent Protein Kinases Gene Family in Potato Under Drought Stress. Front Genet 2022; 13:874397. [PMID: 35669192 PMCID: PMC9164159 DOI: 10.3389/fgene.2022.874397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 04/20/2022] [Indexed: 12/13/2022] Open
Abstract
Calcium-dependent protein kinases (CDPKs) are a class of serine/threonine protein kinases encoded by several gene families that play key roles in stress response and plant growth and development. In this study, the BLAST method was used to search for protein sequences of the potato Calcium-dependent protein kinase gene family. The chromosome location, phylogeny, gene structures, gene duplication, cis-acting elements, protein-protein interaction, and expression profiles were analyzed. Twenty-five CDPK genes in the potato genome were identified based on RNA-seq data and were clustered into four groups (I-IV) based on their structural features and phylogenetic analysis. The result showed the composition of the promoter region of the StCDPKs gene, including light-responsive elements such as Box4, hormone-responsive elements such as ABRE, and stress-responsive elements such as MBS. Four pairs of segmental duplications were found in StCDPKs genes and the Ka/Ks ratios were below 1, indicating a purifying selection of the genes. The protein-protein interaction network revealed defense-related proteins such as; respiratory burst oxidase homologs (RBOHs) interacting with potato CDPKs. Transcript abundance was measured via RT-PCR between the two cultivars and their relative expression of CDPK genes was analyzed after 15, 20, and 25 days of drought. There were varied expression patterns of StCDPK3/13/21 and 23, between the two potato cultivars under mannitol induced-drought conditions. Correlation analysis showed that StCDPK21/22 and StCDPK3 may be the major differentially expressed genes involved in the regulation of malondialdehyde (MDA) and proline content in response to drought stress, opening a new research direction for genetic improvement of drought resistance in potato.
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Affiliation(s)
- Simon Dontoro Dekomah
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
| | - Yihao Wang
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
| | - Tianyuan Qin
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
| | - Derong Xu
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
| | - Chao Sun
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
| | - Panfeng Yao
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
| | - Yuhui Liu
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
| | - Zhenzhen Bi
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
- *Correspondence: Zhenzhen Bi, ; Jiangping Bai,
| | - Jiangping Bai
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou, China
- *Correspondence: Zhenzhen Bi, ; Jiangping Bai,
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11
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Iqbal Z, Memon AG, Ahmad A, Iqbal MS. Calcium Mediated Cold Acclimation in Plants: Underlying Signaling and Molecular Mechanisms. FRONTIERS IN PLANT SCIENCE 2022; 13:855559. [PMID: 35574126 PMCID: PMC9094111 DOI: 10.3389/fpls.2022.855559] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/31/2022] [Indexed: 05/23/2023]
Abstract
Exposure of plants to low temperatures adversely affects plant growth, development, and productivity. Plant response to cold stress is an intricate process that involves the orchestration of various physiological, signaling, biochemical, and molecular pathways. Calcium (Ca2+) signaling plays a crucial role in the acquisition of several stress responses, including cold. Upon perception of cold stress, Ca2+ channels and/or Ca2+ pumps are activated, which induces the Ca2+ signatures in plant cells. The Ca2+ signatures spatially and temporally act inside a plant cell and are eventually decoded by specific Ca2+ sensors. This series of events results in the molecular regulation of several transcription factors (TFs), leading to downstream gene expression and withdrawal of an appropriate response by the plant. In this context, calmodulin binding transcription activators (CAMTAs) constitute a group of TFs that regulate plant cold stress responses in a Ca2+ dependent manner. The present review provides a catalog of the recent progress made in comprehending the Ca2+ mediated cold acclimation in plants.
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Affiliation(s)
- Zahra Iqbal
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
| | - Anjuman Gul Memon
- Department of Biochemistry, College of Medicine, Qassim University, Buraydah, Saudi Arabia
| | - Ausaf Ahmad
- Amity Institute of Biotechnology, Amity University Lucknow, Lucknow, India
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Deepika D, Poddar N, Kumar S, Singh A. Molecular Characterization Reveals the Involvement of Calcium Dependent Protein Kinases in Abiotic Stress Signaling and Development in Chickpea ( Cicer arietinum). FRONTIERS IN PLANT SCIENCE 2022; 13:831265. [PMID: 35498712 PMCID: PMC9039462 DOI: 10.3389/fpls.2022.831265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Calcium-dependent protein kinases (CDPKs) are a major group of calcium (Ca2+) sensors in plants. CDPKs play a dual function of "Ca2+ sensor and responder." These sensors decode the "Ca2+ signatures" generated in response to adverse growth conditions such as drought, salinity, and cold and developmental processes. However, knowledge of the CDPK family in the legume crop chickpea is missing. Here, we have identified a total of 22 CDPK genes in the chickpea genome. The phylogenetic analysis of the chickpea CDPK family with other plants revealed their evolutionary conservation. Protein homology modeling described the three-dimensional structure of chickpea CDPKs. Defined arrangements of α-helix, β-strands, and transmembrane-helix represent important structures like kinase domain, inhibitory junction domain, N and C-lobes of EF-hand motifs. Subcellular localization analysis revealed that CaCDPK proteins are localized mainly at the cytoplasm and in the nucleus. Most of the CaCDPK promoters had abiotic stress and development-related cis-regulatory elements, suggesting the functional role of CaCDPKs in abiotic stress and development-related signaling. RNA sequencing (RNA-seq) expression analysis indicated the role of the CaCDPK family in various developmental stages, including vegetative, reproductive development, senescence stages, and during seed stages of early embryogenesis, late embryogenesis, mid and late seed maturity. The real-time quantitative PCR (qRT-PCR) analysis revealed that several CaCDPK genes are specifically as well as commonly induced by drought, salt, and Abscisic acid (ABA). Overall, these findings indicate that the CDPK family is probably involved in abiotic stress responses and development in chickpeas. This study provides crucial information on the CDPK family that will be utilized in generating abiotic stress-tolerant and high-yielding chickpea varieties.
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Affiliation(s)
- Deepika Deepika
- Stress Signaling Lab, National Institute of Plant Genome Research, New Delhi, India
| | - Nikita Poddar
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi, India
| | - Shailesh Kumar
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi, India
| | - Amarjeet Singh
- Stress Signaling Lab, National Institute of Plant Genome Research, New Delhi, India
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13
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Yang S, Cai W, Shen L, Cao J, Liu C, Hu J, Guan D, He S. A CaCDPK29-CaWRKY27b module promotes CaWRKY40-mediated thermotolerance and immunity to Ralstonia solanacearum in pepper. THE NEW PHYTOLOGIST 2022; 233:1843-1863. [PMID: 34854082 DOI: 10.1111/nph.17891] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 11/18/2021] [Indexed: 06/13/2023]
Abstract
CaWRKY40 in pepper (Capsicum annuum) promotes immune responses to Ralstonia solanacearum infection (RSI) and to high-temperature, high-humidity (HTHH) stress, but how it interacts with upstream signalling components remains poorly understood. Here, using approaches of reverse genetics, biochemical and molecular biology we functionally characterised the relationships among the WRKYGMK-containing WRKY protein CaWRKY27b, the calcium-dependent protein kinase CaCDPK29, and CaWRKY40 during pepper response to RSI or HTHH. Our data indicate that CaWRKY27b is upregulated and translocated from the cytoplasm to the nucleus upon phosphorylation of Ser137 in the nuclear localisation signal by CaCDPK29. Using electrophoretic mobility shift assays and microscale thermophoresis, we observed that, due to the replacement of Q by M in the conserved WRKYGQK, CaWRKY27b in the nucleus failed to bind to W-boxes in the promoters of immunity- and thermotolerance-related marker genes. Instead, CaWRKY27b interacted with CaWRKY40 and promoted its binding and positive regulation of the tested marker genes including CaNPR1, CaDEF1 and CaHSP24. Notably, mutation of the WRKYGMK motif in CaWRKY27b to WRKYGQK restored the W-box binding ability. Our data therefore suggest that CaWRKY27b is phosphorylated by CaCDPK29 and acts as a transcriptional activator of CaWRKY40 during the pepper response to RSI and HTHH.
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Affiliation(s)
- Sheng Yang
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Weiwei Cai
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Lei Shen
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jianshen Cao
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Cailing Liu
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, 350002, China
| | - Jiong Hu
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Deyi Guan
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Shuilin He
- National Education Ministry Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
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14
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Yadav V, Wang Z, Yang X, Wei C, Changqing X, Zhang X. Comparative Analysis, Characterization and Evolutionary Study of Dirigent Gene Family in Cucurbitaceae and Expression of Novel Dirigent Peptide against Powdery Mildew Stress. Genes (Basel) 2021; 12:genes12030326. [PMID: 33668231 PMCID: PMC7996225 DOI: 10.3390/genes12030326] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 12/16/2022] Open
Abstract
Dirigent (DIR) proteins are induced under various stress conditions and involved in sterio- and regio-selective coupling of monolignol. A striking lack of information about dirigent genes in cucurbitaceae plants underscores the importance of functional characterization. In this study, 112 DIR genes were identified in six species, and 61 genes from major cultivated species were analyzed. DIRs were analyzed using various bioinformatics tools and complemented by expression profiling. Phylogenetic analysis segregated the putative DIRs into six distinctively known subgroups. Chromosomal mapping revealed uneven distribution of genes, whereas synteny analysis exhibited that duplication events occurred during gene evolution. Gene structure analysis suggested the gain of introns during gene diversification. Gene ontology (GO) enrichment analysis indicates the participation of proteins in lignification and pathogen resistance activities. We also determined their organ-specific expression levels in three species revealing preferential expression in root and leaves. Furthermore, the number of CmDIR (CmDIR1, 6, 7 and 12) and ClDIR (ClDIR2, 5, 8, 9 and 17) genes exhibited higher expression in resistant cultivars after powdery mildew (PM) inoculation. In summary, based on the expression and in-silico analysis, we propose a role of DIRs in disease resistance mechanisms.
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Affiliation(s)
- Vivek Yadav
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, China; (V.Y.); (Z.W.); (X.Y.); (C.W.); (X.C.)
| | - Zhongyuan Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, China; (V.Y.); (Z.W.); (X.Y.); (C.W.); (X.C.)
| | - Xiaozhen Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, China; (V.Y.); (Z.W.); (X.Y.); (C.W.); (X.C.)
- Xi’an Agriculture Technology, Extension Center, Xi’an 710000, China
| | - Chunhua Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, China; (V.Y.); (Z.W.); (X.Y.); (C.W.); (X.C.)
| | - Xuan Changqing
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, China; (V.Y.); (Z.W.); (X.Y.); (C.W.); (X.C.)
| | - Xian Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, China; (V.Y.); (Z.W.); (X.Y.); (C.W.); (X.C.)
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin 300384, China
- Correspondence: ; Tel.: +86-186-2909-2147
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15
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Zhao P, Liu Y, Kong W, Ji J, Cai T, Guo Z. Genome-Wide Identification and Characterization of Calcium-Dependent Protein Kinase ( CDPK) and CDPK-Related Kinase ( CRK) Gene Families in Medicago truncatula. Int J Mol Sci 2021; 22:1044. [PMID: 33494310 PMCID: PMC7864493 DOI: 10.3390/ijms22031044] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 11/16/2022] Open
Abstract
Calcium-dependent protein kinase (CDPK or CPK) and CDPK-related kinase (CRK) play an important role in plant growth, development, and adaptation to environmental stresses. However, their gene families had been yet inadequately investigated in Medicago truncatula. In this study, six MtCRK genes were computationally identified, they were classified into five groups with MtCDPKs based on phylogenetic relationships. Six pairs of segmental duplications were observed in MtCDPK and MtCRK genes and the Ka/Ks ratio, an indicator of selection pressure, was below 0.310, indicating that these gene pairs underwent strong purifying selection. Cis-acting elements of morphogenesis, multiple hormone responses, and abiotic stresses were predicted in the promoter region. The spatial expression of MtCDPKs and MtCRKs displays diversity. The expression of MtCDPKs and MtCRKs could be regulated by various stresses. MtCDPK4, 14, 16, 22, and MtCRK6 harbor both N-myristoylation site and palmitoylation site and were anchored on plasma membrane, while MtCDPK7, 9, and 15 contain no or only one N-acylation site and were distributed in cytosol and nucleus, suggesting that the N-terminal acylation sites play a key role in subcellular localization of MtCDPKs and MtCRKs. In summary, comprehensive characterization of MtCDPKs and MtCRKs provide a subset of candidate genes for further functional analysis and genetic improvement against drought, cold, salt and biotic stress.
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Affiliation(s)
| | | | | | | | | | - Zhenfei Guo
- College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China; (P.Z.); (Y.L.); (W.K.); (J.J.); (T.C.)
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16
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Yadav A, Garg T, Singh H, Yadav SR. Tissue-specific expression pattern of calcium-dependent protein kinases-related kinases (CRKs) in rice. PLANT SIGNALING & BEHAVIOR 2020; 15:1809846. [PMID: 32835584 PMCID: PMC7588190 DOI: 10.1080/15592324.2020.1809846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/09/2020] [Accepted: 08/10/2020] [Indexed: 05/23/2023]
Abstract
Calcium-dependent protein kinases-related kinases (CDPK-related kinases; CRKs) are Ser/Thr kinases that bind with Ca2+/Calmodulin and play crucial roles in signal transduction pathways during plant growth, development, and responses to multiple stresses. In this study, we have studied detailed organ and tissue-specific expression patterns of rice CRK genes. Our organ-specific RT-PCR analyzes show the differential expression pattern of these genes in various organs of rice. Moreover, our RNA-RNA in situ hybridization study in rice stem base containing developing crown root primordia demonstrates that the expression of CRK genes is spatially restricted to the developing crown root primordia, suggesting their putative role in protein phosphorylation-dependent cellular signaling during rice crown root development. Furthermore, organ-specific differentially expression pattern of CRK genes during floral organogenesis further support for the organ-specific cell signaling during organogenesis. Thus, our study provides a developmentally regulated expression pattern of rice CRK genes, though they are broadly expressed and a basic foundation for functional characterizations of CRK gene members to unravel their specific functions during plant growth and development.
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Affiliation(s)
- Akhilesh Yadav
- Department of Biotechnology, Indian Institute of Technology, Roorkee, India
| | - Tushar Garg
- Department of Biotechnology, Indian Institute of Technology, Roorkee, India
| | - Harshita Singh
- Department of Biotechnology, Indian Institute of Technology, Roorkee, India
| | - Shri Ram Yadav
- Department of Biotechnology, Indian Institute of Technology, Roorkee, India
- CONTACT : Shri Ram Yadav Department of Biotechnology, Indian Institute of Technology, Roorkee247667, India
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17
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Zhang M, Liu Y, He Q, Chai M, Huang Y, Chen F, Wang X, Liu Y, Cai H, Qin Y. Genome-wide investigation of calcium-dependent protein kinase gene family in pineapple: evolution and expression profiles during development and stress. BMC Genomics 2020; 21:72. [PMID: 31973690 PMCID: PMC6979071 DOI: 10.1186/s12864-020-6501-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 01/16/2020] [Indexed: 11/25/2022] Open
Abstract
Background Calcium-dependent protein kinase (CPK) is one of the main Ca2+ combined protein kinase that play significant roles in plant growth, development and response to multiple stresses. Despite an important member of the stress responsive gene family, little is known about the evolutionary history and expression patterns of CPK genes in pineapple. Results Herein, we identified and characterized 17 AcoCPK genes from pineapple genome, which were unevenly distributed across eight chromosomes. Based on the gene structure and phylogenetic tree analyses, AcoCPKs were divided into four groups with conserved domain. Synteny analysis identified 7 segmental duplication events of AcoCPKs and 5 syntenic blocks of CPK genes between pineapple and Arabidopsis, and 8 between pineapple and rice. Expression pattern of different tissues and development stages suggested that several genes are involved in the functional development of plants. Different expression levels under various abiotic stresses also indicated that the CPK family underwent functional divergence during long-term evolution. AcoCPK1, AcoCPK3 and AcoCPK6, which were repressed by the abiotic stresses, were shown to be function in regulating pathogen resistance. Conclusions 17 AcoCPK genes from pineapple genome were identified. Our analyses provide an important foundation for understanding the potential roles of AcoCPKs in regulating pineapple response to biotic and abiotic stresses
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Affiliation(s)
- Man Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Center for Genomics and Biotechnology, College of Plant Protection, College of life science, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China
| | - Yanhui Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Center for Genomics and Biotechnology, College of Plant Protection, College of life science, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China
| | - Qing He
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Center for Genomics and Biotechnology, College of Plant Protection, College of life science, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China
| | - Mengnan Chai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Center for Genomics and Biotechnology, College of Plant Protection, College of life science, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China
| | - Youmei Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Center for Genomics and Biotechnology, College of Plant Protection, College of life science, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China
| | - Fangqian Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Center for Genomics and Biotechnology, College of Plant Protection, College of life science, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China
| | - Xiaomei Wang
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning Investigation Station of South Subtropical Fruit Trees, Ministry of Agriculture, Nanning, 530007, China
| | - Yeqiang Liu
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning Investigation Station of South Subtropical Fruit Trees, Ministry of Agriculture, Nanning, 530007, China
| | - Hanyang Cai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Center for Genomics and Biotechnology, College of Plant Protection, College of life science, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China.
| | - Yuan Qin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Center for Genomics and Biotechnology, College of Plant Protection, College of life science, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China. .,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530004, China.
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18
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Atif RM, Shahid L, Waqas M, Ali B, Rashid MAR, Azeem F, Nawaz MA, Wani SH, Chung G. Insights on Calcium-Dependent Protein Kinases (CPKs) Signaling for Abiotic Stress Tolerance in Plants. Int J Mol Sci 2019; 20:E5298. [PMID: 31653073 PMCID: PMC6862689 DOI: 10.3390/ijms20215298] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 12/18/2022] Open
Abstract
Abiotic stresses are the major limiting factors influencing the growth and productivity of plants species. To combat these stresses, plants can modify numerous physiological, biochemical, and molecular processes through cellular and subcellular signaling pathways. Calcium-dependent protein kinases (CDPKs or CPKs) are the unique and key calcium-binding proteins, which act as a sensor for the increase and decrease in the calcium (Ca) concentrations. These Ca flux signals are decrypted and interpreted into the phosphorylation events, which are crucial for signal transduction processes. Several functional and expression studies of different CPKs and their encoding genes validated their versatile role for abiotic stress tolerance in plants. CPKs are indispensable for modulating abiotic stress tolerance through activation and regulation of several genes, transcription factors, enzymes, and ion channels. CPKs have been involved in supporting plant adaptation under drought, salinity, and heat and cold stress environments. Diverse functions of plant CPKs have been reported against various abiotic stresses in numerous research studies. In this review, we have described the evaluated functions of plant CPKs against various abiotic stresses and their role in stress response signaling pathways.
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Affiliation(s)
- Rana Muhammad Atif
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan.
- Center for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad 38040, Pakistan.
| | - Luqman Shahid
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan.
| | - Muhammad Waqas
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan.
| | - Babar Ali
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan.
| | - Muhammad Abdul Rehman Rashid
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan.
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China.
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38040, Pakistan.
| | - Muhammad Amjad Nawaz
- Education Scientific Center of Nanotechnology, Far Eastern Federal University, 690950 Vladivostok, Russia.
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar 190001, India.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam 59626, Korea.
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Li M, Hu W, Ren L, Jia C, Liu J, Miao H, Guo A, Xu B, Jin Z. Identification, Expression, and Interaction Network Analyses of the CDPK Gene Family Reveal Their Involvement in the Development, Ripening, and Abiotic Stress Response in Banana. Biochem Genet 2019; 58:40-62. [PMID: 31144068 DOI: 10.1007/s10528-019-09916-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 03/27/2019] [Indexed: 11/25/2022]
Abstract
Calcium-dependent protein kinases (CDPKs) play vital roles in the regulation of plant growth, development, and tolerance to various abiotic stresses. However, little information is available for this gene family in banana. In this study, 44 CDPKs were identified in banana and were classified into four groups based on phylogenetic, gene structure, and conserved motif analyses. The majority of MaCDPKs generally exhibited similar expression patterns in the different tissues. Transcriptome analyses revealed that many CDPKs showed strong transcript accumulation at the early stages of fruit development and postharvest ripening in both varieties. Interaction network and co-expression analysis further identified some CDPKs-mediated network that was potentially active at the early stages of fruit development. Comparative expression analysis suggested that the high levels of CDPK expression in FJ might be related to its fast ripening characteristic. CDPK expression following the abiotic stress treatments indicated a significant transcriptional response to osmotic, cold, and salt treatment, as well as differential expression profiles, between BX and FJ. The findings of this study elucidate the transcriptional control of CDPKs in development, ripening, and the abiotic stress response in banana. Some tissue-specific, development/ripening-dependent, and abiotic stress-responsive candidate MaCDPK genes were identified for further genetic improvement of banana.
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Affiliation(s)
- Meiying Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Licheng Ren
- Department of Biology, Hainan Medical College, Haikou, China
| | - Caihong Jia
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Juhua Liu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Hongxia Miao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China
| | - Anping Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
| | - Biyu Xu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
| | - Zhiqiang Jin
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, Hainan, China.
- Key Laboratory of Genetic Improvement of Bananas, Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.
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Wei C, Zhang R, Yang X, Zhu C, Li H, Zhang Y, Ma J, Yang J, Zhang X. Comparative Analysis of Calcium-Dependent Protein Kinase in Cucurbitaceae and Expression Studies in Watermelon. Int J Mol Sci 2019; 20:ijms20102527. [PMID: 31126008 PMCID: PMC6566760 DOI: 10.3390/ijms20102527] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/03/2019] [Accepted: 05/20/2019] [Indexed: 11/30/2022] Open
Abstract
Both the calcium-dependent protein kinases (CDPKs) and CDPK-related kinases (CRKs) play numerous roles in plant growth, development, and stress response. Despite genome-wide identification of both families in Cucumis, comparative evolutionary and functional analysis of both CDPKs and CRKs in Cucurbitaceae remain unclear. In this study, we identified 128 CDPK and 56 CRK genes in total in six Cucurbitaceae species (C. lanatus, C. sativus, C. moschata, C. maxima, C. pepo, and L. siceraria). Dot plot analysis indicated that self-duplication of conserved domains contributed to the structural variations of two CDPKs (CpCDPK19 and CpCDPK27) in C. pepo. Using watermelon genome as reference, an integrated map containing 25 loci (16 CDPK and nine CRK loci) was obtained, 16 of which (12 CDPK and four CRK) were shared by all seven Cucurbitaceae species. Combined with exon-intron organizations, topological analyses indicated an ancient origination of groups CDPK IV and CRK. Moreover, the evolutionary scenario of seven modern Cucurbitaceae species could also be reflected on the phylogenetic trees. Expression patterns of ClCDPKs and ClCRKs were studied under different abiotic stresses. Some valuable genes were uncovered for future gene function exploration. For instance, both ClCDPK6 and its ortholog CsCDPK14 in cucumber could be induced by salinity, while ClCDPK6 and ClCDPK16, as well as their orthologs in Cucumis, maintained high expression levels in male flowers. Collectively, these results provide insights into the evolutionary history of two gene families in Cucurbitaceae, and indicate a subset of candidate genes for functional characterizations in the future.
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Affiliation(s)
- Chunhua Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Ruimin Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Xiaozhen Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Chunyu Zhu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Hao Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Yong Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Jianxiang Ma
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Jianqiang Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Xian Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, China.
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Yang X, Li H, Yang Y, Wang Y, Mo Y, Zhang R, Zhang Y, Ma J, Wei C, Zhang X. Identification and expression analyses of WRKY genes reveal their involvement in growth and abiotic stress response in watermelon (Citrullus lanatus). PLoS One 2018; 13:e0191308. [PMID: 29338040 PMCID: PMC5770075 DOI: 10.1371/journal.pone.0191308] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/02/2018] [Indexed: 12/16/2022] Open
Abstract
Despite identification of WRKY family genes in numerous plant species, a little is known about WRKY genes in watermelon, one of the most economically important fruit crops around the world. Here, we identified a total of 63 putative WRKY genes in watermelon and classified them into three major groups (I-III) and five subgroups (IIa-IIe) in group II. The structure analysis indicated that ClWRKYs with different WRKY domains or motifs may play different roles by regulating respective target genes. The expressions of ClWRKYs in different tissues indicate that they are involved in various tissue growth and development. Furthermore, the diverse responses of ClWRKYs to drought, salt, or cold stress suggest that they positively or negatively affect plant tolerance to various abiotic stresses. In addition, the altered expression patterns of ClWRKYs in response to phytohormones such as, ABA, SA, MeJA, and ETH, imply the occurrence of complex cross-talks between ClWRKYs and plant hormone signals in regulating plant physiological and biological processes. Taken together, our findings provide valuable clues to further explore the function and regulatory mechanisms of ClWRKY genes in watermelon growth, development, and adaption to environmental stresses.
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Affiliation(s)
- Xiaozhen Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
| | - Hao Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
| | - Yongchao Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
- Wenshan Academy of Agricultural Sciences, Wenshan, China
| | - Yongqi Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
- Hanzhong City Agro-technology Extension Center, Hanzhong, China
| | - Yanling Mo
- Yangtze Normal University, Fuling, China
| | - Ruimin Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
| | - Yong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
| | - Jianxiang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
| | - Chunhua Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
- * E-mail: (CHW); (XZ)
| | - Xian Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China
- * E-mail: (CHW); (XZ)
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Li TG, Zhang DD, Zhou L, Kong ZQ, Hussaini AS, Wang D, Li JJ, Short DPG, Dhar N, Klosterman SJ, Wang BL, Yin CM, Subbarao KV, Chen JY, Dai XF. Genome-Wide Identification and Functional Analyses of the CRK Gene Family in Cotton Reveals GbCRK18 Confers Verticillium Wilt Resistance in Gossypium barbadense. FRONTIERS IN PLANT SCIENCE 2018; 9:1266. [PMID: 30254650 PMCID: PMC6141769 DOI: 10.3389/fpls.2018.01266] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 08/10/2018] [Indexed: 05/07/2023]
Abstract
Cysteine-rich receptor-like kinases (CRKs) are a large subfamily of plant receptor-like kinases that play a critical role in disease resistance in plants. However, knowledge about the CRK gene family in cotton and its function against Verticillium wilt (VW), a destructive disease caused by Verticillium dahliae that significantly reduces cotton yields is lacking. In this study, we identified a total of 30 typical CRKs in a Gossypium barbadense genome (GbCRKs). Eleven of these (>30%) are located on the A06 and D06 chromosomes, and 18 consisted of 9 paralogous pairs encoded in the A and D subgenomes. Phylogenetic analysis showed that the GbCRKs could be classified into four broad groups, the expansion of which has probably been driven by tandem duplication. Gene expression profiling of the GbCRKs in resistant and susceptible cotton cultivars revealed that a phylogenetic cluster of nine of the GbCRK genes were up-regulated in response to V. dahliae infection. Virus-induced gene silencing of each of these nine GbCRKs independently revealed that the silencing of GbCRK18 was sufficient to compromise VW resistance in G. barbadense. GbCRK18 expression could be induced by V. dahliae infection or jasmonic acid, and displayed plasma membrane localization. Therefore, our expression analyses indicated that the CRK gene family is differentially regulated in response to Verticillium infection, while gene silencing experiments revealed that GbCRK18 in particular confers VW resistance in G. barbadense.
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Affiliation(s)
- Ting-Gang Li
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dan-Dan Zhang
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lei Zhou
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhi-Qiang Kong
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Adamu S. Hussaini
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dan Wang
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun-Jiao Li
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dylan P. G. Short
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
- U.S. Agricultural Research Station, Salinas, CA, United States
| | - Nikhilesh Dhar
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
- U.S. Agricultural Research Station, Salinas, CA, United States
| | - Steven J. Klosterman
- Crop Improvement and Protection Research Unit, United States Department of Agriculture, Agricultural Research Service, Salinas, CA, United States
| | - Bao-Li Wang
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chun-Mei Yin
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Krishna V. Subbarao
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
- U.S. Agricultural Research Station, Salinas, CA, United States
- *Correspondence: Krishna V. Subbarao, Jie-Yin Chen, Xiao-Feng Dai,
| | - Jie-Yin Chen
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Krishna V. Subbarao, Jie-Yin Chen, Xiao-Feng Dai,
| | - Xiao-Feng Dai
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Krishna V. Subbarao, Jie-Yin Chen, Xiao-Feng Dai,
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23
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Yang S, Li L, Zhang J, Geng Y, Guo F, Wang J, Meng J, Sui N, Wan S, Li X. Transcriptome and Differential Expression Profiling Analysis of the Mechanism of Ca 2+ Regulation in Peanut ( Arachis hypogaea) Pod Development. FRONTIERS IN PLANT SCIENCE 2017; 8:1609. [PMID: 29033956 PMCID: PMC5625282 DOI: 10.3389/fpls.2017.01609] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 09/04/2017] [Indexed: 05/23/2023]
Abstract
Calcium not only serves as a necessary nutrient for plant growth but also acts as a ubiquitous central hub in a large number of signaling pathways. Free Ca2+ deficiency in the soil may cause early embryo abortion, which eventually led to abnormal development of peanut pod during the harvest season. To understand the mechanisms of Ca2+ regulation in pod development, transcriptome analysis of peanut gynophores and pods was performed by comparing the treatments between free Ca2+ sufficiency and free Ca2+ deficiency using Illumina HiSeq™ 2000. 9,903,082,800 nt bases are generated totally. After assembly, the average length of 102,819 unigenes is 999 nt, N50 is 1,782 nt. RNA-seq based gene expression profilings showed a large number of genes at the transcriptional level changed significantly between the aerial pegs and underground swelling pods under free Ca2+ sufficienct or deficiency treatments, respectively. Genes encoding key members of Ca2+ signaling transduction pathway, enzymes for hormone metabolism, cell division and growth, transcriptional factor as well as embryo development were highlighted. This information provides useful information for our further study. The results of digital gene expression (DGE) indicated that exogenous calcium might contribute to the development of peanut pod through its signal transduction pathway, meanwhile, promote the normal transition of the gynophores to the reproductive development.
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Affiliation(s)
- Sha Yang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Lin Li
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Jialei Zhang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yun Geng
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Feng Guo
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jianguo Wang
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Jingjing Meng
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Na Sui
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Shubo Wan
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xinguo Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
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