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Geng X, Zhang C, Wei L, Lin K, Xu ZF. Genome-Wide Identification and Expression Analysis of Cytokinin Response Regulator (RR) Genes in the Woody Plant Jatropha curcas and Functional Analysis of JcRR12 in Arabidopsis. Int J Mol Sci 2022; 23:ijms231911388. [PMID: 36232689 PMCID: PMC9570446 DOI: 10.3390/ijms231911388] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
The cytokinin (CK) response regulator (RR) gene family plays a pivotal role in regulating the developmental and environmental responses of plants. Axillary bud outgrowth in the perennial woody plant Jatropha curcas is regulated by the crosstalk between CK and gibberellins (GA). In this study, we first analyzed the effects of gibberellin A3 (GA3), lovastatin (a CK synthesis inhibitor), decapitation, and their interaction, on the outgrowth of axillary buds. The results indicate that lovastatin completely inhibited GA-promoted axillary bud outgrowth and partially weakened the decapitation-promoted axillary bud outgrowth. To further characterize and understand the role of CK signaling in promoting the development of female flowers and branches, we performed bioinformatics and expression analyses to characterize the CK RR gene (JcRR) family in J. curcas. A total of 14 members of the JcRR family were identified; these genes were distributed on 10 chromosomes. Phylogenetic analysis indicated that the corresponding RR proteins are evolutionarily conserved across different plant species, and the Myb-like DNA-binding domain divides the 14 members of the JcRR family into type-A and type-B proteins. Further analysis of cis-acting elements in the promoter regions of JcRRs suggests that JcRRs are expressed in response to phytohormones, light, and abiotic stress factors; thus, JcRRs may be involved in some plant development processes. Genomic sequence comparison revealed that segmental duplication may have played crucial roles in the expansion of the JcRR gene family, and five pairs of duplicated genes were all subjected to purifying selection. By analyzing RNA sequencing (RNA-seq) and quantitative reverse transcription-polymerase chain reaction (qRT–PCR) data, we characterized that the temporospatial expression patterns of JcRRs during the development of various tissues and the response of these genes to phytohormones and abiotic stress. The JcRRs were mainly expressed in the roots, while they also exhibited differential expression patterns in other tissues. The expression levels of all six type-A and one type-B JcRRs increased in response to 6-benzylaminopurine (6-BA), while the four type-B JcRRs levels decreased. The expression levels of two type-B JcRRs increased in response to exogenous GA3 treatment, while those of three type-A and three type-B JcRRs decreased. We found that type-A JcRRs may play a positive role in the continuous growth of axillary buds, while the role of type-B JcRRs might be the opposite. In response to abiotic stress, the expression levels of two type-A and three type-B JcRRs strongly increased. The overexpression of JcRR12 in Arabidopsis thaliana slightly increased the numbers of rosette branches after decapitation, but not under normal conditions. In conclusion, our results provide detailed knowledge of JcRRs for further analysis of CK signaling and JcRR functions in J. curcas.
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Affiliation(s)
- Xianchen Geng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning 530004, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning 530004, China
| | - Chun Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning 530004, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning 530004, China
| | - Lida Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning 530004, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning 530004, China
| | - Kai Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning 530004, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning 530004, China
| | - Zeng-Fu Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning 530004, China
- Key Laboratory of National Forestry and Grassland Administration for Fast-Growing Tree Breeding and Cultivation in Central and Southern China, College of Forestry, Guangxi University, Nanning 530004, China
- Correspondence:
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Al-Khayri JM, Sudheer WN, Preetha TR, Nagella P, Rezk AA, Shehata WF. Biotechnological Research Progress in Jatropha, a Biodiesel-Yielding Plant. PLANTS (BASEL, SWITZERLAND) 2022; 11:1292. [PMID: 35631717 PMCID: PMC9147403 DOI: 10.3390/plants11101292] [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: 03/29/2022] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Environmental pollution is one of the most pressing challenges in today's world. The main cause of this pollution is fuel emissions from automobiles and other sources. As industrialization progresses, we will be unable to compromise on the use of energy to power heavy machines and will be forced to seek out the best options. As a consequence, utilizing green fuel, such as biodiesel derived from natural sources, is a realistic option. Jatropha curcas L. (Euphorbiaceae) is recognized as the greatest feedstock for biodiesel production throughout the world, and it has gained a huge market value in the recent years. Conventional cultivation alone will not be sufficient to meet the global need for the plant's biomass for the production of biodiesel. Adoption of plant tissue culture techniques that improve the biomass availability is an immediate need. The present review provides detailed information regarding in-vitro plant propagation (direct and indirect organogenesis), somatic embryogenesis, and acclimatization protocols of plantlets for stabilized production of biomass. The review also focuses on biotechnological approaches such as gene transformation studies, production of haploids, and double haploids for developing elite germplasm for high biomass and improved traits for the production of biodiesel.
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Affiliation(s)
- Jameel M. Al-Khayri
- Department of Agricultural Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia; (A.A.R.); (W.F.S.)
| | - Wudali N. Sudheer
- Department of Life Sciences, CHRIST (Deemed to be University), Bengaluru 560029, India; (W.N.S.); (T.R.P.)
| | - Thenmozhi R. Preetha
- Department of Life Sciences, CHRIST (Deemed to be University), Bengaluru 560029, India; (W.N.S.); (T.R.P.)
| | - Praveen Nagella
- Department of Life Sciences, CHRIST (Deemed to be University), Bengaluru 560029, India; (W.N.S.); (T.R.P.)
| | - Adel A. Rezk
- Department of Agricultural Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia; (A.A.R.); (W.F.S.)
- Agricultural Research Center, Virus and Phytoplasma Research Department, Plant Pathology Research Institute, Giza 12619, Egypt
| | - Wael F. Shehata
- Department of Agricultural Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia; (A.A.R.); (W.F.S.)
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Zhang X, Li J, Pan BZ, Chen W, Chen M, Tang M, Xu ZF, Liu C. Extended mining of the oil biosynthesis pathway in biofuel plant Jatropha curcas by combined analysis of transcriptome and gene interactome data. BMC Bioinformatics 2021; 22:409. [PMID: 34407772 PMCID: PMC8375076 DOI: 10.1186/s12859-021-04319-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Jatropha curcas L. is an important non-edible oilseed crop with a promising future in biodiesel production. However, little is known about the molecular biology of oil biosynthesis in this plant when compared with other established oilseed crops, resulting in the absence of agronomically improved varieties of Jatropha. To extensively discover the potentially novel genes and pathways associated with the oil biosynthesis in J. curcas, new strategy other than homology alignment is on the demand. RESULTS In this study, we proposed a multi-step computational framework that integrates transcriptome and gene interactome data to predict functional pathways in non-model organisms in an extended process, and applied it to study oil biosynthesis pathway in J. curcas. Using homologous mapping against Arabidopsis and transcriptome profile analysis, we first constructed protein-protein interaction (PPI) and co-expression networks in J. curcas. Then, using the homologs of Arabidopsis oil-biosynthesis-related genes as seeds, we respectively applied two algorithm models, random walk with restart (RWR) in PPI network and negative binomial distribution (NBD) in co-expression network, to further extend oil-biosynthesis-related pathways and genes in J. curcas. At last, using k-nearest neighbors (KNN) algorithm, the predicted genes were further classified into different sub-pathways according to their possible functional roles. CONCLUSIONS Our method exhibited a highly efficient way of mining the extended oil biosynthesis pathway of J. curcas. Overall, 27 novel oil-biosynthesis-related gene candidates were predicted and further assigned to 5 sub-pathways. These findings can help better understanding of the oil biosynthesis pathway of J. curcas, as well as paving the way for the following J. curcas breeding application.
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Affiliation(s)
- Xuan Zhang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, 666303, Yunnan, China.,The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, 666303, Yunnan, China.,The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Bang-Zhen Pan
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, 666303, Yunnan, China.,The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Wen Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Maosheng Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, 666303, Yunnan, China.,The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Mingyong Tang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, 666303, Yunnan, China.,The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Zeng-Fu Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China. .,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, 666303, Yunnan, China. .,The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China. .,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, 666303, Yunnan, China. .,The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
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Xu CJ, Zhao ML, Chen MS, Xu ZF. Silencing of the Ortholog of DEFECTIVE IN ANTHER DEHISCENCE 1 Gene in the Woody Perennial Jatropha curcas Alters Flower and Fruit Development. Int J Mol Sci 2020; 21:ijms21238923. [PMID: 33255510 PMCID: PMC7727821 DOI: 10.3390/ijms21238923] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/17/2020] [Accepted: 11/21/2020] [Indexed: 01/12/2023] Open
Abstract
DEFECTIVE IN ANTHER DEHISCENCE 1 (DAD1), a phospholipase A1, utilizes galactolipids (18:3) to generate α-linolenic acid (ALA) in the initial step of jasmonic acid (JA) biosynthesis in Arabidopsis thaliana. In this study, we isolated the JcDAD1 gene, an ortholog of Arabidopsis DAD1 in Jatropha curcas, and found that it is mainly expressed in the stems, roots, and male flowers of Jatropha. JcDAD1-RNAi transgenic plants with low endogenous jasmonate levels in inflorescences exhibited more and larger flowers, as well as a few abortive female flowers, although anther and pollen development were normal. In addition, fruit number was increased and the seed size, weight, and oil contents were reduced in the transgenic Jatropha plants. These results indicate that JcDAD1 regulates the development of flowers and fruits through the JA biosynthesis pathway, but does not alter androecium development in Jatropha. These findings strengthen our understanding of the roles of JA and DAD1 in the regulation of floral development in woody perennial plants.
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Affiliation(s)
- Chuan-Jia Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Innovative Academy for Seed Design, Chinese Academy of Sciences, Menglun, Mengla 666303, Yunnan, China; (C.-J.X.); (M.-L.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla 666303, Yunnan, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mei-Li Zhao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Innovative Academy for Seed Design, Chinese Academy of Sciences, Menglun, Mengla 666303, Yunnan, China; (C.-J.X.); (M.-L.Z.)
| | - Mao-Sheng Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Innovative Academy for Seed Design, Chinese Academy of Sciences, Menglun, Mengla 666303, Yunnan, China; (C.-J.X.); (M.-L.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla 666303, Yunnan, China
- Correspondence: (M.-S.C.); (Z.-F.X.)
| | - Zeng-Fu Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Innovative Academy for Seed Design, Chinese Academy of Sciences, Menglun, Mengla 666303, Yunnan, China; (C.-J.X.); (M.-L.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla 666303, Yunnan, China
- Correspondence: (M.-S.C.); (Z.-F.X.)
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Juntawong P, Butsayawarapat P, Songserm P, Pimjan R, Vuttipongchaikij S. Overexpression of Jatropha curcas ERFVII2 Transcription Factor Confers Low Oxygen Tolerance in Transgenic Arabidopsis by Modulating Expression of Metabolic Enzymes and Multiple Stress-Responsive Genes. PLANTS 2020; 9:plants9091068. [PMID: 32825465 PMCID: PMC7570394 DOI: 10.3390/plants9091068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 12/13/2022]
Abstract
Enhancing crop tolerance to waterlogging is critical for improving food and biofuel security. In waterlogged soils, roots are exposed to a low oxygen environment. The group VII ethylene response factors (ERFVIIs) were recently identified as key regulators of plant low oxygen response. Oxygen-dependent N-end rule pathways can regulate the stability of ERFVIIs. This study aims to characterize the function of the Jatropha curcas ERFVIIs and the impact of N-terminal modification that stabilized the protein toward low oxygen response. This study revealed that all three JcERFVII proteins are substrates of the N-end rule pathway. Overexpression of JcERFVII2 conferred tolerance to low oxygen stress in Arabidopsis. In contrast, the constitutive overexpression of stabilized JcERFVII2 reduced low oxygen tolerance. RNA-seq was performed to elucidate the functional roles of JcERFVII2 and the impact of its N-terminal modification. Overexpression of both wildtype and stabilized JcERFVII2 constitutively upregulated the plant core hypoxia-responsive genes. Besides, overexpression of the stabilized JcERFVII2 further upregulated various genes controlling fermentative metabolic processes, oxidative stress, and pathogen responses under aerobic conditions. In summary, JcERFVII2 is an N-end rule regulated waterlogging-responsive transcription factor that modulates the expression of multiple stress-responsive genes; therefore, it is a potential candidate for molecular breeding of multiple stress-tolerant crops.
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Affiliation(s)
- Piyada Juntawong
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (P.B.); (P.S.); (R.P.); (S.V.)
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Correspondence: or ; Tel.: +66-02-562-5555
| | - Pimprapai Butsayawarapat
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (P.B.); (P.S.); (R.P.); (S.V.)
| | - Pattralak Songserm
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (P.B.); (P.S.); (R.P.); (S.V.)
| | - Ratchaneeporn Pimjan
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (P.B.); (P.S.); (R.P.); (S.V.)
| | - Supachai Vuttipongchaikij
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (P.B.); (P.S.); (R.P.); (S.V.)
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
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