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Luo S, Huang J, Jin L, Zou J, Zheng Y, Li D. Transcription factor EgGRP2A regulates EgFATA expression and promotes oleic acid accumulation in oil palm (Elaeis guineensis). JOURNAL OF PLANT PHYSIOLOGY 2024; 299:154263. [PMID: 38772323 DOI: 10.1016/j.jplph.2024.154263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/18/2024] [Accepted: 04/30/2024] [Indexed: 05/23/2024]
Abstract
The oil palm (Elaeis guineensis) is emerging as the world's most important and prolific oilseed crop, celebrated for its impressive oil yield. However, the molecular intricacies that govern lipid metabolism and fatty acid accumulation in oil palm fruits remain relatively underexplored. This study reveals a significant correlation between the expression of EgGRP2A, a transcription factor, and the expression of EgFATA in the oil palm. Yeast one-hybrid analysis and electrophoretic mobility shift assays (EMSA) reveal and confirm the binding interactions between EgGRP2A and the promoter region of EgFATA. Subsequent experiments in oil palm protoplasts show that transient overexpression of EgGRP2A leads to a marked upregulation of EgFATA expression. Conversely, downregulation of EgGRP2A in transgenic oil palm embryoids leads to a significant reduction in EgFATA expression. Metabolite profiling in the transgenic embryoids reveals a significant reduction in unsaturated fatty acids, particularly oleic acid. These findings promise profound insights into the regulatory orchestration of EgFATA and the synthesis of fatty acids, particularly oleic acid, in the oil palm. Furthermore, the results lay the foundation for future breeding and genetic improvement efforts aimed at increasing oleic acid content in oil palm varieties.
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Affiliation(s)
- Shaojie Luo
- School of Life and Health Sciences, Hainan University, Hainan, 570228, China
| | - Jing Huang
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Liu Jin
- School of Life and Health Sciences, Hainan University, Hainan, 570228, China
| | - Jixin Zou
- Rubber Research Institute of Chinese Academy of Tropical Agricultural Sciences (CATAS), China
| | - Yusheng Zheng
- School of Life and Health Sciences, Hainan University, Hainan, 570228, China.
| | - Dongdong Li
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China.
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Wang Y, Yan J, Yang M, Zou J, Zheng Y, Li D. EgMADS3 directly regulates EgLPAAT to mediate medium-chain fatty acids (MCFA) anabolism in the mesocarp of oil palm. PLANT CELL REPORTS 2024; 43:107. [PMID: 38558250 DOI: 10.1007/s00299-024-03200-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 03/19/2024] [Indexed: 04/04/2024]
Abstract
KEY MESSAGE EgMADS3, a pivotal transcription factor, positively regulates MCFA accumulation via binding to the EgLPAAT promoter, advancing lipid content in mesocarp of oil palm. Lipids function as the structural components of cell membranes, which serve as permeable barriers to the external environment of cells. The medium-chain fatty acid in the stored lipids of plants is an important renewable energy. Most research on MCFA production in plant lipid synthesis is based on biochemical methods, and the importance of transcriptional regulation in MCFA synthesis and its incorporation into TAGs needs further research. Oil palm is the most productive oil crop in the world and has the highest productivity among the main oil crops. In this study, the MADS transcription factor (EgMADS3) in the mesocarp of oil palm was characterized. Through the VIGS-virus induced gene silencing, it was determined that the potential target gene of EgMADS3 was related to the biosynthesis of medium-chain fatty acid (MCFA). Transient transformation in protoplasts and qRT-PCR analysis showed that EgMADS3 positively regulated the expression of EgLPAAT. The results of the yeast one-hybrid assays and EMSA indicated the interaction between EgMADS3 and EgLPAAT promoter. Through genetic transformation and fatty acid analysis, it is concluded that EgMADS3 directly regulates the mid-chain fatty acid synthesis pathway of the potential target gene EgLPAAT, thus promotes the accumulation of MCFA and improves the total lipid content. This study is innovative in the functional analysis of the MADS family transcription factor in the metabolism of medium-chain fatty acids (MCFA) of oil palm, provides a certain research basis for improving the metabolic pathway of chain fatty acids in oil palm, and improves the synthesis of MCFA in plants. Our results will provide a reference direction for further research on improving the oil quality through biotechnology of oil palm.
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Affiliation(s)
- Yaning Wang
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Jinqi Yan
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China
| | | | - Jixin Zou
- Rubber Research Institute of Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, China
| | - Yusheng Zheng
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Dongdong Li
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China.
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3
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Cao J, Wang W, Xu X, Li SY, Zheng Y, Li DD. Identification and Analysis of MADS-Box Genes Expressed in the Mesocarp of Oil Palm Fruit (Elaeis guineensis Jacq.). Biochem Genet 2023; 61:2382-2400. [PMID: 37060482 DOI: 10.1007/s10528-023-10376-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 03/14/2023] [Indexed: 04/16/2023]
Abstract
Oil palm (Elaeis guineensis) is the most important tropical oil-bearing crop species worldwide. MADS-box proteins, which play crucial roles in plant growth and development and are involved in various physiological and biochemical processes, compose one of the largest families of plant transcription factors. In this study, 42 MADS-box genes were screened from the mesocarp transcriptome database of oil palm fruit, and their phylogenetic relationships with Arabidopsis thaliana MADS-box genes were analyzed. Based on the results, MADS-box genes from oil palm mesocarp were classified into four groups: MIKCc-type, MIKC*-type, Mα-type, and Mγ-type MADS-box genes. Members of the subfamilies were classified according to the presence of three specific protein motifs. To explore the differential expression of the MADS-box genes, the dynamic expression of all selected MADS-box genes in oil palm was measured by RNA-seq. The high expression of specific MADS-box genes in the mesocarp of oil palm during different developmental stages indicates that those genes may play important roles in the cell division of and metabolite accumulation in the fruit and could become important targets for fruit development and oil accumulation research in oil palm.
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Affiliation(s)
- Jiaqi Cao
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Wei Wang
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Xin Xu
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Si-Yu Li
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Yusheng Zheng
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Dong-Dong Li
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China.
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Badai SS, Rasid OA, Masani MYA, Chan KL, Chan PL, Shaharuddin NA, Abdullah MP, Parveez GKA, Ho CL. Functional characterization of the MSP-C6 promoter as a potential tool for mesocarp-preferential expression of transgenes. JOURNAL OF PLANT PHYSIOLOGY 2023; 289:154080. [PMID: 37699261 DOI: 10.1016/j.jplph.2023.154080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/14/2023]
Abstract
Modification of lipid composition in the mesocarp tissue of oil palm involves genetic manipulation of multiple genes. More than one mesocarp-preferential promoter is necessary for the expression of individual transgenes in the same plant to obviate transcriptional gene silencing. This study aimed to identify genes that are preferentially expressed in the mesocarp tissue and characterize selected candidate mesocarp-preferential promoters. Ten transcripts that were preferentially expressed in the mesocarp tissue were identified from the analysis of 82 transcriptome datasets of 12 different oil palm tissues. The expression of two candidate genes, MSP-C1 and MSP-C6, was verified to be preferentially expressed in the mesocarp tissues and shown to have a low expression level in non-mesocarp tissues by reverse transcription quantitative real-time PCR (RT-qPCR). MSP-C6 promoter fragments of different lengths were transformed into tomato plants for further characterization. Both unripe and ripe fruits of transgenic tomato plants transformed with a construct harboring the MSP-C6-F1 (2014 bp) promoter were shown to have high beta-glucuronidase (GUS) activities. The findings of this study suggest the potential applications of the MSP-C6 promoter as a molecular tool for genetic engineering of novel traits in fruit crops.
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Affiliation(s)
- Siti Suriawati Badai
- Advanced Biotechnology and Breeding Centre (ABBC), Malaysian Palm Oil Board (MPOB), No. 6 Persiaran Institusi, Bandar Baru Bangi 43000, Kajang, Selangor, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia.
| | - Omar Abd Rasid
- Advanced Biotechnology and Breeding Centre (ABBC), Malaysian Palm Oil Board (MPOB), No. 6 Persiaran Institusi, Bandar Baru Bangi 43000, Kajang, Selangor, Malaysia
| | - Mat Yunus Abdul Masani
- Advanced Biotechnology and Breeding Centre (ABBC), Malaysian Palm Oil Board (MPOB), No. 6 Persiaran Institusi, Bandar Baru Bangi 43000, Kajang, Selangor, Malaysia
| | - Kuang Lim Chan
- Advanced Biotechnology and Breeding Centre (ABBC), Malaysian Palm Oil Board (MPOB), No. 6 Persiaran Institusi, Bandar Baru Bangi 43000, Kajang, Selangor, Malaysia
| | - Pek Lan Chan
- Advanced Biotechnology and Breeding Centre (ABBC), Malaysian Palm Oil Board (MPOB), No. 6 Persiaran Institusi, Bandar Baru Bangi 43000, Kajang, Selangor, Malaysia
| | - Noor Azmi Shaharuddin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Mohd Puad Abdullah
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Ghulam Kadir Ahmad Parveez
- Advanced Biotechnology and Breeding Centre (ABBC), Malaysian Palm Oil Board (MPOB), No. 6 Persiaran Institusi, Bandar Baru Bangi 43000, Kajang, Selangor, Malaysia
| | - Chai Ling Ho
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia.
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Apriyanto A, Compart J, Fettke J. Transcriptomic analysis of mesocarp tissue during fruit development of the oil palm revealed specific isozymes related to starch metabolism that control oil yield. FRONTIERS IN PLANT SCIENCE 2023; 14:1220237. [PMID: 37554560 PMCID: PMC10405827 DOI: 10.3389/fpls.2023.1220237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/05/2023] [Indexed: 08/10/2023]
Abstract
The oil palm (Elaeis guineensis Jacq.) produces a large amount of oil from the fruit. However, increasing the oil production in this fruit is still challenging. A recent study has shown that starch metabolism is essential for oil synthesis in fruit-producing species. Therefore, the transcriptomic analysis by RNA-seq was performed to observe gene expression alteration related to starch metabolism genes throughout the maturity stages of oil palm fruit with different oil yields. Gene expression profiles were examined with three different oil yields group (low, medium, and high) at six fruit development phases (4, 8, 12, 16, 20, and 22 weeks after pollination). We successfully identified and analyzed differentially expressed genes in oil palm mesocarps during development. The results showed that the transcriptome profile for each developmental phase was unique. Sucrose flux to the mesocarp tissue, rapid starch turnover, and high glycolytic activity have been identified as critical factors for oil production in oil palms. For starch metabolism and the glycolytic pathway, we identified specific gene expressions of enzyme isoforms (isozymes) that correlated with oil production, which may determine the oil content. This study provides valuable information for creating new high-oil-yielding palm varieties via breeding programs or genome editing approaches.
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Affiliation(s)
- Ardha Apriyanto
- Biopolymer Analytics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
- Research and Development, PT. Astra Agro Lestari Tbk, Jakarta Timur, Indonesia
| | - Julia Compart
- Biopolymer Analytics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Joerg Fettke
- Biopolymer Analytics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
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Martin JJJ, Wu Q, Feng M, Li R, Zhou L, Zhang S, Yang C, Cao H. Lipidomic Profiles of Lipid Biosynthesis in Oil Palm during Fruit Development. Metabolites 2023; 13:727. [PMID: 37367885 DOI: 10.3390/metabo13060727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/12/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
The fruit of the oil palm (Elaeis guineensis Jacq.) has fleshy mesocarpic tissue rich in lipids. This edible vegetable oil is economically and nutritionally significant across the world. The core concepts of oil biosynthesis in oil palms remain to be researched as the knowledge of oil biosynthesis in plants improves. In this study, we utilized a metabolite approach and mass spectral analysis to characterize metabolite changes and identify the sequences of protein accumulation during the physiological processes that regulate oil synthesis during oil palm fruit ripening. Here, we performed a comprehensive lipidomic data analysis in order to understand the role of lipid metabolism in oil biosynthesis mechanisms. The experimental materials were collected from the mesocarp of oil palm (Tenera) at 95 days (early accumulation of fatty acid, first stage), 125 days (rapid growth of fatty acid accumulation, second stage), and 185 days (stable period of fatty acid accumulation, third stage) after pollination. To gain a clear understanding of the lipid changes that occurred during the growth of the oil palm, the metabolome data were found using principal component analysis (PCA). Furthermore, the accumulations of diacylglycerols, ceramides, phosphatidylethanolamine, and phosphatidic acid varied between the developmental stages. Differentially expressed lipids were successfully identified and functionally classified using KEGG analysis. Proteins related to the metabolic pathway, glycerolipid metabolism, and glycerphospholipid metabolism were the most significantly changed proteins during fruit development. In this study, LC-MS analysis and evaluation of the lipid profile in different stages of oil palm were performed to gain insight into the regulatory mechanisms that enhance fruit quality and govern differences in lipid composition and biosynthesis.
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Affiliation(s)
- Jerome Jeyakumar John Martin
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang 571339, China
| | - Qiufei Wu
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang 571339, China
| | - Meili Feng
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang 571339, China
| | - Rui Li
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang 571339, China
| | - Lixia Zhou
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang 571339, China
| | - Shuyan Zhang
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang 571339, China
| | - Cheng Yang
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang 571339, China
| | - Hongxing Cao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang 571339, China
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Chauhan AS, Tiwari M, Indoliya Y, Mishra SK, Lavania UC, Chauhan PS, Chakrabarty D, Tripathi RD. Identification and validation of reference genes in vetiver ( Chrysopogon zizanioides) root transcriptome. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:613-627. [PMID: 37363421 PMCID: PMC10284770 DOI: 10.1007/s12298-023-01315-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 06/27/2023]
Abstract
Vetiver [Vetiveria zizanioides (L.) Roberty] is a perennial C-4 grass traditionally valued for its aromatic roots/root essential oil. Owing to its deep penetrating web-forming roots, the grass is now widely used across the globe for phytoremediation and the conservation of soil and water. This study has used the transcriptome data of vetiver roots in its two distinct geographic morphotypes (North Indian type A and South Indian type B) for reference gene(s) identification. Further, validation of reference genes using various abiotic stresses such as heat, cold, salt, and drought was carried out. The de novo assembly based on differential genes analysis gave 1,36,824 genes (PRJNA292937). Statistical tests like RefFinder, NormFinder, BestKeeper, geNorm, and Delta-Ct software were applied on 346 selected contigs. Eleven selected genes viz., GAPs, UBE2W, RP, OSCam2, MUB, RPS, Core histone 1, Core histone 2, SAMS, GRCWSP, PLDCP along with Actin were used for qRT-PCR analysis. Finally, the study identified the five best reference genes GAPs, OsCam2, MUB, Core histone 1, and SAMS along with Actin. The two optimal reference genes SAMS and Core histone 1 were identified with the help of qbase + software. The findings of the present analyses have value in the identification of suitable reference gene(s) in transcriptomic and molecular data analysis concerning various phenotypes related to abiotic stress and developmental aspects, as well as a quality control measure in gene expression experiments. Identifying reference genes in vetiver appears important as it allows for accurate normalization of gene expression data in qRT-PCR experiments. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01315-7.
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Affiliation(s)
- Abhishek Singh Chauhan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
- Molecular Biology and Biotechnology Division, CSIR – National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Madhu Tiwari
- Molecular Biology and Biotechnology Division, CSIR – National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Yuvraj Indoliya
- Molecular Biology and Biotechnology Division, CSIR – National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Shashank Kumar Mishra
- Microbial Technologies Division, CSIR – National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Umesh Chandra Lavania
- CSIR – National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Puneet Singh Chauhan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
- Microbial Technologies Division, CSIR – National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Debasis Chakrabarty
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
- Molecular Biology and Biotechnology Division, CSIR – National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
| | - Rudra Deo Tripathi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
- Plant Ecology and Environmental Science Division, CSIR – National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 India
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Elbar S, Maytal Y, David I, Carmeli-Weissberg M, Shaya F, Barnea-Danino Y, Bustan A, Harpaz-Saad S. Abscisic acid plays a key role in the regulation of date palm fruit ripening. FRONTIERS IN PLANT SCIENCE 2023; 13:1066142. [PMID: 36874915 PMCID: PMC9981646 DOI: 10.3389/fpls.2022.1066142] [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: 10/10/2022] [Accepted: 12/21/2022] [Indexed: 06/18/2023]
Abstract
The date palm (Phoenix dactylifera L.) fruit is of major importance for the nutrition of broad populations in the world's desert strip; yet it is sorely understudied. Understanding the mechanism regulating date fruit development and ripening is essential to customise date crop to the climatic change, which elaborates yield losses due to often too early occurring wet season. This study aimed to uncover the mechanism regulating date fruit ripening. To that end, we followed the natural process of date fruit development and the effects of exogenous hormone application on fruit ripening in the elite cultivar 'Medjool'. The results of the current study indicate that the onset of fruit ripening occurre once the seed had reached maximum dry weight. From this point, fruit pericarp endogenous abscisic acid (ABA) levels consistently increased until fruit harvest. The final stage in fruit ripening, the yellow-to-brown transition, was preceded by an arrest of xylem-mediated water transport into the fruit. Exogenous ABA application enhanced fruit ripening when applied just before the green-to-yellow fruit color transition. Repeated ABA applications hastened various fruit ripening processes, resulting in earlier fruit harvest. The data presented supports a pivotal role for ABA in the regulation of date fruit ripening.
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Affiliation(s)
- Saar Elbar
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of Jerusalem, Rehovot, Israel
| | - Yochai Maytal
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of Jerusalem, Rehovot, Israel
| | - Itzhak David
- Ramat-Negev Desert Agro-Research Centre, Halutza, Israel
| | - Mira Carmeli-Weissberg
- Department of Fruit Tree Sciences, The Volcani Center, Agricultural Research Organization, Rishon LeZion, Israel
| | - Felix Shaya
- Department of Fruit Tree Sciences, The Volcani Center, Agricultural Research Organization, Rishon LeZion, Israel
| | | | - Amnon Bustan
- Ramat-Negev Desert Agro-Research Centre, Halutza, Israel
| | - Smadar Harpaz-Saad
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of Jerusalem, Rehovot, Israel
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Apriyanto A, Compart J, Zimmermann V, Alseekh S, Fernie AR, Fettke J. Indication that starch and sucrose are biomarkers for oil yield in oil palm (Elaeis guineensis Jacq.). Food Chem 2022; 393:133361. [DOI: 10.1016/j.foodchem.2022.133361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 05/02/2022] [Accepted: 05/29/2022] [Indexed: 11/04/2022]
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10
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Comparative transcriptome profiling and molecular marker development for oil palm fruit color. Sci Rep 2022; 12:15507. [PMID: 36109663 PMCID: PMC9478095 DOI: 10.1038/s41598-022-19890-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 09/06/2022] [Indexed: 12/02/2022] Open
Abstract
Oil palm harvesting is normally determined by fruit exocarp color. To detect expressed sequence tag (EST)-simple sequence repeat (SSR) markers in oil palm hybrid populations, de novo transcriptomic profiling of Nigeria black and Suratthani 1 (Deli × Calabar) plants was performed. More than 46 million high-quality clean reads with a mean length of 1117 bp were generated. Functional annotation and gene ontology (GO) enrichment analysis of differentially expressed genes (DEGs) revealed that the genes were involved in fruit color development and pigment synthesis. Comparison of immature/mature DEGs indicated that nigrescent fruit color was driven by the anthocyanin biosynthesis pathway (ABP); however, the carotenoid biosynthesis pathway (CBP) was involved in the color development of both fruit types. The transcripts of both unique and different genes involved in the ABP and CBP in higher plants were highlighted for further study, especially 3GT, downstream genes in the ABP, and DEARF27 in the CBP. Additionally, SSR primer motifs, namely, 9949, discovered from the DEGs upregulated in the virescent type that encode vacuolar iron transporter (VIT), could separate the nigrescence and virescence traits of Nigeria hybrids. This novel primer has potential to be used as a molecular for further selection in breeding programs especially involving the specific genetic backgrounds described in this study.
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Zhang Q, Jin YH, Zou JX, Zheng YS, Li DD. Characterization and functional analysis of the MADS-box EgAGL9 transcription factor from the mesocarp of oil palm (Elaeis guineensis Jacq.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 321:111317. [PMID: 35696917 DOI: 10.1016/j.plantsci.2022.111317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/06/2022] [Accepted: 05/08/2022] [Indexed: 06/15/2023]
Abstract
Oil palm (Elaeis guineensis Jacq.) is one of the most important oil crops in the world, and compared to all oil crops, it has the highest productive efficiency. In the present study, a MADS-box transcription factor of the AGAMOUS class, named EgAGL9, was identified by expression profile analysis in the different developmental stages of oil palm mesocarp. Real-time quantitative PCR results confirmed that the expression of EgAGL9 increased rapidly during the last stages of oil palm mesocarp development. Then, three downstream genes, including EgSAD (Stearoyl-ACP desaturase), EgTSA (Tryptophan synthase) and EgSDH (Succinate dehydrogenase), were screened by ChIP-Seq and data analysis. EMSA analysis verified that EgAGL9 interacted with the promoter regions of EgSAD, EgTSA and EgSDH. Moreover, the expression levels of EgSAD, EgTSA and EgSDH were downregulated in EgAGL9-overexpressing protoplasts and calli of oil palm. Compared to WT, the total lipid content and ratio of unsaturated fatty acids in transgenic calli (including oleic acid, linoleic acid and linolenic acid) were significantly decreased. Together, these results revealed that these three EgAGL9-regulated genes are involved in regulatory pathways in the oil palm mesocarp. Compared with previous studies, the present study provides a new research strategy for understanding of the molecular regulatory pathways of lipid metabolism in mesocarp of oil palm. The obtained results will bring a new perspective for a comprehensive understanding of the regulation of the metabolic accumulation in the oil palm mesocarp.
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Affiliation(s)
- Qing Zhang
- College of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan 570228, China
| | - Yuan-Hang Jin
- College of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan 570228, China
| | - Ji-Xin Zou
- College of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan 570228, China; Rubber Research Institute of Chinese Academy of Tropical Agricultural Sciences (CATAS), China
| | - Yu-Sheng Zheng
- College of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan 570228, China
| | - Dong-Dong Li
- College of Tropical Crops, Sanya Nanfan Research Institute, Hainan University, Hainan 570228, China.
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Yang M, Yarra R, Zhang R, Zhou L, Jin L, Martin JJJ, Cao H. Transcriptome analysis of oil palm pistil during pollination and fertilization to unravel the role of phytohormone biosynthesis and signaling genes. Funct Integr Genomics 2022; 22:261-278. [PMID: 35229235 DOI: 10.1007/s10142-022-00834-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 02/11/2022] [Accepted: 02/13/2022] [Indexed: 11/28/2022]
Abstract
Phytohormones play an important role in the pollination and fertilization of crops, but the regulatory mechanisms of oil palm pollination and fertilization are unclear. The purpose of this study is to explore the hormonal changes of oil palm pistils during flowering. We used RNA sequencing to evaluate differentially expressed genes (DEGs) in oil palm pistils at the pollination and non-pollination stages. In this study, we found that the hormone contents of oil palm pistil changed drastically after pollination. The transcriptome of the oil palm pistil without pollination and at 2 h, 4 h, 12 h, 24 h, and 48 h after pollination was comprehensively analyzed, and a large number of differential genes and metabolic pathways were explored. Based on the transcriptome data, it could be recognized that the changes of indoleacetic acid (IAA), zeatin riboside (ZR), and abscisic acid (ABA) during pollination were consistent with the changes in the corresponding gene transcripts. Differentially expressed genes during pollination and fertilization of oil palm were mainly related to energy metabolism and hormone signal transduction. It provides new insights to elucidate the interaction and regulation mechanisms of plant hormones before and after oil palm pollination, providing a theoretical basis and reference for the research on sexual reproduction of oil palm.
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Affiliation(s)
- Mengdi Yang
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, 571339, People's Republic of China.,Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, People's Republic of China.,College of Tropical Crops, Hainan University, Haikou, Hainan, 570228, People's Republic of China
| | - Rajesh Yarra
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, 571339, People's Republic of China.,Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, People's Republic of China
| | - Ruining Zhang
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, 571339, People's Republic of China.,Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, People's Republic of China.,College of Horticulture, Hainan University, Haikou, Hainan, 570228, People's Republic of China
| | - Lixia Zhou
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, 571339, People's Republic of China.,Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, People's Republic of China
| | - Longfei Jin
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, 571339, People's Republic of China.,Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, People's Republic of China
| | - Jerome Jeyakumar John Martin
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, 571339, People's Republic of China.,Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, People's Republic of China
| | - Hongxing Cao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, 571339, People's Republic of China. .,Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, People's Republic of China.
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Sá ACDS, Omena-Garcia RP, Pereira GL, Rodrigues-Salvador A, Araújo WL, Motoike SY, Nunes-Nesi A. Spatio-temporal characterization of the fruit metabolism in contrasting accessions of Macauba (Acrocomia aculeata). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 171:14-25. [PMID: 34968988 DOI: 10.1016/j.plaphy.2021.12.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/12/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Although Macauba (Acrocomia aculeata) has been highlighted by its high-quality oil to fit edible and nonedible purposes, data addressing carbon and nitrogen metabolism underlying development and ripening of fruits remain scarce. In addition, accessions of Macauba exibit varied oil yield in fruits, including during the fruit development stages. Here, we monitored contents of carbohydrates, proteins, amino acids and lipids in the mesocarp and endosperm of Macauba fruits until ripening. We selected three accessions from different Brazilian regions (southeast, MG; northeast, PE; and central-west, MS) that differ in the mesocarp lipid content of ripe fruits. Despite the anatomical differences, mesocarp and endosperm exhibited similar trends of metabolite accumulation for most of the analyzed compounds. In the mesocarp, total soluble protein, free amino acids, sucrose, starch and total lipids accumulate towards ripening, while glucose and fructose declined in all accessions. Endosperm differed from mesocarp solely in the amino acid content, which decreased in ripe fruits. In the endosperm, accessions accumulated carbohydrates differently. Accession PE showed comparable fructose and starch contents in the endosperm between the beginning of fruit development and ripening, while in accessions MG and MS, both compounds decreased and increased, respectively, towards ripening. Accession MG was highlighted by its highest lipid content in the two tissues indicating its potential for energy and cosmetic industries. Our results provide novel insights into metabolic changes underlying development and ripening of Macauba fruits and variability in oil content among accessions, indicating new targets for breeding programs.
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Affiliation(s)
- Ana Carolina Dos Santos Sá
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | | | - Greice Leal Pereira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Acácio Rodrigues-Salvador
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Wagner L Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | | | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.
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14
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Chew CL, Tan BA, Low JYS, Mohd Hakimi NIN, Kua SF, Lim CM. Exogenous ethylene application on postharvest oil palm fruit bunches improves crude palm oil quality. Food Sci Nutr 2021; 9:5335-5343. [PMID: 34646505 PMCID: PMC8498053 DOI: 10.1002/fsn3.2423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 11/23/2022] Open
Abstract
Quality and food safety are of paramount importance to the palm oil industry. In this work, we investigated the practicability of ethylene gas exogenous application on post-harvested oil palm fruit bunches to improve the crude palm oil (CPO) quality. The bunches were first exposed to ethylene gas for 24 hr to induce abscission of palm fruits from bunches. The detached fruits were then subjected to heat treatment, mechanical extraction, clarification and drying to produce CPO. Critical quality parameters of CPO produced, that is free fatty acid, deterioration of the bleachability index and triacylglycerol showed improvement with ethylene gas treatment. Contaminant content that is phosphorus, chloride, iron, and copper also showed a reduction in the CPO derived from ethylene-treated bunches. These findings corresponded with low levels of contaminants such as 3-monochloropropane-1,2-diol esters and glycidyl esters in refined oil. The implementation strategy and practicability of this method is herein proposed and discussed. Ethylene application not only improves the CPO quality, but could potentially enhance the process sustainability of palm oil mills.
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Affiliation(s)
- Chien Lye Chew
- Sime Darby Plantation Research, R&D Centre – Carey IslandPulau CareyMalaysia
- Chemical Engineering DisciplineSchool of EngineeringMonash University MalaysiaBandar SunwayMalaysia
- Monash‐Industry Palm Oil Education and Research PlatformSchool of EngineeringMonash University MalaysiaBandar SunwayMalaysia
| | - Bee Aik Tan
- Sime Darby Plantation Technology CentreUPM‐MTDC Technology Centre IIISerdangMalaysia
| | - Jaime Yoke Sum Low
- Sime Darby Plantation Technology CentreUPM‐MTDC Technology Centre IIISerdangMalaysia
| | | | - Shwu Fun Kua
- Sime Darby Plantation Technology CentreUPM‐MTDC Technology Centre IIISerdangMalaysia
| | - Chin Ming Lim
- Sime Darby Plantation Technology CentreUPM‐MTDC Technology Centre IIISerdangMalaysia
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15
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Wang Y, Zou J, Zhao J, Zheng Y, Li D. EgmiR5179 Regulates Lipid Metabolism by Targeting EgMADS16 in the Mesocarp of Oil Palm ( Elaeis guineensis). FRONTIERS IN PLANT SCIENCE 2021; 12:722596. [PMID: 34381490 PMCID: PMC8350733 DOI: 10.3389/fpls.2021.722596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
EgMADS16, one of the MADS-box transcription factors in oil palm, has a high expression level in the late fruit development of the oil palm fruit mesocarp. At the same time, it is also predicted to be the target gene of EgmiR5179, which has been identified in previous research. In this paper, we focused on the function and regulatory mechanism of the EgMADS16 gene in oil palm lipid metabolism. The results indicated that the transcription level of EgMADS16 was highest in the fourth stage, and a dual-luciferase reporter assay proved that the EgMADS16 expression level was downregulated by EgmiR5179. In both the OXEgMADS16 Arabidopsis seeds and oil palm embryonic calli, the total lipid contents were significantly decreased, but the contents of C18:0 and C18:3 in OXEgMADS16 lines were significantly increased. As expected, EgmiR5179 weakened the inhibitory effect of EgMADS16 on the oil contents in transgenic Arabidopsis plants that coexpressed EgmiR5179 and EgMADS16 (OXEgmiR5179-EgMADS16). Moreover, yeast two-hybrid and BiFC analyses suggested that there was an interaction between the EgMADS16 protein and EgGLO1 protein, which had been proven to be capable of regulating fatty acid synthesis in our previous research work. In summary, a model of the molecular mechanism by which miRNA5179 targets EgMADS16 to regulate oil biosynthesis was hypothesized, and the research results provide new insight into lipid accumulation and molecular regulation in oil palm.
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Affiliation(s)
- Yifei Wang
- College of Tropical Crops, Hainan University, Haikou, China
| | - Jixin Zou
- College of Tropical Crops, Hainan University, Haikou, China
- Rubber Research Institute of Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, China
| | - Jin Zhao
- College of Tropical Crops, Hainan University, Haikou, China
| | - Yusheng Zheng
- College of Tropical Crops, Hainan University, Haikou, China
| | - Dongdong Li
- College of Tropical Crops, Hainan University, Haikou, China
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CANDIDATE GENES IDENTIFICATION OF OIL PALM (Elaeis guineensis Jacq.) INTEREST CHARACTERS USING PUBLISHED DATABASE. BIOVALENTIA: BIOLOGICAL RESEARCH JOURNAL 2021. [DOI: 10.24233/biov.7.1.2021.188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Palm oil has supplied more than 30% of vegetable oil consumption worldwide. Rising demand has pushed oil palm plantations to increase the yield. It is well known that genetic has played a significant role in phenotypic performance. Moreover, in recent years, genomic data has emerged tremendously. Unfortunately on the gene related to oil palm yield. Therefore, a preliminary study to classify and select oil palm candidate genes associated with characteristic by scanning existing genes in oil palm or other in-silico species were conducted. Based on Blast2Go results, 22 genes related to oil biosynthesis, two specifically related to fruit number and fruit weight were analysed. Furthermore, 19 candidate genes were able to amplify.
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17
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Fooyontphanich K, Morcillo F, Joët T, Dussert S, Serret J, Collin M, Amblard P, Tangphatsornruang S, Roongsattham P, Jantasuriyarat C, Verdeil JL, Tranbarger TJ. Multi-scale comparative transcriptome analysis reveals key genes and metabolic reprogramming processes associated with oil palm fruit abscission. BMC PLANT BIOLOGY 2021; 21:92. [PMID: 33573592 PMCID: PMC7879690 DOI: 10.1186/s12870-021-02874-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Fruit abscission depends on cell separation that occurs within specialized cell layers that constitute an abscission zone (AZ). To determine the mechanisms of fleshy fruit abscission of the monocot oil palm (Elaeis guineensis Jacq.) compared with other abscission systems, we performed multi-scale comparative transcriptome analyses on fruit targeting the developing primary AZ and adjacent tissues. RESULTS Combining between-tissue developmental comparisons with exogenous ethylene treatments, and naturally occurring abscission in the field, RNAseq analysis revealed a robust core set of 168 genes with differentially regulated expression, spatially associated with the ripe fruit AZ, and temporally restricted to the abscission timing. The expression of a set of candidate genes was validated by qRT-PCR in the fruit AZ of a natural oil palm variant with blocked fruit abscission, which provides evidence for their functions during abscission. Our results substantiate the conservation of gene function between dicot dry fruit dehiscence and monocot fleshy fruit abscission. The study also revealed major metabolic transitions occur in the AZ during abscission, including key senescence marker genes and transcriptional regulators, in addition to genes involved in nutrient recycling and reallocation, alternative routes for energy supply and adaptation to oxidative stress. CONCLUSIONS The study provides the first reference transcriptome of a monocot fleshy fruit abscission zone and provides insight into the mechanisms underlying abscission by identifying key genes with functional roles and processes, including metabolic transitions, cell wall modifications, signalling, stress adaptations and transcriptional regulation, that occur during ripe fruit abscission of the monocot oil palm. The transcriptome data comprises an original reference and resource useful towards understanding the evolutionary basis of this fundamental plant process.
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Affiliation(s)
- Kim Fooyontphanich
- UMR DIADE, Institut de Recherche Pour le Développement, Université de Montpellier, IRD Centre de Montpellier, 911 Avenue Agropolis BP 64501, 34394 Cedex 5, Montpellier, France
- Grow A Green Co, Ltd. 556 Maha Chakraphat Rd. Namaung, Chachoengsao, Chachoengsao Province, 24000, Thailand
| | - Fabienne Morcillo
- UMR DIADE, Institut de Recherche Pour le Développement, Université de Montpellier, IRD Centre de Montpellier, 911 Avenue Agropolis BP 64501, 34394 Cedex 5, Montpellier, France
- CIRAD, DIADE, F-34398, Montpellier, France
| | - Thierry Joët
- UMR DIADE, Institut de Recherche Pour le Développement, Université de Montpellier, IRD Centre de Montpellier, 911 Avenue Agropolis BP 64501, 34394 Cedex 5, Montpellier, France
| | - Stéphane Dussert
- UMR DIADE, Institut de Recherche Pour le Développement, Université de Montpellier, IRD Centre de Montpellier, 911 Avenue Agropolis BP 64501, 34394 Cedex 5, Montpellier, France
| | - Julien Serret
- UMR DIADE, Institut de Recherche Pour le Développement, Université de Montpellier, IRD Centre de Montpellier, 911 Avenue Agropolis BP 64501, 34394 Cedex 5, Montpellier, France
| | - Myriam Collin
- UMR DIADE, Institut de Recherche Pour le Développement, Université de Montpellier, IRD Centre de Montpellier, 911 Avenue Agropolis BP 64501, 34394 Cedex 5, Montpellier, France
| | | | - Sithichoke Tangphatsornruang
- National Science and Technology Development Agency, 111 Thailand Science Park, Phahonyothin Road, Pathum Thani, Thailand
| | - Peerapat Roongsattham
- UMR DIADE, Institut de Recherche Pour le Développement, Université de Montpellier, IRD Centre de Montpellier, 911 Avenue Agropolis BP 64501, 34394 Cedex 5, Montpellier, France
- Department of Genetics, Faculty of Science, Kasetsart University Bangkhen Campus, 50 Phahonyothin Road Jatujak, Bangkok, Thailand
| | - Chatchawan Jantasuriyarat
- Department of Genetics, Faculty of Science, Kasetsart University Bangkhen Campus, 50 Phahonyothin Road Jatujak, Bangkok, Thailand
| | - Jean-Luc Verdeil
- CIRAD, UMR AGAP, F-34398, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Timothy J Tranbarger
- UMR DIADE, Institut de Recherche Pour le Développement, Université de Montpellier, IRD Centre de Montpellier, 911 Avenue Agropolis BP 64501, 34394 Cedex 5, Montpellier, France.
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18
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Wang W, Feng J, Wei L, Khalil-Ur-Rehman M, Nieuwenhuizen NJ, Yang L, Zheng H, Tao J. Transcriptomics Integrated with Free and Bound Terpenoid Aroma Profiling during "Shine Muscat" ( Vitis labrusca × V. vinifera) Grape Berry Development Reveals Coordinate Regulation of MEP Pathway and Terpene Synthase Gene Expression. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:1413-1429. [PMID: 33481572 DOI: 10.1021/acs.jafc.0c06591] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Terpenes and their derivatives are important biomarkers of grape quality as they contribute to the flavor and aroma of grapes. However, the molecular basis of terpene biosynthesis throughout the grapevine phenological developmental cycle remains elusive. Our current study investigates the free and bound terpene biosynthesis of berries at different phenological stages from preveraison to harvest. Detailed gene expression (transcriptomics) analysis, terpenoid volatile production by gas chromatography-mass spectrometry (GC-MS), and in planta transient expression were employed. Our results show that concentrations of most individual terpenes at different stages are distinctive and increase from preveraison to the veraison stage followed by a decrease from veraison to maturity. The combined transcriptomic analysis and terpene profiling revealed that 22 genes belonging to the MEP pathway and multiple classes of transcription factor family members including bHLH and several hormone biosynthesis- or signaling-related genes likely participate in the regulation of terpenoid biosynthesis according to their specific expression patterns in berries. Quantitative real-time polymerase chain expression analysis of 8 key differentially expressed genes in MEP pathways and further 12 randomly selected genes was performed during 8 sampling stages and validated the RNA-seq-derived expression profiles. To further confirm the function of a subset of the differentially expressed genes, we investigated the effects of combined overexpression of 1-deoxy-d-xylulose-5-phosphate synthase (VvDXS1-LOC100249323), 1-deoxy-d-xylulose-5-phosphate reductoisomerase (VvDXR-LOC100248516), and terpene synthase (VvTPS56-LOC100266449) on the production of terpenes by transient overexpression in Nicotiana benthamiana leaves. The overall developmental patterns of total terpenes and gene expression profiles will help guide the functional analyses of further candidate genes important for terpene biosynthesis of grape as well as identifying the master transcriptional and hormonal regulators of this pathway in the future.
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Affiliation(s)
- Wu Wang
- College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jiao Feng
- College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Lingling Wei
- College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | | | - Niels J Nieuwenhuizen
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Private Bag 92169 Auckland, New Zealand
| | - Lina Yang
- Division of Plant and Soil Sciences, West Virginia University, 3425 New Agricultural Sciences Building, 26506-6201 Morgantown, West Virginia, United States
| | - Huan Zheng
- College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jianmin Tao
- College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
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Huang H, Liang J, Tan Q, Ou L, Li X, Zhong C, Huang H, Møller IM, Wu X, Song S. Insights into triterpene synthesis and unsaturated fatty-acid accumulation provided by chromosomal-level genome analysis of Akebia trifoliata subsp. australis. HORTICULTURE RESEARCH 2021; 8:33. [PMID: 33518712 PMCID: PMC7848005 DOI: 10.1038/s41438-020-00458-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 11/16/2020] [Accepted: 11/20/2020] [Indexed: 05/10/2023]
Abstract
Akebia trifoliata subsp. australis is a well-known medicinal and potential woody oil plant in China. The limited genetic information available for A. trifoliata subsp. australis has hindered its exploitation. Here, a high-quality chromosome-level genome sequence of A. trifoliata subsp. australis is reported. The de novo genome assembly of 682.14 Mb was generated with a scaffold N50 of 43.11 Mb. The genome includes 25,598 protein-coding genes, and 71.18% (485.55 Mb) of the assembled sequences were identified as repetitive sequences. An ongoing massive burst of long terminal repeat (LTR) insertions, which occurred ~1.0 million years ago, has contributed a large proportion of LTRs in the genome of A. trifoliata subsp. australis. Phylogenetic analysis shows that A. trifoliata subsp. australis is closely related to Aquilegia coerulea and forms a clade with Papaver somniferum and Nelumbo nucifera, which supports the well-established hypothesis of a close relationship between basal eudicot species. The expansion of UDP-glucoronosyl and UDP-glucosyl transferase gene families and β-amyrin synthase-like genes and the exclusive contraction of terpene synthase gene families may be responsible for the abundant oleanane-type triterpenoids in A. trifoliata subsp. australis. Furthermore, the acyl-ACP desaturase gene family, including 12 stearoyl-acyl-carrier protein desaturase (SAD) genes, has expanded exclusively. A combined transcriptome and fatty-acid analysis of seeds at five developmental stages revealed that homologs of SADs, acyl-lipid desaturase omega fatty acid desaturases (FADs), and oleosins were highly expressed, consistent with the rapid increase in the content of fatty acids, especially unsaturated fatty acids. The genomic sequences of A. trifoliata subsp. australis will be a valuable resource for comparative genomic analyses and molecular breeding.
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Affiliation(s)
- Hui Huang
- Key Laboratory of Research and Utilization of Ethnomedicinal Plant Resources of Hunan Province, College of Biological and Food Engineering, Huaihua University, Huaihua, 418000, China
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Juan Liang
- Key Laboratory of Research and Utilization of Ethnomedicinal Plant Resources of Hunan Province, College of Biological and Food Engineering, Huaihua University, Huaihua, 418000, China
| | - Qi Tan
- Key Laboratory of Research and Utilization of Ethnomedicinal Plant Resources of Hunan Province, College of Biological and Food Engineering, Huaihua University, Huaihua, 418000, China
| | - Linfeng Ou
- Key Laboratory of Research and Utilization of Ethnomedicinal Plant Resources of Hunan Province, College of Biological and Food Engineering, Huaihua University, Huaihua, 418000, China
| | - Xiaolin Li
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Beijing, 100700, China
| | - Caihong Zhong
- Key Laboratory of Research and Utilization of Ethnomedicinal Plant Resources of Hunan Province, College of Biological and Food Engineering, Huaihua University, Huaihua, 418000, China
| | - Huilin Huang
- Key Laboratory of Research and Utilization of Ethnomedicinal Plant Resources of Hunan Province, College of Biological and Food Engineering, Huaihua University, Huaihua, 418000, China
| | - Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Flakkebjerg, DK-4200, Slagelse, Denmark
| | - Xianjin Wu
- Key Laboratory of Research and Utilization of Ethnomedicinal Plant Resources of Hunan Province, College of Biological and Food Engineering, Huaihua University, Huaihua, 418000, China
| | - Songquan Song
- Key Laboratory of Research and Utilization of Ethnomedicinal Plant Resources of Hunan Province, College of Biological and Food Engineering, Huaihua University, Huaihua, 418000, China.
- Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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20
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Candidate genes linked to QTL regions associated with fatty acid composition in oil palm. Biologia (Bratisl) 2021. [DOI: 10.2478/s11756-020-00563-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Ge Y, Zang X, Yang Y, Wang T, Ma W. In-depth analysis of potential PaAP2/ERF transcription factor related to fatty acid accumulation in avocado (Persea americana Mill.) and functional characterization of two PaAP2/ERF genes in transgenic tomato. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 158:308-320. [PMID: 33234384 DOI: 10.1016/j.plaphy.2020.11.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 11/13/2020] [Indexed: 05/24/2023]
Abstract
Fatty acids in avocado fruit are crucial components influencing taste as well as fruit quality and nutritional value. Changes to fatty acid contents and concentrations in avocado fruit are important because of the associated effects on sensory properties. Hence, plant physiologists and molecular biologists interested in elucidating the influence of transcription factors on fatty acid accumulation in avocado fruit. In this study, APETALA2/ethylene-responsive factor (AP2/ERF) family members in avocado (Persea americana Mill.) were systematically and comprehensively analyze to identify potential PaAP2/ERF genes related to fatty acid accumulation. The results of bioinformatics analysis and the expression profiles of the AP2/ERF members suggested that 10 highly expressed PaAP2/ERF genes may encode transcription factors with functions related to the fatty acid accumulation in the avocado mesocarp. Furthermore, PaWRI1 and PaWRI2, two AP2/ERF transcription factor genes in avocado, were functionally characterized regarding their effects on fatty acid accumulation. The transcriptome and biochemical analyses of PaWRI1-2-overexpressing transgenic tomato plants revealed the up-regulated expression of 17 unigenes related to fatty acid synthesis and triacylglycerol assembly as well as increased fatty acid contents relative to the corresponding levels in the wild-type plants. In contrast, the overexpression of PaWRI2 in transgenic tomato plants up-regulated the expression of only six unigenes associated with fatty acid synthesis and triacylglycerol assembly and negligibly affected fatty acid accumulation when compared with wild-type plants. This systematic analysis provides a foundation for future studies regarding AP2/ERF functions associated with fatty acid accumulation.
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Affiliation(s)
- Yu Ge
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 570102, China.
| | - Xiaoping Zang
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 570102, China
| | - Ying Yang
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 570102, China
| | - Tao Wang
- Institute of Vegetable, Liaoning Academy of Agricultural Sciences, Shenyang, Liaoning, 110161, China
| | - Weihong Ma
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 570102, China.
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de Vries J, Ischebeck T. Ties between Stress and Lipid Droplets Pre-date Seeds. TRENDS IN PLANT SCIENCE 2020; 25:1203-1214. [PMID: 32921563 DOI: 10.1016/j.tplants.2020.07.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/24/2020] [Accepted: 07/30/2020] [Indexed: 05/12/2023]
Abstract
Seeds were a key evolutionary innovation. These durable structures provide a concerted solution to two challenges on land: dispersal and stress. Lipid droplets (LDs) that act as nutrient storage reservoirs are one of the main cell-biological reasons for seed endurance. Although LDs are key structures in spermatophytes and are especially abundant in seeds, they are found across plants and algae, and increase during stress. Further, the proteins that underpin their form and function often have deep homologs. We propose an evolutionary scenario in which (i) the generation of LDs arose as a mechanism to mediate general drought and desiccation resilience, and (ii) the required protein framework was co-opted by spermatophytes for a seed-specific program.
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Affiliation(s)
- Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstrasse 1, 37077 Goettingen, Germany; University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidtstrasse 1, 37077 Goettingen, Germany.
| | - Till Ischebeck
- University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), 37077 Goettingen, Germany; University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, Justus-von-Liebig-Weg 11, 37077 Goettingen, Germany.
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23
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Kok SY, Namasivayam P, Ee GCL, Ong-Abdullah M. Comparative proteomic analysis of oil palm (Elaeis guineensis Jacq.) during early fruit development. J Proteomics 2020; 232:104052. [PMID: 33262095 DOI: 10.1016/j.jprot.2020.104052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 11/11/2020] [Accepted: 11/15/2020] [Indexed: 01/04/2023]
Abstract
To gain insights on protein changes in fruit setting and growth in oil palm, a comparative proteomic approach was undertaken to study proteome changes during its early development. The variations in the proteome at five early developmental stages were investigated via a gel-based proteomic technique. A total of 129 variant proteins were determined using mass spectrometric analysis, resulting in 80 identifications. The majority of the identified protein species were classified as energy and metabolism, stress response/defence and cell structure during early oil palm development representing potential candidates for the control of final fruit size and composition. Seven prominent protein species were then characterised using real-time polymerase chain reaction to validate the mRNA expression against the protein abundant profiles. Transcript and protein profiles were parallel across the developmental stages, but divergent expression was observed in one protein spot, indicative of possible post-transcriptional events. Our results revealed protein changes in early oil palm fruit development provide valuable information in the understanding of fruit growth and metabolism during early stages that may contribute towards improving agronomic traits. BIOLOGICAL SIGNIFICANCE: Two-dimensional gel electrophoresis coupled with mass spectrometry approach was used in this study to identify differentially expressed proteins during early oil palm fruit development. A total of 80 protein spots with significant change in abundance were successfully identified and selected genes were analysed using real time PCR to validate their expression. The dynamic changes in oil palm fruit proteome during early development were mostly active in primary and energy metabolism, stress responses, cell structure and protein metabolism. This study reveals the physiological processes during early oil palm fruit development and provides a reference proteome for further improvements in fruit quality traits.
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Affiliation(s)
- Sau-Yee Kok
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), No. 6 Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia; Division of Genetics, Cancer Research Institute, Kanazawa University, Kanazawa, Japan
| | - Parameswari Namasivayam
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia; Institute of Tropical Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Gwendoline Cheng-Lian Ee
- Department of Chemistry, Faculty of Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Meilina Ong-Abdullah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), No. 6 Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia.
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24
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Li SY, Zhang Q, Jin YH, Zou JX, Zheng YS, Li DD. A MADS-box gene, EgMADS21, negatively regulates EgDGAT2 expression and decreases polyunsaturated fatty acid accumulation in oil palm (Elaeis guineensis Jacq.). PLANT CELL REPORTS 2020; 39:1505-1516. [PMID: 32804247 DOI: 10.1007/s00299-020-02579-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/06/2020] [Indexed: 05/13/2023]
Abstract
EgMADS21 regulates PUFA accumulation in oil palm. Oil palm (Elaeis guineensis Jacq.) is the most productive world oil crop, accounting for 36% of world plant oil production. However, the molecular mechanism of the transcriptional regulation of fatty acid accumulation and lipid synthesis in the mesocarp of oil palm by up- or downregulating the expression of genes involved in related pathways remains largely unknown. Here, an oil palm MADS-box gene, EgMADS21, was screened in a yeast one-hybrid assay using the EgDGAT2 promoter sequence as bait. EgMADS21 is preferentially expressed in early mesocarp developmental stages in oil palm fruit and presents a negative correlation with EgDGAT2 expression. The direct binding of EgMADS21 to the EgDGAT2 promoter was confirmed by electrophoretic mobility shift assay. Subsequently, transient expression of EgMADS21 in oil palm protoplasts revealed that EgMADS21 not only binds to the EgDGAT2 promoter but also negatively regulates the expression of EgDGAT2. Furthermore, EgMADS21 was stably overexpressed in transgenic oil palm embryoids by Agrobacterium-mediated transformation. In three independent transgenic lines, EgDGAT2 expression was significantly suppressed by the expression of EgMADS21. The content of linoleic acid (C18:2) in the three transgenic embryoids was significantly decreased, while that of oleic acid (C18:1) was significantly increased. Combined with the substrate preference of EgDGAT2 identified in previous research, the results demonstrate the molecular mechanism by which EgMADS21 regulates EgDGAT2 expression and ultimately affects fatty acid accumulation in the mesocarp of oil palm.
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Affiliation(s)
- Si-Yu Li
- College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Qing Zhang
- College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Yuan-Hang Jin
- College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Ji-Xin Zou
- College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Yu-Sheng Zheng
- College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Dong-Dong Li
- College of Tropical Crops, Hainan University, Hainan, 570228, China.
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25
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Sun R, Gao L, Mi Z, Zheng Y, Li D. CnMADS1, a MADS transcription factor, positively modulates cell proliferation and lipid metabolism in the endosperm of coconut (Cocos nucifera L.). PLANTA 2020; 252:83. [PMID: 33040224 DOI: 10.1007/s00425-020-03490-3] [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: 09/24/2020] [Accepted: 10/04/2020] [Indexed: 06/11/2023]
Abstract
The function of the first MADS-box transcription factor from endosperm of coconut, CnMADS1, was characterized via seed-specific overexpression in Arabidopsis seeds and further confirmed in protoplasts of coconut. Coconut (Cocos nucifera L.), which belongs to the palm family (Arecaceae), is one of the world's most useful economical tropical crops. However, few genes related to coconut endosperm development have been studied. In previous research, an AGAMOUS-like (AGL) MADS-box transcription factor, named CnMADS1, was identified in the endosperm of coconut through the SSH cDNA library. In this paper, functional characterization of the CnMADS1 gene was carried out by seed-specific overexpression in A. thaliana seeds and protoplasts of coconut. The results indicated that in the twelve independent T2 transgenic Arabidopsis lines with high overexpression of CnMADS1, the size of the mature seeds of transgenic plants was increased significantly (19.64% increase in the long axis and 8.6% increase in the short axis) compared to that of the wild-type seeds. Moreover, the total lipid content also increased significantly in mature seeds of transgenic plants. After comparing the expression of related genes in wild-type and transgenic plants and confirmation by EMSA, AtOSR1, a regulatory gene related to seed size, was proven to be significantly up-regulated by CnMADS1 in transgenic plants. Moreover, the transient transformation of protoplasts of coconut also proved that CnLECRK3 (the homologous gene of AtOSR1 in coconut) is up-regulated by the CnMADS1 gene in the same way. All these results indicated that a similar regulation mode existed in Arabidopsis and the endosperm of coconut and ultimately affected the yield and quality of coconut copra.
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Affiliation(s)
- RuHao Sun
- College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Li Gao
- College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Zhiqi Mi
- College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Yusheng Zheng
- College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Dongdong Li
- College of Tropical Crops, Hainan University, Hainan, 570228, China.
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26
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Ting NC, Sherbina K, Khoo JS, Kamaruddin K, Chan PL, Chan KL, Halim MAA, Sritharan K, Yaakub Z, Mayes S, Massawe F, Chang PL, Nuzhdin SV, Sambanthamurthi R, Singh R. Expression of fatty acid and triacylglycerol synthesis genes in interspecific hybrids of oil palm. Sci Rep 2020; 10:16296. [PMID: 33004875 PMCID: PMC7529811 DOI: 10.1038/s41598-020-73170-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 08/10/2020] [Indexed: 11/09/2022] Open
Abstract
Evaluation of transcriptome data in combination with QTL information has been applied in many crops to study the expression of genes responsible for specific phenotypes. In oil palm, the mesocarp oil extracted from E. oleifera × E. guineensis interspecific hybrids is known to have lower palmitic acid (C16:0) content compared to pure African palms. The present study demonstrates the effectiveness of transcriptome data in revealing the expression profiles of genes in the fatty acid (FA) and triacylglycerol (TAG) biosynthesis processes in interspecific hybrids. The transcriptome assembly yielded 43,920 putative genes of which a large proportion were homologous to known genes in the public databases. Most of the genes encoding key enzymes involved in the FA and TAG synthesis pathways were identified. Of these, 27, including two candidate genes located within the QTL associated with C16:0 content, showed differential expression between developmental stages, populations and/or palms with contrasting C16:0 content. Further evaluation using quantitative real-time PCR revealed that differentially expressed patterns are generally consistent with those observed in the transcriptome data. Our results also suggest that different isoforms are likely to be responsible for some of the variation observed in FA composition of interspecific hybrids.
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Affiliation(s)
- Ngoot-Chin Ting
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia.,Biotechnology Research Centre, School of Biosciences, University of Nottingham Malaysia Campus, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Katrina Sherbina
- Quantitative and Computational Biology Section, University of Southern California, 1050 Childs Way, Los Angeles, CA, USA
| | - Jia-Shiun Khoo
- Codon Genomics Sdn. Bhd. Malaysia, No. 26, Jalan Dutamas 7, Taman Dutamas, Balakong, 43200, Seri Kembangan, Selangor, Malaysia
| | - Katialisa Kamaruddin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Pek-Lan Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Kuang-Lim Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Mohd Amin Ab Halim
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Kandha Sritharan
- United Plantations Bhd, Jendarata Estate, 36009, Teluk Intan, Perak, Malaysia
| | - Zulkifli Yaakub
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Sean Mayes
- Plant and Crop Sciences, Sutton Bonington Campus, Sutton Bonington, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Festo Massawe
- Biotechnology Research Centre, School of Biosciences, University of Nottingham Malaysia Campus, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Peter L Chang
- Molecular and Computational Biology Section, University of Southern California, 1050 Childs Way, Los Angeles, CA, USA
| | - Sergey V Nuzhdin
- Molecular and Computational Biology Section, University of Southern California, 1050 Childs Way, Los Angeles, CA, USA
| | - Ravigadevi Sambanthamurthi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Rajinder Singh
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia.
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27
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Tisné S, Denis M, Domonhédo H, Pallas B, Cazemajor M, Tranbarger TJ, Morcillo F. Environmental and trophic determinism of fruit abscission and outlook with climate change in tropical regions. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2020; 1:17-28. [PMID: 37284128 PMCID: PMC10168054 DOI: 10.1002/pei3.10011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/20/2020] [Accepted: 03/03/2020] [Indexed: 06/08/2023]
Abstract
Fruit abscission facilitates the optimal conditions and timing of seed dispersal. Environmental regulation of tropical fruit abscission has received little attention, even though climate change may have its strongest impacts in tropical regions. In this study, oil palm fruit abscission was monitored during multiple years in the Benin Republic to take advantage of the climatic seasonality and the continuous fruit production by this species. An innovative multivariable statistical method was used to identify the best predictors of fruit abscission among a set of climate and ecophysiological variables, and the stage of inflorescence and fruit bunch development when the variables are perceived. The effects of climate scenarios on fruit abscission were then predicted based on the calibrated model. We found complex regulation takes place at specific stages of inflorescence and bunch development, even long before the fruit abscission zone is competent to execute abscission. Among the predictors selected, temperature variations during inflorescence and fruit bunch development are major determinants of the fruit abscission process. Furthermore, the timing of ripe fruit drop is determined by temperature in combination with the trophic status. Finally, climate simulations revealed that the abscission process is robust and is more affected by seasonal variations than by extreme scenarios. Our investigations highlighted the central function of the abscission zone as the sensor of environmental signals during reproductive development. Coupling ecophysiological and statistical modeling was an efficient approach to disentangle this complex environmental regulation.
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Affiliation(s)
- Sébastien Tisné
- CiradUMR AGAPMontpellierFrance
- AGAPUniv MontpellierCIRADINRAMontpellier SupAgroMontpellierFrance
| | - Marie Denis
- CiradUMR AGAPMontpellierFrance
- AGAPUniv MontpellierCIRADINRAMontpellier SupAgroMontpellierFrance
| | | | - Benoît Pallas
- AGAPUniv MontpellierCIRADINRAMontpellier SupAgroMontpellierFrance
| | - Michel Cazemajor
- CRA‐PP/INRABRépublique du Bénin
- PalmElit SASMontferrier‐sur‐LezFrance
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28
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Vallarino JG, Merchante C, Sánchez‐Sevilla JF, de Luis Balaguer MA, Pott DM, Ariza MT, Casañal A, Posé D, Vioque A, Amaya I, Willmitzer L, Solano R, Sozzani R, Fernie AR, Botella MA, Giovannoni JJ, Valpuesta V, Osorio S. Characterizing the involvement of FaMADS9 in the regulation of strawberry fruit receptacle development. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:929-943. [PMID: 31533196 PMCID: PMC7061862 DOI: 10.1111/pbi.13257] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 09/03/2019] [Accepted: 09/08/2019] [Indexed: 05/08/2023]
Abstract
FaMADS9 is the strawberry (Fragaria x ananassa) gene that exhibits the highest homology to the tomato (Solanum lycopersicum) RIN gene. Transgenic lines were obtained in which FaMADS9 was silenced. The fruits of these lines did not show differences in basic parameters, such as fruit firmness or colour, but exhibited lower Brix values in three of the four independent lines. The gene ontology MapMan category that was most enriched among the differentially expressed genes in the receptacles at the white stage corresponded to the regulation of transcription, including a high percentage of transcription factors and regulatory proteins associated with auxin action. In contrast, the most enriched categories at the red stage were transport, lipid metabolism and cell wall. Metabolomic analysis of the receptacles of the transformed fruits identified significant changes in the content of maltose, galactonic acid-1,4-lactone, proanthocyanidins and flavonols at the green/white stage, while isomaltose, anthocyanins and cuticular wax metabolism were the most affected at the red stage. Among the regulatory genes that were differentially expressed in the transgenic receptacles were several genes previously linked to flavonoid metabolism, such as MYB10, DIV, ZFN1, ZFN2, GT2, and GT5, or associated with the action of hormones, such as abscisic acid, SHP, ASR, GTE7 and SnRK2.7. The inference of a gene regulatory network, based on a dynamic Bayesian approach, among the genes differentially expressed in the transgenic receptacles at the white and red stages, identified the genes KAN1, DIV, ZFN2 and GTE7 as putative targets of FaMADS9. A MADS9-specific CArG box was identified in the promoters of these genes.
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Affiliation(s)
- José G. Vallarino
- Departamento de Biología Molecular y Bioquímica. Campus de TeatinosInstituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de Málaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
- Unidad Asociada IFAPA‐CSIC Biotecnología y Mejora en FresaMálagaSpain
| | - Catharina Merchante
- Departamento de Biología Molecular y Bioquímica. Campus de TeatinosInstituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de Málaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
| | - José F. Sánchez‐Sevilla
- Unidad Asociada IFAPA‐CSIC Biotecnología y Mejora en FresaMálagaSpain
- Genómica y BiotecnologíaCentro de MálagaInstituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA)MálagaSpain
| | - María Angels de Luis Balaguer
- Plant and Microbial Biology DepartmentNorth Carolina State UniversityRaleighNCUSA
- Present address:
Precision Biosciences, Inc.DurhamNCUSA
| | - Delphine M. Pott
- Departamento de Biología Molecular y Bioquímica. Campus de TeatinosInstituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de Málaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
- Unidad Asociada IFAPA‐CSIC Biotecnología y Mejora en FresaMálagaSpain
| | - María T. Ariza
- Departamento de Biología Molecular y Bioquímica. Campus de TeatinosInstituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de Málaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
- Unidad Asociada IFAPA‐CSIC Biotecnología y Mejora en FresaMálagaSpain
| | - Ana Casañal
- Departamento de Biología Molecular y Bioquímica. Campus de TeatinosInstituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de Málaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
| | - David Posé
- Departamento de Biología Molecular y Bioquímica. Campus de TeatinosInstituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de Málaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
- Unidad Asociada IFAPA‐CSIC Biotecnología y Mejora en FresaMálagaSpain
| | - Amalia Vioque
- Departamento de Biología Molecular y Bioquímica. Campus de TeatinosInstituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de Málaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
| | - Iraida Amaya
- Unidad Asociada IFAPA‐CSIC Biotecnología y Mejora en FresaMálagaSpain
- Genómica y BiotecnologíaCentro de MálagaInstituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA)MálagaSpain
| | - Lothar Willmitzer
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
| | - Roberto Solano
- Departmento de Genética Molecular de PlantasCentro Nacional de BiotecnologíaConsejo Superior de Investigaciones Científicas (CNB‐CSIC)MadridSpain
| | - Rosangela Sozzani
- Plant and Microbial Biology DepartmentNorth Carolina State UniversityRaleighNCUSA
- Biomathematics ProgramNorth Carolina State UniversityRaleighNCUSA
| | - Alisdair R. Fernie
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
| | - Miguel A. Botella
- Departamento de Biología Molecular y Bioquímica. Campus de TeatinosInstituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de Málaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
- Unidad Asociada IFAPA‐CSIC Biotecnología y Mejora en FresaMálagaSpain
| | - James J. Giovannoni
- Boyce Thompson Institute for Plant Research and USDA‐ARSRobert W. Holley CenterCornell University CampusIthacaNYUSA
| | - Victoriano Valpuesta
- Departamento de Biología Molecular y Bioquímica. Campus de TeatinosInstituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de Málaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
- Unidad Asociada IFAPA‐CSIC Biotecnología y Mejora en FresaMálagaSpain
| | - Sonia Osorio
- Departamento de Biología Molecular y Bioquímica. Campus de TeatinosInstituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’Universidad de Málaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
- Unidad Asociada IFAPA‐CSIC Biotecnología y Mejora en FresaMálagaSpain
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29
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Amiruddin N, Chan PL, Azizi N, Morris PE, Chan KL, Ong PW, Rosli R, Masura SS, Murphy DJ, Sambanthamurthi R, Haslam RP, Chye ML, Harwood JL, Low ETL. Characterization of Oil Palm Acyl-CoA-Binding Proteins and Correlation of Their Gene Expression with Oil Synthesis. PLANT & CELL PHYSIOLOGY 2020; 61:735-747. [PMID: 31883014 DOI: 10.1093/pcp/pcz237] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 12/22/2019] [Indexed: 05/18/2023]
Abstract
Acyl-CoA-binding proteins (ACBPs) are involved in binding and trafficking acyl-CoA esters in eukaryotic cells. ACBPs contain a well-conserved acyl-CoA-binding domain. Their various functions have been characterized in the model plant Arabidopsis and, to a lesser extent, in rice. In this study, genome-wide detection and expression analysis of ACBPs were performed on Elaeis guineensis (oil palm), the most important oil crop in the world. Seven E. guineensis ACBPs were identified and classified into four groups according to their deduced amino acid domain organization. Phylogenetic analysis showed conservation of this family with other higher plants. All seven EgACBPs were expressed in most tissues while their differential expression suggests various functions in specific tissues. For example, EgACBP3 had high expression in inflorescences and stalks while EgACBP1 showed strong expression in leaves. Because of the importance of E. guineensis as an oil crop, expression of EgACBPs was specifically examined during fruit development. EgACBP3 showed high expression throughout mesocarp development, while EgACBP1 had enhanced expression during rapid oil synthesis. In endosperm, both EgACBP1 and EgACBP3 exhibited increased expression during seed development. These results provide important information for further investigations on the biological functions of EgACBPs in various tissues and, in particular, their roles in oil synthesis.
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Affiliation(s)
- Nadzirah Amiruddin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor 43000, Malaysia
| | - Pek-Lan Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor 43000, Malaysia
| | - Norazah Azizi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor 43000, Malaysia
| | - Priscilla Elizabeth Morris
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor 43000, Malaysia
| | - Kuang-Lim Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor 43000, Malaysia
| | - Pei Wen Ong
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor 43000, Malaysia
| | - Rozana Rosli
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor 43000, Malaysia
| | - Subhi Siti Masura
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor 43000, Malaysia
| | - Denis J Murphy
- School of Applied Sciences, University of South Wales, Pontypridd CF37 1DL, UK
| | - Ravigadevi Sambanthamurthi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor 43000, Malaysia
| | - Richard P Haslam
- Department of Plant Sciences, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Mee-Len Chye
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - John L Harwood
- School of Biosciences, University of Cardiff, Cardiff CF10 3AX, UK
| | - Eng-Ti Leslie Low
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor 43000, Malaysia
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Ischebeck T, Krawczyk HE, Mullen RT, Dyer JM, Chapman KD. Lipid droplets in plants and algae: Distribution, formation, turnover and function. Semin Cell Dev Biol 2020; 108:82-93. [PMID: 32147380 DOI: 10.1016/j.semcdb.2020.02.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/28/2020] [Accepted: 02/29/2020] [Indexed: 01/02/2023]
Abstract
Plant oils represent an energy-rich and carbon-dense group of hydrophobic compounds. These oils are not only of economic interest, but also play important, fundamental roles in plant and algal growth and development. The subcellular storage compartments of plant lipids, referred to as lipid droplets (LDs), have long been considered relatively inert oil vessels. However, research in the last decade has revealed that LDs play far more dynamic roles in plant biology than previously appreciated, including transient neutral lipid storage, membrane remodeling, lipid signaling, and stress responses. Here we discuss recent developments in the understanding of LD formation, turnover and function in land plants and algae.
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Affiliation(s)
- Till Ischebeck
- University of Göttingen, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), Department of Plant Biochemistry, 37077, Göttingen, Germany.
| | - Hannah E Krawczyk
- University of Göttingen, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center for Molecular Biosciences (GZMB), Department of Plant Biochemistry, 37077, Göttingen, Germany
| | - Robert T Mullen
- University of Guelph, Department of Molecular Cell Biology, Guelph, Ontario, N1G 2W1, Canada
| | - John M Dyer
- United States Department of Agriculture, Agriculture Research Service, US Arid-Land Agricultural Research Center, Maricopa, AZ, 85138, USA
| | - Kent D Chapman
- University of North Texas, BioDiscovery Institute, Department of Biological Sciences, Denton, TX, 76203, USA
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31
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Guerin C, Serret J, Montúfar R, Vaissayre V, Bastos-Siqueira A, Durand-Gasselin T, Tregear J, Morcillo F, Dussert S. Palm seed and fruit lipid composition: phylogenetic and ecological perspectives. ANNALS OF BOTANY 2020; 125:157-172. [PMID: 31665224 PMCID: PMC7080222 DOI: 10.1093/aob/mcz175] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/30/2019] [Accepted: 10/23/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Palms are vital to worldwide human nutrition, in particular as major sources of vegetable oils. However, our knowledge of seed and fruit lipid diversity in the family Arecaceae is limited. We therefore aimed to explore relationships between seed and fruit lipid content, fatty acid composition in the respective tissues, phylogenetic factors and biogeographical parameters. METHODS Oil content and fatty acid composition were characterized in seeds and fruits of 174 and 144 palm species respectively. Distribution, linear regression and multivariate analyses allowed an evaluation of the chemotaxonomic value of these traits and their potential relationship with ecological factors. KEY RESULTS A considerable intra-family diversity for lipid traits was revealed. Species with the most lipid-rich seeds belonged to the tribe Cocoseae, while species accumulating oil in the mesocarp occurred in all subfamilies and two-thirds of the tribes studied. Seed and fruit lipid contents were not correlated. Fatty acid composition of mesocarp oil was highly variable within tribes. By contrast, within-tribe diversity for seed lipid traits was low, whereas between-tribe variability was high. Consequently, multivariate analyses of seed lipid traits produced groupings of species belonging to the same tribe. Medium-chain fatty acids predominated in seeds of most palm species, but they were also accumulated in the mesocarp in some cases. Seed unsaturated fatty acid content correlated with temperature at the coldest latitude of natural occurrence. CONCLUSION Several previously uncharacterized palms were identified as potential new sources of vegetable oils for comestible or non-food use. Seed lipid traits reflect genetic drift that occurred during the radiation of the family and therefore are highly relevant to palm chemotaxonomy. Our data also suggest that seed unsaturated fatty acids may provide an adaptive advantage in the coldest environments colonized by palms by maintaining storage lipids in liquid form for efficient mobilization during germination.
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Affiliation(s)
| | | | - Rommel Montúfar
- Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
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Zhang Q, Sun R, Zheng Y, Yuan Y, Li D. Isolation and characterization of the EgWRI1 promoter from oil palm (Elaeis guineensis Jacq.) and its response to environmental stress and ethylene. PLoS One 2019; 14:e0225115. [PMID: 31800586 PMCID: PMC6892528 DOI: 10.1371/journal.pone.0225115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/28/2019] [Indexed: 11/18/2022] Open
Abstract
WRI1 is a plant-specific transcription factor that enhances the accumulation of oils through the upregulation of the expression of genes involved in glycolysis and fatty acid biosynthesis. In this study, the EgWRI1 promoter from oil palm was isolated and characterized in transgenic Arabidopsis. The sequence analysis results revealed that various putative plant regulatory elements are present in the EgWRI1 promoter region. The EgWRI1 promoter and beta-glucuronidase (GUS) reporter gene were transcriptionally fused and transformed into Arabidopsis thaliana. Histochemical analysis revealed that GUS staining was very strong in whole seedlings, especially the stems, leaves, and siliques. Moreover, GUS staining was strong in the silique coats but weak in the seeds. Furthermore, to detect whether EgWRI1 was induced by environmental stress, we detected the expression efficiency of the EgWRI1 promoter in transgenic Arabidopsis treated with low temperature, darkness, and exogenous ethylene. The results showed that the activity of the EgWRI1 promoter was induced by darkness but suppressed significantly when exposed to exogenous ethylene. When treated with low temperature, the activity of the EgWRI1 promoter was first reduced after 24 hours but recovered after 48 hours. Taken together, these results reveal the features of the EgWRI1 promoter from oil palm, which will be helpful for improving oil accumulation in oil palm via reasonable cultivation methods.
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Affiliation(s)
- Qing Zhang
- Department of Biotechnology, College of Tropical Crops, Hainan University, Hainan, China
| | - Ruhao Sun
- Department of Biotechnology, College of Tropical Crops, Hainan University, Hainan, China
| | - Yusheng Zheng
- Department of Biotechnology, College of Tropical Crops, Hainan University, Hainan, China
| | - Yijun Yuan
- Department of Bioengineering, College of Life Sciences and Pharmacy, Hainan University, Haikou, Hainan, China
- * E-mail: (YY); (DL)
| | - Dongdong Li
- Department of Biotechnology, College of Tropical Crops, Hainan University, Hainan, China
- * E-mail: (YY); (DL)
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Li F, Wu B, Yan L, Hao C, Qin X, Lai J, Song Y. Transcriptional profiling reveals differentially expressed genes involved in lipid biosynthesis during cacao seed development. Sci Rep 2019; 9:17263. [PMID: 31754164 PMCID: PMC6872657 DOI: 10.1038/s41598-019-53959-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 11/05/2019] [Indexed: 11/09/2022] Open
Abstract
Theobroma cacao is a plant of economic value due to the use of its seed lipid for chocolate, confectionery, and cosmetic industries. The seed lipid contains a stable ratio of saturated and unsaturated fatty acids, which determines its unique melting temperature. However, little is known about the molecular mechanism determining the fatty acid ratio and lipid content in cacao. To gain insight into the unique properties of lipid synthesis in cacao, biochemical and transcriptomic approaches were used to compare the lipid accumulation between high and low lipid content cacao accessions. Lipid accumulation rates and lipid content were different between the two accessions. Moreover, differentially expressed genes were detected between high and low lipid content cacao accessions. The data allowed the identification of distinct candidate genes and furthered our understanding of lipid accumulation, potentially explaining the differences in lipid content between various cacao accessions. The results might be used to develop molecular tools and engineer alternative pathways for cacao breeding with improved lipid production potentials.
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Affiliation(s)
- Fupeng Li
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning, 571533, P.R. China
| | - Baoduo Wu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning, 571533, P.R. China
| | - Lin Yan
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning, 571533, P.R. China
| | - Chaoyun Hao
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning, 571533, P.R. China
| | - Xiaowei Qin
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning, 571533, P.R. China
| | - Jianxiong Lai
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning, 571533, P.R. China
| | - Yinghui Song
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Genetic Resources Utilization of Spice and Beverage Crops, Ministry of Agriculture, Wanning, 571533, P.R. China.
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Lau BYC, Othman A. Evaluation of sodium deoxycholate as solubilization buffer for oil palm proteomics analysis. PLoS One 2019; 14:e0221052. [PMID: 31415606 PMCID: PMC6695131 DOI: 10.1371/journal.pone.0221052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 07/29/2019] [Indexed: 11/29/2022] Open
Abstract
Protein solubility is a critical prerequisite to any proteomics analysis. Combination of urea/thiourea and 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS) have been routinely used to enhance protein solubilization for oil palm proteomics studies in recent years. The goals of these proteomics analysis are essentially to complement the knowledge regarding the regulation networks and mechanisms of the oil palm fatty acid biosynthesis. Through omics integration, the information is able to build a regulatory model to support efforts in improving the economic value and sustainability of palm oil in the global oil and vegetable market. Our study evaluated the utilization of sodium deoxycholate as an alternative solubilization buffer/additive to urea/thiourea and CHAPS. Efficiency of urea/thiourea/CHAPS, urea/CHAPS, urea/sodium deoxycholate and sodium deoxycholate buffers in solubilizing the oil palm (Elaeis guineensis var. Tenera) mesocarp proteins were compared. Based on the protein yields and electrophoretic profile, combination of urea/thiourea/CHAPS were shown to remain a better solubilization buffer and additive, but the differences with sodium deoxycholate buffer was insignificant. A deeper mass spectrometric and statistical analyses on the identified proteins and peptides from all the evaluated solubilization buffers revealed that sodium deoxycholate had increased the number of identified proteins from oil palm mesocarps, enriched their gene ontologies and reduced the number of carbamylated lysine residues by more than 67.0%, compared to urea/thiourea/CHAPS buffer. Although only 62.0% of the total identified proteins were shared between the urea/thiourea/CHAPS and sodium deoxycholate buffers, the importance of the remaining 38.0% proteins depends on the applications. The only observed limitations to the application of sodium deoxycholate in protein solubilization were the interference with protein quantitation and but it could be easily rectified through a 4-fold dilution. All the proteomics data are available via ProteomeXchange with identifier PXD013255. In conclusion, sodium deoxycholate is applicable in the solubilization of proteins extracted from oil palm mesocarps with higher efficiency compared to urea/thiourea/CHAPS buffer. The sodium deoxycholate buffer is more favorable for proteomics analysis due to its proven advantages over urea/thiourea/CHAPS buffer.
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Affiliation(s)
- Benjamin Yii Chung Lau
- Malaysian Palm Oil Board, No 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Abrizah Othman
- Malaysian Palm Oil Board, No 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia
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Zafar S, Li YL, Li NN, Zhu KM, Tan XL. Recent advances in enhancement of oil content in oilseed crops. J Biotechnol 2019; 301:35-44. [PMID: 31158409 DOI: 10.1016/j.jbiotec.2019.05.307] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/14/2019] [Accepted: 05/29/2019] [Indexed: 10/26/2022]
Abstract
Plant oils are very valuable agricultural commodity. The manipulation of seed oil composition to deliver enhanced fatty acid compositions, which are appropriate for feed or fuel, has always been a main objective of metabolic engineers. The last two decennary have been noticeable by numerous significant events in genetic engineering for identification of different gene targets to improve oil yield in oilseed crops. Particularly, genetic engineering approaches have presented major breakthrough in elevating oil content in oilseed crops such as Brassica napus and soybean. Additionally, current research efforts to explore the possibilities to modify the genetic expression of key regulators of oil accumulation along with biochemical studies to elucidate lipid biosynthesis will establish protocols to develop transgenic oilseed crops along much improved oil content. In this review, we describe current distinct genetic engineering approaches investigated by researchers for ameliorating oil content and its nutritional quality. Moreover, we will also discuss some auspicious and innovative approaches and challenges for engineering oil content to yield oil at much higher rate in oilseed crops.
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Affiliation(s)
- Sundus Zafar
- School of Agricultural Equipment Engineering, Jiangsu University, Zhenjiang 212013, People's Republic of China; Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Yu-Long Li
- Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Nan-Nan Li
- School of Resource and Environment, Southwest University, Chongqing, 400715, People's Republic of China
| | - Ke-Ming Zhu
- Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Xiao-Li Tan
- Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, People's Republic of China.
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36
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Alotaibi MD, Alshammari BA, Saba N, Alothman OY, Sanjay M, Almutairi Z, Jawaid M. Characterization of natural fiber obtained from different parts of date palm tree (Phoenix dactylifera L.). Int J Biol Macromol 2019; 135:69-76. [DOI: 10.1016/j.ijbiomac.2019.05.102] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/09/2019] [Indexed: 10/26/2022]
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37
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Tranbarger TJ, Domonhédo H, Cazemajor M, Dubreuil C, Fischer U, Morcillo F. The PIP Peptide of INFLORESCENCE DEFICIENT IN ABSCISSION Enhances Populus Leaf and Elaeis guineensis Fruit Abscission. PLANTS (BASEL, SWITZERLAND) 2019; 8:E143. [PMID: 31151222 PMCID: PMC6630328 DOI: 10.3390/plants8060143] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 05/23/2019] [Accepted: 05/28/2019] [Indexed: 01/18/2023]
Abstract
The programmed loss of a plant organ is called abscission, which is an important cell separation process that occurs with different organs throughout the life of a plant. The use of floral organ abscission in Arabidopsis thaliana as a model has allowed greater understanding of the complexities of organ abscission, but whether the regulatory pathways are conserved throughout the plant kingdom and for all organ abscission types is unknown. One important pathway that has attracted much attention involves a peptide ligand-receptor signalling system that consists of the secreted peptide IDA (INFLORESCENCE DEFICIENT IN ABSCISSION) and at least two leucine-rich repeat (LRR) receptor-like kinases (RLK), HAESA (HAE) and HAESA-LIKE2 (HSL2). In the current study we examine the bioactive potential of IDA peptides in two different abscission processes, leaf abscission in Populus and ripe fruit abscission in oil palm, and find in both cases treatment with IDA peptides enhances cell separation and abscission of both organ types. Our results provide evidence to suggest that the IDA-HAE-HSL2 pathway is conserved and functions in these phylogenetically divergent dicot and monocot species during both leaf and fruit abscission, respectively.
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Affiliation(s)
- Timothy John Tranbarger
- UMR DIADE, Institut de Recherche pour le Développement, Université de Montpellier, 34394 Montpellier, France.
- Ecology and Genetics Laboratory, Pontificia Universidad Católica del Ecuador (PUCE), 17-01-21-84 Quito, Ecuador.
| | | | - Michel Cazemajor
- CRAPP, INRAB, BP 1 Pobè, Benin.
- PalmElit SAS, F-34980 Montferrier-sur-Lez, France.
| | - Carole Dubreuil
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden.
- DRT DPACA, CEA Tech Cadarache, 13108 Saint Paul Lez Durance, France.
| | - Urs Fischer
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden.
- KWS SAAT SE, RD-BT, 37574 Einbeck, Germany.
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38
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Zheng Y, Chen C, Liang Y, Sun R, Gao L, Liu T, Li D. Genome-wide association analysis of the lipid and fatty acid metabolism regulatory network in the mesocarp of oil palm (Elaeis guineensis Jacq.) based on small noncoding RNA sequencing. TREE PHYSIOLOGY 2019; 39:356-371. [PMID: 30137626 DOI: 10.1093/treephys/tpy091] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/12/2018] [Accepted: 07/25/2018] [Indexed: 05/20/2023]
Abstract
Oil palm (Elaeis guineensis Jacq.) is the highest oil-yielding crop in the plant kingdom and accumulates 90% of palm oil in the mesocarp. However, the regulatory mechanisms of lipid and fatty acid (FA) metabolism in oil palm are just beginning to be understood, and more studies are needed, especially in the understanding of small noncoding RNA (ncRNA) and mRNA. Based on the deep sequencing of small noncoding RNAs and the degradome in five developmental mesocarp stages, 452 microRNAs (miRNAs), including 170 conserved known-miRNAs (kn-miRNAs) and 282 novel-miRNA (nov-miRNAs), were identified. After predicting the targets of those miRNAs to 37 FA synthesis-related genes, we found that 22 kn-miRNAs and 14 nov-miRNAs might be involved in FA metabolism pathways. Among them, eg-miR156c, eg-miR397, eg-miR444b and nov-miR129 regulated FA synthesis in plastids and the transport of FA-ACP from plastids to the endoplasmic reticulum by targeting acetyl-CoA carboxylase 1 (ACC1), long-chain acyl-CoA synthetase 9 (LACS9), LACS4 and enoyl-ACP reductase (ENR), respectively. Nov-miR138 and nov-miR59 targeted glycerol-3-phosphate acyltransferase (GPAT), and nov-miR274 targeted phosphatidate phosphatase 1 (PAP1). Both target genes are involved in triacylglycerol synthesis in the endoplasmic reticulum. Eg-miR156e and eg-miR156j played pivotal roles by targeting β-ketoacyl-CoA synthase 12 (KCS12), and nov-miR201 targets very-long-chain enoyl-CoA reductase (ECR). Several miRNAs were also predicted to indirectly regulate FA synthesis and lipid metabolism through the squamosa promoter-binding protein-like gene (SPL), NAC and MYB transcription factors. As a whole, indications of a complex and extensive miRNA-mRNA regulatory network associated with FA metabolism in the mesocarp of the oil palm is presented. The results help to broaden the knowledge of potential mechanisms that might be regulated by miRNAs through modulation of the expression of FA-related target gene metabolism in the oil palm.
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Affiliation(s)
- Yusheng Zheng
- Department of Biotechnology, Hainan Key Laboratory for Sustainable Utilization of Tropic Bioresource, Hainan University, Haikou, Hainan, China
| | | | - Yuanxue Liang
- Department of Biotechnology, Hainan Key Laboratory for Sustainable Utilization of Tropic Bioresource, Hainan University, Haikou, Hainan, China
| | - Ruhao Sun
- Department of Biotechnology, Hainan Key Laboratory for Sustainable Utilization of Tropic Bioresource, Hainan University, Haikou, Hainan, China
| | - Lingchao Gao
- Department of Biotechnology, Hainan Key Laboratory for Sustainable Utilization of Tropic Bioresource, Hainan University, Haikou, Hainan, China
| | - Tao Liu
- Annoroad Gene Technology Co., Ltd, Beijing, China
| | - Dongdong Li
- Department of Biotechnology, Hainan Key Laboratory for Sustainable Utilization of Tropic Bioresource, Hainan University, Haikou, Hainan, China
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Vanhercke T, Dyer JM, Mullen RT, Kilaru A, Rahman MM, Petrie JR, Green AG, Yurchenko O, Singh SP. Metabolic engineering for enhanced oil in biomass. Prog Lipid Res 2019; 74:103-129. [PMID: 30822461 DOI: 10.1016/j.plipres.2019.02.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/21/2019] [Accepted: 02/21/2019] [Indexed: 02/06/2023]
Abstract
The world is hungry for energy. Plant oils in the form of triacylglycerol (TAG) are one of the most reduced storage forms of carbon found in nature and hence represent an excellent source of energy. The myriad of applications for plant oils range across foods, feeds, biofuels, and chemical feedstocks as a unique substitute for petroleum derivatives. Traditionally, plant oils are sourced either from oilseeds or tissues surrounding the seed (mesocarp). Most vegetative tissues, such as leaves and stems, however, accumulate relatively low levels of TAG. Since non-seed tissues constitute the majority of the plant biomass, metabolic engineering to improve their low-intrinsic TAG-biosynthetic capacity has recently attracted significant attention as a novel, sustainable and potentially high-yielding oil production platform. While initial attempts predominantly targeted single genes, recent combinatorial metabolic engineering strategies have focused on the simultaneous optimization of oil synthesis, packaging and degradation pathways (i.e., 'push, pull, package and protect'). This holistic approach has resulted in dramatic, seed-like TAG levels in vegetative tissues. With the first proof of concept hurdle addressed, new challenges and opportunities emerge, including engineering fatty acid profile, translation into agronomic crops, extraction, and downstream processing to deliver accessible and sustainable bioenergy.
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Affiliation(s)
- Thomas Vanhercke
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia.
| | - John M Dyer
- USDA-ARS, US Arid-Land Agricultural Research Center, Maricopa, AZ, USA
| | - Robert T Mullen
- Department of Molecular and Cellular Biology, University of Guelph, ON, Canada
| | - Aruna Kilaru
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, USA
| | - Md Mahbubur Rahman
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, USA
| | - James R Petrie
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia; Folear, Goulburn, NSW, Australia
| | - Allan G Green
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia
| | - Olga Yurchenko
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Surinder P Singh
- CSIRO Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia
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Xiao Y, Xia W, Mason AS, Cao Z, Fan H, Zhang B, Zhang J, Ma Z, Peng M, Huang D. Genetic control of fatty acid composition in coconut (Cocos nucifera), African oil palm (Elaeis guineensis), and date palm (Phoenix dactylifera). PLANTA 2019; 249:333-350. [PMID: 30194535 DOI: 10.1007/s00425-018-3003-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 09/03/2018] [Indexed: 05/26/2023]
Abstract
Predominant gene isoforms and expression bias in lipid metabolism pathways are highly conserved between oil-producing Arecaceae crop species coconut and oil palm, but diverge in non-oil-producing species date palm. Coconut (Cocos nucifera), African oil palm (Elaeis guineensis) and date palm (Phoenix dactylifera) are three major crop species in the Arecaceae family for which genome sequences have recently become available. Coconut and African oil palm both store oil in their endosperms, while date palm fruits contain very little oil. We analyzed fatty acid composition in three coconut tissues (leaf, endosperm and embryo) and in two African oil palm tissues (leaf and mesocarp), and identified 806, 840 and 848 lipid-related genes in 22 lipid metabolism pathways from the coconut, African oil palm and date palm genomes, respectively. The majority of lipid-related genes were highly homologous and retained in homologous segments between the three species. Genes involved in the conversion of pyruvate to fatty acid had a five-to-sixfold higher expression in the coconut endosperm and oil palm mesocarp than in the leaf or embryo tissues based on Fragments Per Kilobase of transcript per Million mapped reads values. A close evolutionary relationship between predominant gene isoforms and high conservation of gene expression bias in the lipid and carbohydrate gene metabolism pathways was observed for the two oil-producing species coconut and oil palm, differing from that of date palm, a non-oil-producing species. Our results elucidate the similarities and differences in lipid metabolism between the three major Arecaceae crop species, providing important information for physiology studies as well as breeding for fatty acid composition and oil content in these crops.
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Affiliation(s)
- Yong Xiao
- Coconut Research Institute, CATAS, Wenchang, 571339, Hainan, People's Republic of China
| | - Wei Xia
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, People's Republic of China.
| | - Annaliese S Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Zengying Cao
- MOA Key Laboratory of Tropical Crop Biology and Genetic Resources Utilization, Institute of Tropical Bioscience and Biotechnology, CATAS, Haikou, 571101, Hainan, People's Republic of China
| | - Haikuo Fan
- Coconut Research Institute, CATAS, Wenchang, 571339, Hainan, People's Republic of China
| | - Bo Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, People's Republic of China
| | - Jinlan Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, People's Republic of China
| | - Zilong Ma
- MOA Key Laboratory of Tropical Crop Biology and Genetic Resources Utilization, Institute of Tropical Bioscience and Biotechnology, CATAS, Haikou, 571101, Hainan, People's Republic of China
| | - Ming Peng
- MOA Key Laboratory of Tropical Crop Biology and Genetic Resources Utilization, Institute of Tropical Bioscience and Biotechnology, CATAS, Haikou, 571101, Hainan, People's Republic of China
| | - Dongyi Huang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, People's Republic of China
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Cultrera NGM, Sarri V, Lucentini L, Ceccarelli M, Alagna F, Mariotti R, Mousavi S, Ruiz CG, Baldoni L. High Levels of Variation Within Gene Sequences of Olea europaea L. FRONTIERS IN PLANT SCIENCE 2019; 9:1932. [PMID: 30671076 PMCID: PMC6331486 DOI: 10.3389/fpls.2018.01932] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 12/12/2018] [Indexed: 05/08/2023]
Abstract
Gene sequence variation in cultivated olive (Olea europaea L. subsp. europaea var. europaea), the most important oil tree crop of the Mediterranean basin, has been poorly evaluated up to now. A deep sequence analysis of fragments of four genes, OeACP1, OeACP2, OeLUS and OeSUT1, in 90 cultivars, revealed a wide range of polymorphisms along all recognized allele forms and unexpected allele frequencies and genotype combinations. High linkage values among most polymorphisms were recorded within each gene fragment. The great sequence variability corresponded to a low number of alleles and, surprisingly, to a small fraction of genotype combinations. The distribution, frequency, and combination of the different alleles at each locus is possibly due to natural and human pressures, such as selection, ancestrality, or fitness. Phylogenetic analyses of allele sequences showed distant and complex patterns of relationships among cultivated olives, intermixed with other related forms, highlighting an evolutionary connection between olive cultivars and the O. europaea subspecies cuspidata and cerasiformis. This study demonstrates how a detailed and complete sequence analysis of a few gene portions and a thorough genotyping on a representative set of cultivars can clarify important issues related to sequence polymorphisms, reconstructing the phylogeny of alleles, as well as the genotype combinations. The identification of regions representing blocks of recombination could reveal polymorphisms that represent putatively functional markers. Indeed, specific mutations found on the analyzed OeACP1 and OeACP2 fragments seem to be correlated to the fruit weight.
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Affiliation(s)
- Nicolò G. M. Cultrera
- Institute of Biosciences and Bioresources, National Research Council, Perugia, Italy
| | - Vania Sarri
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Livia Lucentini
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Marilena Ceccarelli
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Fiammetta Alagna
- ENEA Italian National Agency for New Technologies Energy and Sustainable Economic Development, Trisaia Research Center, Rotondella, Italy
| | - Roberto Mariotti
- Institute of Biosciences and Bioresources, National Research Council, Perugia, Italy
| | - Soraya Mousavi
- Institute of Biosciences and Bioresources, National Research Council, Perugia, Italy
| | | | - Luciana Baldoni
- Institute of Biosciences and Bioresources, National Research Council, Perugia, Italy
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Hassan H, Amiruddin MD, Weckwerth W, Ramli US. Deciphering key proteins of oil palm (Elaeis guineensis
Jacq.) fruit mesocarp development by proteomics and chemometrics. Electrophoresis 2018; 40:254-265. [DOI: 10.1002/elps.201800232] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 10/22/2018] [Accepted: 10/25/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Hasliza Hassan
- Advanced Biotechnology and Breeding Centre (ABBC); Malaysian Palm Oil Board (MPOB); Selangor Malaysia
| | - Mohd Din Amiruddin
- Advanced Biotechnology and Breeding Centre (ABBC); Malaysian Palm Oil Board (MPOB); Selangor Malaysia
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology; Faculty of Life Sciences; University of Vienna; Vienna Austria
- Vienna Metabolomics Center (VIME); University of Vienna; Vienna Austria
| | - Umi Salamah Ramli
- Advanced Biotechnology and Breeding Centre (ABBC); Malaysian Palm Oil Board (MPOB); Selangor Malaysia
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Rosli R, Chan PL, Chan KL, Amiruddin N, Low ETL, Singh R, Harwood JL, Murphy DJ. In silico characterization and expression profiling of the diacylglycerol acyltransferase gene family (DGAT1, DGAT2, DGAT3 and WS/DGAT) from oil palm, Elaeis guineensis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 275:84-96. [PMID: 30107884 DOI: 10.1016/j.plantsci.2018.07.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 07/05/2018] [Accepted: 07/25/2018] [Indexed: 05/14/2023]
Abstract
The diacylglycerol acyltransferases (DGAT) (diacylglycerol:acyl-CoA acyltransferase, EC 2.3.1.20) are a key group of enzymes that catalyse the final and usually the most important rate-limiting step of triacylglycerol biosynthesis in plants and other organisms. Genes encoding four distinct functional families of DGAT enzymes have been characterised in the genome of the African oil palm, Elaeis guineensis. The contrasting features of the various isoforms within the four families of DGAT genes, namely DGAT1, DGAT2, DGAT3 and WS/DGAT are presented both in the oil palm itself and, for comparative purposes, in 12 other oil crop or model/related plants, namely Arabidopsis thaliana, Brachypodium distachyon, Brassica napus, Elaeis oleifera, Glycine max, Gossypium hirsutum, Helianthus annuus, Musa acuminata, Oryza sativa, Phoenix dactylifera, Sorghum bicolor, and Zea mays. The oil palm genome contains respectively three, two, two and two distinctly expressed functional copies of the DGAT1, DGAT2, DGAT3 and WS/DGAT genes. Phylogenetic analyses of the four DGAT families showed that the E. guineensis genes tend to cluster with sequences from P. dactylifera and M. acuminata rather than with other members of the Commelinid monocots group, such as the Poales which include the major cereal crops such as rice and maize. Comparison of the predicted DGAT protein sequences with other animal and plant DGATs was consistent with the E. guineensis DGAT1 being ER located with its active site facing the lumen while DGAT2, although also ER located, had a predicted cytosol-facing active site. In contrast, DGAT3 and some (but not all) WS/DGAT in E. guineensis are predicted to be soluble, cytosolic enzymes. Evaluation of E. guineensis DGAT gene expression in different tissues and developmental stages suggests that the four DGAT groups have distinctive physiological roles and are particularly prominent in developmental processes relating to reproduction, such as flowering, and in fruit/seed formation especially in the mesocarp and endosperm tissues.
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Affiliation(s)
- Rozana Rosli
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, CF37 1DL, United Kingdom; Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Pek-Lan Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Kuang-Lim Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Nadzirah Amiruddin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Eng-Ti Leslie Low
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Rajinder Singh
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - John L Harwood
- School of Biosciences, University of Cardiff, Cardiff, CF10 3AX, United Kingdom
| | - Denis J Murphy
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, CF37 1DL, United Kingdom.
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Hanifiah FHA, Abdullah SNA, Othman A, Shaharuddin NA, Saud HM, Hasnulhadi HAH, Munusamy U. GCTTCA as a novel motif for regulating mesocarp-specific expression of the oil palm (Elaeis guineensis Jacq.) stearoyl-ACP desaturase gene. PLANT CELL REPORTS 2018; 37:1127-1143. [PMID: 29789886 DOI: 10.1007/s00299-018-2300-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 05/15/2018] [Indexed: 06/08/2023]
Abstract
TAAAAT and a novel motif, GCTTCA found in the oil palm stearoyl-ACP desaturase (SAD1) promoter are involved in regulating mesocarp-specific expression. Two key fatty acid biosynthetic genes, stearoyl-ACP desaturase (SAD1), and acyl-carrier protein (ACP3) in Elaeis guineensis (oil palm) showed high level of expression during the period of oil synthesis in the mesocarp [12-19 weeks after anthesis (w.a.a.)] and kernel (12-15 w.a.a.). Both genes are expressed in spear leaves at much lower levels and the expression increased by 1.5-fold to 2.5-fold following treatments with ethylene and abscisic acid (ABA). Both SAD1 and ACP3 promoters contain phytohormone-responsive, light-responsive, abiotic factors/wounding-responsive, endosperm specificity and fruit maturation/ripening regulatory motifs. The activities of the full length and six 5' deletion fragments of the SAD1 promoter were analyzed in transiently transformed oil palm tissues by quantitative β-glucuronidase (GUS) fluorometric assay. The highest SAD1 promoter activity was observed in the mesocarp followed by kernel and the least in the leaves. GUS activity in the D3 deletion construct (- 486 to + 108) was the highest, while the D2 (- 535 to + 108) gave the lowest suggesting the presence of negative cis-acting regulatory element(s) in the deleted - 535 to - 486 (49 bp). It was found that the 49-bp region binds to the nuclear protein extract from mesocarp but not from leaves in electrophoretic mobility shift assay (EMSA). Further fine-tuned analysis of this 49-bp region using truncated DNA led to the identification of GCTTCA as a novel motif in the SAD1 promoter. Interestingly, another known fruit ripening-related motif, LECPLEACS2 (TAAAAT) was found to be required for effective binding of the novel motif to the mesocarp nuclear protein extract.
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Affiliation(s)
- Farah Hanan Abu Hanifiah
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Siti Nor Akmar Abdullah
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
- Laboratory of Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
| | - Ashida Othman
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Noor Azmi Shaharuddin
- Laboratory of Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Halimi Mohd Saud
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Hasnul Abdul Hakim Hasnulhadi
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Umaiyal Munusamy
- Laboratory of Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
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Schex R, Lieb VM, Jiménez VM, Esquivel P, Schweiggert RM, Carle R, Steingass CB. HPLC-DAD-APCI/ESI-MS n analysis of carotenoids and α-tocopherol in Costa Rican Acrocomia aculeata fruits of varying maturity stages. Food Res Int 2018; 105:645-653. [DOI: 10.1016/j.foodres.2017.11.041] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/15/2017] [Accepted: 11/19/2017] [Indexed: 11/16/2022]
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46
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Sanusi NSNM, Rosli R, Halim MAA, Chan KL, Nagappan J, Azizi N, Amiruddin N, Tatarinova TV, Low ETL. PalmXplore: oil palm gene database. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:5098614. [PMID: 30239681 PMCID: PMC6146135 DOI: 10.1093/database/bay095] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 08/16/2018] [Indexed: 12/20/2022]
Abstract
A set of Elaeis guineensis genes had been generated by combining two gene prediction pipelines: Fgenesh++ developed by Softberry and Seqping by the Malaysian Palm Oil Board. PalmXplore was developed to provide a scalable data repository and a user-friendly search engine system to efficiently store, manage and retrieve the oil palm gene sequences and annotations. Information deposited in PalmXplore includes predicted genes, their genomic coordinates, as well as the annotations derived from external databases, such as Pfam, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. Information about genes related to important traits, such as those involved in fatty acid biosynthesis (FAB) and disease resistance, is also provided. The system offers Basic Local Alignment Search Tool homology search, where the results can be downloaded or visualized in the oil palm genome browser (MYPalmViewer). PalmXplore is regularly updated offering new features, improvements to genome annotation and new genomic sequences. The system is freely accessible at http://palmxplore.mpob.gov.my.
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Affiliation(s)
- Nik Shazana Nik Mohd Sanusi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Rozana Rosli
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia.,Genomics and Computational Biology Research Group, University of South Wales,Pontypridd, Wales, UK
| | - Mohd Amin Ab Halim
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Kuang-Lim Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Jayanthi Nagappan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Norazah Azizi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Nadzirah Amiruddin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Tatiana V Tatarinova
- Department of Biology, University of La Verne,1950 Third Street La Verne, CA, USA
| | - Eng-Ti Leslie Low
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia
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47
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Chan KL, Tatarinova TV, Rosli R, Amiruddin N, Azizi N, Halim MAA, Sanusi NSNM, Jayanthi N, Ponomarenko P, Triska M, Solovyev V, Firdaus-Raih M, Sambanthamurthi R, Murphy D, Low ETL. Evidence-based gene models for structural and functional annotations of the oil palm genome. Biol Direct 2017; 12:21. [PMID: 28886750 PMCID: PMC5591544 DOI: 10.1186/s13062-017-0191-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 08/07/2017] [Indexed: 11/13/2022] Open
Abstract
Background Oil palm is an important source of edible oil. The importance of the crop, as well as its long breeding cycle (10-12 years) has led to the sequencing of its genome in 2013 to pave the way for genomics-guided breeding. Nevertheless, the first set of gene predictions, although useful, had many fragmented genes. Classification and characterization of genes associated with traits of interest, such as those for fatty acid biosynthesis and disease resistance, were also limited. Lipid-, especially fatty acid (FA)-related genes are of particular interest for the oil palm as they specify oil yields and quality. This paper presents the characterization of the oil palm genome using different gene prediction methods and comparative genomics analysis, identification of FA biosynthesis and disease resistance genes, and the development of an annotation database and bioinformatics tools. Results Using two independent gene-prediction pipelines, Fgenesh++ and Seqping, 26,059 oil palm genes with transcriptome and RefSeq support were identified from the oil palm genome. These coding regions of the genome have a characteristic broad distribution of GC3 (fraction of cytosine and guanine in the third position of a codon) with over half the GC3-rich genes (GC3 ≥ 0.75286) being intronless. In comparison, only one-seventh of the oil palm genes identified are intronless. Using comparative genomics analysis, characterization of conserved domains and active sites, and expression analysis, 42 key genes involved in FA biosynthesis in oil palm were identified. For three of them, namely EgFABF, EgFABH and EgFAD3, segmental duplication events were detected. Our analysis also identified 210 candidate resistance genes in six classes, grouped by their protein domain structures. Conclusions We present an accurate and comprehensive annotation of the oil palm genome, focusing on analysis of important categories of genes (GC3-rich and intronless), as well as those associated with important functions, such as FA biosynthesis and disease resistance. The study demonstrated the advantages of having an integrated approach to gene prediction and developed a computational framework for combining multiple genome annotations. These results, available in the oil palm annotation database (http://palmxplore.mpob.gov.my), will provide important resources for studies on the genomes of oil palm and related crops. Reviewers This article was reviewed by Alexander Kel, Igor Rogozin, and Vladimir A. Kuznetsov. Electronic supplementary material The online version of this article (doi:10.1186/s13062-017-0191-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kuang-Lim Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.,Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Tatiana V Tatarinova
- Department of Biology, University of La Verne, La Verne, California, 91750, USA.,Spatial Sciences Institute, University of Southern California, Los Angeles, CA, 90089, USA
| | - Rozana Rosli
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.,Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, CF371DL, UK
| | - Nadzirah Amiruddin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Norazah Azizi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Mohd Amin Ab Halim
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Nik Shazana Nik Mohd Sanusi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Nagappan Jayanthi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Petr Ponomarenko
- Spatial Sciences Institute, University of Southern California, Los Angeles, CA, 90089, USA
| | - Martin Triska
- Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA, 90089, USA
| | - Victor Solovyev
- Softberry Inc., 116 Radio Circle, Suite 400, Mount Kisco, NY, 10549, USA
| | - Mohd Firdaus-Raih
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Ravigadevi Sambanthamurthi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Denis Murphy
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, CF371DL, UK
| | - Eng-Ti Leslie Low
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
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49
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Yeap WC, Lee FC, Shabari Shan DK, Musa H, Appleton DR, Kulaveerasingam H. WRI1-1, ABI5, NF-YA3 and NF-YC2 increase oil biosynthesis in coordination with hormonal signaling during fruit development in oil palm. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:97-113. [PMID: 28370622 DOI: 10.1111/tpj.13549] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 03/03/2017] [Accepted: 03/09/2017] [Indexed: 05/24/2023]
Abstract
The oil biosynthesis pathway must be tightly controlled to maximize oil yield. Oil palm accumulates exceptionally high oil content in its mesocarp, suggesting the existence of a unique fruit-specific fatty acid metabolism transcriptional network. We report the complex fruit-specific network of transcription factors responsible for modulation of oil biosynthesis genes in oil palm mesocarp. Transcriptional activation of EgWRI1-1 encoding a key master regulator that activates expression of oil biosynthesis genes, is activated by three ABA-responsive transcription factors, EgNF-YA3, EgNF-YC2 and EgABI5. Overexpression of EgWRI1-1 and its activators in Arabidopsis accelerated flowering, increased seed size and oil content, and altered expression levels of oil biosynthesis genes. Protein-protein interaction experiments demonstrated that EgNF-YA3 interacts directly with EgWRI1-1, forming a transcription complex with EgNF-YC2 and EgABI5 to modulate transcription of oil biosynthesis pathway genes. Furthermore, EgABI5 acts downstream of EgWRKY40, a repressor that interacts with EgWRKY2 to inhibit the transcription of oil biosynthesis genes. We showed that expression of these activators and repressors in oil biosynthesis can be induced by phytohormones coordinating fruit development in oil palm. We propose a model highlighting a hormone signaling network coordinating fruit development and fatty acid biosynthesis.
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Affiliation(s)
- Wan-Chin Yeap
- Sime Darby Plantation, Research and Development, Biotechnology and Breeding, Sime Darby Technology Centre Sdn. Bhd., Serdang, Selangor Darul Ehsan, 43400, Malaysia
| | - Fong-Chin Lee
- Sime Darby Plantation, Research and Development, Biotechnology and Breeding, Sime Darby Technology Centre Sdn. Bhd., Serdang, Selangor Darul Ehsan, 43400, Malaysia
| | - Dilip Kumar Shabari Shan
- Sime Darby Plantation, Research and Development, Biotechnology and Breeding, Sime Darby Technology Centre Sdn. Bhd., Serdang, Selangor Darul Ehsan, 43400, Malaysia
| | - Hamidah Musa
- Sime Darby Plantation, Research and Development, Biotechnology and Breeding, Sime Darby Technology Centre Sdn. Bhd., Serdang, Selangor Darul Ehsan, 43400, Malaysia
| | - David Ross Appleton
- Sime Darby Plantation, Research and Development, Biotechnology and Breeding, Sime Darby Technology Centre Sdn. Bhd., Serdang, Selangor Darul Ehsan, 43400, Malaysia
| | - Harikrishna Kulaveerasingam
- Sime Darby Plantation, Research and Development, Sime Darby Research Sdn Bhd, R&D Centre-Upstream, Pulau Carey, Kuala Langat, Selangor Darul Ehsan, 42960, Malaysia
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50
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Wong YC, Teh HF, Mebus K, Ooi TEK, Kwong QB, Koo KL, Ong CK, Mayes S, Chew FT, Appleton DR, Kulaveerasingam H. Differential gene expression at different stages of mesocarp development in high- and low-yielding oil palm. BMC Genomics 2017; 18:470. [PMID: 28637447 DOI: 10.1186/s12864-017-3855-3857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 06/09/2017] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND The oil yield trait of oil palm is expected to involve multiple genes, environmental influences and interactions. Many of the underlying mechanisms that contribute to oil yield are still poorly understood. In this study, we used a microarray approach to study the gene expression profiles of mesocarp tissue at different developmental stages, comparing genetically related high- and low- oil yielding palms to identify genes that contributed to the higher oil-yielding palm and might contribute to the wider genetic improvement of oil palm breeding populations. RESULTS A total of 3412 (2001 annotated) gene candidates were found to be significantly differentially expressed between high- and low-yielding palms at at least one of the different stages of mesocarp development evaluated. Gene Ontologies (GO) enrichment analysis identified 28 significantly enriched GO terms, including regulation of transcription, fatty acid biosynthesis and metabolic processes. These differentially expressed genes comprise several transcription factors, such as, bHLH, Dof zinc finger proteins and MADS box proteins. Several genes involved in glycolysis, TCA, and fatty acid biosynthesis pathways were also found up-regulated in high-yielding oil palm, among them; pyruvate dehydrogenase E1 component Subunit Beta (PDH), ATP-citrate lyase, β- ketoacyl-ACP synthases I (KAS I), β- ketoacyl-ACP synthases III (KAS III) and ketoacyl-ACP reductase (KAR). Sucrose metabolism-related genes such as Invertase, Sucrose Synthase 2 and Sucrose Phosphatase 2 were found to be down-regulated in high-yielding oil palms, compared to the lower yield palms. CONCLUSIONS Our findings indicate that a higher carbon flux (channeled through down-regulation of the Sucrose Synthase 2 pathway) was being utilized by up-regulated genes involved in glycolysis, TCA and fatty acid biosynthesis leading to enhanced oil production in the high-yielding oil palm. These findings are an important stepping stone to understand the processes that lead to production of high-yielding oil palms and have implications for breeding to maximize oil production.
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Affiliation(s)
- Yick Ching Wong
- Sime Darby Technology Centre Sdn Bhd, 1st Floor, Block B, UPM-MTDC Technology Centre III, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Huey Fang Teh
- Sime Darby Technology Centre Sdn Bhd, 1st Floor, Block B, UPM-MTDC Technology Centre III, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Katharina Mebus
- Centre for Research in Biotechnology for Agriculture (CEBAR), Level 3, Institute of Research Management & Monitoring (IPPP), Research Management & Innovation Comlex, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Tony Eng Keong Ooi
- Sime Darby Technology Centre Sdn Bhd, 1st Floor, Block B, UPM-MTDC Technology Centre III, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Qi Bin Kwong
- Sime Darby Technology Centre Sdn Bhd, 1st Floor, Block B, UPM-MTDC Technology Centre III, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Ka Loo Koo
- Sime Darby Technology Centre Sdn Bhd, 1st Floor, Block B, UPM-MTDC Technology Centre III, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Chuang Kee Ong
- European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Sean Mayes
- Plant and Crop Sciences, Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Fook Tim Chew
- Department of Biological Sciences, Faculty of Science, National University of Singapore, off Lower Kent Ridge Road, Singapore, 117543, Singapore
| | - David R Appleton
- Sime Darby Technology Centre Sdn Bhd, 1st Floor, Block B, UPM-MTDC Technology Centre III, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Harikrishna Kulaveerasingam
- Sime Darby Technology Centre Sdn Bhd, 1st Floor, Block B, UPM-MTDC Technology Centre III, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
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