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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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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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Linkage-based genome assembly improvement of oil palm (Elaeis guineensis). Sci Rep 2019; 9:6619. [PMID: 31036825 PMCID: PMC6488618 DOI: 10.1038/s41598-019-42989-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 04/12/2019] [Indexed: 01/01/2023] Open
Abstract
Meiotic crossovers in outbred species, such as oil palm (Elaeis guineensis Jacq., 2n = 32) contribute to allelic re-assortment in the genome. Such genetic variation is usually exploited in breeding to combine positive alleles for trait superiority. A good quality reference genome is essential for identifying the genetic factors underlying traits of interest through linkage or association studies. At the moment, an AVROS pisifera genome is publicly available for oil palm. Distribution and frequency of crossovers throughout chromosomes in different origins of oil palm are still unclear. Hence, an ultrahigh-density genomic linkage map of a commercial Deli dura x AVROS pisifera family was constructed using the OP200K SNP array, to evaluate the genetic alignment with the genome assembly. A total of 27,890 linked SNP markers generated a total map length of 1,151.7 cM and an average mapping interval of 0.04 cM. Nineteen linkage groups represented 16 pseudo-chromosomes of oil palm, with 61.7% of the mapped SNPs present in the published genome. Meanwhile, the physical map was also successfully extended from 658 Mb to 969 Mb by assigning unplaced scaffolds to the pseudo-chromosomes. A genic linkage map with major representation of sugar and lipid biosynthesis pathways was subsequently built for future studies on oil related quantitative trait loci (QTL). This study improves the current physical genome of the commercial oil palm, and provides important insights into its recombination landscape, eventually unlocking the full potential genome sequence-enabled biology for oil palm.
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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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Zhang L, Wu P, Lu W, Lü S. Molecular mechanism of the extended oil accumulation phase contributing to the high seed oil content for the genotype of tung tree (Vernicia fordii). BMC PLANT BIOLOGY 2018; 18:248. [PMID: 30340540 PMCID: PMC6195728 DOI: 10.1186/s12870-018-1458-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/02/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Oil from seeds of the tung tree (Vernicia fordii) has unique drying properties that are industrially important. We found that the extended oil accumulation period was related to the high seed oil content at maturity among tung tree population. In order to understand the molecular mechanism underlying the high oil content in tung tree seed, Tree H and L were adopted for the further investigation, with seed oil content of about 70 and 45%, respectively. We compared the transcriptomic changes of seed at various times during oil accumulation between the two trees. RESULTS Transcriptomes analysis revealed that many genes involved in glycolysis, fatty acid synthesis, and tri-acyl glyceride assembly still kept high expression in the late period of seed oil accumulation for Tree H only. Many genes in fatty acid degradation pathway were largely up regulated in the late period of seed oil accumulation for Tree L only. Four transcription factors related to fatty acid biosynthesis had different expression pattern in the seed oil accumulation period for the two trees. WRI1 was down regulated and kept the low expression in the late period of seed oil accumulation for the two trees. PII, LEC1 and LEC1-LIKE extended the high expression in the late period of seed oil accumulation in Tree H only. CONCLUSIONS The continued accumulation of oil in the late period of seed oil accumulation for Tree H was associated with relatively high expression of the relevant genes in glycolysis, fatty acid synthesis and tri-acyl glyceride assembly. PII, LEC1, and LEC1-LIKE rather than WRI1 should play an important role in the oil continual accumulation in the late period of seed oil accumulation in Tree H. This study provides novel insight into the variation in seed oil content and informs plant breeding strategies to maximize oil yield.
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Affiliation(s)
- Lingling Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, and Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 Hubei China
| | - Pan Wu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, and Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 Hubei China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Wenying Lu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, and Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 Hubei China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Shiyou Lü
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, and Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074 Hubei China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074 China
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Ruzlan N, Low YSJ, Win W, Azizah Musa N, Ong AL, Chew FT, Appleton D, Mohd Yusof H, Kulaveerasingam H. Key glycolytic branch influences mesocarp oil content in oil palm. Sci Rep 2017; 7:9626. [PMID: 28852058 PMCID: PMC5575415 DOI: 10.1038/s41598-017-10195-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/22/2017] [Indexed: 11/08/2022] Open
Abstract
The fructose-1,6-bisphosphate aldolase catalyzed glycolysis branch that forms dihydroxyacetone phosphate and glyceraldehyde-3-phosphate was identified as a key driver of increased oil synthesis in oil palm and was validated in Saccharomyces cerevisiae. Reduction in triose phosphate isomerase (TPI) activity in a yeast knockdown mutant resulted in 19% increase in lipid content, while yeast strains overexpressing oil palm fructose-1,6-bisphosphate aldolase (EgFBA) and glycerol-3-phosphate dehydrogenase (EgG3PDH) showed increased lipid content by 16% and 21%, respectively. Genetic association analysis on oil palm SNPs of EgTPI SD_SNP_000035801 and EgGAPDH SD_SNP_000041011 showed that palms harboring homozygous GG in EgTPI and heterozygous AG in EgGAPDH exhibited higher mesocarp oil content based on dry weight. In addition, AG genotype of the SNP of EgG3PDH SD_SNP_000008411 was associated with higher mean mesocarp oil content, whereas GG genotype of the EgFBA SNP SD_SNP_000007765 was favourable. Additive effects were observed with a combination of favourable alleles in TPI and FBA in Nigerian x AVROS population (family F7) with highest allele frequency GG.GG being associated with a mean increase of 3.77% (p value = 2.3E-16) oil content over the Family 1. An analogous effect was observed in yeast, where overexpressed EgFBA in TPI - resulted in a 30% oil increment. These results provide insights into flux balances in glycolysis leading to higher yield in mesocarp oil-producing fruit.
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Affiliation(s)
- Nurliyana Ruzlan
- Sime Darby Renewables, Sime Darby Plantation Sdn Bhd, Selangor, Malaysia.
| | - Yoke Sum Jaime Low
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor, Malaysia
| | - Wilonita Win
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor, Malaysia
| | - Noor Azizah Musa
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor, Malaysia
| | - Ai-Ling Ong
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor, Malaysia
| | - Fook-Tim Chew
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - David Appleton
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor, Malaysia
| | - Hirzun Mohd Yusof
- Sime Darby Renewables, Sime Darby Plantation Sdn Bhd, Selangor, Malaysia
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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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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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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. [PMID: 28637447 PMCID: PMC5480177 DOI: 10.1186/s12864-017-3855-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] 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. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3855-7) contains supplementary material, which is available to authorized users.
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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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Ooi TEK, Yeap WC, Daim LDJ, Ng BZ, Lee FC, Othman AM, Appleton DR, Chew FT, Kulaveerasingam H. Differential abundance analysis of mesocarp protein from high- and low-yielding oil palms associates non-oil biosynthetic enzymes to lipid biosynthesis. Proteome Sci 2015; 13:28. [PMID: 26617468 PMCID: PMC4661986 DOI: 10.1186/s12953-015-0085-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 11/22/2015] [Indexed: 12/04/2022] Open
Abstract
Background The oil palm Elaeis guineensis Jacq. which produces the highest yield per unit land area of the oil crops is the most important commercial oil crop in South East Asia. The fleshy mesocarp of oil palm fruit, where oil is mostly derived from, contains up to 90 % dry weight of oil (one of the most concentrated in plant tissues). Hence, there is attention given to gain insights into the processes of oil deposition in this oil rich tissue. For that purpose, two-dimensional differential gel electrophoresis (DIGE) coupled with western assays, were used here to analyze differential protein levels in genetically-related high-and low-yielding oil palm mesocarps. Results From the DIGE comparative analysis in combination with western analysis, 41 unique differentially accumulated proteins were discovered. Functional categorization of these proteins placed them in the metabolisms of lipid, carbohydrate, amino acids, energy, structural proteins, as well as in other functions. In particular, higher abundance of fructose-1,6-biphosphate aldolase combined with reduced level of triosephosphate isomerase and glyceraldehyde-3-phosphate dehydrogenase may be indicative of important flux balance changes in glycolysis, while amino acid metabolism also appeared to be closely linked with oil yield. Conclusions Forty-one proteins in several important biological pathways were identified as exhibiting differential in abundance at critical oil production stages. These confirm that oil yield is a complex trait involving the regulation of genes in multiple biological pathways. The results also provide insights into key control points of lipid biosynthesis in oil palm and can assist in the development of genetic markers for use in oil palm breeding programmes. Electronic supplementary material The online version of this article (doi:10.1186/s12953-015-0085-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tony Eng Keong Ooi
- Sime Darby Technology Centre Sdn. Bhd., UPM-MTDC Technology Centre III, Lebuh Silikon, Universiti Putra Malaysia, 1st Floor, Block B, 43400 Serdang, Selangor Malaysia
| | - Wan Chin Yeap
- Sime Darby Technology Centre Sdn. Bhd., UPM-MTDC Technology Centre III, Lebuh Silikon, Universiti Putra Malaysia, 1st Floor, Block B, 43400 Serdang, Selangor Malaysia
| | - Leona Daniela Jeffery Daim
- Sime Darby Technology Centre Sdn. Bhd., UPM-MTDC Technology Centre III, Lebuh Silikon, Universiti Putra Malaysia, 1st Floor, Block B, 43400 Serdang, Selangor Malaysia
| | - Boon Zean Ng
- Agro-Biotechnology Institute Malaysia, National Institutes of Biotechnology Malaysia, c/o MARDI Headquarters, 43400 Serdang, Selangor Malaysia
| | - Fong Chin Lee
- Sime Darby Technology Centre Sdn. Bhd., UPM-MTDC Technology Centre III, Lebuh Silikon, Universiti Putra Malaysia, 1st Floor, Block B, 43400 Serdang, Selangor Malaysia
| | - Ainul Masni Othman
- Sime Darby Technology Centre Sdn. Bhd., UPM-MTDC Technology Centre III, Lebuh Silikon, Universiti Putra Malaysia, 1st Floor, Block B, 43400 Serdang, Selangor Malaysia
| | - David Ross Appleton
- Sime Darby Technology Centre Sdn. Bhd., UPM-MTDC Technology Centre III, Lebuh Silikon, Universiti Putra Malaysia, 1st Floor, Block B, 43400 Serdang, Selangor Malaysia
| | - Fook Tim Chew
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Kent Ridge Road, Singapore, 117543 Singapore
| | - Harikrishna Kulaveerasingam
- Sime Darby Technology Centre Sdn. Bhd., UPM-MTDC Technology Centre III, Lebuh Silikon, Universiti Putra Malaysia, 1st Floor, Block B, 43400 Serdang, Selangor Malaysia
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Sood A, Chauhan RS. Regulation of FA and TAG biosynthesis pathway genes in endosperms and embryos of high and low oil content genotypes of Jatropha curcas L. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 94:253-67. [PMID: 26134579 DOI: 10.1016/j.plaphy.2015.06.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 06/05/2015] [Accepted: 06/17/2015] [Indexed: 05/22/2023]
Abstract
The rising demand for biofuels has raised concerns about selecting alternate and promising renewable energy crops which do not compete with food supply. Jatropha (Jatropha curcas L.), a non-edible energy crop of the family euphorbiaceae, has the potential of providing biodiesel feedstock due to the presence of high proportion of unsaturated fatty acids (75%) in seed oil which is mainly accumulated in endosperm and embryo. The molecular basis of seed oil biosynthesis machinery has been studied in J. curcas, however, what genetic differences contribute to differential oil biosynthesis and accumulation in genotypes varying for oil content is poorly understood. We investigated expression profile of 18 FA and TAG biosynthetic pathway genes in different developmental stages of embryo and endosperm from high (42%) and low (30%) oil content genotypes grown at two geographical locations. Most of the genes showed relatively higher expression in endosperms of high oil content genotype, whereas no significant difference was observed in endosperms versus embryos of low oil content genotype. The promoter regions of key genes from FA and TAG biosynthetic pathways as well as other genes implicated in oil accumulation were analyzed for regulatory elements and transcription factors specific to oil or lipid accumulation in plants such as Dof, CBF (LEC1), SORLIP, GATA and Skn-1_motif etc. Identification of key genes from oil biosynthesis and regulatory elements specific to oil deposition will be useful not only in dissecting the molecular basis of high oil content but also improving seed oil content through transgenic or molecular breeding approaches.
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Affiliation(s)
- Archit Sood
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan 173 215, H.P., India
| | - Rajinder Singh Chauhan
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan 173 215, H.P., India.
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