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Li X, Cai K, Zhang Q, Pei X, Chen S, Jiang L, Han Z, Zhao M, Li Y, Zhang X, Li Y, Zhang S, Chen S, Qu G, Tigabu M, Chiang VL, Sederoff R, Zhao X. The Manchurian Walnut Genome: Insights into Juglone and Lipid Biosynthesis. Gigascience 2022; 11:6619298. [PMID: 35764602 PMCID: PMC9239856 DOI: 10.1093/gigascience/giac057] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 03/20/2022] [Accepted: 05/24/2022] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Manchurian walnut (Juglans mandshurica Maxim.) is a tree with multiple industrial uses and medicinal properties in the Juglandaceae family (walnuts and hickories). J. mandshurica produces juglone, which is a toxic allelopathic agent and has potential utilization value. Furthermore, the seed of J. mandshurica is rich in various unsaturated fatty acids and has high nutritive value. FINDINGS Here, we present a high-quality chromosome-scale reference genome assembly and annotation for J. mandshurica (n = 16) with a contig N50 of 21.4 Mb by combining PacBio high-fidelity reads with high-throughput chromosome conformation capture data. The assembled genome has an estimated sequence size of 548.7 Mb and consists of 657 contigs, 623 scaffolds, and 40,453 protein-coding genes. In total, 60.99% of the assembled genome consists of repetitive sequences. Sixteen super-scaffolds corresponding to the 16 chromosomes were assembled, with a scaffold N50 length of 33.7 Mb and a BUSCO complete gene percentage of 98.3%. J. mandshurica displays a close sequence relationship with Juglans cathayensis, with a divergence time of 13.8 million years ago. Combining the high-quality genome, transcriptome, and metabolomics data, we constructed a gene-to-metabolite network and identified 566 core and conserved differentially expressed genes, which may be involved in juglone biosynthesis. Five CYP450 genes were found that may contribute to juglone accumulation. NAC, bZip, NF-YA, and NF-YC are positively correlated with the juglone content. Some candidate regulators (e.g., FUS3, ABI3, LEC2, and WRI1 transcription factors) involved in the regulation of lipid biosynthesis were also identified. CONCLUSIONS Our genomic data provide new insights into the evolution of the walnut genome and create a new platform for accelerating molecular breeding and improving the comprehensive utilization of these economically important tree species.
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Affiliation(s)
| | | | | | | | - Song Chen
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Luping Jiang
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Zhiming Han
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Minghui Zhao
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Yan Li
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Xinxin Zhang
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Yuxi Li
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Shikai Zhang
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Mulualem Tigabu
- Southern Swedish Forest Research Center, Faculty of Forest Science, Swedish University of Agricultural Sciences, Lomma SE-234 22, Sweden
| | - Vincent L Chiang
- State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Ronald Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Xiyang Zhao
- Correspondence address. Xiyang Zhao, E-mail:
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Tandukar Z, Chopra R, Frels K, Heim B, Marks MD, Anderson JA. Genetic dissection of seed characteristics in field pennycress via genome-wide association mapping studies. THE PLANT GENOME 2022; 15:e20211. [PMID: 35484973 DOI: 10.1002/tpg2.20211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
Field pennycress (Thlaspi arvense L.) is a new winter annual cash cover crop with high oil content and seed yield, excellent winter hardiness, early maturation, and resistance to most pests and diseases. It provides living cover on fallow croplands between summer seasons, and in doing so reduces nutrient leaching into water sources, mitigates soil erosion, and suppresses weed growth. The first ever genome-wide association study (GWAS) was conducted on a pennycress diversity panel to identify marker trait associations with important seed size and composition related traits. The entire population was phenotyped in three total environments over 2 yr, and seed area, length, width, thousand grain weight, total oil, and total protein were measured post-harvest with specialized high-throughput imaging and near-infrared spectroscopy. Basic unbiased linear prediction values were calculated for each trait. Seed size traits tended to have higher entry mean reliabilities (0.76-0.79) compared with oil content (0.51) and protein content (0.37). Genotyping-by-sequencing identified 33,606 high quality genome-wide single nucleotide polymorphism (SNPs) that were coupled with phenotypic data to perform GWAS for seed area, length, width, thousand grain weight, total oil, and total protein content. Fifty-nine total marker-trait associations were identified revealing genomic regions controlling each trait. The significant SNPs explained 0.06-0.18% of the total variance for that trait in our population. A list of candidate genes was identified based on their functional annotations and characterization in other species. Our results confirm that GWAS is an efficient strategy to identify significant marker-trait associations that can be incorporated into marker-assisted selection pipelines to accelerate pennycress breeding progress.
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Affiliation(s)
- Zenith Tandukar
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, Saint Paul, MN, USA
| | - Ratan Chopra
- Dep. of Plant and Microbial Biology, Univ. of Minnesota, Saint Paul, MN, USA
| | - Katherine Frels
- Dep. of Agronomy and Horticulture, Univ. of Nebraska, Lincoln, NE, USA
| | - Brett Heim
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, Saint Paul, MN, USA
| | - M David Marks
- Dep. of Plant and Microbial Biology, Univ. of Minnesota, Saint Paul, MN, USA
| | - James A Anderson
- Dep. of Agronomy and Plant Genetics, Univ. of Minnesota, Saint Paul, MN, USA
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Wang J, Singh SK, Geng S, Zhang S, Yuan L. Genome-wide analysis of glycerol-3-phosphate O-acyltransferase gene family and functional characterization of two cutin group GPATs in Brassica napus. PLANTA 2020; 251:93. [PMID: 32246349 DOI: 10.1007/s00425-020-03384-4] [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: 02/10/2020] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
Genome-wide identification, spatio-temporal expression analysis and functional characterization of selected Brassica napus GPATs highlight their roles in cuticular wax biosynthesis and defense against fungal pathogens. Glycerol-3-phosphate 1-O-acyltransferase (GPAT) is a key enzyme in the biosynthesis of glycerolipids, a major component of cellular membranes and extracellular protective layers, such as cuticles in plants. Brassica napus is an economically important crop and cultivated worldwide mostly for its edible oil. The B. napus GPATs (BnGPATs) are insufficiently characterized. Here, we performed genome-wide analysis to identify putative GPATs in B. napus and its diploid progenitors B. rapa and B oleracea. The 32 B. napus BnGPATs are phylogenetically divided into three major groups, cutin, suberin, and diverse ancient groups. Analysis of transcriptomes of different tissues and seeds at different developmental stages revealed the spatial and temporal expression profiles of BnGPATs. The yield and oil quality of B. napus are adversely affected by the necrotrophic fungus, Sclerotinia sclerotiorum. We showed that several BnGPATs, including cutin-related BnGPAT19 and 21, were upregulated in the S. sclerotiorum resistant line. RNAi-mediated suppression of BnGPAT19 and 21 in B. napus resulted in thinner cuticle, leading to rapid water and chlorophyll loss in toluidine blue staining and leaf bleaching assays. In addition, the RNAi plants also developed severe necrotic lesions following fungal inoculation compared to the wild-type plants, indicating that BnGPAT19 and 21 are likely involved in cuticular wax biosynthesis that is critical for initial pathogen defense. Taken together, we provided a comprehensive account of GPATs B. napus and characterized BnGPAT19 and 21 for their potential roles in cuticular wax biosynthesis and defense against fungal pathogens.
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Affiliation(s)
- Jingxue Wang
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China.
| | - Sanjay Kumar Singh
- Department of Plant and Soil Sciences and the Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Siyu Geng
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China
| | - Shanshan Zhang
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China
| | - Ling Yuan
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China.
- Department of Plant and Soil Sciences and the Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA.
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Comparative Transcriptome Analysis of Developing Seeds and Silique Wall Reveals Dynamic Transcription Networks for Effective Oil Production in Brassica napus L. Int J Mol Sci 2019; 20:ijms20081982. [PMID: 31018533 PMCID: PMC6515390 DOI: 10.3390/ijms20081982] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/09/2019] [Accepted: 04/19/2019] [Indexed: 02/07/2023] Open
Abstract
Vegetable oil is an essential constituent of the human diet and renewable raw material for industrial applications. Enhancing oil production by increasing seed oil content in oil crops is the most viable, environmentally friendly, and sustainable approach to meet the continuous demand for the supply of vegetable oil globally. An in-depth understanding of the gene networks involved in oil biosynthesis during seed development is a prerequisite for breeding high-oil-content varieties. Rapeseed (Brassica napus) is one of the most important oil crops cultivated on multiple continents, contributing more than 15% of the world’s edible oil supply. To understand the phasic nature of oil biosynthesis and the dynamic regulation of key pathways for effective oil accumulation in B. napus, comparative transcriptomic profiling was performed with developing seeds and silique wall (SW) tissues of two contrasting inbred lines with ~13% difference in seed oil content. Differentially expressed genes (DEGs) between high- and low-oil content lines were identified across six key developmental stages, and gene enrichment analysis revealed that genes related to photosynthesis, metabolism, carbohydrates, lipids, phytohormones, transporters, and triacylglycerol and fatty acid synthesis tended to be upregulated in the high-oil-content line. Differentially regulated DEG patterns were revealed for the control of metabolite and photosynthate production in SW and oil biosynthesis and accumulation in seeds. Quantitative assays of carbohydrates and hormones during seed development together with gene expression profiling of relevant pathways revealed their fundamental effects on effective oil accumulation. Our results thus provide insights into the molecular basis of high seed oil content (SOC) and a new direction for developing high-SOC rapeseed and other oil crops.
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Szczepaniak A, Książkiewicz M, Podkowiński J, Czyż KB, Figlerowicz M, Naganowska B. Legume Cytosolic and Plastid Acetyl-Coenzyme-A Carboxylase Genes Differ by Evolutionary Patterns and Selection Pressure Schemes Acting before and after Whole-Genome Duplications. Genes (Basel) 2018; 9:genes9110563. [PMID: 30469317 PMCID: PMC6265850 DOI: 10.3390/genes9110563] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/09/2018] [Accepted: 11/15/2018] [Indexed: 01/01/2023] Open
Abstract
Acetyl-coenzyme A carboxylase (ACCase, E.C.6.4.1.2) catalyzes acetyl-coenzyme A carboxylation to malonyl coenzyme A. Plants possess two distinct ACCases differing by cellular compartment and function. Plastid ACCase contributes to de novo fatty acid synthesis, whereas cytosolic enzyme to the synthesis of very long chain fatty acids, phytoalexins, flavonoids, and anthocyanins. The narrow leafed lupin (Lupinus angustifolius L.) represents legumes, a plant family which evolved by whole-genome duplications (WGDs). The study aimed on the contribution of these WGDs to the multiplication of ACCase genes and their further evolutionary patterns. The molecular approach involved bacterial artificial chromosome (BAC) library screening, fluorescent in situ hybridization, linkage mapping, and BAC sequencing. In silico analysis encompassed sequence annotation, comparative mapping, selection pressure calculation, phylogenetic inference, and gene expression profiling. Among sequenced legumes, the highest number of ACCase genes was identified in lupin and soybean. The most abundant plastid ACCase subunit genes were accB. ACCase genes in legumes evolved by WGDs, evidenced by shared synteny and Bayesian phylogenetic inference. Transcriptional activity of almost all copies was confirmed. Gene duplicates were conserved by strong purifying selection, however, positive selection occurred in Arachis (accB2) and Lupinus (accC) lineages, putatively predating the WGD event(s). Early duplicated accA and accB genes underwent transcriptional sub-functionalization.
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Affiliation(s)
- Anna Szczepaniak
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland.
| | - Michał Książkiewicz
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland.
| | - Jan Podkowiński
- Department of Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland.
| | - Katarzyna B Czyż
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland.
| | - Marek Figlerowicz
- Department of Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland.
| | - Barbara Naganowska
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznań, Poland.
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Wang J, Wang X, Geng S, Singh SK, Wang Y, Pattanaik S, Yuan L. Genome-wide identification of hexokinase gene family in Brassica napus: structure, phylogenetic analysis, expression, and functional characterization. PLANTA 2018; 248:171-182. [PMID: 29644447 DOI: 10.1007/s00425-018-2888-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 04/01/2018] [Indexed: 06/08/2023]
Abstract
Genome-wide identification, expression analysis, and functional characterization of previously uncharacterized hexokinase family of oil crop, Brassica napus, underscore the importance of this gene family in plant growth and development. In plants, the multi-gene family of dual-function hexokinases (HXKs) plays important roles in sugar metabolism and sensing that affect growth and development. Rapeseed (Brassica napus L.) is an important oil crop; however, little is known about the B. napus HXK gene family. We identified 19 putative HXKs in B. napus genome. B. rapa and B. oleracea, the two diploid progenitors of B. napus, contributed almost equally to the BnHXK genes. Phylogenetic analysis divided the 19 BnHXKs into four groups. The exon-intron structures of BnHXKs share high similarity to those of HXKs in Arabidopsis and rice. The group III and IV BnHXKs are highly expressed in roots, whereas group I members preferentially express in leaves. Analysis of seed transcriptomes at different developmental stages showed that most of group I and IV HXKs are highly expressed 2-weeks after pollination (2WAP), compared to 4WAP for group III. BnHKXs are differentially expressed in susceptible and tolerant B. napus cultivars after fungal infection, suggesting the possible involvement in defense response. We generated rapeseed RNAi lines for BnHXK9, a member of relatively less characterized group IV, by pollen-mediated gene transformation. The seedlings of BnHXK9-RNAi lines showed delayed growth compared to the wild type. The RNAi plants were dwarf with curly leaves, suggesting the involvement of BnHXK9 in plant development. Collectively, our findings provides a comprehensive account of BnHXK gene family in an important crop and a starting point for further elucidation of their roles in sugar metabolism and sensing, as well as plant growth and development.
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Affiliation(s)
- Jingxue Wang
- School of Life Sciences, Shanxi University, Taiyuan, 030006, Shanxi, China.
| | - Xiaomin Wang
- School of Life Sciences, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Siyu Geng
- School of Life Sciences, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Sanjay K Singh
- Department of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Yaohui Wang
- School of Life Sciences, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Sitakanta Pattanaik
- Department of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Ling Yuan
- School of Life Sciences, Shanxi University, Taiyuan, 030006, Shanxi, China.
- Department of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA.
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Ding J, Ruan C, Guan Y, Krishna P. Identification of microRNAs involved in lipid biosynthesis and seed size in developing sea buckthorn seeds using high-throughput sequencing. Sci Rep 2018; 8:4022. [PMID: 29507325 PMCID: PMC5838164 DOI: 10.1038/s41598-018-22464-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/23/2018] [Indexed: 12/20/2022] Open
Abstract
Sea buckthorn is a plant of medicinal and nutritional importance owing in part to the high levels of essential fatty acids, linoleic (up to 42%) and α-linolenic (up to 39%) acids in the seed oil. Sea buckthorn can produce seeds either via the sexual pathway or by apomixis. The seed development and maturation programs are critically dependent on miRNAs. To understand miRNA-mediated regulation of sea buckthorn seed development, eight small RNA libraries were constructed for deep sequencing from developing seeds of a low oil content line ‘SJ1’ and a high oil content line ‘XE3’. High-throughput sequencing identified 137 known miRNA from 27 families and 264 novel miRNAs. The potential targets of the identified miRNAs were predicted based on sequence homology. Nineteen (four known and 15 novel) and 22 (six known and 16 novel) miRNAs were found to be involved in lipid biosynthesis and seed size, respectively. An integrated analysis of mRNA and miRNA transcriptome and qRT-PCR identified some key miRNAs and their targets (miR164d-ARF2, miR168b-Δ9D, novelmiRNA-108-ACC, novelmiRNA-23-GPD1, novelmiRNA-58-DGAT1, and novelmiRNA-191-DGAT2) potentially involved in seed size and lipid biosynthesis of sea buckthorn seed. These results indicate the potential importance of miRNAs in regulating lipid biosynthesis and seed size in sea buckthorn.
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Affiliation(s)
- Jian Ding
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, China
| | - Chengjiang Ruan
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian, 116600, China.
| | - Ying Guan
- Institute of Berries, Heilongjiang Academy of Agricultural Sciences, Suiling, 152200, China
| | - Priti Krishna
- School of Science and Health, Western Sydney University, Penrith, NSW 2751, Australia
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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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