251
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Xiao Y, Zhou L, Xia W, Mason AS, Yang Y, Ma Z, Peng M. Exploiting transcriptome data for the development and characterization of gene-based SSR markers related to cold tolerance in oil palm (Elaeis guineensis). BMC PLANT BIOLOGY 2014; 14:384. [PMID: 25522814 PMCID: PMC4279980 DOI: 10.1186/s12870-014-0384-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 12/12/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND The oil palm (Elaeis guineensis, 2n = 32) has the highest oil yield of any crop species, as well as comprising the richest dietary source of provitamin A. For the tropical species, the best mean growth temperature is about 27°C, with a minimal growth temperature of 15°C. Hence, the plantation area is limited into the geographical ranges of 10°N to 10°S. Enhancing cold tolerance capability will increase the total cultivation area and subsequently oil productivity of this tropical species. Developing molecular markers related to cold tolerance would be helpful for molecular breeding of cold tolerant Elaeis guineensis. RESULTS In total, 5791 gene-based SSRs were identified in 51,452 expressed sequences from Elaeis guineensis transcriptome data: approximately one SSR was detected per 10 expressed sequences. Of these 5791 gene-based SSRs, 916 were derived from expressed sequences up- or down-regulated at least two-fold in response to cold stress. A total of 182 polymorphic markers were developed and characterized from 442 primer pairs flanking these cold-responsive SSR repeats. The polymorphic information content (PIC) of these polymorphic SSR markers across 24 lines of Elaeis guineensis varied from 0.08 to 0.65 (mean = 0.31 ± 0.12). Using in-silico mapping, 137 (75.3%) of the 182 polymorphic SSR markers were located onto the 16 Elaeis guineensis chromosomes. Total coverage of 473 Mbp was achieved, with an average physical distance of 3.4 Mbp between adjacent markers (range 96 bp - 20.8 Mbp). Meanwhile, Comparative analysis of transcriptome under cold stress revealed that one ICE1 putative ortholog, five CBF putative orthologs, 19 NAC transcription factors and four cold-induced orhologs were up-regulated at least two fold in response to cold stress. Interestingly, 5' untranslated region of both Unigene21287 (ICE1) and CL2628.Contig1 (NAC) both contained an SSR markers. CONCLUSIONS In the present study, a series of SSR markers were developed based on sequences differentially expressed in response to cold stress. These EST-SSR markers would be particularly useful for gene mapping and population structure analysis in Elaeis guineensis. Meanwhile, the EST-SSR loci were inducible expressed in response to low temperature, which may have potential application in identifying trait-associated markers in oil palm in the future.
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Affiliation(s)
- Yong Xiao
- />Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan 571339 P.R. China
| | - Lixia Zhou
- />Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan 571339 P.R. China
| | - Wei Xia
- />Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan 571339 P.R. China
| | - Annaliese S Mason
- />School of Agriculture and Food Sciences and Centre for Integrative Legume Research, the University of Queensland, 4072 Brisbane, Australia
| | - Yaodong Yang
- />Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan 571339 P.R. China
| | - Zilong Ma
- />Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, Hainan 571101 P. R. China
| | - Ming Peng
- />Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, Hainan 571101 P. R. China
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252
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Somyong S, Poopear S, Jomchai N, Uthaipaisanwong P, Ruang-areerate P, Sangsrakru D, Sonthirod C, Ukoskit K, Tragoonrung S, Tangphatsornruang S. The AKR gene family and modifying sex ratios in palms through abiotic stress responsiveness. Funct Integr Genomics 2014; 15:349-62. [DOI: 10.1007/s10142-014-0423-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/17/2014] [Accepted: 11/24/2014] [Indexed: 11/29/2022]
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253
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Expression Comparison of Oil Biosynthesis Genes in Oil Palm Mesocarp Tissue Using Custom Array. MICROARRAYS 2014; 3:263-81. [PMID: 27600348 PMCID: PMC4979054 DOI: 10.3390/microarrays3040263] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 09/22/2014] [Accepted: 11/03/2014] [Indexed: 11/20/2022]
Abstract
Gene expression changes that occur during mesocarp development are a major research focus in oil palm research due to the economic importance of this tissue and the relatively rapid increase in lipid content to very high levels at fruit ripeness. Here, we report the development of a transcriptome-based 105,000-probe oil palm mesocarp microarray. The expression of genes involved in fatty acid (FA) and triacylglycerol (TAG) assembly, along with the tricarboxylic acid cycle (TCA) and glycolysis pathway at 16 Weeks After Anthesis (WAA) exhibited significantly higher signals compared to those obtained from a cross-species hybridization to the Arabidopsis (p-value < 0.01), and rice (p-value < 0.01) arrays. The oil palm microarray data also showed comparable correlation of expression (r2 = 0.569, p < 0.01) throughout mesocarp development to transcriptome (RNA sequencing) data, and improved correlation over quantitative real-time PCR (qPCR) (r2 = 0.721, p < 0.01) of the same RNA samples. The results confirm the advantage of the custom microarray over commercially available arrays derived from model species. We demonstrate the utility of this custom microarray to gain a better understanding of gene expression patterns in the oil palm mesocarp that may lead to increasing future oil yield.
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254
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Jazayeri SM, Melgarejo-Muñoz LM, Romero HM. RNA-SEQ: A GLANCE AT TECHNOLOGIES AND METHODOLOGIES. ACTA BIOLÓGICA COLOMBIANA 2014. [DOI: 10.15446/abc.v20n2.43639] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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255
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Meerow AW, Noblick L, Salas-Leiva DE, Sanchez V, Francisco-Ortega J, Jestrow B, Nakamura K. Phylogeny and historical biogeography of the cocosoid palms (Arecaceae, Arecoideae, Cocoseae) inferred from sequences of six WRKY gene family loci. Cladistics 2014; 31:509-534. [DOI: 10.1111/cla.12100] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Alan W. Meerow
- USDA-ARS-SHRS-National Germplasm Repository; 13601 Old Cutler Rd. Miami FL 33158 USA
| | - Larry Noblick
- Montgomery Botanical Center; 11901 Old Cutler Rd. Coral Gables FL 33156 USA
| | - Dayana E. Salas-Leiva
- USDA-ARS-SHRS-National Germplasm Repository; 13601 Old Cutler Rd. Miami FL 33158 USA
- Montgomery Botanical Center; 11901 Old Cutler Rd. Coral Gables FL 33156 USA
- Department of Biological Sciences; Florida International University; 11200 SW 8th St. Miami FL 33199 USA
| | - Vanessa Sanchez
- USDA-ARS-SHRS-National Germplasm Repository; 13601 Old Cutler Rd. Miami FL 33158 USA
| | - Javier Francisco-Ortega
- Department of Biological Sciences; Florida International University; 11200 SW 8th St. Miami FL 33199 USA
- Kushlan Tropical Science Institute; Fairchild Tropical Botanical Garden; 10901 Old Cutler Rd. Miami FL 33156 USA
| | - Brett Jestrow
- Kushlan Tropical Science Institute; Fairchild Tropical Botanical Garden; 10901 Old Cutler Rd. Miami FL 33156 USA
| | - Kyoko Nakamura
- USDA-ARS-SHRS-National Germplasm Repository; 13601 Old Cutler Rd. Miami FL 33158 USA
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256
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Carrasco LR, Larrosa C, Milner-Gulland EJ, Edwards DP. Conservation. A double-edged sword for tropical forests. Science 2014; 346:38-40. [PMID: 25278600 DOI: 10.1126/science.1256685] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- L R Carrasco
- Department of Biological Sciences, National University of Singapore, 117543 Singapore
| | - C Larrosa
- Department of Biological Sciences, National University of Singapore, 117543 Singapore. Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire SL5 7PY, UK.
| | - E J Milner-Gulland
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire SL5 7PY, UK
| | - D P Edwards
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
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257
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Alves AA, Pereira VM, Leão AP, Formigheri EF, de Capdeville G, Souza Junior MT. Advancing palm genomics by developing a high-density battery of molecular markers for Elaeis oleifera for future downstream applications. BMC Proc 2014. [PMCID: PMC4204137 DOI: 10.1186/1753-6561-8-s4-p96] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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258
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McClure KA, Sawler J, Gardner KM, Money D, Myles S. Genomics: a potential panacea for the perennial problem. AMERICAN JOURNAL OF BOTANY 2014; 101:1780-90. [PMID: 25326620 DOI: 10.3732/ajb.1400143] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Perennial crops represent important fresh and processed food sources worldwide, but advancements in breeding perennials are often impeded due to their very nature. The perennial crops we rely on most for food take several years to reach production maturity and require large spaces to grow, which make breeding new cultivars costly compared with most annual crops. Because breeding perennials is inefficient and expensive, they are often grown in monocultures consisting of small numbers of elite cultivars that are vegetatively propagated for decades or even centuries. This practice puts many perennial crops at risk for calamity since they remain stationary in the face of evolving pest and disease pressures. Although there is tremendous genetic diversity available to them, perennial crop breeders often struggle to generate commercially successful cultivars in a timely and cost-effective manner because of the high costs of breeding. Moreover, consumers often expect the same cultivars to be available indefinitely, and there is often little or no incentive for growers and retailers to take the risk of adopting new cultivars. While genomics studies linking DNA variants to commercially important traits have been performed in diverse perennial crops, the translation of these studies into accelerated breeding of improved cultivars has been limited. Here we explain the "perennial problem" in detail and demonstrate how modern genomics tools can significantly improve the cost effectiveness of breeding perennial crops and thereby prevent crucial food sources from succumbing to the perils of perpetual propagation.
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Affiliation(s)
- Kendra A McClure
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Jason Sawler
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
| | - Kyle M Gardner
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
| | - Daniel Money
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
| | - Sean Myles
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
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259
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De novo transcriptome sequence assembly from coconut leaves and seeds with a focus on factors involved in RNA-directed DNA methylation. G3-GENES GENOMES GENETICS 2014; 4:2147-57. [PMID: 25193496 PMCID: PMC4232540 DOI: 10.1534/g3.114.013409] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Coconut palm (Cocos nucifera) is a symbol of the tropics and a source of numerous edible and nonedible products of economic value. Despite its nutritional and industrial significance, coconut remains under-represented in public repositories for genomic and transcriptomic data. We report de novo transcript assembly from RNA-seq data and analysis of gene expression in seed tissues (embryo and endosperm) and leaves of a dwarf coconut variety. Assembly of 10 GB sequencing data for each tissue resulted in 58,211 total unigenes in embryo, 61,152 in endosperm, and 33,446 in leaf. Within each unigene pool, 24,857 could be annotated in embryo, 29,731 could be annotated in endosperm, and 26,064 could be annotated in leaf. A KEGG analysis identified 138, 138, and 139 pathways, respectively, in transcriptomes of embryo, endosperm, and leaf tissues. Given the extraordinarily large size of coconut seeds and the importance of small RNA-mediated epigenetic regulation during seed development in model plants, we used homology searches to identify putative homologs of factors required for RNA-directed DNA methylation in coconut. The findings suggest that RNA-directed DNA methylation is important during coconut seed development, particularly in maturing endosperm. This dataset will expand the genomics resources available for coconut and provide a foundation for more detailed analyses that may assist molecular breeding strategies aimed at improving this major tropical crop.
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260
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Camillo J, Leão AP, Alves AA, Formighieri EF, Azevedo ALS, Nunes JD, de Capdeville G, de A Mattos JK, Souza MT. Reassessment of the Genome Size in Elaeis guineensis and Elaeis oleifera, and Its Interspecific Hybrid. GENOMICS INSIGHTS 2014; 7:13-22. [PMID: 26203259 PMCID: PMC4504075 DOI: 10.4137/gei.s15522] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/11/2014] [Accepted: 05/11/2014] [Indexed: 11/13/2022]
Abstract
Aiming at generating a comprehensive genomic database on Elaeis spp., our group is leading several R&D initiatives with Elaeis guineensis (African oil palm) and Elaeis oleifera (American oil palm), including the whole-genome sequencing of the last. Genome size estimates currently available for this genus are controversial, as they indicate that American oil palm genome is about half the size of the African oil palm genome and that the genome of the interspecific hybrid is bigger than both the parental species genomes. We estimated the genome size of three E. guineensis genotypes, five E. oleifera genotypes, and two interspecific hybrids genotypes. On average, the genome size of E. guineensis is 4.32 ± 0.173 pg, while that of E. oleifera is 4.43 ± 0.018 pg. This indicates that both genomes are similar in size, even though E. oleifera is in fact bigger. As expected, the hybrid genome size is around the average of the two genomes, 4.40 ± 0.016 pg. Additionally, we demonstrate that both species present around 38% of GC content. As our results contradict the currently available data on Elaeis spp. genome sizes, we propose that the actual genome size of the Elaeis species is around 4 pg and that American oil palm possesses a larger genome than African oil palm.
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Affiliation(s)
- Julceia Camillo
- Laboratory of Genetics and Biotechnology, Embrapa Agroenergy, Brasília, DF, Brazil
- Faculty of Agronomy and Veterinary Medicine, University of Brasilia, Brasília, DF, Brazil
| | - André P Leão
- Laboratory of Genetics and Biotechnology, Embrapa Agroenergy, Brasília, DF, Brazil
| | - Alexandre A Alves
- Laboratory of Genetics and Biotechnology, Embrapa Agroenergy, Brasília, DF, Brazil
| | | | - Ana LS Azevedo
- Laboratory of Plant Genetics, Embrapa Dairy Cattle, Juiz de Fora, MG, Brazil
| | - Juliana D Nunes
- Laboratory of Plant Genetics, Embrapa Dairy Cattle, Juiz de Fora, MG, Brazil
| | - Guy de Capdeville
- Laboratory of Genetics and Biotechnology, Embrapa Agroenergy, Brasília, DF, Brazil
| | - Jean K de A Mattos
- Faculty of Agronomy and Veterinary Medicine, University of Brasilia, Brasília, DF, Brazil
| | - Manoel T Souza
- Laboratory of Genetics and Biotechnology, Embrapa Agroenergy, Brasília, DF, Brazil
- Graduate Program in Plant Biotechnology, Federal University of Lavras, Lavras, MG, Brazil
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261
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Ma B, Luo Y, Jia L, Qi X, Zeng Q, Xiang Z, He N. Genome-wide identification and expression analyses of cytochrome P450 genes in mulberry (Morus notabilis). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:887-901. [PMID: 24304637 DOI: 10.1111/jipb.12141] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 12/01/2013] [Indexed: 05/13/2023]
Abstract
Cytochrome P450s play critical roles in the biosynthesis of physiologically important compounds in plants. These compounds often act as defense toxins to prevent herbivory. In the present study, a total of 174 P450 genes of mulberry (Morus notabilis C.K.Schn) were identified based on bioinformatics analyses. These mulberry P450 genes were divided into nine clans and 47 families and were found to be expressed in a tissue-preferential manner. These genes were compared to the P450 genes in Arabidopsis thaliana. Families CYP80, CYP92, CYP728, CYP733, CYP736, and CYP749 were found to exist in mulberry, and they may play important roles in the biosynthesis of mulberry secondary metabolites. Analyses of the functional and metabolic pathways of these genes indicated that mulberry P450 genes may participate in the metabolism of lipids, other secondary metabolites, xenobiotics, amino acids, cofactors, vitamins, terpenoids, and polyketides. These results provide a foundation for understanding of the structures and biological functions of mulberry P450 genes.
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Affiliation(s)
- Bi Ma
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400715, China
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262
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Chalhoub B, Denoeud F, Liu S, Parkin IAP, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, Corréa M, Da Silva C, Just J, Falentin C, Koh CS, Le Clainche I, Bernard M, Bento P, Noel B, Labadie K, Alberti A, Charles M, Arnaud D, Guo H, Daviaud C, Alamery S, Jabbari K, Zhao M, Edger PP, Chelaifa H, Tack D, Lassalle G, Mestiri I, Schnel N, Le Paslier MC, Fan G, Renault V, Bayer PE, Golicz AA, Manoli S, Lee TH, Thi VHD, Chalabi S, Hu Q, Fan C, Tollenaere R, Lu Y, Battail C, Shen J, Sidebottom CHD, Wang X, Canaguier A, Chauveau A, Bérard A, Deniot G, Guan M, Liu Z, Sun F, Lim YP, Lyons E, Town CD, Bancroft I, Wang X, Meng J, Ma J, Pires JC, King GJ, Brunel D, Delourme R, Renard M, Aury JM, Adams KL, Batley J, Snowdon RJ, Tost J, Edwards D, Zhou Y, Hua W, Sharpe AG, Paterson AH, Guan C, Wincker P. Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 2014; 345:950-3. [PMID: 25146293 DOI: 10.1126/science.1253435] [Citation(s) in RCA: 1408] [Impact Index Per Article: 140.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.
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Affiliation(s)
- Boulos Chalhoub
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France.
| | - France Denoeud
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France. Université d'Evry Val d'Essone, UMR 8030, CP5706, Evry, France. Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada.
| | - Haibao Tang
- J. Craig Venter Institute, Rockville, MD 20850, USA. Center for Genomics and Biotechnology, Fujian Agriculture and Forestry, University, Fuzhou 350002, Fujian Province, China
| | - Xiyin Wang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA. Center of Genomics and Computational Biology, School of Life Sciences, Hebei United University, Tangshan, Hebei 063000, China
| | - Julien Chiquet
- Laboratoire de Mathématiques et Modélisation d'Evry-UMR 8071 CNRS/Université d'Evry val d'Essonne-USC INRA, Evry, France
| | - Harry Belcram
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Chaobo Tong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Birgit Samans
- Department of Plant Breeding, Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Margot Corréa
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Corinne Da Silva
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Jérémy Just
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Cyril Falentin
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Chu Shin Koh
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Isabelle Le Clainche
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Maria Bernard
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Pascal Bento
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Benjamin Noel
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Adriana Alberti
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Mathieu Charles
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Dominique Arnaud
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Hui Guo
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Christian Daviaud
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91000 Evry, France
| | - Salman Alamery
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Kamel Jabbari
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France. Cologne Center for Genomics, University of Cologne, Weyertal 115b, 50931 Köln, Germany
| | - Meixia Zhao
- Department of Agronomy, Purdue University, WSLR Building B018, West Lafayette, IN 47907, USA
| | - Patrick P Edger
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Houda Chelaifa
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - David Tack
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Gilles Lassalle
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Imen Mestiri
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Nicolas Schnel
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Marie-Christine Le Paslier
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Guangyi Fan
- Beijing Genome Institute-Shenzhen, Shenzhen 518083, China
| | - Victor Renault
- Fondation Jean Dausset-Centre d'Étude du Polymorphisme Humain, 27 rue Juliette Dodu, 75010 Paris, France
| | - Philippe E Bayer
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Agnieszka A Golicz
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Sahana Manoli
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Tae-Ho Lee
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Vinh Ha Dinh Thi
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Smahane Chalabi
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Qiong Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Reece Tollenaere
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Yunhai Lu
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Christophe Battail
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | | | - Xinfa Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Aurélie Canaguier
- Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Aurélie Chauveau
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Aurélie Bérard
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Gwenaëlle Deniot
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Mei Guan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Zhongsong Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Fengming Sun
- Beijing Genome Institute-Shenzhen, Shenzhen 518083, China
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon-305764, South Korea
| | - Eric Lyons
- School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ, USA
| | | | - Ian Bancroft
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jianxin Ma
- Department of Agronomy, Purdue University, WSLR Building B018, West Lafayette, IN 47907, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | - Dominique Brunel
- INRA, Etude du Polymorphisme des Génomes Végétaux, US1279, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Régine Delourme
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Michel Renard
- INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP) UMR1349, BP35327, 35653 Le Rheu Cedex, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France
| | - Keith L Adams
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Jacqueline Batley
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia. School of Plant Biology, University of Western Australia, WA 6009, Australia
| | - Rod J Snowdon
- Department of Plant Breeding, Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Jorg Tost
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-IG, 2 rue Gaston Crémieux, 91000 Evry, France
| | - David Edwards
- Australian Centre for Plant Functional Genomics, School of Agriculture and Food Sciences, University of Queensland, St. Lucia, QLD 4072, Australia. School of Plant Biology, University of Western Australia, WA 6009, Australia.
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
| | - Wei Hua
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of People's Republic of China, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Andrew G Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada.
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA.
| | - Chunyun Guan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China.
| | - Patrick Wincker
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, BP5706, 91057 Evry, France. Université d'Evry Val d'Essone, UMR 8030, CP5706, Evry, France. Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France.
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Jiao Y, Li J, Tang H, Paterson AH. Integrated syntenic and phylogenomic analyses reveal an ancient genome duplication in monocots. THE PLANT CELL 2014; 26:2792-802. [PMID: 25082857 PMCID: PMC4145114 DOI: 10.1105/tpc.114.127597] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/03/2014] [Accepted: 07/10/2014] [Indexed: 05/18/2023]
Abstract
Unraveling widespread polyploidy events throughout plant evolution is a necessity for inferring the impacts of whole-genome duplication (WGD) on speciation, functional innovations, and to guide identification of true orthologs in divergent taxa. Here, we employed an integrated syntenic and phylogenomic analyses to reveal an ancient WGD that shaped the genomes of all commelinid monocots, including grasses, bromeliads, bananas (Musa acuminata), ginger, palms, and other plants of fundamental, agricultural, and/or horticultural interest. First, comprehensive phylogenomic analyses revealed 1421 putative gene families that retained ancient duplication shared by Musa (Zingiberales) and grass (Poales) genomes, indicating an ancient WGD in monocots. Intergenomic synteny blocks of Musa and Oryza were investigated, and 30 blocks were shown to be duplicated before Musa-Oryza divergence an estimated 120 to 150 million years ago. Synteny comparisons of four monocot (rice [Oryza sativa], sorghum [Sorghum bicolor], banana, and oil palm [Elaeis guineensis]) and two eudicot (grape [Vitis vinifera] and sacred lotus [Nelumbo nucifera]) genomes also support this additional WGD in monocots, herein called Tau (τ). Integrating synteny and phylogenomic comparisons achieves better resolution of ancient polyploidy events than either approach individually, a principle that is exemplified in the disambiguation of a WGD series of rho (ρ)-sigma (σ)-tau (τ) in the grass lineages that echoes the alpha (α)-beta (β)-gamma (γ) series previously revealed in the Arabidopsis thaliana lineage.
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Affiliation(s)
- Yuannian Jiao
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
| | - Jingping Li
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602 Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602
| | - Haibao Tang
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province 350002, China J. Craig Venter Institute, Rockville, Maryland 20850
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602
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264
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Singh R, Low ETL, Ooi LCL, Ong-Abdullah M, Nookiah R, Ting NC, Marjuni M, Chan PL, Ithnin M, Manaf MAA, Nagappan J, Chan KL, Rosli R, Halim MA, Azizi N, Budiman MA, Lakey N, Bacher B, Van Brunt A, Wang C, Hogan M, He D, MacDonald JD, Smith SW, Ordway JM, Martienssen RA, Sambanthamurthi R. The oil palm VIRESCENS gene controls fruit colour and encodes a R2R3-MYB. Nat Commun 2014; 5:4106. [PMID: 24978855 PMCID: PMC4078410 DOI: 10.1038/ncomms5106] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 05/13/2014] [Indexed: 11/17/2022] Open
Abstract
Oil palm, a plantation crop of major economic importance in Southeast Asia, is the predominant source of edible oil worldwide. We report the identification of the VIRESCENS (VIR) gene, which controls fruit exocarp colour and is an indicator of ripeness. VIR is a R2R3-MYB transcription factor with homology to Lilium LhMYB12 and similarity to Arabidopsis PRODUCTION OF ANTHOCYANIN PIGMENT1 (PAP1). We identify five independent mutant alleles of VIR in over 400 accessions from sub-Saharan Africa that account for the dominant-negative virescens phenotype. Each mutation results in premature termination of the carboxy-terminal domain of VIR, resembling McClintock’s C1-I allele in maize. The abundance of alleles likely reflects cultural practices, by which fruits were venerated for magical and medicinal properties. The identification of VIR will allow selection of the trait at the seed or early-nursery stage, 3-6 years before fruits are produced, greatly advancing introgression into elite breeding material. Fruit colour is a trait that affects the harvesting, and therefore oil yield, of the economically important oil palm. Here, the authors identify a gene that may control fruit colour in the oil palm and suggest that selection for this gene during early development could advance the breeding potential of this important crop.
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Affiliation(s)
- Rajinder Singh
- Malaysian Palm Oil Board, Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Eng-Ti Leslie Low
- Malaysian Palm Oil Board, Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Leslie Cheng-Li Ooi
- Malaysian Palm Oil Board, Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Meilina Ong-Abdullah
- Malaysian Palm Oil Board, Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Rajanaidu Nookiah
- Malaysian Palm Oil Board, Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Ngoot-Chin Ting
- Malaysian Palm Oil Board, Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Marhalil Marjuni
- Malaysian Palm Oil Board, Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Pek-Lan Chan
- Malaysian Palm Oil Board, Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Maizura Ithnin
- Malaysian Palm Oil Board, Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Mohd Arif Abdul Manaf
- Malaysian Palm Oil Board, Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Jayanthi Nagappan
- Malaysian Palm Oil Board, Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Kuang-Lim Chan
- Malaysian Palm Oil Board, Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Rozana Rosli
- Malaysian Palm Oil Board, Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Mohd Amin Halim
- Malaysian Palm Oil Board, Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Norazah Azizi
- Malaysian Palm Oil Board, Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | | | - Nathan Lakey
- Orion Genomics, 4041 Forest Park Ave., St. Louis, Missouri 63108, USA
| | - Blaire Bacher
- Orion Genomics, 4041 Forest Park Ave., St. Louis, Missouri 63108, USA
| | - Andrew Van Brunt
- Orion Genomics, 4041 Forest Park Ave., St. Louis, Missouri 63108, USA
| | - Chunyan Wang
- Orion Genomics, 4041 Forest Park Ave., St. Louis, Missouri 63108, USA
| | - Michael Hogan
- Orion Genomics, 4041 Forest Park Ave., St. Louis, Missouri 63108, USA
| | - Dong He
- Orion Genomics, 4041 Forest Park Ave., St. Louis, Missouri 63108, USA
| | - Jill D MacDonald
- Orion Genomics, 4041 Forest Park Ave., St. Louis, Missouri 63108, USA
| | - Steven W Smith
- Orion Genomics, 4041 Forest Park Ave., St. Louis, Missouri 63108, USA
| | - Jared M Ordway
- Orion Genomics, 4041 Forest Park Ave., St. Louis, Missouri 63108, USA
| | - Robert A Martienssen
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Ravigadevi Sambanthamurthi
- Malaysian Palm Oil Board, Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
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265
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Chan PL, Rose RJ, Abdul Murad AM, Zainal Z, Leslie Low ET, Ooi LCL, Ooi SE, Yahya S, Singh R. Evaluation of reference genes for quantitative real-time PCR in oil palm elite planting materials propagated by tissue culture. PLoS One 2014; 9:e99774. [PMID: 24927412 PMCID: PMC4057393 DOI: 10.1371/journal.pone.0099774] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 05/19/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The somatic embryogenesis tissue culture process has been utilized to propagate high yielding oil palm. Due to the low callogenesis and embryogenesis rates, molecular studies were initiated to identify genes regulating the process, and their expression levels are usually quantified using reverse transcription quantitative real-time PCR (RT-qPCR). With the recent release of oil palm genome sequences, it is crucial to establish a proper strategy for gene analysis using RT-qPCR. Selection of the most suitable reference genes should be performed for accurate quantification of gene expression levels. RESULTS In this study, eight candidate reference genes selected from cDNA microarray study and literature review were evaluated comprehensively across 26 tissue culture samples using RT-qPCR. These samples were collected from two tissue culture lines and media treatments, which consisted of leaf explants cultures, callus and embryoids from consecutive developmental stages. Three statistical algorithms (geNorm, NormFinder and BestKeeper) confirmed that the expression stability of novel reference genes (pOP-EA01332, PD00380 and PD00569) outperformed classical housekeeping genes (GAPDH, NAD5, TUBULIN, UBIQUITIN and ACTIN). PD00380 and PD00569 were identified as the most stably expressed genes in total samples, MA2 and MA8 tissue culture lines. Their applicability to validate the expression profiles of a putative ethylene-responsive transcription factor 3-like gene demonstrated the importance of using the geometric mean of two genes for normalization. CONCLUSIONS Systematic selection of the most stably expressed reference genes for RT-qPCR was established in oil palm tissue culture samples. PD00380 and PD00569 were selected for accurate and reliable normalization of gene expression data from RT-qPCR. These data will be valuable to the research associated with the tissue culture process. Also, the method described here will facilitate the selection of appropriate reference genes in other oil palm tissues and in the expression profiling of genes relating to yield, biotic and abiotic stresses.
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Affiliation(s)
- Pek-Lan Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Ray J. Rose
- Australian Research Council Centre of Excellence for Integrative Legume Research, School of Environmental and Life Sciences, The University of Newcastle, New South Wales, Australia
| | - Abdul Munir Abdul Murad
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Zamri Zainal
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Eng-Ti Leslie Low
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Leslie Cheng-Li Ooi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Siew-Eng Ooi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia
| | - Suzaini Yahya
- Sime Darby Biotech Laboratories Sdn Bhd, Km10, Jalan Banting-Kelanang, Banting, Selangor, Malaysia
| | - Rajinder Singh
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), No. 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, Malaysia
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266
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Analysis of multiple transcriptomes of the African oil palm (Elaeis guineensis) to identify reference genes for RT-qPCR. J Biotechnol 2014; 184:63-73. [PMID: 24862192 DOI: 10.1016/j.jbiotec.2014.05.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 04/12/2014] [Accepted: 05/10/2014] [Indexed: 01/22/2023]
Abstract
The African oil palm (Elaeis guineensis), which is grown in tropical and subtropical regions, is a highly productive oil-bearing crop. For gene expression-based analyses such as reverse transcription-quantitative real time PCR (RT-qPCR), reference genes are essential to provide a baseline with which to quantify relative gene expression. Normalization using reliable reference genes is critical in correctly interpreting expression data from RT-qPCR. In order to identify suitable reference genes in African oil palm, 17 transcriptomes of different tissues obtained from NCBI were systematically assessed for gene expression variation. In total, 53 putative candidate reference genes with coefficient of variation values <3.0 were identified: 18 in reproductive tissue and 35 in vegetative tissue. Analysis for enriched functions showed that approximately 90% of identified genes were clustered in cell component gene functions, and 12 out of 53 genes were traditional housekeeping genes. We selected and validated 16 reference genes chosen from leaf tissue transcriptomes by using RT-qPCR in sets of cold, drought and high salinity treated samples, and ranked expression stability using statistical algorithms geNorm, Normfinder and Bestkeeper. Genes encoding actin, adenine phosphoribosyltransferase and eukaryotic initiation factor 4A genes were the most stable genes over the cold, drought and high salinity stresses. Identification of stably expressed genes as reference gene candidates from multiple transcriptome datasets was found to be reliable and efficient, and some traditional housekeeping genes were more stably expressed than others. We provide a useful molecular genetic resource for future gene expression studies in African oil palm, facilitating molecular genetics approaches for crop improvement in this species.
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267
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Montoya C, Cochard B, Flori A, Cros D, Lopes R, Cuellar T, Espeout S, Syaputra I, Villeneuve P, Pina M, Ritter E, Leroy T, Billotte N. Genetic architecture of palm oil fatty acid composition in cultivated oil palm (Elaeis guineensis Jacq.) compared to its wild relative E. oleifera (H.B.K) Cortés. PLoS One 2014; 9:e95412. [PMID: 24816555 PMCID: PMC4015976 DOI: 10.1371/journal.pone.0095412] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 03/26/2014] [Indexed: 12/02/2022] Open
Abstract
We searched for quantitative trait loci (QTL) associated with the palm oil fatty acid composition of mature fruits of the oil palm E. guineensis Jacq. in comparison with its wild relative E. oleifera (H.B.K) Cortés. The oil palm cross LM2T x DA10D between two heterozygous parents was considered in our experiment as an intraspecific representative of E. guineensis. Its QTLs were compared to QTLs published for the same traits in an interspecific Elaeis pseudo-backcross used as an indirect representative of E. oleifera. Few correlations were found in E. guineensis between pulp fatty acid proportions and yield traits, allowing for the rather independent selection of both types of traits. Sixteen QTLs affecting palm oil fatty acid proportions and iodine value were identified in oil palm. The phenotypic variation explained by the detected QTLs was low to medium in E. guineensis, ranging between 10% and 36%. The explained cumulative variation was 29% for palmitic acid C16:0 (one QTL), 68% for stearic acid C18:0 (two QTLs), 50% for oleic acid C18:1 (three QTLs), 25% for linoleic acid C18:2 (one QTL), and 40% (two QTLs) for the iodine value. Good marker co-linearity was observed between the intraspecific and interspecific Simple Sequence Repeat (SSR) linkage maps. Specific QTL regions for several traits were found in each mapping population. Our comparative QTL results in both E. guineensis and interspecific materials strongly suggest that, apart from two common QTL zones, there are two specific QTL regions with major effects, which might be one in E. guineensis, the other in E. oleifera, which are independent of each other and harbor QTLs for several traits, indicating either pleiotropic effects or linkage. Using QTL maps connected by highly transferable SSR markers, our study established a good basis to decipher in the future such hypothesis at the Elaeis genus level.
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Affiliation(s)
- Carmenza Montoya
- Oil Palm Biology and Breeding Program, Corporación Centro de Investigación en Palma de Aceite (Cenipalma), Bogotá D.C., Colombia
| | - Benoit Cochard
- Umr Agap, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Montpellier, France
| | - Albert Flori
- Umr Agap, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Montpellier, France
| | - David Cros
- Umr Agap, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Montpellier, France
| | - Ricardo Lopes
- Laboratory of Molecular Biology, Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), Manaus, Brazil
| | - Teresa Cuellar
- Umr Agap, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Montpellier, France
| | - Sandra Espeout
- Umr Agap, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Montpellier, France
| | - Indra Syaputra
- Agricultural Department, SOCFINDO (PT Socfin-Indonesia), Medan, Indonesia
| | - Pierre Villeneuve
- Umr Iate 1208, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Montpellier, France
| | - Michel Pina
- Umr Iate 1208, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Montpellier, France
| | - Enrique Ritter
- Biotechnology Department, Instituto Vasco de Investigación y Desarrollo Agrario (NEIKER), Vitoria, Spain
| | - Thierry Leroy
- Umr Agap, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Montpellier, France
| | - Norbert Billotte
- Umr Agap, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Montpellier, France
- * E-mail:
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268
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High density SNP and SSR-based genetic maps of two independent oil palm hybrids. BMC Genomics 2014; 15:309. [PMID: 24767304 PMCID: PMC4234488 DOI: 10.1186/1471-2164-15-309] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 03/25/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Oil palm is an important perennial oil crop with an extremely long selection cycle of 10 to 12 years. As such, any tool that speeds up its genetic improvement process, such as marker-assisted breeding is invaluable. Previously, genetic linkage maps based on AFLP, RFLP and SSR markers were developed and QTLs for fatty acid composition and yield components identified. High density genetic maps of crosses of different genetic backgrounds are indispensable tools for investigating oil palm genetics. They are also useful for comparative mapping analyses to identify markers closely linked to traits of interest. RESULTS A 4.5 K customized oil palm SNP array was developed using the Illumina Infinium platform. The SNPs and 252 SSRs were genotyped on two mapping populations, an intraspecific cross with 87 palms and an interspecific cross with 108 palms. Parental maps with 16 linkage groups (LGs), were constructed for the three fruit forms of E. guineensis (dura, pisifera and tenera). Map resolution was further increased by integrating the dura and pisifera maps into an intraspecific integrated map with 1,331 markers spanning 1,867 cM. We also report the first map of a Colombian E. oleifera, comprising 10 LGs with 65 markers spanning 471 cM. Although not very dense due to the high level of homozygosity in E. oleifera, the LGs were successfully integrated with the LGs of the tenera map. Direct comparison between the parental maps identified 603 transferable markers polymorphic in at least two of the parents. Further analysis revealed a high degree of marker transferability covering 1,075 cM, between the intra- and interspecific integrated maps. The interspecific cross displayed higher segregation distortion than the intraspecific cross. However, inclusion of distorted markers in the genetic maps did not disrupt the marker order and no map expansion was observed. CONCLUSIONS The high density SNP and SSR-based genetic maps reported in this paper have greatly improved marker density and genome coverage in comparison with the first reference map based on AFLP and SSR markers. Therefore, it is foreseen that they will be more useful for fine mapping of QTLs and whole genome association mapping studies in oil palm.
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Mathew LS, Spannagl M, Al-Malki A, George B, Torres MF, Al-Dous EK, Al-Azwani EK, Hussein E, Mathew S, Mayer KFX, Mohamoud YA, Suhre K, Malek JA. A first genetic map of date palm (Phoenix dactylifera) reveals long-range genome structure conservation in the palms. BMC Genomics 2014; 15:285. [PMID: 24735434 PMCID: PMC4023600 DOI: 10.1186/1471-2164-15-285] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 04/04/2014] [Indexed: 12/22/2022] Open
Abstract
Background The date palm is one of the oldest cultivated fruit trees. It is critical in many ways to cultures in arid lands by providing highly nutritious fruit while surviving extreme heat and environmental conditions. Despite its importance from antiquity, few genetic resources are available for improving the productivity and development of the dioecious date palm. To date there has been no genetic map and no sex chromosome has been identified. Results Here we present the first genetic map for date palm and identify the putative date palm sex chromosome. We placed ~4000 markers on the map using nearly 1200 framework markers spanning a total of 1293 cM. We have integrated the genetic map, derived from the Khalas cultivar, with the draft genome and placed up to 19% of the draft genome sequence scaffolds onto linkage groups for the first time. This analysis revealed approximately ~1.9 cM/Mb on the map. Comparison of the date palm linkage groups revealed significant long-range synteny to oil palm. Analysis of the date palm sex-determination region suggests it is telomeric on linkage group 12 and recombination is not suppressed in the full chromosome. Conclusions Based on a modified gentoyping-by-sequencing approach we have overcome challenges due to lack of genetic resources and provide the first genetic map for date palm. Combined with the recent draft genome sequence of the same cultivar, this resource offers a critical new tool for date palm biotechnology, palm comparative genomics and a better understanding of sex chromosome development in the palms.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Joel A Malek
- Genomics Laboratory, Weill Cornell Medical College in Qatar, Qatar Foundation, Doha, Qatar.
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270
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Identification of proteins of altered abundance in oil palm infected with Ganoderma boninense. Int J Mol Sci 2014; 15:5175-92. [PMID: 24663087 PMCID: PMC3975447 DOI: 10.3390/ijms15035175] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/05/2014] [Accepted: 03/05/2014] [Indexed: 01/19/2023] Open
Abstract
Basal stem rot is a common disease that affects oil palm, causing loss of yield and finally killing the trees. The disease, caused by fungus Ganoderma boninense, devastates thousands of hectares of oil palm plantings in Southeast Asia every year. In the present study, root proteins of healthy oil palm seedlings, and those infected with G. boninense, were analyzed by 2-dimensional gel electrophoresis (2-DE). When the 2-DE profiles were analyzed for proteins, which exhibit consistent significant change of abundance upon infection with G. boninense, 21 passed our screening criteria. Subsequent analyses by mass spectrometry and database search identified caffeoyl-CoA O-methyltransferase, caffeic acid O-methyltransferase, enolase, fructokinase, cysteine synthase, malate dehydrogenase, and ATP synthase as among proteins of which abundances were markedly altered.
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271
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Wang E, Chinni S, Bhore SJ. Three-dimensional (3D) structure prediction of the American and African oil-palms β-ketoacyl-[ACP] synthase-II protein by comparative modelling. Bioinformation 2014; 10:130-7. [PMID: 24748752 PMCID: PMC3974239 DOI: 10.6026/97320630010130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 03/06/2014] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The fatty-acid profile of the vegetable oils determines its properties and nutritional value. Palm-oil obtained from the African oil-palm [Elaeis guineensis Jacq. (Tenera)] contains 44% palmitic acid (C16:0), but, palm-oil obtained from the American oilpalm [Elaeis oleifera] contains only 25% C16:0. In part, the b-ketoacyl-[ACP] synthase II (KASII) [EC: 2.3.1.179] protein is responsible for the high level of C16:0 in palm-oil derived from the African oil-palm. To understand more about E. guineensis KASII (EgKASII) and E. oleifera KASII (EoKASII) proteins, it is essential to know its structures. Hence, this study was undertaken. OBJECTIVE The objective of this study was to predict three-dimensional (3D) structure of EgKASII and EoKASII proteins using molecular modelling tools. MATERIALS AND METHODS The amino-acid sequences for KASII proteins were retrieved from the protein database of National Center for Biotechnology Information (NCBI), USA. The 3D structures were predicted for both proteins using homology modelling and ab-initio technique approach of protein structure prediction. The molecular dynamics (MD) simulation was performed to refine the predicted structures. The predicted structure models were evaluated and root mean square deviation (RMSD) and root mean square fluctuation (RMSF) values were calculated. RESULTS The homology modelling showed that EgKASII and EoKASII proteins are 78% and 74% similar with Streptococcus pneumonia KASII and Brucella melitensis KASII, respectively. The EgKASII and EoKASII structures predicted by using ab-initio technique approach shows 6% and 9% deviation to its structures predicted by homology modelling, respectively. The structure refinement and validation confirmed that the predicted structures are accurate. CONCLUSION The 3D structures for EgKASII and EoKASII proteins were predicted. However, further research is essential to understand the interaction of EgKASII and EoKASII proteins with its substrates.
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Affiliation(s)
- Edina Wang
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong-Semeling Road, Bedong, 08100, Kedah, Malaysia
| | - Suresh Chinni
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong-Semeling Road, Bedong, 08100, Kedah, Malaysia
| | - Subhash Janardhan Bhore
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong-Semeling Road, Bedong, 08100, Kedah, Malaysia
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272
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Jaligot E, Hooi WY, Debladis E, Richaud F, Beulé T, Collin M, Agbessi MDT, Sabot F, Garsmeur O, D'Hont A, Alwee SSRS, Rival A. DNA methylation and expression of the EgDEF1 gene and neighboring retrotransposons in mantled somaclonal variants of oil palm. PLoS One 2014; 9:e91896. [PMID: 24638102 PMCID: PMC3956824 DOI: 10.1371/journal.pone.0091896] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 02/17/2014] [Indexed: 11/30/2022] Open
Abstract
The mantled floral phenotype of oil palm (Elaeis guineensis) affects somatic embryogenesis-derived individuals and is morphologically similar to mutants defective in the B-class MADS-box genes. This somaclonal variation has been previously demonstrated to be associated to a significant deficit in genome-wide DNA methylation. In order to elucidate the possible role of DNA methylation in the transcriptional regulation of EgDEF1, the APETALA3 ortholog of oil palm, we studied this epigenetic mark within the gene in parallel with transcript accumulation in both normal and mantled developing inflorescences. We also examined the methylation and expression of two neighboring retrotransposons that might interfere with EgDEF1 regulation. We show that the EgDEF1 gene is essentially unmethylated and that its methylation pattern does not change with the floral phenotype whereas expression is dramatically different, ruling out a direct implication of DNA methylation in the regulation of this gene. Also, we find that both the gypsy element inserted within an intron of the EgDEF1 gene and the copia element located upstream from the promoter are heavily methylated and show little or no expression. Interestingly, we identify a shorter, alternative transcript produced by EgDEF1 and characterize its accumulation with respect to its full-length counterpart. We demonstrate that, depending on the floral phenotype, the respective proportions of these two transcripts change differently during inflorescence development. We discuss the possible phenotypical consequences of this alternative splicing and the new questions it raises in the search for the molecular mechanisms underlying the mantled phenotype in the oil palm.
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Affiliation(s)
| | - Wei Yeng Hooi
- UMR DIADE, CIRAD, Montpellier, France
- FELDA Biotechnology Centre, FASSB, Bandar Enstek, Malaysia
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273
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Zhang J, Nieminen K, Serra JAA, Helariutta Y. The formation of wood and its control. CURRENT OPINION IN PLANT BIOLOGY 2014; 17:56-63. [PMID: 24507495 DOI: 10.1016/j.pbi.2013.11.003] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 10/25/2013] [Accepted: 11/06/2013] [Indexed: 05/21/2023]
Abstract
Wood continues to increase in importance as a sustainable source of energy and shelter. Wood formation is a dynamic process derived from plant secondary (radial) growth. Several experimental systems have been employed to study wood formation and its regulation. The use of genetic manipulation approaches and genome-wide analyses in model plants have significantly advanced our understanding of wood formation. In this review, we provide an update of our knowledge of the genetic and hormonal regulation of wood formation based on research in different plants systems, as well as considering the subject from an evo-devo perspective.
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Affiliation(s)
- Jing Zhang
- Department of Biological and Environmental Sciences, Institute of Biotechnology, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland
| | - Kaisa Nieminen
- Department of Biological and Environmental Sciences, Institute of Biotechnology, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland; Finnish Forest Research Institute, P.O. Box 18, 01301 Vantaa, Finland
| | - Juan Antonio Alonso Serra
- Department of Biological and Environmental Sciences, Institute of Biotechnology, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland
| | - Ykä Helariutta
- Department of Biological and Environmental Sciences, Institute of Biotechnology, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland.
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274
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Low ETL, Rosli R, Jayanthi N, Mohd-Amin AH, Azizi N, Chan KL, Maqbool NJ, Maclean P, Brauning R, McCulloch A, Moraga R, Ong-Abdullah M, Singh R. Analyses of hypomethylated oil palm gene space. PLoS One 2014; 9:e86728. [PMID: 24497974 PMCID: PMC3907425 DOI: 10.1371/journal.pone.0086728] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Accepted: 12/15/2013] [Indexed: 12/21/2022] Open
Abstract
Demand for palm oil has been increasing by an average of ∼8% the past decade and currently accounts for about 59% of the world's vegetable oil market. This drives the need to increase palm oil production. Nevertheless, due to the increasing need for sustainable production, it is imperative to increase productivity rather than the area cultivated. Studies on the oil palm genome are essential to help identify genes or markers that are associated with important processes or traits, such as flowering, yield and disease resistance. To achieve this, 294,115 and 150,744 sequences from the hypomethylated or gene-rich regions of Elaeis guineensis and E. oleifera genome were sequenced and assembled into contigs. An additional 16,427 shot-gun sequences and 176 bacterial artificial chromosomes (BAC) were also generated to check the quality of libraries constructed. Comparison of these sequences revealed that although the methylation-filtered libraries were sequenced at low coverage, they still tagged at least 66% of the RefSeq supported genes in the BAC and had a filtration power of at least 2.0. A total 33,752 microsatellites and 40,820 high-quality single nucleotide polymorphism (SNP) markers were identified. These represent the most comprehensive collection of microsatellites and SNPs to date and would be an important resource for genetic mapping and association studies. The gene models predicted from the assembled contigs were mined for genes of interest, and 242, 65 and 14 oil palm transcription factors, resistance genes and miRNAs were identified respectively. Examples of the transcriptional factors tagged include those associated with floral development and tissue culture, such as homeodomain proteins, MADS, Squamosa and Apetala2. The E. guineensis and E. oleifera hypomethylated sequences provide an important resource to understand the molecular mechanisms associated with important agronomic traits in oil palm.
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Affiliation(s)
- Eng-Ti L. Low
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Rozana Rosli
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Nagappan Jayanthi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Ab Halim Mohd-Amin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Norazah Azizi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Kuang-Lim Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | | | - Paul Maclean
- AgResearch Ruakura Research Centre, Hamilton, New Zealand
| | - Rudi Brauning
- AgResearch Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Alan McCulloch
- AgResearch Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Roger Moraga
- AgResearch Grasslands Research Centre, Palmerston North, New Zealand
| | - Meilina Ong-Abdullah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Rajinder Singh
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
- * E-mail:
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275
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276
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Singh R, Low ETL, Ooi LCL, Ong-Abdullah M, Ting NC, Nagappan J, Nookiah R, Amiruddin MD, Rosli R, Manaf MAA, Chan KL, Halim MA, Azizi N, Lakey N, Smith SW, Budiman MA, Hogan M, Bacher B, Van Brunt A, Wang C, Ordway JM, Sambanthamurthi R, Martienssen RA. The oil palm SHELL gene controls oil yield and encodes a homologue of SEEDSTICK. Nature 2013; 500:340-4. [PMID: 23883930 PMCID: PMC4209285 DOI: 10.1038/nature12356] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 06/07/2013] [Indexed: 11/21/2022]
Abstract
A key event in the domestication and breeding of the oil palm, Elaeis guineensis, was loss of the thick coconut-like shell surrounding the kernel. Modern E. guineensis has three fruit forms, dura (thick-shelled), pisifera (shell-less) and tenera (thin-shelled), a hybrid between dura and pisifera1–4. The pisifera palm is usually female-sterile but the tenera yields far more oil than dura, and is the basis for commercial palm oil production in all of Southeast Asia5. Here, we describe the mapping and identification of the Shell gene responsible for the different fruit forms. Using homozygosity mapping by sequencing we found two independent mutations in the DNA binding domain of a homologue of the MADS-box gene SEEDSTICK (STK) which controls ovule identity and seed development in Arabidopsis. The Shell gene is responsible for the tenera phenotype in both cultivated and wild palms from sub-Saharan Africa, and our findings provide a genetic explanation for the single gene heterosis attributed to Shell, via heterodimerization. This gene mutation explains the single most important economic trait in oil palm, and has implications for the competing interests of global edible oil production, biofuels and rainforest conservation6.
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Affiliation(s)
- Rajinder Singh
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
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