201
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Ithnin M, Teh CK, Ratnam W. Genetic diversity of Elaeis oleifera (HBK) Cortes populations using cross species SSRs: implication's for germplasm utilization and conservation. BMC Genet 2017; 18:37. [PMID: 28420332 PMCID: PMC5395919 DOI: 10.1186/s12863-017-0505-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 04/12/2017] [Indexed: 11/25/2022] Open
Abstract
Background The Elaeis oleifera genetic materials were assembled from its center of diversity in South and Central America. These materials are currently being preserved in Malaysia as ex situ living collections. Maintaining such collections is expensive and requires sizable land. Information on the genetic diversity of these collections can help achieve efficient conservation via maintenance of core collection. For this purpose, we have applied fourteen unlinked microsatellite markers to evaluate 532 E. oleifera palms representing 19 populations distributed across Honduras, Costa Rica, Panama and Colombia. Results In general, the genetic diversity decreased from Costa Rica towards the north (Honduras) and south-east (Colombia). Principle coordinate analysis (PCoA) showed a single cluster indicating low divergence among palms. The phylogenetic tree and STRUCTURE analysis revealed clusters based on country of origin, indicating considerable gene flow among populations within countries. Based on the values of the genetic diversity parameters, some genetically diverse populations could be identified. Further, a total of 34 individual palms that collectively captured maximum allelic diversity with reduced redundancy were also identified. High pairwise genetic differentiation (Fst > 0.250) among populations was evident, particularly between the Colombian populations and those from Honduras, Panama and Costa Rica. Crossing selected palms from highly differentiated populations could generate off-springs that retain more genetic diversity. Conclusion The results attained are useful for selecting palms and populations for core collection. The selected materials can also be included into crossing scheme to generate offsprings that capture greater genetic diversity for selection gain in the future. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0505-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maizura Ithnin
- Malaysian Palm Oil Board (MPOB), P.O.Box 10620, 50720, Kuala Lumpur, Malaysia.
| | - Chee-Keng Teh
- Malaysian Palm Oil Board (MPOB), P.O.Box 10620, 50720, Kuala Lumpur, Malaysia.,Present Address: Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, 43400, Selangor, Malaysia
| | - Wickneswari Ratnam
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
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202
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Transcriptome and functional analysis reveals hybrid vigor for oil biosynthesis in oil palm. Sci Rep 2017; 7:439. [PMID: 28348403 PMCID: PMC5428490 DOI: 10.1038/s41598-017-00438-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 02/22/2017] [Indexed: 01/09/2023] Open
Abstract
Oil palm is the most productive oil crop in the world and composes 36% of the world production. However, the molecular mechanisms of hybrids vigor (or heterosis) between Dura, Pisifera and their hybrid progeny Tenera has not yet been well understood. Here we compared the temporal and spatial compositions of lipids and transcriptomes for two oil yielding organs mesocarp and endosperm from Dura, Pisifera and Tenera. Multiple lipid biosynthesis pathways are highly enriched in all non-additive expression pattern in endosperm, while cytokinine biosynthesis and cell cycle pathways are highly enriched both in endosperm and mesocarp. Compared with parental palms, the high oil content in Tenera was associated with much higher transcript levels of EgWRI1, homolog of Arabidopsis thaliana WRINKLED1. Among 338 identified genes in lipid synthesis, 207 (61%) has been identified to contain the WRI1 specific binding AW motif. We further functionally identified EgWRI1-1, one of three EgWRI1 orthologs, by genetic complementation of the Arabidopsis wri1 mutant. Ectopic expression of EgWRI1-1 in plant produced dramatically increased seed mass and oil content, with oil profile changed. Our findings provide an explanation for EgWRI1 as an important gene contributing hybrid vigor in lipid biosynthesis in oil palm.
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203
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Armero A, Baudouin L, Bocs S, This D. Improving transcriptome de novo assembly by using a reference genome of a related species: Translational genomics from oil palm to coconut. PLoS One 2017; 12:e0173300. [PMID: 28334050 PMCID: PMC5363918 DOI: 10.1371/journal.pone.0173300] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 02/17/2017] [Indexed: 01/20/2023] Open
Abstract
The palms are a family of tropical origin and one of the main constituents of the ecosystems of these regions around the world. The two main species of palm represent different challenges: coconut (Cocos nucifera L.) is a source of multiple goods and services in tropical communities, while oil palm (Elaeis guineensis Jacq) is the main protagonist of the oil market. In this study, we present a workflow that exploits the comparative genomics between a target species (coconut) and a reference species (oil palm) to improve the transcriptomic data, providing a proteome useful to answer functional or evolutionary questions. This workflow reduces redundancy and fragmentation, two inherent problems of transcriptomic data, while preserving the functional representation of the target species. Our approach was validated in Arabidopsis thaliana using Arabidopsis lyrata and Capsella rubella as references species. This analysis showed the high sensitivity and specificity of our strategy, relatively independent of the reference proteome. The workflow increased the length of proteins products in A. thaliana by 13%, allowing, often, to recover 100% of the protein sequence length. In addition redundancy was reduced by a factor greater than 3. In coconut, the approach generated 29,366 proteins, 1,246 of these proteins deriving from new contigs obtained with the BRANCH software. The coconut proteome presented a functional profile similar to that observed in rice and an important number of metabolic pathways related to secondary metabolism. The new sequences found with BRANCH software were enriched in functions related to biotic stress. Our strategy can be used as a complementary step to de novo transcriptome assembly to get a representative proteome of a target species. The results of the current analysis are available on the website PalmComparomics (http://palm-comparomics.southgreen.fr/).
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Affiliation(s)
- Alix Armero
- Montpellier SupAgro, UMR AGAP, Montpellier, France
| | | | - Stéphanie Bocs
- CIRAD, UMR AGAP, Montpellier, France
- South Green Bioinformatics Platform, Montpellier, France
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204
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Abstract
Background Emerging evidence indicates that plant miRNAs can present within human circulating system through dietary intake and regulate human gene expression. Hence we deduced that comestible plants miRNAs can be identified in the public available small RNA sequencing data sets. Results In this study, we identified abundant plant miRNAs sequences from 410 human plasma small RNA sequencing data sets. One particular plant miRNA miR2910, conserved in fruits and vegetables, was found to present in high relative amount in the plasma samples. This miRNA, with same 6mer and 7mer-A1 target seed sequences as hsa-miR-4259 and hsa-miR-4715-5p, was predicted to target human JAK-STAT signaling pathway gene SPRY4 and transcription regulation genes. Conclusions Through analysis of public available plasma small RNA sequencing data, we found the supporting evidence for the plant miRNAs cross kingdom RNAi within human circulating system. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3502-3) contains supplementary material, which is available to authorized users.
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205
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Reconstructing the genome of the most recent common ancestor of flowering plants. Nat Genet 2017; 49:490-496. [DOI: 10.1038/ng.3813] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 02/14/2017] [Indexed: 01/24/2023]
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206
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Babu BK, Mathur RK, Kumar PN, Ramajayam D, Ravichandran G, Venu MVB, Babu SS. Development, identification and validation of CAPS marker for SHELL trait which governs dura, pisifera and tenera fruit forms in oil palm (Elaeis guineensis Jacq.). PLoS One 2017; 12:e0171933. [PMID: 28192462 PMCID: PMC5305241 DOI: 10.1371/journal.pone.0171933] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 01/28/2017] [Indexed: 11/18/2022] Open
Abstract
The oil palm fruit forms (dura, pisifera and tenera) governed by the shell thickness gene (Sh) plays a major role in identification of fruit type and also influences palm oil yield. Identification of desired fruit type is a major asset to the breeders and oil palm workers for applications in breeding, seed certification and to reduce time, space and money spent on identification of fruit form. In the present study, we developed Sh gene specific primer pairs and bulk segregant analysis was done using 300 genomic and 8 genic SSR markers. We identified one cleaved amplified polymorphic site (CAPS) marker for differentiation of oil palm fruit type which produced two alleles (280 and 250bp) in dura genotypes, three alleles in tenera genotypes (550, 280, and 250bp) and one allele in pisifera genotypes (550bp). The shell allele sequencing results showed that two SNPs were present, of which SNP2 contributed for variation of fruit forms. The nucleotide ‘A’ was present in only dura genotypes, where as ‘T’ was present only in pisifera genotypes, which in turn led to the change of amino acid lysine to aspargine. The identified CAPS marker was validated on 300 dura, 25 pisifera and 80 tenera genotypes, 80 dura/ pisifera cross progenies and 60 lines of tenera/ tenera cross progeny. Association mapping of marker data with phenotypic data of eight oil yield related traits resulted in identification of seven significant QTLs by GLM approach, four by MLM approach at a significant threshold (P) level of 0.001. Significant QTLs were identified for fruit to bunch and oil to bunch traits, which explained R2 of 12.9% and 11.5% respectively. The CAPS marker used in the present study facilitate selection and timely distribution of desirable high yielding tenera sprouts to the farmers instead of waiting for 4–5 years. This saves a lot of land, time and money which will be a major breakthrough to the oil palm community.
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Affiliation(s)
- B. Kalyana Babu
- ICAR-Indian Institute of Oil Palm Research, Pedavegi, West Godavari (Dt), Andhrapradesh, India
- * E-mail: ,
| | - R. K. Mathur
- ICAR-Indian Institute of Oil Palm Research, Pedavegi, West Godavari (Dt), Andhrapradesh, India
| | - P. Naveen Kumar
- ICAR-Indian Institute of Oil Palm Research, Pedavegi, West Godavari (Dt), Andhrapradesh, India
| | - D. Ramajayam
- ICAR-Indian Institute of Oil Palm Research, Pedavegi, West Godavari (Dt), Andhrapradesh, India
| | - G. Ravichandran
- ICAR-Indian Institute of Oil Palm Research, Pedavegi, West Godavari (Dt), Andhrapradesh, India
| | - M. V. B. Venu
- ICAR-Indian Institute of Oil Palm Research, Pedavegi, West Godavari (Dt), Andhrapradesh, India
| | - S. Sparjan Babu
- ICAR-Indian Institute of Oil Palm Research, Pedavegi, West Godavari (Dt), Andhrapradesh, India
- KL University, Guntur (Dt), Andhra Pradesh, India
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207
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Field Guide to Plant Model Systems. Cell 2017; 167:325-339. [PMID: 27716506 DOI: 10.1016/j.cell.2016.08.031] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 07/28/2016] [Accepted: 08/15/2016] [Indexed: 12/20/2022]
Abstract
For the past several decades, advances in plant development, physiology, cell biology, and genetics have relied heavily on the model (or reference) plant Arabidopsis thaliana. Arabidopsis resembles other plants, including crop plants, in many but by no means all respects. Study of Arabidopsis alone provides little information on the evolutionary history of plants, evolutionary differences between species, plants that survive in different environments, or plants that access nutrients and photosynthesize differently. Empowered by the availability of large-scale sequencing and new technologies for investigating gene function, many new plant models are being proposed and studied.
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208
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Jourda C, Cardi C, Gibert O, Giraldo Toro A, Ricci J, Mbéguié-A-Mbéguié D, Yahiaoui N. Lineage-Specific Evolutionary Histories and Regulation of Major Starch Metabolism Genes during Banana Ripening. FRONTIERS IN PLANT SCIENCE 2016; 7:1778. [PMID: 27994606 PMCID: PMC5133247 DOI: 10.3389/fpls.2016.01778] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/11/2016] [Indexed: 05/24/2023]
Abstract
Starch is the most widespread and abundant storage carbohydrate in plants. It is also a major feature of cultivated bananas as it accumulates to large amounts during banana fruit development before almost complete conversion to soluble sugars during ripening. Little is known about the structure of major gene families involved in banana starch metabolism and their evolution compared to other species. To identify genes involved in banana starch metabolism and investigate their evolutionary history, we analyzed six gene families playing a crucial role in plant starch biosynthesis and degradation: the ADP-glucose pyrophosphorylases (AGPases), starch synthases (SS), starch branching enzymes (SBE), debranching enzymes (DBE), α-amylases (AMY) and β-amylases (BAM). Using comparative genomics and phylogenetic approaches, these genes were classified into families and sub-families and orthology relationships with functional genes in Eudicots and in grasses were identified. In addition to known ancestral duplications shaping starch metabolism gene families, independent evolution in banana and grasses also occurred through lineage-specific whole genome duplications for specific sub-families of AGPase, SS, SBE, and BAM genes; and through gene-scale duplications for AMY genes. In particular, banana lineage duplications yielded a set of AGPase, SBE and BAM genes that were highly or specifically expressed in banana fruits. Gene expression analysis highlighted a complex transcriptional reprogramming of starch metabolism genes during ripening of banana fruits. A differential regulation of expression between banana gene duplicates was identified for SBE and BAM genes, suggesting that part of starch metabolism regulation in the fruit evolved in the banana lineage.
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Affiliation(s)
- Cyril Jourda
- CIRAD, UMR AGAPMontpellier, France
- CIRAD, UMR PVBMTSaint-Pierre, France
| | | | - Olivier Gibert
- CIRAD, UMR QUALISUDMontpellier, France
- CIRAD, UMR QUALISUDJakarta, Indonesia
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209
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Badenes ML, Fernández I Martí A, Ríos G, Rubio-Cabetas MJ. Application of Genomic Technologies to the Breeding of Trees. Front Genet 2016; 7:198. [PMID: 27895664 PMCID: PMC5109026 DOI: 10.3389/fgene.2016.00198] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/31/2016] [Indexed: 12/22/2022] Open
Abstract
The recent introduction of next generation sequencing (NGS) technologies represents a major revolution in providing new tools for identifying the genes and/or genomic intervals controlling important traits for selection in breeding programs. In perennial fruit trees with long generation times and large sizes of adult plants, the impact of these techniques is even more important. High-throughput DNA sequencing technologies have provided complete annotated sequences in many important tree species. Most of the high-throughput genotyping platforms described are being used for studies of genetic diversity and population structure. Dissection of complex traits became possible through the availability of genome sequences along with phenotypic variation data, which allow to elucidate the causative genetic differences that give rise to observed phenotypic variation. Association mapping facilitates the association between genetic markers and phenotype in unstructured and complex populations, identifying molecular markers for assisted selection and breeding. Also, genomic data provide in silico identification and characterization of genes and gene families related to important traits, enabling new tools for molecular marker assisted selection in tree breeding. Deep sequencing of transcriptomes is also a powerful tool for the analysis of precise expression levels of each gene in a sample. It consists in quantifying short cDNA reads, obtained by NGS technologies, in order to compare the entire transcriptomes between genotypes and environmental conditions. The miRNAs are non-coding short RNAs involved in the regulation of different physiological processes, which can be identified by high-throughput sequencing of RNA libraries obtained by reverse transcription of purified short RNAs, and by in silico comparison with known miRNAs from other species. All together, NGS techniques and their applications have increased the resources for plant breeding in tree species, closing the former gap of genetic tools between trees and annual species.
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Affiliation(s)
- Maria L Badenes
- Instituto Valenciano de Investigaciones Agrarias Valencia, Spain
| | - Angel Fernández I Martí
- Hortofruticulture Department, Agrifood Research and Technology Centre of AragonZaragoza, Spain; Genome Center, University of California, Davis, Davis, CAUSA
| | - Gabino Ríos
- Instituto Valenciano de Investigaciones Agrarias Valencia, Spain
| | - María J Rubio-Cabetas
- Hortofruticulture Department, Agrifood Research and Technology Centre of Aragon Zaragoza, Spain
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210
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Guerin C, Joët T, Serret J, Lashermes P, Vaissayre V, Agbessi MDT, Beulé T, Severac D, Amblard P, Tregear J, Durand-Gasselin T, Morcillo F, Dussert S. Gene coexpression network analysis of oil biosynthesis in an interspecific backcross of oil palm. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:423-41. [PMID: 27145323 DOI: 10.1111/tpj.13208] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/27/2016] [Accepted: 04/27/2016] [Indexed: 05/25/2023]
Abstract
Global demand for vegetable oils is increasing at a dramatic rate, while our understanding of the regulation of oil biosynthesis in plants remains limited. To gain insights into the mechanisms that govern oil synthesis and fatty acid (FA) composition in the oil palm fruit, we used a multilevel approach combining gene coexpression analysis, quantification of allele-specific expression and joint multivariate analysis of transcriptomic and lipid data, in an interspecific backcross population between the African oil palm, Elaeis guineensis, and the American oil palm, Elaeis oleifera, which display contrasting oil contents and FA compositions. The gene coexpression network produced revealed tight transcriptional coordination of fatty acid synthesis (FAS) in the plastid with sugar sensing, plastidial glycolysis, transient starch storage and carbon recapture pathways. It also revealed a concerted regulation, along with FAS, of both the transfer of nascent FA to the endoplasmic reticulum, where triacylglycerol assembly occurs, and of the production of glycerol-3-phosphate, which provides the backbone of triacylglycerols. Plastid biogenesis and auxin transport were the two other biological processes most tightly connected to FAS in the network. In addition to WRINKLED1, a transcription factor (TF) known to activate FAS genes, two novel TFs, termed NF-YB-1 and ZFP-1, were found at the core of the FAS module. The saturated FA content of palm oil appeared to vary above all in relation to the level of transcripts of the gene coding for β-ketoacyl-acyl carrier protein synthase II. Our findings should facilitate the development of breeding and engineering strategies in this and other oil crops.
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Affiliation(s)
- Chloé Guerin
- PalmElit SAS, Montferrier-sur-Lez, F-34980, France
| | - Thierry Joët
- IRD, UMR DIADE, 911 Av. Agropolis, Montpellier, 34394, France
| | - Julien Serret
- IRD, UMR DIADE, 911 Av. Agropolis, Montpellier, 34394, France
| | | | | | | | | | - Dany Severac
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, 141 Rue de la Cardonille, Montpellier Cedex 5, 34094, France
| | | | - James Tregear
- IRD, UMR DIADE, 911 Av. Agropolis, Montpellier, 34394, France
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211
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Kwong QB, Teh CK, Ong AL, Heng HY, Lee HL, Mohamed M, Low JZB, Apparow S, Chew FT, Mayes S, Kulaveerasingam H, Tammi M, Appleton DR. Development and Validation of a High-Density SNP Genotyping Array for African Oil Palm. MOLECULAR PLANT 2016; 9:1132-1141. [PMID: 27112659 DOI: 10.1016/j.molp.2016.04.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/21/2016] [Accepted: 04/17/2016] [Indexed: 05/18/2023]
Abstract
High-density single nucleotide polymorphism (SNP) genotyping arrays are powerful tools that can measure the level of genetic polymorphism within a population. To develop a whole-genome SNP array for oil palms, SNP discovery was performed using deep resequencing of eight libraries derived from 132 Elaeis guineensis and Elaeis oleifera palms belonging to 59 origins, resulting in the discovery of >3 million putative SNPs. After SNP filtering, the Illumina OP200K custom array was built with 170 860 successful probes. Phenetic clustering analysis revealed that the array could distinguish between palms of different origins in a way consistent with pedigree records. Genome-wide linkage disequilibrium declined more slowly for the commercial populations (ranging from 120 kb at r(2) = 0.43 to 146 kb at r(2) = 0.50) when compared with the semi-wild populations (19.5 kb at r(2) = 0.22). Genetic fixation mapping comparing the semi-wild and commercial population identified 321 selective sweeps. A genome-wide association study (GWAS) detected a significant peak on chromosome 2 associated with the polygenic component of the shell thickness trait (based on the trait shell-to-fruit; S/F %) in tenera palms. Testing of a genomic selection model on the same trait resulted in good prediction accuracy (r = 0.65) with 42% of the S/F % variation explained. The first high-density SNP genotyping array for oil palm has been developed and shown to be robust for use in genetic studies and with potential for developing early trait prediction to shorten the oil palm breeding cycle.
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Affiliation(s)
- Qi Bin Kwong
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia.
| | - Chee Keng Teh
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia
| | - Ai Ling Ong
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia
| | - Huey Ying Heng
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia
| | - Heng Leng Lee
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia
| | - Mohaimi Mohamed
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia
| | - Joel Zi-Bin Low
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia
| | - Sukganah Apparow
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia
| | - Fook Tim Chew
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Sean Mayes
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Nr Loughborough LE12 5RD, UK
| | | | - Martti Tammi
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia
| | - David Ross Appleton
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor 43400, Malaysia
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212
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Jin J, Lee M, Bai B, Sun Y, Qu J, Rahmadsyah, Alfiko Y, Lim CH, Suwanto A, Sugiharti M, Wong L, Ye J, Chua NH, Yue GH. Draft genome sequence of an elite Dura palm and whole-genome patterns of DNA variation in oil palm. DNA Res 2016; 23:527-533. [PMID: 27426468 PMCID: PMC5144676 DOI: 10.1093/dnares/dsw036] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 06/14/2016] [Indexed: 11/26/2022] Open
Abstract
Oil palm is the world’s leading source of vegetable oil and fat. Dura, Pisifera and Tenera are three forms of oil palm. The genome sequence of Pisifera is available whereas the Dura form has not been sequenced yet. We sequenced the genome of one elite Dura palm, and re-sequenced 17 palm genomes. The assemble genome sequence of the elite Dura tree contained 10,971 scaffolds and was 1.701 Gb in length, covering 94.49% of the oil palm genome. 36,105 genes were predicted. Re-sequencing of 17 additional palm trees identified 18.1 million SNPs. We found high genetic variation among palms from different geographical regions, but lower variation among Southeast Asian Dura and Pisifera palms. We mapped 10,000 SNPs on the linkage map of oil palm. In addition, high linkage disequilibrium (LD) was detected in the oil palms used in breeding populations of Southeast Asia, suggesting that LD mapping is likely to be practical in this important oil crop. Our data provide a valuable resource for accelerating genetic improvement and studying the mechanism underlying phenotypic variations of important oil palm traits.
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Affiliation(s)
- Jingjing Jin
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore.,School of Computing, National University of Singapore, Singapore
| | - May Lee
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore
| | - Bin Bai
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore
| | - Yanwei Sun
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore.,State key laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jing Qu
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore
| | - Rahmadsyah
- R & D Department, Wilmar International Plantation, Palembang, Indonesia
| | - Yuzer Alfiko
- Biotech Lab, Wilmar International, Jakarta, Indonesia
| | - Chin Huat Lim
- R & D Department, Wilmar International Plantation, Palembang, Indonesia
| | | | | | - Limsoon Wong
- School of Computing, National University of Singapore, Singapore
| | - Jian Ye
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore .,State key laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Nam-Hai Chua
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore .,Laboratory of Plant Molecular Biology, The Rockefeller University, New York, USA
| | - Gen Hua Yue
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore .,Department of Biological Sciences, National University of Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore 637551, Republic of Singapore
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213
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Identification of a Δ12 fatty acid desaturase from oil palm (Elaeis guineensis Jacq.) involved in the biosynthesis of linoleic acid by heterologous expression in Saccharomyces cerevisiae. Gene 2016; 591:21-26. [PMID: 27370696 DOI: 10.1016/j.gene.2016.06.039] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 06/17/2016] [Accepted: 06/20/2016] [Indexed: 11/22/2022]
Abstract
Oil palm (Elaeis guineensis Jacq.) is one of the highest oil-yield crops in the world. A Δ12-desaturases associated with the primary steps of long-chain polyunsaturated fatty acid (LC-PUFA) biosynthesis were successfully cloned from oil palm and their functions identified. The open reading frames (ORFs) of egFAD2 (GenBank accession: KT023602) consisted of 1176bp and code for 391 amino acids. Their deduced polypeptides showed 75-93% identity to microsomal Δ12-desaturases from other higher plants, and each contained the three histidine clusters typical of the catalytic domains of such enzymes. RT-PCR experiment indicated that the egFAD2 gene exhibited the highest accumulation in the mesocarp of fruits at 120-140 DAP (i.e. the fourth period of fruit development) and, despite having different expression levels, the other four stages were at significantly lower levels compared with the fourth stage. Plasmid pYES2-egFAD2 was transformed into Saccharomyces cerevisiae strain INVSc1 using lithium acetate method for expression under the induction of galactose. Yeast cells transformed with plasmid constructs containing egFAD12 produced an appreciable amount of linoleic acids (18:2(Δ9,)(12)), not normally present in wild-type yeast cells, indicating that the genes encoded functional Δ12-desaturase enzymes.
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214
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Baker MR, Tabb DL, Ching T, Zimmerman LJ, Sakharov IY, Li QX. Site-Specific N-Glycosylation Characterization of Windmill Palm Tree Peroxidase Using Novel Tools for Analysis of Plant Glycopeptide Mass Spectrometry Data. J Proteome Res 2016; 15:2026-38. [DOI: 10.1021/acs.jproteome.6b00205] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Margaret R. Baker
- Department
of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - David L. Tabb
- Department
of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37205, United States
| | - Travers Ching
- Department
of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
| | - Lisa J. Zimmerman
- Department
of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37205, United States
| | - Ivan Y. Sakharov
- Department
of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Qing X. Li
- Department
of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, Hawaii 96822, United States
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215
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da Silva AC, Grativol C, Thiebaut F, Hemerly AS, Ferreira PCG. Computational identification and comparative analysis of miRNA precursors in three palm species. PLANTA 2016; 243:1265-1277. [PMID: 26919984 DOI: 10.1007/s00425-016-2486-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/09/2016] [Indexed: 06/05/2023]
Abstract
In the present study, miRNA precursors in the genomes of three palm species were identified. Analyzes of sequence conservation and biological function of their putative targets contribute to understand the roles of miRNA in palm biology. MicroRNAs are small RNAs of 20-25 nucleotides in length, with important functions in the regulation of gene expression. Recent genome sequencing of the palm species Elaeis guineensis, Elaeis oleifera and Phoenix dactylifera have enabled the discovery of miRNA genes, which can be used as biotechnological tools in palm trees breeding. The goal of this study is the identification of miRNA precursors in the genomes of these species and their possible biological roles suggested by the mature miRNA-based regulation of target genes. Mature miRNA sequences from Arabidopsis thaliana, Oryza sativa, and Zea mays available at the miRBase were used to predict microRNA precursors in the palm genomes. Three hundred and thirty-eight precursors, ranging from 76 to 220 nucleotide (nt) in size and distributed in 33 families were identified. Moreover, we also identified 266 miRNA precursors of Musa acuminata, which are phylogenetically close to palms species. To understand the biological function of palm miRNAs, 374 putative miRNA targets were identified. An enrichment analysis of target-gene function was carried out using the agriGO tool. The results showed that the targets are involved in plant developmental processes, mainly regulating root development. Our findings contribute to increase the knowledge on microRNA roles in palm biology and could help breeding programs of palm trees.
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Affiliation(s)
- Aline Cunha da Silva
- Universidade Federal Rural da Amazonia, Belém, Brazil
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, CCS, Bl.L-29ss, Cidade Universitária, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Clícia Grativol
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Av. Alberto Lamego, 2000, P5-227A, Parque Califórnia, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Flávia Thiebaut
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, CCS, Bl.L-29ss, Cidade Universitária, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Adriana Silva Hemerly
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, CCS, Bl.L-29ss, Cidade Universitária, Rio de Janeiro, RJ, 21941-599, Brazil
| | - Paulo Cavalcanti Gomes Ferreira
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, CCS, Bl.L-29ss, Cidade Universitária, Rio de Janeiro, RJ, 21941-599, Brazil.
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216
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Ting NC, Yaakub Z, Kamaruddin K, Mayes S, Massawe F, Sambanthamurthi R, Jansen J, Low LET, Ithnin M, Kushairi A, Arulandoo X, Rosli R, Chan KL, Amiruddin N, Sritharan K, Lim CC, Nookiah R, Amiruddin MD, Singh R. Fine-mapping and cross-validation of QTLs linked to fatty acid composition in multiple independent interspecific crosses of oil palm. BMC Genomics 2016; 17:289. [PMID: 27079197 PMCID: PMC4832457 DOI: 10.1186/s12864-016-2607-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 03/28/2016] [Indexed: 12/21/2022] Open
Abstract
Background The commercial oil palm (Elaeis guineensis Jacq.) produces a mesocarp oil (commonly called ‘palm oil’) with approximately equal proportions of saturated and unsaturated fatty acids (FAs). An increase in unsaturated FAs content or iodine value (IV) as a measure of the degree of unsaturation would help to open up new markets for the oil. One way to manipulate the fatty acid composition (FAC) in palm oil is through introgression of favourable alleles from the American oil palm, E. oleifera, which has a more unsaturated oil. Results In this study, a segregating E. oleifera x E. guineensis (OxG) hybrid population for FAC is used to identify quantitative trait loci (QTLs) linked to IV and various FAs. QTL analysis revealed 10 major and two putative QTLs for IV and six FAs, C14:0, C16:0, C16:1, C18:0, C18:1 and C18:2 distributed across six linkage groups (LGs), OT1, T2, T3, OT4, OT6 and T9. The major QTLs for IV and C16:0 on LGOT1 explained 60.0 – 69.0 % of the phenotypic trait variation and were validated in two independent BC2 populations. The genomic interval contains several key structural genes in the FA and oil biosynthesis pathways such as PATE/FATB, HIBCH, BASS2, LACS4 and DGAT1 and also a relevant transcription factor (TF), WRI1. The literature suggests that some of these genes can exhibit pleiotropic effects in the regulatory networks of these traits. Using the whole genome sequence data, markers tightly linked to the candidate genes were also developed. Clustering trait values according to the allelic forms of these candidate markers revealed significant differences in the IV and FAs of the palms in the mapping and validation crosses. Conclusions The candidate gene approach described and exploited here is useful to identify the potential causal genes linked to FAC and can be adopted for marker-assisted selection (MAS) in oil palm. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2607-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ngoot-Chin Ting
- Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia.,School of Biosciences, University of Nottingham Malaysia Campus, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Zulkifli Yaakub
- Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | | | - Sean Mayes
- Plant and Crop Sciences, Sutton Bonington Campus, University of Nottingham, Sutton Bonington, Loughborough, LE12 5RD, UK
| | - Festo Massawe
- School of Biosciences, University of Nottingham Malaysia Campus, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | | | - Johannes Jansen
- Biometris, Wageningen University and Research Centre, P.O. Box 100, 6700 AC, Wageningen, The Netherlands
| | - Leslie Eng Ti Low
- Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Maizura Ithnin
- Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Ahmad Kushairi
- Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Xaviar Arulandoo
- United Plantations Bhd., Jendarata Estate, 36009, Teluk Intan, Perak, Malaysia
| | - Rozana Rosli
- Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Kuang-Lim Chan
- Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Nadzirah Amiruddin
- Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Kandha Sritharan
- United Plantations Bhd., Jendarata Estate, 36009, Teluk Intan, Perak, Malaysia
| | - Chin Ching Lim
- United Plantations Bhd., Jendarata Estate, 36009, Teluk Intan, Perak, Malaysia
| | - Rajanaidu Nookiah
- Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Mohd Din Amiruddin
- Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia
| | - Rajinder Singh
- Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia.
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217
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Comer JR, Zomlefer WB, Barrett CF, Stevenson DW, Heyduk K, Leebens-Mack JH. Nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae). Mol Phylogenet Evol 2016; 97:32-42. [DOI: 10.1016/j.ympev.2015.12.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 12/04/2015] [Accepted: 12/23/2015] [Indexed: 02/02/2023]
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218
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Huq A, Akter S, Nou IS, Kim HT, Jung YJ, Kang KK. Identification of functional SNPs in genes and their effects on plant phenotypes. ACTA ACUST UNITED AC 2016. [DOI: 10.5010/jpb.2016.43.1.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Amdadul Huq
- Department of Horticulture, Hankyong National University, Ansung City, Gyeonggi-do, 17579, Republic of Korea
| | - Shahina Akter
- Department of Horticulture, Hankyong National University, Ansung City, Gyeonggi-do, 17579, Republic of Korea
| | - Ill Sup Nou
- Department of Horticulture, Sunchon National University, 255, Jungang-ro, Suncheon, Jeonam-do, 57922, Korea
| | - Hoy Taek Kim
- Department of Horticulture, Sunchon National University, 255, Jungang-ro, Suncheon, Jeonam-do, 57922, Korea
| | - Yu Jin Jung
- Department of Horticulture, Hankyong National University, Ansung City, Gyeonggi-do, 17579, Republic of Korea
| | - Kwon Kyoo Kang
- Department of Horticulture, Hankyong National University, Ansung City, Gyeonggi-do, 17579, Republic of Korea
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219
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Abstract
We have witnessed an explosion in our understanding of the evolution and structure of plant genomes in recent years. Here, we highlight three important emergent realizations: (1) that the evolutionary history of all plant genomes contains multiple, cyclical episodes of whole-genome doubling that were followed by myriad fractionation processes; (2) that the vast majority of the variation in genome size reflects the dynamics of proliferation and loss of lineage-specific transposable elements; and (3) that various classes of small RNAs help shape genomic architecture and function. We illustrate ways in which understanding these organism-level and molecular genetic processes can be used for crop plant improvement.
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Affiliation(s)
- Jonathan F Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, 50011, USA.
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA.,Division of Plant Sciences, University of Missouri-Columbia, 52 Agriculture Laboratory, Columbia, MO, 65211, USA
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences and Department of Ecology and Evolutionary Biology, Tucson, AZ, 85750, USA.,T.T. Chang Genetic Resource Center, International Rice Research Institute, Los Baños, Laguna, Philippines
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220
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ACC oxidase and miRNA 159a, and their involvement in fresh fruit bunch yield (FFB) via sex ratio determination in oil palm. Mol Genet Genomics 2016; 291:1243-57. [DOI: 10.1007/s00438-016-1181-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 02/06/2016] [Indexed: 10/22/2022]
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221
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Thottathil GP, Jayasekaran K, Othman AS. Sequencing Crop Genomes: A Gateway to Improve Tropical Agriculture. Trop Life Sci Res 2016; 27:93-114. [PMID: 27019684 PMCID: PMC4807965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023] Open
Abstract
Agricultural development in the tropics lags behind development in the temperate latitudes due to the lack of advanced technology, and various biotic and abiotic factors. To cope with the increasing demand for food and other plant-based products, improved crop varieties have to be developed. To breed improved varieties, a better understanding of crop genetics is necessary. With the advent of next-generation DNA sequencing technologies, many important crop genomes have been sequenced. Primary importance has been given to food crops, including cereals, tuber crops, vegetables, and fruits. The DNA sequence information is extremely valuable for identifying key genes controlling important agronomic traits and for identifying genetic variability among the cultivars. However, massive DNA re-sequencing and gene expression studies have to be performed to substantially improve our understanding of crop genetics. Application of the knowledge obtained from the genomes, transcriptomes, expression studies, and epigenetic studies would enable the development of improved varieties and may lead to a second green revolution. The applications of next generation DNA sequencing technologies in crop improvement, its limitations, future prospects, and the features of important crop genome projects are reviewed herein.
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Affiliation(s)
- Gincy Paily Thottathil
- Centre for Chemical Biology, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia
| | - Kandakumar Jayasekaran
- Centre for Chemical Biology, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543
| | - Ahmad Sofiman Othman
- Centre for Chemical Biology, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia
- School of Biological Sciences, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia
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222
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Genome-wide association study identifies three key loci for high mesocarp oil content in perennial crop oil palm. Sci Rep 2016; 6:19075. [PMID: 26743827 PMCID: PMC4705476 DOI: 10.1038/srep19075] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 12/02/2015] [Indexed: 11/25/2022] Open
Abstract
GWAS in out-crossing perennial crops is typically limited by insufficient marker density to account for population diversity and effects of population structure resulting in high false positive rates. The perennial crop oil palm is the most productive oil crop. We performed GWAS for oil-to-dry-mesocarp content (O/DM) on 2,045 genotyped tenera palms using 200K SNPs that were selected based on the short-range linkage disequilibrium distance, which is inherent with long breeding cycles and heterogeneous breeding populations. Eighty loci were significantly associated with O/DM (p ≤ 10−4) and three key signals were found. We then evaluated the progeny of a Deli x AVROS breeding trial and a 4% higher O/DM was observed amongst those having the beneficial genotypes at two of the three key loci (p < 0.05). We have initiated MAS and large-scale planting of elite dura and pisifera parents to generate the new commercial tenera palms with higher O/DM potential.
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223
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Xiao Y, Xia W, Ma J, Mason AS, Fan H, Shi P, Lei X, Ma Z, Peng M. Genome-Wide Identification and Transferability of Microsatellite Markers between Palmae Species. FRONTIERS IN PLANT SCIENCE 2016; 7:1578. [PMID: 27826307 PMCID: PMC5078683 DOI: 10.3389/fpls.2016.01578] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/06/2016] [Indexed: 05/18/2023]
Abstract
The Palmae family contains 202 genera and approximately 2800 species. Except for Elaeis guineensis and Phoenix dactylifera, almost no genetic and genomic information is available for Palmae species. Therefore, this is an obstacle to the conservation and genetic assessment of Palmae species, especially those that are currently endangered. The study was performed to develop a large number of microsatellite markers which can be used for genetic analysis in different Palmae species. Based on the assembled genome of E. guineensis and P. dactylifera, a total of 814 383 and 371 629 microsatellites were identified. Among these microsatellites identified in E. guineensis, 734 509 primer pairs could be designed from the flanking sequences of these microsatellites. The majority (618 762) of these designed primer pairs had in silico products in the genome of E. guineensis. These 618 762 primer pairs were subsequently used to in silico amplify the genome of P. dactylifera. A total of 7 265 conserved microsatellites were identified between E. guineensis and P. dactylifera. One hundred and thirty-five primer pairs flanking the conserved SSRs were stochastically selected and validated to have high cross-genera transferability, varying from 16.7 to 93.3% with an average of 73.7%. These genome-wide conserved microsatellite markers will provide a useful tool for genetic assessment and conservation of different Palmae species 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 SciencesWenchang, China
- *Correspondence: Yong Xiao
| | - Wei Xia
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural SciencesWenchang, China
- College of Agriculture, Hainan UniversityHaikou, China
| | - Jianwei Ma
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural SciencesWenchang, China
| | - Annaliese S. Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University GiessenGiessen, Germany
| | - Haikuo Fan
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural SciencesWenchang, China
| | - Peng Shi
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural SciencesWenchang, China
| | - Xintao Lei
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural SciencesWenchang, China
- Xintao Lei
| | - Zilong Ma
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural ScienceHaikou, China
| | - Ming Peng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural ScienceHaikou, China
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224
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Ooi LCL, Low ETL, Abdullah MO, Nookiah R, Ting NC, Nagappan J, Manaf MAA, Chan KL, Halim MA, Azizi N, Omar W, Murad AJ, Lakey N, Ordway JM, Favello A, Budiman MA, Van Brunt A, Beil M, Leininger MT, Jiang N, Smith SW, Brown CR, Kuek ACS, Bahrain S, Hoynes-O’Connor A, Nguyen AY, Chaudhari HG, Shah SA, Choo YM, Sambanthamurthi R, Singh R. Non-tenera Contamination and the Economic Impact of SHELL Genetic Testing in the Malaysian Independent Oil Palm Industry. FRONTIERS IN PLANT SCIENCE 2016; 7:771. [PMID: 27446094 PMCID: PMC4914825 DOI: 10.3389/fpls.2016.00771] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/17/2016] [Indexed: 05/18/2023]
Abstract
Oil palm (Elaeis guineensis) is the most productive oil bearing crop worldwide. It has three fruit forms, namely dura (thick-shelled), pisifera (shell-less) and tenera (thin-shelled), which are controlled by the SHELL gene. The fruit forms exhibit monogenic co-dominant inheritance, where tenera is a hybrid obtained by crossing maternal dura and paternal pisifera palms. Commercial palm oil production is based on planting thin-shelled tenera palms, which typically yield 30% more oil than dura palms, while pisifera palms are female-sterile and have little to no palm oil yield. It is clear that tenera hybrids produce more oil than either parent due to single gene heterosis. The unintentional planting of dura or pisifera palms reduces overall yield and impacts land utilization that would otherwise be devoted to more productive tenera palms. Here, we identify three additional novel mutant alleles of the SHELL gene, which encode a type II MADS-box transcription factor, and determine oil yield via control of shell fruit form phenotype in a manner similar to two previously identified mutant SHELL alleles. Assays encompassing all five mutations account for all dura and pisifera palms analyzed. By assaying for these variants in 10,224 mature palms or seedlings, we report the first large scale accurate genotype-based determination of the fruit forms in independent oil palm planting sites and in the nurseries that supply them throughout Malaysia. The measured non-tenera contamination rate (10.9% overall on a weighted average basis) underscores the importance of SHELL genetic testing of seedlings prior to planting in production fields. By eliminating non-tenera contamination, comprehensive SHELL genetic testing can improve sustainability by increasing yield on existing planted lands. In addition, economic modeling demonstrates that SHELL gene testing will confer substantial annual economic gains to the oil palm industry, to Malaysian gross national income and to Malaysian government tax receipts.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Wahid Omar
- Malaysian Palm Oil BoardKajang, Malaysia
| | | | - Nathan Lakey
- Orion Genomics, LLC, St. LouisMO, USA
- Orion Biosains Sdn BhdPuchong, Malaysia
| | - Jared M. Ordway
- Orion Genomics, LLC, St. LouisMO, USA
- Orion Biosains Sdn BhdPuchong, Malaysia
| | - Anthony Favello
- Orion Genomics, LLC, St. LouisMO, USA
- Orion Biosains Sdn BhdPuchong, Malaysia
| | | | | | | | | | - Nan Jiang
- Orion Genomics, LLC, St. LouisMO, USA
| | | | | | | | | | | | | | | | | | | | | | - Rajinder Singh
- Malaysian Palm Oil BoardKajang, Malaysia
- *Correspondence: Rajinder Singh,
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225
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Lamade E, Tcherkez G, Darlan NH, Rodrigues RL, Fresneau C, Mauve C, Lamothe-Sibold M, Sketriené D, Ghashghaie J. Natural (13) C distribution in oil palm (Elaeis guineensis Jacq.) and consequences for allocation pattern. PLANT, CELL & ENVIRONMENT 2016; 39:199-212. [PMID: 26228944 DOI: 10.1111/pce.12606] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 06/26/2015] [Indexed: 06/04/2023]
Abstract
Oil palm has now become one of the most important crops, palm oil representing nearly 25% of global plant oil consumption. Many studies have thus addressed oil palm ecophysiology and photosynthesis-based models of carbon allocation have been used. However, there is a lack of experimental data on carbon fixation and redistribution within palm trees, and important C-sinks have not been fully characterized yet. Here, we carried out extensive measurement of natural (13) C-abundance (δ(13) C) in oil palm tissues, including fruits at different maturation stages. We find a (13) C-enrichment in heterotrophic organs compared to mature leaves, with roots being the most (13) C-enriched. The δ(13) C in fruits decreased during maturation, reflecting the accumulation in (13) C-depleted lipids. We further used observed δ(13) C values to compute plausible carbon fluxes using a steady-state model of (13) C-distribution including metabolic isotope effects ((12) v/(13) v). The results suggest that fruits represent a major respiratory loss (≈39% of total tree respiration) and that sink organs such as fruits are fed by sucrose from leaves. That is, glucose appears to be a quantitatively important compound in palm tissues, but computations indicate that it is involved in dynamic starch metabolism rather that C-exchange between organs.
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Affiliation(s)
- Emmanuelle Lamade
- UPR34 Performance of Perennial Cropping Systems, CIRAD-PERSYST, Montpellier, 34398, France
| | - Guillaume Tcherkez
- Research School of Biology, College of Medicine, Biology and Environment, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
| | - Nuzul Hijri Darlan
- Indonesian Oil Palm Research Institute, IOPRI, Jl. Brigjen Katamso 51, Medan, North Sumatra, Indonesia
| | | | - Chantal Fresneau
- ESE, Université Paris-Sud, CNRS UMR 8079, Orsay cedex, 91405, France
| | - Caroline Mauve
- Plateforme Métabolisme-Métabolome, Université Paris-Sud, IPS2, Orsay cedex, 91405, France
| | - Marlène Lamothe-Sibold
- Plateforme Métabolisme-Métabolome, Université Paris-Sud, IPS2, Orsay cedex, 91405, France
| | - Diana Sketriené
- ESE, Université Paris-Sud, CNRS UMR 8079, Orsay cedex, 91405, France
| | - Jaleh Ghashghaie
- ESE, Université Paris-Sud, CNRS UMR 8079, Orsay cedex, 91405, France
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226
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AJAMBANG W, VOLKAERT H, SUDARSONO S. Carbohydrate deprivation upsurges the expression of genes responsible for programmed cell death in inflorescence tissues of oil palm (Elaeis guineensis Jacq.). Turk J Biol 2016. [DOI: 10.3906/biy-1602-26] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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227
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Pootakham W, Sonthirod C, Naktang C, Jomchai N, Sangsrakru D, Tangphatsornruang S. Effects of methylation-sensitive enzymes on the enrichment of genic SNPs and the degree of genome complexity reduction in a two-enzyme genotyping-by-sequencing (GBS) approach: a case study in oil palm ( Elaeis guineensis). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2016; 36:154. [PMID: 27942246 PMCID: PMC5104780 DOI: 10.1007/s11032-016-0572-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 10/20/2016] [Indexed: 05/08/2023]
Abstract
Advances in next generation sequencing have facilitated a large-scale single nucleotide polymorphism (SNP) discovery in many crop species. Genotyping-by-sequencing (GBS) approach couples next generation sequencing with genome complexity reduction techniques to simultaneously identify and genotype SNPs. Choice of enzymes used in GBS library preparation depends on several factors including the number of markers required, the desired level of multiplexing, and whether the enrichment of genic SNP is preferred. We evaluated various combinations of methylation-sensitive (AatII, PstI, MspI) and methylation-insensitive (SphI, MseI) enzymes for their effectiveness in genome complexity reduction and enrichment of genic SNPs. We discovered that the use of two methylation-sensitive enzymes effectively reduced genome complexity and did not require a size selection step. On the contrary, the genome coverage of libraries constructed with methylation-insensitive enzymes was quite high, and the additional size selection step may be required to increase the overall read depth. We also demonstrated the effectiveness of methylation-sensitive enzymes in enriching for SNPs located in genic regions. When two methylation-insensitive enzymes were used, only 16% of SNPs identified were located in genes and 18% in the vicinity (± 5 kb) of the genic regions, while most SNPs resided in the intergenic regions. In contrast, a remarkable degree of enrichment was observed when two methylation-sensitive enzymes were employed. Almost two thirds of the SNPs were located either inside (32-36%) or in the vicinity (28-31%) of the genic regions. These results provide useful information to help researchers choose appropriate GBS enzymes in oil palm and other crop species.
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Affiliation(s)
- Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani, 12120 Thailand
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani, 12120 Thailand
| | - Chaiwat Naktang
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani, 12120 Thailand
| | - Nukoon Jomchai
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani, 12120 Thailand
| | - Duangjai Sangsrakru
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani, 12120 Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani, 12120 Thailand
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He Z, Zhang Z, Guo W, Zhang Y, Zhou R, Shi S. De Novo Assembly of Coding Sequences of the Mangrove Palm (Nypa fruticans) Using RNA-Seq and Discovery of Whole-Genome Duplications in the Ancestor of Palms. PLoS One 2015; 10:e0145385. [PMID: 26684618 PMCID: PMC4684314 DOI: 10.1371/journal.pone.0145385] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 12/03/2015] [Indexed: 11/19/2022] Open
Abstract
Nypa fruticans (Arecaceae) is the only monocot species of true mangroves. This species represents the earliest mangrove fossil recorded. How N. fruticans adapts to the harsh and unstable intertidal zone is an interesting question. However, the 60 gene segments deposited in NCBI are insufficient for solving this question. In this study, we sequenced, assembled and annotated the transcriptome of N. fruticans using next-generation sequencing technology. A total of 19,918,800 clean paired-end reads were de novo assembled into 45,368 unigenes with a N50 length of 1,096 bp. A total of 41.35% unigenes were functionally annotated using Blast2GO. Many genes annotated to "response to stress" and 15 putative positively selected genes were identified. Simple sequence repeats were identified and compared with other palms. The divergence time between N. fruticans and other palms was estimated at 75 million years ago using the genomic data, which is consistent with the fossil record. After calculating the synonymous substitution rate between paralogs, we found that two whole-genome duplication events were shared by N. fruticans and other palms. These duplication events provided a large amount of raw material for the more than 2,000 later speciation events in Arecaceae. This study provides a high quality resource for further functional and evolutionary studies of N. fruticans and palms in general.
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Affiliation(s)
- Ziwen He
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China
| | - Zhang Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China
| | - Wuxia Guo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China
| | - Ying Zhang
- College of Life Sciences, Hainan Normal University, Haikou, Hainan 571158, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China
- * E-mail:
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229
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Ganie SH, Upadhyay P, Das S, Prasad Sharma M. Authentication of medicinal plants by DNA markers. PLANT GENE 2015; 4:83-99. [PMID: 32289060 PMCID: PMC7103949 DOI: 10.1016/j.plgene.2015.10.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 10/01/2015] [Accepted: 10/07/2015] [Indexed: 11/21/2022]
Abstract
Medicinal plants have been used worldwide for centuries to maintain health and to treat diseases, more so chronic diseases. However, adulteration and use of spurious materials as substitutes have become a major concern for users and industry for reasons of safety and efficacy. Therefore, authentication of medicinal plants is of utmost importance. Morphological, anatomical, chemical and DNA markers solve the problem by differentiating the genuine material from the adulterants, substitutes and spurious drugs. DNA markers use nucleotide sequences to identify species; it takes preference over the other two markers being not age dependent, tissue specific and having a higher discriminating power. Therefore, characterization of plants with such markers is an ideal approach for identification of medicinal plant species and populations/varieties of the same species. Availability of certified taxonomic specimens in herbaria is certainly required for unambiguous confirmation through final visual comparison and analysis.
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Affiliation(s)
| | - Priti Upadhyay
- Dept. of Botany, University of Delhi, Delhi 110007, India
| | - Sandip Das
- Dept. of Botany, University of Delhi, Delhi 110007, India
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230
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Ming R, VanBuren R, Wai CM, Tang H, Schatz MC, Bowers JE, Lyons E, Wang ML, Chen J, Biggers E, Zhang J, Huang L, Zhang L, Miao W, Zhang J, Ye Z, Miao C, Lin Z, Wang H, Zhou H, Yim WC, Priest HD, Zheng C, Woodhouse M, Edger PP, Guyot R, Guo HB, Guo H, Zheng G, Singh R, Sharma A, Min X, Zheng Y, Lee H, Gurtowski J, Sedlazeck FJ, Harkess A, McKain MR, Liao Z, Fang J, Liu J, Zhang X, Zhang Q, Hu W, Qin Y, Wang K, Chen LY, Shirley N, Lin YR, Liu LY, Hernandez AG, Wright CL, Bulone V, Tuskan GA, Heath K, Zee F, Moore PH, Sunkar R, Leebens-Mack JH, Mockler T, Bennetzen JL, Freeling M, Sankoff D, Paterson AH, Zhu X, Yang X, Smith JAC, Cushman JC, Paull RE, Yu Q. The pineapple genome and the evolution of CAM photosynthesis. Nat Genet 2015; 47:1435-42. [PMID: 26523774 PMCID: PMC4867222 DOI: 10.1038/ng.3435] [Citation(s) in RCA: 310] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/05/2015] [Indexed: 12/21/2022]
Abstract
Pineapple (Ananas comosus (L.) Merr.) is the most economically valuable crop possessing crassulacean acid metabolism (CAM), a photosynthetic carbon assimilation pathway with high water-use efficiency, and the second most important tropical fruit. We sequenced the genomes of pineapple varieties F153 and MD2 and a wild pineapple relative, Ananas bracteatus accession CB5. The pineapple genome has one fewer ancient whole-genome duplication event than sequenced grass genomes and a conserved karyotype with seven chromosomes from before the ρ duplication event. The pineapple lineage has transitioned from C3 photosynthesis to CAM, with CAM-related genes exhibiting a diel expression pattern in photosynthetic tissues. CAM pathway genes were enriched with cis-regulatory elements associated with the regulation of circadian clock genes, providing the first cis-regulatory link between CAM and circadian clock regulation. Pineapple CAM photosynthesis evolved by the reconfiguration of pathways in C3 plants, through the regulatory neofunctionalization of preexisting genes and not through the acquisition of neofunctionalized genes via whole-genome or tandem gene duplication.
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Affiliation(s)
- Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Robert VanBuren
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Ching Man Wai
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Haibao Tang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
- iPlant Collaborative/University of Arizona, Tuscon, AZ 85719, USA
| | | | - John E. Bowers
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Eric Lyons
- iPlant Collaborative/University of Arizona, Tuscon, AZ 85719, USA
| | - Ming-Li Wang
- Hawaii Agriculture Research Center, Kunia, HI 96759, USA
| | - Jung Chen
- Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, HI 96822, USA
| | - Eric Biggers
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724, USA
| | - Jisen Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Lixian Huang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Lingmao Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Wenjing Miao
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jian Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Zhangyao Ye
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Chenyong Miao
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Zhicong Lin
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Hao Wang
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Hongye Zhou
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Won C. Yim
- Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV 89557-0330, USA
| | | | - Chunfang Zheng
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Canada K1N 6N5
| | - Margaret Woodhouse
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Patrick P. Edger
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Romain Guyot
- IRD, UMR DIADE, EVODYN, BP 64501, 34394 Montpellier Cedex 5, France
| | - Hao-Bo Guo
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Hong Guo
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Guangyong Zheng
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ratnesh Singh
- Texas A&M AgriLife Research, Department of Plant Pathology & Microbiology, Texas A&M University System, Dallas, TX 75252, USA
| | - Anupma Sharma
- Texas A&M AgriLife Research, Department of Plant Pathology & Microbiology, Texas A&M University System, Dallas, TX 75252, USA
| | - Xiangjia Min
- Department of Biological Sciences, Youngstown State University, Youngstown, OH 44555, USA
| | - Yun Zheng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Hayan Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724, USA
| | - James Gurtowski
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY11724, USA
| | | | - Alex Harkess
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | | | - Zhenyang Liao
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jingping Fang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Juan Liu
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Xiaodan Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Qing Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Weichang Hu
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Yuan Qin
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Kai Wang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Li-Yu Chen
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Neil Shirley
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus Urrbrae, South Australia 5064, Australia
| | - Yann-Rong Lin
- Department of Agronomy, National Taiwan University, Taipei 10617, Taiwan
| | - Li-Yu Liu
- Department of Agronomy, National Taiwan University, Taipei 10617, Taiwan
| | - Alvaro G. Hernandez
- W.M. Keck Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chris L. Wright
- W.M. Keck Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Vincent Bulone
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus Urrbrae, South Australia 5064, Australia
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Katy Heath
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Francis Zee
- USDA-ARS, Pacific Basin Agricultural Research Center, Hilo, HI 96720, USA
| | - Paul H. Moore
- Hawaii Agriculture Research Center, Kunia, HI 96759, USA
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, 246 Noble Research Center, Oklahoma State University, Stillwater, OK 74078, USA
| | | | - Todd Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | - Michael Freeling
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - David Sankoff
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Canada K1N 6N5
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Xinguang Zhu
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - J. Andrew C. Smith
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - John C. Cushman
- Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV 89557-0330, USA
| | - Robert E. Paull
- Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, HI 96822, USA
| | - Qingyi Yu
- Texas A&M AgriLife Research, Department of Plant Pathology & Microbiology, Texas A&M University System, Dallas, TX 75252, USA
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Schilling S, Gramzow L, Lobbes D, Kirbis A, Weilandt L, Hoffmeier A, Junker A, Weigelt-Fischer K, Klukas C, Wu F, Meng Z, Altmann T, Theißen G. Non-canonical structure, function and phylogeny of the Bsister MADS-box gene OsMADS30 of rice (Oryza sativa). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:1059-1072. [PMID: 26473514 DOI: 10.1111/tpj.13055] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 10/02/2015] [Accepted: 10/06/2015] [Indexed: 06/05/2023]
Abstract
Bsister MADS-box genes play key roles in female reproductive organ and seed development throughout seed plants. This view is supported by their high conservation in terms of sequence, expression and function. In grasses, there are three subclades of Bsister genes: the OsMADS29-, the OsMADS30- and the OsMADS31-like genes. Here, we report on the evolution of the OsMADS30-like genes. Our analyses indicate that these genes evolved under relaxed purifying selection and are rather weakly expressed. OsMADS30, the representative of the OsMADS30-like genes from rice (Oryza sativa), shows strong sequence deviations in its 3' region when compared to orthologues from other grass species. We show that this is due to a 2.4-kbp insertion, possibly of a hitherto unknown helitron, which confers a heterologous C-terminal domain to OsMADS30. This putative helitron is not present in the OsMADS30 orthologues from closely related wild rice species, pointing to a relatively recent insertion event. Unlike other Bsister mutants O. sativa plants carrying a T-DNA insertion in the OsMADS30 gene do not show aberrant seed phenotypes, indicating that OsMADS30 likely does not have a canonical 'Bsister function'. However, imaging-based phenotyping of the T-DNA carrying plants revealed alterations in shoot size and architecture. We hypothesize that sequence deviations that accumulated during a period of relaxed selection in the gene lineage that led to OsMADS30 and the alteration of the C-terminal domain might have been a precondition for a potential neo-functionalization of OsMADS30 in O. sativa.
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Affiliation(s)
- Susanne Schilling
- Department of Genetics, Friedrich Schiller University Jena, Jena, D-07743, Germany
| | - Lydia Gramzow
- Department of Genetics, Friedrich Schiller University Jena, Jena, D-07743, Germany
| | - Dajana Lobbes
- Department of Genetics, Friedrich Schiller University Jena, Jena, D-07743, Germany
| | - Alexander Kirbis
- Department of Genetics, Friedrich Schiller University Jena, Jena, D-07743, Germany
| | - Lisa Weilandt
- Department of Genetics, Friedrich Schiller University Jena, Jena, D-07743, Germany
| | - Andrea Hoffmeier
- Department of Genetics, Friedrich Schiller University Jena, Jena, D-07743, Germany
| | - Astrid Junker
- Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, D-06466, Germany
| | - Kathleen Weigelt-Fischer
- Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, D-06466, Germany
| | - Christian Klukas
- Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, D-06466, Germany
| | - Feng Wu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zheng Meng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Thomas Altmann
- Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, D-06466, Germany
| | - Günter Theißen
- Department of Genetics, Friedrich Schiller University Jena, Jena, D-07743, Germany
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Beulé T, Agbessi MD, Dussert S, Jaligot E, Guyot R. Genome-wide analysis of LTR-retrotransposons in oil palm. BMC Genomics 2015; 16:795. [PMID: 26470789 PMCID: PMC4608283 DOI: 10.1186/s12864-015-2023-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 10/07/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The oil palm (Elaeis guineensis Jacq.) is a major cultivated crop and the world's largest source of edible vegetable oil. The genus Elaeis comprises two species E. guineensis, the commercial African oil palm and E. oleifera, which is used in oil palm genetic breeding. The recent publication of both the African oil palm genome assembly and the first draft sequence of its Latin American relative now allows us to tackle the challenge of understanding the genome composition, structure and evolution of these palm genomes through the annotation of their repeated sequences. METHODS In this study, we identified, annotated and compared Transposable Elements (TE) from the African and Latin American oil palms. In a first step, Transposable Element databases were built through de novo detection in both genome sequences then the TE content of both genomes was estimated. Then putative full-length retrotransposons with Long Terminal Repeats (LTRs) were further identified in the E. guineensis genome for characterization of their structural diversity, copy number and chromosomal distribution. Finally, their relative expression in several tissues was determined through in silico analysis of publicly available transcriptome data. RESULTS Our results reveal a congruence in the transpositional history of LTR retrotransposons between E. oleifera and E. guineensis, especially the Sto-4 family. Also, we have identified and described 583 full-length LTR-retrotransposons in the Elaeis guineensis genome. Our work shows that these elements are most likely no longer mobile and that no recent insertion event has occurred. Moreover, the analysis of chromosomal distribution suggests a preferential insertion of Copia elements in gene-rich regions, whereas Gypsy elements appear to be evenly distributed throughout the genome. CONCLUSIONS Considering the high proportion of LTR retrotransposon in the oil palm genome, our work will contribute to a greater understanding of their impact on genome organization and evolution. Moreover, the knowledge gained from this study constitutes a valuable resource for both the improvement of genome annotation and the investigation of the evolutionary history of palms.
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Affiliation(s)
- Thierry Beulé
- CIRAD, UMR DIADE (IRD, UM), 34394, Montpellier, France.
| | | | | | | | - Romain Guyot
- IRD, UMR IPME (IRD, CIRAD, UM), 34394, Montpellier, France.
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Gunn BF, Baudouin L, Beulé T, Ilbert P, Duperray C, Crisp M, Issali A, Konan JL, Rival A. Ploidy and domestication are associated with genome size variation in Palms. AMERICAN JOURNAL OF BOTANY 2015; 102:1625-1633. [PMID: 26437888 DOI: 10.3732/ajb.1500164] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 08/24/2015] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY The genome size of a species (C-value) is associated with growth, development and adaptation to environmental changes. Angiosperm C-values range 1200-fold and frequently vary within species, although little is known about the impacts of domestication on genome size. Genome size variation among related species of palms is of evolutionary significance because changes characterize clades and may be associated with polyploidy, transposon amplifications, deletions, or rearrangements. Further knowledge of genome size will provide crucial information needed for planning of whole genome sequencing and accurate annotations. We studied the genome size of Cocos nucifera and its variation among cultivars, and compared it to values for related palms from the Attaleinae subtribe. METHODS Flow cytometric analysis of isolated nuclei from young palm leaves was used to estimate genome sizes of 23 coconut cultivars (Talls, Dwarfs, and hybrids) worldwide and 17 Cocoseae species. Ancestral genome size was reconstructed on a maximum likelihood phylogeny of Attaleinae from seven WRKY loci. KEY RESULTS The coconut genome is large-averaging 5.966 pg-and shows intraspecific variation associated with domestication. Variation among Tall coconuts was significantly greater than among Dwarfs. Attaleinae genomes showed moderate size variation across genera, except polyploids Jubaeopsis caffra, Voanioala gerardii, Beccariophoenix alfredii, and Allagoptera caudescens, which had larger genomes. CONCLUSIONS Our results contribute to the understanding of the relationship between domestication and genome size in long-lived tree crops and provide a basis for whole-genome sequencing of the coconut and other domesticated plants. Polyploidy evolved independently in two clades within Attaleinae.
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Affiliation(s)
- Bee F Gunn
- Research School of Biology, Division of Evolution, Ecology and Genetics, The Australian National University, Acton, ACT 2601, Australia
| | | | | | | | - Christophe Duperray
- Montpellier Rio Imaging, IRB, INSERM U1040, CHU de Montpellier 34295 Montpellier, France
| | - Michael Crisp
- Research School of Biology, Division of Evolution, Ecology and Genetics, The Australian National University, Acton, ACT 2601, Australia
| | - Auguste Issali
- Station de Recherche Marc Delorme, Port Bouët. 07 BP 13 Abidjan, Côte d'Ivoire
| | - Jean-Louis Konan
- Station de Recherche Marc Delorme, Port Bouët. 07 BP 13 Abidjan, Côte d'Ivoire
| | - Alain Rival
- CIRAD, UMR DIADE, F-34398 Montpellier, France
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Ong-Abdullah M, Ordway JM, Jiang N, Ooi SE, Kok SY, Sarpan N, Azimi N, Hashim AT, Ishak Z, Rosli SK, Malike FA, Bakar NAA, Marjuni M, Abdullah N, Yaakub Z, Amiruddin MD, Nookiah R, Singh R, Low ETL, Chan KL, Azizi N, Smith SW, Bacher B, Budiman MA, Van Brunt A, Wischmeyer C, Beil M, Hogan M, Lakey N, Lim CC, Arulandoo X, Wong CK, Choo CN, Wong WC, Kwan YY, Alwee SSRS, Sambanthamurthi R, Martienssen RA. Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm. Nature 2015; 525:533-7. [PMID: 26352475 PMCID: PMC4857894 DOI: 10.1038/nature15365] [Citation(s) in RCA: 271] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 08/10/2015] [Indexed: 12/25/2022]
Abstract
Somaclonal variation arises in plants and animals when differentiated somatic cells are induced into a pluripotent state, but the resulting clones differ from each other and from their parents. In agriculture, somaclonal variation has hindered the micropropagation of elite hybrids and genetically modified crops, but the mechanism responsible remains unknown. The oil palm fruit 'mantled' abnormality is a somaclonal variant arising from tissue culture that drastically reduces yield, and has largely halted efforts to clone elite hybrids for oil production. Widely regarded as an epigenetic phenomenon, 'mantling' has defied explanation, but here we identify the MANTLED locus using epigenome-wide association studies of the African oil palm Elaeis guineensis. DNA hypomethylation of a LINE retrotransposon related to rice Karma, in the intron of the homeotic gene DEFICIENS, is common to all mantled clones and is associated with alternative splicing and premature termination. Dense methylation near the Karma splice site (termed the Good Karma epiallele) predicts normal fruit set, whereas hypomethylation (the Bad Karma epiallele) predicts homeotic transformation, parthenocarpy and marked loss of yield. Loss of Karma methylation and of small RNA in tissue culture contributes to the origin of mantled, while restoration in spontaneous revertants accounts for non-Mendelian inheritance. The ability to predict and cull mantling at the plantlet stage will facilitate the introduction of higher performing clones and optimize environmentally sensitive land resources.
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Affiliation(s)
- Meilina Ong-Abdullah
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Jared M Ordway
- Orion Genomics, 4041 Forest Park Avenue, St Louis, Missouri 63108, USA
| | - Nan Jiang
- Orion Genomics, 4041 Forest Park Avenue, St Louis, Missouri 63108, USA
| | - Siew-Eng Ooi
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Sau-Yee Kok
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Norashikin Sarpan
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Nuraziyan Azimi
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Ahmad Tarmizi Hashim
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Zamzuri Ishak
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Samsul Kamal Rosli
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Fadila Ahmad Malike
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Nor Azwani Abu Bakar
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Marhalil Marjuni
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Norziha Abdullah
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Zulkifli Yaakub
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Mohd Din Amiruddin
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Rajanaidu Nookiah
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Rajinder Singh
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Eng-Ti Leslie Low
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Kuang-Lim Chan
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Norazah Azizi
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Steven W Smith
- Orion Genomics, 4041 Forest Park Avenue, St Louis, Missouri 63108, USA
| | - Blaire Bacher
- Orion Genomics, 4041 Forest Park Avenue, St Louis, Missouri 63108, USA
| | | | - Andrew Van Brunt
- Orion Genomics, 4041 Forest Park Avenue, St Louis, Missouri 63108, USA
| | - Corey Wischmeyer
- Orion Genomics, 4041 Forest Park Avenue, St Louis, Missouri 63108, USA
| | - Melissa Beil
- Orion Genomics, 4041 Forest Park Avenue, St Louis, Missouri 63108, USA
| | - Michael Hogan
- Orion Genomics, 4041 Forest Park Avenue, St Louis, Missouri 63108, USA
| | - Nathan Lakey
- Orion Genomics, 4041 Forest Park Avenue, St Louis, Missouri 63108, USA
| | - Chin-Ching Lim
- United Plantations Berhad, Jendarata Estate, 36009 Teluk Intan, Perak, Malaysia
| | - Xaviar Arulandoo
- United Plantations Berhad, Jendarata Estate, 36009 Teluk Intan, Perak, Malaysia
| | - Choo-Kien Wong
- Applied Agricultural Resources Sdn Bhd, No. 11, Jalan Teknologi 3/6, Taman Sains Selangor 1, 47810 Kota Damansara, Petaling Jaya, Selangor, Malaysia
| | - Chin-Nee Choo
- Applied Agricultural Resources Sdn Bhd, No. 11, Jalan Teknologi 3/6, Taman Sains Selangor 1, 47810 Kota Damansara, Petaling Jaya, Selangor, Malaysia
| | - Wei-Chee Wong
- Applied Agricultural Resources Sdn Bhd, No. 11, Jalan Teknologi 3/6, Taman Sains Selangor 1, 47810 Kota Damansara, Petaling Jaya, Selangor, Malaysia
| | - Yen-Yen Kwan
- FELDA Global Ventures R&D Sdn Bhd, c/o FELDA Biotechnology Centre, PT 23417, Lengkuk Teknologi, 71760 Bandar Enstek, Negeri Sembilan, Malaysia
| | - Sharifah Shahrul Rabiah Syed Alwee
- FELDA Global Ventures R&D Sdn Bhd, c/o FELDA Biotechnology Centre, PT 23417, Lengkuk Teknologi, 71760 Bandar Enstek, Negeri Sembilan, Malaysia
| | | | - Robert A Martienssen
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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235
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Cloning and Expression of Oil Palm (Elaeis guineensis Jacq.) Type 2 Ribosome Inactivating Protein in Escherichia coli. Int J Pept Res Ther 2015. [DOI: 10.1007/s10989-015-9485-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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236
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Ho CL, Tan YC. Molecular defense response of oil palm to Ganoderma infection. PHYTOCHEMISTRY 2015; 114:168-77. [PMID: 25457484 DOI: 10.1016/j.phytochem.2014.10.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 10/01/2014] [Accepted: 10/16/2014] [Indexed: 05/15/2023]
Abstract
Basal stem rot (BSR) of oil palm roots is due to the invasion of fungal mycelia of Ganoderma species which spreads to the bole of the stem. In addition to root contact, BSR can also spread by airborne basidiospores. These fungi are able to break down cell wall components including lignin. BSR not only decreases oil yield, it also causes the stands to collapse thus causing severe economic loss to the oil palm industry. The transmission and mode of action of Ganoderma, its interactions with oil palm as a hemibiotroph, and the molecular defence responses of oil palm to the infection of Ganoderma boninense in BSR are reviewed, based on the transcript profiles of infected oil palms. The knowledge gaps that need to be filled in oil palm-Ganoderma molecular interactions i.e. the associations of hypersensitive reaction (HR)-induced cell death and reactive oxygen species (ROS) kinetics to the susceptibility of oil palm to Ganoderma spp., the interactions of phytohormones (salicylate, jasmonate and ethylene) at early and late stages of BSR, and cell wall strengthening through increased production of guaiacyl (G)-type lignin, are also discussed.
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Affiliation(s)
- C-L Ho
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM-Serdang, Selangor, Malaysia; Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400 UPM-Serdang, Selangor, Malaysia.
| | - Y-C Tan
- Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400 UPM-Serdang, Selangor, Malaysia
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237
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Yan L, Wang X, Liu H, Tian Y, Lian J, Yang R, Hao S, Wang X, Yang S, Li Q, Qi S, Kui L, Okpekum M, Ma X, Zhang J, Ding Z, Zhang G, Wang W, Dong Y, Sheng J. The Genome of Dendrobium officinale Illuminates the Biology of the Important Traditional Chinese Orchid Herb. MOLECULAR PLANT 2015; 8:922-34. [PMID: 25825286 DOI: 10.1016/j.molp.2014.12.011] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 12/15/2014] [Accepted: 12/16/2014] [Indexed: 05/05/2023]
Abstract
Dendrobium officinale Kimura et Migo is a traditional Chinese orchid herb that has both ornamental value and a broad range of therapeutic effects. Here, we report the first de novo assembled 1.35 Gb genome sequences for D. officinale by combining the second-generation Illumina Hiseq 2000 and third-generation PacBio sequencing technologies. We found that orchids have a complete inflorescence gene set and have some specific inflorescence genes. We observed gene expansion in gene families related to fungus symbiosis and drought resistance. We analyzed biosynthesis pathways of medicinal components of D. officinale and found extensive duplication of SPS and SuSy genes, which are related to polysaccharide generation, and that the pathway of D. officinale alkaloid synthesis could be extended to generate 16-epivellosimine. The D. officinale genome assembly demonstrates a new approach to deciphering large complex genomes and, as an important orchid species and a traditional Chinese medicine, the D. officinale genome will facilitate future research on the evolution of orchid plants, as well as the study of medicinal components and potential genetic breeding of the dendrobe.
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Affiliation(s)
- Liang Yan
- College of Life Science, Jilin University, Changchun 130012, China; Pu'er Institute of Pu-er Tea, Pu'er 665000, China
| | - Xiao Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China
| | - Hui Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China
| | - Yang Tian
- College of Life Science, Jilin University, Changchun 130012, China; Key Laboratory of Puerh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Jinmin Lian
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Ruijuan Yang
- Pu'er Institute of Pu-er Tea, Pu'er 665000, China
| | - Shumei Hao
- Yunnan University, Kunming 650091, China
| | - Xuanjun Wang
- Key Laboratory of Puerh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Shengchao Yang
- Key Laboratory of Puerh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Qiye Li
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Shuai Qi
- Agri-Biotech Lab, Kunming 650502, China
| | - Ling Kui
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China
| | - Moses Okpekum
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China
| | - Xiao Ma
- Key Laboratory of Puerh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Jiajin Zhang
- School of Science and Information Engineering, Yunnan Agricultural University, Kunming 650201, China
| | - Zhaoli Ding
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China
| | - Guojie Zhang
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China
| | - Yang Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China; Laboratory of Applied Genomics and Synthetic Biology, College of Life Science, Kunming University of Science and Technology, Kunming 650500, China.
| | - Jun Sheng
- College of Life Science, Jilin University, Changchun 130012, China; Key Laboratory of Puerh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China.
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238
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Hollender CA, Dardick C. Molecular basis of angiosperm tree architecture. THE NEW PHYTOLOGIST 2015; 206:541-56. [PMID: 25483362 DOI: 10.1111/nph.13204] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 10/30/2014] [Indexed: 05/24/2023]
Abstract
The architecture of trees greatly impacts the productivity of orchards and forestry plantations. Amassing greater knowledge on the molecular genetics that underlie tree form can benefit these industries, as well as contribute to basic knowledge of plant developmental biology. This review describes the fundamental components of branch architecture, a prominent aspect of tree structure, as well as genetic and hormonal influences inferred from studies in model plant systems and from trees with non-standard architectures. The bulk of the molecular and genetic data described here is from studies of fruit trees and poplar, as these species have been the primary subjects of investigation in this field of science.
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Affiliation(s)
- Courtney A Hollender
- Appalachian Fruit Research Station, Agricultural Research Service, United States Department of Agriculture, 2217 Wiltshire Rd, Kearnysville, WV, 25430, USA
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239
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Parveez GKA, Rasid OA, Masani MYA, Sambanthamurthi R. Biotechnology of oil palm: strategies towards manipulation of lipid content and composition. PLANT CELL REPORTS 2015; 34:533-43. [PMID: 25480400 DOI: 10.1007/s00299-014-1722-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 11/22/2014] [Accepted: 11/25/2014] [Indexed: 05/13/2023]
Abstract
Oil palm is a major economic crop for Malaysia. The major challenges faced by the industry are labor shortage, availability of arable land and unstable commodity price. This has caused the industry to diversify its applications into higher value products besides increasing its yield. While conventional breeding has its limitations, biotechnology was identified as one of the tools for overcoming the above challenges. Research on biotechnology of oil palm began more than two decades ago leveraging a multidisciplinary approach involving biochemical studies, gene and promoter isolation, transformation vector construction and finally genetic transformation to produce the targeted products. The main target of oil palm biotechnology research is to increase oleic acid in the mesocarp. Other targets are stearic acid, palmitoleic acid, ricinoleic acid, lycopene (carotenoid) and biodegradable plastics. Significant achievements were reported for the biochemical studies, isolation of useful oil palm genes and characterization of important promoters. A large number of transformation constructs for various targeted products were successfully produced using the isolated oil palm genes and promoters. Finally transformation of these constructs into oil palm embryogenic calli was carried out while the regeneration of transgenic oil palm harboring the useful genes is in progress.
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Affiliation(s)
- Ghulam Kadir Ahmad Parveez
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, P.O. Box 10620, 50720, Kuala Lumpur, Malaysia,
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240
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Cros D, Denis M, Sánchez L, Cochard B, Flori A, Durand-Gasselin T, Nouy B, Omoré A, Pomiès V, Riou V, Suryana E, Bouvet JM. Genomic selection prediction accuracy in a perennial crop: case study of oil palm (Elaeis guineensis Jacq.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:397-410. [PMID: 25488416 DOI: 10.1007/s00122-014-2439-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 11/27/2014] [Indexed: 05/18/2023]
Abstract
Genomic selection empirically appeared valuable for reciprocal recurrent selection in oil palm as it could account for family effects and Mendelian sampling terms, despite small populations and low marker density. Genomic selection (GS) can increase the genetic gain in plants. In perennial crops, this is expected mainly through shortened breeding cycles and increased selection intensity, which requires sufficient GS accuracy in selection candidates, despite often small training populations. Our objective was to obtain the first empirical estimate of GS accuracy in oil palm (Elaeis guineensis), the major world oil crop. We used two parental populations involved in conventional reciprocal recurrent selection (Deli and Group B) with 131 individuals each, genotyped with 265 SSR. We estimated within-population GS accuracies when predicting breeding values of non-progeny-tested individuals for eight yield traits. We used three methods to sample training sets and five statistical methods to estimate genomic breeding values. The results showed that GS could account for family effects and Mendelian sampling terms in Group B but only for family effects in Deli. Presumably, this difference between populations originated from their contrasting breeding history. The GS accuracy ranged from -0.41 to 0.94 and was positively correlated with the relationship between training and test sets. Training sets optimized with the so-called CDmean criterion gave the highest accuracies, ranging from 0.49 (pulp to fruit ratio in Group B) to 0.94 (fruit weight in Group B). The statistical methods did not affect the accuracy. Finally, Group B could be preselected for progeny tests by applying GS to key yield traits, therefore increasing the selection intensity. Our results should be valuable for breeding programs with small populations, long breeding cycles, or reduced effective size.
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Affiliation(s)
- David Cros
- CIRAD, UMR AGAP (Genetic Improvement and Adaptation of Mediterranean and Tropical Plants Research Unit), 34398, Montpellier, France,
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241
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Hoen DR, Bureau TE. Discovery of novel genes derived from transposable elements using integrative genomic analysis. Mol Biol Evol 2015; 32:1487-506. [PMID: 25713212 DOI: 10.1093/molbev/msv042] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Complex eukaryotes contain millions of transposable elements (TEs), comprising large fractions of their nuclear genomes. TEs consist of structural, regulatory, and coding sequences that are ordinarily associated with transposition, but that occasionally confer on the organism a selective advantage and may thereby become exapted. Exapted transposable element genes (ETEs) are known to play critical roles in diverse systems, from vertebrate adaptive immunity to plant development. Yet despite their evident importance, most ETEs have been identified fortuitously and few systematic searches have been conducted, suggesting that additional ETEs may await discovery. To explore this possibility, we develop a comprehensive systematic approach to searching for ETEs. We use TE-specific conserved domains to identify with high precision genes derived from TEs and screen them for signatures of exaptation based on their similarities to reference sets of known ETEs, conventional (non-TE) genes, and TE genes across diverse genetic attributes including repetitiveness, conservation of genomic location and sequence, and levels of expression and repressive small RNAs. Applying this approach in the model plant Arabidopsis thaliana, we discover a surprisingly large number of novel high confidence ETEs. Intriguingly, unlike known plant ETEs, several of the novel ETE families form tandemly arrayed gene clusters, whereas others are relatively young. Our results not only identify novel TE-derived genes that may have practical applications but also challenge the notion that TE exaptation is merely a relic of ancient life, instead suggesting that it may continue to fundamentally drive evolution.
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Affiliation(s)
- Douglas R Hoen
- Department of Biology, McGill University, Montréal, QC, Canada
| | - Thomas E Bureau
- Department of Biology, McGill University, Montréal, QC, Canada
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242
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Pootakham W, Jomchai N, Ruang-Areerate P, Shearman JR, Sonthirod C, Sangsrakru D, Tragoonrung S, Tangphatsornruang S. Genome-wide SNP discovery and identification of QTL associated with agronomic traits in oil palm using genotyping-by-sequencing (GBS). Genomics 2015; 105:288-95. [PMID: 25702931 DOI: 10.1016/j.ygeno.2015.02.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 02/03/2015] [Accepted: 02/12/2015] [Indexed: 11/24/2022]
Abstract
Oil palm has become one of the most important oil crops in the world. Marker-assisted selections have played a pivotal role in oil palm breeding programs. Here, we report the use of genotyping-by-sequencing (GBS) approach for a large-scale SNP discovery and genotyping of a mapping population. Reduced representation libraries of 108 F2 progeny were sequenced and a total of 524 million reads were obtained. We detected 21,471 single nucleotide substitutions, most of which (62.6%) represented transition events. Of 3417 fully informative SNP markers, we were able to place 1085 on a linkage map, which spanned 1429.6 cM and had an average of one marker every 1.26 cM. Three QTL affecting trunk height were detected on LG 10, 14 and 15, whereas a single QTL associated with fruit bunch weight was identified on LG 3. The use of GBS approach proved to be rapid, cost-effective and highly reproducible in this species.
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Affiliation(s)
- Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand.
| | - Nukoon Jomchai
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand.
| | - Panthita Ruang-Areerate
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand.
| | - Jeremy R Shearman
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand.
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand.
| | - Duangjai Sangsrakru
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand.
| | - Somvong Tragoonrung
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand.
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand.
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243
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A consensus linkage map of oil palm and a major QTL for stem height. Sci Rep 2015; 5:8232. [PMID: 25648560 PMCID: PMC4316154 DOI: 10.1038/srep08232] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 01/12/2015] [Indexed: 11/08/2022] Open
Abstract
Oil palm (Elaeis guinensis Jacquin) is the most important source of vegetable oil and fat. Several linkage maps had been constructed using dominant and co-dominant markers to facilitate mapping of QTL. However, dominant markers are not easily transferable among different laboratories. We constructed a consensus linkage map for oil palm using co-dominant markers (i.e. microsatellite and SNPs) and two F1 breeding populations generated by crossing Dura and Pisifera individuals. Four hundreds and forty-four microsatellites and 36 SNPs were mapped onto 16 linkage groups. The map length was 1565.6 cM, with an average marker space of 3.72 cM. A genome-wide scan of QTL identified a major QTL for stem height on the linkage group 5, which explained 51% of the phenotypic variation. Genes in the QTL were predicted using the palm genome sequence and bioinformatic tools. The linkage map supplies a base for mapping QTL for accelerating the genetic improvement, and will be also useful in the improvement of the assembly of the genome sequences. Markers linked to the QTL may be used in selecting dwarf trees. Genes within the QTL will be characterized to understand the mechanisms underlying dwarfing.
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244
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Barcelos E, Rios SDA, Cunha RNV, Lopes R, Motoike SY, Babiychuk E, Skirycz A, Kushnir S. Oil palm natural diversity and the potential for yield improvement. FRONTIERS IN PLANT SCIENCE 2015; 6:190. [PMID: 25870604 PMCID: PMC4375979 DOI: 10.3389/fpls.2015.00190] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 03/09/2015] [Indexed: 05/07/2023]
Abstract
African oil palm has the highest productivity amongst cultivated oleaginous crops. Species can constitute a single crop capable to fulfill the growing global demand for vegetable oils, which is estimated to reach 240 million tons by 2050. Two types of vegetable oil are extracted from the palm fruit on commercial scale. The crude palm oil and kernel palm oil have different fatty acid profiles, which increases versatility of the crop in industrial applications. Plantations of the current varieties have economic life-span around 25-30 years and produce fruits around the year. Thus, predictable annual palm oil supply enables marketing plans and adjustments in line with the economic forecasts. Oil palm cultivation is one of the most profitable land uses in the humid tropics. Oil palm fruits are the richest plant source of pro-vitamin A and vitamin E. Hence, crop both alleviates poverty, and could provide a simple practical solution to eliminate global pro-vitamin A deficiency. Oil palm is a perennial, evergreen tree adapted to cultivation in biodiversity rich equatorial land areas. The growing demand for the palm oil threatens the future of the rain forests and has a large negative impact on biodiversity. Plant science faces three major challenges to make oil palm the key element of building the future sustainable world. The global average yield of 3.5 tons of oil per hectare (t) should be raised to the full yield potential estimated at 11-18t. The tree architecture must be changed to lower labor intensity and improve mechanization of the harvest. Oil composition should be tailored to the evolving needs of the food, oleochemical and fuel industries. The release of the oil palm reference genome sequence in 2013 was the key step toward this goal. The molecular bases of agronomically important traits can be and are beginning to be understood at the single base pair resolution, enabling gene-centered breeding and engineering of this remarkable crop.
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Affiliation(s)
- Edson Barcelos
- Embrapa Amazonia Ocidental, Empresa Brasileira de Pesquisa Agropecuária, Manaus, Brazil
- *Correspondence: Edson Barcelos, Embrapa Amazonia Ocidental, Empresa Brasileira de Pesquisa Agropecuária, Rodovia AM 010, Km 29, Manaus, Amazonas 69011-970, Brazil
| | - Sara de Almeida Rios
- Embrapa Amazonia Ocidental, Empresa Brasileira de Pesquisa Agropecuária, Manaus, Brazil
| | - Raimundo N. V. Cunha
- Embrapa Amazonia Ocidental, Empresa Brasileira de Pesquisa Agropecuária, Manaus, Brazil
| | - Ricardo Lopes
- Embrapa Amazonia Ocidental, Empresa Brasileira de Pesquisa Agropecuária, Manaus, Brazil
| | - Sérgio Y. Motoike
- Department of Phytotechnology, Federal University of Viçosa, Viçosa, Brazil
| | - Elena Babiychuk
- Department of Sustainable Development, Vale Institute of Technology, Belém, Brazil
| | - Aleksandra Skirycz
- Department of Sustainable Development, Vale Institute of Technology, Belém, Brazil
| | - Sergei Kushnir
- Department of Sustainable Development, Vale Institute of Technology, Belém, Brazil
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Sampedro J, Guttman M, Li LC, Cosgrove DJ. Evolutionary divergence of β-expansin structure and function in grasses parallels emergence of distinctive primary cell wall traits. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:108-20. [PMID: 25353668 DOI: 10.1111/tpj.12715] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/19/2014] [Accepted: 10/21/2014] [Indexed: 05/06/2023]
Abstract
Expansins are wall-loosening proteins that promote the extension of primary cell walls without the hydrolysis of major structural components. Previously, proteins from the EXPA (α-expansin) family were found to loosen eudicot cell walls but to be less effective on grass cell walls, whereas the reverse pattern was found for EXPB (β-expansin) proteins obtained from grass pollen. To understand the evolutionary and structural bases for the selectivity of EXPB action, we assessed the extension (creep) response of cell walls from diverse monocot families to EXPA and EXPB treatments. Cell walls from Cyperaceae and Juncaceae (families closely related to grasses) displayed a typical grass response ('β-response'). Walls from more distant monocots, including some species that share with grasses high levels of arabinoxylan, responded preferentially to α-expansins ('α-response'), behaving in this regard like eudicots. An expansin with selective activity for grass cell walls was detected in Cyperaceae pollen, coinciding with the expression of genes from the divergent EXPB-I branch that includes grass pollen β-expansins. The evolutionary origin of this branch was located within Poales on the basis of phylogenetic analyses and its association with the 'sigma' whole-genome duplication. Accelerated evolution in this branch has remodeled the protein surface in contact with the substrate, potentially for binding highly substituted arabinoxylan. We propose that the evolution of the divergent EXPB-I group made a fundamental change in the target and mechanism of wall loosening in the grass lineage possible, involving a new structural role for xylans and the expansins that target them.
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Affiliation(s)
- Javier Sampedro
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
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246
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Tanaka T, Maeda Y, Veluchamy A, Tanaka M, Abida H, Maréchal E, Bowler C, Muto M, Sunaga Y, Tanaka M, Yoshino T, Taniguchi T, Fukuda Y, Nemoto M, Matsumoto M, Wong PS, Aburatani S, Fujibuchi W. Oil accumulation by the oleaginous diatom Fistulifera solaris as revealed by the genome and transcriptome. THE PLANT CELL 2015; 27:162-76. [PMID: 25634988 PMCID: PMC4330590 DOI: 10.1105/tpc.114.135194] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 12/10/2014] [Accepted: 01/08/2015] [Indexed: 05/19/2023]
Abstract
Oleaginous photosynthetic organisms such as microalgae are promising sources for biofuel production through the generation of carbon-neutral sustainable energy. However, the metabolic mechanisms driving high-rate lipid production in these oleaginous organisms remain unclear, thus impeding efforts to improve productivity through genetic modifications. We analyzed the genome and transcriptome of the oleaginous diatom Fistulifera solaris JPCC DA0580. Next-generation sequencing technology provided evidence of an allodiploid genome structure, suggesting unorthodox molecular evolutionary and genetic regulatory systems for reinforcing metabolic efficiencies. Although major metabolic pathways were shared with nonoleaginous diatoms, transcriptome analysis revealed unique expression patterns, such as concomitant upregulation of fatty acid/triacylglycerol biosynthesis and fatty acid degradation (β-oxidation) in concert with ATP production. This peculiar pattern of gene expression may account for the simultaneous growth and oil accumulation phenotype and may inspire novel biofuel production technology based on this oleaginous microalga.
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Affiliation(s)
- Tsuyoshi Tanaka
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan JST, CREST, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Yoshiaki Maeda
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Alaguraj Veluchamy
- Environmental and Evolutionary Genomics Section, CNRS UMR8197 INSERM U1024, Institut de Biologie de l'Ecole Normale Supérieure, 75005 Paris, France
| | - Michihiro Tanaka
- Center for iPS Cell Research and Application, Kyoto University, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
| | - Heni Abida
- Environmental and Evolutionary Genomics Section, CNRS UMR8197 INSERM U1024, Institut de Biologie de l'Ecole Normale Supérieure, 75005 Paris, France
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, CNRS-CEA-INRA-Université Grenoble Alpes, CEA Grenoble, 38054, Grenoble Cedex 09, France
| | - Chris Bowler
- Environmental and Evolutionary Genomics Section, CNRS UMR8197 INSERM U1024, Institut de Biologie de l'Ecole Normale Supérieure, 75005 Paris, France
| | - Masaki Muto
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan JST, CREST, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Yoshihiko Sunaga
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan JST, CREST, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Masayoshi Tanaka
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan JST, CREST, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Tomoko Yoshino
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | | | - Yorikane Fukuda
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Michiko Nemoto
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Mitsufumi Matsumoto
- JST, CREST, Chiyoda-ku, Tokyo 102-0075, Japan Biotechnology Laboratory, Electric Power Development Co., Wakamatsu-ku, Kitakyusyu, Fukuoka 808-0111, Japan
| | - Pui Shan Wong
- Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
| | - Sachiyo Aburatani
- Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
| | - Wataru Fujibuchi
- Center for iPS Cell Research and Application, Kyoto University, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
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247
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Clément Y, Fustier MA, Nabholz B, Glémin S. The bimodal distribution of genic GC content is ancestral to monocot species. Genome Biol Evol 2014; 7:336-48. [PMID: 25527839 PMCID: PMC4316631 DOI: 10.1093/gbe/evu278] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
In grasses such as rice or maize, the distribution of genic GC content is well known to be bimodal. It is mainly driven by GC content at third codon positions (GC3 for short). This feature is thought to be specific to grasses as closely related species like banana have a unimodal GC3 distribution. GC3 is associated with numerous genomics features and uncovering the origin of this peculiar distribution will help understanding the potential roles and consequences of GC3 variations within and between genomes. Until recently, the origin of the peculiar GC3 distribution in grasses has remained unknown. Thanks to the recent publication of several complete genomes and transcriptomes of nongrass monocots, we studied more than 1,000 groups of one-to-one orthologous genes in seven grasses and three outgroup species (banana, palm tree, and yam). Using a maximum likelihood-based method, we reconstructed GC3 at several ancestral nodes. We found that the bimodal GC3 distribution observed in extant grasses is ancestral to both grasses and most monocot species, and that other species studied here have lost this peculiar structure. We also found that GC3 in grass lineages is globally evolving very slowly and that the decreasing GC3 gradient observed from 5′ to 3′ along coding sequences is also conserved and ancestral to monocots. This result strongly challenges the previous views on the specificity of grass genomes and we discuss its implications for the possible causes of the evolution of GC content in monocots.
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Affiliation(s)
- Yves Clément
- Montpellier SupAgro, Unité Mixte de Recherche 1334, Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, Montpellier, France Institut des Sciences de l'Evolution de Montpellier, Unité Mixte de Recherche 5554, Centre National de la Recherche Scientifique, Université Montpellier, France
| | | | - Benoit Nabholz
- Institut des Sciences de l'Evolution de Montpellier, Unité Mixte de Recherche 5554, Centre National de la Recherche Scientifique, Université Montpellier, France
| | - Sylvain Glémin
- Institut des Sciences de l'Evolution de Montpellier, Unité Mixte de Recherche 5554, Centre National de la Recherche Scientifique, Université Montpellier, France
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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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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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250
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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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