Abstract
Oil palm produces two types of edible oil, namely palm oil and palm kernel oil that are important sources of food and raw materials for industries, such as cosmetics, biofuels, pharmaceutical and oleochemicals. It is harvested all year round and has the highest oil yield per hectare compared to other edible oil crops. Nevertheless, its yields have stagnated for the past three decades and continuous improvements are required to keep up with future demands of the growing world population. The need to improve productivity motivated the research community and the oil palm industry to jointly embrace the latest biotechniques to study and understand the crop. This partnership paved the way for the development of more comprehensive research programmes that resulted in the release of the assembled oil palm genome sequence, identification of genes/markers associated with traits of interest, and development of new tools. The most important successes to date are the identification of two genes linked to important agronomic traits, i.e. shell phenotype and fruit colour, and a gene that causes the abnormal mantled somaclonal variant. These discoveries have since been translated into diagnostic assays that can be used to screen and select planting materials as early as at the seed or nursery stage, allowing planters to only plant palms with the desired traits. This chapter explores the developments leading to the sequencing of the oil palm genome and its subsequent application in the development of new knowledge and tools that will help shape the next generation of planting materials.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Aberlenc-Bertossi F, Chabrillange N, Duval Y, Tregear J (2008) Contrasting globulin and cysteine proteinase gene expression patterns reveal fundamental developmental differences between zygotic and somatic embryos of oil palm. Tree Physiol 28(8):1157–1167. https://doi.org/10.1093/treephys/28.8.1157
Abrizah O, Lazarus C, Fraser T, Stobart K (2000) Cloning of a palmitoyl-acyl carrier protein thioesterase from oil palm. Biochem Soc Trans 28(6):619–622. https://doi.org/10.1042/BST0280619
Adam H, Jouannic S, Escoute J, Duval Y, Verdeil JL, Tregear JW (2005) Reproductive developmental complexity in the African oil palm (Elaeis guineensis, Arecaceae). Am J Bot 92(11):1836–1852
Adam H, Jouannic S, Morcillo F, Richaud F, Duval Y, Tregear JW (2006) MADS box genes in oil palm (Elaeis guineensis): Patterns in the evolution of the SQUAMOSA, DEFICIENS, GLOBOSA, AGAMOUS, and SEPALLATA subfamilies. J Mol Evol 62(1):15–31. https://doi.org/10.1007/s00239-005-0333-7
Adam H, Jouannic S, Orieux Y, Morcillo F, Richaud F, Duval Y, Tregear JW (2007) Functional characterization of MADS box genes involved in the determination of oil palm flower structure. J Exp Bot 58(6):1245–1259. https://doi.org/10.1093/jxb/erl263
Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, **ao H, Merril CR, Wu A, Olde B, Moreno RF, Et A (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252(5013):1651–1656. https://doi.org/10.1126/science.2047873
Alban C, Job D, Douce R (2000) Biotin metabolism in plants. Annu Rev Plant Physiol Plant Mol Biol 51(1):17–47. https://doi.org/10.1146/annurev.arplant.51.1.17
Alexandrov NN, Brover VV, Freidin S, Troukhan ME, Tatarinova TV, Zhang H, Swaller TJ, Lu Y-PP, Bouck J, Flavell RB, Feldmann KA (2009) Insights into corn genes derived from large-scale cDNA sequencing. Plant Mol Biol 69(1–2):179–194. https://doi.org/10.1007/s11103-008-9415-4
Al-Mssallem IS, Hu S, Zhang X, Lin Q, Liu W, Tan J, Yu X, Liu J, Pan L, Zhang T, Yin Y, **n C, Wu H, Zhang G, Ba Abdullah MM, Huang D, Fang Y, Alnakhli YO, Jia S, Yin A, Alhuzimi EM, Alsaihati BA, Al-Owayyed SA, Zhao D, Zhang S, Al-Otaibi NA, Sun G, Majrashi MA, Li F, Wang J, Yun Q, Alnassar NA, Wang L, Yang M, Al-Jelaify RF, Liu K, Gao S, Chen K, Alkhaldi SR, Liu G, Zhang M, Guo H, Yu J (2013) Genome sequence of the date palm Phoenix dactylifera L. Nat Commun 4:2274. https://doi.org/10.1038/ncomms3274
Alwee SS, Van Der Linden CG, Van Der Schoot J, De Folter S, Angenent GC, Cheah SC, Smulders MJM (2006) Characterization of oil palm MADS box genes in relation to the mantled flower abnormality. Plant Cell, Tissue Organ Cult 85(3):331–344. https://doi.org/10.1007/s11240-006-9084-4
Bai B, Wang L, Lee M, Zhang Y, Alfiko Y, Ye BQ, Wan ZY, Lim CH, Suwanto A, Chua NH, Yue GH (2017) Genome-wide identification of markers for selecting higher oil content in oil palm. BMC Plant Biol 17:93. https://doi.org/10.1186/s12870-017-1045-Z
Bai B, Wang L, Zhang YJ, Lee M, Rahmadsyah R, Alfiko Y, Ye BQ, Purwantomo S, Suwanto A, Chua NH, Yue GH (2018) Develo** genome-wide SNPs and constructing an ultrahigh-density linkage map in oil palm. Sci Rep 8:691. https://doi.org/10.1038/s41598-017-18613-2
Beirnaert A, Vanderweyen R (1941) Contribution a` l’e´tude ge´ne´tique et biome´trique des varie´tie´s d’Elaeis guineensis Jacq. Publ Inst Nat Etude Agron Congo Belge Ser Sci 27:1–101
Belkhadir Y, Subramaniam R, Dangl JL (2004) Plant disease resistance protein signaling: NBS–LRR proteins and their partners. Curr Opin Plant Biol 7(4):391–399. https://doi.org/10.1016/j.pbi.2004.05.009
Beulé T, Camps C, Debiesse S, Tranchant C, Dussert S, Sabau X, Jaligot E, Alwee SSRS, Tregear JW (2011) Transcriptome analysis reveals differentially expressed genes associated with the mantled homeotic flowering abnormality in oil palm (Elaeis guineensis). Tree Genet Genomes 7(1):169–182. https://doi.org/10.1007/s11295-010-0323-9
Beulé T, Agbessi MDT, Dussert S, Jaligot E, Guyot R (2015) Genome-wide analysis of LTR-retrotransposons in oil palm. BMC Genom 16:795. https://doi.org/10.1186/s12864-015-2023-1
Billotte N, Risterucci AM, Barcelos E, Noyer JL, Amblard P, Baurens FC (2001) Development, characterisation, and across-taxa utility of oil palm (Elaeis guineensis Jacq.) microsatellite markers. Genome 44(3):413–425. https://doi.org/10.1139/gen-44-3-413
Billotte N, Marseillac N, Risterucci A-M, Adon B, Brottier P, Baurens F-C, Singh R, Herrán A, Asmady H, Billot C, Amblard P, Durand-Gasselin T, Courtois B, Asmono D, Cheah SC, Rohde W, Ritter E, Charrier A (2005) Microsatellite-based high density linkage map in oil palm (Elaeis guineensis Jacq.). Theor Appl Genet 110(4):754–765. https://doi.org/10.1007/s00122-004-1901-8
Billotte N, Jourjon MF, Marseillac N, Berger A, Flori A, Asmady H, Adon B, Singh R, Nouy B, Potier F, Cheah SC, Rohde W, Ritter E, Courtois B, Charrier A, Mangin B (2010) QTL detection by multi-parent linkage map** in oil palm (Elaeis guineensis Jacq.). Theor Appl Genet 120(8):1673–1687. https://doi.org/10.1007/s00122-010-1284-y
Bonaldo MF, Lennon G, Soares MB (1996) Normalization and subtraction: two approaches to facilitate gene discovery. Genome Res 6(9):791–806. https://doi.org/10.1101/gr.6.9.791
Borevitz JO, **a Y, Blount J, Dixon RA, Lamb C (2000) Activation tagging identifies a conserved MYB regulator of phenylpropanoid biosynthesis. Plant Cell 12(12):2383–2394. https://doi.org/10.2307/3871236
Bourgis F, Kilaru A, Cao X, Ngando-Ebongue G-F, Drira N, Ohlrogge JB, Arondel V (2011) Comparative transcriptome and metabolite analysis of oil palm and date palm mesocarp that differ dramatically in carbon partitioning. Proc Natl Acad Sci 108(30):12527–12532. https://doi.org/10.1073/pnas.1106502108
Budiman MA, Singh R, Low ETL, Nunberg A, Citek R, Rohlfing TJ, Bedell A, Lakey ND, Martienssen RA, Cheah CS (2005) Sequencing of the oil palm genespace. In: Proceedings of PIPOC2005 international palm oil congress (agriculture, biotechnology and sustainability conference). Petaling Jaya, Selangor, Malaysia, pp 628–639
Campbell WH, Gowri G (1990) Codon usage in higher plants, green algae, and cyanobacteria. Plant Physiol 92(1):1–11. https://doi.org/10.1104/pp.92.1.1
Castilho AM, Vershinin AV, Heslop-Harrison JS (2000) Repetitive DNA and the chromosomes in the genome of oil palm (Elaeis guineensis). Ann Bot 85(6):837–844. https://doi.org/10.1006/anbo.2000.1145
Chan PL, Ma LS, Low ETL, Shariff EM, Ooi LCL, Cheah SC, Singh R (2010) Normalized embryoid cDNA library of oil palm (Elaeis guineensis). Electron J Biotechnol 13(1):14. https://doi.org/10.2225/vol13-issue1-fulltext-14
Chan K-L, Rosli R, Tatarinova TV, Hogan M, Firdaus-Raih M, Low E-TL (2017a) Seq**: Gene prediction pipeline for plant genomes using self-training gene models and transcriptomic data. BMC Bioinformatics 18(Suppl1):29. https://doi.org/10.1186/s12859-016-1426-6
Chan K-L, Tatarinova TV, Rosli R, Amiruddin N, Azizi N, Halim MAA, Sanusi NSNM, Jayanthi N, Ponomarenko P, Triska M, Solovyev V, Firdaus-Raih M, Sambanthamurthi R, Murphy D, Low E-TL (2017b) Evidence-based gene models for structural and functional annotations of the oil palm genome. Biol Direct 12(1):21. https://doi.org/10.1186/s13062-017-0191-4
Chin CW (1995) Oil palm planting materials and quality control. In: Proceedings of the 1995 PORIM national oil conference-tech in plant, pp 38–47
Clément Y, Fustier M-A, Nabholz B, Glémin S (2015) The bimodal distribution of genic GC content is ancestral to monocot species. Genome Biol Evol 7(1):336–348. https://doi.org/10.1093/gbe/evu278
Cochard B, Durand-Gasselin T, Amblard P, Konan EK, Gogor S (1999) Performance of adult oil palm clones. In: Ariffin D, Chan KW, Sharifah SSA (eds) Emerging technologies and opportunities in the next millennium. Agriculture conference: proceedings of 1999 PORIM International Palm Oil Congress. PORIM, Kuala Lumpur, pp 53–64
Corley RHV (2005) Illegitimacy in oil palm breeding—a review. J Oil Palm Res 17:64–69
Corley RHV, Law IH (1997) The future for oil palm clones. In: Pushparajah E (ed) Plantation Management for the 21st Century. Incorporated Society of Planters, pp 279–289
Corley RHV, Lee CH, Law IM, Wong CY (1986) Abnormal flower development in oil palm clones. Planter 62(723):233–240
D’Hont A, Denoeud F, Aury J-M, Baurens F-C, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, Da Silva C, Jabbari K, Cardi C, Poulain J, Souquet M, Labadie K, Jourda C, Lengellé J, Rodier-Goud M, Alberti A, Bernard M, Correa M, Ayyampalayam S, Mckain MR, Leebens-Mack J, Burgess D, Freeling M, Mbéguié-A-Mbéguié D, Chabannes M, Wicker T, Panaud O, Barbosa J, Hribova E, Heslop-Harrison P, Habas R, Rivallan R, Francois P, Poiron C, Kilian A, Burthia D, Jenny C, Bakry F, Brown S, Guignon V, Kema G, Dita M, Waalwijk C, Joseph S, Dievart A, Jaillon O, Leclercq J, Argout X, Lyons E, Almeida A, Jeridi M, Dolezel J, Roux N, Risterucci A-M, Weissenbach J, Ruiz M, Glaszmann J-C, Quétier F, Yahiaoui N, Wincker P (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488(7410):213–217. https://doi.org/10.1038/nature11241
Devuyst A (1953) Selection of the oil palm (Elaeis guineensis) in Africa. Nature 172:685–686. https://doi.org/10.1038/172685a0
Dong Q (2004) PlantGDB, plant genome database and analysis tools. Nucleic Acids Res 32(90001):354D–459D. https://doi.org/10.1093/nar/gkh046
Droc G, Larivière D, Guignon V, Yahiaoui N, This D, Garsmeur O, Dereeper A, Hamelin C, Argout X, Dufayard J-F, Lengelle J, Baurens F-C, Cenci A, Pitollat B, D’Hont A, Ruiz M, Rouard M, Bocs S (2013) The Banana Genome Hub. Database 2013:bat035. https://doi.org/10.1093/database/bat035
Durand-Gasselin T, Le Guen VL, Konan E, Duval Y (1990) Oil palm (Elaeis guineensis Jacq.) plantations in Cote d’Ivoire obtained through in vitro culture—First results. Ole ́agineux 45:1–11
Dussert S, Guerin C, Andersson M, Joët T, Tranbarger TJ, Pizot M, Sarah G, Omore A, Durand-Gasselin T, Morcillo F (2013) Comparative transcriptome analysis of three oil palm fruit and seed tissues that differ in oil content and fatty acid composition. Plant Physiol 162(3):1337–1358. https://doi.org/10.1104/pp.113.220525
Eilbeck K, Moore B, Holt C, Yandell M (2009) Quantitative measures for the management and comparison of annotated genomes. BMC Bioinformatics 10(1):67. https://doi.org/10.1186/1471-2105-10-67
Elhaik E, Pellegrini M, Tatarinova TV (2014) Gene expression and nucleotide composition are associated with genic methylation level in Oryza sativa. BMC Bioinform 15(1):23. https://doi.org/10.1186/1471-2105-15-23
Fawcett JA, Maere S, Van de Peer Y (2009) Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event. Proc Natl Acad Sci 106(14):5737–5742. https://doi.org/10.1073/pnas.0900906106
Filho JAF, de Brito LS, Leão AP, Alves AA, Formighieri EF, Souza MT (2017) In silico approach for characterization and comparison of repeats in the genomes of oil and date palms. Bioinform Biol Insights 11:117793221770238. https://doi.org/10.1177/1177932217702388
Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A (2016) The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 44(D1):D279–D285. https://doi.org/10.1093/nar/gkv1344
Gaj MD, Zhang S, Harada JJ, Lemaux PG (2005) Leafy cotyledon genes are essential for induction of somatic embryogenesis of Arabidopsis. Planta 222(6):977–988. https://doi.org/10.1007/s00425-005-0041-y
Galperin MY, Cochrane GR (2009) Nucleic acids research annual database issue and the NAR online molecular biology database collection in 2009. Nucleic Acids Res 37:D1–D4. https://doi.org/10.1093/nar/gkn942
Gan ST, Wong WC, Wong CK, Soh AC, Kilian A, Low E-TL, Massawe F, Mayes S (2018) High density SNP and DArT-based genetic linkage maps of two closely related oil palm populations. J Appl Genet 59(1):23–34. https://doi.org/10.1007/s13353-017-0420-7
Gene Ontology Consortium (2015) Gene ontology consortium: going forward. Nucleic Acids Res 43(D1):D1049–D1056. https://doi.org/10.1093/nar/gku1179
Gonzalez A, Zhao M, Leavitt JM, Lloyd AM (2008) Regulation of the anthocyanin biosynthetic pathway by the TTG1/bHLH/Myb transcriptional complex in Arabidopsis seedlings. Plant J 53:814–827. https://doi.org/10.1111/j.1365-313X.2007.03373.x
Hartley CWS (1988) The oil palm (Elaeis guineesis Jacq.). Longman Scientific & Technical, England
He Z, Zhang C, Liu W, Lin Q, Wei T, Aljohi HA, Chen W-H, Hu S (2017) DRDB: an online date palm genomic resource database. Front Plant Sci 8:1889. https://doi.org/10.3389/fpls.2017.01889
Hershberg R, Petrov DA (2008) Selection on codon bias. Annu Rev Genet 42(1):287–299. https://doi.org/10.1146/annurev.genet.42.110807.091442
Ho CL, Kwan YY, Choi MC, Tee S-SS, Ng W-HH, Lim KA, Lee Y-PP, Ooi SE, Lee W-WW, Tee JM, Tan SH, Kulaveerasingam H, Alwee SSRS, Abdullah MO (2007) Analysis and functional annotation of expressed sequence tags (ESTs) from multiple tissues of oil palm (Elaeis guineensis Jacq.). BMC Genomics 8:381. doi: https://doi.org/10.1186/1471-2164-8-381
Ho C-L, Tan Y-C, Yeoh K-A, Ghazali A-K, Yee W-Y, Hoh C-C (2016) De novo transcriptome analyses of host-fungal interactions in oil palm (Elaeis guineensis Jacq.). BMC Genomics 17(1):66. https://doi.org/10.1186/s12864-016-2368-0
Ho H, Gudimella R, Ong-Abdullah M, Harikrishna JA (2017) Expression of microRNAs during female inflorescence development in African oil palm (Elaeis guineensis Jacq.). Tree Genet Genomes 13(2):35. https://doi.org/10.1007/s11295-017-1120-5
Ho C-L, Tan Y-C, Yeoh K-A, Lee W-K, Ghazali A-K, Yee W-Y, Hoh C-C (2018) Transcriptional response of oil palm (Elaeis guineensis Jacq.) inoculated simultaneously with both Ganoderma boninense and Trichoderma harzianum. Plant Gene 13:56–63. https://doi.org/10.1016/j.plgene.2018.01.003
Holt C, Yandell M (2011) MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinform 12(1):491. https://doi.org/10.1186/1471-2105-12-491
Ikeda M, Umehara M, Kamada H (2006) Embryogenesis-related genes; Its expression and roles during somatic and zygotic embryogenesis in carrot and Arabidopsis. Plant Biotechnol 23(2):153–161. https://doi.org/10.5511/plantbiotechnology.23.153
Iriarte A, Baraibar JD, Romero H, Castro-Sowinski S, Musto H (2013) Evolution of optimal codon choices in the family Enterobacteriaceae. Microbiology 159(Pt_3):555–564. https://doi.org/10.1099/mic.0.061952-0
Jaiswal P (2006) Gramene: a bird’s eye view of cereal genomes. Nucleic Acids Res 34(90001):D717–D723. https://doi.org/10.1093/nar/gkj154
Jaligot E, Rival A, Beulé T, Dussert S, Verdeil J-L (2000) Somaclonal variation in oil palm (Elaeis guineensis Jacq.): the DNA methylation hypothesis. Plant Cell Rep 19(7):684–690. https://doi.org/10.1007/s002999900177
Jaligot E, Hooi WY, Debladis E, Richaud F, Beulé T, Collin M, Agbessi MDT, Sabot F, Garsmeur O, D’Hont A, Alwee SSRS, Rival A (2014) DNA methylation and expression of the EgDEF1 gene and neighboring retrotransposons in mantled somaclonal variants of oil palm. PLoS ONE 9(3):e91896. https://doi.org/10.1371/journal.pone.0091896
Jiao Y, Li J, Tang H, Paterson AH (2014) Integrated syntenic and phylogenomic analyses reveal an ancient genome duplication in monocots. Plant Cell 26(7):2792–2802. https://doi.org/10.1105/tpc.114.127597
** J, Lee M, Bai B, Sun Y, Qu J, Rahmadsyah Alfiko Y, Lim CH, Suwanto A, Sugiharti M, Wong L, Ye J, Chua N-H, Yue GH (2016) Draft genome sequence of an elite Dura palm and whole-genome patterns of DNA variation in oil palm. DNA Res 23(6):527–533. https://doi.org/10.1093/dnares/dsw036
** J, Sun Y, Qu J, Syah R, Lim C-H, Alfiko Y, Rahman N, Suwanto A, Yue G, Wong L, Chua N-H, Ye J (2017) Transcriptome and functional analysis reveals hybrid vigor for oil biosynthesis in oil palm. Sci Rep 7(1):439. https://doi.org/10.1038/s41598-017-00438-8
Jones L (1974) Propagation of clonal palms by tissue culture. Oil Palm News 17:1–8
Jouannic S, Argout X, Lechauve F, Fizames C, Borgel A, Morcillo F, Aberlenc-Bertossi F, Duval Y, Tregear J (2005) Analysis of expressed sequence tags from oil palm (Elaeis guineensis). FEBS Lett 579(12):2709–2714. https://doi.org/10.1016/j.febslet.2005.03.093
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J (2005) Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110(1–4):462–467. https://doi.org/10.1159/000084979
Kanchanapoom K, Domyoas P (1999) The origin and development of embryoids in oil palm (Elaeis guineensis Jacq) embryo culture. Science Asia 25(4):195. https://doi.org/10.2306/scienceasia1513-1874.1999.25.195
Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M (2016) KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 44(D1):D457–D462. https://doi.org/10.1093/nar/gkv1070
Kersey PJ, Staines DM, Lawson D, Kulesha E, Derwent P, Humphrey JC, Hughes DST, Keenan S, Kerhornou A, Koscielny G, Langridge N, McDowall MD, Megy K, Maheswari U, Nuhn M, Paulini M, Pedro H, Toneva I, Wilson D, Yates A, Birney E (2012) Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. Nucleic Acids Res 40(D1):D91–D97. https://doi.org/10.1093/nar/gkr895
Khaw CH, Ng SK (1998) Performance of commercial scale clonal oil palm (Elaeis guineensis Jacq.) plantings in Malaysia. Acta Hortic 461:251–258. https://doi.org/10.17660/ActaHortic.1998.461.27
Korf I (2004) Gene finding in novel genomes. BMC Bioinformatics 5:59. https://doi.org/10.1186/1471-2105-5-59
Kubis SE, Castilho AMMF, Vershinin AV, Heslop-Harrison JSP (2003) Retroelements, transposons and methylation status in the genome of oil palm (Elaeis guineensis) and the relationship to somaclonal variation. Plant Mol Biol 52(1):69–79. https://doi.org/10.1023/A:1023942309092
Kushairi A, Rajanaidu N (2000) Breeding populations, seed production and nursery management. In: Basiron Y, Jalani BS, Chan KW (eds) Advances in oil palm research, pp 39–98
Kwong QB, Teh CK, Ong AL, Chew FT, Mayes S, Kulaveerasingam H, Tammi M, Yeoh SH, Appleton DR, Harikrishna JA (2017) Evaluation of methods and marker Systems in Genomic Selection of oil palm (Elaeis guineensis Jacq.). BMC Genet 18(1):107. https://doi.org/10.1186/s12863-017-0576-5
Latiff A (2000) The biology of the genus Elaeis. In: Basiron Y, Jalani BS, Chan KW (eds) Advances in oil palm research, vol 1. Malaysian Palm Oil Board, Selangor, pp 19–38
Lee M, **a JH, Zou Z, Ye J, Rahmadsyah Alfiko Y, ** J, Lieando JV, Purnamasari MI, Lim CH, Suwanto A, Wong L, Chua N-H, Yue GH (2015) A consensus linkage map of oil palm and a major QTL for stem height. Sci Rep 5(1):8232. https://doi.org/10.1038/srep08232
Li R, Reddy VA, ** J, Rajan C, Wang Q, Yue G, Lim CH, Chua N-H, Ye J, Sarojam R (2017) Comparative transcriptome analysis of oil palm flowers reveals an EAR-motif-containing R2R3-MYB that modulates phenylpropene biosynthesis. BMC Plant Biol 17(1):219. https://doi.org/10.1186/s12870-017-1174-4
Lin H-C, Morcillo F, Dussert S, Tranchant-Dubreuil C, Tregear JW, Tranbarger TJ (2009) Transcriptome analysis during somatic embryogenesis of the tropical monocot Elaeis guineensis: evidence for conserved gene functions in early development. Plant Mol Biol 70(1–2):173–192. https://doi.org/10.1007/s11103-009-9464-3
Llorens C, Futami R, Covelli L, Domínguez-Escribá L, Viu JM, Tamarit D, Aguilar-Rodríguez J, Vicente-Ripolles M, Fuster G, Bernet GP, Maumus F, Munoz-Pomer A, Sempere JM, Latorre A, Moya A (2011) The gypsy database (GyDB) of mobile genetic elements: release 2.0. Nucleic Acids Res 39:D70–D74. https://doi.org/10.1093/nar/gkq1061
Low ETL, Tan JS, Chan PL, Boon SH, Wong YL, Rozana R, Ooi L-L, Ma LS, Ong-Abdullah M, Cheah SC, Ra**der S (2006) Developments toward the application of DNA chip technology in oil palm tissue culture. J Oil Palm Res (Special Issue-April 2006):87–98
Low E-TL, Alias H, Boon S-H, Shariff EM, Tan C-YA, Ooi LC, Cheah S-C, Raha A-R, Wan K-L, Singh R (2008) Oil palm (Elaeis guineensis Jacq.) tissue culture ESTs: Identifying genes associated with callogenesis and embryogenesis. BMC Plant Biol 8(1):62. https://doi.org/10.1186/1471-2229-8-62
Low E-TL, Rosli R, Jayanthi N, Mohd-Amin AH, Azizi N, Chan K-L, Maqbool NJ, Maclean P, Brauning R, McCulloch A, Moraga R, Ong-Abdullah M, Singh R (2014) Analyses of hypomethylated oil palm gene space. PLoS ONE 9(1):e86728. https://doi.org/10.1371/journal.pone.0086728
Low ETL, Singh R, Rajanaidu N, Ong-Abdullah M, Ooi LCL, Lakey ND, Smith SW, Ordway JMJ, Sambanthamurthi R (2016) New frontiers for the oil palm industry through genome technology. Planter 92(1087):701–710
Low E-TL, Jayanthi N, Chan K-L, Sanusi NSNM, Halim MAA, Rosli R, Azizi N, Amiruddin N, Angel LPL, Ong-Abdullah M, Singh R, Manaf MAA, Sambanthamurthi R, Parveez GKA, Kushairi A (2017) The oil palm genome revolution. J Oil Palm Res 29(4):456–468. https://doi.org/10.21894/jopr.2017.00018
Maizura I, Rajanaidu N, Zakri AH, Cheah SC (2006) Assessment of genetic diversity in oil palm (Elaeis guineensis Jacq.) using Restriction Fragment Length Polymorphism (RFLP). Genet Resour Crop Evol 53(1):187–195. https://doi.org/10.1007/s10722-004-4004-0
Majoros WH, Pertea M, Salzberg SL (2004) TigrScan and GlimmerHMM: Two open source ab initio eukaryotic gene-finders. Bioinformatics 20(16):2878–2879. https://doi.org/10.1093/bioinformatics/bth315
Malaysian Palm Oil Board (2017) Review of the Malaysian oil palm industry 2016
Mathew LS, Spannagl M, Al-Malki A, George B, Torres MF, Al-Dous EK, Al-Azwani EK, Hussein E, Mathew S, Mayer KF, Mohamoud Y, Suhre K, Malek JA (2014) A first genetic map of date palm (Phoenix dactylifera) reveals long-range genome structure conservation in the palms. BMC Genom 15(1):285. https://doi.org/10.1186/1471-2164-15-285
Matthes M, Singh R, Cheah S-C, Karp A (2001) Variation in oil palm (Elaeis guineensis Jacq.) tissue culture-derived regenerants revealed by AFLPs with methylation-sensitive enzymes. TAG Theor Appl Genet 102(6–7):971–979. https://doi.org/10.1007/s001220000491
Mayes S, Jack PL, Corley RHV, Marshall DF (1997) Construction of a RFLP genetic linkage map for oil palm (Elaeis guineensis Jacq.). Genome 40(1):116–122. https://doi.org/10.1139/g97-016
Mazumdar P, Binti Othman R, Mebus K, Ramakrishnan N, Ann Harikrishna J (2017) Codon usage and codon pair patterns in non-grass monocot genomes. Ann Bot 120(6):893–909. https://doi.org/10.1093/aob/mcx112
McClintock B (1951) Chromosome organization and genic expression. Cold Spring Harb Symp Quant Biol 16:13–47. https://doi.org/10.1101/SQB.1951.016.01.004
McHale L, Tan X, Koehl P, Michelmore RW (2006) Plant NBS-LRR proteins: adaptable guards. Genome Biol 7(4):212. https://doi.org/10.1186/gb-2006-7-4-212
McKain MR, Tang H, McNeal JR, Ayyampalayam S, Davis JI, DePamphilis CW, Givnish TJ, Pires JC, Stevenson DW, Leebens-Mack JH (2016) A phylogenomic assessment of ancient polyploidy and genome evolution across the Poales. Genome Biol Evol 8(4):1150–1164. https://doi.org/10.1093/gbe/evw060
Montoya C, Lopes R, Flori A, Cros D, Cuellar T, Summo M, Espeout S, Rivallan R, Risterucci A-M, Bittencourt D, Zambrano JR, Alarcón G WH, Villeneuve P, Pina M, Nouy B, Amblard P, Ritter E, Leroy T, Billotte N (2013) Quantitative trait loci (QTLs) analysis of palm oil fatty acid composition in an interspecific pseudo-backcross from Elaeis oleifera (H.B.K.) Cortés and oil palm (Elaeis guineensis Jacq.). Tree Genet Genomes 9(5):1207–1225. https://doi.org/10.1007/s11295-013-0629-5
Morcillo F, Hartmann C, Duval Y, Tregear JW (2001) Regulation of 7S globulin gene expression in zygotic and somatic embryos of oil palm. Physiol Plant 112(2):233–243. https://doi.org/10.1034/j.1399-3054.2001.1120212.x
Morcillo F, Gallard A, Pillot M, Jouannic S, Aberlenc-Bertossi F, Collin M, Verdeil JL, Tregear JW (2007) EgAP2-1, an AINTEGUMENTA-like (AIL) gene expressed in meristematic and proliferating tissues of embryos in oil palm. Planta 226(6):1353–1362. https://doi.org/10.1007/s00425-007-0574-3
Moretzsohn MC, Nunes CDM, Ferreira ME, Grattapaglia D (2000) RAPD linkage map** of the shell thickness locus in oil palm (Elaeis guineensis Jacq.). TAG Theor Appl Genet 100(1):63–70. https://doi.org/10.1007/s001220050009
NCBI (2018) txid51952[Organism:exp]—EST—NCBI. https://www.ncbi.nlm.nih.gov/nucest/?term=txid51952[Organism:exp]. Accessed 9 Jul 2018
Nurniwalis AW, Suhaimi N, Siti Nor Akmar A, Aminah S, Mohamad Arif MA (2008) Gene discovery via expressed sequence tags from the oil palm (Elaeis guineensis Jacq.) mesocarp. J Oil Palm Res 87–96
Okoye MN, Bakoumé C, Uguru MI, Singh R, Okwuagwu CO (2016) Genetic relationships between elite oil palms from Nigeria and selected breeding and germplasm materials from Malaysia via simple sequence repeat (SSR) markers. J Agric Sci 8(2):159. https://doi.org/10.5539/jas.v8n2p159
Omar WSW, Willis LB, Rha C, Sinskey AJ, Ramli US, Yunus AMM, Parveez GKA, Sambanthamurthi R (2008) Isolation and utilization of acetyl-coa carboxylase from oil palm (Elaeis guineensis) mesocarp. J Oil Palm Res 2:97–107
Ong PW, Maizura I, Abdullah NAP, Rafii MY, Ooi LCL, Low ETL, Singh R (2015) Development of SNP markers and their application for genetic diversity analysis in the oil palm (Elaeis guineensis). Genet Mol Res 14(4):12205–12216. https://doi.org/10.4238/2015.October.9.9
Ong PW, Maizura I, Marhalil M, Rajanaidu N, Abdullah NAP, Rafii MY, Ooi LCL, Low ETL, Singh R (2018) Association of SNP markers with height increment in mpob-angolan natural oil palm populations. J Oil Palm Res 30:61–70. https://doi.org/10.21894/jopr.2017.0003
Ong-Abdullah M, Ooi S (2006) Biomarkers: finding a niche in oil palm tissue culture. Part 1—laying the foundation. Oil Palm Bull 53:36–48
Ong-Abdullah M, Ordway JM, Jiang N, Ooi S-E, Kok S-Y, 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 E-TL, Chan K-L, Azizi N, Smith SW, Bacher B, Budiman MA, Van Brunt A, Wischmeyer C, Beil M, Hogan M, Lakey N, Lim C-C, Arulandoo X, Wong C-K, Choo C-N, Wong W-C, Kwan Y-Y, Alwee SSRS, Sambanthamurthi R, Martienssen RA (2015) Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm. Nature 525(7570):533–537. https://doi.org/10.1038/nature15365
Ong-Abdullah M, Ordway JM, Nan J, Ooi SE, Mokri A, Kok SY, Sarpan N, Azimi N, Hashim AT, Ishak Z, Rosli SK, Nookiah R, Singh R, Low ETL, Sachdeva M, Smith SW, Lakey N, Martienssen RA, Sambanthamurthi R (2016) Tissue culture and epigenetics. Planter 92(1087):741–749
Ooi LC-L, Low E-TL, Abdullah MO, Nookiah R, Ting NC, Nagappan J, Manaf MAA, Chan K-L, 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 Y-M, Sambanthamurthi R, Singh R (2016) Non-tenera contamination and the economic impact of SHELL genetic testing in the Malaysian independent oil palm industry. Front Plant Sci 7:771. https://doi.org/10.3389/fpls.2016.00771
Osborne DJ, Henderson J, Corley RH (1992) Controlling fruit-shedding in the oil palm. Endeavour 16(4):173–177. https://doi.org/10.1016/0160-9327(92)90044-P
Ouyang S, Buell CR (2004) The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants. Nucleic Acids Res 32:D360–D363. https://doi.org/10.1093/nar/gkh099
Pootakham W, Jomchai N, Ruang-areerate P, Shearman JR, Sonthirod C, Sangsrakru D, Tragoonrung S, Tangphatsornruang S (2015) Genome-wide SNP discovery and identification of QTL associated with agronomic traits in oil palm using genoty**-by-sequencing (GBS). Genomics 105(5–6):288–295. https://doi.org/10.1016/j.ygeno.2015.02.002
Raberchault H, Ahee J, Guenin G (1970) Colonies cellulaires et formes èmbryos in vitro a patir de cultures d’embryons de palmier a huile (Elaeis guineensis Jacq.) al’aide de cultures de tissue foliares. Comptes Rendus l’Académie des Sci Paris Série D283:1735–1737
Rao V, Kushairi A (1999) Quality of oil palm planting material. In: Rajanaidu N, Jalani BS (eds) 1996 seminar on sourcing of oil palm planting materials for local and overseas joint ventures. PORIM, Bangi, pp 188–197
Rhoads A, Au KF (2015) PacBio sequencing and its applications. Genomics Proteomics Bioinformatics 13(5):278‐289. https://doi.org/10.1016/j.gpb.2015.08.002
Riju A, Chandrasekar A, Arunachalam V (2007) Mining for single nucleotide polymorphisms and insertions/deletions in expressed sequence tag libraries of oil palm. Bioinformation 2(4):128–131. https://doi.org/10.6026/97320630002128
Rival A (2000) Somatic embryogenesis in oil palm. In: Jain SM, Gupta PK, Newton RJ (eds) Somatic embryogenesis in woody plants, vol 6. Kluwer Academic Publishers, Massachusetts, pp 249–290
Rival A, Tregear J, Jaligot E, Morcillo F, Aberlenc F, Billotte N, Richaud F, Beule T, Borgel A, Duval Y (2001) Oil Palm Biotechnology at CIRAD. In: The 2001 PIPOC on cutting edge technologies for sustained competitiveness. Malaysian Palm Oil Board, pp 51–82
Rohani O, Sharifah S, Rafii M, Ong M, Tarmizi A, Zamzuri I (2000) Tissue culture of oil palm. In: Basiron Y, Jalani BS, Chan KW (eds) Advances in oil palm research. Malaysian Palm Oil Board, Bangi, pp 238–283
Rosli R, Amiruddin N, Ab Halim MA, Chan P-L, Chan K-L, Azizi N, Morris PE, Leslie Low E-T, Ong-Abdullah M, Sambanthamurthi R, Singh R, Murphy DJ (2018) Comparative genomic and transcriptomic analysis of selected fatty acid biosynthesis genes and CNL disease resistance genes in oil palm. PLoS ONE 13(4):e0194792. https://doi.org/10.1371/journal.pone.0194792
Royal Botanic Gardens Kew (1909) Bulletin of miscellaneous information. Springer on behalf of Royal Botanic Gardens. Royal Botanic Gardens, Kew
Sambanthamurthi R, Abrizah O, Umi Salamah R (1999) Biochemical factors that control oil composition in the oil palm. J Oil Palm Res (Special Issue):23–33
Sarpan N, Kok S-Y, Chai S-K, Fitrianto A, Nuraziyan A, Zamzuri I, Ong-Abdullah M, Ooi S-E (2015) A model for predicting flower development in Elaeis guineensis Jacq. J Oil Palm Res 27(4):315–325
Schweikert G, Zien A, Zeller G, Behr J, Dieterich C, Ong CS, Philips P, De Bona F, Hartmann L, Bohlen A, Kruger N, Sonnenburg S, Ratsch G (2009) mGene: Accurate SVM-based gene finding with an application to nematode genomes. Genome Res 19(11):2133–2143. https://doi.org/10.1101/gr.090597.108
Seng T-Y, Ritter E, Mohamed Saad SH, Leao L-J, Harminder Singh RS, Qamaruz Zaman F, Tan S-G, Syed Alwee SSR, Rao V (2016) QTLs for oil yield components in an elite oil palm (Elaeis guineensis) cross. Euphytica 212(3):399–425. https://doi.org/10.1007/s10681-016-1771-6
Shearman JR, Jantasuriyarat C, Sangsrakru D, Yoocha T, Vannavichit A, Tragoonrung S, Tangphatsornruang S (2013) Transcriptome analysis of normal and mantled develo** oil palm flower and fruit. Genomics 101(5):306–312. https://doi.org/10.1016/j.ygeno.2013.02.012
Sim S-C, Durstewitz G, Plieske J, Wieseke R, Ganal MW, Van Deynze A, Hamilton JP, Buell CR, Causse M, Wijeratne S, Francis DM (2012) Development of a large SNP genoty** array and generation of high-density genetic maps in tomato. PLoS ONE 7(7):e40563. https://doi.org/10.1371/journal.pone.0040563
Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31(19):3210–3212. https://doi.org/10.1093/bioinformatics/btv351
Singh R, Soon-guan T, Panandam J, Rahman RA (2008a) Identification of cDNA-RFLP markers and their use for molecular map** in oil palm (Elaeis guineensis). Asia Pacific J Mol Biol Biotechnol 16(3):53–63
Singh R, Zaki N, Ting N-C, Rosli R, Tan S-G, Low E-T, Ithnin M, Cheah S-C (2008b) Exploiting an oil palm EST database for the development of gene-derived SSR markers and their exploitation for assessment of genetic diversity. Biologia 63(2):227–235. https://doi.org/10.2478/s11756-008-0041-z
Singh R, Tan SG, Panandam JM, Rahman R, Ooi LC, Low E-TL, Sharma M, Jansen J, Cheah S-C (2009) Map** quantitative trait loci (QTLs) for fatty acid composition in an interspecific cross of oil palm. BMC Plant Biol 9(1):114. https://doi.org/10.1186/1471-2229-9-114
Singh R, Low E-TL, Ooi LC-L, Ong-Abdullah M, Ting N-C, Nagappan J, Nookiah R, Amiruddin MD, Rosli R, Manaf MAA, Chan K-L, Halim MA, Azizi N, Lakey N, Smith SW, Budiman MA, Hogan M, Bacher B, Van Brunt A, Wang C, Ordway JM, Sambanthamurthi R, Martienssen RA (2013a) The oil palm SHELL gene controls oil yield and encodes a homologue of SEEDSTICK. Nature 500(7462):340–344. https://doi.org/10.1038/nature12356
Singh R, Ong-Abdullah M, Low E-TL, Manaf MAA, Rosli R, Nookiah R, Ooi LC-L, Ooi S, Chan K-L, Halim MA, Azizi N, Nagappan J, Bacher B, Lakey N, Smith SW, He D, Hogan M, Budiman MA, Lee EK, DeSalle R, Kudrna D, Goicoechea JL, Wing RA, Wilson RK, Fulton RS, Ordway JM, Martienssen RA, Sambanthamurthi R (2013b) Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds. Nature 500(7462):335–339. https://doi.org/10.1038/nature12309
Singh R, Low E-TL, Ooi LC-L, Ong-Abdullah M, Nookiah R, Ting N-C, Marjuni M, Chan P-L, Ithnin M, Manaf MAA, Nagappan J, Chan K-L, Rosli R, Halim MA, Azizi N, Budiman MA, Lakey N, Bacher B, Van Brunt A, Wang C, Hogan M, He D, MacDonald JD, Smith SW, Ordway JM, Martienssen RA, Sambanthamurthi R (2014) The oil palm VIRESCENS gene controls fruit colour and encodes a R2R3-MYB. Nat Commun 5(1):4106. https://doi.org/10.1038/ncomms5106
Singh R, Ong-Abdullah M, Low E, Nookiah R, Abd Manaf M, Sambanthamurthi R (2015) SureSawitTM SHELL—a diagnostic assay to predict fruit forms of the oil palm. Oil Palm Bull 70:13–16
Siqueira JF, Fouad AF, Rôças IN (2012) Pyrosequencing as a tool for better understanding of human microbiomes. J Oral Microbiol 4(1):10743. https://doi.org/10.3402/jom.v4i0.10743
Smith SA, Donoghue MJ (2008) Rates of molecular evolution are linked to life history in flowering plants. Science 322(5898):86–89. https://doi.org/10.1126/science.1163197
Snyder EE, Stormo GD (1995) Identification of protein coding regions in genomic DNA. J Mol Biol 248:1–18. https://doi.org/10.1006/jmbi.1995.0198
Soares MB, Bonaldo MF, Jelene P, Su L, Lawton L, Efstratiadis A (1994) Construction and characterization of a normalized cDNA library. Proc Natl Acad Sci 91(2):9228–9232. https://doi.org/10.1073/pnas.91.20.9228
Solovyev V, Kosarev P, Seledsov I, Vorobyev D (2006) Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biol 7(Suppl 1):S10.1–S10.12. https://doi.org/10.1186/gb-2006-7-s1-s10
Soltani MF, Hadizadeh M, Soltani Banavandi MJ, Yazdizadeh A (2014) Bioinformatics comparison of codon usage of genes encoding phosphate transporter in terms of salt tolerance, day length, temperature and pollination in different plants. Int J Adv Biol Biomed Res 2(2):504–509
Stanke M, Waack S (2003) Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19:ii215–ii225. https://doi.org/10.1093/bioinformatics/btg1080
Stanke M, Diekhans M, Baertsch R, Haussler D (2008) Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24(5):637–644. https://doi.org/10.1093/bioinformatics/btn013
Stein LD (2013) Using GBrowse 2.0 to visualize and share next-generation sequence data. Brief Bioinform 14(2):162–171. https://doi.org/10.1093/bib/bbt001
Sundararajan A, Dukowic-Schulze S, Kwicklis M, Engstrom K, Garcia N, Oviedo OJ, Ramaraj T, Gonzales MD, He Y, Wang M, Sun Q, Pillardy J, Kianian SF, Pawlowski WP, Chen C, Mudge J (2016) Gene evolutionary trajectories and GC patterns driven by recombination in Zea mays. Front Plant Sci 7:1433. https://doi.org/10.3389/fpls.2016.01433
Syed Alwee S, Seng T, Mohamed Saad S (2014) Applications of molecular markers for oil palm crop improvement. Planter 90(1057):281–291
Tatarinova TV, Alexandrov NN, Bouck JB, Feldmann KA (2010) GC3 biology in corn, rice, sorghum and other grasses. BMC Genom 11(1):308. https://doi.org/10.1186/1471-2164-11-308
Tatarinova T, Elhaik E, Pellegrini M (2013) Cross-species analysis of genic GC3 content and DNA methylation patterns. Genome Biol Evol 5(8):1443–1456. https://doi.org/10.1093/gbe/evt103
Tee S-S, Tan Y-C, Abdullah F, Ong-Abdullah M, Ho C-L (2013) Transcriptome of oil palm (Elaeis guineensis Jacq.) roots treated with Ganoderma boninense. Tree Genet Genomes 9(2):377–386. https://doi.org/10.1007/s11295-012-0559-7
Teh C-K, Ong A-L, Kwong Q-B, Apparow S, Chew F-T, Mayes S, Mohamed M, Appleton D, Kulaveerasingam H (2016) Genome-wide association study identifies three key loci for high mesocarp oil content in perennial crop oil palm. Sci Rep 6(1):19075. https://doi.org/10.1038/srep19075
Teh C-K, Muaz SD, Tangaya P, Fong P-Y, Mayes A-LO, Chew FT, Kulaveerasingam H, Appleton D (2017) Characterizing haploinsufficiency of SHELL gene to improve fruit form prediction in introgressive hybrids of oil palm. Sci Rep 7:3118. https://doi.org/10.1038/s41598-017-03225-7
Teoh WC, Cheah SC, Harikrishna K, Tan SH (2003) Isolation and characterization of Myb-related genes from oil palm (Elaeis guineensis Jacq.). J Plant Biol 46(2):95–104. https://doi.org/10.1007/BF03030437
Ter-Hovhannisyan V, Lomsadze A, Chernoff YO, Borodovsky M (2008) Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training. Genome Res 18(12):1979–1990. https://doi.org/10.1101/gr.081612.108
Ting NC, Cheah SC, Ishak Z, Tan SG, Faridah QZ, Maizura I, Singh R (2006) Statistical map** of quantitative trait loci controlling the time to first callusing in oil palm (Elaeis guineensis Jacq.) Tissue Culture. Pertanika J Trop Agric Sci 29(2006):35–45
Ting N-C, Zaki NM, Rosli R, Low E-TL, Ithnin M, Cheah S-C, Tan S-G, Singh R (2010) SSR mining in oil palm EST database: application in oil palm germplasm diversity studies. J Genet 89(2):135–145. https://doi.org/10.1007/s12041-010-0053-7
Ting N-C, Jansen J, Nagappan J, Ishak Z, Chin C-W, Tan S-G, Cheah S-C, Singh R (2013) Identification of QTLs associated with callogenesis and embryogenesis in oil palm using genetic linkage maps improved with SSR markers. PLoS ONE 8(1):e53076. https://doi.org/10.1371/journal.pone.0053076
Ting N-CC, Jansen J, Mayes S, Massawe F, Sambanthamurthi R, Ooi LCL, Chin CW, Arulandoo X, Seng T-YY, Alwee SSRS, Ithnin M, Singh R, Cheng-Li OL, Chin CW, Arulandoo X, Seng T-YY, Alwee SSRS, Ithinin M, Singh R (2014) High density SNP and SSR-based genetic maps of two independent oil palm hybrids. BMC Genom 15(1):309. https://doi.org/10.1186/1471-2164-15-309
Ting N-C, Yaakub Z, Kamaruddin K, Mayes S, Massawe F, Sambanthamurthi R, Jansen J, Low LET, Ithnin M, Kushairi A, Arulandoo X, Rosli R, Chan K-L, Amiruddin N, Sritharan K, Lim CC, Nookiah R, Amiruddin MD, Singh R (2016) Fine-map** and cross-validation of QTLs linked to fatty acid composition in multiple independent interspecific crosses of oil palm. BMC Genom 17(1):289. https://doi.org/10.1186/s12864-016-2607-4
Tisné S, Denis M, Cros D, Pomiès V, Riou V, Syahputra I, Omoré A, Durand-Gasselin T, Bouvet J-M, Cochard B (2015) Mixed model approach for IBD-based QTL map** in a complex oil palm pedigree. BMC Genom 16(1):798. https://doi.org/10.1186/s12864-015-1985-3
Tranbarger TJ, Dussert S, Joët T, Argout X, Summo M, Champion A, Cros D, Omore A, Nouy B, Morcillo F, Joet T, Argout X, Summo M, Champion A, Cros D, Omore A, Nouy B, Morcillo F (2011) Regulatory mechanisms underlying oil palm fruit mesocarp maturation, ripening, and functional specialization in lipid and carotenoid metabolism. Plant Physiol 156(2):564–584. https://doi.org/10.1104/pp.111.175141
Tranbarger TJ, Fooyontphanich K, Roongsattham P, Pizot M, Collin M, Jantasuriyarat C, Suraninpong P, Tragoonrung S, Dussert S, Verdeil J-L, Morcillo F (2017) Transcriptome analysis of cell wall and NAC domain transcription factor genes during Elaeis guineensis fruit ripening: evidence for widespread conservation within monocot and eudicot lineages. Front Plant Sci 8:603. https://doi.org/10.3389/fpls.2017.00603
Ukoskit K, Chanroj V, Bhusudsawang G, Pipatchartlearnwong K, Tangphatsornruang S, Tragoonrung S (2014) Oil palm (Elaeis guineensis Jacq.) linkage map, and quantitative trait locus analysis for sex ratio and related traits. Mol Breed 33(2):415–424. https://doi.org/10.1007/s11032-013-9959-0
Van de Peer Y, Fawcett JA, Proost S, Sterck L, Vandepoele K (2009) The flowering world: a tale of duplications. Trends Plant Sci 14(12):680–688. https://doi.org/10.1016/j.tplants.2009.09.001
Wang H-C, Hickey DA (2007) Rapid divergence of codon usage patterns within the rice genome. BMC Evol Biol 7:S6. https://doi.org/10.1186/1471-2148-7-S1-S6
Wang X, Wu J, Liang J, Cheng F, Wang X (2015) Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources. Database 2015:bav093. https://doi.org/10.1093/database/bav093
Weissman SM (1987) Molecular genetic techniques for map** the human genome. Mol Biol Med 4:133–143
Wong G, Tan C, Soh A (1997) Large scale propagation of oil palm clones: experiences to date. Acta Hortic 447:649–658
Wong YC, Teh HF, Mebus K, Ooi TEK, Bin Kwong Q, Koo KL, Ong CK, Mayes S, Chew FT, Appleton DR, Kulaveerasingam H (2017) Differential gene expression at different stages of mesocarp development in high- and low-yielding oil palm. BMC Genom 18(1):470. https://doi.org/10.1186/s12864-017-3855-7
Wooi K (1990) Oil palm (Elaeis guineensis Jacq.): tissue culture and micropropagation. In: Bajaj YPS (ed) Biotechnology in agriculture and forestry 10: legumes and oilseed crops. Springer, Berlin, pp 569–592
Wooi KC (1995) Oil palm tissue culture-current practice and constraints. In: Rao V, Henson IE, Rajanaidu N (eds) 1993 ISOPB international symposium on recent developments in oil palm tissue culture and biotechnology. PORIM, Kuala Lumpur, pp 21–32
**e M, Yu B (2015) siRNA-directed DNA Methylation in Plants. Curr Genomics 16(1):23–31. https://doi.org/10.2174/1389202915666141128002211
Xu L, Yuan Y, Zhang L, Wan L, Zheng Y, Zhou P, Li D (2011) Identification and characterization of differential gene expression in the mesocarp and kernel of oil palm nuts using suppression subtractive hybridization. Tree Genet Genomes 7(5):999–1010. https://doi.org/10.1007/s11295-011-0390-6
Yamagishi M, Yoshida Y, Nakayama M (2012) The transcription factor LhMYB12 determines anthocyanin pigmentation in the tepals of Asiatic hybrid lilies (Lilium spp.) and regulates pigment quantity. Mol Breed 30(2):913–925. https://doi.org/10.1007/s11032-011-9675-6
Yang X, Wang J (2016) Genome-wide analysis of NBS-LRR genes in sorghum genome revealed several events contributing to NBS-LRR gene evolution in grass species. Evol Bioinforma 12:9–21. https://doi.org/10.4137/EBO.S36433
Ying XU, Mural RJ, Ralph Einstein J, Shah MB, Uberbacher EC (1996) GRAIL: a multi-agent neural network system for gene identification. Proc IEEE 84(10):1544–1551. https://doi.org/10.1109/5.537117
Zaki NM, Singh R, Rosli R, Ismail I (2012) Elaeis oleifera genomic-SSR markers: exploitation in oil palm germplasm diversity and cross-amplification in Arecaceae. Int J Mol Sci 13(4):4069–4088. https://doi.org/10.3390/ijms13044069
Zeven AC (1967) The semi-wild oil palm and its industry in Africa. Agric Res Rep 689:28–33
Zulkifli Y, Ra**der S, Mohd Din A, Ting NC, Rajanaidu N, Kushairi A, Musa B, Mohamad O, Ismanizan I (2014) Inheritance of SSR and SNP loci in an oil palm interspecific hybrid backcross (BC2) population. J Oil Palm Res 26:203–213
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Low, ET.L. et al. (2020). Oil Palm Genome: Strategies and Applications. In: Ithnin, M., Kushairi, A. (eds) The Oil Palm Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-22549-0_7
Download citation
DOI: https://doi.org/10.1007/978-3-030-22549-0_7
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-22548-3
Online ISBN: 978-3-030-22549-0
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)