Molecular Evolution and Genetic Diversity of Oil Palm Based on Sequencing and Analysis with Molecular Markers

  • Parisa Azizi
  • Mohamed Musa HanafiEmail author
  • Mohamad Osman
  • Mohd Rafii Yusop
  • Maizura Ithnin
  • Sima Taheri
  • Mahbod Sahebi
Part of the Compendium of Plant Genomes book series (CPG)


Molecular marker advancement and utilization to exploit and identify genetic diversity are the most key developments in molecular genetic studies. Molecular markers are the most common tool for exploring plant genetic diversity and area pre- requisite for gene mapping, segregation and genetic analysis, forensic assessment, phylogenetic analysis, and the achievement of many other biological goals. Despite the development of several molecular marker types that are regularly applied in plant breeding, majority of these markers are confined in their functions due to their limited accessibility and the cost of analyses carried out on a large scale. However, the advent of sequencing technologies, including next-generation sequencing (NGS) and genotyping by sequencing (GBS), has transformed plant breeding via SSR and SNP development. To date, different types of sequencing technologies have been generated and reviewed. This chapter provides insight into the spectrum of molecular marker-based detection methods and their role in determining the genetic diversity of oil palms based on sequencing.


Molecular markers Oil palm genetic diversity Genotyping by sequencing Next-generation sequencing 



The authors wish to acknowledge Universiti Putra Malaysia (UPM) for support.


  1. Abdullah N, Yusop MR, Ithnin M, Saleh G, Latif M (2011) Genetic variability of oil palm parental genotypes and performance of its’ progenies as revealed by molecular markers and quantitative traits. CR Biol 334:290–299CrossRefGoogle Scholar
  2. Ajambang W, Asmono D, Toruan N (2012) Microsatellite markers reveal Cameroon’s wild oil palm population as a possible solution to broaden the genetic base in the Indonesia-Malaysia oil palm breeding programs. Afr J Biotech 11:13244–13249CrossRefGoogle Scholar
  3. Arias D, Montoya C, Rey L, Romero H (2012) Genetic similarity among commercial oil palm materials based on microsatellite markers. Agronomía Colombiana 30:188–195Google Scholar
  4. Arias D, González M, Romero H (2015) Genetic diversity and establishment of a core collection of oil palm (Elaeis guineensis Jacq.) based on molecular data. Plant Genet Resour 13:256–265CrossRefGoogle Scholar
  5. Ataga C, Fatokun C (1989) Disc polyacrylamide gel electrophoresis of pollen proteins in the oil palm (Elaeis). Euphytica 40:83–88Google Scholar
  6. Babu K et al (2019) Development and validation of whole genome-wide and genic microsatellite markers in oil palm (Elaeis guineensis Jacq.): first microsatellite database (OpSatdb). Sci Rep 9:1899Google Scholar
  7. Bai B et al (2018) Developing genome-wide SNPs and constructing an ultrahigh-density linkage map in oil palm. Sci Rep 8:691PubMedCrossRefPubMedCentralGoogle Scholar
  8. Bakoumé C et al (2011) DNA sequence-based markers for verification of ramet-to-ortet relationship in oil palm (Elaeis guineensis Jacq.). Am J Plant Sci 2:539Google Scholar
  9. Bakoumé C, Wickneswari R, Rajanaidu N, Kushairi A, Amblard P, Billotte N (2007) Allelic diversity of natural oil palm (Elaeis guineensis Jacq.) populations detected by microsatellite markers: implications for conservation. Plant Genet Resour 5:104–107CrossRefGoogle Scholar
  10. Bakoumé C, Wickneswari R, Siju S, Rajanaidu N, Kushairi A, Billotte N (2015) Genetic diversity of the world’s largest oil palm (Elaeis guineensis Jacq.) field genebank accessions using microsatellite markers. Genet Resour Crop Evol 62:349–360CrossRefGoogle Scholar
  11. Barcelos E, Amblard P, Berthaud J, Seguin M (2002) Genetic diversity and relationship in American and African oil palm as revealed by RFLP and AFLP molecular markers. Pesquisa Agropecuária Brasileira 37:1105–1114CrossRefGoogle Scholar
  12. Beirnaert ADF, Vanderweyen R (1941) Contribution à l’étude génétique et biométrique des variétés d’Elaeis guineensis Jacquin. East African StandardGoogle Scholar
  13. Bhagya H, Babu BK, Naika MB, Mathur R, Gangadharappa P, Satisha D, Naik R (2018) Identification and utilization of polymorphic SSR markers for genetic diversity studies in oil palm. Int J Curr Microbiol App Sci 7:333–341CrossRefGoogle Scholar
  14. Billotte N, Risterucci A-M, Barcelos E, Noyer J-L, Amblard P, Baurens F-C (2001) Development, characterisation, and across-taxa utility of oil palm (Elaeis guineensis Jacq.) microsatellite markers. Genome 44:413–425PubMedCrossRefGoogle Scholar
  15. Billotte N et al (2005) Microsatellite-based high density linkage map in oil palm (Elaeis guineensis Jacq.). Theor Appl Genet 110:754–765PubMedCrossRefGoogle Scholar
  16. Cardona CCC, Coronado YM, Conronado ACM, Ochoa I (2018) Genetic diversity in oil palm (Elaeis guineensis Jacq.) using RAM (random amplified microsatellites). Bragantia 77:546–556CrossRefGoogle Scholar
  17. Cheah S, Ooi L (1999) Development of genetic markers for the oil palm based on simple sequence repeat (SSR) DNA. In: Colloquium on advances in oil palm research under IRPA-funded programmes in the 7th Malaysian Plan, pp 1–2Google Scholar
  18. Cheah SC, Ooi LCL, Rahimah AR (1995) Polymorphic DNA in oil palm amplified by simple sequence repeat (SSR) primed polymerase chain reactions. Paper presented at the In The VII National Biotechnology Seminar (Seminar Bioteknologi Kebangsaan ke VII), Langkawi Island, Malaysia, 20–22 NovemberGoogle Scholar
  19. Chee WW, Jit TC, Kien WC, Mayes S, Singh R, Chin S (2015) Development of an effective SSR-based fingerprinting system for commercial planting materials and breeding applications in oil palm. J Oil Palm Res 27:113–127Google Scholar
  20. Chun TC et al (2018) Genetic diversity and inbreeding level in deli dura and avros advanced breeding materials in oil palm (Elaeis guineensis Jacq.) using microsatellite markers. J Oil Palm Res 30:366–379Google Scholar
  21. Constantin M, Ridwani S, Syukur M, Suwarno WB, Godswill N-N (2017) Genetic Diversity and Interrelationship among Some Dura × Tenera Oil Palm (Elaeis guineensis Jacq.) Genotypes in Cameroon. J Agric Sci Technol 7:81–90Google Scholar
  22. Dhanapal AP et al (2015) Genome-wide association analysis of diverse soybean genotypes reveals novel markers for nitrogen traits. Plant Genome 8Google Scholar
  23. França LT, Carrilho E, Kist TB (2002) A review of DNA sequencing techniques. Q Rev Biophys 35:169–200PubMedCrossRefGoogle Scholar
  24. Govindaraj M, Vetriventhan M, Srinivasan M (2015) Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives. Genet Res Int 2015:1–14CrossRefGoogle Scholar
  25. Hama-Ali EO, Alwee SSRS, Tan SG, Panandam JM, Ling HC, Namasivayam P, Peng HB (2015) Illegitimacy and sibship assignments in oil palm (Elaeis guineensis Jacq.) half-sib families using single locus DNA microsatellite markers. Mol Biol Rep 42:917–925PubMedCrossRefGoogle Scholar
  26. Hardon J, Thomas R (1968) Breeding and selection of the oil palm in Malaya. Oléagineux 23:85–90Google Scholar
  27. Hartley C (1988) The oil palm, 3rd edn. Longman, LondonGoogle Scholar
  28. Hayati A, Wickneswari R, Maizura I, Rajanaidu N (2004) Genetic diversity of oil palm (Elaeis guineensis Jacq.) germplasm collections from Africa: implications for improvement and conservation of genetic resources. Theor Appl Genet 108:1274–1284PubMedCrossRefGoogle Scholar
  29. Hiremath PJ et al (2012) Large-scale development of cost-effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes. Plant Biotechnol J 10:716–732PubMedCrossRefPubMedCentralGoogle Scholar
  30. Huang X et al (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42:961PubMedCrossRefGoogle Scholar
  31. Jacobson A, Hedrén M (2007) Phylogenetic relationships in Alisma (Alismataceae) based on RAPDs, and sequence data from ITS and trnL. Plant Syst Evol 265:27–44CrossRefGoogle Scholar
  32. Jayanthi M, Mandal P, Sujatha G, Sri K, Rao G, Sunitha B, Babu M (2008) Simple sequence repeats and RAPD primers for assessment of genetic uniformity among the field planted clones of oil palm. J Plant Crops 36:235–238Google Scholar
  33. Jin J et al (2016) Draft genome sequence of an elite Dura palm and whole-genome patterns of DNA variation in oil palm. DNA Res 23:527–533PubMedCrossRefPubMedCentralGoogle Scholar
  34. Jouannic S et al (2005) Analysis of expressed sequence tags from oil palm (Elaeis guineensis). FEBS Lett 579:2709–2714PubMedCrossRefGoogle Scholar
  35. Khomphet T, Eksomtramage T, Duangpan S (2018) Genetic variation of improved oil palm Tenera hybrid populations using morphological and SSR markers. Songklanakarin J Sci Technol 40Google Scholar
  36. Kularatne R (2000) Assessment of genetic diversity in natural oil palm (Elaeis guineensis Jacq.) populations using amplified fragment length polymorphism markers. Ph. D. Dissertation, Universiti Kebangsaan Malaysia, Kuala Lumpur, MalaysiaGoogle Scholar
  37. Kularatne R, Shah F, Rajanaidu N (2001) The evaluation of genetic diversity of Deli dura and African oil palm germplasm collection by AFLP techniqueGoogle Scholar
  38. Ling AH (2019) Global palm oil trade—prospect and outlook. Paper presented at Malaysia—China Business Forum, Kuala Lumpur, 4th March 2019Google Scholar
  39. Maizura I, Cheah S, Rajanaidu N (2001) Genetic diversity of oil palm germplasm collections using RFLPs. In: Cutting-edge technologies for sustained competitiveness: Proceedings of the 2001 PIPOC International Palm Oil Congress, Agriculture Conference, Kuala Lumpur, Malaysia, 20–22 August 2001, Malaysian Palm Oil Board (MPOB), pp 526–535Google Scholar
  40. Maizura I, Rajanaidu N, Zakri A, Cheah S (2006) Assessment of genetic diversity in oil palm (Elaeis guineensis Jacq.) using restriction fragment length polymorphism (RFLP). Genet Resour Crop Evol 53:187–195CrossRefGoogle Scholar
  41. Mandal PK, Malliah P, Sireesha K, Shamila S, Aruna C (2004) The use of RAPD markers for molecular characterization of oil palm (Elaeis guineensis Jacq.) germplasm. J Plant Crops 32:131–133Google Scholar
  42. Mohan M, Nair S, Bhagwat A, Krishna T, Yano M, Bhatia C, Sasaki T (1997) Genome mapping, molecular markers and marker-assisted selection in crop plants. Mol Breeding 3:87–103CrossRefGoogle Scholar
  43. Moretzsohn MdC, Ferreira M, Amaral Z, Coelho PJdA, Grattapaglia D, Ferreira ME (2002) Genetic diversity of Brazilian oil palm (Elaeis oleifera HBK) germplasm collected in the Amazon Forest. Euphytica 124:35CrossRefGoogle Scholar
  44. Norziha A, Rafii M, Maizura I, Mohd Din A (2008) Genetic diversity among oil palm parental genotypes revealed by microsatellite polymorphism and its relationship to progeny performanceGoogle Scholar
  45. Nugroho Y et al (2019) Genome-wide SNP-discovery and analysis of genetic diversity in oil palm using double digest restriction site associated DNA sequencing. In: IOP conference series: earth and environmental science, vol 1. IOP Publishing, p 012041Google Scholar
  46. Okoye M, Bakoumé C, Uguru M, Singh R, Okwuagwu C (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 8Google Scholar
  47. Okoye MN, Bakoume C, Uguru MI, Singh R (2018) Genetic diversity and relatedness of oil palm progenies determined by microsatellite and agronomic markers. Afr J Biotech 17:614–625CrossRefGoogle Scholar
  48. Ong P, Maizura I, Abdullah N, Rafii M, Ooi L, Low E, Singh R (2015) Development of SNP markers and their application for genetic diversity analysis in the oil palm (Elaeis guineensis). Genet Mol Res 14:12205–12216PubMedCrossRefGoogle Scholar
  49. Paterson AH (1996) Genome mapping in plants. RG Landes Co.Google Scholar
  50. Pereira V, Leao A, Forimighieri E, Souza Junior M, Rios SdA, Alves A (2015) Molecular characterization and genetic structure of american oil palm (Elaeis oleifera) based on genome-wide SNP markers. In: Embrapa Agroenergia-Resumo em anais de congresso (ALICE). Encontro De Pesquisa E Inovação Da Embrapa Agroenergia. Brasília, DF. Anais… Brasília, DF: Embrapa AgroenergiaGoogle Scholar
  51. Pootakham W, Uthaipaisanwong P, Sangsrakru D, Yoocha T, Tragoonrung S, Tangphatsornruang S (2013) Development and characterization of single-nucleotide polymorphism markers from 454 transcriptome sequences in oil palm (Elaeis guineensis). Plant Breeding 132:711–717CrossRefGoogle Scholar
  52. Pootakham W et al (2015) Genome-wide SNP discovery and identification of QTL associated with agronomic traits in oil palm using genotyping-by-sequencing (GBS). Genomics 105:288–295PubMedCrossRefGoogle Scholar
  53. Purba AR, Noyer J-L, Baudouin L, Perrier X, Hamon S, Lagoda P (2000) A new aspect of genetic diversity of Indonesian oil palm (Elaeis guineensis Jacq.) revealed by isoenzyme and AFLP markers and its consequences for breeding. Theor Appl Genet 101:956–961CrossRefGoogle Scholar
  54. Putri LAP, Rivallan R, Puspitaningrum Y, Perrier X, Asmono D, Billotte N (2010) Allelic diversity of 22 Sampoerna Agro’s oil palm pisifera based on microsatellite markersGoogle Scholar
  55. Rajanaidu N, Maizura I, Cheah S (2006) Screening of oil palm natural populations using RAPD and RFLP molecular markers. Malaysian Palm Oil Board (MPOB)Google Scholar
  56. Riju A, Chandrasekar A, Arunachalam V (2007) Mining for single nucleotide polymorphisms and insertions/deletions in expressed sequence tag libraries of oil palm. Bioinformation 2:128PubMedCrossRefPubMedCentralGoogle Scholar
  57. Rival A, Bertrand L, Beulé T, Combes M-C, Trouslot P, Lashermes P (1998) Suitability of RAPD analysis for the detection of somaclonal variants in oil palm (Elaeis guineensis Jacq.). Plant Breeding 117:73–76CrossRefGoogle Scholar
  58. Sathish D, Mohankumar C (2007) RAPD markers for identifying oil palm (Elaeis guineensis Jacq.) parental varieties (dura & pisifera) and the hybrid teneraGoogle Scholar
  59. Shah F, Rashid O, Simons A, Dunsdon A (1994) The utility of RAPD markers for the determination of genetic variation in oil palm (Elaeis guineensis). Theor Appl Genet 89:713–718PubMedCrossRefGoogle Scholar
  60. Singh R, Nagappan J, Tan SG, Panandam JM, Cheah SC (2007) Development of simple sequence repeat (SSR) markers for oil palm and their application in genetic mapping and fingerprinting of tissue culture clones. APJMBB 15:121–131Google Scholar
  61. Singh R, Nagappan J, Tan S-G, Panandam JM, Cheah SC (2007) Development of simple sequence repeat (SSR) markers for oil palm and their application in genetic mapping and fingerprinting of tissue culture clones. Asia Pac J Mol Biol Biotechnol 15:121–131Google Scholar
  62. Singh R et al (2008) Exploiting an oil palm EST database for the development of gene-derived SSR markers and their exploitation for assessment of genetic diversity. Biologia 63:227–235CrossRefGoogle Scholar
  63. Solin NWNM, Toruan-Mathius N (2014) Genetic diversity of D×P population yield component in oil palm’s paternal half-sib family based on microsatellite markers. Energy Procedia 47:196–203CrossRefGoogle Scholar
  64. Squirrell J, Hollingsworth P, Woodhead M, Russell J, Lowe A, Gibby M, Powell W (2003) How much effort is required to isolate nuclear microsatellites from plants? Mol Ecol 12:1339–1348PubMedCrossRefGoogle Scholar
  65. Taeprayoon P, Tanya P, Lee S-H, Srinives P (2015) Genetic background of three commercial oil palm breeding populations in Thailand revealed by SSR markers. Aust J Crop Sci 9:281Google Scholar
  66. Taeprayoon P, Tanya P, Kang YJ, Limsrivilai A, Lee S-H, Srinives P (2016) Genome-wide SSR marker development in oil palm by Illumina HiSeq for parental selection. Plant Genet Resour 14:157–160CrossRefGoogle Scholar
  67. Teh C-K et al (2016) Genome-wide association study identifies three key loci for high mesocarp oil content in perennial crop oil palm. Sci Rep 6:19075PubMedCrossRefPubMedCentralGoogle Scholar
  68. Thawaro S, Te-chato S (2010) Verification of legitimate tenera oil palm hybrids using SSR and propagation of hybrids by somatic embryogenesis. Songklanakarin J Sci Technol 32Google Scholar
  69. Ting N-C et al (2010) SSR mining in oil palm EST database: application in oil palm germplasm diversity studies. J Genet 89:135–145PubMedCrossRefGoogle Scholar
  70. Ting N-C et al (2014) High density SNP and SSR-based genetic maps of two independent oil palm hybrids. BMC Genom 15:309CrossRefGoogle Scholar
  71. Tranbarger TJ, Dussert S, Joët 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 156:564–584Google Scholar
  72. Uthaipaisanwong P, Somyong S, Tangphatsornruang S, Yoocha T, Jantasuriyarat C (2017) Development and characterization of simple sequence repeats derived from mitochondrial genome of oil palm using next generation sequencing. Thai J Sci Technol 6:288–300Google Scholar
  73. Varshney R et al (2008) Identification and validation of a core set of informative genic SSR and SNP markers for assaying functional diversity in barley. Mol Breeding 22:1–13CrossRefGoogle Scholar
  74. Wang DG et al (1998) Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280:1077–1082PubMedCrossRefGoogle Scholar
  75. Weising K, Nybon H, Wolff K, Kahl G (2005) Applications of DNA fingerprinting in plant sciences. DNA Fingerprinting in plants-principles, methods, and applications, pp 235–276Google Scholar
  76. Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18:7213–7218PubMedCrossRefPubMedCentralGoogle Scholar
  77. Xia W et al (2019) Development of high-density SNP markers and their application in evaluating genetic diversity and population structure in Elaeis guineensis. Front Plant Sci 10:130PubMedCrossRefPubMedCentralGoogle Scholar
  78. Xiao Y, Zhou L, Xia W, Mason AS, Yang Y, Ma Z, Peng M (2014) Exploiting transcriptome data for the development and characterization of gene-based SSR markers related to cold tolerance in oil palm (Elaeis guineensis). BMC Plant Biol 14:384PubMedCrossRefPubMedCentralGoogle Scholar
  79. Xiao Y et al (2016) Genome-wide identification and transferability of microsatellite markers between Palmae species. Front Plant Sci 7:1578PubMedPubMedCentralGoogle Scholar
  80. Zaki NM, Ismail I, Rosli R, Chin TN, Singh R (2010) Development and characterization of Elaeis oleifera microsatellite markers. Sains Malaysiana 39:909–912Google Scholar
  81. 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 13:4069–4088PubMedCrossRefPubMedCentralGoogle Scholar
  82. Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isolation: a review. Mol Ecol 11:1–16PubMedCrossRefGoogle Scholar
  83. Zulkifli Y, Maizura I, Rajinder S (2009) Genetic diversity study of Elaeis guineensis germplasm using EST-SSRs. In: Actas de la international society for oil palm breeders (ISOPB) seminar. KLCC, Kuala LumpurGoogle Scholar

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© Springer Nature Switzerland AG 2020

Authors and Affiliations

  • Parisa Azizi
    • 1
    • 2
  • Mohamed Musa Hanafi
    • 1
    • 2
    • 3
    Email author
  • Mohamad Osman
    • 4
  • Mohd Rafii Yusop
    • 2
  • Maizura Ithnin
    • 5
  • Sima Taheri
    • 6
  • Mahbod Sahebi
    • 2
  1. 1.Laboratory of Plantation Science and TechnologyInstitute of Plantation Studies, Universiti Putra MalaysiaSerdangMalaysia
  2. 2.Laboratory of Climate-Smart Food Crop ProductionInstitute of Tropical Agriculture and Food Security, Universiti Putra MalaysiaSerdangMalaysia
  3. 3.Department of Land Management, Faculty of AgricultureUniversiti Putra MalaysiaSerdangMalaysia
  4. 4.Prime Minister’s DepartmentMalaysian Industry-Government Group for High Technology (MIGHT)CyberjayaMalaysia
  5. 5.Advanced Biotechnology and Breeding CentreMalaysian Palm Oil BoardKajangMalaysia
  6. 6.Centre of Research in Biotechnology for Agriculture (CEBAR), University of MalayaKuala LumpurMalaysia

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