DNA intensity and genetic diversity of oil palm (Elaeis guineensis) to determine an elite low lipase line
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Abstract. Angkat NU, Siregar LAM, Basyuni M, Afandi D, Syahputra I. 2021. DNA intensity and genetic diversity of oil palm (Elaeis guineensis) to determine an elite low lipase line. Biodiversitas 22: 900-905. The acidification of palm oil due to lipase activity in the mesocarp is assessed under genetic control. Three molecular markers have been established to gauge the lipase gene in oil palm. Lower lipase activity is desired for good quality edible oil. This study aims to identify the genetic diversity by screening groups/families to determine an elite low lipase genotype of oil palm. Genetic diversity and population structure of 15 groups of oil palm were investigated by using three specific markers with GenAlex 6.502 software. Results show that the Polymorphic Informative Content (PIC) value of markers was around 0,985-0,993, which indicates that these markers are effective in determining the diversity of lipase activity in oil palm. Analysis of molecular variance (AMOVA) revealed that genetic diversity varies within individuals (54%), among individuals (31%), and among population (15%). The value of number of alleles (Na), number of effective alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He), and number of allele migration (Nm) indicate that the genetic diversity in this population is relatively low. Phylogenetic analysis identified two main groups as high lipase and low lipase activity groups based on DNA intensity.
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References
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Berger KG. 2006. Undersatnding oil and fats. Global oil fats business magazine 3:4 (50-53).
Bariyah K, Nuri A, Purwiyatno H. 2017. Reduction of Diglycerides and Free Fatty Acids in Crude Palm Oil Using Adsorbents. AGRITECH, Vol. 37 (1) : 48-58.
Budiman LF, Ardha A, Adi P, Sudarsono S. 2019. Genetic diversity analysis of Tenera × Tenera and Tenera × Pisifera Crosses and D self of oil palm (Elaeis guineensis) parental populations originating from Cameroon. Biodiversitas 20 : 937-949.
Constant LLB, Ntsomboh NG, Ngando E, George F, Ngalle BH, Nyouma A, and Joseph M. 2017. A review of main factors affecting palm oil acidity within the smallholder oil palm ( Elaeis guineensis Jacq) sector in Cameroon. African Journal of Food Science. Vol. 11(9) : 296-301.
Corley, R.H.V, Tinker PB. 2003. Molecular markers in oil palm breeding. The Oil palm forth edition : 163.
Corley R.H.V., Tinker,P.B. 2016. The oil palm, Fifth edn. John Wiley & Sons, Ltd., Oxford
Domonhédo, H., Cuéllar, T., Espeout, S., Droc, G., Summo, M., Rivallan, R., Cros, D., Nouy, B., Omore, A., Nodichao, L., Arondel, F., Ahanhanzo, C., Bilotte, N.,2018.Genomic structure, QTLmapping, and molecular markers of lipase genes responsible for palm oil acidity in the oil palm (Elaeis guineensis Jacq.).Tree Genetics & Genomes: https// doi.org/10.1007/s11295-018-1284-7.
Morcillo F, Cros D, Bilotte N, Ngando-Ebongue GF, Domonhédo H., Pizot M, Cuéllar T, Espéout S, Dhouib, R, Bourgis F, Claverol S, Tranbarger TJ, Nouy B, Arondel V. 2013. Improving palm oil quality through identification and mapping of the lipase gene causing oil deterioration. Nature Communications 4, Article number :2160 doi:10.1038/ncomms3160.
Maimun T, Nasrul, Fikriatul AH, Putri R. 2017. Inhibition of Increased Free Fatty Acid Levels in Oil Palm Fruits Using Liquid Smoke. JTIPI : https://doi.org/10.17969/jtipi.v9i2.8469
Mateescue RG, Zhang Z, Tsai J, Phavaphutanon NI, Burton WG, Lust R, Quaas K, Murphy GM, Acland RJ, Todhunter. 2005. Analysis of allele fidelity, polymorphic information content, and density of microsatellites in a genome-wide screening for hip dysplasia in a crossbreed pedigree. J. Hered. 96:847- 853
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Nei M, Chesser RK. 1983. Estimation of fixation indices and gene diversities. Ann Hum Genet 47 (3): 253-259
Orozco-Castillo K, J Chalmers, R Waugh, W Powell. 1994. Detection of genetic diversity and selective gene introgression in coffee using RAPD markers. Theer. Appl. Gent. 87 : 934-940.
Pacheco P. 2012. Soybean and Oil Palm Expansion in Sout America. A review of main trends and implications. Working Paper 90. CIFOR, Bogor, Indonesia.
Peakall and Smouse. 2012. Introduction to population genetic analysis. GenAlex Genetic Analysis in Excel. Based on material provided at the national graduate workshop An Introduction to Genetic Analysis for Populations Studies offered by Rod Peakall and Peter Smouse at the Australian National University, Canberra, Australia, July 2009.
Roy H and Krecik SG. 2016. Smallholder Palm Oil Financing in Indinesia : Needs and Opportunities for Sustainable Finance Intervention. www.rainforest-alliance.org
Roubos K, Moustakas M, Aravanopoulos FA. 2010. Moleculer identification of Greek olive (Olea europaea) based on microsatellite loci. Genet.Mol.Res 9: 1865-1876
Sarimana U, Nurcahyono I, Javier H., Pratiwi E, Fahmi W, Zulhermana Z, Dwi A. 2019. Genetic Diversity Preliminary Study of Cameroon Origin Oil Palm at PT. Binasawit Makmur. Journal of Suboptimal Lands Vol 8:130. DOI: https://doi.org/10.33230/JLSO.8.2.2019.424. Vol.8, No.2 :126-133
Suroso, A.S. 2013. Quality of Used Cooking Oil in terms of Peroxide Number, Acid Number and Water Content. Indoensia Pharmacy Journal Vol 3(2).
USDA Foreign Agriculture Service. 2018. Indonesia Oilseed Products and Annual. Gain Report Number : 1807.
Val, ADB, Ferreira J, Veira N, M Pasqual, A F de Oleiveira, A Boren and GMA Cancado. 2012. Genetic diversity of Brazilian and Introduced olive germplasm based on microsatellite markers. Genetic and Moleculer Research 11 (1) : 556-571.
Wong YT, Kushairi A, Rajanaidu N, Osman M., Wicknesmwari R, Sambhanthamurti R. 2015. Screening of wild oil palm (Elaeis guineensis) germplasm for lipase activity. Journal of Agricultural Science. doi:10.1017/S0021859615001112
Yono D, Wahyu Y, Sobur and Mathius NT. 2017. Identification of SSR Markers Associated with Oil Palm (Elaeisguineensis Jacq.) Bunch Weight. J. Agron. Indonesia 45 (1): 79-85 DOI:https://dx.doi.org/10.24831/jai.v45i1.14014
Berger KG. 2006. Undersatnding oil and fats. Global oil fats business magazine 3:4 (50-53).
Bariyah K, Nuri A, Purwiyatno H. 2017. Reduction of Diglycerides and Free Fatty Acids in Crude Palm Oil Using Adsorbents. AGRITECH, Vol. 37 (1) : 48-58.
Budiman LF, Ardha A, Adi P, Sudarsono S. 2019. Genetic diversity analysis of Tenera × Tenera and Tenera × Pisifera Crosses and D self of oil palm (Elaeis guineensis) parental populations originating from Cameroon. Biodiversitas 20 : 937-949.
Constant LLB, Ntsomboh NG, Ngando E, George F, Ngalle BH, Nyouma A, and Joseph M. 2017. A review of main factors affecting palm oil acidity within the smallholder oil palm ( Elaeis guineensis Jacq) sector in Cameroon. African Journal of Food Science. Vol. 11(9) : 296-301.
Corley, R.H.V, Tinker PB. 2003. Molecular markers in oil palm breeding. The Oil palm forth edition : 163.
Corley R.H.V., Tinker,P.B. 2016. The oil palm, Fifth edn. John Wiley & Sons, Ltd., Oxford
Domonhédo, H., Cuéllar, T., Espeout, S., Droc, G., Summo, M., Rivallan, R., Cros, D., Nouy, B., Omore, A., Nodichao, L., Arondel, F., Ahanhanzo, C., Bilotte, N.,2018.Genomic structure, QTLmapping, and molecular markers of lipase genes responsible for palm oil acidity in the oil palm (Elaeis guineensis Jacq.).Tree Genetics & Genomes: https// doi.org/10.1007/s11295-018-1284-7.
Morcillo F, Cros D, Bilotte N, Ngando-Ebongue GF, Domonhédo H., Pizot M, Cuéllar T, Espéout S, Dhouib, R, Bourgis F, Claverol S, Tranbarger TJ, Nouy B, Arondel V. 2013. Improving palm oil quality through identification and mapping of the lipase gene causing oil deterioration. Nature Communications 4, Article number :2160 doi:10.1038/ncomms3160.
Maimun T, Nasrul, Fikriatul AH, Putri R. 2017. Inhibition of Increased Free Fatty Acid Levels in Oil Palm Fruits Using Liquid Smoke. JTIPI : https://doi.org/10.17969/jtipi.v9i2.8469
Mateescue RG, Zhang Z, Tsai J, Phavaphutanon NI, Burton WG, Lust R, Quaas K, Murphy GM, Acland RJ, Todhunter. 2005. Analysis of allele fidelity, polymorphic information content, and density of microsatellites in a genome-wide screening for hip dysplasia in a crossbreed pedigree. J. Hered. 96:847- 853
Nurniwalis AW. 2017. Physiological, biochemical and molecular analyses of fruit development in oil palm (Elaeis guineensis Jacq.). PhD thesis, University of Nottingham Malaysia Campus
Nei M. 1978. Estimation of average heterozygosity and genetic from small number of individual . Genet 89 : 583-590
Nei M, Chesser RK. 1983. Estimation of fixation indices and gene diversities. Ann Hum Genet 47 (3): 253-259
Orozco-Castillo K, J Chalmers, R Waugh, W Powell. 1994. Detection of genetic diversity and selective gene introgression in coffee using RAPD markers. Theer. Appl. Gent. 87 : 934-940.
Pacheco P. 2012. Soybean and Oil Palm Expansion in Sout America. A review of main trends and implications. Working Paper 90. CIFOR, Bogor, Indonesia.
Peakall and Smouse. 2012. Introduction to population genetic analysis. GenAlex Genetic Analysis in Excel. Based on material provided at the national graduate workshop An Introduction to Genetic Analysis for Populations Studies offered by Rod Peakall and Peter Smouse at the Australian National University, Canberra, Australia, July 2009.
Roy H and Krecik SG. 2016. Smallholder Palm Oil Financing in Indinesia : Needs and Opportunities for Sustainable Finance Intervention. www.rainforest-alliance.org
Roubos K, Moustakas M, Aravanopoulos FA. 2010. Moleculer identification of Greek olive (Olea europaea) based on microsatellite loci. Genet.Mol.Res 9: 1865-1876
Sarimana U, Nurcahyono I, Javier H., Pratiwi E, Fahmi W, Zulhermana Z, Dwi A. 2019. Genetic Diversity Preliminary Study of Cameroon Origin Oil Palm at PT. Binasawit Makmur. Journal of Suboptimal Lands Vol 8:130. DOI: https://doi.org/10.33230/JLSO.8.2.2019.424. Vol.8, No.2 :126-133
Suroso, A.S. 2013. Quality of Used Cooking Oil in terms of Peroxide Number, Acid Number and Water Content. Indoensia Pharmacy Journal Vol 3(2).
USDA Foreign Agriculture Service. 2018. Indonesia Oilseed Products and Annual. Gain Report Number : 1807.
Val, ADB, Ferreira J, Veira N, M Pasqual, A F de Oleiveira, A Boren and GMA Cancado. 2012. Genetic diversity of Brazilian and Introduced olive germplasm based on microsatellite markers. Genetic and Moleculer Research 11 (1) : 556-571.
Wong YT, Kushairi A, Rajanaidu N, Osman M., Wicknesmwari R, Sambhanthamurti R. 2015. Screening of wild oil palm (Elaeis guineensis) germplasm for lipase activity. Journal of Agricultural Science. doi:10.1017/S0021859615001112
Yono D, Wahyu Y, Sobur and Mathius NT. 2017. Identification of SSR Markers Associated with Oil Palm (Elaeisguineensis Jacq.) Bunch Weight. J. Agron. Indonesia 45 (1): 79-85 DOI:https://dx.doi.org/10.24831/jai.v45i1.14014
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