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Genetic diversity and establishment of a core collection of oil palm (Elaeis guineensis Jacq.) based on molecular data

Published online by Cambridge University Press:  08 December 2014

Diana Arias ,
Maria González  and
Hernán Romero
Diana Arias
Affiliation:
Oil Palm Biology and Breeding Program, Oil Palm Research Center, Calle 21 No. 42-55, Bogotá, Colombia
Maria González
Affiliation:
Oil Palm Biology and Breeding Program, Oil Palm Research Center, Calle 21 No. 42-55, Bogotá, Colombia
Hernán Romero*
Affiliation:
Oil Palm Biology and Breeding Program, Oil Palm Research Center, Calle 21 No. 42-55, Bogotá, Colombia Department of Biology, Universidad Nacional de Colombia, Bogotá, Colombia
*
*Corresponding author. E-mail: hmromeroa@unal.edu.co
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Abstract

Understanding of genetic diversity and its distribution is essential for promoting the use of genetic resources. The development of core collections using molecular tools has been proposed as a strategy for increasing the economical use and conservation of genetic resources. In this study, we investigated the genetic variation among different geographical origins and potential entries that constituted a core collection of oil palm, using 29 microsatellite markers and by evaluating 788 oil palm accessions. Our results revealed important genetic diversity (HT= 0.759) between oil palm accessions from Angola and Cameroon, which exhibited a low coefficient of genetic differentiation between populations (GST= 0.022). However, the inclusion of oil palm accessions from Indonesia in the analysis resulted in a high coefficient of genetic differentiation between populations (GST= 0.251). We found that the combination of stratified sampling based on a sorting method and a heuristic algorithm was the most effective method for the development of an oil palm core collection set. Using this method, two core collections were identified. The first core collection, comprising 289 entries, contained 271 retained alleles in a sample representing 37% of the entire collection. The second one is a mini core collection, comprising 91 entries, that contained 271 retained alleles with a total He value of 0.72 in a sample representing 11% of the entire collection. The information reported in this study will be of great interest to oil palm researchers because new strategies for breeding programmes can be developed based on these advances.

Keywords

genetic resourcesmicrosatellite markersmini core collectionoil palm
Type
Research Article
Information
Plant Genetic Resources , Volume 13 , Issue 3 , November 2015 , pp. 256 - 265
Copyright
Copyright © NIAB 2014 

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References

Arias, DM, Montoya, C and Romero, HM (2010) Preliminary results on the molecular characterization of oil palm using microsatellites markers. PALMAS 31: 35–45.Google Scholar
Arias, D, Montoya, C and Romero, H (2013a) Molecular characterization of oil palm Elaeis guineensis Jacq. materials from Cameroon. Plant Genetic Resources: Characterization and Utilization 11(2): 140–148. doi: http://dx.doi.org/10.1017/S1479262112000482 .Google Scholar
Arias, D, González, M, Prada, F, Restrepo, E and Romero, H (2013b) Morpho-agronomic and molecular characterisation of oil palm Elaeis guineensis Jacq. material from Angola. Tree Genetics & Genomes 9: 1283–1294.Google Scholar
Bakoumé, C, Wickneswari, R, Rajanaidu, N, Kushairi, A, Amblard, P, and Billotte, N (2007) Allelic diversity of natural oil palm (Elaeis guineensis Jacq.) populations detected by microsatellite markers: implications for conservation. Plant Genetic Resources: Characterization and Utilization 5(2): 104–107. doi: 10.1017/S1479262107710870.Google Scholar
Barcelos, E, Amblard, P, Berthaud, J and 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: 1105–1114.Google Scholar
Billotte, N, Risterucci, AM, Barcelos, E, Noyer, JL, Amblard, P and Baurens, FC (2001) Development, characterisation, and across-taxa utility of oil palm (Elaeis guineensis Jacq.) microsatellite markers. Genome 44: 413–425.CrossRefGoogle ScholarPubMed
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 and Mangin, B (2010) QTL detection by multi-parent linkage mapping in oil palm (Elaeis guineensis Jacq.). Theoretical and Applied Genetics 120: 1673–1687.Google Scholar
Billotte, N, Marseillac, N, Risterucci, AM, Adon, B, Brottier, P, Baurens, FC, Singh, R, Herrán, A, Asmady, H, Billot, C, Amblard, P, Durand-Gasselin, T, Courtois, B, Asmono, D, Cheah, SC, Rohde, W, Ritter, E and Charrier, A (2005) Microsatellite-based high density linkage map in oil palm (Elaeis guineensis Jacq.). Theoretical and Applied Genetics 110: 754–765.Google Scholar
Bowcock, AM, Ruiz-Linares, A, Tomfohrde, J, Minch, E, Kidd, JR and Cavalli-Sforza, LL (1994) High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368: 455–457.Google Scholar
Brown, AHD (1989) Core collections: a practical approach to genetic resources management. Genome 31: 818–824.Google Scholar
Chung, JW, Kim, KW, Chung, JW, Lee, JR, Lee, SY, Dixit, A, Kang, HK, Zhao, W, McNally, KL, Hamilton, RS, Gwag, JG and Park, YJ (2009) Development of a core set from a large rice collection using a modified heuristic algorithm to retain maximum diversity. Journal of Integrative Plant Biology 51: 1116–1125.Google Scholar
Cochard, B, Adon, B, Rekima, S, Billotte, N, Desmier de Chenon, R, Koutou, A, Nouy, B, Omoré, A, Purba, AR, Glazsmann, JC and Noyer, JL (2009) Geographic and genetic structure of African oil palm diversity suggests new approaches to breeding. Tree Genetics & Genomes 5: 493–504.Google Scholar
Cochran, WG (1977) Sampling Techniques, 3rd edn. New York: John Wiley and Sons.Google Scholar
Corley, RHV and Tinker, PB (2003) The Oil Palm, 4th edn. World Agricultural Series. Oxford UK: Blackwell Publishers Ltd.CrossRefGoogle Scholar
Diwan, N, McIntosh, MS and Bauchan, GR (1995) Methods of developing a core collection of annual Medicago species. Theoretical and Applied Genetics 90: 755–761.Google Scholar
FAOSTAT(2010) FAO Statistical Yearbook. World Food and Agriculture. Food and Agriculture Organization of the United Nations. Available at http://faostat.fao.org/site/ (accessed accessed 11 October 2012).Google Scholar
Gerritsma, W and Wessel, M (1997) Oil palm: domestication achieved? Netherlands Journal of Agricultural Science 45: 463–475.Google Scholar
Gimlet, VN (2002) GIMLET: a computer program for analyzing genetic individual identification data. Molecular Ecology Notes 2: 377–379.Google Scholar
Goudet, J (2002) Institute of Ecology, Biology Building, UNIL Software (FSTAT), Version 2.9.3.2 . http://www2.unil.ch/popgen/softwares/fstat.htm.Google Scholar
Hao, CY, Dong, YC, Wang, LF, You, GX, Zhang, HN, Ge, HM, Jia, JZ and Zhang, XY (2008) Genetic diversity and construction of core collection in Chinese wheat genetic resources. Chinese Science Bulletin 53: 1518–1526.Google Scholar
Hayati, A, Wickneswari, R, Maizura, I and Rajanaidu, N (2004) Genetic diversity of oil palm (Elaeis guineensis Jacq.) germplasm collections from Africa: implications for improvement and conservation of genetic resources. Theoretical and Applied Genetics 108: 1274–1284.Google Scholar
Hodgkin, T, Roviglioni, R, de Vicente, MC and Dudnik, N (2001) Molecular methods in the conservation and use of plant genetic resources. Acta Horticulturae 546: 107–118.Google Scholar
Kalia, RK, Rai, MK, Kalia, S, Singh, R and Dhawan, AK (2011) Microsatellite markers: an overview of the recent progress in plants. Euphytica 177: 309–334. doi: 10.1007/s10681-010-0286-9.Google Scholar
Kim, KW, Chung, HK, Cho, GT, Ma, KH, Chandrabalan, D, Gwag, JG, Kim, TS, Cho, EG and Park, YJ (2007) PowerCore: a program applying the advanced M strategy with a heuristic search for establishing core sets. Bioinformatics 23: 2155–2162.Google Scholar
Kularatne, RS, Shah, FH and Rajanaidu, N (2001) The evaluation of genetic diversity of Deli dura and African oil palm germplasm collection by AFLP technique. Tropical Agricultural Research 13: 1–12.Google Scholar
Kuroda, Y, Tomooka, N, Kapa, A, Wanigadea, SM and Vaughan, D (2009) Genetic diversity of wild soybean (Glycine soja Sieb. et Zucc.) and Japanese cultivated soybeans [G. max (L.) Merr.] based on microsatellite (SSR) analysis and the selection of a core collection. Genetic Resources and Crop Evolution 56: 1045–1055.Google Scholar
Laurentin, H (2009) Data analysis for molecular characterization of plant genetic resources. Genetic Resources and Crop Evolution 56(2): 277–292. doi: 10.1007/s10722-008-9397-8.Google Scholar
Le Cunff, L, Fournier-Level, A, Laucou, V, Vezzulli, S, Lacombe, T, Adam-Blondon, AF, Boursiquot, JM and This, P (2008) Construction of nested genetic core collections to optimize the exploitation of natural diversity in Vitis vinifera L. subsp. sativa. BMC Plant Biology 8: 31.Google Scholar
Li, ZC, Zhang, HL, Zeng, YW, Yang, ZY, Shen, SQ, Sun, CQ and Wang, XK (2002) Studies on sampling schemes for the establishment of core collection of rice landrace in Yunnan, China. Genetic Resources and Crop Evolution 49: 67–74.Google Scholar
Maizura, I, Rajanaidu, N, Zakri, A and Cheah, S (2006) Assessment of genetic diversity in oil palm (Elaeis guineensis Jacq.) using restriction fragment length polymorphism (RFLP). Genetic Resources and Crop Evolution 53: 187–195.Google Scholar
Moe, KT, Gwag, JG and Park, YJ (2012) Efficiency of PowerCore in core set development using amplified fragment length polymorphic markers in mungbean. Plant Breeding 131: 110–117.Google Scholar
Montoya, C, Arias, DM, Rey, L, and Rocha, PJ (2005) Caracterización molecular de materiales de E. guineensis Jacq. Procedentes de Angola. Fitotecnia Colombiana 5(2): 1–10.Google Scholar
Nei, M and Li, WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences 76: 5269– 5273.Google Scholar
Nei, M (1987) Molecular Evolutionary Genetics. New York: Colombia University Press.Google Scholar
Peakall, R and Smouse, P (2006) GENALEX6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6 288–295.Google Scholar
Qu, L, Li, X, Wu, G and Yang, N (2005) Efficient and sensitive method of DNA silver staining in polyacrylamide gels. Electrophoresis 26: 99–101.Google Scholar
Rohlf, FJ (2000) Statistical power comparisons among alternative morphometric methods. American Journal Physical Anthropology 111: 463–478.Google Scholar
Rey, L, Gómez, PL, Ayala, I, Delgado, W and Rocha, P (2004) Colecciones genéticas de palma de aceite Elaeis guineensis (Jacq.) y Elaeis oleifera (H.B.K.) de Cenipalma: Características de importancia en el sector palmicultor. PALMAS 25: 39–48.Google Scholar
Sangiri, C, Kaga, A, Tomooka, N, Vaughan, DA and Srinives, P (2007) Genetic diversity of the mungbean (Vigna radiata, Leguminosae) gene pool on the basis of microsatellite analysis. Australian Journal of Botany 55: 837–847. doi:10.1071/BT07105 .Google Scholar
Spagnoletti, PL and Qualset, CO (1993) Evaluation of five strategies for obtaining a core subset from a large genetic resource collection of durum wheat. Theoretical and Applied Genetics 87: 295–304.Google Scholar
Singh, R, Mohd, N, Ting, N, Rosli, R, Tan, S, Leslie, E, Ithnin, M and Cheah, S (2008) Exploiting an oil palm EST database for the development of gene-derived SSR markers and their exploitation for assessment of genetic diversity. Biologic 63: 227–235 Section Cellular and Molecular Biology. doi: 10.2478/s11756-008-0041-z.Google Scholar
van Hintum, T, Brown, AHD, Spillane, C and Hodgkin, T (2000) Core Collections of Plant Genetics Resources. IPGRI Technical Bulletin No. 3. Rome, Italy: International Plant Genetic Resources Institute.Google Scholar
Yan, WG, Rutger, N, Bryant, R, Bockelman, HE, Fjellstrom, RG, Chen, MH, Tai, T and McClung, A (2007) Development and evaluation of a core subset of the USDA rice germplasm collection. Crop Science 47: 869–876. doi: 10.2135/cropsci2006.07.0444 .Google Scholar
Zewdie, Y, Tong, N and Bosland, P (2004) Establishing a core collection of Capsicum using a cluster analysis with enlightened selection of accessions. Genetic Resources and Crop Evolution 51: 147–151.Google Scholar
Zhang, H, Zhang, D, Wang, M, Sun, J, Qi, Y, Li, J, Wei, X, Han, L, Qiu, Z, Tang, S and Li, Z (2011) A core collection and mini core collection of Oryza sativa L. in China. Theoretical and Applied Genetics 122: 49–61.Google Scholar
Zhao, WG, Cho, GT, Ma, KH, Chung, JW, Gwag, JG and Park, YJ (2010) Development of an allele-mining set in rice using a heuristic algorithm and SSR genotype data with least redundancy for the post-genomic era. Molecular Breeding 26: 639–651.Google Scholar
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