Advertisement

Diversity Studies Using Molecular Markers

  • Chandrika Perera
  • H. D. Dharshani Bandupriya
  • Regi J. Thomas
  • Roland Bourdeix
Chapter
  • 22 Downloads

Abstract

The introduction of molecular markers in the latter part of the twentieth century denoted a major advancement in the research on plant genetics. Molecular markers have become highly advantageous to help overcome certain inherent difficulties associated with the genetic improvement of perennial crops such as coconut. Starting from the middle of the 1990s, considerable progress has been achieved in the genetic diversity analysis of coconut. The early attempts of molecular research on coconut used the common molecular marker systems of the time, such as randomly amplified polymorphic DNA and amplified fragment length polymorphism. Later, the generation of coconut-specific DNA markers and the adoption of high-throughput systems have paved the way for an acceleration, with greater accuracy, in using molecular markers for diversity studies in coconut. Molecular markers have also been used in the development of linkage maps and the identification of quantitative trait loci (QTL) in coconut. The research using molecular markers has been used, and will be further useful, in formulating and refining the further collection and conservation of coconut germplasm, the management of genebanks, identification of duplicates, and determining the strategies for rejuvenation of the existing field genebanks. The data can further be used in the parental selection in the coconut breeding programmes aimed at combining the desirable characters from diverse parents into novel cultivars. The availability of high-throughput marker systems will increase the accuracy and precision of genetic and QTL mapping via linkage analysis. Further, association studies which facilitate the use of existing populations in QTL mapping will be an important tool in moving towards marker-assisted selection of coconuts for desirable traits to ensure sustainability of the coconut industry.

Keywords

Molecular markers Phenotypic variation Coconut varieties Domestication Genetic erosion Genetic variability 

References

  1. Ashburner GR, Thompson WK, Halloran GM et al (1997a) Fruit component analysis of south Pacific coconut palm populations. Genet Resour Crop Evol 44:327–355Google Scholar
  2. Ashburner GR, Thompson WK, Halloran GM (1997b) RAPD analysis of South Pacific coconut palm populations. Crop Sci 37:992–997Google Scholar
  3. Bandaranayake CK (2006) An effective population size for reliable map resolution of Coconut (Cocos nucifera L.). CORD 22(2):33–40Google Scholar
  4. Baudouin L, Lebrun P (2002) The development of a microsatellite kit and dedicated software use with coconuts. Burotrop Bull 17:16–20Google Scholar
  5. Baudouin L, Lebrun P, Konan JL et al (2006) QTL analysis of fruit components in the progeny of a Rennell Island Tall coconut (Cocos nucifera L.) individual. Theor Appl Genet 112:258–268PubMedGoogle Scholar
  6. Benbadis BK (1992) Coconut and date palm. In: Hammerschlag FA, Litz RW (eds) Biotechnology of perennial fruit crops. CAB International, Wallingford, pp 383–400Google Scholar
  7. Bourdeix R, Santos G, Labouisse JP et al (2005) Useful definition of terms and nomenclature. In: Batugal P, Ramanatha Rao V, Oliver J (eds) Coconut genetic resources. IPGRI, Rome, pp 9–10Google Scholar
  8. Coppens G, Gunn B, Baudouin L (2018) Coconut domestication - Chapter 2. Where we are today. In R. Bourdeix & A. Prades (Eds.), A Global Strategy for the Conservation and Use of Coconut Genetic Resources 2018–2028 (pp 36–38) Montpellier, France. Bioversity InternationalGoogle Scholar
  9. Daher RF, Pereira MG, Tupinamba EA et al (2002) Assessment of coconut tree genetic divergence by compound sample RAPD marker analysis. Crop Breed Appl Biotechnol 3(2):431–438Google Scholar
  10. Dasanayaka PN, Everard JMDT, Karunanayake EH et al (2003) Characterization of coconut germplasm by microsatellite markers. Trop Agric Res 15:51–61Google Scholar
  11. Duran Y, Rohde W, Kullaya A et al (1997) Molecular analysis of east African Tall coconut genotypes by DNA marker technology. J Genet Breed 51:279–288Google Scholar
  12. Everard JMDT (1996) Use of molecular markers for breeding of the coconut palm (Cocos nucifera L.). MSc. Thesis, University of New England, Armidale, AustraliaGoogle Scholar
  13. Foale MA (1991) Coconut genetic diversity: present knowledge and future research needs. In: Papers of the IBPGR workshop on coconut genetic resources held in Cipanas, Indonesia, 8–11 October 1999. IBPGR, Rome, pp 46–53Google Scholar
  14. Fremond Y, Ziller R, de Nuce de Lamothe M (1966) Le cocotier. Maisonneuve and Larose, ParisGoogle Scholar
  15. Gangolly SR, Satyabalan K, Pandalai KM (1957) Varieties of coconut. Indian Cocon J 10:3–28Google Scholar
  16. Gunn BF, Baudouin L, Olsen KM (2011) Independent origins of cultivated coconut (Cocos nucifera L.) in the old-world tropics. Plos One 6(6):e21143PubMedPubMedCentralGoogle Scholar
  17. Gunn B, Myrie WW, Baudouin L (2018) Origin, history and dynamics of coconut cultivation - Chapter 1. Introduction to the Global Coconut Strategy In R Bourdeix & A Prades (Eds.), A Global Strategy for the Conservation and Use of Coconut Genetic Resources 2018–2028 (pp 3–7). Montpellier, France. Bioversity InternationalGoogle Scholar
  18. Glenn R. Summerhayes (2018) Coconuts on the Move: Archaeology of Western Pacific. The Journal of Pacific History 53(4):375–396Google Scholar
  19. Hamelin C, Bourdeix R, Baudouin L (2005) The international coconut genetic resources database. In: Batugal P, Ramanatha Rao V, Oliver J (eds) Coconut genetic resources. IPGRI, Rome, pp 282–301Google Scholar
  20. Harries HC (1978) The evolution, dissemination and classification of Cocos nucifera L. Bot Rev 44:205–317Google Scholar
  21. Herran A, Estioko L, Becker D et al (2000) Linkage mapping and QTL analysis in coconut (Cocos nucifera L.). Theor Appl Genet 101:292–300Google Scholar
  22. Jayalekshmy VG, Sree Rangasamy SR (2002) Cluster analysis in coconut (Cocos nucifera L.). J Plant Crop 30(2):18–22Google Scholar
  23. Kamaral LCJ, Perera SACN, Perera KLNS et al (2014) Genetic diversity of the Sri Lanka yellow dwarf form as revealed by microsatellite markers. Trop Agric Res 26(1):131–139Google Scholar
  24. Kamaral LCJ, Dassanayaka PN, Perera KLNS et al (2016) SSR markers reveal the population structure of yellow (dwarf) coconuts in Sri Lanka. Tree Genet Genomes 12(6):116Google Scholar
  25. Kandoliya UK, Joshi AK, Mori DS et al (2018) Genetic diversity analysis of coconut (Cocos nucifera L.) genotypes and hybrids using molecular marker. Indian J Agric Biochem 31(1):25–32Google Scholar
  26. Kearsey MJ, Luo ZW (2003) Mapping, characterization and deployment of quantitative trait loci. In: Plant molecular breeding. Blackwell Publishing Ltd, Oxford, pp 1–29Google Scholar
  27. Konan KJN, Koffi KE, Konan KJL et al (2007a) Microsatellite gene diversity in coconut (Cocos nucifera L.) accessions resistant to lethal yellowing disease. Afr J Biotechnol 6(4):341–347Google Scholar
  28. Konan KJL, Konan KJN, Koffi KE et al (2007b) Coconut microsatellite gene diversity analysis technology transfer to Cote d’ Ivoire. Biotechnology 6(3):383–387Google Scholar
  29. Kriswiyanti E, Temaja GRM, Sudana IM et al (2013) Genetic variation of coconut Tall (Cocos nucifera L.) in Bali, Indonesia based on microsatellite DNA. J Biol Agric Healthc 13:208–224Google Scholar
  30. Lebrun P, N’Cho YP, Seguin M et al (1998) Genetic diversity in coconut (Cocos nucifera L.) revealed by restriction fragment length polymorphism (RFLP) markers. Euphytica 101:103–108Google Scholar
  31. Lebrun P, Baudouin L, Bourdeix R et al (2001) Construction of a linkage map of the Rennell Island Tall coconut type (Cocos nucifera L.) and QTL analysis for yield characters. Genome 44:962–970PubMedGoogle Scholar
  32. Liyanage DV (1958) Varieties and forms of coconut palms grown in Ceylon. Ceylon Cocon Quart 9:1–10Google Scholar
  33. Loiola CM, Azevedo AON, Diniz LEC et al (2016) Genetic relationships among tall coconut palm (Cocos nucifera L.) accessions of the International Coconut Genebank for Latin America and the Caribbean (ICG-LAC), evaluated using microsatellite markers (SSRs). Plos One 11(3):e0151309PubMedPubMedCentralGoogle Scholar
  34. Meerow AW, Wisser RJ, Brown JS et al (2003) Analysis of genetic diversity and population structure within Florida coconut (Cocos nucifera L.) germplasm using microsatellite DNA, with special emphasis on the Fiji Dwarf cultivar. Theor Appl Genet 106:715–726PubMedGoogle Scholar
  35. Menon KPV, Pandalai KM (1958) The coconut, a monograph. Indian Central Coconut Committee, ErnakulamGoogle Scholar
  36. Narayana GV, John CM (1949) Varieties and forms of coconut. Madras Agric J 36:349–366Google Scholar
  37. Oyoo ME, Muhammed N, Cyrus KN et al (2016) Assessment of the genetic diversity of Kenyan coconut germplasm using simple sequence repeat (SSR) markers. Afr J Biotechnol 15(40):2215–2223Google Scholar
  38. Perera L (1999) Assessing genetic diversity in coconut using molecular markers. Ph.D Thesis, University of Dundee, ScotlandGoogle Scholar
  39. Perera L (2002) Chloroplast DNA variation of coconut is opposite to its nuclear DNA variation. CORD 18(2):56–73Google Scholar
  40. Perera SACN (2010) QTL analysis in coconut via genome mapping: principles, requirements and prospects. Cocos 20:57–65Google Scholar
  41. Perera SACN, Ekanayake GK (2008) Characterization of Sri Lankan indigenous coconut (Cocos nucifera L.) varieties for diversity in quantitative morphology. Trop Agric 157:25–42Google Scholar
  42. Perera SACN, Kilian A (2008) Diversity arrays technology: a high throughput molecular marker system for coconut. Pragna (IFS Newsl Sri Lanks) xix (1 Special issue), pp 60–64Google Scholar
  43. Perera L, Russell JR, Provan J (1998) Evaluating genetic relationships between indigenous coconut (Cocos nucifera L.) accessions from Sri Lanka by means of AFLP profiling. Theor Appl Genet 96:545–550PubMedGoogle Scholar
  44. Perera L, Russell JR, Provan J (1999) Identification and characterization of microsatellites in coconut (Cocos nucifera L.) and the analysis of coconut populations in Sri Lanka. Mol Ecol 8:344–346PubMedGoogle Scholar
  45. Perera L, Russell JR, Provan J et al (2000) Use of microsatellite DNA markers to investigate the level of genetic diversity and population genetic structure of coconut (Cocos nucifera L.). Genome 43:15–21PubMedGoogle Scholar
  46. Perera L, Russell JR, Provan J et al (2001) Levels and distribution of genetic diversity of coconut (Cocos nucifera L., var. Typica form typica) from Sri Lanka assessed by microsatellite markers. Euphytica 122:381–389Google Scholar
  47. Perera L, Russell JR, Provan J et al (2003) Studying genetic relationships among coconut varieties/populations using microsatellite markers. Euphytica 132:121–123Google Scholar
  48. Perera L, Fernando WBSF, Hearth N et al (2004) Use of microsatellite DNA markers for population analysis, variety identification and for hybridity testing of coconut in Sri Lanka. In: Peiris TSG, Ranasinghe CS (eds) Proceedings of the international conference to mark the 75th anniversary of Coconut Research Institute, Sri Lanka, Part II. Ceylon Printers, Colombo, pp 3–15Google Scholar
  49. Perera SACN, Ekanayake GK, Attanayake RB (2009) Characterization of conserved coconut germplasm in Sri Lanka with morphological descriptors. CORD 25(1):46–53Google Scholar
  50. Perera SACN, Gunn B, Rivera RI (2018) 3.9.4 DNA analysis in farmer’s fields – chapter 3. Where we need to be to secure diversity and promote use. In: Bourdeix R, Prades A (eds) A global strategy for the conservation and use of coconut genetic resources 2018–2028, Montpellier, pp 171–172Google Scholar
  51. Pokou DN, Manimekelai R, Fan HK (2018) 3.9.3 DNA analysis in ex situ genebanks – chapter 3. Where we need to be to secure diversity and promote use. In: Bourdeix R, Prades A (eds) A global strategy for the conservation and use of coconut genetic resources 2018–2028, Montpellier, p 171Google Scholar
  52. Pradeepkumar S, Manimekalai R, Ranjithakumari BD (2011) Microsatellite marker-based characterization of south pacific coconut (Cocos nucifera L.) accessions. Int J Plant Breed Genet 5(1):34–43Google Scholar
  53. Rajesh MK, Nagarajan P, Jerard BA et al (2008) Microsatellite variability of coconut accessions (Cocos nucifera L.) from Andaman and Nicobar Islands. Curr Sci 94(12):1627–1631Google Scholar
  54. Rajesh MK, Thomas RJ, Rijith J et al (2012) Genetic purity assessment of D X T hybrids in coconut with SSR markers. Indian J Genet Plant Breed 72(4):472–474Google Scholar
  55. Ratnambal MJ, Kumaran PM, Arunachala V et al (2001) Coconut genetic resources and molecular approaches. Indian J Plant Genet Resour 14(2):182–184Google Scholar
  56. Ribeiro FE, Baudouin L, Lebrun P et al (2010) Population structures of Brazilian Tall coconut (Cocos nucifera L.) by microsatellite markers. Genet Mol Biol 33(4):696–702PubMedPubMedCentralGoogle Scholar
  57. Ritter E, Rodriguez MJB, Herran A et al (2000) Analysis of quantitative trait loci (QTL) based on linkage maps in coconut (Cocos nucifera L.). In: Arencibia A (ed) Plant genetic engineering towards the third millennium. Elsevier, Amsterdam, pp 42–48Google Scholar
  58. Rivera R, Edwards KJ, Barker JHA et al (1999) Isolation and characterization of polymorphic microsatellites in Cocos nucifera L. Genome 42:668–675PubMedGoogle Scholar
  59. Rohde W, Kullaya A, Rodriguez J et al (1995) Genome analysis of Cocos nucifera L. by PCR amplification of spacer sequences separating a subset of copia-like 16RI repetitive elements. J Genet Breed 49:179–186Google Scholar
  60. Rohde W, Becker D, Kullaya A et al (1999) Analysis of coconut germplasm biodiversity by DNA marker technologies and construction of a first genetic linkage map. In: Oropeza C, Verdeil JL, Ashburner GR, Cardena R, Santamaria JM (eds) Current advances in coconut biotechnology. Kluwer, Dordrecht, pp 99–120Google Scholar
  61. Rohde W, Herran A, Estioko L et al (2000) Mapping of DNA markers, homeotic genes and QTLs in coconut (Cocos nucifera L.) and synteny studies with oil palm. In: Proceedings of the international symposium on oil palm genetic resources and utilization, Kuala Lumpur, pp pAC1–AC21Google Scholar
  62. Sankaran M, Damodaran V, Singh DR et al (2012) Characterization and diversity assessment in coconut collections of Pacific Ocean Islands and Nicobar Islands. Afr J Biotechnol 11(97):16320–16329Google Scholar
  63. Shalini KMS, Lebrun PBA, Baudouin L et al (2007) Identification of molecular markers associated with mite resistance in coconut (Cocos nucifera L.). Genome 50:35–42PubMedGoogle Scholar
  64. Teulat B, Aldam C, Trehin R (2000) An analysis of genetic diversity in coconut (Cocos nucifera) populations from across the geographic range using sequence-tagged microsatellites (SSRs) and AFLPs. Theor Appl Genet 100:764–771Google Scholar
  65. Thomas RJ, Rajesh MK, Kalavathi S et al (2013) Analysis of genetic diversity in coconut and its conservation in root (wilt) disease affected areas of Kerala: a community participatory approach. Indian J Genet Plant Breed 73(3):295–301Google Scholar
  66. Upadhyay A, Jose J, Manimekalai R et al (2002) Managing plant genetic diversity. Proceedings of international conference, Kula lumpur, Malaysia, p 61–66Google Scholar
  67. Whitehead RA (1976) Coconut. In: Simmonds NW (ed) Evolution of crop plants. Longman, London, pp 221–225Google Scholar
  68. Yong X, Luo Y, Yang Y et al (2013) Development of microsatellite markers in Cocos nucifera and their application in evaluating the level of genetic diversity of Cocos nucifera. Plant Omics 6(3):193–200Google Scholar
  69. Yao SDM, Konan KJL, Pokou ND et al (2013) Assessment of the genetic diversity conservation in three tall coconut (Cocos nucifera L.) accessions regenerated by controlled pollination, using microsatellite markers. Afr J Biotechnol 12(20): 2808–2815 Google Scholar
  70. Zizumbo-Villarreal D, Fernandez-Barrera M, Torres-Hernandez N et al (2005) Morphological variation of fruit in Mexican populations of Cocos nucifera L. (Arecaceae) under in situ and ex situ conditions. Genet Resour Crop Evol 52:421–434Google Scholar

Copyright information

© Springer Nature Switzerland AG 2020

Authors and Affiliations

  • Chandrika Perera
    • 1
  • H. D. Dharshani Bandupriya
    • 2
  • Regi J. Thomas
    • 3
  • Roland Bourdeix
    • 4
    • 5
  1. 1.Faculty of AgricultureUniversity of PeradeniyaPeradeniyaSri Lanka
  2. 2.Department of Plant SciencesUniversity of ColomboColomboSri Lanka
  3. 3.The Central Plantation Crops Research InstituteKasargodIndia
  4. 4.CIRAD – UMR AGAP, CIRAD (Agricultural Research for Development)MontpellierFrance
  5. 5.AGAP, University of Montpellier, CIRAD, INRA, Montpellier SupAgroMontpellierFrance

Personalised recommendations