Genetic Diversity Evaluation of MARDI’s Coconut (Cocos nucifera L.) Germplasm using Simple Sequence Repeats
Abstract
A total of 18 simple sequence repeat (SSR) markers have been optimized and used to genotype coconut (Cocos nucifera L.). These markers were used to genotype 23 coconut varieties that were maintained in MARDI’s germplasm collection. Fifteen SSR loci were polymorphic markers while the remaining three SSR were monomorphic. The number of alleles ranged from 2 to 19 with a mean number of 8.53 per locus. The expected heterozygosity values in each variety ranged from 0.07 to 0.61, with an average value of 0.52. Several varieties could be successfully differentiated by using these 15 SSR markers such as Cameroon Red Dwarf x West African Tall hybrid, Mawa hybrid, Malayan Tall x Cameroon Red Dwarf hybrid, Malayan Red Dwarf x Rotuman hybrid, Catigan, Pandan and Laguna. A UPGMA Dendogram showed Niu Damu as an outlying group with high dissimilarity from all other varieties. Analyses using the STRUCTURE software showed all 23 varieties to be clustered into 21 genotypic groups. This new information will greatly contribute towards characterization of the MARDI’s coconut germplasm collection and to develop a SSR tool for the identification of new coconut varieties in Malaysia.
References
Baudouin, L. et al. (2006) QTL analysis of fruit components in the progeny of a Rennell Island Tall coconut (Cocos nucifera L.) individual. Theoretical and applied genetics, 112(2), 258-268.
Dasanayaka, P. N. et al. (2009) Analysis of coconut (Cocos nucifera L.) diversity using microsatellite markers with emphasis on management and utilisation of genetic resources. Journal of the National Science Foundation of Sri Lanka, 37(2).
Falush, D. et al. (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics, 164(4), 1567-1587.
Garza, J. C., & Williamson, E. G. (2001) Detection of reduction in population size using data from microsatellite loci. Molecular ecology, 10(2), 305-318.
Glaubitz, J. C. (2004) Convert: A user‐friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Molecular Ecology Notes, 4(2), 309-310.
Meerow, A. W. 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. Theoretical and Applied Genetics, 106(4), 715-726.
Pritchard, J. K. et al. (2000) Inference of population structure using multilocus genotype data. Genetics, 155(2), 945-959.
Perera, L. et al. (2003) Studying genetic relationships among coconut varieties/populations using microsatellite markers. Euphytica,132(1), 121-128.
Rivera, R. et al. (1999) Isolation and characterization of polymorphic microsatellites in Cocos nucifera L. Genome, 42(4), 668-675.
