The traditional method of hybrid identification and genetic diversity evaluation based on differences in range of expressions of morphological and agronomical characters has been routinely employed in the assessment of oil palm germplasm and breeding populations at the Nigerian Institute of Oil Palm Research (NIFOR). Considering the limitations of this conventional method and the advantages of molecular markers in complementing conventional breeding methods, this study was conducted to determine the legitimacy of NIFOR oil palm progenies and to assess the genetic variations and relationships existing among the breeding populations using microsatellite (SSR) markers. Ten microsatellite markers were used to screen 226 oil palm samples which included 215 samples from NIFOR and 11 other samples belonging to the Malaysian Palm Oil Board (MPOB) advanced breeding lines and germplasm materials. Results obtained revealed that out of 200 F1 oil palm progeny derived from 11 of the 15 parents evaluated, 57% (114) were true-to-type and 43% (86) were contaminated. Almost all the contamination or illegitimacy detected was due to pollination errors. High genetic diversity was detected among the 15 NIFOR parents with the NIFOR tenera parents recording the highest number of alleles (5), rare alleles (17), and gene diversity (0.650) when compared to the Deli dura NIFOR and NIFOR dura parents. With reference to the MPOB breeding materials, the various oil palm sources showed significant and large value of genetic differentiation (FST= 0.177, P = 0.001) due to variations within the sources of parental materials. Rogers’ dissimilarity coefficient matrix displayed two main clusters, one separating MPOB Madagascar accessions from the rest of the samples. Principal co-ordinates analysis (PCoA) showed that the NIFOR breeding parents clustered closely with the MPOB Nigeria and Angola derived materials indicating a common origin of mainland genotypes. A comparative assessment of molecular and morphological methods of describing genetic relationships in the NIFOR oil palm progenies showed that SSR analysis recorded the highest level of polymorphism (100%) in all the progenies. Although the correlation between agronomic and genetic distance matrices was very low and insignificant (r = 0.2989), both matrices discriminated the progenies effectively into two groups as per their agronomic performance and pedigree or origin, respectively.
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