Maizura Ithnin

Exploiting an oil palm EST database for the development of gene-derived SSR markers and their exploitation for assessment of genetic diversity.

A total of 5,521 expressed sequence tags (ESTs) from oil palm were used to search for type and frequency of simple sequence repeat (SSR) markers. Dimeric repeat motifs appeared to be the most abundant, followed by tri-nucleotide repeats. Redundancy was eliminated in the original EST set, resulting in 145 SSRs in 136 unique ESTs (114 singletons and 22 clusters). Primers were designed for 94 (69.1%) of the unique ESTs (consisting of 14 consensus and 80 singletons). Primers for 10 EST-SSRs were developed and used to evaluate the genetic diversity of 76 accessions of oil palm originating from seven countries in Africa, and the standard Deli dura population. The average number of observed and effective alleles was 2.56 and 1.84, respectively. The EST-SSR markers were found to be polymorphic with a mean polymorphic information content value of 0.53. Genetic differentiation (FST) among the populations studied was 0.2492 indicating high level of genetic divergence. Moreover, the UPGMA (unweighted pair-group method with arithmetic mean) analysis revealed a strong association between genetic distance and geographic location of the populations studied. The germplasm materials exhibited higher diversity than Deli dura, indicating their potential usefulness in oil palm improvement programmes. The study also revealed that the populations from Nigeria, Congo and Cameroon showed the highest diversity among the germplasm evaluated in this study. The EST-SSRs further demonstrated their worth as a new source of polymorphic markers for phylogenetic analysis, since a high percentage of the markers showed transferability across species and palm taxa.

SSR mining in oil palm EST database: application in oil palm germplasm diversity studies

This study reports on the detection of additional expressed sequence tags (EST) derived simple sequence repeat (SSR) markers for the oil palm. A large collection of 19243 Elaeis guineensis ESTs were assembled to give 10258 unique sequences, of which 629 ESTs were found to contain 722 SSRs with a variety of motifs. Dinucleotide repeats formed the largest group (45.6%) consisting of 66.9% AG/CT, 21.9% AT/AT, 10.9% AC/GT and 0.3% CG/CG motifs. This was followed by trinucleotide repeats, which is the second most abundant repeat types (34.5%) consisting of AAG/CTT (23.3%), AGG/CCT (13.7%), CCG/CGG (11.2%), AAT/ATT (10.8%), AGC/GCT (10.0%), ACT/AGT (8.8%), ACG/CGT (7.6%), ACC/GGT (7.2%), AAC/GTT (3.6%) and AGT/ACT (3.6%) motifs. Primer pairs were designed for 405 unique EST-SSRs and 15 of these were used to genotype 105 E. guineensis and 30 E. oleifera accessions. Fourteen SSRs were polymorphic in at least one germplasm revealing a total of 101 alleles. The high percentage (78.0%) of alleles found to be specific for either E. guineensis or E. oleifera has increased the power for discriminating the two species. The estimates of genetic differentiation detected by EST-SSRs were compared to those reported previously. The transferability across palm taxa to two Cocos nucifera and six exotic palms is also presented. The polymerase chain reaction (PCR) products of three primer-pairs detected in E. guineensis, E. oleifera, C. nucifera and Jessinia bataua were cloned and sequenced. Sequence alignments showed mutations within the SSR site and the flanking regions. Phenetic analysis based on the sequence data revealed that C. nucifera is closer to oil palm compared to J. bataua; consistent with the taxanomic classification.

Genetic variability of oil palm parental genotypes and performance of its' progenies as revealed by molecular markers and quantitative traits.

Studies were conducted to assess the genetic relationships between the parental palms (dura and pisifera) and performance of their progenies based on nine microsatellite markers and 29 quantitative traits. Correlation analyses between genetic distances and hybrids performance were estimated. The coefficients of correlation values of genetic distances with hybrid performance were non-significant, except for mean nut weight and leaf number. However, the correlation coefficient of genetic distances with these characters was low to be used as predicted value. These results indicated that genetic distances based on the microsatellite markers may not be useful for predicting hybrid performance. The genetic distance analysis using UPGMA clustering system generated 5 genetic clusters with coefficient of 1.26 based on quantitative traits of progenies. The genotypes, DP16, DP14, DP4, DP13, DP12, DP15, DP8, DP1 and DP2 belonging to distant clusters and greater genetic distances could be selected for further breeding programs.

Coconut, Date, and Oil Palm Genomics

The palm family, consisting of over 2,500 species arrayed among ca. 200 genera, is the third most economically important family of plants after the grasses and legumes. Three palm species account for the large majority of the family’s economic importance: coconut (Cocos nucifera), African oil palm (Elaeis guineensis), and date palm (Phoenix dactylifera). Of the three, genomics has been least developed in the coconut, where molecular tools have largely been used to characterize germplasm, and, to a lesser extent, develop quantitative trait loci (QTL). Both date palm and oil palm have recently had their genomes sequenced. The application of genomic tools to these palm species will result in enormous advances in the genetic improvement of all three crops.

Oil Palm Genomics

Publisher Summary Plant genomics is reversing the previous paradigm of identifying genes behind biological functions and instead focuses on finding biological functions behind genes. The oil palm belongs to the genus Elaeis, which contains two species, E. Guineensis and E. oleifera. It is regarded as the most efficient oil-bearing crop in the world compared to other crops of the same genre in terms of land use. However, the oil yield of oil palm has reached stagnation of late and there is an urgent need for improvement. Hence, this chapter discusses the current trend of leveraging genomics in the production of new and improved planting materials. The genomic platforms form the resource toward achieving the target of producing superior oil palms. As with other plant genomes, the oil palm has now been sequenced and with the plummeting price of sequencing as time goes by, more genomes will follow suit. Malaysian Palm Oil Board (MPOB) is known to have the largest oil palm germplasm collection in the world. That is an ideal source for identifying new alleles essential for breeding.

Biodiversity and Conservation of Elaeis Species

The current oil palm planting materials yield three times more than the figure recorded six decades ago. This was partly achieved through genetic improvement and selection procedures imposed on the oil palm breeding populations. The repeated cycles of selection applied had removed a lot of ‘unwanted’ alleles from the breeding populations. However, this might have affected the populations’ ability to withstand environmental threat and genetic gains in the future. Realizing the important role of oil palm germplasms in harmonizing these effects, several research organizations had accumulated a large number of Elaeis guineensis and Elaeis oleifera accessions from their centers of origin. These materials exhibit greater genetic diversity and can offer genes for many economically important traits valuable for future oil palm improvement. These potential germplasm materials should be strategically conserved to ensure effective and continuous accessibility, in line with the long-term breeding cycle of the oil palm. Core collection can effectively preserve the genetic diversity of the oil palm germplasms. Apart from maintaining the genetic resources in the living ex situ field plots, in vitro methods of storing genetic materials within smaller size facilities are also available. These methods offer conservation of high numbers of materials, protection from diseases and low cost of maintenance. Both, the ex situ and in vitro methods provide complementary means for effective long-term conservation of the oil palm genetic materials for posterity.

Genetic diversity of Elaeis oleifera (HBK) Cortes populations using cross species SSRs: implication’s for germplasm utilization and conservation

BackgroundThe Elaeis oleifera genetic materials were assembled from its center of diversity in South and Central America. These materials are currently being preserved in Malaysia as ex situ living collections. Maintaining such collections is expensive and requires sizable land. Information on the genetic diversity of these collections can help achieve efficient conservation via maintenance of core collection. For this purpose, we have applied fourteen unlinked microsatellite markers to evaluate 532 E. oleifera palms representing 19 populations distributed across Honduras, Costa Rica, Panama and Colombia.ResultsIn general, the genetic diversity decreased from Costa Rica towards the north (Honduras) and south-east (Colombia). Principle coordinate analysis (PCoA) showed a single cluster indicating low divergence among palms. The phylogenetic tree and STRUCTURE analysis revealed clusters based on country of origin, indicating considerable gene flow among populations within countries. Based on the values of the genetic diversity parameters, some genetically diverse populations could be identified. Further, a total of 34 individual palms that collectively captured maximum allelic diversity with reduced redundancy were also identified. High pairwise genetic differentiation (Fst > 0.250) among populations was evident, particularly between the Colombian populations and those from Honduras, Panama and Costa Rica. Crossing selected palms from highly differentiated populations could generate off-springs that retain more genetic diversity.ConclusionThe results attained are useful for selecting palms and populations for core collection. The selected materials can also be included into crossing scheme to generate offsprings that capture greater genetic diversity for selection gain in the future.