Development of simple sequence repeat (SSR) markers for oil palm and their application in genetic mapping and fingerprinting of tissue culture clones

This study describes the application of a simple and effective method to isolate SSR markers from oil palm genomic sequences. A total of 12 informative SSR markers are described. The SSR markers were found suitable for genome analysis and DNA fingerprinting of oil palm tissue culture clones. Eleven of the 12 SSR markers exhibited expected Mendelian segregation ratios when tested on a mapping population, indicating their suitability for genetic mapping studies. The markers identified in the species Elaeis oleifera also showed applicability in a second species, that is Elaeis guineensis. Apart from genetic mapping, the SSR markers also showed promise as molecular probes for DNA fingerprinting of oil palm tissue culture clones. The SSR markers can be used for clonal identification, monitoring line uniformity between and within clones and detecting culture mix-up

Identification of cDNA-RFLP markers and their use for molecular mapping in oil palm (Elaeis guineensis)

Restriction fragment length polymorphic (RFLP) probes derived from complementary DNA (cDNA) clones were developed for oil palm genome analysis. A total of 321 cDNA-RFLP probes were evaluated for their ability to detect polymorphism in a mapping family derived from the selfing of a Tenera guineensis palm (palm T128). Approximately 38% (123 probes) revealed polymorphism with at least one restriction enzyme. All the 123 informative probes were used to genotype the mapping family. Majority of the markers (80%) showed expected segregation ratios, indicating that most of the RFLP markers were inherited in a Mendelian manner. A total of 116 segregating markers were assigned to 20 linkage groups spanning 693cM. The RFLP markers were found to be largely well distributed and did not show excessive clustering in any particular region. This is the first published map for oil palm containing gene specific markers. The cDNA-RFLP probes mapped will not be merely anonymous markers with symbols, but point to the actual location of specific genes. The map also proved useful in revealing QTL associated with oil to wet mesocarp (O/WM) content

Statistical mapping of quantitative trait loci controlling the time to first callusing in oil palm (elaeis guineensis Jacq.) tissue culture

An additional 400 genetic markers (126 RFLPs, 274 AFLPs) were successfully mapped on the earlier developed linkage maps using 87 F1 progenies derived from Deli dura X Yangambi pisifera cross. This resulted in a denser map with coverage length of 1, 714cM and 1,225cM for pisifera and dura, respectively. Further exploration to searchfor quantitative trait loci (QTL) associated with time to first callusing (TFC) was carried out by Kosambi Interval Mapping using the computer program MapQTL Version 4. O. The tissue culture trait data showed a continuous distribution. In this paper; three likelihood QTLs were detected in pisifera and two QTLs in dura at 99% and 95% significant thresholds. These QTL locations can be designated as statistically significant for contributing to the variation of TFG. Therefore, the information points to a genomic loci affecting tissue culturability in oil palm

Mapping quantitative trait loci (QTLs) for fatty acid composition in an interspecific cross of oil palm

Background: Marker Assisted Selection (MAS) is well suited to a perennial crop like oil palm, in which the economic products are not produced until several years after planting. The use of DNA markers for selection in such crops can greatly reduce the number of breeding cycles needed. With the use of DNA markers, informed decisions can be made at the nursery stage, regarding which individuals should be retained as breeding stock, which are satisfactory for agricultural production, and which should be culled. The trait associated with oil quality, measured in terms of its fatty acid composition, is an important agronomic trait that can eventually be tracked using molecular markers. This will speed up the production of new and improved oil palm planting materials. Results: A map was constructed using AFLP, RFLP and SSR markers for an interspecific cross involving a Colombian Elaeis oleifera (UP1026) and a Nigerian E. guinneensis (T128). A framework map was generated for the male parent, T128, using Joinmap ver. 4.0. In the paternal (E. guineensis) map, 252 markers (199 AFLP, 38 RFLP and 15 SSR) could be ordered in 21 linkage groups (1815 cM). Interval mapping and multiple-QTL model (MQM) mapping (also known as composite interval mapping, CIM) were used to detect quantitative trait loci (QTLs) controlling oil quality (measured in terms of iodine value and fatty acid composition). At a 5% genome-wide significance threshold level, QTLs associated with iodine value (IV), myristic acid (C14:0), palmitic acid (C16:0), palmitoleic acid (C16:1), stearic acid (C18:0), oleic acid (C18:1) and linoleic acid (C18:2) content were detected. One genomic region on Group 1 appears to be influencing IV, C14:0, C16:0, C18:0 and C18:1 content. Significant QTL for C14:0, C16:1, C18:0 and C18:1 content was detected around the same locus on Group 15, thus revealing another major locus influencing fatty acid composition in oil palm. Additional QTL for C18:0 was detected on Group 3. A minor QTL for C18:2 was detected on Group 2. Conclusion: This study describes the first successful detection of QTLs for fatty acid composition in oil palm. These QTLs constitute useful tools for application in breeding programmes

Oil palm (Elaeis guineensis Jacq.) tissue culture ESTs: identifying genes associated with callogenesis and embryogenesis

Background: Oil palm (Elaeis guineensis Jacq.) is one of the most important oil bearing crops in the world. However, genetic improvement of oil palm through conventional breeding is extremely slow and costly, as the breeding cycle can take up to 10 years. This has brought about interest in vegetative propagation of oil palm. Since the introduction of oil palm tissue culture in the 1970s, clonal propagation has proven to be useful, not only in producing uniform planting materials, but also in the development of the genetic engineering programme. Despite considerable progress in improving the tissue culture techniques, the callusing and embryogenesis rates from proliferating callus cultures remain very low. Thus, understanding the gene diversity and expression profiles in oil palm tissue culture is critical in increasing the efficiency of these processes. Results: A total of 12 standard cDNA libraries, representing three main developmental stages in oil palm tissue culture, were generated in this study. Random sequencing of clones from these cDNA libraries generated 17,599 expressed sequence tags (ESTs). The ESTs were analysed, annotated and assembled to generate 9,584 putative unigenes distributed in 3,268 consensi and 6,316 singletons. These unigenes were assigned putative functions based on similarity and gene ontology annotations. Cluster analysis, which surveyed the relatedness of each library based on the abundance of ESTs in each consensus, revealed that lipid transfer proteins were highly expressed in embryogenic tissues. A glutathione S-transferase was found to be highly expressed in non-embryogenic callus. Further analysis of the unigenes identified 648 non-redundant simple sequence repeats and 211 putative full-length open reading frames. Conclusion: This study has provided an overview of genes expressed during oil palm tissue culture. Candidate genes with expression that are modulated during tissue culture were identified. However, in order to confirm whether these genes are suitable as early markers for embryogenesis, the genes need to be tested on earlier stages of tissue culture and a wider range of genotypes. This collection of ESTs is an important resource for genetic and genome analyses of the oil palm, particularly during tissue culture development

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 trinucleotide 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 (F ST) 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