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Conventional quantitative trait loci (QTL) analysis of a mapping family is carried out to generate molecular tools for development of compact interspecific hybrid palms that can be planted more closely for higher yields per unit land area. Genetic maps were constructed for an interspecific backcross two (BC2) oil palm population using single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers. A total of 1744 markers were mapped onto 16 linkage groups, spanning 1499.5 cM with an average marker interval of 0.86 cM. Using empirical genome and chromosome-wide thresholds, QTL analysis yielded a number of significant associations with vegetative characters for palm compactness. Subsequent QTL analysis revealed two major and two putative QTL linked to rachis length and petiole cross-section, two important characters for palm compactness. The QTL identified are an important step towards the implementation of marker assisted selection (MAS), enabling breeders to make early informed decisions on improving interspecific hybrids.

Background - The commercial oil palm (Elaeis guineensis Jacq.) produces a mesocarp oil (commonly called ‘palm oil’) with approximately equal proportions of saturated and unsaturated fatty acids (FAs). An increase in unsaturated FAs content or iodine value (IV) as a measure of the degree of unsaturation would help to open up new markets for the oil. One way to manipulate the fatty acid composition (FAC) in palm oil is through introgression of favourable alleles from the American oil palm, E. oleifera, which has a more unsaturated oil.Results - In this study, a segregating E. oleifera x E. guineensis (OxG) hybrid population for FAC is used to identify quantitative trait loci (QTLs) linked to IV and various FAs. QTL analysis revealed 10 major and two putative QTLs for IV and six FAs, C14:0, C16:0, C16:1, C18:0, C18:1 and C18:2 distributed across six linkage groups (LGs), OT1, T2, T3, OT4, OT6 and T9. The major QTLs for IV and C16:0 on LGOT1 explained 60.0 – 69.0 % of the phenotypic trait variation and were validated in two independent BC2 populations. The genomic interval contains several key structural genes in the FA and oil biosynthesis pathways such as PATE/FATB, HIBCH, BASS2, LACS4 and DGAT1 and also a relevant transcription factor (TF), WRI1. The literature suggests that some of these genes can exhibit pleiotropic effects in the regulatory networks of these traits. Using the whole genome sequence data, markers tightly linked to the candidate genes were also developed. Clustering trait values according to the allelic forms of these candidate markers revealed significant differences in the IV and FAs of the palms in the mapping and validation crosses.Conclusions - The candidate gene approach described and exploited here is useful to identify the potential causal genes linked to FAC and can be adopted for marker-assisted selection (MAS) in oil palm

Clonal reproduction of oil palm by means of tissue culture is a very inefficient process. Tissue culturability is known to be genotype dependent with some genotypes being more amenable to tissue culture than others. In this study, genetic linkage maps enriched with simple sequence repeat (SSR) markers were developed for dura (ENL48) and pisifera (ML161), the two fruit forms of oil palm, Elaeis guineensis. The SSR markers were mapped onto earlier reported parental maps based on amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers. The new linkage map of ENL48 contains 148 markers (33 AFLPs, 38 RFLPs and 77 SSRs) in 23 linkage groups (LGs), covering a total map length of 798.0 cM. The ML161 map contains 240 markers (50 AFLPs, 71 RFLPs and 119 SSRs) in 24 LGs covering a total of 1,328.1 cM. Using the improved maps, two quantitative trait loci (QTLs) associated with tissue culturability were identified each for callusing rate and embryogenesis rate. A QTL for callogenesis was identified in LGD4b of ENL48 and explained 17.5% of the phenotypic variation. For embryogenesis rate, a QTL was detected on LGP16b in ML161 and explained 20.1% of the variation. This study is the first attempt to identify QTL associated with tissue culture amenity in oil palm which is an important step towards understanding the molecular processes underlying clonal regeneration of oil palm.

Enroute to mapping QTLs for yield components in oil palm, we constructed the linkage map of a FELDA high yielding oil palm (Elaeis guineensis), hybrid cross. The parents of the mapping population are a Deli dura and a pisifera of Yangambi origin. The cross out-yielded the average by 8–21% in four trials all of which yielded comparably to the best current commercial planting materials. The higher yield derived from a higher fruit oil content. SSR markers in the public domain - from CIRAD and MPOB, as well as some developed in FELDA - were used for the mapping, augmented by locally-designed AFLP markers. The female parent linkage map comprised 317 marker loci and the male parent map 331 loci, both in 16 linkage groups each. The number of markers per group ranged from 8–47 in the former and 12–40 in the latter. The integrated map was 2,247.5 cM long and included 479 markers and 168 anchor points. The number of markers per linkage group was 15–57, the average being 29, and the average map density 4.7 cM. The linkage groups ranged in length from 77.5 cM to 223.7 cM, with an average of 137 cM. The map is currently being validated against a closely related population and also being expanded to include yield related QTLs.

Tissue culture is employed for the large scale production of elite planting materials in the oil palm plantation industry of Malaysia. The advantage of this technique is the homogeneous quality that can be produced across the clones. However, the production cost is high compared to conventional seedlings due to some unpredictable constraints. One of the major problems that has been reported is the average low rate of regeneration among the clones. Inconsistencies have been reported in that both callogenesis and embryogenesis varied among the lines. Attempts were made to generate restriction fragment length polymorphism (RFLP) and amplified fragment length polymorphism (AFLP). These DNA markers were used for constructing genetic linkage maps for two commercial palms namely, Ulu Remis Deli dura (ENL48) and Yangambi pisifera (ML161). Both maps were used as frameworks to detect quantitative trait loci (QTL) associated with the traits of tissue culture amenability. The generation of DNA markers involved the genotyping of 87 F1 palms using 70 cDNA probes and 16 EcoRI/MseI and 8 PstI/MseI primer-pairs. This produced a total of 36 RFLPs and 43 AFLPs for ENL48 and 66 RFLPs and 58 AFLPs for ML161. The data were integrated into the existing database for the mapping analysis by using JoinMap®3.0 at LOD 4.0 and recombination frequency θ <0.400. The ENL48 linkage map was constructed by using 87 RFLPs and 123 AFLPs. These markers were grouped into 25 linkage groups covering a total genetic distance of 1,136.3cM. A denser map of ML161 was obtained with 147 RFLPs and 225 AFLPs which resulted in 16 linkage groups with a total map length of 1,755.7cM. The QTL for tissue culture amenability were determined using interval mapping and multiple quantitative mapping (MQM) with the help of the MapQTL® 4.0 software. The LOD thresholds were estimated using the permutation test. The QTLs for the callusing rate (CR) were detected at linkage groups D9 and P7 on the ENL48 and the ML161 maps, resp

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.

The African oil palm (Elaeis guineensis Jacq.) is a highly valued oil producing perennial crop with a productive lifespan of about 25 years. Although benefiting from a long productivity period, oil palm genetic improvement is a slow and tedious process which requires between 10 to 12 years to complete one selection cycle. As such, marker-assisted selection (MAS) is an invaluable tool for yield improvement in oil palm. In particular, MAS could be used to facilitate efforts to increase the unsaturated fatty acid content of palm oil by introgression of desired alleles from the American species, E. oleifera which produces highly unsaturated oil. In order to help achieve this, high density genetic linkage maps were constructed for a commercial Deli dura (maternal) x Yangambi pisifera (paternal) breeding population (P2) and a Colombian E. oleifera (maternal) x Nigerian E. guineensis (paternal) interspecific hybrid population (OxG). The P2 and OxG mapping populations were screened with approximately 700 oil palm SSR primer-pairs and genotyped with a 4.5K customized oil palm SNP array to identify informative markers. The P2 and OxG populations consisted of 87 and 108 palms, respectively. Genetic linkage maps were first constructed for the individual parental palms of the mapping populations and followed by integration of the two parental maps. A P2 integrated map with 1,331 markers spanning 1,867 cM over the 16 linkage groups was constructed, representing the 16 chromosome pairs in oil palm. This study for the first time reports the genetic map for the Colombian E. oleifera, although the map only comprises of ten linkage groups with 65 markers spanning 471 cM. The Colombian E. oleifera map was also successfully integrated with the Nigerian E. guineensis parental map, resulting in a partial integrated map for OxG. The genetic maps and the available phenotypic data were successfully used to identify 22 quantitative trait loci (QTLs) associated with various yield components (Y