Elaeis guineensis and E. oleifera are the two species of oil palm. E. guineensis is the most widely cultivated commercial species, and introgression of desirable traits from E. oleifera is ongoing. We report an improved E. guineensis genome assembly with substantially increased continuity and completeness, as well as the first chromosome-scale E. oleifera genome assembly. Each assembly was obtained by integration of long-read sequencing, proximity ligation sequencing, optical mapping, and genetic mapping. High interspecific genome conservation is observed between the two species. The study provides the most extensive gene annotation to date, including 46,697 E. guineensis and 38,658 E. oleifera gene predictions. Analyses of repetitive element families further resolve the DNA repeat architecture of both genomes. Comparative genomic analyses identified experimentally validated small structural variants between the oil palm species and resolved the mechanism of chromosomal fusions responsible for the evolutionary descending dysploidy from 18 to 16 chromosomes.
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Basal stem rot (BSR) is one of the main oil palm diseases that have led to tremendous losses in oil yields for almost a century. Having markers, especially those that are linked to resistance (R) genes could potentially alleviate this problem by providing the tools to select palms that are tolerant or resistant to the disease. This study aimed to develop oil palm genomic markers that can distinguish oil palm plants with different levels of resistance to BSR. We identified 144 homologous R genes in the oil palm genome based on the conserved domain structure of known R proteins. Six simple sequence repeat markers were identified and used to genotype 40 palms with different levels of resistance to BSR. The observed and effective number of alleles ranged from 2.00 to 7.00 and 1.57 to 4.30, respectively. The observed heterozygosity ranged from 0.13 to 0.67, with a mean of 0.46 while the expected heterozygosity ranged from 0.40 to 0.78, with a mean of 0.51. Analysis of genetic distances from the set of markers was able to differentiate susceptible and tolerant palm samples. These results may help in the early selection of durable BSR disease resistant oil palm cultivars
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A high-quality reference genome is an important resource that can help decipher the genetic basis of traits in combination with linkage or association analyses. The publicly available oil palm draft genome sequence of AVROS pisifera (EG5) accounts for 1.535 Gb of the 1.8 Gb oil palm genome. However, the assemblies are fragmented, and the earlier assembly only had 43% of the sequences placed on pseudo-chromosomes. By integrating a number of SNP and SSR-based genetic maps, a consensus map (AM_EG5.1), comprising of 828.243 Mb genomic scaffolds anchored to 16 pseudo-chromosomes, was generated. This accounted for 54% of the genome assembly, which is a significant improvement to the original assembly. The total length of N50 scaffolds anchored to the pseudo-chromosomes increased by ∼18% compared to the previous assembly. A total of 139 quantitative trait loci for agronomically important quantitative traits, sourced from literature, were successfully mapped on the new pseudo-chromosomes. The improved assembly could also be used as a reference to identify potential errors in placement of specific markers in the linkage groups of the genetic maps used to assemble the consensus map. The 3422 unique markers from five genetic maps, anchored to the pseudo-chromosomes of AM_EG5.1, are an important resource that can be used preferentially to either construct new maps or fill gaps in existing genetic maps. Synteny analysis further revealed that the AM_EG5.1 had high collinearity with the date palm genome cultivar 'Barhee BC4' and shared most of its segmental duplications. This improved chromosomal-level genome is a valuable resource for genetic research in oil palm.
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Co-dominant simple sequence repeat (SSRs) are popular DNA markers, widely applied in oil palm genetic studies, especially in genetic mapping, marker-trait association, diversity analysis and detecting illegitimacy. A repository having detailed information on SSRs and their inheritance profiles in specific breeding lines is lacking in Malaysia. Such a database enables prioritising polymorphic SSRs for screening, identification of which otherwise can be expensive and time consuming. As such, to facilitate and accelerate development of informative SSRs, oil palm SSR resource interface (OPSRI) was established and currently contains information on 1983 markers that were genotyped successfully across several oil palm breeding lines. OPSRI is a well-structured database that can expedite marker development and reduce redundancy in the on-going efforts at developing DNA markers for genetic analysis of oil palm. The system has been integrated with MISA, Primer3, ORF search script and BLAST to enable SSR identification. This study also characterised a large number of expressed sequence tags (EST)-SSRs using an in-silico approach. The information within the OPSRI database can help accelerate research in oil palm as well as in crops such as coconut and date palm which have a high level of synteny and marker-transferability with oil palm.
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A set of reliable reference genes is essential for accurate quantification and interpretation of gene expression data using reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR). In this study, Roche-454 RNA-seq reads from 27 libraries of various oil palm tissues were systematically analysed to identify a set of potential reference genes. Eleven candidate reference genes were identified from the transcriptome data. These genes, together with three oil palm reference genes previously identified for tissue culture samples (PD000380, PD00569, pOP-EA01332) and five classical housekeeping genes [glyceraldehyde-3-phosphate dehydrogenase (GAPDH), NAD5, TUBULIN, UBIQUITIN, ACTIN] were analysed across samples collected from various tissues from mature oil palm (leaf, root, endosperm, mesocarp, female flowers) and stages of tissue culture (non-embryogenic callus, embryogenic callus, polyembryoids, and shoots from polyembryoids). The expression levels of these genes were compared and evaluated using geNorm. Three genes (EgREF_5, EgREF_7 and EgREF_11) were found to be appropriate reference genes for normalising gene expression data from both mature plant and tissue culture samples.
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Oil palm produces a quarter of the world.s total vegetable oil. In line with its global importance, an initiative to sequence the oil palm genome was carried out successfully, producing huge amounts of sequence information, allowing SNP discovery. High-capacity SNP genotyping platforms have been widely used for marker.trait association studies in oil palm. Besides genotyping, a SNP array is also an attractive tool for understanding aberrations in chromosome inheritance. Exploiting this, the present study utilized chromosome-wide SNP allelic distributions to determine the ploidy composition of over 1,000 oil palms from a commercial F1 family, including 197 derived from twin-embryo seeds. Our method consisted of an inspection of the allelic intensity ratio using SNP markers. For palms with a shifted or abnormal distribution ratio, the SNP allelic frequencies were plotted along the pseudo-chromosomes. This method proved to be efficient in identifying whole genome duplication (triploids) and aneuploidy. We also detected several loss of heterozygosity regions which may indicate small chromosomal deletions and/or inheritance of identical by descent regions from both parents. The SNP analysis was validated by flow cytometry and chromosome counts. The triploids were all derived from twin-embryo seeds. This is the first report on the efficiency and reliability of SNP array data for karyotyping oil palm chromosomes, as an alternative to the conventional cytogenetic technique. Information on the ploidy composition and chromosomal structural variation can help to better understand the genetic makeup of samples and lead to a more robust interpretation of the genomic data in marker.trait association analyses.
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The high yielding tenera is the commercial oil palm planting material of choice in Southeast Asia. Notwithstanding this, there is continuous effort to further improve the yield and one way to do this is by addressing the yield components (YCs). Using 4451 SNP and over 600 SSR markers, this study revealed quantitative trait loci (QTL) associated with YCs in two breeding populations, a Deli dura.×Yangambi pisifera (P2) and a Deli dura.×AVROS pisifera (KULIM DxP). Thirteen and 29 QTLs were identified in P2 and KULIM DxP, respectively. They were compared to other YC-linked QTLs reported previously for different genetic backgrounds by mapping the QTL-linked markers to the oil palm genome. The comparison revealed four common chromosomes containing QTLs influencing various YCs. The results reveal the possible presence of closely linked loci or pleiotropic genes influencing YCs in oil palm. Exploiting the genome data has also facilitated the discovery of candidate genes within or near the QTL regions including those related to glycosylation, fatty acid and oil biosynthesis, and development of flower, seed and fruit.
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Identification of novel genes that are specifically expressed in root is essential for isolation and characterisation of root-specific promoters. Mining the transcriptome of various oil palm tissue-specific data generated from ribonucleic acid-sequencing (RNA-Seq) technology has enabled the discovery of rootspecific genes. A total of seven candidates of root-specifically or preferentially expressed genes were selected from RNA-Seq analysis, and the gene expression profiles were validated using real-time quantitative polymerase chain reaction (RT-qPCR). The relative fold change of transcript expression in RT-qPCR was statistically analysed by comparing with root tissues at the in vitro culture stage (RS1). Results showed that the transcript annotated as an oil palm metallothionine (EgMT) gene was significantly upregulated at around 7 to 170-fold across the different developmental stages of root tissues. A proline-rich protein (EgPRP1) transcript was also significantly upregulated by about 7 to 55-fold. Both EgMT and EgPRP1 transcripts had relatively low expressions in the other tissues studied. The high levels of expression of EgMT and EgPRP1 in roots highlighted the genes. promoter.s potential to regulate a strong expression level of transgenes in a root-specific manner.
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