Land-use change from market responses to oil palm intensification in Indonesia.

Oil palm is a major driver of tropical deforestation. A key intervention proposed to reduce the footprint of oil palm is intensifying production to free up spare land for nature, yet the indirect land-use implications of intensification through market forces are poorly understood. We used a spatially explicit land-rent modeling framework to characterize the supply and demand of oil palm in Indonesia under multiple yield improvement and demand elasticity scenarios and explored how shifts in market equilibria alter projections of crop expansion. Oil palm supply was sensitive to crop prices and yield improvements. Across all our scenarios, intensification raised agricultural rents and lowered the effectiveness of reductions in crop expansion. Increased yields lowered oil palm prices, but these price-drops were not sufficient to prevent further cropland expansion from increased agricultural rents under a range of price elasticities of demand. Crucially, we found that agricultural intensification might only result in land being spared when the demand relationship was highly inelastic and crop prices were very low (i.e., a 70% price reduction). Under this scenario, the extent of land spared (∼0.32 million ha) was countered by the continued establishment of new plantations (∼1.04 million ha). Oil palm intensification in Indonesia could exacerbate current pressures on its imperiled biodiversity and should be deployed with stronger spatial planning and enforcement to prevent further cropland expansion.

Cambios en el uso de suelo causados por la reacción del mercado a la intensificación de la palma aceitera en Indonesia Resumen La palma aceitera es una de las principales causas de la deforestación. Una intervención importante propuesta para reducir la huella de esta palma es la intensificación de la producción para que el suelo sobrante sea usado por la naturaleza, pero se sabe muy poco sobre las implicaciones del uso indirecto de suelo de la intensificación a través de las fuerzas del mercado. Usamos un marco de modelos de renta de suelo espacialmente explícito para caracterizar la oferta y demanda de la palma aceitera en Indonesia bajo varios escenarios de mejoras en la producción y elasticidad de demandas y exploramos cómo los cambios en el equilibrio del mercado alteran las proyecciones de la expansión agrícola. La oferta de palma aceitera fue susceptible a los precios de los cultivos y a las mejoras en la producción. La intensificación elevó la renta agrícola y redujo la efectividad de la reducción de la expansión agrícola en todos nuestros escenarios. El aumento en la producción bajó los precios de la palma, pero estas caídas no fueron suficientes para evitar la expansión agrícola a partir de las rentas agrícolas elevadas bajo un rango de elasticidad de precios de demanda. Más importante, descubrimos que la intensificación agrícola puede sólo resultar en que sobre el suelo cuando la relación de demanda casi no sea elástica y los precios de las cosechas sean muy bajos (una reducción del 70% en los precios). Bajo este escenario, la extensión de suelo sobrante (∼0.32 millones de ha) fue contrarrestado por el establecimiento continuo de nuevos sembradíos (∼1.04 millones de ha). La intensificación de la palma aceitera en Indonesia podría agravar las presiones existentes sobre su biodiversidad en peligro y debería implementarse con una mayor planeación espacial y aplicación para prevenir una expansión agrícola superior.

Genetic Structure of Ganoderma boninense Populations Associated with Oil Palm at Neighboring Fields with Different Planting Ages in Malaysia.

Ganoderma boninense is a basidiomycete pathogen of African oil palm (Elaeis guineensis) and the causal agent of basal stem rot (BSR) disease, which is the most destructive fungal disease of oil palm in Southeast Asia. The disease is fatal for infected palms and can result in 50 to 80% losses in oil yields because of a reduction in productive life span and a yield decline of infected oil palms. In this study, G. boninense isolates collected from different locations and planting blocks with different palm ages were molecularly characterized using microsatellite genotyping. Results showed high pathogen genetic diversity (He = 0.67 to 0.74) among planting blocks and between oil palm estates. Two nearby planting blocks with similar planting ages (i.e., 1999 and 2001) had a similar percentage of BSR incidence (>20%) but showed distinct Ganoderma genetic structure as detected using STRUCTURE. Similar results were obtained from another trial site where planting blocks differing in planting age but located only less than 1 km apart showed a diverse genetic background. The pathogen genetic admixture of the oldest planting (>30% BSR incidence) differed significantly from the younger planting (1.8 to 2.8% BSR incidence, breeding trial block), suggesting that the host-pathogen genotype interaction may impact the Ganoderma genetic variation over time. The genetic structure of G. boninense, as revealed in this study, implies positive selection resulting from the pathogen genetic variation, host-pathogen interaction, and possible introductions of novel genetic variants (through spores) from adjacent plantings. These findings offer new insights into the genetic changes of G. boninense over time. The information is essential to design disease management strategies and breeding for BSR resistance in oil palm.

Molecular network of the oil palm root response to aluminum stress.

BACKGROUND: The solubilization of aluminum ions (Al3+) that results from soil acidity (pH < 5.5) is a limiting factor in oil palm yield. Al can be uptaken by the plant roots affecting DNA replication and cell division and triggering root morphological alterations, nutrient and water deprivation. In different oil palm-producing countries, oil palm is planted in acidic soils, representing a challenge for achieving high productivity. Several studies have reported the morphological, physiological, and biochemical oil palm mechanisms in response to Al-stress. However, the molecular mechanisms are just partially understood. RESULTS: Differential gene expression and network analysis of four contrasting oil palm genotypes (IRHO 7001, CTR 3-0-12, CR 10-0-2, and CD 19 - 12) exposed to Al-stress helped to identify a set of genes and modules involved in oil palm early response to the metal. Networks including the ABA-independent transcription factors DREB1F and NAC and the calcium sensor Calmodulin-like (CML) that could induce the expression of internal detoxifying enzymes GRXC1, PER15, ROMT, ZSS1, BBI, and HS1 against Al-stress were identified. Also, some gene networks pinpoint the role of secondary metabolites like polyphenols, sesquiterpenoids, and antimicrobial components in reducing oxidative stress in oil palm seedlings. STOP1 expression could be the first step of the induction of common Al-response genes as an external detoxification mechanism mediated by ABA-dependent pathways. CONCLUSIONS: Twelve hub genes were validated in this study, supporting the reliability of the experimental design and network analysis. Differential expression analysis and systems biology approaches provide a better understanding of the molecular network mechanisms of the response to aluminum stress in oil palm roots. These findings settled a basis for further functional characterization of candidate genes associated with Al-stress in oil palm.

Occurrence of triploids in oil palm and their origin.

BACKGROUND AND AIMS: Oil palms showing exceptional vigour and dubbed as 'giant palms' were identified in some progeny during breeding. A panel of phenotypical traits were studied to characterize these trees. The hypothesis that gigantism and other anomalies might be linked to polyploidy was investigated. METHODS: Twenty sib pairs of palms from different crosses, each comprising a giant and a normal oil palm, were studied by flow cytometry with rice 'Nipponbare' as standard reference. In parallel, palms were assessed in the field using 11 phenotypic traits. A principal component analysis (PCA) was conducted to define relationships between these phenotypical traits, and a linear discriminant analysis (LDA) to predict ploidy level and giant classification. Finally, a co-dominant molecular marker study was implemented to highlight the sexual process leading to the formation of 2n gametes. KEY RESULTS: The first group of oil palms presented an oil palm/rice peak ratio of around 4.8 corresponding to diploid oil palms, whereas the second group presented a ratio of around 7, classifying these plants as triploid. The PCA enabled the classification of the plants in three classes: 21 were normal diploid palms; ten were giant diploid palms; while 11 were giant triploid palms. The LDA revealed three predictors for ploidy classification: phyllotaxy, petiole size and circumference of the plant, but surprisingly not height. The molecular study revealed that triploid palms arose from 2n gametes resulting from the second division restitution of meiosis in parents. CONCLUSIONS: This study confirms and details the process of sexual polyploidization in oil palm. It also identifies three phenotypical traits to assess the ploidy level of the giant oil palms in the field. In practical terms, our results provide a cheap scientific method to identify polyploid palms in the field.

Identification of microRNAs involved in the Phosphate starvation response in Oil Palm (Elaeis guineensis Jacq.).

BACKGROUND: Plant microRNA, often known as miRNA, is a novel form of gene expression regulator that is known to play a significant role in phosphate starvation. The identification of microRNAs involved in the response to phosphate starvation in oil palms is beneficial for breeding programs. METHOD: The main nursery stage seedlings of two oil palm progenies were treated with three different fertiliser namely: complete fertiliser with urea, P2O5, K2O, and MgO based on the standard procedure as a control (C); fertiliser with urea, K2O, MgO without P2O5 (P0); and no fertiliser (F0) for 24 weeks. A total of six oil palm roots were subjected to RNA isolation, followed by miRNA sequencing using the Illumina HiSeq 4000 platform, and all reads were computationally analysed. RESULTS: In total, 119 potential miRNAs related to 5,891 genes were identified. The P-specific miRNAs were assumed based on the miRNAs that identified without P fertilizer treatment, resulted of twenty miRNA sequences in the treatment comparison of (C vs P0) vs (C vs F0). Those 20 miRNA sequences were grouped into 9 families, namely EgmiR319; EgmiR399; EgmiR396; EgmiR172; EgmiR156; EgmiR157; miR5648; miR5645; and EgmiRNA_unidentified. Two miRNAs were selected for RT-qPCR validation, namely EgMir399 and EgMir172. Their expression pattern was similar with the RNA sequencing results and shown opposite expression pattern with their target genes, UBC E2 24 and APETALA2, respectively. CONCLUSIONS: The nine micro RNA families was identified in oil palm root tissue at phosphate starvation.

High-resolution genetic linkage map and height-related QTLs in an oil palm (Elaeis guineensis) family planted across multiple sites.

A refined SNP array containing 92,459 probes was developed and applied for chromosome scanning, construction of a high-density genetic linkage map and QTL analysis in a selfed Nigerian oil palm family (T128). Genotyping of the T128 mapping family generated 76,447 good quality SNPs for detailed scanning of aberration and homozygosity in the individual pseudo-chromosomes. Of them, 25,364 polymorphic SNPs were used for linkage analysis resulting in an 84.4% mapping rate. A total of 21,413 SNPs were mapped into 16 linkage groups (LGs), covering a total map length of 1364.5 cM. This genetic map is 16X denser than the previous version used to establish pseudo-chromosomes of the oil palm reference genome published in 2013. The QTLs associated with height, height increment and rachis length were identified in LGs TT05, 06, 08, 15 and 16. The present QTLs as well as those published previously were tagged to the reference genome to determine their chromosomal locations. Almost all the QTLs identified in this study were either close to or co-located with those reported in other populations. Determining the QTL position on chromosomes was also helpful in mining for the underlying candidate genes. In total, 55 putative genes and transcription factors involved in the biosynthesis, conjugation and signalling of the major phytohormones, especially for gibberellins and cell wall morphogenesis were found to be present in the identified genomic QTL regions, and their potential roles in plant dwarfism are discussed. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-023-01360-2.

Transcriptome analysis reveals key developmental and metabolic regulatory aspects of oil palm (Elaeis guineensis Jacq.) during zygotic embryo development.

BACKGROUND: Oil palm is the most efficient oil-producing crop in the world, and the yield of palm oil is associated with embryonic development. However, a comprehensive understanding of zygotic embryo development at the molecular level remains elusive. In order to address this issue, we report the transcriptomic analysis of zygotic embryo development in oil palm, specifically focusing on regulatory genes involved in important biological pathways. RESULTS: In this study, three cDNA libraries were prepared from embryos at S1 (early-stage), S2 (middle-stage), and S3 (late-stage). There were 16,367, 16,500, and 18,012 genes characterized at the S1, S2, and S3 stages of embryonic development, respectively. A total of 1522, 2698, and 142 genes were differentially expressed in S1 vs S2, S1 vs S3, and S2 vs S3, respectively. Using Gene Ontology (GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis to identify key genes and pathways. In the hormone signaling pathway, genes related to auxin antagonize the output of cytokinin which regulates the development of embryo meristem. The genes related to abscisic acid negatively regulating the synthesis of gibberellin were strongly up-regulated in the mid-late stage of embryonic development. The results were reported the early synthesis and mid-late degradation of sucrose, as well as the activation of the continuous degradation pathway of temporary starch, providing the nutrients needed for differentiation of the embryonic cell. Moreover, the transcripts of genes involved in fatty acid synthesis were also abundantly accumulated in the zygotic embryos. CONCLUSION: Taken together, our research provides a new perspective on the developmental and metabolic regulation of zygotic embryo development at the transcriptional level in oil palm.

Chromosome identification in oil palm (Elaeis guineensis) using in situ hybridization with massive pools of single copy oligonucleotides and transferability across Arecaceae species.

Chromosome identification is essential for linking sequence and chromosomal maps, verifying sequence assemblies, showing structural variations and tracking inheritance or recombination of chromosomes and chromosomal segments during evolution and breeding programs. Unfortunately, identification of individual chromosomes and chromosome arms has been a major challenge for some economically important crop species with a near-continuous chromosome size range and similar morphology. Here, we developed oligonucleotide-based chromosome-specific probes that enabled us to establish a reference chromosome identification system for oil palm (Elaeis guineensis Jacq., 2n = 32). Massive oligonucleotide sequence pools were anchored to individual chromosome arms using dual and triple fluorescent in situ hybridization (EgOligoFISH). Three fluorescently tagged probe libraries were developed to contain, in total 52,506 gene-rich single-copy 47-mer oligonucleotides spanning each 0.2-0.5 Mb across strategically placed chromosome regions. They generated 19 distinct FISH signals and together with rDNA probes enabled identification of all 32 E. guineensis chromosome arms. The probes were able to identify individual homoeologous chromosome regions in the related Arecaceae palm species: American oil palm (Elaeis oleifera), date palm (Phoenix dactylifera) and coconut (Cocos nucifera) showing the comparative organization and concerted evolution of genomes in the Arecaceae. The oligonucleotide probes developed here provide a valuable approach to chromosome arm identification and allow tracking chromosome transfer in hybridization and breeding programs in oil palm, as well as comparative studies within Arecaceae.

Expression analysis of miRNAs and their putative target genes confirm a preponderant role of transcription factors in the early response of oil palm plants to salinity stress.

BACKGROUND: Several mechanisms regulating gene expression contribute to restore and reestablish cellular homeostasis so that plants can adapt and survive in adverse situations. MicroRNAs (miRNAs) play roles important in the transcriptional and post-transcriptional regulation of gene expression, emerging as a regulatory molecule key in the responses to plant stress, such as cold, heat, drought, and salt. This work is a comprehensive and large-scale miRNA analysis performed to characterize the miRNA population present in oil palm (Elaeis guineensis Jacq.) exposed to a high level of salt stress, to identify miRNA-putative target genes in the oil palm genome, and to perform an in silico comparison of the expression profile of the miRNAs and their putative target genes. RESULTS: A group of 79 miRNAs was found in oil palm, been 52 known miRNAs and 27 new ones. The known miRNAs found belonged to 28 families. Those miRNAs led to 229 distinct miRNA-putative target genes identified in the genome of oil palm. miRNAs and putative target genes differentially expressed under salinity stress were then selected for functional annotation analysis. The regulation of transcription, DNA-templated, and the oxidation-reduction process were the biological processes with the highest number of hits to the putative target genes, while protein binding and DNA binding were the molecular functions with the highest number of hits. Finally, the nucleus was the cellular component with the highest number of hits. The functional annotation of the putative target genes differentially expressed under salinity stress showed several ones coding for transcription factors which have already proven able to result in tolerance to salinity stress by overexpression or knockout in other plant species. CONCLUSIONS: Our findings provide new insights into the early response of young oil palm plants to salinity stress and confirm an expected preponderant role of transcription factors - such as NF-YA3, HOX32, and GRF1 - in this response. Besides, it points out potential salt-responsive miRNAs and miRNA-putative target genes that one can utilize to develop oil palm plants tolerant to salinity stress.

Multi-scale comparative transcriptome analysis reveals key genes and metabolic reprogramming processes associated with oil palm fruit abscission.

BACKGROUND: Fruit abscission depends on cell separation that occurs within specialized cell layers that constitute an abscission zone (AZ). To determine the mechanisms of fleshy fruit abscission of the monocot oil palm (Elaeis guineensis Jacq.) compared with other abscission systems, we performed multi-scale comparative transcriptome analyses on fruit targeting the developing primary AZ and adjacent tissues. RESULTS: Combining between-tissue developmental comparisons with exogenous ethylene treatments, and naturally occurring abscission in the field, RNAseq analysis revealed a robust core set of 168 genes with differentially regulated expression, spatially associated with the ripe fruit AZ, and temporally restricted to the abscission timing. The expression of a set of candidate genes was validated by qRT-PCR in the fruit AZ of a natural oil palm variant with blocked fruit abscission, which provides evidence for their functions during abscission. Our results substantiate the conservation of gene function between dicot dry fruit dehiscence and monocot fleshy fruit abscission. The study also revealed major metabolic transitions occur in the AZ during abscission, including key senescence marker genes and transcriptional regulators, in addition to genes involved in nutrient recycling and reallocation, alternative routes for energy supply and adaptation to oxidative stress. CONCLUSIONS: The study provides the first reference transcriptome of a monocot fleshy fruit abscission zone and provides insight into the mechanisms underlying abscission by identifying key genes with functional roles and processes, including metabolic transitions, cell wall modifications, signalling, stress adaptations and transcriptional regulation, that occur during ripe fruit abscission of the monocot oil palm. The transcriptome data comprises an original reference and resource useful towards understanding the evolutionary basis of this fundamental plant process.

Detection of ploidy and chromosomal aberrations in commercial oil palm using high-throughput SNP markers.

MAIN CONCLUSION: Karyotyping using high-density genome-wide SNP markers identified various chromosomal aberrations in oil palm (Elaeis guineensis Jacq.) with supporting evidence from the 2C DNA content measurements (determined using FCM) and chromosome counts. 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.

Analysis of genetic diversity and discrimination of Oil Palm DxP populations based on the origins of pisifera elite parents.

A total of 251 Dura cross Pisifera (DxP) hybrid palms from six populations descending from six parental African Pisifera origins and involving 12 progenies were analyzed with 19 selected Simple Sequence Repeats (SSR) markers. A total of 110 alleles were produced, ranging from three to eight per SSR, with a mean of 5.8 alleles per SSR locus. Of these, 68.5% were considered shared alleles by more than one population and the remaining 31.5% were population specific alleles. They generated between six and 21 haplotypes in all populations, and depending on the SSR marker, between one and 10 haplotypes within populations. Various parameters for analyzing genetic variability, differentiation and genetic structure were computed using GenAlEx, Structure and Darwin software. The obtained results confirmed microsatellites as a robust, feasible and trustful method for obtaining DNA fingerprints, tracing the source of oil palm samples. With respect to the authenticity of materials or for solving legitimacy issues, accession belonging to each population by SSR markers could be distinguished, but additional SSR should be screened for improving this process.

Optimised and systematic suitable climate modelling confirms future longitudinal-trends for growing oil palm in Africa.

Palms are iconic plants. Oil palms are very important economically and originate in Africa where they can act as a model for palms in general. The effect of future climate on the growth of oil palm will be very detrimental. Latitudinal migration of tropical crops to climate refuges may be impossible, and longitudinal migration has only been confirmed for oil palm, of all the tropical crops. The previous method to determine the longitudinal trend for oil palm used the longitudes of various countries in Africa and plotted these against the percentage suitable climate for growing oil palms in each country. An increasing longitudinal trend was observed from west to east. However, the longitudes of the countries were randomly distributed which may have introduced bias and the procedure was time consuming. The present report presents an optimised and systematic procedure that divided the regions, as presented on a map derived from a CLIMEX model, into ten equal sectors and the percentage suitable climates for growing oil palm were determined for each sector. This approach was quicker, systematic and straight forward and will be useful for management of oil palm plantations under climate change. The method confirmed and validated the trends reported in the original method although the suitability values were often lower and there was less spread of values around the trend. The values for the CSIRO MK3.0 and MIROC H models demonstrated considerable similarities to each other, contributing to validation of the method. The procedure of dividing maps equally into sectors derived from models, could be used for other crops, regions, or systems more generally, where the alternative may be a more superficial visual examination of the maps. Methods are required to mitigate the effects of climate change and stakeholders need to contribute more actively to the current climate debate with tangible actions.

Phenomics, genomics of oil palm (Elaeis guineensis Jacq.): way forward for making sustainable and high yielding quality oil palm.

Oil palm (Elaeis guineensis Jacq.) is a heterogeneous, perennial crop having long breeding cycle with a genome size of 1.8 Gb. The demand for vegetable oil is steadily increasing, and expected that nearly 240-250 million tons of vegetable oil may be required by 2050. Genomics and next generation technologies plays crucial role in achieving the sustainable availability of oil palm with good yield and high quality. A successful breeding programme in oil palm depends on the availability of diverse gene pool, ex-situ conservation and their proper utilization for generating elite planting material. The major breeding methods adopted in oil palm are either modified recurrent selection or the modified reciprocal recurrent selection method. The QTLs of yield and related traits are chiefly located on chromosome 4, 10, 12 and 15 which is discussed in the current review. The probable chromosomal regions influencing the less height increment is observed to be on chromosomes 4, 10, 14 and 15. Advanced genomic approaches together with bioinformatics tools were discussed thoroughly for achieving sustainable oil palm where more efforts are needed. Major emphasis is given on oil palm crop improvement using holistic approaches of various genomic tools. Also a road map given on the milestones in the genomics and way forward for making oil palm to high yielding quality oil palm.

Characterization of Oil Palm Acyl-CoA-Binding Proteins and Correlation of Their Gene Expression with Oil Synthesis.

Acyl-CoA-binding proteins (ACBPs) are involved in binding and trafficking acyl-CoA esters in eukaryotic cells. ACBPs contain a well-conserved acyl-CoA-binding domain. Their various functions have been characterized in the model plant Arabidopsis and, to a lesser extent, in rice. In this study, genome-wide detection and expression analysis of ACBPs were performed on Elaeis guineensis (oil palm), the most important oil crop in the world. Seven E. guineensis ACBPs were identified and classified into four groups according to their deduced amino acid domain organization. Phylogenetic analysis showed conservation of this family with other higher plants. All seven EgACBPs were expressed in most tissues while their differential expression suggests various functions in specific tissues. For example, EgACBP3 had high expression in inflorescences and stalks while EgACBP1 showed strong expression in leaves. Because of the importance of E. guineensis as an oil crop, expression of EgACBPs was specifically examined during fruit development. EgACBP3 showed high expression throughout mesocarp development, while EgACBP1 had enhanced expression during rapid oil synthesis. In endosperm, both EgACBP1 and EgACBP3 exhibited increased expression during seed development. These results provide important information for further investigations on the biological functions of EgACBPs in various tissues and, in particular, their roles in oil synthesis.

Variation for heterodimerization and nuclear localization among known and novel oil palm SHELL alleles.

Oil palm breeding involves crossing dura and pisifera palms to produce tenera progeny with greatly improved oil yield. Oil yield is controlled by variant alleles of a type II MADS-box gene, SHELL, that impact the presence and thickness of the endocarp, or shell, surrounding the fruit kernel. We identified six novel SHELL alleles in noncommercial African germplasm populations from the Malaysian Palm Oil Board. These populations provide extensive diversity to harness genetic, mechanistic and phenotypic variation associated with oil yield in a globally critical crop. We investigated phenotypes in heteroallelic combinations, as well as SHELL heterodimerization and subcellular localization by yeast two-hybrid, bimolecular fluorescence complementation and gene expression analyses. Four novel SHELL alleles were associated with fruit form phenotype. Candidate heterodimerization partners were identified, and interactions with EgSEP3 and subcellular localization were SHELL allele-specific. Our findings reveal allele-specific mechanisms by which variant SHELL alleles impact yield, as well as speculative insights into the potential role of SHELL in single-gene oil yield heterosis. Future field trials for combinability and introgression may further optimize yield and improve sustainability.

Sphingomonas palmae sp. nov. and Sphingomonas gellani sp. nov., endophytically associated phyllosphere bacteria isolated from economically important crop plants.

In this study, two endophytic bacterial strains designated JS21-1T and S6-262T isolated from leaves of Elaeis guineensis and stem tissues of Jatropha curcas respectively, were subjected for polyphasic taxonomic approach. On R2A medium, colonies of strains JS21-1T and S6-262T are orange and yellow, respectively. Phylogenetic analyses using 16S rRNA gene sequencing and whole-genome sequences placed the strains in distinct clades but within the genus Sphingomonas. The DNA G + C content of JS21-1T and S6-262T were 67.31 and 66.95%, respectively. Furthermore, the average nucleotide identity and digital DNA-DNA hybridization values of strains JS21-1T and S6-262T with phylogenetically related Sphingomonas species were lower than 95% and 70% respectively. The chemotaxonomic studies indicated that the major cellular fatty acids of the strain JS21-1T were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C16:0, and C14:0 2OH; strain S6-262T possessed summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH) and summed feature 8 (C18:1 ω6c and/or C18:1 ω7c). The major quinone was Q10, and the unique polyamine observed was homospermidine. The polar lipid profile comprised of mixture of sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and certain uncharacterised phospholipids and lipids. Based on this polyphasic evidence, strains JS21-1T and S6-262T represent two novel species of the genus Sphingomonas, for which the names Sphingomonas palmae sp. nov. and Sphingomonas gellani sp. nov. are proposed, respectively. The type strain of Sphingomonas palmae sp. nov. is JS21-1T (= DSM 27348T = KACC 17591T) and the type strain of Sphingomonas gellani sp. nov. is S6-262T (= DSM 27346T =  KACC 17594T).

Early nodulin 93 protein gene: essential for induction of somatic embryogenesis in oil palm.

KEY MESSAGE: Transcript profiling during the early induction phase of oil palm tissue culture and RNAi studies in a model somatic embryogenesis system showed that EgENOD93 expression is essential for somatic embryogenesis. Micropropagation of oil palm through tissue culture is vital for the generation of superior and uniform elite planting materials. Studies were carried out to identify genes to distinguish between leaf explants with the potential to develop into embryogenic or non-embryogenic callus. Oil palm cDNA microarrays were co-hybridized with cDNA probes of reference tissue, separately with embryo forming (media T527) and non-embryo (media T694) forming leaf explants sampled at Day 7, Day 14 and Day 21. Analysis of the normalized datasets has identified 77, 115 and 127 significantly differentially expressed genes at Day 7, Day 14, and Day 21, respectively. An early nodulin 93 protein gene (ENOD93), was highly expressed at Day 7, Day 14, and Day 21 and in callus (media T527), as assessed by RT-qPCR. Validation of EgENOD93 across tissue culture lines of different genetic background and media composition showed the potential of this gene as an embryogenic marker. In situ RNA hybridization and functional characterization in Medicago truncatula provided additional evidence that ENOD93 is essential for somatic embryogenesis. This study supports the suitability of EgENOD93 as a marker to predict the potential of leaf explants to produce embryogenic callus. Crosstalk among stresses, auxin, and Nod-factor like signalling molecules likely induces the expression of EgENOD93 for embryogenic callus formation.

Multilocus phylogeography of the world populations of Elaeidobius kamerunicus (Coleoptera, Curculionidae), pollinator of the palm Elaeis guineensis.

Elaeidobius kamerunicus Faust (Coleoptera, Curculionidae) is one of the specific pollinators on inflorescences of the African oil palm Elaeis guineensis Jacquin. This derelomine weevil is native to tropical Africa. During the late 20th century, it was introduced into all tropical regions where E. guineensis is grown, in order to improve its pollination and fruit set. Despite an overall success, a decline in pollination efficiency has been documented in several regions. In this study, we reconstructed a multilocus phylogeography of the world populations of E. kamerunicus, in order to explore its genetic diversity in its native and introduced ranges. Our results showed that African populations of E. kamerunicus are forming two differentiated mitochondrial clusters in West and central Africa, forming a contact zone along the Cameroon Volcanic Line. The existence of this sharp contact zone along this weak altitudinal barrier suggests that other parameters, such as climate, may be driving the distribution of populations. A differential genetic structure between mitochondrial and nuclear genes, and the strong level of genetic structure of the mitochondrial gene, also suggest sex-biased dispersal in this species, with males dispersing more than females. The genetic structure inferred from Asian and South American populations suggests that they originate from populations of both western and central tropical Africa and that a bottleneck has probably been experienced by these populations.

Adsorption and Desorption Properties of Total Flavonoids from Oil Palm (Elaeis guineensis Jacq.) Mature Leaf on Macroporous Adsorption Resins.

Three different macroporous resins (XAD7HP, DAX-8, and XAD4) were evaluated for their adsorption and desorption properties in preparing flavonoid-enriched oil palm (Elaeis guineensis Jacq.) leaf extract. The influences of initial concentration, solution pH, contact time, and desorption solvent (ethanol) concentration were determined by static sorption/desorption methods. The optimal condition for adsorption of flavonoids was achieved when the solution of the extract was adjusted to pH 7, reaching equilibrium after 1440 min at 298 K. The adsorption process was well described by a pseudo-second-order kinetics model, while the adsorption isotherm data fitted well with a Freundlich model. The adsorption by each resin was via an exothermic and physical adsorption process. Based on the static experiment results, XAD7HP was found to be the most appropriate adsorbent, while 80% ethanol was the best solvent for desorbent. Further evaluation of its dynamic adsorption and desorption characteristics on a packed glass column showed that XAD7HP could enrich the OPL total flavonoid content by a 3.57-fold increment. Moreover, UHPLC-UV/PDA and UHPLC-MS/MS analysis revealed that apigenin and luteolin derivatives were selectively adsorbed by XAD7HP. Additionally, both the crude OPL extract and the flavonoid-enriched fraction have good DPPH and NO free radical scavenging activities. Multiple interactions between the flavonoids and cross-linked polymeric XAD7HP resin through van der Waals forces and hydrogen bonding described the sorption processes. Therefore, by utilizing this method, the flavonoid-enriched fraction from crude OPL extract could be used as a potential bioactive ingredient in nutraceutical and pharmaceutical applications at minimum cost with optimum efficiency.