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

Ting NC, Chan PL, Buntjer J, Ordway JM, Wischmeyer C, Ooi LC, et al.

Physiol Mol Biol Plants, 2023 Sep;29(9):1301-1318.
PMID: 38024957 DOI: 10.1007/s12298-023-01360-2

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.
Fulltext An integrated linkage map of interspecific backcross 2 (BC2) populations reveals QTLs associated with fatty acid composition and vegetative parameters influencing compactness in oil palm

Yaakub Z, Kamaruddin K, Singh R, Mustafa S, Marjuni M, Ting NC, et al.

BMC Plant Biol, 2020 Jul 29;20(1):356.
PMID: 32727448 DOI: 10.1186/s12870-020-02563-5

BACKGROUND: Molecular breeding has opened new avenues for crop improvement with the potential for faster progress. As oil palm is the major producer of vegetable oil in the world, its improvement, such as developing compact planting materials and altering its oils' fatty acid composition for wider application, is important.
RESULTS: This study sought to identify the QTLs associated with fatty acid composition and vegetative traits for compactness in the crop. It integrated two interspecific backcross two (BC2) mapping populations to improve the genetic resolution and evaluate the consistency of the QTLs identified. A total 1963 markers (1814 SNPs and 149 SSRs) spanning a total map length of 1793 cM were integrated into a consensus map. For the first time, some QTLs associated with vegetative parameters and carotene content were identified in interspecific hybrids, apart from those associated with fatty acid composition. The analysis identified 8, 3 and 8 genomic loci significantly associated with fatty acids, carotene content and compactness, respectively.
CONCLUSIONS: Major genomic region influencing the traits for compactness and fatty acid composition was identified in the same chromosomal region in the two populations using two methods for QTL detection. Several significant loci influencing compactness, carotene content and FAC were common to both populations, while others were specific to particular genetic backgrounds. It is hoped that the QTLs identified will be useful tools for marker-assisted selection and accelerate the identification of desirable genotypes for breeding.
Fulltext Assessment of Oil Palm Pollinating Weevil (Elaeidobius kamerunicus) Population Density in Biparental dura × pisifera Hybrids on Deep Peat-Soil in Perak State, Malaysia

Swaray S, Y Rafii M, Din Amiruddin M, Firdaus Ismail M, Jamian S, Jalloh M, et al.

Insects, 2021 Mar 04;12(3).
PMID: 33806613 DOI: 10.3390/insects12030221

This study was conducted to assess the Elaeidobius kamerunicus (EK) population density among the biparental dura × pisifera hybrids' palms on deep peat-soil. Twenty-four hybrids derived from 10 genetic sources were used. Variance analysis showed that the EK population density varies between different oil palm hybrids, with a more noticeable variation of a low population mean in the male weevil across the hybrids. The highest weevil population mean/spikelet was attained on the third day of anthesis. The maximum monthly population of EK/spikelet (12.81 ± 0.23) and population density of EK (1846.49 ± 60.69) were recorded in January. Accordingly, 41.67% of the hybrids recorded an EK population density greater than the trial means of 973.68 weevils. Hybrid ECPHP550 had the highest mean of EK/spikelet (10.25 ± 0.11) and the highest population density of EK/palm (1241.39 ± 73.74). The parental mean population was 963.24 weevils and parent Deli-Banting × AVROS recorded the highest EK population density (1173.01). The overall results showed a notable disparity in the EK population among the biparental hybrids. Parental Deli-Banting × AVROS and hybrid ECPHP550 could be more useful to optimize the weevil population for pollination improvements in palm plantations. However, we suggest that volatile production should be included as a desirable trait in oil palm selective breeding.
Fulltext Genetic Diversity Assessment of MPOB-Senegal Oil Palm Germplasm Using Microsatellite Markers

Myint KA, Yaakub Z, Rafii MY, Oladosu Y, Samad MYA, Ramlee SI, et al.

Biomed Res Int, 2021;2021:6620645.
PMID: 33997027 DOI: 10.1155/2021/6620645

Molecular characterization of oil palm germplasm is crucial in utilizing and conserving germplasm with promising traits. This study was conducted to evaluate the genetic diversity structures and relationships among 26 families of MPOB-Senegal oil palm germplasm using thirty-five microsatellite markers. High level of polymorphism (P = 96.26%), number of effective allele (N e = 2.653), observed heterozygosity (H o = 0.584), expected heterozygosity (H e = 0.550), total heterozygosity (H T = 0.666), and rare alleles (54) were observed which indicates that MPOB-Senegal germplasm has a broad genetic variation. Among the SSR markers, sMo00053 and sMg00133 were the most informative markers for discrimination among the MPOB-Senegal oil palm germplasm for having the highest private alleles and the rare alleles. For selection and conservation, oil palm populations with high rare alleles and Nei's gene diversity index should be considered as these populations may possess unique genes for further exploitation.
Genomic diversity and genome-wide association analysis related to yield and fatty acid composition of wild American oil palm

Ithnin M, Vu WT, Shin MG, Suryawanshi V, Sherbina K, Zolkafli SH, et al.

Plant Sci, 2021 Mar;304:110731.
PMID: 33568284 DOI: 10.1016/j.plantsci.2020.110731

Existing Elaeis guineensis cultivars lack sufficient genetic diversity due to extensive breeding. Harnessing variation in wild crop relatives is necessary to expand the breadth of agronomically valuable traits. Using RAD sequencing, we examine the natural diversity of wild American oil palm populations (Elaeis oleifera), a sister species of the cultivated Elaeis guineensis oil palm. We genotyped 192 wild E. oleifera palms collected from seven Latin American countries along with four cultivated E. guineensis palms. Honduras, Costa Rica, Panama and Colombia palms are panmictic and genetically similar. Genomic patterns of diversity suggest that these populations likely originated from the Amazon Basin. Despite evidence of a genetic bottleneck and high inbreeding observed in these populations, there is considerable genetic and phenotypic variation for agronomically valuable traits. Genome-wide association revealed several candidate genes associated with fatty acid composition along with vegetative and yield-related traits. These observations provide valuable insight into the geographic distribution of diversity, phenotypic variation and its genetic architecture that will guide choices of wild genotypes for crop improvement.
Fulltext The oil palm VIRESCENS gene controls fruit colour and encodes a R2R3-MYB

Singh R, Low ET, Ooi LC, Ong-Abdullah M, Nookiah R, Ting NC, et al.

Nat Commun, 2014 Jun 30;5:4106.
PMID: 24978855 DOI: 10.1038/ncomms5106

Oil palm, a plantation crop of major economic importance in Southeast Asia, is the predominant source of edible oil worldwide. We report the identification of the virescens (VIR) gene, which controls fruit exocarp colour and is an indicator of ripeness. VIR is a R2R3-MYB transcription factor with homology to Lilium LhMYB12 and similarity to Arabidopsis production of anthocyanin pigment1 (PAP1). We identify five independent mutant alleles of VIR in over 400 accessions from sub-Saharan Africa that account for the dominant-negative virescens phenotype. Each mutation results in premature termination of the carboxy-terminal domain of VIR, resembling McClintock's C1-I allele in maize. The abundance of alleles likely reflects cultural practices, by which fruits were venerated for magical and medicinal properties. The identification of VIR will allow selection of the trait at the seed or early-nursery stage, 3-6 years before fruits are produced, greatly advancing introgression into elite breeding material.
Fulltext Variation for heterodimerization and nuclear localization among known and novel oil palm SHELL alleles

Singh R, Low EL, Ooi LC, Ong-Abdullah M, Ting NC, Nookiah R, et al.

New Phytol, 2020 04;226(2):426-440.
PMID: 31863488 DOI: 10.1111/nph.16387

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.
Chromosome-scale Elaeis guineensis and E. oleifera assemblies: comparative genomics of oil palm and other Arecaceae

Low EL, Chan KL, Zaki NM, Taranenko E, Ordway JM, Wischmeyer C, et al.

G3 (Bethesda), 2024 Sep 04;14(9).
PMID: 38918881 DOI: 10.1093/g3journal/jkae135

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.
Fulltext Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm

Ong-Abdullah M, Ordway JM, Jiang N, Ooi SE, Kok SY, Sarpan N, et al.

Nature, 2015 Sep 24;525(7570):533-7.
PMID: 26352475 DOI: 10.1038/nature15365

Somaclonal variation arises in plants and animals when differentiated somatic cells are induced into a pluripotent state, but the resulting clones differ from each other and from their parents. In agriculture, somaclonal variation has hindered the micropropagation of elite hybrids and genetically modified crops, but the mechanism responsible remains unknown. The oil palm fruit 'mantled' abnormality is a somaclonal variant arising from tissue culture that drastically reduces yield, and has largely halted efforts to clone elite hybrids for oil production. Widely regarded as an epigenetic phenomenon, 'mantling' has defied explanation, but here we identify the MANTLED locus using epigenome-wide association studies of the African oil palm Elaeis guineensis. DNA hypomethylation of a LINE retrotransposon related to rice Karma, in the intron of the homeotic gene DEFICIENS, is common to all mantled clones and is associated with alternative splicing and premature termination. Dense methylation near the Karma splice site (termed the Good Karma epiallele) predicts normal fruit set, whereas hypomethylation (the Bad Karma epiallele) predicts homeotic transformation, parthenocarpy and marked loss of yield. Loss of Karma methylation and of small RNA in tissue culture contributes to the origin of mantled, while restoration in spontaneous revertants accounts for non-Mendelian inheritance. The ability to predict and cull mantling at the plantlet stage will facilitate the introduction of higher performing clones and optimize environmentally sensitive land resources.