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 micropropagation of elite hybrids and genetically modified crops, but the mechanism remains a mystery1. The oil palm fruit abnormality, mantled, is a somaclonal variant arising from tissue culture that drastically reduces yield, and has largely halted efforts to clone elite hybrids for oil production2–4. Widely regarded as epigenetic5, mantling has defied explanation, but here we identify the MANTLED gene using Epigenome Wide Association Studies. 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 (the Good Karma epiallele) predicts normal fruit set, while hypomethylation (the Bad Karma epiallele) predicts homeotic transformation, parthenocarpy and dramatic loss of yield. Loss of Karma methylation and 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.

BackgroundThe 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.ResultsIn 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2607-4) contains supplementary material, which is available to authorized users.

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Summary 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.

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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.

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 (BC 2) 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.