The genome sequence of the African oil palm, the main source of oil production, is used to predict at least 34,802 genes, including oil biosynthesis genes; comparison with the draft sequence of the South American oil palm reveals that the two species may have diverged in the New World and that segmental duplications of chromosome arms define the palaeotetraploid origin of palm trees. Two papers published in this issue of Nature deal with the genetics of two variants of one of the most important crops in use today — the African oil palm Elaeis guineensis and its South American cousin Elaeis oleifera. Palm oil accounts for almost half the edible oil consumed worldwide and is also a biofuel, although not without controversy, as in many areas palm oil monoculture has replaced valuable natural forest. Analyses of the 1.8-gigabase genome sequence of E. guineensis and draft sequence of E. oleifera provide insights into oil biosynthesis genes and their regulators, and a record of genome evolution. A key event in the domestication and breeding of the oil palm was loss of the thick, coconut-like shell. The second of the two papers identifies mutations the SHELL gene that specify the different fruit forms found in the oil palm and shows that SHELL gene mutations that originated in pre-colonial Africa are responsible for the single gene hybrid vigour and high yields attained by the oil palm. Oil palm is the most productive oil-bearing crop. Although it is planted on only 5% of the total world vegetable oil acreage, palm oil accounts for 33% of vegetable oil and 45% of edible oil worldwide, but increased cultivation competes with dwindling rainforest reserves. We report the 1.8-gigabase (Gb) genome sequence of the African oil palm Elaeis guineensis, the predominant source of worldwide oil production. A total of 1.535 Gb of assembled sequence and transcriptome data from 30 tissue types were used to predict at least 34,802 genes, including oil biosynthesis genes and homologues of WRINKLED1 (WRI1), and other transcriptional regulators1, which are highly expressed in the kernel. We also report the draft sequence of the South American oil palm Elaeis oleifera, which has the same number of chromosomes (2n = 32) and produces fertile interspecific hybrids with E. guineensis2 but seems to have diverged in the New World. Segmental duplications of chromosome arms define the palaeotetraploid origin of palm trees. The oil palm sequence enables the discovery of genes for important traits as well as somaclonal epigenetic alterations that restrict the use of clones in commercial plantings3, and should therefore help to achieve sustainability for biofuels and edible oils, reducing the rainforest footprint of this tropical plantation crop.

The oil palm fruit ‘mantled’ abnormality is a somaclonal variant that markedly reduces yield; here, a genome-wide DNA methylation analysis finds that hypomethylation of a single Karma family retrotransposon embedded in a homeotic gene intron is common to all mantled clones and is associated with aberrant splicing and termination of the gene transcript, and that loss of methylation predicts a loss of oil palm yield. A flower and fruit abnormality known as 'mantled' can develop in some agricultural oil palm cultivars derived from tissue culture and the resulting mantled palms can become unproductive. Mantling is widely regarded as an epigenetic trait, but has not been fully explained. Meilina Ong-Abdullah et al. have undertaken a genome-wide, unbiased, DNA methylation analysis to look for loci epigenetically associated with the mantled phenotype. They find that hypomethylation of a single Karma family retrotransposon embedded in the intron of a homeotic gene is common to all mantled clones and associated with aberrant splicing and termination of the gene transcript. Loss of methylation — dubbed the Bad Karma epiallele — predicts a loss of oil palm yield and this property should enable screening for higher-performing clones at the plantlet stage. 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 unknown1. 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 production2,3,4. Widely regarded as an epigenetic phenomenon5, ‘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.

Genetic mapping and whole-genome sequencing studies identify the SHELL gene (a homologue of Arabidopsis SEEDSTICK) as responsible for the three different fruit forms in oil palm (Elaeis guineesis); this has important economic implications for modulating SHELL activity to breed desired fruit forms and enhance oil yields. Two papers published in this issue of Nature deal with the genetics of two variants of one of the most important crops in use today — the African oil palm Elaeis guineensis and its South American cousin Elaeis oleifera. Palm oil accounts for almost half the edible oil consumed worldwide and is also a biofuel, although not without controversy, as in many areas palm oil monoculture has replaced valuable natural forest. Analyses of the 1.8-gigabase genome sequence of E. guineensis and draft sequence of E. oleifera provide insights into oil biosynthesis genes and their regulators, and a record of genome evolution. A key event in the domestication and breeding of the oil palm was loss of the thick, coconut-like shell. The second of the two papers identifies mutations the SHELL gene that specify the different fruit forms found in the oil palm and shows that SHELL gene mutations that originated in pre-colonial Africa are responsible for the single gene hybrid vigour and high yields attained by the oil palm. A key event in the domestication and breeding of the oil palm Elaeis guineensis was loss of the thick coconut-like shell surrounding the kernel. Modern E. guineensis has three fruit forms, dura (thick-shelled), pisifera (shell-less) and tenera (thin-shelled), a hybrid between dura and pisifera1,2,3,4. The pisifera palm is usually female-sterile. The tenera palm yields far more oil than dura, and is the basis for commercial palm oil production in all of southeast Asia5. Here we describe the mapping and identification of the SHELL gene responsible for the different fruit forms. Using homozygosity mapping by sequencing, we found two independent mutations in the DNA-binding domain of a homologue of the MADS-box gene SEEDSTICK (STK, also known as AGAMOUS-LIKE 11), which controls ovule identity and seed development in Arabidopsis. The SHELL gene is responsible for the tenera phenotype in both cultivated and wild palms from sub-Saharan Africa, and our findings provide a genetic explanation for the single gene hybrid vigour (or heterosis) attributed to SHELL, via heterodimerization. This gene mutation explains the single most important economic trait in oil palm, and has implications for the competing interests of global edible oil production, biofuels and rainforest conservation6.

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.

Oil palm is the second largest source of edible oil which contributes to approximately 20% of the world's production of oils and fats. In order to understand the molecular biology involved in in vitro propagation, flowering, efficient utilization of nitrogen sources and root diseases, we have initiated an expressed sequence tag (EST) analysis on oil palm.