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. 2013 Aug 15;500(7462):340-4.
doi: 10.1038/nature12356. Epub 2013 Jul 24.

The Oil Palm SHELL Gene Controls Oil Yield and Encodes a Homologue of SEEDSTICK

Free PMC article

The Oil Palm SHELL Gene Controls Oil Yield and Encodes a Homologue of SEEDSTICK

Rajinder Singh et al. Nature. .
Free PMC article


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 pisifera. 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 Asia. 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 conservation.


Figure 1
Figure 1. Fruit forms of the African oil palm Elaeis guineensis
a, Dura (Sh/Sh) fruit forms have a thick lignified shell surrounding the kernel, which is absent in pisifera (sh/sh). F1 hybrid palms (Sh/sh) have an intermediate fruit form (tenera) which is much higher yielding than either parent in terms of mesocarp oil. b, Dura, tenera and pisifera fruit stained for lignin (red) with phloroglucinol.
Figure 2
Figure 2. Homozygosity mapping of the shell trait
a, AVROS pedigree palms heterozygous (tenera, pink) and homozygous (pisifera, blue and green) for Shell are indicated, linked to parents and progeny planted over 5 decades. Individually sequenced palms are indicated (green). Three additional pisifera palms from this extended pedigree were also individually sequenced (not shown). The remaining pisifera palms were sequenced as a pool. b, The Shell locus was mapped onto scaffold p3-sc00043 (3.4Mb) and SNP density was plotted along the scaffold (upper panel). Markers surrounding Shell are plotted against the % of pisifera palms with the SNP haplotype in the Nigerian T128 F1 mapping population. Shell was mapped between flanking markers, denoted by blue diamonds, at 400 Kb and 1 Mb. A local diversity minimum of 200 Kb was found within this interval (inset). c, Genes (green) and transposons (red) are indicated as boxes. The local diversity minimum contained 4 homozygous genes (boxed), only one of which (Shell) was located between the flanking markers in panel b.
Figure 3
Figure 3. Sequence diversity of Shell
Multiple sequence alignment of Arabidopsis STK (AEE82818.1) and SHP1 (P29381.1) proteins, rice protein OsMADS13 (AAF13594.1), poplar predicted protein (XP_002327282.1), grape MADS-box protein 5 (XP_002281890.1), tomato TAGL1 (AAM33101.2) and peach SHATTERPROOF-like (ABG75908.1) (Out Groups), E. oleifera, E. guineensis and exemplars of Deli dura (Oil Palm – Dura Allele) and pisifera from T128 – Nigerian and AVROS – Congo (Oil Palm – Pisifera Allele). The pisifera fruit form is caused by two disruptive SNPs that affect a highly conserved amino acid motif in the MADS-box DNA binding and dimerization domain. Gene names (out group examples) or sample identifiers (oil palm examples) are in parentheses.
Figure 4
Figure 4. Expression of Shell in early oil palm fruit
Longitudinal sections of 1 WAA Dura fruit (a, b) and cross sections of 5 WAA pisifera fruit (c, d) were hybridized to a pool of two unique Shell locked nucleic acid (LNA) probes (a, c) or to a scrambled sequence LNA negative control probe (b, d). Colorimetric in situ hybridization probe detection is blue and all sections were counterstained red. The scale bar (0.8 mm) shown in panel b applies to all four panels. Structural hallmarks of fruits are indicated by labeled arrows in panels a and c.

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