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The oil palm SHELL gene controls oil yield and encodes a homologue of SEEDSTICK

Nature volume 500, pages 340–344 (2013)Cite this article

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Abstract

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.

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Figure 1: Fruit forms of the African oil palm Elaeis guineensis.
Figure 2: Homozygosity mapping of the shell trait.
Figure 3: Sequence diversity of SHELL.
Figure 4: Expression of SHELL in early oil palm fruit.

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Accession codes

Primary accessions

GenBank/EMBL/DDBJ

Data deposits

E. guineensis and E. oleifera genome sequences have been deposited at DDBJ/EMBL/GenBank under the accessions ASJS00000000 and ASIR00000000, respectively. Gene sets are available at http://genomsawit.mpob.gov.my.

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Acknowledgements

We thank J. Jansen for assistance with JoinMap, and Beijing Genome Institute, The Genome Institute at Washington University, Tufts University Core Facility and the Arizona Genome Institute for mapping and genome sequencing. We thank Kulim, Sime Darby, FELDA Agricultural Services, United Plantations and Applied Agricultural Resources for providing materials and phenotype information of individual palms. Phylogeny, Inc. performed in situ hybridization services. Creative Biolabs performed yeast two-hybrid co-transformations and interaction assays. We thank J. Birchler and Z. Lippman for discussions on hybrid vigour. We appreciate the constant support of Y. M. Choo, and the Ministry of Plantation Industries and Commodities, Malaysia. The project was endorsed by the Cabinet Committee on the Competitiveness of the Palm Oil Industry (CCPO) and funded by the Malaysian Palm Oil Board. R.A.M. is supported by a grant from National Science Foundation 0421604 ‘Genomics of Comparative Seed Plant Evolution’.

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Authors and Affiliations

  1. Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia,

    Rajinder Singh, Eng-Ti Leslie Low, Leslie Cheng-Li Ooi, Meilina Ong-Abdullah, Ngoot-Chin Ting, Jayanthi Nagappan, Rajanaidu Nookiah, Mohd Din Amiruddin, Rozana Rosli, Mohamad Arif Abdul Manaf, Kuang-Lim Chan, Mohd Amin Halim, Norazah Azizi & Ravigadevi Sambanthamurthi

  2. Orion Genomics, 4041 Forest Park Avenue, St Louis, 63108, Missouri, USA

    Nathan Lakey, Steven W. Smith, Muhammad A. Budiman, Michael Hogan, Blaire Bacher, Andrew Van Brunt, Chunyan Wang & Jared M. Ordway

  3. Howard Hughes Medical Institute–Gordon and Betty Moore Foundation, Cold Spring Harbor Laboratory, Cold Spring Harbor, 11724, New York, USA

    Robert A. Martienssen

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  1. Rajinder Singh
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Contributions

R.S. initiated work on the SHELL marker/gene. R.S., E.-T.L.L., M.O.-A. and R.S. conceptualized the research programme. R.S., E.-T.L.L., M.O.-A., R.N., M.A.A.M., N.L., S.W.S., J.M.O., R.S. and R.A.M. developed the overall strategy, designed experiments and coordinated the project. R.A.M. conceptualized the homozygosity mapping strategy. R.S., R.N. and R.A.M identified samples for homozygosity mapping. R.N. and M.D.A. developed and maintained the mapping population and assisted in phenotyping. R.S., M.O.-A., L.C.-L.O., N.-C.T., J.N., N.L., M.A.B., B.B., A.V.B., C.W., J.M.O. and R.S. conducted laboratory experiments and data analyses. R.S. and L.C.-L.O. constructed the genetic map. E.-T.L.L., R.R., K.-L.C., M.A.H., N.A., S.W.S., M.H., A.V.B. and C.W. performed bioinformatics analyses. N.L., A.V.B., C.W., J.M.O., R.S. and R.A.M. resequenced the candidate gene and characterized the mutations. R.S., E.-T.L.L., M.O.-A., R.N., N.L., S.W.S., J.M.O., R.S. and R.A.M. prepared and revised the manuscript.

Corresponding authors

Correspondence to Rajinder Singh, Ravigadevi Sambanthamurthi or Robert A. Martienssen.

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Competing interests

R.A.M. is a consultant for Orion Genomics, LLC.

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Singh, R., Low, ET., Ooi, LL. et al. The oil palm SHELL gene controls oil yield and encodes a homologue of SEEDSTICK. Nature 500, 340–344 (2013). https://doi.org/10.1038/nature12356

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