Cacao Tree's Genetic Secrets May Bolster the Chocolate Supply

By Eliza Strickland | September 15, 2010 2:10 pm

cacaoIt’s the most delicious genetic breakthrough yet. A consortium led by Mars Inc., the company behind such treats as M&Ms and Snickers, has announced the rough draft of the cacao tree’s genome, and researchers say the information could lead to improvements in the chocolate supply.

While the scientists are just beginning to analyze the genome, understanding the tree’s innermost workings could lead to breeding programs for drought- or disease-resistant varieties, or even for trees that produce tastier or healthier cocoa. The consortium has put the data online at the Cacao Genome Database for use by any and all.

The tree, known officially as Theobroma cacao (meaning “food of the gods”), contains about 420 million DNA units, represented by the letters A, C, G and T. That is fairly small for a plant. The human genome has about three billion units. [New York Times]

In a strange twist, the quest for the cacao tree genome became a race between two companies that typically compete in the candy aisle of your local drug store, Mars and Hershey. According to a New York Times report, the Hershey-led research project has also finished a rough draft of the genome, but can’t discuss its work until a journal article is published.

The genetic data will be precious to those who cultivate and rely on the cacao tree, researchers say.

Despite its seeming ubiquity on newsstands, chocolate is reliant on a notoriously fragile crop that has been plagued by pests and disease. In the 1980s, Brazil was a top cocoa exporter. Then a fungus known as witches’ broom infected cacao trees and decimated the industry. [Time]

After that crash in the South American cacao market, production shifted to Africa.
Today, about 70 percent of the world crop is grown in West Africa, and several million small farmers depend on it for their livelihoods. Scientists say it might be possible to as much as quintuple the output of beans per acre in Africa through breeding that relies on genetic information. [New York Times]

Related Content:
Image: Wikimedia Commons
CATEGORIZED UNDER: Living World
  • Brian Too

    How did Africa escape the witches’ broom fungus?

  • news reader

    “Mars Inc. Cacao Genome Database claims Open Access, public domain: falls short”
    1 Comment – Hide Original Post
    This initially looked very promising: Mars, along with a number of collaborators (USDA, IBM, Clemson University Genomics Institute; Public Intellectual Property Resource for Agriculture at the University of California-Davis; National Center for Genome Resources; Center for Genomics and Bioinformatics at Indiana University; HudsonAlpha Institute for Biotechnology; and Washington State University), have sequenced the cacao genome and released it “Open Access” and “public domain” for the benefit of all, at a site called the Cacao Genome Project:
    McLean, VA –Today, Mars, Incorporated, the U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), and IBM released the preliminary findings of their breakthrough cacao genome sequence and made it available in the public domain.
    – From the Mars Inc. press release 15 September 2010
    A quote from the Independent article on the release (First rice, then wheat – now cocoa genome unravelled 15 Sep 2010) from one of the collaborators on the project:
    Professor Shapiro, a molecular biologist, said: “We thought: ‘Let’s put this in the public domain so everyone has free access to it for eternity’. It could be patented and it can’t be now. We have full open access.
    “public domain”

    “full open access”

    As this is data, we could also be talking about Open Data.

    Let’s take a look at how ‘open’ this Cacao Genome Project is by examining the fine print (of the license):

    In order to get access to the data, you have to get an account (no anonymous access; obligatory registration is pretty counter-Open Access and arguably not ‘public domain’). In order to get an account, you have to agree to a license.

    Registration & license

    From the license:
    The Provider is making available the information and data found in the cocoa genome databases for general information purposes for scientific research, germplasm conservation and enhancement such as plant breeding, technical training, general education, academic use, or personal use.
    Restricted use, appearing not to include commercial use. So more of a GPL-ish license as opposed to a BSD-ish license (before anyone calls me out, but I am not saying GPL is NOT commercial, just generally viewed as less commercial-friendly than BSD).

    Moving on:
    Anytime the User consults the data base through the cocoa genome database web site, he/she shall be bound to the same obligations under this IAA. Should the User store the information and data for future use he/she shall be bound to the same obligations under this IAA.

    The User shall not transfer the information referred to in this agreement, or any copy of them, to a third party without obtaining written authorization from the Providers which will only be provided subject to the third party user entering into this same IAA.
    Wow. That is particularly extraordinary. A WTF moment.

    Fortunately I didn’t agree to the license so I AM able to talk about it now.

    Not allowing third parties to see a license is inherently incompatible to the idea of Open Access, Open Source, Open Data and public domain.

    It is simply bizarre in these modern times.

    Moving on:
    The User shall not claim legal ownership over the information and data found in the data base nor seek intellectual property protection under any form over these information, data and data base. For clarity, the user agrees not to claim any of the sequences disclosed in these databases in any patent application.

    Translation: Don’t claim legal ownership, because we own the IP for the data AND the sequences, and (maybe) we will be claiming patents, etc some time in the future. I have not been able to find anything on the site to the contrary (see below ‘Deluded or Disengenuous’ below).

    Moving on:
    However, the foregoing shall not prevent the User from releasing, reproducing or seeking intellectual property protection on improved seeds or plants that may be developed using the information for purposes of making such seeds or plants available to farmers for cultivation.
    This appears to allow commercial use of the database (“make available” can include selling the seeds), which seeds to conflict with the earlier clause.

    Conclusion
    Clearly, this data set has not been released as Open Access and certainly not released into the public domain.

    Instead of Open Access or public domain, they have a restrictive license, which allows gated access for a restricted set of uses.

    They should therefore not be claiming Open Access or public domain for this data.

    Deluded or disingenuous?
    The “About” page of the Cacao Genome Project claims that the license is in place to defensibly block patents of the sequences. While this may be true, claiming an Open Access AND public domain release of the data is either disingenuous or deluded.
    Public access to the genome will be available permanently without
    patent via the Cacao Genome Database. Before viewing the data, users
    have to agree that they will not seek any intellectual property
    protection over the data, including gene sequences contained in the
    database. The Information Access Agreement allows any cacao breeders
    and other researchers to freely use the genome information to develop
    new cacao varieties. This allows for a level playing field and a
    healthy competitive environment that will ultimately benefit the
    sustainability of cacao production in the long term.

    ‘Free’ as in ‘beer’ they should have said.
    posted by Glen Newton at 10:30 AM on 17-Sep-2010

    newsreader said…
    Not only that, but during the first day of the website, it also stated that if you use the data you could not publish any articles with it until some unspecified time in the future, not that I would ever know what to do with it;) but someone out there must ….. so where does that leave them? but it changed the next day… so which version is accurate if you enter the first day…

    18 September, 2010 17:25

    https://www.blogger.com/comment.g?blogID=29304736&postID=57472949342457933&page=1&token=1284845116110_AIe9_BFjpN4aWvnACOt7I0MdbCdDb8jPLzdnPhPQMzHVJI_2GnJv5ff0R8FzI5R-ISxxGt0JZjXHXIBFIKuhN7RjAtbki-nja2qg5omupI01AKDmCM8Tp4aMD7mZJBDJDaTplO5gPw2gAU7ngKwMBsMQMJdcSf4vXaQcife6ZldkzwBN9FWFkTs8CNALFUu8cfKWuGwv-iItzK3mcFoXIw8MVCdCd3_nvSQzWPQTNY6uua6yPkctG9wgRUsjEQCk3PWhRiW6I8TXkB5PRZ_H3E98E-oasEnnj3LMc7gFfbOakbYG0Jp1QOsSUT0kgkRNuMBAPNffRWzKXNhUv9c-KQcIU4kKjWucbSA0jV5efkDj92h7KYYj040TKzPY7JstBeO970Kk33xKxCEE-gz4lZMx9wJZt2oHwh_EvpS68Un3e7Cikx9ms7XHU6xz_xJSgBN-8XS3rx5yepqJY1WEyi3iZVUdC_4lKO3TqYX63Wc4IBnvIpo3EVJaL75LehLvhq9pGuwBf9T-CtBdt2LBpUSej2-ASq40FVgQW4dBJR4D1kv5oi8acCMVoP-mLJv5j8mNsv5ZQfMBlafYgbB7r9MbJkxcE5wM1sTSI1EzobeD0_8au_LFhkgyQYW5ZOVp5iiciBed5HCXyzVMp7vHlDXrU_W92BL6RXdXUHxu3YFmDW1A9Btj93nl5vVv4aSUgC9pxe4loqO5

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