Jul 24 2012

The Banana Genome

Published in Nature this month is a report of the entire genetic sequence of Musa acuminata – the Cavendish banana. The banana is the most popular fruit in the industrialized world. Banana varieties are also an important staple crop in much of the world. The Cavendish, however, is threatened by two fungal infections – Panama disease and black leaf streak disease. Hopefully knowledge gained from the banana genome will lead to new varieties of acuminata that are resistant.

Part of the problem is that the Cavendish is a highly cultivated variety. Starting about 7,000 years ago the banana was cultivated by hybridization of various varieties. Interestingly, most acuminata varieties are triploid, meaning they have three copies of each chromosome, while some are diploid with two copies. Diploid and triploid varieties were hybridized together.

One trait in particular that was selected for was being seedless. Most banana varieties contain numerous large seeds. The Cavendish has none, which makes it an attractive variety as a dessert fruit. However, this also means that there is no longer any sexual recombination within the Cavendish variety. Every Cavendish banana  plant (representing about half of all bananas in the world) is a somaclone derived from the single variety. A somaclone refers to a plant derived ultimately from a single somatic parent cell. This means that every Cavendish banana plant is virtually identical genetically to every other. They are not strictly identical because somaclone variability is possible through spontaneous somatic mutations.  But variation is minimal.

The same it true, by the way, in some other cultivated plants, such as grape vines. Vines can be spread by taking a cutting from an adult vine, resulting in a somaclone.

While this may be efficient for industrialized production, having plant cultivars that are largely somaclones has one huge significant downside – the lack of genetic diversity. This means that pests and diseases have the opportunity to evolve to highly efficiently infect and infest the somaclone variety. The Cavendish banana industry is a huge evolutionary opportunity for any fungus, for example, that evolves traits that allow it to infect this common plant. That is exactly what is happening.

This issue goes beyond bananas and even somaclone varieties. Humans have cultivated many species of plants, and those cultivars that have the most desirable traits (including being the most profitable) have tended to predominate. This is happening at the expense of local varieties. As genetic diversity of cultivated plants decreases, they are more susceptible to diseases and blight. This is a serious threat to the sustainability of our crops. Bananas may be the most vulnerable at the moment, but they are not alone in being threatened by disease.

There are possible solutions, however. One easy solution (meaning it does not require any technological or scientific advances) is simply protecting local varieties of cultivated plants. We may need to pay a little extra for these varieties, but it is an important hedge against crop blight.

Sequencing the banana genome is part of a high tech approach to the problem. If somaclones do not contain much genetic diversity, then perhaps we can generate that diversity ourselves. We can cultivate or genetically engineer new varieties to increase genetic diversity, and specifically to provide resistance to emerging threats like Panama disease. Researchers, for example, and sequences DH-Pahang variety of Musa acuminata, an ancestral variety to the Cavendish. DH-Pahang is resistant to the fungal diseases that threatens the Cavendish. If researchers can identify the genes responsible for this resistance and introduce them back into the Cavendish variety, that could result in a new variety that is also resistant.

This may prevent history from repeating itself. A century ago the primary commercial banana variety being shipped to industrial nations was not the Cavendish but the Gros Michel. This was a larger, creamier, and by all accounts better variety of M. acuminata than the Cavendish we have today. It was wiped out (not extinct, but not commercially viable) by the early 1960s, and was replaced with the Cavendish. We got 50 years out of the Cavendish, but now it may go the way of the Gros Michel if it’s not saved.

Perhaps, with some genetic tweaking thanks to the knowledge gained from sequencing the M. acuminata genome, scientists can not only save the Cavendish but bring back the Gros Michel, newly resistant to the fungus that previously wiped it out. That would be something. I have never tried a Gros Michel. Perhaps one day I will be able to buy them at the local supermarket.

Of course, any genetic tweaks we make now will only be a temporary solution, as the fungi are not likely to give up but will continue to evolve and spread in an evolutionary arms race. Long term it seems we need to reverse the practice of depending upon very few cultivars for most of our food production. We need to build greater genetic diversity back into our plant production on a large scale.

 

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19 responses so far

19 Responses to “The Banana Genome”

  1. DevoutCatalyston 24 Jul 2012 at 8:42 am

    Build a hardy banana and grow it nearer the point of sale. Become a charter member of the Connecticut Banana Growers Association and perhaps wave goodbye to tropical fungi.

  2. shawmutton 24 Jul 2012 at 9:28 am

    Obviously the atheist’s worst nightmare. I don’t know if I heard about it on the SGU or another podcast, but there’s a whole book on the history of the banana called “Banana: The Fate of the Fruit That Changed the World”.

  3. ConspicuousCarlon 24 Jul 2012 at 11:56 am

    Sequencing the banana genome is part of a high tech approach to the problem.

    It’s also part of the low-tech solution if we want to be sure that any two specific local varieties actually are different in any non-cosmetic way. Then we can avoid unnecessary localization and for all we know maybe also find non-visible variations which we otherwise wouldn’t know to separate.

  4. Steven Novellaon 24 Jul 2012 at 12:43 pm

    I’m actually growing a wild banana plant in my back yard. It’s pretty fun – they grow fast. I’ve been reading about how to care for and propagate banana plants – very interesting, and a bit complicated. Hopefully I will have my first fruit by the Fall, if not then maybe next Spring. I’m still tweaking the fertilizer, watering schedule and now I have to deal with the suckers. Apparently there are three different kinds. I need to identify the proper one to propagate, which ones to get rid of immediately, and which one to leave behind to replace the spent plant after fruiting. Ack.

  5. ConspicuousCarlon 24 Jul 2012 at 1:16 pm

    Please be careful. Every time produce mutates into self-awareness and acquires a taste for human blood, it’s always because some guy plucked the wrong shoot.

  6. ChrisHon 24 Jul 2012 at 3:05 pm

    Dr. Novella:

    I’m actually growing a wild banana plant in my back yard.

    I’m attempting to grow two Improved Meyer’s Lemon trees on my deck. I have had issues with just keeping them alive between outside weather and inside pests (spider mites and aphids). Right now one has grown back all of the leaves that fell off when it was inside but it has no fruit, and the other has yellowing leaves that are falling off and is covered in blossoms (which is common with a stressed plant).

    If I make it to TAM next year, I may start talking to you about adventures in gardening.

  7. SARAon 24 Jul 2012 at 3:20 pm

    When I first learned about this banana crisis I was sort of shocked. I assumed, foolishly, that different parts of the world were eating different types of bananas.

    I grew up in Puerto Rico. We grew banana trees in the backyard. I think it was a local variety, because you could buy the same thing in the grocery. You could also get “normal” bananas. The local variety were small, fatter, and very sweet. Cavendish are amazingly bland compared to them. We called them apple bananas, but I have no idea what they were really called. When we moved back to the States I looked in vain for those bananas.

    It seems to me that from a marketing point of view, developing a large variety of bananas would be a good thing for the Chiquitas of the world. The populations of Industrial Nations revel in finding subtle and overt variations in their food choices. Think coffee, apples, beer, wine….Proper marketing would support the science of variation in the banana.

  8. BillyJoe7on 24 Jul 2012 at 5:29 pm

    “Every time produce mutates into self-awareness …”

    Haven’t you heard? They already are. Even the lowly bacteria are self-aware. They purposefully get together to plan their attack on their human victims and party afterwards in an orgy of self-congratulation.

    http://mic.sgmjournals.org/content/151/3/637.full

  9. Steven Novellaon 24 Jul 2012 at 5:36 pm

    Yeah – I never understood why there were so many varieties of apples, pears, oranges, grapes, etc. – but only one banana (before I realized there are actually many kinds of bananas). But in the US there is one – because it is the only variety that ripens slowly enough after picking that it can be shipped around the world, and because it’s a somaclone.

    But I agree. It seems to me there is a huge incentive to develop cultivars of the Cavendish that would provide some variety in the market. I’m assuming that it’s difficult for some reason. Perhaps now the process will be easier with the genome sequence.

  10. HHCon 24 Jul 2012 at 5:45 pm

    I like the baby bananas from Equador.

  11. sonicon 24 Jul 2012 at 6:35 pm

    It does seem that having genetic diversity is a good way to assure future food supply.
    I have two gardens now– one that feeds just two– the other is good for 5 now, we are expanding it for 20 people.
    When I plant I usually plant a few different cultivars of each food. Some years one cultivar will do well and another not so well. The next year it might be the other way around.
    What is odd is that the cultivars that do well in one garden one year might be the ones that do poorly in the other garden that year… and the gardens aren’t very far apart.
    So from a personal experience kinda deal– genetic diversity is a good way to assure food production.
    This is a big deal in the farm world now– if you want to support this you can buy ‘heirloom’ cultivars (heirloom in this case means ‘breeds true’… a special definition).

    Dr.N.-
    good luck with the bananas.

  12. ChrisHon 24 Jul 2012 at 6:54 pm

    A century ago the primary commercial banana variety being shipped to industrial nations was not the Cavendish but the Gros Michel. This was a larger, creamier, and by all accounts better variety of M. acuminata than the Cavendish we have today. It was wiped out (not extinct, but not commercially viable) by the early 1960s, and was replaced with the Cavendish.

    I wonder if they could find some of Gros Michel bananas if they could also get its genome, and use it to create another slow ripening tasty banana that can be shipped.

  13. Mlemaon 24 Jul 2012 at 7:00 pm

    decreased diversity threatens the world’s agriculture. Monsanto, the biggest global threat to plant diversity, needs to be reined in.

    http://www.ucsusa.org/food_and_agriculture/science_and_impacts/impacts_genetic_engineering/eight-ways-monsanto-fails.html

  14. davewon 25 Jul 2012 at 9:54 am

    In Hawaii once I got to sample a few different kinds of bananas. One was 1/3 the size of the Cavendish, dark brown when ripe, and utterly delicious.

  15. Pjaypton 25 Jul 2012 at 1:27 pm

    “Obviously the atheist’s worst nightmare. I don’t know if I heard about it on the SGU or another podcast, but there’s a whole book on the history of the banana called “Banana: The Fate of the Fruit That Changed the World””

    I found this very fruitful:

    http://www.scientificamerican.com/podcast/episode.cfm?id=7BA7726C-EBE6-29DB-B21F7FF464B293E9

    I should warn I went bananas after hearing this podcast! :-)

  16. ccbowerson 26 Jul 2012 at 12:28 am

    “Yeah – I never understood why there were so many varieties of apples, pears, oranges, grapes, etc…”

    One obstacle is the price of bananas. Per pound they are among the least expensive fruit in a supermarket. In the US, bananas are primarily eaten as a sweet fruit, so many bananas which are starchier (plantains) are really a different type of food altogether, as they are eaten and cooked more like potatoes or sweet potatoes. Introducing a new type of sweet banana is difficult, because the marketing would need to find an angle to overcome the initial hesitation of trying something new plus the need to justify a higher price for something viewed traditionally as an inexpensive food.

    The large number of apple varietals that have become popular lately have had names with marketing in mind, but they differential themselves by various attributes: crisp versus soft, sweet versus tart, and various flavor characteristics, depending on personal preferences- or if needed for cooking applications. Bananas are not viewed as having distinguishing characteristics in the US, because there is really only one sweet banana type widely available.

  17. BillyJoe7on 26 Jul 2012 at 6:30 am

    Do you have Lady Finger bananas in America?
    They are about the best tasting of all the Australian varieties.

    http://www.australiantropicalfruits.org.au/tropical_fruits/produce_types/banana/lady_finger/

  18. DevoutCatalyston 26 Jul 2012 at 7:47 am

    BillyJoe7, my local grocer says they’re available, but they don’t sell well here. Go figure. Hobbyists have access to all manner of banana varieties in the USA,

    http://going-bananas.com/bananaplantdescriptions.htm

  19. ccbowerson 26 Jul 2012 at 11:35 pm

    One chain of supermarkets where I live in upstate New York carries those small thin skinned sweet bananas that come in a semicircle bunch, which I believe are the lady finger type you are refering to, but it is an exceptional supermarket and isnt probably representative of the US in general. Other more typical grocer stores or supermarkets do not carry this type. I tried them several years ago and did not notice a significant difference other than size and skin thickness. Perhaps I will try them again

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