Category: DNA

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“It is silly to think of one solution”

Johan Schut pulled a folding knife from his hip pocket, inserted the tip into the base of a bright, crispy head of romaine lettuce and severed it in two.

“See there, the little brown specks with black legs?” He lifted one of the busy beasts onto the tip of his blade. “It’s a family of aphids. This is a non-resistant lettuce.”

Gotta love the New York Times ledes (as we ex-reptiles call them). This one certainly got me reading, and probably would have done even if I weren’t interested in “entrepreneurs and scientists [who] are trying to use all available techniques, including genetic modification, to improve agriculture around the world.”

It’s all there; cisgenesis, AFLP and MAS, arms races, private-public partnerships, options up the wazoo. Go Wageningen!

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Nibbles: Climate, Money, Wine, Rice, Photosynthesis, Diversity

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It’s been a good week for the genomes

Cucumber. Tomato. Pig. Horse. A veritable cornucopia of crops and livestock. And from it will doubtless emerge fascinating scientific insights.

  • “[H]orses have a newly forming part in their genetic make-up which shows the evolutionary process in action in a way that has not been seen before.”
  • “[N]ew research applications and innovations at many points in the pork chain.”
  • “[F]ar more is going on in the phloem than anybody … had previously expected.”

(The tomato is just an advanced map; no giant claims there, yet.)

This is really important science, no doubt about it. But I’d like to see a moratorium on claims that any of this is going to improve anybody’s food security. It hasn’t, yet. And personally I doubt that it ever will, but maybe that’s just me. I bought into the dream along with everyone else. Back in 1982 I agreed that cereals would fix their own nitrogen, that photosynthesis would be rejigged to become more efficient, that seed storage proteins would be made more completely nutritious.

The thing is, cereals don’t need to be engineered. It might help, but it hasn’t happened yet and in the meantime legumes are there to take up the slack. Changing C3 plants into C4 plants hasn’t happened yet either, and one has to wonder how much it will help poor farmers in the hot environments that make C4 more efficient. Seed storage proteins have been rejigged; Monsanto built a high-lysine maize, but it vanished more or less without trace because conventionally-bred high-lysine maizes are far cheaper and more attractive to the small-scale farmers who really need better nutrition. Nobody back then was too worried about drought or flooding; tolerance to submersion has now been engineered into rice and could be useful.

Overall, though, I wonder how much more progress might have been made had “ordinary” plant breeding been as easy and attractive as messing about with DNA directly. I also wonder how many surprises like this one are in store:

Indirect costs of a nontarget pathogen mitigate the direct benefits of a virus-resistant transgene in wild Cucurbita

Translation: Transgenic squashes — and almost all of them being grown commercially in the US and Mexico are transgenic — are protected from zucchini yellow mosaic virus. Plants that carry the resistance genes suffer considerably more wilt disease as a result. Hey ho, let’s see if we can add wilt resistance to the mix, shall we?

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Lost apples found

ResearchBlogging.org It is an incontestable fact that of 7100 named varieties of apples grown in the United States in the 1800s, 6800 are extinct, “no longer to be seen again” according to Cary Fowler.

Or, maybe not.

A press release gives an insight into a study on the Identification of Historic Apple Trees in the Southwestern United States and Implications for Conservation. ((Kanin J. Routson, Ann A. Reilley, Adam D. Henk, & Gayle M. Volk (2009). Identification of Historic Apple Trees in the Southwestern United States and Implications for Conservation Horticultural Science, 44, 589-594)) The bad news is that 11 varieties now account for 90% of all apple sales in the US, with 41% down to a single variety. The good news is that apple trees can live to a good old age, and if the land they’re on isn’t needed for anything else, old trees can still be found.

Kanin J. Routson of the University of Arizona and Ann A. Reilley, Adam D. Henk and Gayle M. Volk at the USDA’s National Center for Genetic Resources Preservation looked at 280 apple trees growing in 43 historic farmstead and orchard sites in Arizona, Utah, and New Mexico. They compared DNA from those trees to 109 known apple varieties that were introduced to the American southwest around the end of the 19th century. The 280 samples harboured 144 different genotypes, 34 of which could be identified with known varieties introduced by commercial nurseries and the USDA. Those 34 covered 120 of the trees. That left 160 trees, and 110 genotypes, with “unique fingerprints that did not match any of the fingerprinted cultivars”.

Of course, some of the unidentified varieties might still be traceable to varieties held in the USDA Apple Collection, not all of which have been DNA fingerprinted. Others could well be seedlings, kept because people valued their fruits. A close look at their fingerprints might reveal parentage. But some, surely, are bound to be lost varieties that once had names. As DNA sequencing becomes cheaper and cheaper, one could hope that even herbarium specimens would be put into the line-up to see whether any of the lost varieties are actually alive and well and holed up somewhere in the American southwest.

Stop Press: Yesterday’s New York Times editorialised on the same subject.

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Nibbles: Climate change, Papaya sex, Inheritance, AGCommons