Category: DNA

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Potato salad

I don’t know if it’s because of the International Year of the Potato, but there’s been a fair amount on the spud in the news lately. I nibbled a few days ago news of a paper which will cause a major rethink on the worldwide spread of the potato. Virtually all modern potato varieties are derived from landraces from the lowlands of southern and central Chile. Why? Some people think it’s because those are the first ones that arrived in Europe. Others that there were also highland Andean varieties in Europe, but that they got wiped out by late blight. But analyzing DNA from old herbarium specimens shows that both types of potatoes were grown in Europe both before and after late blight hit. So a new theory is needed.

Then there was a short piece on the CIP collection in LatinAmericaPress. Note the cool picture of diversity in the colour of potato flesh. I’m not sure what prompted the article, but it may have been a CGIAR press release on how the international centres, including CIP, are sending germplasm for safety duplication in Svalbard in time for the opening in three weeks’ time.

CIP was also in the news with the announcement of the establishment of Red Latinpapa. That’s the Latin American Network for Innovation on Potato Improvement and Dissemination. Its “aim is to help poor potato farmers in Latin America improve their income and reduce costs by making it easier for them to access new technologies and varieties and getting their input into what traits are most useful.” Among other things, “Latinpapa will stimulate exchange and analysis of genetic material between researchers in the region.” A busy time ahead for the CIP genebank, and national genebanks around the region, I guess.

And finally, a bit of fun. Remember the picture of sliced potatoes in the LatinAmericaPress article showing lots of different colours and patterns? Of course, because of the relatively narrow base of modern potato varieties, as described in that USDA paper I started with, we don’t get potato chips (crisps for the Brits among us) in all these different colours. Bummer.

But maybe we will soon. Someone in Switzerland is indeed working on a blue chip. But in fact mixtures of blue and white chips are already commercially available in the US. Although they “have a weird flavor that is not quite potato.” Sounds intriguing…

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Soybeans and its bottlenecks (or lack of them)

All too often crop genetic diversity studies — even ones published in peer-reviewed journals – are not really testing a clearly set out hypothesis. Markers are chosen and scored for each accession in a germplasm collection, and that’s basically it. Oh sure, estimates of various genetic parameters for the collection as a whole are provided, and there are dendrograms aplenty to illustrate the relationships among accessions. Which is fine, that sort of information can be useful. But one sometimes wishes that more focused questions had been asked — and answered.

Which is why recent work on soybean from USDA and visiting scientists from China and Korea is so interesting. I saw it reported in the February issue of Biodiesel magazine, but the original news item goes back to late last year. What the USDA team did is not just fingerprint material from the 17,000-strong USDA Soybean Germplasm Collection maintained at Urbana, Illinois and publish a nice dendrogram showing how Chinese accessions are related among themselves and to Korean ones, for example. ((Although someone probably did that as well!)) They defined four distinct sets of germplasm, each of which was derived from the one before, and tested the specific hypothesis that each process of derivation caused significant narrowing of genetic diversity, i.e. was associated with a “genetic bottleneck.” The sets of material were:

  1. 26 accessions of wild soybeans 
  2. 52 Asian landraces derived from them
  3. the 17 Asian landraces introduced to the US in the 20th century
  4. 25 elite modern cultivars which have been bred from them

What they found is that genetic diversity (as measured by gene sequencing) in wild soybeans was much greater than in landraces, which is fair enough. Most crops go through a very strong genetic bottleneck at domestication. What was more surprising is that the loss of genetic diversity caused by the introduction of only a few landraces to North America, followed by intensive breeding, amounted to only about 25%. This was much less than expected. The genetic base of US soybeans is narrow, yes, but not that narrow, it turns out.

What this means is that randomly introducing more landraces into soybean breeding programmes will not be very effective. The authors suggest that landraces should instead be carefully selected from the Urbana collection based on what the specific breeding objectives are at any one time. So, if breeding for resistance to the Asian aphid is the aim, landraces from areas of Asia where this pest is found should be the ones to be thawed out of genebank and crossed with the elite material.

All very logical. But I wonder. Was all that gene sequencing really necessary to reach this conclusion? I mean, wouldn’t you want to be somewhat selective in the landraces you introduce into a breeding programme even if the genetic base of the crop had been narrower? Maybe a breeder will help me out here. But anyway, it was good to see a real hypothesis of practical significance clearly set out and tested through specific comparisons in a crop molecular diversity study.

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Pussy Galore

A paper appeared in Science last year which used mitochondrial DNA and microsatellites to determine the geographic origin of the domesticated cat. We blogged about it back in June, albeit briefly. The major conclusion was that the cat was domesticated once, in the Fertile Crescent, about 9000 years ago, at about the time that agriculture started to take off. A paper just out in Genomics now takes the story on from there, by looking in more detail at the relationship among pure breeds and random-bred local populations from all over the world. ((Monika J. Lipinski, Lutz Froenicke, Kathleen C. Baysac, Nicholas C. Billings, Christian M. Leutenegger, Alon M. Levy, Maria Longeri, Tirri Niini, Haydar Ozpinar, Margaret R. Slater, Niels C. Pedersen and Leslie A. Lyons. (2008) The ascent of cat breeds: Genetic evaluations of breeds and worldwide random-bred populations. Genomics 91:12-21. doi:10.1016/j.ygeno.2007.10.009))

Using microsatellites, which are best suited to resolving more recent changes in genetic diversity, the authors of this latest study tried to reconstruct what happened when domestic cats left their Middle Eastern cradle and spread all over the world, presumably with the first agriculturalists and then with merchants and other travellers. It turns out that the diversity of the genepool has not decreased much overall during the past several thousand years. But it has fragmented. So now you have quite genetically differentiated groupings among the world’s cats: in the Mediterranean, Western Europe (+ the Americas), Asia and East Africa. The Asian group is particularly interesting, being the most distinct and the one with the most internal patterning. This shows that cats went to Asia early, and became relatively isolated there, from the rest of the world and from each other. ((Don’t I remember something similar for wheat? Must look it up. Later: ok, it was barley.))

There’s interesting stuff in the paper on the relationship among pure-bred breeds. They’re apparently mostly relatively young (less that 150 years old), and there’s not really that many of them (41 are recognized by cat enthusiasts), certainly compared to dogs and livestock like cattle and sheep. And it seems they’re all derived from 16 so-called “foundation” breeds, such as the Persian, for example. These in turn mostly — there are some exceptions — originated from random-bred cats from their region of origin, i.e. Persia, in the case of the Persian. Unsurprisingly, the development of pure-bred breeds from local common-or-garden cats has been associated with a narrowing of genetic diversity. And with the accumulation of deleterious mutations. It’s only in pure-bred cats that genetic disorders have been spotted. This study should lead to better plans for breed management, that could avoid such problems, the authors hope.