Category: DNA

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Who to believe?

RSS feeds can be pretty unforgiving, capturing those momentary lapses that not even the fastest fingers can recover. Take, for example, Exhibit A, pictured below. (Click to embiggen.)

Someone clearly thought better about the “fact” that a genetically modified cowpea (“actually a bean”) could generate US$1 billion for small farmers. So it got downgraded to a claim by scientists ((And we all know how unreliable they are.)) that will still deliver US$1 billion … without specifying to whom exactly.

The story? Oh, you don’t want to bother with that.

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Nibbles:Collecting missions, Grapes, Beans, Genome, Local markets, Water

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Insights into watermelon genetic diversity

ResearchBlogging.org There’s no doubt that most of the time when we non-experts think of genetic diversity in DNA terms, we think about alterations in the actual DNA sequence. Change the genetic code and there’s a chance you change the nature of a gene and as a result change the outward appearance, the phenotype, of an organism. There have been lots of studies relating the differences among species to differences in the DNA code of this sort, but far fewer looking at the differences among varieties of a single species. Amnon Levi and his colleagues looked at the sequence differences among heirloom watermelon varieties and were surprised by the lack of diversity. Despite the fact that heirloom watermelons differ in highly complex ways in a whole slew of traits, ((Parris, 1949, is the motherlode on this, if you can get it.)) Levi and colleagues concluded that “there is a very narrow genetic diversity at the DNA sequence level”.

There are, however, other sources of variation that are not reflected in the DNA sequence. Once such is methylation, the attachment of a methyl group to two of the four letters that make up the genetic code. Methylation is closely involved in whether a gene is active or not, and the same gene with two different methylation patterns in two different individuals can be expressed differently, resulting in different phenotypes despite genotypes that are similar in sequence (though obviously not in methylation). Methylation patterns are inherited, but they are not strictly speaking genetic; they are one kind of epigenetic inheritance.

Levi and his group turned their attention to the methylation pattern of 47 watermelon varieties. ((Not including, alas, the famed Moon and Stars watermelon.)) The epigenetic diversity varied from 16-43%, while diversity measured by conventional DNA sequence markers ranged from 3-20%. “Diversity at the methylation level is three times higher than the genetic diversity revealed by DNA markers on the same set of heirloom DNAs,” the authors conclude. ((Nimmakayala, P., Vajja, G., Gist, R., Tomason, Y., Levi, A., & Reddy, U. (2010). Effect of DNA methylation on molecular diversity of watermelon heirlooms and stability of methylation specific polymorphisms across the genealogies Euphytica DOI: 10.1007/s10681-010-0259-z)) The vast majority of methylation patterns are inherited stably from the variety’s parents, with very few arising fresh.

The bit I really do not understand in all this is the extent to which the relationships among varieties deduced from methylation patterns match those derived from DNA sequence differences. The new paper and one from 2001 both contain tree diagrams of the relationships, but there is no direct comparison. ((I’m not even sure if that is doable.)) Eyeballing the trees, and looking only at the nearest neighbours, the overlap does not seem all that impressive. I’d like to know more.

That 2001 paper also uses the low genetic diversity (at the DNA sequence level) to argue for “the need to broaden the genetic base of cultivated watermelon”. That idea seems to have fallen by the wayside as the diversity in epigenetic factors has emerged. Is there a more general conclusion to be drawn?

This observation of greater methylation than DNA sequence differences adds to the growing importance of epigenetics in studies of diversity, and may become important in breeding new varieties with specific desired traits. If the methylation patterns can be linked to phenotypic traits, as has already been shown in Arabidopsis, it could be possible to alter methylation without needing to do crosses and selection.

Bonus factoid: “Watermelon is the fifth most economically important vegetable crop and is grown in 44 states in the United States.”

Bonus hint: Don’t go searching Google images for “watermelon diversity”. You’ll likely be disgusted.

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Getting the most out of wild tomatoes

ResearchBlogging.orgWhere should breeders look for traits like drought resistance among the landraces and wild relatives of crops? The FIGS crowd says: in dry places, of course. And they have a point. But it may not be as simple as that, as a recent paper on wild tomatoes shows. ((XIA, H., CAMUS-KULANDAIVELU, L., STEPHAN, W., TELLIER, A., & ZHANG, Z. (2010). Nucleotide diversity patterns of local adaptation at drought-related candidate genes in wild tomatoes Molecular Ecology DOI: 10.1111/j.1365-294X.2010.04762.x))

The authors looked at the diversity of two genes implicated in drought tolerance, nucleotide by nucleotide, in three populations of each of two closely related wild tomato species from the arid coastal areas of central Peru to northern Chile. Annual precipitation at the collecting sites ranged from 5 to 235 mm. As another recent paper put it, the tomato genepool “has both the requisite genetic tools and ecological diversity to address the genetics of drought responses, both for plant breeding and evolutionary perspectives.” Here’s where the populations came from: 1-3 are Solanum peruvianum, 4-6 are S. chilense.

These places are pretty dry. Here’s what a close-up of the driest (number 3) looks like:

Anyway, Hui Xia et al. found evidence of purifying or stabilizing selection at one gene, called LeNCED1. So far so good. But they also found a pattern of variation at the other gene, pLC30-15, in one of the populations (number 4, S. chilense from Quicacha in southern Peru) which they interpreted as evidence of diversifying selection, where “two alleles compete against each other in the fixation process.”

Now, that would arguably be a more interesting population for a breeder to investigate than any of the others, but the observation “is difficult to explain based on the environmental variables of the populations investigated.” Ouch, say the FIGS crowd! ((Actually, it’s not as bad as that, that other paper I quoted earlier has this to say: “We confirmed that several eco-physiological traits show significant trait-climate associations among climate-differentiated populations of S. pimpinellifolium, including strong association between native precipitation and whole-plant tolerance to water stress.”)) But is it perhaps that the authors just considered average rainfall, and not how variable rainfall was at the site, from year to year? The best they can suggest by way of explanation is that S. chilense is an endemic with a very narrow ecological amplitude. In contrast, S. peruvianum is more of a generalist, with larger, expanding populations, found in both dry and mesic locations: “this may not be favourable for the occurrence of adaptive evolution, either because phenotypic plasticity can be promoted rather than local adaptation or because beneficial mutations are more likely recruited from the higher genetic standing variation.”

So, target dry areas for adaptation to drought tolerance, by all means, but the environment is not all, and some wild species may be more useful than others in providing interesting diversity depending on their ecological strategies and population dynamics.

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Cattle’s great adventure

ResearchBlogging.orgEvolutionary Anthropology has a nice paper summarizing the history of domestic cattle, based on the latest molecular marker data. ((Ajmone-Marsan, P., Garcia, J., & Lenstra, J. (2010). On the origin of cattle: How aurochs became cattle and colonized the world Evolutionary Anthropology: Issues, News, and Reviews, 19 (4), 148-157 DOI: 10.1002/evan.20267)) Unusually, the authors at least attempt a flowing account of the origin and spread of a domesticated species, and even more unusually actually achieve it in places. Alas, the details of haplogroups and mtDNA vs Y-chromosome markers will keep intruding. Someone will write a review paper some day which gets the geeky stuff of summarizing all the molecular and other data out of the way upfront, and then just tells the story of domestication and dispersal as the old-fashioned, and no doubt now out of fashion, narrative historians used to do. Rather than annoyingly mixing up the two.

Anyway, that story can be summarized for cattle in one map, and here it is:

Which is cool enough. But actually what stays in the mind — or, at any rate, my mind — is, as ever, the little things. Here are three that did it for me.

First, a rare attempt to link up genetic patterns in a domesticated species and the associated human population:

Four ancient Tuscan breeds all had haplotypes also found in Anatolia, near the sites of domestication. [This] … may indicate a secondary migration from Anatolia to Italy, [which] … would be in line with the classical accounts of Etruscans arriving in Italy from either Lydia or the isle of Lemnos. An Etruscan representation of cattle resembles the semi-feral Maremmana cattle in southern Tuscany. Interestingly, inhabitants of two small Tuscan cities with Etruscan origins also had southwest-Asian mtDNA signatures.

Second, a simple historical explanation for a fairly obvious feature of modern European cattle diversity, to wit, that there isn’t much of it in the Netherlands.

Seventeenth-century Dutch paintings show cattle with a large variety of coat colors. After three catastrophic rinderpest epidemics in the eighteenth century, cattle herds were repopulated by mass imports of black-pied cattle from the Holstein region.

And finally, the story of the Brazilian zebu herd, which caught my eye because of the reference to it in a recent Economist article.

This started during the nineteenth century with the purchase of a few animals and was followed by mass imports of Guzerat (1975), Gir (1890), and Ongole (1895, in Brazil denoted as Nelore) animals to improve the national herds. The same zebu breeds were also imported into the U.S. These imports consisted mainly of bulls. The percentage of animals with zebu mtDNA varies in Brazil from 37% in the Gir breed to 43% in the Nelore and 69% in the Guzerat breeds. As shown by the distribution of the indicine Y-chromosomes and microsatellite analysis, zebu bulls were crossed in several South American Criollo populations… Today, Brazil holds the largest commercial cattle population worldwide, with 200 million heads. Together with descendants of other indicine and taurine imports, Nelore make up the bulk of this intensively managed population.

You see what I mean about the geeky stuff interrupting the flow, right? Anyway, the particularly fun detail about this Brazilian zebu story is the fact that one Nelore bull, called Karvadi, “became the ancestor of thousands of Brazilian zebu cattle.” There’s a photograph of him in the paper, courtesy of the Archives of the VR Artificial Insemination Center, Araçatuba, and very handsome he is too.