Category: DNA

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The diverse uses of genebank collections

It’s easy to assume that it’s only plant breeders that use genebank collections. But in fact there are clever people out there who are delving into genebanks for all kinds of different reasons. Two recent articles on rice illustrate this nicely.

In the latest Rice Today Tom Hargrove tells the story of the global odyssey of the rice varieties called Carolina Gold and White.

Carolina Gold and White show how genes of good crop varieties spread. The seeds made a remarkable journey: from Indonesia to Madagascar by boat almost 2,000 years ago, then to the wealthy and slave-driven Carolina plantations. Her seeds seem to have helped war-weary Confederate veterans start a new life along the Amazon in South America. Freed slaves may have taken her seeds back to Africa, which she once called home. Carolina Gold recently started a new life in South Carolina, and her white-hulled sister is a parent of an improved variety for upland rice farmers in Colombia and Panama.

Hargrove describes how it was by comparing contemporary seeds with genebank samples that part of that epic story was pieced together, and how it was from genebank samples that Carolina Gold cultivation was revived, albeit it on a much smaller scale, in the State which gave it its name, after almost a hundred years.

Meanwhile, EurekAlert has a piece on another famous, though rather more modern, rice variety: IR8. One of the Green Revolution varieties,

IR8 used to produce 9.5 to 10.5 tons per hectare, significantly more than other varieties in the 1960s when average global rice yields were around only 2 tons per hectare. But, when grown today, IR8 can yield only around 7 tons per hectare.

Why? Is it nature or nurture? Researchers “grew rice from original IR8 seeds preserved in the International Rice Genebank and compared it to rice grown from IR8 seeds continuously grown and harvested over the last few decades.” Genetically, they were found to be similar, so the 15% decrease in yield must be down to environmental changes, possibly including hotter nights:

the findings demonstrate the need for ongoing or “maintenance” breeding because it allows rice plants to cope with a changing environment.

So, even when genebank accessions are not used by breeders, the results can end up being of use to breeders.

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Nibbles: Musa wild relative, Soil biodiversity, Wild sorghum hybrids, Millet diversity, Bees, Garlic core collection, Heirloom seed saving, Nutrition, Fungal conservation, Sacred places

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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.