Category: DNA

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Genotyping Support Service

The CGIAR’s Generation Challenge Programme‘s mission is

To use advanced genomics science and plant genetic diversity to overcome complex agricultural bottlenecks that condemn millions of the world’s neediest people to a future of poverty and hunger

They’ve just announced a new service: the Genotyping Support Service. What will GSS do?

Here’s a sample of what our latest service offers: assessing proposals, hiring genotyping services from the best providers, taking care of the administrative hassles, ensuring the generation of high-quality data and training participating researchers to interpret and work with the data to optimise outputs. In this way, researchers get to use the technology right away, while also learning how to get the greatest mileage out of the technology, thus creating local capacity. As such, GSS contributes to GCP’s effort to support and motivate plant breeding ‘champions’ in developing regions.

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All cows are not equal

Cows produce milk, right? Its qualities vary among breeds, with creamy Jersey milk at one end and that skimmed milk cow at the other. And the quantity varies within a breed, which is how we got to the monster lactation machines that are the modern Friesian. But until this morning I had no idea that there was a distinct difference in the type of milk produced by cows within a breed.

Apparently, the major protein in milk, beta-casein, comes in two different forms, called A1 and A2 (original, huh). Some cows have both forms of casein in their milk, some only A1 and some only A2. (Students of genetics will want to know the ratios. I can’t seem to find them.) The A2 corporation, which has registered and trademarked A2 milkâ„¢, says that the A2 form is the original, and that at some point in the past a mutation produced A1. It also hints strongly that as a result, pure A2 milk is better for you. There seems to be some evidence floating around out there, but none of it is overwhelmingly positive.

Anyway, one can determine which cows produce what milk with a simple DNA test, and this morning’s awakening came from a report about the first dairy farm in the US to separate the milk from its A2 cows. A dairy company in Lincoln, Nebraska has started to market A2 milk in the US. To say they are cagey about the exact health claims they are making for this premium priced product would be the understatement of the week.

“To say there is no controversy over this would not be correct,” said Timothy Thietje, CEO of The Original Foods Company, a Nebraska-based marketer of A2 Milk.

“But to say there’s a substantial body of evidence both in terms of science and the response from people who use the product is correct.”

Right.

All this started in New Zealand and Australia, where the milk is marketed without the approval of the milk boards; what would all those other farmers do? But could this, just possibly, be a case in which reducing diversity might be good for you?

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A second helping of rice

More today to satisfy your hunger for rice information, hot on the heels of the recent paper trying to explain the pattern of genetic variation across and within two subspecies of cultivated rice, discussed by Jeremy a couple of days ago.

First there’s a paper ((Global Dissemination of a Single Mutation Conferring White Pericarp in Rice. Sweeney MT, Thomson MJ, Cho YG, Park YJ, Williamson SH, et al. PLoS Genetics Vol. 3, No. 8.)) looking at how the red pericarp of wild rice became the white pericarp of cultivated rice. The answer is that a mutation arose in the japonica subspecies, crossed to the indica and became fixed in both under very strong selection pressure by ancient rice farmers. They must have really liked those funny mutant white grains when they first noticed them! Oh to have been a fly on the wall — or a brown plant hopper on the rice stalk — when the white pericarp mutation was first noticed in some ancient paddy…

Then comes news that the three CGIAR centres with an interest in rice — IRRI, WARDA and CIAT — are to boost their collaboration to solve the pressing production problems of Africa. There’s talk of forming a consortium. More flags being prepared.

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Diversity in rice varieties: what caused it?

Larry Moran has a very good article on the genetic diversity found in the DNA of rice varieties. I won’t try to summarize what he has to say, because he says it so well. But I will emphasize something that he doesn’t. The biologists who looked at rice wanted to know what caused the pattern of diversity they see across rice vareties. One possibility is selection. The other is the founder effect, where a very small subset of a larger population gives rise to a new species (or variety) so that the new species contains less diversity than the ancestor population from which it sprang. In rice, neither explanation on its own is sufficient.

An agricultural scientist might not care one bit, or might simply assume that it was all due to selection by farmers. But the truth is that it needed a combination of the founder effect and positive selection to create modern rice diversity. The founder effect relates to the fact that Oryza sativa indica and Oryza sativa japonica were both domesticated independently from the wild Oryza rufipogon, maybe a few times. The results of those early events set up the foundation genes for rice. Then selection was brought to bear and created the diversity we now see. Luck and hard work, every time.