Domestication

Michael’s post on water buffalo genetic diversity and domestication reminded me that I was intending to point you all in the direction of Dienekes’ Anthropology Blog. Although Dienekes mainly blogs about the genetic diversity and evolution of humans, he does occasionally link to papers on animal domestication and related issues. He has an RSS feed, which makes it easy to monitor his blog. In the past couple of years he has pointed to interesting papers on:

Incidentally, a great paper reviewing the use of genetics and archaeology to document domestication came out last year and you can see the abstract here. Now, what’s really needed is for someone to bring together the human, livestock and crop genetic data.

Water buffalo diversity

Michael Kubisch is a geneticist and reproductive physiologist working at the Tulane National Primate Research Center in the New Orleans area. He’s sent us his take on a recent paper on the genetics of the water buffalo. We really welcome this kind of contribution from our readers. Keep ’em coming! Here’s what Michael has to say:

Results of an interesting study by Chinese researchers have just been published, describing an extensive analysis of the genetics of Chinese swamp water buffalo (Bubalus bubalis). The Chinese swamp-type buffalo differs from the Indian river-type buffalo by the fact that it has 48 chromosomes compared to the 50 found in the latter. There is a third subspecies, the wild water buffalo, which may still exist in Southeast Asia, although its population size and genetic status are unknown and the animal is listed on the IUCN red list as being threatened. Based on analysis of mitochondrial DNA (which is solely inherited from one’s mother and consequently ideal for tracing maternal inheritance patterns), it appears that river and swamp buffalo split about 28,000 years ago with a further split in the swamp buffalo into two maternal lines taking place about 18,000 years ago. The genetic diversity varies between the two swamp buffalo matrilines in China and the authors suggest that the difference between the two lines might in part be due to the fact that occasional genetic introgression from wild swamp buffalo might have taken place into one of the lines. Interestingly, domestication of water buffalo seems to have occurred independently in India and China, most likely as a result of rice cultivation. Substantial numbers of water buffalo outside exist Asia, among other countries in Italy, where, as any cheese afficionado will know, their milk is used for the production of mozzarella.

Mapping underutilized genomes

It seems you can hardly open a newspaper these days — or open a news website — without reading that someone somewhere has mapped yet another genome, whether human, Neanderthal, sheep, mouse or bee. It hasn’t received any press coverage at all, but the taro (Colocasia esculenta) genome has now been added to the list. CIRAD scientists working in Vanuatu, in the South Pacific, and others just announced this at the recent meeting of the International Society for Tropical Root Crops held in Kerala, India.

One thing to note is that these are not all really genome mapping projects. Despite the many headlines to that effect, scientists are not mapping the Neanderthal genome. What they’re doing is sequencing it — or a small bit of it. There is a difference.

Sequencing means determining the (correct!) order of all the DNA bases — the letters of the genetic code — of an organism. Besides some very fancy hardware and software, you need the DNA of just one individual to do this. Mapping is both rather less and rather more.

Less, because it only aims to determine the relative location of some major landmarks of the genome. That is, not the order of all the letters in the book of life, but rather the relative positions of the pages where some choice quotations can be found.

More, because some of those genomic landmarks may be close to genes associated with predisposition to a disease or some other interesting trait. To find that out you need DNA from whole families, or populations, rather than a single individual — in the case of taro, the family was all the progeny from a couple of crosses between local ni-Vanuatu varieties. You trace the inheritance of the trait you’re interested in together with that of specific “markers” (any observable variation in the DNA sequence), and, hey presto, if you’re lucky you have a much more readily documented proxy for the trait.

With the new genome map, we now have genetic proxies for things like the yield and dimensions of the underground corm of taro. This edible aroid is an important staple in Oceania and parts of South and South East Asia, Africa and the Caribbean, but there are few breeding programmes around the world, which is why it often ends up on lists of so-called “neglected and underutilized species.” This map should make it easier to screen the hundreds of seeds that can result from crossing two varieties and select only the best individuals for further testing (this is called marker-assisted selection). It should therefore stimulate people to set up taro improvement programmes.

These are much needed. Mainly vegetatively propagated by farmers, taro is genetically fairly uniform in many places, making it susceptible to pests and diseases. It was almost wiped out in the South Pacific country of Samoa in the mid-1990s by taro leaf blight, a fungal disease. It has recovered at least in part because a regional project (called TaroGen) was set up by Pacific countries with support from Australia to breed — in collaboration with farmers — and disseminate resistant varieties.

Biotechnology means GMOs to many people, but this is a case where biotechnology is facilitating conventional breeding — nothing to do with genetic engineering. It may not have made the news like other mapping projects, but the new genome map means taro breeding should prove a little bit easier in the future.

Wild sheep don’t drift

The moufflon is a wild sheep from Corsica, Sardina and Cyprus. In 1957, a male and a female from Corsica were taken to another island, this one in the southern Indian Ocean, in an attempt to establish a herd for sport hunting. The pair thrived on Haute Island, and the resulting population peaked at about 700 head in the 1970’s, thereafter oscillating between 200 and 600. Ok, so far so weird, but so what? Well it turns out that genetic diversity hasn’t behaved as expected. By rights in such a small, isolated, inbred population it should have decreased markedly as a result of genetic drift. But according to this, it hasn’t. The reason is probably strong natural selection, according to the authors of the study, who compared DNA from the original founding couple to that of the present herd.

Late blight origins

Ask anyone working in plant genetic resources for an example of the importance of growing genetically diverse crops and chances are that sooner or later they’ll mention the Irish potato famine, caused by the late blight fungus Phytophtora infestans in the 1840s. But for such an important – and iconic – disease, it is amazing how what we think we know about it keeps changing. There’s been a re-think recently about which strain of the fungus actually caused the outbreak in Ireland. And now there’s DNA work to figure out where the pathogen came from. The debate on that point seems now to have been decided in favour of the Andes.