Genetic diversity

June 22, 2011June 22, 2011

Rice domestication roundup

In the past few weeks there’s been a number of papers on the genetics of rice domestication. I’ll just give you the main findings here, and leave you to battle with the details on your own. With the help of various other bloggers.

Dorian Fuller did a great job of summarizing the multiple domestication (or indica and japonica) theory at The Archaeobotanist a couple of weeks back. This seems to have the upper hand at the moment. Wild perennial rice is cultivated in wetland margins in the Neolithic Yangtze, and as the water ecology begins to be altered by humans, creating seasonal drought conditions to stimulate seed production, particular adaptations are selected (annuality, short stature, less branching etc.), which leads to the domestication of japonica rice. This is then taken to the area of an independently-domesticated proto-indica, probably around 3800-4000 years ago, and some genes are exchanged. So far, so good, and there is now a pretty comprehensive database of rice archaeology to back up the recent studies of single and multiple genes.

Well, certainly the “genetic and selective basis for domestication” seem to be different for japonica and indica, but another recent paper throws some doubt on the multiple domestication idea. Now, I’ve briefly discussed this with people who know a lot more about rice than I do and it seems the main sticking (as it were) point is the dating of the indica-japonica split to 3,900 years ago. Previous estimate were in the hundreds of thousands of years, supporting the multiple domestication theory, but the problem is that the newer, lower estimate was based on domestication genes only. Lots more argument on the horizon, I suspect.

June 20, 2011June 20, 2011

Nibbles: Seed savers, Lemons, Assam Rice, Striga control, Amaranth, Bearded pigs, Banana, Early nutrition

Seed savers: everyone’s got an angle, from Seeds of Hope and Change to Seed Bank Bingo.
Italian lemons enjoying a renaissance. In California, natch.
India registers Assam farmers’ traditional rice varieties. In other news, rice water “is also used as shampoo, according to community elders”.
US$9 million to “implement and evaluate four approaches” to controlling Striga in Africa. One day we’ll know.
Denver Botanic Gardens does amaranth.
Evolution of bearded pigs. Good to know. Good to eat?
Bioversity banana team guest blogs at Annals of Botany. But surely they have a blog of their own. No, wait…
Agriculture is bad for your health.

June 19, 2011

The diversity of Andean diversity festivals

Hot on the heels of the Fifth Potato Festival in Peru, which we mentioned a few days ago, comes the Festival Nacional de la Agrobiodiversidad Frutos de la Tierra, also in Peru, 24-26 June. And, not to be outdone, Ecuador weighs in with the I Seminario Internacional de la Papa, also on 24 June. One has to wonder what is driving this proliferation of agricultural events in the region. And since we’re on the subject of Andean diversity, does anyone else think that some of the potato varieties illustrated by National Geographic are nothing of the sort?

June 13, 2011June 13, 2011

Brainfood: Bean diversity, Rice domestication, Microbial interactions squared, Threat of extinction, Agroforestry, Species diversity

Population structure and genetic differentiation among the USDA common bean (Phaseolus vulgaris L.) core collection. Subpopulations detected within usual Middle American and Andean genepools. The former was more diverse. Diversity was lower for domestication loci. One wonders whether game worth candle.
Artificial selection for a green revolution gene during japonica rice domestication. There’s nothing new under the sun. Fuller fills us in.
Positive plant microbial interactions in perennial ryegrass dairy pasture systems. Plant-microbe interactions can have significant positive impact on production of, and chemical inputs into and losses from, perennial ryegrass dairy pasture systems. Gotta love that agrobiodiversity.
Plant growth promoting potential of Pontibacter niistensis in cowpea (Vigna unguiculata (L.) Walp.). And another one. New bacterium from Western Ghats fertilizes soil and helps cowpea to grow.
Extinction risk and diversification are linked in a plant biodiversity hotspot. That would the Cape. Extinction threat (IUCN categories) is better explained by phylogeny than by human activity or plant traits. Go figure.
The framework tree species approach to conserve medicinal trees in Uganda. Sort of like artificial keystone species. Lots of other cool stuff in the same issue of Agroforestry Systems.
Use of topographic variability for assessing plant diversity in agricultural landscapes. By and large, more environmental variability means more plant diversity, in Switzerland. Maybe some crop wild relatives in there?

June 7, 2011

A more strategic approach to evaluation?

I feel we need evaluation data on ‘agronomic’ performance. Morphological description, in most cases, totally pointless.

That was the first response to my posting of the rice sheath blight story on GIPB the other day.

Somewhat provoked, one of the authors of the paper prepared this reposte.

Consider this like a “morphological FIGS” (Focused Identification of Germplasm Strategy), selecting the “best bet” set of accessions to meet the researchers’ objectives.

Yes of course we need more evaluation.

But look at the effort that went in to the screening of these 200. Imagine scaling that up to the whole collection of 110,000+ accessions. Impossible. Imagine even scaling up to the 5,000 we can characterize in one year. Impossible.

Then consider all the evaluation data IRRI has collected in the past on the genebank accessions and effectively discarded. (“Don’t throw it away! Give it to me … Thank you … Oh, I see what you mean. Throw it away” is the typical sequence of reactions we get from people convinced we shouldn’t discard it). Why discard it? Because it was all done using the quick-and-dirty anything-is-better-than-nothing approach of genebanks to characterizing and evaluating large collections. The experts won’t do it, we don’t know how to do it properly, so let’s just do what we can do. Silly.

When we evaluate accessions we have to evaluate them properly, led by the trait experts, and we can only ever hope to do that for small subsets of accessions.

Then consider the lack of progress even by the experts in evaluating diverse subsets (dare I say core collections?) for resistance to sheath blight.

Sheath blight is an unusual disease. Because of the mode of spread from one plant to the next (by fungal hyphae), the rate of spread is highly dependent on plant architecture. The experts felt this “noise” might be hiding the signal of physiological resistance that they wanted to detect. Therefore they should control for canopy architecture; therefore we should use characterization data to select accessions for evaluation.

The real message is not that characterization data are useful. The real message is that evaluation efforts must be focused more carefully on the right subset of accessions, choosing the “best bet” set for each request. Characterization data are just another type of data that may or may not help us to choose in the concept elaborated in FIGS.

Let the debate continue!