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?
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?
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!
The revenge of characterization data
It is a truth universally acknowledged that characterization data are useless to breeders. Well, universally acknowledged by breeders anyway. Morphological data are all well and good for genebank curators looking for duplicates and old-fashioned taxonomists, they say. But what we need is evaluation data, and lots of it.
As usual, I exaggerate; for effect, as usual. But I think it would certainly be true to say that detailed morphological descriptions of germplasm are not the highest priority thing breeders want out of genetic resources databases. That would probably be information on resistance to biotic and abiotic stresses.
And yet a paper just out in Euphytica shows that the former can be clues to the latter. A team at IRRI ((And thanks to IRRI for the photo.)) looked at the susceptibility of rice to sheath blight, an important disease throughout rice-growing areas, especially under intensive systems. ((Susceptibility of rice to sheath blight: an assessment of the diversity of rice germplasm according to genetic groups and morphological traits. L. Willocquet, M. Noel, R. Sackville Hamilton and S. Savary. Euphytica. Online first. May 2011. DOI: 10.1007/s10681-011-0451-9.)) They measured how 200 accessions did when inoculated with Rhizoctonia solani in the field. So far, so conventional.
But because the accessions were very carefully chosen (out of a total of over 100,000 in the IRRI genebank), the team, which included the genebank manager, were able to estimate to what extent differences in disease intensity were due to plant and canopy architecture — in other words, morphology — and how much to genetic susceptibility.
The accessions tested were selected to represent contrasting morphologies (based on leaf length, leaf angle and number of tillers, typical characterization descriptors), different phenologies (number of days to 80% flowering) and all the major varietal groups (indica, aus, aromatic, temperate, japonica and tropical japonica). It turned out that the lowest levels of disease intensity were found on a particular morpho-phenological group, and that this effect of morphology on disease intensity was much greater than any effect of genetic group, although the aus varietal group was markedly superior to the others.
The authors therefore recommend that breeders looking for sources of reduced susceptibility to sheath blight will find it most efficient to select taller accessions with wider leaves. Let us see what the breeders think. I’ll post this on GIPB and report back if there’s any reaction.
Brainfood: Cabbages, Crops in Darfur, Sowing dates, People and biodiversity, Honeybees, Rhizobium, Figs, Urban ag, Wild olives, Ancient textiles, Ducks, Wheat introgression, Food citizenship, Crop models, Trifolium, Variety choice
- Genetic diversity of Brassica oleracea var. capitata gene bank accessions assessed by AFLP. Czech genebank; subgroups reflected place of origin.
- Optimizing the cropping mix in North Darfur State, Sudan. A study of Umkdada district. “…the results of the model were different from the real practices of the farmers.” Oh dear. To improve the fit, schoolboys should work in the fields more. And crops should fetch more. The dismal science indeed.
- Climate-driven simulation of global crop sowing dates. Ok, this model works. You can predict sowing dates under rainfed conditions for various annual crops from climatic conditions. Not entirely sure why you would want to, though.
- Exploring some of the myths of land use change: Can rural to urban migration drive declines in biodiversity? Yes, counter-intuitively, at least in the forests of Mexico’s southwestern highlands. More from Conservation Magazine.
- Pollination services in the UK: How important are honeybees? Quite a bit, but maybe not as much as previously thought. It’s the wild bees, stupid!
- Genetic diversity and symbiotic effectiveness of rhizobia isolated from root nodules of Phaseolus vulgaris L. grown in soils of Iran. It is high, and it varies, respectively.
- Interspecific hybridization of fig (Ficus carica L.) and Ficus erecta Thunb., a source of Ceratocystis canker resistance. It’s a breakthrough!
- Exploring the diversity of urban and peri-urban agricultural systems in Sudano-Sahelian West Africa: An attempt towards a regional typology. There are 6 types. Not 5; not 7. On this one, the journey is more interesting than the destination.
- Variability of wild olives (Olea europaea subsp. europaea var. sylvestris) analyzed by agro-morphological traits and SSR markers. There’s a lot of variabzzzzzzzzzz…
- Hemp in ancient rope and fabric from the Christmas Cave in Israel: Talmudic background and DNA sequence identification. Mainly flax, but some hemp, from both Roman and Chalcolithic periods. But can you smoke it?
- Modelling the distribution of domestic ducks in Monsoon Asia. Low resolution data, plus fancy modelling, can be used to get pretty good high resolution predictions.
- Gene flow between wheat and wild relatives: empirical evidence from Aegilops geniculata, Ae. neglecta and Ae. triuncialis. It happens, a lot.
- Toward food system sustainability through school food system change: Think&EatGreen@School and the making of a community-university research alliance. Food citizenship?
- Simulation of winter wheat yield and its variability in different climates of Europe: A comparison of eight crop growth models. Big differences among models, so best thing to do is to use the mean of all of them.
- The potential of plant viruses to promote genotypic diversity via genotype × environment interactions. The negative effect of White Clover Mosaic Virus (WCMV) infection on performance differs from white clover genotype to genotypes, which means differential selection, which means negative frequency-dependent selection in host populations, which means diversity. Via.
- Amplifying the benefits of agroecology by using the right cultivars. Why should we summarize, when an author has already done so?