Category: Genetic diversity

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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!

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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.

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Snow White and the Four Coconut Types

Over at the Coconut Google Group, Hugh Harris has had enough.

Snow White had no problem – not only was the name of each Disney dwarf carved on the end of the bed, they were identified by easily distinguished features: Happy, Sleepy, Bashful, Sneezy, Dopey, Grumpy and Doc.

Dwarf coconut names are not so simple.

  • Dr Nair is looking for a source of green Malayan Dwarf
  • Roland thinks there may be half a dozen green dwarf populations in Malaysia, not just one, pure green dwarf
  • Dr Srinivasan calls for more insights on the distribution pattern of Malayan Green Dwarf, Brazil Green Dwarf etc.
  • Elan Star wants to know about the Samoan or Tongan dwarf in Hawaii.

So perhaps this is a good time to suggest that what is needed now is a Global Coconut Genome Consortium.

For a fee, anyone should be able to send a coconut tissue sample (dwarf, tall, hybrid or unknown) to a collaborating laboratory for a DNA analysis that would identify that sample in terms of its similarity to, or difference from, all previously analysed samples.

The technology is available in many countries on all continents (except Africa?); there are already laboratories able to handle coconut samples in Australia, China, Europe, the USA and Brazil, and probably elsewhere (and the cost is coming down).

There is an International Botanical Congress in Melbourne, Australia, this July. If anyone reading this email is going to that meeting, or knows someone who will be there, please make an opportunity to talk about starting a Global Coconut Genome Consortium (GCGC or GC^2).

In the meantime, returning to the subject of dwarf coconuts, there can never be a 100% “pure” green dwarf or any other coconut (until in vitro propagation methods are a practical possibility).

Indeed, all coconut “varieties” are no more or less than local populations that look phenotypically similar to other populations that share a recent common ancestor.

At the risk of causing more, not less, confusion, I would like to suggest that the commonplace distinction of “tall or dwarf” should be forgotten and replaced. Instead we should recognise four “basic” plant habit phenotypes:

  1. the tall wild type (with large and small fruited sub-types)
  2. the tall domestic type (with different fruit-colour sub-types)
  3. the dwarf domestic type (with different fruit-size and -colour sub-types)
  4. the compact-habit dwarf (which has all the tall features except internode length)

But each of these basic phenotypes, and particularly the first two, are locally introgressed, so that there appears to be a fifth, intermediate, phenotype. For want of any accepted term, this can be thought of as the common cultivated coconut.

And, Elan, your dwarf is number 4 but if you look around you will certainly see number 3 as well.

So, a Global Coconut Genome Consortium. Any takers?