Comments on: Making that haystack smaller

By: Aninformedsource

Aninformedsource — Thu, 16 Jul 2009 08:27:01 +0000

I can see a debate that may be there but shouldn’t. It should be simple — we give each user what (s)he needs. Users studying diversity need core collections. Users trying to identify genes for a trait need diversity for that trait, uniformity for everything else. Users needing a particular trait need just that – with trait-specific subsets if the phenotyping data are available, or based on predictions such as provided through FIGS. The only problem with core collections is they’ve been pushed for purposes they weren’t intended for.

By: Ahmed Amri

Ahmed Amri — Sat, 11 Jul 2009 11:23:29 +0000

The recent examples at ICARDA of FIGS approach to better target sources of valuable traits are first sign of the relevance of the approach. I am sure the approach can be further refined and is pursued at ICARDA with partners. The success of such approach will rely, in addition to available environmental layers, on the availability of information of distribution of stresses and on the virulence spectra in case of biotic stresses. Subsets established for a given biotic stress could differt from one region to the other based on the virulence of the populations.

By: Jacob

Jacob — Fri, 10 Jul 2009 19:49:56 +0000

To me, the potato results mean that we shouldn’t be looking at selection, but at migration and drift.

Selection reduces diversity, migration and drift determine where it goes.

By: DannyH

DannyH — Thu, 09 Jul 2009 15:19:55 +0000

The same authors in a recent Crop Science paper tested taxonomic and biogeographic associations with 10,738 disease and pest evaluations, derived from the literature and genebank records, of 32 pest and diseases in five classes of organisms (bacteria, fungi, insects, nematodes, and virus). The data showed that ratings for only Colorado potato beetle [Leptinotarsa decemlineata (Say)] and one pathogen (Potato M Carlavirus) are reliably predicted both by host taxonomy and climatic variables.
http://tech.groups.yahoo.com/group/CropWildRelativesGroup/message/490

By: Ken Street

Ken Street — Thu, 09 Jul 2009 14:09:34 +0000

Populations of wild potatoes and their pests are biological entities and as such will be subject to evolutionary processes driven by selection pressures placed on them by their environments. FIGS seeks to use environmental parameters to predict where certain selection pressures occur that would favor sought after traits.

In developing FIGS we used geographic information to define environments where we have found resistance before and then looked in similar environments to find new sources. Or we defined environments that would favor high population densities of the pest – it proved more successful than using a random set selection process or a core set.

The fact that the studies by Jansky et al did not find a clear correlation between the distribution of resistance for some pests could be a function of the algorithms they used and the environmental data they used. Other niche modeling exercises have found that the BIOS parameters within the Worldclim suite of surfaces seem to be of more significance than .

Further, what level of statistical significance is used to say something is correlated to a particular trait or not is open to debate. The 5% or even the 10% rule, while rigorous, are arbitrary and may preclude certain possibilities. Thus when applying these models in a germplasm selection context we perhaps need to play with accepting a lower level of significance if we are to maximize our chance of putting together a set of material that contains a higher proportion of the sought after trait.

Finally – FIGS is an approach that has potential to evolve into a pragmatic tool given further intellectual input.

By: Michael

Michael — Thu, 09 Jul 2009 10:33:09 +0000

All good points. The FIGS approach is not intended to be a universal panacea. It should mainly be considered for finding adaptive trait variation. Unlike the core collection concept, it does not try to concentrate all the available genetic variation in a 5-10% sub-sample of the original collection. The approach has been demonstrated to be effective with powdery mildew, CCN tolerance, boron toxicity tolerance, Sunn pest, RWA and is showing initial promise for salinity tolerance – all with respect to bread wheat. We should just think of FIGS as a strategy for linking breeders, and other users, to the ‘candidate’ accessions (good chance of having the genetic variation they are looking for) in ex situ collections. At the same time we should expect that there will be other strategies (or methods) around, or under development, that will build further on Vavilov’s (1957) concept of “starting with the right material” to ensure success in plant improvement.

A general observation after about 30 years in the game: Common sense seems to be more effective in exploiting plant genetic resources than rocket science. Perhaps this might stimulate some interesting discussion?

Vavilov, N.I., 1957. World resources of cereals, grain leguminous crops and flax and their utilization in plant breeding. Agroecological survey of the principal field crops. Izdatel’stvo Akademii Nauk SSR, Moskva, Leningrad, 463 p.

By: Nigel

Nigel — Thu, 09 Jul 2009 09:25:03 +0000

Yes the case of potatoes is very interesting indeed, but is it typical? There are numerous papers showing that using ecogeography as a predictor of patterns of genetic diversity does not always work, but ecogeography is still widely used because in the absence of clear genetic diversity or characterisation / evaluation data there is practically no alternative. Predictive characterisation using the FIGS approach will I feel be a similar case, although it may not be perfect it is an excellent pragmatic tool.