50 whys to look for genes: 12. Similar varieties respond similarly in similar locations

In agricultural trials, where a number of varieties or animals or plants can be raised or grown in multiple replicates in many locations, varieties can be grouped by similarity in responses across all locations using techniques of cluster analysis (Byth et al. 1976).  Varieties in any resulting group tend to be above average for a location in the same locations and below average in the same location… The wider the range of locations in the measurements on which the grouping is based, the more likely it is that the ups and downs shared by varieties in a group are produced by the same conjunctions of measurable factors [genes and environmental factors].

For example, imagine a group of plant varieties that originated from particular parental or ancestral stock that is more susceptible to plant rusts (a form of parasitic fungi), and that these varieties had a poor yield in locations where rainfall occurred in concentrated periods on poorly drained soils. The obvious hypothesis about genetic factors modulated by environmental factors is that these varieties share genes from the parental stock that are related to rust susceptibility and this susceptibility is evident in the measurements of yield in locations where the rainfall pattern enhances rusts. Through additional research to compare the variety and ancestral genomes, it may be possible to identify specific sets of genes that are shared, to investigate whether and how each one contributes to rust susceptibility, and to use that knowledge in planting recommendations for locations like those observed in the trial and for subsequent research that might extend beyond the observed varieties and locations.

Complications:

It becomes more difficult to distinguish groups of varieties by similarity of responses across locations when varieties are observed in only a few locations or when the locations are not the same from one variety to the next. [This approach] becomes infeasible when analyzing measurements from studies of human twins because such studies have only two replicates (twins) in one or at most two locations (families).

References

The quotes above are from pages 95ff  in Taylor, Peter J. (2014) Nature-Nurture? No: Moving the Sciences of Variation and Heredity Beyond the Gaps.

Byth, D. E., R. L. Eisemann, et al. (1976). “Two-way pattern analysis of a large data set to evaluate genotypic adaptation.” Heredity 37(2): 215-230.

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(Introduction to this series of posts)

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