Question: Calculating correlation of same trait between environments for estimating genotype-environment interaction
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gravatar for therealybq
4.1 years ago by
therealybq20
Singapore
therealybq20 wrote:

Hi everyone,

I am new to the fields of quantitative genetics and bioinformatics, and this is my first post on Biostars. :)

I have a few specific questions about the estimation of genotype-environment (gxe) interaction.

Recently, I have been reading a paper by Mr Jose Domingos from James Cook University, which is downloadable from Researchgate:

http://www.researchgate.net/publication/256917392_Heritability_of_harvest_growth_traits_and_genotypeenvironment_interactions_in_barramundi_Lates_calcarifer_%28Bloch%29

In it, his team inferred the level of gxe interaction of each trait based on the correlation of the same trait between two environments. The higher the correlation, the lower the gxe.

According to my understanding of this method, for each trait, there needs to be more than one value for each genotype: at least one for each environment.

Normally, I would assume that each individual represents its own phenotype.

However, it seems impossible to have one individual inhabiting two environments at the same time. Also, near the top right corner of page 69, it is written: "... only one observation per trait was taken for each individual ..." so it seems the individual is not what represents each genotype in the calculation of correlation for estimating gxe.

So what constitutes each genotype in the calculation? Offspring of the same sire-dam pair? identical twins/triplets?

If it is, say, offspring of the same sire-dam pair (i.e. a family), then do we take the means for every family in one environment as data values, then pair them with the correpsonding means in the other environment when calculating the correlation for each trait?

Thank you very much for your replies in advance!

ADD COMMENTlink written 4.1 years ago by therealybq20
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