I’m looking for possible genetic markers that are associated with “performance” in Pacific cod, measured via growth, condition, and survival. I am particularly intersted in markers that are associated with these metrics in cod exposed to warming. I performed GWAS analyses a couple days ago to identify sites where performance metrics differ among genotype probabilities, using temperature treatemnt as a covariate. Here I’ll show results from sites associated with a computed “composite performance index” from four metrics that we have for all fish: standard growth rate (standard length), standard growth length (wet weight), hepatosomatic index (“HSI”, i.e. liver condition), and condition index based on wet weight (“Kwet”). I rescaled all these metrics across all fish from 0-1, then added them to create a composite performance index, with max value of 4.

Here is a manhatton plot showing the GWAS results. The values are log10-pvalues computed based on chisquare distribution of likelihood ratios ( pchisq(lrt.gc1_filt$LRT, df=1, lower=F)). In green are markers with log10-pvalue > 3, which I’ve selected as a cutoff (somewhat arbitrarily) to further explore:

I pulled genotype probabilties for the putative growth/condition markers (those in green above) by subsetting the experimental fish beagle file, then ran PCAngsd on just those sites. This generated a covariance matrix, which I brought into R to run PCA. Here is a PCA biblot of experimental fish (PC1 x PC2). PC1 explains 66% of the variation in these putative performance markers. I’ve color-coded points by the composite index, with highest numbers in yellow (on the left) indicating fish with high growth/condition.

The GWAS was run using a composite index, which correlates very nicely with PC1:

But how about the original growth and condition metrics? The putative markers do a pretty good job of predicting growth rate, especially in the warmest temperature, and predicting HSI (liver condition) in the coldest temperature. Very interesting!

Here’s is the relationship among PC1 and standard growth rate (standard length):

Here’s is the relationship among PC1 and standard growth rate (wet weight):

Here’s is the relationship among PC1 and hepatosomatic index (liver condition):

Here’s is the relationship among PC1 and condition index based on wet weight (Kwet):

Are these putative “performance” markers associated with specific genes / processes?

Here are genes containing putative growth/condition markers (in gene bodies, or within 2kb -i.e. promoter region). I will perform functional enrichment later.