Livestock Breeding and Genomics - Notebook 5

Problem 1: QTL Data

Estimate genotypic values \(a\) and \(d\) and predict breeding values for all animals using the QTL-data given under:

https://charlotte-ngs.github.io/lbgfs2023/data/p1_qtl_1_loci.csv

Your Solution

• Start by re-formatting the paternal and maternal alleles into a genotype
• Use a linear regression to estimate genotypic values
• Predict breeding values for all animals

Problem 2: Increase Effects of Genotype on Phenotype

Change the phenotypic records in the above given dataset such that the QTL explains \(50%\) of the genetic variation when a heritability of \(0.45\) is assumed. It is assumed that the QTL acts purely additively, hence the genotypic value of the heterozygotes can be set to \(d=0\).

Show the results as a scatter plot of all phenotypic values for the QTL genotypes.

Your Solution

• Compute the genetic variance that can be attributed to the QTL based on the phenotypic variance on the heritability and on the amount of variation explained by the QTL.
• Read the data and convert the paternal and the maternal alleles to QTL-genotypes
• Compute allele frequencies
• Compute the genotypic value \(a\) from the QTL variance
• Add genotypic value to the phenotypes according to the QTL-Genotype
• Fit regression of new phenotypes on genotypes
• Show the results with plots

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Latest Changes: 2023-10-13 09:09:07 (pvr)