Dissecting the genetic architecture of quantitative traits using genome-wide identity-by-descent sharing

Additive and dominance genetic variances underlying the expression of quantitative traits are important quantities for predicting short-term responses to selection, but they are notoriously challenging to estimate in most non-model wild populations. Specifically, large-sized or panmictic populations may be characterized by low variance in genetic relatedness among individuals which in turn, can prevent accurate estimation of quantitative genetic parameters. We used estimates of genome-wide identity-by-descent (IBD) sharing from autosomal SNP loci to estimate quantitative genetic parameters for ecologically important traits in nine-spined sticklebacks (Pungitius pungitius) from a large, outbred population. Using empirical and simulated datasets, with varying sample sizes and pedigree complexity, we assessed the performance of different crossing schemes in estimating additive genetic variance and heritability for all traits. We found that low variance in relatedness characteristic of wild..., , , # Dissecting the genetic architecture of quantitative traits using genome-wide identity-by-descent sharing

This repository contains all data and code necessary to reproduce the analyses and figures performed in the manuscript.

## Directories

1. root directory: this directory contains the R codes necessary to format the data and produce the \"DataAndGRMsHelsinki.RData\" input file (see below), construct the GRMs, run the animal models, perform the correction from Legarra et al. 2015 and perform QTL mapping.

2. \"data\": this directory contains the raw genotypic (genotypeTable & genotypeMap) and phenotypic (complete_pheno_data.txt) data for the article. It also contains a summarized .RData file (\"DataAndGRMsHelsinki.RData\") containing the ready-to-use formated data combining both genotype and phenotype data.

3. \"figures&tables\": this directory contains all R codes to reproduce the figures from main text and supplementary material. Code for Fig.1 and Fig.6 are embeded in their ...