Original title: SNP Allocation For Estimating Heritability (SAFE-h2): A tool to explore genomic origins of phenotypes for estimation of SNP heritability using additive-only allelic effects or additive and non-additive allelic effects
Authors: Behrooz Darbani,Mogens Nicolaisen
In this article, the authors discuss the importance of SNP heritability in determining genetic gains. They explain that extreme polygenicity, which refers to the presence of many small effect-size causal SNPs, is a key factor in estimating heritability. However, they also argue that non-causal SNPs can lead to underestimation of heritability levels. They suggest that this is because non-causal SNPs make negative contributions to heritability, which is biologically unrealistic.
To address this issue, the authors introduce a tool called SAFE-h2 (SNP Allocation For Estimating Heritability) that utilizes association p-values to filter out SNPs that contribute negatively to heritability estimations. They demonstrate the effectiveness of SAFE-h2 using both simulated and real datasets from plant and animal species.
Additionally, SAFE-h2 is able to capture non-additive effects by making allelic adjustments within loci. This improves the accuracy of SNP heritability estimations for various phenotypes.
Overall, the authors find that the EMMAX algorithm is the most stable and accurate model for SNP heritability profiling using SAFE-h2. They declare no competing interests in conducting this research.
Original article: https://www.biorxiv.org/content/10.1101/2023.08.28.555092v3