GWAS & Selection signatures

Allelic properties of quantitative trait loci (QTL) in Australian dairy cattle

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Abstract

Pinpointing causal variants for quantitative traits is complicated by linkage disequilibrium, multiple nearby signals, and effects on multiple traits. We aimed to identify 100kb windows containing quantitative trait loci (QTL) and determine if these windows are likely to contain a single major causal variant affecting a single trait. Alternatively, if multiple traits are affected at a locus, are the effects pleiotropic or are there multiple causal variants? We analysed up to 71,972 Australian Holstein, Jersey, Australian Red and crossbred cows for 16 (decorrelated) traits. Genotypes included 5,364,143 autosomal imputed sequence variants (INFO > 0.4; MAF > 0.005) LD-pruned at pairwise r² 1à—10⁻⁴, sum of PIPs > 0.8, and ≥1 variant exceeding the genome-wide false discovery rate ≤ 0.01. Windows within 1Mb were merged into regions across traits. Per region, we choose a 'leading window' which maximised local GEBV variance across traits. We used the distribution of local GEBV haplotypes in the 100kb windows to determine if there was likely one or multiple causal variants in the segment. We identified 202 qualifying windows clustering into 92 regions (each region comprising one or more 100kb windows). Most leading windows (59/92; 64%) were consistent with a single major causal variant affecting a one (decorrelated) trait. The remaining 33 regions had multiple traits that passed our selection criteria. Of these, we classified just under half (14/33) as pleiotropic (that is, a single causal variant affecting multiple traits) and the remainder as having two or more independent causal variants. In conclusion, it is usually possible to map significant loci to within a 100kb segment and most of the loci we examined appear compatible with a single dominant causal variant. These loci are strong candidates for further fine-mapping and functional follow-up. A small number of regions displayed high degrees of local complexity - either multiple alleles at one locus or distinct nearby QTL with divergent multi-trait effects - highlighting the need for novel approaches which accommodate multiple causal variants and multi-trait heterogeneity in small genomic regions.

Keywords: 2026

How to Cite:

Kemper, K., Xiang, R., Breen, E. & Goddard, M., (2026) “Allelic properties of quantitative trait loci (QTL) in Australian dairy cattle”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2279707. doi: https://doi.org/10.31274/wcgalp.24548

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