MATN3 underlies a QTL for stature in cattle

Abstract

Live weight (LWT) in dairy cattle is associated with milk production efficiency, and also has a high genetic correlation with stature. To identify genetic regions impacting stature and LWT, we conducted a genome-wide association study using 65,500 mixed-breed NZ dairy cattle and 16,243,015 imputed genotypes. We identified a quantitative trait locus (QTL) at BTA11:78-79Mbp for stature that was significant at a genome-wide level (β=3.98mm ± 0.56; P=1.6×10-12) but not significant for LWT (β=1.253 ± 0.393 kg; P=1.4×10-3). Ensembl’s Variant Effect Predictor was used to search for coding variants to attempt to identify a candidate causative gene for this QTL, and gene expression from RNA sequence data representing 373 cows were analysed for 16 genes and 3,640 markers to highlight expression QTL (eQTL) in this region. The gene with the most significant eQTL was MATN3 (ENSBTAG00000020893; P=2.5×10-38), encoding a protein which is involved in bone development. The correlation between variant effects (-log p-values) was calculated for the stature QTL and MATN3 eQTL (r=0.584), with the same variant (rs475277351) most significant for both QTL. This suggests a common genetic signal underlying both QTL, supporting the hypothesis that the MATN3 gene underlies the stature QTL.