Genetic and genomic characterization followed by single-step genomic evaluation of withers height in German Warmblood horses

Abstract

Reliability of genomic predictions is influenced by the size and genetic composition of the reference population. For German Warmblood horses, compilation of a reference population has been enabled through the cooperation of five German breeding associations. In this study, preliminary data from this joint reference population were used to genetically and genomically characterize withers height and to apply single-step methodology for estimating genomic breeding values for withers height. Using data on 2113 mares and their genomic information considering about 62,000 single nucleotide polymorphisms (SNPs), analysis of the genomic relationship revealed substructures reflecting breed origin and different breeding goals of the contributing breeding associations. A genome-wide association study confirmed a known quantitative trait locus (QTL) for withers height on equine chromosome (ECA) 3 close to LCORL and identified a further significant peak on ECA 1. Using a single-step approach with a combined relationship matrix, the estimated heritability for withers height was 0.31 (SE = 0.08) and the corresponding genomic breeding values ranged from − 2.94 to 2.96 cm. A mean reliability of 0.38 was realized for these breeding values. The analyses of withers height showed that compiling a reference population across breeds is a suitable strategy for German Warmblood horses. The single-step method is an appealing approach for practical genomic prediction in horses, because not many genotypes are available yet and animals without genotypes can by this way directly contribute to the estimation system.

Replacement of microsatellite markers by imputed medium-density SNP arrays for parentage control in German warmblood horses

“…A high similarity of breeds at a MS level could therefore be assumed. Combined with the rather strong connectedness between the breeds (Nolte et al 2019 ; Vosgerau et al 2022 ), an imputation of all breeds together seemed feasible.…”

Prediction of body condition in Jersey dairy cattle from 3D-images using machine learning techniques

“…Haberland et al (2012) observed that, for animals with a large number of progeny records available, additional gain in accuracy from GEBV is small. In the same way, in the study of Vosgerau et al (2022) about withers height, the increase in reliability was greater for animals with a small number of offspring.…”

“…The impact of genomic breeding values (GEBVs) on the accuracy of EBVs has been analysed in previous studies (Haberland et al, 2012;Vosgerau et al, 2022). Haberland et al (2012) observed that, for animals with a large number of progeny records available, additional gain in accuracy from GEBV is small.…”

“…Their estimates ranged between 0.34 to 0.64 (DsD and SiL, respectively) for conformation traits and 0.02 to 0.23 (IF12 and AFF-RE, respectively) for the reproductive ones. In the literature, high heritability estimates were reported for conformation traits in horse breeds (Solé et al, 2014 in Menorca horse population;Gómez et al, 2021 in PRE horse breed;Vosgerau et al, 2022 in German Warmblood horses). However, for fertility, lower heritability values were observed (Mantovani et al, 2020;Perdomo-González et al, 2021).…”

764. Recent advances in genomics of equine health, welfare and performance

“…Reproduction and behaviour traits are the least reported in the HorseQTLdb. Among the most recent studies of important Equine QTLs are; Osteochondrosis (Drabbe et al 2022), Height at Withers (Vosgerau et al 2022), and gait and racing performance (Ricard and Duluard 2022). The difficulties in recording behaviour phenotypes probably reflect the small number of genetic associations reported in both OMIA and HorseQTLdb.…”