Genome‐wide association mapping and examination of possible maternal effect for the pace trait of horses

Abstract

Previously, a single nucleotide polymorphism (SNP) related to gait type was identified at position 22 999 655 of chromosome 23 in the coding region of DMRT3 (DMRT3:Ser301Ter) by showing that a cytosine (C) to adenine (A) mutation of this SNP induced pace in the Icelandic horse. We investigated the effect of DMRT3:Ser301Ter on the gait of Hokkaido Native Horses, a Japanese native breed, and examined genetic factors other than DMRT3 by exploring genome-wide SNPs related to gait determination. All animals exhibiting pace were AA for DMRT3:Ser301Ter, confirming the association of DMRT3:Ser301Ter with gait determination; however, 14.3% of the animals exhibiting trot also had AA for DMRT3:Ser301Ter, suggesting the presence of another factor(s) cooperatively working with DMRT3:Ser301Ter for gait determination. SNPs on chromosomes 13 and 23 were detected by genome-wide association analysis (false discovery rate <0.05), although SNPs on chromosome 23 were all located in the vicinity of DMRT3:Ser301Ter, confirming the association with DMRT3. A genome-wide association study targeting only animals with AA for DMRT3:Ser301Ter to examine genetic factors cooperatively working with DMRT3:Ser301Ter for gait determination suggested associations of 23 SNPs on six chromosomes. In a series of analyses of the effect of a maternal factor (dam's gait) on gait determination, the effect was suggested in comparison of the frequencies of exhibiting pace in gait checks in only two animal groups having dams with different DMRT3:Ser301Ter genotypes (P < 0.05), suggesting that the gait of the dam does not have a major effect on whether progeny homozygous for the DMRT3:Ser301Ter mutation will preferentially pace or trot.

Distribution of the mutant allele of the DMRT3 gene associated with ambling gaits in Japanese native horse populations

“…In Japan, a considerable part of horses in the Medieval ages to early modern periods were expected to exhibit ambling gaits (Kozasa, 2011; Sawazaki, 1994) because they were preferable for comfortable riding. Furthermore, many Hokkaido horses perform ambling gaits and reported to be homozygous for DMRT3:p.Ser301Ter due to selection for this trait (Amano et al., 2018). While the frequency of DMRT3:p.Ser301Ter is reported to be high in Hokkaido horses (Amano et al., 2018; Promerová et al., 2014), the distribution of DMRT3:p.Ser301Ter in the eight Japanese native horse populations currently remains unknown.…”

“…Furthermore, many Hokkaido horses perform ambling gaits and reported to be homozygous for DMRT3:p.Ser301Ter due to selection for this trait (Amano et al., 2018). While the frequency of DMRT3:p.Ser301Ter is reported to be high in Hokkaido horses (Amano et al., 2018; Promerová et al., 2014), the distribution of DMRT3:p.Ser301Ter in the eight Japanese native horse populations currently remains unknown. Therefore, we herein investigated the distribution and allele frequencies of DMRT3:p.Ser301Ter in the eight populations of Japanese native horse.…”

Genomic analysis of gaits and racing performance of the French trotter

“…We did not find other QTNs for both trotting technique and racing performances. We did not find any effect of SNPs found by GWAS on gait traits in gaited horses (Amano et al., 2018; Bussiman et al., 2020; Fegraeus, Hirschberg, et al., 2017; Staiger et al., 2016) or those found in Standardbred to differentiate trotters from pacers (McCoy et al., 2019).…”

“…In these cases, the relationship with pace was sometimes exclusive with all pacer AA and all non‐pacer CC (Novoa‐Bravo et al., 2018). However, in most breeds, there were several AA horses that were unable to pace, even if none of the CC horse were able to pace (Amano et al., 2018; Fegraeus, Hirschberg, et al., 2017; Jaderkvist et al., 2015; Kristjansson et al., 2014) or all AA horses were able to pace, and some CC horses too ( Jaderkvist, Kangas, et al., 2014). However, there has been an established relationship between genotype at DMRT3 and the ability to pace (Han & Peñagaricano, 2016).…”

“…More than 50% of the significant SNPs were not in the SNP list retained in our study, principally due to low MAF or low other quality controls. We also checked SNPs found in GWAS analysis in gaited horses (Amano et al., 2018; Bussiman et al., 2020; Fegraeus, Hirschberg, et al., 2017; Staiger et al., 2016) and those found in Standardbred to differentiate trotters from pacers (McCoy et al., 2019) with no success. Particular adaptations of each breed or population to the same racing performance depended on different genes according to its overall genetic background.…”