Heritability and genome-wide association mapping for supernumerary teats in French Alpine and Saanen dairy goats

Abstract

This paper reports a quantitative genetics and genomic analysis of undesired presence of supernumerary teats (SNT) in goats. Supernumerary teats are a problem in goat breeding as they can considerably impede machine milking efficiency, leading to increased milking time and injury. This phenotype has routinely been recorded for the past 15 yr in French Alpine and Saanen goats. Around 4% of the females had been assigned the SNT phenotype and consequently could not be included in the breeding program as elite animals. The heritability of this binary trait, estimated by applying linear logistic polygenic models to 32,908 Alpine and 23,217 Saanen females, was 0.40 and 0.44, respectively. A genome-wide association study was implemented using a daughter design composed of 810 Saanen goats sired by 9 artificial insemination bucks and 1,185 Alpine goats sired by 11 bucks, genotyped with the goatSNP50 chip (Illumina Inc., San Diego, CA). This association study was based on logistic polygenic models, one with separately taken single nucleotide polymorphisms and the other with haplotypes as fixed effects. The 2 breeds were analyzed together and separately. No region was found to be significant at the genome level, but 17 regions on 10 chromosomes were significant at the chromosome level. These signals were always only slightly above the chromosome significance threshold and only a few of them overlapped across analyses. No evidence of segregation of a major gene in our Saanen and Alpine populations was observed, suggesting that SNT presence is inherited in a polygenic fashion. This conclusion regarding SNT determinism agrees with recent association analyses in cattle, and one locus was even found in an orthologous region. The possibility of applying markers-based selection on the SNT trait is therefore unlikely, but, as this trait is heritable and routinely recorded, it could be managed by attributing a dedicated estimated breeding value.