Fine-mapping and identification of candidate causal genes for tail length in the Merinolandschaf breed

AbstractBackgroundDocking the tails of young lambs in long-tailed sheep breeds is a common practice worldwide. This practice is associated with pain, suffering and damage to the affected animals. Breeding for a shorter tail in long-tailed sheep breeds could offer one of the alternatives. This study aimed to analyze the natural tail length variation in the most common German Merino variety, and to identify possible causal alleles for the short tail phenotype segregating within a typical long-tailed breed.ResultsHaplotype-based mapping in 362 genotyped (Illumina OvineSNP50) and phenotyped Merinolandschaf lambs resulted in a genome-wide significant mapping at position 37,111,462 bp on sheep chromosome 11 and on chromosome 2 at position 94,538,115 bp (Oar_v4.0). Targeted capture sequencing of these regions in 48 selected sheep and comparative analyses of WGS data of various long and short-tailed sheep breeds as well as wild sheep subspecies identified a SNP and a SINE element as the promising candidates. The PCR genotyping of these candidates revealed complete linkage of both the candidate variants. The SINE element is located in the promotor region of HOXB13, while the SNP was located in the first exon of HOXB13 and predicted to result in a nonsynonymous mutation.ConclusionsOur approach successfully identified HOXB13 as candidate genes and the likely causal variants for tail length segregating within a typical long-tailed Merino breed. This would enable more precise breeding towards shorter tails, improve animal welfare by amplification of ancestral alleles and contribute to a better understanding of differential embryonic development.