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

Abstract

Background: Docking 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.Results: Haplotype-based mapping in 362 genotyped (Illumina OvineSNP50) and pehenotyped 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. Conclusions: Our 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.

Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes

“…More recently, Li et al [ 13 ] emphasized the significance of both PDGFD and BMP2 signals in sheep tail formation, and described a new variant based on a 169-bp insertion close to the 5′-UTR region of HOXB13 , which is likely to be associated with the long tail phenotype. This variant was further confirmed as a 167-bp segment with a linked missense mutation ( c.23C > G ) in Merinolandschaf sheep [ 32 ]. It is likely that multiple genes may contribute to the configuration of sheep tails since tail phenotype and related fat deposition levels vary greatly between different sheep breeds from different geographical regions.…”

Ovine HOXB13: expanding the gene repertoire of sheep tail patterning and implications in genetic improvement

“…These include the platelet derived growth factor D (PDGFD) gene 1,11,12 and the intergenic region between the bone morphogenetic protein 2 (BMP2) and hydroxyacid oxidase 1 (HAO1) genes, referred to as the IBH region [13][14][15] linked with the fat-tail phenotype, and the T-box transcription factor T (TBXT) gene [16][17][18] linked with variations in caudal vertebrae. Recent studies highlighted a new gene, HOXB13, which is highly associated with the sheep tail length [19][20][21][22][23] (Table 1). Of these studies, two independent efforts, one recently published in Communications Biology 23 and the other published as a preprint 21 , strongly highlighted a structural variation (SV) in the form of a short insertion associated with the longtail phenotype, adding a new critical member to the gene repertoire of the sheep tail configuration.…”

“…HOXB13 as a controller of long and short tails: variant determination in the ovine context In recent studies [21][22][23] , the HOXB13 gene was first highlighted to be significantly associated with the sheep tail phenotype in a genomic comparison that included Ethiopian fat-rumped and short fat-tailed sheep breeds vs. Ethiopian long fat-tailed and Sudanese long thin-tailed sheep breeds 22 . In this genomic analysis, a haplotype specific to Ethiopian long fat-tailed and Sudanese long thin-tailed sheep breeds was highlighted (top variant: rs428121282; chr11:37,338,422; Oar_v3.1) 22 .…”

“…These include six highly differentiated SVs in the IBH selective region (the largest event was a 7728-bp insertion) and three SVs in the PDGFD selective region (the largest one was an 867-bp insertion) 21 . More recently, in the Merinolandschaf breed, the same variant was highlighted as a 167-bp insertion in the promotor region of HOXB13 with a completely linked nonsynonymous mutation in the first exon of HOXB13 located 132 bp downstream of the insertion (rs413316737; chr11:37,290,361; OAR_v4.0; c.C23G) 23 . This 167-bp insertion was flanked by 14-bp direct repeats (CTGCCAGCGATTTA) on both sides, which suggests the potential that this insertion is a short interspersed nuclear element (SINE) 23 .…”

“…More recently, in the Merinolandschaf breed, the same variant was highlighted as a 167-bp insertion in the promotor region of HOXB13 with a completely linked nonsynonymous mutation in the first exon of HOXB13 located 132 bp downstream of the insertion (rs413316737; chr11:37,290,361; OAR_v4.0; c.C23G) 23 . This 167-bp insertion was flanked by 14-bp direct repeats (CTGCCAGCGATTTA) on both sides, which suggests the potential that this insertion is a short interspersed nuclear element (SINE) 23 . Differences in the length and position of variant were indicated as a result of sequencing error due to the presence of a long 'T' base homopolymer in the detected SINE repeat element 23 .…”