Genome data uncover four synergistic key regulators for extremely small body size in horses

Abstract

Background: Miniature size in horses represents an extreme reduction of withers height that originated after domestication. In some breeds, it is a highly desired trait representing a breed- or subtype-specific feature. The genomic changes that emerged due to strong-targeted selection towards this distinct type remain unclear.

Results: Comparisons of whole-genome sequencing data from two Miniature Shetland ponies and one standard-sized Shetland pony, performed to elucidate genetic determinants for miniature size, revealed four synergistic variants, limiting withers height to 34.25 in. (87 cm). Runs of homozygosity regions were detected spanning these four variants in both the Miniature Shetland ponies and the standard-sized Shetland pony. They were shown to be characteristic of the Shetland pony breed, resulting in a miniature type under specific genotypic combinations. These four genetic variants explained 72% of the size variation among Shetland ponies and related breeds. The length of the homozygous regions indicate that they arose over 1000 years ago. In addition, a copy number variant was identified in DIAPH3 harboring a loss exclusively in ponies and donkeys and thus representing a potential height-associated variant.

Conclusion: This study reveals main drivers for miniature size in horses identified in whole genome data and thus provides relevant candidate genes for extremely short stature in mammals.

Keywords: Body size; Horse; Miniature; Next generation sequencing; Pony; ROH; Synergism.

Fig. 1

Pairwise Fst between three Shetland ponies and a pool of 24 equids. The individual chromosomes are plotted against Fst detected in windows of 50,000 bp

Fig. 2

Genotype distribution of height associated variants. The withers height of the investigated Shetland ponies and related breeds is compared with the variant genotypes of ADAMTS17, OSTN, GH1 and HMGA2 (a). General linear model analysis confirmed a significant association of variant genotypes with height at the withers. A considerably lower withers height can be seen in ponies with a homozygous mutant genotype for all four variants. Comparative evaluation of all four genotypes shows a powerful synergistic effect (b). None of the horses with homozygous mutant genotypes of all variants or homozygous mutant genotypes of three variants plus a heterozygous genotype of the fourth variant shows a withers height higher than 87 cm

Fig. 3

Shetland pony specific deletion located in DIAPH3. Integrated Genomics Viewer (IGV) shows bam-files of all three Shetland ponies derived from whole-genome sequencing analysis harbouring a deletion of an estimated size of 7245 bp. In contrast, all control horses reveal an insertion in this region (exemplary display of three Hanoverian horses)

Fig. 4

Shetland pony specific deletion located in VWA8. Integrated Genomics Viewer (IGV) shows bam-files of all three Shetland ponies derived from whole-genome sequencing analysis harbouring a deletion of an estimated size of 21,284 bp. In contrast, all control horses reveal an insertion in this region (exemplary display of three Hanoverian horses)

Fig. 5

Frequency of DIAPH3 deletion in horse breeds/ populations. CNV detection in the whole validation sample set reveals copy numbers of 1 or 0 exclusively in the Shetland ponies and related breeds as well as in the Icelandic horse, Lewitzer, Welsh and Donkey

Fig. 6

Pony-specific deletion found in DIAPH3. Graphical representation of a region of DIAPH3 revealing a 7245 bp loss in intron 3, which can be observed in the Shetland pony and in one ancient Berel’ horse