Limits...
A Non-Synonymous HMGA2 Variant Decreases Height in Shetland Ponies and Other Small Horses.

Frischknecht M, Jagannathan V, Plattet P, Neuditschko M, Signer-Hasler H, Bachmann I, Pacholewska A, Drögemüller C, Dietschi E, Flury C, Rieder S, Leeb T - PLoS ONE (2015)

Bottom Line: This suggests that the HMGA2 variant also affects DNA binding in vivo and thus leads to reduced growth and a smaller stature in Shetland ponies.The identified HMGA2 variant also segregates in several other pony breeds but was not found in regular-sized horse breeds.We therefore conclude that we identified a quantitative trait nucleotide for height in horses.

View Article: PubMed Central - PubMed

Affiliation: Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland; Agroscope, Swiss National Stud Farm, 1580, Avenches, Switzerland; Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL & Agroscope, 3001, Bern, Switzerland.

ABSTRACT
The identification of quantitative trait loci (QTL) such as height and their underlying causative variants is still challenging and often requires large sample sizes. In humans hundreds of loci with small effects control the heritable portion of height variability. In domestic animals, typically only a few loci with comparatively large effects explain a major fraction of the heritability. We investigated height at withers in Shetland ponies and mapped a QTL to ECA 6 by genome-wide association (GWAS) using a small cohort of only 48 animals and the Illumina equine SNP70 BeadChip. Fine-mapping revealed a shared haplotype block of 793 kb in small Shetland ponies. The HMGA2 gene, known to be associated with height in horses and many other species, was located in the associated haplotype. After closing a gap in the equine reference genome we identified a non-synonymous variant in the first exon of HMGA2 in small Shetland ponies. The variant was predicted to affect the functionally important first AT-hook DNA binding domain of the HMGA2 protein (c.83G>A; p.G28E). We assessed the functional impact and found impaired DNA binding of a peptide with the mutant sequence in an electrophoretic mobility shift assay. This suggests that the HMGA2 variant also affects DNA binding in vivo and thus leads to reduced growth and a smaller stature in Shetland ponies. The identified HMGA2 variant also segregates in several other pony breeds but was not found in regular-sized horse breeds. We therefore conclude that we identified a quantitative trait nucleotide for height in horses.

No MeSH data available.


Multiple species alignment of the first 37 amino acids of HMGA2.The first AT-hook domain of HMGA2 is shaded in orange. Position 28 with the p.G28E variant in Shetland ponies is fully conserved in all analyzed vertebrate species including zebrafish The sequences were derived from the following accession numbers: Equus caballus, LN849001; Homo sapiens, NP_003474.1; Pan troglodytes, XP_009423258.1; Bos taurus, XP_002687694.2; Sus scrofa, XP_005664014.1; Mus musculus, NP_034571.1; Rattus norvegicus, NP_114459.1; Gallus gallus, NP_990332.1; Danio rerio, NP_997845.1.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4608717&req=5

pone.0140749.g002: Multiple species alignment of the first 37 amino acids of HMGA2.The first AT-hook domain of HMGA2 is shaded in orange. Position 28 with the p.G28E variant in Shetland ponies is fully conserved in all analyzed vertebrate species including zebrafish The sequences were derived from the following accession numbers: Equus caballus, LN849001; Homo sapiens, NP_003474.1; Pan troglodytes, XP_009423258.1; Bos taurus, XP_002687694.2; Sus scrofa, XP_005664014.1; Mus musculus, NP_034571.1; Rattus norvegicus, NP_114459.1; Gallus gallus, NP_990332.1; Danio rerio, NP_997845.1.

Mentions: As the NGS data did not contain any variant calls in the gap region, we PCR-amplified a region containing the first exon from the two Shetland ponies used in the initial variant analysis. We sequenced the PCR products using the Sanger method and identified an additional non-synonymous variant, HMGA2:c.83G>A. This variant is predicted to result in the exchange of a neutral glycine residue to a negatively charged glutamate in the HMGA2 protein (p.G28E). The major HMGA2 protein isoform is highly conserved across vertebrates and contains 109 amino acids. It is a DNA-binding protein with 3 so-called AT-hooks, strongly positively charged domains, which bind to the minor groove of DNA. The p.G28E exchange is located in the first of these AT-hooks. We hypothesized that the additional negative charge would impair the binding of this domain to the likewise negatively charged DNA. PolyPhen-2 also predicted this variant to be probably damaging (score = 0.999) [16]. The extremely high conservation of the first AT-hook of HMGA2 is shown in Fig 2.


A Non-Synonymous HMGA2 Variant Decreases Height in Shetland Ponies and Other Small Horses.

Frischknecht M, Jagannathan V, Plattet P, Neuditschko M, Signer-Hasler H, Bachmann I, Pacholewska A, Drögemüller C, Dietschi E, Flury C, Rieder S, Leeb T - PLoS ONE (2015)

Multiple species alignment of the first 37 amino acids of HMGA2.The first AT-hook domain of HMGA2 is shaded in orange. Position 28 with the p.G28E variant in Shetland ponies is fully conserved in all analyzed vertebrate species including zebrafish The sequences were derived from the following accession numbers: Equus caballus, LN849001; Homo sapiens, NP_003474.1; Pan troglodytes, XP_009423258.1; Bos taurus, XP_002687694.2; Sus scrofa, XP_005664014.1; Mus musculus, NP_034571.1; Rattus norvegicus, NP_114459.1; Gallus gallus, NP_990332.1; Danio rerio, NP_997845.1.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4608717&req=5

pone.0140749.g002: Multiple species alignment of the first 37 amino acids of HMGA2.The first AT-hook domain of HMGA2 is shaded in orange. Position 28 with the p.G28E variant in Shetland ponies is fully conserved in all analyzed vertebrate species including zebrafish The sequences were derived from the following accession numbers: Equus caballus, LN849001; Homo sapiens, NP_003474.1; Pan troglodytes, XP_009423258.1; Bos taurus, XP_002687694.2; Sus scrofa, XP_005664014.1; Mus musculus, NP_034571.1; Rattus norvegicus, NP_114459.1; Gallus gallus, NP_990332.1; Danio rerio, NP_997845.1.
Mentions: As the NGS data did not contain any variant calls in the gap region, we PCR-amplified a region containing the first exon from the two Shetland ponies used in the initial variant analysis. We sequenced the PCR products using the Sanger method and identified an additional non-synonymous variant, HMGA2:c.83G>A. This variant is predicted to result in the exchange of a neutral glycine residue to a negatively charged glutamate in the HMGA2 protein (p.G28E). The major HMGA2 protein isoform is highly conserved across vertebrates and contains 109 amino acids. It is a DNA-binding protein with 3 so-called AT-hooks, strongly positively charged domains, which bind to the minor groove of DNA. The p.G28E exchange is located in the first of these AT-hooks. We hypothesized that the additional negative charge would impair the binding of this domain to the likewise negatively charged DNA. PolyPhen-2 also predicted this variant to be probably damaging (score = 0.999) [16]. The extremely high conservation of the first AT-hook of HMGA2 is shown in Fig 2.

Bottom Line: This suggests that the HMGA2 variant also affects DNA binding in vivo and thus leads to reduced growth and a smaller stature in Shetland ponies.The identified HMGA2 variant also segregates in several other pony breeds but was not found in regular-sized horse breeds.We therefore conclude that we identified a quantitative trait nucleotide for height in horses.

View Article: PubMed Central - PubMed

Affiliation: Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland; Agroscope, Swiss National Stud Farm, 1580, Avenches, Switzerland; Swiss Competence Center of Animal Breeding and Genetics, University of Bern, Bern University of Applied Sciences HAFL & Agroscope, 3001, Bern, Switzerland.

ABSTRACT
The identification of quantitative trait loci (QTL) such as height and their underlying causative variants is still challenging and often requires large sample sizes. In humans hundreds of loci with small effects control the heritable portion of height variability. In domestic animals, typically only a few loci with comparatively large effects explain a major fraction of the heritability. We investigated height at withers in Shetland ponies and mapped a QTL to ECA 6 by genome-wide association (GWAS) using a small cohort of only 48 animals and the Illumina equine SNP70 BeadChip. Fine-mapping revealed a shared haplotype block of 793 kb in small Shetland ponies. The HMGA2 gene, known to be associated with height in horses and many other species, was located in the associated haplotype. After closing a gap in the equine reference genome we identified a non-synonymous variant in the first exon of HMGA2 in small Shetland ponies. The variant was predicted to affect the functionally important first AT-hook DNA binding domain of the HMGA2 protein (c.83G>A; p.G28E). We assessed the functional impact and found impaired DNA binding of a peptide with the mutant sequence in an electrophoretic mobility shift assay. This suggests that the HMGA2 variant also affects DNA binding in vivo and thus leads to reduced growth and a smaller stature in Shetland ponies. The identified HMGA2 variant also segregates in several other pony breeds but was not found in regular-sized horse breeds. We therefore conclude that we identified a quantitative trait nucleotide for height in horses.

No MeSH data available.