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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.


Electrophoretic mobility shift assay (EMSA).We incubated a double-stranded oligonucleotide (dsDNA) with increasing concentrations of peptides containing either the wildtype (28Gly) or mutant (28Glu) sequence of the first AT-hook of the HMGA2 protein. With the wildtype sequence a partial shift of the dsDNA band could already be observed at the lowest concentration of peptide corresponding to a molar ratio of peptide to DNA of 1.4. At the highest concentration of the wildtype peptide, the majority of the DNA was in the DNA-protein complex. In contrast, with the mutant peptide the band shift was only observed at higher peptide concentrations and a smaller proportion of DNA was bound.
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pone.0140749.g005: Electrophoretic mobility shift assay (EMSA).We incubated a double-stranded oligonucleotide (dsDNA) with increasing concentrations of peptides containing either the wildtype (28Gly) or mutant (28Glu) sequence of the first AT-hook of the HMGA2 protein. With the wildtype sequence a partial shift of the dsDNA band could already be observed at the lowest concentration of peptide corresponding to a molar ratio of peptide to DNA of 1.4. At the highest concentration of the wildtype peptide, the majority of the DNA was in the DNA-protein complex. In contrast, with the mutant peptide the band shift was only observed at higher peptide concentrations and a smaller proportion of DNA was bound.

Mentions: To assess the functional consequences of the amino acid exchange we performed an electrophoretic mobility shift assay (EMSA). We incubated peptides comprising 11 amino acids with the first AT-hook domain of either the wildtype or mutant HMGA2 protein with a double-stranded oligonucleotide containing an HMGA2 binding site. The EMSA experiment showed that the mutant peptide bound with greatly reduced affinity to the DNA compared to the peptide with the wildtype sequence (Fig 5).


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)

Electrophoretic mobility shift assay (EMSA).We incubated a double-stranded oligonucleotide (dsDNA) with increasing concentrations of peptides containing either the wildtype (28Gly) or mutant (28Glu) sequence of the first AT-hook of the HMGA2 protein. With the wildtype sequence a partial shift of the dsDNA band could already be observed at the lowest concentration of peptide corresponding to a molar ratio of peptide to DNA of 1.4. At the highest concentration of the wildtype peptide, the majority of the DNA was in the DNA-protein complex. In contrast, with the mutant peptide the band shift was only observed at higher peptide concentrations and a smaller proportion of DNA was bound.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0140749.g005: Electrophoretic mobility shift assay (EMSA).We incubated a double-stranded oligonucleotide (dsDNA) with increasing concentrations of peptides containing either the wildtype (28Gly) or mutant (28Glu) sequence of the first AT-hook of the HMGA2 protein. With the wildtype sequence a partial shift of the dsDNA band could already be observed at the lowest concentration of peptide corresponding to a molar ratio of peptide to DNA of 1.4. At the highest concentration of the wildtype peptide, the majority of the DNA was in the DNA-protein complex. In contrast, with the mutant peptide the band shift was only observed at higher peptide concentrations and a smaller proportion of DNA was bound.
Mentions: To assess the functional consequences of the amino acid exchange we performed an electrophoretic mobility shift assay (EMSA). We incubated peptides comprising 11 amino acids with the first AT-hook domain of either the wildtype or mutant HMGA2 protein with a double-stranded oligonucleotide containing an HMGA2 binding site. The EMSA experiment showed that the mutant peptide bound with greatly reduced affinity to the DNA compared to the peptide with the wildtype sequence (Fig 5).

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.