GWAS Identifies a Region Containing the SALL1 Gene in Variation of Pigmentation Intensity Within the Chestnut Coat Color of Horses.
Abstract: Chestnut coat color in horses is determined by a missense mutation within the MC1R gene. However, the intensity of the chestnut color can vary widely within individuals possessing this genotype. Here, we investigated this variation using standardized photographs of 96 horses. Each horse was ranked lightest to darkest within the cohort for phenotype by 3 blinded observers. A genome-wide association study utilizing the relative shade ranking as the phenotype and using 268 487 single-nucleotide polymorphisms (SNPs) genotyped using the Affymetrix Equine 670k array identified a single significantly associated region on chromosome 3 (P = 2.934 × 10-8). Analysis of whole-genome sequences for horses spanning the diverse range of chestnut color identified candidate SNPs within the coding sequence of the only gene in the region: SALL1. The function of SALL1 is largely unknown, though it is predicted to interact with the Hermansky-Pudlak Syndrome type 1 (HPS1) protein, which causes partial albinism in humans. However, with only one study suggesting a circumstantial influence of the SALL1 protein on pigmentation, additional work is needed to confirm this new coat color locus in larger populations and investigate the function of this protein for impacts on equine health.
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Publication Date: 2021-08-04 PubMed ID: 34343312PubMed Central: PMC8386761DOI: 10.1093/jhered/esab037Google Scholar: Lookup
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Summary
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The research article is about the findings of a genome-wide study conducted to understand the genetic basis of chestnut color intensity variations in horses. The study identified a region on chromosome 3, specifically the SALL1 gene, which influences this color variation.
Introduction to the Study
- This research investigates the chestnut coat color variation in horses. While the chestnut coat coloration is determined by a change in the MC1R gene, significant variations in the intensity of this color within horses possessing this genotype have been observed. The specific factors causing this variation were hitherto unknown.
- The goal is to understand what genetic elements are influencing this color intensity fluctuation. The researchers achieved this by carrying out a genome-wide association study (GWAS).
Methodology
- The researchers collected standardized photographs of 96 horses for this study. Three impartial observers were used to rank each horse from lightest to darkest based on their chestnut color intensity.
- Using these ranks as phenotypes, the team undertook a GWAS. They used a specific gene chip, an Affymetrix Equine 670k array, to genotype 268 487 single-nucleotide polymorphisms (SNPs), which are genetic markers, in each horse.
Findings of the GWAS
- Through the GWAS, the team identified one region on the horse’s Chromosome 3 that was significantly associated with the variation (P = 2.934 × 10-8).
- In-depth analysis of the whole genome sequences of the horses representing the chestnut color intensity spectrum led to the identification of candidate SNPs within the coding sequence of the SALL1 gene. This gene was the only one identified within the significant region located on chromosome 3.
Implications
- The role of the SALL1 gene is largely unknown, but it is thought to interact with the Hermansky-Pudlak Syndrome type 1 (HPS1) protein. Dysfunction of the HPS1 protein in humans leads to partial albinism, indicating a possible role of this gene and its protein in pigmentation.
- These findings lay the groundwork for further research aimed at confirming the influence of SALL1 on the horse’s coat color in a larger population.
- Future research might also investigate the impact of SALL1 on equine health, given the suggested connection with the HPS1 protein which, in humans, causes a form of albinism.
Cite This Article
APA
Hammons V, Ribeiro L, Munyard K, Sadeghi R, Miller D, Antczak D, Brooks SA.
(2021).
GWAS Identifies a Region Containing the SALL1 Gene in Variation of Pigmentation Intensity Within the Chestnut Coat Color of Horses.
J Hered, 112(5), 443-446.
https://doi.org/10.1093/jhered/esab037 Publication
Researcher Affiliations
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.
- Department of Animal Sciences, UF Genetics Institute, University of Florida, 2250 Shealy Dr, Gainesville, FL, USA.
- Royal Veterinary College, University of London, London, UK.
- Department of Animal Sciences, UF Genetics Institute, University of Florida, 2250 Shealy Dr, Gainesville, FL, USA.
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, Australia.
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
- Department of Animal Sciences, UF Genetics Institute, University of Florida, 2250 Shealy Dr, Gainesville, FL, USA.
MeSH Terms
- Animals
- Genome
- Genome-Wide Association Study
- Genotype
- Horses / genetics
- Phenotype
- Pigmentation / genetics
Grant Funding
- 202802/Z/16/Z / Wellcome Trust
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