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Home / Equine Research Bank / Animals (Basel) / SNP-Based Heritability of Osteochondrosis Dissecans in Hanov...
Animals : an open access journal from MDPI2023; 13(9); doi: 10.3390/ani13091462

SNP-Based Heritability of Osteochondrosis Dissecans in Hanoverian Warmblood Horses.

Abstract: Before the genomics era, heritability estimates were performed using pedigree data. Data collection for pedigree analysis is time consuming and holds the risk of incorrect or incomplete data. With the availability of SNP-based arrays, heritability can now be estimated based on genotyping data. We used SNP array and 1.6 million imputed genotype data with different minor allele frequency restrictions to estimate heritabilities for osteochondrosis dissecans in the fetlock, hock and stifle joints of 446 Hanoverian warmblood horses. SNP-based heritabilities were estimated using a genomic restricted maximum likelihood (GREML) method and accounting for patterns of regional linkage disequilibrium in the equine genome. In addition, we employed GREML for family data to account for different degrees of relatedness in the study population. Our results indicate that we were able to capture a larger proportion of additive genetic variance compared to pedigree-based estimates in the same population of Hanoverian horses. Heritability estimates on the linear scale for fetlock-, hock- and stifle-osteochondrosis dissecans were 0.41-0.43, 0.62-0.63, and 0.23-0.25, respectively, with standard errors of 0.11-0.14. Accounting for linkage disequilibrium patterns had an upward effect on the imputed data and a downward impact on the SNP array genotype data. GREML for family data resulted in higher heritability estimates for fetlock-osteochondrosis dissecans and slightly higher estimates for hock-osteochondrosis dissecans, but had no effect on stifle-osteochondrosis dissecans. The largest and most consistent heritability estimates were obtained when we employed GREML for family data with genomic relationship matrices weighted through patterns of regional linkage disequilibrium. Estimation of SNP-based heritability should be recommended for traits that can only be phenotyped in smaller samples or are cost-effective.
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Publication Date: 2023-04-25 PubMed ID: 37174498PubMed Central: PMC10177438DOI: 10.3390/ani13091462Google Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

The study focuses on using a new method (genotype data from SNP arrays) to estimate the heritability of osteochondrosis dissecans, a common joint disorder in Hanoverian warmblood horses, and shows that this method provides more accurate estimates compared to the traditional pedigree analysis.

Background and Methodology

  • The researchers conducted an investigation on osteochondrosis dissecans, a common ailment in Hanoverian warmblood horses, affecting the fetlock, hock, and stifle joints. The aim was to use Single Nucleotide Polymorphism (SNP)-based genotyping data to estimate the heritability of this disorder in these horses.
  • In the past, heritability estimates relied largely on pedigree data – a slow, possibly imprecise method due to potential inaccuracies or omissions in the data.
  • Using SNP array and 1.6 million imputed genotype data with varied minor allele frequency restrictions enabled the researchers to utilize a contemporary method for the heritability estimation.
  • The application of a genomic restricted maximum likelihood (GREML) method, which takes into account the regional correlation within the genes (termed “linkage disequilibrium”), was instrumental in SNP-based heritability estimation.
  • Also, this study factored in different relationships in the horse population by utilizing GREML for family data.

Results and Implication

  • The SNP-based heritability method showed better capture of the additive genetic variance when compared to pedigree-based estimates, depicting it as a more precise approach.
  • This study provided distinct heritability estimates for each osteochondrosis dissecans type. The fetlock, hock, and stifle estimates were 0.41-0.43, 0.62-0.63, and 0.23-0.25, respectively.
  • Careful consideration of linkage disequilibrium patterns influenced the accuracy of the data. They elevated the imputed data’s effect and reduced the impact of the SNP array genotype data.
  • GREML for family data significantly increased the heritability estimates for fetlock- and hock-osteochondrosis dissecans, but made no difference for stifle-osteochondrosis dissecans.
  • The study indicated that the most accurate heritability estimates resulted from implementing GREML for family data, especially when genomic relationship matrices were weighted by patterns of regional linkage disequilibrium.
  • The abstract concludes by advocating for the use of SNP-based heritability estimation methods for traits prone to be phenotyped in smaller samples or for cost-effective pursuits.

Cite This Article

APA
Zimmermann E, Distl O. (2023). SNP-Based Heritability of Osteochondrosis Dissecans in Hanoverian Warmblood Horses. Animals (Basel), 13(9). https://doi.org/10.3390/ani13091462

Publication

Animals : an open access journal from MDPI
ISSN: 2076-2615
NlmUniqueID: 101635614
Country: Switzerland
Language: English
Volume: 13
Issue: 9

Researcher Affiliations

Zimmermann, Elisa
  • Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover (Foundation), 30559 Hannover, Germany.
Distl, Ottmar
  • Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover (Foundation), 30559 Hannover, Germany.

Conflict of Interest Statement

The authors declare no conflict of interest.

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