SNP-Based Heritability of Osteochondrosis Dissecans in Hanoverian Warmblood Horses
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 us...
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MDPI AG
2023-04-01
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| Series: | Animals |
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| Online Access: | https://www.mdpi.com/2076-2615/13/9/1462 |
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| author | Elisa Zimmermann Ottmar Distl |
| author_facet | Elisa Zimmermann Ottmar Distl |
| author_sort | Elisa Zimmermann |
| collection | DOAJ |
| description | 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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| language | English |
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| publishDate | 2023-04-01 |
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| series | Animals |
| spelling | doaj.art-47b9b1911a8c480cbcddccb3f696f2c32023-11-17T22:29:26ZengMDPI AGAnimals2076-26152023-04-01139146210.3390/ani13091462SNP-Based Heritability of Osteochondrosis Dissecans in Hanoverian Warmblood HorsesElisa Zimmermann0Ottmar Distl1Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover (Foundation), 30559 Hannover, GermanyInstitute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover (Foundation), 30559 Hannover, GermanyBefore 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.https://www.mdpi.com/2076-2615/13/9/1462equidosteochondrosisgenetic parametersgenomic relationship matricesSNP-based heritabilitylinkage disequilibrium |
| spellingShingle | Elisa Zimmermann Ottmar Distl SNP-Based Heritability of Osteochondrosis Dissecans in Hanoverian Warmblood Horses Animals equid osteochondrosis genetic parameters genomic relationship matrices SNP-based heritability linkage disequilibrium |
| title | SNP-Based Heritability of Osteochondrosis Dissecans in Hanoverian Warmblood Horses |
| title_full | SNP-Based Heritability of Osteochondrosis Dissecans in Hanoverian Warmblood Horses |
| title_fullStr | SNP-Based Heritability of Osteochondrosis Dissecans in Hanoverian Warmblood Horses |
| title_full_unstemmed | SNP-Based Heritability of Osteochondrosis Dissecans in Hanoverian Warmblood Horses |
| title_short | SNP-Based Heritability of Osteochondrosis Dissecans in Hanoverian Warmblood Horses |
| title_sort | snp based heritability of osteochondrosis dissecans in hanoverian warmblood horses |
| topic | equid osteochondrosis genetic parameters genomic relationship matrices SNP-based heritability linkage disequilibrium |
| url | https://www.mdpi.com/2076-2615/13/9/1462 |
| work_keys_str_mv | AT elisazimmermann snpbasedheritabilityofosteochondrosisdissecansinhanoverianwarmbloodhorses AT ottmardistl snpbasedheritabilityofosteochondrosisdissecansinhanoverianwarmbloodhorses |