Should we use the single nucleotide polymorphism linked to in genomic evaluation of French trotter?
Abstract: An A/C mutation responsible for the ability to pace in horses was recently discovered in the gene. It has also been proven that allele C has a negative effect on trotters' performances. However, in French trotters (FT), the frequency of allele A is only 77% due to an unexpected positive effect of allele C in late-career FT performances. Here we set out to ascertain whether the genotype at SNP (linked to ) should be used to compute EBV for FT. We used the genotypes of 630 horses, with 41,711 SNP retained. The pedigree comprised 5,699 horses. Qualification status (trotters need to complete a 2,000-m race within a limited time to begin their career) and earnings at different ages were precorrected for fixed effects and evaluated with a multitrait model. Estimated breeding values were computed with and without the genotype at SNP as a fixed effect in the model. The analyses were performed using pedigree only via BLUP and using the genotypes via genomic BLUP (GBLUP). The genotype at SNP was removed from the file of genotypes when already taken into account as a fixed effect. Alternatively, 3 groups of 100 candidates were used for validation. Validations were also performed on 50 random-clustered groups of 126 candidates and compared against the results of the 3 disjoint sets. For performances on which has a minor effect, the coefficients of correlation were not improved when the genotype at SNP was a fixed effect in the model (earnings at 3 and 4 yr). However, for traits proven strongly related to , the accuracy of evaluation was improved, increasing +0.17 for earnings at 2 yr, +0.04 for earnings at 5 yr and older, and +0.09 for qualification status (with the GBLUP method). For all traits, the bias was reduced when the SNP linked to was a fixed effect in the model. This work finds a clear rationale for using the genotype at for this multitrait evaluation. Genomic selection seemed to achieve better results than classic selection.
Publication Date: 2015-11-03 PubMed ID: 26523557DOI: 10.2527/jas.2015-9224Google Scholar: Lookup
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- Journal Article
- Research Support
- Non-U.S. Gov't
Summary
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The study focuses on evaluating whether the genotype at Single Nucleotide Polymorphism (SNP), linked to a genetic mutation, should be used for predicting the estimated breeding values (EBV) of French Trotter horses. The results show that for traits strongly related to SNP, accuracy of evaluation improves significantly, thus supporting the use of this genotype for multitrait evaluation. Genomic selection also appeared to provide more accurate results than traditional selection methods.
Research Methodology
- The study involved the assessment of genotypes from 630 horses.
- 41,711 SNP were retained, with a pedigree encompassing 5,699 horses.
- The researchers considered two key areas in evaluating the horses: a 2,000 meter race qualification status and earnings at different ages.
- These traits were precorrected for fixed effects and evaluated using a multitrait model.
- The Estimated Breeding Values (EBV) were computed with the genotype at SNP being included and excluded as a fixed effect in the model.
- Analyses were performed using the genotypes through genomic BLUP (GBLUP) method, with SNP genotype removed from the genotype file when it was already considered as a fixed effect.
- Three subsets of 100 candidates each were used for validation, alongside 50 randomly-clustered groups of 126 candidates.
Key Findings
- For performance indicators that had minor relation to SNP (like earnings at ages 3 and 4), the coefficients of correlation did not improve when genotype at SNP was included as a fixed effect in the model.
- However, for those traits which were strongly related to SNP, the accuracy of evaluation saw significant improvement. Specifically, there was an increase of +0.17 in 2-year-old earnings, +0.04 for 5-year-old and older earnings, and +0.09 for qualification status.
- Across all traits studied, the bias was reduced when the SNP linked to the gene mutation was included as a fixed effect in the model.
Conclusion
- This study identifies a sound rationale for using the genotype at Single Nucleotide Polymorphism in the multitrait evaluation model
- In comparison to classic selection techniques, genomic selection appears to produce better accuracy results in assessment of French Trotter horses.
Cite This Article
APA
Brard S, Ricard A.
(2015).
Should we use the single nucleotide polymorphism linked to in genomic evaluation of French trotter?
J Anim Sci, 93(10), 4651-4659.
https://doi.org/10.2527/jas.2015-9224 Publication
Researcher Affiliations
MeSH Terms
- Alleles
- Animals
- Breeding
- Databases, Factual
- Genomics / methods
- Genotype
- Horses / genetics
- Mutation
- Pedigree
- Polymorphism, Single Nucleotide
- Reproducibility of Results
- Transcription Factors / genetics
- Transcription Factors / metabolism
Citations
This article has been cited 2 times.- Ricard A, Duluard A. Genomic analysis of gaits and racing performance of the French trotter. J Anim Breed Genet 2021 Mar;138(2):204-222.
- Legarra A, Ricard A, Varona L. GWAS by GBLUP: Single and Multimarker EMMAX and Bayes Factors, with an Example in Detection of a Major Gene for Horse Gait. G3 (Bethesda) 2018 Jul 2;8(7):2301-2308.
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