Dominanssin vaikutus eläinten jalostusarvojen ennustamisessa

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Identification of runs of homozygosity affecting female fertility and milk production traits in Finnish Ayrshire cattle

Inbreeding gives rise to continuous lengths of homozygous genotypes called runs of homozygosity (ROH) that occur when identical haplotypes are inherited from both parents. ROHs are enriched for deleterious recessive alleles and can therefore be linked to inbreeding depression, defined as decreased phenotypic performance of the animals. However, not all ROHs within a region are expected to have harmful effects on the trait of interest. We aimed to identify ROHs that unfavourably affect female fertility and milk production traits in the Finnish Ayrshire population. The estimated effect of ROHs with the highest statistical significance varied between parities from 9 to 17 days longer intervals from calving to first insemination, from 13 to 38 days longer intervals from first to last insemination and from 0.3 to 1.0 more insemination per conception. Similarly, for milk production traits ROHs were associated with a reduction of 208 kg for milk yield, 7 kg for protein yield and 16 kg for fat yield. We also found regions where ROHs displayed unfavourable effects across multiple traits. Our findings can be exploited for more efficient control of inbreeding depression, for example by minimizing the occurrence of unfavourable haplotypes as homozygous state in breeding programmes.yPeer reviewe

Effect of genomic selection on genetic variability in chromosomal level in the Finnish Ayrshire

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A combination of two variants in PRKAG3 is needed for a positive effect on meat quality in pigs

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Relationship between bull dam herd characteristics and bias in estimated breeding value of bull

The objective of the study was to relate estimated breeding values (EBVs) of the parents’ 305-days protein production and the bull dam herd-year characteristics to the empirical bias in pedigree indices (difference between the pedigree index and the final proof) of young bulls. Two animal model evaluations were carried out; one included records up to 1990 and the other up to spring 1992. The final data set included 242 bulls with pedigree indices, final proofs, parents’ EBVs, production and herd information (the size, the average production and the intraherd standard deviation) of the dams. The average empirical bias in pedigree indices was 13.6 kg. The correlation between the final proof of the bull and the EBVs of the bull sire or dam were 0.45 and 0.17, respectively. The low correlation with bull dam EBV indicates the unreliability of the bull dam EBVs. Size of the herd and the standard deviation of production in the herd when bull dam produced its third lactation were correlated with the empirical bias in pedigree index. Pedigree indices of the bulls coming from small herds with high intraherd standard deviation were more biased than those from the big herds with low intraherd standard deviation. The best bulls, when grouped according to their final proofs, were sons of the highest EBV sires. EBVs of bull dams did not differ in the highest and the lowest final proof groups, but the dams of the best bull group had a higher first lactation record than the dams of the other bull groups

Heritability of hypothyroidism in the Finnish Hovawart population

Background: The Hovawart is a working and companion dog breed of German origin. A few hundred Hovawart dogs are registered annually in Finland. The most common disease with a proposed genetic background in Hovawarts is hypothyroidism. The disease is usually caused by lymphocytic thyroiditis, an autoimmune disorder which destroys the thyroid gland. Hypothyroidism can be treated medically with hormone replacement. Its overall incidence could also be reduced through selection, provided that the trait shows an adequate genetic basis. The aim of this study was to estimate the heritability of hypothyroidism in the Finnish Hovawart population. Results: The pedigree data for the study were provided by the Finnish Kennel Club and the hypothyroidism data by the Finnish Hovawart Club. The data included 4953 dogs born between 1990 and 2010, of which 107 had hypothyroidism and 4846 were unaffected. Prior to the estimation of heritability, we studied the effects of gender, birth year, birth month, and inbreeding on susceptibility to hypothyroidism. Heritability was estimated with the probit model both via restricted maximum likelihood (REML) and Gibbs sampling, using litter and sire of the dog as random effects. None of the studied systematic effects or level of inbreeding had a significant effect on susceptibility to hypothyroidism. The estimated heritability of hypothyroidism varied from 0.47 (SE=0.18) using REML to 0.62 (SD=0.21) using Gibbs sampling. Conclusions: Based on our analysis, the heritability of hypothyroidism is moderate to high, suggesting that its prevalence could be decreased through selection. Thus, breeders should notify the breed association of any affected dogs, and their use for breeding should be avoided.Peer reviewe

Heritability of hypothyroidism in the Finnish Hovawart population

Background: The Hovawart is a working and companion dog breed of German origin. A few hundred Hovawart dogs are registered annually in Finland. The most common disease with a proposed genetic background in Hovawarts is hypothyroidism. The disease is usually caused by lymphocytic thyroiditis, an autoimmune disorder which destroys the thyroid gland. Hypothyroidism can be treated medically with hormone replacement. Its overall incidence could also be reduced through selection, provided that the trait shows an adequate genetic basis. The aim of this study was to estimate the heritability of hypothyroidism in the Finnish Hovawart population. Results: The pedigree data for the study were provided by the Finnish Kennel Club and the hypothyroidism data by the Finnish Hovawart Club. The data included 4953 dogs born between 1990 and 2010, of which 107 had hypothyroidism and 4846 were unaffected. Prior to the estimation of heritability, we studied the effects of gender, birth year, birth month, and inbreeding on susceptibility to hypothyroidism. Heritability was estimated with the probit model both via restricted maximum likelihood (REML) and Gibbs sampling, using litter and sire of the dog as random effects. None of the studied systematic effects or level of inbreeding had a significant effect on susceptibility to hypothyroidism. The estimated heritability of hypothyroidism varied from 0.47 (SE=0.18) using REML to 0.62 (SD=0.21) using Gibbs sampling. Conclusions: Based on our analysis, the heritability of hypothyroidism is moderate to high, suggesting that its prevalence could be decreased through selection. Thus, breeders should notify the breed association of any affected dogs, and their use for breeding should be avoided.Peer reviewe

Identification of copy number variations and candidate genes for reproduction traits in Finnish pig populations

Animal breeding programs can be improved by genetic markers associated with production and reproduction traits. Reproduction traits are important for economic success of pig production and therefore development of genetic tools for selection is of high interest to pig breeding. In this study our objective was to identify genomic regions as-sociated with fertility traits in two Finnish pig breeds using large scale SNP genotyping and genome wide association analysis and characterization of copy number variations (CNV). Since CNVs are structural variations of the genome they potentially have a large effect on gene expression and protein function. We analyzed 1265 genotyped boars for nine different reproduction traits and identified 46 CNV regions encompassing 13 genes. 11 of the CNV regions were shared between the breeds, 20 were unique to the Finnish Yorkshire and 15 to the Finnish Landrace. The ge-nome wide association (GWAS) analysis identified zero to five reproduction associated genomic regions per trait. Furthermore, we identified 23 genomic regions with 20 candidate genes associated with fertility traits using GWAS analysis. The identified CNV regions were compared against GWAS regions to detect candidate regions with an ef-fect on reproduction traits. This study reports candidate genes and genomic regions within two Finnish pig breeds for reproduction traits, which can be utilized in breeding programs.Peer reviewe

Whole-genome association analysis of pork meat pH revealed three significant regions and several potential genes in Finnish Yorkshire pigs

Background: One of the most commonly used quality measurements of pork is pH measured 24 h after slaughter. The most probable mode of inheritance for this trait is oligogenic with several known major genes, such as PRKAG3. In this study, we used whole-genome SNP genotypes of over 700 AI boars; after a quality check, 42,385 SNPs remained for association analysis. All the boars were purebred Finnish Yorkshire. To account for relatedness of the animals, a pedigree-based relationship matrix was used in a mixed linear model to test the effect of SNPs on pH measured from loin. A bioinformatics analysis was performed to identify the most promising genes in the significant regions related to meat quality. Results: Genome-wide association study (GWAS) revealed three significant chromosomal regions: one on chromosome 3 (39.9 Mb-40.1 Mb) and two on chromosome 15 (58.5 Mb-60.5 Mb and 132 Mb-135 Mb including PRKAG3). A conditional analysis with a significant SNP in the PRKAG3 region, MARC0083357, as a covariate in the model retained the significant SNPs on chromosome 3. Even though linkage disequilibrium was relatively high over a long distance between MARC0083357 and other significant SNPs on chromosome 15, some SNPs retained their significance in the conditional analysis, even in the vicinity of PRKAG3. The significant regions harbored several genes, including two genes involved in cyclic AMP (cAMP) signaling: ADCY9 and CREBBP. Based on functional and transcription factor-gene networks, the most promising candidate genes for meat pH are ADCY9, CREBBP, TRAP1, NRG1, PRKAG3, VIL1, TNS1, and IGFBP5, and the key transcription factors related to these genes are HNF4A, PPARG, and Nkx2-5. Conclusions: Based on SNP association, pathway, and transcription factor analysis, we were able to identify several genes with potential to control muscle cell homeostasis and meat quality. The associated SNPs can be used in selection for better pork. We also showed that post-GWAS analysis reveals important information about the genes' potential role on meat quality. The gained information can be used in later functional studies.Peer reviewe