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- Rius-Vilarrasa, Elisenda Rius, et al.
(författare)
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Influence of model specifications on the reliabilities of genomic prediction in a Swedish-Finnish red breed cattle population
- 2012
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Ingår i: Journal of Animal Breeding and Genetics. - : Wiley. - 0931-2668 .- 1439-0388. ; 129, s. 369-379
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Tidskriftsartikel (refereegranskat)abstract
- Using a combined multi-breed reference population, this study explored the influence of model specification and the effect of including a polygenic effect on the reliability of genomic breeding values (DGV and GEBV). The combined reference population consisted of 2986 Swedish Red Breed (SRB) and Finnish Ayrshire (FAY) dairy cattle. Bayesian methodology (common prior and mixture models with different prior distribution settings for the marker effects) as well as a best linear unbiased prediction with a genomic relationship matrix [genomic best linear unbiased predictor (GBLUP)] was used in the prediction of DGV. Mixture models including a polygenic effect were used to predict GEBV. In total, five traits with low, high and medium heritability were analysed. For the models using a mixture prior distribution, reliabilities of DGV tended to decrease with an increasing proportion of markers with small effects. The influence of the inclusion of a polygenic effect on the reliability of DGV varied across traits and model specifications. Average correlation between DGV with the Mendelian sampling term, across traits, was highest (R2 = 0.25) for the GBLUP model and decreased with increasing proportion of markers with large effects. Reliabilities increased when DGV and parent average information were combined in an index. The GBLUP model with the largest gain across traits in the reliability of the index achieved the highest DGV mean reliability. However, the polygenic models showed to be less biased and more consistent in the estimation of DGV regardless of the model specifications compared with the mixture models without the polygenic effect.
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- Rius-Vilarrasa, Elisenda Rius, et al.
(författare)
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Reliabilities of genomic prediction using combined reference data of the Nordic Red dairy cattle populations
- 2011
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Ingår i: Journal of Dairy Science. - : American Dairy Science Association. - 0022-0302 .- 1525-3198. ; 94, s. 4700-4707
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Tidskriftsartikel (refereegranskat)abstract
- This study investigated the possibility of increasing the reliability of direct genomic values (DGV) by combining reference populations. The data were from 3,735 bulls from Danish, Swedish, and Finnish Red dairy cattle populations. Single nucleotide polymorphism markers were fitted as random variables in a Bayesian model, using published estimated breeding values as response variables. In total, 17 index traits were analyzed. Reliabilities were estimated using a 5-fold cross validation, and calculated as the within-year squared correlation between estimated breeding values and DGV. Marker effects were estimated using reference populations from individual countries, as well as using a combined reference population from all 3 countries. Single-country reference populations gave mean reliabilities across 17 traits of 0.19 to 0.23, whereas the combined reference gave mean reliabilities of 0.26 for all populations. Using marker effects from 1 population to predict the other 2 gave a loss in mean reliability of 0.14 to 0.21 when predicting Swedish or Finnish animals with Danish marker effects, or vice versa. Using Swedish or Finnish marker effects to predict each other only showed a loss in mean reliability of 0.03 to 0.05. A combined Swedish-Finnish reference population led to an average reliability as high as that from the 3-country reference population, but somewhat different for individual traits. The results from this study show that it is possible to increase the reliability of DGV by combining reference populations from related populations.
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- Tarekegn, Getinet Mekuriaw, et al.
(författare)
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Genetic parameters of endocrine fertility traits based on in-line milk progesterone profiles in Swedish Red and Holstein dairy cows
- 2019
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Ingår i: Journal of Dairy Science. - : American Dairy Science Association. - 0022-0302 .- 1525-3198. ; 102, s. 11207-11216
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Tidskriftsartikel (refereegranskat)abstract
- Evaluating fertility traits based on endocrine progesterone profiles is becoming a promising option to improve dairy cow fertility. Several studies have been conducted on endocrine fertility traits, mainly in the Holstein breed. In this study, focusing also on the Swedish Red (SR) breed, genetic parameters were estimated for classical and endocrine fertility traits, the latter based on in-line milk progesterone records obtained for 14 Swedish herds using DeLaval Herd Navigator (DeLaval International, Tumba, Sweden). A total of 210,403 observations from 3,437 lactations of 1,107 SR and 1,538 Holstein cows were used. Mixed linear animal models were used for estimation of genetic parameters. Least squares means analysis showed that Holstein cows had a 2.5-d-shorter interval from calving to commencement of luteal activity (C-LA) and longer length of first inter-ovulatory interval (IOI) than SR cows. The highest mean interval for C-LA, IOI, and first luteal phase length (LPL) was observed in the fourth parity. The incidence of short (<18 d), normal, (18-24 d), and long (>24 d) IOI was 29.3, 40.7, and 30%, respectively. Genetic analysis indicated moderate heritability (h(2)) for C-LA (h(2) = 0.24), luteal activity during the first 60 d in milk (LA60, h(2) = 0.15), proportion of samples with luteal activity (PLA, h(2) = 0.13), and calving to first heat (CFH, h(2) = 0.18), and low heritability estimates for LPL (h(2) = 0.08) and IOI (h(2) = 0.03) in the combined data set for both breeds. Similar heritability estimates were obtained for each breed separately except for IOI and LPL in SR cows, for which heritability was estimated to be zero. Swedish Red cows had 0.01 to 0.06 higher heritability estimates for C-LA, LA60, and PLA than did Holstein cows. Calving interval had moderate heritability among the classical traits for Holstein and the combined data set, but h(2) was zero for SR. Commencement of luteal activity had a strong genetic correlation with LA60 (mean +/- SE; -0.88 +/- 0.06), PLA (-0.72 +/- 0.11), and CFH (0.90 +/- 0.04). Similarly, CFH had a strong genetic correlation with IOI (0.98 +/- 0.20). Number of inseminations per series showed a weak genetic correlation with all endocrine traits except IOI. Overall, endocrine traits had higher heritability estimates than classical traits in both breeds, and may have a better potential to explain the actual reproductive status of dairy cows than classical traits. This might favor inclusion of some endocrine fertility traits-especially those related to commencement of luteal activity as selection criteria and breeding goal traits if recording becomes more common in herds. Further studies on genetic and genomic evaluations for endocrine fertility traits may help to provide firm conclusions. A prerequisite is that the data from automatic devices be made available to recording and breeding organizations in the future and included in a central database.
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