Genomic and conventional breeding values for clinical mastitis

Conventional and genomic breeding values for clinical mastitis were estimated,based on a dataset of 15,905 cows (36,250 lactations) from 10 farms, calving years from 1996 to 2014. The number of genotyped bulls was 2647 and 799 of them had offspring among the surveyed cows. Pedigree consisted of 64,306 individuals. Analyzed trait was defined as the number of incidence of clinical mastitis per standard lactation. Parity was limited from 1 to 7. The highest proportion of mastitis disease was observed in early lactation and decreased with month of lactation, while there was an upswing of diseases with parity. Genetic trend for cows showed a deteriorating tendency for clinical mastitis. From 1992 to 2010 there was a rise in the relative values of breeding values from 88% to 112% (worsening). Relative breeding values of these bulls were on average above 100%. The correlations between classical genomic breeding values and the values were high: 93% for the whole sample, 81% to 48 young genomic bulls without daughters born in years 2011 and 2012

ECONOMIC SUSTAINABILITY OF THE LOCAL DUAL-PURPOSE CATTLE

Base economic characteristics (total revenues, total costs, profit and profitability ratio) of the Slovak Pinzgau breed were calculated in this study. Under the actual production and economic conditions of the breed, production system is operated with loss (-457 € per cow and per year) and with negative profitability ratio (-20%). Optimisation of the production parameters on the level defined in the breed standard (5,200 kg milk per cow and year, 92% for conception rate of cows, 404 days of calving interval and 550 g in daily gain of reared heifers) and improved udder health traits (clinical mastitis incidence and somatic cells score) was of positive impact on the total revenues (+34%), on the effective utilisation of costs (+105%) and balanced profit of dairy systems. Next to the positive profitability of the system, higher quality and security of dairy milk products should be mentioned there. Moreover, direct subsidies as an important factor of positive economic result of dairy cattle systems has to be pointed as well. Subsidies should be provided to compensate the real biological limitation of the local breed farmed in marginal areas. However, improvement of the production parameters of the Slovak Pinzgau breed is recommended with the same attention to reach the economic sustainability of dairy production system. To reach economic sustainability of the breed from practical point of view, the farmer activity should be aimed especially to the enhanced herd management

Bio-economic Models for Efficient Dairy Cattle Breeding

The objective of this study was to define the main principles when the economic weights of traits are defined to be applicate in dairy cattle breeding. The competitive farming is a function of additive genetic values of traits weighted with economic values. For the calculation of economic values, the bio-economic models are mostly used. These models should reflect the production circumstances of evaluated production systems and be flexible to fit other production situations. Except of the production traits, the functional traits and traits for feed intake utilization are very important for the sustainable production. The environmental benefits (e. g. reduction of greenhouse gas emissions, welfare) should be mentioned as well. Results based on the bio-economic models provide the first information whether the breeding goal for cattle would be redefined. Moreover, flexibility of the bio-economic models enables to evaluate the breeding goals for different customer groups and for different cattle breeds. They are beneficial tools for comprehensive evaluation of the economic values for the most important traits in cattle and in sheep

Analysis of foot and claw diseases/disorders in Czech Holstein cows

Received: 2018-05-07 | Accepted: 2018-05-14 | Available online: 2018-11-26https://doi.org/10.15414/afz.2018.21.04.194-196Foot and claw diseases/disorders from 24 545 lactations of 10 340 Holstein cows were recorded on 7 farms in the Czech Republic from 1999 to 2018. There were defined a three groups of foot and claw disorders/diseases: diseases of skin (SD), which cover digital, interdigital dermatitis and interdigital phlegmon; then disorders of the claw horn (CH) including ulcers, white line disease, horn fissures, together with double sole and  overall claw diseases (OCD) ingluding all the recorded disorders. The OCD ratio observed during 1th and 305th days of lactation was  52.56% of all evaluated lactations. The observed ratio of SD and CH  were 28.61% and 27.15%, respectively. A foot and claw disorders were defined as 0/1 occurrence per lactation, for the purposes of analyses,. Genetic parameters were estimated using by linear animal models for evaluated traits. Models  included the random additive genetic effect of animal (A), the permanent environmental effect of cow (PE), fixed effects of parity, farm, year and season of calving, and age at calving as discreet variables in classes. The estimated heritability were 13.84%, 12.64% and 9.83%, 8.73% and 9.97%, for OCD, CH, SD, ulcers (U) and for dermatitis digitalis and interdigitalis (DD), respectively. Genetic correlation was 17.66% between SD and CH, whereas traits SD and DD equal high genetic similarity (98.4%). Also correlation between CH and U traits was high (92.62%). The presented results indicate to possibility of selection against foot and claw disorders/diseases for Czech Holstein population. The work was supported by the project QJ1510144 and the institutional support MZE-RO0718 of the Ministry of Agriculture of the Czech Republic.Keywords: cattle, foot and claw disorders, genetic parameters, health traits, uddeReferencesBuch, L. H., A. C. Sørensen, J. Lassen, P. Berg, J. A. Eriksson, J. H. Jakobsen,  M. K. Sørensen (2011) Hygiene-related and feed-related hoof diseases show different patterns of genetic correlations to clinical mastitis and female fertility. J. Dairy Sci., 94, 1540-1551.Chapinal, N., A. Koeck, A. Sewalem, D. F. Kelton, S. Mason, G. Cramer,F. Miglior (2013) Genetic parameters for hoof lesions and their relationship with feet and leg traits in Canadian Holstein cows. J. Dairy Sci., 96, 2596-2604.Egger-Danner, C., O.K. Hansen, K. Stock, J.E. Pryce, J. Cole, N. Gengler, B. Heringstad (2013) Challenges and benefits of health data recording in the context of food chain quality, management and breeding. ICAR Technical Series.Groeneveld, E., M. Kovač, and N. Mielenz (2008) VCE User’s Guide and Reference Manual, Version 6.0. Krpálková, L., M. Štípková & M. Krejčová, 2016. Vliv zdraví paznehtů a úrovně reprodukce na výkonnost a zisk stáda dojnic. Náš chov, 76 (9), 58-63.Krupová, Z., Krupa, E., Michaličková, M., Wolfová, M., Kasarda, R. (2016) Economic values for health and feed efficiency traits of dual-purpose cattle in marginal areas. Journal of Dairy Science, ,. 99,  s. 644-656.Madsen, P. , J. Jensen. 2010. DMU – a package for analysing multivariate mixed models. Version 6, release 5.0., Aarhus University, Foulum, Denmark.Pérez-Cabal, M. A. ,N. Charfeddine, N. (2015) Models for genetic evaluations of claw health traits in Spanish dairy cattle.   J. Dairy Sci., 98 (11), 8186-8194.Sogstad, A. M., T. Fjeldaas, O. Østerås,  K. P. Forshell. (2005) Prevalence of claw lesions in Norwegian dairy cattle housed in tie stalls and free stalls. Prev. Vet. Med., 70, 191-209.van der Spek, D., J.A. van Arendonk, A.A. Vallée, H. Bovenhuis (2013) Genetic parameters for claw disorders and the effect of preselecting cows for trimming. J Dairy Sci., 96 (9), 6070-6078.van der Waaij, E. H., M. Holzhauer, E. Ellen, C. Kamphuis, G.de Jong. (2005) Genetic parameters for claw disorders in Dutch dairy cattle and correlations with conformation traits. J. Dairy Sci., 88, 3672-3678

GWAS in practical cattle breeding in Czech Republic, single step method, genetic progress

Development of genetic evaluation of animals is permanent process. It was going from estimated breeding value (EBV) calculated by CC-test, across a BLUP – animal model and RR-TDM, to the genomic enhanced breeding value (GEBV) using genetic markers. Methods of genetic evaluation become a part of marketing strategies of insemination companies. Therefore all countries and association of breeders seek to be compatible with others. Now we are in a period of massive global implementation of genomic evaluation, which combines traditional BLUP with huge quantity of genetic SNP markers. Multi-step procedures are now usual in practice, which work with deregressed proofs. Development of methods attained to the single-step procedure (ssGBLUP) which overcomes some difficulties of previous methods, improves reliabilities of evaluation and compares all animals, genotyped and ungenotyped, in entire nation-wide population. Genomic evaluation influence above all young genotyped animals. In Czech Republic single-step procedure is routinely used for national evaluation of milk, linear type traits, reproduction and longevity. GEBVs are accompanied by genomic reliabilities. Genetic trends over last 20 years are in some traits different for genomic evaluation compared to traditional BLUP evaluation, although input data and genetic parameters (heritability) are the same and genotyped animals were only small proportion from entire evaluated population. Differences in genetic trends increase mainly in new batches of animals. Reason of it could be in the changed variability of breeding values and “genomic correction” of relationship between animals, which is expanded from genotyped animals to others individuals in a population. Keywords: genomic breeding value, single-step, genomic relationship, genetic trend, SNP ReferencesBauer, J. et al. (2014) Approximation of the reliability of single-step genomic breeding values for dairy cattle in the Czech Republic. Anim. Sci. Papers and Reports, 32, pp. 301-306.Bauer, J., Přibyl, J. and Vostrý, L. (2015) Contribution of domestic production records and Interbull EBV on approximate reliabilities of single-step genomic breeding values in dairy cattle. Czech J. Anim. Sci., 60, 263-267.Candrák, J., Kadlečík O. and Schaeffer L.R. (1997) The use of test-day model for Slovak cattle populations. In: Proc. 48th Annual Meeting of the European Association for Animal Production, Vienna, Austria, August 25–28.Christensen,  O.F. and Lund, M.S. (2010) Genomic prediction when some animals are not genotyped. Genet.Sel.Evol. 42, pp. 2.Fisher, R.A. (1918) The correlation between relatives in the supposition of Mendelianinheritance. Trans. Roy. Soc. Edinb. 52, pp. 399-433.            Fragomeni, B.O. et al. (2015) Hot topic: Use of genomic recursions in single-step genomic best linear unbiased predictor (BLUP) with a large number of genotypes. J. Dairy Sci., 98, pp. 4090-4094.Gao, H. et al. (2012) Comparison on genomic predictions using three GBLUP methods and two single step blending methods in the Nordic Holstein population. Genet. Sel.Evol. 44, pp. 8.Legarra A., Aguilar I. and Misztal, I. (2009) A relationship matrix including full pedigree and genomic information. J. Dairy Sci., 92, pp. 4656-4663.Masuda, Y. et al. (2016) Implementation of genomic recursions in single-step genomic best linear unbiased predictor for US Holsteins with a large number of genotyped animals. J. Dairy Sci., 99, pp. 1968-1974.Mendel, G.J. (1866) Versuche über Pflanzen-Hybriden. Verh. Naturforsch. Ver. Brünn 4, pp. 3–47 (1901, J. R. Hortic. Soc. 26, pp. 1–32).Meuwissen, T.H.E., Hayes, B.J. and Goddard, M.E. (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics, 157, pp. 1819–1829.Misztal, I., Legarra A. and Aguilar, I. (2009) Computing procedures for genetic evaluation including phenotypic, full pedigree, and genomic information. J. Dairy Sci., 92, pp. 4648–4655.Misztal, I. et al. (2013) Methods to approximate reliabilities in single-step genomic evaluation. J. Dairy Sci., 96, pp. 647-654.Pešek, P., Přibyl, J. and Vostrý, L. (2015) Genetic variances of SNP loci for milk yield in dairy cattle. J. Appl. Genet., 56, pp. 339-347.Přibyl, J. et al. (2014) Domestic and Interbull information in the single step genomic evaluation of Holstein milk production.  Czech J. Anim. Sci., 59, pp. 409-415.Přibyl, J. et al. (2015) Domestic estimated breeding values and genomic enhanced breeding values of bulls in comparison with their foreign genomic enhanced breeding values. Animal, 9, pp. 1635-1642.VanRaden, P.M. (2008) Efficient methods to compute genomic predictions. J. Dairy Sci., 91, pp. 4414–4423.VanRaden, P.M. et al. (2011) Genomic evaluations with many more genotypes. Genet. Sel.Evol. 43, pp. 10.Wright, S. (1921) Systems of mating. Genetics. 6, pp. 111-178.Zavadilová, L. et al. (2014) Single-step genomic evaluation for linear type traits of Holstein cows in Czech Republic. Anim. Sci. Papers and Reports vol. 32, pp. 201-208.

Genetic Parameters for a Weighted Analysis of Survivability in Dairy Cattle

The genetic parameters for the survival of Holstein cows, analysed in nine consecutive time periods during the first three calving intervals, were estimated. The earlier the animals are culled, the more they are informationally underestimated. This undervaluing can be remedied by using a weighted analysis that balances the amount of information. If the method of estimating breeding values changes, the genetic parameters will also change. The Holstein cattle dataset from 2005 to 2017 used in this study included 1,813,636 survival records from 298,290 cows. The pedigree with three generations of ancestors included 660,476 individuals. Linear repeatability models estimated genetic parameters for overall and functional survivability. Due to weights, heritability increased from 0.013 to 0.057. Repeatability with weights was 0.505. The standard deviations of breeding values were 1.75 and 2.18 without weights and 6.04 and 6.20 with weights. Including weights in the calculation increased the additive variance proportion and the breeding values’ reliabilities. We conclude that the main contribution of the weighted method we have presented is to compensate for the lack of records in culled individuals with a positive impact on the reliability of the breeding value

Comparison of genomic breeding values of Holstein in Czech Republic

Genomic evaluation by single-step procedure allows efficient implanting of genetic SNP markers into complicated procedure of random regression test-day-model of milk traits. Test-day records and pedigree files on nation-wide scale are combined with genomic relationship into common evaluation of both genotyped and ungenotyped animals. Due to strong import of foreign sperm into small national populations is the reliability of evaluation of young animals low. This is particularly seen in evaluation of young bulls, which frequently have both parents foreign. Genomic evaluation helps and notably improves reliability of evaluation. ssGBLUP procedure is advantageous especially for small populations. Domestic genomic evaluation of young animals has medium to high correlation with foreign Interbull values. Interbull conversion of values of bulls according MACE, which works with progeny tested bulls, is more reliable than conversion according GMACE procedure, which works with genomic evaluation of young animals.  Keywords: genomic breeding value, ssGBLUP, test day model, MACE, GMACEReferencesBauer, J. et al. (2014) Approximation of the reliability of single-step genomic breeding values for dairy cattle in the Czech Republic. Anim. Sci. Papers and Reports, 32, pp. 301-306.Bauer, J., Přibyl, J. and Vostrý, L. (2015) Contribution of domestic production records and Interbull EBV on approximate reliabilities of single-step genomic breeding values in dairy cattle. Czech J. Anim. Sci., 60, 263-267.Christensen,  O.F. and Lund, M.S. (2010) Genomic prediction when some animals are not genotyped. Genet.Sel.Evol. 42, pp. 2.Forni, S., Aguilar I. and Misztal, I. (2011) Different genomic relationship matrices for single step analysis using phenotypic, pedigree and genomic information. Genet. Sel. Evol., 43, pp. 1.Legarra A., Aguilar I. and Misztal, I. (2009) A relationship matrix including full pedigree and genomic information. J. Dairy Sci., 92, pp. 4656-4663.Meuwissen, T.H.E., Hayes, B.J. and Goddard, M.E. (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics, 157, pp. 1819–1829.Misztal, I., Legarra A. and Aguilar, I. (2009) Computing procedures for genetic evaluation including phenotypic, full pedigree, and genomic information. J. Dairy Sci., 92, pp. 4648–4655.Pešek, P., Přibyl, J. and Vostrý, L. (2015) Genetic variances of SNP loci for milk yield in dairy cattle. J. Appl. Genet., 56, pp. 339-347.Plemdat, (2015) Descriptions of Breeding values Evaluation.  Retrieved on 10th June 2015 From www.plemdat.cz.Přibyl, J. et al. (2014) Domestic and Interbull information in the single step genomic evaluation of Holstein milk production.  Czech J. Anim. Sci., 59, pp. 409-415.Přibyl, J. et al. (2015) Domestic estimated breeding values and genomic enhanced breeding values of bulls in comparison with their foreign genomic enhanced breeding values. Animal, 9, pp. 1635-1642.Vitezica, Z.G. et al. (2011) Bias in genomic predictions for populations under selection. Genet. Res. (Camb), 93, pp. 357-366.Zavadilová, L., Jamrozik, J. and Schaeffer, L.R. (2005a) Genetic parameters for test-day model with random regressions for production traits of Czech Holstein cattle. Czech J. Anim. Sci., 50, pp. 142-154.Zavadilová, L., Němcová, E. and Wolf, J. (2005b) Definition of subgroups for fixedregression in the test-day animal model for milk production of Holstein cattle in the CzechRepublic. Czech J. Anim. Sci., 50, pp. 7-13.Zavadilová, L. et al. (2014) Single-step genomic evaluation for linear type traits of Holstein cows in Czech Republic. Anim. Sci. Papers and Reports vol. 32, pp. 201-208