Estimation and comparison of conventional and genomic breeding values in Holstein cattle of Antioquia, Colombia

A, Juan Zambrano; F, Juan Rincón; H, Albeiro López; Z, Julián Echeverri

doi:10.21897/rmvz.44

Cited by 5 publications

(3 citation statements)

References 20 publications

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“…Animal model consider that throughout all period of lactation, the environment has the same effect and because of that, some animals can appear with high or low breeding values. Similar results proclaim (Zambrano et al, 2015) at Holstein cattle breed. The test day model follows the lactation curve and for each point from the curve, the model made the corrections for the most important effect for that moment and not for the whole lactation.…”

Section: Comparison Between Estimation Modelssupporting

confidence: 80%

Preliminary study regarding use of genomic selection in Romanian cattle breeds evaluation

Gras,

Rotar,

Grosu

et al. 2023

Archiva Zootechnica

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In Romania, the livestock is very scattered on the diverse environmental conditions. Due to difficulties regarding data collection, with the help of genomic selection, the paradigm of genetic improvement of economical traits in Romanian cattle breeds can be changed. Population studied in this paper consist in animals genotyped using 60k SNP panel. Association studies were performed for estimate the effect of SNP polymorphism on milk yield at 305 days. Genetic evaluation was compared under four statistical methodologies were compared under six scenarios 5k, 10k, 15k, 20k, 25k and 37k SNP panels. High association with phenotypes were displayed by 38 SNP’s. Generally, accuracy of the studied models, tend to increase with complexity (informational input). The model with the lowest accuracy was Sire-Model (36.6% accuracy). Adding information in Animal Model increase accuracy of estimation and finally, adding genomic information the accuracy was maximized to 69.9%. For each lactation all the statistical models return highly correlated breeding values. The highest (97.2%) and the lowest (79.2%) rank correlation are registered between Test-Day and Animal Model for the first and second lactation. Genomic evaluation is a more feasible methodology than classical breeding value estimation, in term of accuracy of selection and the quality of the parentage information.

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Section: Comparison Between Estimation Modelssupporting

confidence: 80%

Preliminary study regarding use of genomic selection in Romanian cattle breeds evaluation

Gras,

Rotar,

Grosu

et al. 2023

Archiva Zootechnica

View full text Add to dashboard Cite

show abstract

“…In contrast, genomic estimated breeding values provide more accurate reliabilities for animals without performance data (Muir, 2007;Zambrano et al, 2015). This supports the benefits of using genomic calculations for selection at an early age, especially for hardto-measure traits.…”

Section: Discussionsupporting

confidence: 52%

Estimation of genetic parameters and breeding values for feed intake and energy balance using pedigree relationships or single-step genomic evaluation in Holstein Friesian cows

Harder

Stamer²,

Junge

et al. 2020

Journal of Dairy Science

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At the beginning of lactation, high-performing dairy cows often experience a severe energy deficit, which in turn is associated with metabolic stress. Increasing feed intake (FI) or reducing the energy deficit during this period could improve the metabolic stability and thus the health of the animals. Genomic selection for the first time enables the inclusion of this hard-to-measure trait in breeding programs. The objective of the current study was the estimation of genetic parameters and genomic breeding values for FI and energy balance (EB). For this purpose, 1,374 Holstein Friesian (HF) dairy cows from 8 German research farms were phenotyped with standardized FI data protocols. After data editing, phenotypic data of HF comprised a total of 40,012 average weekly FI records with a mean of 21.8 ± 4.3 kg/d. For EB 33,376 average weekly records were available with a mean of 3.20 ± 29.4 MJ of NE L /d. With the Illumina Bovine SNP50 BeadChip (Illumina Inc., San Diego, CA) 1,128 of phenotyped cows were genotyped. Thirty-five female candidates of the HF population were genotyped but not phenotyped. Pedigree information contained sires and dams 4 generations back. The random regression animal model included the fixed effects of herd test week (alternatively, herd group test week), parity, and stage of lactation, modeled by the function according to Ali and Schaeffer (1987). For both the random permanent environmental effect across lactations and the random additive genetic effect, third-order Legendre polynomials were chosen. Additionally, a random permanent environmental cow effect within lactation was included. Analyses for heritabilities, genetic correlations between different lactation stages, and breeding values were estimated using, respectively, pedigree relationships and single-step genomic evaluation, carried out with the DMU software package (Madsen et al., 2013). This allowed for comparison of conventional reliabilities with genomic-assisted reliabilities based on real data, to evaluate the gain of genotyping. Heritability estimates ranged between 0.12 and 0.50 for FI, and 0.15 and 0.48 for EB, and increased toward the end of lactation. Genetic correlations were weak between early and late lactation, with a value of 0.05 for FI and negative with a value of −0.05 for EB. Reliabilities for genomic values of cows for FI and EB ranged between 0.33 and 0.61, and 0.27 and 0.47, respectively. For the genotyped cows without phenotypes, the inclusion of genomic relationship leads to an increase of the average reliability of the breeding value for FI by nearly 9% and for EB by 4%. The results show the possibility of combining pedigree, genotypes, and phenotypes for increasing FI or EB to reduce health and reproductive problems, especially at the beginning of lactation. Nevertheless, the reference population needs to be extended to reach higher breeding value reliabilities.

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“…Zambrano et al -Evaluación genómica en ganado Holstein Colombiano leche (18,19), en razas criollas (20), así como en ganado de carne (21). El objetivo de esta investigación fue determinar la precisión y el sesgo de valores genómicos directos (VGD) usando genotipos imputados a densidad media, en características productivas y reproductivas en ganado Holstein de Antioquia, Colombia.…”

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Evaluación genómica en ganado Holstein Colombiano, usando genotipos imputados a densidad media

2019

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Objetivo. Determinar la precisión y el sesgo de predicción de valores genómicos directos (VGD) usando genotipos imputados a densidad media, en características productivas y reproductivas en ganado Holstein de Antioquia, Colombia. Materiales y métodos. Fueron genotipificados 31 animales con el chip Illumina BovineLD, 64 con el chip Illumina BovineSNP50v2 y 48 con el chip Illumina BovineHD. La imputación se realizó usando dos paneles de SNPs (6K y 40K) a una densidad 44K, usando el programa FINDHAP.f90 v4. Los efectos de los SNPs fueron estimados mediante el método bayes_C, usando genotipos de baja densidad (6K) y genotipos imputados a una densidad media (44_imputado). La precisión y el sesgo de los VGDs fueron determinados mediante validación cruzada. Las características evaluadas fueron: producción de leche (PL), porcentaje de proteína (PRO), porcentaje de grasa (GRA), puntaje de células somáticas (SCS), intervalo entre partos (IEP) y días abiertos (DA). Resultados. Las precisiones de VGD (rpVGD;EBV) en todas las características evaluadas oscilaron entre 0.19 y 0.24 y el sesgo (bVGD;EBV) entre 0.03 y 0.16 cuando se usó el panel 6K y usando el panel 44K_imputado las precisiones fueron mayores, oscilado entre 0.24 y 0.33 y sesgo entre 0.03 y 0.26. Conclusiones. La precisión de predicción de los VGDs fue mayor cuando se usaron genotipos imputados a densidad media, en comparación con la precisión de predicción obtenida empleando genotipos de baja densidad. Por lo cual, en este estudio se concluye que la imputación de genotipos es muy útil dado que aumenta la confiabilidad de la evaluación genómica.

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Estimation and comparison of conventional and genomic breeding values in Holstein cattle of Antioquia, Colombia

Cited by 5 publications

References 20 publications

Preliminary study regarding use of genomic selection in Romanian cattle breeds evaluation

Preliminary study regarding use of genomic selection in Romanian cattle breeds evaluation

Estimation of genetic parameters and breeding values for feed intake and energy balance using pedigree relationships or single-step genomic evaluation in Holstein Friesian cows

Evaluación genómica en ganado Holstein Colombiano, usando genotipos imputados a densidad media

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