scholarly journals The impact of genetic relationship information on genomic breeding values in German Holstein cattle

2010 ◽  
Vol 42 (1) ◽  
Author(s):  
David Habier ◽  
Jens Tetens ◽  
Franz-Reinhold Seefried ◽  
Peter Lichtner ◽  
Georg Thaller
Keyword(s):  
Genetic Relationship ◽  
Holstein Cattle ◽  
Genomic Breeding ◽  
Breeding Values ◽  
The Impact

scholarly journals GPS Coordinates for Modelling Correlated Herd Effects in Genomic Prediction Models Applied to Hanwoo Beef Cattle

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 2050
Author(s):  
Beatriz Castro Dias Cuyabano ◽  
Gabriel Rovere ◽  
Dajeong Lim ◽  
Tae Hun Kim ◽  
Hak Kyo Lee ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Genomic Prediction ◽  
Prediction Models ◽  
Phenotypic Expression ◽  
Genetic Evaluation ◽  
Genomic Breeding ◽  
Breeding Values ◽  
Korean Cattle ◽  
Evaluation Programs ◽  
The Impact

It is widely known that the environment influences phenotypic expression and that its effects must be accounted for in genetic evaluation programs. The most used method to account for environmental effects is to add herd and contemporary group to the model. Although generally informative, the herd effect treats different farms as independent units. However, if two farms are located physically close to each other, they potentially share correlated environmental factors. We introduce a method to model herd effects that uses the physical distances between farms based on the Global Positioning System (GPS) coordinates as a proxy for the correlation matrix of these effects that aims to account for similarities and differences between farms due to environmental factors. A population of Hanwoo Korean cattle was used to evaluate the impact of modelling herd effects as correlated, in comparison to assuming the farms as completely independent units, on the variance components and genomic prediction. The main result was an increase in the reliabilities of the predicted genomic breeding values compared to reliabilities obtained with traditional models (across four traits evaluated, reliabilities of prediction presented increases that ranged from 0.05 ± 0.01 to 0.33 ± 0.03), suggesting that these models may overestimate heritabilities. Although little to no significant gain was obtained in phenotypic prediction, the increased reliability of the predicted genomic breeding values is of practical relevance for genetic evaluation programs.

scholarly journals Association of HindIII-polymorphism in kappa-casein gene with milk, fat and protein yield in holstein cattle*

2018 ◽  
Vol 65 (3) ◽  
Author(s):  
Martina Miluchová ◽  
Michal Gábor ◽  
Juraj Candrák ◽  
Anna Trakovická ◽  
Kristína Candráková
Keyword(s):  
Information Content ◽  
Milk Production ◽  
Polymorphism Information Content ◽  
Milk Fat ◽  
Breeding Value ◽  
Holstein Cattle ◽  
Cattle Population ◽  
Effective Number ◽  
Breeding Values ◽  
The Impact

The aim of the paper was to evaluate the effect of genetic polymorphism of kappa-casein on the milk production in Holstein cattle. A total 210 cows of Holstein cattle were use in this study. On the basis of PCR-RFLP analyses we established genotype structure of cattle population and calculated allelic frequencies. In Holstein cattle population was detected all three genotypes – AA (69.52%), AB (27.62%) and BB (2.86%). The frequency of allele A was 83.33% and allele B was 16.67%. Effectiveness of allele incidence and genetic diversity was evaluated with following parameters: theoretical heterozygosity (Heexp), experimental heterozygosity (Heobs), polymorphism information content (PIC), expected homozygosity (E), effective number of alleles (ENA), level of possible variability realization (V%). The Holstein cattle kept in Slovak Republic exhibit high value of homozygosity and low values of polymorphism information content, effective number of alleles and level of possible variability realization. The effect of polymorphism of CSN3 gene on average breeding values for milk production traits as the yield of milk, fat and protein in kilograms as well as contents of fat and protein in percentages was detected using by the packed SAS 9.3 of SAS Enterprise Guide 5.1. We detected statistical significant difference between genotypes only at an average breeding value for the percentage of protein in milk during assessment the variability of observed traits in depending on polymorphism of CSN3 gene. For other breeding values the impact of individual genotypes CSN3 gene on their variability was not observed.

scholarly journals The Impact of Genetic Relationship Information on Genome-Assisted Breeding Values

Genetics ◽  
2007 ◽  
Vol 177 (4) ◽  
pp. 2389-2397 ◽  
Author(s):  
D. Habier ◽  
R. L. Fernando ◽  
J. C. M. Dekkers
Keyword(s):  
Genetic Relationship ◽  
Breeding Values ◽  
The Impact

scholarly journals Claw health and feed efficiency as new selection criteria in the Czech Holstein cattle Krupová Z., Wolfová M., Krupa E., Přibyl J., Zavadilová L.

2018 ◽  
Vol 63 (No. 10) ◽  
pp. 408-418 ◽  
Author(s):  
Z. Krupová ◽  
M. Wolfová ◽  
E. Krupa ◽  
J. Přibyl ◽  
L. Zavadilová
Keyword(s):  
Feed Intake ◽  
Feed Efficiency ◽  
Disease Incidence ◽  
Selection Index ◽  
Residual Feed Intake ◽  
Selection Response ◽  
Holstein Cattle ◽  
Breeding Objective ◽  
Economic Weights ◽  
The Impact

The objective of this study was to calculate economic weights for ten current breeding objective traits and for four new traits characterising claw health and feed efficiency in Czech Holstein cattle and to investigate the impact of different selection indices on the genetic responses for these traits. Economic weights were estimated using a bio-economic model, while applying actual (2017) and predicted (2025) production and economic circumstances. For the actual situation, the economic weights of claw disease incidence were –100.1 € per case, and those of daily residual feed intake in cows, breeding heifers, and fattened animals were –79.37, –37.16, and –6.33 €/kg dry matter intake per day, respectively. In the predicted situation, the marginal economic weights for claw disease and feed efficiency traits increased on average by 38% and 20%, respectively. The new traits, claw disease incidence and daily residual feed intake, were gradually added to the 17 current Holstein selection index traits to improve the new traits. Constructing a comprehensive index with 21 traits and applying the general principles of the selection index theory, a favourable annual genetic selection response was obtained for the new traits (–0.008 cases of claw disease incidence and –0.006 kg of daily residual feed intake across all cattle categories), keeping the annual selection response of the most important current breeding objective traits at a satisfactory level (e.g., 73 kg of milk yield per lactation, 0.016% of milk fat). Claw health and feed efficiency should be defined as new breeding objectives and new selection index traits of local dairy population.

scholarly journals Genotype imputation from various low-density SNP panels and its impact on accuracy of genomic breeding values in pigs

animal ◽  
2018 ◽  
Vol 12 (11) ◽  
pp. 2235-2245 ◽  
Author(s):  
D.A. Grossi ◽  
L.F. Brito ◽  
M. Jafarikia ◽  
F.S. Schenkel ◽  
Z. Feng
Keyword(s):  
Genotype Imputation ◽  
Low Density ◽  
Genomic Breeding ◽  
Breeding Values ◽  
Snp Panels

scholarly journals Genomic Breeding Values for Claw Diseases/Disorders in Czech Holstein Cows

2019 ◽  
Vol 67 (5) ◽  
pp. 1245-1251
Author(s):  
Ludmila Zavadilová ◽  
Eva Kašná ◽  
Zuzana Krupová
Keyword(s):  
Infectious Diseases ◽  
Fixed Effects ◽  
Genetic Correlations ◽  
Genetic Effect ◽  
Holstein Cows ◽  
Additive Genetic Effect ◽  
Genomic Information ◽  
White Line ◽  
Genomic Breeding ◽  
Breeding Values

Genomic breeding values (GEBV) were predicted for claw diseases/disorders in Holstein cows. The data sets included 6,498, 6,641 and 16,208 cows for the three groups of analysed disorders. The analysed traits were infectious diseases (ID), including digital and interdigital dermatitis and interdigital phlegmon, and non-infectious diseases (NID), including ulcers, white line disease, horn fissures, and double sole and overall claw disease (OCD), comprising all recorded disorders. Claw diseases/disorders were defined as 0/1 occurrence per lactation. Linear animal models were employed for prediction of conventional breeding values (BV) and genomic breeding values (GEBV), including the random additive genetic effect of animal and the permanent environmental effect of cow and fixed effects of parity, herd, year and month of calving. Both high and intermediate weights (80% and 50%, respectively) of genomic information were employed for GEBV50 and GEBV80 prediction. The estimated heritability for ID was 3.47%, whereas that for NID 4.61% and for OCD was 2.29%. Approximate genetic correlations among claw diseases/disorders traits ranged from 19% (ID x NID) to 81% (NID x OCD). The correlations between predicted BV and GEBV50 (84–99%) were higher than those between BV and GEBV80 (70–98%). Reliability of breeding values was low for each claw disease/disorder (on average, 3.7 to 14.8%) and increased with the weight of genomic information employed.

scholarly journals Effect of unfavourable population structure on estimates of heritability, systematic effects and breeding values

2008 ◽  
Vol 51 (6) ◽  
pp. 601-610
Author(s):  
A. P. Kominakis
Keyword(s):  
Population Structure ◽  
Mean Squared Error ◽  
Heritability Estimate ◽  
Breeding Values ◽  
Parameter Estimations ◽  
Squared Error ◽  
Heritability Estimation ◽  
Population Structures ◽  
Systematic Effects ◽  
The Impact

Abstract. Empirical estimations of heritability, systematic effects and predictions of sires’ breeding values (BVs) were obtained under various population structures for simulated populations consisted of n = 400 animals in 5 herds for a trait of medium heritability (h2 = 0.30). An infinitesimal additive genetic animal model was assumed while simulating data. Population structure was varied to allow for good and poor connectedness across herds and (non)random association between the genetic and the environmental effects. The impact of the various population structures on the parameter estimation(s) was assessed using Mean Squared Error (MSE) and Pearson’s correlations. Allowing sires to have progenies in more than one herd (good herd connectedness) and random use of sires across herds generally resulted in good parameter estimations. Poor connectedness significantly affected herd effects estimation and BV prediction but not heritability estimation as long as random usage of sires across environments was guaranteed. Selective use of the best sires in the best herds along with poor connectedness resulted in poorest estimations of all parameters examined. In the latter case, heritability was seriously underestimated (h2 = 0.06) while highest error, lowest accuracies for the BVs and a remarkable underestimation of the genetic gain were observed. Use of reference sires on a natural mating basis to create genetic links between herds has served a good solution for both heritability and BVs estimation under unfavorable structure. Mating 0.25 of the herd ewes with reference sires resulted in a heritability estimate close to the simulated one. Significantly better estimates of systematic effects and BVs were, however, obtained when 0.5 of the herd ewes were mated by reference sires.

scholarly journals Prediction of genomic breeding values for growth, carcass and meat quality traits in a multi-breed sheep population using a HD SNP chip

BMC Genetics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Luiz F. Brito ◽  
Shannon M. Clarke ◽  
John C. McEwan ◽  
Stephen P. Miller ◽  
Natalie K. Pickering ◽  
...  
Keyword(s):  
Meat Quality ◽  
Quality Traits ◽  
Sheep Population ◽  
Genomic Breeding ◽  
Breeding Values ◽  
Snp Chip ◽  
Meat Quality Traits ◽  
Breed Sheep

scholarly journals Genomic selection for white spot syndrome virus resistance in whiteleg shrimp boosts survival under an experimental challenge test

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Marie Lillehammer ◽  
Rama Bangera ◽  
Marcela Salazar ◽  
Sergio Vela ◽  
Edna C. Erazo ◽  
...  
Keyword(s):  
Genomic Selection ◽  
Genetic Improvement ◽  
White Spot Syndrome Virus ◽  
Random Mating ◽  
Challenge Test ◽  
White Spot ◽  
Breeding Value ◽  
Genomic Breeding ◽  
Breeding Values ◽  
White Spot Syndrome

AbstractWhite spot syndrome virus (WSSV) causes major worldwide losses in shrimp aquaculture. The development of resistant shrimp populations is an attractive option for management of the disease. However, heritability for WSSV resistance is generally low and genetic improvement by conventional selection has been slow. This study was designed to determine the power and accuracy of genomic selection to improve WSSV resistance in Litopenaeus vannamei. Shrimp were experimentally challenged with WSSV and resistance was evaluated as dead or alive (DOA) 23 days after infestation. All shrimp in the challenge test were genotyped for 18,643 single nucleotide polymorphisms. Breeding candidates (G0) were ranked on genomic breeding values for WSSV resistance. Two G1 populations were produced, one from G0 breeders with high and the other with low estimated breeding values. A third population was produced from “random” mating of parent stock. The average survival was 25% in the low, 38% in the random and 51% in the high-genomic breeding value groups. Genomic heritability for DOA (0.41 in G1) was high for this type of trait. The realised genetic gain and high heritability clearly demonstrates large potential for further genetic improvement of WSSV resistance in the evaluated L. vannamei population using genomic selection.

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