New approaches to genetic evaluation of beef cattle

1988 ◽  
Vol 12 ◽  
pp. 99-110
Author(s):  
E. John Pollak
Keyword(s):  
Animal Model ◽  
Beef Cattle ◽  
Mixed Model ◽  
The United States ◽  
Genetic Evaluation ◽  
Beef Industry ◽  
Widespread Application ◽  
Cattle Industry ◽  
Reduced Animal Model ◽  
Genetic Evaluations

The beef cattle industry in the United States has undergone dramatic changes over the past decade with the adoption of genetic evaluation programs. The method of choice has been Henderson's mixed model methodology for best linear unbiased prediction (BLUP). The most prevalently used model is the animal model (Henderson and Quaas, 1976) computed by the equivalent reduced animal model (Quaas and Pollak, 1980).Neither the methodology or the models being used are particularly new. What is new in this industry is the widespread application of these techniques to the analysis of the data banks maintained by the breed organizations. Today many breed associations publish a national sire evaluation, and most of these have published their first in the last three years. This rapid proliferation of published evaluations has coincided with an attitude in the industry of promoting specification beef and predictable performance. Genetic evaluations provide information not only to achieve goals in selection but as well for merchandizing cattle based on quantifiable potential. The enthusiasm for genetic evaluations right now in the U.S. beef industry is high.

scholarly journals Development of a genetic evaluation for hair shedding in American Angus cattle to improve thermotolerance

2020 ◽  
Author(s):  
Harly J. Durbin ◽  
Duc Lu ◽  
Helen Yampara-Iquise ◽  
Stephen P. Miller ◽  
Jared E. Decker
Keyword(s):  
Beef Cattle ◽  
Tall Fescue ◽  
The United States ◽  
Early Summer ◽  
Genetic Evaluation ◽  
Functional Enrichment ◽  
Fescue Toxicosis ◽  
Beef Industry ◽  
Angus Cattle ◽  
Genetic Evaluations

AbstractBackgroundHeat stress and fescue toxicosis caused by ingesting tall fescue infected with the endophytic fungus Epichloë coenophiala represent two of the most prevalent stressors to beef cattle in the United States, costing the beef industry millions of dollars each year. The rate at which a beef cow sheds her winter coat early in the summer is an indicator of adaptation to heat and an economically relevant trait in many parts of the U.S. Further, research suggests that early-summer hair shedding may be reflective of tolerance to fescue toxicosis, as vasoconstriction induced by fescue toxicosis limits the ability of an animal to shed its winter coat. Here, we developed parameters for routine genetic evaluation of hair shedding score in American Angus cattle and identified genomic loci associated with variation in hair shedding score via genome-wide association analysis (GWAA).ResultsHair shedding score was found to be moderately heritable (h2 = 0.34 to 0.40), with differing repeatability estimates between cattle grazing versus not grazing endophyte-infected tall fescue. Our results suggest modestly negative genetic and phenotypic correlations between a dam’s hair shedding score (lower score is earlier shedding) and the weaning weight of her calf, one metric of performance. Together, these results indicate that economic gains can be made via the use of hair shedding score breeding values to select for heat tolerant cattle. GWAA identified 176 variants significant at FDR < 0.05. Functional enrichment analyses using genes within 50 Kb of these variants identified pathways involved in keratin formation, prolactin signaling, host-virus interaction, and other biological processes.ConclusionsThis work contributes to a continuing trend in the development of genetic evaluations for environmental adaptation. The results of this work will aid beef cattle producers in selecting more sustainable and climate-adapted cattle, as well as enable the development of similar routine genetic evaluations in other breeds.

scholarly journals Applications of an Animal Model in the United States Beef Cattle Industry

1988 ◽  
Vol 71 ◽  
pp. 35-53 ◽  
Author(s):  
L.L. Benyshek ◽  
M.H. Johnson ◽  
D.E. Little ◽  
J.K. Bertrand ◽  
L.A. Kriese
Keyword(s):  
United States ◽  
Animal Model ◽  
Beef Cattle ◽  
The United States ◽  
Cattle Industry

scholarly journals Development of a genetic evaluation for hair shedding in American Angus cattle to improve thermotolerance

2020 ◽  
Vol 52 (1) ◽  
Author(s):  
Harly J. Durbin ◽  
Duc Lu ◽  
Helen Yampara-Iquise ◽  
Stephen P. Miller ◽  
Jared E. Decker
Keyword(s):  
Heat Stress ◽  
Beef Cattle ◽  
Tall Fescue ◽  
The United States ◽  
Genetic Evaluation ◽  
Functional Enrichment ◽  
Fescue Toxicosis ◽  
Weaning Weight ◽  
Angus Cattle ◽  
Genetic Evaluations

Abstract Background Heat stress and fescue toxicosis caused by ingesting tall fescue infected with the endophytic fungus Epichloë coenophiala represent two of the most prevalent stressors to beef cattle in the United States and cost the beef industry millions of dollars each year. The rate at which a beef cow sheds her winter coat early in the summer is an indicator of adaptation to heat and an economically relevant trait in temperate or subtropical parts of the world. Furthermore, research suggests that early-summer hair shedding may reflect tolerance to fescue toxicosis, since vasoconstriction induced by fescue toxicosis limits the ability of an animal to shed its winter coat. Both heat stress and fescue toxicosis reduce profitability partly via indirect maternal effects on calf weaning weight. Here, we developed parameters for routine genetic evaluation of hair shedding score in American Angus cattle, and identified genomic loci associated with variation in hair shedding score via genome-wide association analysis (GWAA). Results Hair shedding score was moderately heritable (h2 = 0.34 to 0.40), with different repeatability estimates between cattle grazing versus not grazing endophyte-infected tall fescue. Our results suggest modestly negative genetic and phenotypic correlations between a dam’s hair shedding score (lower score is earlier shedding) and the weaning weight of her calf, which is one metric of performance. Together, these results indicate that economic gains can be made by using hair shedding score breeding values to select for heat-tolerant cattle. GWAA identified 176 variants significant at FDR < 0.05. Functional enrichment analyses using genes that were located within 50 kb of these variants identified pathways involved in keratin formation, prolactin signalling, host-virus interaction, and other biological processes. Conclusions This work contributes to a continuing trend in the development of genetic evaluations for environmental adaptation. Our results will aid beef cattle producers in selecting more sustainable and climate-adapted cattle, as well as enable the development of similar routine genetic evaluations in other breeds.

Genetic evaluation for the beef industry in Australia

2005 ◽  
Vol 45 (8) ◽  
pp. 913 ◽  
Author(s):  
H-U. Graser ◽  
B. Tier ◽  
D. J. Johnston ◽  
S. A. Barwick
Keyword(s):  
Beef Cattle ◽  
Evaluation System ◽  
Carcass Characteristics ◽  
Genetic Evaluation ◽  
Beef Industry ◽  
Linear Unbiased Prediction ◽  
Cattle Industry ◽  
Evaluation Procedures ◽  
Complex Models ◽  
Best Linear Unbiased

Genetic evaluation for beef cattle in Australia has been performed using an animal model with best linear unbiased prediction since 1984. The evaluation procedures have evolved from simple to more complex models and from few to a large number of traits, including traits for reproduction, growth and carcass characteristics. This paper describes in detail the current beef cattle genetic evaluation system ‘BREEDPLAN’ used for the Australian beef cattle industry, the traits analysed and underlying models, and presents a short overview of the challenges and planned developments of coming years.

scholarly journals Reduced Animal Models Fitting Only Equations for Phenotyped Animals

2021 ◽  
Vol 12 ◽  
Author(s):  
Mohammad Ali Nilforooshan ◽  
Dorian Garrick
Keyword(s):  
Animal Model ◽  
Animal Models ◽  
Mixed Model ◽  
Reduced Model ◽  
Relationship Matrix ◽  
Full Model ◽  
Breeding Values ◽  
Reduced Animal Model ◽  
Numerator Relationship Matrix ◽  
Model Equations

Reduced models are equivalent models to the full model that enable reduction in the computational demand for solving the problem, here, mixed model equations for estimating breeding values of selection candidates. Since phenotyped animals provide data to the model, the aim of this study was to reduce animal models to those equations corresponding to phenotyped animals. Non-phenotyped ancestral animals have normally been included in analyses as they facilitate formation of the inverse numerator relationship matrix. However, a reduced model can exclude those animals and obtain identical solutions for the breeding values of the animals of interest. Solutions corresponding to non-phenotyped animals can be back-solved from the solutions of phenotyped animals and specific blocks of the inverted relationship matrix. This idea was extended to other forms of animal model and the results from each reduced model (and back-solving) were identical to the results from the corresponding full model. Previous studies have been mainly focused on reduced animal models that absorb equations corresponding to non-parents and solve equations only for parents of phenotyped animals. These two types of reduced animal model can be combined to formulate only equations corresponding to phenotyped parents of phenotyped progeny.

The characterization of the cow-calf, stocker and feedlot cattle industry water footprint to assess the impact of livestock water use sustainability

2020 ◽  
Vol 158 (5) ◽  
pp. 416-430
Author(s):  
H. M. Menendez ◽  
L. O. Tedeschi
Keyword(s):  
Beef Cattle ◽  
Water Use ◽  
Water Footprint ◽  
Current Model ◽  
The United States ◽  
Independent Study ◽  
Model Parameters ◽  
Cattle Industry ◽  
Freshwater Use ◽  
The Impact

AbstractPerception of freshwater use varies between nations and has led to concerns of how to evaluate water use for sustainable food production. The water footprint of beef cattle (WFB) is an important metric to determine current levels of freshwater use and to set sustainability goals. However, current WFB publications provide broad WF values with inconsistent units preventing direct comparison of WFB models. The water footprint assessment (WFA) methodologies use static physio-enviro-managerial equations, rather than dynamic, which limits their ability to estimate cattle water use. This study aimed to advance current WFA methods for WFB estimation by formulating the WFA into a system dynamics methodology to adequately characterize the major phases of the beef cattle industry and provide a tool to identify high-leverage solutions for complex water use systems. Texas is one of the largest cattle producing areas in the United States, a significant water user. This geolocation is an ideal template for WFB estimation in other regions due to its diverse geography, management-cultures, climate and natural resources. The Texas Beef Water Footprint model comprised seven submodels (cattle population, growth, nutrition, forage, WFB, supply chain and regional water use; 1432 state variables). Calibration of our model replicated initial WFB values from an independent study by Chapagain and Hoekstra in 2003 (CH2003). This CH2003 v. Texas production scenarios evaluated model parameters and assumptions and estimated a 41–66% WFB variability. The current model provides an insightful tool to improve complex, unsustainable and inefficient water use systems.

Results of multivariate individual animal model genetic evaluations of british pedigree beef cattle

1997 ◽  
Vol 65 (2) ◽  
pp. 199-207 ◽  
Author(s):  
R. E. Crumps ◽  
G. Simm ◽  
D. Nicholson ◽  
R. H. Findlay ◽  
J. G. E. Bryan ◽  
...  
Keyword(s):  
Animal Model ◽  
Birth Weight ◽  
Beef Cattle ◽  
Fixed Effects ◽  
Breeding Value ◽  
Individual Animal ◽  
Group Sex ◽  
The Uk ◽  
Genetic Evaluations ◽  
Genetic Trends

AbstractThis paper reports the procedures put into place in the UK for the genetic evaluation of pedigree beef cattle and estimation of genetic trends using a comprehensive model to allow critical analysis of progress made under previous data recording schemes. Live weights of Simmental, Limousin, Charolais, South Devon and Aberdeen Angus beef cattle, recorded by the Meat and Livestock Commission (MLC) from 1970 to 1992 were analysed, as part of a project to introduce best linear unbiased predictions (BLUP) of breeding value in the British beef industry. Birth weights were available from MLC or the relevant breed society, (4000 to 84000 records, depending on the breed) and 200- and 400-day weights were estimated by within-animal linear regression on all available weights (resulting in 8000 to 48000 records per breed). Animals were retrospectively assigned to contemporary groups within herds, separately for each trait, taking account of observed calving patterns. Records were adjusted to correct for heterogeneity of variance between herds. BLUP evaluations were then performed within breed, fitting a multivariate individual animal model. In addition to additive direct genetic effects, additive maternal genetic and dam permanent environmental effects were included for birth weight and 200-day weight. Unknown parents were assigned to genetic groups, based on estimated date of birth. The model included fixed effects for contemporary group, sex, month of birth, birth type (single or multiple), embryo transfer births, fostered calves, breed of dam, proportion purebred and age of dam. Genetic trends were estimated by regressing estimated breeding values for animals on their year of birth. Trends in birth weight, 200-day weight and 400-day weight between 1970 and 1992 were approximately 0·09, 0·73 and 1·38 kg per annum respectively for the Charolais breed; 0·08, 0·76 and 1·33 kg per annum for the Simmental; 0·06, 0·53 and 0·89 kg per annum for the Limousin; 0·12, 1·02 and 1·86 kg per annum for the Aberdeen Angus; and 0·03, 0·38 and 0·82 kg per annum for the South Devon breed.

52 Genomic selection in the beef industry: Current achievements and future directions

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 54-55
Author(s):  
Daniel W Moser ◽  
Stephen P Miller ◽  
Kelli J Retallick ◽  
Duc Lu ◽  
Larry A Kuehn
Keyword(s):  
Beef Cattle ◽  
Genomic Selection ◽  
Large Scale ◽  
Genetic Evaluation ◽  
Fiscal Year ◽  
Genomic Testing ◽  
Routine Practice ◽  
The Past ◽  
Angus Cattle ◽  
Genetic Evaluations

Abstract In the past decade, genomic testing of beef cattle has evolved from applications in research to a routine practice for many beef cattle seedstock breeders. Testing for lethal genetic conditions or parentage was many breeders’ first experience with genomic testing. While the American Angus Association (AAA) began utilizing 384 SNP genotypes in genetic evaluations in 2009, the adoption of genotyping with higher density (~50,000 SNP) arrays by AAA in 2010 launched large-scale genotyping of Angus cattle for genetic evaluation. AAA transitioned from semi-annual to weekly genetic evaluations in 2010, and cost of genotyping decreased from $139 per animal in 2011, to $37 in 2017. In fiscal year 2018, AAA members genotyped over 160,000 animals for genetic evaluation, and as of April 2019, the AAA and Canadian Angus Association joint genetic evaluation includes over 635,000 genotyped animals. Now genotyping arrays with Angus-specific SNP content are used. The primary benefit to Angus breeders has been increased accuracy of genetic prediction for young animals, especially for traits with limited phenotypic information such as carcass traits, feed intake and mature cow size. Future benefits from genotyping include identification and selection against embryonic lethal alleles, better characterization of inbreeding, and selection tools for additional traits relevant to or measured in unique environments. Electronic sensors and other novel approaches may yield previously unmeasurable phenotypes for health and efficiency traits, which can be extended to wider populations for selection using genomics. New techniques such as DNA pooling and genotyping by sequencing may reduce costs enabling widespread testing in commercial cow-calf and cattle feeding enterprises. The application of genomic selection has clearly been a significant advancement in genetic selection in Angus cattle in the past ten years. This early adoption will expedite subsequent genomic tools at an increasing rate and will foster innovation.

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