ASSIGNMENT

SUBJECT: ANIMAL BREEDING PLANS (ABG-703)

TOPIC: MIX MODEL SOLUTIONS AND BEST LINEAR

UNBIASED PREDICTIONS (BLUP)

SUBMITTED TO DR. SAIF UR REHMAN

SUBMITTED BY MUHAMMAD ADNAN SHAHID

2019-AG-283
Msc. Animal Breeding and Genetics.
 Best Linear Unbiased Prediction (BLUP)

Best linear unbiased predictions are similar to empirical Bayes estimates of random effects in
linear mixed models, except that in the latter case, where weights depend on unknown values of
components of variance, these unknown variances are replaced by sample-based estimates.
In practice, it is often the case that the parameters associated with the random effect(s) term(s)
are unknown; these parameters are the variances of the random effects and residuals. Typically
the parameters are estimated and plugged into the predictor, leading to the Empirical Best
Linear Unbiased Predictor (EBLUP). Notice that by simply plugging in the estimated parameter
into the predictor, additional variability is unaccounted for, leading to overly optimistic prediction
variances for the EBLUP.
The use of the term "prediction" may be because in the field of animal breeding in which
Henderson worked, the random effects were usually genetic merit, which could be used to
predict the quality of offspring (Robinson[1] page 28)). However, the equations for the "fixed"
effects and for the random effects are different.
In statistics, best linear unbiased prediction (BLUP) is used in linear mixed models for the
estimation of random effects. BLUP was derived by Charles Roy Henderson in 1950 but the
term "best linear unbiased predictor" (or "prediction") seems not to have been used until
1962.[1] "Best linear unbiased predictions" (BLUPs) of random effects are similar to best linear
unbiased estimates (BLUEs) (see Gauss–Markov theorem) of fixed effects. The distinction
arises because it is conventional to talk about estimating fixed effects but predicting random
effects, but the two terms are otherwise equivalent. (This is a bit strange since the random
effects have already been "realized"; they already exist.

USES:
BLUP is a modern genetic evaluation system for all breeding organizations. It estimates genetic
merit of individuals using observations and genetic similarity, given the components of variance.
BLUP offers the potential to accelerate genetic progress in your breeding population. BLUP is
easy to use, fast, suitable for simultaneous analysis of a large number of traits and able to fit
complex models.
It supports a wide range of methods to specify genetic similarity between individuals, such as
pedigree relationships and genomic relationships plus regression,

BLUP usage?
In general, it is a method of estimating random effects

Advantages :
BLUP allows you to use sophisticated models in estimation of breeding values for all animal
species. BLUP uses a fast, state-of-the-art solving algorithm. This ensures fast computation of
estimated breeding values even if your evaluation model is complex and your animal population
is large. BLUP can be used in practice for modern applications, such as random regression
models and social interaction models. Genetic similarity between individuals can be specified
with pedigree and genomic information. Gene and marker assisted genetic evaluation is also
supported.

The software is used worldwide in national and international evaluations for cattle but also for
pigs, horses, sheep, goats, fish, foxes, poultry and barley

Calcultaion of breeding values?

Softwares available using BLUP?

 MixBLUP
 Selegen-REML/BLUP
 Mix99
 GRAMBLUP
 Sas/Stat
 Genomatrix
 BESSiE
 RBIO

Why Use a Mixed Model?

As stated above, mixed models have several advantages over traditional linear models.
Just a few are listed here.

 • Specifying More Appropriate Variance-Covariance Structures for Longitudinal Data:

The ability to fit complex covariance patterns provides more appropriate fixed effect
estimates and standard errors.
  • Analysis Assuming Unequal Group Variances: Different variances can be fit for each
treatment group.
 • Analysis of Longitudinal Data with Unequal Time Points: Mixed models allow for the
analysis of data in which the measurements were made at random (varying) time points.
 • Analysis of Longitudinal Data with Missing Response Data: Problems caused by
missing data in repeated measures and cross-over trials are eliminated.
 • Greater Flexibility in Modeling Covariates: Covariates can be modeled as fixed or
random and more accurately represent their true contribution in the model.

 Mixed models are particularly useful in medical studies where a wide variety of factors
influence the response to a treatment of interest. For example, suppose that an
experimental treatment is being administered to a group of patients desiring to lose
weight. Traditional statistical methodologies (e.g., ANOVA, multiple regression, etc.)

Mixed Model Solutions

A mixed model (or more precisely mixed error-component model) is a statistical

model containing both fixed effects and random effects.[1] These models are useful in a
wide variety of disciplines in the physical, biological and social sciences. They are
particularly useful in settings where repeated measurements are made on the
same statistical units (longitudinal study), or where measurements are made on clusters
of related statistical units. Because of their advantage in dealing with missing values,
mixed effects models are often preferred over more traditional approaches such as
repeated measures ANOVA.
The Mixed Models procedure analyzes results from a wide variety of experimental
designs in which the outcome (response) is continuous, including
 • Two-sample designs (replacing the t-test)
 • One-way layout designs (replacing one-way ANOVA)
 • Factorial designs (replacing factorial GLM)
 • Split-plot designs (replacing split-plot GLM)

USES:

The Mixed Models procedure can be used to test and estimate means (including pair-wise
comparisons among levels), compare models, estimate variance-covariance matrix
components, and produce graphs of means and repeated measurements of subjects.
REFERENCES:
https://gsejournal.biomedcentral.com/articles/10.1186/s12711-016-0241-x
http://www.afhalifax.ca/magazine/wp-
content/sciences/LaGenetique/EstimateBreedingValues/Software%20in%20animal%20breeding
.htm
https://www.mixblup.eu/
https://www.ncss.com/
https://en.wikipedia.org/wiki/Best_linear_unbiased_prediction
http://www.biometria.ufv.br/?page_id=17
https://www.luke.fi/en/business-solutions/expertise-areas/livestock-and-feed/mix99-solving-
large-mixed-model-equations/