Enhanced comment feature has been enabled for all readers including those not logged in. Click on the Discussion tab (top left) to add or reply to discussions.

Multiple Trait Evaluation: Difference between revisions

From BIF Guidelines Wiki
No edit summary
No edit summary
 
(6 intermediate revisions by 3 users not shown)
Line 1: Line 1:
Multiple-trait genetic evaluation differs from a single-trait evaluation in that several phenotypic traits are evaluated at the same time. Reasons for doing a multiple trait genetic evaluation include greater prediction [[Accuracy| accuracy]] and reduced [[Prediction Bias |prediction bias]].  
[[Category: Genetic Evaluation]]
Multiple-trait genetic evaluation differs from a single-trait evaluation in that several phenotypic traits are evaluated at the same time. Reasons for doing a multiple-trait genetic evaluation include greater prediction [[Accuracy| accuracy]] and reduced [[Prediction Bias |prediction bias]].  


As with single-trait genetic evaluation most traits use [[Best Linear Unbiased Prediction | BLUP]] to obtain [[Expected Progeny Difference| EPD]] by solving the mixed-model equations. For single traits with breeding values as the only random effect the mixed-model equations take the form
As with single-trait genetic evaluation most traits use [[Best Linear Unbiased Prediction | BLUP]] to obtain [[Expected Progeny Difference| EPD]] by solving the mixed-model equations. For single traits with breeding values as the only random effect the mixed-model equations take the form
Line 18: Line 19:
</math>
</math>
</center>
</center>
where <math>\mathbf{X}</math> and <math>\mathbf{Z}</math> are the incidence matrices for the fixed and random effects, <math>\mathbf{K}</math> is a relationship relationship matrix, <math>\hat\boldsymbol{\beta}</math> are estimated fixed effects, <math>\hat\mathbf{u}</math> the predicted breeding values, <math>\mathbf{y}</math> the vector of observed phenotypes, and <math>\lambda=\sigma^2_e/\sigma^2_g</math> is the ratio of the environmental variance <math>\sigma^2_e</math> and the additive genetic variance <math>\sigma^2_g</math>.
where <math>\mathbf{X}</math> and <math>\mathbf{Z}</math> are the incidence matrices for the fixed and random effects, <math>\mathbf{K}</math> is a relationship matrix, <math>\hat\boldsymbol{\beta}</math> are estimated fixed effects, <math>\hat\mathbf{u}</math> the predicted breeding values, <math>\mathbf{y}</math> the vector of observed phenotypes, and <math>\lambda=\sigma^2_e/\sigma^2_g</math> is the ratio of the environmental variance <math>\sigma^2_e</math> and the additive genetic variance <math>\sigma^2_g</math>.


In a multiple-trait genetic evaluation  we have covariances in addition to addition to variances associated with the random effects. In addition, different animals could have observed phenotypes for different subsets of traits. In the case where we have two traits and with breeding values as the only random effects, the mixed model equations take the form
In a multiple-trait genetic evaluation  we have covariances in addition to variances associated with the random effects<ref> Henderson, C. R., and  R. L. Quaas. 1976. Multiple trait evaluation using relatives' records, J. Anim. Sci.  43:1188–1197.</ref><ref>Mrode, R. A. 2005. Best linear unbiased prediction of breeding value: multivariate models. In: Linear models for the prediction of animal breeding values 2nd ed. CAB Int., Wallingford, Oxfordshire, UK. p. 83-119. </ref>. In addition, different animals could have observed phenotypes for different subsets of traits. In the case where we have two traits and with breeding values as the only random effects, the mixed-model equations take the form
<center>
<center>
<math>
<math>
Line 39: Line 40:
where <math>\mathbf{G}</math> is the genetic covariance matrix and is a function of a relationship matrix <math>\mathbf{K}</math> and genetic variances of the two traits and the genetic covariance between the two traits, and <math>\mathbf{R}</math> is the environmental covariance matrix and is a function of the  environmental variances of the two traits and the environmental covariance between the two traits.
where <math>\mathbf{G}</math> is the genetic covariance matrix and is a function of a relationship matrix <math>\mathbf{K}</math> and genetic variances of the two traits and the genetic covariance between the two traits, and <math>\mathbf{R}</math> is the environmental covariance matrix and is a function of the  environmental variances of the two traits and the environmental covariance between the two traits.


[WE NEED CITATIONS]
==References==
 
<references />

Latest revision as of 09:59, 6 April 2022

Multiple-trait genetic evaluation differs from a single-trait evaluation in that several phenotypic traits are evaluated at the same time. Reasons for doing a multiple-trait genetic evaluation include greater prediction accuracy and reduced prediction bias.

As with single-trait genetic evaluation most traits use BLUP to obtain EPD by solving the mixed-model equations. For single traits with breeding values as the only random effect the mixed-model equations take the form

where and are the incidence matrices for the fixed and random effects, is a relationship matrix, are estimated fixed effects, the predicted breeding values, the vector of observed phenotypes, and is the ratio of the environmental variance and the additive genetic variance .

In a multiple-trait genetic evaluation we have covariances in addition to variances associated with the random effects[1][2]. In addition, different animals could have observed phenotypes for different subsets of traits. In the case where we have two traits and with breeding values as the only random effects, the mixed-model equations take the form

where is the genetic covariance matrix and is a function of a relationship matrix and genetic variances of the two traits and the genetic covariance between the two traits, and is the environmental covariance matrix and is a function of the environmental variances of the two traits and the environmental covariance between the two traits.

References

  1. Henderson, C. R., and R. L. Quaas. 1976. Multiple trait evaluation using relatives' records, J. Anim. Sci. 43:1188–1197.
  2. Mrode, R. A. 2005. Best linear unbiased prediction of breeding value: multivariate models. In: Linear models for the prediction of animal breeding values 2nd ed. CAB Int., Wallingford, Oxfordshire, UK. p. 83-119.