Recent talks

Genomska selekcija rjave pasme goveda v Sloveniji

Use of AlphaDrop in the simulation approach to genomic selection and mate allocation Genomska selekcija

InterBull: Partitioning of international genetic trends by origin in Brown Swiss bulls

I attended the InterBull meeting this year in Stavanger (Norway), which was jointly organised with the EAAP conference in the same place. I participated with contribution titled "Partitioning of international genetic trends by origin in Brown Swiss bulls" co-authored with colleagues. In essence we partitioned  breeding values of Brown Swiss animals by origin of selection and summarized those partitions as origin specific genetic trends. This gives us an opportunity to evaluate the effect of selection performed in different countries and how this affects the global genetic trends. Results for this breed are quite shocking! Look into the paper and talk (see bellow) for more ;)

We were looking forward for comments and/or critiques about the applied method from the audience, but did not get any direct questions. Several people approached me after the talk and one of the comments was that our method is nothing more than multiplying breeding values by the share of genes coming from different origin. This is not true and I will demonstrate this in with a simple example.

Let us assume that we have a simple small pedigree as shown bellow with R code, where column names are: id =individual code, fid = father code, mid = mother code, ori = origin, and bv = breeding value. This pedigree could represent situation where we constantly use foreign sires - here only two generations are being shown. Origin represents the country of registering/selecting aninmal.

## Simple example
example <- data.frame( id=c(  1,   2,   3,   4,   5),
                      fid=c( NA,  NA,   1,  NA,   3),
                      mid=c( NA,  NA,   2,  NA,   4),
                      ori=c("A", "B", "A", "B", "A"),
                       bv=c(100, 106, 104, 106, 103))

Now we would like to perform gene proportion analysis and partitioning of supplied breeding values, both according to origin. This is easy to achieve "by hand" for this simple example (see paper bellow for maths), but tedious for bigger examples. I have wrote an R package partAGV (not yet publicly available, but you can contact me) that can be used for such analyses.

## For gene proportion analysis
example$gp <- 1
 
library(partAGV)
partAGV(example, colAGV=6:5)
 
## Gene proportions
##    id  fid  mid ori gp gp_pa gp_w gp_A gp_B
## 1   1 <NA> <NA>   A  1     0    1 1.00 0.00
## 2   2 <NA> <NA>   B  1     0    1 0.00 1.00
## 3   3    1    2   A  1     1    0 0.50 0.50
## 4   4 <NA> <NA>   B  1     0    1 0.00 1.00
## 5   5    3    4   A  1     1    0 0.25 0.75
 
## Partitions of breeding values 
##    id  fid  mid ori  bv bv_pa bv_w  bv_A  bv_B
## 1   1 <NA> <NA>   A 100     0  100 100.0   0.0
## 2   2 <NA> <NA>   B 106     0  106   0.0 106.0
## 3   3    1    2   A 104   103    1  51.0  53.0
## 4   4 <NA> <NA>   B 106     0  106   0.0 106.0
## 5   5    3    4   A 103   105   -2  23.5  79.5

As we can see gene proportions are as expected: 1/2 for each origin in individual 3 and 1/4 vs. 3/4 for individual 5. Partitions of breeding values show that in animal 5 we 23.5 (out of 105) is attributed to selection work done in country A and 79.5 is attributed to selection work done in country B. Now, if we multiply breeding value of individual 5 (105) by origin specific gene proportions (1/4 and 3/4) we get 25.75 and 77.5, which is similar to partitions, but not the same. This shows that our method enables separation of gene flow and selection work preformed by particular country. In order to see this algebraically we can write breeding values of this individual as:

a_5   = 1/2 a_3 + 1/2 a_4 + w_5

      = 1/2 (1/2 a_1 + 1/2 a_2   +     w_3)  + 1/2 w_4 + w_5

      =      1/4 a_1 + 1/4 a_2   + 1/2 w_3   + 1/2 w_4 + w_5

      =      1/4 w_1 + 1/4 w_2   + 1/2 w_3   + 1/2 w_4 + w_5

      =      1/4 100 + 1/4 106   + 1/2   1   + 1/2 106 +  -2

      =           25 +      26.5 +       0.5 +      53 +  -2

If we now collect terms specific to each origin we get:

a_5_A =           25 +                   0.5 +         +  -2 = 23.5

a_5_B =                     26.5 +                  53       = 79.5

Partitioning of international genetic trends by origin in Brown Swiss bulls

Partitioning of international genetic trends by origin in Brown Swiss bulls

Use of INLA for animal breeding applications

I am working with Ingelin Steinsland and Sara Martino on the use of approximate Bayesian method called Integrated Nested Laplace Approximation (INLA). We presented some of our preliminary results at Workshop in Bayesian Inference for Latent Gaussian Models with Applications in Zurich (Switzerland). We had two contributions:

• Application of Integrated Nested Laplace Approximation to Survival Models as used in Animal Breeding
• Use of Integrated Nested Laplace Approximation for Pedigree Based Mixed Models

Evaluation of different approaches for the estimation of daily yield from single milk testing scheme in cattle

Janez finnished and submitted the paper "Evaluation of different approaches for the estimation of daily yield from single milk testing scheme in cattle". He did the majority of job! I improved his work a bit with the comments and restructuring/rewritting some parts of the paper.

Evaluation of different approaches for the estimation of daily yield from single milk testing scheme in cattle

Fun picture of genetic experiments with cattle

Source: Cécile Dumas, AUG Liege

Loking for cattle genetics presentations?

Go here - courtesy of Kent A. Weigel.

Genes for cowboys

I rally like the title of this "material": Genes for cowboys. I still need to parse the content.

Genomic selection in beef cattle

Stephen P. Miller has wrote two short articles about application of genomic selection in beef cattle:

• Genomics - A Fast Train Coming
• Harnessing the Power of Genomics for Beef - A Collaborative Approach

Genomska selekcija

Danes sva imela s Potočnik Klemnom predstavitev o genomski selekciji. Jaz sem na splošno predstavil "klasično" selekcijo in v čem se razlikuje genomska selekcija, medtem ko je Klemen predstavil vtise in informacije z Interbull delavnice. Moj del predstavitve je na voljo tukaj, za pregled stanja pa lahko sledite tej povezavi.

Genomska selekcija

Financiranje rejskega programa za lisasto pasmo govedi v Italiji

Te dni se mudim v Italiji na tečaju, ki ga vodi Ignacy Misztal. Tečaj sicer organizira ANAPRI - rejsko organizacija za lisasto pasmo govedi v Italiji. Po pogovoru z gostitelji sem izvedel, da se rejski program financira v grobem na sledeči način: 60 % iz proračuna, 15 % s strani rejcev in ostalo z "aktivnostjo" same zveze. Rejci morajo na kravo na leto plačati 11 EUR. S tem prispevajo del stroškov za izvajanje kontrole in ostale dejavnosti povezane s selekcijo.