Semiparametric regression via penalized splines literature

Interested in semiparametric regression via penalized splines? Take a look here.

Kako ravnajo s poginulimi živalmi čez lužo

Glej "Dealing With Deadstock". Pri nas pa v določenih pogledih pretiravamo do skrajne mere. Se povsem strinjam, da mora biti ta segment živinoreje primerno urejen, a za to izvajati "vesoljske" procese ni razumno.

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

Progress bar in R

Nice summary on how to use progress bars in R. I am posting this here in order to have a note for later searches.

Weather change - shit!

See here what kind of problems are Australian farmers facing due to weather changes.

How Ant Subterrain Structure's Looks Like?

Describing genetic variability

One of paramount interests of quantitative geneticists is the knowledge about how much visible (phenotypic) variability is due to genetic variability. To describe this we usually compute narrow sense heritability h² = Var(a) / Var(y), where y is phenotypic and a is additive genetic value (see book by Falconer and MacKay). A usual result from analyses is that fitness related traits have much lower heritability (say 0.1 or similar) than morphological traits (say 0.5 or even more). This eventually leads to the conclusion that selection will not be effective for fitness related traits, since there is not much additive genetic variability. However, this can only be partialy true. The heritability can have a small value due to small additive genetic variance and/or large phenotypic variance. It is clear that if there is a lot of environmental variability that the selection can not be the prime force to change the population. However, this still does not mean that we should neglect the genetic variability. David Houle has dealt with this issue and published a paper in Genetics (1992). I have read that paper several times and I always forget the exact conclusion. Well, there is no exact conclusion. However, Houle suggests that heritability is not a good measure of evolvability (ability of population to respond to selection) or variability (strength of forces that maintain and deplete genetic variation). He suggests that standardizing the additive genetic variance with a mean is better, which in turn leads to the suggestion that additive genetic coefficient of variation (CV_a = Var(a) / Mean(y)) is a more informative measure than heritability. There is also some more recent work by Houle (his pub. webpage, this looks very interesting), that I need to digest - sometime.

An example: we have two populations A and B (this could also be two different traits!), with means 5 and 10, additive genetic variance 5 and 5, heritabilities 0.2 and 0.2. Based on heritabilities we could conclude that selection will have the same effect in both populations, but this is not true in relative meaning. In population A the additive genetic variance is euqal to the mean, whereas it is only half of the mean in population B. The additive genetic coefficient of variations would be 0.45 and 0.22 for population A and B, respectively. This means that we can achive relatively greater response to selection in population A than in population B.

Video lectures about genetics (biology)

In addition to YouTube videos about genetics there is also a huge number of video lectures at http://videolectures.net/. There is a lot of material on machine learning, statistics, ..., but also biology - see Introduction to Biology which is a course from MIT. Bellow is a link to first lecture on Genetics given by Lander.

Lecture 6: Genetics 1
Eric Lander

Slick spline plot in SAS

Here is an example of a slick spline (using penalized b-splines) plot in SAS. The plot is created with SGPLOT procedure. I hope SAS will add such "functions" also to model based procedures such as GLM, MIXED, GENMOD, ...

European Master in Animal Breeding and Genetics

Posredujem novico o štipendijah za študij "European Master in Animal Breeding and Genetics". Kratek pregled predmetnikov (Course contents) na spletni strani http://www.emabg.eu pokaže, da je večina predmetov na temo genetike in selekcije na splošno in ločeno po vrstah živali, ki so pomembne za živinorejo. Je pa na voljo tudi nekaj bolj splošnih predmetov, ki bi lahko bili zelo zanimivi - psi in mačke!

Dear all
Scholarships are available for students from EU countries that want to participate in the European Master in Animal Breeding and Genetics (EMABG) starting in August 2009. Deadlines for applications: May 1st 2009. The deadline for non-EU students that want to participate in course starting this year has passed but they can applied before January 15th 2010 for the next academic year. Information on program and scholarships can be found at www.emabg.eu

The European Master in Animal Breeding is accepted by the European Union as an Erasmus Mundus MSc programme for a five-year period starting in 2007. In 2007, 24 students started the program followed by 21 students in 2008. The universities participating in the EM-ABG are Wageningen University (the Netherlands), University of Natural Resources and Applied Life Sciences (Austria), Christian-Albrechts-Universität (Germany), AgroParisTech (France), Swedish University of Agricultural Sciences (Sweden) and The Norwegian University of Life Sciences (Norway). These groups have a long tradition of collaboration and a strong profile in the area of Animal Breeding and Genetics.

For more information and application, please contact:
EM-ABG secretary, Animal Breeding and Genomics Centre, Wageningen University, PO Box 338, NL 6700 AH Wageningen, The Netherlands, emabg@wur.nl

Kindest regards

Johan van Arendonk
Co-ordinator of EMABG

YouTube videos about genetics

While browsing for SNP chips for sheep I found out that there are some very nice videos on YouTube about genetics. Here is a list of some, but be free to explore further on!

• Genetics 101 Part 1: What are genes?
• Genetics 101 Part 2: What are SNPs?
• Genetics 101 Part 3: Where do your genes come from?
• Genetics 101 Part 4: What is phenotype?
• Gregor Mendel and Genetics
• Heredity
  

• Microarrays
• DNA microarrays
• Microarray Method for Genetic Testing

• Pamela Anderson Illustrates Genetics? - PowerPoint Comedy --> it nicely explains the linkage disequilibrium ;)
  

Chip for sheep

There is a lot of work in the area of SNP-chips for sheep. See:

• International Sheep Genomics Consortium (YouTube video)
• Australian Sheep Gene Mapping Web Site
• Sheep Genomics
• ...

However, genomic selection with "standard" chips might not be so successful in all sheep populations since there is a lot of variation in a sense that that the linkage disequilibrium is not so strong as in cattle - though I am saying that without having much experience!

3D health card

This is cool! Click on video if you do not speak Slovenian.

Growth performance of station tested rams in Slovenia

This is our short communication for ASD 2009.

Update 2009-03-13: We had to shorten the manuscript to three pages. This of course lead to the exclusion of some results that will be published elsewhere.

Growth performance of station tested rams in Slovenia

Publish at Scribd or explore others: Draft Research Academic Work growth Sheep

Substantial update of "Evolution and Selection of Quantitative Traits"

Bruce Walsh send an e-mail to AGDG list about the substantial update of their forthcoming book "Evolution and Selection of Quantitative Traits". After very successful volume 1, we are all eagerly waiting for this volume!

Armidale Animal Breeding Summer Course 2009 Materials

UNE in Armidale organizes each year an Animal Breeding Summer Course. This year they hosted Bruce Walsh (Quantitative Genetic Theory and Analysis: Selection Theory) and Pieter Bijma (Quantitative Genetic Models for social interaction and GxE and inherited variability). What I really like about this course is that all the materials are posted on the website (follow this link for materials for this year). Therefore, all of us that did not had the opportunity to go down under can still study!

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