Archive for the ‘Genomic Selection’ Category

Recent articles

February 28, 2014 Leave a comment

Just a small review of the articles I went through recently :

  • A surprising results on sex bias in Holstein. Huge impact on the industry could be thought of, if the figure are confirmed and impact better estimated (I mean, conventional semen give 50% of females. So the worst case scenario against which +450 kg more milk at the end of the second lactation could be produced…is not the common situation).
  • Analysis of selective sweep in cattle with sequence data.
  • Some hints on way to correct for population stratification
  • The funny article of the month, a compression exercise with all the results included (Side effect of the OpenData policy ? …lots of information you’ll never really use ?)

Recent articles

January 21, 2014 Leave a comment

Just a small review of the articles I went through recently :

Recent articles

October 31, 2013 Leave a comment

Just a small review of the articles I went through recently :

Recent articles

July 8, 2013 Leave a comment

Just a small review of the articles I went through recently :

Sufficiently rare to be mentioned, Bayes theorem in Science  by  Efron , with a nice follow-up post on the og

Although the lab technicalities were far beyond my understanding, the questions raised by this article on Evolution of  essential gene, stroke me !

I wish I had time to have a look on these kind of procedure during my  Ph’D, a simple permutation algorithm to compute significance threshold. By the way, I also learned a new distribution : the Rademacher distribution

I was eager to see this article, the Rat Genome Sequencing and Mapping consortium  made a very interesting piece of work combining sequence and genetic mapping in outbred rats. A lot of questions came to my mind based on these results…yeah hunting the so called “causal mutation” may not be that easy.

And last the funny  article of the month ! This kind of question could have been seen on  Freakonometrics

Are bets following mendel’s law ?

June 14, 2013 Leave a comment

IMG_20130603_114814My parents just got two cute calves. Their parents are both heterozygous at the polled locus, furthermore their sire is heterozygous at the Red Factor (Rr). As a breeder I hope they’ll be both homozygous polled (PP) and red factor (Rr)…as a scientist, (or just a realistic breeder) I know the odds for such an event are low, so I tried to bet for something more realistic — which in fact is not that easy !  This lead me to the question :

Do bets on genotypes follow mendel’s law ?

I’ve set a quick and dirty survey  to collect data, in the hope that it may help to answer this question. So if you’ve got time to fill the form, I’ll be more than happy !

PS : These calves will be tested on the new Eurogenomics LD chip so real genotypes /status will be available in a month or two….with hopefully some first analysis of the results.

Recent articles

June 5, 2013 Leave a comment

Just a small review of the articles I went through recently :

  • A good article on covariance matrices regularization, the latter point to another article that turns out to be a generalization of methods we’ve tested for genomic selection (I wish I knew them some times ago).
  • Two articles on Genomic Selection, the first one made me think about discussion we had with David after my PhD defense. The second one  although  “less humourous than the original submission”, make a nice review of “the Bayesian alphabet”, explaining and pointing out a lot of interesting facts on Bayesian analysis.
  • A nice article on a minute plant genome, that could be related to the ongoing encode’s discussion.
  • An interesting article on LongRNA .
  • The funny article of the month

Sources of proudness

May 18, 2013 Leave a comment

taurusastronautmodelsA2evolutionjpgApril have been the occasion of several changes and achievements on my parents’ farm.

Milking robots

First and foremost, after milking something like 1 Millions cows (~30 years,  ~50 cows, 2X a day…figures got impressive !), my parents invested in a milking robot. Launching was pretty challenging, since cows have to bear a pretty disruptive change in their life style (from a gregarious behavior to autonomy in fact). I took a whole week of “holidays” to  help for the switch between milking parlor to automate milking. Despite the 4 hours of sleep per day (we were handling cows 24/7) I really enjoyed the experience (and guess what, I’ve been pretty efficient reading articles in the night, while cows were being milked !).

A second achievement, related to the previous one, is that after one month using the robots three cows outperform our previous milking record per day (mostly the effect of being milked more often), so 3 cows reached 60Kg/milk per day, the best being able to produce 70kg/day. For those of my INRA’s colleagues lacking some references, I generally turn this into “These cows produce around 3 time their weight in a month, producing almost 2 tonnes of milk…which won’t be enough to pay the rent of my flat in Paris’ suburbs 😦 (The milk price was 299€/1000 l for 2013-1) …this is essentially why I don’t own a cow at home ! The impact of robots milking on production is pretty well known, I am just happy to witness it so quickly. Recently one of our first cow out of a “genomic sire” also reached an impressive 50kg milk per day, which is pretty nice for a first lactation…and a sign that our gEBV are not so bad (isn’t it ?)!

Production improvements

A third nice news –still regarding productivity– is that my parents ranked 35th in France in the last “Top List” (the latter rank herd based on their average productivity). The herd reach an average of 11500 kg milk (305d) per cow @ 32 Protein and 34 Fat. While we’ve been for decade within the top ranked ISU herd in France, this is always nice to see that genetic is not disconnected from phenotypes ! I am eager to see what our results will be next year, with the automated milking !

anzeige-hi-13-05-de-bossA forth (maybe a bit outdated) event was that we had our first cow reaching a total life production of 100 000 kg of milk. A funny story is that I used to tell Vincent Ducrocq (ages ago, when I was in master degree) that this cow was the living proof that we believed in the longevity index since her sire had a strong longevity index and was chosen on purpose. Years later, I also wan’t to see here a proof that longevity index are also verified on farms !

Radieuse’s great grand sons on the top gRZG

Last, the new gRZG leader in germany Boss is a great grand son of Radieuse (born and raised on our farm), and its half-brothers ranked 22nd (Platin) and 33rd (Sharp) in gRZG. While we already had several sires positively progeny tested, out of our cows, none reached a “leader” status. So I am very proud to see that this family of cow give such good results abroad.