Blog: A Steak in Genomics

[HerefordGuy]

A Steak in Genomics
2015 Angus Convention to Host First-Ever International Genomics Symposium
http://steakgenomics.blogspot.com/2015/02/2015-angus-convention-to-host-first.html

Plus, check out my "snow steer" on the Facebook page: https://www.facebook.com/SteakGenomics/posts/1534916270096619

 

[librarian]

Could a study be done similar to the DNA study where Native, Milking, Irish and Generic Shorthorns were compared for relatedness be done where the analysis included Maine, Chi and Galloway samples as well?
Just to see which direction which groups of Shorthorns tend to creed toward?
Also Shorthorns from Australia, South America and Europe.
Maybe also include Ayrshire and Red Holstein, Red Poll and Red Angus?

 

[HerefordGuy]

Could a study be done similar to the DNA study where Native, Milking, Irish and Generic Shorthorns were compared for relatedness be done where the analysis included Maine, Chi and Galloway samples as well?
Just to see which direction which groups of Shorthorns tend to creed toward?
Also Shorthorns from Australia, South America and Europe.
Maybe also include Ayrshire and Red Holstein, Red Poll and Red Angus?

Most of the data you talk about has already been generated and published. http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004254
For example, representatives from Maine, Chi, Galloway, Ayrshire, Holstein, Red Poll, and Red Angus are in the PLOS Genetics paper.

What is not available is man hours. If you know of a student at Mizzou who would like to work on this, I would be happy to guide them through the process. Or, even a Mid-Missouri high school student looking for a science fair project.
Have them contact me: http://web.missouri.edu/~deckerje/people.html

 

[librarian]

Thank you. I have read the PLOS Genetics paper and have wondered if that work has paved the way for testing specific animals for infusions of breeds outside the pedigree.
There is so much mythology about "impure blood" in pedigrees. When there is a question, it seems that semen samples  could be tested for breed DNA affinities.
The DNA study involving Native Shorthorns includes data on Irish influenced Shorthorns. Could that be run against the PLOS data for Galloway or other breeds to illuminate the persistent mystery surrounding Improver? 
I would like to study Red Galloway DNA and compare it to other red beef breeds.
If we had the samples, that is.
I did read in the Plos paper that fine distinctions between breeds of British cattle could be as much a matter of management, geography and culture as DNA?

 

[knabe]

matter of management, geography and culture as DNA?

all breeds, species are created this way.  only part of that is reflected in DNA, the rest, we are only just beginning to unravel.

 

[librarian]

Actually, I had read the older paper, MacHugh DE, Shriver MD, Loftus RT, Cunningham P, Bradley DG (1997) Microsatellite DNA variation and the evolution, domestication and phylogeography of taurine and zebu cattle (Bos taurus and Bos indicus). Genetics 146: 1071–1086 Available: http://www.genetics.org/cgi/content/abst​ract/146/3/1071.
thank you for posting this one.

 

[HerefordGuy]

A Steak in Genomics
Register for NCBA Cattlemens Webinar:
New Tools in Bull Selection
Understanding and Using Selection Indexes
http://steakgenomics.blogspot.com/2015/02/register-for-ncba-cattlemens-webinar.html

 

[HerefordGuy]

A Steak in Genomics
Articles of Note from Drovers CattleNetwork​
http://steakgenomics.blogspot.com/2015/03/articles-of-note-drovers-cattlenetwork.html

 

[HerefordGuy]

A Steak in Genomics
Big Number, Little Calf.
Story by Mizzou College of Agriculture, Food and Natural Resources​
http://steakgenomics.blogspot.com/2015/03/a-big-number-for-little-calf-mus-dairy.html

 

[HerefordGuy]

A Steak in Genomics
Why do many reasonable people doubt science?
http://steakgenomics.blogspot.com/2015/03/why-do-many-reasonable-people-doubt.html

 

[knabe]

A Steak in Genomics
Why do many reasonable people doubt science?
http://steakgenomics.blogspot.com/2015/03/why-do-many-reasonable-people-doubt.html

the strength of science is that it doubts science.  all too often we don't.

http://www.reuters.com/article/2012/03/28/us-science-cancer-idUSBRE82R12P20120328

 

[HerefordGuy]

the strength of science is that it doubts science.  all too often we don't.

http://www.reuters.com/article/2012/03/28/us-science-cancer-idUSBRE82R12P20120328

Public acceptance of science and reproducibility of science are two separate issues. The article you shared refers to the reproducibility of science. The article I shared pointed out in several places that science is self-correcting. The quotes I shared highlighted that science is judgemental of science ("doubts science" in your terms). The issue of reproducibility of science slows the pace of scientific discovery and means more effort and time is needed for science to self-correct.

Public doubt is separate from the scientific process. Public doubt of science doesn't perform preliminary, follow-up, or replication studies. Public doubt doesn't peer-review literature. But, public doubt does lead to whether or not scientific knowledge is accepted and applied. Public doubt does affect whether the general population acts on scientific knowledge or if their actions reflect a rejection of science (e.g. not vaccinating, buying raw milk, not trusting agriculture, etc.) I am not concerned about whether or not the public accepts cutting edge or basic research. I am concerned when they don't accept validated, replicated science. (Just so we are clear, genomic prediction is a validated, replicated scientific technology.)

 

[knabe]

The public in general isn't looking for definitions, they are only looking for one exception to the rule to prove the rule that they don't trust science.


I guess the problem I have with genetic prediction is who's prediction to trust.


The Holstein heifer you guys labeled as predictive of performance will go a long way towards your position if she performs as predicted.


To me, the markers are still just hi res parentage maps that are markers that may contain causative elements.  I guess I still haven't seen a tool that will help me in a breed other than angus and Holstein. The companies that took our money still haven't recovered from that public relations disaster.


Hopefully we can start finding causative markers and find other markers in other breeds that may have utility before everything is gone instead of just focusing on angus and Holstein and narrowing those gene pools to the point that all other cattle go extinct. I guess I just don't see the performance difference to warrant elimination of wide swaths of diversity yet.


It would be useful if the space could focus on heterosis.  Perhaps it's just not necessary any more with magical angus as their performance in some lines exceeds hybrid vigor.

 

[HerefordGuy]

In Holstein cattle, the approach they use is basically a hi-res parentage test, but it also includes relationships to the entire breed. This is not a design flaw but a strength! This is the reason it works. Looking at observed relationships rather than expected relationships. I need to write a blog post on this, but likely won't be till June.

The work towards causative variants is beginning, but that is a very long row to hoe.

 

[knabe]

I know it's a strength because it includes things we don't understand. It's been my position all along.


I just think we need to be careful about diversity to avoid 1974 corn.

 

[HerefordGuy]

A Steak in Genomics
Are We Embracing Science and Technology?
http://blog.steakgenomics.org/2015/05/are-we-embracing-science-and-technology.html

 

[knabe]

http://bombsight.org/#12/51.5047/-0.1001


neat way to visualize data.


interesting that big ben wasn't hit.


http://www.slate.com/blogs/quora/2015/05/25/world_war_ii_why_wasn_t_big_ben_bombed_during_the_blitz.html?wpisrc=obnetwork


must be hard to keep track of all those markers.

 

[knabe]

A Steak in Genomics
Are We Embracing Science and Technology?
http://blog.steakgenomics.org/2015/05/are-we-embracing-science-and-technology.html

i would turn it around.  is science and technology embracing new (or old) ways to deliver data to the end user?


there currently is not a method to introgress data points.  we just have to keep taking science and technology's word that things work.


i think science and technology have not adequately explained that the star system was a fraud and how they are overcoming $80/test or more and yet have no real explanation of how to introgress anything and how an investment that doesn't allow that is going to allow rapid progress other than to single out the magic individual and then market that as a success.

 

[knabe]

http://news.yahoo.com/study-reveals-flaws-gene-testing-results-often-conflict-145515442--finance.html

 

[knabe]

Interesting. Not saying the cattle genomics arena is guilty of this,


http://io9.com/i-fooled-millions-into-thinking-chocolate-helps-weight-1707251800