Blog: A Steak in Genomics

interesting way to represent data.  caution, slow to load


https://vimeo.com/128373915


makes me wonder if WWI and WWII never happened what our challenges today would be.


mao and stalin almost match WWII in deaths.  amazing.


interesting comment was that there were more deaths proportionately speaking from other conflicts.


mongol conquest and lushan rebellion, amazing.


scale is hard to assess.

sort of reminds me of this.


http://www.edwardtufte.com/tufte/posters

First 2015 BIF blog post up.
A Steak in Genomics: Assessing the Economic Impacts of Estrus Synchronization & FTAI in Beef Production
http://blog.steakgenomics.org/2015/06/assessing-economic-impacts-of-estrus.html

A Steak in Genomics
2015 BIF posts from Tuesday evening and Wednesday morning.

Temperament and Acclimation to Human Handling Impact Productive and Reproductive Efficiency in Bos indicus-Influenced Cattle
http://blog.steakgenomics.org/2015/06/temperament-and-acclimation-to-human.html

Drought Was Just One Reason the US Cow Inventory Declined
http://blog.steakgenomics.org/2015/06/drought-was-just-one-reason-us-cow.html

Sustainability: What is it and why does it matter?
http://blog.steakgenomics.org/2015/06/sustainability-what-is-it-and-why-does.html

Sustainability: What Does the Data Say About the Beef Industry
http://blog.steakgenomics.org/2015/06/sustainability-what-does-data-say-about.html

How Do Current Market Incentives Affect Genetic Selection Decisions?
http://blog.steakgenomics.org/2015/06/how-do-current-market-incentives-affect.html

A Steak in Genomics
Cow Lifetime Productivity Task Force
http://blog.steakgenomics.org/2015/06/cow-lifetime-productivity-task-force.html

one could compare two extremes.


buying 3 in one packages where one can sell the calf, the cow is pregnant and one can sell the calf against raising a calf for two years before it has a calf to sell and how long it is necessary to break even and replacement costs at the end of the individuals production.


obviously this is just one scenario, but it is at the extreme ends.


have a friend that continually did the first scenario and also sold the cow. this is the first time he has produced his own females as he bought when prices were low, bought some decent bulls and source for those replacements dried up due to drought etc.


one could graph this and also add in different scenarios.

knabe said:

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

Click to expand...

knabe-
Sorry for the lack of response to your posts. Busy writing grants and traveling. Trying to catch up now.

Here are my thoughts on the Yahoo article.

When deciding to get tested, either through a doctor's office or by sending in a swab to a private company, "patients need to choose labs that are sharing their data" with the broader research community so scientists can compare and learn from the results and make testing more accurate for everyone, she said.

Click to expand...

The genetic testing companies in the livestock sector are doing this.
A further difference between the human disease testing and genomic-enhanced EPDs in cattle is the reliance on a single DNA variant. In human disease genetics they typically make a yes or no decisions (mastectomy or not) based on a single variant or a small number of variants. If those variants are not genotyped accurately, this causes major problems (needless surgery). In genomic-enhanced EPDs we test a large number of variants at a time, thus no single variant has a big impact. Further, the SNP chip technology we use is highly accurate. The biggest issue with genomic-enhanced EPDs is the quality of sample sent in.
See http://blog.steakgenomics.org/2015/02/avoid-headache-properly-submitting-dna.html and http://blog.steakgenomics.org/2012/09/take-care-when-collecting-hair-samples.html.
The Yahoo article is more similar to genetic defect testing in livestock. The recent scare with a Simmental bull is an example. The Gelbvieh issue is another. http://blog.steakgenomics.org/2014/01/fawn-calf-genetic-test-being-redesigned.html. But, beef breeders are very astute and don't let these errors last for long.

A Steak in Genomics
eBEEF.org launched at BIF
http://blog.steakgenomics.org/2015/06/ebeeforg-launched-at-bif.html

knabe said:

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.

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knabe-
I tried to explain why what I refer to as "gene tests" were not effective in my BIF talk, but perhaps I wasn't blunt enough.
The file is large (3.5 MB pdf) so it might take a second to download.
http://www.bifconference.com/bif2015/documents/2015BIF-SelectionDecisions-Decker.pdf
The audio is also available. http://www.bifconference.com/bif2015/newsroom.html

HerefordGuy said:

Busy writing grants

Click to expand...

any broad stroke hints on grants? genetic basis for hybrid vigor, inbreeding depression, inbreeding without depression etc?


sequencing chillingham cattle?

HerefordGuy said:

I wasn't blunt enough.

Click to expand...

you don't have to be blunt, just effective.


the industry needs to move on from the star mentality and they really don't understand the existing technology. i don't either, but then i don't have angus.


sure would like to see why some individuals have absolutely no milk and why once it's gone, it's so hard to put back in.


conversely, too much milk as well.


butterfat % too.  chi's supposedly have high butterfat but no milk.  lots of interesting things to do.


really the only way to do that is to become a professor, but i was never good enough in the genetics coursework.

knabe said:

HerefordGuy said:

Busy writing grants

Click to expand...

any broad stroke hints on grants? genetic basis for hybrid vigor, inbreeding depression, inbreeding without depression etc?
sequencing chillingham cattle?

Click to expand...

No sequencing of Chillingham cattle, but did you see our Chirikof Island Cattle preprint? http://biorxiv.org/content/early/2015/01/26/014415

Wrote 2 USDA grants, one looking at fertility and the other at local adaptation.
Sent research proposals to 6 breed association foundations.

knabe said:

HerefordGuy said:

I wasn't blunt enough.

Click to expand...

you don't have to be blunt, just effective.


the industry needs to move on from the star mentality and they really don't understand the existing technology. i don't either, but then i don't have angus.


sure would like to see why some individuals have absolutely no milk and why once it's gone, it's so hard to put back in.


conversely, too much milk as well.


butterfat % too.  chi's supposedly have high butterfat but no milk.  lots of interesting things to do.


really the only way to do that is to become a professor, but i was never good enough in the genetics coursework.

Click to expand...

The way we estimate milk in beef production should take energy density of the milk into account.

I don't know how my smartphone works. But, I know it does work, I trust it, and use it all the time.
I don't think most crop guys understand hybrid corn breeding or genetic modification introducing Roundup Ready plants. But, they still use the improved crops and reap the benefits.

cool on the alaska cattle.  my dad told me about them years ago.  completely forgot about them.


fertility.  how about a fertility study where some cows give a range of eggs when flushed.

absolutely love the horns.


https://en.wikipedia.org/wiki/Yakutian_cattle


holy crap.  someone needs to get on this if contextually true.


The meat of Yakutian cattle is known for its natural [/size]marbling[/size].[/size][5]

A Steak in Genomics
Red Angus Releases Herd Navigator DNA test
http://blog.steakgenomics.org/2015/06/red-angus-releases-herd-navigator-dna.html

The Breeders Equation
http://www.nature.com/scitable/knowledge/library/the-breeder-s-equation-24204828

And yes, there are people out there arguing about the longevity of castrated salmon
https://westhunt.wordpress.com/2015/06/24/make-room-make-room/

Applications of Population Genetics to Animal Breeding, from Wright, Fisher and Lush to Genomic Prediction  http://www.genetics.org/content/196/1/1.full
From which the review on J. Lush's work was interesting in its old fashioned applicability.

And another thing to think about, Evolutionary Game Theory
https://en.m.wikipedia.org/wiki/Evolutionary_game_theory

A Steak in Genomics

Live blog posts from Texas A&M Beef Cattle Short Course.

Selection and Use of Breeds and Breedtypes
http://blog.steakgenomics.org/2015/08/selection-and-use-of-breeds-and.html

Heterozygosity and heterosis consideration for the beef industry.
http://blog.steakgenomics.org/2015/08/heterozygosity-and-heterosis.html

Genetics for Today's Cattlemen (and Women)
http://blog.steakgenomics.org/2015/08/genetics-for-todays-cattlemen-and-women.html

A Steak in Genomics
Purebred cattle marketing
http://blog.steakgenomics.org/2015/08/purebred-cattle-marketing-texas-beef.html