Blog: A Steak in Genomics

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knabe

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what about other predictive tools?


the return on investment with snps seems rather low (not just with cattle, but everything other than basic research).


Of course every new technology promises to save the world, but what new technologies/approaches do you see emerging to augment/replace snps to create actionable results for producers?
 

HerefordGuy

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knabe said:
what about other predictive tools?


the return on investment with snps seems rather low (not just with cattle, but everything other than basic research).


Of course every new technology promises to save the world, but what new technologies/approaches do you see emerging to augment/replace snps to create actionable results for producers?

To be honest with you knabe most producers aren't using the current tools correctly. See http://steakgenomics.blogspot.com/2014/06/economically-relevant-traits-for-new.html We would see more improvement if breeders quite double counting (select on actual BW, BW EPD, and CED at the same time), coming up with ad hoc mental indexes, selecting on indicator traits, selecting on phenotypes (most important criteria to most producers is actual birth weight) etc.

I think the swine and dairy industry would disagree with your point about ROI on SNP genotypes. Where's your data to support that claim? I see most industries and producers investing more in genomics, not backing away from it.
 

knabe

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Just personal exp w snps. Swine has a lot more interval on it and Holstein is much tighter bred so correlation has higher probability. Only beef breed similar is angus and all previous across breed work is useless. There doesn't seem to be much economic need for it in beef as everyone knows what to buy already without it for what they want. pretty easy to get marbling, growth, bw, or efficiency. There isn't snps for two shots, weaned and certified for a premium. Find some snps to allow coastal cattle to be bought by Harris or others. They are avoided like the plague by buyers or discounted as everyone knows they are going to get sick and expose them to sickness and death loss not to mention spread of disease. I'm sure pork would want to reduce their death loss about now rather than have some more snp data.
 

knabe

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HerefordGuy said:
How many of you have heard about the new research into the environmental impact of cattle? How many of you have heard about the new documentary "Cowspiracy"? I discuss in my new blog post.
A Steak in Genomics
Look in the Mirror:
What do We Need to Change?
http://steakgenomics.blogspot.com/2014/07/look-in-mirror-what-do-we-need-to-change.html


300 lb calves are 800 bucks today. that's almost cull cow prices for hamburger 2 months ago for an 1100 lb cow.  beef cattle has been slow to adopt a margin mentality and is too obsessed with negative margin for tax purposes.


if i was capitalized, i would locate near major transit highways and move cattle closer and closer to corn a couple of times, say calve in eastern oregon, wean and ship somewhere closer to corn and save money on freight and logistics rather than be so obsessed with genetics that are not in demand but merely serve a purpose in a urination contest.


trucking is finally more expensive in CA. those who didn't get a taxpayer subsidized smog cleanup had to buy a new truck.  the trucks traded in can't drive in CA.  good trucks can be bought cheap.  guys are trading them in out of state for CA qualified trucks. those not in compliance now are getting tickets.
 

knabe

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microbial studies have been done, though i don't know if it's been done comparing large numbers of animals with known efficiency differences before hand.  i do have a friend that tried forever to change the rumen population for his Ph.D. and it kept reverting back to it's original population and ratio's. said he was really disappointed.


i would say one reason beef has been slow to adopt new stuff, is that they did for a while and they were continually burned.


margin probably is in the stool rather than the carcass.
 

librarian

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knabe said:
...
are there models that show the ability to take individuals with say an easily measurable reduction of markers in individuals with little overlap, and then combine them to reproduce an animal that has the macroset of markers and achieve the same results in the initially observed phenotype?
....
it worries me that in identifying phenotypes that with elimination of genetic diversity through heavily marketed lines that important sources of diversity and desirable traits will be lost.  no one that i know of has addressed this problem. "alternative alleles or genes for the same traits but perhaps with different pathways affecting the same trait but not yet stacked serendipitously or stacked through easy observation as it was low hanging fruit in heavily promoted bloodlines. too many times things have not been where we thought they were" 

Knabe,
Would you please dumb down the first question so that I can see the picture better?  I am getting a strong intuition that you are getting at something very interesting, but the gap between intuition and insight is making my imagination balk.

The second question:
How would one address this problem of recovering diversity, at home with no tools other than observation?  Not exactly recovery; more like extinction intervention?
And what exactly do you mean here,
"alternative alleles or genes for the same traits but perhaps with different pathways affecting the same trait but not yet stacked serendipitously or stacked through easy observation as it was low hanging fruit in heavily promoted bloodlines. too many times things have not been where we thought they were"
I am interpreting your remarks to suggest that something fixed in a certain bloodlines undoubtedly exists elsewhere with other associations understood, misunderstood and never to be understood. And we should look for those traits in other places,and save the seed, rather than just use the same set of instructions until they wear thin and mutate? Because genetic diversity is like the volume of a stream and we are carving a narrow channel that may become an empty canyon some day?

I believe this shaded stream bank is where most of my questions dwell, and I cannot almost see you pointing into the high branches of an old old tree for a single Fameuse Snow apple , but I am just not quite grasping it.

 

knabe

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librarian said:
knabe said:
...
are there models that show the ability to take individuals with say an easily measurable reduction of markers in individuals with little overlap, and then combine them to reproduce an animal that has the macroset of markers and achieve the same results in the initially observed phenotype?


it's just a control for markers.  find animals with the markers, make the markers different, absent or whatever, then put them back in and see if you get the same observed results.  no one will ever do this.
 

librarian

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”We especially need imagination in science. It is not all mathematics, nor all logic,
but it is somewhat beauty and poetry.” Maria Mitchell

and so with markers, the sum always being more than the parts
 

knabe

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Would like raw data pics on those graphs over time.


GIGO


How does one account for environment?
 

HerefordGuy

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I think whole herd reporting helps with the Garbage In Garbage Out problem. But, at the end of the day, the quality of the data is dependent on the breeders reporting it. I think a strength of Angus's BRS reporting system (http://www.angus.org/Performance/AHIR/PerfGuidelines.aspx) is that they collect data from commercial producers who don't have a financial interest in how purebred animals rank.

Right now herd effects control for environmental differences. I think there may be value in calculating region specific EPDs in the future.
 

knabe

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I seriously doubt everyone's reporting techniques would pass a clia inspection

It sure would be nice to see operator to operator variation and scatter plots using the same bull with calves verified to ensure cleanup bull wasn't included.
 

HerefordGuy

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knabe said:
I seriously doubt everyone's reporting techniques would pass a clia inspection

It sure would be nice to see operator to operator variation and scatter plots using the same bull with calves verified to ensure cleanup bull wasn't included.
I seriously doubt anyone's reporting techniques would pass a CLIA inspection! :)
Two weeks after reading this post, I still can't believe you would compare to CLIA...
 

knabe

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HerefordGuy said:
I seriously doubt anyone's reporting techniques would pass a CLIA inspection! :)
Two weeks after reading this post, I still can't believe you would compare to CLIA...


CLIA has been my life for a while. FDA is even more rigorous and has bigger feet.
 

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