Steer Planet - Show Steers and Club Calves Forum

Steer Planet Chat => The Big Show => Topic started by: librarian on April 07, 2014, 10:56:53 PM

Title: Obese gene
Post by: librarian on April 07, 2014, 10:56:53 PM
I've been thinking about something AJ said a while back about backfat on cows.
Back fat on a steer in a feedlot is waste. Backfat on a cow on a "sawdust and sand" nutrional diet is a source of survival. A cow can store up fat and save the energy for tough times. I think IMF is probably kinda corelated with the ability to back fat.....just a guess though.

And I was wondering about the "obesity gene" which I saw that 6807 might carry. When someone says, 'that's a 6807 type cow', it's usually a cow that looks pretty good to me.
I don't really understand this obesity gene, but maybe I have been selecting for it. Lots of folks around here are talking about how skinny looking cows that raise a big calf are so great because they don't eat much.  They might actually eat a lot, but that's not the point, right now. In the natural world, some animals kind of track the environment with their reproductive effort and will cut their losses if the environment takes a real turn for the worse in any given breeding season. It seems like cows with more back fat would be better in harsh situations.  Which is stored first, back fat or intramuscular fat? Which is burned first?
I also hear about "selfish" cows that stay so fat that they don't put any energy into milk for their offspring.
I wonder if that happens every year, or just in bad years?  How do all those environmental triggers that operate on genetic expression figure into this?
 
Then I read this: (they are trying to sell us bulls wit the tt variant of the obese gene)
http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CC0QFjAA&url=http%3A%2F%2Fwww.cattlelandfeedyards.com%2FGenomics___Genetic_Breeder_Alliance.pdf&ei=OmlDU4W7L6vgsAScioGQDA&usg=AFQjCNGWZ_kA-MCOm2ug9hS8e90__YHnYQ&bvm=bv.64367178,d.cWc&cad=rja (http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CC0QFjAA&url=http%3A%2F%2Fwww.cattlelandfeedyards.com%2FGenomics___Genetic_Breeder_Alliance.pdf&ei=OmlDU4W7L6vgsAScioGQDA&usg=AFQjCNGWZ_kA-MCOm2ug9hS8e90__YHnYQ&bvm=bv.64367178,d.cWc&cad=rja)
GENOMICS
Through ongoing genomic research with Quantum Genetics in Saskatoon, Cattleland has identified
significant performance benefits in feeding cattle with certain variants in the obese gene, or Leptin gene.
The obese gene, which produces the hormone leptin, has three variants identified. These are either
normal (cc), one copy variant (ct), or two copies variant (tt). Cattleland believes that feeding of known ct
and tt marketing groups results in more consistent quality carcasses which are ready for slaughter earlier
than a cc animal.Significant amounts of research have also been conducted highlighting that ct and tt
cows wean heavier calves when compared to cc cows. These tt cows also have higher rebreeding rates
and a longer productive life than cc cows.
CATTLELAND GENETIC BREEDER ALLIANCE
Aim
Breeding and feeding the right cattle
Using superior sires of known genomic make-up for the improvement of overall profitability and
marketability of the calf crop. To feed the most efficient cattle in the feedyard to produce a consistent,
quality carcass. The alliance is designed for the cow-calf operator interested in genetic improvement
while reducing the capital investment required to do so.
Background
Cattleland Feedyards in Strathmore, Alberta is a vertically integrated agricultural enterprise with a one-
time feeding capacity of over 30,000 head. Reliability and consistency of end product are of great
importance for Cattleland and the company is continually looking for ways to guarantee quality supply to
the end user, the consumer. Through ongoing genomic research with Quantum Genetics in Saskatoon,
Cattleland has identified significant performance benefits in feeding cattle with certain variants in the
obese gene, or Leptin gene. The obese gene, which produces the hormone leptin, has three variants
identified. These are either normal (cc), one copy variant (ct), or two copies variant (tt). Cattleland
believes that feeding of known ct and tt marketing groups results in more consistent quality carcasses
which are ready for slaughter earlier than a cc animal. Significant amounts of research have also been
conducted highlighting that ct and tt cows wean heavier calves when compared to cc cows. These tt cows
also have higher rebreeding rates and a longer productive life than cc cows.
Figure 1 demonstrates that ct and tt cows have a higher level of back fat at a lower body weight in both
the spring prior to calving, as well as in the fall at weaning. This higher back fat has a direct correlation
with body condition score which in turn affects reproduction rates. Figure 1 also shows that the higher
weaning weights and daily gains of ct and tt calves.

Would someone please educate me about this obese gene? Thanks.
Title: Re: Obese gene
Post by: knabe on April 07, 2014, 11:39:45 PM
i remember talking with a prominent angus breeder about this years ago and how he noticed it was segregating and where the segregating bulls ended up.  would be interesting if this was a marker for it. it would also explain the variability he was noticing.  this type of thing will probably show up more often as it's figured out and that variability is due to these types of things rather than the cattle just being labeled as variable. good post. it might turn out that superiority in other traits are simply nucleotides and energy just not being wasted on truncated proteins and or copies that are silenced that are not needed and energy can either not be used and less input needed or that it shows up in other pathways not being short of building blocks.  this type of research and thinking is important.
Title: Re: Obese gene
Post by: librarian on April 08, 2014, 02:48:10 PM
Thank you. Now I just need to go educate myself enough to grasp this education.  It is very interesting and I'm glad for the help.
Any chance you would mention where the segregated bulls ended up?
I ask because the same folks who love their skinny cows always say that if one breeds OCC into them, they will lose fertility.  I have never believed this, especially when I see at least one shot of OCC in what looks to me to be their best animals.
Title: Re: Obese gene
Post by: HerefordGuy on April 08, 2014, 02:59:23 PM
I find it ridiculous that in 2014 people are still trying to use single gene tests to predict performance of traits that are controlled by hundreds of genes. The reported p-values are not impressive and would not be noteworthy in a genome-wide analysis.
You would be much better served by purchasing bulls based on a feedlot index, like $BEEF or CHB$, or using a marbling EPD, especially if it is a genomic-enhanced EPD, to increase fat deposition. Or, if you are interested in cows that will do well in harsh environments, select on a $EN. http://www.angusbeefbulletin.com/articlePDF/By%20the%20numbers%2001_09%20ABB.pdf (http://www.angusbeefbulletin.com/articlePDF/By%20the%20numbers%2001_09%20ABB.pdf)

Here is my take on gene tests versus genomic prediction.
http://steakgenomics.blogspot.com/2012/08/gene-tests-vs-genomic-selection.html (http://steakgenomics.blogspot.com/2012/08/gene-tests-vs-genomic-selection.html)

Please post on my blog or email me if you have further questions.
Title: Re: Obese gene
Post by: Duncraggan on April 08, 2014, 03:03:33 PM
librarian and HerefordGuy, I like your thinking on this topic!
Title: Re: Obese gene
Post by: knabe on April 08, 2014, 04:44:05 PM
I find it ridiculous that in 2014 people are still trying to use single gene tests to predict performance of traits that are controlled by hundreds of genes.


yup. as long as there are hundreds, it's not that big of a deal to track them.

someone with perl, tcl/tk experience should be able to easily make a program even the most ignorant breeder could use to introgress markers.

genomics has been at a standstill for too long.
Title: Re: Obese gene
Post by: librarian on April 08, 2014, 06:23:51 PM
I just like to learn about genetics, environment and expression. I think all the testing, other than for genetic defects, is kind of bogus and just another thing they are marketing.
Title: Re: Obese gene
Post by: HerefordGuy on April 08, 2014, 08:01:52 PM
I find it ridiculous that in 2014 people are still trying to use single gene tests to predict performance of traits that are controlled by hundreds of genes.


yup. as long as there are hundreds, it's not that big of a deal to track them.

someone with perl, tcl/tk experience should be able to easily make a program even the most ignorant breeder could use to introgress markers.

genomics has been at a standstill for too long.
knabe-
You want to introgress marbling alleles from Angus? Cross your Maines with top Angus sires, make F2s, test with the GeneMax test and keep the animals that score higher on the marbling score. This should select animals that have the Angus haplotype. You might want to also select for Maine breed characteristics to make them look like Maines. This should be an effective way to select for hundreds of loci containing variants affecting marbling in Angus.
Title: Re: Obese gene
Post by: HerefordGuy on April 08, 2014, 08:14:54 PM
I just like to learn about genetics, environment and expression. I think all the testing, other than for genetic defects, is kind of bogus and just another thing they are marketing.
You have the right to your opinion, but your opinion is not backed up by evidence. The rate of genetic progress has increased dramatically (I  can't share the specific amount because Curt Van Tassell has not yet published his research) in dairy cattle since they started using genomic predictions. The pork and poultry industry have adopted genomic predictions, because they work. 40% of the genetic variation in typical traits are explained by genomic predictions. That's the same amount of information as 20 progeny records.

Other livestock industries are much quicker to adopt new technologies that work. Genomic predictions are one of those technologies.

The single-gene test (like the one you posted) are very close to simply being a marketing scam. But, as I discussed on my blog, genomic predictions are completely different.

I'm watching for the beef breeders who realize the potential of genomic predictions and has the creativity, courage, and independence of thought to do something really cool with the technology.
Title: Re: Obese gene
Post by: knabe on April 08, 2014, 08:26:12 PM
No. But I do have an angus project in mind.

I realize that there are no causal markers, simply parentage markers that are closer to the causality, ie a qtl, be it whatever mechanism than parentage verification.

I also realize individual snps are mostly useless and only serve as a road sign for a stretch of DNA that may do something.

I really just think this whole genomics thing has retuned so little value that it's way past time to ask the question are we using the right tools looking for causes of variability in traits of interest.

What I'm really after within any breed is a way to capture the difference in expression and allow producers to introgress the combinations they want, validate them and make breed crosses if they so desire and make combinations they want. There is too much power in the hands of too few, similar to our problem in government. We need more freedom, not less, we need more ideas, not less. We need more people with more ideas, yes understanding the failure of gwa and the limitations of screening snps. The p values are pathetic for just about every discovery project of this type. It's time to look for something different.
Title: Re: Obese gene
Post by: librarian on April 08, 2014, 08:30:21 PM
Yes, like he said. Introgress the technology with evolutionary intent.
Title: Re: Obese gene
Post by: knabe on April 08, 2014, 08:49:52 PM
i would also add that there is probably some low hanging fruit with regard to dairy and beef animals with regard to how and where fat is deposited.  there can't be hundreds of genes responsible for higher kph, lower backfat, higher marbling, higher fat inside the rib instead of on the outside. is it known what makes marbling disappear and the pathway for that and what management techniques other than the obvious ones that makes more marbling?  there should be management epd's which probably have just as much effect as the genetic effect, yet aren't leveraged with the same romantic notions that all this genomic windbagging generates.
Title: Re: Obese gene
Post by: Charguy on April 08, 2014, 09:41:08 PM
Here is a link to a simple paper by the University of Saskatchewan.

http://homepage.usask.ca/~schmutz/leptin.html (http://homepage.usask.ca/~schmutz/leptin.html)

Unlike the others posting and bashing the test, I can attest that I do believe in the marker and I have seen increased profitability when I use TT bulls on my herd of simmi/angus females and retain ownership until slaughter. In my experience the cattle with at least one T, finish between 10-21 days sooner then calves without the gene and more consistently hit the top grade, earning me a premium for my calves. That is not to say that CC cattle do not marble or hit the top grade, but inorder to get them there it takes longer.

Of course if I do not feed the calves out and simply dump them in a sales barn, I do not receive any of the benefit from the gene. The person feeding the calf will, but traditional marketing makes it difficult to extract a premium. After being proactive and using this simple, inexpensive test, I know have feedlots calling me to buy the calves direct because the feedlots know they can make money feeding my cattle.

Its an unexpensive test and it makes me money. I use TT bulls so I know every calf I have has at least one copy of the gene. I dont need to test the cows but I know several are at least CT as I have been using TT bulls for years. If a breeder doesnt want to test, I dont buy a bull.

My 2 cents and you dont have to agree with me. It is something that has been proven and you can say thathere is several factors contributing and you are right. But if you can easily select for one of those things that is a contributing factor, and is proven to have influence and can make you more money, it is pretty silly to ignore it and pass it off as a marketing scam.
Title: Re: Obese gene
Post by: librarian on April 08, 2014, 11:06:52 PM
My understanding of all this is kind of like black and white TV. Really I just wonder how this obesity gene looks on the outside.  Is it something like this, or much more extreme? What is an example of a Shorthorn expressing this?
O C C Kiddo 832K   
      Q A S Traveler 23-4    AAA #9250717
   D H D Traveler 6807    AAA #10858958    
      Bemindful Maid D H D 0807    AAA #9680345
O C C Emblazon 854E    AAA #+12514348       
      PBC 707 1M F0203    AAA #8252710
   Dixie Erica of C H 1019    AAA 9973782    
      Dixie Erica of C H 615    AAA 8783516
         
      D H D Traveler 6807    AAA #10858958
   O C C Anchor 771A    AAA #11684971    
      O C C Juanada 709V    AAA 11012561
O C C Juanada 957F    AAA +12834913       
      N Bar Emulation EXT    AAA #10776479
   O C C Juanada 775C    AAA 12058322    
      O C C Juanada 709V    AAA 11012561

or this? Limestone Missing Link W269

                O C C Emblazon 854E    AAA #+12514348
   O C C Headliner 661H    AAA 13235201    
      O C C Juanada 858F    AAA #+12740290
O C C Missing Link 830M    AAA #14456399       
      O C C Glory 950G    AAA #13096423
   O C C Dixie Erica 946K    AAA +13890899    
      O C C Dixie Erica 816B    AAA +11770426
         
      D H D Traveler 6807    AAA #10858958
   O C C Emblazon 854E    AAA #+12514348    
      Dixie Erica of C H 1019    AAA 9973782
O C C Dixie Erica 688J    AAA +13395145       
      D H D Traveler 6807    AAA #10858958
   O C C Dixie Erica 816B    AAA +11770426    
      Dixie Erica of C H 1019    AAA 9973782

or just Emblazon?
maybe the "obese" cows would look like this?
Title: Re: Obese gene
Post by: knabe on April 08, 2014, 11:24:19 PM
You should just ask him. He knows who has it and where it came from.
Title: Re: Obese gene
Post by: Charguy on April 08, 2014, 11:28:03 PM
You cannot tell the difference between a CC bull and a TT bull or cow by looking at a picture. Like I said before you can feed CC cattle to be fat. It just takes longer
Title: Re: Obese gene
Post by: knabe on April 09, 2014, 12:06:28 AM
I am talking about something different.
Title: Re: Obese gene
Post by: aj on April 09, 2014, 07:56:38 AM
Kit Pharo uses Ohldes genetics some.
Title: Re: Obese gene
Post by: HerefordGuy on April 09, 2014, 10:20:42 AM
Yes, like he said. Introgress the technology with evolutionary intent.
knabe is not talking about introgressing technology, he is  interested in introgressing genes like they do in plant genetics.
Title: Re: Obese gene
Post by: HerefordGuy on April 09, 2014, 10:23:30 AM
i would also add that there is probably some low hanging fruit with regard to dairy and beef animals with regard to how and where fat is deposited.  there can't be hundreds of genes responsible for higher kph, lower backfat, higher marbling, higher fat inside the rib instead of on the outside. is it known what makes marbling disappear and the pathway for that and what management techniques other than the obvious ones that makes more marbling?  there should be management epd's which probably have just as much effect as the genetic effect, yet aren't leveraged with the same romantic notions that all this genomic windbagging generates.
When we do genome-wide analysis for marbling in Angus, we don't see any large effects, all we see is thousands of small effects. I disagree that there is low-hanging fruit, especially for marbling.
Title: Re: Obese gene
Post by: knabe on April 09, 2014, 10:29:28 AM
When we do genome-wide analysis for marbling in Angus, we don't see any large effects, all we see is thousands of small effects. I disagree that there is low-hanging fruit, especially for marbling.


i don't mean low hanging fruit for marbling, sorry, i mean how fat is deposited, which can include marbling, but since it's overall percentage is low, to me, that could break either way.


i guess one thing i don't understand or forgot, is how thousands of small effects don't get lost due to error, especially if the training population is diverse and the pathways have little overlap between individuals. to me, this marbling thing seems to be left over pathway energy as opposed to any direct effect.


i forget the papers, but there is these little cells, and their number and distribution and distribution density may vary, but for some reason, they fill with fat, or lose fat or something, depending upon available energy and it's use, ie foraging in the wild versus statically in a feedlot like a glutton.
Title: Re: Obese gene
Post by: knabe on April 09, 2014, 10:41:59 AM
When we do genome-wide analysis for marbling in Angus, we don't see any large effects, all we see is thousands of small effects. I disagree that there is low-hanging fruit, especially for marbling.


is it possible to discuss how the animals were chosen for the GWA and reservations you had with regard to their accuracy and any other considerations?


did you make pools of samples?
Title: Re: Obese gene
Post by: HerefordGuy on April 09, 2014, 10:56:10 AM
How much of the phenotypic or genetic variance is this leptin test accounting for?
If this leptin variant was a causal mutation of large (or moderate) effect, the p-values would be very small and highly significant. It would also be replicated across independent experiments. In 2006, Taylor's group tried to replicate the leptin result, and it was not significant.

The only genes I know of that would be worth introgressing would be CAPN1 and CAST for tenderness, PLAG1 for growth, and DGAT for milk protein. For quantitative traits, large effect gene variants are the rare exception, not the rule. Evolution uses thousands of small effects to influence the genetic variation for complex and quantitative traits. This is why genetic prediction (EPDs and PTAs) and genomic predictions work. With EPDs we use pedigrees and progeny records to account for thousands of small effects. With genomic predictions we use the sum of thousands of DNA markers to account for thousands of small effects.
Title: Re: Obese gene
Post by: HerefordGuy on April 09, 2014, 11:48:32 AM
When we do genome-wide analysis for marbling in Angus, we don't see any large effects, all we see is thousands of small effects. I disagree that there is low-hanging fruit, especially for marbling.



is it possible to discuss how the animals were chosen for the GWA and reservations you had with regard to their accuracy and any other considerations?


did you make pools of samples?

Here is the research paper.
http://www.biomedcentral.com/1471-2164/13/606 (http://www.biomedcentral.com/1471-2164/13/606) Plots are in the supplementary material.
We collected as many Angus AI sires as we could get our hands on. Most of these represent Angus sires with large numbers of progeny, but also includes unique populations like the Wye herd.
We weighted each animal's EPD by its accuracy, less accurate EPDs received less emphasis in the analysis. We removed parent average effects from the EPDs. So, we explicit modeled the inaccuracy and dependency between samples in this analysis (by using a mixed-model analysis).
Other papers and other groups are seeing the same results, thousands of loci of small effect. Human research also finds these same results. Evolutionary theory also says we should expect these results.
Title: Re: Obese gene
Post by: HerefordGuy on April 09, 2014, 11:49:45 AM
When we do genome-wide analysis for marbling in Angus, we don't see any large effects, all we see is thousands of small effects. I disagree that there is low-hanging fruit, especially for marbling.


is it possible to discuss how the animals were chosen for the GWA and reservations you had with regard to their accuracy and any other considerations?


did you make pools of samples?
Animals were not pooled, each animal was individually genotyped.
Title: Re: Obese gene
Post by: librarian on April 09, 2014, 12:13:58 PM
Sorry, I was being a smart alec about introgression, never a good idea.  There is a lot of philosophical territory here that maybe isn't quite appropriate for Steerplanet, but why not?  From my 5 minute study of this word that is new to me (but the idea seems to guide me), introgression can occur naturally, or can be accomplished through genetic engineering.  A smart alec might suggest that we splice an intention to evolve into the genetic technology so that the organism can short circuit our scientific notions of what is profitable.
I am always interested in what old time breeders "see" when they study cattle. The breeder knabe referred to early in this discussion figured this out through observation, I assume, not genomic analysis.  Even if you ask and even if you are told what bloodline carries a trait, you have to be able to see  what you are looking at.  I have a friend who thinks people don't spend enough time on observation any more, because the world has gotten so full of demands on our time.  I think there is truth in that. It's like when big pharma synthesizes a drug that grows wild in the Amazon, making the Amazon irrelevant.
So, knabe says
i guess one thing i don't understand or forgot, is how thousands of small effects don't get lost due to error, especially if the training population is diverse and the pathways have little overlap between individuals. to me, this marbling thing seems to be left over pathway energy as opposed to any direct effect.
i forget the papers, but there is these little cells, and their number and distribution and distribution density may vary, but for some reason, they fill with fat, or lose fat or something, depending upon available energy and it's use, ie foraging in the wild versus statically in a feedlot like a glutton.
be says


That part gets more to what I am pondering.  What would be the natural history of that left over pathway and what would have been the trade off.  It seems analogous to obesity in native human populations who have evolved on a low carbohydrate diet and then been switched over to white flour and sugar.  Big trade off in survivability for an increased ability to store fat.
Wikipedia tells me, "Introgression is an important source of genetic variation in natural populations and may contribute to adaptation and even adaptive radiation.[1"
Our attempts to reclaim the ability to fatten on grass alone across diverse environments seems to call for releasing the gene pool from streamlined combinations of ultimate fitness for the feedlot to get on with re-adaptive radiation.
and this from knabe
What I'm really after within any breed is a way to capture the difference in expression and allow producers to introgress the combinations they want, validate them and make breed crosses if they so desire and make combinations they want.


How would you make this capture? Would the introgression be natural or technological?
Title: Re: Obese gene
Post by: librarian on April 09, 2014, 12:22:56 PM
My whole long and winding road with crossbreeding started with reading about the Nazi's (sorry, but it was them) attempt to breed back to the Aurochs by combining and recombining all the available cattle genetics and selecting for Aurochs type.  At that time I read that they actually accomplished this in only about 12 years, with Heck's cattle. Turns out is wasn't quite like that, but I figured if they can re-breed an Aurochs, I should be able to re-breed a Scotch Shorthorn. 
As usual, one has to be careful what they wish for.  I think these Scotch types may have the obesity gene.
Now I'm trying to figure out if that is a good or bad thing.
Title: Re: Obese gene
Post by: knabe on April 09, 2014, 12:24:34 PM
It makes sense that evolution generally wouldn't have large effect genes for many pathways.
Title: Re: Obese gene
Post by: knabe on April 09, 2014, 12:29:15 PM
Sorry I meant pooling after data collection.

I will read paper.

Was there any pair wise substitution on associations to eliminate candidates or how did you eliminate candidates if effect is so low and were there any interesting dependicies?

Probably my choice of the word pooling is technically incorrect.
Title: Re: Obese gene
Post by: librarian on April 09, 2014, 02:07:40 PM
I thought this was the cool part of the conclusions:

"Finally, our results suggest that natural selection has also acted in this domesticated population to increase immunity and possibly to buffer the organism against the effects of inbreeding depression"
Title: Re: Obese gene
Post by: -XBAR- on April 10, 2014, 07:30:14 AM
My whole long and winding road with crossbreeding started with reading about the Nazi's (sorry, but it was them)

There is much to learn from their approach.  If only the Nazi ideology had been applied to livestock and not humans.   

 'Keep your blood pure,
 It is not yours alone,
 It comes from far away,
 It flows into the distance
 Laden with thousands of ancestors,
 And it holds the entire future!
 It is your eternal life'

-There is no substitute for observation-
Title: Re: Obese gene
Post by: knabe on April 10, 2014, 09:04:11 AM
Nice paper. Need to reread.
Title: Re: Obese gene
Post by: knabe on April 10, 2014, 09:10:57 AM
Nazi model was flawed due to anthropogenic projection.

Model required constant repetition of a lie, almost chant like.

Title: Re: Obese gene
Post by: librarian on April 10, 2014, 06:44:10 PM
Do you think the tt cows would have more fat deposition in their udders? 
I have heard that one of the reasons Shorthorns fell out of favor was that they got hog fat in feedyards after WWII when they started really pushing corn.  Is that accurate?
Title: Re: Obese gene
Post by: librarian on April 10, 2014, 07:01:15 PM
And here is a picture. The caption goes:
Lutz Heck (far left) and Hermann Göring (not surprisingly, on the far right) examining a relief map of the Białowieża Forest. The tiny figures represent characteristic game animals (elk, red deer, etc.); in the background a stuffed European bison looms. The horn sitting on the map is perhaps from a Heck aurochs. Image from Waidwerk der Welt, a catalogue published to accompany the 1937 International Hunting Exposition in Berlin.
Title: Re: Obese gene
Post by: HerefordGuy on April 11, 2014, 02:48:43 PM
And here is a picture. The caption goes:
Lutz Heck (far left) and Hermann Göring (not surprisingly, on the far right) examining a relief map of the Białowieża Forest. The tiny figures represent characteristic game animals (elk, red deer, etc.); in the background a stuffed European bison looms. The horn sitting on the map is perhaps from a Heck aurochs. Image from Waidwerk der Welt, a catalogue published to accompany the 1937 International Hunting Exposition in Berlin.
Because so much variation was lost when cattle were domesticated, I don't think you can reconstruct aurochs from domestic cattle. You can make something that looks similar, but the DNA is not necessarily the same.
Title: Re: Obese gene
Post by: HerefordGuy on April 11, 2014, 02:59:37 PM
i guess one thing i don't understand or forgot, is how thousands of small effects don't get lost due to error, especially if the training population is diverse and the pathways have little overlap between individuals. to me, this marbling thing seems to be left over pathway energy as opposed to any direct effect.
Are you talking metabolic pathways?

The larger the effect the more accurate the estimated effect size is. The smaller the effect, the less accurately its effect is estimated. But, when we do the analysis, even though the effects are small they cluster in the same gene networks. In my mind this highlights that individually each gene/variant (which is tagged by a marker) has little/no predictive ability. But, if we look at hundreds or thousands of effects we now have predictive ability.

The populations are not diverse, they usually contain individuals from a single population/breed.

Because we are dealing with small effects, we need large sample sizes. That is why we don't even attempt to create a genomic prediction unless we have over 1,000 samples. The larger the sample, the better the effect is estimated.



Title: Re: Obese gene
Post by: librarian on April 11, 2014, 03:04:37 PM
after that detour, back to the selection pressure for fat deposition question

Biosci Biotechnol Biochem. 2000 Oct;64(10):2240-2. http://www.ncbi.nlm.nih.gov/pubmed/11129604 (http://www.ncbi.nlm.nih.gov/pubmed/11129604)
Differential response of obese gene expression from fasting in bovine adipose tissues.
Kim H1, Chi Y, Chung K, Kim K, Choi Y, Baik M.
Abstract
To understand the molecular mechanism for intramuscular fat deposition, the expression of the obese gene was examined in response to fasting. Food deprivation for 48 h induced a decrease in the level of obese mRNA in pooled adipose tissues (abdominal, perirenal, subcutaneous, intermuscular and intramuscular). The expression of obese mRNA was examined for individual adipose tissue from several fat depots. It was highly expressed in perirenal adipose tissue, but fasting did not affect its expression level in this tissue. Moderate levels were detected in subcutaneous and intermuscular adipose tissues, and a fasting-induced decrease in obese mRNA was apparent in these tissues. The expression level of the obese gene in intramuscular adipose tissue was very low and did not respond to fasting.

So, yes, it seems to be about those little cells filling up or emptying out depending upon the energy requirements.  But, rather than thinking about this in terms of gluttony and a fast track to marbling, I am trying to think of it in terms of reproductive fitness.  I think it was Mill Iron who said that cows are supposed to fluctuate in weight between winter and summer, and his made up for their weight loss over the winter by getting fat in the summer.  Seems natural enough.  I read in one of those old accounts of cattle in Scotland, that the best meat was the "new meat" laid on in the summer after the animal had starved over the winter.  The experts always tell us once you lose that fat, the meat will never marble, but I wonder.

But about fertility and milk production vs. fat deposition.  I was thinking about my Galloway cattle, who seem to have not much milk, but what they have seems to be "thick" and "high test".  The Galloways also store fat in the muscle instead of between the muscles or as back fat.  Maybe they can get it out faster that way.  These cattle are evolved to survive hard times in a cold wet climate with scant forage. They fatten easily.
Studying that, I came up with this about the Obese Gene and Milk Fat
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0063406 (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0063406)
excerpts for those who don't like to plow through all that jargon:

Although a number of cellular, molecular and genetic studies have been performed with FTO, its functions and effects are far from being understood. Even less is known about RPGRIP1L. Considering that the FTO gene including its linked genomic neighborhood affects fat deposition in humans, the question arises, whether this gene region also affects the amount of fat delivered in milk during lactation. If the FTO locus does not only affect fat synthesis but is also involved in the regulation of energy balance, we would also expect additional effects on other milk components.

Our findings suggest that the FTO region not only regulates milk fat yield, but also the total energy content of milk. With regard to GWAS in humans, the FTO region has been repeatedly associated with body mass index and obesity. However, studies with lean mass have not been performed. To further test the pleiotropic effects of the FTO region, the analysis of traits characterizing body composition would be of interest. But body mass measurement of dairy cattle is not a matter of routine under production conditions.

The effects of the genetic variation in the FTO region accounted for about 1% of the corresponding traits variance in the analyzed cattle population. Even if the effect is small, it seems to be consistent across species and deserves more attention as a factor contributing to complex traits, which are expected to be formed by small effects of many loci [7].

In summary, our study in dairy cattle provides evidence that the obesity-associated FTO gene region accounts for variation in milk fat yield. For the first time, we show that the region does not only control fat but also protein yield and that both milk composition traits are regulated in the same direction. Therefore, we suggest that the FTO gene region controls the energy amount secreted during lactation. The position of the associated haplotype blocks and SNPs, their direction of effect and allele frequency distribution detected in our cattle study suggest that at least two causative variants account for differences between genotype classes. These mutations most likely underlie different selection pressure for production traits. In turn, this indicates different biological functions of the involved gene variants with respect to control and regulation of fat and protein metabolic pathways and in regard to maintaining energy homeostasis and controlling energy partitioning. Besides FTO, the neighboring upstream gene RPGRIP1L and the downstream non-coding genes U6ATAC and 5 S rRNA have functional relevance for milk fat and protein yield.
Title: Re: Obese gene
Post by: knabe on April 11, 2014, 03:40:48 PM
Are you talking metabolic pathways? yes

The populations are not diverse, they usually contain individuals from a single population/breed.
the sources of contributions are not diverse within a population?
the locations of effects are not diverse?


if one looks across breeds, understanding the divergence past the markers (or the marker not even being present, rendering them with lower utility, what percent snp difference is there over the entire regions of interest? what is the distribution of snps past the markers? ie are they random, in upstream, downstream regions, within introns, within exons or both compared to upstream downstream regions or is it all just random, understanding random is a relative term and certain regions have different levels of conservation/pressure.
Title: Re: Obese gene
Post by: HerefordGuy on April 11, 2014, 04:35:53 PM
Quote from: knabe link=topic=48527.msg404825#msg404825 date=1397248848
[color=#ff0000
if one looks across breeds, understanding the divergence past the markers (or the marker not even being present, rendering them with lower utility, what percent snp difference is there over the entire regions of interest? what is the distribution of snps past the markers? ie are they random, in upstream, downstream regions, within introns, within [/color]exons or both compared to upstream downstream regions or is it all just random, understanding random is a relative term and certain regions have different levels of conservation/pressure.
We haven't had the sequence data to look at this yet.

The region of interest is the entire genome. We don't pick out gene regions in a genomic prediction. We fit the entire genome.
Title: Re: Obese gene
Post by: HerefordGuy on April 11, 2014, 05:59:34 PM
Speaking of FTO. http://www.nature.com/news/new-contender-for-fat-gene-found-1.14863 (http://www.nature.com/news/new-contender-for-fat-gene-found-1.14863)
Title: Re: Obese gene
Post by: knabe on April 11, 2014, 09:01:36 PM
did i read that right? a behavior "gene".


perhaps ext without his behavior gene has more marbling.


one would think so as he's low, but some of his offspring are triple him and grand get some are even higher.


perhaps his behavior is masking a lot of marbling.
Title: Re: Obese Gene: Survival of the Fattest?
Post by: librarian on April 12, 2014, 12:06:10 PM
I have often wondered the same about EXT, because I see that he does seem to transmit marbling.  Every time I tell myself that disposition influences marbling, I think, yeah but EXT was a supposed to be jerk and look what he did for carcass quality.

I think the management EPD would probably the most useful information in all this.
 
All this came up because I had a couple mid August calves that stayed on their mothers all winter and were weaned a couple weeks ago.  The mothers had grass hay, all they wanted, and minerals over the winter .  These are the fattest weaning calves I have ever had.  Usually I calve in March and wean in November.
The mothers are in really good condition and we had a long, cold winter.  One mom was a first calf Shorthorn heifer out of my Scotch type bull.  I was kind of knocking this heifer at one point for being too fat and carrying a lot of fat in her brisket.  The other was an old Angus cow that could get fat on "sawdust and sand".  Both calves are out of my Scotch Type bull (the Shorthorn calf is double bred). The double bred calf is an exaggerated version of another heifer I got out of that bull.
I saw a picture (attached) of another related heifer built the same way.
A smart person said the heifer in this picture might have the obese gene, and I assumed that was a bad thing.  Now I am rethinking it.
I am just posting the picture as an example of phenotype. I have no idea what her genotype is and I am not saying she has the obese gene, just saying all these animals are built the same way.

Title: Re: Obese gene
Post by: Okotoks on April 12, 2014, 01:12:30 PM
There were some studies a few years ago that showed a direct correlation between disposition and the ability to marble. Maybe the descendants of EXT that had marbling just didn't get the bad disposition/poor marbling gene passed to them. (I am making an assumption they were better dispositions which might be wrong!)

http://www.cabpartners.com/articles/news/244/ritchie_asistaffpaper.pdf (http://www.cabpartners.com/articles/news/244/ritchie_asistaffpaper.pdf)

Title: Re: Obese gene
Post by: librarian on April 13, 2014, 03:43:18 PM
I have often studied harlan Richie's Historical Review of Cattle Type
https://www.msu.edu/~ritchieh/historical/cattletype.html (https://www.msu.edu/~ritchieh/historical/cattletype.html)
Does the marbling come from Emulation 31 or the ornery gene?

These are my fat calves.  I will just have to get the test, I guess, to check out the hypothesis.
Old timers, is the short fat calf the type that used to be around?  Probably the type Oakview says we are better off without.  I do think she is too extreme.
Yes, she has horns.
Title: Re: Obese gene
Post by: GONEWEST on April 14, 2014, 02:13:21 PM
I am sure there are lots of good things to come out of all this sort of discussion and research. But the fact remains that there is much more variation in carcass related traits BETWEEN breeds than WITHIN breeds. Everyone knows that Angus and Angus cross cattle, Galloways and I am sure Shorthorns if given the opportunity, grade better. European breeds yield higher. Over the last decade Angus breeders have shown us that the animals selected for high carcass trait EPD's are slab sided razor backs that can't cut it in a commercial environment. A tremendous amount carcass quality depends on environment. Days on high quality feed. IMO, and with that fact in mind and knowing that there is not nearly as much variation within a breed, any effort to try to identify animals who are superior in carcass traits is practically useless. As an example, the American Simmental Association has spent no telling how many thousands of dollars and research time so that they can tell me that if I use the highest Rib Eye EPD bull in the breed I can expect to get a carcass with less than one half of one square inch of Rib Eye larger than if my neighbors average Simmental bull gets in the pasture and breeds my cows. Did I REALLY need to know that?????? It would have been much more practical and more advantageous to members of the Simmental Association if the money and effort would have been spent promoting and selling the breed and its advantages. But then these EPD inventors that work for the breed associations wouldn't have any way to justify their high paying jobs.

There are practical reasons that prohibit beef production from being compared with that of swine, poultry or milk production as far as genetic technology is concerned. Chief among these is environment. Swine and poultry and to a lesser extent dairy are all produced in a controlled environment. These industries are dominated by one breed or breed cross of the applicable species. That can't be done in beef production. No one breed or cross fits all the different environments that have to be used to make beef. In any species when you select for one individual trait or even one set of important traits, you lose others. In poultry, pork or dairy production that might be fine. For instance losing the mothering ability in Holsteins. But in beef production, due to the diverse environments used to produce beef, these trade offs can be impractical. Therefore the genetic progress in beef production is slower because there are practical factors that hold it back. The lack of progress does not come from an unwillingness to embrace new technology but from practical reasons that must be addressed before anything else.
Title: Re: Obese gene
Post by: chambero on April 14, 2014, 03:01:30 PM
Gonewest - that's a good way of putting it.  In reality, pork and poultry have largely eliminated environment as a variable due the animals much shorter growth periods and smaller size which works together to allow for indoor or highly confined feeding.

I think environment plays an equal role to genetics on many cattle traits including calving ease and rate of gain
Title: Re: Obese gene
Post by: GONEWEST on April 14, 2014, 03:43:34 PM
With more and bigger dry lot dairies, milk production is becoming an even more controlled environment, too.
Title: Re: Obese gene
Post by: aj on April 14, 2014, 06:34:53 PM
I really don't know what the heck you guys are talking about. I'd say say 20 replacement heifer calves.....wean them......run them with the cows all winter on stalks.....grass....NO GRAIN. Keep the top 50% and dump the rest. All the talk does NOTHING! Either use natural pressure or shut up. jmo
Title: Re: Obese gene
Post by: librarian on April 14, 2014, 07:53:13 PM
Right, let the environment do the sorting rather than a DNA test.  But you could do a DNA test on the cows that are working in your environment to figure out why. Maybe.
The part that I find interesting is the role environment plays in how and when genes are expressed. I wasn't curious about marbling, I was curious about if a cow that raises a fat calf over the winter and stays fat doing it might have the obese gene, and if that were so, then maybe that gene disposed them to put extra fat into their milk as well as on their back.  That type of cow might work well in a fall calving situation, overwintering on a lot of over ripe hay or stockpiled grass.
Most of us think about different types of cattle all the time, and which type is working best for us.
But yes, it is totally using a canon to kill an ant to think about all those proteins and pathways etc.

Title: Re: Obese gene
Post by: knabe on April 15, 2014, 10:11:35 AM
Hereford guy, are there any line element differences in any of the studies you have seen?
Title: Re: Obese gene
Post by: librarian on April 15, 2014, 02:17:27 PM
from Darwin, Origin of Species, page 284:
...the difficulty lies in understanding how such correlated modifications of structure could have been slowly accumulated by natural selection.
This difficulty, though appearing insuperable, is lessened, or, as I believe, disappears, when it is remembered that selection may be applied to the family, as well as to the individual, and may thus gain the desired end.  Thus, breeders of cattle wish the flesh and fat to be well marbled together; the animal has been slaughtered, but the breeder has gone with confidence to the same stock and has succeeded. ..


In the chart about incidence of tt bulls in various breeds, the highest percentage was in the Hereford breed.  http://homepage.usask.ca/~schmutz/leptin.html (http://homepage.usask.ca/~schmutz/leptin.html)
Couldn't some grad student look at this across other breeds, especially the British breeds and see how the expression relates to management?

These questions and observations are not new, and I refer to Dr. Clarke from his book Cattle Problems Explained, from 1880.
http://books.google.com/books?id=kDFFAAAAYAAJ&dq=cattle%20problems%20explained&pg=PA164#v=onepage&q=cattle%20problems%20explained&f=false (http://books.google.com/books?id=kDFFAAAAYAAJ&dq=cattle%20problems%20explained&pg=PA164#v=onepage&q=cattle%20problems%20explained&f=false)
CHAPTER XVIII.
The Saving Of Muscle In Fattening Cattle.
Exercise and Juicy Meat versus Waste and Degeneration of the Muscles.

The practice of Mr. John D. Gillette, of Logan Co., 111., and others, in exercising their cattle, including the famous prize steers of 1877, led to much more discussion than would have taken place if he had failed to carry off the prizes at Chicago. But the superior quality of the beef produced by his out-door feeding, under the exercise incident to it, suggests a little further inquiry as to the causes of such a juicy and superior quality in his grade Short-horns, or any other cattle, there having been many other successes in feeding under such or similar management.

In many instances, prize cattle in the London market and elsewhere, have been affected with '' fatty degeneration," or degeneration of the muscles; and, as this condition is met with in stall-fed cattle, while cattle having moderate exercise are not so affected, the origin of fatty degeneration requires some thought. It appears most conspicuously in a degenerated condition of the muscles that are necessarily used during exercise, suggesting the idea that inactivity gives rise to it, as this disorder is known to result from disuse, or inaction, in other parts of the system. It is necessary, first, to see how the size of the muscles is maintained, so that causes and consequences may be compared in ascertaining why the size and substance are reduced, or changed, under certain artificial conditions. Motion in the muscles causes wearing change; wear gives occasion for renewal, causing a demand for nutritive blood supply, in proportion to motion and waste.

Many fat cattle have sufficient vigor of muscle and circulation to escape this disorganizing process—the fatty degeneration of the muscles. But others are seriously affected by it. The disorganization of the fibres and fascicles of the muscles results from disuse and inaction in the legs or other affected parts of the animal; this inaction itself resulting from reduced or prohibited exercise.

In alluding to the practice of Mr. John D. Gillette, and others of Central Illinois, in fattening cattle in their groves and pasture lots, thus allowing them to indulge in considerable voluntary exercise, it was stated that other successes from similar management had been observed. For instance, Hereford steers have been, and probably still are, frequently fatted and finished off in England on good grass, in open pastures, and without night penning; and the juicy quality of their beef is abundantly well known in the London and other markets of that country. On a more extended scale, Short-horn grades and fine common steers and heifers, in hundreds of herds, and many thousands of instances, fatten rapidly and well on the ample, open Western ranges of rich grass, fully maintaining their muscular proportion by adequate daily exercise. And many steers are fatted during winter weather in ample yards, provided with simple sheds, these cattle voluntarily seeking shelter or indulging in gentle activity, as they require.




Title: Re: Obese gene
Post by: librarian on November 30, 2014, 06:57:52 AM
Repost
Title: Re: Obese gene
Post by: aj on November 30, 2014, 09:01:38 AM
Thank you.
Title: Re: Obese gene
Post by: aj on November 30, 2014, 09:25:51 PM
Can you........could I send in blood for a test......the cc   tt    thing a mcfloppy? I had a cow that was fat all the time....used two of her sons heavily.......she raised good calves......milked good.....is the test like the 50 k test?