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Offline librarian

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Obese gene
« 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
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.
'Those who do not understand the old will not understand the new'. -farmers quote

Offline knabe

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Re: Obese gene
« Reply #1 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.
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Offline librarian

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Re: Obese gene
« Reply #2 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.
'Those who do not understand the old will not understand the new'. -farmers quote

Offline HerefordGuy

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Re: Obese gene
« Reply #3 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

Here is my take on gene tests versus genomic prediction.
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.

Offline Duncraggan

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Re: Obese gene
« Reply #4 on: April 08, 2014, 03:03:33 PM »
librarian and HerefordGuy, I like your thinking on this topic!

Offline knabe

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Re: Obese gene
« Reply #5 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.
« Last Edit: April 08, 2014, 04:56:29 PM by knabe »
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Offline librarian

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Re: Obese gene
« Reply #6 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.
'Those who do not understand the old will not understand the new'. -farmers quote

Offline HerefordGuy

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Re: Obese gene
« Reply #7 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.

Offline HerefordGuy

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Re: Obese gene
« Reply #8 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.

Offline knabe

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Re: Obese gene
« Reply #9 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.
« Last Edit: April 08, 2014, 10:32:15 PM by knabe »
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Offline librarian

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Re: Obese gene
« Reply #10 on: April 08, 2014, 08:30:21 PM »
Yes, like he said. Introgress the technology with evolutionary intent.
'Those who do not understand the old will not understand the new'. -farmers quote

Offline knabe

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Re: Obese gene
« Reply #11 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.
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Offline Charguy

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Re: Obese gene
« Reply #12 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

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.

Offline librarian

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Re: Obese gene
« Reply #13 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?
'Those who do not understand the old will not understand the new'. -farmers quote

Offline knabe

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Re: Obese gene
« Reply #14 on: April 08, 2014, 11:24:19 PM »
You should just ask him. He knows who has it and where it came from.
"The generation that told us to question authority, has now become the Authority we cannot question!"

 

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