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Offline Charguy

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Re: Obese gene
« Reply #15 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

Offline knabe

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Re: Obese gene
« Reply #16 on: April 09, 2014, 12:06:28 AM »
I am talking about something different.
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Offline aj

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Re: Obese gene
« Reply #17 on: April 09, 2014, 07:56:38 AM »
Kit Pharo uses Ohldes genetics some.
People can't believe we have such a big moon for such a small town.

Offline HerefordGuy

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Re: Obese gene
« Reply #18 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.

Offline HerefordGuy

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Re: Obese gene
« Reply #19 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.

Offline knabe

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Re: Obese gene
« Reply #20 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.
« Last Edit: April 09, 2014, 10:33:26 AM by knabe »
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Offline knabe

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Re: Obese gene
« Reply #21 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?
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Offline HerefordGuy

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Re: Obese gene
« Reply #22 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.

Offline HerefordGuy

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Re: Obese gene
« Reply #23 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 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.

Offline HerefordGuy

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Re: Obese gene
« Reply #24 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.

Offline librarian

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Re: Obese gene
« Reply #25 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?
« Last Edit: April 09, 2014, 12:17:50 PM by librarian »
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Offline librarian

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Re: Obese gene
« Reply #26 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.
'Those who do not understand the old will not understand the new'. -farmers quote

Offline knabe

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Re: Obese gene
« Reply #27 on: April 09, 2014, 12:24:34 PM »
It makes sense that evolution generally wouldn't have large effect genes for many pathways.
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Offline knabe

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Re: Obese gene
« Reply #28 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.
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Offline librarian

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Re: Obese gene
« Reply #29 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"
'Those who do not understand the old will not understand the new'. -farmers quote

 

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