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Offline HerefordGuy

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Re: Blog: A Steak in Genomics
« Reply #60 on: May 12, 2014, 09:18:27 PM »
New blog post at Steak in Genomics about new Simmental TraitTrac system.
http://steakgenomics.blogspot.com/2014/05/american-simmental-associations-updates.html

Offline HerefordGuy

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Re: Blog: A Steak in Genomics
« Reply #61 on: May 14, 2014, 09:20:06 PM »
Few updates and questions about my blog.

First off, I have created a Facebook page for my blog and extension program. If Facebook is your thing and you enjoy beef genetics and genomics, please like my Facebook page and share it with your friends. https://www.facebook.com/SteakGenomics

Second, new blog post announcing the Cattlemen's Boot Camp we will be hosting this July. http://steakgenomics.blogspot.com/2014/05/cattlemens-boot-camp-at-mizzou.html Let me know if you have questions about the Boot Camp.

Third, I have received complaints about being a troll on another message board http://www.cattletoday.com/forum/viewtopic.php?f=6&t=90965&p=1132929#p1132929. (I guess this is karma for me, knabe?  ;) ) I assume those of you interested in my blog, click on the new posts. Those of you not interested in the blog scroll on by. If this is not the case and this thread bothers you, send me a message and I will stop posting about my blog on SteerPlanet.

I appreciate all of the visits to my blog by SteerPlaneteers.

Thanks,
Jared Decker
« Last Edit: May 14, 2014, 09:21:22 PM by HerefordGuy »

Offline knabe

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Re: Blog: A Steak in Genomics
« Reply #62 on: May 15, 2014, 12:42:59 AM »
HG. Don't worry about the troll. I think part of your mission is to reach out to cattle laymen who don't understand genomics. Most of my questions comments on grnomics are attempts to tee it up for you. At this point, I think people are sort of fed up with the genomics thing. The first markers were bogus like most firsts, the second round was bogus, they took away tools to introgress , survey individuals and introgress, then numbers were suspect and rightly or wrongly, to me the markers today are just a higher resolution parentage set with tracking of large segments of DNA with higher correlation to trait of interest. Yes we understand all the markers are low impact on an individual basis ie 1% or less and people question the return of testing especially for producers that try to buy cheap and sell higher and don't need cattle that are trying to get that extra 5%. They are more interested in something more tangible either in explanations or results or both and are leery of turning over their genetics to companies or the aaa. I don't think people trust the industry anymore.

Offline HerefordGuy

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Re: Blog: A Steak in Genomics
« Reply #63 on: May 15, 2014, 08:41:15 AM »
Thanks for the feedback knabe.

In terms of high resolution parentage testing, I think you are right, but I am going to write a blog post about why that is a good thing and the benefits of that. (Thanks for teeing up another post!)

As I've mentioned before, I think you could use genomic selection to introgress. I need to think about this more.

I accept that people do not trust the industry. I think industry being transparent may help this some. But there are beef producers who do not trust technologies that have been around for decades. I wonder what portion of the beef industry are "laggards"?
http://suewaters.wikispaces.com/Rogers

Offline knabe

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Re: Blog: A Steak in Genomics
« Reply #64 on: May 15, 2014, 09:48:47 AM »
I wouldn't worry about the laggards. They are a diverse group and have their reasons. I know several who are extremely successful and don't just jump on stuff. They focus on spread of the price of bought and sold and seem to be in the ranch business for profit rather than cattleman. They don't worry about opportunity rather than big hats.


Like anything, I would prioritize the market.

What is the most useful information you have found about older angus if anything?

Yes we know they don't have the growth, have higher bw, lower marbling later maturing, I guess the genomics industry has the appearance of a self fulfilling prophecy to use fewer and newer bulls. I guess its hard for me to believe nothing interesting is in the older cattle.
« Last Edit: May 15, 2014, 09:52:22 AM by knabe »

Offline knabe

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Re: Blog: A Steak in Genomics
« Reply #65 on: May 15, 2014, 07:01:43 PM »

Third, I have received complaints about being a troll on another message board http://www.cattletoday.com/forum/viewtopic.php?f=6&t=90965&p=1132929#p1132929. (I guess this is karma for me, knabe?  ;) )



I would put that in the breeds thread instead of the coffee shop thread. the other guy was the troll.

Offline HerefordGuy

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Re: Blog: A Steak in Genomics
« Reply #66 on: May 21, 2014, 10:22:14 AM »
Register now for the 2014 Beef Improvement Federation Annual Convention! See blog post for more details.
http://steakgenomics.blogspot.com/2014/05/2014-beef-improvement-federation-annual.html

Have any of you attended BIF before? What did you think? What improvements in the meeting would you like to see?

Offline knabe

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Re: Blog: A Steak in Genomics
« Reply #67 on: May 21, 2014, 10:51:05 AM »

looks like a good lineup.  wish i could go.

what are some successes of observed traits with causality other than parentage.

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?

to me, many of the papers are self-reinforcing rather than independent validation.

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.
« Last Edit: May 21, 2014, 10:57:37 AM by knabe »

Offline HerefordGuy

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Re: Blog: A Steak in Genomics
« Reply #68 on: May 29, 2014, 10:36:27 AM »
A Steak in Genomics: Charolais Association will host a tour prior to BIF to discuss development of genomic-enhanced EPDs. https://www.facebook.com/SteakGenomics/posts/1436960666558847

Offline HerefordGuy

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Re: Blog: A Steak in Genomics
« Reply #69 on: May 30, 2014, 04:03:57 PM »
A Steak in Genomics: Jim Womack gave an update about the USDA CAP project on Bovine Respiratory Disease.
http://steakgenomics.blogspot.com/2014/05/jim-womack-update-on-bovine-respiratory.html

Offline knabe

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Re: Blog: A Steak in Genomics
« Reply #70 on: May 30, 2014, 04:52:40 PM »
A Steak in Genomics: Jim Womack gave an update about the USDA CAP project on Bovine Respiratory Disease.
http://steakgenomics.blogspot.com/2014/05/jim-womack-update-on-bovine-respiratory.html



cool. what's your take on the genomic regions? 


any blood taken and RNA expression assessed?

Offline HerefordGuy

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Re: Blog: A Steak in Genomics
« Reply #71 on: June 02, 2014, 01:45:22 PM »
A Steak in Genomics: Jim Womack gave an update about the USDA CAP project on Bovine Respiratory Disease.
http://steakgenomics.blogspot.com/2014/05/jim-womack-update-on-bovine-respiratory.html



cool. what's your take on the genomic regions? 


any blood taken and RNA expression assessed?

The genomic regions make sense. Genes involved with innate immunity, such as the interleukins, were in the identified regions.

The research team did a challenge experiment where they infected cattle with 7 different pathogens. They collected tissues from the challenge animals and have done an RNA-seq experiment on the lymph nodes. I think the RNA-seq data is either submitted or currently being written up for publication.

Offline knabe

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Re: Blog: A Steak in Genomics
« Reply #72 on: June 02, 2014, 02:56:56 PM »
is the rna count based from ngs only, how did they control for that between individuals (from personal experience, it's an issue), and did they assess potential modifications, snps between rna /dna and within rna individual species or should i just wait for publication?

Offline librarian

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Re: Blog: A Steak in Genomics
« Reply #73 on: June 04, 2014, 01:07:00 PM »
This is good education.  Thanks for the posts.
'Those who do not understand the old will not understand the new'. -farmers quote

Offline HerefordGuy

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Re: Blog: A Steak in Genomics
« Reply #74 on: June 06, 2014, 03:57:12 PM »
I believe the BRD team is using the same or similar methods as the rat developmental liver transcriptome paper that Taylor's group published.  http://physiolgenomics.physiology.org/content/physiolgenomics/45/8/301.full.pdf
So, I believe they are using FPKM.
I don't think they are looking at RNA editing in this analysis. (Chris Elsik has a graduate student who is looking at RNA editing in honeybee.)
I think they look at expression at both a gene and isoform level. But, for most of the details you will have to wait for publication.

 

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