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Offline HerefordGuy

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Blog: A Steak in Genomics
« on: July 10, 2012, 11:17:06 PM »
Please check out my new blog, A Steak in Genomics: A blog for stakeholders in animal production and genomics.  http://steakgenomics.blogspot.com/

What questions would you like answered on my blog?

I am welcome to any suggestions or critiques.   
« Last Edit: February 08, 2014, 06:20:44 PM by HerefordGuy »

Offline knabe

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Re: New Blog: A Steak in Genomics
« Reply #1 on: July 10, 2012, 11:39:10 PM »
Hi Jared. Thanks for starting the blog.  Congratulations on getting your Ph. D. Been waiting to see what you would do next.

So many questions.

Do you yet have enough info to know yet what percent of marbling is controlled within genes or in regulatory regions or by some other mechanism?  Somewhat loaded question.

Are there any known markers for either tenderness or marbling that work across breeds, even one?

Is RT pcr yet usable to measure marbling or tenderness? Of the five or do variants of double muscling is the one besides the piedmontaise that imparts tenderness or increased muscle mass in a hetero state?
« Last Edit: July 10, 2012, 11:43:50 PM by knabe »

Offline HerefordGuy

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Re: New Blog: A Steak in Genomics
« Reply #2 on: July 10, 2012, 11:55:54 PM »
I will work on answering these in future blog posts.  Thanks for the great questions!

Offline HerefordGuy

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Re: New Blog: A Steak in Genomics
« Reply #3 on: July 11, 2012, 12:19:43 AM »
Just published a new post.  Accuracy improvement from Genomic-Enhanced EPDs expressed as progreny equivalents http://steakgenomics.blogspot.com/2012/07/accuracy-improvement-from-genomic.html

Offline Diamond

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Re: New Blog: A Steak in Genomics
« Reply #4 on: July 11, 2012, 05:22:27 AM »
I look forward to reading, keep up the good
Life is short. Play Hard.

Offline aj

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Re: New Blog: A Steak in Genomics
« Reply #5 on: July 11, 2012, 07:09:01 AM »
Cool deal!
People can't believe we have such a big moon for such a small town.

Offline HerefordGuy

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Re: New Blog: A Steak in Genomics
« Reply #6 on: August 07, 2012, 10:50:05 PM »
Latest blog post is finally out. http://steakgenomics.blogspot.com/2012/08/gene-tests-vs-genomic-selection.html

Knabe, to answer your questions: CAPN and CAST are predictive across breeds, at least the breeds in our recent study.  From the data I have seen, marbling has no genes of large effect, meaning it will require genomic selection. Most (not all) variation that influences complex traits currently appears to be in regulatory elements.  Most everyone is using SNP markers (rather than RT PCR or other assays) due to the scalability and throughput of SNP genotyping.

Offline knabe

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Re: New Blog: A Steak in Genomics
« Reply #7 on: August 07, 2012, 11:16:49 PM »
Latest blog post is finally out. http://steakgenomics.blogspot.com/2012/08/gene-tests-vs-genomic-selection.html

Knabe, to answer your questions: CAPN and CAST are predictive across breeds, at least the breeds in our recent study.  From the data I have seen, marbling has no genes of large effect, meaning it will require genomic selection. Most (not all) variation that influences complex traits currently appears to be in regulatory elements.  Most everyone is using SNP markers (rather than RT PCR or other assays) due to the scalability and throughput of SNP genotyping.


thanks hg.  i know about the low effect for marbling.  hence why i keep bellyaching about having a spreadsheet with them as it's tooooo easy to have individuals with the same marbling "score" to have a completely different set.  companies offer no one any chance at tracking introgression.  at previous job, we almost never found snps of any value within genes, only regulatory as well, same at current job.  aptamers may be a bridge to specificity depending upon ph and throughput.  snp genotyping has yet to provide anything at work.....yet.  we are getting more thorough.  as usual, the training set, depth and region are important.

we use snps and rt back and forth. it allows to have small impact genes in our assay to cumulatively attain power.  yes, it can be improved.
« Last Edit: August 07, 2012, 11:26:38 PM by knabe »

Offline knabe

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Re: New Blog: A Steak in Genomics
« Reply #8 on: August 07, 2012, 11:44:26 PM »
any thought of having a marker on both sides of regions after/before known crossover points, region containing causal agent or does the 770 chip do this or does the 50k chip do this. one could do this to see if there is an upstream or downstream regulator element or even epigenetic.  maybe they are just more evenly or strategically spread out now?  if causal is in the regulatory region, anyone doing knockouts or another technique to measure effect.  probably something else is required since effect is so low.  again, maybe aptamers is a solution to screen.
« Last Edit: August 07, 2012, 11:45:02 PM by knabe »

Offline HerefordGuy

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Re: New Blog: A Steak in Genomics
« Reply #9 on: August 14, 2012, 08:10:25 PM »
New Post.  Quality Beef.  http://steakgenomics.blogspot.com/2012/08/quality-beef-result-of-reproductive.html
Please contact Dave Patterson if you have questions about the Quality Beef program.

Offline HerefordGuy

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Re: New Blog: A Steak in Genomics
« Reply #10 on: August 18, 2012, 09:26:38 PM »
New Post.  Asking the Right Questions.  http://steakgenomics.blogspot.com/2012/08/asking-right-questions.html

I don't want to spam Steerplanet, so if you all are tired of me posting on this thread when I publish a new blog post just let me know.  :)
Thanks!

Offline knabe

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Re: New Blog: A Steak in Genomics
« Reply #11 on: August 18, 2012, 10:21:59 PM »
Keep posting.

Hands on research is in short supply.

Maybe post about your Herefords, thrasch herefords or what ohlde bought.
« Last Edit: August 19, 2012, 11:54:22 AM by knabe »

Offline Cruiser

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Re: New Blog: A Steak in Genomics
« Reply #12 on: August 19, 2012, 10:39:58 PM »
I really like your blog..interesting reads!

Offline HerefordGuy

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Re: New Blog: A Steak in Genomics
« Reply #13 on: September 08, 2012, 12:26:24 AM »

Offline HerefordGuy

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Re: New Blog: A Steak in Genomics
« Reply #14 on: September 14, 2012, 07:07:15 AM »

 

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