Blog: A Steak in Genomics

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knabe

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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?
 

HerefordGuy

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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.
 

knabe

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HerefordGuy said:
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.
 

knabe

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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.
 

knabe

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Keep posting.

Hands on research is in short supply.

Maybe post about your Herefords, thrasch herefords or what ohlde bought.
 

knabe

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Gentlemen gentlemen no fighting over the reference sequence.

Did the same thing on human and cdnas. It's fun.

Hopefully u get to ask for more clones, sequence source types , longer reads different chemistry and sequence sources and maybe different animals.  Thank goodness you don't have celera/ventner cheating while you do this taking credit for all your work declaring the strategy worthless but the whole time using your sequence as a backbone and verification/validation.

Make sure u contact Ron Myers lab in Alabama for tips. They are probably the best finishers in the world.
 

HerefordGuy

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New blog post describing a new method, called Birth Date Selection Mapping, to identify genes responding to selection. We were able to show that weaning weight, milking ability, calving ease, and marbling were the traits under the strongest selection in Angus.  http://steakgenomics.blogspot.com/2012/11/birth-date-selection-mapping.html
Let me know if you have suggestions to make the blog easier to understand.
 

comercialfarmer

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Just got around to reading some of your blog.  Had to spray some WD40 on old parts in my brain I haven't used in a while.  Glad you take the time to write it.  


If you ever get a moment for a question, I have pondered something for a while and you may be able to shed some light on it.  When I read, "Our results also suggests that the immune system is under selection in cattle."  It reminded me of it.  


It is apparent that highland cattle are much more resistant to pneumonia causing pathogens than other breeds of cattle.  Have you ran across any information suggesting this is this simply due to anatomical differences, for example something like they have a larger lung volume to body ratio vs other breeds, etc...  or is there any known evidence that they have a more aggressive or competent immune system defense.    If it is the later, I've always thought that they may hold a key to decreasing millions of dollars of losses in the cattle industry.  
 
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