Potential genetic defect in Shorthorn cattle

[aj]

I heard someone mention a 50 k chip or model or something........is this kind of a road map........identification  of genes.........or something?

 

[DL]

I heard someone mention a 50 k chip or model or something........is this kind of a road map........identification  of genes.........or something?

aj - here is info about the 50K SNP Chip from MSU extension

SNP Chips

As mentioned earlier, there is a SNP about every 700 base pairs in the Bos taurus genome, and since the genome is about 2.8 billion base pairs in length, there are about 4 million SNPs. There are too many SNPs to deal with all of them practically, so smaller samples of SNPs are used. Specific SNPs can be identified in a variety of ways, but the current, most practical approach is the SNP chip, which is a small piece of plastic or glass with dozens to hundreds of thousands of small dots on it that bind DNA. Each dot corresponds to a specific SNP and a small bit of adjacent DNA, and for a given animal, the SNP can be present in zero, one, or two copies, corresponding to having been inherited from neither, one, or both parents. The most common SNP chip used for cattle is from the company Illumina (Illumina Inc., San Diego, CA). This chip has around 50,000 SNPs and thus is called a 50K SNP chip, but only about 40,000 of these are reasonably useful for a variety of reasons; for example, some SNPs provide redundant or ambiguous information. An attempt was made to scatter these SNPs throughout the 2.8 billion base pair genome so if evenly spaced (and they are not), the 40,000 SNPs would provide a marker at about 70,000 base pair intervals. Although far from perfect, this number of SNPs turns out to be very useful for selection purposes in some populations of dairy cattle. Subsets of 10,000 SNPs are almost as useful as the 40,000 (VanRaden et al. 2009). Much larger and more expensive SNP chips are used for studying the genetic basis of disease in human populations (Edelson 2008), and much smaller and cheaper SNP chips are being planned for cattle (e.g., choosing the 300 most useful SNPs from the Illumina 50K chip). The current cost to researchers for one 50K SNP chip plus analysis is around US$200; smaller chips could cost as little as US$20 to $50.

 

[knabe]

http://en.wikipedia.org/wiki/DNA_microarray

 

[DL]

NOBODY. call the Maine and Chi assoc and see what they have to say about this.

Ya know it's funny - I was basically asked the same question and I though why does it matter? We have information on an abnormality described in Shorthorn calves sired by a certain Shorthorn bull or his sons - so clearly this is a Shorthorn issue - could it be an issue in another breed - sure - but why does that matter?? It is clearly a Shorthorn issue - a potential genetic issue in Shorthorn cattle.

To clarify another issue -

[size=10pt]DR BEEVER WANTS SAMPLES AND HE WANTS THEM ASAP -​

[size=10pt]whoever said "Beever doesn't want samples yet" IS FLAT OUT WRONG​

and as an aside calling me a *itch doesn't make you right  ;D

ps modify - seems I can't spell

 

[aj]

If you go through intellectual exercise of trying to think of enviromental factors that would cause deformed calves what is there out there. Junk batteries in a pasture. Tainted lot of protein tubs? Bad vaccine of some sort? Ground water contamination? Show additives being fed to a bred show heifer. Bulls being co-mingled in different owners cow herds? Nitrates if feed or grazed forages? Alien space ship experiments? Drought? Contaminated salt? Nuclear waste? Down wind of a meth lab?

 

[knabe]

remember, kill the messenger.

if you call the associations they basically have the same answer.

good people are working on these defects.

again, some of the biggest complainers are people who dont even understand recessive genes.

yes, its hard to understand.

 

[trevorgreycattleco]

Kool aid? Come on. I asked him lots of questions. He answered them? Have you talked to Pat DL? Instead of beating each other up all the time, how about overcoming our pride or stubborness or whatever it is and get SOMETHING DONE. If a guy tells me for over an hour all he knows about this and I believe him, I drank the kool aid? I repect what you say DL but that comment stunk. The one thing I know is somebody is lieing. Period. I dont know who but somebody is full of crap.I will find out soon enough. Just like the rest of us. Instead of using steerplanet to throw shots around. Lets get on the phone and talk. Work it out and show the other breeds that we are legit. Right now, legit is the last word used to describe this deal. I can assure you Pat got a earful from me and he never wavered from what he said. Isnt it his job to be in charge of this investigation? It sure isnt mine. It sure isnt yours DL. Thats what we pay him to do. Let him do his job. Call him. Ask him like I did and form your own opinion. We all loose if the number one bull in the breed gets wacked form a defect. Thats a fact. DL has made many good points. Nobody is arguing this. Lets try and look at the big picture and work toward that. Witch hunts and public berating gets all of us nowhere. Even if the ball has been dropped badly already, it doesnt mean we cant still fix what needs fixed. Remember the Jim Valvano speech? "Never give up. Don't ever give up." Thats how I roll.

 

[trevorgreycattleco]

NOBODY. call the Maine and Chi assoc and see what they have to say about this.

Ya know it's funny - I was basically asked the same question and I though why does it matter? We have information on an abnormality described in Shorthorn calves sired by a certain Shorthorn bull or his sons - so clearly this is a Shorthorn issue - could it be an issue in another breed - sure - but why does that matter?? It is clearly a Shorthorn issue - a potential genetic issue in Shorthorn cattle.

To clarify another issue -

[size=10pt]DR BEEVER WANTS SAMPLES AND HE WANTS THEM ASAP -​

[size=10pt]whoever said "Beever doesn't want samples yet" IS FLAT OUT WRONG​

and as an aside calling me a *itch doesn't make you right  ;D

ps modify - seems I can't spell

Guess I need to call Dr B.

 

[DL]

Kool aid? Come on. I asked him lots of questions. He answered them? Have you talked to Pat DL? Instead of beating each other up all the time, how about overcoming our pride or stubborness or whatever it is and get SOMETHING DONE. If a guy tells me for over an hour all he knows about this and I believe him, I drank the kool aid? I repect what you say DL but that comment stunk. The one thing I know is somebody is lieing. Period. I dont know who but somebody is full of crap.I will find out soon enough. Just like the rest of us. Instead of using steerplanet to throw shots around. Lets get on the phone and talk. Work it out and show the other breeds that we are legit. Right now, legit is the last word used to describe this deal. I can assure you Pat got a earful from me and he never wavered from what he said. Isnt it his job to be in charge of this investigation? It sure isnt mine. It sure isnt yours DL. Thats what we pay him to do. Let him do his job. Call him. Ask him like I did and form your own opinion. We all loose if the number one bull in the breed gets wacked form a defect. Thats a fact. DL has made many good points. Nobody is arguing this. Lets try and look at the big picture and work toward that. Witch hunts and public berating gets all of us nowhere. Even if the ball has been dropped badly already, it doesnt mean we cant still fix what needs fixed. Remember the Jim Valvano speech? "Never give up. Don't ever give up." Thats how I roll.

was it grape?

I was asked to email him asap - I did (this was before Christmas) - I was told to call him back Monday after Christmas - there has been an exchange of multiple emails - I was given no information to dispute my statements. I have formed my opinion and I stand by what I have posted

- you and everyone else can form and own your own opinion

this is not a witch hunt, nor is it public berating - it is simply information
- the goal is to obtain samples from Shorthorn calves that have a distal hind limb deformity to determine if the cause of the deformity is genetic (or not)
- obtaining samples requires that Shorthorn breeder be aware of the potential genetic defect prior to calving season so the appropriate number of sample can be obtained so that it can be determined if the cause of the hind limb deformity is genetic (or not)
-the big picture is we need samples and to get them people need to be aware
-it ain't really all that hard

 

[jaimiediamond]

I enjoy grape Kool-Aid myself its better then the vinegar water you serve inquiring minds As it is purely foolish to believe everything one reads on the internet I contacted some people and was informed that at this time there are no conclusive results.  That doesn't mean I need to glue feathers to my bottom and put my head in the sand but it does mean I am intelligent enough to question what I read and confirm things without foolishly following an unknown person. TGCC was perhaps your biggest defender and has always been someone who speaks what he thinks.  Is it wrong that there are more opinions than your own? 

 

[DL]

I enjoy grape Kool-Aid myself its better then the vinegar water you serve inquiring minds As it is purely foolish to believe everything one reads on the internet I contacted some people and was informed that at this time there are no conclusive results.  That doesn't mean I need to glue feathers to my bottom and put my head in the sand but it does mean I am intelligent enough to question what I read and confirm things without foolishly following an unknown person. TGCC was perhaps your biggest defender and has always been someone who speaks what he thinks.  Is it wrong that there are more opinions than your own? 

No one has said there  are "conclusive results" - to get "conclusive results" we need more samples - to determine if the hind limb defect seen in Shorthorn cattle is genetic (or not) we need more samples - to obtain more samples people need to be informed -

you are certainly entitled to own your own opinion - I have presented what I know and I stand by it, you can decide what you want, if anything, to do with that information

 

[trevorgreycattleco]

Fair enough. Thats the beauty of the good ol USA. We can all form our own opinions. I agree we need to be informed asap but if the facts havent been proven with out a doubt, we dont need to argue. We need to work together.  I stand up for the breed before anybody. Period.

DL, I dont know what to tell you. He called me. Squeaky wheel gets the grease.

 

[knabe]

No one is in charge or is supposed to be..  It is a collaborative project comprised of a team of people.

Its a mirror of the ag community which is full of chiefs and very few if any Indians.

Thank goodness peoplle have the foresight to turn in samples, find the gene and develop a test.

Really it's nothing more than that and all this other stuff makes the breed look bad, not the defect.

Really is it that hard?  There's too many other interesting things to improve like that Ulysses bull up in Canada and some of these other programs people have.

Its pretty interesting to think one bull, defect, or breeder makes a breed.

 

[sue]

Fair enough. Thats the beauty of the good ol USA. We can all form our own opinions. I agree we need to be informed asap but if the facts havent been proven with out a doubt, we dont need to argue. We need to work together.  I stand up for the breed before anybody. Period.

DL, I dont know what to tell you. He called me. Squeaky wheel gets the grease.

 Potential genetic defect - is like a bad dream, can it go away or can I just wait to hear about after  I  buy or sell  my next bull?  Let's just gather the information, turn in samples and let everyone make the choices they want to make.  Do you need the phone number?

 

[sue]

DL
I would like to just say- you're post are very easy to comprehend. Over the years talking with Beever - alot of what he explains over the phone is not as clear.  I visited with him a little recently and reading your posts helped me out a bunch more!?  Again the articles over the years that you have written I feel reach alot of us. So thank you again. 

 

[DL]

Fair enough. Thats the beauty of the good ol USA. We can all form our own opinions. I agree we need to be informed asap but if the facts havent been proven with out a doubt, we dont need to argue. We need to work together.  I stand up for the breed before anybody. Period.

DL, I dont know what to tell you. He called me. Squeaky wheel gets the grease.

not to belabor the point - what facts are you talking about?

The fact that 6 of 7 Shorthorn calves with a hind limb deformity are homozygous for a 2.7 Mb region?
The fact that 7 of 7 calves have been sired by one bull or his sons?
The fact that there is geographic variability in the reported cases?
The fact that these data suggest (but do not prove) that the hind limb deformity in Shorthorn cattle is genetic?
The fact that we need more samples of Shorthorn calves with the hind limb deformity to determine if the abnormality is genetic (or not)?
The fact that to obtain more samples all breeders (not just a select few)  need to be aware of what to look for?

Which if these facts is an issue for you?

ps thanks sue, the messenger always takes a beating so your comments are much appreciated 

 

[aj]

Jamie......the history of the world did not start when you graduated high school. DL is not an unknown enity. She was raising questions on the other internet board around the time you were seventeen years old. Ah those were the days. I remember the day the breeder or owner of Windstar got on the board and declared his bull was not a pha carrier! Beever and he had heated words on the board. I remember telos and his studying and knowledge of the old maine pedigrees. I remember suggesting the book "The battle of the bull runts" which is a book describing the dwarfism problem in the Herford breed. I really enjoyed the one chapter where the investigator actually kinda got one breeder drunk to ply some info out of him. He went and got 2 pedigree's out of a whole in the wall after half a fifth that finally broke the trail wide open on the old St. Louis Lad bull that was born in the 1890's or whenever it was.There is science behind all this stuff. Now it is easy with the genetic dna and everything. Remember the "Bulldog defect"(pha). Telos and knabe were wracking their brains out on the old main pedigrees. There were dead ends and pedigrees that weren't right and people raising hell all over the place. It got to a point where the steerplanet.com banned defect discussions. I really love the genetics of one of the questioned bulls. I hope and pray that he ends up being clean. This ain't the first time a defect has occured. In the herford dwarfism deal that kinda surfaced around the 1950's the bull that started it all was born in 1896 or so. It took 50 years for the thing to surface. It was spread all over the damn place. Herds were washed up . Peoples lives were essentially destroyed over night. There were no genetic dna testing going on so the breeders used carrier cows(tester cows) to figure out the clean lines. It was terrible slow. I think if people know the history of events like these they have a better chance of understanding this potential deal. jmo

 

[aj]

I guess maybe it was showsteer.com that banned the defect talk. Wow I googled "The battle of the bull runts" by L.P.McCann. Amazon had 2 used at 125 bucks a piece. I think I paid 20 for mine. Must be a collectors item.

 

[frostback]

I tried to add this to a thread where it is said that only shorthorn samples are wanted but it wouldnt let me. Anyway,, why are they only wanting shorthorns. Wouldnt you want any suspicious calves samples. Wouldnt that help rule stuff out or confirm others. Are there not Maines or Chis that may trace back to shorthorns? What about Durham reds?

 

[knabe]

I think I paid 40 a couple years ago.

I got a two vol set of consular reports "cattle and dairy farming" published in 1888 commissioned by congress.  Kinda cool.

Seems a lot of copies got destroyed by people removing the plates and selling them individually.

Wilpost a couple of pics.