Genome of a Bull

[inyati13]

Preface: The following is presented to generate creative thought. A phenotype can tell lies. A proven genotype has a pedigree to stand on. Have fun.

Definitions:

Genotype: the genetic constitution of an individual organism.

Genome: the complete set of genes or genetic material present in a cell or organism.

Phenotype: the set of observable characteristics of an individual resulting from the interaction of its genotype with the environment.

Background: When you look at a cow, you are seeing a fraction of what is contained in the genotype. It is analogous to looking at the tip of the iceberg. The domestic cow (Bos taurus) has 60 chromosomes. The size of the bovine genome is 3 Gb (3 billion base pairs). It contains approximately 22,000 genes of which 14,000 are common to all mammalian species. Bovines share 80 percent of their genes with humans. The genome of a cow is the largest genome ever sequenced.
The percentage of the genotype expressed in the phenotype is infinitely small. For example, the genes that provide the blueprint for the physiological functions are not visible in the phenotype.

More important to this message is that many genes go unexpressed in the phenotype. Those genes are still present in the animal's genome. They may be expressed in the phenotype of the off-spring. Some of the unexpressed genes maybe superior, some may be inferior.

Question: The debate is open. Is a bull with a great phenotype and a mediocre genotype preferable to a bull with a mediocre phenotype and a superior genotype?

 

[Ebenezer]

And genes can turn on and off in generational skips and such. Maternal programing is an influence. Where are you getting the genotype data? I don't think that what is currently available to reinforce EPDs (remember the word is "estimated") comes close to telling you much about the 3 billion base pairs.

So, let's say that somebody has a post legged bull for sale with limited heart girth. Regardless of any other data the bull is flawed. His rear legs will not last to breed cows as long as a bull with proper leg set. His daughters (opinion) will be harder calving heifers and cows.

Best of both worlds: find a breeder who linebreeds, culls and keeps. Buy some that he is selling from his keepers. The more similar his environment and management is to yours - the better.

 

[sim.-ang.king]

Is this thread because some people didn't like your bull?

 

[inyati13]

And genes can turn on and off in generational skips and such. Maternal programing is an influence. Where are you getting the genotype data? I don't think that what is currently available to reinforce EPDs (remember the word is "estimated") comes close to telling you much about the 3 billion base pairs.

So, let's say that somebody has a post legged bull for sale with limited heart girth. Regardless of any other data the bull is flawed. His rear legs will not last to breed cows as long as a bull with proper leg set. His daughters (opinion) will be harder calving heifers and cows.

Best of both worlds: find a breeder who linebreeds, culls and keeps. Buy some that he is selling from his keepers. The more similar his environment and management is to yours - the better.

Ebenezer, please post the most current data you have on the genome. This is 2009 data from a US Dept of Agriculture funded study of the genome of a Hereford cow. I am on a cell phone currently but will be happy to provide a proper reference when I have access to my laptop.

 

[inyati13]

Is this thread because some people didn't like your bull?

Yes. That thread generated my idea for this question. Responses like Ebenezer's is what I was hoping to get.

 

[inyati13]

:wave: Ebenezer:

Reference: Elsik, C.G. et al, (Bovine Genome Sequencing and Analysis Consortium) (2009). "The genome sequence of taurine cattle: a window to ruminant biology and evolution". Science 324 (5926): 522–528. doi:10.1126/science.1169588. PMC 2943200. PMID 19390049

 

[Jake]

Until there is a fully mapped out genome and accurate testing to be able to track what will be expressed a person cannot for certain know if an animal will outproduce his phenotype. Even when you stack genetics in a pedigree you will end up with the undesirable pieces of the paired genotypes.

The most accurate way we have today of judging an animals genotype is by looking at his phenotype and then controlling for the environment. Just because an animal is out of a "great" doesn't mean he inherited all the "great" genes and today we don't have an accurate way of testing that.

Now this goes back to the origin of this question, the faults I found in your calf are faults that I find in a large portion of the Dream On sired animals I have seen pictured.

 

[inyati13]

Until there is a fully mapped out genome and accurate testing to be able to track what will be expressed a person cannot for certain know if an animal will outproduce his phenotype. Even when you stack genetics in a pedigree you will end up with the undesirable pieces of the paired genotypes.

The most accurate way we have today of judging an animals genotype is by looking at his phenotype and then controlling for the environment. Just because an animal is out of a "great" doesn't mean he inherited all the "great" genes and today we don't have an accurate way of testing that.

Now this goes back to the origin of this question, the faults I found in your calf are faults that I find in a large portion of the Dream On sired animals I have seen pictured.

Thank you for the tone of your response. It resonates well with the intent of my question. You might take a look at the study. There has been considerable work on the genome. In fact, I don't fully understand how it works but the breed associations are using the advances in genomics to refine their EPD numbers. Just got off the phone with an animal science professor who was explaining it to me. So maybe we are not that far off. Thank you. Intelligent men can have intelligent exchanges.

 

[TennesseeTuxedo]

I am following this thread with great interest.

 

[TennesseeTuxedo]

Ron, you prompted me to go back and dig up this thread from 2014.

viewtopic.php?f=12&t=90602

 

[Jake]

Thank you for the tone of your response. It resonates well with the intent of my question. You might take a look at the study. There has been considerable work on the genome. In fact, I don't fully understand how it works but the breed associations are using the advances in genomics to refine their EPD numbers. Just got off the phone with an animal science professor who was explaining it to me. So maybe we are not that far off. Thank you. Intelligent men can have intelligent exchanges.

I do believe they get closer and closer all the time. Will be interesting to see how quickly they can add to the profitability of an operation when we get to the point of being able to use genomics to their potential.

 

[inyati13]

Ron, you prompted me to go back and dig up this thread from 2014.

http://www.cattletoday.com/forum/viewto ... 12&t=90602

Some good information in that.

 

[Ebenezer]

A phenotype can tell lies.

Is this true in the sense of structural or many convenience faults? I understand growth, milk production, size and many things cannot be correctly expressed but are we to believe that blatant faults are the problem of environment? I think not. Incorrect structure, low udder quality, pinched heart girth, dipped back, poor foot angle, bad hooves, poor disposition and much more are not going to be disappearing if they are in the parents.

We can use faulty animals, sure, but not without consequences. You can cover faults by selecting the offspring that do not express the faults. Outcrossing and crossbreeding helps tremendously. But there is still a % loss and an introduction of faults into the genepool. This is the problem with some breeds that now have foot, leg and fertility issues: problems are introduced and folks either are going to lose money or sell all by "value" of parentage and connections. It does not make the problems go away and does not make the breed better.

So what if, (big if) an animal has poor phenotype and futuristic genetic testing of more than 50% of the pairs says that is should have correct structure, right amount of growth, right amount of milk, mild temperament, ... Is it an animal to keep and use as a building block? There are stories that defy the odds: Jim Lingle recommending that a friend buy a roach back bull from an old Wye sale, a famous breeder using a small and poor performing bull named Bob to create a famous line, and probably more. But they are known because they were _____? (Maybe the word is "exceptions"?)

 

[inyati13]

A phenotype can tell lies.

Is this true in the sense of structural or many convenience faults? I understand growth, milk production, size and many things cannot be correctly expressed but are we to believe that blatant faults are the problem of environment? I think not. Incorrect structure, low udder quality, pinched heart girth, dipped back, poor foot angle, bad hooves, poor disposition and much more are not going to be disappearing if they are in the parents.

We can use faulty animals, sure, but not without consequences. You can cover faults by selecting the offspring that do not express the faults. Outcrossing and crossbreeding helps tremendously. But there is still a % loss and an introduction of faults into the genepool. This is the problem with some breeds that now have foot, leg and fertility issues: problems are introduced and folks either are going to lose money or sell all by "value" of parentage and connections. It does not make the problems go away and does not make the breed better.

So what if, (big if) an animal has poor phenotype and futuristic genetic testing of more than 50% of the pairs says that is should have correct structure, right amount of growth, right amount of milk, mild temperament, ... Is it an animal to keep and use as a building block? There are stories that defy the odds: Jim Lingle recommending that a friend buy a roach back bull from an old Wye sale, a famous breeder using a small and poor performing bull named Bob to create a famous line, and probably more. But they are known because they were _____? (Maybe the word is "exceptions"?)

"A phenotype can tell lies". In practice, producing the best cattle warrants using every tool in the box. Breeders select for the best phenotype possible. Phenotype sells. But so does genotype. The only difference between the Bulls that sell for 5k versus the ones that sell for 3k is more often than not genotype. Maybe buyers are making a mistake but the money is real. Try selling a bull at the Bulls of the Bluegrass that is from a herd bull.

The thread TT referenced raises the same issue. A phenotype can hide a plethora of undesired traits. Genotype has a track record.

Your question about can it be structural. Yes. I am not clear on what you mean by convenience faults. An explanation would help. Remember, for every gene that is expressed in a phenotype there is the homologous gene that is not! However, depending on how the chromosomes are sorted during meiosis in the formation of the gamete, that non-expressed gene may express itself. That gene could affect the form and/or function of the off-spring. Thereby, affecting structure.

You stated: Incorrect structure, low udder quality, pinched heart girth, dipped back, poor foot angle, bad hooves, poor disposition and much more are not going to be disappearing if they are in the parents.

I agree. If observed in the phenotype, they are also in the genotype. But study of the animals pedigree can be utilized to avoid these undesirable traits. I know Rocking P will not use Upgrade in their herd because they don't like his foot structure.

 

[Lazy M]

Why would anyone settle for poor geno or phenotype? There are enough bulls for sale that look good and have the paperwork to match. My thought is that a bull with obvious physical flaws would have a greater propensity to express those same flaws in their calves. Also most/all epds that I'm aware of only address birth factors and performance factors not structural defects..

 

[inyati13]

Why would anyone settle for poor geno or phenotype? There are enough bulls for sale that look good and have the paperwork to match. My thought is that a bull with obvious physical flaws would have a greater propensity to express those same flaws in their calves. Also most/all epds that I'm aware of only address birth factors and performance factors not structural defects..

Everyone probably agrees with you. Nevertheless, the issue comes up. The old thread posted by TT also raises the question.

 

[jscunn]

Ron,
Two things..

1. The association dont have a freaking clue as to what genomes they are looking for yet. If they tell you they do they are lying.. If they knew they wouldnt have to "recalibrate" every year.

2. Now lets assume that they have all the genes figured out for BW WW YW Milk, CW marbl, etc.. This particular bull was in the top 1% for every trait they listed. However..he was pretty badly sickle hocked and his front feet turned out.. Would you buy him? Better question would you sell him??

 

[gizmom]

I have read through this thread and the other thread that was referenced. I admit that genotype is important to me, but it is also important to use a knife on bull calves that have exceptional genotype but don't have adequate phenotype to go with it. If a bull calf can't walk no matter how great his genotype he needs to be a steer. I confess much of the mumbo jumbo of genomes is Greek to me, science is a great tool I believe in using every tool available but you better be measuring the performance of your calves and using your eyes to evaluate that calf as well as using genomes, if you want to have longevity in the cattle business.

Gizmom

 

[Lazy M]

Ron,
Two things..

2. Now lets assume that they have all the genes figured out for BW WW YW Milk, CW marbl, etc.. This particular bull was in the top 1% for every trait they listed. However..he was pretty badly sickle hocked and his front feet turned out.. Would you buy him? Better question would you sell him??

Might as well, GAR has been offering up poor phenotype/great genotype bulls as seedstock for years :roll:

 

[inyati13]

Ron,
Two things..

1. The association dont have a freaking clue as to what genomes they are looking for yet. If they tell you they do they are lying.. If they knew they wouldnt have to "recalibrate" every year.

2. Now lets assume that they have all the genes figured out for BW WW YW Milk, CW marbl, etc.. This particular bull was in the top 1% for every trait they listed. However..he was pretty badly sickle hocked and his front feet turned out.. Would you buy him? Better question would you sell him??

Thanks for all the comments. It is during the recalibration process that a member with a registered animal can submit genomic data on their animal and the data is used to better support the EPD numbers. I don't have a command on how it works but as you infer they seem to be looking for genes in the genome of the subject that supports one of those traits reflected in the EPDs. If another user understands the process that the associations employ to enhance the EPDs by applying actual genomics data, please fill in the details.

NO. I would not buy a bull with a compromised phenotype. For one reason, I service my small herd via AI. I do not employ ET at this time. The bull in the pictures came to me as an embryo calf in a heifer I purchased from Fire Sweep Simmentals. I am extremely happy with the purchase.

I would avoid selling a bull that people I consult with tell me is not appropriate to use for breeding.