Genotype and Phenotype

[inyati13]

Definitions: Genotype; The genetic constitution of an individual organism. Phenotype; The set of observable characteristics of an individual resulting from the interaction of its genotype with the environment.

Unless you can take a Bovine to a lab and do a total genetic makeup on it, the evidence of its genetic constitution is revealed by its pedigree and what you can see with your eye. EPDs are data collected on the animals performance. The performance reflected in the EPD data is influenced by the animals genotype and the environment. The best bull in the world could have poor WW data, if the cows he bred did not produce adequate milk to wean healthy calves.

These are fundamental concepts and I provide them because despite their simplicity, I see statements on CT that fail to acknowledge these concepts. For example, there was a thread that diminished the importance of looking at the bulls phenotype in favor of looking at the data. My question is this: where do you put the most emphasis as a breeder in your effort to evaluate the genetic quality of a Bovine?

I am not a breeder but from my understanding of genetics, I would think the order of importance unless you had a complete annotated genetic map of the animals DNA to study, would be: First, the Phenotype; Second the Pedigree: and third the data on the Bovines performance as reflected in the EPDs.

Here is why I would put Phenotype first. The Phenotype is the most direct insight into the animals genotype. Everyone is knowledgeable that in looking at a Bull that you see only those characteristics that are expressed and that defects my be hidden by the recessive genes. Conversely, there may be superior characteristics expressed if the bull was mated to a cow that would help uncover that characteristic. But when you look at a Bull you can only judge him as he is. Obviously if you know the cows you plan to mate him too you have more information to perform you evaluation. But in the science of genetics the dice have been rolled and what you see in the Phenotype is the result of all the genetic mechanisms having been played out. Mutations, meiosis, dominance, recessiveness, fertilization, crossing over of limbs of DNA strands, etc. Yet I talk to breeders around here who tell me they put more value on the EPDs. To the point that they exclude bulls or cows sight-unseen. I could see that if you needed a bull just for heifers and you were interested in CE only. Thanks. I hope this generates some entertaining debate. Let the fun begin.

PS. Can we agree to exclude the exceptions and focus on the fundamentals. I know you could justify using EPDs in exceptions like the CE point above. What is the general practice? That is what this is about. Thanks.

 

[cmf1]

...And if you had access to a DNA profile, (Bovigen, Igenity, etc.) how much would that weigh in to your matings?

Inyati, if I'm hijacking please tell me and I'll delete, but it seems like the DNA profiles are a pretty useful tool to have available alongside the aforementioned.

 

[3waycross]

Well in fact if i understand it correctly the newer genetic test reveal more and more all the time so I suppose that it is a tool that should be included.

Having said that here's how i select;

Pour over pedigrees, epd's and gene tests and eliminate everything that DOES NOT reflect the traits i want or that eliminates itself by exhibiting bloodlines, traits or genetic flaws, that are not acceptable in my program!

THEN

I select by phenatype. It works for me that doesn't mean you have to use my system. It just means it works for me!

 

[KNERSIE]

The best pedigree in the world combined with the "best" breeding values, means diddly squat if it isn't expressed in the phenotype. All the tools are just that, tools! Use all of them!

 

[3waycross]

The best pedigree in the world combined with the "best" breeding values, means diddly squat if it isn't expressed in the phenotype. All the tools are just that, tools! Use all of them!

I believe that's what i just said!

I just find it easier to select my way, rather than run around the country looking at bulls that really look good and then eliminating them for some fatal flaw in their numbers. For example why would i care what a bull looks like if his PAP score is above the minimum required for my altitude.

THAT is what i mean by a FATAL FLAW. That's how i use ALL the tools. I just make it a point to not fall in love with a bull based on his looks and then end up having to cull him for PAP.

BEEN THERE DONE THAT GOT THE T_SHIRT

Case in point. Fell in love with this fella at 4 months bought him at 7 months and 785lbs. PAP'd him at 9 months he scored a 42. PAP'd him at 12 months , he scored a 52.

Found him a home in Nebraska......cost me a net loss of $500 for that little experiment. I won't do it again.

 

[inyati13]

...And if you had access to a DNA profile, (Bovigen, Igenity, etc.) how much would that weigh in to your matings?

Inyati, if I'm hijacking please tell me and I'll delete, but it seems like the DNA profiles are a pretty useful tool to have available alongside the aforementioned.

Thanks for asking about the hijacking but that is the best outcome to a question, in fact, this is why I raised the question. What is the scope of the DNA profile? I don't know the extent to which the DNA of domestic cattle has been mapped. My son is doing his PhD at Vanderbilt Universtiy and he tells me the genome of the lab mouse is mapped to the extent that the loci of every gene is known. Is the same true of domestic cattle? I don't know, and even if the location of the genes are known and the traits that are controled by each of those identified genes has been determined, how do you know how they are going to affect the Phenotype. I want to be clear, it is one thing to know which chromosome a gene is on and what trait it controls, but how do you look at it and tell exactly how it affects the Phenotype. For example, if I know that 5 genes will be involved in determining the color of a cows face. And I know which chromesomes those genes are on. And I know the loci of those genes on those specific chromosomes, how do I look at those and tell whether the face is going to be white, black or blazed. That is part of the reason I started this thread. If you are a breeder, what are you doing to get the phenotype you want. It gets more complicated. Some characteristics are not visual in the phenotype. For example, rate of growth, size of offspring, amount of milk produced. Those characteristics are not going to be visual in the phenotype. And that is where the EPD data comes in. But when all is said and done, the best tool seems to be the phenotype.

 

[redcowsrule33]

Selecting for one and not the other is a dangerous game. In my mind it's akin to single trait selection. My methods for evaluating cattle are similar to 3way's.

In reading one of our local ag papers I came across an article about a talk a prominent seedstock producer gave at a conference recently. Bothered me a bit. An excerpt:

"Genetic improvement and profitability were not necessarily correlated in the past.
"When we go back to the '80s and '90s, we were using EPDs to grow cattle faster. But when we look back over that 10 year selection period between 1985 and 1995, that index didn't change," he said, noting that the increased output did not equate to increased profit as costs continued to rise.
However, the early 1990s brought about downward pressure on cow size and upward pressure on carcass size. As cattle changed, so did profitability, measured by the rate of genetic change which calculated out to roughly $2 per head per year.
A metric more familiar to the dairy, poultry and swine industries, rate of genetic change has now become a profitability measure for cattle as well, estimated at $15 per head per year. As Leachman pointed out, not playing the game today is like leaving money on the table. Those producers who did not focus on that figure 30 years ago did not miss out as the rate saw very little change. If you sat out during the 1990s, he said, you are behind $20.
As more data is gathered, collected, analyzed and indexed, it becomes more apparent that numbers don't lie. "We are going to be better served by using this technology than looking at the cattle visually," he stated. "We don't think those visual techniques are effective at predicting the profitability of the animal."

I realize that he is pimping his program, but encouraging people to put more pressure on numbers and less on the phenotype bugs me to say the least. This is an art that shouldn't be lost. My thought is use all the information you can, visually and on paper, to select, but don't let one thing overshadow the rest.

Link to the full article: http://www.agriview.com/news/livest...cle_83a476f2-867c-11e2-b1cd-0019bb2963f4.html

 

[inyati13]

Selecting for one and not the other is a dangerous game. In my mind it's akin to single trait selection. My methods for evaluating cattle are similar to 3way's.

In reading one of our local ag papers I came across an article about a talk a prominent seedstock producer gave at a conference recently. Bothered me a bit. An excerpt:

"Genetic improvement and profitability were not necessarily correlated in the past.
"When we go back to the '80s and '90s, we were using EPDs to grow cattle faster. But when we look back over that 10 year selection period between 1985 and 1995, that index didn't change," he said, noting that the increased output did not equate to increased profit as costs continued to rise.
However, the early 1990s brought about downward pressure on cow size and upward pressure on carcass size. As cattle changed, so did profitability, measured by the rate of genetic change which calculated out to roughly $2 per head per year.
A metric more familiar to the dairy, poultry and swine industries, rate of genetic change has now become a profitability measure for cattle as well, estimated at $15 per head per year. As Leachman pointed out, not playing the game today is like leaving money on the table. Those producers who did not focus on that figure 30 years ago did not miss out as the rate saw very little change. If you sat out during the 1990s, he said, you are behind $20.
As more data is gathered, collected, analyzed and indexed, it becomes more apparent that numbers don't lie. "We are going to be better served by using this technology than looking at the cattle visually," he stated. "We don't think those visual techniques are effective at predicting the profitability of the animal."

I realize that he is pimping his program, but encouraging people to put more pressure on numbers and less on the phenotype bugs me to say the least. This is an art that shouldn't be lost. My thought is use all the information you can, visually and on paper, to select, but don't let one thing overshadow the rest.

Link to the full article: http://www.agriview.com/news/livest...cle_83a476f2-867c-11e2-b1cd-0019bb2963f4.html

Thank you for that. I agree with you. He is using the numbers to the exclusion of looking at the phenotype. His point is pretty good but I just don't see the strength he does in the numbers. Use all the tools but to say to use the numbers rather "than looking at the cattle visually" seems a real stretch. I know when we used fruit flies to conduct genetic research in school, you still had to sit down and describe the phenotype before you could identify how the genes paired out. But as Tom Selleck said in "Quigley Down Under", This ain't Dodge City and you ain't Bill Hickok.

 

[cmf1]

I'm well south of being an experienced breeder, but I do factor in what little I know.
Phenotype is what forces me to look at other data.
If an animal is not to my liking phenotypically, I don't have any interest in knowing anymore about him.
Still developing my "eye" as well.
I'm sure not savvy enough to stray away from that first criteria on "scientific blending" of numbers so to speak.
But after having some semen DNA profiled, I am amazed at the information that can be attributed to an animal from this process.
I am curious as to whether or not experienced breeders are accepting DNA scores as readily as EPDs.
Seems to me DNAs would be even more reliable than EPDs as outcome predictors. Not the absolute final word, but more concise information to decide with.
Eh?

 

[cow pollinater]

I'm pretty much on 3ways system but I quit registering anything and its all bulls for my own use now so I'm not as picky since the end result for most of the calves is slaughter. If I'm wrong once in awhile it's MY problem and not someone elses.
I always want cattle that LOOK like they're going to do what I want them to do but I like to see numbers that back that up. I start with numbers and work backwards.

Sometimes you'll be surprised once the bull is proven. I've seen a number of bulls that you'd look in at person and see just an average bull with a few flaws and shrug and walk away but when we prove them out we find explosive growth and carcass traits that we didn't see, etc. Since my business(the cow calf part) is making calves to sell by the pound, should I care if the calves LOOK like they're going to grow or should I choose a sire whose calves have proven that they GROW. I sell by the pound and the guys that are buying them care less about "ideal" than I do.
You'd also be surprised by how many bulls with near perfect phenotype and pedigree don't measure up once they've been proven.

Go through any studs catalog and try to guess the Angus bulls $EN just by looking at his picture. Pick a few traits and try to guess what that sire will do based on phenotype and then look at the numbers on sires with accuracy of .70 plus and see how you've done.

FWIW, the army told me I'm to lame phenotypically to do road marches about fifteen years ago but I've been walking ten miles a day seven days a week on concrete every since and I'm no more sound in my foot structure now than I was then. :lol:

 

[cow pollinater]

Seems to me DNAs would be even more reliable than EPDs as outcome predictors. Not the absolute final word, but more concise information to decide with.
Eh?

On the dairy side of things we consider a genomic proof/epd to be the equivilant of ten progeny on the ground. It is nowhere near the kind of reliability that progeny proven provides but it's an early indicator. A few of the studs jumped on it early and charged a bunch of money to their customers for up and coming bulls (the genetics of tommorrow are the embroys that aren't even born yet) that were not progeny proven and are now backpedaling and trying desperatly to keep business because about half of the bulls they were selling didn't match up to the price they were selling them for.

 

[bse]

I do like all the others i like a combination of all things i look at a sale book pick out what i like by the numbers and pedigree then get there and start the elimination process by phenotype.
I flushed a cow and had to do the parentage on her so i did the HD50K Genomic test and this is for Angus im sure other breeds have it now but i can only say about Angus it has 50k markers on about 25 traits , i like the information it told me, an example her CE tanked but i know now what type bull i need to use to improve on that and it put true numbers on all traits where several traits had no numbers or Interum numbers so all purebred heifers retained from now on will have the HD50K and its just another tool.
I believe in the very near future it will be playing a bigger part in bull selection JMO.

 

[robert]

If you allow nature to eliminate problems then you will find that functional characteristics will multiply simply due to survival of the fittest (fit for their environment). However the temptation is always to modify that type to fit your own 'ideal', for example if you dislike more set to the hind legs than that which has emerged naturally over time then cattle with straighter hind legs get preferred over those with more set and for that there will be a consequence. An example of this is the dairy industry where classification of animals is done to a breed standard yet after fertility feet and legs remain a major reason to cull, I suspect that selection for environment ( in the case of dairy that would be concrete rather than pasture) has not been allowed to occur.

 

[HOSS]

I work on a similar system as bse does. I look at the epd's and arrange the cattle by priority just viewing their epd profile. Once I get to the sale I look at my epd prioritized list and match them up with the phenotype of the actual cattle. The phenotype may move an animal up or down on my priority list. I have seen some animals with epd's that I had lower on my list for some number or another not being exactly what I am looking for but the phenotype expressed in the actual animal trumped that particular epd shortcoming. Once I have my list prioritized I bid according to the list. Sometimes the top animal on my list goes too high and I move on to my #2 priority.

 

[inyati13]

I do like all the others i like a combination of all things i look at a sale book pick out what i like by the numbers and pedigree then get there and start the elimination process by phenotype.
I flushed a cow and had to do the parentage on her so i did the HD50K Genomic test and this is for Angus im sure other breeds have it now but i can only say about Angus it has 50k markers on about 25 traits , i like the information it told me, an example her CE tanked but i know now what type bull i need to use to improve on that and it put true numbers on all traits where several traits had no numbers or Interum numbers so all purebred heifers retained from now on will have the HD50K and its just another tool.
I believe in the very near future it will be playing a bigger part in bull selection JMO.

bse, thanks. this is what I was looking for, "The High-Density panel is made up of more than 50,000 single nucleotide polymorphisms (SNP), also known as DNA markers that have been identified in the bovine genome. The test utilises SNPs spaced evenly across the entire genome, providing High-Density genomic trait predictions to cover specifictraits of interest. In our initial product these include various economically important traits for calving,growth, carcase and feed efficiency." Notice that utilizes is spelled with an "s". That is over-seas English, probably written in Australia. Not important other than they probably participated in the research but it was underwritten by Pfizer. I thought there must be something like this being done. It said there is 13 well established traits in the HD panel. DNA (Deoxyribonucleic acid) is a polynucleotide chain with two strands to form the double helix. A gene is actually a region or section of a DNA macropolymer that controls a trait or characteristic. So thank you. You provided me with something I was looking for so I could determine if this had been done in cattle which I was most certain had to be. Lab mice and Drosophlia (fruit flies) have been through this for years because they are used in genetic research. For example, eye color and shape are the traits you do in your beginning genetic class. No doubt this will be done for more traits and breeds in the future.

But even with this, you still must look to the phenotype for confirmation. Thanks to everyone. I appreciate the information and I bet you guys find what you do rewarding.

 

[inyati13]

If you allow nature to eliminate problems then you will find that functional characteristics will multiply simply due to survival of the fittest (fit for their environment). However the temptation is always to modify that type to fit your own 'ideal', for example if you dislike more set to the hind legs than that which has emerged naturally over time then cattle with straighter hind legs get preferred over those with more set and for that there will be a consequence. An example of this is the dairy industry where classification of animals is done to a breed standard yet after fertility feet and legs remain a major reason to cull, I suspect that selection for environment ( in the case of dairy that would be concrete rather than pasture) has not been allowed to occur.

robert, you are headed into the science of Speciation (Ernest Mayr). I had Speciation under Dr. Madison E. Pryor who in 1959 was the only US scientist to travel to Antartica with a Russian Expedition. It was one of the first joint efforts of those countries. Dr. Pryor learned Russian in about 6 weeks at a miliary training facility. He then was able to teach it. If you google him you will discover that he has a Glacier named for him in Antartica. He was my mentor. Speciation is the process by which species are formed and it goes on every day, it is not w/o flaws (yes, nature is not perfect, if it was we would still have dinosaurs). It takes a long time but if it don't work it will never come to exist. People ask me why I believe in evolution, well look at breeding, it is evolution being directed by humans. I don't find cover in not believeing what my mind tells me is a truth. Better not mess too much with the way a quadapeds legs are made. It just took about 750,000 million years to get them to work as well as they do.

 

[robert]

as I see it the major flaw in DNA technology as marketed by Pfizer and Igenity is that hey give you a score of 1 thru 10 on each of the traits they measure, but for example if there are 20 markers for say calving ease and your animal scores a 5 that may mean she has 10 of those 20 markers, you take her and mate her to a bull who also has a score of 5, meaning he too has 10 of those 20 markers, but which ones? Conceivably in this mating you could end up with anything from a score of 1 to 10 but you have no way of knowing, nor of continuing selection pressure as it is still random recombination. I have no doubt that DNA technology is the future of genetic selection, the big question is whether it is the current genomic profiling or if it will be a more targeted marker driven science that allows selection towards homozygous trait carriers, I would rather the latter!

 

[robert]

If you allow nature to eliminate problems then you will find that functional characteristics will multiply simply due to survival of the fittest (fit for their environment). However the temptation is always to modify that type to fit your own 'ideal', for example if you dislike more set to the hind legs than that which has emerged naturally over time then cattle with straighter hind legs get preferred over those with more set and for that there will be a consequence. An example of this is the dairy industry where classification of animals is done to a breed standard yet after fertility feet and legs remain a major reason to cull, I suspect that selection for environment ( in the case of dairy that would be concrete rather than pasture) has not been allowed to occur.

robert, you are headed into the science of Speciation (Ernest Mayr). I had Speciation under Dr. Madison E. Pryor who in 1959 was the only US scientist to travel to Antartica with a Russian Expedition. It was one of the first joint efforts of those countries. Dr. Pryor learned Russian in about 6 weeks at a miliary training facility. He then was able to teach it. If you google him you will discover that he has a Glacier named for him in Antartica. He was my mentor. Speciation is the process by which species are formed and it goes on every day, it is not w/o flaws (yes, nature is not perfect, if it was we would still have dinosaurs). It takes a long time but if it don't work it will never come to exist. People ask me why I believe in evolution, well look at breeding, it is evolution being directed by humans. I don't find cover in not believeing what my mind tells me is a truth. Better not mess too much with the way a quadapeds legs are made. It just took about 750,000 million years to get them to work as well as they do.

It's likely I wasn't clear, I was more pointing out that when we refuse to accept the form that evolves under the pressure of environment / management because it doesn't meet our minds eye vision of perfection and end up distorting true functional selection in favor of idyllic phenotypic expression. Regarding Dairy type I wonder if the judging team ideal of hind leg set / foot angle / heel depth / pastern strength is in reality unsuited for life on concrete and is an obstruction to actual improvement?

 

[inyati13]

If you allow nature to eliminate problems then you will find that functional characteristics will multiply simply due to survival of the fittest (fit for their environment). However the temptation is always to modify that type to fit your own 'ideal', for example if you dislike more set to the hind legs than that which has emerged naturally over time then cattle with straighter hind legs get preferred over those with more set and for that there will be a consequence. An example of this is the dairy industry where classification of animals is done to a breed standard yet after fertility feet and legs remain a major reason to cull, I suspect that selection for environment ( in the case of dairy that would be concrete rather than pasture) has not been allowed to occur.

robert, you are headed into the science of Speciation (Ernest Mayr). I had Speciation under Dr. Madison E. Pryor who in 1959 was the only US scientist to travel to Antartica with a Russian Expedition. It was one of the first joint efforts of those countries. Dr. Pryor learned Russian in about 6 weeks at a miliary training facility. He then was able to teach it. If you google him you will discover that he has a Glacier named for him in Antartica. He was my mentor. Speciation is the process by which species are formed and it goes on every day, it is not w/o flaws (yes, nature is not perfect, if it was we would still have dinosaurs). It takes a long time but if it don't work it will never come to exist. People ask me why I believe in evolution, well look at breeding, it is evolution being directed by humans. I don't find cover in not believeing what my mind tells me is a truth. Better not mess too much with the way a quadapeds legs are made. It just took about 750,000 million years to get them to work as well as they do.

It's likely I wasn't clear, I was more pointing out that when we refuse to accept the form that evolves under the pressure of environment / management because it doesn't meet our minds eye vision of perfection and end up distorting true functional selection in favor of idyllic phenotypic expression. Regarding Dairy type I wonder if the judging team ideal of hind leg set / foot angle / heel depth / pastern strength is in reality unsuited for life on concrete and is an obstruction to actual improvement?

No Sir. It was very clear and that is exactly what I took your meaning to be. I hear you loud and clear. Biological systems are complex. When it comes to genetics we are in the stone age or at least the iron age. You and I are on the same page. Breeding had to be done only with the phenotype before we knew what DNA was or had EPDs. Man has performed marvels breeding domestic animals. They did by evaluating the phenotype. I think what some people may miss here is this; if you can observe performance and you can (i.e., you can look at a cow and see that see is growing fast, producing milk, etc.), that is all part of the phenotype. The observable characteriestics produced by the genotype. Good point on the Dairy cow feet. Nature exerts its selective pressures on populations. Seems when man gets involved he does it on what you say is the mind eye vision. May get what he wants but cause imbalance somewhere else. Thanks. Appreciate your help in understanding how you guys do this.

 

[bse]

There are differences in Igenity and Pfizer (now Zoeitis)geonomic tests in the way the info is sent back to you, Igenity does the 1 to 10 scale some traits 1 being best some 10 being best with the Zoeitis HD50K all traits are ranked 1 to 100, If you rank a 1 your in the top 1% of the breed for that trait a 100 your in the bottom and its still not gonna tell you on which side of 50 what is wraped what way(all thats above me) but i can choose better and roll the dice for improving that trait. I like the info from Zoeitis better because its all one way not some traits this way some the other.