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PostSubject: Re: genotype evaluation   Mon Nov 15, 2010 8:29 pm

MKeeney wrote:
df wrote:
MKeeney wrote:
df wrote:
Commercial cattlemen don't measure genotypes.
Do you think registered breeders measure genotypes Question

Purebred breeders largely record observations such as weaning weight and the resulting genetic evaluations are largely the result of additive genes. Certainly higher accuracy bulls have had a fair comparison of their breeding value.

I seriously doubt there is much hybrid vigor in crossing lines within a breed and certainly not as much as crossing breeds of cattle.

so measuring phenotype gives us the genotype? how would you account for a 25% IBC in a so called "GENETIC EVALUATION" using phenotype? if there`s no hybrid vigor in outcrossing within a breed, why don`t more REGISTERED breeders linebreed instead of constantly searching for outcrosses? what is a breed Dennis? no need for them anymore? put them all back together, and the next step is to re-select new breeds? define hybrid vigor?

Phenotype = genotype + environment so NO, phenotype is not genotype. I think I am interested in two things; the genetic merit of the sire and his ability to not cause me problems. I want a higher percent of my calves to be marketable or usable as replacements. Can I eliminate dinks?

The genetic merit is derived from ranking animals within their contemporary groups.

Consistency would be nice although I find it a little odd that bulls that are deemed "consistent" are not used in more linebreeding programs. I would think the bulls not promoted as consistent (when others in the same herd are "consistent) would be discriminated against.

Inbreeding coefficients are not currently accounted for in a genetic evaluation. However, if an inbred bull was used on enough of the population, the EPDs would reflect the breeding value of the bull. I suspect EPDs (low accuracy) do not account for IBC very well. I would bet that Ext is pretty well characterized for genetic value.

I think registered breeders are attracted to the next greatest and want to avoid linebreeding so they can minimize the potential for genetic defects. I am sure there is some inbreeding depression they would also like to avoid. I think producers have heard a bit about dwarfs in the 1930's-1950's and want to avoid the financial losses. I did not say there was NO hybrid vigor; I said there is not much compared to crossing breeds.

What is a breed? Great question. Funny, I just heard a presentation from a geneticists that stated composites are considered purebred IF they are recorded with a breed association. Can't agree with that!!

Is there a need for breeds? Not if you ask the swine and poultry folks. Seems they have lines that do specific things, then they cross those lines. Don't really know if they use breeds in the traditional sense. I suspect they might take a segment of the population of each breed and create a line but not sure if they believe the breeds themselves are that important.

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PostSubject: Re: genotype evaluation   Mon Nov 15, 2010 9:49 pm

[quote="dwight@steadfastbeef.com"]
MKeeney wrote:
[quote="dwight@steadfastbeef.comCall me an idiot, but my lifetime is too short to take that many chances.

Maybe I am too much of a coward to use a bull I can't stand looking at, but I wasn't afraid to share one of my "filters." Perhaps I should keep my other filters to myself.
It might be time to sit and watch that inbred, prepotent parentstock plot of corn not grow as well as the field corn you wrote your "perspectives " about ...it`s a disappointing day when inbreeding regression sorts the linebreeders ....



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PostSubject: Re: genotype evaluation   Mon Nov 15, 2010 9:54 pm

[quote="MKeeney"]
dwight@steadfastbeef.com wrote:
MKeeney wrote:
[quote="dwight@steadfastbeef.comCall me an idiot, but my lifetime is too short to take that many chances.

Maybe I am too much of a coward to use a bull I can't stand looking at, but I wasn't afraid to share one of my "filters." Perhaps I should keep my other filters to myself.
It might be time to sit and watch that inbred, prepotent parentstock plot of corn not grow as well as the field corn you wrote your "perspectives " about ...it`s a disappointing day when inbreeding regression sorts the linebreeders ....




Actually I was thinking why some don't cull the rogues within the designated male rows, or be able to spot them.
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PostSubject: Re: genotype evaluation   Mon Nov 15, 2010 9:56 pm

[quote="dwight@steadfastbeef.com"]
MKeeney wrote:
dwight@steadfastbeef.com wrote:
MKeeney wrote:
[quote="dwight@steadfastbeef.comCall me an idiot, but my lifetime is too short to take that many chances.

Maybe I am too much of a coward to use a bull I can't stand looking at, but I wasn't afraid to share one of my "filters." Perhaps I should keep my other filters to myself.
It might be time to sit and watch that inbred, prepotent parentstock plot of corn not grow as well as the field corn you wrote your "perspectives " about ...it`s a disappointing day when inbreeding regression sorts the linebreeders ....




Actually I was thinking why some don't cull the rogues within the designated male rows, or be able to spot them.
Anyone can sort. Very few really breed
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PostSubject: Re: genotype evaluation   Mon Nov 15, 2010 10:07 pm

Excellent post Dwight. Not saying that either is worthy of being pulled by the root, but I would think that sometimes it is needed. A linebreeding program that doesn't cull wouldn't accompoish much.
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PostSubject: Re: genotype evaluation   Tue Nov 16, 2010 3:55 pm

AX- wrote:
Excellent post Dwight. Not saying that either is worthy of being pulled by the root, but I would think that sometimes it is needed. A linebreeding program that doesn't cull wouldn't accompoish much.
Brian,
do you linebreed ? What is the highest IBC level you have created from your matings?
Dwight, explain to me how you build prepotency without regression? will higher levels of homozygousity create more "rogues"? what level of inbreeding defined by IBC have you created?
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PostSubject: Re: genotype evaluation   Tue Nov 16, 2010 6:04 pm

Mike, I have outlined some of our linebreeding in the thread I started about our Red cattle. What I left out is that there are quite a few matings from our 801 bull and daughters from our 26L bull, who is out of the grand dam of 801. Also trying to line up or Lana cows so that 205 cow and sisters are in there twice to this point. On our black cattle we have linebred to CSU Ram Time 0115 to some extent - don't have enough blacks to get a big sample, but our pet project is breeding all daughters of our Ram Time son to a 1/2 brother. The resulting progeny (Now bred heifers) are bred back to Ram Time 0115. Also do the occasional sire / daughter mating with the reds and had all of our Black Bred Heifers a year ago bred back to their sire. So basically, yes we do linebreed to some extent, not on everything, but do try to line up our top cows in a pedigree and our Gambler bull in a pedigree, granted nothing super long term as I'm only 36, but it's a start.
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PostSubject: genotype evaluation   Tue Nov 16, 2010 6:10 pm

AX- wrote:
Mike, I have outlined some of our linebreeding in the thread I started about our Red cattle. What I left out is that there are quite a few matings from our 801 bull and daughters from our 26L bull, who is out of the grand dam of 801. Also trying to line up or Lana cows so that 205 cow and sisters are in there twice to this point. On our black cattle we have linebred to CSU Ram Time 0115 to some extent - don't have enough blacks to get a big sample, but our pet project is breeding all daughters of our Ram Time son to a 1/2 brother. The resulting progeny (Now bred heifers) are bred back to Ram Time 0115. Also do the occasional sire / daughter mating with the reds and had all of our Black Bred Heifers a year ago bred back to their sire. So basically, yes we do linebreed to some extent, not on everything, but do try to line up our top cows in a pedigree and our Gambler bull in a pedigree, granted nothing super long term as I'm only 36, but it's a start.

good deal; show us some sire/daughter matings pictures...do you see regression in sire/dau matings?
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PostSubject: Re: genotype evaluation   Tue Nov 16, 2010 9:52 pm

Mike, I don't have any pics of the sire daughters this year. They were all out of heifers so they were a little smaller and shaped fine. The biggest problem we got was a lot of white - the Bull (Black) had a little white underneath and sure passed it on. I culled three of them for that. I'll get a pic of a couple Reds in the next few days. One was our top performing heifer calf of that year. I saw no ill effects on her at all (GamblerxGambler Mating).
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PostSubject: Re: genotype evaluation   Wed Nov 17, 2010 2:58 am

AX- wrote:
Mike, I don't have any pics of the sire daughters this year. They were all out of heifers so they were a little smaller and shaped fine. The biggest problem we got was a lot of white - the Bull (Black) had a little white underneath and sure passed it on. I culled three of them for that. I'll get a pic of a couple Reds in the next few days. One was our top performing heifer calf of that year. I saw no ill effects on her at all (GamblerxGambler Mating).
Some, for instance early line 1 herefords, propose to linebreed while increasing performance...though like Falloon in his closed herd, the line 1 now seeks to minimize linebreeding levels...will you cull linebreds that don`t measure up to the average or expected phenotype of the herd?
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PostSubject: Re: genotype evaluation   Wed Nov 17, 2010 6:31 am

The genomic selection process at Accelerated Genetics can be easiest explained when looking at full siblings as all are assigned same Traditional PAs. Only after getting the genomic estimates for their PTAs and STAs can you really see the differences between full sibling bull calves. And sometimes the difference between full siblings can be significant.



Table 1. Application of Genomic PTAs to Contract Bulls

Animal
Traditional NM$
Genomic NM$
Traditional PL
Genomic PL
Bull A
415.5
411
1.3
1.3
Bull B
415.5
207
1.3
-0.2
Bull C
415.5
472
1.3
1.4



For example in Table 1, we compared three full sibling bull calves using Net Merit (NM$) and Productive Life (PL) as traits. In the past a bull stud may have chosen Bull B, based on his physical appearance and conformation. Now, with the help of genomic analysis, it is clear that Bull B is not even close to his siblings on NM$ or PL. So the bull stud would want to avoid Bull B and purchase Bull C, whose Genomic NM$ is clearly higher than his Traditional NM$. The same would be true for females genomically tested.
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PostSubject: Re: genotype evaluation   Wed Nov 17, 2010 9:30 am

MikeK wrote:
...will you cull linebreds that don`t measure up to the average or expected phenotype of the herd?
This is where I get lost. Everything I read by Dr. Bonsma, he eventually brings in the endocrine system, the nervous system, and total environment and talks of the different pathways by which they influence morphology of the genotype. How do you ever know what the "expected phenotype" is until your cattle are well adapted to their environment? How do you know when they are well adapted?

I think I understand that neither of those questions can be answered if genetics are continually being changed.

That's why I asked the question about Larry's cattle(genetics) in your Kentucky environment. If you breed Larry's cows to a bull of Larry's genetics(essentially the same genotype), is there a difference in phenotype of the progeny due to the different environments?
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PostSubject: Re: genotype evaluation   Wed Nov 17, 2010 10:08 am

Quote :
That's why I asked the question about Larry's cattle(genetics) in your Kentucky environment. If you breed Larry's cows to a bull of Larry's genetics(essentially the same genotype), is there a difference in phenotype of the progeny due to the different environments?

The definition of phenotype includes the environment.

Quote :
the visible characteristics of an organism resulting from the interaction between its genetic makeup and the environment
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PostSubject: Re: genotype evaluation   Wed Nov 17, 2010 10:13 am

[quote="RobertMac"]
MikeK wrote:
...will you cull linebreds that don`t measure up to the average or expected phenotype of the herd?

I cull the males a lot harder than the females (closebred or otherwise) that do not fit my critetia, as one way to reduce risk. I may miss out on some but it fits better with the materials I have to build with. Where there is a major communication problem is that no two people have the same exact criteria. If we all had the same base material and used the same strain building materials with the same criteria then there MAY NOT be enough difference between these evolving strains to really reap the benefits of of the Tru-Line goal?
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PostSubject: Re: genotype evaluation   Wed Nov 17, 2010 10:33 am

RobertMac wrote:
MikeK wrote:
...will you cull linebreds that don`t measure up to the average or expected phenotype of the herd?
This is where I get lost. Everything I read by Dr. Bonsma, he eventually brings in the endocrine system, the nervous system, and total environment and talks of the different pathways by which they influence morphology of the genotype. How do you ever know what the "expected phenotype" is until your cattle are well adapted to their environment? How do you know when they are well adapted?

I think I understand that neither of those questions can be answered if genetics are continually being changed.

That's why I asked the question about Larry's cattle(genetics) in your Kentucky environment. If you breed Larry's cows to a bull of Larry's genetics(essentially the same genotype), is there a difference in phenotype of the progeny due to the different environments?
the type is the same...maybe it`s time to question Bonsma a bit...was he a breeder ? or an observer of type? why did both he and lasater put breeds together and re-select a new breed?
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PostSubject: Re: genotype evaluation   Wed Nov 17, 2010 10:34 am

[quote="dwight@steadfastbeef.com"]
RobertMac wrote:
MikeK wrote:
...will you cull linebreds that don`t measure up to the average or expected phenotype of the herd?

I cull the males a lot harder than the females (closebred or otherwise) that do not fit my critetia, as one way to reduce risk. I may miss out on some but it fits better with the materials I have to build with. Where there is a major communication problem is that no two people have the same exact criteria. If we all had the same base material and used the same strain building materials with the same criteria then there MAY NOT be enough difference between these evolving strains to really reap the benefits of of the Tru-Line goal?
risk of what?
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PostSubject: Re: genotype evaluation   Wed Nov 17, 2010 10:37 am

[quote="MKeeney"]
dwight@steadfastbeef.com wrote:
RobertMac wrote:
MikeK wrote:
...will you cull linebreds that don`t measure up to the average or expected phenotype of the herd?

I cull the males a lot harder than the females (closebred or otherwise) that do not fit my critetia, as one way to reduce risk. I may miss out on some but it fits better with the materials I have to build with. Where there is a major communication problem is that no two people have the same exact criteria. If we all had the same base material and used the same strain building materials with the same criteria then there MAY NOT be enough difference between these evolving strains to really reap the benefits of of the Tru-Line goal?
risk of what?

Fixing (making homozygous) a trait/observation (chose your own word) that does not fit towards the ideal of the strain developer.
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PostSubject: Re: genotype evaluation   Wed Nov 17, 2010 2:25 pm

MKeeney wrote:
RobertMac wrote:
MikeK wrote:
...will you cull linebreds that don`t measure up to the average or expected phenotype of the herd?
This is where I get lost. Everything I read by Dr. Bonsma, he eventually brings in the endocrine system, the nervous system, and total environment and talks of the different pathways by which they influence morphology of the genotype. How do you ever know what the "expected phenotype" is until your cattle are well adapted to their environment? How do you know when they are well adapted?

I think I understand that neither of those questions can be answered if genetics are continually being changed.

That's why I asked the question about Larry's cattle(genetics) in your Kentucky environment. If you breed Larry's cows to a bull of Larry's genetics(essentially the same genotype), is there a difference in phenotype of the progeny due to the different environments?
the type is the same...maybe it`s time to question Bonsma a bit...was he a breeder ? or an observer of type? why did both he and lasater put breeds together and re-select a new breed?
Dr. Bonsma developed the Bonsmara breed
Tom Lasater developed the Beefmaster breed
Dr. Ensminger defines a breeder as the person that owns the cow at the time of service and was responsible for selecting the sire.
I guess I'm not sure of who is a "breeder".

I wouldn't have thought that there was enough difference in Wyoming and Kentucky environments to make great changes in phenotype, but that's why I asked. My other question might not have been worded very well, so I'll ask them again...

How does a cattleman ever know what the "expected phenotype" is until his cattle are well adapted to their environment?
How does the cattleman know when they are well adapted?

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PostSubject: Re: genotype evaluation   Wed Nov 17, 2010 4:32 pm

This may be elementary to all, but I think the degree of prepotency expected from an inbred animal is nearly exactly the same as the inbreeding depression observed. If a phenotype of a potential "inbred" parent isn't compromised, then I'd bet the expected inbreeding homozygosity for the genes controlling that phenotye just didn't happen, and the potential parent is not truly inbred for those genes.

If this is right, a breeder interested in linebreeding would first line up the pedigrees, then find the best performers, and be rid of them as potential parents.
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PostSubject: Re: genotype evaluation   Wed Nov 17, 2010 8:12 pm

Mean Spirit wrote:
This may be elementary to all, but I think the degree of prepotency expected from an inbred animal is nearly exactly the same as the inbreeding depression observed. If a phenotype of a potential "inbred" parent isn't compromised, then I'd bet the expected inbreeding homozygosity for the genes controlling that phenotye just didn't happen, and the potential parent is not truly inbred for those genes.

If this is right, a breeder interested in linebreeding would first line up the pedigrees, then find the best performers, and be rid of them as potential parents.

I am not sure that would be considered elementary, I have no experience with seed stock breeding but I would sure like discussion on this “elementary” observation or principal from breeders with experience using unacceptable breeding stock and acceptable breeding stock, with the same line bred pedigree and type depth back 4 generations or better. Then comparing the progeny in groups large enough to determine an average in order to measure consistence of the preferred type...

It sounds about right to me, as I just can’t see having it both ways.

Mean, it's good to have you back...was about to send a search party... Smile
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PostSubject: Re: genotype evaluation   Wed Nov 17, 2010 10:14 pm

RobertMac wrote:
MKeeney wrote:
RobertMac wrote:
MikeK wrote:
...will you cull linebreds that don`t measure up to the average or expected phenotype of the herd?
This is where I get lost. Everything I read by Dr. Bonsma, he eventually brings in the endocrine system, the nervous system, and total environment and talks of the different pathways by which they influence morphology of the genotype. How do you ever know what the "expected phenotype" is until your cattle are well adapted to their environment? How do you know when they are well adapted?

I think I understand that neither of those questions can be answered if genetics are continually being changed.

That's why I asked the question about Larry's cattle(genetics) in your Kentucky environment. If you breed Larry's cows to a bull of Larry's genetics(essentially the same genotype), is there a difference in phenotype of the progeny due to the different environments?
the type is the same...maybe it`s time to question Bonsma a bit...was he a breeder ? or an observer of type? why did both he and lasater put breeds together and re-select a new breed?
Dr. Bonsma developed the Bonsmara breed
Tom Lasater developed the Beefmaster breed
Dr. Ensminger defines a breeder as the person that owns the cow at the time of service and was responsible for selecting the sire.
I guess I'm not sure of who is a "breeder".

I wouldn't have thought that there was enough difference in Wyoming and Kentucky environments to make great changes in phenotype, but that's why I asked. My other question might not have been worded very well, so I'll ask them again...

How does a cattleman ever know what the "expected phenotype" is until his cattle are well adapted to their environment?
How does the cattleman know when they are well adapted?



Interesting point that makes you think...
Personally I prefer to buy cattle that have been born and raised in an enviroment close to mine-- which is why I prefer the Montana/ND/WY/SD folks-- BUT with AI over the last 50 years the genetics on many have been spread everywhere....

We've preferred buying from the years of maternal breeding Taylor has done at Whitney Creek- Greg at Cole Creek- orDeboos at Diamond D type breeding-- who have used/interspersed a mixture of of Wye- Shoshone- Juanada- old Rito- old N-Bar-even some Basin- mostly all bloodlines long used and proven in our country.....

The other day I had a chance to bid on some of Taylors heifers-and since circumstances didn't work out to go to the sale to see the cattle- and knowing and respecting Taylors program- so knew he wasn't going to pawn off a pud or dink-- bid on them only because of the pedigrees and the cow families in their past...

SO- just thinking about the topic of genotypes- and thinking out loud now for the reasons I and/or my son picked these cattle:

I never have saw OCC Prestige in my life-- but knowing what Emblazon (Prestiges paternal grandsire) and Headliner (his sire)- along with another Headliner son- Missing Link has contributed to some cattle in our area- and knowing that Prestiges dam was Emblazons full sister (and a cow that Tim Ohlde told a neighbor was maybe his best ever raised )-- and then the fact that the heifer in questions dam was sired by a Shoshone bull (Shoshone Felix 6310 J O D) which I'd heard praise and raves about once or twice somewhere over the last few years Wink Razz Laughing - and who apparently thrived (and produced daughters/sons) both in our droughted and short grass country- and Mikes fescue country....

The other was a unique bloodline to me-- Octoraro Ballot STO 6 daughter-- which goes back to the old Ballot of Belladrum bull (which I know little about- but respect Sam Wileys breeding program)-- but better was the fact he (Octoraro 6) had two bulls on the maternal side that I knew had done wonders in maternal breeding in our area- Rito 054 GDAR as mgs and Shoshone Viking GD60 as mggs... And on the dams side had Logan of Wye as mgs... Along with a long list of cattle that had came from this part of the country- and pretty well showed what they could do....

I would have bid on all Taylors Bannons (because I think they make great mommas) - but because I have some of his Bannon daughters- and a son which I'm going to use some more- and are starting to wind some tight thought I'd like to see how these new genotypes (which are much the same phenotype) would work into the whole mess.....Then hopefully throw some more Shoshone/Wye/Rito 707/Juanada ALREADY ENVIROMENTALLY PROVEN BLOODLINES back on top of them and see what comes out....And a few years down the line hopefully hit them hard with the Bannon of Wye blood again..

For a couple of years I've really like the looks of the Tender Ten bull- his 5522 pedigree connections- his disposition reports- his BW and CED-- and I have even communicated with the Texas folks that own him---- but what has kept me away from him is the majority of his family history (long term almost one ranch breeding) is Texas enviroment bred- which is a hell of a lot different then Montana enviroment bred which is now looking at 15 BELOW temps by next week..... Wink santa rendeer
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