Inbred selection

What criteria should be used for selection of the inbred? How critical do we need to be on the female's ability.

If you're looking for the most prepotent ones, keep the ones others don't want. If you select the phentypically best ones, I think you are keeping the ones who aren't, in fact, all that homozygous.

Wouldn't that depend on what traits you are trying to concentrate?

I guess so. I'm really just thinking out loud here, but I'd expect that the "keep the depressed phenotype" rule would necessarily be limited to traits that we'd be smart enough to recognize inbreeding depression in, ie traits that are easily measured. And it'd probably be limited somewhat by the number of genes controlling the trait.

Obviously, if you are selecting for one trait, like marbling, you wouldn't gain any prepotency by selecting the parents who are phenotypically depressed in growth. But I'd wager that you wouldn't get far with marbling by picking the highest IMF animals as parents. The theory is that a lack of phenotypic depression indicates a lack of genotypic homozygosity.

Kinda depressing really. Maybe I'm wrong.

Mean Spirit wrote:

I guess so. I'm really just thinking out loud here, but I'd expect that the "keep the depressed phenotype" rule would necessarily be limited to traits that we'd be smart enough to recognize inbreeding depression in, ie traits that are easily measured. And it'd probably be limited somewhat by the number of genes controlling the trait.

Obviously, if you are selecting for one trait, like marbling, you wouldn't gain any prepotency by selecting the parents who are phenotypically depressed in growth. But I'd wager that you wouldn't get far with marbling by picking the highest IMF animals as parents. The theory is that a lack of phenotypic depression indicates a lack of genotypic homozygosity.

Kinda depressing really. Maybe I'm wrong.

Take this for what it is worth:
While in school we were discussing inbreeding and the Prof told a story. There was a hog farmer that heard that inbred hogs were actually superior to non-inbreds so he started inbreeding. He had also heard that inbreeding produced regression so he assumed that the "most regressed appearing" hogs were more inbred so he kept those that appeared to him to be "the most regressed." After several generations he could not understand why his closed herd was so pitiful and difficult breeders. After all they were inbred so they were supposed to be much better than they were.

Added point:
The generation interval of swine is much shorter than cattle. Plus hogs have litters. The above story is about selection. The good part about breeding cattle as compared to hogs is that if the breeder doesn't make appropriate selections the population wont wreck as fast as other species with shorter generation intervals and have multiples at birth.
Try working with mice. The have approximately 8 pups per litter. A female mouse can concieve at 6 weeks of age and the gestation period is 3 weeks.

That farmer had a "definition" problem--- what does "superior" mean?

I think he was probably on the correct track, more or less, for making the most prepotent parents. He just needed to take the next step-- the outcross for the commercial guy- to see it.

Or maybe they were just sorry pigs. How can you tell a sorry pig from a genetic powerhouse pig that is 40% inbred? And even if you could manage to convince yourself that they are powerhouses and notjust sorry, and you could manage to keep them alive and reproducing, how do you sell the product? There's some chance peoplewho visit the herd will be less than impressed. The "pig digest" adwill have someugly pictures. The epds are gonna be abysmal.

Which is why it's a little depressing to think about.

dwight@steadfastbeef.com wrote:

Mean Spirit wrote:

I guess so. I'm really just thinking out loud here, but I'd expect that the "keep the depressed phenotype" rule would necessarily be limited to traits that we'd be smart enough to recognize inbreeding depression in, ie traits that are easily measured. And it'd probably be limited somewhat by the number of genes controlling the trait.

Obviously, if you are selecting for one trait, like marbling, you wouldn't gain any prepotency by selecting the parents who are phenotypically depressed in growth. But I'd wager that you wouldn't get far with marbling by picking the highest IMF animals as parents. The theory is that a lack of phenotypic depression indicates a lack of genotypic homozygosity.

Kinda depressing really. Maybe I'm wrong.

Take this for what it is worth:
While in school we were discussing inbreeding and the Prof told a story. There was a hog farmer that heard that inbred hogs were actually superior to non-inbreds so he started inbreeding. He had also heard that inbreeding produced regression so he assumed that the "most regressed appearing" hogs were more inbred so he kept those that appeared to him to be "the most regressed." After several generations he could not understand why his closed herd was so pitiful and difficult breeders. After all they were inbred so they were supposed to be much better than they were.

Added point:
The generation interval of swine is much shorter than cattle. Plus hogs have litters. The above story is about selection. The good part about breeding cattle as compared to hogs is that if the breeder doesn't make appropriate selections the population wont wreck as fast as other species with shorter generation intervals and have multiples at birth.
Try working with mice. The have approximately 8 pups per litter. A female mouse can concieve at 6 weeks of age and the gestation period is 3 weeks.

Dwight,

Did he use the inbreds to crossbreed?

Keystone wrote:

dwight@steadfastbeef.com wrote:

Mean Spirit wrote:

I guess so. I'm really just thinking out loud here, but I'd expect that the "keep the depressed phenotype" rule would necessarily be limited to traits that we'd be smart enough to recognize inbreeding depression in, ie traits that are easily measured. And it'd probably be limited somewhat by the number of genes controlling the trait.

Obviously, if you are selecting for one trait, like marbling, you wouldn't gain any prepotency by selecting the parents who are phenotypically depressed in growth. But I'd wager that you wouldn't get far with marbling by picking the highest IMF animals as parents. The theory is that a lack of phenotypic depression indicates a lack of genotypic homozygosity.

Kinda depressing really. Maybe I'm wrong.

Take this for what it is worth:
While in school we were discussing inbreeding and the Prof told a story. There was a hog farmer that heard that inbred hogs were actually superior to non-inbreds so he started inbreeding. He had also heard that inbreeding produced regression so he assumed that the "most regressed appearing" hogs were more inbred so he kept those that appeared to him to be "the most regressed." After several generations he could not understand why his closed herd was so pitiful and difficult breeders. After all they were inbred so they were supposed to be much better than they were.

Added point:
The generation interval of swine is much shorter than cattle. Plus hogs have litters. The above story is about selection. The good part about breeding cattle as compared to hogs is that if the breeder doesn't make appropriate selections the population wont wreck as fast as other species with shorter generation intervals and have multiples at birth.
Try working with mice. The have approximately 8 pups per litter. A female mouse can concieve at 6 weeks of age and the gestation period is 3 weeks.

Dwight,

Did he use the inbreds to crossbreed?

No. He did not. He lost so much money in the process he sold the inbreds out of both frustration and financial need.

It bothers me that the mood here has been consumed with regression. Perhaps it also needs to be brought up again that a strain, in order to be useful in a cross, should bring SOME superior traits to the cross that the strain has in a homozygous state. Using a plant breeding example, if one wants to create a hybrid that has both exceptional root strength AND stalk strength then usually one parent is exceptional (and homozygous) for one trait and the second parent is exceptional (and homozygous) for the other trait. Why are some being so consumed with the half empty part of the glass? What if the best way to create a "full glass" is to combine two glasses that are exceptionally half-full. Are we forgetting Gavin Faloon's analogy of two pieces if paper that have holes in them? Are we forgetting Hagedoorn's analogy of two curtains with holes in them? Are we instead being suduced back into the mindset of wanting to "have it all" in one strain that consistantly replicates all of the things we want all if the time?

dwight@steadfastbeef.com wrote:

It bothers me that the mood here has been consumed with regression. Perhaps it also needs to be brought up again that a strain, in order to be useful in a cross, should bring SOME superior traits to the cross that the strain has in a homozygous state. Using a plant breeding example, if one wants to create a hybrid that has both exceptional root strength AND stalk strength then usually one parent is exceptional (and homozygous) for one trait and the second parent is exceptional (and homozygous) for the other trait. Why are some being so consumed with the half empty part of the glass? What if the best way to create a "full glass" is to combine two glasses that are exceptionally half-full. Are we forgetting Gavin Faloon's analogy of two pieces if paper that have holes in them? Are we forgetting Hagedoorn's analogy of two curtains with holes in them? Are we instead being suduced back into the mindset of wanting to "have it all" in one strain that consistantly replicates all of the things we want all if the time?

I have one paper and am waiting conformation of a second paper(Oddly neither are registration papers ) and I plan on crossing them to increase my profit, I certainly don’t think one strain will do it all and if I have come across that way it was unintentional.

What is regression?

Let’s say for example one seed stock provider is focusing on udders and they have a pedigree 15 cows deep of exceptional udders which have been line bred to some degree back 4 generations, the breeder decides they have deep enough pedigree and experience with the cattle, they decide to do a father- daughter flush... The resulting offspring are not as uniform as they were expecting some look more acceptable in the traditional sense of the word then the others...

But one bull calf from the flush is picture perfect the kind they want to put their brand on, thankful for the success they pick him to carry on the strain as they are 20 years into the plan time is critical....

To my way of thinking it would take a unique individual to go against traditional selection and progeny test the more unacceptable offspring against the Top to analysis things unseen....

I realize this example is hypothetical and hence has little merit... best to stick to real experiences but that would eliminate me

Mean Spirit wrote:

That farmer had a "definition" problem--- what does "superior" mean?

I think he was probably on the correct track, more or less, for making the most prepotent parents. He just needed to take the next step-- the outcross for the commercial guy- to see it.

Or maybe they were just sorry pigs. How can you tell a sorry pig from a genetic powerhouse pig that is 40% inbred? And even if you could manage to convince yourself that they are powerhouses and notjust sorry, and you could manage to keep them alive and reproducing, how do you sell the product? There's some chance peoplewho visit the herd will be less than impressed. The "pig digest" adwill have someugly pictures. The epds are gonna be abysmal.

Which is why it's a little depressing to think about.

How can you tell a sorry pig from a genetic powerhouse pig that is 40% inbred?
How can you tell a sorry pig from a genetic powerhouse pig when both are outcrossed? Gavin Falloon bought some hogs to breed because he realized he could see the lifetime production and variation of offspring of a cow in one sow`s litter...anyone yearning to linebreed cattle should start with hogs for some first hand linebreeding experience in a speeded up version. Doesn`t outcrossing confuse proper selection of parent material to the same degree inbreeding does?

It bothers me that the mood here has been consumed with regression. Perhaps it also needs to be brought up again that a strain, in order to be useful in a cross, should bring SOME superior traits to the cross that the strain has in a homozygous state. Using a plant breeding example, if one wants to create a hybrid that has both exceptional root strength AND stalk strength then usually one parent is exceptional (and homozygous) for one trait and the second parent is exceptional (and homozygous) for the other trait. Why are some being so consumed with the half empty part of the glass? What if the best way to create a "full glass" is to combine two glasses that are exceptionally half-full. Are we forgetting Gavin Faloon's analogy of two pieces if paper that have holes in them? Are we forgetting Hagedoorn's analogy of two curtains with holes in them? Are we instead being suduced back into the mindset of wanting to "have it all" in one strain that consistantly replicates all of the things we want all if the time?[/quote]

Anyone honestly breeding knows holes exist...Are you suggesting that the desired traits will be expressed phenotypically in superor fashion in the inbred strain ? Will the root strength of the inbred parent equal the root stength of the plant crossed for root strength AND stalk strength?

MKeeney wrote:

Mean Spirit wrote:

That farmer had a "definition" problem--- what does "superior" mean?

I think he was probably on the correct track, more or less, for making the most prepotent parents. He just needed to take the next step-- the outcross for the commercial guy- to see it.

Or maybe they were just sorry pigs. How can you tell a sorry pig from a genetic powerhouse pig that is 40% inbred? And even if you could manage to convince yourself that they are powerhouses and notjust sorry, and you could manage to keep them alive and reproducing, how do you sell the product? There's some chance peoplewho visit the herd will be less than impressed. The "pig digest" adwill have someugly pictures. The epds are gonna be abysmal.

Which is why it's a little depressing to think about.

How can you tell a sorry pig from a genetic powerhouse pig that is 40% inbred?
How can you tell a sorry pig from a genetic powerhouse pig when both are outcrossed? Gavin Falloon bought some hogs to breed because he realized he could see the lifetime production and variation of offspring of a cow in one sow`s litter...anyone yearning to linebreed cattle should start with hogs for some first hand linebreeding experience in a speeded up version. Doesn`t outcrossing confuse proper selection of parent material to the same degree inbreeding does?

Porcine Genetic Powerhouses from inbred populations. Nearly all candidates for this honor come from plain jane females that were not at the top of the class. Matter of fact they were usually retained to fill a production quota. Currently I concentrate most of my efforts on the Berkshires due to demand. The emerging top sire is a product of just such a female. This pig (24-10) was from an exceptional litter from which 2 littermate males were selected by breeders looking for more complete (mature looking) individuals. When you apply these experiences to the latest hot AI promoted bull one can not be surprised when they fall on their ass. Difficult concepts to comprehend when you have been told from day one that "Like begets like". MikeL

What I was thinking mike... The best root strength parents are gonna be the ones who are homozygous for the genes that control root strength to be sure-- but are they phenotypically the ones with the strongest roots? I think what we know about heterosis suggests otherwise- the best ones at many traits are probably not homozygous, no matter what their pedigree says.

My thinking has always been linebreed the pedigrees, then select the "best" ones as parents to move on- if I got a half sib mating that was awesome phenotypically, I win!! I get my inbreeding for consistency and I get cattle I want to be around. But I'm thinking that phenotypically superior inbred animal might in fact be a failure genetically.

So tell me again-- how do you select inbred parent stock? Picking the poor ones really does seem like a pretty bad way to proceed- maybe as bad as picking the best ones. Hilly's progeny test would work, but that is some kind of slow. All of this is making me reevaluate my skepticism about genomic testing for those traits that are available. Combining genomc test results with selection might be a way to ID parents with specific genes that are also phenotypically acceptable.

And another question- Epds are based largely on collections of contemporary group data from an animal, his progeny, and his pedigree relatives. If any of this stuff I'm writing is right, aren't epds seriously flawed, to the point of being nearly useless?

Mean Spirit wrote:

What I was thinking mike... The best root strength parents are gonna be the ones who are homozygous for the genes that control root strength to be sure-- but are they phenotypically the ones with the strongest roots? I think what we know about heterosis suggests otherwise- the best ones at many traits are probably not homozygous, no matter what their pedigree says.

My thinking has always been linebreed the pedigrees, then select the "best" ones as parents to move on- if I got a half sib mating that was awesome phenotypically, I win!! I get my inbreeding for consistency and I get cattle I want to be around. But I'm thinking that phenotypically superior inbred animal might in fact be a failure genetically.

So tell me again-- how do you select inbred parent stock? Picking the poor ones really does seem like a pretty bad way to proceed- maybe as bad as picking the best ones. Hilly's progeny test would work, but that is some kind of slow. All of this is making me reevaluate my skepticism about genomic testing for those traits that are available. Combining genomc test results with selection might be a way to ID parents with specific genes that are also phenotypically acceptable.

And another question- Epds are based largely on collections of contemporary group data from an animal, his progeny, and his pedigree relatives. If any of this stuff I'm writing is right, aren't epds seriously flawed, to the point of being nearly useless?

If you compare this corn, yes epds can be usuless. Remember the final harvest is the "fruit". i.e. the black baldy steer. MikeL

I'm probably being too cynical, but it seems to me that most "linebreeders" are getting this wrong. Inbreeding followed by culling the unacceptable phenotypes- big percentages of the crop, they all say, must be culled- aren't they taking one step forward, then two steps back?

And taking the steps metaphor a little further, when is the linebreeders journey finished?

Honestly, we all know how to make nice cattle. Mike L, I think it is, roughly, like begets like, keeping the pedigrees fresh, keeping inbreeding pretty low, Cull the ones that didn't work out, feed them well. But making cattle that are actually better for the commercial cattleman? That's a tricky mother. It really is.

Mean Spirit wrote:

What I was thinking mike... The best root strength parents are gonna be the ones who are homozygous for the genes that control root strength to be sure-- but are they phenotypically the ones with the strongest roots? I think what we know about heterosis suggests otherwise- the best ones at many traits are probably not homozygous, no matter what their pedigree says.

My thinking has always been linebreed the pedigrees, then select the "best" ones as parents to move on- if I got a half sib mating that was awesome phenotypically, I win!! I get my inbreeding for consistency and I get cattle I want to be around. But I'm thinking that phenotypically superior inbred animal might in fact be a failure genetically.

So tell me again-- how do you select inbred parent stock? Picking the poor ones really does seem like a pretty bad way to proceed- maybe as bad as picking the best ones. Hilly's progeny test would work, but that is some kind of slow. All of this is making me reevaluate my skepticism about genomic testing for those traits that are available. Combining genomc test results with selection might be a way to ID parents with specific genes that are also phenotypically acceptable.

And another question- Epds are based largely on collections of contemporary group data from an animal, his progeny, and his pedigree relatives. If any of this stuff I'm writing is right, aren't epds seriously flawed, to the point of being nearly useless?

MS, ...DNA holds the key to hasten the process of homozygousity evaluation; other wise, trust ancestry and breed it...why the hell keep pedigrees if you only trust the phenotype standing in front of you.
epd`s; even dna enhanced epds, are a measure of averages; useless to breeders seeking to minimize the spread of variation in progeny

Mean Spirit wrote:

I'm probably being too cynical, but it seems to me that most "linebreeders" are getting this wrong. Inbreeding followed by culling the unacceptable phenotypes- big percentages of the crop, they all say, must be culled- aren't they taking one step forward, then two steps back?

And taking the steps metaphor a little further, when is the linebreeders journey finished?

Honestly, we all know how to make nice cattle. Mike L, I think it is, roughly, like begets like, keeping the pedigrees fresh, keeping inbreeding pretty low, Cull the ones that didn't work out, feed them well. But making cattle that are actually better for the commercial cattleman? That's a tricky mother. It really is.

The line breeders journey is never finished. My plans for future genetic exploits are to retain all the females and let the results influence the next steps. Indexes and visual appraisals do not tell one the degree or level of homozygosity or the the concentration of genes responsibile for the expression of specific l traits. Hopefully as dna research progresses we can better understand and evaluate the individual profiles. MikeL

MKeeney wrote:

Mean Spirit wrote:

What I was thinking mike... The best root strength parents are gonna be the ones who are homozygous for the genes that control root strength to be sure-- but are they phenotypically the ones with the strongest roots? I think what we know about heterosis suggests otherwise- the best ones at many traits are probably not homozygous, no matter what their pedigree says.

My thinking has always been linebreed the pedigrees, then select the "best" ones as parents to move on- if I got a half sib mating that was awesome phenotypically, I win!! I get my inbreeding for consistency and I get cattle I want to be around. But I'm thinking that phenotypically superior inbred animal might in fact be a failure genetically.

So tell me again-- how do you select inbred parent stock? Picking the poor ones really does seem like a pretty bad way to proceed- maybe as bad as picking the best ones. Hilly's progeny test would work, but that is some kind of slow. All of this is making me reevaluate my skepticism about genomic testing for those traits that are available. Combining genomc test results with selection might be a way to ID parents with specific genes that are also phenotypically acceptable.

And another question- Epds are based largely on collections of contemporary group data from an animal, his progeny, and his pedigree relatives. If any of this stuff I'm writing is right, aren't epds seriously flawed, to the point of being nearly useless?

MS, ...DNA holds the key to hasten the process of homozygousity evaluation; other wise, trust ancestry and breed it...why the hell keep pedigrees if you only trust the phenotype standing in front of you.
epd`s; even dna enhanced epds, are a measure of averages; useless to breeders seeking to minimize the spread of variation in progeny

How much are the variation of progeny of inbreds reduced compred to non-inbred lines?

df wrote:

MKeeney wrote:

Mean Spirit wrote:

What I was thinking mike... The best root strength parents are gonna be the ones who are homozygous for the genes that control root strength to be sure-- but are they phenotypically the ones with the strongest roots? I think what we know about heterosis suggests otherwise- the best ones at many traits are probably not homozygous, no matter what their pedigree says.

My thinking has always been linebreed the pedigrees, then select the "best" ones as parents to move on- if I got a half sib mating that was awesome phenotypically, I win!! I get my inbreeding for consistency and I get cattle I want to be around. But I'm thinking that phenotypically superior inbred animal might in fact be a failure genetically.

So tell me again-- how do you select inbred parent stock? Picking the poor ones really does seem like a pretty bad way to proceed- maybe as bad as picking the best ones. Hilly's progeny test would work, but that is some kind of slow. All of this is making me reevaluate my skepticism about genomic testing for those traits that are available. Combining genomc test results with selection might be a way to ID parents with specific genes that are also phenotypically acceptable.

And another question- Epds are based largely on collections of contemporary group data from an animal, his progeny, and his pedigree relatives. If any of this stuff I'm writing is right, aren't epds seriously flawed, to the point of being nearly useless?

MS, ...DNA holds the key to hasten the process of homozygousity evaluation; other wise, trust ancestry and breed it...why the hell keep pedigrees if you only trust the phenotype standing in front of you.
epd`s; even dna enhanced epds, are a measure of averages; useless to breeders seeking to minimize the spread of variation in progeny

How much are the variation of progeny of inbreds reduced compred to non-inbred lines?

CONSIDERABLE...wait a second...how do you get a non-inbred line?

MikeK wrote:

epd`s; even dna enhanced epds, are a measure of averages; useless to breeders seeking to minimize the spread of variation in progeny

EPDs point you in a direction, but they don't tell you if you're on the right road to get where you want to go.
EPDs do not equal genotype
My opinion.

Can you "have it all" if all you want isn't too much?

Dr. Bonsma wrote:

So our steps are...first of all, getting adaptability; secondly, to get functional efficiency; next, to get metabolic efficiency--the animal that can convert its feed into an end product in a most efficient way.

RobertMac wrote:

MikeK wrote:

epd`s; even dna enhanced epds, are a measure of averages; useless to breeders seeking to minimize the spread of variation in progeny

EPDs point you in a direction, but they don't tell you if you're on the right road to get where you want to go.
EPDs do not equal genotype
My opinion.

Absolutely. EPDs are a measurement of the expression of the genotype. They are by definition phenotypes, not genotypes.

RobertMac wrote:

Can you "have it all" if all you want isn't too much?

Would that be considered enough

MKeeney wrote:

DNA holds the key to hasten the process of homozygousity evaluation; other wise, trust ancestry and breed it...why the hell keep pedigrees if you only trust the phenotype standing in front of you.

I find this to be a good point, Larry often reiterates the importance of the ancestry, making this is a long process ...

"As always, intimate familiarity of the ancestry is very important"

"It is unimportant as to how far any of us get, it is only the continuation of the constant direction that counts."

This makes sense to me:

“I have come to believe the phenotypic selection criteria self-governs the level of inbreeding or degree of prepotency; that production levels are self-governed by the environment; that milk levels and carcass values are self-governed by their effect on composition and that composition has the greatest impact on functional reproductivity. So improving prepotency of composition once identified seems to be ‘priority 1′ at ANY preferred production level.” - Larry Leonhardt

I had to start this post because things seemed to stray from it a bit.