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Offline knabe

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cow genome
« on: April 23, 2009, 03:59:37 PM »
http://www.genomeweb.com/node/915449?emc=el&m=370499&l=2&v=aea3af4a27

The resulting assembly has around 91% of the assembled genome anchored onto chromosomes.

when human was first announced finished with clinton, blair, francis collins,and the dude from celera, i think it was 95% finished.  human is over 99.5% finished.

not sure yet what they mean when they say anchored.  in a worse case scenario, it could mean the reads are anchored onto 30 chromosomes with further editing and resequencing to be done, best case, is that 91% is really done.  this leaves vast gaps for repeats such as huntingtons in human which wasn't unraveled till a repeat area was discovered in assembly.

"The team's analyses also suggest that the cattle genome has undergone numerous rearrangements, spurred by repetitive elements and duplications such as segmental duplication, retrotransposons, and retroviral long terminal repeats. For example, they found 1,020 segmental duplications involving more than three percent of the genome. and with these duplications sometimes occuring in areas that are harder to tease out through the sequencing data assembly process, there will be more.

In particular, the cattle genome contained duplications in genes involved in immune function, olfactory receptors, reproduction, lactation, and digestion. Ten immune system-related genes were also among the 71 genes under positive selection in the domestic cow genome."

positive selection increases the prevalence of adaptive traits.  meaning man can influence this through selection without knowing it.

"The bovine HapMap data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation," University of Missouri researcher Jerry Taylor, who was part of the Bovine HapMap team, said in a statement. "The recent decline in diversity is sufficiently rapid that loss of diversity should be of concern to animal breeders."  NO KIDDING.

with such recent relative inbreeding in several breeds including angus, hereford, maine anjou, it's pretty clear, at least to me, there are obvious opportunities/problems and not just from a defect perspective.
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Offline knabe

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Re: cow genome
« Reply #1 on: April 23, 2009, 04:07:53 PM »
thought i would add this reference as well.

http://news.bbc.co.uk/2/hi/science/nature/6749213.stm

Dr Hubbard said: "We are now seeing the majority of the rest of the genome is active to some extent."

He explained that the study had found junk DNA was being transcribed, or copied, into RNA - an active molecule that relays information from DNA to the cellular machinery.

He added: "This is a remarkable finding, since most prior research suggested only a fraction of the genome was transcribed."

'Complex picture'

Dr Birney added that many of the RNA molecules were copying overlapping sequences of DNA.

He said: "The genome looks like it is far more of a network of RNA transcripts that are all collaborating together. Some go off and make proteins; [and] quite a few, although we know they are there, we really do not have a good understanding of what they do.

"This leads to a much more complex picture."

The researchers now hope to scale up their efforts to look at the other 99% of the genome.

I have always thought this to be the case.
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Offline HerefordGuy

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Re: cow genome
« Reply #2 on: April 24, 2009, 01:13:24 AM »
Knabe,
Your statement "
positive selection increases the prevalence of adaptive traits.  meaning man can influence this through selection without knowing it"
confuses me.  Are you implying that this is a problem?  If so, I kindly disagree.

If you read the actual report, it is clear that the positive selection they are discussing is happening over millions of years on an evolutionary time scale, not likely due to artificial selection by humans.  This selection may be do to ruminants having a rumen filled with microbes, or from the fact that they live in herds and diseases are easily passed between individuals. 

But, humans not knowing what genes they are affecting by selection has been occurring since cattle were domesticated 10,000 years ago.  In fact, in order for a species to be domesticated, its genome must be altered in order that it will be docile enough to live with man.  When you use EPDs to make selection decisions, you do not know the genes underlying that EPD, but the EPD still works with out problems.  Hope this clarifies. 

This is such an exciting day for the cattle community.  Thanks for starting this post!  With this new resource, mutations causing genetic deficts, such as Curly Calf, can be identified much more rapidly.  The dairy industry is already using genomic breeding values, and in time the beef industry will follow.  This means that we will know a calf's breeding value based on a DNA profile, rather than waiting years to record his progeny performance.  This resource and the technologies that come from it will revolutionize the industry the same way EPDs, AI and ET have in the past. 
 (clapping)

Offline HerefordGuy

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Re: cow genome
« Reply #3 on: April 24, 2009, 01:22:33 AM »
Knabe,
To reply to some of your other comments:
The University of Maryland has made a separate assembly of the genome that appears superior to Baylor's.  The genome reference sequence will continue to be improved upon and refined.

I think that as cattle breeders, it is very important that we try to keep inbreeding at low levels.  We still need to use all of the technology available such as EPDs, AI and ET, but we need to make sure that we are using a diverse set of high quality cattle.  My understanding of the Curly Calf situation is that it was discovered by a rancher doing lots of father-daughter matings.  Never a good idea.

Offline knabe

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Re: cow genome
« Reply #4 on: April 24, 2009, 09:53:37 AM »
Knabe,
Your statement "
positive selection increases the prevalence of adaptive traits.  meaning man can influence this through selection without knowing it"
confuses me.  Are you implying that this is a problem?  If so, I kindly disagree.  i'm saying it can be a problem. selection for performance or other traits, could come at the expense of environmental adaptivity.  i wonder what the dystocia rate of wildebeasts is?  i wonder what it would be under selection pressure for depth of body, spring of rib, straight hocks, level hips, more bone, more hair, smaller head, polled, more rear, more sogginess, zipper fronted, rocket fronted, gain on grass, gain on grain.  i wonder if parasite resistance, behavior such as migration in response to stimuli such as fly season is changed by performance selection.


If you read the actual report, it is clear that the positive selection they are discussing is happening over millions of years on an evolutionary time scale, not likely due to artificial selection by humans.  This selection may be do to ruminants having a rumen filled with microbes, or from the fact that they live in herds and diseases are easily passed between individuals.  yes, it is clear, but the bottlenecks created in the last 200 years have decreased diversity as evidenced in the difference in diversity between indicus and taurus, with taurus under more recent bottlenecking and the removal of large segments of millions of years of selection.  are you referring to microbe diversity in the rumen, or diversity within the microbe genome.  there isn't much and it's difficult to influence, select for change in that.  worked with a guy who's Ph.D. was specifically that.

But, humans not knowing what genes they are affecting by selection has been occurring since cattle were domesticated 10,000 years ago.  In fact, in order for a species to be domesticated, its genome must be altered in order that it will be docile enough to live with man.  When you use EPDs to make selection decisions, you do not know the genes underlying that EPD, but the EPD still works with out problems.  Hope this clarifies.  if you read courageous cattlemen and responses to that direction, you will know that EPD's do not come without problems.  i'm confused, other than domestication, which seems to be able to happen more quickly in some species than others, that if man simply picked out the easiest to domesticate way back in the day, they were picking out the animals that required on average, the least genetic change for domestication.  it's not like they said, hey, lets make a controlled experiment, pick a diversity of animals that have various aversions to us.

This is such an exciting day for the cattle community.  Thanks for starting this post!  With this new resource, mutations causing genetic deficts, such as Curly Calf, can be identified much more rapidly.  The dairy industry is already using genomic breeding values, and in time the beef industry will follow.  This means that we will know a calf's breeding value based on a DNA profile, rather than waiting years to record his progeny performance.  This resource and the technologies that come from it will revolutionize the industry the same way EPDs, AI and ET have in the past.  since i work for a company that is using genetic profiles, there is a danger there in that it is difficult to say do you have proof of absence of disease or just proof of no presence of disease or whatever trait you are working on in the opposite orientation for say a positive trait.


which genetic changes have bottlenecked the genome the most?  domestication, EPD's.  evolutionary time scales are compressed by selection, or the equivalent of bottlenecking and creating essentially land races.  human selection can and does overcome establishing heterozygosity.

more later.
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Offline HerefordGuy

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Re: cow genome
« Reply #5 on: April 24, 2009, 10:34:01 AM »
With domestication, humans now provide the environment for cattle.  So, cattle only have to fit the environment supplied by their owners. 

I think you and I would agree that we need to be careful in selecting extremes for aesthetic purposes.

The HapMap paper says indicus were domesticated from a population that was more diverse.  Indicus were more diverse even before domestication.
I was referring to the fact that early ruminants evolved a large sac in their bodies filled with potentially harmful microbes.  Ruminants need to support the "good" microbes and fend off the "bad" microbes.

I believe you and I agree that inbreeding should be a concern to producers.

During domestication, early herdsman picked the most docile of the wild auroch.  But these were still wild.  These first cattle then had progeny.  The progeny then had a distribution of temperment, from wild to docile.  The early herdsman then selected the most docile of the progeny.  Thus, they were selecting for temperment.  If a species, such as auroch, has tens of thousands of animals, and you domesticate a few hundred animals, that is a much more sever bottleneck then caused by selection for EPDs.  See fig 2 of HapMap paper.

http://www.sciencemag.org/cgi/content/full/324/5926/528

I feel that the HapMap paper showed that current levels of diversity are higher than expected and at the moment are fine.  The problem comes when breeders are not concerned with inbreeding and diversity is substantually decreased.

Article on genomic breeding values

http://genex.crinet.com/page2348/Genomics1

Offline knabe

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Re: cow genome
« Reply #6 on: April 24, 2009, 11:18:46 AM »

Article on genomic breeding values

http://genex.crinet.com/page2348/Genomics1


50% is random.  working for a company with 80% on coronary heart disease at 80%, this still isn't that great, although a great improvement over current guesses.

i'd still rather have markers in the trait or regulatory element as links can be broken very easily from personal knowledge in lettuce, especially if you are making divergent crosses.
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Offline knabe

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Re: cow genome
« Reply #7 on: April 24, 2009, 04:53:13 PM »

I feel that the HapMap paper showed that current levels of diversity are higher than expected and at the moment are fine.  The problem comes when breeders are not concerned with inbreeding and diversity is substantually decreased.


would like to see experiment repeated with DNA from taurine breeds from 50, 100 and 200 years ago vs inducus and see if minor allele frequencies are the same.  would also be interesting to see if any cattle are found preserved in peat bogs and other preservation sites.

also, the mutation rate comments are misleading as cows don't have wars eliminating vast swaths of the population.  they obviously do have disease, but not cities and this could account for snp rates/bp.

also, cattle domestication could have been a novelty, started with different numbers of animals in different areas of the world, rather than heavy selection pressure in the beginning, essentially, a form of line breeding from the beginning similar to dogs, but allowed to accumulate snps rather than decrease them by adding to the population as cattle raising became successful but the major allele frequencies were somewhat more fixed, but not by selection.

oh well.
« Last Edit: April 24, 2009, 04:59:53 PM by knabe »
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