Shikoku Genome Sequencing

the_november_rainthe_november_rain
edited January 2012 in Shikoku Ken (四国犬)
Genome sequencing has been touched upon before in reference to shikokus. Money aside, I was wondering if someone could clarify the overall benefits or advantages of getting the genome sequencing of the shikoku.

Comments

  • NWshibanutNWshibanut
    Sequencing the genome might allow us to better understand the genetic diversity (or lack thereof) in the Shikoku gene pool. It could possibly identify which deleterious genes are present in high frequency, and allow breeders to select against them, or breed them out through selective outcrossings.
  • dlrobertsdlroberts
    To add to that, it allows for extensive genetic testing, so as perfect a picture of an individual dog's health that is scientifically possible can be painted. Unfortunately, even with a complete sequencing there will still be unknowns as there is still a lot to learn about how specific gene variants lead to specific diseases or specific genetic traits. But, with a record of a dog's genome, as more and more information about gene variants and diseases becomes available, a more detailed picture of each dog's contribution to their progeny can be painted.

    Even with the unknowns, having a complete genome sequence allows breeders to select breedings that will serve a specific purpose. For example, it will enable them to determine the pair with maximally different genomes, or identify a line that carries a variation in some genes that isn't present in their lines.

    Basically, it would allow breeders to come as close as scientifically possible to knowing exactly what a breeding will contribute to the gene pool.
  • CrimsonO2CrimsonO2
    Gattaca!!!

    Jesse
  • ttddinhttddinh
    Adding to dlroberts' comments, it also has been used as a tool to map mutations. In arabidopsis, a mustard plant with only 5 chromosomes, there are still problems with mapping a mutation when a phenotype is contribute by more than one loci ( more than one genetic mutation). So what we have done is do whole genome sequencing for 5-10 plants and compare the genome-wide sequences for all plants and using statistical analyses, identify mutations that are common in all 10 plants that have the same mutated phenotype. In the case of Shikoku or any other breed, if we had a mapping population of say 10-20 dogs and they all have hip dysplasia or some other phenotype we are interested in, we could potentially identify those genes responsible for that phenotype. It's a very powerful tool.
  • BradnJessBradnJess
    edited January 2012
    Not to pull the discussion too far off track (and anyone who is more well-versed in genetics than I am [biologically speaking, I don't usually study farther than the brain] please correct me), but SNP (single nucleotide polymorphisms) genotyping, to my understanding, is a more economical and efficient way to look at the genetic diversity of a population. This genotyping typically only looks at, in most populations, far less than 1% of of the genome - the proportion of which SNPs make up of the genome. What is important, however, is that SNPs are largely responsible for genetic variation (anybody correct me here if I'm wrong, my course in adaptability is now a while back) and are, at least in human populations, related to a significant proportion of diseases relative to other genetic material.

    I just bring this up because, if this is a serious consideration for the preservation effort, it seems important to have something economical enough to justify spending money on a genetic test vs. an import. Last quote I heard for genome wide sequencing, the price would make you vomit. However, my anthropology professor was talking about the liklihood that it may be reduced to a much more affordable price for scholarly use (he hopes in the range of $300 - 500 per). I'm not sure about what how pricing would be for commercial use, however. :(

    Again, disclaimer: NOT a student of biology, correct me if I am wrong.
  • aykayk
    Maybe people could explore this as an alternative:

    http://www.wisdompanel.com/optimal_selection/

    http://www.wisdompanel.com/assets/1/7/canine_chronicle.pdf

  • ttddinhttddinh
    When I was advocating for whole genome sequencing, I was doing it purely from the standpoint of using technology to its fullest and asking questions/designing experiments that will most likely to get funded (by a grant agency). Furthermore, I was going in with the mindset that the mapping population is small (less than 50). There are certainly advantages and disadvantages to both methods.

    SNPs

    1) Have been shown to be implicated in diseases and since they are usually conserved, they could be used to study variation.

    http://jhered.oxfordjournals.org/content/98/5/428.full

    SNP overview http://w.nslij-genetics.org/ld/hirschhorn05.pdf

    2) SNP analysis is cheaper than whole genome sequencing

    3) whole genome SNP analysis could be done
    http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010809

    4) However, SNP analysis only provide a snapshot of the whole genome (as you said @BradNJess, it represents only 1% of the genome)

    5) No matter how much one claims about the grandeur of SNPs, there are other factors involved in disease and genetic variation.

    6) Have SNPs been shown to be linked to hip dysplasia? I thought some genes have been preliminarily identified. Please correct me if I am wrong, I don't keep up with canine genetics.

    Whole genome sequencing

    1) The bad thing: it relatively expensive

    2) It can be done and would provide a vast amount of information that could be mined

    3) Bioinformatic analyses take A REALLY LONG TIME.

    To be quite honest though, we would be VERY hard-pressed to fund this ourselves. It would get REALLY expensive. @BradNJess, I hope I answered some of your concerns, if not, please let me know, perhaps over the weekend, I would have more time to clarify things. :)




  • the_november_rainthe_november_rain
    @ttddinh -how long does it take?
  • ttddinhttddinh
    @the_november_rain--How long does what take?

    If it is the bioinformatic analyses, it depends on the person and what it is that you want them to do. If they are busy it could take 4-5 months, if they are not, a couple of weeks.
  • hotarujishinhotarujishin
    edited March 2012
    Or you might use this:
    http://www.genoscoper.com/in_english2/gene_tests/gene_tests/dla_diversity/

    The cost is far less than genome sequencing, I would think.
    The price list is there.
  • lwrothlwroth
    I'd be really excited about it if I had a rare breed with small numbers and had a chance to see their genetic profile. I sent a canine geneticist an abstract of the recent Japanese study on aggression in Japanese Akita males--Androgen receptor gene polymorphisms are associated with aggression in Japanese Akita Inu.
    Konno A. Inoue-Murayama M. Hasegawa T.
    Biology Letters. 7(5):658-60, 2011 Oct 23.
    UI: 21450727--and he commented looking at a single gene for a relationship wasn't so good as looking at the whole genome and proposed a study with 50 aggressive Akita males and 50 non-aggressive males. I don't think it will work out, hard to get samples for one thing, but we have a vet behaviorist who's also an Akita breeder who was willing to help with a definition of "aggression" for the study. I hope in the not far future we can do something further in looking at autoimmune diseases in Akitas, something like the project now being finished with Poodles,
  • lwrothlwroth
    When I post a URL I cut and pasted from a Safari window, it ends up a lot longer and more confusing. I don't know if I'm doing something wrong, and I don't know if people can look at the linked pages if they want to.
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