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Re: [SANET-MG] MAS and organics



Dale Wilson wrote:
Hi Joe,


RA Fisher first described quantitative traits (QTL) and theorized
that the QTL mainly added minute additive contributions to size,
etc.


Well, "quantitative trait" and "quantitative trait loci" are not quite
the same thing.
ans: Your point is peculiar, Fisher described QTL as I said.


The big discussion in MAS now is about the cost ineffectiveness
of MAS when Fisher's rule applies, there a are very many minute
contributions.


These quantitative, statistical models were used by Hardy and Weinberg
and by Fisher because they are simple and elegant.  But you can't take
them too seriously.  Given a little environmental interaction even 2-3
segregating loci produce enough phenotypes that they look like many
genes, and can fit the classic quantitative genetic models.
ans: Please excuse me but Hardy-Weinberg is fundamental and it is still valid. Fisher's methods and theories are still valid and discussed. I think your comment is just grotesque! without merit!


Yet, even when there *are* many genes affecting a trait, QTL analysis
often identifies a few major QTL's.  Yeah, they may be artifacts that
disappear with more data.  But these QTL's can *still* work in practice
for two reasons: 1) narrow genetic context and disequilibrium.
ans:Linkage disequilibrium
Linkage disequilibrium is often termed "allelic association." When alleles at two distinctive loci occur in gametes more frequently than expected given the known allele frequencies and recombination fraction between the two loci, the alleles are said to be in linkage disequilibrium. Evidence for linkage disequilibrium can be helpful in mapping disease genes since it suggests that the two may be very close to one another.
Source : PhRMA Genomics

The issue in MAS is mainly the strength of (quality) of QTL and their number. Professionals generally agree that many QTL each with minute contribution cannot be cost effectively studied by MAS. Use of MAS in such cases is fruitless.

The population at hand is genetically narrow in many breeding
situations.  There may be many genes involved in a trait species-wide,
but most are fixed in the population.
ans: Please excuse, but that statement does not make sense?

Commercial breeding populations tend to be very far from linkage
equilibrium.  The old quantitative genetic models assume linkage
equilibrium.  Breeders in practice are not selecting genes, but
relatively large chunks of chromosomes.  This is where QTL's shine.
ans: Not really, not at all!


Regarding Wytze's point about patents, I believe the markers can be patented but the linked loci are separate. Plant patents may be
acquired using MAS but those patents are no different from the
current plant patents, I think.


I think Wytze's point was that all these high-tech, gee-whiz methods
promote the issuance of *utility patents* on plants.  I don't think you
can patent markers per se, because they are just features that
naturally occur on the chromosome.  One has to invent something to get
a patent.
ans: Traditionally, plant patents never invented, they selected. The invention lies in the breeders eye and mind, not in the crop plant.


If courts were fair and honest MAS would block patents because
the QTL are in wild populations. However, it  is clear that
courts are neither fair nor honest , so all bets are off.


A great deal of effort goes into finding and assembling all the genetic
pieces into useful crop (and animal) varieties.  Don't you think that
breeders should be able to protect their inventions from people who
would steal them?  I am not sure if utility patents are the best way to
do this, in part, because patenting is too expensive for ordinary folk.
 I would rather see use of the PVP.
ans: It is hard to see where MAS causes more plant patents than does traditional selection, except in the outlay of operating expenses for MAS which may prompt more pressure to provide plant patents.

Dale
Finally,
It was nice, but strange, to hear from you. I think your genetic theories are different from anything in the real world. However, I hate to interfere with you flights of fantasy. sincerely,Joe Cummins

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