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Re: [SANET-MG] MAS and organics



Hello Dale,
This discussion is not going anywhere. I will make a few comments below then leave it for good! sincerely,Joe Cummins
Dale Wilson wrote:
Joe,


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.


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!


Well, Joe, sometimes reality is unpleasant!  These quantitative genetic
models are over-simplifications, limiting cases.  Most real-life
breeding problems do not hinge on very large numbers of genes.  In
situations where a few genes are important (pest resistance, quite
often) marker-assisted selection for QTL's is efficient.
ans: the reference I provided , the 2005 science article, showed that major traits such as oil in maize and size in chickens are determined by very many genes each contributing very small amounts. In such cases , maybe , the most important commercial traits MAS is not cost effective, patient selection works.


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 linkage disequilibrium.
ans: as I pointed out earlier tight linkage of QTL is far less commonplace than unlinked or loosely linked QTL.


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.


Precisely! The greater the linkage disequilibrium, the better MAS works
(or appears to work, depending on your objective).  The "QTL's"
elborated in such a situation may be only localized tools not useable
in general in the species.  But, suppose your job were to transfer
soybean cyst nematode resistance into a thousand lines of US maturity
group IV soybeans, ASAP.
ans: tight linkage is nice if you can get it but it is not usual,.

Dekker has a nice easy-to understand paper that explains the linkage
equilibrium issue in marker-assisted selection:
http://jas.fass.org/cgi/content/full/82/13_suppl/E313


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.


Commercially the objective is not to "study QTL's" the objective is to
make rapid genetic progress.
ans: I would think that one major goal of a breeding program is not to squander corporate or government funds on a MAS breeding program that is not cost effective because there are many QTL each contributing small amounts.That is the way it works in thew real world. If you are advising your company the area of QTL they are certain go broke really fast! Or is that your intention?

Here are some links to additional background information:
http://www.leafyvegetables.nl/download/21_125-130_Peleman.pdf
http://www.cropscience.org.au/icsc2004/symposia/3/4/133_schmidtdh.htm
http://www.animalgenome.org/edu/QTL/Julius_notes/15_basics_mas.PDF
http://www.animalgenome.org/edu/MAS/Dekkers/PAGVII/
http://www.fao.org/biotech/logs/C10/summary.htm

Dale

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