From: toby@milton.u.washington.edu (Toby Bradshaw)
Subject: Re: plant phys use in breeding
Organization: University of Washington, Seattle
Date: Fri, 11 Sep 1992 15:55:37 GMT

>Steve Modena
>re: RAPDs and Ron Sederoff
>Keith Robison made a similar recommendation months ago.  
>Whooten in that lab has a BitNet account and knows about bionet.
>My email to them has not been treated with a courtesy of a reply.  ;^)

Probably Ross don't realize his name has been changed from
"Whetten" to "Whooten".

>What one "knows" via propaganda versus what one hears in the 
>hallways is often quite a contrast.  I stand on my skepticism.
>No one better than Sederoff's lab to explain specifics to
>enquiring minds.

Could be that they're too busy doing science instead of
just talking about it :)

>Ron Sederoff's telephone number is:  1-919-515-7800 and no email
>address listed in the 1991-92 Campus Telephone Directory.  Go ahead:
>call them and invite them to engage.

I don't really need to call Ron, since I see him every couple
of months at some meeting or other.  I've talked at length with
him in the past three weeks, and one of his students was here
in Seattle a couple of weeks ago.  I suggest that you might
offer to buy Ron lunch, and find out for yourself what they're
doing.  Ron has an email address but never reads it.

>tb>...found a RAPD linked to the "nectarine" phenotype in peach.
>
>I sat in a seminar here a month ago and the visiting-scientist
>said that RAPDs are good for the particular set of plants
>being investigated.  Switch the genetic composition of the
>plants under investigation and you can throw your RAPDs primers
>away and start the search over......I don't do this stuff, I just
>watch the one who do.

Whether markers linked to a trait in one pedigree will be
informative in other pedigrees depends on many things, like
whether the population is in linkage equilibrium, how often
the mutation ("tangerine") has arisen in peaches, how many
loci can produce "tangerine" phenotypes, how tightly the
marker is linked, and how much polymorphism exists in the
peach breeding population.  Some markers, like the
Huntington's disease RFLP in humans, are applicable
across all pedigrees because the disease seems to have
arisen only once in human history and the marker is fairly
tightly linked.  Thus, while the conservative approach
is to assume that a given marker may be informative only
in the original mapping pedigree, it is not always so.
There are many ways to get around the problem of
linkage equilibrium; the ultimate is to walk to the
gene and identify the polymorphism that gives rise to
the trait of interest.  

>So, short of giving out Pioneer's secrets, I'd love to hear from
>someone online who can be specific about a specific crop.  I have
>a very recent dissertation in hand on earliness QTLs via RFLP
>analysis.  That one, like a couple of others on the shelf here
>at Hill Library, do not appear to be earth shattering.  The thesis
>work is *good* and my conclusion is the technique is not *yet*
>earth shattering.

Will you be impressed when the first plant disease resistance
locus is cloned?  It probably has been in Tanksley's lab, by
saturating the locus with RAPDs and walking.  The candidate
gene they showed at a recent meeting is Seattle looks like
a winner.

>>OP corn used to be traditional, too, and costs less than controlled
>>crosses.  It's the return on investment that counts, not just the
>>up-front costs.
>
>That's not exactly correct: it's the return on investment IN THE FACE OF
>up-front costs, don't you think?  

That's why I said not *just* the up-front costs.

>When I took Experimental Design at Missouri, Gary Krause said: "You didn't
>need Statistics to see what hybrid corn meant.  40% yield increment
>right across the board needs no statistics.  On the other hand, you
>may need very good statistical evaluation to 'prove' a 1% yield
>increment.
>
>So...what is the likely return on investment in maize breeding *today*
>(not 1938) when breeders are proud of the *steady* 1%-per-year
>progress that has been the hallmark of maize genetic improvement over
>the last 30 years?  What does RFLP breeding promise?  Be specific.

How about a molecular understanding of general and specific
combining ability?  I don't follow the maize RFLP stuff all that
closely, but "big" questions like this are amenable to
analysis if you have enough markers.

>What is the return on investment?

Unknown to me, and of very little concern to me.

>What has been the progress on
>achieving a saturation RFLP marker map?

It depends on what you mean by "saturated" of course.  A 20cM
map useful for QTL mapping can be done with RAPDs in a few weeks,
given a suitable mapping pedigree.

>What are the problems?

$$ :)

>Why did the Genetics Institute get out of the saturation marker game?

Who knows?  Beancounters rule in most companies.

>You were much more detailed about the flight worthiness of the F-15
>than about commercial or scientific progress with RFLP-based breeding. :^)

The history of fighter aircraft is 75 years, RFLPs weren't even
conceived of until the 80s.  The Plant Genome panel of the
USDA NRI Competitive Grants Program gives out about the same
amount of money that it takes to put the 6 Phoenix missiles on
the belly of 1 F-14.

>Well, why get exotic:  the F-111 is a killer and *never* was a stable
>aircraft.  And the old Star Fighters did none-too-well in the
>-electronically-over-loaded-mode the Luftwaffe had them in.

This is a terrible forum to discuss fighter aircraft, but
here goes:  The F-111 was/is a piece of junk, but it was/is
stable statically and dynamically, as are all operational
fighter aircraft.  Static stability requires the CG forward
of the center of lift, and dynamic stability means that
deviations from trimmed flight are damped rather that
amplified.  Stability is the antithesis of maneuverability,
so fighters are "less stable" than transports, but they
are stable in the aerodynamic senses.

>Some people swear by the F100 and others say it was unstable.
>
>F-4 and SkyHawks are stable, which is why they are still being
>*built* after *38* years of service.

Geez.  M-D hasn't built a new F-4 since Christ was a pup.  Both
aircraft are still in service, but haven't been built for
many years.

>....and neither would I cite the Pentagon or the aircraft manufacturer.

I have a more reliable source, since my father is a fighter
pilot and has flown most of the current batch of fighter
aircraft :)  According to him, the hardest to fly is the
AV-8A Harrier in hover, where the wingtip puffer ducts cannot
overcome large roll inputs and have a nasty tendency to
turn turtle.

>Are trees plants?  ;^)

Only on the outside.  On the inside they're an advanced composite
of cellulose fiber-reinforced lignoplastic, suitable for construction
of the spars on a Pitts Special.

Toby Bradshaw
Department of Biochemistry and College of Forest Resources
University of Washington, Seattle
toby@u.washington.edu



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