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Re: yellow inheritance, Gen 101, and Sayonara, for now...

halinar@open.org wrote:

Hi Joe,
First, let me say thanks for the Genetics 101 refresher.  I seemed to have skipped to 451 and then am working backwards which is often how I learn things. :-)  From studying the CD-ROM of the A. Thaliana genome, and some of the sequence analysis sites, there are basics that I've skipped.  Of course, one of the advantages of doing it this way is that one doesn't run as much risk of adopting theories that have subsequently been proven inaccurate.  Once the genome and proteome of Hosta is mapped, then we will be better able to speak about what is ACTUALLY happening, and not have to operate on simply what we BELIEVE may be happening.

RE:>> Thus, for every gene at a certain locus there are many different possible alleles, but a diploid can only contain two
alleles of each gene, one from the pod parent and one from the pollen parent.
Are you purporting that the coloration in Hosta is controlled by but one gene?  The theory of one allele per gene is part of basic Mendelian Genetics yet when adding linkage mapping for groups of alleles, sorted out onto each chromosome, the puzzle can get quite complex.  This is where Mendel became limited--he only had his punnett-squares and an insatiable appetite for rigor in two dimensional arrays.   I'm not certain of this (so far I haven't found research), but it seems likely that the statement "a diploid can only contain two alleles of each gene, one from the pod parent and one from the pollen parent" is true to the extent that there are homologous chromosomes, and heterozygous chromosomes, and traits controlled by but one gene.  I believe this statement may address only part of the story, however, when talking about traits controlled by multiple genes.

Since one trait can be influenced by multiple genes, the trait of coloration in Hosta could easily be spread across multiple chromosomes, or there could be several linkages of coloration alleles on one chromosome.   Whether you call this Bio 101, Gen 101, or Genetics 451 with a twist, I don't know.  However, without a gene map that helps to explain linkages, the hybridizer is relagated to utilizing linkage mapping and probability theory, best understood by humans through utilizing these two-dimensional arrays, for which Mendel became famous.  Unfortunately, Hosta reproduce relatively slowly compared to Drosophila so gathering statistics on the percentage of recombinants in gametes relative to the positions of genes along a chromosome could take some serious man years.  

This, incidentally, is why I chuckle when people exclaim, "we have too many Hostas cultivars registered already!".  They have not allowed their minds to venture into new territories.  How about a purple and red leaf?  How about yellow, purple, red and green, all into the leaf?  There are lots of plants that have these characteristics and I wonder if we couldn't gradually force these different gene pools into a Hosta?  Maybe not this decade, or this century, but like I said, being disappointed that we have so many varieties of Hosta is extremely limited thinking.  Just look at what we've seen in the last few years!  Think of what Ran could be working on there in his genetics lab with flowers on Hosta.  Unfortunately, all of this takes time because we only get one generation per year (on average).

RE:>>The biosynthesis of chlorophyll is VERY complex and there are probably a hundred or more genes involved in chlorophyll synthesis.
Perhaps contrary to the opinion of some here, I am not able to simply pick up an issue of Nature re the genome mapping of A. Thaliana, sit in a chair with my feet propped up, light the fire, sip the coffee and commence to consume through osmosis an issue of Nature cover to cover.  To the contrary.  My first read yielded about 1-10% comprehension, at best. Some paragraphs I still have only minimal comprehension.  However, now that I have poured over many segments multiple times, referenced the glossaries and done my homework by studying the sequenceing and genome/proteome information for many months, some of this is actually starting to sink in.

Without going into all of the details of my investigation, let me just quote a section specifically relating to this VERY complex chlorophyll systhesis matter to which you refer:

"For pigment biosynthesis, 16 genes in chorophyll biosysthesis and 31 genes in carotenoid biosynthesis were found.  (Supplementary Information Table 8).  Our analyses have identified several potential components of the light perception pathway, and have revealed the complex distribution of components of the photosynthetic apparatus between nuclear and plastid genomes." (Nature: 14 Ded 2000, Pg 810.)  (This author's note -- and interesting ratio, Joe; 16 chlorophyll genes and 31 carotenoid genes... hhhhmmmm).

While it is complex, this does not mean that we cannot undertake the study and make some progress.  Apparently these folks have, and while the findings don't unravel mysteries about Hosta per se, there is considerable support for the notion that much of these findings will extrapolate quite nicely into the genome map of other eukaryotics, including humans.  e.g. on Pg 802, they list 36 Arabidopsis genes with similarities to human disease genes.  And these are just the DISEASE genes.  I wonder how many other genes are similar.  With BLAST and FASTA and other bioinformatics database tools, answers that were once elusive can now be unravelled, albeit with some serious comsumption of processor ticks.

RE:>>A mutation in any one of these genes could result in the failure of the plant to produce chlorophyll if it occurs in the early to mid part of the biosynthesis, while it can result in a yellow pigment that is close to a fully formed chlorophyll molecule, but not quite complete, if the mutation is in a gene at the end of the process.  These late forms of chlorophyll are generally yellow pigments.
"These late forms of chlorophyll" - You meant to say these "latter" forms, not late or later--right?  I'm not certain but this is how I read it.

Ref. Jim Hawes, in "Those Blasted Plastids" --I love that title.  The yellow pigments to which you refer, and the chromoplasts that contain these carotenoid yellow pigments, seem less common but that is part of the reason we like their colors so much.  While I love a beautiful green Hosta, its beauty is not diminished but enhanced when placed next to a plant that is filled with carotenoids but quite lacking in chloroplasts.   And mix in a plant with a nice combination of chloroplasts, chromoplasts and amyloplasts (Great Expectations, June, Paradise Joyce?), and that plant catches the eye!  It is one of the reasons we all LOVE Hostas!   But to better understand sports, I need to test Ben's "Rules of Thumb" more thoroughly.  I cannot do this with my present level of understanding.

I'm only beginning to learn about these things, but I found a statement in Nature (ibid, pg 802) to be very illucidative on this subject of Sports.  Parts of it, Jim Hawes will relate to quite well (and he may sit back and raise his hands to extoll, "Hip, hip, hurray!.  By jove, I think he's got it!);  to wit:

"The three genomes in the plant cell--those of the nucleus, the plastids (chloroplasts) and the mitochrondria--differ markedly in gene number, organization and stability.  Plastid genes are densely packed in an order highly conserved in all plants whereas mitochondrial genes are widely dispersed and subjected to extensive recombination.  (Sato, S. "Complete structure of the chloroplast genome of A. Thaliana.  DNA Research 6, 283-290 (1999)),

"Organellar genomes are remnants of independent organisms--plastids are derived from the cyanobacterial lineage and mitochondria are derived from the a-Proteobacteria (there is that ASCII limitation again).  The remaining genes in plastids include those that encode subunits of the photosystem and the electron transport chain, whereas the genes in mitochondria encode essential subunits of the respiratory chain.  Both organelles contain sets of specific membrane proteins that, together with housekeeping proteins, account for 61% of the genes in chloroplast and 88% in the mitochondria (Table 4).  The balances are involved in transcription and translation". (ibid, pg 802).

I've got to stop there, but needless to say, I am trying to relate portions that pertain specifically to the discussion at hand.

RE:>>(a more more recent post). "You really need to get hold of some older genetics book from the 60's or 70's that actually covers Mendelian genetics".
Joe, I read this and just had to chuckle.  Mendel was a genious.  Way ahead of his time.  However, "Mendel could do no more than analyze the numerical results from his dihybrid crosses, because he didn't know that seven pairs of homologous chromosomes carry the pea plant's "units' of inheritance." (As he referred to them)". (Starr and Taggart, 1998).  This independent assortment theory was best represented in a two dimensional array that we know of as the punnett-square.  They state further, "In a monohybrid cross involving only a single gene pair, three genotypes are possible: AA, Aa, and aa.  We can represent this as 3n where n is the number of gene pairs.... Today, Mendel's theory of segregation still stands.  Hereditary material is indeed organized in units (genes) that retain their identity and are segregated from each other for distribution of different gametes.  However, the theory of independent assortment has undergone some modification". (ibid)

Now, I don't know much about genetics, but I do know that the punnett-square is used to help man understand what is going on with heredity when he did not have today's modern lab analysis equipment.  What an admirable job he did.   This gave man a graphical tool that explained much of what he could not see to examine further.  It does not, however, control the plant and how its genes really function.

By using rigorous mathematics and the disciplined application of the scientific method of analysis, Mendel made great strides forward in genetics.  However, I have the feeling that your asking me to grab a genetics book from the 60's or 70's is analygous to me asking you to grab a computer book from the same era in order to understand IV6 of the TCP/IP numbering scheme; the use of 6 sets of octets may be relevant, but beyond that, not much is to be gained (and maybe you already know this.  In that case, it's like asking me to use an 8-bit 8086 to run software designed for a 64-bit GUI machine. Try to load Win 2000 onto an 1983 IBM-PC.  Please don't limit me that much).  

This is not to poo-poo the importance of this basic understanding.  I am just saying that I want to understand this from the INSIDE out first, not the OUTSIDE in.   There are plenty of researchers working on the outside in approach and they don't need my assistance, I can assure you.  I won't name all of the great hybridizers because I would have to list hundreds.

Does my approach make sense to you?  No?  Yes?  Don't give a rip?

RE:>>Genes come in different flavors called alleles.
Well, kind of.  It's not worth debating with you about nomenclature when I don't yet understand the mechanism.  What we want to call a phenomena sometimes limits how we understand the phenomena.  I want to better understand the phenomena FIRST and then hunt for the terms that apply.  Sometimes, when we try to force old terms into explaining heretofore undefinable phenomena, we become limited by the terms in our ability to understand and explain what is REALLY happening.  I'm not saying this is the case, but I am saying that I can take a fresh approach because I am unencumbered by what may be but partial truths.  I don't really KNOW anything, so at least I have the benefit of knowing that half of what I know is NOT incorrect!   I simply don't have much knowledge on the subject at all!  (But I have an appointment with someone who does and this could be loads of fun!!!  Unfortunately, that person did not know what a Hosta was so our marketing department still has a lot of work to do!).

Does that make sense?

RE:>>There is a non-active allele of this gene called y that does not function, hence it does not produce yellow leaves.  There could also be other alleles of the "yellow leaf" gene that are only partly functional.
Now we're making some progress.  This I have no trouble with a'tall.

RE:>>These alleles differ in their base pair arrangment so that they produce a enzyme that has a different amino acid at a certain location.  That different amino acid may not have any effect on the functioning of the enzyme, or it could totally shut down the enzyme.  It could also make the enyzme function at a much slower rate.  Thus, for every gene at a certain locus there are many
different possible alleles, but a diploid can only contain two alleles of each gene, one from the pod parent and one from the pollen parent.
And here is where we go into uncharted territory, but I believe this becomes necessary.  Have you identified these alleles?  Have you or other researchers identified these genes?   Who is working on this in a lab somewhere?  Ben is doing some DNA analysis re: ploidy and there are others working with BAP, but I'm trying to find researchers who are actively involved with protein sequencing or gene mapping in Hosta.  This does not detract from the work of the micro biologist or the hybridizer, and it doesn't mean that I can't be all confused about micro bio concepts (because as you point out, I sure as hell may be :-)), but do you understand that I don't really need to understand this that well when what I'm wanting to do is gain some understanding of the plant, but from the inside out?  I'm wanting to advance my knowledge at the MOLECULAR level and much more quickly than at the micro level.     

For example, in A. Thaliana, (Nature, ibid pg 810) "... of the nine subunits of the chloroplast ATP synthase complex, there are encoded in the nucleus, including the II-, gamma?, and S-subunits (there is that ASCII problem again);  The remaining subunits (I, II, iV, gamma, Beta, and Epsilon?) are encoded in the chloroplast.  (Maier, Nickerman, Igloi, Kossel.  "Complete sequence of the maize chloroplast genome; gene content, hotspots for divergence and fine tuning of the genetic information by transcript editing." J. Mol. Biol.  251, 614-28 (1995)).

I believe that once I understand more from the molecular point of view, the micro level will come easy.  

Now, in order to advance my understanding, I'm going to have to spend a lot more time in the books and at the research lab.  In between my efforts that appear to be "tinkering" with computers, and my efforts to grow better Hostas (and I WILL condense thirty years of others experience into a three year learning curve, or so I am willing to both publicly and vehemently purport), I will be finding time to advance my understanding.  To enable that to happen efficiently, however, I believe I am going to have to sign off of the hosta-open and most certainly the Phoenix (gag).

I have enjoyed these discussions, and I've made a number of cyber friends whom I shall miss.  However, there are SO many serious issues that call me that I must gain back some of my time.  I will attempt to carry on some of this discussion in the new Hosta Discussion Forum at http://dev.hostahaven.com, and IF YOU WISH, I will communicate some privately, in a format that I feel is more conducive to learning and less encumbered by off topic conversations (especially mine!)   Please don't "write me off" saying what an "arrogant idiot".   A humble idiot, perhaps, but hopefully never an arrogant one in spite of my "dumbing down" fau paux.      

God bless you all.  I hope to meet more of you at future Hosta shindigs.

And to Ben Z., Joe H., James H., Ran L., Bill M., Dan N., Preston L., Roy D. Narda M., Jim T. and many, many other others that have tolerated my long posts and occassionally enjoyed them, "Thank you".  I've really enjoyed the communications and learned a lot.  I'll probably be back in the early winter, but Joe is probably right--I need to not only be intelligent, but to be smart.

Hosta la Vista!   (And remember, after this post, I'm no longer a registered user.  This is only to gain some time back.  You will all be missed).    

Right now I hear my mother-in-law calling, so it's time to start being smart ... :-)

Andrew Lietzow
#1 Plantsman at http://hostahaven.com
1250 41st St
Des Moines, IA 50311-2516

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