Bio-types vs. clones???

JamieGoode has a good discussion on varieties vs. clones:
Jamie:Varieties/Clones

OK...so this is pretty much as I understand it. A few salient points:

1. You cross Pinot & GouaisBlanc, plant the seed, you do not get Chard...you get a new variety. Yet Chard, as it's vegetatively propogated, is a cross between Pinot X Gouais Blanc. OK...that makes sense.

2. As a given variety grows in the vnyd, it can spontaneous mutate. If you propagate from one of these mutated plants, you get a new clone of that variety. When you do the DNA on those clones, looking at only 10-12 or so "sites", the are identically the same variety. The DNA, as done w/ only a few "sites" can't distinguish between clones.
But we have 3 varieties that are DNA-wise identical: PinotNoir/PinotBlanc/PinotGris. Even though those are genetically identical, they are recognized as different varieties. OK....that makes sense.
However, if you you look at more than 10-12 different "sites" (or regions as Jamie calls them), if you do the full DNA analysis...wouldn't that more extensive analysis pick up differences in the various clones??

3. When investigating the subject of Prunent/Nebbiolo, most folks I corresponded with felt that Prunent (as grown in the Val d'Ossola) was just the local name for Nebbiolo (as is Chiavennasca in the Valtelline, Spanna in Gattinara, Picptendre in the Val d'Aosta). However, I was assured by one person that Prunent is not a synonym or local name for Prunent, but that Prunent is a different bio-type of Nebbiolo. D'Agata frequently refers in his book to bio-types of grapes, w/o defining the differences (that I could find). To my knowledge, the DNA on Prunent has not been done.
What the heck is a "bio-type" and how does it differ from a clone. If you do the DNA on various bio-types, using only 10-12 "sites", will the DNA identify them as being different? Or do you have to do many more "sites" to distinguish between bio-types?? Would the full DNA sequence distinguish between "bio-types"??

This stuff is all so complicated & confusing. Makes the Higg's Boson seem like child's play. Somebody help me out here.
Tom

[Robin Garr]

Way above my pay grade, Tom, but fascinating stuff. Thanks for posting, and if any of the gang feels competent to take it on (or stands ready to take it on without competence), I'll be here to read.

I do have a question about the Higgs Boson, though. If some crafty wine maker found a way to make a wine with the H.B. somehow involved in the process, would it still be a Natural Wine?

[David M. Bueker]

This is a job for Carole Meredith.

Nature loves diversity. Even among so-called “pure” cultivars (selected wild vines that have been asexual reproduced for centuries by man) you are going to see diversity (thus various bio types). So-called population of “pure” cultivars would be “unnatural”. Aren’t various clones of a given bio type identified by looking at phenotype characteristics (size, shape, number of wings of a cluster; uniform or non uniform size of berry, size of berry, skin thickness of berry, color of berry; number of seeds, hardness of seeds, etc) or a behavior characteristic (vigor, time of ripening; disease resistance, etc)? The question now for me becomes-how much of these bio type characteristics are due to ”terroir” (the actual place and piece of dirt man decided to plant the vine)?

Salute

This is a job for Carole Meredith.

Yup, David. She's on the way..over on WB.
Tom

From googling for a definition of bio type it reads to me that bio type is another word for clone

From googling for a definition of bio type it reads to me that bio type is another word for clone

Google didn't give me a whole lot of info on bio-type, Peter. Carole is going to set me straight soon.
Here's what I had to say on WB:

So...I finally waded thru all Carole's comments in the Rhys/Carricante thread.

To my understanding, "bio-type" is a rather nebulous term, mostly used by the Italians, d'Agata and OliverMcCrum (well...Oliver's a Scotsman, not Italian, but
he should be an Italian). It refers to an arbitrary grouping of clones that display "distinctly" different characteristics. Thus, PinotNoir/PinotGris/PinotBlanc/etc,
although, technically, by DNA, are the same variety, they are not clones of Pinot, but "bio-types".
As for Primitivo/Zinfandel; the side-by-side plantings I've observed are distinctly different to my untrained eye. They are, technically, clones I guess. But they
perhaps should be distinguished as "bio-types"??

Thus, it seems to me, that "bio-types" is a rather arbitrary term. I'm curious what DNA would tell you about "bio-types". They would, based at looking at 10-12 sites,
say they are the same?? Would looking at more sites allow you to distinguish them by DNA??

Carole should be along sometime to set us all straight..hopefully.

This stuff is all so confusing & I'm not making any sense out of it all. I'm going back to work on the equations for showing the existence of an anti-Higg'sBoson with a charm of 3.78.
It's a whole lot simpler!!

So "bio-type doesn't seem to have a clear definition that I can decypher...just a sort of grouping of clones that have
some sort of commonality.
Tom

Genetics indeed can be confusing. Taking Tom's first two points:

[1] Growing a grapevine from seed is conventional sexual reproduction and behaves just as animal reproduction does regarding genetics. Two seeds resulting from a cross of Pinot and Goulais Blanc bear the same genetic relationship as two brothers or sisters sharing the same parents. They may resemble each other, but they will have significant differences. That is the whole point of sexual reproduction: genetic recombination.

[2] Cloning is the creation of a new, complete individual from a piece of a previous individual. This is very commonplace in plants--stem or root cuttings can be broken off and new, complete plants grown from them. Many higher plants propagate almost exclusively this way and only rarely by sexual reproduction (flowers and seeds). Since you're not recombining the genetic material with that from another individual, a clone is genetically identical to the individual it was cloned from. Some animal phyla reproduce by cloning (jellyfish, hydra, and sponges, for example), but it's uncommon in higher animals. In humans, we only see cloning up to the four-cell stage of a new human embryo, and even then relatively rarely. We call the resulting clones identical twins, triplets, or quadruplets.

Now it's not quite true that a clone will always end up completely genetically identical to the individual it was cloned from. This is because the propagation of genetic information during cell division isn't perfect--there can be mutations--small changes in the genetic code. An example: there is a cell in a vine whose descendants will become a new branch on the vine. This cell picks up a mutation that causes it to be unable to produce blue anthocyanin pigment. The grapes that grow on that branch will not turn purple in the fall--they will be white. Now suppose that a vine-grower cuts off a part of this branch and clones a new vine from it. That vine will produce exclusively white grapes, although it is otherwise genetically identical to the red-grape-producing branches of the vine it was cloned from. The process I just described has happened at least three times to pinot noir vines. The results are pinot blanc and pinot gris. Very recently one of the pinot vines in the Musigny vineyard grew a branch with albino grapes on it, and the vineyard owner has cloned "Musigny blanc" vines from it.

Geneticists usually don't look at the entire genetic sequence when comparing the genomes of individual plants or animals. As you mentioned, they only look at a relatively small number of short sequences in the genome (the twelve "sites"). You are correct that, if they compared the whole genome of pinot blanc, pinot noir, and pinot gris (and Musigny blanc), there would be differences. Specifically, there would be a difference somewhere in the genes involved in the process of producing purple pigmentation as the grapes mature. It could be that a gene encoding an enzyme critical for production of the pigment is faulty, so that the pigment can't be produced. Or the fault might be in a gene encoding a protein involved in the process that triggers the production of the pigment as the grape matures, so that even though it's capable of synthesizing the pigment, it doesn't do so.

So yes, more extensive genetic analysis would pick up differences between the clones.

-Paul W.

Genetics indeed can be confusing. ...

Thanks for taking the time to respond. That helps quite a bit my understanding. A bit clearer than mud now.

Let me know when you need help on the Higg's Boson!!
Tom

[1] Growing a grapevine from seed is conventional sexual reproduction and behaves just as animal reproduction does regarding genetics. Two seeds resulting from a cross of Pinot and Goulais Blanc bear the same genetic relationship as two brothers or sisters sharing the same parents. They may resemble each other, but they will have significant differences. That is the whole point of sexual reproduction: genetic recombination.

True. It's also BTW true that if you that if you pollenate a Chardonnay flower with Chardonnay pollen you don't get Chardonnay.

In in his book Native Wine Grapes of Italy, d'Agata defines biotypes on page 22. He says that they are subvarieties, i.e. "varieties" (using the word loosely) that DNA sequencing show to be identical, but which have obvious morphological and physiological differences. Those differences would be due a set of mutations that were deemed to be desirable. Thus Pinot Noir, Blanc and Gris would be biotypes.

Unfortunately I cannot track the page down, but I am pretty sure that in the same book he also points out that even if vines have absolutely identical DNA, the genes may express themselves differently due to the environment, resulting in vines/grapes that look like different varieties. Not sure if they are biotypes too. I guess in most cases we cannot in practice yet distinguish properly between this case and the difference that are due to a set of mutations.

As posted on WB, where CaroleMeredith made some comments:

Well...thanks to Carole's (and others) explanations of the subject, it's starting to make some sense. I went back and re-read
Ian d'Agata's discussion on the subject (pg 22 & 27). Now makes more sense. Some of the things I've come away with:

1. We know that Science tells us, via DNA profiling, that Pinot Noir/Gris/Blanc are one & the same variety. When you look at the vines/grapes/wines,
clearly there are differences...vast differences. According to the TTB, these are distinct/different varieties. If you did the full DNA sequence on those
three, you would find differences. This is not done and seems of limited value. You can look at the friggin' vines and see the differences. So...in this
case the Science misleads us and the TTB & the vnyd farmers are correct...they are different varieties. Science doesn't really mislead us, it just doesn't
tell us the full story.

2. As a plant geneticist, Carole has a different view on the subject from the rest of us wine geeks. Which is fine. She is reluctant to use the
term "clone" but seems to have given up the battle on its usage. But she doesn't want to accept "biotype" because it adds another (ill-defined/
arbitrary) level of complexity to the subject. Least that's my take on what she thinks. Fine enough w/ me.

3. d'A points out that "biotype" is often used interchangeably w/ "clone". He rejects that interchangeability and asserts that they are different terms.
But offers no support for that assertion.

4. Another gem from d'A's discussion. We all "know" that Nebbiolo and Pinot are more prone to mutate than any other of the varieties. We do "know" that,
don't we?? We've been told that by the "experts" for yrs. d'A disputes that claim. He asserts that that idea has only come about because these are
ancient grape varieties. Therefore, they have just had a longer time thru history to mutate, given that grapevines are mutating all the time (heck....I bet
there's some Mondeuse mutating, as we speak, up on MtVeeder..it must be an ugly sight to watch!!). Not that those varieties are more prone to mutate inherently.

5. d'A cites the case of Pigato/Vermentino/Favorita/Rolle. The DNA profiling tells us that those are the identical variety (though the Wikipedia entry on Favorita
asserts, from Jancis, that DNA tells us that Favorita is a distinct variety from the other three). He cites the case of Angelo Negro, in the Roero, planted
Favorita and Pigato side by side in the same vnyd. It was clear to Angelo that the vines/grapes, and wines were distinctly different...were not the same
variety. The growers in Liguria have planted Vermentino and Pigato side-by-side there and assert, quite forcefully, that they are different varieties. Yet the
DNA profile assures that they are the same variety. Once again, DNA science misleads us...or, at least, doesn't tell us the whole story. So...are
Pigato & Vermentino & Favorita different "biotypes"?? d'A doesn't address that issue and doesn't tell us who makes that decision that they are different
biotypes. So...it seems a bit arbitrary & confusing if they are. Score one for Carole.

6. d'A frequently refers in his Nebbiolo section to "Nebbiolo (bio-type Lampia)" (Michet being a virused version of Lampia). So who has defined biotype Lampa??
d'A? The Italian gummint?? The growers in B/B?? Are Lampia/Michet/Chiavvanasca/Picotondre/Prunent all different clones or different biotypes, even though they
are, by DNA, identical varieties?? At least, when d'A refers to Nebbiolo (biotype Lampia), I do know what he's talking about..Nebbiolo as grown in the B/B area.

7. So.....what the heck is a "bio-type" of a grape variety?? Who the heck defines a biotype of a certain grape variety?? Some mustache-Pete farmer out in the vnyd??
d'A and Alice?? The gummint?? The TTB?? It all seems a bit arbitrary & confusing. Score one for Carole.
So...my understanding of a biotype: You take a particular grape variety (say Nebbiolo), plant it in a certain region of Italy, and grow it there for hunnerds of yrs. Those vines
mutate. Eventually they become different from their original source vines. Are these (now) mutated vines a biotype or a clone. Are Lampia/Spanna/Picotondre/Prunent/Chiavannasca
different biotypes or merely clones of Nebbiolo. If I declare that Prunent is a biotype of Nebbiolo, will the World accept my declaration?? Prolly not. If d'A declares that Lampia
is a biotype of Nebbiolo, will the World accept that declaration?? Perhaps. Perhaps not.
So....to my thinking....biotype is nothing more than a collection of clones that have been growing in a particular region of Italy (not seen the use of biotype in Calif or any
other wine growing region that I can recall) for many yrs. Sometimes these biotypes will be markedly different from biotypes in other regions, sometimes not.
So...that's my story & I'm sticking to it!!! [snort.gif]

It's still all pretty confusing, but I think I understand it all a bit better. Thanks to Carole and all others for contributing to my edumacation. Back to the Higg's Boson, a subject
that seems a whole lot simpler to me.

Tom

From googling for a definition of bio type it reads to me that bio type is another word for clone

Google didn't give me a whole lot of info on bio-type, Peter. Carole is going to set me straight soon.
Here's what I had to say on WB:

So...I finally waded thru all Carole's comments in the Rhys/Carricante thread.

To my understanding, "bio-type" is a rather nebulous term, mostly used by the Italians, d'Agata and OliverMcCrum (well...Oliver's a Scotsman, not Italian, but
he should be an Italian). It refers to an arbitrary grouping of clones that display "distinctly" different characteristics. Thus, PinotNoir/PinotGris/PinotBlanc/etc,
although, technically, by DNA, are the same variety, they are not clones of Pinot, but "bio-types".
As for Primitivo/Zinfandel; the side-by-side plantings I've observed are distinctly different to my untrained eye. They are, technically, clones I guess. But they
perhaps should be distinguished as "bio-types"??

.......

So "bio-type doesn't seem to have a clear definition that I can decypher...just a sort of grouping of clones that have
some sort of commonality.
Tom

Well, I suppose its the responsibility of the writer who used the term bio type to define what he means by it, but from all so far in this thread it is what we here all call a clone.

Since all propated vines are produced by cloning he seems to be using bio type to distinguish those clones that demonstrate different character is tics, e.g. Pi not noir is a clone but Pi not gris is a bio-type.

But this is a definition too far. The use of the word clone in itself means a variation.

When vineyards buy Pi not noir vines they don't order (say ) 1,000 Pinotnoir, they order so many clones by name or number, 777, Precoce, or etc.

I think on all vine catalogues vines are listed by clone and the characteristics of the clone. Even on the relatively young Pinotage (my speciality) there were three distinct clones, and more coming.

Where a clone is very different it gets a name as a new variety, e.g. Pi not gris, Gamay droit.

I think I got his meaning.

A bio type is variety that is in fact a clone of another, viz Pi not gris is a variety but a biotype because its a clone of Pi not noir.

He's arguing Prunent is a bio type ?

I think the key difference between a biotype on the one hand, and any old mutated clone on the other, is that biotypes have "clear physiological and morphological differences". So much seems easy in principle to grasp, and I can understand why the term is used. There is a degree of arbitrariness in what is a clear physiological and morphological difference. But our definition of variety is also rather arbitrary - it is based on the number of DNA sites we have decided are worth looking at.

I am not sure how useful all these terms are, but I do see the motivation for using the word biotype. Just wish everyone could agree on the terminology.

I think the key difference between a biotype on the one hand, and any old mutated clone on the other, is that biotypes have "clear physiological and morphological differences". So much seems easy in principle to grasp, and I can understand why the term is used. There is a degree of arbitrariness in what is a clear physiological and morphological difference. But our definition of variety is also rather arbitrary - it is based on the number of DNA sites we have decided are worth looking at.

I am not sure how useful all these terms are, but I do see the motivation for using the word biotype. Just wish everyone could agree on the terminology.

Yup, Steve....that's pretty much the conclusion I've reached. There's a certain degree of arbitrariness there in the
use of "biotype". But I think it can be a useful term.
Tom

I think I got his meaning.

A bio type is variety that is in fact a clone of another, viz Pi not gris is a variety but a biotype because its a clone of Pi not noir.

He's arguing Prunent is a bio type ?

So this whole discussion of Biotype vs clone was precipitated by my interest in Prunent, grown in the Val d'Ossola of the NW Piemonte.
So...I went back & reread d'Agata's discussion of Nebbiolo. What I learned:

1. NebbioloLampia/NebbioloMichet/Spanna/Chiavanasca/Picontondre/Prunent are, by DNA profiling, true Nebbiolo.
However, but looking at 28-53 micro-satellites, they identified only two genotypes (what the heck is that term mean?) of Nebbiolo:
Nebbiolo Lampia and Nebbiolo Rose. Nebbiolo Rose is identified as a member of the Nebbiolo family (but not a biotype) but a distinct/separate
variety, related to Nebbiolo. It is only the Nebbiolo (biotype Lampia), as grown in Barbaresco/Barolo, that he labels as a "biotype". So what are
Spanna/Chiavanasca/Picotondre/Prunent?? Are they biotypes or clones of Nebbiolo?? He really doesn't say. But it's clear that he
regards Nebbiolo (biotype Lampia) as the one true Nebbiolo to which all others are derived.

2. d'A's only mention of Prunent, of the Val d'Ossola is that it was the first mention in the literature, back in 13??, of Nebbiolo.
With no additional comment. Does that imply that Prunent is the original source of Nebbiolo?? The cantineGarrone folks ([url]cantinegarrone.it/en[/url]
label those vines in the Vd'O as the "grandfather" of Nebbiolo. Not sure exactly what that means. To my knowledge, there has been no DNA profiling
of the Vd'O Prunent. I will be in touch with them to find out what they actually know. But I suspect the folks in B/B would be incensed but that
claim that Nebbiolo originated in the Vd'O. EmilySchindler/WineMonger gifted me a btl of the Garrone Prunent to try. I can hardly wait to see what
it's like.

All very fascinating stuff. Now back to the Higg's Boson.

Tom

However, but looking at 28-53 micro-satellites, they identified only two genotypes (what the heck is that term mean?) of Nebbiolo: Nebbiolo Lampia and Nebbiolo Rose.

It means that for vines called Nebbiolo, looking at those micro-satellites only, there are only two DNA sequences. Effectively there are two varieties, but I think genotype is more precise because it emphasises that only limited regions of DNA were tested. Heck, it is difficult picking the right words!

As d'Agata refers to Prunent as a synonym of Nebbiolo (I just checked), I would assume it is not a biotype.

However, but looking at 28-53 micro-satellites, they identified only two genotypes (what the heck is that term mean?) of Nebbiolo: Nebbiolo Lampia and Nebbiolo Rose.

It means that for vines called Nebbiolo, looking at those micro-satellites only, there are only two DNA sequences. Effectively there are two varieties, but I think genotype is more precise because it emphasises that only limited regions of DNA were tested. Heck, it is difficult picking the right words!

As d'Agata refers to Prunent as a synonym of Nebbiolo (I just checked), I would assume it is not a biotype.

That's sorta the problem, Steve. Who exactly defines/decides whether Prunent is a bio-type or just a synonym??
It all seems a bit fuzzy and arbitrary.
Tom

It's also BTW true that if you that if you pollinate a Chardonnay flower with Chardonnay pollen you don't get Chardonnay.

Yep. The seed from which the original chardonnay vine was grown contains two complete sets of genes: one from each of the parent vines. The technical term is that their cells are diploid. But pollen cells, and the ova that they fertilize to form the seed, have only one set of genes (technical term: haploid). And here's the kicker: that set of genes is NOT a complete set from either of chardonnay's parents. They're a mixture of genes from either parent.

Chardonnay is a cross between pinot noir and goulais blanc. Chardonnay cells have one set of chromosomes (large bundles of genes) from pinot noir, and one from goulais blanc. Pollen and ova in chardonnay flowers have only one set of chromosomes, and for each chromosome it's more or less random whether it is the one from pinot or the one from goulais. So the result of breeding chardonnay with chardonnay will most likely be a seed that has some chromosomes both of which are pinot-based and some where both are goulias-based. The result is a different genetic makeup than chardonnay.

The production of pollen and ova also involves a process called crossing-over, where two chromosomes exchange pieces of their genomes. So you can end up with chromosomes with some genes that came from pinot and some from goulais. This will further cause the offspring to diverge genetically from the parents.

-Paul W.

However, but looking at 28-53 micro-satellites, they identified only two genotypes (what the heck is that term mean?) of Nebbiolo:
Nebbiolo Lampia and Nebbiolo Rose

"Genotype" means "set of genes". In contrast to "phenotype", which means "physical characteristic". I don't want to write a book on genetics here; suffice it to say that there is not a one-to-one correspondence between a physical characteristic (such as white grapes) and a gene. A physical characteristic may be caused by multiple genes acting singly or in concert (polygenic inheritance), and a single gene may influence multiple physical characteristics (plieotropic effect).

In this usage, they mean that they analyzed 28-53 small sequences of genetic DNA (the micro-satellites). They found that in nebbiolo, there are only two differences in these sequences. One is always found in the sub-variety (or biotype) we call nebbiolo lampia, and the other is always found in the sub-variety we call nebbiolo rose.

-Paul W.

Who exactly defines/decides whether Prunent is a bio-type or just a synonym??
It all seems a bit fuzzy and arbitrary.

It's completely arbitrary. All of taxonomy (the grouping of individual organisms into breeds, races, species, genera, families, phyla, etc.) is arbitrary. Nature has organisms that produce offspring, very often by exchanging genetic material with other organisms. The grouping of these organisms into species and phyla and whatnot is a human construct that we use to classify organisms into groups so that we can more easily understand them. There are rules for these categories, but they are OUR rules, not nature's, and nature isn't always as tidy as we would like.

So turning to grapevines: the Eurasian plant from which most wine is made is the species Vitis vinifera. The main rule for classifying organisms as a "species" is that members of one species don't (in most cases, can't) interbreed with members of another species. This isn't strictly true for vines--you can cross Vitis vinifera with other species in the genus Vitis (the Vitis vinifera variety Aramon crossed with Vitis rupestris [a North American vine species] produced the AxR #1 plants used as rootstock for V. vinifera grafts in vineyards).

As we previously discussed, vines with useful characteristics don't breed true--their seeds don't consistently inherit the characteristics that make the parent agriculturally valuable. So instead we clone the vines with the useful characteristics. A "variety" is a group of vines that are clones of each other.

But as also previously discussed, over time mutations occur so that clones in the same variety aren't necessarily completely identical genetically. Sometimes these mutations result in a change in appearance (phenotype) that is agriculturally significant and causes us to want to classify the vines with the divergent characteristics as a separate group, even though they are clones of the parent group. The lack of pigmentation in pinot blanc, pinot gris, and Musigny blanc vs. pinot noir is an example. Apparently the term "biotype" is used for this concept. I have been using the term "sub-variety". Mutations may result in phenotypic effects that are not as dramatic as white vs. purple grapes. For example, some clones resist disease or grow better in arid soil than others. Whether or not you decide to assign new names to clones with these differences depends on whether they are significant to you.

"Synonym" of course means "another name for the same thing". So the variety called Malbec is also known in some places as Auxerrois or Cot. But all three names refer to the same set of vine clones.

-Paul W.

Genetic variations, either natural or induced (bio-type sounds a little more “natural” than somaclone) are critical in crop management and improvement in quality of the fruit. Understanding gene function will help in grasping genetic diversity in grape vines, and understand why one vine has a given set of characteristics and another vine has another given set of characteristics. Man’s long history with the grape vine and his viticultural practices and techniques has more or less determined the genetic diversity in vines that exist today (this by no way means the vine has lost its ability to diversify, it’s a function of all living things). IMHO, man, without any knowledge of genetics and genes did a fine job in making selections just by using his sense of sight and taste. Today you have the vine-growers do what they do best in the vineyard and the researches in the labs doing what they can do and we’re gaining knowledge.

Salute