Can plants recover alleles lost on one of the homologous chromosomes?

[stcordova (Salvador Cordova)]

From:

Raising a glass to grapes’ surprising genetic diversity: Could contribute to wine’s varying flavors, aromas, researchers say – ScienceDaily

Each of us inherits one copy of their gene from their mother and one from their father," said Professor Gaut. “One would assume that the grapes inherit two copies of every gene, too, with one coming from each of their two parents. However, we found there was just one copy, not two, for 15 percent of the genes in Chardonnay , and it was also true of Cabernet Sauvignon grapes. Together, that means that grape varieties differ in the presence or absence of thousands of genes.”

I found another paper for an apparently wild-type plant species:
https://www.nature.com/articles/s41467-018-04721-8

C. australis genome harbors 19,671 protein-coding genes, and importantly, 11.7% of the conserved orthologs in autotrophic plants are lost in C. australis . Many of these gene loss events likely result from its parasitic lifestyle and the massive changes of its body plan. Moreover, comparison of the gene expression patterns in Cuscuta prehaustoria/haustoria and various tissues of closely related autotrophic plants suggests that Cuscuta haustorium formation requires mostly genes normally involved in root development. The C. australis genome provides important resources for studying the evolution of parasitism, regressive evolution, and evo-devo in plant parasites.

Is there a mechanism that can easily restore the missing allele/gene/loci on one chromosome from the homologous chromsome that still has a copy? As in, if a grape plant has lost 15% of it’s genes on one chromosome, how likely is it that it can get back that very same 15% or even a good fraction of the 15% once it is lost?

It seems there is a lot of pressure to lose genes, more so than to make new ones.

[evograd (Blogging Graduate Student)]

With the grapes, it’s pretty clear that our selective breeding of different varieties has led to the accumulation of significant structural variants, and the paper even says in the abstract that there is strong natural selection against these.

The second example is in a parasitic plant, and it’s very well known that parasitic organisms evolve streamlined genomes, losing genes whose functions are no longer required in a parasitic lifestyle.

[stcordova (Salvador Cordova)]

@evograd

The second example is in a parasitic plant, and it’s very well known that parasitic organisms evolve streamlined genomes, losing genes whose functions are no longer required in a parasitic lifestyle.

Thank you for you reply.

Are you aware of a mechanism that could restore the missing genes once they are gone from a lineage. In the case of the domesticated grapes, the missing genes are at least on one of the homologous chromosomes. Do you expect there could ever be anywhere near a full restoration if there were a change in selective pressure?

I’m not aware of any large scale resotoration mechanism even in the case of the grapes.

[evograd (Blogging Graduate Student)]

Why do you think, or expect us to think, that such a “large scale restoration mechanisms” exists?

It’s obviously different in the case of the domesticated graphs, as the genes aren’t “gone from a lineage”, their frequency is just reduced. Presumably if there was a dramatic shift in selection pressures they could amplify the frequency of gene copies back to two per diploid genome.

[Art (Arthur Hunt)]

@stcordova

As in, if a grape plant has lost 15% of it’s genes on one chromosome, how likely is it that it can get back that very same 15% or even a good fraction of the 15% once it is lost?

Did you bother to read the paper, @stcordova? Do you know anything at all about grape cultivation? Do you know how irrelevant your questions are? Do you worry that there may be some in your YEC classes that know the answers and will immediately see how uninformed you really are, if and when you start to go on about how grapes refute evolution and support YEC? Remember, there are many vineyards in your area (several of which I have visited), and most of the proprietors are likely going to know something about this.

[stcordova (Salvador Cordova)]

@Art

Do you know anything at all about grape cultivation?

Nope, that’s why I was asking around.

if a grape plant has lost 15% of it’s genes on one chromosome, how likely is it that it can get back that very same 15% or even a good fraction of the 15% once it is lost?

So is the chance high say above 50% or low, like say close to 0%.

Thanks for responding and your criticisms of me, but I am curious since you’re a plant biologist.

[Art (Arthur Hunt)]

@stcordova

if a grape plant has lost 15% of it’s genes on one chromosome, how likely is it that it can get back that very same 15% or even a good fraction of the 15% once it is lost?

So is the chance high say above 50% or low, like say close to 0%.

In this context, the question makes no sense. This is because grapes are vegetatively propagated. Mitosis, no meiosis.

[John_Harshman]

@Art

In this context, the question makes no sense.

Does it make sense in any context? Once a gene is lost, it doesn’t come back. How would it?

[stcordova (Salvador Cordova)]

@Art

In this context, the question makes no sense. This is because grapes are vegetatively propagated. Mitosis, no meiosis.

Thanks for your reply, but not all grapes are vegitatively propagated, right? How else did they lose those genes?

Granted, these are domestic plants, but how do they get bred if they are only vegitatively propagated?

I can understand such a technique of vegitative propagation for seedless grapes, for example.

As far as relevance, I passed this data point to Dr. Sanford. He was astonished at the level of gene loss. This discovery was recent, relatively speaking. He felt it might be relevant to the Young Life case.

Neither he nor I have pursued the matter that much as we think we might have to wait on more data. It just came to mind to discuss some more.

Thanks for your reply.

[Art (Arthur Hunt)]

@Art

@Art

In this context, the question makes no sense.

Does it make sense in any context? Once a gene is lost, it doesn’t come back. How would it?

These plants have functioning copies of the genes, so they are not completely lost.

[stcordova (Salvador Cordova)]

@John_Harshman

Does it make sense in any context? Once a gene is lost, it doesn’t come back. How would it?

I can only imagine one route in this case. The grape goes through a polyploid form, and if it reverts to the diploid form, it loses the chromosomes with the missing gene.

[Art (Arthur Hunt)]

@stcordova

Thanks for your reply, but not all grapes are vegitatively propagated, right?

Grapes are vegetatively propagated. This is to speed the re-populating of vineyard and to preserve the special characteristics of different varieties.

@stcordova

Granted, these are domestic plants, but how do they get bred if they are only vegitatively propagated?

Desirable traits and plants are selected and propagated vegetatively. This allows one to isolate and multiply novel and attractive traits at one fell swoop, without “traditional” breeding.

@stcordova

As far as relevance, I passed this data point to Dr. Sanford. He was astonished at the level of gene loss. This discovery was recent, relatively speaking. He felt it might be relevant to the Young Life case.

Sanford should know better than to latch onto this phenomenon to support his absurd suppositions. After all, he is a plant scientist, one who works in the wine country of NY to boot.

[stcordova (Salvador Cordova)]

@stcordova

I can only imagine one route in this case. The grape goes through a polyploid form, and if it reverts to the diploid form, it loses the chromosomes with the missing gene.

That’s however on the generous assumption all gene losses are on the same chromosome!

[Art (Arthur Hunt)]

@stcordova

The grape goes through a polyploid form, and if it reverts to the diploid form,

I suggest you look up the term “hemizygous”.

[stcordova (Salvador Cordova)]

@Art

I suggest you look up the term “hemizygous”.

Thanks, Art.

[stcordova (Salvador Cordova)]

It just occurred to me that a plant might recover a single or a few loci if the loci that are missing are on the same chromosome.

If the paternal and maternal gametes that make an offspring both have the chromosome with all the loci, then an offspring with all the loci can be made. The converse is unfortunately true where the maternal and paternal gametes both have the chromosome which has all the missing loci, then the offspring will have the loci gone for good. The situation is even more complicated when there are loci are missing from either chromosome of a homologous pair, and not just one of the chromosomes of the pair. And further, a single offspring is not fixation of the genome.

But this got me thinking…

Here is a diagram relating the synteny of the human genome to the mouse genome.

What is not shown in the graph is the implicit homologous paring of the human chromosomes. I would assume since they show only one representation of each human chromosome, that the synteny on one chromosome is mostly identical on the corresponding homologous chromosome.

Translocations can happen. Here is a classification of some of the kinds of translocations:

But if translocations such as the above happens between chromosomes, how does the homologous partner get synchronized with the partner that is out of balance so that the synteny is preserved over time between homologous chromosomes in a species.
This would be the problem described for the grapes all over again.

Wouldn’t there be a lot of chance events and/or selection such that individuals from the same ancestor that introduced the translocation, join up and then their offspring manage to get the right pair of chromsomes so that they are homologous again? Then this offspring’s karyotype has to somehow fix into the population?

The alternative is that this is done somehow to 4 chromosomes simulataneously. For example Human Chromosome 3 has a region form Mouse Chromosome 16. Suppose for the sake of argument the ancestor of both man and mouse had something closer to the Mouse arrangement.

Did 2 mostly identical segments from the homologous pair of Chromosome 16A and 16B simultaneously migrate to the ancestor of the human Chromosome 3A and 3B and insert in about the same locations? What would be the mechanism for this to happen?

The alternative is to do this piecemeal as described above with the grapes.

Finally translocation has consequences. From wiki:

Chromosomal translocation - Wikipedia

carriers of balanced reciprocal translocations have increased risks of creating gametes with unbalanced chromosome translocations, leading to Infertility, miscarriages or children with abnormalities.

[John_Harshman]

Typical Sal: lots of gibberish misusing technical terms, emphasized with colorful diagrams.

[T_aquaticus]

@stcordova

Are you aware of a mechanism that could restore the missing genes once they are gone from a lineage. In the case of the domesticated grapes, the missing genes are at least on one of the homologous chromosomes.

If the gene is present in the population somewhere, wild or cultivated, then it isn’t lost. If no living grape plant, living or wild, lacks a gene then it is gone forever.

[stcordova (Salvador Cordova)]

Ploidy changes in plants and ploidy even changes in some human somatic cells like cardiace myocites.

Notwithstanding ploidy changes, there is the problem that synteny changes would pose to the 4D nucleome gene regulation:

It’s premature to assert that synteny changes can happen with high probability without bad consequences. Natural selection might resist such changes rather than facilitate them!

The above diagram was from:

Genomic Views of Transcriptional Enhancers: Essential Determinants of...

[John_Harshman]

Can anyone figure out what Sal is trying to claim here?