hybrids Transposons and Capsicum evolution

[Max Burn]

I've been studying hybridization and evolution of plants and took an interest in the role that transposable elements play in this.

A recent paper called Transposon proliferation drives genome architecture and regulatory evolution in wild and domesticated peppers is worth checking out.

It relate to genomic shock and subgenomic dominance in hybrids. Subgenomic dominance is when one parental genome is expressed more strongly than the other in a hybrid. This relates to inhibitors of transposable elements that can lose their function in hybrids, which allows transposable elements to operate to try to facilitate cooperation between two divergent genomes. This can cause significant restructuring of genetic elements which plays a major role in plant evolution.

Previous theory on evolution postulates a major role of mutation in the creation of new forms and species, but newer evidence is showing that hybridization is more significant in terms of evolution. A good example of this in Capsicum is the emergence of super-hot genetics from an interspecific hybridization event of Capsicum. Such genetic interactions allow for existing genes to become modified in their expression, as well as inhibited. This creates genomic conflict and facilitates escape from adaptive conflict where existing genes become expressed differently through the actions of transposons and other interactions. In the case of the example this results in the creation of pepper lines that have capsaicinoids expressed in non-placental tissues or in the case of the bubble gum lines we see pigments expressed in the peduncles.

The more divergent two parental subgenomes are, the more likely it is that there will be genomic shock, where there are issues with compatibility of cytoplasmic and nuclear elements in terms of expression, this leads to issues like negative sense heterosis or dwarfism, or decreased viability of gametes like pollen, leading to decreased formation of seeds or reduced viability of seeds that do form. Reduced fertility can prevent F2 formation, but may allow back-crossing to parental forms, which can facilitate introgression of traits in some cases, which is useful for those who are breeding the plants.

It's a moderately complicated topic, but basically hybridization plays an important role in the evolution of plants, often much more so than mutation does. This is quite useful for breeders, but it's important to note that to take advantage of such things that often a large scale effort is required and then recombinant phenotypes and emergent traits need to be searched for and selected. This makes it difficult to exploit these types of interactions using low plant numbers and crosses. The more plants you work with, the more likely it is that you can find and propagate new traits that emerge from transposition of existing genes, which results in a modified expression.

Interestingly this type of interaction isn't just limited to Capsicum or plants, it's now known to play a major role in evolution of nearly all organisms which are diploid or have more than two copies of genomes, which are known as polyploids. It's something that we can exploit in terms of peppers, as well as many other domesticated plants.

Many studies and papers have been published on this topic in the past few years, it's part of the cutting edge of genetic research into plant evolution and hybridization.

It's definitely food for thought, if you are into that kind of thing.

 

[Max Burn]

Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation - Nature Communications

Existing genetics and genomics studies of peppers mainly focus on single species. Here, the authors report a pepper graph pan-genome and a genome variation map of 500 accessions from five domesticated species and close wild relatives to reveal their domestication, introgression and population...

www.nature.com

A link to another paper on Capsicum evolution:

Genomes of cultivated and wild Capsicum species provide insights into pepper domestication and population differentiation

 

[Pepper-Guru]

Everything is a hybrid and numbers of seed sown matters a whole hell of a lot in terms of whether or not you’ll see those special gifts nature provides. Nice. Great article.

 

[Hammer Town]

This explains why many seed sellers give caveats about “this is only F3 or F4 so you might get different results” .
I for one am puzzled why, for instance, the MOA scotch bonnet shapes are somewhat all over the place despite having been bred for who knows how many decades. You’d think that they would have been able to breed in the signature 4 lobed , bonnet on top shape by now.
The ghost pepper type on the other hand displays very good genetic stability. Every time I grow a ghost I get consistently good production with the trademark size, shape and colour etc.

 

[Hammer Town]

Everything is a hybrid and numbers of seed sown matters a whole hell of a lot in terms of whether or not you’ll see those special gifts nature provides. Nice. Great article.

Yes, growing out a thousand plants of one type will give you a very high probability of getting at least some results that would be desirable, or with the typical sought after genetic traits. Or produce something atypical that one would want to jump on and grow out .
There seems to be a lot of people who get an unexpected result in their garden and all of the sudden there’s a “new” strain on the market.
The idea of breeding two lower heat types together and getting a super hot, or even the reverse, seems pretty commonplace these days.

 

[Max Burn]

https://www.mdpi.com/2223-7747/14/14/2136

The Dynamics of Long Terminal Repeat Retrotransposon Proliferation and Decay Drive the Evolution of Genome Size Variation in Capsicum

One of the tangents that interests me is that an enormous amount of domestication for numerous plant species took place in the Andes thousands of years ago. It's gets mysterious, take corn for example, it is said to have been domesticated in Mexico, but the oldest corn from Mexico is only partially domesticated and the oldest corn from the Andes is a thousand years older and it's fully domesticated.

Peppers themselves have a similar situation, a lot of ancestral species appear to originate in South America. It's not really useful knowledge, just trivia, but it appears that Capsicum chinense has origin in or near the Amazon. I have my own theories about some of the domestications over time and their relationship to various regions but those theories are educated guesses at best. What is clear is that the botanical achievements of precolumbian New World cultures are remarkable.

Sometimes I wonder if some of what we consider to be native species of various plants are actually just feral populations that have drifted and homogenized over millennia. I don't actually believe we can calculate dates of hybridization and evolutionary divergence using concepts of genetic mutation rates. I think that is more like genomic astrology than an actual science, no offense intended.

 

[Hammer Town]

https://www.mdpi.com/2223-7747/14/14/2136

The Dynamics of Long Terminal Repeat Retrotransposon Proliferation and Decay Drive the Evolution of Genome Size Variation in Capsicum

One of the tangents that interests me is that an enormous amount of domestication for numerous plant species took place in the Andes thousands of years ago. It's gets mysterious, take corn for example, it is said to have been domesticated in Mexico, but the oldest corn from Mexico is only partially domesticated and the oldest corn from the Andes is a thousand years older and it's fully domesticated.

Peppers themselves have a similar situation, a lot of ancestral species appear to originate in South America. It's not really useful knowledge, just trivia, but it appears that Capsicum chinense has origin in or near the Amazon. I have my own theories about some of the domestications over time and their relationship to various regions but those theories are educated guesses at best. What is clear is that the botanical achievements of precolumbian New World cultures are remarkable.

Sometimes I wonder if some of what we consider to be native species of various plants are actually just feral populations that have drifted and homogenized over millennia. I don't actually believe we can calculate dates of hybridization and evolutionary divergence using concepts of genetic mutation rates. I think that is more like genomic astrology than an actual science, no offense intended.

The prevailing opinion does seem to be of a South American/Andes origination for capsicums. What I would find interesting would be finding out how the various types such as chinense, anuum, frurescens etc came about and whether they are mutations that came about naturally over time, or whether there was some human intervention in them or ???.
I suspect that the full answer will never be fully and conclusively found.

 

[Hammer Town]

https://www.mdpi.com/2223-7747/14/14/2136

The Dynamics of Long Terminal Repeat Retrotransposon Proliferation and Decay Drive the Evolution of Genome Size Variation in Capsicum

One of the tangents that interests me is that an enormous amount of domestication for numerous plant species took place in the Andes thousands of years ago. It's gets mysterious, take corn for example, it is said to have been domesticated in Mexico, but the oldest corn from Mexico is only partially domesticated and the oldest corn from the Andes is a thousand years older and it's fully domesticated.

Peppers themselves have a similar situation, a lot of ancestral species appear to originate in South America. It's not really useful knowledge, just trivia, but it appears that Capsicum chinense has origin in or near the Amazon. I have my own theories about some of the domestications over time and their relationship to various regions but those theories are educated guesses at best. What is clear is that the botanical achievements of precolumbian New World cultures are remarkable.

Sometimes I wonder if some of what we consider to be native species of various plants are actually just feral populations that have drifted and homogenized over millennia. I don't actually believe we can calculate dates of hybridization and evolutionary divergence using concepts of genetic mutation rates. I think that is more like genomic astrology than an actual science, no offense intended.

I hypothesize that shifting climates and habitat over millennia have led to the necessary mutation and adaptation of flora and fauna to survive over time. Those that did not adapt , or could not adapt, become extinct.
I saw a video the other day that claimed that something like 47 species of animals are going extinct every day. I also saw a story a couple of days ago about an “extinct bird from New Zealand” was recently found in New York City .

 

[CaneDog]

Thanks for sharing Max and welcome back!

 

[Max Burn]

Thanks!

I suppose there is a bit of a semantics issue here. A person could consider a gene duplication or sequence inversion, which are results of transposable elements, as resulting in types of mutation. However when they occur due to hybridization interactions I think of them as recombinations. I suspect that both ways of framing the distinction have value. However I tend to think of mutations as spontaneous things that occur in a given population as opposed to interactions of genomic conflict in hybrids of distinct populations.


On that note:

Reproductive compatibility in Capsicum is not necessarily reflected in genetic or phenotypic similarity between species complexes

Wild relatives of domesticated Capsicum represent substantial genetic diversity and thus sources of traits of potential interest. Furthermore, the hybridization compatibility between members of Capsicum species complexes remains unresolved. Improving our understanding of the relationship between...

journals.plos.org

Reproductive compatibility in Capsicum is not necessarily reflected in genetic or phenotypic similarity between species complexes

I suspect that sometimes our taxonomic preconceptions are a bit limiting in terms of ratiocinatoric endeavors. It's all too common to try to alter observations to fit beliefs as opposed to ensuring that belief fits the observation, at least in my experience, which is to say I've often realized I was wrong as I learned more about a subject.

I wonder, if I lived over a 100,000 years from now and encountered fossils of a Great Dane and a Chihuahua, would I be able to recognize them as distinct forms of a single diverse species or would I consider them separate related species?

In some ways taxonomy is a convenient way of framing observable relationships but it is also a form of contrivance, a type of intellectual contraption or a machination. Species is a convenient word to employ, but it's a made up word that attempts to describe a relationship which isn't nearly so standardized and well defined as we would prefer it to be.

It's curious that many species appear to be created as a result of two distinct parental species mating successfully against the odds and producing offspring that are unlike either parent, despite being formed from them. That there are genetic elements that can self modify, resulting in genes moving around, genomes being reorganized, sequences being inverted or duplicated or even eliminated makes this subject as complex as it is intriguing.

Ordinarily the elements that can cause such profound genetic restructuring exist in a regulated or inhibited form in organisms, but when two dissimilar genomes are combined in some hybridizations a conflict arises in which such limitations and inhibitions are decreased and dramatic interactions occur. It is as if the cells and their machinery and their genetic information have mechanisms that try to reshuffle and fix incompatibility and make it all work again. It also seems clear that some of the most interesting and dramatic changes are among the least frequent. Some hybridizations in some plants may succeed only a few times, out of hundreds of thousands of crosses and yet in those cases produce unique outcomes.

Consider, for example, the recently published case of the origin of a relative of Capsicum, Solanum tuberosum, aka the potato:

Redirecting

Ancient hybridization underlies tuberization and radiation of the potato lineage

Another case of a species originating from a restructuring of a hybrid! The paper claims this occurred 8-9 million years ago, but I suspect that our methods of arriving at such dates are themselves contrivances though not impossibilities, I think the dating of such events is much less certain than the observation that such events certainly occurred and did so long ago.

It's clear as well that transposable elements also played important roles in such events which produced radical phenotypes from distinct parental populations that were quite unlike the eventual result.

I can't help but think of human chromosome #2 when I read of such things either, which is a chromosome that was the result of the fusion of two ancestral chromosomes. Could such a restructuring in our own genomes have arisen from transposition and hybridization? I cannot help but think that's at least one of the possibilities, but of course that's neither here nor there, it's just wondrous trivia.

In terms of utility of knowledge, being able to take our understanding and apply it to something productive, it's useful to know that two related species that are typically unable to produce offspring may in some cases produce them infrequently and that the result is an often peculiar combination where one parental genome is much more strongly expressed than the other, which is a thing that is called subgenomic dominance. Such offspring are not equal mixes of both parents.

It's also interesting that often reluctant hybrids are incapable of self pollination, but may still be able to pollinate a parental form or yet another close relative. This is a numbers game, if the combination of distinct genomes is only able to produce a viable gamete one out of a thousand times then the odds of self pollination are extremely low, yet pollen is produced in amounts large enough that it's sometimes possible for a plant with such reduced fertility to pollinate a parental form or a close relative.

We also know that a lot of combinations of hybrids don't work so well, the plants may be dwarfed, they may stop growing or exhibit symptoms as if they are infected by a virus. In terms of crosses that is not a bad sign per say, because it's a sign of plants trying to make their distinct subgenomes work together anyway and typically if you have enough plants from a cross that tends to exhibit such traits, a minority of them will grow well. It's a numbers game.

We often see such cases where the majority of plants produced by such hybridizations are such miserable beings that we feel as if the effort is unwarranted or results in a weakening or dilution of genetic strength, yet even the desirable forms of plants that we breed together in pure forms were themselves once formations of hybridizations that themselves resulted in largely miserable results as well, with only a few of the combinations being successful and healthy. Moreover some combinations, even when infrequent, can still produce specimens which exhibit unusual vigor and health, in addition to unique and desirable traits.

The indication is, then, that hybrid results like viruses-like symptoms or dwarfism are not a bad sign, for they indicate that the genomes of the parents are attempting to work together, meaning that such populations are where much more interesting and desirable forms are likely to be found, despite being in the minority.

This is apparent in many hybridization efforts, not merely those of Capsicum. When learning that 90% of a certain cross tend to exhibit dwarfism or grow poorly, for example, this potentially means that 10% grow just fine. It is my suggestion that such ratios should not be discouraging or considered as problematic as they might at first seem, but rather that it can also be said of such populations that; this is where the magic happens.

At the same time there is nothing magical about plants that grow poorly and one must be willing to grow many plants, select the few and discard the rest, to be able to beat exploit the interactions and recombinations of which I write about.

Indeed, much as long ago there was no such thing as a potato, there was no such thing as a hot pepper whatsoever, but at some point recombinations resulted in their creation, so too does the future potentially contain plants and combinations of them which today do not even exist. It's entirely possible, for example, that one day a Capsicum line will be developed which produces capsaicinoids in and or on its leaves. It's even possible that such a plant has arisen and gone undetected and then died off in the past. In fact many botanical possibilities exist that are presently beyond our imagination or realization, even without the use of GMO technology.

Many beloved plants originated as hybrids like potatoes, peppers, corn, poppies and more.

We often think that everything that can be done or will be done has been done and we are just repeating or doing it again, but consider even a deck of cards, in a deck of 52 cards the possibility of combinations is 52^52, that is 52 to the exponential value of 52, which is an enormous number larger than the number of all humans who have ever lived. Odds are that when you shuffle a physical deck of cards that the combination you create has literally never been done before.

Plants have thousands of genes, with far more possibilities than a deck of cards, the potential combinations are incalculable even without the use of advanced genetic technology but it requires time and effort, as well as a bit of faith and encouragement. Each year new varieties and combinations of pepper genetics are formed which have never before existed on this planet. There are already thousands of varieties of Capsicum in existence, the potential for amazing new combinations is tremendous. Go for it.

I hope you enjoy this topic as much as I do.

 

[SatanicFlatIron]

Thanks, MN. Your thoughts on the topic are the kind of content I really enjoy reading.
This type of mechanism could explain the genesis of mutations such as anthocyanin retention in Pimenta da Neyde, the numbers game that allows the viability of some interspecific hybrids with zygotic barriers (e.g. C. annuum x C. baccatum), the recently documented possibility of crossing the purple corolla clade with other clades besides C. pubescens (C. baccatum x C. eximium), and the fact that not all C. chinense x C. annuum hybrids exhibit dwarfism or VL syndrome. The topic of backcrossing is also certainly interesting and I'll keep it in mind if some of my interspecific hybrids fail to self-pollinate.

When learning that 90% of a certain cross tend to exhibit dwarfism or grow poorly, for example, this potentially means that 10% grow just fine.

Is this percentage an example, or do you think it could also be applied to some of the interspecific examples I mentioned?

 

[Max Burn]

With the hybrid dwarfism I was referring to, I had poppy hybrids in mind specifically, where a majority of certain crosses between species are dwarfed but a minority of around 10-30% are not.

In regards to Capsicum it's trickier.

https://www.researchgate.net/publication/372156731_Understanding_and_overcoming_hybrid_lethality_in_seed_and_seedling_stages_as_barriers_to_hybridization_and_gene_flow

The above link has a paper about overcoming hybrid lethality barriers and it mentions specifically that Capsicum can have temperature dependent issues wherein plants grown at higher temperatures can overcome the issue.

The higher temps are basically 85-95 degrees fahrenheit or so, as discussed in this paper:

Temperature-dependent sugar accumulation in interspecific Capsicum F1 plants showing hybrid weakness - Journal of Plant Research

In plants, F1 hybrids showing hybrid weakness exhibit weaker growth than their parents. The phenotypes of hybrid weakness are often suppressed at certain temperatures. However, it is unclear whether hybrid weakness in Capsicum annuum × C. chinense is temperature-dependent or not. Our study...

link.springer.com

Another paper on hybrid weakness:

Evolution and Molecular Control of Hybrid Incompatibility in Plants - PMC

Postzygotic reproductive isolation (RI) plays an important role in speciation. According to the stage at which it functions and the symptoms it displays, postzygotic RI can be called hybrid inviability, hybrid weakness or necrosis, hybrid sterility, ...

pmc.ncbi.nlm.nih.gov

Another paper from the 1990s called

Genetic analysis of stunted growth by nuclear-cytoplasmic interaction in interspecific hybrid of Capsicum by using RAPD markers
Discussed how hybrid weakness, despite relating to specific inherited alleles or genes is due, nevertheless, to interactions between nuclear genetics and cytoplasmic elements.

Here is another link to another paper on the topic:

Capsicum annuum with causal allele of hybrid weakness is prevalent in Asia - PMC

Reproductive isolation, including hybrid weakness, plays an important role in the formation of species. Hybrid weakness in Capsicum, the cessation of plant growth, is caused by two complementary dominant genes, A from C. chinense or C. frutescens ...

pmc.ncbi.nlm.nih.gov

That one discusses prevalence of genetics involved.

Here is another paper link:

Successful Wide Hybridization and Introgression Breeding in a Diverse Set of Common Peppers (Capsicum annuum) Using Different Cultivated Ají (C. baccatum) Accessions as Donor Parents

Capsicum baccatum, commonly known as ají, has been reported as a source of variation for many different traits to improve common pepper (C. annuum), one of the most important vegetables in the world. However, strong interspecific hybridization barriers exist between them. A comparative study of...

journals.plos.org

Successful Wide Hybridization and Introgression Breeding in a Diverse Set of Common Peppers (Capsicum annuum) Using Different Cultivated Ají (C. baccatum) Accessions as Donor Parents

This one contains some useful information.

Virus-like-syndrome or dwarfism was observed in F1 hybrids when both C. chinense and C. frutescens were used as female parents.

This is useful because in some cases the reciprocal cross of a hybrid that exhibits dwarfism: doesn't. This also shows that cytoplasmic inheritance plays a role in this. Since plants inherit cytoplasmic contents and mitochondria from their mothers, and this acts like hardware, while the nuclear genetics inherited from both mother and fathers, so to speak, act like software, it's easy to see how some sets of software might be less compatible with some sets of software.

In some cases issues arise because the hardware, like chloroplasts, inherited from the mother have two distinct sets of distinct instructions from each parent, instructions which cannot both be followed. Interestingly cacti can sometimes appear to follow both sets of instructions and a single meristem can give rise to two distinct types of tissues together, but that's not something that appears to happen in most plants.

Theoretically because of genetic mixing events in both meiosis and when gametes fuse in fertilization, even hybrids that tend to produce dwarfism and hybrid weakness or lethality should have some potential combinations where this does not occur. It could be the case that only a few combinations in a thousand or a hundred thousand fertilizations grow well. With Capsicum, which does not produce thousands of seeds per fruit, this makes it challenging to overcome lethality by using large numbers of seeds, but not totally impossible. However using strategies like growing seedlings at higher temperatures appears to be a more viable solution, but one must at some point envision growing offspring at lower temperatures and obviously creating a line of plants that cannot be grown at lower temperatures is not convenient. This means at some point a breeding approach will require a different strategy that likely relies on numbers, even when hybrid lethality is overcome using other strategies at first.

That shouldn't be too difficult if an F2 generation can be achieved. While certain F1 combinations result in fairly consistent hybrid lethality or dwarfism, if a strategy like using heat allows this to be overcome some of the F2 combinations should lack the incompatibility of the F1. (Aa in F1, aa: Aa/aA: AA in F2)

However it might also be a viable or even a preferred strategy to avoid F2 and if using heat to overcome hybrid lethality the plants are then backcrossed to a parental form using the F1 as the pollen donor, again giving rise to a generation where the hybrid lethal combination is less frequent.

In poppies hybrid lethality is also known, but they can often produce several thousand seeds per fruit and are easy to sow in large numbers and obviously, plants that don't suffer from the lethality grow well and so it's a easier to use the numbers strategy than it is with Capsicum. This makes it easier to use cross species introgression, but many aspects of hybrid lethality are similar in numerous types of plants where the issue is that the meristem (to return to the previous analogy which I find useful) is trying to use a maternal set of cytoplasmic hardware with two sets of distinct software that provide different or conflicting instructions, including one of which is potentially incompatible with the hardware.

I suspect altering the ploidy may also be a viable strategy, where one could use a chemical agent on geminating seeds, which promotes an increase in the number of chromosomes in the population, to compensate for the incompatibilities, which I believe fall under the category of genomic shock, but that's more speculative in terms of strategies I have studied or observed. It is known however than spontaneous changes in ploidy are involved in some plant strategies to overcome barriers to hybrid fertility, such as has been recently identified in the evolutionary history of Ipomoea batatas, for example. More about that can be found here:

Scientists Finally Unravel the Sweet Potato’s Ancient Genetic Secret

Across bustling markets in Nairobi, rural fields in Malawi, and backyard gardens in Peru, the sweet potato is more than…

www.sciencenewstoday.org

It appears that there are a few ways that plants and the people who grow them can overcome some of the issues that potentially arise due to genomic shock in hybrids.

 

[Max Burn]

More on the theory about hybrid weakness and overcoming it via heat. I realize this is not the same topic as transposons in Capsicum evolution, but felt like hybrid lethality and dwarfism relates to this thread and is such a niche topic that few readers are going to have an in-depth interest in it so I'm just writing about it here as a tangent related to the discussion. Thank you for your patience.

https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.12711

Capsicum annuum S (CaS) promotes reproductive transition and is required for flower formation in pepper (Capsicum annuum)

This paper is interesting in relation to hybrid lethality and dwarfism, as the onset of such lethality or dwarfism occurs typically around the time in the life of a seedling when it is transitioning to adulthood, a time when ordinarily the plant begins to form flowers.

As mentioned in this paper, in Capsicum and it's close relatives this transition phase typically involves the primary meristem terminating and then growth occurs from lateral meristems which form reproductive organs in which gamete formation occurs.

plants in the family Solanaceae, such as petunia (Petunia hybrida), tomato (Solanum lycopersicum) and pepper (Capsicum annuum), are characterized by sympodial shoot architecture: the SAM terminates in an IM, and plant growth continues from lateral meristems, termed sympodial meristems (SYMs), which develop in the axil of the youngest leaf below the apical inflorescence (Schmitz & Theres, 1999). The SYM develops into a shoot segment termed the sympodial unit (SU), consisting of vegetative and reproductive organs in a species-specific pattern, and new SYMs are repeatedly formed from the axils of the uppermost leaves of the preceding SU.

Note that above this is stated to occur in a species specific manner. It is typically at this stage when hybrid lethality occurs, where growth ceases, the original SAM or shoot apical meristem terminates but is not replaced by new flower producing growth.

The paper goes on to describe a transcription factor called LFY or Leafy, which plays a role in this process.

Transcription factor - Wikipedia

en.wikipedia.org

A transcription factor is a special protein, like a little machine, that interacts with DNA sequences and turns them on and or off at the right times, allowing their encoded instructions to operate.

It's not difficult to see how the genes of an organism work closely with its transcription factors like LFY and how different combinations of such factors and genes can lead to complications.

Many transcription factors are inherently maternally, from the mother. Meaning that if the pollen of a father has genes that the transcription factor is not accustomed to, the relationship between the genes and the transcription factor will not function in an ideal way.

In this manner, the transcription factor of one species may not work well with the genes of another closely related species. This type of situation is not uncommon in terms of hybridization of closely related species where offspring form but their ability to grow and mature is adversely affected.

The transcription factor LFY is often called a meristem identity gene. It is required for the production of flower tissue and is found in all flowering plants. Because it interacts with the genes of an organism different subgenomes may not have equal compatibility with it. Notably in seeds, a meristem already exists in dormant form, which uses the cells of the mother to form and gain its cytoplasmic contents. However as it matures when the seed becomes a plant, it needs to work with the subgenomes of the mother and father and thus complications can arise.

So far LFY is known to interact with three distinct target genes , AGAMOUS, APETALA3 and APETALA1. The first two are floral homeotic genes involved in flower formation while the last is a meristem identity pathway gene.

https://en.wikipedia.org/wiki/ABC_model_of_flower_development

Above is a link discussing a theory of flower formation involving floral homeotic genes and meristem.

https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.20017

Above is a paper discussing heat stress proteins, which are themselves often transcription factors relating to survival of plants in hot environments. What is interesting is that high temperatures can be used to overcome Capsicum hybrid lethality and dwarfism, using temperatures in the 85-95 degrees Fahrenheit range. Heat stress proteins help ensure plant survival and recovery from the effects of heat, which can inhibit transcription by affecting multiple aspects of growth and function, like enzymatic rates of operation and protein structure. Essentially it appears that issues of maturation in terms of hybrid incompatibility are able to be compensated for by the same proteins that compensate for issues related to heat stress.

In effect heat exposure potentially activates plant elements that work to ensure survival and function.

Unlike maternally inherited transcription factors, heat stress proteins are typically produced from nuclear genes which are activated when heat stress occurs, meaning that they can promote the production of encoded transcription factors from a subgenome which are compatible with that subgenome, to replace the potentially heat damaged transcription factors in the cytoplasm. This can potentially compensate for compatibility issues in terms of cytonuclear interactions.

Heat can harm proteins like LFY, which then need to be replaced to ensure plant survival and growth and so heat stress pathways include means to replace damaged cytoplasmic contents using nuclear genetic instructions, which then can overcome incompatibilities that existed with the maternally inherited transcription factors by replacing them with compatible ones. In theory at least, this is what makes sense to me. I could be wrong and if you have information that contradicts what I understand and believe please feel free to present it.

 

[Max Burn]

Regarding Genomic Shock and transposable element activation in hybrids, this is well known in Nightshades by analysis of genomes.

From:

The Genomic Shock Hypothesis: Genetic and Epigenetic Alterations of Transposable Elements after Interspecific Hybridization in Plants - PMC

Transposable elements (TEs) are major components of plant genomes with the ability to change their position in the genome or to create new copies of themselves in other positions in the genome. These can cause gene disruption and large-scale genomic ...

pmc.ncbi.nlm.nih.gov

3.12. Nicotiana

In Nicotiana sylvestris × N. tomentosiformis hybrid (synthetic N. tabacum allotetraploid), a significant increase of Tnt1 LTR retrotransposon copy number was observed derived from maternal elements

3.16. Solanum

Raza et al. (2017) [109] performed a comparative analysis of the DNA methylation patterns in Solanum lycopersicum, S. pimpinellifolium, and their reciprocal hybrids and found that the reciprocal hybrids had lower levels of DNA methylation in LTR retrotransposons than their parents...

In general, in the Solanum species hybridization seems to activate certain TEs accompanied by a reduction in DNA methylation.

Solanoideae is a subfamily of Solanaceae, it includes about a dozen closely related tribes, which contain both Solanum and Capsicums

Solaneae, which includes tomatoes and Potatoes as well as other plants, and Physaleae which includes ground cherries and tomatillos and Capsiceae which includes Capsicum; are known to be a well-supported monophyletic group.

The occurrence of genomic shock and transposable element mobilization in interspecific hybrids in these Solanoideae plants is well supported by both analysis and observation.

It is true that some organisms exhibit genomic shock and that some do not, in terms of hybrid observations. It is variable and specific to the organisms. It is something well known in Solanum and Capsicum species, from genomic analysis and observation.

 

[Bou]

Lots of interesting reading herethanks for sharing.