What do you mean by genome organisation or architecture?

Dear Abhijeet...

We can never assume that the different genomes belong to the same level of complexity and organization. Some traits are simply under the genetic control, while in the other traits both genetic and epigenetic mechanisms sharing control over their inheritance. Therefore, we always tend to deal with simpler and less complex genomes for better understanding. Thanks.

Sorry, you need to define what you mean by "higher organized genome". This term has no real scientific meaning. Breeding and domestication will select for certain traits that can be bred out of a wild-type population, but this should not affect the genome at the gross level. In general, selective breeding over hundreds of years will not create a new species. Just consider dogs as an example, domestication selected for traits (allelic variants) and breeds, but they are still dogs and can still be bred to each other.

Dear Gregory...

It is very simple!! Some traits are fully controlled by nuclear genes, while other traits both nuclear and cytoplasmic genes participated in its inheritance! Again, some traits are controlled by genetic effects, whereas other traits organized via genetic and epigenetic effects. Now, which mechanism is more organized (has different levels of organization, genetic and epigenetic), that with genetic effects or the one with genetic and epigenetic effects??

This is a philosophical question. There are not enough detailed studies that could concern all aspects of genome architecture and epigenetic to draw any conclusions about it.

Dear Stephan...

Your opinion is highly respected. If we have no or a little knowledge about a specific theory this will not make a question about it "Philosophical"!! For me, I will try to answer this question through suitable methods, this is the positive way to react!!!

Thanks.

Actually you cannot analyse the genome architecture and epigenetic of enough individuals from diverse species to draw a general conclusion about that.

But please write me if you have a result and which methods you have used and how many Individuals you have analysed.

OK, Keep in touch!!

not clear

You should have said that wild plants have more diverse genes than cultivated counterparts. Through systematic breeding, many genes (responsible for not-desirable traits for human consumption) are selected out for current cultivated elite lines. And the loss of some important genes can make these cultivated lines more vulnerable to, for example, disease resistance.

@ Ayoob Obaid Alfalahi,

I think I know what you tried to say. Wild species usually give small fruits, lower yields...and, on the other hand, cultivated elite lines usually give better fruits quality and better yields. So, you think that these results are due to a 'higher organized genome'. However, the term is not correctly used here. Instead, through continuous breeding, favorable alleles are artificially selected for and accumulated. And this causes the better performance of these cultivated lines (**this is the essence of plant breeding and cultivar development). A better performance of a cultivar is not only due to genotype, it also links to the interaction of genotypes and environments (i.e. GxE effect).

Yuan is correct, that selective breeding in domesticated species selects for traits from a wild-type population by enriching for specific allelic variants. This is not due to epigentic effects nor does it change the structure or organization of the genome. Epigenetic modifications act on the genome to regulate gene expression, silence some genes, and mark enhancers/promoters. Such modifications are methylation of histones and/or CpG dinucleotides, for example. Whether these are trans-generational, i.e.inherited from parent to offspring is still quite controversial.

I'm really appreciated for all these valuable inputs, and I like to make something clear:

1. Traits inheritance is controlled by different genes, hence different mechanisms.

2. These different mechanisms are involved genetic and/or epigenetic effects!

3. The inheritance of trait that only submitted to genetic effects is not complicated as trait submitted to both, genetic and epigenetic effects!!!

Now, which trait has the higher level of organization??

@ Ayoob Obaid Alfalahi,

I just carefully read your earlier reponse to Gregory. What makes you think that 'the WILD species' have no such phenomena (of 'genetic effect' and 'epigenetic effect'), or teamwork (between 'genetic effect' and 'epigenetic effect'), compared to its cultivar counterpart?

@ Gregory Dressler,

Thanks for the response. But I was thinking: will the 'epigenetic' mechnism in the 'wild' species change a bit (due to evolution) [ex. becoming simpler or more complicated] on the course the wild species domesticates into a specific environment? Have you heard about anything like that??

Epigenetic mechanisms, such as Polycomb mediated repression or trithorax mediated activation or DNA methyltransferases, will be found in WT and domesticated species because they are essential for gene control and for development. Domestication is unlikley to change those mechanisms because the traits selected for are unlikely to be linked to these genes. However, it is formally possible that a variant in a Polycomb gene could be selected for because it may affects crop yields, but such a variant would affect hundreds of genes and would likely affect hundreds of traits. Regardless, any trait and any allelic variant can be subjected to epigenetic modifications by the environment, which can up or down regulated gene expression, but that generally is not inherited in the next generation.

Ayoob, we still do not know what higher level of organization you refer to? All genes have higher structural organization, i.e. nucleosomes, chromatin, compaction, etc.

@ Ayoob Obaid Alfalahi,

Sorry, I just saw your last post:

"3. The inheritance of trait that only submitted to genetic effects is not complicated as trait submitted to both genetic and epigenetic effects!!! Now, which trait has the higher level of organization??"

If the statement is ture, I would probably carefully say: "the later trait is more tightly controlled". It is not much to do with 'higher genome organization'.

Dear Dr.Yuan-Yeu, thanks for these reasonable statements.

This is very close to what I meant, I used the term "Highly Organized Genome" to describe the genomes through which "Traits are Tightly Controlled".

Thanks Sir.

Hi Ayoob,

Yes, I know what you tried to say. But using the term 'highly organized genome' will confuse people. When you said 'highly organized genome', the image (see attachment) will pop out automatically for many people...It generally refers to how the DNA is organized and packed into chromosomes in the nucleus (eukaryotes).......That is why we have this long discussion.

But it is a good discussion, though.