Dear Shu Chen,

this phenomenon is common in plant species. In White clover (Allotetraploid) a similar situation exists - the subgenome from one progenitor is almost perfectly retained, while the other subgenome contains many genetic variations and deletions. I am not entirely sure why one sub-genome is retained with higher fidelity than the other, but the redundancy does mean that one homeologue is free to evolve rapidly.  The formation of hybrids (including allo-polyploidy) does introduce one genome to the si/TaSi/miRNAs generated from the other.  This is thought to contribute significantly to the epigenetic regulation of the hybrid - which is significant for phenomena such as heterosis/hybrid vigour.

I'm sure others will have additional comments of use.

Cheers,

Nick

Dear Shu Chen,

In human Genetics, there are significant differences in recombination fraction between males and females. We can see result of this in Mapping; the genetic length in females(4460 cM) is 72% greater than the genetic length of males(2590cM). In human this phenomenon has not been solved exactly but It is strongly speculate that female gamete precursors remain long time (many years) in Meiosis I before ovulation different than males. I hope this may help you.

Wishing you all the best for your career.

Kenan Delil.

Dear Nick Albert,

Thank you very much for your reply. Could you show me the paper about the subgenome variation in white clover? 

When you say "The formation of hybrids (including allo-polyploidy) does introduce one genome to the si/TaSi/miRNAs generated from the other.", do you mean that the parental subgenome is more likely to change because subjected to the si/TaSi/miRNAs regulation from a foreign cytoplasmic environment? But is it always the case that maternal subgenome shows less genetic variation since hybridization? I remember I read a literature review about a subgenome will evolve less drastically if from a population was experiencing a severe bottleneck before hybridization.

Hi Shu Chen,

First off, this isn't my field of expertise, but rather something I've noticed having worked on an allopolyploid - you should also try to get in touch with people who work on polyploidy specifically. So with this in mind, here are some further comments that I hope will help: 

The full report of the white clover sub-genomes isn't yet published, but those of us working on genes from clovers have noted it previously.  I've certainly found this on the genes I worked on in Trifolium (Anthocyanin MYB genes - I could easily distinguish where some of the genes came from). The genome of white clover + progenitors has been sequenced, and I believe is being prepared for publication - see this conference abstract https://pag.confex.com/pag/xxi/webprogram/Paper7698.html.

You might also find some useful comments in Williams et al. BMC Plant Biology 2012, 12:55 http://www.biomedcentral.com/1471-2229/12/55.

My comment about the small RNAs refers to the events that happen during hybridisation of distinct genomes. Even in Arabidopsis accessions, crosses that exhibit heterosis display dramatic changes in the 24nt siRNAs, and also some very interesting alterations in gene expression from both parental alleles (http://www.pnas.org/content/108/6/2617.abstract) .  I don't think this is limited to the maternal parent.

It seems plausible that if one progenitor was highly homozygous, and the other was heterozygous that might account for some differences in the genetic diversity in the polyploid hybrid. But I'm not sure if this would explain the dramatic gene loss that can occur within one sub-genome.

I hope this helps,

Cheers,

Nick

Perhaps the organism treats its two genomes differently.  This sounds far-fetched but there is an example in amphibians:  _Rana esculenta_ has haploid genomes from two different ancestors, but during gametogenesis it destroys the set that came from _R. ridabunda_ and only propagates the set that came from _R. lessonae_.

That specific thing won't be happening in your plants, but if one ancestral genome is sequestered or suppressed in some way, it will have a very different substitution rate than the other one.