If a plant has high genetic variation, it indicates that the plant has a high chance of adopting the natural environmental conditions and vice versa. The percentage of DNA polymorphism always remains high in the case of DNA extracted from callus and in vitro callus derived shoots. I am working on some endangered plants with very few individuals in each pocket with low genetic variation (polymorphism). If I find sufficient polymorphism in in vitro callus generated shoots due to somaclonal variation, that means plants have a higher adaption power due to that variation compared to natural genetic variation and are supposed to survive in their natural habitats, if transferred. There may be some epigenetic changes to generate that variation. If I check polymorphisms that with the plant's natural genetic polymorphism will it help me to understand epigenetic changes during callus mediated organogenesis?
The most important aspect is to have solid phenotypes/phenotyping. That is use same genetic material and firmly show that exposure to a different environment resulting in lasting changed phenotypes (that is mitotically or meiotically) propagated (i.e obtain epitypes).
It is important to know what kind of plasticity you are planning to look at and to appreciate that there are many different types of plasticity. Some that are caused by epigenetic mechanism (but no changes in the primary DNA sequence) and some that are not (i.e changes in the primary DNA sequence) such as caused by chromosomal rearrangements or mutations.
You can look at some of our publications on how we found the epigetic phenomenon in our systems even before we started to use molecular methods.
Look at these and references therein:
An adaptive epigenetic memory in conifers with important implications for seed production 2012
Differential gene expression related to an epigenetic memory affecting climatic adaptation in Norway spruce. 2011
MicroRNAs, the epigenetic memory and climatic adaptation in Norway spruce. 2010
Hi Biswajit
If you want to check epigenetics changes and don't have facility for MSAP analysis you can use MS-RAPD.
You can use the protocol proposed by Luis Valledor https://www.researchgate.net/publication/234158987_Is_the_Interplay_between_Epigenetic_Markers_Related_to_the_Acclimation_of_Cork_Oak_Plants_to_High_Temperatures?ev=prf_pub
Good luck
Rodrigo
Article Is the Interplay between Epigenetic Markers Related to the A...
The most important aspect is to have solid phenotypes/phenotyping. That is use same genetic material and firmly show that exposure to a different environment resulting in lasting changed phenotypes (that is mitotically or meiotically) propagated (i.e obtain epitypes).
It is important to know what kind of plasticity you are planning to look at and to appreciate that there are many different types of plasticity. Some that are caused by epigenetic mechanism (but no changes in the primary DNA sequence) and some that are not (i.e changes in the primary DNA sequence) such as caused by chromosomal rearrangements or mutations.
You can look at some of our publications on how we found the epigetic phenomenon in our systems even before we started to use molecular methods.
Look at these and references therein:
An adaptive epigenetic memory in conifers with important implications for seed production 2012
Differential gene expression related to an epigenetic memory affecting climatic adaptation in Norway spruce. 2011
MicroRNAs, the epigenetic memory and climatic adaptation in Norway spruce. 2010
Thanks Dr. Carl Gunnar Fossdal. Actually I have some morphotypes of some high altitude Himalayan plants. Same plant grow at lower altitude(9500 ft) show big leaves and rhizomes and same at quite high altitude (14500 ft) show dwarf nature. But at the same time, some at base of Mt. Kanchenjongha (17000 ft) show big leaves and rhizomes. More over that plants have the adaptability to survive at quite lower altitude (5000 ft), but, a similar species (needs taxonomic revision) can not thrive at lower altitude (5000 ft). Both the species are critically endangered in their natural habitats. How is that possible?
It may well be that there is epigenetic effects at play but then you must describe to us how they were propagated. Have you vegetatively propagated them? Or made seeds from the same parents at different altitudes? And performed common garden type experiments? Have you ruled out that different soil conditions (i.e lack of Nitrogen, Mg, Fe, P, S) or even if mycorrhiza is a factor? Is the reason why they are critically endangered known?
They are main propagated by rhizome cuttings and seeds also. But, from seeds, the percentage is less in nature. Those morphotypes are found at different altitudes separated from at least 50-60 kms. No sir, I am able to grow them in vitro but in field conditions, they are unable to grow for long time as temperature and altitude is a factor. yes, mycorrhizal association was reported for their better association of roots and growth.
Sounds interesting, but it must be very challenging to perform the experiment., I guess use of controlled growth chambers or the like is not possible for you? But certainly the chance to find epigenetic effects should be good.
Bose, A more probable solution is to rule out all soil related factors under controlled environment at the altitude the species could not survive in natural habitat. If all these factors are checked, you may establish the cause of mortality at the deleterious altitude. More so, what is the collection pressure associated with the species? The regeneration rate may affect its population especially if it has limited adaption and genetic variation in its natural habitat.
yes Francis. I am able to grow all of them in in vitro conditions with special experimental design. They all respond well. But, I must say, it was quite difficult to regenerate them. I observed that if one really works with some real endangered species, he/she must find out the reasons for endangerment of that species. If the reason is just over exploitation or anthropocentric activities, then those species respond well in invitro conditions. But, if other factors are associated with the reason for getting endangered, they didn't. As per my experience. In that case we must find those hidden treasure to save them.
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