Thursday, 10 September 2015

Mutant Clones? Not Darwinian But Science Explains Them

Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm | Nature.

Despite its daunting title, this research paper shows the explanatory power of the recently-discovered field of epigenetics.

For those not familiar with this science, epigenetics is the study of the way, in complex multicellular organisms where cells are highly differentiated and specialised to perform very different functions, the same genome is made to perform different functions. Clearly, the genes needed to make and work muscles in mammals or leaves in trees, are not the same as those needed to grow and work brains in mammals or fruit in tees.

In fact, the control is fairly simple - a methyl chemical group is added at certain points in the unwanted genes to switch them off. These methylation groups are the epigenes and most of them will be added after fertilisation when the cells begin to differentiate.

This has now been used to explain why clones of oil date palms failed to be as productive as the trees from which leaf cells were taken and grown in laboratories to produce seedlings. It had been hoped that by cloning the most productive palms, the land area needed to produce enough palm oil to meet the demand would be greatly reduced. The opposite turned out to be true, however, because vary many of the clones turned out to have malformed and useless fruits - something that was not discovered until they had been growing for some 30 years.

The problem was that the leaf cells had the wrong set of epigenes and weren't like the normal stem cells produced by normal fertilization. In fact, the problem wasn't that the wrong genes had been methylated but that a key one had not been.

The same sort of problem is also found in other clones crops so cloning has failed to produce the expected results in terms of high yield from cloned specimens which was hoped would eliminate the uncertainties of normal sexual breeding and the impracticality of labour-intensive grafting.

Somaclonal variation arises in plants and animals when differentiated somatic cells are induced into a pluripotent state, but the resulting clones differ from each other and from their parents. In agriculture, somaclonal variation has hindered the micropropagation of elite hybrids and genetically modified crops, but the mechanism responsible remains unknown1. The oil palm fruit ‘mantled’ abnormality is a somaclonal variant arising from tissue culture that drastically reduces yield, and has largely halted efforts to clone elite hybrids for oil production. Widely regarded as an epigenetic phenomenon, ‘mantling’ has defied explanation, but here we identify the MANTLED locus using epigenome-wide association studies of the African oil palm Elaeis guineensis. DNA hypomethylation of a LINE retrotransposon related to rice Karma, in the intron of the homeotic gene DEFICIENS, is common to all mantled clones and is associated with alternative splicing and premature termination. Dense methylation near the Karma splice site (termed the Good Karma epiallele) predicts normal fruit set, whereas hypomethylation (the Bad Karma epiallele) predicts homeotic transformation, parthenocarpy and marked loss of yield. Loss of Karma methylation and of small RNA in tissue culture contributes to the origin of mantled, while restoration in spontaneous revertants accounts for non-Mendelian inheritance. The ability to predict and cull mantling at the plantlet stage will facilitate the introduction of higher performing clones and optimize environmentally sensitive land resources.

Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm.
Meilina Ong-Abdullah, Jared M. Ordway, et al.
Nature (2015) doi:10.1038/nature15365

Copyright © 2015, Rights Managed by Nature Publishing Group. Reproduced with permission under licence No. 3705370920738

Epigenetics is interesting because it marks a departure from strictly Darwinian evolution, which assumes that all characteristics are inherited at conception, unlike the earlier and largely discredited Lamarckian theory of evolution which had been proposed by Jean Baptiste Lamarck, which assumed that characters aquired after conception could be passed on to offspring. Epigenetics has now blurred this distinction and shown that, in limited situations, epigenes acquired after conception can be inherited.

This in no way undermines the principles of Darwinian evolution by natural selection of course, because the vast majority of characteristics are inherited the way Darwin proposed, but it demonstrates that genetic engineering followed by extensive cloning to quickly produce commercial quantities of genetically engineered plants without losing the engineered genes by hybridization with 'normal' forms, may not be a straightforward as it once seemed. Clearly, cloning is not simply a matter of selecting easily-cloned cells, such as those in a highly specialised part of the plant like a leaf or a root.

So, rather than reacting against something that seems on the face of it to go against a fundamental principle of biology and so rejecting it with the wave of a hand, what science has done with epigenetics is to accept that inheritance is not wholly Darwinian and that, in a limited sense, Lamarck was not entirely wrong. So, they are now using this new knowledge to solve previous mysteries.

How very unlike a religion where basic dogmas are sacred and to abandon them when the evidence demands it is to abandon the religion itself.

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