Epigenetic modifications result in genetic degradation. Here's the evidence.
It's obvious that current plant/animal breeding techniques have reduced genetic diversity of food varieties. Breeding is kind of artificial selection of desired traits and characteristics. This can be done by epigenetic amplification or silencing of desired traits as in dog breeding. The most modern techniques try to manipulate genetic information in different ways. Scientists are even able to transfer genes between organisms. Results have been almost catastrophical; ~90% of food varieties have disappeared during the last 100 years. This is why farmers are looking for safer and more efficient techniques for plant/animal breeding.
Keywords: breeding reduces genetic diversity, epigenetic breeding
The latest and the best solution is epigenetic breeding. But will it result in improvement of genetic diversity? No. Just like in the wild, epigenetic modifications result in genetic errors and low genetic diversity. This happens slower than in traditonal breeding techniques but anyway, it's an inevitable phenomenon. Here's the evidence. Changes in epigenetic information profiles result in genetic errors:
"Many studies have reported that CpG-SNPs are associated with different diseases, such as type 2 diabetes, breast cancer, coronary heart disease, and psychosis which show a clear interaction between genetic (SNPs) and epigenetic (DNA methylation) regulation."
"Loss of expression of the O6-methylguanine DNA methyltransferase (MGMT) protein is a frequent occurrence in many types of cancer, including 30–46% of sporadic colorectal cancers.9, 10, 11, 12, 13 This is almost invariably associated with methylation of the MGMT promoter.9 MGMT is a ubiquitously expressed DNA repair protein that protects against mutagenesis by repairing mutagenic O6-methylguanines within DNA. By direct cleavage of the methyl adducts, the enzyme can restore the affected guanine nucleotides to normal.14 If this fails to occur, O6-methylguanines can pair erroneously with thymine during DNA replication, resulting in G:C>A:T transitions in the DNA, which can be important in neoplastic transformation."
"Recently, MGMT methylation was found to be closely associated with the C>T SNP (rs16906252) within the first exon of MGMT in colorectal cancer."
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Epigenetic marks respond to internal and environmental cues (A) resulting in various effects on chromatic conformation and gene expression.
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"Surprisingly, hydroxymethylated sites are consistently associated with elevated C to G transversion rates at the level of segregating polymorphisms, fixed substitutions, and somatic mutations in tumors."
"DNA hypomethylation promotes genomic instability 4, in many cases leading to an increased mutational load and activation of proto-oncogenes."
"DNA methylation has been linked to mismatch repair (MMR) deficiency and genomic instability in multiple contexts, in both cell lines and in disease. In the HCT116 colorectal cancer cell line, ablation of catalytically active DNMT1 causes cell cycle arrest and apoptosis due to increased chromosomal instability. In mouse ES cells, loss of Dnmt1 also causes global hypomethylation and increased mutation rates."
"If we assume that CpHpG methylation also occurs in the germline, and that 5mC deamination can occur within a CpHpG context, then we might surmise that methylated CpHpG sites could also constitute mutation hotspots causing human genetic disease. To test this postulate, 54,625 missense and nonsense mutations from 2,113 genes causing inherited disease were retrieved from the Human Gene Mutation Database (http://www.hgmd.org). Some 18.2 per cent of these pathological lesions were found to be C > T and G > A transitions located in CpG dinucleotides (compatible with a model of methylation-mediated deamination of 5mC), an approximately ten-fold higher proportion than would have been expected by chance alone."
"Altered DNA methylation and genome instability: A new pathway to cancer"
"This increased genome instability is characterized by increased occurrences of mutations, cells with incorrect chromosome number, loss of heterochromatin and mistakes in transcription."
"A reduction in DNA methylation leads to genomic instability, accumulation of endogenous DNA damage, and sensitivity to DNA-damaging agents."
"CpG methylation reduces genomic instability."
"As well, DNA methylation is thought to be a major contributor of point mutations leading to human genetic disease, when it precedes deamination of 5-methylcytosine (m5C) present within CpG dinucleotides. CpG dinucleotides are hypothesized to be a hotspot for mutations in a variety of genes, where a substantial proportion of intragenic single base-pair mutations (35%) occur in CpG dinucleotides and are the result of C>T or G>A transitions. Consequently, the rate of transitions at CpGs is suggested to be 20-fold higher than transitions at non-CpG sites."
"When cytosine is mutated to uracil by spontaneous deamination, the DNA glycosylase enzyme UDG (uracil DNA glycosylase) reverses the damage, in a base excision repair mechanism. When the equivalent deamination reaction occurs on 5-methylcytosine, however, the product, thymine, is not repaired by DNA repair enzymes."
"I show that sites methylated by the Dcm enzyme exhibit an 8-fold increase in mutation rate in natural bacterial populations. I also show that modifications at other sites in various bacteria also increase the mutation rate, in some cases by a factor of forty or more."
"The architecture of the chromatin itself and its level of condensation can greatly impact the expression of genes as well as the sensitivity of the DNA to damage."
"For example, DNA is more highly methylated, and therefore compacted, in areas that contain repetitive sequences to prevent the expression of non-coding DNA, induction of double-stranded breaks (DSBs), transposable elements and inappropriate recombination events likely to occur at repetitive DNA sequences. These events can lead to mutations, genome instability and cancer development."
"When chromatin is more 'open,' major genetic disruption is more likely. And when the researchers inhibited an epigenetic modifier called G9a, they found that chromatin accessibility, or openness, increased substantially."
