What is the frequency or rate of somaclonal variation in terms of percentage or per 1000 plants in tissue cultured plants?
In trees: ... the somatic point mutation rate in poplar is 1.33 × 10− 10 (95% CI 1.53 × 10− 11–4.18 × 10− 10) per base per haploid genome per year...
Hofmeister, B.T., Denkena, J., Colomé-Tatché, M. et al. A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa. Genome Biol 21, 259 (2020). https://doi.org/10.1186/s13059-020-02162-5
In vitro plants: Two cell lines of Oryza sativa cultivated for more than 20 years accumulated single nucleotide substitutions in two housekeeping genes encoding 5- enolpyruvylshikimate-3-phosphate synthase and ribosomal protein small subunit 20 at a level 3.2-3.4 9 10-3 per nucleotide (Noro et al. 2007)
Two transgenes (nptII and rolC) transferred to the cell cultures of Panax ginseng by Agrobacterium-mediated transformation accumulated single nucleotide substitutions during 13 years of continuous subculturing of the cell lines. The mutation frequency was 1.21 9 10-3 per nucleotide in 1995 and 1.37 9 10-3 per nucleotide in 2007, which was a significant 13% increase (Kiselev et al. 2009)
P. ginseng accumulated single nucleotide substitutions in the endogenous genes encoding actin, phenylalanine ammonia-lyase, dammarenediol synthase and somatic embryogenesis receptor kinase during long-term propagation of cell cultures over a period of 20 years. The mutation frequency was 0.67 9 10-3 , 0.72 9 10-3 , 1.09 9 10-3 per nucleotide in cultivated plants, 2-year-old cell culture and 20-year-old cell culture, respectively (Kiselev et al. 2011, 2013b)
Cited after Dubrovina AS, Kiselev KV. Age-associated alterations in the somatic mutation and DNA methylation levels in plants. Plant Biol (Stuttg). 2016 Mar;18(2):185-96. doi: 10.1111/plb.12375. Epub 2015 Aug 12. PMID: 26211365
Thus, if it is correct to compare the data, in vitro culture has 10E7 more mutations per site per year than natural rate in growing plants.
You should add more and publish a review Alex. Thanks for sharing. Of course the rates will vary both in tissue culture and in natural environment depending on the growth conditions. There is a limit to subculture in micropropagation and it varies by species
Chet Ram
hexaploid bread wheat genome has 15 344 693 583 bases (Zimin, et al., The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum, GigaScience, Volume 6, Issue 11, November 2017, gix097).
In vitro culture it can get 10 millions mutated nucleotides per year. (with 1.5 *10-3 mutations per nucleotide per year).
According to Sònia Garcia,et al. (Recent updates and developments to plant genome size databases, Nucleic Acids Research, Volume 42, Issue D1, 1 January 2014, Pages D1159–D1166), the total amount of DNA in the unreplicated haploid nucleus of an organism across eukaryotes varies approximately 66 000-fold. The smallest genome so far reported is found in the parasitic microsporidian Encephalitozoon intestinalis with a C-value of just 2,300,000 bp, the largest reliable genome size estimate is for the angiosperm Paris japonica with a C-value of 148 880 000 000 bp. (=10 genomes of wheat)
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