Genomic Variations of Rice Regenerants from Tissue Culture Revealed by Whole Genome Re-Sequencing

Yang, Qin; Shin, Kong-Sik; Woo, Hee-Jong; Lim, Myung-Ho

doi:10.9787/pbb.2018.6.4.426

Cited by 9 publications

(12 citation statements)

References 19 publications

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“…Genetic or epigenetic purity of regenerants can be perturbed by e.g. chromosomal changes [ 1 ], point mutations [ 2 ], movement of transposable elements [ 3 ], or changes in methylation status of DNA [ 4 ] originating due to numerous stresses (sterilization factors [ 5 ], media components [ 6 ], light conditions [ 7 ] or humidity [ 8 ]). The extent of changes may depend on a type of explants [ 9 ], genotype [ 10 ], or time of culture on induction medium [ 11 , 12 ].…”

Section: Introductionmentioning

confidence: 99%

Barley somatic embryogenesis-an attempt to modify variation induced in tissue culture

Orłowska

2021

J of Biol Res-Thessaloniki

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Background Somatic embryogenesis is a phenomenon carried out in an environment that generates abiotic stress. Thus, regenerants may differ from the source of explants at the morphological, genetic, and epigenetic levels. The DNA changes may be the outcome of induction media ingredients (i.e., copper and silver ions) and their concentrations and time of in vitro cultures. Results This study optimised the level of copper and silver ion concentration in culture media parallel with the induction medium longevity step towards obtaining barley regenerants via somatic embryogenesis with a minimum or maximum level of tissue culture-induced differences between the donor plant and its regenerants. The optimisation process is based on tissue culture-induced variation evaluated via the metAFLP approach for regenerants derived under varying in vitro tissue culture conditions and exploited by the Taguchi method. In the optimisation and verification experiments, various copper and silver ion concentrations and the different number of days differentiated the tested trials concerning the tissue culture-induced variation level, DNA demethylation, and de novo methylation, including symmetric (CG, CHG) and asymmetric (CHH) DNA sequence contexts. Verification of optimised conditions towards obtaining regenerants with minimum and maximum variability compared to donor plants proved useful. The main changes that discriminate optimised conditions belonged to DNA demethylation events with particular stress on CHG context. Conclusions The combination of tissue culture-induced variation evaluated for eight experimental trials and implementation of the Taguchi method allowed the optimisation of the in vitro tissue culture conditions towards the minimum and maximum differences between a source of tissue explants (donor plant) and its regenerants from somatic embryos. The tissue culture-induced variation characteristic is mostly affected by demethylation with preferences towards CHG sequence context.

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Section: Introductionmentioning

confidence: 99%

Barley somatic embryogenesis-an attempt to modify variation induced in tissue culture

Orłowska

2021

J of Biol Res-Thessaloniki

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“…Somaclonal variation can lead to genome-wide SNVs, indels, variations in chromosome number, chromosome rearrangements, the activation of transposable elements, and epigenetic alterations (Karp and Maddock, 1984;Lee and Phillips, 1987;Jiang et al, 2011;Miguel and Marum, 2011). In rice, mutations in the range of tens to tens of thousands of SNVs and indels per individual plant have been observed following tissue culture (Miyao et al, 2012;Zhang, Wang, et al, 2014;Wei et al, 2016;Qin et al, 2018;Tang et al, 2018). Similarly, between 9 and 65 novel homozygous SNVs and 2-6 homozygous indels have been discerned in the R1 generation compared to its progenitor plant in Arabidopsis (Jiang et al, 2011).…”

Section: A Introgression Through Crossingmentioning

confidence: 99%

“…Given that traditional breeding can elicit substantial genetic changes during the development of new crop cultivars, and spontaneously-derived genetic variation is prevalent in all species, it is not surprising that genetic variation between traditionally-bred cultivars of the same species can be immense. For example, between approximately 25,000 to 9.8 million SNVs and 1,400 to 1.4 million indels have been observed between individuals of different cultivars/accessions of soybean (Lam et al, 2010;Yadav et al, 2015;Anderson et al, 2016), cotton (Li, Manghwar, et al, 2019), sweet cherry (Xanthopoulou et al, 2020), maize (Sun et al, 2018), rice (e.g., Subbaiyan et al, 2012;Kawakatsu et al, 2013;Fu et al, 2016;Qin et al, 2018;Wang, Mauleon, et al, 2018), and tomato (Causse et al, 2013), respectively (Table 1). Indeed, SNVs have been found to be present on average every 61-540 bp in maize, wheat, soybean, B. oleracea and rice cultivars (Ching et al, 2002;Somers et al, 2003;Van et al, 2005;Subbaiyan et al, 2012;Agnieska et al, 2016;Fu et al, 2016;Golicz et al, 2016;Sun et al, 2018), while indels have been estimated to occur every 126-900 bp in maize lines (Ching et al, 2002;Sun et al, 2018).…”

Section: A Introgression Through Crossingmentioning

confidence: 99%

Genetic Variation and Unintended Risk in the Context of Old and New Breeding Techniques

Singer

Laurie

Bilichak

et al. 2021

Critical Reviews in Plant Sciences

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For thousands of years, humans have been improving crops to better suit their needs. These enhancements are driven by changes in the genetic makeup of the plant. While this was initially unintentional, there has been a steady push to increase the pace and precision of crop breeding, something that has occurred alongside a growing understanding of genetics and an escalating capacity to thoroughly assess genomes at the molecular level. With the advent and rapid uptake of molecular breeding techniques, such as transgenics and genome editing over the past few decades, there has been much trepidation regarding the possibility of off-target effects derived from unanticipated mutations at loci other than those intended for alteration, and the unintended risks that this might confer. These concerns persist regardless of the fact that a growing number of studies indicate that the occurrence of off-target mutations derived from newer biotechnological breeding techniques are negligible compared to what is observed with many conventional breeding approaches, and even spontaneously from one generation to the next. Given the impending food security crisis that we are facing in the short-term, there is a critical need to implement a wide range of breeding tools as a means of meeting growing demand, withstanding climate change-related pressures, increasing nutrition, and providing environmental benefits. While food safety is clearly of the utmost importance, now is certainly not the time to prevent the use of particular breeding technologies based on unfounded doubts. Therefore, in this review, we attempt to shed light on these apprehensions by putting purported "risks" into the context of plant breeding as a whole by comparing frequencies of spontaneous mutations with those (both anticipated and unanticipated) that occur through various conventional and biotechnological breeding approaches, including transgenics and genome editing. We then consider how these changes may, or may not, translate into unanticipated risk, and discuss the current global regulatory asynchrony surrounding genome edited crops.

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“…However, the TCIV and SV terms are often used mutually [7]. TCIV may be pronounced at the morphological [8], biochemical [9], genetic [10] and epigenetic [11] levels, which do not necessarily overlap [12]. Possibly the most investigated level is based on DNA markers.…”

Section: Introductionmentioning

confidence: 99%

Understanding In Vitro Tissue Culture-Induced Variation Phenomenon in Microspore System

Bednarek

Pachota

Dynkowska

et al. 2021

IJMS

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In vitro tissue culture plant regeneration is a complicated process that requires stressful conditions affecting the cell functioning at multiple levels, including signaling pathways, transcriptome functioning, the interaction between cellular organelles (retro-, anterograde), compounds methylation, biochemical cycles, and DNA mutations. Unfortunately, the network linking all these aspects is not well understood, and the available knowledge is not systemized. Moreover, some aspects of the phenomenon are poorly studied. The present review attempts to present a broad range of aspects involved in the tissue culture-induced variation and hopefully would stimulate further investigations allowing a better understanding of the phenomenon and the cell functioning.

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Genomic Variations of Rice Regenerants from Tissue Culture Revealed by Whole Genome Re-Sequencing

Cited by 9 publications

References 19 publications

Barley somatic embryogenesis-an attempt to modify variation induced in tissue culture

Barley somatic embryogenesis-an attempt to modify variation induced in tissue culture

Genetic Variation and Unintended Risk in the Context of Old and New Breeding Techniques

Understanding In Vitro Tissue Culture-Induced Variation Phenomenon in Microspore System

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