Evidence for an evolutionary force that prevents epigenetic silencing between tail-to-tail rice genes with a short spacer

Kobayashi, Sohei; Noro, Yuji; Nagano, Hironori; Yoshida, Kaoru; Takano-Shimizu, Toshiyuki; Kishima, Yuji; Sano, Yoshio

doi:10.1016/j.gene.2004.11.012

Cited by 2 publications

(1 citation statement)

References 33 publications

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“…The transition/transversion ratio found in natural mutation of AA‐genome Oryza species was 1.92 (Kobayashi et al, 2005). In contrast, transition and transversion mutations in LPT123‐TC171 were found in 389 and 204 positions, respectively, which gave the ratio of approximately 2.16.…”

Section: Discussionmentioning

confidence: 98%

Molecular Karyotyping and Exome Analysis of Salt‐Tolerant Rice Mutant from Somaclonal Variation

et al. 2014

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LPT123-TC171 is a salt-tolerant (ST) and drought-tolerant (DT) rice line that was selected from somaclonal variation of the original Leuang Pratew 123 (LPT123) rice cultivar. The objective of this study was to identify the changes in the rice genome that possibly lead to ST and/or DT characteristics. The genomes of LPT123 and LPT123-TC171 were comparatively studied at the four levels of whole chromosomes (chromosome structure including telomeres, transposable elements, and DNA sequence changes) by using next-generation sequencing analysis. Compared with LPT123, the LPT123-TC171 line displayed no changes in the ploidy level, but had a significant deficiency of chromosome ends (telomeres). The functional genome analysis revealed new aspects of the genome response to the in vitro cultivation condition, where exome sequencing revealed the molecular spectrum and pattern of changes in the somaclonal variant compared with the parental LPT123 cultivar. Mutation detection was performed, and the degree of mutations was evaluated to estimate the impact of mutagenesis on the protein functions. Mutations within the known genes responding to both drought and salt stress were detected in 493 positions, while mutations within the genes responding to only salt stress were found in 100 positions. The possible functions of the mutated genes contributing to salt or drought tolerance were discussed. It was concluded that the ST and DT characteristics in the somaclonal variegated line resulted from the base changes in the salt-and drought-responsive genes rather than the changes in chromosome structure or the large duplication or deletion in the specific region of the genome.

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Section: Discussionmentioning

confidence: 98%

Molecular Karyotyping and Exome Analysis of Salt‐Tolerant Rice Mutant from Somaclonal Variation

et al. 2014

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Genetic variations in rice in vitro cultures at the EPSPs–RPS20 region

et al. 2006

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In vitro cultures of plant cells have often been utilized to generate genetic variations, which are designated somaclonal variations. Little is known about the major genetic alterations in the cultured cells and the nature of these genetic changes. Here, we examined different lines of rice Oc cells that have been cultured for more than 20 years on agar media or in liquid media. We surveyed 35 clones obtained from PCR amplification of the 3-kb EPSPs-RPS20 region. The sequence divergence among the Oc cells was even greater than that between Japonica and Indica rice cultivars. The divergent sequences appeared to be maintained as multiple copies in a single cell. Surprisingly, the nucleotide substitutions in the Oc cells were characterized by an extremely high frequency of transition mutations of A/T-to-G/C, a feature which is similar to that of the mutations caused by chemical mutagens such as 5-bromouracil and 2-aminopurine. Although no replacements in the exons of this region were observed among the AA-genome Oryza species, our results revealed that the nucleotide substitutions of the cultured cell lines occurred more frequently at replacement sites in the exons than at synonymous sites. These distinct mutation biases found in rice in vitro cultures might contribute importantly to somaclonal variations.

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Evidence for an evolutionary force that prevents epigenetic silencing between tail-to-tail rice genes with a short spacer

Cited by 2 publications

References 33 publications

Molecular Karyotyping and Exome Analysis of Salt‐Tolerant Rice Mutant from Somaclonal Variation

Molecular Karyotyping and Exome Analysis of Salt‐Tolerant Rice Mutant from Somaclonal Variation

Genetic variations in rice in vitro cultures at the EPSPs–RPS20 region

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