Identification of minor DNA variations in rice somaclonal variants

Chowdari, Kodavali V.; Ramakrishna, Wusirika; Tamhankar, Shubhada; Hendre, R.R.; Gupta, Vidya S.; Sahasrabudhe, N.A.; Ranjekar, P. K.

doi:10.1007/s002990050531

Cited by 23 publications

(4 citation statements)

References 13 publications

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“…Insertion of plant retrotransposons into coding regions in protoplasts or cell cultures has been demonstrated in tobacco (Grandbastien et al 1989) and rice (Hirochika et al 1996). Sequence amplifications or deletions are another cause of somaclonal mutations (Chowdari et al 1998). M M 1 1 2 2 3 3 4 4 5 5 6 6 7 7 8 8 9 9 1 10 0 1 11 1 1 12 2 1 13 3 1 14 4 1 15 5 1 16 6 A A X X Y Y Tissue culture has been extensively used to propagate apple clones, but there are only a few reports on the assessment of genetic fidelity of regenerated plants, and most of these are based on RAPD marker analysis.…”

Section: Resultsmentioning

confidence: 98%

ISSR assay for ascertaining genetic fidelity of micropropagated plants of apple rootstock Merton 793

Pathak

Dhawan

2011

In Vitro Cell.Dev.Biol.-Plant

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With the current trends in high density plantations of fruit trees, numerous clonal rootstocks of apple have been developed through various breeding programs. Among them, Merton 793 is the most popular in India because of the desirable traits of vigorous growth and resistance to woolly apple aphid and collar rot. The planting material of this rootstock cannot be multiplied at a desirable rate by means of conventional vegetative propagation methods, so micropropagation techniques are being explored to augment scarce planting material. Large number of plants can be produced in vitro under aseptic conditions, but there is always a danger of producing somaclonal variants by tissue culture technology. Thus, it is advisable to check the clonal fidelity of in vitro raised plants, especially of perennials prior to their field transplantation. The genetic stability of in vitro raised plants of apple rootstock Merton 793, multiplied through enhanced axillary bud proliferation up to 22 subculture passages, was tested by intersimple sequence repeat (ISSR) assay. Of 24 ISSR primers screened, 15 primers produced clear reproducible bands, resulting in a total of 134 distinct bands with an average of 8.9 bands per primer. Apple rootstock MM 111 and scion Jonathan, taken as outliers with tissue culture-raised progenies of Merton 793, ruled out the possibility that the invariant banding pattern occurred because of inefficiency of ISSR primers in detecting variations. The homogenous amplification profile observed for all the micropropagated plants compared to the donor plant confirmed the clonal fidelity of the tissue culture-raised Merton 793 plants. This suggests that axillary bud multiplication is the safest mode for multiplication of true-to-type plants. This is the first study that evaluates the applicability of ISSR markers in establishing clonal fidelity of tissue culture-raised apple plants.

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Section: Resultsmentioning

confidence: 98%

ISSR assay for ascertaining genetic fidelity of micropropagated plants of apple rootstock Merton 793

Pathak

Dhawan

2011

In Vitro Cell.Dev.Biol.-Plant

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“…Insertion of plant retrotransposons into coding regions after protoplast or cell culture has been demonstrated in tobacco (Grandbastien et al 1989) and rice (Hirochika et al 1996). Sequence amplifications or deletions are another cause of somaclonal mutations (Chowdari et al 1998;Rostiana et al 1999). Somaclonal variation is genotype-specific and its rate is variable between and within species.…”

Section: Introductionmentioning

confidence: 97%

Somaclonal variation in rye (Secale cereale L.) analyzed using polymorphic and sequenced AFLP markers

Puente

González

Ruiz

et al. 2008

In Vitro Cell.Dev.Biol.-Plant

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Amplified fragment length polymorphism (AFLP) analysis of 24 in vitro regenerated rye plants was performed in order to evaluate the somaclonal variation rate in this species and to identify rye genomic regions where mutations are preferentially promoted by in vitro culture processes. Regenerated plants were obtained from cell lines derived from immature embryos and plants were regenerated by somatic embryogenesis. Twenty-three regenerants showed variation when compared against sibling plants obtained from the same cell line. A total number of 887 AFLP markers were scored, and 8.8% identified the same polymorphism in plants obtained independently from different cell lines, revealing putative mutational hot spots. Using controlled crossings and analysis of the corresponding progenies, we were able to verify the genetic stability in the next generation for only five of these polymorphisms. The nucleotide sequence of the AFLP amplicon of four of the polymorphic markers was obtained, but only the sequence of two markers was clearly identified in the databases. The sequence of marker A1-303 was identified as part of a tandemly repeated sequence, the 120-bp family, which is located at telomeric regions and is widely distributed among rye chromosomes. The marker A5-375 showed high similarity with regions of Angela retrotransposons.

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“…SSRs are reported to play significant roles in the characterization of DNA changes of somaclonal mutants. Previously, Chowdari et al (1998) have used SSRs to detect differences between somaclonal mutants of rice and their wild-type genotype, Indrayani; however, a minor sequence variation at a microsatellite locus is revealed only following DNA digestion with restriction endonucleases. Recently, Ngezahayo et al (2007) have analyzed 2-year-old calli of Nipponbare and their regenerated plants, and have detected 21 and 17% genomic polymorphisms using 24 RAPD and 20 SSR markers, respectively.…”

Section: Introductionmentioning

confidence: 99%

Detection of DNA changes in somaclonal mutants of rice using SSR markers and transposon display

Gao

Vallejo

et al. 2009

Plant Cell Tiss Organ Cult

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Identification of minor DNA variations in rice somaclonal variants

Cited by 23 publications

References 13 publications

ISSR assay for ascertaining genetic fidelity of micropropagated plants of apple rootstock Merton 793

ISSR assay for ascertaining genetic fidelity of micropropagated plants of apple rootstock Merton 793

Somaclonal variation in rye (Secale cereale L.) analyzed using polymorphic and sequenced AFLP markers

Detection of DNA changes in somaclonal mutants of rice using SSR markers and transposon display

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