Identification of minor DNA variations in rice somaclonal variants

• Published in: Plant cell reports 1998-11, Vol.18 (1/2), p.55-58
• Main Authors: Chowdari, K.V, Ramakrishna, W, Tamhankar, S.A, Hendre, R.R, Gupta, V.S, Sahasrabudhe, N.A, Ranjekar, P.K
• Format: Article
• Language: English
• Subjects: Agronomy. Soil science and plant productions; Amplification; Biological and medical sciences; Callus; clones; culture media; Deoxyribonucleic acid; Digestion; DNA; DNA probes; Fingerprinting; Fundamental and applied biological sciences. Psychology; Genetic analysis; Genetic markers; genetic techniques and protocols; genetic variation; Genetics; Genetics and breeding of economic plants; genotype; Haploidy, in vitro culture applications, somatic hybrids; Hybridization; Loci; methodology; micropropagation; Microsatellites; molecular sequence data; nucleotide sequences; Oligonucleotides; Oryza sativa; Plant breeding: fundamental aspects and methodology; Progeny; Regeneration; regenerative ability; Rice; somaclonal variation; tissue culture
• ISSN: 0721-7714; 1432-203X
• DOI: 10.1007/s002990050531

Some somaclonal variants derived from a landrace rice variety, Indrayani, were shown to be high yielding and resistant to multiple diseases in previous analysis carried out in our laboratory. An attempt was made to assess the effect of culturing and regeneration of rice plants on DNA variation at microsatellite loci in R2 progeny of callus-derived rice plants. Different somaclones of the rice line Indrayani differing in yield and disease response (high, low and no change in yield, as compared to the original genotype) were used as genetic material for these analyses. Analysis of microsatellite loci was accomplished by digesting DNA from regenerated rice somaclones and assaying for polymorphisms at microsatellite loci by in-gel hybridization with synthetic oligonucleotide probes such as (GATA)4, (CAC)5 and (TG)10. Specific variation at a PCR-amplified locus containing three internal microsatellite repeats (1E6) using restriction site fingerprinting was also investigated. The locus-specific amplification of a sequence-tagged microsatellite marker followed by digestion with HinfI and Sau3AI restriction endonucleases showed differences in some somaclonal variants. The technique used in this study enables monitoring of DNA changes in successive generations of somaclonal variants as a measure of DNA variability and possibly to identify the regions which are responsible for specific traits.