Comparative Study of High Quality Genomic DNA Extraction  Protocols in Rice and Tomato Crops

Dubey, Shiv Mani; Kumar, Sanjeev; Antre, Suresh H.; Gowda, P. H. R.

doi:10.20546/ijcmas.2017.611.327

Cited by 2 publications

(1 citation statement)

References 19 publications

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“…Optimized protocol for DNA extraction For tomatoes (Solanum lycopersicum sp. ), like for many other plant species, numerous methods for DNA extraction have been tested (Ahmed et al, 2009;Mamidala and Nanna, 2009;Dubey et al, 2017). For any investigation at the DNA level, the primary condition is to obtain a genomic DNA of sufficient quantity and of good quality.…”

Section: Morphological Characterizationmentioning

confidence: 99%

New varieties of tomato - morphological aspects and molecular characterisation with RAPD and SSR markers

et al. 2020

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This study presents the main morphological features and the first molecular investigations of four new tomato varieties (Solanum lycopersicum), aiming to obtain their complete characterisation. Evaluation with the standard descriptors for tomato revealed specific and distinct traits for each analysed variety. The molecular analyses for variety identification started with testing three methods for DNA extraction. With an optimized method, which doesn’t need liquid nitrogen for plant tissue disruption, good quality DNA was obtained, in adequate quantities, and well preserved when stored at -20 °C. To highlight the genetic differences among the analysed tomato varieties, nine RAPD primers and ten SSR primers were tested. Of these, the optimal amplification protocols for five RAPD primers and five SSR primers were established. The amplified products obtained with RAPD primers revealed an average number of bands per primer of 8.8 and a total rate of polymorphism of 59.1%; with OPB10 primer was seen the highest number of DNA bands (11), and with OPA07 primer was registered the highest degree of genetic variability among the studied varieties (77.7%). Two SSR markers (SSR 20 and SSR T107) amplified monomorphic banding patterns corresponding to 170 base pairs and 250 base pairs, respectively, for all varieties; with SSR T7, SSR T62, and SSR T70 primers were generated multiple amplification bands, with a different distribution of the bands into the agarose gel for each analysed tomato variety.

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Section: Morphological Characterizationmentioning

confidence: 99%

New varieties of tomato - morphological aspects and molecular characterisation with RAPD and SSR markers

et al. 2020

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Genetic variability analysis of partially salt tolerant local and inbred rice (Oryza sativa L.) through molecular markers

Mazumder

Hoque

Sinha

et al. 2020

Heliyon

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Random Amplified Polymorphic DNA (RAPD) analysis was performed to assess the genetic variability in sixteen selected germplasms of rice, Oryza sativa L. using eight decamer RAPD primers. The data obtained from this investigation reveals a high level of polymorphism between cultivars. The primers produced a total of 255 bands of which all 255 bands were polymorphic indicating 100% polymorphism. The size of the amplified bands ranged from 220 bp to 2290 bp. The number of polymorphic fragments ranged from 24 to 49 with an average of 32 polymorphic fragments for each primer. The primer OPX04 produced the maximum number (49) of polymorphic bands while the OPB04 and OPB17 produced the minimum number (24) of polymorphic bands. The polymorphic information content (PIC) values ranged from 0.6616 to 0.8845 with an average of 0.832. The highest PIC value (0.8845) was obtained for primer OPL03. The RAPD data was analyzed to determine the pair-wise genetic similarity coefficients which ranged from 0.00 to 0.83. The BRRIdhan 23 and the BRRIdhan 41 varieties were the closest genotypes with the highest similarity index of 83%. This was followed by 77% similarity between a pair of cultivars Kalamona and Horkuch. On the other hand, 100% dissimilarity was seen between BRRIdhan 53, BRRIdhan 50, BRRIdhan 10, BRRIdhan 70, BRRIdhan 54, BRRIdhan 40, BRRIdhan 23, BRRIdhan 47, BRRIdhan 41 and Dadsail respectively and between BRRIdhan 53 and Horkuch; indicating a high level of variability between paired genotypes. Cluster analysis was performed using Unweighted Paired Group of Arithmetic Means (UPGMA). The UPGMA dendrogram resolved the selected rice cultivars into four clusters.

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Comparative Study of High Quality Genomic DNA Extraction Protocols in Rice and Tomato Crops

Cited by 2 publications

References 19 publications

New varieties of tomato - morphological aspects and molecular characterisation with RAPD and SSR markers

New varieties of tomato - morphological aspects and molecular characterisation with RAPD and SSR markers

Genetic variability analysis of partially salt tolerant local and inbred rice (Oryza sativa L.) through molecular markers

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