Comparative evaluation of DNA extraction from rice’s root-associated bacterial consortium for population structure study

Nichapat Kittiborwornkul; S.T Anne Sahithi; Jirapa Phetsom; Theerawut Phusantisampan; Wasinee Pongprayoon; Malinee Sriariyanun

doi:10.1051/e3sconf/202130202014

All issues

Volume 302 (2021)

E3S Web Conf., 302 (2021) 02014

References

Open Access

Issue		E3S Web Conf. Volume 302, 2021 2021 Research, Invention, and Innovation Congress (RI²C 2021)


Article Number		02014
Number of page(s)		7
Section		Environmental Science and Engineering
DOI		https://doi.org/10.1051/e3sconf/202130202014
Published online		10 September 2021

A. Abdel-Latif and G. Osman, Comparison of three genomic DNA extraction methods to obtain high DNA quality from maize, Plant Methods. 13, 1(2017): 1. [PubMed] [Google Scholar]
A. Cachada, T. Rocha-Santos, and A.C. Duarte, Soil and Pollution, Soil Pollution. (2018): 1–28. [Google Scholar]
Y.S. Cheng, P. Mutrakulcharoen, S. Chuetor, K. Cheenkachorn, P. Tantayotai, E.J. Panakkal, M. Sriariyanun, Recent Situation and Progress in Biorefining Process of Lignocellulosic Biomass: Toward Green Economy, Applied Science and Engineering Progress. 13, 4 (2020): 299–311. [Google Scholar]
N. Chairerk, P. Pongyeela, J. Chungsiriporn, and N. Rakmak, Ethanol Extraction of Active Ingredients and Antioxidants from Germinated Sangyod Rice, Applied Science and Engineering Progress. 14(1), (2021). [Google Scholar]
H. Liu, L.C. Carvalhais, M. Crawford, et al., Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria., Frontiers in Microbiology. 8, (2017). [Google Scholar]
P. Songkumarn, P. Chaijuckam, V. Tongsri, and J.J.G. Guerrero, Expression Analysis of Defense Related Genes in Rice Response to Bipolaris oryzae, the Causal Agent of Rice Brown Spot, Applied Science and Engineering Progress. 12(2), (2018). [Google Scholar]
P. Songkumarn, P. Chaijuckam, and J.J.G. Guerrero, Genetic Diversity and Aggressiveness of Bipolaris oryzae in North-Central Thailand, Applied Science and Engineering Progress. 12(2), (2018). [Google Scholar]
W. Pongprayoon, T. Siringam, A. Panya, and S. Roytraku, Application of Chitosan in Plant Defense Responses to Biotic and Abiotic Stresses, Applied Science and Engineering Progress. 15(1), (2022) [Google Scholar]
J.M. Awika, Major Cereal Grains Production and Use around the World, Presented at the January (2011). [Google Scholar]
M.A. Mohamad Roslan, M.A. Naim Mohamad, and S. Mohd Omar, High-Quality DNA From Peat Soil For Metagenomics Studies: A Minireview On DNA Extraction Methods, Science Heritage Journal. 1, 2(2017): 01–06. [Google Scholar]
M.D. Braid, L.M. Daniels, and C.L. Kitts, Removal of PCR inhibitors from soil DNA by chemical flocculation, Journal of Microbiological Methods. 52, 3(2003): 389–393. [PubMed] [Google Scholar]
M. Majaneva, O.H. Diserud, S.H.C. Eagle, M. Hajibabaei, and T. Ekrem, Choice of DNA extraction method affects DNA metabarcoding of unsorted invertebrate bulk samples, Metabarcoding and Metagenomics. 2, (2018). [Google Scholar]
M. Sriariyanun, P. Yasurin, P. Pornwongthong and, K. Cheenkachorn, Production, purification and characterization of an ionic liquid tolerant cellulase from Bacillus sp. Isolated from rice paddy field soil, Electronic Journal of Biotechnology. 19, (2015). [Google Scholar]
N. Atheeqah-Hamzah, C.S.Y. Yong, and U.K. Yusuf, Extraction of High-quality RNA from Metabolite and Pectin Rich Recalcitrant Calyx Tissue of Hibiscus sabdariffa L, Pertanika Journal of Tropical Agricultural Science. 43, 4(2020). [Google Scholar]
R. Backer, J.S. Rokem, G. Ilangumaran, et al., Plant Growth-Promoting Rhizobacteria: Context, Mechanisms of Action, and Roadmap to Commercialization of Biostimulants for Sustainable Agriculture, Frontiers in Plant Science. 9, (2018). [Google Scholar]
R.S. Pickard and B.J. McKevith, The Role Of Cereals In The Diet, Using Cereal Science and Technology for the Benefit of Consumers. 89 (2005). [Google Scholar]
R. Von Post, L. Von Post, C. Dayteg, M. Nilsson, B.P. Forster, and S. Tuvesson, A high-throughput DNA extraction method for barley seed, Euphytica. 130, 2(2003): 255–260. [Google Scholar]
S. Khalid, M. Shahid, N.K. Niazi, B. Murtaza, I. Bibi, and C. Dumat, A comparison of technologies for remediation of heavy metal contaminated soils, Journal of Geochemical Exploration. 182, (2017): 247–268. [Google Scholar]
X. Ren, B. Kang, and Z. Zhang, Understanding tumor ecosystems by single-cell sequencing: promises and limitations, Genome Biology. 19, 1(2018): 211. [PubMed] [Google Scholar]
R. Akkharasinphonrat, T. Douzou, M. Sriariyanun, Development of ionic liquid utilization in biorefinery process of lignocellulosic biomass, King Mongkut’s University of Technology North Bangkok International Journal of Applied Science and Technology, 10, 2 (2017): 89–96. [Google Scholar]

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[1] A. Abdel-Latif and G. Osman, Comparison of three genomic DNA extraction methods to obtain high DNA quality from maize, Plant Methods. 13, 1(2017): 1. [PubMed] [Google Scholar]

[2] A. Cachada, T. Rocha-Santos, and A.C. Duarte, Soil and Pollution, Soil Pollution. (2018): 1–28. [Google Scholar]

[3] Y.S. Cheng, P. Mutrakulcharoen, S. Chuetor, K. Cheenkachorn, P. Tantayotai, E.J. Panakkal, M. Sriariyanun, Recent Situation and Progress in Biorefining Process of Lignocellulosic Biomass: Toward Green Economy, Applied Science and Engineering Progress. 13, 4 (2020): 299–311. [Google Scholar]

[4] N. Chairerk, P. Pongyeela, J. Chungsiriporn, and N. Rakmak, Ethanol Extraction of Active Ingredients and Antioxidants from Germinated Sangyod Rice, Applied Science and Engineering Progress. 14(1), (2021). [Google Scholar]

[5] H. Liu, L.C. Carvalhais, M. Crawford, et al., Inner Plant Values: Diversity, Colonization and Benefits from Endophytic Bacteria., Frontiers in Microbiology. 8, (2017). [Google Scholar]

[6] P. Songkumarn, P. Chaijuckam, V. Tongsri, and J.J.G. Guerrero, Expression Analysis of Defense Related Genes in Rice Response to Bipolaris oryzae, the Causal Agent of Rice Brown Spot, Applied Science and Engineering Progress. 12(2), (2018). [Google Scholar]

[7] P. Songkumarn, P. Chaijuckam, and J.J.G. Guerrero, Genetic Diversity and Aggressiveness of Bipolaris oryzae in North-Central Thailand, Applied Science and Engineering Progress. 12(2), (2018). [Google Scholar]

[8] W. Pongprayoon, T. Siringam, A. Panya, and S. Roytraku, Application of Chitosan in Plant Defense Responses to Biotic and Abiotic Stresses, Applied Science and Engineering Progress. 15(1), (2022) [Google Scholar]

[9] J.M. Awika, Major Cereal Grains Production and Use around the World, Presented at the January (2011). [Google Scholar]

[10] M.A. Mohamad Roslan, M.A. Naim Mohamad, and S. Mohd Omar, High-Quality DNA From Peat Soil For Metagenomics Studies: A Minireview On DNA Extraction Methods, Science Heritage Journal. 1, 2(2017): 01–06. [Google Scholar]

[11] M.D. Braid, L.M. Daniels, and C.L. Kitts, Removal of PCR inhibitors from soil DNA by chemical flocculation, Journal of Microbiological Methods. 52, 3(2003): 389–393. [PubMed] [Google Scholar]

[12] M. Majaneva, O.H. Diserud, S.H.C. Eagle, M. Hajibabaei, and T. Ekrem, Choice of DNA extraction method affects DNA metabarcoding of unsorted invertebrate bulk samples, Metabarcoding and Metagenomics. 2, (2018). [Google Scholar]

[13] M. Sriariyanun, P. Yasurin, P. Pornwongthong and, K. Cheenkachorn, Production, purification and characterization of an ionic liquid tolerant cellulase from Bacillus sp. Isolated from rice paddy field soil, Electronic Journal of Biotechnology. 19, (2015). [Google Scholar]

[14] N. Atheeqah-Hamzah, C.S.Y. Yong, and U.K. Yusuf, Extraction of High-quality RNA from Metabolite and Pectin Rich Recalcitrant Calyx Tissue of Hibiscus sabdariffa L, Pertanika Journal of Tropical Agricultural Science. 43, 4(2020). [Google Scholar]

[15] R. Backer, J.S. Rokem, G. Ilangumaran, et al., Plant Growth-Promoting Rhizobacteria: Context, Mechanisms of Action, and Roadmap to Commercialization of Biostimulants for Sustainable Agriculture, Frontiers in Plant Science. 9, (2018). [Google Scholar]

[16] R.S. Pickard and B.J. McKevith, The Role Of Cereals In The Diet, Using Cereal Science and Technology for the Benefit of Consumers. 89 (2005). [Google Scholar]

[17] R. Von Post, L. Von Post, C. Dayteg, M. Nilsson, B.P. Forster, and S. Tuvesson, A high-throughput DNA extraction method for barley seed, Euphytica. 130, 2(2003): 255–260. [Google Scholar]

[18] S. Khalid, M. Shahid, N.K. Niazi, B. Murtaza, I. Bibi, and C. Dumat, A comparison of technologies for remediation of heavy metal contaminated soils, Journal of Geochemical Exploration. 182, (2017): 247–268. [Google Scholar]

[19] X. Ren, B. Kang, and Z. Zhang, Understanding tumor ecosystems by single-cell sequencing: promises and limitations, Genome Biology. 19, 1(2018): 211. [PubMed] [Google Scholar]

[20] R. Akkharasinphonrat, T. Douzou, M. Sriariyanun, Development of ionic liquid utilization in biorefinery process of lignocellulosic biomass, King Mongkut’s University of Technology North Bangkok International Journal of Applied Science and Technology, 10, 2 (2017): 89–96. [Google Scholar]