Root sampling and RNA extraction methods for field-based gene expression analysis of soybeans

References

• Darko, E., Végh, B., Khalil, R., Marček, T., Szalai, G., Pál, M., & Janda, T. (2019). Metabolic responses of wheat seedlings to osmotic stress induced by various osmolytes under iso-osmotic conditions. PLoS ONE, 14(12), e0226151. https://doi.org/10.1371/journal.pone.0226151
   Web of Science ®Google Scholar
• Deepa, K., Sheeja, T. E., Santhi, R., Sasikumar, B., Cyriac, A., Deepesh, P. V., & Prasath, D. (2014). A simple and efficient protocol for isolation of high quality functional RNA from different tissues of turmeric (Curcuma longa L.). Physiology and Molecular Biology of Plants, 20(2), 263–271. https://doi.org/10.1007/s12298-013-0218-y
   Web of Science ®Google Scholar
• Henry, A., Cal, A. J., Batoto, T. C., Torres, R. O., & Serraj, R. (2012). Root attributes affecting water uptake of rice (Oryza sativa) under drought. Journal of Experimental Botany, 63(13), 4751–4763. https://doi.org/10.1093/jxb/ers150
   PubMed Web of Science ®Google Scholar
• Ishikawa, J. (2016) Role of soybean aquaporins in inhibition of water uptake under flooding. KAKEN Final Research Report. *in japanese with English abstract. https://kaken.nii.ac.jp/ja/file/KAKENHI-PROJECT-25450031/25450031seika.pdf
   Google Scholar
• Kawai, M., Smamarajeewa, P. K., Barrero, R. A., Nishiguchi, M., & Uchiyama, H. (1998). Cellular dissection of the degradation pattern of cortical cell death during aerenchyma formation of rice roots. Planta, 204(3), 277–287. https://doi.org/10.1007/s004250050257
   Web of Science ®Google Scholar
• Matsunami, M., Hayashi, H., Tominaga, Y., Nagamura, Y., Murai-Hatano, M., & Ishikawa-Sakurai, J. (2018). Effective methods for practical application of gene expression analysis in field-grown rice roots. Plant and Soil, 433(1–2), 173–187. https://doi.org/10.1007/s11104-018-3834-z
   Web of Science ®Google Scholar
• Muoki, R.C., Paul, A., Kumari, A., Singh, K. & Kumar, S. An improved protocol for the isolation of RNA from roots of tea (Camellia sinensis (L.) O. Kuntze). Mol Biotechnol. 2012 Sep; 52(1), 82–88. doi: 10.1007/s12033-011-9476-5. PMID: 22144070
   Google Scholar
• Nagano, A. J., Sato, Y., Mihara, M., Antonio, B. A., Motoyama, R., Itoh, H., Nagamura, Y. & Izawa, T. (2012) Deciphering and prediction of transcriptome dynamics under fluctuating field conditions. Cell 141(6), 1358–1369. https://doi.org/10.1016/j.cell.2012.10.048
   Google Scholar
• Ouyang, K., Li, J., Huang, H., Que, Q., Li, P., & Chen, X. (2014). A simple method for RNA isolation from various tissues of the tree Neolamarckia cadamba. Biotechnology & Biotechnological Equipment, 28(6), 1008–1013. https://doi.org/10.1080/13102818.2014.981086
   PubMed Web of Science ®Google Scholar
• Prince, S. J., Valliyodan, B., Ye, H., Yang, M., Tai, S., Hu, W., Murphy, M., Durnell, L. A., Song, L., Joshi, T., Liu, Y., Van de Velde, J., Vandepoele, K., Grover Shannon, J., & Nguyen, H. T. (2019). Understanding genetic control of root system architecture in soybean: Insights into the genetic basis of lateral root number. Plant, Cell & Environment, 42(1), 212–229. https://doi.org/10.1111/pce.13333
   Web of Science ®Google Scholar
• Sah, S. K., Kaur, G., & Kaur, A. (2014). Rapid and reliable method of high-quality RNA extraction from diverse plants. American Journal of Plant Sciences, 5(21), 3129–3139. https://doi.org/10.4236/ajps.2014.521329
   Google Scholar
• Suralta, R. R., & Yamauchi, A. (2008). Root growth, aerenchyma development, and oxygen transport in rice genotypes subjected to drought and waterlogging. Environmental and Experimental Botany, 64(1), 75–82. https://doi.org/10.1016/j.envexpbot.2008.01.004
   Web of Science ®Google Scholar
• Wang, Y., Hayatsu, M., & Fujii, T. (2012). Extraction of bacterial RNA from soil: Challenges and solutions. Microbes Environment, 27(2), 111–121. https://doi.org/10.1264/jsme2.ME11304
   Web of Science ®Google Scholar
• Yamaguchi, M., Valliyodan, B., Zhang, J., Lenoble, M. E., Yu, O., Rogers, E. E., Nguyen, H. T., & Sharp, R. E. (2010). Regulation of growth response to water stress in the soybean primary root. I. Proteomic analysis reveals region‐specific regulation of phenylpropanoid metabolism and control of free iron in the elongation zone. Plant, Cell & Environment, 33(2), 223–243. https://doi.org/10.1111/j.1365-3040.2009.02073x
   Web of Science ®Google Scholar
• Yuan, S., Li, R., Chen, H., Zhang, C., Chen ,Li., Hao, Q., Chen, S., Shan, Z., Yang, Z., Zhang, X., Qiu, D., Zhou, X. (2017). RNA-Seq analysis of nodule development at five different developmental stages of soybean (Glycine max) inoculated with Bradyrhizobium japonicum strain 113-2. Scientific Reports, 7, 42248. https://doi.org/10.1038/srep42248
   Web of Science ®Google Scholar
• Yuan, S., Li, R., Chen, S., Chen, H., Zhang, C., Chen, L., Hao, Q., Shan, Z., Yang, Z., Qiu, D., Zhang, X., & Zhou, X. (2016). RNA-Seq analysis of differential gene expression responding to different rhizobium strains in soybean (Glycine max) roots. Frontiers in Plant Science, 7, 721. https://doi.org/10.3389/fpls.2016.00721
   Web of Science ®Google Scholar
• Zhang, D. Y., Ali, Z., Wang, C. B., Xu, L., Yi, J. X., Xu, Z. L., Liu, X. Q., He, X. L., Huang, Y. H., Khan, I. A., Trethowan, R. M., & Ma, H. X. (2013). Genome-wide sequence characterization and expression analysis of major intrinsic proteins in soybean (Glycine max L.). PloS one, 8(2), e56312. https://doi.org/10.1371/journal.pone.0056312
   Google Scholar