509
Views
0
CrossRef citations to date
0
Altmetric
SOIL & CROP SCIENCES

Effects of electrophoresis buffer, electrophoresis time, and annealing temperature on the quality of SSR molecular detection in rice varieties

, , , , , & show all
Article: 2275414 | Received 03 Jul 2023, Accepted 21 Oct 2023, Published online: 09 Nov 2023

References

  • Ashraf, H., Husaini, A. M., Ashraf Bhat, M., Parray, G. A., Khan, S., & Ganai, N. A. (2016, October). SSR based genetic diversity of pigmented and aromatic rice (Oryzasativa L.) genotypes of the western Himalayan region of India. Physiology and Molecular Biology of Plants., 22(4), 547–9. https://doi.org/10.1007/s12298-016-0377-8
  • Azqueta, A., Gutzkow, K. B., & Brunborg, G. (2011, September 18). Towards a more reliable comet assay: Optimising agarose concentration, unwinding time and electrophoresis conditions. Mutation Research, 724(1–2), 41–45. https://doi.org/10.1016/j.mrgentox.2011.05.010
  • Cao, Q., Lu, B. R., Xia, H., RONG, J., SALA, F., SPADA, A., & GRASSI, F. (2006, December). Genetic diversity and origin of weedy rice (Oryza sativa f. spontanea) populations found in North-eastern China revealed by simple sequence repeat (SSR) markers. Annals of Botany, 98(6), 1241–1252. https://doi.org/10.1093/aob/mcl210
  • Chen, J., Xie, W., & Wang, T. (2017). Genetic diversity analysis of photoperiod and temperature-sensitive male sterile lines in rice based on SSR markers. Jiangxi Journal of Agricultural Sciences, 29(3), 1–6.
  • Gunson, R., Gillespie, G., & Carman, W. F. (2003, April). Optimisation of PCR reactions using primer chessboarding. Journal of Clinical Virology, 26(3), 369–373. https://doi.org/10.1016/S1386-6532(03)00006-4
  • Hu, W., Zhou, T., Wang, P., Wang, B., Song, J., Han, Z., Chen, L., Liu, K., & Xing, Y. (2020, January). Development of whole-genome agarose-resolvable LInDel markers in rice. Rice (N Y), 13(1), 1. https://doi.org/10.1186/s12284-019-0361-3
  • Ishii, K., & Fukui, M. (2001, August). Optimization of annealing temperature to reduce bias caused by a primer mismatch in multitemplate PCR. Applied & Environmental Microbiology, 67(8), 3753–3755. https://doi.org/10.1128/AEM.67.8.3753-3755.2001
  • Jasim Aljumaili, S., Rafii, M. Y., Latif, M. A., Sakimin, S. Z., Arolu, I. W., & Miah, G. (2018, March 15). Genetic diversity of aromatic rice germplasm revealed by SSR markers. BioMed Research International, 2018, 1–11. https://doi.org/10.1155/2018/7658032
  • Jayabalan, S., Pulipati, S., Ramasamy, K., Jaganathan, D., Venkatesan, S. D., Vijay, G., Kumari, K., Raju, K., Hariharan, G. N., & Venkataraman, G. (2019, September 10). Analysis of genetic diversity and population structure using SSR markers and validation of a Cleavage Amplified Polymorphic Sequences (CAPS) marker involving the sodium transporter OsHKT1;5 in saline tolerant rice (Oryza sativa L.) landraces. Gene, 713, 143976. https://doi.org/10.1016/j.gene.2019.143976
  • Kaur, S., Panesar, P. S., Bera, M. B., & Kaur, V. (2015). Simple sequence repeat markers in genetic divergence and marker-assisted selection of rice cultivars: A review. Critical Reviews in Food Science and Nutrition, 55(1), 41–49. https://doi.org/10.1080/10408398.2011.646363
  • Killgore, G. E., Holloway, B., & Tenover, F. C. (2000, July). A 5’ nuclease PCR (TaqMan) high-throughput assay for detection of the mecA gene in staphylococci. Journal of Clinical Microbiology, 38(7), 2516–2519. https://doi.org/10.1128/JCM.38.7.2516-2519.2000
  • Lee, P. Y., Costumbrado, J., Hsu, C. Y., & Kim, Y. H. (2012, April). Agarose gel electrophoresis for the separation of DNA fragments. Journal of Visualized Experiments: JoVe, 20(62), 3923. https://doi.org/10.3791/3923
  • Liu, Q., Ding, X., & Zhang, P. (2021). Purity identification of hybrid rice Seed using SSR molecular markers. Anhui Agricultural Bulletin, 27(5), 9–10.
  • O’Conner, J. L., Wade, M. F., & Zhou, Y. (1991, March). Control of buffer pH during agarose gel electrophoresis of glyoxylated RNA. Biotechniques, 10(3), 300–302.
  • Rychlik, W., Spencer, W. J., & Rhoads, R. E. (1990, November). Optimization of the annealing temperature for DNA amplification in vitro;. Nucleic Acids Research, 18(21), 6409–6412. https://doi.org/10.1093/nar/18.21.6409
  • Wang, X. (2006). Construction of rice characteristic fingerprint and analysis of seed purity using SSR markers. Fujian Agriculture and Forestry University.
  • Xiaoyue, Y., Hua, Y., & Fanggang, Z. (2016). Effect of annealing temperature, DNA polymerase, and thermal cycler on the quality of rice variety authenticity SSR molecular marker detection. Jiangsu Agricultural Sciences, 44(11), 57–60.
  • Yang, G., Yang, Y., Guan, Y., Xu, Z., Wang, J., Yun, Y., Yan, X., & Tang, Q. (2021, October 19). Genetic diversity of Shanlan Upland rice (Oryza sativa L.) and association analysis of SSR markers linked to agronomic traits. BioMed Research International, 2021, 1–11. https://doi.org/10.1155/2021/7588652
  • Yao, G., Lu, L., & Dan, Z. (2013). Screening and evaluation of agarose gel electrophoresis polymorphic SSR markers between indica and japonica subspecies. Henan Agricultural Sciences, 42(08), 16–20. https://doi.org/10.15933/j.cnki.1004-3268.2013.08.030
  • Zhou, H., Li, S., Liu, J., Hu, J., Le, S., & Li, M. (2023, February). Identification and analysis of the genetic integrity of different types of rice resources through SSR markers. Scientific Reports, 13(1), 2428. https://doi.org/10.1038/s41598-023-29514-y