|
Screening of Different Rice Genotypes Using Functional Markers Related to Gn1a gene
|
Smaeil Talebi Kouyakhi   , Bahram Maleki Zanjani , Mostafa Modarresi * , Alireza Tarang |
| Rice Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Rasht, Iran , m.modaresi@areeo.ac.ir |
|
|
Abstract: (732 Views) |
Global food security is endanged by various factors, with one of the most significant being the quantitative and qualitative increase in agricultural production. Given the vital role of rice in the daily nutrition of Iranians and the necessity to enhance the efficiency of limited land resources, it is imperative to increase the yield per unit area. Identifying genotypes carrying alleles of genes associated with grain yield improvement is one of the methods to breed rice plant. Therefore, breeding rice genotypes can be used in breeding programs, to produce high-yield varieties. Given the importance of the number of grain per panicle and its impact on increasing rice grain yield per unit area, this study aimed to screen rice genotypes using a functional marker associated with the Gn1a gene, among several genes related to yield. In this research, 52 localraces and improved genotypes of rice were obtaied from the collection of the Rice Research Institute of Iran. The grain number trait was evaluated based on phenotypic and molecular evaluations in the field related to the band pattern amplified by gene specific primer pairs for Grain number 1a gene (Gn1a), controlling the grain number trait. The genetic evaluation identified 15 cultivars with the allele associated with a large panicle (more than 121 grains per panicle) and 37 cultivars without this allele. This finding, confirmed by phenotypic evaluation, demonstrates the reliability and accuracy of the marker used to predict and differentiate cultivars for upcoming breeding programs. The logistic regression results also supported this outcome. However, several other examined samples exhibited a high number of seeds, indicating the presence of additional genes influencing the seed count per panicle in those lines.
|
|
| Keywords: Rice, Number of grain per panicle trait, Genetic screening, functional marker efficiency |
|
|
Full-Text [PDF 625 kb]
(156 Downloads)
|
|
Type of Study: Research |
Subject:
Plant improvement
|
|
|
|
|
|
|
| References |
1. Andersen, J.R. and Lübberstedt, T. (2003). Functional markers in plants. Trends in Plant Science, 8: 554-560. [ DOI:10.1016/j.tplants.2003.09.010] 2. Ashikari, M., Sakakibara, H., Lin, S., Yamamoto, T., Takashi, T., Nishimura, A., Angeles, E.R., Qian, Q., Kitano, H. and Matsuoka, M. (2005). Cytokinin oxidase regulates rice grain production. Science, 309: 741-745. [ DOI:10.1126/science.1113373] 3. Doyle, J. and Doyle, J.L. (1990). Isolation of plant DNA from faesh tissue. Focus, 12: 13-15. [ DOI:10.2307/2419362] 4. Fernando, A., Selvaraj, M., Chavarriaga, P., Valdes, S. and Tohme, J. (2021). A clearinghouse for genome-edited crops and field testing. Molecular Plant, 14: 3-5. [ DOI:10.1016/j.molp.2020.12.010] 5. Gouda, G., Parida, M., Donde, R., Gupta, M.K., Kumar, J., Mohanty, S., Panda, R., Dash, S., Pradhan, S., Mohapatra, T. and Behera, L. (2019). Identification of high grain number genes and assessment of genetic diversity in high and low grain number rice genotypes useful for marker-assisted selection breeding programs. Annals of Plant and Soil Research, 21(4): 301-311. 6. Gouda, G., Gupta, M.K., Donde, R., Kumar, J., Parida, M., Mohapatra, T., Dash, S.K., Pradhan, S.K. and Behera, L. (2020). Characterization of haplotypes and single nucleotide polymorphisms associated with Gn1a for high grain number formation in rice plant. Genomics, 112(3): 2647-2657. [ DOI:10.1016/j.ygeno.2020.02.016] 7. Halilu, Z., Rabi'u Aliyu Umar, R.A., Shehu, A.A,. Turaki, A.A., Balarabe, A.H. and Gumi, A.M. (2020). Studies on some major yield responsive genes in selected rice (Oryza species) cultivars grown in Nigeria using candidate gene SSR-based markers approach. African Journal of Biotechnology, 19: 33-42. [ DOI:10.5897/AJB2018.16567] 8. Ikeda, M., Miura, K., Aya, K., Kitano, H. and Matsuoka, M. (2013). Genes offering the potential for designing yield-related traits in rice. Current opinion in Plant Biology, 16: 213-220. [ DOI:10.1016/j.pbi.2013.02.002] 9. Huang, Y., Dong, H., Shang, M. and Wang, K. (2021). CRISPR/Cas systems: the link between functional genes and genetic improvement. The Crop Journal, 9(3): 678-687. [ DOI:10.1016/j.cj.2021.03.004] 10. Jiang, S., Sun, S., Bai, L., Ding, G., Wang, T., Xia, T., Jiang, H., Zhang, X. and Zhang, F. (2017). Resequencing and variation identification of whole genome of the japonica rice variety" Longdao24" with high yield. PLoS One, 12: e0181037. [ DOI:10.1371/journal.pone.0181037] 11. Kaab Omeyr, A., PourMohammadi, P., Gilani, A., Alami-Saeid, K. and Fakhari, M. (2022). Investigation of genetic diversity and classification of aerobic and local rice genotypes in Khuzestan province. Plant Genetic Researches, 8(2):103-116 (In Persian). [ DOI:10.52547/pgr.8.2.8] 12. Li, G., Xu, B., Zhang, Y., Xu, Y., Khan, N.U., Xie, J., Sun, X., Guo, H., Wu, Z.and Wang, X. (2022a). RGN1 controls grain number and shapes panicle architecture in rice. Plant Biotechnology Journal, 20: 158-167. [ DOI:10.1111/pbi.13702] 13. Li, M., Pan, X. and Li, H. (2022b). Pyramiding of gn1a, gs3, and ipa1 exhibits complementary and additive effects on rice yield. International Journal of Molecular Sciences, 23: 12478. [ DOI:10.3390/ijms232012478] 14. Liu, M., Fan, F., He, S., Guo, Y., Chen, G., Li, N., Li, N., Yuan, H., Si, F. and Yang, F. (2022). Creation of elite rice with high-yield, superior-quality and high resistance to brown planthopper based on molecular design. Rice, 15: 1-13. [ DOI:10.1186/s12284-022-00563-7] 15. Liu, X., Zhou, S., Wang, W., Ye, Y., Zhao, Y., Xu, Q., Zhou, C., Tan, F., Cheng, S. and Zhou, D.X. (2015). Regulation of histone methylation and reprogramming of gene expression in the rice inflorescence meristem. The Plant Cell, 27: 1428-1444. [ DOI:10.1105/tpc.15.00201] 16. Lübberstedt, T., Melchinger, A.E., Fähr, S., Klein, D., Dally, A. and Westhoff, P. (1998). QTL mapping in testcrosses of flint lines of maize: III. Comparison across populations for forage traits. Crop Science, 38: 1278-1289. [ DOI:10.2135/cropsci1998.0011183X003800050027x] 17. Lübberstedt, T., Zein, I., Andersen, J.R., Wenzel, G., Krützfeldt, B., Eder, J., Ouzunova, M. and Chun, S. (2005). Development and application of functional markers in maize. Euphytica, 146: 101-108. [ DOI:10.1007/s10681-005-0892-0] 18. Ma, F., Zhu, X., Wang, H., Wang, S., Cui, G., Zhang, T., Yang, Z., He, G., Ling, Y. and Wang, N. (2019). Identification of QTL for kernel number-related traits in a rice chromosome segment substitution line and fine mapping of qSP1. The Crop Journal, 7: 494-503. [ DOI:10.1016/j.cj.2018.12.009] 19. MirMohammadi Maibody, S.A.M. and Golkar, P. (2019). Application of DNA molecular markers in plant breeding Plant Genetic Researches, 6(1):1-30 (In Persian). [ DOI:10.29252/pgr.6.1.1] 20. Nellemann, C. (2009). The Environmental Food Crisis: The Environment's Role In Averting Future Food Crises: A UNEP Rapid Response Assessment. UNEP/Earthprint, United Nations Avenue, Gigiri Nairobi, KENY. 21. Nishimura, C., Ohashi, Y., Sato, S., Kato, T., Tabata, S. and Ueguchi, C. (2004). Histidine kinase homologs that act as cytokinin receptors possess overlapping functions in the regulation of shoot and root growth in Arabidopsis. The Plant Cell, 16: 1365-1377. [ DOI:10.1105/tpc.021477] 22. Qian, Q., Guo, L., Smith, S.M. and Li, J. (2016). Breeding high-yield superior quality hybrid super rice by rational design. National Science Review, 3: 283-294. [ DOI:10.1093/nsr/nww006] 23. Riefler, M., Novak, O., Strnad, M. and SchmüLling, T. (2006). Arabidopsis cytokinin receptor mutants reveal functions in shoot growth, leaf senescence, seed size, germination, root development, and cytokinin metabolism. The Plant Cell, 18: 40-54. [ DOI:10.1105/tpc.105.037796] 24. Salami, H. and Bastani, M. (2017). Is rice import unjustified in Iran?. Journal of Agricultural Economics and Development, 31(3): 268-278 (In Persian). 25. Sharifi, P. and Aminpanah, H. (2017). Evaluation of genotype × environment interactions, stability and a number of genetic parameters in rice genotypes. Plant Genetic Researches, 3(2): 25-42 (In Persian). [ DOI:10.29252/pgr.3.2.25] 26. Shen, L., Wang, C., Fu, Y., Wang, J., Liu, Q., Zhang, X., Yan, C., Qian, Q. and Wang, K (2018). QTL editing confers opposing yield performance in different rice varieties. Journal of Integrative Plant Biology, 60: 89-93. [ DOI:10.1111/jipb.12501] 27. Varshney, R.K., Singh, V.K., Kumar, A., Powell, W. and Sorrells, M.E. (2018). Can genomics deliver climate-change ready crops? Current Opinion in Plant Biology, 45: 205-211. [ DOI:10.1016/j.pbi.2018.03.007] 28. Xu, Z., Miao, Y., Chen, Z., Gao, H., Wang, R., Zhao, D., Zhang, B., Zhou, Y., Tang, S. and Zhang, H. (2019). Identification and fine mapping of qGN1c, a QTL for grain number per panicle, in rice (Oryza sativa). Molecular Breeding, 39: 1-12. [ DOI:10.1007/s11032-019-1039-7] 29. Yan, C.J., Yan, S., Yang, Y.C., Zeng, X.H., Fang, Y.W., Zeng, S.Y., Tian, C.Y., Sun, Y.W., Tang, S.Z. and Gu, M.H. (2009). Development of gene-tagged markers for quantitative trait loci underlying rice yield components. Euphytica, 169: 215-226. [ DOI:10.1007/s10681-009-9937-0] 30. Yang, Y., Shen, Z., Xu, C., Guo, M., Li, Y., Zhang, Y., Zhong, C., Sun, S. and. Yan, C. (2020). Genetic improvement of panicle-erectness japonica rice toward both yield and eating and cooking quality. Molecular Breeding, 40: 1-12. [ DOI:10.1007/s11032-020-01127-7] 31. Zeng, D., Tian, Z., Rao, Y., Dong, G., Yang, Y., Huang, L., Leng, Y., Xu, J., Sun, C., Zhang, G. and Hu, J. (2017). Rational design of high-yield and superior-quality rice. Nature plants, 3(4): 1-5. [ DOI:10.1038/nplants.2017.31] 32. Zhang, G.H., Li, S.Y., Wang, L., Ye, W.J., Zeng, D.L., Rao, Y.C., Peng, Y.L., Hu, J., Yang, Y.L., Xu, J. Ren, D.Y., Gao, Z.Y., Zhu, L., Dong, G.J., Hu, X.M., Yan, M.X., Guo, L.B. , Li, C.Y. and Qian, Q. (2014). LSCHL4 from japonica cultivar, which is allelic to NAL1, increases yield of indica super rice 93-11. Molecular Plant, 7: 1350-1364. [ DOI:10.1093/mp/ssu055] |
|
| Send email to the article author |
|
|
|
Research code: 17-04-04-005-00180
Talebi Kouyakhi S, Maleki Zanjani B, Modarresi M, Tarang A. Screening of Different Rice Genotypes Using Functional Markers Related to Gn1a gene. pgr 2024; 11 (1) :37-46 URL: http://pgr.lu.ac.ir/article-1-299-en.html
|
