Introgression of Sub1 QTL (Submergence tolerant QTL) into the elite rice variety Jaya by Marker Assisted Backcross Breeding
Keywords:
Rice, Submergence tolerance, Marker Assisted Backcross Breeding, Polymorphic SSR markersAbstract
Rice (Oryza sativa L.) is the most important staple food crop of Asia. Submergence is the third important abiotic stress affecting rice crop in coastal ecosystems of Kerala due to heavy showers of South-West monsoon. The most viable solution to overcome this problem is to introgress submergence tolerant gene into high yielding elite rice varieties. Hence, the present study was undertaken to introgress submergence tolerant gene (Sub1 gene) into the elite rice variety Jaya through Marker Assisted Backcross Breeding (MABB). Polymorphism assay using 625 SSR markers could select two polymorphic foreground markers, seven polymorphic recombinant markers and 76 polymorphic genome wide markers. The genotypic selection of heterozygous plants was made in F1 and in each backcross generation and in selfed progeny homozygous plants were selected using the selected foreground and recombinant markers. The Sub1 region of the selected BC2F2 progeny ranged from 0.5-5.6 mb and had ≥ 85% homozygosity to that of recurrent parent. These selected progeny were screened for submergence tolerance in vitro and scored according to SES by IRRI which showed similar score to that of the donor parent. Our work could introgress the abiotic stress submergence tolerance controlled by Sub1 gene into the popular rice variety Jaya. The developed abiotic stress tolerant rice lines are under field evaluation and can be cultivated profitably in the coastal ecosystem where flood is the major constraint limiting rice production.References
Alexandratos, N., and Bruinsma, J., 2012. World agriculture towards 2030/2050: the 2012 revision, global perspective studies team, FAO, Agricultural Development Economics Division, 1-154.
Benbouza, H., Jacquemin, J.M., Baudoin, J.P. and Mergeai, G. 2006. Optimization of a reliable, fast, cheap and sensitive silver staining method to detect ssr markers in polyacrylamide gels. Biotechnol. Agron. Soc. Environ., 10(2): 77-81.
CESS, 2010. Plan project 239. Detailed project report.
Cuc, Luu M., Huyen, Luu T. N., Hien, Pham T. M., Hang, Vu T. T., Dam, Nguyen Q., Mui, Pham T., Quang, Vu D., Ismail, Abdelbagi M., Ham, Le H. 2012. Application of marker assisted backcrossing to introgress the submergence tolerance QTL SUB1 into the Vietnam elite rice variety - AS996. American Journal of Plant Sciences, 3: 528-536.
Das, Gitishree., and Rao, G., J., N. 2015. Molecular marker assisted gene stacking for biotic and abiotic stress resistance genes in an elite rice cultivar. Front. Plant Sci., 6:698.
Doyle, J.J. and Doyle, J.L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin, 19: 11-15.
FAO, Food and Agricultural Organization of the United Nations. Statistical Yearbook 2017. Rome. Italy.
Fukao, T., Xu, K., Ronald P.C., Bailey-Serres J. 2006. A variable cluster of ethylene response factor-like genes regulates metabolic and developmental acclimation responses to submergence in rice. Plant Cell 18:2021–2034.
Hasan, M. M., Rafi, M. M. Y., Ismail, M. R., Mahmood, M., Rahim, H. A., Alam, M. A., Ashkani, S., Malek, M. A., and Latif, M. A. 2015. Marker - assisted backcrossing: A useful method for rice improvement. Taylor & Francis, 29 (2): 237-254.
Hospital, F. 2003. Marker - assisted breeding. In: Newbury, H.J. (ed.), Plant Molecular Breeding, Blackwell Publishing, Oxford, pp. 30 - 59.
Hospital, F. and Charcosset, A. 1997. Marker - assisted introgression of quantitative trait loci. Genetics., 147: 1469 -1485.
Iftekharuddaula, K., Newaz, M. and Salam, M. 2011. Rapid and high-precision marker assisted backcrossing to introgress the SUB1 QTL into BR11, the rainfed lowland rice mega variety of Bangladesh. Euphytica., 178(1): 83-97.
IRRI, 1988. Standard evaluation system for rice testing programme (IRTP), Rice Manual 3rd Ed., International Rice Research Institute, Manila (Philippines), p.19.
IRGSP, 2005. The map - based sequence of the rice genome. Nature, 436: 793–800.
KAU. 2016. Package of Practices Recommendations - Crops, 15 Ed., Directorate of Extension, Kerala Agricultural University, Thrissur, p.19.
Manzanilla, D. O., Paris, T. R., Vergara, G. V., Is-mail, A. M., Pandey, S., Labios, R. V., Tatlonghari, G. T., Acda, R. D., Chi, T. T. N., Duoangsila, K., Siliphouthone, I., Manikmas, M. O. A., and Mackill, D. J. 2011. Submergence risks and farmers’ preferences: implications for breeding Sub1 rice in Southeast Asia, Agricultural Systems, 104 (4): 353-347.
Mccouch, Sr., Teytelman, L., Xu, Y., Lobos, Kb., Clare, K., Walton, M., 2002. Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Research 9: 199 - 207.
Nandi, S., Subudhi, P. K., Senadhira, D., Manigbas, N. L., Sen - Mandi, S. and Huang, N. 1997. Mapping QTL for submergence tolerance in rice by AFLP analysis and selective genotyping. Mol. Gen. Genet., 255: 1 - 8.
Neeraja, C., Maghirang, R. R., Pamplona, A., Heuer, S., Collard, B.C.Y., Septiningsih, E.M., Vergara, G., Sanchez, D., Xu, K., Ismail, A.M. and Mackill, D. J. 2007. A marker - assisted backcross approach for developing submergence- tolerant rice cultivars. Theor. Appl. Genet., 115(6): 767-776.
Pradhan, S, K., Barik, S. R., Sahoo, J., Pandit, E., Nayak, D. K., Pani, D. R., Anandan, A. 2015. Comparison of Sub1 makers and their combinations for submergence tolerance and analysis of adaptation strategies of rice in rainfed lowland ecology. Science Direct, 338 (10):650-659.
Ralph, V. B. 2008. GGT 2.0: Versatile software for visualization and analysis of genetic data. J. Hered., 99(2): 232 - 236.
Sarkar, R. K. and Bhattacharjee, B. 2012. Rice genotypes with SUB1 QTL differ in submergence tolerance, elongation ability during submergence and re – generation growth at re – emergence. Rice 5:7.
Septiningsih, E.M., Pamplona, A.M., Sanchez, D.L., Neeraja, C.N., Vergara, G.V., Heuer, S., Ismail, A.M. and Mackill, D.J., 2009. Development of submergence tolerant rice cultivars: The SUB1 locus and beyond. Ann. Bot., 103(2): 151-160.
Tanksley, S.D., Young, N.D., Paterson, A.H. and Bonierbale, M.W. 1989. RFLP mapping in plant breeding: new tools for an old science. Biotech., 7: 257 - 264.
Temnykh, S., Clerck, G.D., Lukashova, A., Lipovich, L., Carthinour. S., McCouch, S.R., 2001. Computational and experimental analysis of microsatellites in rice (O. sativa L.): Frequency, length variation, transposon associations, and genetic marker potential. Genome Res., 11(8): 1441 - 1452.
Toojinda, T., Siangliw, M., Tragoonrung, S., Vanavichit, A. 2003. Molecular genetics of submergence tolerance in rice: QTL analysis of key traits, Ann. Bot. 91: 243–253.
Xu, K., and Mackill, D.J. 1996. A major locus for submergence tolerance mapped on rice chromosome 9. Mol. Breed., 2: 219 - 224.
Xu, K., Xia, X., Fukao, T., Canlas, P., Maghirang, R.R., Heuer, S., Ismail, A.I., Bailey-Serres, J., Ronald, P.C. and Mackill, D.J. 2006. Sub1A is an ethylene response factor-like gene that confers submergence tolerance to rice. Nature., 442: 705 - 708.
Xu, K., Xu, X., Ronald, P.C. and Mackill, D.J. 2000.A high-resolution linkage map in the vicinity of the rice submergence tolerance locus Sub1. Mol. Genet., 263: 681 - 689.
Downloads
Published
How to Cite
Issue
Section
License
Copyright © 2001-11 Kerala Agricultural University. Some rights reserved. This journal and the individual contributions contained in it are protected under copyright by the Kerala Agricultural University and the following terms and conditions apply to their use; Photocopying Single photocopies of single articles may be made for personal use as allowed by national copyright laws. Permission of the publisher and payment of a fee is required for all other photocopying including multiple or systematic copying, copying for advertising or promotional purposes, resale, and all forms of document delivery. Permission may be sought directly from the Editor, Journal of Tropical Agriculture, Department of Agronomy, College of Horticulture,, Kerala Agricultural University, KAU PO, Thrissur 680 656, Kerala, India. (Phone: +91-487-2438325; Fax +91-487-2371040; E-mail: editor.jta@kau.in. Derivative works Subscribers may reproduce tables of contents or prepare lists of articles including abstracts for internal circulation within their institution. Permission of the Publisher is required for resale or distribution outside the institution. Permission of the Publisher is required for all other derivative works, including compilations and translations. Notice No responsibility is assumed by the Publisher for any injury and/or damage to persons or property as a matter of products, liability, negligence, or otherwise, or from any use of any methods, products, instructions or ideas contained in the material herein.