Nitrogen-Use Efficiency Evaluation and Genome Survey of Vietnamese Rice Landraces (Oryza sativa L.)

Date Received: Oct 19, 2018

Date Accepted: Oct 22, 2018

Date Published: Oct 22, 2018

DOI: https://doi.org/10.31817/vjas.2018.1.2.04

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Issue: Vol. 1 No. 2 (2018): Vietnam Journal of Agricultural Sciences

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ENGINEERING AND TECHNOLOGY

How to Cite:

Nguyen, H., Dinh, T. L., Nguyen, T., & Pham, C. (2018). Nitrogen-Use Efficiency Evaluation and Genome Survey of Vietnamese Rice Landraces (Oryza sativa L.). Vietnam Journal of Agricultural Sciences, 1(2), 142–155. https://doi.org/10.31817/vjas.2018.1.2.04

Nitrogen-Use Efficiency Evaluation and Genome Survey of Vietnamese Rice Landraces (Oryza sativa L.)

Hanh Thi Thuy Nguyen (*) 1 , Thuy Linh Mai Dinh 2 , Trung Quoc Nguyen 1   , Cuong Van Pham 3

  • Corresponding author: ntthanh.sh@vnua.edu.vn
  • 1 Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi 131000, Vietnam
  • 2 Center of International Plant Research Vietnam and Japan (CIPR), Hanoi 131000, Vietnam
  • 3 Faculty of Agronomy, Vietnam National University of Agriculture, Hanoi 131000, Vietnam

    • Keywords

    Genome survey, Local rice landrace (Oryza sativa L.), Nitrogen use efficiency (NUE)

    Abstract


    The overuse of fertilizers can result in many adverse effects such as decreasing fertilizer use efficiency of plants, wasting resources, increasing farming costs, and polluting our environment. Local rice landraces including indigenous and local rice varieties, may contain considerable genetic diversity that can serve as sources of germplasm for genetic improvements of nutrient use efficiency, yield, resistance to pests and pathogens, and important agronomic traits. Increasing the fertilizer use efficiency of crops by developing new rice varieties is necessary for sustainable agriculture. In this study, six rice varieties, Chiem Tay (CT), Te Tep (TT), Re Bac Ninh (RB), IR24, P6DB, and Khang Dan 18 (KD18), were evaluated for nitrogen use efficiency. Two landraces, P6DB and CT, which showed the lowest and highest values of nitrogen use efficiencies, were selected for a genome survey. Ninety-seven out of the 1051 surveyed markers indicated polymorphisms. These polymorphic markers were distributed along to each of the 12 chromosomes and were either scattered quite evenly on a chromosome or were condensed at particular regions in the physical map. The obtained information on nitrogen use efficiency (NUE) variation and the marker map should be very useful to further identify QTLs/genes involving in NUE as well as other genetic analyses toward the development of sustainable agriculture.

    References

    Amano T., Zhu Q., Wang Y., Inoue N. and Tanaka H. (1993). Case studies on high yields of paddy rice in Jiangsu province, China. I. Characteristics of grain production. Japanese Journal of Crop Science. Vol 62. pp. 267-274.

    Bing Z., Qi-Ming D., Qi-Jun Z., Jie-Qin L., Shao-Ping Y., Yong-Shu L., Yong P. and Ping L. (2006). Analysis of segregation distortion of molecular markers in F2 population of rice. Acta Genetica Sinica. Vol 33 (5). pp. 449-457.

    Broadbent F. E., de Datta S. K. and Laureles E. V. (1987). Measurement of nitrogen utilization efficiency in rice genotypes. Agronomy Journal. Vol 79. pp. 786-791.

    Chandra R., Takeuchi H. and Hasegawa T. (2012). Hydrothermal pretreatment of rice straw biomass: a potential and promising method for enhanced methane production. Applied Energy. Vol 94. pp. 129-140.

    Cuong P. V., Huong N. T., Hang D. T. T., Hanh T. T., Takuya A. and Toshihiro M. (2010). Nitrogen Use efficiency in F1 hybrid, Improved and Local Cultivars of rice (Oryza Sativa L.) during different cropping seasons. Journal of Science & Development. Vol 8 (Eng. Iss. 1). pp. 59-68.

    Davies D. B. and Sylvester-Bradley R. (1995). The contribution of fertilizer nitrogen to leachable nitrogen in the UK: a review. Journal of The Science of Food and Agriculture. Vol 68. pp. 399-406.

    De Datta S. K. and Broadbent F. E. (1993). Development changes related to nitrogen-use efficiency in rice. Field Crop Research. Vol 34. pp. 47-56.

    Dellaporta S. L., Wood J. and Hicks J. B. (1983). A plant DNA minipreparation: version II. Plant molecular biology reporter. Vol 1 (4). pp. 19-21.

    Ferguson R. B., Hergert G. W., Schepers J. S., Gotway C. A., Cahoon J. E. and Peterson T. A. (2002). Site-specific nitrogen management of irrigated maize, yield and soil residual nitrate effects. Soil Science Society of America Journal. Vol 66. pp. 544-553.

    Guong V. T., Lap T. T., Hoa N. M., Castillo E. G., Padilla J. L. and Singh U. (1995). Nitrogen-use efficiency in direct-seeded rice in the Mekong River Delta: varietal and phosphorus response. Agricultural Information Management Standards. pp. 151-159.

    Hamaoka N., Uchida Y., Tomita M., Kumagai E., Araki T. and Ueno O. (2013). Genetic variations in dry matter production, nitrogen uptake, and nitrogen use efficiency in the AA genome Oryzaspecies grown under different nitrogen conditions. Plant Production Science. Vol 16. pp. 107-116.

    Hanh N. T. T., Cuong P. V. and Bertin P. (2014). The effect of nitrogen concentration on nitrogen use efficiency and related traits in cultivated rices (Oryza sativa L. subsp. indica and japonica and O. glaberrima Steud.) in hydroponics. Euphytica. Vol 198. pp. 137-151.

    Harushima Y., Yano M., Shomura A., Sato M., Shimano T., Kuboki Y., Yamamoto T., Lin S. Y., Antonio B. A., Parco A., Kajiya H., Huang N., Tamamoto K., Nagamura Y., Kurata N., Khush G. S. and Sakaki T. (1998). A high-density rice genetic map with 2,275 markers using a single F2 population. Genetics. Vol 148. pp. 479-494.

    Hashimoto M., Herai Y., Nagaoka T. and Kouno K. (2007). Nitrate leaching in granitic regosol as affected by N uptake and transpiration by corn. Soil Science and Plant Nutrition. Vol 53. pp. 300-309.

    Hasegawa H. (2003). High-yielding rice cultivars perform best even at reduced nitrogen fertilizer rate. Crop Science. Vol 43. pp. 921-926.

    Hawkesford M. J. (2011). An overview of nutrient use efficiency and strategies for crop improvement. Wiley, Sussex. pp. 5-19.

    Hung N. N., Singh U., Xuan V.T., Buresh R. J., Padilla J. L., Lap T. T. and Nga T. T. (1995). Improving nitrogen-use efficiency of direct-seeded rice on alluvial soils of the Mekong River Delta. AGRIS. pp.138-149.

    Inthapanya P., Sipaseuth, Sihavong P., Sihathep V., Chanphengsay M., Fukai S. and Basnayake J. (2000). Genotype differences in nutrient uptake and utilization for grain yield production of rainfed lowland rice under fertilized and non-fertilized conditions. Field Crops Research. Vol 65. pp. 57-68.

    Ju J., Yamamoto Y., Wang Y., Shan Y., Dong G., Miyazaki A. and Yoshida T. (2009). Genotypic differences in dry matter accumulation, nitrogen use efficiency and harvest index in recombinant inbred lines of rice under hydroponic culture. Plant Production Science. Vol 12. pp. 208-216.

    Kjeldahl J. (1883). New method for the determination of nitrogen in organic substances. Zeitschrift für analytische Chemie, Vol 22 (1). pp. 366-383.

    Koutroubas S. D. and Ntanos D. A. (2003). Genotypic differences for grain yield and nitrogenutilization in Indica and Japonica rice under Mediterranean conditions. Field Crops Research. Vol 83. pp. 251-260.

    Mae T., Inaba A., Kaneta Y., Masaki S., Sasaki M., Aizawa M., Okawa S., Hasegawa S. and Makino A. (2006). A large-grain rice cultivar, Akita 63, exhibits high yields with high physiological N-use efficiency. Field Crops Research. Vol 97. pp. 227-237.

    McCouch S. R., Kochert G., Yu Z. H., Wang Z. Y., Khush G. S., Coffman W. R. and Tanksley S. D. (1988). Molecular mapping of rice chromosomes. Theoretical and Applied Genetics. Vol 76 (6). pp. 815-829.

    McCouch S. R., Teytelman L., Xu Y., Lobos K. B., Clare K., Walton M., Fu B., Maghirang R., Li Z., Xing Y., Zhang Q., Kono I., Yano M., Fjellstrom R., DeClerck G., Schneider D., Cartinhour S., Ware D. and Stein L. (2002). Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Research. Vol 9 (6). pp. 199-207.

    Misselbrook T. H., Van der Weerden Y. J., Pain B. F., Jarvis S. C., Chambers B. J., Smith K. A., Phillips V. R. and Demmers T. G. M. (2000). Ammonia emission factors for UK agriculture. Atmospheric Environment. Vol 34. pp. 871-880.

    Muhammad A. V., Fahrul Z. H., Takashige I., Azma A. S., Tariq M., Muhammad S. H. and Muhammad S. (2013). Construction of microsatellite linkage map and detection of segregation distortion in Indica rice (Oryza Sativa L.). Pakistan Journal of Botany. Vol 45 (6). pp. 2085-2092.

    Namai S., Toriyama K. and Fukuta Y. (2009). Genetic variation in dry matter production and physiological nitrogen use efficiency in rice (Oryza sativa L.) varieties. Breeding Science. Vol 59. pp. 269-276.

    Pathak R. R., Ahmed A., Lachab S. and Raghuram N. (2008). Molecular physiology of plant nitrogen use efficiency and biotechnological options for its enhancement. Current Science. Vol 94. pp. 1394-1401.

    Peng S., Cassman K. G., Virmani S. S., Sheehy J. and Khush G. S. (1999) Yield potential trends of tropical rice since the release of IR8 and the challenge of increasing rice yield potential. Crop Science. Vol 39. pp. 1552-1559.

    PRC - Plant Resources Center (2017). Plant germplasm information online. Retrieved on December 10, 2016 at http://csdl.prc.org.vn/Default.aspx.

    Septiningsih E. M., Sanchez D. L., Singh N., Sendon P. M. D., Pamplona A. M., Heuer S. and Mackill D. J. (2012). Identifying novel QTLs for submergence tolerance in rice cultivars IR72 and Madabaru. Theoretical and Applied Genetics. Vol 124. pp. 867-874.

    Singh U., Ladha J. K., Castillo E. G., Punzalan G., Tirol-Padre A. and Duqueza M. (1998). Genotypic variation in nitrogen use efficiency in medium and long duration rice. Field Crops Research. Vol 58. pp. 35-53.

    Socolow R. H. (1999). Nitrogen management and the future of food: lessons from the management of energy and carbon. Proceedings of the National Academy of Science of the United States of American. Vol 96. pp. 6001-6008.

    Song W., Chen X. Y., Xu J. R. and Zhang Z. Y. (2003). Research progress in forest tree genetic linkage map construction and its future prospects. Yi Chuan. Vol 25 (6). pp. 749-756.

    Tirol-Padre A., Ladha J. K., Singh U., Laureles E., Punzalan G. and Akita S. (1996). Grain yield performance of rice genotypes at suboptimal levels of soil N as affected by N uptake and utilization efficiency. Field Crops Research. Vol 46. pp. 127-143.

    Ut T. T and Kei K. (2006). The impact of green revolution on rice production in Vietnam. The Developing Economies. Vol 2. pp. 167-189.

    Vitousek P. M., Naylor R., Crews T., David M. B., Drinkwater L. E., Holland E., Johnes P. J., Katzenberger J., Martinelli L. A., Matson P. A., Nziguheba G., Ojima D., Palm C. A., Robertson G. P., Sanchez P. A., Townsend A. R. and Zhang F. S. (2009). Nutrient imbalances in agricultural development. Science. Vol 324. pp. 1519-1520.

    Yang J., Peng S., Zhang Z., Wang Z., Visperas R. M. and Zhu Q. (2002). Grain and dry matter yields and portioning of assimilates in Japonica/Indica hybrid rice. Crop Science. Vol 42. pp. 766-772.