Biochemists and molecular markers associated with water stress tolerance in rice
Keywords:
Oryza sativa L, drought, production, isoenzimes, microsatellite
Abstract
Drought in Venezuela has become a limiting factor for national rice production, as the cultivated varieties traditionally are adapted to high water supply. This study aimed to identify biochemical (isozymes) and molecular markers (microsatellites, SSR) associated with water stress tolerance in rice (Oryza sativa L.). Gene mapping study was conducted in a BC1 F2 crossing (LO2 x Fonaiap 2000) x LO2 using the MapDisto program and the method of one marker at a time. 89 putative quantitative characters (QTLs) associated with vegetative, reproductive and yield traits were identified. Using five isozymes (PRX, G6PDH, ACP, 6PGD, and SDH) and 40 SSR drought susceptibility indexes (ISS) were estimated. Next, the association between isoenzymes, water stress tolerance and ISS in the families of the segregating population was identified for variables related to the vegetative, reproductive and maturation of the grain phase in rice. In the 2 linkage groups (chromosome 3 and 9)4 QTL associated with ISS, 2 regions associated with 50% flowering, 1 for desgrane (chromosome 3) and 1 for fertility (chromosome 9) were detected in RM107, RM442, and RM570. This information can be used as a criterion in molecular marker-assisted selection in future rice breeding programs in order to identify families and genotypes tolerant to the water stress condition
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References
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• Courtois B., D. Filloux, N. Ahmadi, J-L. Noyer, C. Billot y E.P. Guimarães. 2003. Uso de marcadores moleculares para el manejo de poblaciones de arroz mejoradas mediante selección recurrente. pp. 53-76. In: Mejoramiento poblacional, una alternativa para explorar los recursos genéticos del arroz en América Latina. Editor, E.P. Guimarães. CIAT-Colombia. 374 p.
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• Garcia, F. 2008. Caracterización morfoanatómica de genotipos de arroz (Oryza sativa L.) en condiciones de estrés hídrico. Trabajo de grado para optar al título de Ingeniero Agrónomo. Universidad Central de Venezuela. Facultad de Agronomía. 89 p.
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• Grandillo, S. y S. Tanksley. 1996. QTL analysis of horticultural traits differentiating the cultivated tomato from closely related species Lycopersicum pimpinellifolium. Theoretical and Applied Genetics. 92:935-951.
• Lanceras, J., G. Pantuwan, B. Jongdee and T. Toojinda. 2004. Quantitative Trait Loci Associated with Drought Tolerance at Reproductive Stage in Rice. Plant Physiology. 135(1):384-399.
• Lang, N. and B. Buu. 2008. Fine mapping for drought tolerance in rice (Oryza sativa L.) Omonrice. 16:9-15.
• Lafitte, H., A. Blum and G. Atlin. 2003. Using secondary traits to help identify drought- tolerant genotypes. IRRI: Breeding Rice for Drought-Prone Environments. pp. 37-48.
• Lafitte, H., A. Price and B. Courtois. 2004. Yield response to water deficit in an upland rice
mapping population: Associations among traits and genetic markers. Theoretical and Applied Genetics. 109(6):1237-1246.
• Lee, S., C. Oh, J. Suh, S. McCouch and S. Ahn. 2005. Identification of QTLs for domestication – related and agronomic traits in an Oryza sativa x Oryza rufipogon two backcross populations. Theoretical and Applied Genetics. 110:649-659.
• Ortiz, A., O. Gómez y C. Ramis, C. 2004. Caracterización bioquímica de poblaciones del complejo de maleza arroz rojo en Venezuela. Agronomía Trop. 54(3):257-273.
• Lee, B. K., K. Y. Kim, W. J. Jung, J. C. Avice, A. Ourry and T. H. Kim 2007. Peroxidases and lignification in relation to the intensity of water-deficit stress in white clover (Trifolium repens L.). Journal of Experimental Botany. 58(6):1271-1279.
• Lorieux, M. 2008. MapDistoGenetics Software, version 1.7. IRD-CIAT.
• Mackill, D. 2003. What molecular tools are available for selection for drought tolerance? Section 4.4 Breeding Rice for Drought - Prone Environments. IRRI. pp. 55-61.
• Manchenko, G. 1994. Handbook of Detection of Enzymes on Electrophoretic gels. Library of Congress Cataloging-in-Publication Data. 341 p.
• McCouh, S. R., L. Teytelman, Y. Xu, K. B. Lobos, K. Clare, M. Walton, B. Fu, R. Maghirang, Z. Li, Y. Xing, Q. Zhang, L. Kono, M. Yano, R. Fjellstrom, G. DeClerck, D. Schneider, S. Cartinhour, D. Ware and L. Stein. 2002. Development and Mapping of 2240 New SSR Markers for Rice (Oryza sativa L.). DNA Research. 9:199-207.
• McCouch, S., X. Chen, O. Panaud, S. Temnykh, Y. Xu, Y. Cho, N. Huang, T. Ishii and M. Blair. 1997. “Microsatellite marker development, mapping and applications in rice genetics and breeding”. Plant Molecular Biology. 35:89-99.
• McCouch, S. and R. Doerge. 1995. QTL mapping in rice. Trends and Genetics. 11(12):482-487.
• Mei, H., Q. Shu, Y. Wang, C. Ying, Z. Li, L. Guo, X. Yu and L. Luo. 2005. Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and Venezuela. Revista Facultad de Agronomía de la Universidad Central de Venezuela (UCV). 28:117-130.
• Pérez-Almeida, I., E. Torres, L. Angulo y M. Acevedo. 2011. Diversidad genética entre cultivares de arroz de Venezuela con base a la estimación del coeficiente de parentesco y análisis con marcadores moleculares microsatélites (SSR). Interciencia. 36(7):545- 551.
• Pieters, A. J. and M. Núñez. 2008. Photosyntesis, water use efficiency andδ13C in two rice genotypes with contrasting response to water deficit. Photosynthetica. 46(4):574-580.
• Praddep, M., N. Sarla, L. Reddy and E. Siddiq. 2005. Identification and mapping of yield and yield relative QTLs from an Indian accession of Oryza rufipogon. BMC Genetics. BioMed Central. Research article. Available online: https://bit.ly/3aJ1dV2 [Abr. 08,2014].
• Quirós, E. 2003. Evaluación morfológica y molecular de líneas avanzadas de mejoramiento genético de arroz (Oryza sativa) del Instituto de Investigación Agropecuaria de Panamá (IDIAP). Tesis para optar al título de maestría. Escuela de Posgrado, Programa de Educación para el Desarrollo y la Conservación del Centro Agronómico Tropical de Investigación y Enseñanza. 136 p.
• Rudd, S, H. Schoof and K. Mayer. 2005. Plant Markers a database of predicted molecular markers from plants. Nucleic Acids Research. Available online: https://bit.ly/2w2lqGT [Abr. 10, 2014].
• Sarkarung, S. 2002. A regional breeding program to develop drought - tolerant rainfed lowland germoplasm: IRRI´s experience in South and Southeast Asia. Breeding Rice for Drought - Prone Environments. IRRI. pp.70-74.
• Semagn, K., A. Bjornstad and N. Ndjiondjop. 2006. An overview of molecular markers methods for plants. African Journal of Biotechnology. 5(25):2540-2568.
• Septiningshigh, E., J. Prasetiyono, E. Lubis, T. Tai, T. Tjubaryat, S. Moeljopaeiro and S. McCouch. 2003. Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theoretical and Applied Genetics. 107:1419-1432.
• Swarbreck, S., M. Defoin-Platel, M. Hindle, M. Saqi and D. Habash. 2011. New perspectives on glutamine synthetase in grasses. Journal of Experimental Botany. 62(4):1511-1522.
• Takahashi, Y., A. Shomura, T. Sasaki and M. Yano. 2001. Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the α subunit of protein kinaseCK2. Proc Natl Acad USA. Available online: https://bit.ly/39PvXnC 98(14):7922-7927. [Abr. 08, 2014].
• Temnykh, S., W. Ayres, N. Cartinhour, S. Hauck, L. Lipovich, Y. Cho, T. Ishii and S. MCcouch. 2001. Mapping and genome organization of microsatellite sequence in rice (Oryza sativa L.). Theoretical and Applied Genetics. 100(5):697-712.
• Teng, S., Q. Qian, D. L. Zeng, Y. Kunihiro, K.Fujimoto, D. N Huang and L. H Zhu. 2002. Analysis of gene loci and epistasis for drought tolerance in seedling stage of rice (O. sativa L.) Yi Chuan Xue Bao. Available online: www.ncbi.nlm.nih.gov. 29(3):235- 240.
• Toojinda, T. 2002. Molecular genetics of submergence tolerance in rice: Quantitative trait loci (QTL) analysis of traits associated with submergence tolerance. Annals Botan.
• Thomson, M., T. Tai, A. McClung, X.-H. Lai, M. Hinga, K. Lobos, Y. Xu, C. Martínez and S. McCouch. 2003. Mapping quantitative trait loci for yield, yield components and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson. Theoretical and Applied Genetics. 107(3):479-493.
• Toorchi, M., H. Shashidhar, N. Sharma and S. Hittalmani. 2002. Tagging QTLs for maximum root length in rainfed lowland rice (Oryza sativa L.) using molecular markers. Cell Molecular Biology Lett. 7(2B):771-776.
• Torrealba, G. 2010. Identificación de marcadores moleculares asociados a la tolerancia al estrés hídrico en arroz (Oryza sativa L.). Trabajo para optar al título de doctora en Ciencias Agrícolas. Universidad Central de Venezuela (UCV), Facultad de Agronomía. Maracay. 199 p.
• Torrealba, G., I. Pérez, N. Delgado, C. Ramis, L.Angulo, O. León, M. Muñoz y G. Martínez. 2010. Metodología de campo para evaluación de tolerancia al estrés hídrico en el cultivo arroz. INIA Divulga. 16:23-26.
• Velásquez, R. 2001. Control genético de tres sistemas isoenzimáticos en arroz (Oryza sativa L). Trabajo de ascenso a Asistente. Maracay. Universidad Central de Venezuela (UCV), Facultad de Agronomía. 57 p.
• Vikram, P., BP. Mallikarjuna, S. Dixit, H. Uddin, MT. Sta Cruz, A. Kumar and Kumar. A. 2011. qDTY1.1, a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds. BMC Genetics. 12:89-104.
• Wan, X., J. Wan, J. Weng, L. Jiang, J. Bi, C. Wang and H. Zhai. 2005. Stability of QTLs for rice grain dimension and endosperm chalkiness characteristics across eight environments. 2005. Theoretical and Applied Genetics. 110(7):1334-1346.
• Xiao, J., J. Li, S. Grandillo, S. Ahn, L. Yuan, S. D Tanksley and McCouch S. 1998. Identification of trait improving quantitative trait loci alleles from a wild rice relative, Oryza rufipogon. Genetics. 150(2):899-909.
• Babu, R., P. Shanmugasundaram, P. Chezhian, B. Nguyen, P. Jayaprakash, S. Ganesh, V. Chamarerk, A. Palchamy, S. Sadasivam, S. Sarkarung, L. Wade and H. Nguyen.2002. Molecular Dissection of Drought Tolerance in rice: Association between Physiomorphological Traits and Field Performance. In: Field screening for drought tolerance in Crop Plants with Emphasis on Rice. Proceedings of an International Workshop on Field Screening for Drought Tolerance in Rice, 11-14 December 2000, ICRISAT, Patancheru, India. Patancheru 502 324, Andhra Pradesh, India, and the Rockefeller Foundation, New York. pp. 82-87.
• Brondani, C., N. Rangel, V. Brondani and E. Ferreira. 2002. QTL mapping and introgression of yield-related traits from Oryza glumaepatula to cultivated rice (Oryza sativa) using microsatellite markers. Theoretical and Applied Genetics. 104:1192-1203.
• Courtois, B. and R. Lafitte. 2003. Using market- aided selection for a specific drought- tolerance trait. In: Breeding Rice for drought-prone environments. Edited by Fischer, K.S; R., Lafitte; S., Fukai; G., Atlin y B. Gardí. International Rice Research Institute (IRRI), Philippines. pp. 84-89.
• Courtois B., D. Filloux, N. Ahmadi, J-L. Noyer, C. Billot y E.P. Guimarães. 2003. Uso de marcadores moleculares para el manejo de poblaciones de arroz mejoradas mediante selección recurrente. pp. 53-76. In: Mejoramiento poblacional, una alternativa para explorar los recursos genéticos del arroz en América Latina. Editor, E.P. Guimarães. CIAT-Colombia. 374 p.
• Cortés, J. 2004. El Agua en el Mundo: Cooperación y Conflicto. In: Observatori Solidaritat UB. Disponible en línea: https://bit.ly/2vhP9v6. [Abr. 08, 2014].
• FAO. (Food and Agriculture Organization) 2002.El agua: un recurso inapreciable y limitado. Enfoques. Disponible en línea: https://bit.ly/3cL7di9. [Abr.08, 2014].
• Fischer, R. and R. Maurer. 1978. Drought resistance in spring wheat cultivars. I. Grain yield responses, Aust. J. Agric. Res. 29(5):897-912.
• Garcia, F. 2008. Caracterización morfoanatómica de genotipos de arroz (Oryza sativa L.) en condiciones de estrés hídrico. Trabajo de grado para optar al título de Ingeniero Agrónomo. Universidad Central de Venezuela. Facultad de Agronomía. 89 p.
• Ghneim, T., P. Alejandro, I. Pérez, G. Torrealba, C. Martínez, M. Lorieux and J. Tohme. 2005. Plant Breeding News, Edition 160 10. An Electronic Newsletter of Applied Plant Breeding by FAO and Cornell University.
• Ghneim-Herrera, T., A. Rosales, M. Aguilar, P. Alejandro J., I. Pérez-Almeida y G. Torrealba. 2006. Identificación de cultivares de arroz con alta capacidad de ajuste osmótico para el mejoramiento genético de la tolerancia a la sequía. Agronomía Tropical. 56(4):677-687.
• Grandillo, S. y S. Tanksley. 1996. QTL analysis of horticultural traits differentiating the cultivated tomato from closely related species Lycopersicum pimpinellifolium. Theoretical and Applied Genetics. 92:935-951.
• Lanceras, J., G. Pantuwan, B. Jongdee and T. Toojinda. 2004. Quantitative Trait Loci Associated with Drought Tolerance at Reproductive Stage in Rice. Plant Physiology. 135(1):384-399.
• Lang, N. and B. Buu. 2008. Fine mapping for drought tolerance in rice (Oryza sativa L.) Omonrice. 16:9-15.
• Lafitte, H., A. Blum and G. Atlin. 2003. Using secondary traits to help identify drought- tolerant genotypes. IRRI: Breeding Rice for Drought-Prone Environments. pp. 37-48.
• Lafitte, H., A. Price and B. Courtois. 2004. Yield response to water deficit in an upland rice
mapping population: Associations among traits and genetic markers. Theoretical and Applied Genetics. 109(6):1237-1246.
• Lee, S., C. Oh, J. Suh, S. McCouch and S. Ahn. 2005. Identification of QTLs for domestication – related and agronomic traits in an Oryza sativa x Oryza rufipogon two backcross populations. Theoretical and Applied Genetics. 110:649-659.
• Ortiz, A., O. Gómez y C. Ramis, C. 2004. Caracterización bioquímica de poblaciones del complejo de maleza arroz rojo en Venezuela. Agronomía Trop. 54(3):257-273.
• Lee, B. K., K. Y. Kim, W. J. Jung, J. C. Avice, A. Ourry and T. H. Kim 2007. Peroxidases and lignification in relation to the intensity of water-deficit stress in white clover (Trifolium repens L.). Journal of Experimental Botany. 58(6):1271-1279.
• Lorieux, M. 2008. MapDistoGenetics Software, version 1.7. IRD-CIAT.
• Mackill, D. 2003. What molecular tools are available for selection for drought tolerance? Section 4.4 Breeding Rice for Drought - Prone Environments. IRRI. pp. 55-61.
• Manchenko, G. 1994. Handbook of Detection of Enzymes on Electrophoretic gels. Library of Congress Cataloging-in-Publication Data. 341 p.
• McCouh, S. R., L. Teytelman, Y. Xu, K. B. Lobos, K. Clare, M. Walton, B. Fu, R. Maghirang, Z. Li, Y. Xing, Q. Zhang, L. Kono, M. Yano, R. Fjellstrom, G. DeClerck, D. Schneider, S. Cartinhour, D. Ware and L. Stein. 2002. Development and Mapping of 2240 New SSR Markers for Rice (Oryza sativa L.). DNA Research. 9:199-207.
• McCouch, S., X. Chen, O. Panaud, S. Temnykh, Y. Xu, Y. Cho, N. Huang, T. Ishii and M. Blair. 1997. “Microsatellite marker development, mapping and applications in rice genetics and breeding”. Plant Molecular Biology. 35:89-99.
• McCouch, S. and R. Doerge. 1995. QTL mapping in rice. Trends and Genetics. 11(12):482-487.
• Mei, H., Q. Shu, Y. Wang, C. Ying, Z. Li, L. Guo, X. Yu and L. Luo. 2005. Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and Venezuela. Revista Facultad de Agronomía de la Universidad Central de Venezuela (UCV). 28:117-130.
• Pérez-Almeida, I., E. Torres, L. Angulo y M. Acevedo. 2011. Diversidad genética entre cultivares de arroz de Venezuela con base a la estimación del coeficiente de parentesco y análisis con marcadores moleculares microsatélites (SSR). Interciencia. 36(7):545- 551.
• Pieters, A. J. and M. Núñez. 2008. Photosyntesis, water use efficiency andδ13C in two rice genotypes with contrasting response to water deficit. Photosynthetica. 46(4):574-580.
• Praddep, M., N. Sarla, L. Reddy and E. Siddiq. 2005. Identification and mapping of yield and yield relative QTLs from an Indian accession of Oryza rufipogon. BMC Genetics. BioMed Central. Research article. Available online: https://bit.ly/3aJ1dV2 [Abr. 08,2014].
• Quirós, E. 2003. Evaluación morfológica y molecular de líneas avanzadas de mejoramiento genético de arroz (Oryza sativa) del Instituto de Investigación Agropecuaria de Panamá (IDIAP). Tesis para optar al título de maestría. Escuela de Posgrado, Programa de Educación para el Desarrollo y la Conservación del Centro Agronómico Tropical de Investigación y Enseñanza. 136 p.
• Rudd, S, H. Schoof and K. Mayer. 2005. Plant Markers a database of predicted molecular markers from plants. Nucleic Acids Research. Available online: https://bit.ly/2w2lqGT [Abr. 10, 2014].
• Sarkarung, S. 2002. A regional breeding program to develop drought - tolerant rainfed lowland germoplasm: IRRI´s experience in South and Southeast Asia. Breeding Rice for Drought - Prone Environments. IRRI. pp.70-74.
• Semagn, K., A. Bjornstad and N. Ndjiondjop. 2006. An overview of molecular markers methods for plants. African Journal of Biotechnology. 5(25):2540-2568.
• Septiningshigh, E., J. Prasetiyono, E. Lubis, T. Tai, T. Tjubaryat, S. Moeljopaeiro and S. McCouch. 2003. Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theoretical and Applied Genetics. 107:1419-1432.
• Swarbreck, S., M. Defoin-Platel, M. Hindle, M. Saqi and D. Habash. 2011. New perspectives on glutamine synthetase in grasses. Journal of Experimental Botany. 62(4):1511-1522.
• Takahashi, Y., A. Shomura, T. Sasaki and M. Yano. 2001. Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the α subunit of protein kinaseCK2. Proc Natl Acad USA. Available online: https://bit.ly/39PvXnC 98(14):7922-7927. [Abr. 08, 2014].
• Temnykh, S., W. Ayres, N. Cartinhour, S. Hauck, L. Lipovich, Y. Cho, T. Ishii and S. MCcouch. 2001. Mapping and genome organization of microsatellite sequence in rice (Oryza sativa L.). Theoretical and Applied Genetics. 100(5):697-712.
• Teng, S., Q. Qian, D. L. Zeng, Y. Kunihiro, K.Fujimoto, D. N Huang and L. H Zhu. 2002. Analysis of gene loci and epistasis for drought tolerance in seedling stage of rice (O. sativa L.) Yi Chuan Xue Bao. Available online: www.ncbi.nlm.nih.gov. 29(3):235- 240.
• Toojinda, T. 2002. Molecular genetics of submergence tolerance in rice: Quantitative trait loci (QTL) analysis of traits associated with submergence tolerance. Annals Botan.
• Thomson, M., T. Tai, A. McClung, X.-H. Lai, M. Hinga, K. Lobos, Y. Xu, C. Martínez and S. McCouch. 2003. Mapping quantitative trait loci for yield, yield components and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson. Theoretical and Applied Genetics. 107(3):479-493.
• Toorchi, M., H. Shashidhar, N. Sharma and S. Hittalmani. 2002. Tagging QTLs for maximum root length in rainfed lowland rice (Oryza sativa L.) using molecular markers. Cell Molecular Biology Lett. 7(2B):771-776.
• Torrealba, G. 2010. Identificación de marcadores moleculares asociados a la tolerancia al estrés hídrico en arroz (Oryza sativa L.). Trabajo para optar al título de doctora en Ciencias Agrícolas. Universidad Central de Venezuela (UCV), Facultad de Agronomía. Maracay. 199 p.
• Torrealba, G., I. Pérez, N. Delgado, C. Ramis, L.Angulo, O. León, M. Muñoz y G. Martínez. 2010. Metodología de campo para evaluación de tolerancia al estrés hídrico en el cultivo arroz. INIA Divulga. 16:23-26.
• Velásquez, R. 2001. Control genético de tres sistemas isoenzimáticos en arroz (Oryza sativa L). Trabajo de ascenso a Asistente. Maracay. Universidad Central de Venezuela (UCV), Facultad de Agronomía. 57 p.
• Vikram, P., BP. Mallikarjuna, S. Dixit, H. Uddin, MT. Sta Cruz, A. Kumar and Kumar. A. 2011. qDTY1.1, a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds. BMC Genetics. 12:89-104.
• Wan, X., J. Wan, J. Weng, L. Jiang, J. Bi, C. Wang and H. Zhai. 2005. Stability of QTLs for rice grain dimension and endosperm chalkiness characteristics across eight environments. 2005. Theoretical and Applied Genetics. 110(7):1334-1346.
• Xiao, J., J. Li, S. Grandillo, S. Ahn, L. Yuan, S. D Tanksley and McCouch S. 1998. Identification of trait improving quantitative trait loci alleles from a wild rice relative, Oryza rufipogon. Genetics. 150(2):899-909.
Published
2014-12-30
How to Cite
Torrealba-Nuñez, G. T., Pérez-Almeida, I., Ramis, C., Delgado, N., Angulo Graterol, L., De Faría, Y. K., Marín, C., León-Brito, O., & Martínez Zapata, G. C. (2014). Biochemists and molecular markers associated with water stress tolerance in rice. Agronomía Tropical, 64(3-4), 211-226. Retrieved from http://publicaciones.inia.gob.ve/index.php/agronomiatropical/article/view/221
Section
Original research article
Copyright (c) 2014 Gelis T. Torrealba-Nuñez, Iris Pérez-Almeida, Catalina Ramis, Nelly Delgado, Luis Angulo Graterol, Yreny K. De Faría, Carlos Marín, Oralys León-Brito, Getssy C. Martínez Zapata
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
