Mapping genomic regions associated with yield and drought tolerance indices in recombinant inbred lines of rice

Document Type : Research paper


Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, P. O. Box: 41635-1314, Rasht, Iran.


Mapping QTLs with molecular markers can be very useful for plant breeders in agricultural genomics. The identification and introgression of QTLs for grain yield and drought tolerance indicesis an efficient approach to improve the drought tolerance of rice varieties. In this study, QTLs controlling some traits associated with grain yield and drought tolerance indiceswere identified using 150 F8 lines derived from a cross between Sepidroud and Gharib, under non-stress and stress conditions. The genetic linkage map containing 12 ISSR polymorphic markers, 103 SSR, 1 IRAP marker, 11 REMAP markers and 16 combinations of ISSR markers covered 1005.2 cM of the rice genome and a mean distance between adjacent markers was 4.43 cM. In this experiment, two QTLs with main effects were mapped for SSI and YSI indices, three QTLs with main effects for grain yield under non-stress and stress conditions, TOL, STI, GMP, and YI, four QTLs with main effects for MP and HM. One epistatic QTL was mapped for grain yield under non-stress condition and STI index. The phenotypic variation explained by each main effect QTLs and epistatic QTLs ranged from 3.99 to 25.41% and 6.51 to 18.81%, respectively. Fifteen main effect QTLs, including, qGY9, qGY12a, qTOL4,qTOL5, qSSI5, qSSI6, qSTI9, qSTII2, qMP9, qGMP9, qGMP12, qHM12a, qYSI5, qYSI6, and qYI12a as the major QTLs controlling these traits can be considered in rice breeding programs for improving grain yield and drought tolerance after validation. The markers UBC816-2, (Tos2+UBC827)-4, (UBC826+HB12)-6, RM215 and RM5371 located near major QTLs could be used in MAS programs.


Barik S. R., Pandit E., Pradhan S. K., Mohanty S. P., and Mohapatra T. (2019). Genetic mapping of morpho-physiological traits involved during reproductive stage drought tolerance in rice. Plos One, 14(12): e0214979.‏
Bernier J., Kumar A., Ramaiah V., Spaner D., and Atlin G. (2007). A large-effect QTL for grain yield under reproductive-stage drought stress in upland rice. Crop Science, 47: 507–518.
Bhattarai U., and Subudhi P. K. (2018). Genetic analysis of yield and agronomic traits under reproductive-stage drought stress in rice using a high-resolution linkage map. Gene, 669: 69–76.
Bouman B. A. M., and Tuong T. P. (2001). Field water management to save water and increase its productivity in irrigated lowland rice. Agricultural Water Management, 49: 11–30.
Bouslama M., and Schapaugh W. T. (1984). Stress tolerance in soybean. Part 1: evaluation of three screening techniques for heat and drought tolerance. Crop Science, 24: 933–937.
Cattivelli L., Rizza F., Badeck F. W., Mazzucotelli E., Masterangelo A. M., Francia E., Mare C., Tondelli A., and Stanca A. M. (2008). Drought tolerance improvement in crop plants: An integrated view from breeding to genomics. Field Crop Research, 105: 1–14.
Danesh Gilevaei M., Samizadeh Lahigi H. A., and Rabiei B. (2018). Evaluation of drought tolerance in the rice (Oryza sativa L.) cultivars and recombinant inbred lines population. Iranian Journal of Genetics and Plant Breeding, 7(1): 41–49.
Descalsota-Empleo G. I., Amparado A., Inabangan-Asilo M. A., Tesoro F., Stangoulis J., Reinke R., and Swamy B. M. (2019). Genetic mapping of QTL for agronomic traits and grain mineral elements in rice. The Crop Journal, 7: 560–572.
Dixit Sh., Singh A., Cruz M. T. S., Maturan P. T., Amante M., and Kumar A. (2014). Multiple major QTL lead to stable yield performance of rice cultivars across varying drought intensities. BMC Genetics, 15(16): 1–13.
Fernandez G. C. J. (1992). Effective selection criteria for assessing stress tolerance. In Kuo C. G. (Ed.) Proceedings of the International Symposium on Adaptation of Vegetables and Other Food Crops in Temperature and Water Stress Publication Tainan Taiwan, 257–270.
Fischer R. A., and Maurer R. (1978). Drought resistance in spring wheat cultivars. Part 1: grain yield response. Australian Journal of Agricultural Research, 29: 897–912.
Gavuzzi P., Rizza F., Palumbo M., Campanile R. G., Ricciardi G. L., and Borghi B. (1997). Evaluation of field and laboratory predictors of drought and heat tolerance in winter cereals. Canadian Journal of Plant Science, 77(4): 523–531.
Ghimire K. H., Quiatchon L. A., Vikram P., Swamy B. P. M., Dixit Sh., Ahmed H., Hernandez J. E., Borromeo T. H., and Kumar A. (2012). Identification and mapping of a QTL (qDTY1.1) with a consistent effect on grain yield under drought. Field Crops Research, 131: 88–96.
Hittalmani S., Huang N., Courtois B., Venuprasad R., Shashidhar H. E., Bagali G. G., Li Z. K., Zhuang J. Y., Zheng K. L., Liu G. F., Wang G. C., Singh V. P., Sidhu J. S., Srivantaneeyakul S., Mclaren G., and Khush G. S. (2003). Identification of QTLs for growth and grain yield related traits in rice across nine locations in Asia. Theoretical and Applied Genetics, 107: 679–690.
Hu S. P., Yang H., Zou G. H., Liu H. Y., Liu G. L., Mei H. W., Cai R., Li M. S., and Luo L. J. (2007). Relationship between coleoptile length and drought resistance and their QTL mapping in rice. Rice Science, 14: 13–20.
Kosambi D. D. (1943). The estimation of map distances from recombination values. Annals of Eugenics, 12: 172–175.
Lafitte H. R., Yongsheng G., Yan S., and Li Z. K. (2007). Whole plant responses, key processes, and adaptation to drought stress: the case of rice. Journal of Experimental Botany, 58: 169–175.
Lang N. T., Nha C. T., Ha P. T. T., and Buu B. C. (2013). Quantitative trait loci (QTLs) associated with drought tolerance in rice (Oryza sativa L.). SABRAO Journal of Breeding and Genetics, 45(3): 409–421.
Li H., Ribaut J. M., Li Z., and Wang J. (2008). Inclusive composite interval mapping (ICIM) for digenic epistasis of quantitative traits in biparental populations. Theoretical and Applied Genetics, 116: 243–260.
Li H., Ye G., and Wang J. (2007). A modified algorithm for the improvement of composite interval mapping. Genetics, 175: 361–374.
Manickavelu A., Nadarajan N., Ganesh S. K., Gnanamalar R. P., and Babu R. C. (2006). Drought tolerance in rice. Morphological and molecular genetic consideration. Journal of Plant Growth Regulation, 50: 121–138.
Manly K. F., and Olson J. M. (1999). Overview of QTL mapping software and introduction to map manager QTX. Mammalian Genome, 10: 327–334.
Mardani Z., Rabiei B., Sabouri H., and Sabouri A. (2013). Mapping of QTLs for germination characteristics under non-stress and drought stress in rice. Rice Science, 20(6): 391−399.
McPherson M. J., and Møller S. G. (2006). PCR. 2nd Edition, Taylor & Francis Group, London, pp. 292. DOI:
Pramudyawardani, E. F., Aswidinnoor H., Purwoko B. S., Suwarno W. B., Islam M. R., Verdeprado H., and Collard B. C. (2018). Genetic analysis and QTL mapping for agronomic and yield-related traits in ciherang-sub1 rice backcross populations. Plant Breeding and Biotechnology, 6(3): 177−192.‏
Rabiei B., Kordrostami M., and Sabouri A. (2015). Identification of QTLs for yield related traits in Indica type rice using SSR and AFLP markers. Agriculturae Conspectus Scientificus, 80: 91−99.
Rahimi M., Dehghani H., Rabiei B., and Tarang A. R. (2014). Mapping main and epistatic QTLs for drought tolerance indices in F5 population of rice. Journal of Genetics, 8 (4): 435−448. (In Persian).
Rosielle A. A., and Hamblin J. (1981). Theorical aspect of selection for yield in stress and non-stress environment. Crop Science, 21: 943−946.
Sabouri A., Toorchi M., Rabiei B., Aharizad S., Moumeni A., and Singh R. K. (2010). Identification and mapping of QTLs for agronomic traits in Indica-Indica cross of rice (Oryza sativa L.). Cereal Research Communications, 38: 317−326.
Sabouri H., Dadras A. H., Sabouri A., and Katouzi M. (2013). Mapping QTLs for agronomic traits in rice under water stress condition using Iranian recombinant inbred lines population. Journal of Plant Physiology and Breeding, 3(1): 57−69.
Saghi Maroof M. A., Biyashev R. M., Yang G. P., Zhang Q., Allard R. W. (1994). Extraordinarily polymorphic microsatellite DNA in barely species diversity, chromosomal location, and population dynamics. Proceedings of the National Academy of Sciences of the United States of America, 91: 5466−5570.
TianY., Zhang H., Xu P., Chen X., Liao Y., Han B., Chen X., Fu X., and Wu X. (2015). Genetic mapping of a QTL controlling leaf width and grain number in rice. Euphytica, 202: 1–11.
Tiwari S., SL K., Kumar V., Singh B., Rao A., Mithra S. V. A., Rai V., Singh A. K., and Singh N. K. (2016). Mapping QTLs for salt tolerance in rice (Oryza sativa L.) by bulked segregant analysis of recombinant inbred lines using 50K SNP chip. Plos One, 11(4): 1−19.
Vikram P., Swamy B. P., Dixit SH., Ahmed H. U., Sta Cruz M. T., Singh A. K., 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(1): 1−15.
Wang J., Li H., Zhang L., and Meng L. (2012). Users’ manual of QTL IciMapping version 3.2: The Quantitative Genetics Group, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China, and Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600 Mexico, D. F., Mexico.
Wang X., Pang Y., Zhang J., Zhang Q., Tao Y., Feng B., Zheng T., Xu J., and Li Z. (2014). Genetic background effects on QTL and QTL×environment interaction for yield and its component traits as revealed by reciprocal introgression lines in rice. Crop Journal, 2(6): 345−357.
Wu P., Shou H., Xu G., and Lian X. (2013). Improvement of phosphorus efficiency in rice on the basis of understanding phosphate signaling and homeostasis. Current Opinion in Plant Biology, 16: 205−212.
Yadaw R. B., Dixit SH., Raman A., Mishra K. K., Vikram P., Swamy B. P. M., Sta Cruz M. T., Maturan P. T., Pandey M., and Kumar A. (2013). A QTL for high grain yield under lowland drought in the background of popular rice variety Sabitri from Nepal. Field Crops Research, 144: 281–287.
Yue B., Xiong L., Xue W., Xing Y. Z., Luo L., and Xu C. (2005). Genetic analysis for drought resistance of rice at reproductive stage in field with different types of soil. Theoretical and Applied Genetics,111: 1127−1136.
Zhao X., Qin Y., Jia B., KimLee S. M., Eun M. Y., Kim K. M., and Sohn J. K. (2013). Comparison and analysis of QTLs, epistatic effects and QTL×environment interactions for yield traits using DH and RILs populations in rice. Journal of Integrative Agriculture, 12(2): 198−208.
Zhu M., Liu D., Liu W., Li D., Liao Y., Li J., and Ma X. (2017). QTL mapping using an ultra-high-density SNP map reveals a major locus for grain yield in an elite rice restorer R998. Scientific Reports, 7(1): 10914.‏