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Mapping quantitative trait loci associated with yield and yield components under reproductive stage salinity stress in rice (Oryza sativa L.)

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Abstract

Salinity tolerance in rice is critical at reproductive stage because it ultimately determines grain yield. An F2 mapping population derived from a Sadri/FL478 cross was exposed to saline field conditions (6–8 dS m − 1) after the active tillering stage to identify reproductive stage specific QTLs for salinity tolerance. Genetic linkage map was constructed using 123 microsatellite markers on 232 F2 progenies. Totally 35 QTLs for 11 traits under salinity stress were detected with LOD > 3, out of which 28 QTLs that explained from 5.9 to 30.0% phenotypic variation were found to be significant based on permutation test. Three major QTL clusters were found on chromosomes 2 (RM423–RM174), 4 (RM551–RM518) and 6 (RM20224–RM528) for multiple traits under salinity stress. Both parental lines contributed additively for QTLs identified for the yield components. A majority of the QTLs detected in our study are reported for the first time for reproductive stage salinity stress. Fine-mapping of selected putative QTLs will be the next step to facilitate marker-assisted backcrossing and to detect useful genes for salinity tolerance at the reproductive stage in rice.

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References

  • Akbar M., Yabuno T. and Nakao S. 1972 Breeding for saline resistant varieties of rice I. variability for salt tolerance among some rice varieties. Jpn. J. Breed. 22, 277–284.

    Article  Google Scholar 

  • Ammar M. H. M., Pandit A., Singh R. K., Sameena S., Chauhan M. S., Singh A. K. et al. 2009 Mapping of QTLs controlling Na + , K +  and Cl −  ion concentrations in salt tolerant indica rice variety CSR27. J. Plant Biochem. Biotech. 18, 139–150.

    Article  CAS  Google Scholar 

  • Churchill G. A. and Doerge R. W. 1994 Empirical threshold values for quantitative trait mapping. Genetics 138, 963–971.

    CAS  PubMed  Google Scholar 

  • Counce P. A., Keisling T. C. and Mitchell A. J. 2000 A uniform, objective, and adaptive system for expressing rice development. Crop Sci. 40, 436–443.

    Article  Google Scholar 

  • Cui H., Takeoka Y. and Wada T. 1995 Effect of sodium chloride on the panicle and spikelet morphogenesis in rice. Jpn. J. Crop. Sci. 64, 593–600.

    Article  CAS  Google Scholar 

  • Flowers T. J. and Yeo A. 1981 Variability in the resistance of sodium chloride salinity within rice (Oryza sativa L.) varieties. New Phytol. 88, 363–373.

    Article  CAS  Google Scholar 

  • Flowers T. J. and Yeo A. 1995 Breeding for salinity resistance in crop plants—where next? Aust. J. Plant Physiol. 22, 875– 884.

    Article  Google Scholar 

  • Flowers T. J. and Flowers S. A. 2005 Why does salinity pose such a difficult problem for plant breeders? Agric. Water Manage. 78, 15–24.

    Article  Google Scholar 

  • Genc Y., McDonald G. and Tester M. 2007 Reassessment of tissue Na +  concentration as a criterion for salinity tolerance in bread wheat. Plant Cell Environ. 30, 1486–1498.

    Article  CAS  PubMed  Google Scholar 

  • Gregorio G. B. 1997 Tagging salinity tolerance genes in rice using amplified fragment length polymorphism (AFLP). Ph.D. thesis, University of the Philippines, Los Ba nos College, Laguna, Philippines.

  • Gregorio G. B., Senadhira D., Mendoza R. D., Manigbas N. L., Roxas J. P. and Guerta C. Q. 2002 Progress in breeding for salinity tolerance and associated abiotic stresses in rice. Field Crops Res. 76, 91–101.

    Article  Google Scholar 

  • Haq T. U., Gorham J., Akhtar J., Akhtar N. and Steele K. A. 2010 Dynamic quantitative trait loci for salt stress components on chromosome 1 of rice. Funct. Plant Biol. 37, 634– 645.

    Article  Google Scholar 

  • Heenan D. P., Lewin L. G. and McCaffery D. W. 1988 Salinity tolerance in rice varieties at different growth stages. Aust. J. Exp. Agric. 28, 343–349.

    Article  Google Scholar 

  • Islam M. M. 2004 Mapping salinity tolerance genes in rice (Oryza sativa L.) at reproductive stage. Ph.D. dissertation, University of the Philippines, Los Ba nos, Laguna, Philippines.

  • Ismail A. M., Heuer S., Thomson M. J. and Wissuwa M. 2007 Genetic and genomic approaches to develop rice germplasm for problem soils. Plant Mol. Biol. 65, 547–570.

    Article  CAS  PubMed  Google Scholar 

  • Jenks M. A., Hasegawa P. M. and Jain S. M. 2007 Advances in molecular breeding toward drought and salt tolerant crops. Springer, The Netherlands.

    Book  Google Scholar 

  • Joehanes R. and Nelson J. 2008 QGene 4.0, an extensible Java QTLanalysis platform. Bioinformatics 24, 2788–2789.

    Article  CAS  PubMed  Google Scholar 

  • Khatun S., Rizzo C. A. and Flowers T. J. 1995 Genotypic variation in the effect of salinity on fertility in rice. Plant Soil 173, 239–250.

    Article  CAS  Google Scholar 

  • Kim S.-H., Bhat P. R., Cui X., Walia H., Xu J., Wanamaker S. et al. 2009 Detection and validation of single feature polymorphisms using RNA expression data from a rice genome array. BMC Plant Biol. 9, 65.

    Google Scholar 

  • Kosambi D. D. 1944 The estimation of map distances from recombination values. Ann. Eugen. 12, 172–175.

    Article  Google Scholar 

  • Lin H. X., Zhu M. Z., Yano M., Gao J. P., Liang Z. W., Su W. A. et al. 2004 QTLs for Na +  and K +  uptake of the shoots and roots controlling rice salt tolerance. Theor. Appl. Genet. 108, 253–260.

    Article  CAS  PubMed  Google Scholar 

  • Maas E. V. and Hoffmann G. J. 1977 Crop salt tolerance: current assessment. J. Irrig. Drain. Eng.-ASCE. 103, 115–134.

    Google Scholar 

  • Maas E. V. and Grattan S. R. 1999 Crop yields as affected by salinity. In Agricultural drainage (ed. R. W. Skaggs and J. van Schilfgaarde), pp. 55–108. Agron Monograph 38, ASA, CSSA, SSA, Madison, USA.

  • Manly K. F., Cudmore Jr R. H. and Meer J. M. 2001 Map Manager QTX, cross-platform software for genetic mapping. Mamm. Genome 12, 930–932.

    CAS  Google Scholar 

  • McCouch S. R. and CGSNL (Committee on Gene Symbolization, Nomenclature and Linkage, Rice Genetics Cooperative) 2008 Gene nomenclature system for rice. Rice 1, 72–84.

  • McCouch S. R., Chen X., Panaud O., Temnykh S., Xu Y., Cho Y. G. et al. 1997 Microsatellite marker development, mapping and applications in rice genetics and breeding. Plant Mol. Biol. 35, 89–99.

    Article  CAS  PubMed  Google Scholar 

  • Mohammadi-Nejad G., Arzani A., Rezai A. M., Singh R. K. and Gregorio G. B. 2008 Assessment of rice genotypes for salt tolerance using microsatellite markers associated with the saltol QTL. Afr. J. Biotechnol. 7, 730–736.

    Google Scholar 

  • Moradi F., Ismail A. M., Gregorio G. B. and Egdane J. A. 2003 Salinity tolerance of rice during reproductive development and association with tolerance at the seedling stage. Ind. J. Plant Physiol. 8, 105–116.

    Google Scholar 

  • Munns R. and Tester M. 2008 Mechanisms of salinity tolerance. Annu. Rev. Plant Biol. 59, 651–681.

    Article  CAS  PubMed  Google Scholar 

  • Narciso J. and Hossain M. 2002 World rice statistics. IRRI, Los Ba nos, Philippines.

  • Rao P. S., Mishra B., Gupta S. R. and Rathore A. 2008 Reproductive stage tolerance to salinity and alkalinity stresses in rice genotypes. Plant Breed. 127, 256–261.

    Article  Google Scholar 

  • Ren Z. H., Gao J. P., Li G. L., Cai X. L., Huang W., Chao D. Y. et al. 2005 A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat. Genet. 37, 1141–1146.

    Article  CAS  PubMed  Google Scholar 

  • Sarhadi E., Mohammadi-Bazargani M., Sajise A. G., Abdolahi S., Vispo A. N., Arceta M. et al. 2012 Proteomic analysis of rice anthers under salt stress. Plant Physiol. Biochem. 58, 280–287.

    Article  CAS  PubMed  Google Scholar 

  • Singh R. K. and Flowers T. J. 2010 The physiology and molecular biology of the effects of salinity on rice. In Handbook of plant and crop stress, 3rd edition (ed. M. Pessarakli), pp. 901–942. Taylor and Francis, Boca Raton, USA.

  • Singh R. K., Gregorio G. B. and Jain R. K. 2007 QTL mapping for salinity tolerance in rice. Physiol. Mol. Biol. Plants 13, 87–99.

    CAS  Google Scholar 

  • Temnykh S., DeClerck G., Lukashova A., Lipovich L., Cartinhour S. and McCouch S. R. 2001 Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 11, 1441–1452.

    Article  CAS  PubMed  Google Scholar 

  • Thomson M. J., Edwards J. D., Septiningsih E. M., Harrington S. E. and McCouch S. R. 2006 Substitution mapping of dth1.1, a flowering-time quantitative trait locus (QTL) associated with transgressive variation in rice, reveals multiple sub-QTL. Genetics 172, 2501–2514.

    Article  CAS  PubMed  Google Scholar 

  • Thomson M. J., Ocampo M., Egdane J., Rahman M. A., Sajise A. G., Adorada D. L. et al. 2010 Characterizing the Saltol quantitative trait locus for salinity tolerance in rice. Rice 3, 148–160.

    Article  Google Scholar 

  • United States Salinity Laboratory Staff 1954 Diagnosis and improvement of saline and alkali soils. US Department of Agriculture, Agricultural Handbook No. 60. Government Printer, Washington, USA.

  • Veldboom L. R., Lee M. and Woodman W. L. 1994 Molecular-marker facilitated studies in an elite maize population. I. Linkage analysis and determination of QTLs for morphological traits. Theor. Appl. Genet. 88, 7–16.

    Article  CAS  PubMed  Google Scholar 

  • Wang S., Basten C. J. and Zeng Z. B. 2011 Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh, USA. http://statgen.ncsu.edu/qtlcart/WQTLCart.htm

  • Xie X., Jin F., Song M. H., Suh J. P., Hwang H. G., Kim Y.G. et al. 2008 Fine mapping of a yield-enhancing QTL cluster associated with transgressive variation in an Oryza sativa L. × O. rufipogon cross. Theor. Appl. Genet. 116, 613–622.

    Article  PubMed  Google Scholar 

  • Yeo A. R. and Flowers T. J. 1982 Accumulation and localization of sodium ions within the shoots of rice (Oryza sativa) varieties differing in salinity resistance. Physiol. Plant 56, 343–348.

    Article  CAS  Google Scholar 

  • Zang J. P., Sun Y., Wang Y., Yang J., Li F., Zhou Y. L. et al. 2008 Dissection of genetic overlap of salt tolerance QTLs at the seedling and tillering stages using backcross introgression lines in rice. Sci. Chin. Ser. C-Life Sci. 51, 583–591.

    Article  Google Scholar 

  • Zeng L. and Shannon M. C. 2000 Salinity effects on the seedling growth and yield components of rice. Crop Sci. 40, 996–1003.

    Article  Google Scholar 

  • Zeng L., Shannon M. C. and Grieve C. M. 2002 Evaluation of salt tolerance in rice genotypes by multiple agronomic parameters. Euphytica 127, 235–245.

    Article  CAS  Google Scholar 

  • Zeng Z. 1993 Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci. Proc. Natl. Acad Sci. USA 90, 10972–10976.

    Article  CAS  PubMed  Google Scholar 

  • Zeng Z. 1994 Precision mapping of quantitative trait loci. Genetics 136, 1457–1468.

    CAS  PubMed  Google Scholar 

  • Zheng L., Shannon M. C. and Lesch S. M. 2001 Timing of salinity stress affecting rice growth and yield components. Agric. Water Manage. 48, 191–206.

    Article  Google Scholar 

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Acknowledgements

The authors thank A. G. Sajise and N. A. Vispo for technical assistance in the salinity screening, and M. Arceta for technical assistance in the genotyping. We also appreciate Dr Endang M. Septiningsih and Dr Bert C. Y. Collard for their useful suggestions and comments. Technical editing by Dr Bill Hardy is sincerely acknowledged. The help of the head of the Plant Breeding, Genetics and Biotechnology Division is duly acknowledged for permission to conduct the research at IRRI.

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  1. REZA MOHAMMADI

    Present address: Agricultural Biotechnology Research Institute of Iran (ABRII), North West and West Region, Tabriz, Iran

Authors and Affiliations

  1. Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO, Box 7777, Metro Manila, Philippines

    REZA MOHAMMADI, GLENN B. GREGORIO & RAKESH K. SINGH

  2. Genetics and Molecular Biology Division, Institute of Biological Sciences, University of the Philippines, Los Baños, Philippines

    MERLYN S. MENDIORO & GENALEEN Q. DIAZ

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  1. REZA MOHAMMADI
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  2. MERLYN S. MENDIORO
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Correspondence to RAKESH K. SINGH.

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[Mohammadi R., Mendioro M. S., Diaz G. Q., Gregorio G. B. and Singh R. K. 2013 Mapping quantitative trait loci associated with yield and yield components under reproductive stage salinity stress in rice (Oryza sativa L.). J. Genet. 92, xx–xx]

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MOHAMMADI, R., MENDIORO, M.S., DIAZ, G.Q. et al. Mapping quantitative trait loci associated with yield and yield components under reproductive stage salinity stress in rice (Oryza sativa L.) . J Genet 92, 433–443 (2013). https://doi.org/10.1007/s12041-013-0285-4

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