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Evaluation of near-isogenic lines for drought resistance QTL and fine mapping of a locus affecting flag leaf width, spikelet number, and root volume in rice

Abstract

Drought stress is a major limiting factor for crop production and breeding for drought resistance is very challenging due to the complex nature of this trait. Previous studies in rice suggest that the upland japonica variety IRAT109 shows better drought resistance than the lowland indica variety Zhenshan 97. Numerous quantitative trait loci (QTL) have been previously mapped using a recombinant inbred line population derived from these two genotypes. In this study, near-isogenic lines (NILs) for 17 drought resistance-related QTL were constructed and phenotypic variations of these NILs were investigated under drought and normal conditions. Fourteen of these NILs showed significant phenotypic differences relative to the recurrent parent under at least one of the conditions and nine NILs showed significant differences under both conditions. After eliminating the effect of heading date on drought resistance, only four NILs carrying seven QTL (four for the same grain yield-related traits and three for the same or similar root traits QTL) showed differences consistent with the original QTL mapping results. One of these lines (N19) contains qFSR4, a QTL on chromosome 4 controlling root volume per tiller and co-segregating with flag leaf width and spikelet number per panicle. Using a population derived from N19, qFSR4 was mapped to a 38-kb region containing three open reading frames including the previously characterized NARROW LEAF 1 (NAL1) gene. NAL1, which controls leaf width and also affects vein patterning and polar auxin transport, is the most promising candidate genes for qFSR4. Our results underscore the importance of the development of NILs to confirm the identification of QTL affecting complex traits such as drought resistance.

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References

  • Ashraf M (2010) Inducing drought tolerance in plants: recent advances. Biotechnol Adv 28:169–183

    PubMed  Article  CAS  Google Scholar 

  • Bernier J, Kumar A, Serraj R, Spaner D, Atlin G (2008) Review: breeding upland rice for drought resistance. J Sci Food Agric 88:927–939

    Article  CAS  Google Scholar 

  • Courtois B, Ahmadi N, Khowaja F, Price AH, Rami JF, Frouin J, Hamelin C, Ruiz M (2009) Rice root genetic architecture: meta-analysis from a drought QTL database. Rice 2:115–128

    Article  Google Scholar 

  • Farooq M, Tagle AG, Santos RE, Ebron LA, Fujita D, Kobayashi N (2010) Qantitative trait loci mapping for leaf length and leaf width in rice cv. IR64 derived lines. J Integr Plant Biol 52:578–584

    PubMed  Article  CAS  Google Scholar 

  • Friml J, Yang X, Michniewicz M, Weijers D, Quint A, Tietz O, Benjamins R, Ouwerkerk PB, Ljung K, Sandberg G, Hooykaas PJ, Palme K, Offringa R (2004) A PINOID-dependent binary switch in apical-basal PIN polar targeting directs auxin efflux. Science 306:862–865

    PubMed  Article  CAS  Google Scholar 

  • Jiao Y, Wang Y, Xue D, Wang J, Yan M, Liu G, Dong G, Zeng D, Lu Z, Zhu X, Qian Q, Li J (2010) Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet 42:541–544

    PubMed  Article  CAS  Google Scholar 

  • Kamoshita A, Chandra Babu R, Boopathi NM, Fukai S (2008) Phenotypic and genotypic analysis of drought-resistance traits for development of rice cultivars adapted to rainfed environments. Field Crops Res 109:1–23

    Article  Google Scholar 

  • Kobayashi S, Fukuta Y, Morita S, Sato T, Osaki M, Khush GS (2003) Quantitative Trait Loci Affecting Flag Leaf Development in Rice (Oryza sativa L.). Breed Sci 53:255–262

    Article  CAS  Google Scholar 

  • Kobayashi S, Fukuta Y, Yagi T, Sato T, Osaki M, Khush GS (2004) Identification and characterization of quantitative trait loci affecting spikelet number per panicle in rice (Oryza sativa L.). Field Crops Res 89:253–262

    Article  Google Scholar 

  • Lin HX, Ashikari M, Yamanouchi U, Sasaki T, Yano M (2002) Identification and characterization of a quantitative trait locous, Hd9, controlling heading date in rice. Breed Sci 52:35–41

    Article  CAS  Google Scholar 

  • Luo LJ (2010) Breeding for water-saving and drought-resistance rice (WDR) in China. J Exp Bot 61:3509–3517

    PubMed  Article  CAS  Google Scholar 

  • McCouch SR, Teytelman L, Xu Y, Lobos KB, 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, Stein L (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 9:199–207

    PubMed  Article  CAS  Google Scholar 

  • Miura K, Ikeda M, Matsubara A, Song XJ, Ito M, Asano K, Matsuoka M, Kitano H, Ashikari M (2010) OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat Genet 42:545–549

    PubMed  Article  CAS  Google Scholar 

  • Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucl Acids Res 8:4321

    PubMed  Article  CAS  Google Scholar 

  • Nguyen HN, Babu RC, Blum A (1997) Breeding for drought resistance in rice: physiology and molecular genetics consideration. Crop Sci 17:1426–1434

    Article  Google Scholar 

  • Price A, Tomos AD (1997) Genetic dissection of root growth in rice (Oryza sativa L.). II. Mapping quantitative trait loci using molecular markers. Theor Appl Genet 95:143–152

    Article  CAS  Google Scholar 

  • Price A, Courtois B (1999) Mapping QTLs associated with drought resistance in rice: progress, problems and prospects. Plant Growth Regul 29:123–133

    Article  CAS  Google Scholar 

  • Qi J, Qian Q, Bu Q, Li S, Chen Q, Sun J, Liang W, Zhou Y, Chu C, Li X, Ren F, Palme K, Zhao B, Chen J, Chen M, Li C (2008) Mutation of the rice Narrow leaf1 gene, which encodes a novel protein, affects vein patterning and polar auxin transport. Plant Physiol 147:1947–1959

    PubMed  Article  CAS  Google Scholar 

  • Steele KA, Price AH, Shashidhar HE, Witcombe JR (2006) Marker-assisted selection to introgress rice QTLs controlling root traits into an Indian upland rice variety. Theor Appl Genet 112:208–221

    PubMed  Article  CAS  Google Scholar 

  • Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (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

    PubMed  Article  CAS  Google Scholar 

  • Wu KS, Tanksley SD (1993) Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genet 241:225–235

    PubMed  Article  CAS  Google Scholar 

  • Xing Y, Zhang Q (2010) Genetic and molecular bases of rice yield. Annu Rev Plant Biol 61:421–442

    PubMed  Article  CAS  Google Scholar 

  • Xing YZ, Tang WJ, Xue WY, Xu CG, Zhang Q (2008) Fine mapping of a major quantitative trait loci, qSSP7, controlling the number of spikelets per panicle as a single Mendelian factor in rice. Theor Appl Genet 116:789–796

    PubMed  Article  CAS  Google Scholar 

  • Xue W, Xing Y, Weng X, Zhao Y, Tang W, Wang L, Zhou H, Yu S, Xu C, Li X, Zhang Q (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40:761–767

    PubMed  Article  CAS  Google Scholar 

  • Yonemaru J, Yamamoto T, Fukuoka S, Uga Y, Hori K, Yano M (2010) Q-TARO: QTL Annotation Rice Online Database. Rice 3:194–203

    Article  Google Scholar 

  • Yue B (2005) Study on the genetic basis of drought resistance at reproductive stage in rice. Dissertation, Huazhong Agricultural University

  • Yue B, Xiong L, Xue W, Xing Y, Luo L, Xu C (2005) Genetic analysis for drought resistance of rice at reproductive stage in field with different types of soil. Theor Appl Genet 111:1127–1136

    PubMed  Article  Google Scholar 

  • Yue B, Xue W, Xiong L, Yu X, Luo L, Cui K, Jin D, Xing Y, Zhang Q (2006a) Genetic basis of drought resistance at reproductive stage in rice: separation of drought tolerance from drought avoidance. Genetics 172:1213–1228

    PubMed  Article  Google Scholar 

  • Yue B, Xue WY, Luo LJ, Xing YZ (2006b) QTL analysis for flag leaf characteristics and their relationships with yield and yield traits in rice. Acta Genet Sin 33:824–832

    PubMed  Article  CAS  Google Scholar 

  • Zhang Q (2007) Strategies for developing Green Super Rice. Proc Natl Acad Sci USA 104:16402–16409

    PubMed  Article  CAS  Google Scholar 

  • Zhao Y (2010) Auxin biosynthesis and its role in plant development. Annu Rev Plant Biol 61:49–64

    PubMed  Article  CAS  Google Scholar 

  • Zhao Y, Christensen SK, Fankhauser C, Cashman JR, Cohen JD, Weigel D, Chory J (2001) A role for flavin monooxygenase-like enzymes in auxin biosynthesis. Science 291:306–309

    PubMed  Article  CAS  Google Scholar 

  • Zou GH, Mei HW, Liu HY, Liu GL, Hu SP, Yu XQ, Li MS, Wu JH, Luo LJ (2005) Grain yield responses to moisture regimes in a rice population: association among traits and genetic markers. Theor Appl Genet 112:106–113

    PubMed  Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by grants from the National Natural Science Foundation of China (30725021, 30830071, and 30921091), the National Special Key Project of China on Functional Genomics of Major Plants and Animals (2006AA10A103), the National Green Super Rice Project (2010AA101805), and the Bill & Melinda Gates Foundation.

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Correspondence to Lizhong Xiong.

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Communicated by T. Tai.

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Ding, X., Li, X. & Xiong, L. Evaluation of near-isogenic lines for drought resistance QTL and fine mapping of a locus affecting flag leaf width, spikelet number, and root volume in rice. Theor Appl Genet 123, 815–826 (2011). https://doi.org/10.1007/s00122-011-1629-1

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  • DOI: https://doi.org/10.1007/s00122-011-1629-1

Keywords

  • Quantitative Trait Locus
  • Recombinant Inbred Line
  • Drought Resistance
  • Grain Yield
  • Recombinant Inbred Line Population