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Trait identification and QTL validation for reproductive stage drought resistance in rice using selective genotyping of near flowering RILs

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Abstract

Drought resistance is becoming an indispensable character for rice improvement due to the dwindling global water resources. Genetic improvement for drought resistance is achieved through physiological dissection and genetic analysis of independent component traits associated with crop productivity under stress. A subset mapping population of 93 near flowering recombinant inbred lines with uniform phenology was constituted for genetic analysis of reproductive stage drought resistance. The population was phenotyped for 22 physio-morphological traits under two contrasting water regimes imposed at reproductive stage. Broad sense heritabilities of morphological traits were lower under stress than irrigated. Predominant association of plant height, panicle exsertion and harvest index with grain yield were observed under stress. The sustenance of panicle exsertion through maintaining growth during moisture stress was found as a significant trait associated with the grain yield through minimizing spikelet sterility. Selective genotyping was carried out with 23 polymorphic microsatellite markers of the established target genomic regions for drought resistance. The study validated the association of a QTL region on the long arm of chromosome 1 with plant height, panicle length, panicle exsertion, biological yield and stomatal conductance under stress. This region, flanked by markers RM246 and RM315, was known to possess the semi-dwarf gene, sd-1. Role of another major interval lying between RM256 and RM149 on chromosome 8 in defining the drought resistance could be established through identification of QTLs associated with leaf rolling, panicle exsertion, plant height, panicle length, senescence and biological yield under moisture stress condition. Few other QTLs were also identified.

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References

  • Ali ML, Pathan MS, Zhang J, Bai G, Sarkarung S, Nguyen HT (2000) Mapping QTL for root traits in a recombinant inbred population from two indica ecotypes in rice. Theor Appl Genet 101:756–766. doi:10.1007/s001220051541

    Article  CAS  Google Scholar 

  • Babu RC, Nguyen BD, Chamarek V, Shanmugasundaram P, Chezian P, Jeyaprakash P, Ganesh SK, Palchamy A, Sadasivam S, Sarkarung S, Wade LJ, Nguyen HT (2003) Genetic analysis of drought resistance in rice by molecular markers: association between secondary traits and field performance. Crop Sci 43:1457–1469

    CAS  Google Scholar 

  • Barrs HD, Weatherly PE (1962) A re-examination of the relative turgidity technique for estimating water deficits in leaves. Aust J Biol Sci 15:413–428

    Google Scholar 

  • Ceccarelli S (1987) Yield potential and drought tolerance of segregating populations of barley in contrasting environments. Euphytica 36:265–273. doi:10.1007/BF00730673

    Article  Google Scholar 

  • Champoux MC, Wang G, Sarkarung S, Mackill DJ, O’ Toole JC, Huang N, McCouch SR (1995) Locating genes associated with root morphology and drought avoidance in rice via linkage to molecular markers. Theor Appl Genet 90:969–981. doi:10.1007/BF00222910

    Article  CAS  Google Scholar 

  • Courtois B, Huang N, Guiderdoni E (1995) RFLP mapping of genes controlling yield components and plant height in an indica × japonica doubled haploid population. In: Proceedings of the international rice research conference, Los Banos, 13–15 February, pp 963–976

  • Courtois B, McLaren G, Sinha PK, Prasad K, Yadav R, Shen L (2000) Mapping QTLs associated with drought avoidance in upland rice. Mol Breed 6:55–66. doi:10.1023/A:1009652326121

    Article  CAS  Google Scholar 

  • Courtois B, Shen L, Petalcorin W, Carandang S, Mauleon R, Li Z (2003) Locating QTLs controlling constitutive root traits in the rice population IAC 165 × Co39. Euphytica 134:335–345. doi:10.1023/B:EUPH.0000004987.88718.d6

    Article  CAS  Google Scholar 

  • Cruz RT, O’Toole JC (1984) Dry land rice response to an irrigation gradient at flowering stage. Agron J 76:178–183

    Google Scholar 

  • Cui HK, Peng SB, Xing YZ, Yu SB, Xu CG, Zhang Q (2003) Molecular dissection of the genetic relationships of source, sink and transport tissue with yield traits in rice. Theor Appl Genet 106:649–658

    CAS  PubMed  Google Scholar 

  • Fukai S, Pantuwan G, Jongdee B, Cooper M (1999) Screening for drought resistance in rainfed lowland rice. Field Crops Res 64:61–74. doi:10.1016/S0378-4290(99)00051-9

    Article  Google Scholar 

  • Gates DM (1968) Transpiration and leaf temperature. Annu Rev Plant Physiol 19:211–238. doi:10.1146/annurev.pp.19.060168.001235

    Article  Google Scholar 

  • Ingram KT, Bueno FD, Namuco OS, Yambao EB, Beyrouty CA (1994) Rice roots traits for drought resistance and their genetic variation. In: Kirk GRD (ed) Rice roots: nutrient and water use. IRRI, Los Banos, pp 67–77

    Google Scholar 

  • Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:170–175

    Google Scholar 

  • Lafitte HR (2002) Relationship between leaf relative water content during reproductive stage water deficit and grain formation in rice. Field Crops Res 76:165–174. doi:10.1016/S0378-4290(02)00037-0

    Article  Google Scholar 

  • Lafitte HR, Price AH, Courtois B (2004) Yield response to water deficit in an upland rice mapping population; associations among traits and genetic markers. Theor Appl Genet 109:1237–1246. doi:10.1007/s00122-004-1731-8

    Article  CAS  PubMed  Google Scholar 

  • Lanceras JC, Pantuwan G, Jongdee B, Toojinda T (2004) Quantitative trait loci associated with drought tolerance at reproductive stage in rice. Plant Physiol 135:364–399. doi:10.1104/pp.103.035527

    Article  Google Scholar 

  • Lilley JM, Ludlow MM, McCouch SR, O’Toole JC (1996) Locating QTL for osmotic adjustment and dehydration tolerance in rice. J Exp Bot 47:1427–1436. doi:10.1093/jxb/47.9.1427

    Article  CAS  Google Scholar 

  • Loresto GC, Chang TT (1981) Decimal scoring systems for drought reaction and recovery ability in rice screening nurseries. Int Rice Res Newslet 6(2):9–10

    Google Scholar 

  • Ludlow M, Muchow RC (1990) A Critical evaluation of traits for improving crop yields in water-limited environments. Adv Agron 43:107–153. doi:10.1016/S0065-2113(08)60477-0

    Article  Google Scholar 

  • McCouch SR, Temnykh S, Lukashova A, Coburn J, DeClerk G, Cartinhour S, Harington S, Thomson M, Septiningis E, Semon M, Moncada P, Li J (2001) Microsatellite markers in rice: abundance, diversity, and applications. Adv Genet 107:117–135

    Google Scholar 

  • McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Magirang R, Li Z, Xing Y, Zhang Q, Kono I, 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. doi:10.1093/dnares/9.6.199

    Article  CAS  PubMed  Google Scholar 

  • O’Toole JC, Namuco OS (1983) Role of panicle exsertion in water stress induced sterility. Crop Sci 23:1093–1097

    Article  Google Scholar 

  • Pantuwan G, Fukai S, Cooper M, Rajatasereekul S, O’Toole JC (2002) Yield response of rice (Oryza sativa L.) genotypes to different types of drought under rainfed lowlands. Part 2. Selection of drought resistant genotypes. Field Crops Res 73:169–180. doi:10.1016/S0378-4290(01)00195-2

    Article  Google Scholar 

  • Porebski S, Bailey BR, Baum BR (1997) Modification of CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Mol Biol Rep 15:6–15. doi:10.1007/BF02772108

    Article  Google Scholar 

  • Price AH, Courtois B (1999) Mapping QTLs associated with drought resistance in rice: progress, problems and prospects. Plant Growth Regul 29:123–133. doi:10.1023/A:1006255832479

    Article  CAS  Google Scholar 

  • Price AH, Young EM, Tomos AD (1997) Quantitative trait loci associated with stomatal conductance, leaf rolling and heading date mapped in upland rice (Oryza sativa). New Phytol 137:83–91. doi:10.1046/j.1469-8137.1997.00818.x

    Article  CAS  Google Scholar 

  • Price AH, Steele KA, Moore BJ, Barraclough PB, Clark LJ (2000) A combined RFLP and AFLP linkage map of upland rice (Oryza sativa L.) used to identify QTLs for root-penetration ability. Theor Appl Genet 100:49–56. doi:10.1007/s001220050007

    Article  CAS  Google Scholar 

  • Price AH, Steele KA, Moore BJ, Jones RGW (2002) Upland rice grown in soil-filled chambers and exposed to contrasting water-deficit regimes II. Mapping quantitative trait loci for root morphology and distribution. Field Crops Res 76:25–43. doi:10.1016/S0378-4290(02)00010-2

    Article  Google Scholar 

  • Redona ED, Mackill DJ (1996) Mapping quantitative trait loci for seeding vigor using RFLPs. Theor Appl Genet 92:395–492. doi:10.1007/BF00223685

    Article  CAS  Google Scholar 

  • Robin S, Pathan MS, Courtois B, Lafitte R, Carandang C, Lanceras S, Amante M, Nguyen HT, Li Z (2003) Mapping osmotic adjustment in an advanced back-cross inbred population of rice. Theor Appl Genet 107:1288–1296. doi:10.1007/s00122-003-1360-7

    Article  CAS  PubMed  Google Scholar 

  • Robin S, Manimaran R, Pushpa R, Jeyaprakash P, Mahendran S, Lafitte HR, Atlin GN (2004) Development and Characterization of RILs for molecular mapping of reproductive stage moisture stress tolerance in rice. In: New directions for a diverse planet: Proceedings of the 4th international crop science congress, Brisbane, 26 Sep–1 Oct 2004. Accessed from http://www.cropscience.org.au/icsc2004/poster/1/3/4/884_robins.htm on 29 August 2008

  • Shen L, Courtois B, McNally KL, Robin S, Li Z (2001) Evaluation of near-isogenic lines of rice introgressed with QTLs for root depth through marker-aided selection. Theor Appl Genet 103:75–83. doi:10.1007/s001220100538

    Article  CAS  Google Scholar 

  • Spielmeyer W, Ellis MH, Chandler PM (2002) Semidwarf (sd-1), ‘‘green revolution’’ rice, contains a defective gibberellin 20-oxidase gene. Proc Natl Acad Sci USA 99:9043–9048. doi:10.1073/pnas.132266399

    Article  CAS  PubMed  Google Scholar 

  • Temnykh S, Park WD, Ayres N, Castinhour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCouch SR (2000) Mapping and genome organization of microsatellite sequences in rice. Theor Appl Genet 100:697–712. doi:10.1007/s001220051342

    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. doi:10.1101/gr.184001

    Article  CAS  PubMed  Google Scholar 

  • Tripathy JN, Zhang J, Robin S, Nguyen TT, Nguyen HT (2000) QTL for cell membrane stability mapped in rice (Oryza sativa L.). Theor Appl Genet 100:1197–1202. doi:10.1007/s001220051424

    Article  CAS  Google Scholar 

  • Venuprasad R, Shasidhar HE, Hittalmani S, Hemamalini GS (2002) Tagging quantitative trait loci associated with grain yield and root morphological traits in rice (Oryza sativa L.) under contrasting moisture regimes. Euphytica 128:293–300. doi:10.1023/A:1021281428957

    Article  CAS  Google Scholar 

  • Wang S, Basten CJ, Zeng ZB (2005) Windows QTL cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh. Accessed from http://statgen.ncsu.edu/qtlcart/WQTLCart.htm on 29 August 2008

  • Williams SRF (1946) Methods of growth analysis. In: Sestak Z, Catasky J, Jouris PJ (eds) Plant photosynthetic production manual methods. Drow Jenk NU Publishers, The Hague, pp 348–391

    Google Scholar 

  • Xia BS, Hanada K, Kizuzhi F (1991) Character expression of the semi-dwarfism gene sd1in rice. Effect of nitrogen levels on the expression of some agronomic characteristics. Jpn J Crop Sci 60:36–41

    Google Scholar 

  • Yadav R, Courtois B, Huang N, McLaren G (1997) Mapping genes controlling root morphology and root distribution in a doubled-haploid population of rice. Theor Appl Genet 94:619–632. doi:10.1007/s001220050459

    Article  CAS  Google Scholar 

  • Yano M, Sasaki T (1997) Genetic and molecular dissection of quantitative traits in rice. Plant Mol Biol 35:145–153. doi:10.1023/A:1005764209331

    Article  CAS  PubMed  Google Scholar 

  • Yoshida S (1981) Fundamentals of rice crop science. IRRI, Los Banos, p 269

    Google Scholar 

  • Zhang J, Zheng HG, Aarti A, Pantuwan G, Nguyen TT, Tripathy JN, Sarial AK, Robin S, Babu RC, Nguyen BD, Sarkarung S, Blum A, Nguyen HT (2001) Locating Genomic regions associated with components of drought resistance in rice: comparative mapping within and across species. Theor Appl Genet 103:19–29. doi:10.1007/s001220000534

    Article  CAS  Google Scholar 

  • Zheng BS, Yang L, Zhang WP, Mao CZ, Wu YR, Yi KK, Liu FY, Wu P (2003) Mapping QTLs and candidate genes for rice root traits under different water-supply conditions and comparative analysis across three populations. Theor Appl Genet 107:1505–1515. doi:10.1007/s00122-003-1390-1

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

We greatly acknowledge the Rockefeller Foundation, USA for supporting this project on genetic improvement of rice for drought resistance through a food security program grant (No. FS077/2002) awarded to Tamil Nadu Agricultural University, Coimbatore, India.

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Authors and Affiliations

  1. Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, 641003, Tamil Nadu, India

    M. Subashri, S. Robin, S. Rajeswari, K. Mohanasundaram & T. S. Raveendran

  2. Indian Agricultural Research Institute, Rice Breeding and Genetics Research Centre, Aduthurai, 612101, Tamil Nadu, India

    K. K. Vinod

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  1. M. Subashri
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Correspondence to S. Robin.

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Subashri, M., Robin, S., Vinod, K.K. et al. Trait identification and QTL validation for reproductive stage drought resistance in rice using selective genotyping of near flowering RILs. Euphytica 166, 291–305 (2009). https://doi.org/10.1007/s10681-008-9847-6

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  • DOI: https://doi.org/10.1007/s10681-008-9847-6

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