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Quantitative trait loci for panicle size, heading date and plant height co-segregating in trait-performance derived near-isogenic lines of rice (Oryza sativa)

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Abstract

Near-isogenic lines (NILs) are ideal materials for precise estimation of quantitative trait loci (QTL) effects and map-based gene isolation. With the completion of the rice genome sequence, QTL isolation based on NILs is becoming a routine. In this study, a trait-performance derived NIL strategy was adopted to develop NILs. Two plants were identified within one inbred line of recombinant inbred lines (RILs, F7 generation), exhibiting a significant difference in panicle size. By marker screening of the whole genome the genetic background of the two plants was estimated to be 98.7% identical. These two plants were selected as parents to produce a near-isogenic F2 (NIL-F2) population, consisting of 125 individuals, in which spikelets per panicle (SPP), grains per panicle (GPP), heading date (HD) and plant height (PH) were recorded. These four traits expressed discontinuous or bimodal distribution in the NIL-F2 population and followed the expected segregation ratios for a single Mendelian factor by progeny tests. A partial dominant QTL for the four traits was mapped to the same interval flanked by RM310 and RM126 on chromosome 8. The QTL region explained 83.0, 80.2, 94.9 and 93.8% of trait variation of SPP, GPP, HD and PH in the progenies, respectively. Progeny tests also confirmed co-segregation of QTL for the four traits, tall plants consistently flowering late and carrying large panicles. Different NILs development strategies are discussed.

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References

  • Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, Nishimura A, Angeles ER, Qian Q, Kitano H, Matsuoka M (2005) Cytokinin oxidase regulates rice grain production. Science 309(5735):741–745

    Article  PubMed  CAS  Google Scholar 

  • Bernacchi D, Beck-Bunn T, Emmatty D, Eshed Y, Inai S, Lopez J, Petiard V, Sayama H, Uhlig J, Zamir D, Tanksley S (1998) Advanced backcross QTL analysis of tomato. II. Evaluation of near-isogenic lines carrying single-donor introgressions for desirable wild QTL-alleles derived from Lycopersicon hirsutum and L. pimpinellifolium. Theor Appl Genet 97:170–180

    Article  CAS  Google Scholar 

  • Darvasi A, Weinreb A, Minke V, Wellert JI, Soller M (1993) Detecting marker-QTL linkage and estimating QTL gene effect and map location using a saturated genetic map. Genetics 134:943–951

    PubMed  CAS  Google Scholar 

  • Fan CC, Xing YZ, Mao HL, Lu TT, Han B, Xu CG, Li XH, Zhang QF (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet (in press)

  • Frary A, Nesbitt C, Frary A, Grandillo S, Knaap E, Cong B, Liu JP, Meller J, Elber R, Alpert KB, Tanksley SD (2000) fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science 289

  • Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199

    PubMed  CAS  Google Scholar 

  • Li JM, Thomson M, McCouch RS (2004) Fine mapping of a grain-weight quantitative trait locus in the pericentromeric region of rice chromosome 3. Genetics 168:2187–2195

    Article  PubMed  CAS  Google Scholar 

  • Lin HX, Qian HR, Zhuang JY, Lu J, Min SK, Xiong ZM, Huang N, Zheng KL (1996) RFLP mapping of QTLs for yield and related characters in rice (Oryza sativa L.). Theor Appl Genet 92:920–927

    Article  CAS  Google Scholar 

  • Lin HX, Liang ZW, Sasaki T, Yano M (2003) Fine mapping and characterization of quantitative trait loci Hd4 and Hd5 controlling heading date in rice. Breed Sci 53:51–59

    Article  CAS  Google Scholar 

  • Lincoln S, Daley M, Lander E (1992) Constructing genetic maps with MAPMAKER/EXP 3.0. Whitehead Institute Technical Report, 3rd edn. Whitehead Institute, Cambridge

  • Lincoln SE, Daly MJ, Lander ES (1993) Mapping genes controlling quantitative traits with MAPMAKER/QTL1.1: a tutorial and reference manual, 2nd edn. Whitehead Institute Technical Report, Cambridge

  • Lu C, Shen Z, Tan Z, Xu Y, He P, Chen Y, Zhu L (1996) Comparative mapping of QTLs for agronomic traits of rice across environments using a doubled haploid population. Theor Appl Genet 93:1211–1217

    Article  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Nishimura A, Ashikari M, Lin S, Takashi T, Angeles ER, Yamamoto T, Matsuoka M (2005) Isolation of a rice regeneration quantitative trait loci gene and its application to transformation systems. PNAS 102:11940–11944

    Article  PubMed  CAS  Google Scholar 

  • Paterson AH, Damon S, Hewitt JD, Zamir D, Rabinowitch HD, Lincoln SE, Lander ES, Tanksley SD (1991) Mendelian factors underlying quantitative traits in tomato: comparison across species, generations, and environments. Genetics 127(1):181–197

    PubMed  CAS  Google Scholar 

  • Ren ZH, Gao JP, Li LG, Cai XL, Huang W, Chao DY, Zhu MZ, Wang ZY, Luan S, Lin HX (2005) A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat Genet 37(10):1141–1146

    Article  PubMed  CAS  Google Scholar 

  • Spielmeyer W, Ellis MH, Chandler PM (2002) Semidwarf (sd-1), “green revolution” rice, contains a defective gibberellin 20-oxidase gene. PNAS 99:9043–9048

    Article  PubMed  CAS  Google Scholar 

  • Tanksley SD, Nelson JC (1996) Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet 92:191–203

    Article  Google Scholar 

  • Tian F, Li DJ, Fu Q, Zhu ZF, Fu YC, Wang XK, Sun CQ (2005) Construction of introgression lines carrying wild rice (Oryza rufipogon Griff.) segments in cultivated rice (Oryza sativa L.) background and characterization of introgressed segments associated with yield-related traits. Theor Appl Genet

  • Wan XY, Wan JM, Weng JF, Jiang L, Bi JC, Wang CM, Zhai HQ (2005) Stability of QTLs for rice grain dimension and endosperm chalkiness characteristics across eight environments. Theor Appl Genet 110(7):1334–1346

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Xiao J, Li J, Yuan L, Tanksley SD (1996) Identification of QTLs affecting traits of agronomic importance in a recombinant inbred population derived from a subspecific rice cross. Theor Appl Genet 92:230–244

    Article  CAS  Google Scholar 

  • Xiao J, Li J, Grandillo S, Ahn SN, Yuan LP, Tanksley SD, McCouch SR (1998) Identification of trait-improving quantitative trait loci alleles from a wild rice relative, Oryza rufipogon. Genetics 150:899–909

    PubMed  CAS  Google Scholar 

  • Xing YZ, Tan YF, Hua JP, Sun XL, Xu CG, Zhang Q (2002) Characterization of the main effects, epistatic effects and their environmental interactions of QTLs on the genetic basis of yield traits in rice. Theor Appl Genet 105:248–257

    Article  PubMed  CAS  Google Scholar 

  • Xiong L, Liu K, Dai X, Xu C, Zhang Q (1999) Identification of genetic factors controlling domestication-related traits of rice using an F2 population of a cross between Oryza sativa and O. rufipogon. Theor Appl Genet 98:243–251

    Article  CAS  Google Scholar 

  • Yamamoto T, Kuboki Y, Lin SY, Sasaki T, Yano M (1998) Fine mapping of quantitative trait loci Hd-1, Hd-2 and Hd-3, controlling heading date of rice, as single Mendelian factors. Theor Appl Genet 97:37–44

    Article  CAS  Google Scholar 

  • Yamamoto T, Lin HX, Sasaki T, Yano M (2000) Identification of heading date quantitative trait locus Hd6 and characterization of its epistatic interactions with Hd2 in rice using advanced backcross progeny. Genetics 154:885–891

    PubMed  CAS  Google Scholar 

  • Yano M, Nagamura Y, Kurata N, Minobe Y, Sasaki T (1997) Identification of quantitative trait loci controlling heading date in rice using a high density linkage map. Theor Appl Genet 95:1025–1032

    Article  CAS  Google Scholar 

  • Yu SB, Li JX, Xu CG, Tan YF, Gao YJ, Li XH, Zhang QF (1997) Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid. Proc Natl Acad Sci USA 94:9226–9231

    Article  PubMed  CAS  Google Scholar 

  • Yu SB, Li JX, Xu CG, Tan YF, Li XH, Zhang QF (2002) Identification of quantitative trait loci and epistatic interactions for plant height and heading date in rice. Theor Appl Genet 104:619–625

    Article  PubMed  CAS  Google Scholar 

  • Zhuang JY, Lin HX, Lu J, Qian HR, Hittalmani S, Huang N, Zheng KL (1997) Analysis of QTL × environment interaction for yield components and plant height in rice. Theor Appl Genet 95:799–808

    Article  CAS  Google Scholar 

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Acknowledgments

This work was supported in part by grants from the National Program on the Development of Basic Research and the National Natural Science Foundation of China. We thank Dr Jeppe Reitan Andersen in DIAS for helpful comments to the manuscript.

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Authors and Affiliations

  1. National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China

    Yushan Zhang, Caiguo Xu, Qifa Zhang & Yongzhong Xing

  2. Shanghai Agrobiological Gene Center, 2901 Beidi Road, Shanghai, 201106, China

    Lijun Luo

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  1. Yushan Zhang
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  2. Lijun Luo
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  3. Caiguo Xu
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  4. Qifa Zhang
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  5. Yongzhong Xing
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Correspondence to Yongzhong Xing.

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Communicated by H. H. Geiger

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Zhang, Y., Luo, L., Xu, C. et al. Quantitative trait loci for panicle size, heading date and plant height co-segregating in trait-performance derived near-isogenic lines of rice (Oryza sativa). Theor Appl Genet 113, 361–368 (2006). https://doi.org/10.1007/s00122-006-0305-3

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  • DOI: https://doi.org/10.1007/s00122-006-0305-3

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