Skip to main content

Comparison of quantitative trait loci controlling seedling characteristics at two seedling stages using rice recombinant inbred lines

Theoretical and Applied Genetics volume 109, pages 640–647 (2004)Cite this article

Abstract

A better understanding of the genetics of seedling characteristics in rice could be helpful in improving rice varieties. Zhenshan 97 and Minghui 63, the parents of Shanyou 63, an elite hybrid developed during the last decade in China, vary greatly with respect to their physiological and morphological traits at the seedling growth stage. In this study, we used a population of 240 recombinant inbred lines derived from a cross between Zhenshan 97 and Minghui 63 to identify quantitative trait loci (QTL) for seedling characteristics. All plant material was grown in hydroponic culture. Data for the following characters were collected at 30 days and 40 days post-sowing: plant height, shoot dry matter weight (SDW), maximum root length, root dry weight (RDW), total dry weight , and root-shoot ratio (the ratio of SDW to RDW). Analysis using composite interval mapping detected 16 QTL for the six traits in 30-day-old seedlings. Of these 16 QTL, Minghui 63 alleles increased trait values at only two of them. The QTL in the vicinity of R3166 on chromosome 5 simultaneously influenced PH, SDW, MRL, RDW, and TDW in the same direction. Twenty QTL were detected for the same traits in the 40-day-old seedlings. However, at this stage Minghui 63 alleles increased trait values at eight QTL. The QTL linked to R3166 also affected PH, SDW, MRL, RDW, and TDW. Only four QTL were common to the two stages. These results clearly indicate that different genes (QTL) control the same traits during different time intervals. Zhenshan 97 alleles had positive effects during the first 30 days of seedling growth, but thereafter the positive effects of Minghui 63 alleles on seedling growth gradually became more pronounced.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

43,34 €

Price includes VAT (Finland)
Tax calculation will be finalised during checkout.

Fig. 1

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

    Article  CAS  Google Scholar 

  • Asins MJ, Mestre P, Garcia JE, Dicenta F, Carbonell EA (1994) Genotype × environment interaction in QTLs analysis of an intervarietal almond cross by means of genetic markers. Theor Appl Genet 89:358–364

    Google Scholar 

  • Basten CJ, Weir BS, Zeng ZB (2001) qtl cartographer, Version 1.15. Department of Statistics, North Carolina State University, Raleigh

  • Bradshaw HD Jr, Stettler RF (1995) Molecular genetics of growth and development in Populus. IV. Mapping QTLs with large effects on growth, form, and phenology traits in a forest tree. Genetics 139:963–973

    CAS  PubMed  Google Scholar 

  • Cao G, Zhu J, He C, Gao Y, Yan J, Wu P (2001) Impact of epistasis and QTL × environment interaction on the developmental behavior of plant height in rice (Oryza sativa L.). Theor Appl Genet 103:153–160

    CAS  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

    CAS  Google Scholar 

  • Chang TT, Loresto GC, O’ Toole JC, Armenta-Soto JL (1982) Strategy and methodology of breeding rice for drought-prone areas. In: IRRI (ed) Drought resistance in crops with the emphasis on rice. The International Rice Research Institute, Manila, pp 217–244

  • Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971

    CAS  PubMed  Google Scholar 

  • Cui KH, Peng SB, Xing YZ, Xu CG, Yu SB, Zhang Q (2002) Molecular dissection of seedling vigor and associated physiological traits in rice. Theor Appl Genet 105:745–753

    Article  Google Scholar 

  • Ellis RH (1992) Seed and seedling vigor in relation to crop growth and yield. Plant Growth Regul 11:249–255

    Google Scholar 

  • Ingram K, Bueno TFD, Namuco OS, Yambao EB, Beyrouty CA (1994) Rice root traits for drought resistance and their genetic variation. In: Kirk GJD (ed) Rice roots: nutrient and water use. The International Rice Research Institute, Manila, pp 67–77

  • Kamoshita A, Wade LJ, Ali ML, Pathan MS, Zhang J, Sarkarung S, Nguyen HT (2002) Mapping QTLs for root morphology of a rice population adapted to rainfed lowland conditions. Theor Appl Genet 104:880–893

    Article  Google Scholar 

  • Karrel EE, Chandler JM, Foolad MR, Rodriguez RL (1993) Correlation between α-amylase gene expression and seedling vigor in rice. Euphytica 66:163–169

    Google Scholar 

  • Lin SY, Sasaki T, Yano M (1998) Mapping quantitative trait loci controlling seed dormancy and heading date in rice, Oryza sativa L, using backcross inbred lines. Theor Appl Genet 96:997–1003

    CAS  Google Scholar 

  • Lin HX, Ashikari M, Yamanouchi U, Sasaki T, Yano M (2002) Identification and characterization of a quantitative trait locus, controlling heading date in rice. Breed Sci 52:35–42

    Article  CAS  Google Scholar 

  • Loresto GC, Zhang WX, Chaudhary D, Chang TT (1983) Aeroponic technique for screening the drought avoidance mechanism of rice genotypes by root characters. Garcia de Orta 10:77–82

    Google Scholar 

  • McCouch SR, Cho YG, Yano M, Paul E, Blinstruub M (1997) Report on QTL nomenclature. Rice Genet Newsl 14:11–13

    Google Scholar 

  • O’Toole JC, Bland WL (1987) Genotypic variation in crop plant root systems. Adv Agron 41:91–145

    Google Scholar 

  • Plomion C, Durel CE, O’Malley DM (1996) Genetic dissection of height in maritime pine seedlings raised under accelerated growth conditions. Theor Appl Genet 93:849–858

    CAS  Google Scholar 

  • Price AH, 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 AH, Tomos AD, Virk DS (1997) Genetic dissection of root growth in rice (Oryza sativa L.). I. A hydroponic screen. Theor Appl Genet 95:132–142

    Article  Google Scholar 

  • Redoña ED, Mackill DJ (1996a) Genetic variation for seedling vigor traits in rice. Crop Sci 36:285–290

    Google Scholar 

  • Redoña ED, Mackill DJ (1996b) Molecular mapping of quantitative trait loci in japonica rice. Genome 39:395–403

    Google Scholar 

  • Redoña ED, Mackill DJ (1996c) Mapping quantitative trait loci for seedling vigor in rice using RFLPs. Theor Appl Genet 92:395–402

    Google Scholar 

  • StatSoft (1997) Statistica. StatSoft, Tulsa, Okla.

  • Tan YF, Xing YZ, Li JX, Yu SB, Xu CG, Zhang Q (2000) Genetic bases of appearance quality of rice grains in Shanyou 63, an elite rice hybrid. Theor Appl Genet 101:823–829

    CAS  Google Scholar 

  • Verhaegen D, Plomion C, Gion JM, Poitel M, Costa P, Kremer A (1997) Quantitative trait dissection analysis in Eucalyptus using RAPD markers. I. Detection of QTL in interspecific hybrid progeny, stability of QTL expression across different ages. Theor Appl Genet 95:597–608

    Article  Google Scholar 

  • de Vicente MC, Tanksley SD (1993) QTL analysis of transgressive segregation in an interspecific tomato cross. Genetics 134:585–596

    PubMed  Google Scholar 

  • Wu WR, Li WM, Tang DZ, Lu HR, Worland AJ (1999) Time-related mapping of quantitative trait loci underlying tiller number in rice. Genetics 151:297–303

    CAS  PubMed  Google Scholar 

  • Xing YZ, Tan YF, Xu CG, Hua JP, Sun XL (2001) Mapping and isolation of quantitative trait loci controlling plant height and heading date in rice. Acta Bot Sin 43:840–845

    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 in the genetic basis of yield traits in rice. Theor Appl Genet 105:248–257

    CAS  Google Scholar 

  • Yamamoto T, Lin HX, Sasaki T, Yano M (2000) Identification of heading date quantitative trait locus hd6, and characterization of its epistasis interaction with hd2 in rice using advanced backcross progeny. Genetics 154:885–891

    Google Scholar 

  • Yan J, Zhu J, He C, Benmoussa M, Wu P (1998) Molecular dissection of developmental behavior of plant height in rice (Oryza sativa L). Genetics 150:1257–1265

    CAS  PubMed  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

    Article  CAS  Google Scholar 

  • Yoshida S, Hasegawa S (1982) The rice root system: its development and function. In: IRRI (ed) Drought resistance in crops with the emphasis on rice. International Rice Research Institute, Manila, Philippines, pp 83–96

  • Yoshida S, Forno DA, Cock JH, Gomex KA (1976) Laboratory manual for physiological studies of rice. 3rd edn. International Rice Research Institute, Manila, Philippines

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

    CAS  PubMed  Google Scholar 

  • Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136:1457–1468

    CAS  PubMed  Google Scholar 

  • Zheng HG, Babu RC, Pathan MS, Ali ML, Huang N, Courtois B, Nguyen HT (2000) Quantitative trait loci for root penetration ability and root thickness in rice: comparison of genetic backgrounds Genome 43:53–61

    Google Scholar 

Download references

Acknowledgements

We thank Dr. Q. Zhang for his helpful advice at various stages of this investigation. We also thank Ms. Susan M. Wielgus (Horticulture Department, University of Wisconsin-Madison) for correction of the English. This work was supported by a grant from National Key Project of Science and Technology (2002AA2Z1002), a grant from the National Natural Science Foundation of China, a grant from the National Key Program on Basic Research and Development of China, and the special National Key Project on Functional Genomics Bioclip of China.

Author information

Affiliations

  1. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China

    C. G. Xu, X. Q. Li, Y. Xue, Y. W. Huang, J. Gao & Y. Z. Xing

Authors
  1. C. G. Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. X. Q. Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Y. Xue
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Y. W. Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. J. Gao
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Y. Z. Xing
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Y. Z. Xing.

Additional information

Communicated by D.J. Mackill

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Xu, C.G., Li, X.Q., Xue, Y. et al. Comparison of quantitative trait loci controlling seedling characteristics at two seedling stages using rice recombinant inbred lines. Theor Appl Genet 109, 640–647 (2004). https://doi.org/10.1007/s00122-004-1671-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-004-1671-3

Keywords

  • Quantitative Trait Locus
  • Quantitative Trait Locus Analysis
  • Quantitative Trait Locus Mapping
  • Root Trait
  • Coleoptile Length