Skip to main content

Advertisement

SpringerLink
Log in

Localization of QTL for basal root thickness in japonica rice and effect of marker-assisted selection for a major QTL

  • Published:
Euphytica Aims and scope Submit manuscript

Abstract

Root traits are key components of plant adaptation to drought environment. By using a 120 recombined inbred lines (RILs) rice population derived from a cross between IRAT109, a japonica upland rice cultivar and Yuefu, a japonica lowland rice cultivar, a complete genetic linkage map with 201 molecular markers covering 1,833.8 cM was constructed and quantitative trait loci (QTLs) associated with basal root thickness (BRT) were identified. A major QTL, conferring thicker BRT, located on chromosome 4, designated brt4, explained phenotypic variance of 20.6%, was selected as target QTL to study the effects of marker-assisted selection (MAS) using two early segregating populations derived from crosses between IRAT109 and two lowland rice cultivars. The results showed that the flanking markers of brt4 were genetically stable in populations with different genetic backgrounds. In the two populations under upland conditions, the difference between the means of BRT of plants carrying positive and negative favorable alleles at brt4 flanking markers loci was significant. Phenotypic effects of BRT QTL brt4 were 5.05–8.16%. When selected plants for two generations were planted at Beijing and Hainan locations under upland conditions, MAS effects for BRT QTL brt4 were 4.56–18.56% and 15.46–26.52% respectively. The means of BRT for the homozygous plants were greater than that of heterozygous plants. This major QTL might be useful for rice drought tolerance breeding.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

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

    Article  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

    Article  CAS  Google Scholar 

  • Kamoshita A, Zhang J, Siopongco J, Sarkarung S, Nguyen HT, Wade LJ (2002a) Effect of phenotyping environment on identification of quantitative trait loci for rice root morphology under anaerobic conditions. Crop Sci 42:255–265

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Lander ES, Green P, Abraham SJ, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181

    Article  PubMed  CAS  Google Scholar 

  • Lang YZ, Hu J, Yang JC, Zhang ZJ, Zhu QS (2003) Study on morphology and function of root system for drought resistance in rice. J Yangzhou Univ 24(4):58–61

    Google Scholar 

  • Li ZC, Mu P, Li CP, Zhang HL, Li ZK, Gao YM, Wang XQ (2005) QTL mapping of root traits in a doubled haploid population from a cross between upland and lowland japonica rice in three environments. Theor Appl Genet 110:1244–1252

    Article  PubMed  CAS  Google Scholar 

  • Lincoln SE, Daly MJ, Lander ES (1993) Constructing genetic linkage maps with MAPMAKER/EXP VER. 3.0: a tutorial and reference manual, 3rd edn. Technical Report, Whitehead Institute for Biomedical Research, Cambridge, Mass

  • Lilley JM, Ludlow MM, McCouch SR, O′Toole JC (1996) Locating QTL for osmotic adjustment and dehydration tolerance in rice. J Exp Bot 47(30):1427–1436

    Article  CAS  Google Scholar 

  • Ling ZM, Li ZC, Yu R, Mu P (2002) Study on root traits of paddy rice and upland rice. J China Agric Univ 7(3):7–11

    Google Scholar 

  • McCouch SR, Kochert G, Yu ZH, Wang ZY, Khush GS, Coffman WR, Tanksley SD (1988) Molecular mapping of rice chromsomes. Theor Appl Genet 76:815–829

    Article  CAS  Google Scholar 

  • McCouch SR, Temnykh S, Lukashova A, Coburn J, DeClerck G, Cartinhour S, Harrington S, Thomson M, Septiningsih E, Semon M, Moncada P, Li J (2001) Microsatellite markers in rice: abundance, diversity, and applications. In: Khush GS, Brar DS, Hardy B (eds) Rice genetics IV. Proc 4th Int Rice Genet Symp. SciencePubl, New Delhi/International Rice Research Institute, Los Baños, Philippines, pp 117–135

    Chapter  Google Scholar 

  • Neeraja CN, Maghirang-Rodriguez R, Pamplona A, Heuer S, Collard BCY, Septiningsih EM, Vergara G, Sanchez D, Xu K, Ismail AM, Mackill DJ (2007) A marker-assisted backcross approach for developing submergence-tolerant rice cultivars. Theor Appl Genet 115:767–776

    Article  PubMed  CAS  Google Scholar 

  • Nguyen HT, Babu RC, Blum A (1997) Breeding for drought resistance in rice: physiology and molecular genetics consideration. Crop Sci 37:1426–1434

    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 

  • Ray JD, Yu L, McCouch SR, Wang G, Nguyen HT (1996) Mapping quantitative trait loci associated with root penetration ability in rice (Oryza sativa L.). Theor Appl Genet 92:627–636

    Article  CAS  Google Scholar 

  • Ribaut JM, Betrán J (1999) Single large-scale marker-assisted selection (SLS-MAS). Mol Breed 5(6):531–541

    Article  Google Scholar 

  • Romagosa I, Han F, Ullrich SE, Hayes PM, Wesenbery DM (1999) Verification of yield QTL through realized molecular marker-assisted selection responses in a barley cross. Mol Breed 5:143–152

    Article  Google Scholar 

  • Schmierer DA, Kandemir N, Kudrna DA, Jones BL, Ullrich SE, Kleinhofs A (2005) Molecular marker-assisted selection for enhanced yield in malting barley. Mol Breed 14(4):463–473

    Article  Google Scholar 

  • Schneider AK, Mary EB, James DK (1997) Marker-assisted selection to improve drought resistance in common bean. Crop Sci 37:51–60

    CAS  Google Scholar 

  • Shen XL, Guo WZ, Zhu XF, Yuan YL, Yu JZ, Russell JK, Zhang TZ (2005) Molecular mapping of QTLs for fiber qualities in three diverse lines in Upland cotton using SSR markers. Mol Breed 15(2):169–181

    Article  CAS  Google Scholar 

  • Stuber CW (1995) Mapping and manipulating quantitative traits in maize. Trends Genet 11:477–481

    Article  PubMed  CAS  Google Scholar 

  • Temnykh S, Park WD, Ayres N (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697–712

    Article  CAS  Google Scholar 

  • Wang DL, Zhu J, Li ZK, Paterson AH (1999) A computer software for mapping quantitative trait loci with main effects, epistatic effects and QTL × environment interactions. User manual for QTLMAPPER VER.1.0. Texas A & M University, College Station

    Google Scholar 

  • Wang YG, Deng QY, Liang FS, Xing QH, Li JM, Xong YD, Sun SM, Guo BT, Yuan LP, Wang B (2004) Molecular marker assisted selection for yield-enhancing genes in the progeny of Minghui63 × O.rufipogon. Agric Sci China 103:75–83

    Google Scholar 

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

    Article  CAS  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

    Article  CAS  Google Scholar 

  • Zhang TZ, Yuan YL, Yu J., Guo WZ, Kohel JR (2003) Molecular tagging of a major QTL for fiber strength in Upland cotton and its marker-assisted selection. Theor Appl Genet 106:262–268

    PubMed  CAS  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

    Article  PubMed  CAS  Google Scholar 

  • Zhu J (1998) Mixed model approaches for mapping quantitative trait loci. Hereditas 20(Suppl):137–138

    Google Scholar 

Download references

Acknowledgements

We thank the reviewers for their critical reviews and suggestions. This work was supported by the High Technology Research and Development Project of China (2006AA10Z158, 2006AA100101), 948 project [2006-G1(B)] and the Key technologies R&T program of China (2006BAD13B01-6).

Author information

Authors and Affiliations

  1. Key Laboratory of Crop Genomics and Genetic Improvement of Ministry of Agriculture, Key Laboratory of Crop Heterosis and Utilization of Ministry of Education and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100094, China

    Lifeng Liu, Ping Mu, Xueqin Li, Yanying Qu, Yi Wang & Zichao Li

  2. College of Agronomy, Agricultural University of Hebei, Baoding, 071001, China

    Lifeng Liu

  3. College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China

    Zichao Li

Authors
  1. Lifeng Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ping Mu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xueqin Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yanying Qu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yi Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Zichao Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Zichao Li.

Additional information

L. Liu and P. Mu are contributed equally to this work.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Liu, L., Mu, P., Li, X. et al. Localization of QTL for basal root thickness in japonica rice and effect of marker-assisted selection for a major QTL. Euphytica 164, 729–737 (2008). https://doi.org/10.1007/s10681-008-9695-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10681-008-9695-4

Keywords

Search

Navigation