Skip to main content
SpringerLink
Log in

Identification of quantitative trait loci associated with germination using chromosome segment substitution lines of rice (Oryza sativa L.)

  • Original Paper
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

Rapid and uniform seed germination under diverse environmental conditions is a desirable characteristic for most crop plants, such as rice, wheat, and maize. However, the genetic base of the variations in the rate of germination is not well understood. In this study, quantitative trait loci (QTL) for germination rate were mapped with a set of 143 chromosome segment substitution lines (CSSL) each contains a small genomic fragment from a japonica variety Nipponbare in the uniform genetic background of an indica variety Zhenshan97. Nine CSSL showed significantly lower germination rate than that in Zhenshan97. Four germination-related QTL were identified located on chromosomes 2, 5, 6 and 10, at which all japonica alleles decreased germination rate. By using the CSSL-derived F2 population, a major QTL (qGR2) on chromosome 2 was confirmed, and delimited to a 10.4 kb interval containing three putative candidate genes, of which OsMADS29 was only expressed preferentially in the seed. These results would facilitate cloning of the major gene that affects germination rate, and provide an insight into the genetic basis of germination.

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
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  • Alonso-Blanco C, Bentsink L, Hanhart CJ, de Vries Blankestijn H, Koornneef M (2003) Analysis of natural allelic variation at seed dormancy loci of Arabidopsis thaliana. Genetics 164:711–729

    PubMed  CAS  Google Scholar 

  • Arora R, Agarwal P, Ray S, Singh AK, Singh VP, Tyagi AK, Kapoor S (2007) MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress. BMC Genom 8:242

    Article  Google Scholar 

  • Becker A, Theißen G (2003) The major clades of MADS-box genes and their role in the development and evolution of flowering plants. Mol Phylogenet Evol 29:464–489

    Article  PubMed  CAS  Google Scholar 

  • Bentsink L, Jowett J, Hanhart CJ, Koornneef M (2006) Cloning of DOG1, a quantitative trait locus controlling seed dormancy in Arabidopsis. Proc Natl Acad Sci USA 103:17042–17047

    Article  PubMed  CAS  Google Scholar 

  • Bentsink L, Hanson J, Hanhart CJ, de Vries Blankestijn H, Coltrane C, Keizer P, El-Lithy M, Alonso-Blanco C, Teresa de Andrése M, Reymond M, van Eeuwijk F, Smeekens S, Koornneef M (2010) Natural variation for seed dormancy in Arabidopsis is regulated by additive genetic and molecular pathways. Proc Natl Acad Sci USA 107:4264–4269

    Article  PubMed  CAS  Google Scholar 

  • Bewley JD (1997) Seed germination and dormancy. Plant Cell 9:1055–1066

    Article  PubMed  CAS  Google Scholar 

  • Bewley JD, Black M (1985) Seeds: physiology of development and germination. Plenum Press, New York

    Google Scholar 

  • Cai HW, Morishima H (2002) QTL clusters reflect character associations in wild and cultivated rice. Theor Appl Genet 104:1217–1228

    Article  PubMed  CAS  Google Scholar 

  • Carrera E, Holman T, Medhurst A, Peer W, Schmuths H, Footitt S, Theodoulou FL, Holdsworth MJ (2007) Gene expression profiling reveals defined functions of the ATP-binding cassette transporter COMATOSE late in phase II of germination. Plant Physiol 143:1669–1679

    Article  PubMed  CAS  Google Scholar 

  • Chen F, Nonogaki H, Bradford KJ (2002) A gibberellin-regulated xyloglucan endotransglycosylase gene is expressed in the endosperm cap during tomato seed germination. J Exp Bot 53:215–223

    Article  PubMed  CAS  Google Scholar 

  • Chen QQ, Mu JX, Zhou HJ, Yu SB (2007) Genetic effect of japonica alleles detected in indica candidate introgression lines. Sci Agri Sin 40:2379–2387

    Google Scholar 

  • Chiang GCK, Barua D, Kramer EM, Amasino RM, Donohue K (2009) Major flowering time gene, FLOWERING LOCUS C, regulates seed germination in Arabidopsis thaliana. Proc Natl Acad Sci USA 106:11661–11666

    Article  PubMed  CAS  Google Scholar 

  • Copeland LO, McDonald MF (1995) Principles of seed science and technology, 3rd edn. Maxwell MacMillan International, New York

    Book  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  PubMed  CAS  Google Scholar 

  • Delwiche SR, Mckenzie KS, Webb BD (1996) Quality characteristics in rice by near-infrared reflectance analysis of whole-grain milled samples. Cereal Chem 73:257–263

    CAS  Google Scholar 

  • Dingkuhn M, Schnier HF, Javellana C, Pamplona R, De Datta SK (1992) Effect of late season nitrogen application on canopy photosynthesis and yield of transplanted and direct seeded tropical lowland rice. II. Canopy stratification at flowering stage. Field Crops Res 28:235–249

    Article  Google Scholar 

  • Dunnett C (1955) A multiple comparisons procedure for comparing several treatments with a control. J Am Stat Assoc 50:1096–1121

    Article  Google Scholar 

  • Dutt M, Geneve R (2007) Time to radicle protrusion does not correlate with early seedling growth in individual seeds of Impatiens and Petunia. J Amer Soc Hort Sci 132:283–436

    Google Scholar 

  • Fan CC, Xing YZ, Mao HL, Lu TT, Han B, Xu CG, Li XH, Zhang Q (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 112:1164–1171

    Article  PubMed  CAS  Google Scholar 

  • Fujino K, Sekiguchi H, Matsuda Y, Sugimoto K, Ono K, Yano M (2008) Molecular identification of a major quantitative trait locus, qLTG3–1, controlling low-temperature germinability in rice. Proc Natl Acad Sci USA 105:12623–12628

    Article  PubMed  CAS  Google Scholar 

  • Fujino K, Sekiguchi H, Sato T, Kiuchi H, Nonoue Y, Takeuchi Y, Ando T, Lin SY, Yano M (2004) Mapping of quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.). Theor Appl Genet 108:794–799

    Article  PubMed  CAS  Google Scholar 

  • Gu XY, Kianian SF, Foley ME (2004) Multiple loci and epistases control genetic variation for seed dormancy in weedy rice (Oryza sativa). Genetics 166:1503–1516

    Article  PubMed  CAS  Google Scholar 

  • Hou MY, Wang CM, Jiang L, Wan JM, Hideshi Y, Yoshimura A (2004) Inheritance and QTL mapping of low temperature germinability in rice (Oryza sativa L.). Acta Genet Sin 31:701–706

    PubMed  CAS  Google Scholar 

  • Holdsworth MJ, Bentsink L, Soppe WJJ (2008) Molecular networks regulating Arabidopsis seed maturation, afterripening, dormancy and germination. New Phytol 179:33–54

    Article  PubMed  CAS  Google Scholar 

  • Howell KA, Narsai R, Carroll A, Ivanova A, Lohse M, Usade B, Millar AH, Whelan J (2009) Mapping metabolic and transcript temporal switches during germination in rice highlights specific transcription factors and the role of RNA instability in the germination process. Plant Physiol 149:961–980

    Article  PubMed  CAS  Google Scholar 

  • Isshiki M, Tsumoto A, Shimamoto K (2006) The serine/arginine-rich protein family in rice plays important roles in constitutive and alternative splicing of pre-mRNA. Plant Cell 18:146–158

    Article  PubMed  CAS  Google Scholar 

  • Jiang L, Liu SJ, Hou MY, Tang JY, Chen LM, Zhai HQ, Wan JM (2006) Analysis of QTLs for seed low temperature germinability and anoxia germinability in rice (Oryza sativa L.). Field Crops Res 98:68–75

    Article  Google Scholar 

  • Juliano BO, Villareal CP (1993) Grain quality evaluation of world rices. International Rice Research Institute, Manila

    Google Scholar 

  • Limami AM, Rouillon C, Glevarec G, Gallais A, Hirel B (2002) Genetic and physiological analysis of germination efficiency in maize in relation to nitrogen metabolism reveals the importance of cytosolic glutamine synthetase. Plant Physiol 2002:1860–1870

    Article  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

    Article  CAS  Google Scholar 

  • Lincoln S, Daly M, Lander E (1992) Constructing genetics maps with MAPMAKER/EXP 3.0. Whitehead Institute Technical Report. Whitehead Institute, Cambridge

    Google Scholar 

  • McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Zing 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

    Article  PubMed  CAS  Google Scholar 

  • Miura K, Lin SY, Yano M, Nagamine T (2001) Mapping quantitative trait loci controlling low temperature germinability in rice (Oryza sativa L.). Breeding Sci 51:293–299

    Article  CAS  Google Scholar 

  • Morohashi Y (2002) Peroxidase activity develops in the micropylar endosperm of tomato seeds prior to radicle protrusion. J Exp Bot 53:1643–1650

    Article  PubMed  CAS  Google Scholar 

  • Nonogaki H (2006) Seed germination-the biochemical and molecular mechanisms. Breeding Sci 56:93–105

    Article  CAS  Google Scholar 

  • Nonogaki H, Gee OH, Bradford KJ (2000) A germination-specific endo-β-mannanase gene is expressed in the micropylar endosperm cap of tomato seeds. Plant Physiol 123:1235–1245

    Article  PubMed  CAS  Google Scholar 

  • Panaud O, Chen X, McCouch SR (1996) Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet 252:597–607

    PubMed  CAS  Google Scholar 

  • Reddy ASN (2004) Plant serine/arginine-rich proteins and their role in pre-mRNA splicing. Trends Plant Sci 9:541–547

    Article  PubMed  CAS  Google Scholar 

  • Rogers SO, Bendich AJ (1988) Extraction of DNA from plant tissues. In: Gelvin SB, Schilperoort RA (eds) Plant molecular biology manual, pp A6: l–10. Kluwer, Boston

    Google Scholar 

  • Schmuths H, Bachmann K, Weber E, Horres R, Hoffmann M (2006) Effects of preconditioning and temperature during germination of 73 natural accessions of Arabidopsis thaliana. Ann Bot 97:623–634

    Article  PubMed  Google Scholar 

  • Sreenivasulu N, Usadel B, Winter A, Radchuk V, Scholz U, Stein N, Weschke W, Strickert M, Close TJ, Stitt M, Graner A, Wobus U (2008) Barley grain maturation and germination: metabolic pathway and regulatory network commonalities and differences highlighted by new MapMan/PageMan profiling tools. Plant Physiol 146:1738–1758

    Article  PubMed  CAS  Google Scholar 

  • Takeba G (1980) Accumulation of free amino acids in the tips of nonthermodormant embryonic axes accounts for the increase in growth potential of New York lettuce seeds. Plant Cell Physiol 21:1639–1644

    CAS  Google Scholar 

  • Tan YF, Li JX, Yu SB, Xing YZ, Xu CG, Zhang Q (1999) The three important traits for cooking and eating quality of rice grains are controlled by a single locus in an elite rice hybrid, Shanyou 63. Theor Appl Genet 99:642–648

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Wan JM, Cao YJ, Wang CM, Ikehashi H (2005) Quantitative trait loci associated with seed dormancy in rice. Crop Sci 45:712–716

    Article  CAS  Google Scholar 

  • Wang L, Xie W, Chen Y, Tang W, Yang J, Ye R, Liu L, Lin Y, Xu C, Xiao J, Zhang Q (2010) A dynamic gene expression atlas covering the entire life cycle of rice. Plant J 61:752–766

    Article  PubMed  CAS  Google Scholar 

  • Wang LQ, Zhong M, Li XH, Yuan DJ, Xu YB, Liu HF, He YQ, Luo LJ, Zhang Q (2008) The QTL controlling amino acid content in grains of rice (Oryza sativa) are co-localized with the regions involved in the amino acid metabolism pathway. Mol Breed 21:127–137

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported in part by grants from National Program on Key Basic Research Project, National Special Program for Research of Transgenic Plant of China, and the National Natural Science Foundation of China (30971750).

Author information

Authors and Affiliations

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

    Min Li, Penglin Sun, Hongju Zhou & Sibin Yu

  2. College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China

    Min Li, Penglin Sun, Hongju Zhou & Sibin Yu

  3. School of Plant Biology and International Centre for Plant Breeding Education and Research, The University of Western Australia, Crawley, WA, 6009, Australia

    Sheng Chen

Authors
  1. Min Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Penglin Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hongju Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Sheng Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Sibin Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Sibin Yu.

Additional information

Communicated by E. Guiderdoni.

M. Li and P. Sun contributed equally to the work.

Electronic supplementary material

Below is the link to the electronic supplementary material.

122_2011_1593_MOESM1_ESM.pdf

Fig. S1 Time course of germination of seeds incubated at 13°C (A), 18°C (B), 23°C (C) and 28°C (D) in three parental lines. Squares, triangles and circles represent the means of three replicates for ‘ZS97’, ‘CSSL29’ and ‘Nipponbare’ respectively, and vertical bars indicate standard deviation. (PDF 22 kb)

122_2011_1593_MOESM2_ESM.pdf

Fig. S2 Germination (%) of CSSLs containing different substitution fragments overlapping the genomic region of RM485–RM1211 on chromosome 2. The phenotype (means ± SD) and P value of Dunnett’s test against ‘ZS97’ are given for each line. ** Indicates significant difference at p < 0.01. (PDF 28 kb)

122_2011_1593_MOESM3_ESM.pdf

Fig. S3 Relative expression in microarray data of LOC_Os02g07420 and LOC_Os02g07430 at different developmental stages in ‘ZS97’. 1–14, the tissue samples collected and the methods for microarray analysis as described by Wang et al. (2010). (PDF 17 kb)

Table S1 Forty-four rice varieties surveyed for germination rate at 2 and 7 days. (XLS 19 kb)

Table S2 Primers for reverse transcriptase (RT)-PCR of the candidate genes. (DOC 27 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Li, M., Sun, P., Zhou, H. et al. Identification of quantitative trait loci associated with germination using chromosome segment substitution lines of rice (Oryza sativa L.). Theor Appl Genet 123, 411–420 (2011). https://doi.org/10.1007/s00122-011-1593-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-011-1593-9

Keywords

Search

Navigation