Skip to main content
SpringerLink
Log in

Mapping quantitative trait loci for yield components and morphological traits in an advanced backcross population between Oryza grandiglumis and the O. sativa japonica cultivar Hwaseongbyeo

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

Abstract

Introgression has been achieved from wild species Oryza grandiglumis (2n=48, CCDD, Acc. No. 101154) into O. sativa subsp. japonica cv. Hwaseongbyeo as a recurrent parent. An advanced introgression (backcross) line, HG101, produced from a single plant from BC5F3 families resembled Hwaseongbyeo, but it showed differences from Hwaseongbyeo in several traits, including days to heading and culm length. To detect the introgressions, 450 microsatellite markers of known chromosomal position were used for the parental survey. Of the 450 markers, 51 (11.3%) detected O. grandiglumis segments in HG101. To characterize the effects of alien genes introgressed into HG101, an F2:3 population (150 families) from the cross Hwaseongbyeo/HG101 was developed and evaluated for 13 agronomic traits. Several lines outperformed Hwaseongbyeo in several traits, including days to heading. Genotypes were determined for 150 F2 plants using simple sequence repeat markers. Qualitative trait locus (QTL) analysis was carried out to determine the relationship between marker genotype and the traits evaluated. A total of 39 QTL and 1 gene conferring resistance to blast isolate were identified using single-point analysis. Phenotypic variation associated with each QTL ranged from 4.2 to 30.5%. For 18 (46.2%) of the QTL identified in this study, the O. grandiglumis-derived alleles contributed a desirable agronomic effect despite the overall undesirable characteristics of the wild phenotype. Favorable wild alleles were detected for days to heading, spikelets per panicle, and grain shape traits. Grain shape QTL for grain weight, thickness, and width identified in the F2:3 lines were further confirmed based on the F4 progeny test. The confirmed locus, tgw2 for grain weight is of particular interest because of its independence from undesirable height and maturity. Several QTL controlling amylose content and grain traits have not been detected in the previous QTL studies between Oryza cultivars, indicating potentially novel alleles from O. grandiglumis. The QTL detected in this study could be a rich source of natural genetic variation underlying the evolution and breeding of rice.

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

Similar content being viewed by others

References

  • Ahn SN, Kim YK, Hong HC, Han SS, Kwon SJ, Choi HC, Moon HP, McCouch SR (2000) Molecular mapping of a new gene for resistance to rice blast. Euphytica 116:17–22

    Article  CAS  Google Scholar 

  • Ahn SN, Kwon SJ, Suh JP, Kang KH, Kim HJ, Song MT, Hwang HG, Moon HP (2001) Identification of introgressions in a backcross progeny derived from the cross between Oryza sativa and O grandiglumis. Korean J Breed 33:318–323

    Google Scholar 

  • Ahn SN, Kwon SJ, Suh JP, Kang KH, Kim HJ, Hwang HG, Moon HP (2003) Introgression for agronomic from O grandiglumis into rice, O sativa. In: Mew TW, Brar DS, Peng S, Dawe D, Hardy B (eds) Rice science: innovations and impact for livelihood. IRRI, Los Banos, pp 265–274

    Google Scholar 

  • Akimoto M, Morishima H (2003) Genetic population structures of Oryza glumaepatula and O. grandiglumis distributed in Amazon flood area. In: Khush GS, Brar DS, Hardy B (eds) Advances in rice genetics. IRRI, Los Banos, pp 126–127

    Google Scholar 

  • Brar DS, Khush GS (1997) Alien introgression in rice. Plant Mol Biol 35:35–47

    Article  PubMed  CAS  Google Scholar 

  • Brondani C, Rangel PHN, Brondani RPV, Ferreira ME (2002) QTL mapping and introgression of yield-related traits from Oryza glumaepatula to cultivated rice (Oryza sativa) using microsatellite markers. Theor Appl Genet 104:1192–1203

    Article  PubMed  CAS  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 

  • Causse MA, Fulton TM, Cho YG, Ahn SN, Chunwongse J, Wu K, Xiao J, Yu Z, Ronald PC, Harrington SE, Second G, McCouch SR, Tanksley SD (1994) Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics 138:1251–1274

    PubMed  CAS  Google Scholar 

  • Cho YG, Eun MY, McCouch SR, Chae YA (1994) The semidwarf gene, sd-1, of rice (Oryza sativa L). II. Molecular mapping and marker-assisted selection. Theor Appl Genet 89:54–59

    CAS  Google Scholar 

  • Frary A, Nesbitt TC, Frary S, Grandillo S, van der Knapp E, Cong B, Lui J, Meller J, Elber R, Alpert KB, Tanksley SD (2000) fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science 289:85–88

    Article  PubMed  CAS  Google Scholar 

  • Harushima Y, Kurata N, Yano M, Nagamura Y, Sasaki T, Minobe Y, Nakagara M (1996) Detection of segregation distortions in an indica–japonica rice cross using a high-resolution molecular map. Theor Appl Genet 92:145–190

    Article  CAS  Google Scholar 

  • Harushima Y, Nakagahra M, Yano M, Sasaki M, Sasaki T, Kurata N (2002) Diverse variation of reproductive barriers in three intraspecific rice crosses. Genetics 160:313–322

    PubMed  Google Scholar 

  • Heinrichs EA, Medrano FG, Rapusas HR (1985) Genetic evaluation for insect resistance in rice. International Rice Research Institute, Manila

    Google Scholar 

  • Hittalmani S, Huang N, Courtois B, Venuprasad R, Shashidhar HE, Zhuang JY, Zheng KL, Liu GF, Wang GC, Sidhu JS, Srivantaneeyakul S, Singh VP, Bagali PG, Prasanna HC, McLaren G, Khush GS (2003) Identification of QTL for growth- and grain yield-related traits in rice across nine locations of Asia. Theor Appl Genet 107:679–690

    Article  PubMed  Google Scholar 

  • International Rice Genome Sequencing Project (IRGSP) (2005) The map-based sequence of the rice genome. Nature 436:793–800

    Article  Google Scholar 

  • Ishii T, Brar DS, Multani DS, Khush GS (1994) Molecular tagging of genes for brown planthopper resistance and earliness introduced from Oryza australiensis into cultivated rice, O. sativa. Genome 37:217–221

    CAS  Google Scholar 

  • Ishimaru K (2003) Identification of a locus increasing rice yield and physiological analysis of its function. Plant Physiol 133:1083–1090

    Article  PubMed  CAS  Google Scholar 

  • Jena KK, Kochert G (1991) Restriction fragment fragment polymorphism analysis of CCDD genome species of the genus Oryza L. Plant Mol Biol 5:109–118

    Google Scholar 

  • Jena KK, Khush GS, Kochert G (1992) RFLP analysis of rice (Oryza sativa L) introgression lines. Theor Appl Genet 84:608–616

    Article  Google Scholar 

  • Jena KK, Pasalu IC, Rao YK, Varalaxmi Y, Krishnaiah K, Khush GS, Kochert G (2003) Molecular tagging of a gene for resistance to brown planthopper in rice (Oryza sativa L). Euphytica 129:81–88

    Article  CAS  Google Scholar 

  • Juliano BO (1971) A simplified assay for milled-rice amylose. Cereal Sci Today 16:334–360

    Google Scholar 

  • Kim YK, Kim YJ, Choi HC, Han SS (1995) Inheritance of leaf blast reactions to four races of blast fungus in segregating populations of eight rice crosses (In Korean). RDA J Agric Sci 37:283–298

    Google Scholar 

  • Kwon SJ, Ahn SN, Hong HC, Cho YC, Suh JP, Kim YK, Kang KH, Han SS, Choi HC, Moon HP, Hwang HG (2002) Identification of DNA markers linked to resistance genes to rice blast (Pyricularia grisea Sacc). Korean J Breed 34:105–110

    Google Scholar 

  • Li JM, Thomson M, McCouch SR (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 

  • Liu G, Lu G, Zeng L, Wang G-L (2002) Two broad-spectrum blast resistance genes, Pi9(t) and Pi2(t), are physically linked on rice chromosome 6. Mol Genet Genomics 267:472–480

    Article  PubMed  CAS  Google Scholar 

  • McCouch SR, Doerge RW (1995) QTL mapping in rice. Trends Genet 11:482–487

    Article  PubMed  CAS  Google Scholar 

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

  • Mei HW, Luo LJ, Ying CS, Wang YP, Yu XQ, Guo LB, Paterson AH, Li ZK (2003) Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two testcross populations. Theor Appl Genet 107:89–101

    PubMed  CAS  Google Scholar 

  • Moncada P, Martínez CP, Borrero J, Chatel M, Gauch Jr H, Guimarães E, Tohme J, McCouch SR (2001) Quantitative trait loci for yield and yield components in an Oryza sativa ( Oryza rufipogon BC2F2 population evaluated in an upland environment. Theor Appl Genet 102:41–52

    Article  CAS  Google Scholar 

  • Nelson JC (1997) QGENE: software for marker-based genome analysis and breeding. Mol Breed 3:239–245

    Article  CAS  Google Scholar 

  • Nguyen BD, Brar DS, Bui BC, Nguyen TV, Pham LN, Nguyen HT (2003) Identification and mapping of the QTL for aluminum tolerance introgressed from the new source, Oryza rufipogon Griff. into indica rice (O. sativa L). Theor Appl Genet 106:583–593

    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 

  • Paterson AH, DeVerna JW, Lanini B, Tanksley SD (1990) Fine mapping of quantitative trait loci using selected overlapping recombinant chromosomes in an interspecies cross of tomato. Genetics 124:735-742

    PubMed  CAS  Google Scholar 

  • Ryu JD, Yeh WH, Han SS, Lee YH, Lee EJ (1987) Regional and annual fluctuation of races of Pyricularia oryzae during 1977–1985 in Korea. Korean J Plant Pathol 3:174–179

    Google Scholar 

  • Sasaki A, Ashikari M, Ueguchi-Tanaka M, Itoh H, Nishimura A, Swapan D, Ishiyama K, Saito T, Kobayashi M, Khush GS, Kitano H, Matsuoka M (2002) Green revolution: a mutant gibberellin-synthesis gene in rice. Nature 416:701–702

    Article  PubMed  CAS  Google Scholar 

  • Septiningsih EM, Prasetiyono J, Lubis ET, Tai TH, Tjubaryat T, Moeljopawiro S, McCouch SR (2003a) Molecular marker detection of rice (Oryza sativa L) plant architecture under temperate and tropical climates. Theor Appl Genet 107:1350–1356

    Article  CAS  Google Scholar 

  • Septiningsih EM, Trijatmiko KR, Moeljopawiro S, McCouch SR (2003b) Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O rufipogon. Theor Appl Genet 107:1419–1432

    Article  CAS  Google Scholar 

  • Tanksley SD (1993) Mapping polygenes. Annu Rev Genet 27:205–233

    Article  PubMed  CAS  Google Scholar 

  • Temnykh S, Cartinhour S, Park W, Ayres N, Hauck N, Lipovich L, Cho YG, 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 

  • Temnykh S, De Clerck G, Lukashova A, Lipovitch L, Cartinhour S, McCouch SR (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

    Article  PubMed  CAS  Google Scholar 

  • Thomson MJ, Tai TH, McClung AM, Lai XH, Hinga ME, Lobos KB, Xu Y, Martinez CP, McCouch SR (2003) Mapping quantitative trait loci for yield components and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson. Theor Appl Genet 107:479–493

    Article  PubMed  CAS  Google Scholar 

  • Vaughan DA, Morishima H, Kadowaki K (2003) Diversity in the Oryza genus. Curr Opin Plant Biol 6:139–146

    Article  PubMed  CAS  Google Scholar 

  • Wang ZY, Second G, Tanksley SD (1992) Polymorphism and phylogenetic relationships among species in the genus Oryza as determined by analysis of nuclear RFLPs. Theor Appl Genet 83:565–581

    Article  Google Scholar 

  • Williams VR, Wu WT, Tsai HY, Bates HG (1958) Varietal differences in amylase content of rice starch. J Agric Food Chem 8:47–48

    Article  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 cross. Theor Appl Genet 92:230–244

    Article  CAS  Google Scholar 

  • Xiao J, Li J, Grandillo S, Ahn SN, Yuan L, 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 

  • Xiong LZ, Liu KD, Dai XK, Xu CG, 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 

  • Xu Y, Zhu L, Xiao J, Huang N, McCouch SR (1997) Chromosomal regions associated with segregation distortion of molecular markers in F2, backcross, doubled haploid, and recombinant inbred populations in rice (Oryza sativa L). Mol Gen Genet 253:535–545

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y, Sasaki T (2000) Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12:2473–2484

    Article  PubMed  CAS  Google Scholar 

  • Yu GJ, Kwak TS, Kang KH, Moon HP (1997) Efficiency of backcrossing and ovule culture in an interspecific cross between O sativa L and O grandiglumis. Prod Korean J Breed 29:448–452

    Google Scholar 

Download references

Acknowledgements

This study was supported by grants from the Bio Green 21 project of the Rural Development Administration and from the Crop Functional Genomics Center of the 21st Century Frontier Research Program (Project code no. CG3112) funded by the Ministry of Science and Technology, Republic of Korea.

Author information

Authors and Affiliations

  1. Department of Agronomy, College of Agriculture & Life Sciences, Chungnam National University, 305-764, Daejeon, Korea

    D.-B. Yoon, H.-J. Kim, H.-G. Ju & S.-N. Ahn

  2. National Institute of Crop Science, RDA, 441-100, Suwon, Korea

    K.-H. Kang, J.-P. Suh & O.-Y. Jeong

  3. National Institute of Agricultural Biotechnology, RDA, 441-707, Suwon, Korea

    S.-J. Kwon

Authors
  1. D.-B. Yoon
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. K.-H. Kang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. H.-J. Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. H.-G. Ju
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. S.-J. Kwon
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. J.-P. Suh
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. O.-Y. Jeong
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. S.-N. Ahn
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to S.-N. Ahn.

Additional information

Communicated by Q. Zhang

Rights and permissions

Reprints and permissions

About this article

Cite this article

Yoon, DB., Kang, KH., Kim, HJ. et al. Mapping quantitative trait loci for yield components and morphological traits in an advanced backcross population between Oryza grandiglumis and the O. sativa japonica cultivar Hwaseongbyeo. Theor Appl Genet 112, 1052–1062 (2006). https://doi.org/10.1007/s00122-006-0207-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-006-0207-4

Keywords

Search

Navigation