Skip to main content
SpringerLink
Log in

Identification of main effects, epistatic effects and their environmental interactions of QTLs for yield traits in rice

  • Research Article
  • Published:
Genes & Genomics Aims and scope Submit manuscript

Abstract

Quantitative trait loci (QTLs) controlling yield and yield components were identified by using a doubled haploid (DH) population of 120 lines from a sub-specific cross between ‘Samgang’ (Indica) and ‘Nagdong’ (Japonica). Main effects, epistatic effects, their environment interactions of QTLs were analyzed via mixed linear model approach across different environments. A total of 17 putative QTLs were identified on 8 chromosomes and five QTLs were detected over two years. 7 QTLs of main effects and 23 epistatic interactions were observed for five traits. Epistatic interactions played an important role in controlling the expression of yield related traits. The epistatic effects explained higher percentages of phenotype variation for panicles per plant, seed set percentage and yield. Significant QTL×environment (QE) interactions effects were identified for all traits, including 5 main effect QTLs. However, the present study failed to identify the significant interactions between epistatic loci containing main effect QTLs and the environment. The information provided in the present study could be used in the marker-assisted selection to enhance selection efficiency and to improve yield in 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

Similar content being viewed by others

References

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

    Article  CAS  PubMed  Google Scholar 

  • Basten CJ, Weir BS and Zeng ZB (2005) QTL Cartographer, version 1.17.

  • Beavis WD, Grant D, Albertsen M and Fincher R (1991) Quantitative trait loci for plant height in four maize populations and their associations with qualitative genetic loci. Theor. Appl. Genet. 83: 141–145.

    Article  Google Scholar 

  • Berke TG, Baenziger PS and Morris R (1992) Chromosomal Location of Wheat Quantitative Trait Loci Affecting Agronomic Performance of Seven Traits, Using Reciprocal Chromosome Substitutions. Crop Sci. 32: 621–627.

    Article  Google Scholar 

  • Brondani C, Rangel N, Brondani V and Ferreira E (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  CAS  PubMed  Google Scholar 

  • Burr B, Burr FA, Thompson KH, Albertson MC and Stuber CW (1988). Gene mapping with recombinant inbreds in maize. Genetics 118: 519–526.

    CAS  PubMed  Google Scholar 

  • Campbell BT, Baenziger PS, Gill KS, Eskridge KM, Budak H, Erayman M, Dweikat I and Yen Y (2003) Identification of QTLs and Environmental Interactions Associated with Agronomic Traits on Chromosome 3A of Wheat. Crop Sci. 43: 1493–1505.

    CAS  Google Scholar 

  • Cho YG, Kang HJ, Lee JS, Lee YT, Lim SJ, Gauch H, Eun MY and McCouch SR (2007) Identification of Quantitative Trait Loci in Rice for Yield, Yield Components, and Agronomic Traits across Years and Locations. Crop Sci. 47: 2403–2417.

    Article  Google Scholar 

  • Fasoulas AC and Allard RW (1962) Nonallelic Gene Interactions in the Inheritance of Quantitative Characters in Barley. Genetics 47: 899–907.

    CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Ge XJ, Xing YZ, Xu CG and He YQ (2005) QTL analysis of cooked rice grain elongation, volume expansion, and water absorption using a recombinant inbred population. Plant Breed. 124: 121–126.

    Article  CAS  Google Scholar 

  • Guo LB, Xing YZ, Mei HW, Xu CG, Shi CH, Wu P and Luo LJ (2005) Dissection of component QTL expression in yield formation in rice. Plant Breed. 124: 127–132.

    Article  CAS  Google Scholar 

  • Hua JP, Xing YZ, Wu WR, Xu CG, Sun XL, Yu SB and Zhang QF (2003) Single-locus heterotic effects and dominance by dominance interactions can adequately explain the genetic basis of heterosis in an elite rice hybrid. Proc. Natl. Acad. Sci. USA 100: 2574–2579.

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Kato K, Miura H and Sawada S (2000) Mapping QTLs controlling grain yield and its components on chromosome 5A of wheat. Theor. Appl. Genet. 101: 1114–1121.

    Article  CAS  Google Scholar 

  • Kobayashi S, Fukuta Y, Yagi T, Sato T, Osaki M and Khush GS (2004) Identification and characterization of quantitative trait loci affecting spikelet number per panicle in rice (Oryza sativa L.). Field Crops Res. 89: 253–262.

    Article  Google Scholar 

  • Lee SJ, Oh CS, Suh JP, McCouch SR and Ahn SN (2005) Identification of QTLs for domestication-related and agronomic traits in an Oryza sativa×O. rufipogon BC1F7 population. Plant Breed. 124: 209–219.

    Article  CAS  Google Scholar 

  • Li ZK, Pinson SR, Park WD, Paterson AH and Stansel JW (1997) Epistasis for three grain yield components in rice (Oryza sativa L.). Genetics 145: 453–465.

    CAS  PubMed  Google Scholar 

  • Liang F, Deng Q, Wang Y, Xiong Y, Jin D, Li J and Wang B (2004) Molecular marker-assisted selection for yield-enhancing genes in the progeny of “9311×O. rufipogon” using SSR. Euphytica 139: 159–165.

    Article  CAS  Google Scholar 

  • Lin HX, Qian HR, Zhuang JY, Lu J, Min SK, Xiong ZM, Huang N and 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 

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

  • Liu G, Zhang Z, Zhu H, Zhao F, Ding X, Zeng R, Li W and Zhang G (2008) Detection of QTLs with additive effects and additive-by-environment interaction effects on panicle number in rice (Oryza sativa L.) with single-segment substitution lines. Theor. Appl. Genet. 116: 923–931.

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Moncada P, Martinez CP, Borrero J, Chatel M, Gauch H, Guimaraes E, Tohme J and 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 

  • Nagata K, Fukuta Y, Shimizu H, Yagi T and Terao T (2002) Quantitative Trait Loci for Sink Size and Ripening Traits in Rice (Oryza sativa L.). Breed. Sci. 52: 259–273.

    Article  CAS  Google Scholar 

  • Paterson A, Damon S, Hewitt J, Zamir D, Rabinowitch H, Lincoln S, Lander E and Tanksley SD (1991) Mendelian factors underlying quantitative traits in tomato: comparison across species, generations, and environments. Genetics 127: 181–197.

    CAS  PubMed  Google Scholar 

  • Paterson AH, Lander ES, Hewitt JD, Peterson S, Lincoln SE and Tanksley SD (1988) Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature 335: 721–726.

    Article  CAS  PubMed  Google Scholar 

  • Qin Y, Kim SM and Sohn JK (2008) Detection of main effect QTLs, epistatic QTLs and QE interactions for grain appearance of brown rice (Oryza sativa L.). J. Crop Sci. Biotech. 11: 151–156.

    Google Scholar 

  • Rahman ML, Chu SH, Choi MS, Qiao YL, Jiang W, Piao R, Khanam S, Cho YI, Jeung J, Jena KK, et al. (2007) Identification of QTLs for some agronomic traits in rice using an introgression line from Oryza minuta. Mol. Cells 24: 16–26.

    CAS  PubMed  Google Scholar 

  • Redoña ED and Mackill DJ (1998) Quantitative trait locus analysis for rice panicle and grain characteristics. Theor. Appl. Genet. 96: 957–963.

    Article  Google Scholar 

  • Roeder MIS, Huang XQ and Boerner A (2008) Fine mapping of the region on wheat chromosome 7D controlling grain weight. Funct. Integr. Genomics 8: 79–86.

    Article  CAS  Google Scholar 

  • Song XJ, Huang W, Shi M, Zhu MZ and Lin HX (2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat. Genet. 39: 623–630.

    Article  CAS  PubMed  Google Scholar 

  • Tan LB, Zhang PJ, Liu FX, Wang GJ, Ye S, Zhu ZF, Fu YC, Cai HW and Sun CQ (2008) Quantitative trait loci underlying domestication- and yield-related traits in an Oryza sativa×Oryza rufipogon advanced backcross population. Genome 51: 692–704.

    Article  CAS  PubMed  Google Scholar 

  • Tanksley SD and 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 

  • Thomson MJ, Tai TH, McClung AM, Lai XH, Hinga ME, Lobos KB, Xu Y, Martinez CP and McCouch SR (2003) Mapping quantitative trait loci for yield, 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  CAS  PubMed  Google Scholar 

  • Veldboom LR and Lee M (1994) Molecular-marker-facilitated studies of morphological traits in maize. II: Determination of QTLs for grain yield and yield components. Theor. Appl. Genet. 89: 451–458.

    Article  CAS  Google Scholar 

  • Wang DL, Zhu J, Li ZK and Paterson AH (1999) Mapping QTLs with epistatic effects and QTL×environment interactions by mixed linear model approaches. Theor. Appl. Genet. 99: 1255–1264.

    Article  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Xie X, Jin F, Song MH, Suh JP, Hwang HG, Kim YG, McCouch SR and Ahn SN (2008) Fine mapping of a yield-enhancing QTL cluster associated with transgressive variation in an Oryza sativa × O. rufipogon cross. Theor. Appl. Genet. 116: 613–622.

    Article  PubMed  Google Scholar 

  • Xing YZ, Tan YF, Hua JP, Sun XL, Xu CG and Zhang QF (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  CAS  PubMed  Google Scholar 

  • Xu JL, Yu SB, Luo LJ, Zhong DB, Mei HW and Li ZK (2004) Molecular dissection of the primary sink size and its related traits in rice. Plant Breed. 123: 43–50.

    Article  CAS  Google Scholar 

  • Yao FY, Xu CG, Yu SB, Li JX, Gao YJ, Li XH and Zhang QF (1997) Mapping and genetic analysis of two fertility restorer loci in the wild-abortive cytoplasmic male sterility system of rice (Oryza sativa L.). Euphytica 98: 183–187.

    Article  CAS  Google Scholar 

  • Yoon DB, Kang KH, Kim HJ, Ju HG, Kwon SJ, Suh JP, Jeong OY and Ahn SN (2006) 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.

    Article  CAS  PubMed  Google Scholar 

  • You A, Lu X, Jin H, Ren X, Liu K, Yang G, Yang H, Zhu L and He G (2006) Identification of quantitative trait loci across recombinant inbred lines and testcross populations for traits of agronomic importance in rice. Genetics 172: 1287–1300.

    Article  PubMed  Google Scholar 

  • Yu SB, Li JX, Xu CG, Tan YF, Gao YJ, Li XH, Zhang QF and 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.

    Article  CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Zhang ZH, Li P, Wang LX, Hu ZL, Zhu LH and Zhu YG (2004) Genetic dissection of the relationships of biomass production and partitioning with yield and yield related traits in rice. Plant Sci. 167: 1–8.

    Article  CAS  Google Scholar 

  • Zhuang JY, Fan YY, Rao ZM, Wu JL, Xia YW and Zheng KL (2002) Analysis on additive effects and additive-by-additive epistatic effects of QTLs for yield traits in a recombinant inbred line population of rice. Theor. Appl. Genet. 105: 1137–1145.

    Article  CAS  PubMed  Google Scholar 

  • Zhuang JY, Lin HX, Lu J, Qian HR, Hittalmani S, Huang N and Zheng KL (1997) Analysis of QTL×environment interaction for yield components and plant height in rice. Theor. Appl. Genet. 779: 799–808.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. School of Applied Biosicences, Kyungpook National University, Daegu, 702-701, Korea

    Xinhua Zhao, Yang Qin & Jae-Keun Sohn

Authors
  1. Xinhua Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yang Qin
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jae-Keun Sohn
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jae-Keun Sohn.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zhao, X., Qin, Y. & Sohn, JK. Identification of main effects, epistatic effects and their environmental interactions of QTLs for yield traits in rice. Genes Genom 32, 37–45 (2010). https://doi.org/10.1007/s13258-010-0786-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13258-010-0786-y

Keywords

Search

Navigation