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QTL × environment interactions in rice. I. Heading date and plant height

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Abstract

One hundred twenty six doubled-haploid (DH) rice lines were evaluated in nine diverse Asian environments to reveal the genetic basis of genotype × environment interactions (GEI) for plant height (PH) and heading date (HD). A subset of lines was also evaluated in four water-limited environments, where the environmental basis of G × E could be more precisely defined. Responses to the environments were resolved into individual QTL × environment interactions using replicated phenotyping and the mixed linear-model approach. A total of 37 main-effect QTLs and 29 epistatic QTLs were identified. On average, these QTLs were detectable in 56% of the environments. When detected in multiple environments, the main effects of most QTLs were consistent in direction but varied considerably in magnitude across environments. Some QTLs had opposite effects in different environments, particularly in water-limited environments, indicating that they responded to the environments differently. Inconsistent QTL detection across environments was due primarily to non- or weak-expression of the QTL, and in part to significant QTL × environment interaction effects in the opposite direction to QTL main effects, and to pronounced epistasis. QTL × environment interactions were trait- and gene-specific. The greater GEI for HD than for PH in rice were reflected by more environment-specific QTLs, greater frequency and magnitude of QTL × environment interaction effects, and more pronounced epistasis for HD than for PH. Our results demonstrated that QTL × environment interaction is an important property of many QTLs, even for highly heritable traits such as height and maturity. Information about QTL × environment interaction is essential if marker-assisted selection is to be applied to the manipulation of quantitative traits.

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References

  • Austin DF, Lee M (1998) Detection of quantitative trait loci for grain yield and yield components in maize across generations in stress and nonstress environments. Crop Sci 38:1296–1308

    CAS  Google Scholar 

  • Baker RJ (1988) Differential response to environmental stress. In: Weir BS, Eisen EJ, Goodman MM, Namkoong G (eds) Proc 2nd Int Conf on Quantitative Genetics. Sinauer, Sunderland, Massachusetts, pp 492–504

  • Bubeck DM, Goodman MM, Beavis WD, Grant D (1993) Quantitative trait loci controlling resistance to gray leaf spot in maize. Crop Sci 33:838–847

    Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Cooper M, Hammer GL (1996) Plant adaptation and crop improvement. CAB International, Oxon, UK

  • Courtois B, Huang N, Guiderdoni E (1995) RFLP mapping of genes controlling yield components and plant height in an indica × japonica doubled-haploid population. In: Proc Int Rice Research Conf, Los Baños, The Philippines, pp 963–976

  • Crossa J, Vargas M Van Eeuwijk FA, Jiang C, Edmeades GO, Hoisington D (1999) Interpreting genotype × environment interaction in tropical maize using linked molecular markers and environmental covariables. Theor Appl Genet 99:611–625

    Article  Google Scholar 

  • Doebley J, Stec A, Gustus C (1995) teosinte branched l and the origin of maize: evidence for epistasis and the evolution of dominance. Genetics 141:333–346

    CAS  PubMed  Google Scholar 

  • Falconer DS (1981) Introduction to quantitative genetics, 2nd edn. London and New York

  • Georges M (1997) Case history in animal improvement: mapping complex traits in ruminants. In: Paterson AH (ed) Molecular dissection of complex traits. , CRC Press, Boca Raton, Florida, USA, pp 229–240

  • Hayes PM, Liu BH, Knapp SJ, Chen F, Jones B (1993) Quantitative trait loci effects and environmental interaction in a sample of North American barley germplasm. Theor Appl Genet 87:392–401

    Google Scholar 

  • Huang N, McCouch S, Mew T, Parco A, Guiderdoni E (1994) Development of an RFLP map from a doubled-haploid population in rice. Rice Genet Newslett 11:134–137

    Google Scholar 

  • Huang N, Courtois B, Khush GS, Lin H, Wang G (1996) Association of quantitative trait loci for plant height with major dwarfing genes in rice. Heredity 77:130–137

    CAS  Google Scholar 

  • Huang N, Parco A, Mew T, Magpantay G, McCouch S (1997) RFLP mapping of isozymes, RAPD and QTLs for grain shape and brown plant hopper resistance in a doubled-haploid rice population. Mol Breed 3:105–113

    CAS  Google Scholar 

  • Jain SK, Marshall DR (1967) Population studies in predominantly self-pollinated species. X. Variation in natural populations of Avena fatua and A. barbata. Am Nat 101:19–33

    Article  Google Scholar 

  • Jiang C, Edmeades GO, Armstead I, Laffite HR, Hayward MD (1999) Genetic analysis of adaptation difference between highland and lowland tropical maize using molecular markers. Theor Appl Genet 99:1106–1119

    Article  CAS  Google Scholar 

  • Lark KG, Chase K, Adler F, Mansur LM, Orf JH (1995) Interactions between quantitative trait loci in soybean in which trait variation at one locus is conditional upon a specific allele at another. Proc Natl Acad Sci USA 92:4656–4660

    CAS  PubMed  Google Scholar 

  • Lee SH, Bailey MA, Mian MAR, Carter TE, Ashley Jr DA, Hussey RS, Parrott WA, Boerma HR (1996) Molecular markers associated with soybean plant height, lodging, and maturity across locations. Crop Sci 36:728–735

    CAS  Google Scholar 

  • Li ZK, Pinson SRM, Stansel JW, Park WD (1995) Identification of quantitative trait loci (QTLs) for heading date and plant height in cultivated rice (Oryza sativa L.). Theor Appl Genet 91:374–381

    CAS  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Li ZK, Luo LJ, Mei HW, Shu QY, Wang DL (2001) Overdominant epistatic loci are the primary basis of inbreeding depression and heterosis in rice. I. Biomass and grain yield. Genetics 158:1737–1753

    CAS  PubMed  Google Scholar 

  • Lin HX, Yamamoto T, Sasaki T, Yano M (2000) Characterization and detection of epistatic interactions of three QTLs, Hd1, Hd2 and Hd3, controlling heading date in rice using nearly isogenic lines. Theor Appl Genet 101:1021–1028

    CAS  Google Scholar 

  • Luo LJ, Li ZK, Mei HW, Shu QY, Tabien R (2001) Overdominant epistatic loci are the primary basis of inbreeding depression and heterosis in rice. II. Grain yield components. Genetics 158:1755–1771

    CAS  PubMed  Google Scholar 

  • Lu CL, Shen L, Tan Z, Xu Y, He P (1996) Comparative mapping of QTLs for agronomy traits of rice across environments using a doubled-haploid population. Theor Appl Genet 93:1211–1217

    CAS  Google Scholar 

  • Mather K, Jinks JL (1982) Biometrical genetics, Chapman and Hall, London

  • Paterson AH (1995) Molecular dissection of quantitative traits: progress and prospects. Genome Res 5:321–333

    CAS  PubMed  Google Scholar 

  • Paterson AH, Damon S, Hewitt JD, Zamir D, Rabinowitch HD (1991) Mendelian factors underlying quantitative traits in tomato: comparison across species, generations, and environments. Genetics 127:181–197

    CAS  PubMed  Google Scholar 

  • SAS institute Inc (1996) SAS users guide: statistics. SAS Institute, Cary, North Carolina

    Google Scholar 

  • Sripongpangkul K, Posa GBT, Senadhira DW, Brar DS, Huang N, Khush GS, Li ZK (2000) Genes/QTLs affecting flood tolerance in rice. Theor Appl Genet 101:1074–1081

    Article  CAS  Google Scholar 

  • Stuber CW (1997) Case history in crop improvement: yield heterosis in maize. In: Paterson AH (ed) Molecular dissection of complex traits. CRC Press, Boca Raton, Florida, USA, pp 197–206

  • Tinker NA, Mather DE, Rossnagel BG, Kasha KJ, Kleiohofs A (1996) Regions of the genome that affect agronomic performance in two barley cultivars. Crop Sci 36:1053–1062

    Google Scholar 

  • Veldboom LR, Lee M (1996) Genetic mapping of quantitative trait loci in maize in stress and nonstress environments. I. Grain yield and yield components. Crop Sci 36:1310–1319

    CAS  Google Scholar 

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

    Article  Google Scholar 

  • Xiao JH, Li J, Yuan L, Tanksley SD (1995) Dominance is the major genetic basis of heterosis in rice as revealed by QTL analysis using molecular markers. Genetics 140:745–754

    CAS  PubMed  Google Scholar 

  • Xiao JH, Li J, Yuan L, Tanksley SD (1996) Identification of QTLs affecting traits of agronomic importance in a recombinant inbred population derived from a subspecific rice cross. Theor Appl Genet 92:230–244

    Article  CAS  Google Scholar 

  • Yan JQ, 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 

  • Yan JQ, Zhu J, He C, Benmoussa M, Wu P (1999) Molecular marker-assisted dissection of genotype × environment interaction for plant type traits in rice (Oryza sativa L.). Crop Sci 39:538–544

    Google Scholar 

  • Yano M, Marushima Y, Nagamura Y, Kurata N, Minobe Y (1997) Identification of quantitative trait loci controlling heading date in rice using a high-density linkage map. Theor Appl Genet 95:1025–1032

    Google Scholar 

  • Yu SB, Li JX, Xu CG, Gao YF, Li XH (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 

  • Zhou Y, Li W, Wu W, Chen Q, Mao D (2001) Genetic dissection of heading time and its components in rice. Theor Appl Genet 102:1236–1242

    CAS  Google Scholar 

  • Zhu J, Weir B (1996) Mixed model approaches for dialelle analysis based on a bio-model. Genet Res Cambridge 68:233–240

    CAS  Google Scholar 

  • Zhuang JY, Lin HX, Lu J, Qian HR, Hittalmani S, Huang N, Zheng KL (1997) Analysis of QTL × environment interaction for yield components and plant height in rice. Theor Appl Genet 95:799–808

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We are very grateful for valuable comments and suggestions on the manuscript from Dr. Wenzel and two anonymous reviewers. We also thank B. Hardy for his help in editorial work of the MS. Financial support from a BMZ/GTZ grant of the German government and from the Rockefeller Foundation is greatly appreciated.

Author information

Author notes

  1. S. B. Yu

    Present address: National Key Laboratory for Crop Improvement, Huazhong Agricultural University, Wuhan, China

  2. N. Huang

    Present address: Applied Phytologics Incorporated, Sacramento, California, USA

  3. B. Courtois

    Present address: CIRAD-Biotrop, 34398 , Montpellier Cedex 5, France

Authors and Affiliations

  1. Plant Breeding, Genetics, and Biochemistry Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines

    Z. K. Li, S. B. Yu, H. R. Lafitte, N. Huang, B. Courtois, S. Hittalmani, C. H. M. Vijayakumar & G. S. Khush

  2. University of Agricultural Sciences, GKVK, 560 065, Bangalore, India

    S. Hittalmani

  3. South China Agricultural University, Guangzhou, China

    G. F. Liu

  4. Indian Agricultural Research Institute, New Delhi, India

    H. E. Shashidhar

  5. China National Rice Research Institute, Hangzhou, China

    G. C. Wang, J. Y. Zhuang & K. L. Zheng

  6. Punjab Agricultural University, Ludhiana, India

    V. P. Singh

  7. Rice Research Institute, Bangkok, Thailand

    J. S. Sidhu & S. Srivantaneeyakul

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  1. Z. K. Li
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Correspondence to Z. K. Li.

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Communicated by G. Wenzel

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Li, Z.K., Yu, S.B., Lafitte, H.R. et al. QTL × environment interactions in rice. I. Heading date and plant height. Theor Appl Genet 108, 141–153 (2003). https://doi.org/10.1007/s00122-003-1401-2

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  • DOI: https://doi.org/10.1007/s00122-003-1401-2

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