Theoretical and Applied Genetics

, Volume 116, Issue 5, pp 715–722 | Cite as

Detection of quantitative trait loci controlling extremely early heading in rice

  • Y. Nonoue
  • K. Fujino
  • Y. Hirayama
  • U. Yamanouchi
  • S. Y. Lin
  • M. Yano
Original Paper


To clarify the genetic basis of extremely early heading in rice, we conducted quantitative trait locus (QTL) analyses using F2 populations from two genetically wide cross combinations, Hayamasari/Kasalath (HaF2) and Hoshinoyume/Kasalath (HoF2). Hayamasari and Hoshinoyume are extremely early-heading japonica cultivars. Photoperiod sensitivity is completely lost in Hayamasari and weak in Hoshinoyume. Three QTLs, QTL(chr6), QTL(chr7), and QTL(chr8), for days-to-heading (DTH) in HaF2 were detected on chromosomes 6, 7, and 8, respectively, and QTL(chr6) and QTL(chr7) were detected in HoF2. On the basis of the chromosomal locations, QTL(chr6), QTL(chr7), and QTL(chr8) may be likely to be Hd1, Hd4, and Hd5, respectively, which had been detected previously as QTLs for DTH in an F2 population of Nipponbare × Kasalath. Alleles of QTL(chr7) decreased DTH dramatically in both Hayamasari and Hoshinoyume, suggesting that QTL(chr7) has a major role in determining extremely early heading. In addition, allele-specific interactions were detected between QTL(chr6), QTL(chr7) and QTL(chr8). This result suggests that not only allelic differences but also epistatic interactions contribute to extremely early heading. QTL(chr8) was detected in HaF2, but not in HoF2, suggesting that it determines the difference in DTH between Hayamasari and Hoshinoyume. A major QTL was also detected in the region of QTL(chr8) in QTL analysis using an F2 population of Hayamasari × Hoshinoyume. This result supports the idea that QTL(chr8) is a major factor that determines the difference in DTH between Hayamasari and Hoshinoyume, and is involved in photoperiod sensitivity.


Quantitative Trait Locus Quantitative Trait Locus Analysis Quantitative Trait Locus Mapping Epistatic Interaction Photoperiod Sensitivity 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



We thank Dr. Harumi Kikuchi, Hokkaido Central Agricultural Experiment Station, for providing seeds of Hoshinoyume and Hayamasari. This work was supported by the Agri-Bio Project (IP-1001) of the Ministry of Agriculture, Forestry and Fisheries of Japan.


  1. Basten CJ, Weir BS, Zeng ZB (2005) QTL cartographer, ver. 1.17. Department of Statistics, North Carolina State University, RaleighGoogle Scholar
  2. Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971PubMedGoogle Scholar
  3. Doi K, Izawa T, Fuse T, Yamanouchi U, Kubo T, Shimatani Z, Yano M, Yoshimura A (2004) Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1. Genes Dev 18:926–936CrossRefPubMedGoogle Scholar
  4. Fujino K (2003) Photoperiod sensitivity genes controlling heading date in rice cultivars in the northernmost region of Japan. Euphytica 131:97–103CrossRefGoogle Scholar
  5. Fujino K, Sekiguchi H (2005a) Identification of QTLs conferring genetic variation for heading date among rice varieties at the northern-limit of rice cultivation. Breed Sci 55:141–146CrossRefGoogle Scholar
  6. Fujino K, Sekiguchi H (2005b) Mapping of QTLs conferring extremely early heading in rice (Oryza sativa L.). Theor Appl Genet 111:393–398CrossRefPubMedGoogle Scholar
  7. 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 108:794–799CrossRefPubMedGoogle Scholar
  8. Gu XY, Foley ME (2007) Epistatic interaction of three loci regulate flowering time under short and long daylengths in a backcross population of rice. Theor Appl Genet 114:745–754CrossRefPubMedGoogle Scholar
  9. Harushima Y, Yano M, Shomura A, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY, Antonio BA, Parco A, Kajiya H, Huang N, Yamamoto K, Nagamura Y, Kurata N, Khush GS, Sasaki T (1998) A high-density rice genetic linkage map with 2,275 markers using a single F2 population. Genetics 148:479–494PubMedGoogle Scholar
  10. Hayama R, Coupland G (2004) The molecular basis of diversity in the photoperiodic flowering responses of Arabidopsis and rice. Plant Physiol 135:677–684CrossRefPubMedGoogle Scholar
  11. Ichitani K, Okumoto Y, Tanisaka T (1997) Photoperiod sensitivity gene of Se-1 locus in photoperiod insensitive rice cultivars of the northern limit region of rice cultivation. Breed Sci 47:145–152Google Scholar
  12. Ichitani K, Okumoto Y, Tanisaka T (1998a) Genetic analyses of low photoperiod sensitivity of rice cultivars from the northernmost regions of Japan. Plant Breed 117:543–547CrossRefGoogle Scholar
  13. Ichitani K, Okumoto Y, Tanisaka T (1998b) Genetic analyses of the rice cultivar Kasalath with special reference to two photoperiod sensitivity loci, E1 and Se-1. Breed Sci 48:51–57Google Scholar
  14. Izawa T, Takahashi Y, Yano M (2003) Comparative biology comes to bloom: genomic and genetic comparison of flowering pathways in rice and Arabidopsis. Curr Opin Plant Biol 6:113–120CrossRefPubMedGoogle Scholar
  15. Kojima S, Takahashi Y, Kobayashi Y, Monna L, Sasaki T, Araki T, Yano M (2002) Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions. Plant Cell Physiol 43(10):1096–1105CrossRefPubMedGoogle Scholar
  16. Kurata N, Nagamura Y, Yamamoto K, Harushima Y, Sue N, Wu J, Antonio BA, Shomura A, Shimizu T, Lin SY, Inoue T, Fukuda A, Shimano T, Kuboki Y, Toyama T, Miyamoto Y, Kirihara T, Hayasaka H, Miyao A, Monna L, Zhong HS, Tamura Y, Wang ZX, Momma T, Umehara Y, Yano M, Sasaki T, Minobe Y (1994) A 300-kilobase-interval genetic map of rice including 883 expressed sequences. Nature Genet 8:365–372CrossRefPubMedGoogle Scholar
  17. Lander ES, Green P, Abrahamson J, Barlow A, Daley MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181CrossRefPubMedGoogle Scholar
  18. 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 101:1021–1028CrossRefGoogle Scholar
  19. Lin HX, Liang ZW, Sasaki T, Yano M (2003) Fine mapping and characterization of quantitative trait loci Hd4 and Hd5 controlling heading date in rice. Breed Sci 53:51–59CrossRefGoogle Scholar
  20. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325CrossRefPubMedGoogle Scholar
  21. Okumoto Y, Ichitani K, Inoue H, Tanisaka T (1996) Photoperiod insensitivity gene essential to the varieties grown in the northern limit region of paddy rice. Euphytica 92:63–66CrossRefGoogle Scholar
  22. Rice Genome Research Program (2007) The latest high-density rice genetic map, including 3,267 markers.
  23. Sasaki T (2003) Rice genome analysis: understanding the genetic secrets of the rice plant. Breed Sci 53:281–289CrossRefGoogle Scholar
  24. Takahashi Y, Shomura A, Sasaki T, Yano M (2001) Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the α subunit of protein kinase CK2. Proc Natl Acad Sci USA 98:7922–7927CrossRefPubMedGoogle Scholar
  25. Uga Y, Nonoue Y, Liang ZW, Lin HX, Yamamoto S, Yamanouchi U, Yano M (2007) Accumulation of additive effects generates a strong photoperiod sensitivity in the extremely late-heading rice cultivar ‘Nona Bokra’. Theor Appl Genet 114:1457–1466CrossRefPubMedGoogle Scholar
  26. Yamamoto T, Kuboki Y, Lin SY, Sasaki T, Yano M (1998) Fine mapping of quantitative trait loci Hd-1, Hd-2 and Hd-3, controlling heading date of rice, as single Mendelian factors. Theor Appl Genet 97:37–44CrossRefGoogle Scholar
  27. Yamamoto T, Lin HX, Sasaki T, Yano M (2000) Identification of heading date quantitative trait locus Hd6 and characterization of its epistatic interactions with Hd2 in rice using advanced backcross progeny. Genetics 154:885–891PubMedGoogle Scholar
  28. Yano M, Harushima Y, Nagamura Y, Kurata N, Minobe Y, Sasaki T (1997) Identification of quantitative trait loci controlling heading date in rice using a high-density linkage map. Theor Appl Genet 95:1025–1032CrossRefGoogle Scholar
  29. 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 12:2473–2484CrossRefPubMedGoogle Scholar
  30. Yano M, Kojima S, Takahashi Y, Lin HX, Sasaki T (2001) Genetic control of flowering time in rice, a short-day plant. Plant Physiol 127:1425–1429CrossRefPubMedGoogle Scholar
  31. Zeng Z (1993) Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci. Proc Natl Acad Sci USA 90:10972–10976CrossRefPubMedGoogle Scholar
  32. Zeng Z (1994) Precision mapping of quantitative trait loci. Genetics 136:1457–1468PubMedGoogle Scholar

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Y. Nonoue
    • 1
  • K. Fujino
    • 2
  • Y. Hirayama
    • 3
    • 5
  • U. Yamanouchi
    • 4
  • S. Y. Lin
    • 1
    • 6
  • M. Yano
    • 4
  1. 1.Institute of Society for Techno-innovation of Agriculture, Forestry and FisheriesTsukubaJapan
  2. 2.Hokuren Agricultural Research InstituteNaganuma, YubariJapan
  3. 3.Hokkaido Prefectural Kamikawa Agricultural Experiment StationPippu, KamikawaJapan
  4. 4.National Institute of Agrobiological SciencesTsukubaJapan
  5. 5.Hokkaido Central Agricultural Experiment StationIwamizawaJapan
  6. 6.Honda Research Institute Japan Co., LtdKisarazuJapan

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