Plant Molecular Biology Reporter

, Volume 29, Issue 3, pp 702–713 | Cite as

Fine Mapping of qHD4-1, a QTL Controlling the Heading Date, to a 20.7-kb DNA Fragment in Rice (Oryza sativa L.)

  • Binbin Wang
  • Changxiang Zhu
  • Xu Liu
  • Wenying Wang
  • Hanfeng Ding
  • Mingsong Jiang
  • Guangxian Li
  • Wei Liu
  • Fangyin Yao


A library consisting of 1,123 single-segment substitution lines (SSSLs) in the same genetic background of an elite rice variety Huajingxian74 (HJX74) was evaluated for heading date. From this library, the SSSL W05-1-11-5-16-2-5 with the substituted interval of PSM103—RM348-OSR15-PSM382-RM131-RM127—RM280 was found having a gene, which stably performed extreme late heading date which performed stable and late heading in the different environments of Shandong, Guangdong, and Hainan. To map the gene governing heading date, the SSSL W05-1-11-5-16-2-5 was crossed with the recipient HJX74 to develop an F2 segregating population. The distribution of late and early heading plants in this population fitted a segregation ratio of 3:1, indicating the late heading was controlled by a dominant gene. The gene locus for heading date was tentatively designated as qHD4-1. Using a random sample of 460 individuals from the F2 segregation population, the qHD4-1 locus was mapped between two SSR markers RM3335 and RM17572, with genetic distances of 0.1 and 0.2 cM, respectively. For fine mapping of qHD4-1, a large F2:3 segregating population of 3,000 individuals were developed from F2 plants heterozygous in the RM3335-RM17572 region. Recombinants analyses further mapped qHD4-1 to an interval of 20.7-kb-bounded WB05 and the WB06. Sequence analysis of this 20.7-kb region revealed that it contains three open reading frames (ORFs), encoding wall-associated receptor kinase-like 5, putative F-box domain containing protein, and putative arogenate/prephenate dehydratase. Of them, ORF1, predicting to encode serine/threonine kinase, is considered the most likely as the candidate gene. The genetic and physical map of the qHD4-1 locus will be very useful in molecular cloning of the qHD4-1gene.


Oryza sativa Heading date Single-segment substitution line (SSSL) Physical mapping Sequence information 



We are grateful to professor Zhang Guiquan, South China Agricultural University, Guangzhou for kindly providing us with the SSSL populations. This work was financially supported by the National High-Tech “863” Program of P.R. China (No. 2006AA100101), China Science and Technology Support Program (No. 2006BAD13B01-18), the High-Tech Innovation Foundation of Shandong Academy of Agricultural Science (No. 2007YCX007), the Open Foundation of the State Key Laboratory of Crop Biology, China (2009KF05, 2010KF07), and the National Program on Research and the Development of Transgenic Plants (No. 2008ZX08001-001, 2009ZX08001-010B)


  1. Chetelat RT, Meglic V, Cisneros P (2000) A genetic map of tomato based on BC1 Lycopersicon esculentum × Solanum lycopersicoides reveals overall synteny but suppressed recombination between these homeologous genomes. Genetics 154:857–867PubMedGoogle Scholar
  2. Doi K, Iwata N, Yoshimura A (1997) The construction of chromosome substitution lines of African rice (Oryza glaberrima Steud.) in the background of japonica rice (O. sativa L.). Rice Genet Newsl 14:39–41Google Scholar
  3. Doi K, Izawa T, Fuse T, Yamanouchi U, Kubo T, Shimatani Z, Yano M, Yoshimura (2004) A 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 18:926–936PubMedCrossRefGoogle Scholar
  4. Ebitani T, Takeuchi Y, Nonoue Y, Yamamoto T, Takeuchi K, Yano M (2005) Construction and evaluation of chromosome segment substitution lines carrying overlapping chromosome segments of indica rice cultivar ‘Kasalath’ in a genetic background of japonica elite cultivar ‘Koshihikari’. Breed Sci 55:65–73CrossRefGoogle Scholar
  5. Eshed Y, Zamir D (1995) An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL. Genetics 141:1147–1162PubMedGoogle Scholar
  6. Gebbie LK, Burn JE, Hocart CH, Williamson SE (2005) Genes encoding ADP-ribosylation factors in Arabidopsis thaliana L. Heyn.; genome analysis and antisense suppression. J Exp Bot 56:1079–1091PubMedCrossRefGoogle Scholar
  7. Griffiths S, Dunford RP, Coupland G, Lourie DA (2003) The evolution of CONSTAN-like gene families in barley, rice, and Arabidopsis. Plant Physiol 131:1855–1867PubMedCrossRefGoogle Scholar
  8. Guo S, Tian RX, Feng ZW, Zhao CF (2010) Cloning and expression analysis of the mooth-edge seed gene GSE-1 from Cucurbita pepo L. Plant Mol Biol Rep. doi: 10.1007/s11105-010-0253-6 Google Scholar
  9. He FH, Xi ZY, Zeng RZ, Tulukdar A, Zhang GQ (2005a) Mapping of heading date QTLs in rice (Oryza sativa L.) using single segment substitution lines. Scientia Agricultura Sinica 38:1505–1513, In ChineseGoogle Scholar
  10. He FH, Xi ZY, Zeng RZ, Tulukdar A, Zhang GQ (2005b) Identification of QTLs for plant height and its components by using single segment substitution lines in rice (Oryza sativa). Rice Sci 12(3):151–156Google Scholar
  11. Izawa T, Takahashi Y, Yano M (2003) Comparative biology comes into bloom: genomic and genetic comparison of flowering pathways in Rice and Arabidopsis. Curr Opin Plant Biol 6:113–120PubMedCrossRefGoogle Scholar
  12. Jeuken M, Lindhout P (2004) The development of lettuce backcross inbred lines (BILs) for exploitation of the Lactuca saligna (wild lettuce) germplasm. Theor Appl Genet 109:394–401PubMedCrossRefGoogle Scholar
  13. 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 condition. Plant Cell Physiol 43:1096–1105PubMedCrossRefGoogle Scholar
  14. Komiya R, Ikegami A, Tamaki S, Yokoi S, Shimamoto K (2008) Hd3a and RFT1 are essential for flowering in rice. Development 135:767–774PubMedCrossRefGoogle Scholar
  15. Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugene 12:172–175CrossRefGoogle Scholar
  16. Kubo T, Aida Y, Nakamura K, Tsunematsu H, Doi K, Yoshimura A (2002) Reciprocal chromosomal segment substitution series derived from Japonic and Indica cross of rice (Oryza sativa L.). Breed Sci 52:319–325CrossRefGoogle Scholar
  17. Lander ES, Gree P (1987) Construction of multilocus genetic linkage maps in human. Proc Natl Acad Sci USA 84:2363–2367PubMedCrossRefGoogle Scholar
  18. Li ZK, Prison 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 91:374–381Google Scholar
  19. Li WT, Zeng RZ, Zhang ZM, Zhang GQ (2002) Mapping of S-b locus for F1 pollen sterility in cultivated rice using PCR based markers. Acta Bot Sin 44(4):463–467Google Scholar
  20. Lin HX, Qian HR, Xiong ZM, Min SK, Zheng KL (1996) Mapping of major genes and minor genes for heading date in several rice vareties (Oryza sativa L.). Chin J Genet 23:107–114Google Scholar
  21. Lin SY, Sasaki T, Yano M (1998) Mapping quantitative trait loci controlling seed dormancy and heading date in rice, Oryza sativa L. using backrcross inbred lines. Theor Appl Genet 96:997–1003CrossRefGoogle Scholar
  22. Lin HX, Ashikari M, Yamanouchi U, Sasaki T, Yano M (2002) Identification and characterization of a quantitative trait locus, Hd9, controlling heading date in rice. Breed Sci 52:35–41CrossRefGoogle Scholar
  23. 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
  24. Liu GM, Li WT, Zeng RZ, Zhang ZM, Zhang GQ (2004) Identification of QTLs on substituted segments in single segment substitution lines of rice. Acta Genet Sin 31:1395–1400 [In Chinese.]PubMedGoogle Scholar
  25. Liu GF, Zhang ZM, Zhu HT, Zhao FM, Ding XH, Zeng RZ, Li WT, Zhang GQ (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(7):923–931PubMedCrossRefGoogle Scholar
  26. Matus I, Corey A, Filichkin T, Hayes PM, Vales MI, Kling J, Riera-Lizarazu O, Sato K, Powell W, Waugh R (2003) Development and characterization of recombinant chromosome substitution lines (RCSLs) using Hordeum vulgare subsp. spontaneum as a source of donor alleles in a Hordeum vulgare subsp. vulgare background. Genome 46(6):1010–1023PubMedCrossRefGoogle Scholar
  27. McCouch SR, Cho YG, Yano M, Paul E, Blinstrub M (1997) Report on QTL nomenclature. Rice Genet Newsl 14:11–13Google Scholar
  28. Monna L, Lin HX, Kojima S, Sasaki T, Yano M (2002) Genetic dissection of a genomic region for a quantitative trait locus, Hd3, into two loci, Hd3a and Hd3b, ontrolling heading date in rice. Theor Appl Genet 104:772–778PubMedCrossRefGoogle Scholar
  29. 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 252:597–607PubMedGoogle Scholar
  30. Reeves PH, Murtas G, Dash S, Coupl G (2002) Early in short days4, a mutation in Arabidopsis that causes early flowering and reduces the mRNA abundance of the floral repressor FLC. Development 129:5349–5361PubMedCrossRefGoogle Scholar
  31. Sugano S, Andronis C, Ong MS, Green RM, Tobin M (1999) The protein kinase CK2 is involved in regulation of circadian rhythms in Arabidopsis. Proc Natl Acad Sci USA 95:11020–11025CrossRefGoogle Scholar
  32. Takahashi Y, Shomura A, Sasaki T, Yano M (2001) Hd6 a rice quantitative trait locus involved in photoperiod sensitivity, encodes the alpha subunit of protein kinase CK2. Proc Natl Acad Sci USA 98:7922–7927PubMedCrossRefGoogle Scholar
  33. Takeuchi Y, Lin SY, Sasaki T, Yano M (2003) Fine linkage mapping enables dissection of closely linked quantitative trait loci for seed dormancy and heading in rice. Theor Appl Genet 107:1174–1180PubMedCrossRefGoogle Scholar
  34. Wang HD, Makeen K, Yan Y, Cao Y, Sun SB, Xu GH (2010) OsSIZ1 regulates the vegetative growth and reproductive development in rice. Plant Mol Biol Rep. doi: 10.1007/s11105-010-0232-y Google Scholar
  35. Xi ZY, He FH, Zeng RZ, Zhang ZM, Ding XH, Li WT, Zhang GQ (2006) Development of a wide population of chromosome single-segment substitution lines in the genetic background of an elite cultivar of rice (Oryza sativa L.). Genome 49:476–484PubMedCrossRefGoogle Scholar
  36. Xiao J, 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 140:745–754PubMedGoogle Scholar
  37. Xing YZ, Tang WJ, Xue WY, Xu CG, Zhang QF (2008) Fine mapping of a major quantitative trait loci, qSSP7, controlling the number of spikelets per panicle as a single Mendelian factor in rice. Theor Appl Genet 116(6):789–796PubMedCrossRefGoogle Scholar
  38. Xu XB, Liu ZX, Zhang DF, Liu Y, Song WB, Li JS, Dai JR (2009) Isolation and analysis of Rice Rf1-Orthologus PPR Genes Co-segregating with Rf3 in Maize. Plant Mol Biol Rep 27:511–517CrossRefGoogle Scholar
  39. Xue WY, Xing YZ, Weng XY, Zhao Y, Tang WJ, Wang L, Zhou HJ, Yu SB, Xu CG, Li XH, Zhang QF (2008) Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40:761–767PubMedCrossRefGoogle Scholar
  40. 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
  41. Yamamoto T, Lin HX, Sasaki T, Yano M (2000) Identification of heading date quantitative trait locus Hd6, and characterization of its epistatic interaction with Hd2 in rice using advanced backcross progeny. Genetics 154:885–891PubMedGoogle Scholar
  42. 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
  43. Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Nagamura Y, Sasaki T, Umehara Y (2000a) Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopis flowering time gene CONSTANS. Plant Cell 12:2473–2483CrossRefGoogle Scholar
  44. Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamto K, Umehara Y, Nagamura Y, Sasaki T (2000b) Hd-1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12:2473–2483CrossRefGoogle Scholar
  45. Yao FY (2006) Identification of QTLs for heading date and analysis of epistasis based on single segment substitution lines in rice (Oryza sativa L.), Ph.D thesis submitted to the South China Agricultural University, Guangzhou, ChinaGoogle Scholar
  46. Zhang GQ, Zeng RZ, Zhang ZM, Ding XH, Li WT, Liu GM, He FH, Tulukdar A, Huang CF, Xi ZY, Qin LJ, Shi JQ, Zhao FM, Feng MJ, Shan ZL, Chen L, Guo XQ, Zhu HT, Lu YG (2004) The construction of a library of single segment substitution lines in rice(Oryza sativa L.). Rice Genet Newsl 21:85–87Google Scholar
  47. Zhao FM, Liu GF, Zhu HT, Ding XH, Zeng RZ, Zhang ZM, Li WT, Zhang GQ (2008) Unconditional and conditional QTL mapping for tiller number at various stages by using single segment substitution lines in rice (Oryza sativa L.). Agric Sci China 7(3):257–265Google Scholar
  48. Zheng, KL, Huang N, Bennett J, Khush GS (1995) PCR-based marker-assisted selection in rice breeding. In: IRRI discussion paper series. No. 12. International Rice Research Institute, Manila, PhilippinesGoogle Scholar
  49. Zhou XJ, Li J, Cheng W, Liu H, Li MM, Zhang Y, Li WB, Han SC, Wang YD (2010) Gene structure analysis of rice ADP-ribosylation factors (OsARFs) and their mRNA expression in developing rice plants. Plant Mol Biol Rep 28:692–703CrossRefGoogle Scholar
  50. Zhu WY, Lin J, Yang DW, Zhao L, Zhang YD, Zhu Z, Chen T, Wang CL (2009) Development of chromosome segment substitution lines derived from backcross between two sequenced Rice cultivars, Indica recipient 93-11 and Japonica donor Nipponbare. Plant Mol Biol Rep 27:126–131CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Binbin Wang
    • 1
  • Changxiang Zhu
    • 3
  • Xu Liu
    • 1
  • Wenying Wang
    • 1
  • Hanfeng Ding
    • 1
  • Mingsong Jiang
    • 2
  • Guangxian Li
    • 2
  • Wei Liu
    • 1
  • Fangyin Yao
    • 1
  1. 1.High-Tech Research CenterShandong Academy of Agricultural ScienceJinanPeople’s Republic of China
  2. 2.Shandong Rice Research InstituteJiningPeople’s Republic of China
  3. 3.State Key Laboratory of Crop BiologyShandong Agricultural UniversityTai’anPeople’s Republic of China

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