Skip to main content
Log in

Identification of simple sequence repeat markers for utilizing wide-compatibility genes in inter-subspecific hybrids in rice (Oryza sativa L.)

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


Although pronounced heterosis in inter-subspecific hybrids was known in rice for a long time, its utilization for hybrid rice breeding has been limited due to their hybrid sterility (HS). For the last two decades, however, a few inter-subspecific hybrids have been developed by incorporating wide-compatibility genes (WCG) that resolve HS, into parental lines of these inter-subspecific hybrids. For effective use of WCG, it is necessary to find convenient markers linked to WCG of practical importance. In this paper, initially a set of simple sequence repeat (SSR) markers in the vicinity of known WCG loci identified based on comparative linkage maps have been surveyed in a population derived from the three-way cross- IR36/Dular//Akihikari, where a known donor of WCG Dular was crossed to a representative indica and japonica cultivar. Of the five parental polymorphic markers, RM253 and RM276 were found to be closely linked to the WCG locus S5 at a distance of 3.0 and 2.8 cM, respectively. Later, loci for HS were examined in three F2 populations derived from inter-subspecific crosses, with same set of SSR markers. The locus S8 was confirmed to have major influence on HS in the F2 population derived from CHMRF-1/Taichung65 since two SSR markers in its vicinity, RM412 and RM141, co-segregated with HS at a map distance of 7.6 and 4.8 cM, respectively. In the F2 population derived from the cross BPT5204/Taipei309, three SSR markers in the vicinity of S5, RM50, RM276 and RM136 co-segregated with HS at a map distance of 4.2, 3.2 and 7.8 cM, respectively. In the third F2 population derived from Swarna/Taipei309, the SSR markers in the vicinity of S5, RM225, RM253, RM50, RM276 and RM136 were identified to co-segregate with HS at a map distance of 3.2, 2.6, 3.4, 2.6 and 6.6 cM, respectively. These results indicated a clear picture of WCG in Dular as well as the predominant role of HS alleles at S5 locus. The identified SSR markers are expected to be used for incorporation of WCG into parental lines in hybrid rice breeding to solve HS in inter-subspecific hybrids.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2

Similar content being viewed by others


  • Chen X, Temnykh S, Xu Y, Cho YG, McCouch SR (1997) Development of microsatellite framework map providing genome wide coverage in rice (Oryza sativa L). Theor App Genet 95:553–567

    Article  CAS  Google Scholar 

  • Devanand PS, Rangaswamy M, Ikehashi H (2000) Identification of hybrid sterility gene loci in two cytoplasmic male sterile lines in rice. Crop Sci 40:640–646

    Article  Google Scholar 

  • Heuer S, Miézan KM (2003) Assessing hybrid sterility in Oryza glaberrima( O sativa hybrid progenies by PCR marker analysis and crossing with wide compatibility varieties. Theor Appl Genet 107:902–909

    Article  PubMed  CAS  Google Scholar 

  • Ikehashi H, Araki H (1986) Genetics of F1 sterility in remote crosses of rice. In Rice Genetics IRRI:119–130

    Article  Google Scholar 

  • Joshi SP, Ranjekar PK, Gupta VS (1999) Molecular markers in plant genome analysis. Curr Sci 77:230–240

    CAS  Google Scholar 

  • Kato S, Kosaka H, Hara S (1928) On the affinity of rice varieties as shown by the fertility of hybrid plants. Bull Sci Fakult Terkult Kyushu Imp Univ 3:132–147

    Google Scholar 

  • Kosambi DD (1944) The estimation of map distance from recombination values. Ann Eugen 12:172–175

    Google Scholar 

  • Kubo T, Yoshimura A (2001) Linkage analysis of a gene controlling F2 sterility in japonica/ indica backcross progenies of rice. Rice Genet Newsl 18:52–53

    Google Scholar 

  • Kubo T, Eguchi M, Yoshimura A (2000) A new gene for F1 pollen sterility in japonica/ indica cross of rice. Rice Genet Newsl 17:63–64

    Google Scholar 

  • Kubo T, Eguchi M, Yoshimura A (2001) A new gene for F1 pollen sterility on chromosome12 in japonica/ indica cross of rice. Rice Genet Newsl 18:54–55

    Google Scholar 

  • Lander ES, Green P, Abrahmson J, Barloe A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary linkage maps of experimental and natural populations. Genomics 1:174–181

    Article  PubMed  CAS  Google Scholar 

  • Lu CG, Takabatake K, Ikehashi H (2000) Identification of segregation distortion neutral alleles to improve pollen fertility of indica-japonica hybrids in rice. Euphytica 113:101–107

    Article  CAS  Google Scholar 

  • McCouch SR, Leonid T, Yunbi X, Katarzyna BL, Karen C (2002) Development and mapping of 2240 New SSR markers for Rice (Oryza sativa L.). Theor Appl Genet 109:199–207

    Google Scholar 

  • Nagato Y, Yoshimura A (1998) Report of the committee on gene symbolization, nomenclature and linkage groups. Rice Genet Newsl 15:13–74

    Google Scholar 

  • Roder MS, Plaschke J, Konig SU, Borner A, Sorrells ME, Tanksley SD, Ganal MW (1998) Abundance, variability and chromosomal location of microsatellites in wheat. Mol Genet 246:327–333

    Article  Google Scholar 

  • Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual 3rd edn. Cold Spring Harbor, NY, USA pp 5.40–5.46

  • Sano Y (1993) Is an egg killer present in rice. Theor Appl Genet 86:1038–1042

    Article  Google Scholar 

  • Sano Y, Eiguchi M, Hirano HY (1992) Genetic elimination found in the indica-japonica hybrid of rice. Jpn J Breed 42:454–455

    Google Scholar 

  • Sobrizal Y, Matsuzaki P, Yoshimura A (2002) Mapping of pollen semi-sterility gene S-28 (t) on rice chromosome 4. Rice Genet Newsl 19:34–37

    Google Scholar 

  • Taguchi K, Doi K, Yoshimura A (1999) RFLP mapping of S-19, a gene for F1 pollen sterility found in back cross progeny of Oryza sativa and O.glaberrima. Rice Genet Newsl 16:70–71

    Google Scholar 

  • Wan J, Ikehashi H (1995a) Identification of a new locus S-16 causing hybrid sterility in native rice varieties (Oryza sativa L.) from Tai-hu lake region and Yunnan Province, China. Breed Sci 45:461–470

    Google Scholar 

  • Wan J, Ikehashi H (1995b) Loci for hybrid sterility in Basmati crosses. Intl Rice Res Notes 20:4

    Google Scholar 

  • Wan J, Yanagihara S, Kato H, Ikehashi H (1993) Multiple alleles at a new locus causing hybrid sterility between Korean indica variety and a javanica variety in rice (Oryza sativa L.). Jap J Breed 43:507–516

    Google Scholar 

  • Wan J, Yamaguchi Y, Kato H, Ikehashi H (1996) Two new loci for hybrid sterility in rice (Oryza sativa L.). Theor Appl Genet 92:183–190

    Article  CAS  Google Scholar 

  • Wang J, Liu KD, Xu CG, Li XH, Zhang Q (1998) The high level of wide compatibility of variety ‘Dular’ has a complex genetic basis. Theor Appl Genet 97:407–411

    Article  CAS  Google Scholar 

  • Williams CE, Yanagihara S, McCouch SR, Mackill D, Ronald PC (1997) Predicting success of indica/japonica crosses in rice based on a PCR marker for the S-5 n allele at a hybrid-sterility locus. Crop Sci 37:1910–1912

    Article  CAS  Google Scholar 

  • Yanagihara S, Kato H, Ikehashi H (1992) A new locus for multiple alleles causing hybrid sterility between an Aus variety and javanica varieties in rice (Oryza sativa L.). Jap J Breed 42:793–801

    Google Scholar 

  • Yanagihara S, Couch SR, Ishikawa K, Ogi Y, Maruyama K, Ikehashi H (1995) Molecular analysis of the inheritance of the S-5 locus conferring wide compatibility in indica/japonica hybrids of rice (Oryza sativa L.). Theor Appl Genet 90:182–188

    Article  CAS  Google Scholar 

  • Yuan LP (1992) The strategy of the development of hybrid rice breeding. In: Yuan LP (ed) Current stratus of two line hybrid rice research 1–5, In Chinese, English summary. Agricultural Publishing Ltd, Beijing

    Google Scholar 

  • Zheng K, Huang N, Bennet J, Khush GS (1995) PCR based marker-assisted selection in rice breeding. IRRI Discussion paper series No 12. International Rice Research Institute, Manila

    Google Scholar 

  • Zhu S, Wang C, Zheng T, Zhao Z, Ikehashi H, Wan J. (2005) New gene located on chromosome 2 causing hybrid sterility in a remote cross of rice. Plant Breed 124:440–445

    Article  CAS  Google Scholar 

Download references


The authors profusely thank Dr. B. Mishra, Project Director, Directorate of Rice Research, Hyderabad for the kind help and assistance received and research facilities extended to pursue the present study.

Author information

Authors and Affiliations


Corresponding author

Correspondence to E. A. Siddiq.

Additional information

Communicated by T. Sasaki

S.P. Singh , R.M. Sundaram contributed equally

Rights and permissions

Reprints and permissions

About this article

Cite this article

Singh, S.P., Sundaram, R.M., Biradar, S.K. et al. Identification of simple sequence repeat markers for utilizing wide-compatibility genes in inter-subspecific hybrids in rice (Oryza sativa L.). Theor Appl Genet 113, 509–517 (2006).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: