SpringerLink
Log in

Delimitation of the rice wide compatibility gene S5 n to a 40-kb DNA fragment

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

Abstract

Wide compatibility varieties (WCVs) are a special class of rice (Oryza sativa L.) germplasm that produces hybrids with normal pollen and spikelet fertility when crossed with both indica and japonica subspecies. The wide compatibility gene S5 n has been used extensively in intersubspecific hybrid breeding programs. We previously mapped the S5 locus to a 2.2-cM genomic region between RM253 and R2349 on chromosome 6, using a population of 356 F1 plants derived from the three-way cross 02428/Nan**g11//Balilla. In this study, a chromosome walking strategy was employed to construct a physical map covering this genomic region using these two closest markers as the starting points. A physical map consisting of six overlap** BAC clones was formed, spanning a genomic region of 540-kb in length. By analyzing recombination events from a population of 8,000 F1 plants derived from a three-way cross based on near isogenic lines of the S5 locus, the S5 locus was localized to a DNA fragment of 40-kb in length, flanked by two shotgun subclones, 7B1 and 15D2. Sequence analysis of this fragment predicted five open reading frames, encoding xyloglucan fucosyltransferases, dnak-type molecular chaperone BiP, a putative eukaryotic aspartyl protease, and a hypothetical protein. This result will be very useful in molecular cloning of the S5 n allele and marker-assisted transferring of the wide compatibility gene in rice breeding programs.

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

Access this article

Log in via an institution

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.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Birren B, Green ED, Klapholz S, Mayers RM, Roskams J (1997) Genome analysis. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, pp 397–454

    Google Scholar 

  • Causse MA, Fulton TM, Cho YG, Ahn SN, Chunwongse J, Wu KS, **ao JH, Yu ZH, Ronald PC, Harrington SE, Second G, McCouch SR, Tanksley SD (1994) Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics 138:1251–1274

    PubMed  Google Scholar 

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

    Article  Google Scholar 

  • Hammond C, Helenius A (1995) Quality control in the secretory pathway. Curr Opin Cell Biol 7:523–529

    Article  PubMed  Google Scholar 

  • He GH, Zheng JK, Yin GD, Yang ZL (1994) Gamete fertility of F1 between indica and japonica (In Chinese with English abstract). Chin J Rice Sci 8:177–180

    Google Scholar 

  • Ikehashi H, Araki H (1984) Variety screening of compatibility types revealed in F1 fertility of distant crosses in rice. Jpn J Breed 34:304–313

    Google Scholar 

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

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

    Google Scholar 

  • 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 K, Miyao A, Monna L, Zhong HS, Tamura Y, Wang ZX, Momma T, Umehara Y, Yano M, Sasaki T and Minobe Y (1994) A 300 kilobase interval genetic map of rice including 883 expressed sequences. Nat Genet 8:365–372

    Article  PubMed  Google Scholar 

  • Li XQ (1988) Improving the fertility of indica–japonica hybrids by using the wide-compatibility gene. Hybrid Rice 3:31–33

    Google Scholar 

  • Li BJ, Ouyang XZ (1992) Cytological study on the abortion of spikelets of F1 from indica and japonica (In Chinese with English abstract). In: Yuan LP (ed) Current status of two line hybrid rice research. Agricultural Press, Bei**g, pp 286–289

    Google Scholar 

  • Li H, Tang L, Zou J (1991) Marker-based analysis of wide compatibility in rice (in Chinese). Hybrid Rice 4:22–24

    Google Scholar 

  • Ling DH, Ma ZR, Chen MF, Liang CY, He BS (1991) Types of male sterile mutants in somaclones from somatic cell culture of indica rice (In Chinese with English abstract). Acta Genet Sin 18:132–139

    Google Scholar 

  • Liu YG, Whittier RF (1995) Thermal asymmetric interlaced PCR: automatable amplification and sequencing of insert and fragments from P1 and YAC clones for chromosome walking. Genomics 25:674–681

    Article  PubMed  Google Scholar 

  • Liu A, Zhang Q, Li H (1992) Location of a gene for wide-compatibility in the RFLP linkage map. Rice Genet Newsl 9:134–136

    Google Scholar 

  • Liu YS, Zhou KD, Yin GD, Luo WZ (1993) Preliminary cytological observations on female sterility of hybrids between indica and japonica rice (In Chinese with English abstract). Acta Biol Exp Sin 26:95–99

    Google Scholar 

  • Liu KD, Wang J, Li HB, Xu CG, Liu AM, Li XH, Zhang Q (1997a) A genome-wide analysis of wide compatibility in rice and the precise location of the S 5 locus in the molecular map. Theor Appl Genet 95:809–814

    Article  Google Scholar 

  • Liu YS, Sun JS, Zhou KD (1997b) Cytological basis causing spikelet sterility of intersubspecific hybrid in Oryza sativa (In Chinese with English abstract). Acta Biol Exp Sin 30:335–341

    Google Scholar 

  • Liu HY, Xu CG, Zhang Q (2004) Male and female gamete abortions, and reduced affinity between the uniting gametes as the causes for sterility in an indica/japonica hybrid in rice. Sex Plant Reprod 17:55–62

    Article  Google Scholar 

  • Maeka M, Inuka T, Shinbashi N (1991) Spikelet sterility in F1 hybrids between rice varieties Silewah and Hayakogane. Jpn J Breed 41:359–363

    Google Scholar 

  • Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325

    PubMed  Google Scholar 

  • Peng KM, Zhang HB, Zhang Q (1998) A BAC library constructed to the rice cultivar ‘Minghui63‘ for cloning genes of agronomic importance. Acta Bot Sin 40:1108–1114

    Google Scholar 

  • Ramalho-Santos M, Verissimo P, Cortes L, Samyn B, Van Beeumen J, Pires E, Faro C (1998) Identification and proteolytic processing of procardosin A. Eur J Biochem 255:133–138

    Article  PubMed  Google Scholar 

  • Saghai Maroof MA, Yang GP, Biyashev RM, Maughan PJ, Zhang Q (1996) Analysis of the barley and rice genomes by comparative RFLP linkage map**. Theor Appl Genet 92:541–551

    Article  Google Scholar 

  • Sarkinnen P, Kalkkinen N, Tilgman C, Siuro J, Kervinen J, Mikola L (1992) Aspartic proteinases from barley grains is related to mammalian lysosomal cathepsin D. Planta 186:317–323

    Google Scholar 

  • Song X, Qiu SQ, Xu CG, Li XH, Zhang Q (2005) Genetic dissection of embryo-sac fertility, pollen fertility and their contributions to spikelet fertility of an indica–japonica rice hybrid. Theor Appl Genet 110:205–211

    Article  PubMed  Google Scholar 

  • Tao QZ, Zhao HY, Qiu LY, Hong GF (1994) Construction of a full bacterial artificial chromosome (BAC) library of Oryza sativa genome. Cell Res 4:127–133

    Google Scholar 

  • Temnykh S, Park WD, Ayres N, Cartihour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCouch SR (2000) Map** and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697–712

    Article  Google Scholar 

  • Teng JL, Xue QZ, Wang YX (1996) Ultrastructural observations of pollen and anther wall development between subspecies in rice (Oryza sativa L.) (In Chinese with English abstract). J Zhejiang Agr Univ 22:467–473

    Google Scholar 

  • Wang YX, Yan JQ, Xue QZ, Shen SQ (1991) Cytological studies on partial male sterility of F1 hybrids between subspecies in rice (In Chinese). J Zhejiang Agr Univ 17:417–422

    Google Scholar 

  • Wang CL, Zhang ZL, Tang SZ, Shi JD (1992) Exploitation of heterosis between indica and japonica by three-line method. I. Differentiation between indica–japonica sterility and cytoplasmic male sterility (In Chinese with English abstract). Jiangsu J Agr Sci 8:1–7

    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 97:407–412

    Article  Google Scholar 

  • Wu KS, Tanksley SD (1993) Abundance polymorphism and genetic map** of microsatellite in rice. Mol Gen Genet 241:225–235

    Article  PubMed  Google Scholar 

  • Yanagihara S, McCouch 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 (O. sativa L.). Theor Appl Genet 90:182–188

    Article  Google Scholar 

  • Yokoo M (1984) Female sterility in an indica–japonica cross of rice. Jpn J Breed 34:219–227

    Google Scholar 

  • Zhang Q, Zhou ZQ, Yang GP, Xu CG, Liu KD, Saghai Maroof MA (1996) Molecular marker heterozygosity and hybrid performance in indica and japonica rice. Theor Appl Genet 93:1218–1224

    Article  Google Scholar 

  • Zhao MF, Li XH, Yang JB, Xu CG, Hu RY, Liu DJ, Zhang Q (1999) Relationship between molecular marker heterozygosity and hybrid performance in intra- and inter-subspecific crosses in rice. Plant Breed 118:139–144

    Article  Google Scholar 

  • Zheng K, Shen P, Qian H, Wang J (1992) Tagging genes for wide compatibility in rice via linkage to RFLP markers. Chin J Rice Sci 6:145–150

    Google Scholar 

  • Zhu XH, Cao XZ, Zhu QS (1996) Cytological studies on spikelet sterility of indica–japonica hybrids in rice (In Chinese with English abstract). Chin J Rice Sci 10:71–78

    Google Scholar 

Download references

Acknowledgments

This research was supported by grants from the National Program of Research and Development of Transgenic Plants, the National Special Key Project of Functional Genomics and Biochips, the National Natural Science Foundation of China, and an Award to Elite Young Teacher at Universities of China (K Liu).

Author information

Authors and Affiliations

  1. National Key Laboratory of Crop Genetic Improvement, and National Center of Plant Gene Research-Wuhan, Huazhong Agricultural University, Wuhan, 430070, China

    S. Q. Qiu, Kede Liu, J. X. Jiang, X. Song, C. G. Xu, X. H. Li & Qifa Zhang

Authors
  1. S. Q. Qiu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kede Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. J. X. Jiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. X. Song
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. C. G. Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. X. H. Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Qifa Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Kede Liu.

Additional information

Communicated by T. Sasaki

Rights and permissions

Reprints and permissions

About this article

Cite this article

Qiu, S.Q., Liu, K., Jiang, J.X. et al. Delimitation of the rice wide compatibility gene S5 n to a 40-kb DNA fragment. Theor Appl Genet 111, 1080–1086 (2005). https://doi.org/10.1007/s00122-005-0033-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-005-0033-0

Keywords

Search

Navigation