Construction of the primary physical map of rice chromosome 12


A primary physical map of rice chromosome 12 was constructed using marker-based chromosome landing and chromosome walking. A BAC library from IR64 was screened using 84 RFLP markers, 4 STS markers and 6 microsatellite markers on chromosome 12 by colony hybridization and polymerase chain reaction (PCR) amplification. A total of 59 contigs consisting of 419 BAC clones including 5 single-clones were physically aligned on rice chromosome 12 with the largest BAC contig covering 855 kb. The whole physical map had a size of ∼16 Mb and covered about 52% of rice chromosome 12. This physical map will be certainly helpful for map-based gene cloning of agronomically and biological important genes and understanding the genome structure of the chromosome.

This is a preview of subscription content, access via your institution.


  1. [1]

    Arumuganathan K, Earle E D. Nuclear DNA Content of Some Important Plant Species.Plant Mol Bio Rep, 1991,9: 208–218.

    Article  Google Scholar 

  2. [2]

    Causse M A, Fulton T M, Cho Y G,et al. Saturated Molecular Map of the Genome Based of an Interspecific Backcross Population.Genetics, 1994,138: 1251–1274.

    Google Scholar 

  3. [3]

    Harushima Y, Yano M, Shomura A,et al. A Highdensity Rice Genetic Linkage Map with 2275 Markers Using a Single F2 Population.Genetics, 1998,148: 479–494.

    Google Scholar 

  4. [4]

    ZHOU G Y. Distantly Related Hybridization and Genetic Engineering of Crops. In:Rice Genetics (Pro Int Rice Genet Sump). Manila: Island Press, 1986. 867–876.

    Google Scholar 

  5. [5]

    Shimamoto K, Terada R, Izawa T,et al. Fertile Transgenic Rice Plants Regenerated from Transformed Protoplasts.Nature, 1989,338: 274–276.

    Article  Google Scholar 

  6. [6]

    Shizuya H, Birren B, Kim U J,et al. Cloning and Stable Maintenance of 300-kilobase Pair Fragments of Human DNA inEscherichia coli Using an F-factorbased Vector.Proc Natl Acad Sci USA, 1992,89: 8794–8797.

    Article  Google Scholar 

  7. [7]

    WANG Guo-Liang, Thomas E, SONG Wen-Yuan,et al. Construction of a Rice Bacterial Artificial Chromosome Library and Identification of Clones Linked to theXa-21 Disease Resistance.The Plant J, 1995,7 (3): 525–533.

    Article  Google Scholar 

  8. [8]

    ZHANG Hong-Bin, Choi S, Woo S S,et al. Construction and Characterization of Two Bacterial Artificial Chromosome Libraries from the Parents of a Permanent Recombinant Inbred Mapping Population.Mol Breed, 1996(1): 11–24.

    Google Scholar 

  9. [9]

    Monna L, Miyao A, Zhong H S,et al. Saturation Mapping with Subclones of YACs: DNA Marker Production Targeting the Rice Blast Disease Resistance Gene,Pi-b.Theor Appl Genet, 1997,94: 170–176.

    Article  Google Scholar 

  10. [10]

    Sanchez A C, Ilag L L, YANG Dai-Chang,et al. Genetic and Physical Mapping ofXa13, a Recessive Bacterial Blight Resistance Gene in Rice.Theor Appl Genet, 199998: 1022–1028.

    Article  Google Scholar 

  11. [11]

    SONG Wen-Yuan, WANG Guo-Liang, Chen L L,et al. A Receptor Kinase- likes Protein Encoded by the Rice Disease Resistance Genes,Xa-21.Science, 1995,270: 1804–1806.

    Article  Google Scholar 

  12. [12]

    YANG Dai-Chang, Sanchez A, Khush G S,et al. Construction of a BAC Contig Containing theXa5 Locus in Rice.Theor Appl Genet, 1998,97: 1120–1124.

    Article  Google Scholar 

  13. [13]

    YANG Dai-Chang, Parco A, Nandi S,et al. Construction of a Bacterial Artificial Chromosome (BAC) Library and Identification of Overlapping BAC Clones with Chromosome 4 Specific RFLP Markers in Rice.Theor Appl Genet, 1997,95: 1147–1154.

    Article  Google Scholar 

  14. [14]

    Sambrook J, Fritsch E F, Manitiatis T. Molecular cloning: a Laboratory Manual. New York: Cold Spring Harbor Laboratory Press, 1989. 25–26.

    Google Scholar 

  15. [15]

    XU Ji-Chen, YANG Dai-Chang, Domingo J,et al. Screening for Overlapping Bacterial Artificial Chromosome Clones by PCR Analysis with an Arbitrary Primer.Proc Natl Acad Sci USA, 1998,95: 5661–5666.

    Article  Google Scholar 

  16. [16]

    LIU Yao-Guang, Mitsukawa N, Oosumi T,et al. Efficient Isolation and Mapping of Arabidopsis Thaliana T-DNA Insert Junctions by Thermal Asymmetric Interlaced PCR.The Plant Journal, 1995,8: 457–463.

    Article  Google Scholar 

  17. [17]

    ZHANG Hong-Bin, Wing R A. Physical Mapping of the Rice Genome with BACs.Plant Molecular Biology, 1997,35: 115–127.

    Article  Google Scholar 

  18. [18]

    Dhar M S, Dabak M M, Gupta V S,et al. Organization and Properties of Repeated DNA Sequences in Rice Genome.Plant Sci, 1988,55: 43–52.

    Article  Google Scholar 

  19. [19]

    LI Zhi-Kang, Pinson S R M, Marchetti M A,et al. Characterization of Quantitative Trait Loci (QTLs) in Cultivated Rice Contributing to Field Resistance to Sheath Blight (Rhizoctonia solani).Theor Appl Genet, 1995,91: 382–388.

    Google Scholar 

  20. [20]

    Wissuwa M, Yano M, Ae N. Mapping of QTLs for Phosphous-deficiency Tolerance in Rice (Oryza sativa L).Theor Appl Genet, 1998, 97: 777–783.

    Article  Google Scholar 

  21. [21]

    Nagamura Y, Inoue T, Anotnia B A,et al. Extensive Conservation of Duplicated Segments between Rice Chromosome 11 and 12.Breed Sci, 1995,45: 373–376.

    Google Scholar 

  22. [22]

    WU Jian-Zhong, Nori Kurata, Hiroshi Tanoue,et al. Physical Mapping of Duplicated Genomic Regions of Two Chromosome Ends in Rice.Genetics, 1998,150: 1595–1603.

    Google Scholar 

  23. [23]

    Michael D G, Katruen M D. Comparative Genetics in the Grasses.Proc Natl Acad Sci USA, 1998,95: 1971–1974.

    Article  Google Scholar 

  24. [24]

    Izaw T, Shimamoto K. Becoming a Model Plant: The Importance of Rice to Plant Science.Trends in Plant Science, 1996,1(3): 95–99.

    Article  Google Scholar 

  25. [25]

    JIANG Ji-Ming, Gill B S, WANG Guo-Liang,et al. Metaphase and Interphase Fluorescence in site Hybridization Mapping of the Rice Genome with Bacterial Artificial Chromosomes.Proc Natl Acad Sci USA, 1995,92: 4478–4491.

    Google Scholar 

  26. [26]

    YAN Hui-Min, SONG Yun-Chun, LI Li-Jia,et al. Comparative Physical Location of RiceXa21 Gene in Rice and Maize Using BAC-FISH.Acta Botanica Sinica, 1999,41(3): 249–253.

    Google Scholar 

Download references

Author information



Corresponding author

Correspondence to Fu Bin-Ying.

Additional information

Foundation item: Supported by Rockefeller Foundation

Biography: FU Bin-Ying (1965-), male, Ph. D. candidate, Reseach direction: plant molecular genetics.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Bin-Ying, F., Ying-Guo, Z. & Zhi-Kang, L. Construction of the primary physical map of rice chromosome 12. Wuhan Univ. J. Nat. Sci. 5, 238–244 (2000).

Download citation

Key words

  • chromosome landing
  • chromosome walking
  • BAC contigs
  • physical map

CLC number

  • Q 343. 2