Free Access

Identification of Chromosomes from Multiple Rice Genomes Using a Universal Molecular Cytogenetic Marker System

Xiaomin Tang

State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing 100101, China

Search for more papers by this author

Weidong Bao,

Weidong Bao

State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing 100101, China

Search for more papers by this author

Wenli Zhang,

Wenli Zhang

State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing 100101, China

Search for more papers by this author

Zhukuan Cheng,

Corresponding Author

Zhukuan Cheng

State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing 100101, China

*Author for correspondence. Tel: +86 (0)10 6486 8726; Fax: +86 (0)10 6487 3428; E-mail: <[email protected]>.Search for more papers by this author

Xiaomin Tang,

Xiaomin Tang

State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing 100101, China

Search for more papers by this author

Weidong Bao,

Weidong Bao

State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing 100101, China

Search for more papers by this author

Wenli Zhang,

Wenli Zhang

State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing 100101, China

Search for more papers by this author

Zhukuan Cheng,

Corresponding Author

Zhukuan Cheng

State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing 100101, China

*Author for correspondence. Tel: +86 (0)10 6486 8726; Fax: +86 (0)10 6487 3428; E-mail: <[email protected]>.Search for more papers by this author

First published: 15 June 2007

https://doi.org/10.1111/j.1744-7909.2007.00508.x

Citations: 12

Supported by the National Natural Science Foundation of China (30325008, 30428019 and 30530070).

Publication of this paper is supported by the National Natural Science Foundation of China (30624808).

About

PDF

Tools

Share a link

Email
Wechat
Bluesky

Abstract

To develop reliable techniques for chromosome identification is critical for cytogenetic research, especially for genomes with a large number and smaller-sized chromosomes. An efficient approach using bacterial artificial chromosome (BAC) clones as molecular cytological markers has been developed for many organisms. Herein, we present a set of chromosomal arm-specific molecular cytological markers derived from the gene-enriched regions of the sequenced rice genome. All these markers are able to generate very strong signals on the pachytene chromosomes of Oryza sativa L. (AA genome) when used as fluorescence in situ hybridization (FISH) probes. We further probed those markers to the pachytene chromosomes of O. punctata (BB genome) and O. officinalis (CC genome) and also got very strong signals on the relevant pachytene chromosomes. The signal position of each marker on the related chromosomes from the three different rice genomes was pretty much stable, which enabled us to identify different chromosomes among various rice genomes. We also constructed the karyotype for both O. punctata and O. officinalis with the BB and CC genomes, respectively, by analysis of 10 pachytene cells anchored by these chromosomal arm-specific markers.

References

Aggarwal RK, Brar DS, Nandi S, Huang N, Khush GS (1999). Phylogenetic relationships among Oryza species revealed by AFLP markers. Theor. Appl. Genet. 98, 1320–1328.
10.1007/s001220051198
CAS Web of Science® Google Scholar
Ambros PF, Matzke MA, Matzke AJM (1986). Detection of a 17kb unique sequence (T-DNA) in plant chromosomes by in situ hybridization. Chromosoma 94, 11–18.
10.1007/BF00293525
CAS Web of Science® Google Scholar
Arumuganathan K, Earle ED (1991). Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9, 208–218.
10.1007/BF02672069
CAS PubMed Web of Science® Google Scholar
Bao WD, Zhang WL, Yang QY, Zhang Y, Han B, Gu MH et al. (2006). Diversity of centromeric repeats in two closely related wild rice species, O. officinalis an. O. rhizomatis. Mol. Genet. Genomics 275, 421–430.
10.1007/s00438-006-0103-2
CAS PubMed Web of Science® Google Scholar
Chen CC, Chen CM, Hsu FC, Wang CJ, Yang JT, Kao YY (2000). The pachytene chromosomes of maize as revealed by fluorescence in situ hybridization with repetitive DNA sequences. Theor. Appl. Genet. 101, 30–36.
10.1007/s001220051445
CAS Web of Science® Google Scholar
Cheng ZK, Gu MH (1994). Karyotype analysis for pachytene chromosome of indica, japonica rice and their hybrid. Chin. J. Genet. 21, 182–187.
Google Scholar
Cheng ZK, Buell CR, Wing RA, Gu MH, Jiang JM (2001a). Toward a cytological characterization of the rice genome. Genome Res. 11, 2133–2141.
10.1101/gr.194601
CAS PubMed Web of Science® Google Scholar
Cheng ZK, Presting GG, Buell CR, Wing RA, Jiang JM (2001b). High-resolution pachytene chromosome mapping of bacterial artificial chromosomes anchored by genetic markers reveals the centromere location and the distribution of genetic recombination along chromosome 10 of rice. Genetics 157, 1749–1757.
CAS PubMed Web of Science® Google Scholar
Cheng ZK, Dong FG, Langdon T, Shu OY, Buell CR, Gu MH et al. (2002). Rice Centromeres are marked by a satellite repeat and a centromere-specific retrotransposon. Plant Cell 14, 1691–1704.
10.1105/tpc.003079
CAS PubMed Web of Science® Google Scholar
Chung MC, Wu HK (1987). Karyotype analysis of “IR36” and two trisomic lines of rice. Bot. Bull. Acad. Sin. 28, 289–304.
Web of Science® Google Scholar
Dong F, Song J, Naess SK, Helgeson JP, Gebhardt C, Jiang J (2000). Development and applications of a set of chromosome-specific cytogenetic DNA markers in potato. Theor. Appl. Genet. 101, 1001–1007.
10.1007/s001220051573
CAS Web of Science® Google Scholar
Ge S, Sang T, Lu BR, Hong DY (1999). Phylogeny of rice genomes with emphasis on origins of allotetraploid species. Proc. Natl. Acad. Sci. USA 96, 14400–14405.
10.1073/pnas.96.25.14400
CAS PubMed Web of Science® Google Scholar
Gerlach WL, Bedbrook JR (1979). Cloning and characterization of ribosomal RNA genes from wheat and barley. Nucleic Acids Res. 7, 1869–1885.
10.1093/nar/7.7.1869
CAS PubMed Web of Science® Google Scholar
Hanson RE, Zwick MS, Choi S, Islan-Faridi MN, McKnight TD, Wing RA et al. (1995). Fluorescent in situ hybridization of a bacterial artificial chromosome. Genome 38, 646–651.
10.1139/g95-082
CAS PubMed Web of Science® Google Scholar
International Rice Genome Sequencing Project (2005). The map-based sequence of the rice genome. Nature 436, 793–800.
10.1038/nature03895
CAS PubMed Web of Science® Google Scholar
Jiang J, Gill BS (1994). Non-isotopic in situ hybridization and plant genome mapping, the first ten years. Genome 37, 717–725.
10.1139/g94-102
CAS PubMed Web of Science® Google Scholar
Jiang J, Gill BS, Wang G, Ronald PC, Ward DC (1995). Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes. Proc. Natl. Acad. Sci. USA 92, 4487–4491.
10.1073/pnas.92.10.4487
CAS PubMed Web of Science® Google Scholar
Khush GS, Kinoshita T (1991). Rice karyotype, marker genes, and linkage groups. In: GS Khush, GH Toenniessen, eds. Rice Biotechnology. CAB International, Wallingford , UK. pp. 83–108.
Google Scholar
Khush GS, Singh RJ, Sur SC, Librojo AL (1984). Primary trisomics of rice, origin, morphology, cytology, and use in linkage mapping. Genetics 107, 141–163.
CAS PubMed Web of Science® Google Scholar
Khush GS, Singh K, Ishii T, Parco A, Huang N, Brar DS et al. (1996). Centromere mapping and orientation of the cytological, classical, and molecular linkage maps of rice. In: GS Khush, ed. Rice Genetics III. Proceedings of the Third International Rice Genetics Symposium. International Rice Research Institute, Manila . pp. 57–75.
10.1142/9789812814289_0005
Google Scholar
Kurata N, Omura T, Iwata N (1981). Studies on centromere, chromomere and nucleolus in pachytene nuclei of rice, Oryza sativa, microsporocytes. Cytologia 46, 791–800.
10.1508/cytologia.46.791
Web of Science® Google Scholar
Lapitan NLV, Brown SE, Kennard W, Stephens JL, Knudson DL (1997). FISH physical mapping with barley BAC clones. Plant J. 11, 149–156.
10.1046/j.1365-313X.1997.11010149.x
CAS Web of Science® Google Scholar
Li CB, Zhang DM, Ge S, Lu BR, Hong DY (2001). Identification of genome constitution of Oryza malampuzhaensis, O. minuta, and O. punctata by multicolor genomic in situ hybridization. Theor. Appl. Genet. 103, 204–211.
10.1007/s001220100563
CAS Web of Science® Google Scholar
Ren F, Lu BR, Li S, Huang J, Zhu Y (2003). A comparative study of genetic relationships among the AA-genome Oryza species using RAPD and SSR markers. Theor. Appl. Genet. 108, 113–120.
10.1007/s00122-003-1414-x
CAS PubMed Web of Science® Google Scholar
Shastry SVS, Rangao Rao DR, Mistra RN (1960). Pachytene analysis in Oryza. I. Chromosome morphology in Oryza sativa L. Indian J. Genet. Breed. 20, 15–21.
Google Scholar
Shen DL, Wang ZF, Wu M (1987). Gene mapping on maize pachytene chromosomes by in situ hybridization. Heredity 44, 131–149.
Google Scholar
Wu HK (1967). Note on preparing of pachytene chromosomes by double mordant. Sci. Agr. 15, 40–44.
Google Scholar
Wu T, Wu R. (1987). A new rice repetitive DNA sequence shows homology to both 5s RNA and tRNA. Nucleic Acids Res. 15, 5913–5923.
10.1093/nar/15.15.5913
CAS PubMed Web of Science® Google Scholar
Zhang W, Yi C, Bao W, Liu B, Cui J, Yu H et al. (2005). The transcribed 165–bp CentO satellite is the major functional centromeric element in the wild rice specie. Oryza punctata. Plant Physiol. 138, 1205–1215.
Google Scholar

Citing Literature

Volume49, Issue6

June 2007

Pages 953-960

Identification of Chromosomes from Multiple Rice Genomes Using a Universal Molecular Cytogenetic Marker System

Abstract

References

Citing Literature

References

Information

About Wiley Online Library

Help & Support

Opportunities

Connect with Wiley

Identification of Chromosomes from Multiple Rice Genomes Using a Universal Molecular Cytogenetic Marker System

Abstract

References

Citing Literature

References

Related

Information