Chromosome painting using repetitive DNA sequences as probes for somatic chromosome identification in maize

Proc Natl Acad Sci U S A. 2004 Sep 14;101(37):13554-9. doi: 10.1073/pnas.0403659101. Epub 2004 Sep 1.


Study of the maize (Zea mays L.) somatic chromosomes (2n = 20) has been difficult because of a lack of distinguishing characteristics. To identify all maize chromosomes, a multicolor fluorescence in situ hybridization procedure was developed. The procedure uses tandemly repeated DNA sequences to generate a distinctive banding pattern for each of the 10 chromosomes. Fluorescence in situ hybridization screening trials of nonsubtracted or subtracted PCR libraries resulted in the isolation of microsatellite 1-26-2, subtelomeric 4-12-1, and 5S rRNA 2-3-3 clones. These three probes, plus centromeric satellite 4 (Cent4), centromeric satellite C (CentC), knob, nucleolus-organizing region (NOR), pMTY9ER telomere-associated sequence, and tandemly repeated DNA sequence 1 (TR-1) were used as a mixture for hybridization to root-tip chromosomes. All 10 chromosomes were identified by the banding and color patterns in the 14 examined lines. There was significant quantitative variation among lines for the knob, microsatellite, TR-1, and CentC signals. The same probe mixture identifies meiotic pachytene, late prophase I, and metaphase I chromosomes. The procedure could facilitate the study of chromosomal structure and behavior and be adapted for other plant species.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Chromosome Painting / methods*
  • Chromosomes, Plant / genetics*
  • DNA Probes / genetics*
  • Karyotyping
  • Molecular Sequence Data
  • Repetitive Sequences, Nucleic Acid / genetics*
  • Zea mays / genetics*


  • DNA Probes

Associated data

  • GENBANK/CL569181
  • GENBANK/CL569243