High-resolution physical mapping of the secalin-1 locus of rye on extended DNA fibers

High-resolution mapping of secalin-1 <i>(Sec-1)</i> locus has been performed by fluorescence in situ hybridization to extended DNA fibers of rye (<i>Secale cereale</i>, 2n = 14), employing DNA probes of λ phage clones containing the ω-secalin gene. The fluorescent signals to rye extended DNA fibers revealed continuous strings of 45 µm, corresponding to the size of 147 kb DNA. To determine the copy number of <i>Sec-1</i> locus on DNA fibers, a 1.2-kb fragment including the entire coding region of the ω-secalin gene and a 1.0-kb fragment of the promoter region were amplified by PCR as probes for another fiber FISH. The physical position of these sequences was visualized as alternating fluorescent spots by multicolor in situ hybridization. Alternating signals of two DNA probes reflected the tandem repeated organization of the <i>Sec-1</i> locus having 15 copies of the gene. The present findings based on fiber FISH analysis support the contention that the ω-secalin genes are arranged in a head-to-tail fashion separated by 8 kb of spacer sequences with a total length of 145 kb.