A physical map with yeast artificial chromosome (YAC) clones covering 63% of the 12 rice chromosomes

A new YAC (yeast artificial chromosome) physical map of the 12 rice chromosomes was constructed utilizing the latest molecular linkage map. The 1439 DNA markers on the rice genetic map selected a total of 1892 YACs from a YAC library. A total of 675 distinct YACs were assigned to specific chromosomal locations. In all chromosomes, 297 YAC contigs and 142 YAC islands were formed. The total physical length of these contigs and islands was estimated to 270 Mb which corresponds to approximately 63% of the entire rice genome (430 Mb). Because the physical length of each YAC contig has been measured, we could then estimate the physical distance between genetic markers more precisely than previously. In the course of constructing the new physical map, the DNA markers mapped at 0.0-cM intervals were ordered accurately and the presence of potentially duplicated regions among the chromosomes was detected. The physical map combined with the genetic map will form the basis for elucidation of the rice genome structure, map-based cloning of agronomically important genes, and genome sequencing.Key words: physical mapping, YAC contig, rice genome, rice chromosomes.

Identification of YAC clones containing the mutable slender glume locus slg in rice (Oryza sativa L.)

A mutable slender glume gene slg, which often reverts to the wild-type state, was induced by gamma-ray irradiation of seeds of the japonica rice cultivar 'Gimbozu'. The final goal was to understand whether the slender glume mutation was associated with the insertion of a transposable element, utilizing map-based cloning techniques. The RFLP (restriction fragment length polymorphism) analysis revealed that the slg locus was located between two RFLP loci, XNpb33 and R1440, on chromosome 7 with recombination values of 3.1% and 1.0%, respectively. Using these two RFLP loci as probes, five YAC (yeast artificial chromosome) clones containing either of these two loci were selected from a YAC library. Subsequently, both end fragments of these YAC clones, amplified by the inverse PCR (IPCR) method, were used to select new YAC clones more closely located to the slg locus. After repeating such a procedure, we successfully constructed a 6-cM YAC contig, and identified four overlapping YAC clones, Y1774, Y3356, Y5124, and Y5762, covering the slg locus. The chromosomal location of the slg was narrowed down to the region with a physical distance of less than 280 kb between the right-end fragments of Y1774 and Y3356.Key words: Oryza sativa, mutable gene, slender glume mutation, YAC contig.

Linkage Disequilibrium and Physical Mapping of Pas1 in Mice

By using linkage disequilibrium (LD) analysis in 21 strains of known susceptibility to lung cancer and by assembling a YAC contig, we mapped to a ∼1.5-Mb region on distal mouse chromosome 6 the Pas1locus, the major determinant of lung cancer predisposition in mice. Our results, on the basis of haplotype and phenetic analysis, suggest that the Pas1s susceptibility allele is shared by several mouse-inbred strains of independent origin, which show either high or intermediate predisposition to lung tumorigenesis. Therefore, the Pas1s allele is probably derived from an ancestral mouse rather than from independent mutations of the same gene. We showed the feasibility of LD in common inbred strains for the fine mapping of disease loci, and provided the biological basis and the reagents for the cloning of the Pas1 gene.

Mapping of dentin-specific acidic phosphoprotein and integrin-binding sialoprotein in sheep defines an inversion breakpoint with respect to human chromosome 4Q

Genes from sheep chromosome 6 map to human chromosome 4 in the region extending from 4p16 to 4q26. However, there is an inversion of gene order in the central portion of the chromosome with one breakpoint close to secreted phosphoprotein 1 (SPP1). Genes for SPP1, integrin-binding sialoprotein (IBSP) and dentin-specific acidic phosphoprotein (DMP1) are located close together in a YAC contig in the human. RFLP markers were developed for DMP1 and IBSP in sheep and located on the sheep linkage map to further define the breakpoint region. There were no recombinants between SPP1 and IBSP indicating that these loci are close together in sheep, as in humans. DMP1 was located approximately 80 cM from SPP1 in sheep, 7 cM from the microsatellite BMC4203. In the human YAC contig, the order of these genes is SPP1-IBSP-DMP1 with 340 kb separating SPP1 and IBSP and 150 kb between IBSP and DMP1. Therefore, one breakpoint for the inversion in gene order between the sheep and the human has been narrowed to a region of 150 kb on the human map.