Plant Genome IV Conference Plant Genome IV Conference
A physical map of rice will be useful for studying the structure and function of the genome, and for map-based cloning of various genes. We have therefore generated a physical map of the rice genome with yeast artificial chromosome (YAC) clones using DNA markers on our high-density molecular genetic map. The previously described YAC library (Umehara et al. 1994, Molecular Breeding 1: 79-89), which contains about 7,000 clones with average inserts of 350kb and covering about 6 times the rice genome, was screened using the 1,383 mapped DNA markers reported earlier (Kurata et al. 1994, Nature Genetics 8: 365-372). Screening was through the methods of colony hybridization and polymerase chain reaction (PCR). We have nearly completed the construction of a first-generation rice physical map using about 1,300 DNA markers. From a total of 4,757 YAC clones selected by one or more of the 1,033 markers, 2,449 unique clones could be identified. Out of the unique YAC clones, 1,988 were assigned each to a unique location on the chromosomes. The YAC clones aligned on the chromosomes formed 190 contigs, covering a total of 230 cM over the 12 rice linkage groups. It is estimated that these YAC contigs, together with the YAC clones outside contigs cover more than half of the rice genome. Alignment of the YAC clones along the genetic map also revealed that the physical distance corresponding to 1cM genetic distance varied approximately from 90kb to over 2Mb in different regions of the rice genome. More than 600 DNA markers, in addition to the previously mapped 1,383 markers, have been recently mapped in RGP (unpublished data). These markers are also being used for screening our YAC library. In addition, two other approaches, chromosome walking with YAC-end clones and fingerprinting of YAC clones with rice repeated sequences, are also being developed to facilitate making the physical map generated by the above-mentioned methods. We plan to finish soon a second-generation physical map covering more than 80% of the rice genome with YAC clones.