Physical mapping of rice chromosome 1 with yeast artificial chromosomes (YACs)

We have constructed a physical map of rice chromosome 1 using yeast artificial chromosomes (YACs). A YAC library of 350 kb average insert size, covering about 6 rice haploid genome equivalents, was screened using 182 DNA markers which we had previously located on chromosome 1, by colony hybridization and polymerase chain reaction (PCR) amplification. One hundred and sixty-two DNA markers identified at least one YAC each carrying one, two or more marker sequences, for a total of 476 clones. Of these identified YACs, 284 were located in their original positions on chromosome 1. These 284 YACs defined 69 YAC contigs or islands which are estimated to cover more than 60% of the total chromosome length. The use of mapped DNA markers in constructing a physical map facilitates the integration of genetic and physical maps, as well as fine ordering of the DNA markers, especially at sites where the markers are clustered tightly on the genetic map. Our high density molecular map has been proven, by chromosome landing with YACs using mapped DNA markers, to cover more than half of the entire length of chromosome 1. The remaining 192 YACs were selected by other copies of DNA markers that mapped on chromosome 1. This description of the YAC contigs formed on chromosome 1 constitutes the second report of rice physical mapping, following that for chromosome 6.