Construction of YAC contigs on rice chromosome 5.

Abstract

A physical map of rice chromosome 5 was constructed with yeast artificial chromosome (YAC) clones along a high-resolution molecular linkage map carrying 118 DNA markers distributed over 123.7 cM of genomic DNA. YAC clones have been identified by colony and Southern hybridization for 105 restriction fragment length polymorphism (RFLP) markers and by polymerase chain reaction (PCR) screening for 8 sequence-tagged site (STS) markers and 5 randomly amplified polymorphic DNA (RAPD) markers. Of 458 YACs, 235 individual YACs with an average insert length of 350 kb were selected and ordered on chromosome 5 from the YAC library. Forty-eight contigs covering nearly 21 Mb were formed on the chromosome 5; the longest one was 6 cM and covered 1.5 Mb. The length covered with YAC clones corresponded to 62% of the total length, of chromosome 5. There were many multicopy sequences of expressed genes on chromosome 5. The distribution of many copies of these expressed gene sequences was determined by YAC Southern hybridization and is discussed. A physical map with these characteristics provides a powerful tool for elucidation of genome structure and extraction of useful genetic information in rice.