PAG-VI: A 120 KB RESOLUTION CONTIG MAP OF THE RICE GENOME

PAG-VI  Plant & Animal Genome VI Conference

Town & Country Hotel, San Diego, CA, January 18-22, 1998.

W89

A 120 KB RESOLUTION CONTIG MAP OF THE RICE GENOME

GUOFAN HONG1 2, Yuemin Qian1, Shuliang Yu1, Xin Hu1, Jia Zhu1, Wenhua Tao1, Wen Li1, Chen Su1, Haiying Zhao1, Longfang Qiu1, Di Yu1, Xiaohui Liu1, Boqian Wu1, Xianliang Zhang1, Wenhui Zhao1

  1. National Center for Gene Research, CAS, 500 Caobao Road , Shanghai 200233, China
  2. Shanghai Institute of Biochemistry , CAS, 320 Yueyang Road, Shanghai 200031, China

Based on our "BAC-Fingerprinting-Marker Location" strategy, rice contigs were constructed with approx. 92% coverage of the genome. The computer software used in the systematic rice fingerprints analysis was designed at the Sanger's Center, Cambridge, UK. A BAC library of approx. 22000 clones with average inserts of 120 kb (i.e. about 7 equivalents of the rice genome) were used in the map construction. 631 contigs of various length in average depth of approx. 3.5 clones were obtained. Hybridization between BAC clones within contigs of random sampling was performed, which has confirmed the overlaps of fingerprints. Contigs were mapped on the chromosomes with the aid of molecular markers. 161 contigs were found to contain more than two markers (up to 5 markers). The physical distances between molecular markers in these contigs were determined. The majority of markers used in this project was from BS 125. The order on the chromosomes of contigs with these markers was therefore determined based on the marker synteny relationship among cereals. A small number of markers was from Nipponbare. The order of contigs with these markers could not be determined (because the relative location of the markers of the two varieties were not known). These contigs were only temporarily placed at the bottom of chromosomes, to which they belonged. Since the order of the contigs on chromosomes was based on the marker synteny relationship, certain error in their order may be possible, which, however, could be corrected during the course of map refining, gap filling and DNA sequencing. It should be noted that BAC clones located at both extremes of the contigs were often much less of redundancy, therefore, they need to be further checked for their overlapping before using them as extending clones for gap-filling.

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