Development Of A Rice Chromosome 4 Specific Tiling Microarray And Expression Analysis Of Oryza Sativa Japonica Nipponbare Chromosome 4

Abstract As a member of the International Rice Genome Sequencing Project (IRGSP), the National Center for Gene Research (NCGR) took the task of completion of sequence of the Oryza sativa japonica Nipponbare chromosome 4. At the same time, NCGR initiated a genome-sequencing project of the Oryza sativa indica Guangluai 4 chromosome 4 in 1993. High collinearity as they share, construction of the physical map of one rice subspecies can benefit from the sequence scaffolds of the other rice subspecies. Anchoring sequence tag connector (STC) in silico and screening the whole BAC library by hybridization with labelled DNA probes are the major establishing the physical map for both rice subspecies. In this study, a new method of pool PCR was adopted to explore the potential of the available BAC liberaries. Pool PCR can be taken as an alternative for screening the BAC library, which is performed with multiplex DNA templates and multiplex primers in a single reaction system. With primers designed according to the distal sequence of seed BACs, I mapped a contig at the genetic distance 102.3cM by pool PCR.Seven BAC clones were identified partially overlapping the seed BAC H621D04. Six of them were missed from the results of screening BAC library by hybridization, which proves that pool PCR is an efficient method for extension of physical map. Finally I chose a BAC clone H418F10 for sequencing based on the result of fingerprinting. Rice (Oryza sativa) represents a model for cereal as well as monocot plants. The completion of genome sequence of the Oryza sativa japonica Nipponbare...