We have constructed a high resolution rice genetic map containing 1,383 DNA markers at an average interval of 300 kilobases (kb). The markers, distributed along 1,575 cM on 12 linkage groups, comprise 883 cDNAs, 265 genomic DNAs, 147 randomly amplified polymorphic DNAs (RAPD) and 88 other DNAs. cDNAs were derived from rice root and callus, analysed by single-run sequencing and searched for similarities with known proteins. Nearly 260 rice genes are newly identified and mapped, and genomic DNA and cloned RAPD fragments were also sequenced to generate STSs. Our map is the first significant gene expression map in plants. It is also the densest genetic map available in plants and the first to be backed up comprehensively by clone sequence data.
Yeast artificial chromosome (YAC) clones were arranged on the positions of restriction fragment length polymorphism (RFLP) and sequence-tagged site (STS) markers already mapped on the high-resolution genetic maps of rice chromosomes 3 and 11. From a total of 416 and 242 YAC clones selected by colony/Southern hybridization and polymerase chain reaction (PCR) analysis, 238 and 135 YAC clones were located on chromosomes 3 and 11, respectively. For chromosomes 3 and 11, 24 YAC contigs and islands with total coverage of about 46% and 12 contigs and islands with coverage of about 40%, respectively, were assigned. Although many DNA fragments of multiple copy marker sequences could not be mapped to their original locations on the genetic map by Southern hybridization because of a lack of RFLP, the physical mapping of YAC clones could often assign specific locations of such multiple copy sequences on the genome. The information provided here on contig formation and similar sequence distribution revealed by ordering YAC clones will help to unravel the genome organization of rice as well as being useful in isolation of genes by map-based cloning.
Physical maps of rice chromosomes 4 and 7 were constructed by landing yeast artificial chromosomes (YACs) along our high-density molecular linkage map. Using 114 DNA markers, 258 individual YACs were located on chromosome 4. Sixty-two out of 258 YACs carried two or more DNA marker positions and formed 16 contigs which covered a total length of 17.1 cM. The other YACs were arranged to 23 positions. On chromosome 7, 203 individual YACs were landed on 109 DNA markers. Sixty-four out of 203 YACs formed 15 contigs which covered a total length of 21.8 cM and 139 YACs were localized to 26 positions. Chromosomes 4 and 7 were covered with minimum tiling paths of 45 and 48 YACs, respectively. Taking the average size of YAC insert DNA to be 350 kb and the entire genome size to be 430 Mb, about 16-18 Mb of each chromosome or an estimated 50% of their total lengths have been covered with YACs. Physical maps of these 2 chromosomes should be of great help in identifying useful trait genes and unraveling genetic and biological characteristics in rice.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.