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An integrated physical and genetic map of the rice genome

Mingsheng Chen et al. Plant Cell. 2002 Mar.

Abstract

Rice was chosen as a model organism for genome sequencing because of its economic importance, small genome size, and syntenic relationship with other cereal species. We have constructed a bacterial artificial chromosome fingerprint-based physical map of the rice genome to facilitate the whole-genome sequencing of rice. Most of the rice genome ( approximately 90.6%) was anchored genetically by overgo hybridization, DNA gel blot hybridization, and in silico anchoring. Genome sequencing data also were integrated into the rice physical map. Comparison of the genetic and physical maps reveals that recombination is suppressed severely in centromeric regions as well as on the short arms of chromosomes 4 and 10. This integrated high-resolution physical map of the rice genome will greatly facilitate whole-genome sequencing by helping to identify a minimum tiling path of clones to sequence. Furthermore, the physical map will aid map-based cloning of agronomically important genes and will provide an important tool for the comparative analysis of grass genomes.

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Figures

Figure 1.
Figure 1.
BAC-Based Physical Map of the Rice Genome. The RGP genetic markers used for anchoring are listed at right in red. Next to the RGP genetic markers are the genetic positions in centimorgans. In the middle is the physical map on scale. The anchored portions are shown in red and the gaps are shown in black. At left are the contigs in order. The positions of the centromeres are shown in yellow; they are based on the RGP genetic map (Harushima et al., 1998; Saji et al., 2001). The centromeres of chromosomes 1, 6, 7, and 9 are mapped to single genetic positions at 73.4, 65.8, 49.7, and 0.8 cM, respectively. The centromeres of chromosomes 3, 4, 5, 8, 11, and 12 are mapped in genetic intervals of 0.8 cM (85.2 to 86 cM), 3.7 cM (19.6 to 23.3 cM), 1.4 cM (53.2 to 54.6 cM), 3.5 cM (50.8 to 54.3 cM), 1.1 cM (54.8 to 55.9 cM), and 3.3 cM (48.2 to 51.5 cM), respectively. The centromere of chromosome 10 is mapped to 15.4 to 15.9 cM by FISH using a centromere-specific repeat as a probe (Cheng et al., 2001). The centromere of chromosome 2 was mapped originally to 50 to 50.3 cM (Harushima et al., 1998). However, this region (∼900 kb) is located within a single contig with a physical-to-genetic distance ratio of 369 kb/cM, whereas the neighboring contig has severely suppressed recombination (>1 Mb/cM). Therefore, we have included 50 to 54.6 cM as the centromeric region for chromosome 2.
Figure 2.
Figure 2.
FPC Display of Contig 219. Clones highlighted in green are in shotgun sequencing. Clones highlighted in yellow are redigested finished clones from GenBank, and the corresponding BAC clones are shown in gray.
Figure 3.
Figure 3.
Genetic Recombination in Chromosomes 1, 4, and 10. The x axis represents the physical distance in megabases along the chromosome. The y axis represents the ratio of genetic distance to physical distance (cM/Mb). The approximate centromere positions are marked with arrowheads (CEN). The physical distance intervals for which cM/Mb was estimated are based on the size of a single contig if two or more genetic markers were used in contig anchoring or the sizes of two or more contigs if a single genetic marker was used in contig anchoring. Estimated cM/Mb was extended to neighboring gaps in the physical map.
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