Genetic And Comparative Analysis Of Simple Sequence Repeats On Rice Chromosome 4

Computational screening of `the chromosome 4 sequence of the rice Oryzasativa japonica Nipponbare revealed 1844 tandem simple sequence repeats (SSRs)or microsatellites ≥ 20 bp with repeated unit lengths of 1-6 base pairs, thus thefrequency was detected as one SSR in every 18.8 kb on the chromosome. While thedistribution of the SSRs along the chromosome was detected as one SSR per 23.8 kband 16 kb on the short and long arms respectively, there were no SSRs detected inthe core of the centromeric region. Although the poly(AT)n repeats represented themost abundant and length polymorphic class of SSRs on the chromosome, it did notoccur in the exons. GC-rich trinucleotide repeats (TNRs) were the most abundant inthe coding regions, representing 71.69% of the SSRs identified in the exons. 224SSRs were associated with the repetitive DNA sequences, most of them werepoly(AT)n tracts. Sequence variations of SSRs in the two subspecies of the Asiancultivated rice indica and japonica varieties were identified, revealing thatdivergence and convergence of the two subspecies could be traced by analysis ofSSRs. These results provide a great opportunity on SSR-based marker developmentand genome comparative analysis of the two subspecies of the Asian cultivated rice. Computation screening the complete genome sequences of Arabidopsis thalianarevealed 5652 SSRs(≥ 20 bp), the frequency was detected as one SSR in every20.6kb. No conspicuous difference of SSRs densities had been discovered betweenany two chromosomes of A. thaliana. Of 28470 A. thaliana coding sequences(CDSs), only 677 CDSs contained 725 SSRs. Most of codon repeats of A. thalianacorresponded to small hydrophilic amino acids. The SSRs in the conservative genesbetween A. thaliana and rice chromosome 4 showed no conservation. A total of23280 SSRs were found in the whole genome sequences of rice, the frequency was 5水稻基因组第 4 号染色体简单重复序列的遗传分析及比较基因组学研究detected as one SSR in every 15.52 kb. SSRs represented 0.21% of rice genomesequences, whereas SSRs only represented 0.13% of A. thaliana genome sequences.The density of SSRs in rice genome and genes was higher than that in A. thaliana. Itmight be one of reasons why the rice genome size is larger than that of the A.thaliana. Our result suggested that the genes of different species differ in SSRspreference as well as the genome of different species. Some hierarchical satellitesequences in rice and A. thalian are reported. Sequence analysis of a japonica BAC OSJNBa0039K24 identified a cluster ofsix tandemly arranged peroxidase genes, pod1, pod 2, pod3, pod4, pod5, pod6.Comparative and evolutionary analysis of indica and japonica peroxidase familysrevealed that the gene cluster occurred by tandemly gene duplications (osp1→osp2→osp3→osp4→osp5 and pod1→pod2→pod4→pod5→pod6). Pod3 is predicted tobe mitochondrion gene.