Chloroplast DNA Variation between and within Japonica and Indica Rice Subspecies
Date Issued
2005
Date
2005
Author(s)
Yang, Ya-Ching
DOI
en-US
Abstract
Chloroplast genomes in higher plants generally contain two large inverted repeats (IRs), separated by a large single copy region (LSC) and a small single copy region (SSC). In rice, the chloroplast genome is about 134.5-kb in length and comprises at least four rRNA genes, 30 tRNA genes, and over 100 genes that encoding proteins. By summarizing previous studies on DNA polymorphisms resulted from restriction sites analysis in Oryza, the inter-subspecific length-polymorphisms and SNPs between the chloroplast genomes of Japonica and Indica rice were verified. The cpDNAs have been sequenced completely only in three varieties (the Japonica type, Nipponbare and PA64S; and the Indica type, 93-11), and the relative variation between/within subspecies is still unclear due to lack of more representive varieties. In this study, nine varieties of each subspecies were used to elucidate inter- or intra-subspecific chloroplast variations, the chloroplast genes related to these variations, and the evolutionary relationships among chloroplast, nuclear and mitochondrial DNA. In a total sequence of 576-kb in length, 97 variations in the rice chloroplast genomes between Japonica and Indica, including 27 InDels and 70 SNPs, were detected. In the inter-subspecific variations, the InDel rate in the LSC region (0.03%) was much higher than the other regions, and the highest SNP rate was in the SSC region, followed by the LSC region. In addition, an I-35 was found around the 76 kb in the LSC region existed in KS139 merely, and two adjacent SNPs specifically emerged in CHS6, KSS2, TCN1, and TCS17. And the frequency of variation among Indica varieties was 6.6x10-3 per kb larger than that among Japonica varieties (8.2x10-4 per kb). Based on the differences in reverse-complementary sequence variations between Indica and Japonica varieties, and within Indica varieties, the timings of inversion incidents could be traced back at pre- or post-differentiation stages of rice subspecies, respectively. According to the results from BLAST queries, the average number of cpDNA fragments integrated into the nuclear chromosomes was 6.42, which was near to the number of seven of cpDNA flux to the mitochondrial genome, and it appeared that the occurrence of cpDNA transferring to the nuclear or mitochondrial genomes was frequently. And the averaged transferring frequency for a single copy cpDNA fragment was 6.05, and the transferred frequency for cpDNA fragments in the inverted repeat regions was twice (14 on average) more than the single copy regions. It also indicated that the cpDNA fragments transferring to the nuclear genome were distributed evenly over the chloroplast genome. Results of this study not only contribute the information on chloroplast DNA variations among varieties, but also facilitate further researches on the relation between chloroplast genes and important agronomic traits of rice.
Subjects
葉綠體基因體
秈稉
亞種間（內）變異
插入及缺失
單一核苷
酸多型性
重複序列
DNA序列倒置
chloroplast genome
inter- (intra-) subspecific variations between Japonica and Indica rice
InDel
SNP
repeat sequences
DNA sequence inversion
Type
thesis
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