| Rice is the most important crop for human consumption, providing staple food for more than half the world's population. The well-established protocols for high-efficiency genetic transformation, widespread availability of high-density genetic and physical maps , and high degrees of synteny among cereal genomes combine to make rice a unique organism for studying the physiology, developmental biology, genetics, and evolution of plants. Meanwhile , microsatellite marker is an indispensably important tool to study the hypothesis of rice heterosis.A lot of microsatellites exist in rice genome, but it can not been put into practice completely for the sake of expensive investment and development period. However, a new approach should be generated to develop such useful tool through bioinformatics.The main results are summarized as follows:1. With the help of SSR perl script, more than 237 thousand mirosatellite locies were found in 93-11 species, of which there are 14415 microsatellite locies have length polymorphism between 93-11 and Nipponbare species. The most part of microsatellite, whose length is shorter than 10bp, equals to12138.1103 locies distributed from 10bp to 20bp, the remained part, which is longer than 20bp, equal to 1174 or so.2. 505 released primer, published by Temnykh, E.T, were studied on the aspect of average length. Generally speaking, amplified SSR products average length range from 100 to 200.3. 100 randomly selected primers from the database were taken advantaged of verifying their practically amplifying effect, most of them can get the amplified products, and the average length focused on the region of 100bp to 200bp.4. Of the randomly selected 100 primers, 19 primers has the difference less than 10bp,41 primers less than that of 20, and 40 primers more than that of 20bp.Onlynot less than 8bp difference can be distinguished through the 3%, 4v/cm gel and electrophoresis for 2 hours. And the SDS-PAGE can distinguish the difference less than 8 base-pair.5. 87 microsatellites were distributed to certain contigs in 12 chromosomes, of which there were 11 microsatellites were anchored in chromosomel, and the related average coverage area was 16.5 centimorgan. However, Optimistically supposing, the precision can be improved to 0.22 centiMorgan or 57 kilo base-pair on the presumption that half of the entire markers can be utilized.6. 6 rice species 93-17, Nipponbare, Ce64, Minhui63, Zhonghua9 and 02428 were clustered to 2 main classes with 65 markers and hierarchical method: Indica and japonica. It is identical with the genealogical classification of these 6 species, which also proved the validity and particularity of the neodevelopmental Microsatellite markers.7. Of the entire microsatellite sequences, the average length of SSR is 13.2 base-pair in 93-11 and 12.6 base-pair in Nipponbare. The maximum mononucleotide repeat motif is A/T, and the maximum dinucleotide repeat motif is AT/TA, which construct the main part of SSR length difference between 93-11 and Nipponbare. The maximum trinucleotide repeat motif is CGC/GCG, which is closely associated withthe gene according to the prevenient study. The average content of microsatellites is 0.86% in 93-11, and 0.80% in Nipponbare. The part of beyond tetranucleotide repeat motif was not taken into account. |
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