Cloning Orthologous Transcription Factors And The Primary Study On Dynamics Of The Indica And Japonica Genome Differentiation In Rice (Oryza Sativa L.)

The gene annotation, gene function identification and the comparision of functional genes and indica-japonica genome have become the important focus of the study on functional genome since the rice genome sequencing have been completed. According to the sequences in databases of 9311(indica) and Nipponbare (japonica), the transcription factors were cloned and identified, and compared the difference of mPing and Ser/Thr amino acid protein kinase genes between 9311 and Nipponbare genome sequence. The results are as follows:1. An OsMYC gene and a putative OsGAI gene were cloned with homology search and RT-PCR in rice (Oryza sativa L.). The results of molecular structure analysis and homologous alignment of the OsMYC gene indicated that it has a typical DNA binding domain: basic/helix-loop-helix motif at the C-terminus, it has 78%, 48% identity with the MYC7E, AtMYC2, respectively. So the 3 genes may be orthologous genes.2.The OsGAI gene and the OsMYC gene were used to cunstruct overexpressing vectors and transform Arabidopsis with Agrobacterium infection. 36 transgenenic plants with OsMYC gene and 27 with OsGAI gene were obtained, respectively. The height of Arabidopsis plant transformated with OsGAI gene is obviuosly shorter than the control.3. We found there are three kinds of alternative splice varieties of a MYB gene, and cloned all the differrent products.4. The difference of Ser/Thr amino acid protein kinase genes between 9311 and Nipponbare were compared. Six-Two out of 138 Ser/Thr amino acid protein kinase genes had differences between the two genome sequence by sequence alignment. Thirty genes were seleted and investigated by PCR, out of these 6 genes had nucleotide deletion in 9311. We estimated that there were about 12 Ser/Thr amino acid protein kinase genes in Nipponbare which were differrent to 9311. Thus, the ratio of the difference of Ser/Thr amino acid protein kinase gene between 9311 and Nipponbare was about 9%, which was obviously higher than the average difference (2%) between 9311 and Nipponbare genomic sequences. The result showed that Ser/Thr amino acid protein kinase gene may be a hot point of the Indica and Japanica genome differentiation.5. The copy numbers and location of a retrotransposon mPing were compared in 9311 and Nipponbare genome sequences. Twelve copies and 37 copies of mPing existed in 9311 and Nipponbare, respectively. Only one copy lied in the same location in the two genomic sequences. Eight copies existed only in 9311 were tested by PCR. The resultsshowed that there were not mPing at the same location of 9311 in Yuanjiang and Dongxiang common wild rices (Oryza rufipongon Griff.) as well as Japonica varieties, however there were copies in other Indica varieties. The 22 mPing copies of Nipponbare had no copies in the same location of 9311 and two common wild rices. The result indicated that these copies of the mPing retrotransposon came into being during the domestication process of cultivated rice. So the retrotransposon may act as one of the dynamics factors of genome evolution of rice..6.13 SSR and 19 RFLP indica-japonica specific molecular markers were located on rice chromosome with electronic locating. Among them, ten SSR and 13 RFLP markers located in haplotype region of rice chromosome, which is a set of genes or sequences without homologous recombination. The nonradom association of isozyme may be related to haplotype.