| Rice (Oryza sativa L.) is one of the world’s most important food crops, serving as a staple for more than 50% of the world population. Similar to other crops, rice suffers from many plant diseases that play an important role in determining the yield and cost of food. Rice bakanae disease (RBD), caused by the pathogen Fusarium fujikuroi, is becoming severely detrimental to rice production worldwide. Therefore, it is necessary to make a system research of bakanae disease, provide a reference for the breakthrough of the molecular genetic mechanism of resistance to bakanae disease. Identification of resistance genes is for the breeding application. Rice blast, bacterial blight (BB), sheath blight, bakanae disease, false smut, brown planthopper (BPH) and white backed planthopper are all destructive diseases and insects causing significant yield reduction in rice. Breeding new lines with multiple disease and insect resistance genes will ensure the rice yield safety. RNA-Sequencing of transcriptome and relative quantitative analysis of proteome after rice bakanae inoculation are conducted. Meanwhile, RIL permanent populations are used on QTL locating for bakanae disease resistance. Through association analysis of transcriptome and quantitative proteome to identify differentially expressed genes and proteins, and through the analysis of QTL location, the molecular genetic mechanism of resistance to bakanae disease is illustrated, to provide valuable information for future studies on the molecular mechanisms of rice bakanae resistance. In the aspect of breeding application of resistance genes, new restorers with multiple resistances to diseases and BPH are developed using the MAS technique and further evaluated by artificial inoculation in two years. These results impart valuable information for breeding resistance in rice.1. To understand the interaction between rice and F. fujikuroi, a moderate resistant genotype,9311(Oryza sativa indica), and a susceptible genotype, Nipponbare(Oryza sativa japonica), are used for transcriptome analysis. In total,1,152 and 1,052 transcripts are differentially expressed between the controls and the treatments for 9311 and Nipponbare, respectively. Comparative transcriptome analysis reveals different expression patterns for the two genotypes. Although some common defense-related enriched GO terms are shared in both genotypes, specific defense-related terms are enriched exclusively in 9311. A detailed comparison of defense-related DEGs reveals that certain WRKYs, WAK and MAP3Ks are responsible for the RBD resistance in 9311. The OsWAK112d gene is up-regulated in the resistant genotype. The POEI gene response to abiotic stress is modulated in Nipponbare. Combined the specific chromosome distribution of the DEGs ratio to the total transcripts with previous reports regarding QTL location, the defense-related genes WRKYs and MARKs on chromosome 1 that are modulated in 9311 upon infection might play a crucial role in the rice-F. fujikuroi interaction. Further characterization of these resistance genes may provide candidate genes for the development of molecular markers for rice bakanae resistance breeding programs. Transcriptomic dissection of the rice-F. fujikuroi interaction provides valuable information for future studies on the molecular mechanisms of rice bakanae resistance.2. Relative quantitative proteomic level is analyzed using TMT technique on the basic of the tanscriptics research for the 9311 variety after inoculation of the pathogen. Results shows that 8694 proteins are identified and 116 proteins are defined as differentially expressed proteins (DEPs). In the DEPs,89 proteins are up regulated and 27 DEPs are down regulated, which might suggest that more proteins are modulated and up-regulated to defense the invasion of the pathogen when rice suffers disease and other biotic stress. PATHWAY enrichment analysis of the DEPs shows that the highest enriched signaling pathway are Phenylalanine metabolism, Nitrogen metabolism, Phenylpropanoid biosynthesis, Diterpenoid biosynthesis, Arachidonic acid metabolism and Cadherin signaling pathway. These pathways directly or indirectly participate in the defence of rice to rice bakakane disease. Correlation analysis of transcriptome data and proteomics data in 9311 shows that,22 correlated differentially expressed genes are both identified in the two omics. The 22 correlated genes are low possitive correlated. Most of the correlated genes are modulated in the same direction. GO annotation of the 22 correlated genes shows that they are significantly enrich in the terms of ion binding, vesicle and catalytic activity.3.132 Recombinant Inbred Lines (RILs) from PA64S/9311 and 169 RILs from Nipponbare/9311 are evaluated of the seedling elongation character for rice bakanae disease resistance through artificial inoculation. Hereinto, seedling elongation and seedling weight are both evaluated for the RIL population from PA64S/9311. QTL mapping of the two characters is conducted using the two RIL populations. Seven QTLs are identified through the evaluation of the changes of seedling elongation and seedling weight in the two RILs after RBD inoculation. They can explain 11.0%-22.3% of their phenotypic resistance variances. Hereinto, 4 QTLs(qBE1.1, qBE9, qBE1.2 and qBE3) are found on the evaluation of the seedling elongation characters, which are located on chromosome 1,3 and 9, separately. The analysis of correlation between seedling elongation and weight has found that the two characters are significantly positive correlated. Further comparison of QTL physical internal shows that, similar physical internals are found between the QTLs of seedling weight in PA64S/9311 and the QTLs of seedling elongation in Nipponbare/9311. Physical internals of key genes obtained through transcriptomic dissection are listed. The location of the key genes is compared with the QTLs location of this study and previous reports. Results indicate that RBD-resistance-related QTLs or genes are almost distributed on chromosome 1 and 3.4. Ten new lines with BB, blast and/or BPH resistance genes are developed using MAS and ATS methods. Only HR13 with resistance genes to BB, blast and BPH is obtained. Besides BB and blast resistance, four lines (HR39, HR41, HR42 and HR43) demonstrate moderately reisistance to BPH, though MAS for BPH resistance genes is not conducted in developing the four lines. It suggests that there are unknown elite BPH resistance genes in the donor parent Zhongzul4. A more effective defense is demonstrated in the lines with Pi1 and Pi2 genes though the weather in 2012 is favorable to disease incidence. Blast resistance of the lines with one single resistance gene Pita, are easily influenced by the weather. |
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