Genome-wide Association Studies Of Important Agronomic Traits In Rice Germplasm

In this study, 5,291 SNPs were used to analyse genetic structure of 523 rice germplasms and to perform genome-wide association studies(GWASs) for plant type, grain color, direct-seeding and seedling blast resistance related traits. The main results were as follows:1. The results of population structure of 523 accessions indicated that the panel can be divided into indica(469) and japonica(54) subspecies. The population differentiation coefficient(FST) was 0.56 suggesting an obvious population differentiation. Moreover, the indica panel can be divided into four subgroups and one mixed subgroup. The FST value ranged from 0.05 to 0.25 indicating small or middle differentiations among five subgroups.2. The GWASs were performed based on the indica subpopulation. For plant type related traits, 114 and 161 significant loci were identified under Lingshui and Hangzhou environments, respectively, and 10 significant loci were obtained across two environments. For grain color related traits, 12 and 11 significant loci were detected under two environments, respectively, and six significant loci were obtained under two environments. For direct seeding related traits, eight significant loci were detected under two environments, respectively, and two significant loci were identified across two environments. For seedling blast resistance trait, 16 isolates were used for inoculation. A total of 127 significant loci were detected in Hangzhou environment.3. Pleiotropy analyses were performed on the significant loci. For plant type and grain color related traits, 54 significant loci including NAL1 and Rc showed clear signal of pleiotropy. In particular, a long genome region on chromosome 11, including nine loci, was associated with both flag leaf length and ratio of flag leaf length and width. The pleiotropic analyses of blast resistance loci indicated that Pi9、Pi5、Pi56(t) and Pita were detected at least two or more isolates. In addition, there were eight new loci that can be detected at least three isolates. The results indicated that these loci showed a broad spectrum of blast resistance.4. For tiller angle trait, four candidate genes, including LOC_Os08g33150, LOC_Os08g33160, LOC_Os08g33200 and LOC_Os08g33420, with large differences in expression level had been identified. The expression level of LOC_Os08g33160 was 57 fold changes between two groups of accessions with different phenotypes. The sequencing results showed that a C-T key mutation occurred in the fourth exon leading to mRNA from CAA to UAA and causing the translation terminated in advance. Therefore, the gene would be the most likely candidate gene for controlling rice tiller angle.5. For seedling blast resistance trait, 45 R genes including four cloned genes had been obtained. These R genes are mainly distributed on chromosome 11(18 genes), 6(9) and 12(8) displaying a clustered distribution. A previously reported R gene, LOC_Os12g23930, was included in the 45 candidate genes. RT-qPCR results showed that the expression level of this R gene was significantly down-regulated 5.6 times after inoculation, which was in complete agreement with previous report.6. Transcription sequencing of resistant variety inoculated with isolate S182 identified 282 up and 401 down-regulated genes including eight R genes. The LOC_Os01g66020 might be involved in the regulation of rice bacterial blight resistance. Combined with the GWAS results of S182, three candidate genes, including LOC_Os02g02850, LOC_Os02g41590 and LOC_Os02g41630, were obtained by using the two methods. Interestingly, the LOC_Os02g41630, which is highly homologous with OsPAL5, is one member of phenylalanine ammonia-lyase gene family(PAL)(OsPAL1), while another member of PAL, OsPAL4, has a certain resistance to white leaf blight, sheath blight and rice blast implying that the candidate gene might be an important gene for regulating rice seedling blast resistance.