Genome-wide Association Study And Transcriptome Analysis Of Rice Seed Dormancy

Rice seed dormancy is a complex quantitative trait that is influenced by both genetic and environmental factors.In rice production,a moderate and balanced level of seed dormancy is one of the important factors that determine seedling establishment in the early stage or yield formation in the later stage.Therefore,it is important to investigate the genetic characteristics of rice seed dormancy,to explore the key genes of rice seed dormancy,and to cultivate good varieties with moderate and balanced dormancy for rice genetic breeding and food security.In this study,the dormancy of rice was investigated by genome-wide association analysis(GWAS)and transcriptome sequencing(RNA-seq)technology,and the results are as follows:1.195 resequenced germplasm resources were used as materials,and the germplasm dormancy level was measured by the germination rate of germplasm resources under non-dormancy breaking and dormancy breaking(dry heat and GA)treatments,and the results showed that the dormancy phenotypic variation of germplasm resources was wide,and both dry heat and GA treatments could effectively release seed dormancy,and most of the germplasm dormancy levels within the population were low,and a few materials with higher dormancy levels could be used for germplasm genetic improvement.2.GWAS based on a mixed linear model using 1 120 223 high-quality SNPs for germination rate in 195 germplasm resources identified 30 quantitative trait loci(QTLs)significantly associated with seed dormancy(p < 10-4),distributed on 10 chromosomes,explaining 7.3-20.4% of the phenotypic variation.12 of the QTLs overlapped with regions of previously reported QTLs,and the rest were novel loci.3.QTLs detected jointly under two or three treatments(q GR4-4,q GR4-5,q GR8,q GR11-4)and the most significantly associated QTL detected under a single treatment(q GR3)were analyzed and screened for 13 high confidence candidate genes.These genes were strongly expressed during seed germination and during seed development,and were significantly induced by multiple hormone treatments.4.To further understand the biological function and genetic mechanism of seed dormancy in rice,eight high-dormant and ten low-dormant germplasm were used as materials and seeds were germinated and treated for 48 h.Seed dormancy differentially expressed genes(DEGs)were analyzed according to Indica and Japonica subgroups using RNA-seq technique.2,090up-regulated and 2 640 down-regulated DEGs were obtained,and it was found that the number of Indica DEGs was much higher than that of Japonica subpopulation.Based on gene annotation information,transcription factor and protein kinase databases,71hormone-related genes(ABA,GA,IAA,etc.),256 transcription factors(MYB,b HLH,C2H2,NAC and other families)and 185 protein kinases(RLK and other types)were identified.5.GO enrichment analysis revealed that seed dormant DEGs of the Indica subgroup were significantly enriched in structural molecular activity functions,ribosome-related cellular components,and biological processes such as cell cycle,DNA metabolism and nucleic acid metabolism;seed dormant DEGs of the Japonica subgroup were significantly enriched in vesicle-like cellular components and biological processes such as photosynthesis,precursor metabolite and energy production,and secondary metabolism.KEGG enrichment analysis revealed that seed dormancy DEGs in both Indica and Japonica subgroups were significantly enriched in metabolic pathways,protein processing in the endoplasmic reticulum,carbon metabolism and phenylpropanoid biosynthesis pathways in both Indica and Japonica subgroups.The results indicated that hormones,transcription factors,protein kinases,protein synthesis,energy metabolic pathways,redox reactions,cell wall modifications,and chromatin modifications were the factors responsible for the differences in seed dormancy and germination between Indica and Japonica as well as the differences in high and low seed dormancy.6.29 candidate genes for seed dormancy/germination were identified using weighted gene co-expression network analysis(WGCNA)in six modules(pink,purple,blue,brown,turquoise and yellow)associated with hormones,epigenetic modifications,redox,sugar metabolism,cell wall modifications,s HSP,etc.in Indica and Japonica or significantly differentially expressed specifically in high and low dormancy varieties,which may be important factors involved in regulating seed dormancy and germination.