Genome Wide Association Study On Heat Tolerance During Grain-filling Stage And Main Agronomic Traits In Rice

Rice is the main food crop for more than half of the world's population.And maintaining stable yield of rice is crucial.High temperature damage is one of the main abiotic stresses,which poses a great threat to rice yield.Therefore,it is one of the main breeding targets to cultivate rice varieties with high temperature tolerance.In this study,the relative heat-resisting index(RHI)and rice quality were used as the identification criteria to assess the heat resistance of rice during the grain-filling stage,and the heat-resistant QTLs and candidate genes during the grain-filling stage were excavated through genome wide association analysis.Then,micrornas associated with these heat-resistant associated sites were mined by bioinformatics,to explore the possible adaptive mechanism of microRNA under high temperature stress.In addition,the main agronomic traits(rice growing period,plant height,effective panicle number,panicle length,spikelet density,seed setting rate,thousand grains weight,yield per plant,spikelet per panicle and grains per panicle)were analyzed by GWAS to find new genetic sites and find candidate genes to control these traits and provide a theoretical basis for improving comprehensively agronomic traits of rice.The main results are as follows:1.In this study,233 core materials with relatively consistent rice growing period were selected from 3K Rice Genome Project.The variation detection of the resequencing data was conducted using BWA,Samtools,Picard,GATK,Plink with IRGSP1.0 as the reference genome,so as to obtain 2429 kb high-density genotype data.By analyzing the linkage disequilibrium of the whole genome,the average attenuation distance of LD in the whole genome is 63 kb.The structure of the material group was analyzed,and the group was divided into 9 subgroups.2.Three QTLs with relative heat-resisting index during the grain-filling stage were located in the core material and distributed on 2,4 and 8.Among them,q RHI2 is on chromosome 2,and the explanatory rate of phenotype is 15.08%.q RHI4 is on chromosome 4 with a phenotypic explanatory rate of 13.25%.q RHI8 is on chromosome 8,with a phenotypic explanatory rate of 15.70%.q RHI8 has been reported in previous studies.In addition,a total of 28 QTLs related to rice quality were identified after high temperature stress during grain-filling period,all of which were distributed all chromosomes except chr3.Among them,q Ht Gt6 had the highest phenotypic explanatory rate of 28.1%,q Ht CD10 was followed by 24.70%.In addition to q Ht HR9 and q Ht GT6,the other 26 sites were all new loci located in this study.Three candidate genes related to heat resistance during grainfilling stage were selected as LOC?Os06g12450 is related to gelatinization temperature after heat stress,LOC?Os02g34900 and LOC?Os02g47270 is related to gel consistency after heat stress.3.Four heat-related microRNAs of the same family during grain-filling stage were screened by RHI at the QTL locus q RHI8 on chromosome 8,namely osa-mi R395 h,osami R395 i,osa-mi R395 k and osa-mi R395 y respectively.Micro RNAs with genomic differences between heat resistant differences varieties ZS97 b and SYD2 during grainfilling stage were searched,and these microRNAs were co-located with heat-resistant QTLs during grain-filling stage that had been previously located.Three heat-resistant microRNAs of osa-mi R2120-3p,osa-mi R395 w,and osa-mi R812 j during the grain-filling stage were screened.4.A total of 43 loci significantly associated with main agronomic traits were identified in the core material population,including 6 related sites for rice growing period,1 related sites for plant height,9 related sites for effective panicle number,4 related sites for panicle length,10 related sites for spikelet density,2 related sites for seed setting rate,2 related sites for thousand grains weight,1 related sites for yield per plant,1 related sites for spikelet per panicle,7 related sites for grains per panicle.In addition to q RGP7.2,q PH12,q PL6.2,q SD6.2,q TGW1.1,q GP1,q GP5.2,the other 36 are all new loci located in this study.Six candidate genes related to agronomic traits were selected as LOC?Os12g18760 is related to plant height,LOC?Os03g33530 is related to effective panicle number,LOC?Os06g30940 is related to panicle length,LOC?Os01g49810 is related to thousand grains weight,LOC?Os09g25260 is related to yield per plant and LOC?Os09g32620 is related to spikelet density and spikelet per panicle.