Genome-Wide Association Study On Resistance To Rice Black-Streaked Dwarf Virus Disease In Japonica Rice Varieties

Rice black stripe dwarf disease(Rice black-streaked dwarf virus disease,RBSDVD)is a virus disease transmitted by small brown planthopper Laodelphax striatellus Fallén(SBPH),which not only harms rice but also causes maize coarse shrinkage.The plant showed obvious dwarfing and the leaf color became thicker and green,the heading stage is not heading or heading incomplete,the seed setting rate decreases or is not strong,which seriously affects the safe production of rice and corn.So far,the control measures for rice black stripe dwarf disease are various,and the use of chemical pesticides to control the spread of small brown planthopper is the most widely used way.However,the method has a large investment and has an impact on environmental ecological security.It is considered to be the most economical,environmentally friendly and effective control measures to screen high resistant germplasm resources,explore resistance genes and cultivate resistant rice varieties.Nevertheless,because black dwarf virns can not transmit virus through egg,the source of resistance identification needs to be re-toxic in each generation.The procedure of resistance identification is complicated,the period is long and the stability of identification results is poor,which greatly restricts the screening of RBSDVD resistance sources and the discovery of resistance genes.Only a few RBSDVD resistant sources have been reported,but no cloning of resistance genes has been reported.Little is known about the molecular mechanism of rice resistance RBSDVD.Therefore,in order to explore the RBSDVD resistance sources and genes,this study completed the identification of 1072 japonica rice resources from 18 provinces and cities in China,analyzed the resistance differences of japonica rice varieties in different provinces,and identified 187 extrame resistant varieties for two consecutive years.Genome data were obtained by re-sequencing,genome-wide association analysis(GWAS)was used to explore the relevant disease resistance sites,and the candidate genes in the interval were analyzed.The main contents of the study were as follows:1 Identification of resistance to dwarf disease in rice with 1072 japonica riceIn this study,the field natural induced identification method was used to identify the resistance of rice black-streaked dwarf disease on 1072 domestic japonica rice resources from 18 provinces and cities in my country with different germplasm resources.The results showed that the average incidence of the tested materials was 34.33%,of which 54 showed high resistance(incidence<5%),only 5.03%,and the above materials(incidence>15%)accounted for 74.47%.An average incidence rate of 167 local varieties was 44.13%,while the average incidence rate of cultivated varieties was 31.12%,indicating that local varieties RBSDVD more sensitive than cultivated varieties.The results showed that there were great differences in the resistance level of japonica rice varieties cultivated in different provinces.The order of average incidence of different geographical varieties was:Heilongjiang>Hebei>Zhejiang>Ningxia>Hunan>Jilin>Yunnan>Guangxi>Guangdong>Beijing>Fujian>Jiangxi>Liaoning>Xinjiang>Taiwan>Henan>Jiangsu>Shandong.The average incidence rate of japonica rice varieties in Heilongjiang Province was 57.85%,while that of japonica rice varieties in Jiangsu,Henan and Shandong provinces was only 13.22%,16.23%and 10.68%respectively.2 Genome-wide association study on resistance to rice black-streaked dwarf virus disease in Japonica riceAfter that,we selected a total of 187 varieties with high susceptibility or high resistance in 2017,and repeated identification in 2018.The selected varieties were re-sequenced and 5,187,315 SNPs were obtained using Nipponbare as the reference sequence,and combined with the biennial table Genome-wide association analysis was performed on the type data using the mixed linear model(MLM)in the TASSEL software,and significantly associated SNPs were detected on chromosomes 11.We paid attention to the locus on chromosome 11,analyzed the candidate genes in the interval of the associated locus,and conducted preliminary analysis of the three genes LOC_Os11g31940,LOC_Os11g32210,and LOC_Os11g32240 as candidate genes.There were six non-synonymous SNP,in the coding region of LOC_Os11g31940 japonica rice varieties.The gene can be divided into three haplotypes,among which haplotype 2 and haplotype 3 are significantly resistant to RBSDVD.The expression levels of haplotype 1 and haplotype 2 were not significantly different before and after susceptible,and the expression levels of susceptible haplotype 3 in resistant varieties were significantly lower than those of unsensitive varieties.Further analysis of the Rice3K database,there are 8 haplotypes,haplotype 2 and haplotype 3 analyzed by japonica rice also showed haplotype resistance haplotypes in Rice3K.There are six non-synonymous SNP,in the coding region of the LOC_Os11g32210,which can be divided into five haplotypes,haplotypes 3-5 significantly resistant to RBSDVD;expression analysis showed that haplotypes 1 and haplotypes 2 decreased significantly after induction,and haplotypes 3-5 showed little difference before and after induction.There are two non-synonymous SNP,in the coding region of LOC_Os11g32240,which can be divided into two haplotypes,among which haplotype 2 is signfficantly resistant to RBSDVD.Expression analysis showed that haplotype 1 and haplotype 2 increased significantly after infection,and haplotype 2 increased less than haplotype 1.Rice3K database was further analyzed.There were 5 haplotypes.haplotype 1 and haplotype 2 analyzed by japonica rice also showed disease resistance in Rice3K.The discovery of the above sites and the acquisition of candidate genes lay a foundation for the cloning and elucidation of the resistance mechanism of the candidate genes.This study clarifies the resistance differences RBSDVD japonica rice varieties in different provinces of china and provides a reference for guiding resistance breeding.the excavation of the above high resistance varieties and loci provides effective materials and gene resources for resistance breeding,and lays a foundation for the analysis of the mechanism of rice resistance to RBSDVD.