Soybean[Glycine max(L.)Merr.],grown for its edible seed protein and oil,is often called the miracle crop because of its many uses.However,one of the major constrains in soybean production is viral pathogens.Among the various viral diseases,Soybean mosaic disease is reported to be the most destructive viral disease caused by Soybean mosaic virus(SMV)and is found in all over the world including China.Early infection by the virus gives the highest reduction in yield(50-80％).Insecticidal sprays and cultural methods are not always effective.Although,the control of the aphid,the vector has not proved practical or reliable(a means of virus management).Exploitation of host plant resistance by means of growing resistant varieties is the best method of controlling SMV.Soybean is a vital crop in China and represents the major economic crop to small hold farmers.Three major soybean producing regions in China are Northeast China,Huang-Huai Valleys,and Southern China.One of the major constraints hindered in these areas in soybean production is SMV.National centre for soybean improvement(NCSI),China,has been actively working on SMV research for the past few decades.Totally,22strains,(SC1-SC22)were identified from three major soybean producing regions,by different researchers,during the period from1999-2013.NCSI collected soybean cultivars and landraces from China and other countries and they screened against the Chinese SMV strains as well as identified as resistant sources.Meanwhile,identification and analysis of resistant genes for Chinese SMV strains are currently in progress.Recently,China has faced considerable reductions in soybean seed yields due to moderate virulent SMV strains SC5and SC20.Kefeng.No.1and Qihuang.No.1cultivars are showing resistance to SC5and SC20,respectively.However,the genetic and molecular basis of resistance is unknown.Therefore,it is necessary to explore a resistance study for SC5and SC20.That could be utilized in SMV breeding programs for the production and deployment of cultivars containing enhanced SMV resistance.With this background knowledge,the objectives of this study were proposed as;i)Inheritance analysis and identification of the location of the gene conferring resistance to SC5and SC20,ii)Identification of the candidate genes to the resistance genes of SC5and SC20.　　To examine the inheritance of resistance in SC5,P1,P2,F1,F2and RIL populations of the cross Kefeng.No.1(resistant,R)between Nannong1138-2(susceptible,S)were used.F1was the same to Kefeng.No.1,F2and RILs segregated in phenotypic ratios of3R:1S and1R:1S respectively.These results confirmed that a single dominant gene confers the Kefeng No.1resistance to SC5.Subsequently,we tracked the genomic region conferring the SC5resistance.It was found to be Bin352-Bin353of500Kb and is present on the Chromosome2(LG D1b).The location was found out using427RILs and high density bin map composed of4703bin markers.The500Kb genomic regions contained thirty eight putative genes.To find out thepossible candidate geneswe utilized the whole genome resequencing(WGRS)data of427RILs SNPs information.Totally,271SNPs are present in the500kb genomic region.Of these271SNPs,107SNPs were found on the twenty nine genes.Each gene contained one to sixteen SNPs.The remaining nine genes did not contain any SNPs.To know the association between107SNPs and the phenotype data of the427RILs,they were used to testing at cut off p＜0.01and p＜0.001significance level by chi square analysis.This showed that60SNPs were associated with SC5resistance.These60SNPs were found on twenty one genes.Further,we used the concept that all the given SNPs and their corresponding genes are used to associate with the concerned trait.With this concept in mind;we have selected the eleven candidate genes.The functions of these genes are verified by qRT-PCR analysis.