Genome-wide Association Study for Sclerotinia sclerotiorum Resistance of Soybean

doi:10.7668/hbnxb.20190364

Abstract

Abstract: This study aim to find candidate sites or candidate genes that are strongly associated with Sclerotinia sclerotiorum resistance of soybean,and provide reference for the molecular markers development and resistance gene cloning,and serve resistance breeding of soybean.The genomic DNA of 126 Canadian soybean materials was digested using Ape k Ⅰ enzyme and sequenced via the Illumina Hiseq2000 platform and genotyping;The cotton pad technique was used to inoculate the 126 materials with Sclerotinia sclerotiorum and to assess their phenotype. Structure 2.3.4,SPSS 20.0,TASSEL 5.0 and PLINKv 1.07 were used to conduct whole genome association analyses(consider only additive effects).After filtering the polymorphisms with a minor allele frequency(MAF)of 0.01,30 125 SNPs were obtained.Results obtained from two dimensional PCA and population structure analysis were consistent and segregated the 126 soybean samples into 2 sub-populations,the Kappa Index K=0.44.The 126 soybean samples were divided into 3 sub-populations using the neighbor-joining algorithm. If the threshold is set to α ≤ 0.05,in the single SNP-phenotype of association analysis,the locus with the strongest association was identified on physical position 34387780,34387823 and 34387841 of chromosome 3(with a P-value of 8.669E-7)and accounted for 17.80% of the phenotypic variation; other less significant loci appeared on chromosomes 20,1,4,17.In the Haplotype-phenotype of association analysis,the strongest association was found on physical position 5575883/5647814/5648648/5734897 of Chromosome 17(with a P-value of 1.038E-6)and accounted for 17.56% of phenotypic variation. Within 200 kb range,the candidate genes of Chromosome 3 are Glma.03g129100,Glma.03g129200,Glma.03g129300,Glma.03g129500,Glma.03g129800, and Glma.03g129900; Chromosome 17:Glma.17g071300,Glma.17g072200, and Glma.17g073300.

Key words: Soybean, Sclerotinia sclerotiorum, GWAS, Single SNP, Haplotype

CLC Number:

Q78
S432

ZHANG Yu, Francois Belzile. Genome-wide Association Study for Sclerotinia sclerotiorum Resistance of Soybean[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2020, 35(1): 205-213. doi: 10.7668/hbnxb.20190364.

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