大豆抗菌核病的全基因组关联研究

doi:10.7668/hbnxb.20190364

摘要/Abstract

摘要： 找到大豆与抗菌核病强关联的候选位点或候选基因，为抗病基因克隆和抗病分子标记开发提供借鉴，服务大豆抗菌核病育种。对126个加拿大大豆品种的基因组DNA用Ape k Ⅰ酶消化后Illumina Hiseq2000平台测序进行基因分型，供试的126个材料用棉垫接种核盘菌菌丝体进行表型鉴定。采用Structure 2.3.4、SPSS 20.0、TASSEL 5.0和PLINKv 1.07软件分别模拟群体遗传结构、二元主成分分析、邻接法聚类，进行SNP-phenotype和Haplotype-phenotype的关联分析（只考虑加性效应）。最小等位基因频率0.01过滤，得到30 125个SNPs。主成分及群体结构聚类结果中度一致，将126个供试材料划分为2个组群，Kappa聚类一致度检验K=0.44。邻接法（The neighbor-joining algorithm，NJ）聚为3个组群。α≤0.05时，在单个SNP-phenotype的关联研究中，最强关联在3号染色体物理位置34387780、34387823和34387841处（P值都为8.669E-7），可分别解释表型变异的17.80%，其次在20，1，4，17号染色体上。Haplotype-phenotype的关联分析中，最强关联在17号染色体物理位置5575883/5647814/5648648/5734897处（P值为1.038E-6），可解释表型变异的17.56%。200 kb范围内，3号染色体上的候选基因有Glma.03g129100、Glma.03g129200、Glma.03g129300、Glma.03g129500、Glma.03g129800、Glma.03g129900。17号染色体上为Glma.17g071300、Glma.17g072200、Glma.17g073300。

关键词: 大豆, 菌核病, GWAS, 单个SNP, 单倍型

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

中图分类号:

Q78
S432

张羽, Francois Belzile. 大豆抗菌核病的全基因组关联研究[J]. 华北农学报, 2020, 35(1): 205-213. doi: 10.7668/hbnxb.20190364.

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.

http://www.hbnxb.net/CN/Y2020/V35/I1/205

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