title: Inheritance, fine-mapping, and candidate gene analyses of resistance to soybean mosaic virus strain SC5 in soybean.
abstract: Soybean mosaic virus (SMV) is one of the most devastating pathogens for soybeans in China. Among the country-wide 22 strains, SC5 dominates in Huang-Huai and Changjiang valleys. For controlling its damage, the resistance gene was searched through Mendelian inheritance study, gene fine-mapping, and candidate gene analysis combined with qRT-PCR (quantitative real-time polymerase chain reaction) analysis. The parents F1, F2, and RILs (recombinant inbred lines) of the cross Kefeng-1 (Resistance, R) × NN1138-2 (Susceptible, S) were used to examine the inheritance of SC5-resistance. The F1was resistant and the F2and RILs segregated in a 3R:1S and 1R:1S ratio, respectively, indicating a single dominant gene conferring the Kefeng-1 resistance. Subsequently, the genomic region conferring the resistance was found in "Bin 352-Bin353 with 500 kb" on Chromosome 2 using the phenotyping data of the 427 RILs and a high-density genetic map with 4703 bin markers. In the 500 kb genomic region, 38 putative genes are contained. The association analysis between the SNPs in a putative gene and the resistance phenotype for the 427 RILs prioritized 11 candidate genes using Chi-square criterion. The expression levels of these genes were tested by qRT-PCR. On infection with SC5, 7 out of the 11 genes had differential expression in Kefeng-1 and NN1138-2. Furthermore, integrating SNP-phenotype association analysis with qRT-PCR expression profiling analysis, Glyma02g13495 was found the most possible candidate gene for SC5-resistance. This finding can facilitate the breeding for SC5-resistance through marker-assisted selection and provide a platform to gain a better understanding of SMV-resistance gene system in soybean.
authors.affiliation: Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, China.|MOA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China.|MOA Key Laboratory of Biology and Genetic Improvement of Soybean, Nanjing Agricultural University, Nanjing, 210095, China.|National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.|Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
authors.forename: Adhimoolam
authors.initials: A
authors.lastname: Karthikeyan
authors.affiliation: Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, China.|MOA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China.|MOA Key Laboratory of Biology and Genetic Improvement of Soybean, Nanjing Agricultural University, Nanjing, 210095, China.|National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.|Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
authors.forename: Kai
authors.initials: K
authors.lastname: Li
authors.affiliation: Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, China.|MOA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China.|MOA Key Laboratory of Biology and Genetic Improvement of Soybean, Nanjing Agricultural University, Nanjing, 210095, China.|National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.|Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
authors.forename: Hua
authors.initials: H
authors.lastname: Jiang
authors.affiliation: Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, China.|MOA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China.|MOA Key Laboratory of Biology and Genetic Improvement of Soybean, Nanjing Agricultural University, Nanjing, 210095, China.|National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.|Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
authors.forename: Rui
authors.initials: R
authors.lastname: Ren
authors.affiliation: Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, China.|MOA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China.|MOA Key Laboratory of Biology and Genetic Improvement of Soybean, Nanjing Agricultural University, Nanjing, 210095, China.|National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.|Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
authors.forename: Cui
authors.initials: C
authors.lastname: Li
authors.affiliation: Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, China.|MOA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China.|MOA Key Laboratory of Biology and Genetic Improvement of Soybean, Nanjing Agricultural University, Nanjing, 210095, China.|National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.|Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
authors.forename: Haijian
authors.initials: H
authors.lastname: Zhi
authors.affiliation: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
authors.forename: Shouyi
authors.initials: S
authors.lastname: Chen
authors.affiliation: Soybean Research Institute, Nanjing Agricultural University, Nanjing, 210095, China. sri@njau.edu.cn.|MOA National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, 210095, China. sri@njau.edu.cn.|MOA Key Laboratory of Biology and Genetic Improvement of Soybean, Nanjing Agricultural University, Nanjing, 210095, China. sri@njau.edu.cn.|National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China. sri@njau.edu.cn.|Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China. sri@njau.edu.cn.
authors.forename: Junyi
authors.initials: J
authors.lastname: Gai
mesh_terms: D001483:Base Sequence; D002681:China; D002874:Chromosome Mapping; D018744:DNA, Plant / Q000235:genetics*; D030541:Databases, Genetic; D060467:Disease Resistance / Q000235:genetics*; D005799:Genes, Dominant / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D056726:Genetic Association Studies; D008040:Genetic Linkage; D010935:Plant Diseases / Q000276:immunology* / Q000821:virology; D017800:Potyvirus / Q000145:classification / Q000276:immunology*; D060888:Real-Time Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000235:genetics* / Q000254:growth & development* / Q000276:immunology / Q000821:virology
chemical_list: D018744:DNA, Plant
keywords: Candidate resistance gene; Fine-mapping; Inheritance; Soybean (Glycine max (L.) Merr.); Soybean mosaic virus (SMV); qRT-PCR (quantitative real-time polymerase chain reaction)