title: Identification of haplotypes at the Rsv4 genomic region in soybean associated with durable resistance to soybean mosaic virus.
abstract: Discovery of new germplasm sources and identification of haplotypes for the durable Soybean mosaic virus resistance gene, Rsv 4, provide novel resources for map-based cloning and genetic improvement efforts in soybean. The Soybean mosaic virus (SMV) resistance locus Rsv4 is of interest because it provides a durable type of resistance in soybean [Glycine max (L.) Merr.]. To better understand its molecular basis, we used a population of 309 BC3F2 individuals to fine-map Rsv4 to a ~120 kb interval and leveraged this genetic information in a second study to identify accessions 'Haman' and 'Ilpumgeomjeong' as new sources of Rsv4. These two accessions along with three other Rsv4 and 14 rsv4 accessions were used to examine the patterns of nucleotide diversity at the Rsv4 region based on high-depth resequencing data. Through a targeted association analysis of these 19 accessions within the ~120 kb interval, a cluster of four intergenic single-nucleotide polymorphisms (SNPs) was found to perfectly associate with SMV resistance. Interestingly, this ~120 kb interval did not contain any genes similar to previously characterized dominant disease resistance genes. Therefore, a haplotype analysis was used to further resolve the association signal to a ~94 kb region, which also resulted in the identification of at least two Rsv4 haplotypes. A haplotype phylogenetic analysis of this region suggests that the Rsv4 locus in G. max is recently introgressed from G. soja. This integrated study provides a strong foundation for efforts focused on the cloning of this durable virus resistance gene and marker-assisted selection of Rsv4-mediated SMV resistance in soybean breeding programs.
authors.affiliation: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Ilut
authors.affiliation: Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA.
authors.forename: Alexander E
authors.initials: AE
authors.lastname: Lipka
authors.affiliation: Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Ch'ongju, Chungbuk, 28116, Korea.
authors.forename: Namhee
authors.initials: N
authors.lastname: Jeong
authors.affiliation: Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Ch'ongju, Chungbuk, 28116, Korea.
authors.forename: Dong Nyuk
authors.initials: DN
authors.lastname: Bae
authors.affiliation: Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Ch'ongju, Chungbuk, 28116, Korea.
authors.forename: Dong Hyun
authors.initials: DH
authors.lastname: Kim
authors.affiliation: Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Ch'ongju, Chungbuk, 28116, Korea.
authors.forename: Ji Hong
authors.initials: JH
authors.lastname: Kim
authors.affiliation: Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, 24061, USA.
authors.forename: Neelam
authors.initials: N
authors.lastname: Redekar
authors.affiliation: Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Ch'ongju, Chungbuk, 28116, Korea.
authors.forename: Kiwoung
authors.initials: K
authors.lastname: Yang
authors.affiliation: Epigenomics Research Center, Genome Institute, Korea Research Institute of Bioscience and Biotechnology, Taejon, 34141, Korea.|Department of Functional Genomics, Korea University of Science and Technology, Taejon, 34141, Korea.
authors.forename: Won
authors.initials: W
authors.lastname: Park
authors.affiliation: Department of Crop Science and Biotechnology, Dankook University, Cheonan, Chungnam, 31116, Korea.
authors.forename: Sung-Taeg
authors.initials: ST
authors.lastname: Kang
authors.affiliation: Epigenomics Research Center, Genome Institute, Korea Research Institute of Bioscience and Biotechnology, Taejon, 34141, Korea.|Department of Functional Genomics, Korea University of Science and Technology, Taejon, 34141, Korea.
authors.forename: Namshin
authors.initials: N
authors.lastname: Kim
authors.affiliation: National Institute of Crop Science, Rural Development Administration, Wanju, Jeonbuk, 55365, Korea.
authors.forename: Jung-Kyung
authors.initials: JK
authors.lastname: Moon
authors.affiliation: Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, 24061, USA.
authors.forename: M A
authors.initials: MA
authors.lastname: Saghai Maroof
authors.affiliation: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA. mag87@cornell.edu.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Gore
authors.affiliation: Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Ch'ongju, Chungbuk, 28116, Korea. scjeong@kribb.re.kr.
authors.forename: Soon-Chun
authors.initials: SC
authors.lastname: Jeong
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D018744:DNA, Plant / Q000235:genetics; D060467:Disease Resistance / Q000235:genetics*; D017343:Genes, Plant; D006239:Haplotypes; D015810:Linkage Disequilibrium; D009029:Mosaic Viruses / Q000472:pathogenicity*; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics* / Q000821:virology; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000235:genetics* / Q000821:virology
chemical_list: D018744:DNA, Plant