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Identification of haplotypes at the Rsv4 genomic region in soybean associated with durable resistance to soybean mosaic virus

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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.

Abstract

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.

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Acknowledgments

This study in the SCJ lab was supported principally by a grant from the Next-Generation BioGreen 21 Program (PJ01101503), by the Rural Development Administration, and partly supported by the National Research Foundation of Korea grant funded by the Korea government (MSIP) (No. 2015R1A2A2A01002969) and by the Korea Research Institute of Bioscience and Biotechnology Research Initiative Program. MASM acknowledges funding from the Virginia Soybean Board, the Virginia Agricultural Experiment Station and the Hatch Program of the National Institute of Food and Agriculture, US Department of Agriculture. This work was also partly funded by USDA-NIFA/DOE Biomass Research and Development Initiative (BRDI) Grant No. 2012-10006 (MAG), Cornell University startup funds (MAG), and University of Illinois startup funds (AEL).

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Authors and Affiliations

  1. Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA

    Daniel C. Ilut & Michael A. Gore

  2. Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA

    Alexander E. Lipka

  3. Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Ch’ongju, Chungbuk, 28116, Korea

    Namhee Jeong, Dong Nyuk Bae, Dong Hyun Kim, Ji Hong Kim, Kiwoung Yang & Soon-Chun Jeong

  4. Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, 24061, USA

    Neelam Redekar & M. A. Saghai Maroof

  5. Epigenomics Research Center, Genome Institute, Korea Research Institute of Bioscience and Biotechnology, Taejon, 34141, Korea

    Won Park & Namshin Kim

  6. Department of Functional Genomics, Korea University of Science and Technology, Taejon, 34141, Korea

    Won Park & Namshin Kim

  7. Department of Crop Science and Biotechnology, Dankook University, Cheonan, Chungnam, 31116, Korea

    Sung-Taeg Kang

  8. National Institute of Crop Science, Rural Development Administration, Wanju, Jeonbuk, 55365, Korea

    Jung-Kyung Moon

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  1. Daniel C. Ilut
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  15. Soon-Chun Jeong
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Correspondence to Michael A. Gore or Soon-Chun Jeong.

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Communicated by H. T. Nguyen.

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Ilut, D.C., Lipka, A.E., Jeong, N. et al. Identification of haplotypes at the Rsv4 genomic region in soybean associated with durable resistance to soybean mosaic virus. Theor Appl Genet 129, 453–468 (2016). https://doi.org/10.1007/s00122-015-2640-8

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  • DOI: https://doi.org/10.1007/s00122-015-2640-8

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