Theoretical and Applied Genetics

, Volume 132, Issue 12, pp 3413–3424 | Cite as

Genome-wide association study of the seed transmission rate of soybean mosaic virus and associated traits using two diverse population panels

  • Qiong Liu
  • Houston A. Hobbs
  • Leslie L. DomierEmail author
Original Article


Key message

Genome-wide association analyses identified candidates for genes involved in restricting virus movement into embryonic tissues, suppressing virus-induced seed coat mottling and preserving yield in soybean plants infected with soybean mosaic virus.


Soybean mosaic virus (SMV) causes significant reductions in soybean yield and seed quality. Because seedborne infections can serve as primary sources of inoculum for SMV infections, resistance to SMV seed transmission provides a means to limit the impacts of SMV. In this study, two diverse population panels, Pop1 and Pop2, composed of 409 and 199 soybean plant introductions, respectively, were evaluated for SMV seed transmission rate, seed coat mottling, and seed yield from SMV-infected plants. The phenotypic data and genotypic data from the SoySNP50K dataset were analyzed using GAPIT and rrBLUP. For SMV seed transmission rate, a single locus was identified on chromosome 9 in Pop1. For SMV-induced seed coat mottling, loci were identified on chromosome 9 in Pop1 and on chromosome 3 in Pop2. For seed yield from SMV-infected plants, a single locus was identified on chromosome 3 in Pop2 that was within the map interval of a previously described quantitative trait locus for seed number. The high linkage disequilibrium regions surrounding the markers on chromosomes 3 and 9 contained a predicted nonsense-mediated RNA decay gene, multiple pectin methylesterase inhibitor genes (involved in restricting virus movement), two chalcone synthase genes, and a homolog of the yeast Rtf1 gene (involved in RNA-mediated transcriptional gene silencing). The results of this study provided additional insight into the genetic architecture of these three important traits, suggested candidate genes for downstream functional validation, and suggested that genomic prediction would outperform marker-assisted selection for two of the four trait–marker associations.



Funding from the USDA CRIS Project #5012–22,000-022-00D. Mention of a trademark, proprietary product, or vendor does not constitute a guarantee or warranty of the product by the United States Department of Agriculture or the University of Illinois and does not imply its approval to the exclusion of other products or vendors that may also be suitable.

Author contribution statement

QL performed the association mapping and statistical analysis and drafted the manuscript, HAH performed the phenotypic analysis of Pop2, and LLD prepared the manuscript for submission.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

122_2019_3434_MOESM1_ESM.pdf (1.9 mb)
Supplementary file1 (PDF 1967 kb)


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Copyright information

© This is a U.S. government work and its text is not subject to copyright protection in the United States; however, its text may be subject to foreign copyright protection 2019

Authors and Affiliations

  1. 1.Department of Crop SciencesUniversity of IllinoisUrbanaUSA
  2. 2.Soybean/Maize Germplasm, Pathology, and Genetics Research UnitUnited States Department of Agriculture-Agricultural Research ServiceUrbanaUSA

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