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Loci and candidate genes in soybean that confer resistance to Fusarium graminearum

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Association analysis techniques were used to identify and verify twelve single nucleotide polymorphisms (SNPs) associated with Fusarium graminearum resistance. Two novel candidate genes were obtained.


Fusarium graminearum causes seed and root rot and seedling damping-off of soybean, leading to severe yield loss. Presently, the genetic basis of resistance to F. graminearum is elucidated in only four soybean accessions, which is not sufficient for resistance improvement. The objective of the present study was to identify the genome-wide genetic architecture of resistance to F. graminearum in landraces and cultivated soybeans based on a growth room evaluation. The resistance levels of 314 diverse accessions were tested, and 22,888 single nucleotide polymorphisms (SNPs) with a minor allele frequency of > 0.05 were developed using the specific-locus amplified fragment sequencing (SLAF-seq) approach. Twelve SNPs were identified as associated with F. graminearum resistance, and these SNPs were located at 12 genomic regions on eight chromosomes (Chr.) and could explain 5.53–14.71% of the observed phenotypic variation. One SNP, rs9479021, located on Chr.6, overlapped with qRfg_Gm06, the known QTL for resistance to F. graminearum. The other SNPs were novel and associated with resistance to F. graminearum. Nine novel candidate genes were predicted to contribute to resistance to F. graminearum according to the haplotype and transcript abundance analysis of the candidate genes. The identified markers and resistant cultivars are valuable for the improvement of resistance to F. graminearum.

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This study was conducted in the Key Laboratory of Soybean Biology of the Chinese Education Ministry, Soybean Research & Development Center (CARS), and the Key Laboratory of Northeastern Soybean Biology and Breeding/Genetics of the Chinese Agriculture Ministry and was financially supported by the Chinese National Natural Science Foundation (31671717, 31471517), National Key R & D Project for Crop Breeding (2016YFD0100304), the National Supporting Project (2014BAD22B01), the Youth Leading Talent Project of the Ministry of Science and Technology in China (2015RA228), the National Ten-thousand Talents Program, Heilongjiang Provincial Project (GX17B002, JC2018007, C2018016), the ‘Academic Backbone’ Project of Northeast Agricultural University (15XG04, 17XG22), Postdoctoral Fund in Heilongjiang Province (LBH-Z15017, LBH-Q17015), and the ‘Youth Innovation Talent’ Project of the general undergraduate universities in Heilongjiang province (UNPYSCT-2016145).

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Authors and Affiliations



CJZ and XZ conceived the study and contributed to population development. YFQ, WLT, LJQ, and HKZ contributed to genotyping. ZHW contributed to phenotypic evaluation. YPH and WBL contributed to experimental design and writing paper. All authors contributed to and approved the final manuscript.

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Correspondence to Zhenhua Wang or Yingpeng Han.

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The authors declare that they have no conflict of interest.

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The authors have adhered to the ethical responsibilities outlined by Theoretical and Applied Genetics.

Additional information

Communicated by David A. Lightfoot.

Chanjuan Zhang and Xue Zhao have contributed equally to this work.

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Zhang, C., Zhao, X., Qu, Y. et al. Loci and candidate genes in soybean that confer resistance to Fusarium graminearum. Theor Appl Genet 132, 431–441 (2019).

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