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Genome-wide association analysis identified SNPs closely linked to a gene resistant to Soil-borne wheat mosaic virus

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Abstract

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Using association and linkage mapping, two SNP markers closely linked to the SBWMV resistance gene on chromosome 5D were identified and can be used to select the gene in breeding.

Abstract

Soil-borne wheat mosaic virus (SBWMV) disease is a serious viral disease of winter wheat growing areas worldwide. SBWMV infection can significantly reduce grain yield up to 80 %. Developing resistant wheat cultivars is the only feasible strategy to reduce the losses. In this study, wheat Infinium iSelect Beadchips with 9 K wheat SNPs were used to genotype an association mapping population of 205 wheat accessions. Six new SNPs from two genes were identified to be significantly associated with the gene for SBWMV resistance on chromosome 5D. The SNPs and Xgwm469, an SSR marker that has been reported to be associated with the gene, were mapped close to the gene using F6-derived recombinant inbred lines from the cross between a resistant parent ‘Heyne’ and a susceptible parent ‘Trego’. Two representative SNPs, wsnp_CAP11_c209_198467 and wsnp_JD_c4438_5568170, from the two linked genes in wheat were converted into KBioscience Competitive Allele-Specific Polymerase assays and can be easily used in marker-assisted selection to improve wheat resistance to SBWMV in breeding.

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Acknowledgments

This is contribution number 14-056-J from the Kansas Agricultural Experiment Station, Manhattan, KS, USA. This project is partly funded by the National Research Initiative Competitive Grants CAP project 2011- 68002-30029 from the USDA National Institute of Food and Agriculture. The mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture. USDA is an equal opportunity provider and employer.

Conflict of interest

The authors declare that they have no conflict of interest.

Author information

Authors and Affiliations

  1. Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA

    Shubing Liu, Xiping Yang, Dadong Zhang & Guihua Bai

  2. Hard Winter Wheat Genetics Research Unit, USDA-ARS, 4008 Throckmorton Hall, Manhattan, KS, 66506, USA

    Guihua Bai

  3. Cereal Crops Research Unit, USDA-ARS, Fargo, ND, USA

    Shiaoman Chao

  4. Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA

    William Bockus

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  1. Shubing Liu
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  2. Xiping Yang
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  3. Dadong Zhang
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  4. Guihua Bai
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  5. Shiaoman Chao
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  6. William Bockus
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Correspondence to Guihua Bai.

Additional information

Communicated by M. E. Sorrells.

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122_2014_2277_MOESM1_ESM.docx

Supplemental Fig. 1 Linkage disequilibrium analysis indicated the six SNPs were within a strong linkage block with the marker Xgwm469 on wheat chromosome 5DL. The linkage map from Somers et al. (2004) was used as a reference map to indicate that only Xgwm469 had LD with the six SNPs, not other two adjacent markers (Xcfd10 and Xgwm565). Supplemental Fig. 2 KASP assay profiling of SNP wsnp_CAP11_c209_198467 (A) and SNP wsnp_JD_c4438_5568170 (B) in 205 wheat accessions. (A). Allele X (KASPFAM, blue color) represents the A nucleotide, Allele Y (KASPHEX, green color) represents the G nucleotide. (B). Allele X (KASPFAM, blue color) represents the A nucleotide, Allele Y (KASPHEX, green color) represents the G nucleotide. The black dots and crosses in the circle represent water controls and missing data. Supplementary material 1 (DOCX 287 kb)

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Liu, S., Yang, X., Zhang, D. et al. Genome-wide association analysis identified SNPs closely linked to a gene resistant to Soil-borne wheat mosaic virus. Theor Appl Genet 127, 1039–1047 (2014). https://doi.org/10.1007/s00122-014-2277-z

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  • DOI: https://doi.org/10.1007/s00122-014-2277-z

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