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Development and dissection of diagnostic SNP markers for the downy mildew resistance genes Pl Arg and Pl 8 and maker-assisted gene pyramiding in sunflower (Helianthus annuus L.)

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Abstract

Diagnostic DNA markers are an invaluable resource in breeding programs for successful introgression and pyramiding of disease resistance genes. Resistance to downy mildew (DM) disease in sunflower is mediated by Pl genes which are known to be effective against the causal fungus, Plasmopara halstedii. Two DM resistance genes, Pl Arg and Pl 8 , are highly effective against P. halstedii races in the USA, and have been previously mapped to the sunflower linkage groups (LGs) 1 and 13, respectively, using simple sequence repeat (SSR) markers. In this study, we developed high-density single nucleotide polymorphism (SNP) maps encompassing the Pl arg and Pl 8 genes and identified diagnostic SNP markers closely linked to these genes. The specificity of the diagnostic markers was validated in a highly diverse panel of 548 sunflower lines. Dissection of a large marker cluster co-segregated with Pl Arg revealed that the closest SNP markers NSA_007595 and NSA_001835 delimited Pl Arg to an interval of 2.83 Mb on the LG1 physical map. The SNP markers SFW01497 and SFW06597 delimited Pl 8 to an interval of 2.85 Mb on the LG13 physical map. We also developed sunflower lines with homozygous, three gene pyramids carrying Pl Arg , Pl 8 , and the sunflower rust resistance gene R 12 using the linked SNP markers from a segregating F2 population of RHA 340 (carrying Pl 8 )/RHA 464 (carrying Pl Arg and R 12 ). The high-throughput diagnostic SNP markers developed in this study will facilitate marker-assisted selection breeding, and the pyramided sunflower lines will provide durable resistance to downy mildew and rust diseases.

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Acknowledgements

The authors would like to thank Dr. Loren Rieseberg for providing access to the Sunflower Genome Data Repository. We also thank Drs. Gerald Seiler and Zengcui Zhang for critical review of the manuscript, and Angelia Hogness and Cheryl Huckle for technical assistance.

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  1. Northern Crop Science Laboratory, USDA-Agricultural Research Service, 1605 Albrecht Blvd N, Fargo, ND, 58102-2765, USA

    L. L. Qi, B. S. Hulke & M. E. Foley

  2. Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA

    Z. I. Talukder

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  1. L. L. Qi
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  2. Z. I. Talukder
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  3. B. S. Hulke
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  4. M. E. Foley
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Correspondence to L. L. Qi.

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This project was funded by the USDA-ARS CRIS Project No. 3060-21000-039-00D. Mention of trade names or commercial products in this report is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the US Department of Agriculture. The USDA is an equal opportunity provider and employer.

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Qi, L.L., Talukder, Z.I., Hulke, B.S. et al. Development and dissection of diagnostic SNP markers for the downy mildew resistance genes Pl Arg and Pl 8 and maker-assisted gene pyramiding in sunflower (Helianthus annuus L.). Mol Genet Genomics 292, 551–563 (2017). https://doi.org/10.1007/s00438-017-1290-8

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