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Genotyping-by-sequencing targeting of a novel downy mildew resistance gene Pl 20 from wild Helianthus argophyllus for sunflower (Helianthus annuus L.)

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Genotyping-by-sequencing revealed a new downy mildew resistance gene, Pl 20 , from wild Helianthus argophyllus located on linkage group 8 of the sunflower genome and closely linked to SNP markers that facilitate the marker-assisted selection of resistance genes.

Abstract

Downy mildew (DM), caused by Plasmopara halstedii, is one of the most devastating and yield-limiting diseases of sunflower. Downy mildew resistance identified in wild Helianthus argophyllus accession PI 494578 was determined to be effective against the predominant and virulent races of P. halstedii occurring in the United States. The evaluation of 114 BC1F2:3 families derived from the cross between HA 89 and PI 494578 against P. halstedii race 734 revealed that single dominant gene controls downy mildew resistance in the population. Genotyping-by-sequencing analysis conducted in the BC1F2 population indicated that the DM resistance gene derived from wild H. argophyllus PI 494578 is located on the upper end of the linkage group (LG) 8 of the sunflower genome, as was determined single nucleotide polymorphism (SNP) markers associated with DM resistance. Analysis of 11 additional SNP markers previously mapped to this region revealed that the resistance gene, named Pl 20 , co-segregated with four markers, SFW02745, SFW09076, S8_11272025, and S8_11272046, and is flanked by SFW04358 and S8_100385559 at an interval of 1.8 cM. The newly discovered P. halstedii resistance gene has been introgressed from wild species into cultivated sunflower to provide a novel gene with DM resistance. The homozygous resistant individuals were selected from BC2F2 progenies with the use of markers linked to the Pl 20 gene, and these lines should benefit the sunflower community for Helianthus improvement.

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References

  • Ahmed S, de Labrouhe DT, Delmotte F (2012) Emerging virulence arising from hybridization facilitated by multiple introductions of the sunflower downy mildew pathogen Plasmopara halstedii. Fungal Genet Biol 49:847–855

    Article  CAS  PubMed  Google Scholar 

  • Bachlava E, Radwan OE, Abratti G, Tang S, Gao W, Heesacker AF, Bazzalo ME, Zambelli A, Leon AJ, Knapp SJ (2011) Downy mildew (Pl 8 and Pl 14 ) and rust (R Adv ) resistance genes reside in close proximity to tandemly duplicated clusters of non-TIR-like NBS-LRR-encoding genes on sunflower chromosomes 1 and 13. Theor Appl Genet 122:1211–1221

    Article  PubMed  Google Scholar 

  • Baute GJ, Kane NC, Grassa CJ, Lai Z, Rieseberg LH (2015) Genome scans reveal candidate domestication and improvement genes in cultivated sunflower, as well as post-domestication introgression with wild relatives. New Phytol 206:830–838

    Article  CAS  PubMed  Google Scholar 

  • Bert PF, de Labrouhe TD, Philippon J, Mouzeyar S, Jouan I, Nicolas P, Vear F (2001) Identification of a second linkage group carrying genes controlling resistance to downy mildew (Plasmopara halstedii) in sunflower (Helianthus annuus L.). Theor Appl Genet 103:992–997

    Article  CAS  Google Scholar 

  • Bouzidi MF, Franchel J, Tao Q, Stormo K, Mraz A, Nicolas P, Mouzeyar S (2006) A sunflower BAC library suitable for PCR screening and physical mapping of targeted genomic regions. Theor Appl Genet 113:81–89

    Article  CAS  PubMed  Google Scholar 

  • Bowers JE, Bachlava E, Brunick RL, Rieseberg LH, Knapp SJ, Burke JM (2012) Development of a 10,000 locus genetic map of the sunflower genome based on multiple crosses. G3 Genes Genom Genet 2:721–729

    CAS  Google Scholar 

  • Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635

    Article  CAS  PubMed  Google Scholar 

  • Chen J, Hu J, Jan CC (2006) Molecular mapping of a nuclear male sterility gene in sunflower (Helianthus annuus L.) using TRAP and SSR markers. Theor Appl Genet 113:122–127

    Article  CAS  PubMed  Google Scholar 

  • Constantinescu O, Thines M (2010) Plasmopara halstedii is absent from Australia and New Zealand. Pol Bot J 55:293–298

    Google Scholar 

  • de Labrouhe DT, Pilorgé E, Nicola P, Vear F (2000) Le mildiou du tournesol. INRA and CETIOM, Paris

    Google Scholar 

  • de Romano AB, Romano C, Bulos M, Altieri E, Sala C (2010) A new gene for resistance to downy mildew in sunflower. In: Proceedings of Int Symposium “Sunflower breeding on resistance to diseases”, Krasnodar, Russia, June 23–24, 2010

  • Dußle CM, Hahn V, Knapp SJ, Bauer E (2004) Pl Arg from Helianthus argophyllus is unlinked to other known downy mildew resistance genes in sunflower. Theor Appl Genet 109:1083–1086

    Article  PubMed  Google Scholar 

  • Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:e19379

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Flor HH (1955) Host-parasite interaction in flax rust: its genetics and other implications. Phytopathology 45:680–685

    Google Scholar 

  • Franchel J, Bouzidi MF, Bronner G, Vear F, Nicolas P, Mouzeyar S (2013) Positional cloning of a candidate gene for resistance to the sunflower downy mildew, Plasmopara halstedii race 300. Theor Appl Genet 126:359–367

    Article  PubMed  Google Scholar 

  • Gascuel Q, Martinez Y, Boniface MC, Vear F, Pichon M, Godiard L (2015) The sunflower downy mildew pathogen Plasmopara halstedii. Mol Plant Pathol 16:109–122

    Article  PubMed  Google Scholar 

  • Gedil MA, Slabaugh MB, Berry S, Segers B, Peleman J, Michelmore R, Miller JF, Gulya T, Knapp SJ (2001) Candidate disease resistance genes in sunflower cloned using conserved nucleotide binding site motifs: genetic mapping and linkage to downy mildew resistance gene Pl 1 . Genome 44:205–212

    Article  CAS  PubMed  Google Scholar 

  • Gilley M, Misar C, Gulya T, Markell S (2016) Prevalence and virulence of Plasmopara halstedii (downy mildew) in sunflowers. In: Proceeding 38th Sunflower Research Forum. Fargo ND. http://www.sunflowernsa.com/uploads/research/1277/Prevalence.Downey_Gilley.etal_2016.rev.pdf. Accessed 18 Apr 2017

  • GRIN (2017) Germplasm Resources Information Network. United States Department of Agriculture, Agricultural Research Service, Beltsville, MD. http://www.ars-grin.gov/. Accessed 18 Apr 2017

  • Gulya TJ (1985) Registration of five disease-resistant sunflower germplasms. Crop Sci 25:719–720

    Google Scholar 

  • Gulya TJ (2005) Evaluation of wild annual Helianthus species for resistance to downy mildew and Sclerotinia stalk rot. In: Proceeding 27th Sunflower Research Forum. Fargo ND, 12–13 Jan 2005. http://www.sunflowernsa.com/uploads/research/265/GulyaWildHelianthus_studies_05.pdf. Accessed 18 Apr 2017

  • Gulya TJ, Miller JF, Viranyi F, Sackston WE (1991a) Proposed internationally standardized methods for race identification of Plasmopara halstedii. Helia 14:11–20

    Google Scholar 

  • Gulya TJ, Sackston WE, Viranyi F, Masirevic S, Rashid KY (1991b) New races of the sunflower downy mildew pathogen (Plasmopara halstedii) In Europe and North and South America. J Phytopathol 132:303–311

    Article  Google Scholar 

  • Gulya TJ, Due B, Hutter M (2010) New virulent races of downy mildew: distribution, status of DM resistant hybrids, and USDA sources of resistance to races that overcome the Pl 6 gene. In: Proceedings of 32th Sunflower Research Forum. Fargo ND, January 12–13, 2010. http://www.sunflowernsa.com/uploads/16/gulya1_virulentraces_10.pdf. Accessed 18 Apr 2017

  • Gulya TJ, Markell S, McMullen M, Harveson B, Osborne L (2011) New virulent races of downy mildew: distribution, status of DM resistant hybrids, and USDA sources of resistance. In: Proceedings of 33th Sunflower Research Forum. Fargo ND, January 12–13, 2011. http://www.sunflowernsa.com/uploads/17/gulya_virulentracesdownymildew.pdf. Accessed 18 Apr 2017

  • Huang L, Brooks SA, Fellers JP, Gill BS (2003) Map-based cloning of leaf rust resistance gene Lr21 from the large and polyploidy genome of bread wheat. Genetics 164:655–664

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hulke BS, Miller JF, Gulya TJ, Vick BA (2010) Registration of the oilseed sunflower genetic stocks HA 458, HA 459, and HA 460 possessing genes for resistance to downy mildew. J Plant Regist 4:93–97

    Article  Google Scholar 

  • Humann RH, Gulya TJ, Markell SG (2016) Downy Mildew. In: Harveson RM, Markell SG, Block CC, Gulya TJ (eds) Compendium of Sunflower Diseases and Pests. American Phytopathology Press, St. Paul, pp 18–20

    Google Scholar 

  • Hyma KE, Barba P, Wang M, Londo JP, Acharya CB, Mitchell SE, Sun Q, Reisch B, Cadle-Davidson L (2015) Heterozygous mapping strategy (HetMappS) for high resolution genotyping-by-sequencing markers: a case study in grapevine. PLoS One 10:e0134880

    Article  PubMed  PubMed Central  Google Scholar 

  • Islam MR, Shepherd KW (1991) Present status of genetics of rust resistance in flax. Euphytica 55:255–267

    Article  Google Scholar 

  • Jan CC, Rutger JN (1988) Mitomycin C- and streptomycin-induced male sterility in cultivated sunflower. Crop Sci 28:792–795

    Article  CAS  Google Scholar 

  • Jones DA, Dickinson MJ, Balint-Kurti PJ, Dixon MS, Jones JDG (1993) Two complex resistance loci revealed in tomato by classical and RFLP mapping of the Cf-2, Cf-4, Cf-5, and Cf9 genes for resistance to Cladosporium fulvum. Mol Plant Microbe Interact 6:348–357

    Article  CAS  Google Scholar 

  • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu Z, Gulya TJ, Seiler GJ, Vick BA, Jan CC (2012) Molecular mapping of the Pl 16 downy mildew resistance gene from HA-R4 to facilitate marker-assisted selection in sunflower. Theor Appl Genet 125:121–131

    Article  CAS  PubMed  Google Scholar 

  • Long YM, Chao WS, Ma GJ, Xu SS, Qi LL (2016) An innovative SNP genotyping method adapting multiple platforms and throughputs. Theor Appl Genet. doi:10.1007/s00122-016-2838-4

    PubMed  Google Scholar 

  • Markell SG, Humann RH, Gilley M, Gulya TJ (2016) Downy mildew pathogen. In: Harveson RM, Markell SG, Block CC, Gulya TJ (eds) Compendium of sunflower diseases and pests. American Phytopathology Press, St. Paul, pp 15–117

    Google Scholar 

  • Meyers BC, Chin DB, Shen KA, Sivaramakrishnan S, Lavelle DO, Zhang Z, Michelmore RW (1998) The major resistance gene cluster in lettuce is highly duplicated and spans several megabases. Plant Cell 10:1817–1832

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Miller JF, Gulya TJ (1987) Inheritance of resistance to race 3 downy mildew in sunflower. Crop Sci 27:210–212

    Article  Google Scholar 

  • Miller JF, Gulya TJ (1988) Registration of six downy mildew resistant sunflower germplasm lines. Crop Sci 28:1040–1041

    Article  Google Scholar 

  • Miller JF, Gulya TJ (1991) Inheritance of resistance to race 4 of downy mildew derived from interspecific crosses in sunflower. Crop Sci 31:40–43

    Article  Google Scholar 

  • Molinero-Ruiz ML, Melero-Vara JM, Dominguez J (2003) Inheritance of resistance to two races of sunflower downy mildew (Plasmopara halstedii) in two Helianthus annuus L. lines. Euphytica 131:47–51

    Article  CAS  Google Scholar 

  • Mouzeyar S, Roeckel-Drevet P, Gentzbittel L, Philippon J, de Labrouhe DT, Vear F, Nicolas P (1995) RFLP and RAPD mapping of the sunflower Pl 1 locus for resistance to Plasmopara halstedii race 1. Theor Appl Genet 91:733–737

    Article  CAS  PubMed  Google Scholar 

  • Mulpuri S, Liu Z, Feng J, Gulya TJ, Jan CC (2009) Inheritance and molecular mapping of a downy mildew resistance gene, Pl 13 in cultivated sunflower (Helianthus annuus L.). Theor Appl Genet 119:795–803

    Article  CAS  PubMed  Google Scholar 

  • Qi LL, Gulya TJ, Seiler GJ, Hulke BS, Vick BA (2011) Identification of resistance to new virulent races of rust in sunflowers and validation of DNA markers in the gene pool. Phytopathol 101:241–249

    Article  CAS  Google Scholar 

  • Qi LL, Gulya TJ, Hulke BS, Vick BA (2012) Chromosome location, DNA markers and rust resistance of the sunflower gene R 5 . Mol Breeding 30:745–756

    Article  CAS  Google Scholar 

  • Qi LL, Long YM, Jan CC, Ma GJ, Gulya TJ (2015) Pl 17 is a novel gene independent of known downy mildew resistance genes in the cultivated sunflower (Helianthus annuus L.). Theor Appl Genet 128:757–767

    Article  CAS  PubMed  Google Scholar 

  • Qi LL, Foley ME, Cai XW, Gulya TJ (2016a) Genetics and mapping of a novel downy mildew resistance gene, Pl 18 , introgressed from wild Helianthus argophyllus into cultivated sunflower (Helianthus annuus L.). Theor Appl Genet 129:741–752

    Article  CAS  PubMed  Google Scholar 

  • Qi LL, Long YM, Talukder ZI, Seiler GJ, Block CC, Gulya TJ (2016b) Genotyping-by-sequencing uncovers the introgression alien segments associated with Sclerotinia basal stalk rot resistance from wild species—I. Helianthus argophyllus and H. petiolaris. Front Genet 7:219

    PubMed  PubMed Central  Google Scholar 

  • Radwan O, Bouzidi MF, Vear F, Philippon J, de Labrouhe TD, Nicolas P, Mouzeyar S (2003) Identification of non-TIR-NBS-LRR markers linked to the Pl 5 /Pl 8 locus for resistance to downy mildew in sunflower. Theor Appl Genet 106:1438–1446

    Article  CAS  PubMed  Google Scholar 

  • Radwan O, Gandhi S, Heesacker A, Whitaker B, Taylor C, Plocik A, Kesseli R, Kozik A, Michelmore RW, Knapp SJ (2008) Genetic diversity and genomic distribution of homologs encoding NBS-LRR disease resistance proteins in sunflower. Mol Genet Genom 280:111–125

    Article  CAS  Google Scholar 

  • Rahim M, Jan CC, Gulya TJ (2002) Inheritance of resistance to sunflower downy mildew races 1, 2 and 3 in cultivated sunflower. Plant Breed 121:57–60

    Article  Google Scholar 

  • Roeckel-Drevet P, Gagne G, Mouzeyar S, Gentzbittel L, Philippon J, Nicolas P, de Labrouhe DT, Vear F (1996) Colocation of downy mildew (Plasmopara halstedii) resistance genes in sunflower (Helianthus annuus L.). Euphytica 91:225–228

    CAS  Google Scholar 

  • Rogers CE, Thompson TE, Seiler GJ (1982) Sunflower species of the United States. National Sunflower Association, Bismarck, pp 4–22

    Google Scholar 

  • Schilling EE (2006) In: Flora of North America Editorial Committee (eds) Flora of North America North of Mexico. Oxford University Press, New York, Oxford. Helianthus 21:141–169

  • Seiler GJ (1991) Registration of 13 downy mildew tolerant interspecific sunflower germplasm lines derived from wild annual species. Crop Sci 31:1714–1716

    Google Scholar 

  • Seiler GJ (2010) Utilization of wild Helianthus species in breed for disease resistance. In: Proceedings of the International Symposium “Sunflower Breeding on Resistance to Diseases”, Krasnodar, Russia. International Sunflower Association, Paris, France. June 23–24, 2010, pp 37–51

  • Seiler GJ, Qi LL, Marek LF (2017) Utilization of sunflower crop wild relatives for cultivated sunflower improvement. Crop Sci. doi:10.2135/cropsci2016.10.0856

    Google Scholar 

  • Slabaugh MB, Yu JK, Tang SX, Heesacker A, Hu X, Lu GH, Bidney D, Han F, Knapp SJ (2003) Haplotyping and mapping a large cluster of downy mildew resistance gene candidates in sunflower using multilocus intron fragment length polymorphisms. Plant Biotechnol J 1:167–185

    Article  CAS  PubMed  Google Scholar 

  • Song WY, Pi LY, Wang GL, Gardner J, Holsten T, Ronald PC (1997) Evolution of the rice Xa21 disease resistance gene family. Plant Cell 9:1279–1287

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stebbins JC, Winchell CJ, Constable JVH (2013) Helianthus winteri (Asteraceae), a new perennial species from the southern Sierra Nevada foothills, California. Aliso 31:19–24

    Article  Google Scholar 

  • Talukder ZI, Gong L, Hulke BS, Pegadaraju V, Song QJ, Schultz Q, Qi LL (2014) A high-density SNP map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R 12 . PLoS One 9:e98628

    Article  PubMed  PubMed Central  Google Scholar 

  • Van Ooijen JW (2006) JoinMap® 4, Software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, Wageningen, Netherlands. http://www.kyazma.com. Accessed 4 Jan 2016

  • Vear F (1974) Studies on resistance to downy mildew in sunflower (Helianthus annuus L.). In: Proceedings of 6th International Sunflower Conference, 22–24 July, 1974, Bucharest, Romania, pp 297–302

  • Vear F, Leclercq P (1971) Deux nouvea ux genes resistance au mildiou du tournesol. Ann Amelior Plantes 21:251–255

    Google Scholar 

  • Vear F, Gentzbittel L, Philippon J, Mouzeyar S, Mestries E, Roeckel-Drevet P, de Labroube DT, Nicolas P (1997) The genetics of resistance to five races of downy mildew (Plasmopara halstedii) in sunflower (Helianthus annuus L.). Theor Appl Genet 95:584–589

    Article  Google Scholar 

  • Vear F, Seriveys H, Petit A, Serre F, Boudon JP, Roche S, Walser P, de Labrouhe DT (2008) Origins of major genes for downy mildew resistance in sunflower. In: Proceedings of 17th International Sunflower Conference Cordoba, Spain, 2008, pp 125–130

  • Viranyi F, Gulya TJ, Tourieille DL (2015) Recent changes in the pathogenic variability of Plasmopara halstedii (sunflower downy mildew) populations from different continents. Helia 38:149–162

    Google Scholar 

  • Vrânceanu V, Stoenescu F (1970) Immunity to sunflower downy mildew due to a single dominant gene. Probl Agric 22:34–40

    Google Scholar 

  • Vrânceanu VL, Pirvu N, Stoenescu FM (1981) New sunflower downy mildew resistance genes and their management. Helia 4:23–27

    Google Scholar 

  • Zhang ZW, Ma GJ, Zhao J, Markell SG, Qi LL (2017) Discovery and introgression of the wild sunflower-derived novel downy mildew resistance gene Pl 19 in confection sunflower (Helianthus annuus L.). Theor Appl Genet 130:29–39

    Article  CAS  PubMed  Google Scholar 

  • Zimmer DE, Kinman ML (1972) Downy mildew resistance in cultivated sunflower and its inheritance. Crop Sci 12:749–751

    Article  Google Scholar 

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Acknowledgements

The authors thank Dr. Loren Rieseberg for providing access to the Sunflower Genome Data Repository. They also thank Drs. Gerald Seiler and Gongjun Shi for critical review of the manuscript, Angelia Hogness for technical assistance, and Michelle Gilley for P. halstedii isolates. This project was supported by the USDA-AMS Specialty Crop Block Grant Program 15-SCBGP-ND-0026 and 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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  1. Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA

    G. J. Ma & S. G. Markell

  2. Soybean Genomics and Improvement Lab, USDA-Agricultural Research Service, Beltsville, MD, 20705-2350, USA

    Q. J. Song

  3. Red River Valley Agricultural Research Center, USDA-Agricultural Research Service, 1605 Albrecht Blvd N, Fargo, ND, 58102-2765, USA

    L. L. Qi

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  1. G. J. Ma
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Ma, G.J., Markell, S.G., Song, Q.J. et al. Genotyping-by-sequencing targeting of a novel downy mildew resistance gene Pl 20 from wild Helianthus argophyllus for sunflower (Helianthus annuus L.). Theor Appl Genet 130, 1519–1529 (2017). https://doi.org/10.1007/s00122-017-2906-4

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