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Molecular Breeding

, 39:19 | Cite as

Molecular mapping of the downy mildew and rust resistance genes in a sunflower germplasm line TX16R

  • Z. Liu
  • L. Zhang
  • G. J. Ma
  • G. J. Seiler
  • C. C. Jan
  • L. L. QiEmail author
Article
  • 12 Downloads

Abstract

The sunflower germplasm line TX16R is resistant to Plasmopara halstedii (causal agent of sunflower downy mildew) and Puccinia helianthi (causal agent of sunflower rust), which are two destructive foliar diseases in sunflower production worldwide. This study reports the mapping of the downy mildew and rust resistance genes Pl33 and R16 from TX16R, respectively. Progeny testing of test crosses for downy mildew resistance suggested that Pl33 localizes to linkage group (LG) 4 of the sunflower genome. Molecular mapping of Pl33 using simple sequence repeat (SSR) and single-nucleotide polymorphism (SNP) markers identified Pl33 cosegregating with ORS644, ORS963, SFW04901, and SFW04052, and linking to two SNPs, NSA_006089 and NSA_008496, at a genetic distance of 0.2 cM on the proximal side. Bulked segregant analysis using SSR and EST-SSR markers from LGs previously reported for rust genes identified polymorphic SSR markers associated with rust resistance on LG13. R16 was mapped between SFW08875 and SFW04317 on LG13, with a genetic distance of 1.8 and 1.1 cM, respectively. The 15 linked markers span a genetic distance of 27.4 cM in LG13. The cosegregating or closely linked markers to the two resistance genes will facilitate marker-assisted selection (MAS) and gene pyramiding, and will further assist in identifying genes responsible for DM and rust resistance.

Keywords

Sunflower Downy mildew Rust Resistance SSR SNP marker 

Notes

Acknowledgments

The authors are very grateful to Lisa Brown for the technical assistance in this study. We thank Ms. Puying Zheng for her help in molecular marker genotyping and Dr. Fang Wei for his help in phenotyping to rust. We appreciate Drs. Yunming Long and Zahirul Talukder for their help during the SNP primer design. This project was supported by the USDA-ARS CRIS Project No. 3060-21000-043-00D. 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. The USDA is an equal opportunity provider and employer.

Author’s contribution

Conceived and designed the experiments: CCJ, ZL. Performed the experiments: ZL, LZ, GJM, CCJ, GS. Analyzed the data: ZL, GJM, LLQ. Wrote the paper: ZL, LLQ. Commented on the manuscript before submission: CCJ, GJM, GS.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

The experiments were performed in compliment with the current laws of the USA.

Supplementary material

11032_2018_921_MOESM1_ESM.docx (18 kb)
ESM 1 (DOCX 18 kb)
11032_2018_921_MOESM2_ESM.xlsx (13 kb)
ESM 2 (XLSX 12 kb)
11032_2018_921_MOESM3_ESM.pptx (308 kb)
Supplementary Fig. 1 PCR pattern of seven SNP markers for HA 434 (1), TX16R (2) and HA 458 (3). Four SNP markers had the same PCR pattern between TX16R and HA 458. Three SNP markers, i.e., SFW04052, NSA_006089, and SFW06856, showed different alleles between TX16R (Pl33) and HA 458 (Pl17), with HA 458 having the same allele as HA 434. (PPTX 308 kb)

References

  1. Albourie JM, Tourvieille J, Tourvieille de Labrouhe D (1998) Resistance to metalaxyl in isolates of the sunflower pathogen Plasmopara halstedii. European J Plant Pathol 104:2335–2342CrossRefGoogle Scholar
  2. 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 122:1211–1221CrossRefGoogle Scholar
  3. Bert PF, Tourvielle de Labrouhe D, 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 103:992–997CrossRefGoogle Scholar
  4. 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. Genes Genomes Genetics 2:721–729PubMedGoogle Scholar
  5. 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, 2010Google Scholar
  6. 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 109:1083–1086CrossRefGoogle Scholar
  7. Friskop AJ, Gulya TJ, Harveson RH, Humann RM, Acevedo M, Markell SG (2015) Phenotypic diversity of Puccinia helianthi (sunflower rust) in the United States from 2011 and 2012. Plant Dis 99:1604–1609CrossRefGoogle Scholar
  8. Ganal MW, Tanksley SD (1996) Recombination around the Tm2a and Mi resistance genes in different crosses of Lycopersicon peruvianum. Theor Appl Genet 92:101–108CrossRefGoogle Scholar
  9. Gascuel Q, Martinez Y, Boniface MC, Vear F, Pichon M, Godiard L (2015) The sunflower downy mildew pathogen Plasmopara halstedii. Mol Plant Path 16:109–122CrossRefGoogle Scholar
  10. 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 Pl1. Genome 44:205–212CrossRefGoogle Scholar
  11. Gilley MA, Markell SG, Gulya TJ, Misar CG (2016) Prevalence and virulence of Plasmopara halstedii (downy mildew) in sunflowers. Available at http://www.sunflowernsa.com/uploads/research/1277/Prevalence.Downey_Gilley.etal_2016.rev.pdf. Accessed 4 June 2018
  12. Gong L, Hulke BS, Gulya TJ, Markell SG, Qi LL (2013a) Molecular tagging of a novel rust resistance gene R 12 in sunflower (Helianthus annuus L.). Theor Appl Genet 126:93–99CrossRefGoogle Scholar
  13. Gong L, Gulya TJ, Markell SG, Hulke BS, Qi LL (2013b) Genetic mapping of rust resistance genes in confection sunflower line HA-R6 and oilseed line RHA 397. Theor Appl Genet 126:2039–2049CrossRefGoogle Scholar
  14. Gulya TJ (1985) Registration of five disease-resistant sunflower germplasms. Crop Sci 25:719–720Google Scholar
  15. Gulya TJ (2006) The sunflower rust situation: Current races in the northern and central Great Plains, and resistance in oilseed and confection hybrids Available at http://www.sunflowernsa.com/research/researchworkshop/documents/Gulya_Rust_06.pdf. Accessed 4 June 2018
  16. Gulya TJ, Draper M, Harbour J, Holen C, Knodel J, Lamey A, Mason P (1999) Metalaxyl resistance in sunflower downy mildew in North America. Proc. 21st sunflower res. Workshop. p. 118-123, January 14–15Google Scholar
  17. Gulya TJ, Markell S (2009) Sunflower rust status – 2008 race frequency across the Midwest and resistance among commercial hybrids. Available at http://www.sunflowernsa.com/uploads/Gulya_RustStatus_09.pdf. Accessed 4 June 2018
  18. 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. Available at http://www.sunflowernsa.com/uploads/resources/575/gulya_virulentracesdownymildew.pdf. Accessed 4 June 2018
  19. Hulke BS, Grassa CJ, Bowers JE, Burke JM, Qi LL, Talukder ZI, Rieseberg LH (2015) A unified SNP map of sunflower (Helianthus annuus L.) derived from the sunflower genome project resources. Crop Sci 55:1696–1702CrossRefGoogle Scholar
  20. Jan CC, Gulya TJ (2006) Registration of a sunflower germplasm resistant to rust, downy mildew and virus. Crop Sci 46:1829CrossRefGoogle Scholar
  21. Kosambi DD (1943) The estimation of map distances from recombination values. Ann Eugenics 12:172–175CrossRefGoogle Scholar
  22. Livaja M, Wang Y, Wieckhorst S, Haseneyer G, Hahn V, Knapp SJ, Taudien S, Schön CC, Bauer E (2013) BSTA: a targeted approach combines bulked segregant analysis with next-generation sequencing and de novo transcriptome assembly for SNP discovery in sunflower. BMC Genomics 14:628CrossRefGoogle Scholar
  23. 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 125:121–131CrossRefGoogle Scholar
  24. Long YM, Chao WS, Ma GJ, Xu SS, Qi LL (2017) An innovative SNP genotyping method adapting multiple platforms and throughputs. Theor Appl Genet 130:597–607CrossRefGoogle Scholar
  25. Ma GJ, Markell SG, Song QJ, Qi LL (2017) Genotyping-by-sequencing targeting of a novel downy mildew resistance gene Pl 20 from wild Helianthus argophyllus in sunflower (Helianthus annuus L.). Theor Appl Genet 130:1519–1529CrossRefGoogle Scholar
  26. Ma GJ, Song QJ, Markell SG, Qi LL (2018) High throughput genotyping-by-sequencing facilitates molecular tagging of a novel rust resistance gene, R 15, in sunflower (Helianthus annuus L.). Theor Appl Genet 131:1423–1432CrossRefGoogle Scholar
  27. Markell S, Gulya T, McKay K, Hutter M, Hollingsworth C, Ulstad V, Kock R, Knudsvig A (2009) Widespread occurrence of the aecial stage of sunflower rust caused by Puccinia helianthi in North Dakota and Minnesota in 2008. Plant Dis 93:668–669CrossRefGoogle Scholar
  28. Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci U S A 88:9828–9832CrossRefGoogle Scholar
  29. Miller JF, Gulya TJ, Vick BA (2004) Five oil sunflower germplasm. Crop Sci 44:1034CrossRefGoogle Scholar
  30. 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 119:795–803CrossRefGoogle Scholar
  31. Neu C, Stein N, Keller B (2002) Genetic mapping of the Lr20-Pm1 resistance locus reveals suppressed recombination on chromosome arm 7AL in hexaploid wheat. Genome 45:737–744CrossRefGoogle Scholar
  32. Pecrix Y, Buendia L, Penouilh-Suzette C, Maréchaux M, Legrand L, Bouchez Q, Rengel D, Gouzy J, Cottret L, Vear F, Godiard L (2018a) Sunflower resistance to multiple downy mildew pathotypes revealed by recognition of conserved effectors of the oomycete Plasmopara halstedii. The Plant Journal doi.  https://doi.org/10.1111/tpj.14157
  33. Pecrix Y, Penouilh-Suzette C, Stéphane Muños S, Felicity Vear F, Godiard L (2018b) Ten broad spectrum resistances to downy mildew physically mapped on the sunflower genome. Front Plant Sci 9:1780.  https://doi.org/10.3389/fpls.2018.01780 CrossRefPubMedPubMedCentralGoogle Scholar
  34. Qi LL, Wang SL, Chen PD, Liu DJ, Gill BS (1998) Identification and physical mapping of three Haynaldia villosa chromosome-6V deletion lines. Theor Appl Genet 97:1042–1046CrossRefGoogle Scholar
  35. Qi LL, Hulke BS, Vick BA, Gulya TJ (2011) Molecular mapping of the rust resistance gene R 4 to a large NBS-LRR cluster on linkage group 13 of sunflower. Theor Appl Genet 123:351–358CrossRefGoogle Scholar
  36. Qi LL, Gulya TJ, Hulke BS, Vick BA (2012a) Chromosome location, DNA markers and rust resistance of the sunflower gene R 5. Mol Breed 30:745–756CrossRefGoogle Scholar
  37. Qi LL, Seiler GJ, Hulke BS, Vick BA, Gulya TJ (2012b) Genetics and mapping of the R 11 gene conferring resistance to recently emerged rust races, tightly linked to male fertility restoration, in sunflower (Helianthus annuus L.). Theor Appl Genet 125:921–932CrossRefGoogle Scholar
  38. Qi LL, Ma GJ, Long YM, Hulke BS, Markell SG (2015a) Relocation of a rust resistance gene R 2 and its marker-assisted gene pyramiding in confection sunflower (Helianthus annuus L.). Theor Appl Genet 128:477–488CrossRefGoogle Scholar
  39. Qi LL, Long YM, Jan CC, Ma GJ, Gulya TJ (2015b) Pl 17 is a novel gene independent of known downy mildew resistance genes in the cultivated sunflower (Helianthus annuus L.). Theor Appl Genet 128:757–767CrossRefGoogle Scholar
  40. Qi LL, Long YM, Ma GJ, Markell SG (2015c) Map saturation and SNP marker development for the rust resistance genes (R 4, R 5, R 13a, and R 13b) in sunflower (Helianthus annuus L.). Mol Breed 35:196–210CrossRefGoogle Scholar
  41. Qi LL, Foley ME, Cai XW, Gulya TJ (2016) 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 129:741–752CrossRefGoogle Scholar
  42. Qi LL, Talukder ZM, Hulke BS, Foley ME (2017) 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 Gen Genomics 292:551–563CrossRefGoogle Scholar
  43. Radwan O, Bouzidi MF, Vear F, Philippon J, de Labrouhe DT, Nicolas P, Mouzeyar S (2003) Identification of non-TIR-NBS-LRR markers linked to the Pl5/Pl8 locus for resistance to downy mildew in sunflower. Theor Appl Genet 106:1438–1446CrossRefGoogle Scholar
  44. 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 Gen Genomics 280:111–125CrossRefGoogle Scholar
  45. 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 91:225–228Google Scholar
  46. Seiler GJ, Qi LL, Marek LF (2017) Utilization of sunflower crop wild relatives for cultivated sunflower improvement. Crop Sci 57:1083–1011CrossRefGoogle Scholar
  47. Stirling B, Newcombe G, Vrebalov J, Bosdet I, Bradshaw HD Jr (2001) Suppressed recombination around the MXC3 locus, a major gene for resistance to poplar leaf rust. Theor Appl Genet 103:1129–1137CrossRefGoogle Scholar
  48. 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(7):e98628.  https://doi.org/10.1371/journal.pone.0098628 CrossRefPubMedPubMedCentralGoogle Scholar
  49. Van Ooijen JW (2006) JoinMap® 4, software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, WageningenGoogle Scholar
  50. 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 95:584–589CrossRefGoogle Scholar
  51. Vincourt P, As-sadi F, Bordat A, Langlade NB, Gouzy J, Pouilly N, Lippi Y, Serre F, Godiard L, Tourvieille de Labrouhe D, Vear F (2012) Consensus mapping of major resistance genes and independent QTL for quantitative resistance to sunflower downy mildew. Theor Appl Genet 125:909–920CrossRefGoogle Scholar
  52. Viranyi F, Gulya TJ, Tourieille DL (2015) Recent changes in the pathogenic variability of Plasmopara halstedii (sunflower downy mildew) populations from different continents. Helia 0.  https://doi.org/10.1515/helia-2015-0009
  53. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78CrossRefGoogle Scholar
  54. Wei F, Gobelman-Werner K, Morroll SM, Kurth J, Mao L, Wing R, Leister D, Schulze-Lefert P, Wise RP (1999) The Mla (powdery mildew) resistance cluster is associated with three NBS-LRR gene families and suppressed recombination within a 240-kb DNA interval on chromosome 5S (1HS) of barley. Genetics 153:1929–1948PubMedPubMedCentralGoogle Scholar
  55. Wieckhorst S, Bachlava E, Dußle CM, Tang S, Gao W, Saski C, Knapp SJ, Schön CC, Hahn V, Bauer E (2010) Fine mapping of the sunflower resistance locus Pl ARG introduced from the wild species Helianthus argophyllus. Theor Appl Genet 121:1633–1644CrossRefGoogle Scholar
  56. Xie W, Ben-David R, Zeng B, Dinoor A, Xie C, Sun Q, Röder MS, Fahoum A, Fahima T (2012) Suppressed recombination rate in 6VS/6AL translocation region carrying the Pm21 locus introgressed from Haynaldia villosa into hexaploid wheat. Mol Breed 29:399–412CrossRefGoogle Scholar
  57. Yu JK, Tang S, Slabaugh MB, Heesacker A, Cole G, Herring M, Soper J, Han F, Chu WC, Webb DM, Thompson L, Edwards KJ, Berry S, Leon AJ, Grondona M, Olungu C, Maes N, Knapp SJ (2003) Towards a saturated molecular genetic linkage map for cultivated sunflower. Crop Sci 43:367–387CrossRefGoogle Scholar
  58. Zhang M, Liu Z, Jan CC (2016) Molecular mapping of a rust resistance gene R 14 in cultivated sunflower line PH3. Mol Breed 36:32CrossRefGoogle Scholar
  59. Zhang ZW, Ma GJ, Zhao J, Markell SJ, 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 130:29–39Google Scholar

Copyright information

© This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply 2019

Authors and Affiliations

  1. 1.Department of Plant SciencesNorth Dakota State UniversityFargoUSA
  2. 2.Baicheng Academy of Agricultural SciencesBaichengChina
  3. 3.USDA-ARS, Edward T. Schafer Agricultural Research Center, Northern Crop Science LaboratoryFargoUSA

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