Molecular Breeding

, 39:11 | Cite as

Genetic analysis of Phn7.1, a major QTL conferring partial resistance to Phytophthora nicotianae in Nicotiana tabacum

  • Justin M. Ma
  • Crystal Heim
  • Matt Humphry
  • J. M. Nifong
  • Ramsey S. LewisEmail author


The oomycete Phytophthora nicotianae is one of the most economically important pathogens affecting tobacco (Nicotiana tabacum L.). Genetic resistance is a preferred means of managing damage caused by Phytophthora, and genes conferring partial resistance are likely to be more durable over time than those controlling immunity. Characterization of specific genetic variability controlling partial disease resistance may aid the development of long-term strategies for minimizing crop plant disease loss. Previous mapping studies identified a quantitative trait locus (QTL) designated as Phn7.1 controlling partial P. nicotianae resistance. Favorable alleles at this QTL have been identified in cigar tobacco cultivars ‘Beinhart 1000’ and ‘Florida 301,’ and were thought to also be present in most modern elite US flue-cured tobacco germplasm. To gain increased insight of the location and effect of Phn7.1, this QTL was mapped using an increased number of molecular markers (SNPs) in the genomic region of interest. A series of near isogenic lines (NILs) and sub-NILs carrying the Phn7.1-associated genomic region introgressed from Beinhart 1000 in the genetic background of susceptible variety Hicks were developed and evaluated. The region was found to have an additive effect on resistance and the corresponding QTL was localized to within a genetic interval of approximately 3 cM. Genotyping of historical materials with Phn7.1-associated SNP markers strongly suggests that the favorable Phn7.1 allele(s) is present in most modern US flue-cured cultivars and absent in early predecessor germplasm. Information from this study may be useful in marker-assisted selection and for identification of Phn7.1 candidate genes in future investigations.


Nicotiana Phytophthora Black shank Plant disease resistance Quantitative trait locus 


Author contributions

JMM, CM, MH, and JMN performed the research, helped analyze the data, and reviewed the manuscript. RSL designed the research, helped analyzed the data, and drafted the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.


  1. Apple JL (1962) Transfer of resistance to black shank (Phytophthora parasitica var nicotianae) from Nicotiana plumbaginifolia to N. tabacum. Phytopathology (Abstract) 52:1Google Scholar
  2. Bindler G, Plieske J, Bakaher N, Gunduz I, Ivanov N, van der Hoeven R, Ganal M, Donini P (2011) A high density genetic map of tobacco (Nicotiana tabacum L.) obtained from large scale microsatellite marker development. Theor Appl Genet 123:219–230CrossRefGoogle Scholar
  3. Broman KW, Sen S (2009) A guide to QTL mapping with R/qtl in statistics for biology and health. Springer, New YorkCrossRefGoogle Scholar
  4. Chaplin JF (1962) Transfer of black shank resistance from Nicotiana plumbaginifolia to flue-cured N. tabacum. Tob Sci 6:184–189Google Scholar
  5. Corwin JA, Kliebensten DJ (2017) Quantitative resistance: more than just perception of a pathogen. Plant Cell 29:655–665CrossRefGoogle Scholar
  6. Csinos AS (2005) Relationship of isolate origin to pathogenicity of race 0 and 1 of Phytophthora parasitica var. nicotianae on tobacco cultivars. Plant Dis 89:332–337CrossRefGoogle Scholar
  7. Drake KE, Lewis RS (2013) An introgressed Nicotiana rustica genomic region confers resistance to Phytophthora nicotianae in cultivated tobacco. Crop Sci 53:1366–1374CrossRefGoogle Scholar
  8. Drake KE, Moore JM, Bertrand P, Fortnum B, Peterson P, Lewis RS (2015) Black shank resistance and agronomic performance of flue-cured tobacco lines and hybrids carrying the introgressed region, Wz. Crop Sci 55:1–8CrossRefGoogle Scholar
  9. Drake-Stowe K, Bakaher N, Goepfert S, Philippon B, Mark R, Peterson P, Lewis RS (2017) Multiple disease resistance loci affect soilborne disease resistance in tobacco (Nicotiana tabacum). Phytopathology 107:1055–1061CrossRefGoogle Scholar
  10. Edwards K, Fernandez-Pozo N, Drake-Stowe K, Humphry M, Evans AD, Bombarely A, Allen F, Hurst R, White B, Kernodle SP, Bromley JR, Sanchez-Tamburino JP, Lewis RS, Mueller LA (2017) A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen use efficiency. BMC Genomics 18:448CrossRefGoogle Scholar
  11. Gallup CA, McCorkle KL, Ivors K, Shew HD (2017) Characterization of the black shank pathogen, Phytophthora nicotianae, across North Carolina tobacco production areas. Plant Dis 102:1108–1114CrossRefGoogle Scholar
  12. Kenward MG, Roger JH (1997) Small sample inference for fixed effects from restricted maximum likelihood. Biometrics 53:983–997CrossRefGoogle Scholar
  13. Kourelis J, van der Hoorn RAL (2018) Defended to the nines: 25 years of resistance gene cloning identifies nine mechanisms for R protein function. Plant Cell 30:285–299Google Scholar
  14. Krattinger SG, Lagudah ES, Spielmeyer W, Singh RP, Huerta-Espino J, McFadden H, Bossolini E, Selter LL, Keller B (2009) A putative ABC transporter confers durable resistance to multiple fungal pathogens in wheat. Science 323:1360–1363CrossRefGoogle Scholar
  15. Madden LV, Hughes G, van der Bosch F (2007) The study of plant disease epidemics. APS Press, St. PaulGoogle Scholar
  16. McCorkle KL, Lewis RS, Shew HD (2012) Resistance to Phytophthora nicotianae in tobacco breeding lines derived from variety Beinhart 1000. Plant Dis 97:252–258CrossRefGoogle Scholar
  17. McCorkle KL, Drake-Stowe KE, Lewis RS, Shew HD (2017) Characterization of Phytophthora nicotianae resistance conferred by the introgressed Nicotiana rustica region, Wz, in flue-cured tobacco. Plant Dis 102:309–317CrossRefGoogle Scholar
  18. Moore JW, Herrera-Foessel S, Lan C, Schnippenkoetter W, Ayliffe M, Huerta-Espino J, Lillemo M, Viccars L, Milne R, Periyannan S, Kong X, Spielmeyer W, Talbot M, Bariana H, Patrick JW, Dodds P, Singh R, Lagudah E (2015) A recently evolved hexose transporter variant confers resistance to multiple pathogens in wheat. Nat Genet 47:1494–1498CrossRefGoogle Scholar
  19. Poland JA, Balint-Kurti PJ, Wisser RJ, Pratt RC, Nelson RJ (2009) Shades of gray: the world of quantitative disease resistance. Trends Plant Sci 14:21–29CrossRefGoogle Scholar
  20. Saxton AM (1998) A macro for converting mean separation output to letter groupings in Proc Mixed. SAS Users Group Int 23:1243–1246 Accessed 3/16/2016Google Scholar
  21. Schaalje GB, McBride JB, Fellingham GW (2001) Approximations to distributions of test statistics in complex mixed linear models using SAS Proc MIXED. SAS Users Group Int 26:262Google Scholar
  22. Sierro N, van Oeveren J, van Eijk MJT, Martin F, Stormo KE, Peitsch MC, Ivanov NV (2013) Whole genome profiling physical map and ancestral annotation of tobacco Hicks broadleaf. Plant J Cell Mol Biol 75:880–889CrossRefGoogle Scholar
  23. Sierro N, Battey JND, Ouadi S, Bakaher N, Bovet L, Willig A, Goepfert S, Peitsch MC, Ivanov NV (2014) The tobacco genome sequence and its comparison with those of tomato and potato. Nat Commun 5:3833CrossRefGoogle Scholar
  24. Sullivan MJ, Melton TA, Shew HD (2005) Managing the race structure of Phytophthora parasitica var. nicotianae with cultivar rotation. Plant Dis 89:1285–1294CrossRefGoogle Scholar
  25. Tisdale WB (1931) Development of strains of cigar wrapper tobacco resistant to black shank (Phytophthora nicotianae Breda de Haan). Florida Univ Agr Expt Stat Bull 226:1–45Google Scholar
  26. Valleau WE, Stokes GW, Johnson EM (1960) Nine years experience with the Nicotiana longiflora factor for resistance to Phytophthora parasitica var. nicotianae in control of black shank. Tob Sci 4:92–94Google Scholar
  27. Van Ooijen J (2006) JoinMap 4, software for the calculation of genetic linkage maps in experimental populations. Kyazma B.V, WageningenGoogle Scholar
  28. Vontimitta V, Lewis RS (2012) Mapping of quantitative trait loci affecting resistance to Phytophthora nicotianae in tobacco (Nicotiana tabacum L.) line Beinhart-1000. Mol Breed 29:89–98CrossRefGoogle Scholar
  29. Wang Y, Tiwari VK, Rawat N, Gill BS, Huo N, You FM, Coleman-Derr D, Gu YQ (2016) GSP: a web-based platform for designing genome-specific primers in polyploids. Bioinformatics 32:2382–2383CrossRefGoogle Scholar
  30. Wiesner-Hanks T, Nelson R (2016) Multiple disease resistance in plants. Ann Rev Phythopathol 54:229–252CrossRefGoogle Scholar
  31. Xiao B, Drake K, Vontimitta V, Tong Z, Zhang X, Li M, Leng X, Li Y, Lewis RS (2013) Location of genomic regions contributing to resistance in tobacco cultivar Florida 301. Crop Sci 53:473–481CrossRefGoogle Scholar
  32. Yang Q, He Y, Kabahuma M, Chaya T, Kelly A, Borrego E, Bian Y, El Kasmi F, Yang L, Teixeira P, Kolkman J, Nelson R, Kolomiets M, Dangl JL, Wisser R, Caplan J, Li X, Lauter N, Balint-Kurti P (2017) A gene encoding maize caffeoyl-CoA O-methyltransferase confers quantitative resistance to multiple pathogens. Nat Genet 49:1364–1372CrossRefGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Department of Crop and Soil ScienceNorth Carolina State UniversityRaleighUSA
  2. 2.Plant Biotechnology DivisionBritish American Tobacco CompanyCambridgeUK

Personalised recommendations