Identification and editing of a hybrid lethality gene expands the range of interspecific hybridization potential in Nicotiana

Abstract

Key message

Identification and inactivation of hybrid lethality genes can be used to expand the available gene pool for improvement of a cultivated crop species.

Abstract

Hybrid lethality is one genetic mechanism that contributes to reproductive isolation in plants and serves as a barrier to use of diverse germplasm for improvement of cultivated species. A classic example is the seedling lethality exhibited by progeny from the Nicotiana tabacum × N. africana interspecific cross. In order to increase the body of knowledge on mechanisms of hybrid lethality in plants, and to potentially develop tools to circumvent them, we utilized a transposon tagging strategy to identify a candidate gene involved in the control of this reaction. N. tabacum gene Nt6549g30 was identified to code for a class of coiled-coil nucleotide-binding site-leucine-rich repeat (CC-NBS-LRR) proteins, the largest class of plant defense proteins. Gene editing, along with other experiments, was used to verify that Nt6549g30 is the gene at the N. tabacum Hybrid Lethality 1 (NtHL1) locus controlling the hybrid lethality reaction in crosses with N. africana. Gene editing of Nt6549g30 was also used to reverse interspecific seedling lethality in crosses between N. tabacum and eight of nine additional tested species from section Suaveolentes. Results further implicate the role of disease resistance-like genes in the evolution of plant species and demonstrate the possibility of expanding the gene pool for a crop species through gene editing.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3

References

  1. Afanador LK, Haley SD, Kelly JD (1993) Adoption of a mini-prep DNA extraction method for RAPD marker analysis in common bean (Phaseolus vulgaris L.). Annu Rep Bean Improv Coop 36:10–11

    Google Scholar 

  2. An G, Watson BD, Chiang CC (1986) Transformation of tobacco, tomato, potato, and Arabidopsis thaliana using a binary Ti vector system. Plant Physiol 81:301–305

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Ballvora A, Ercolano MR, Weiß J, Meksem K, Bormann CA, Oberhagemann P, Salamini F, Gebhardt C (2002) The R1 gene for potato resistance to late blight (Phytophthora infestans) belongs to the leucine zipper/NBS/LRR class of plant resistance genes. Plant J 30:361–371

    CAS  PubMed  Google Scholar 

  4. 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 123:219–230

    PubMed  PubMed Central  Google Scholar 

  5. Bomblies K, Weigel D (2007) Hybrid necrosis: autoimmunity as a potential gene-flow barrier in plant species. Nat Rev Genet 8:382–393

    CAS  PubMed  Google Scholar 

  6. Brieger F (1929) Vererbung bei Artbastarden unter besonderer Berücksichtigung der Gattung Nicotiana. Zücht 1:140–152

    Google Scholar 

  7. Burk LG, Gerstel DU, Wernsman EA (1979) Maternal haploids of Nicotiana tabacum L. from seed. Science 206:585–585

    CAS  PubMed  Google Scholar 

  8. Casey LW, Lavrencic P, Bentham AR, Cesari S, Ericsson DJ, Croll T, Turk D, Anderson PA, Mark AE, Dodds PN, Mobli M, Kobe B, Williams SJ (2016) The CC domain structure from the wheat stem rust resistance protein Sr33 challenges paradigms for dimerization in plant NLR proteins. Proc Natl Acad Sci USA 113:12856–12861

    CAS  PubMed  Google Scholar 

  9. Cesari S, Bernoux M, Moncuquet P, Kroj T, Dodds PN (2014) A novel conserved mechanism for plant NLR protein pairs: the “integrated decoy” hypothesis. Front Plant Sci 5:606

    PubMed  PubMed Central  Google Scholar 

  10. Cesari S, Moore J, Chen C, Webb D, Periyannan S, Mago R, Bernoux M, Lagudah ES, Dodds PN (2016) Cytosolic activation of cell death and stem rust resistance by cereal MLA-family CC–NLR proteins. Proc Natl Acad Sci USA 113:10204–10209

    CAS  PubMed  Google Scholar 

  11. Chae E, Bomblies K, Kim ST, Karelina D, Zaidem M, Ossowski S, Martín-Pizarro C, Laitinen RA, Rowan BA, Tenenboim H, Lechner S, Demar M, Habring-Muller A, Lanz C, Ratsch G, Weigel D (2014) Species-wide genetic incompatibility analysis identifies immune genes as hot spots of deleterious epistasis. Cell 159:1341–1351

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Chen C, Lin HX (2016) Evolution and molecular control of hybrid incompatibility in plants. Front Plant Sci 7:1208

    PubMed  PubMed Central  Google Scholar 

  13. Clarkson JJ, Knapp S, Garcia VF, Olmstead RG, Leitch AR, Chase MW (2004) Phylogenetic relationships in Nicotiana (Solanaceae) inferred from multiple plastid DNA regions. Mol Phylogenet Evol 33:75–90

    CAS  PubMed  Google Scholar 

  14. Deng J, Fang L, Zhu X, Zhou B, Zhang T (2019) A CC-NBS-LRR gene induces hybrid lethality in cotton. J Expt Botany. https://doi.org/10.1093/jxb/erz312

    Article  Google Scholar 

  15. Dubey N, Singh K (2018) Role of NBS-LRR proteins in plant defense. In: Singh A, Singh K (eds) Molecular aspects of plant-pathogen interaction. Springer, Singapore, pp 115–138

    Google Scholar 

  16. Edwards K, Fernandez-Pozo N, Drake-Stowe K, Humphry M, Evans A, Bombarely A, Allen F, Hurst R, White B, Kernodle S, Bromley JR, Sanchez-Tamburrino JP, Lewis RS, Mueller LA (2017) Map-based cloning of homeologous loci implicated in nitrogen utilization efficiency enabled by an improved Nicotiana tabacum genome assembly. BMC Genom 18:448

    CAS  Google Scholar 

  17. Fitzmaurice WP, Lehman LJ, Nguyen LV, Thompson WF, Wernsman EA, Conkling MA (1992) Development and characterization of a generalized gene tagging system for higher plants using an engineered maize transposon Ac. Plant Mol Biol 20:177–198

    CAS  PubMed  Google Scholar 

  18. Fitzmaurice WP, Nguyen LV, Wernsman EA, Thompson WF, Conkling M (1999) Transposon Tagging of the sulfur gene of tobacco using engineered maize Ac/Ds elements. Genetics 153:1919–1928

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Gerstel DU, Burns JA, Burk LG (1979) Interspecific hybridizations with an African tobacco, Nicotiana africana Merxm. J Hered 70:342–344

    Google Scholar 

  20. Hancock WG, Kuraparthy V, Kernodle SP, Lewis RS (2015) Identification of maternal haploids of Nicotiana tabacum aided by transgenic expression of green fluorescent protein: evidence for chromosome elimination in the N. tabacum × N. africana interspecific cross. Mol Breed 35:179

    Google Scholar 

  21. Hebsgaard SM, Korning PG, Tolstrup N, Engelbrecht J, Rouzé P, Brunak S (1996) Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. Nucleic Acids Res 24:3439–3452

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Huang X, Madan A (1999) CAP3: A DNA sequence assembly program. Genome Res 9:868–877

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Iizuka T, Kuboyama T, Marubashi W, Oda M, Tezuka T (2011) Nicotiana debneyi has a single dominant gene causing hybrid lethality in crosses with N. tabacum. Euphytica 186:321–328

    Google Scholar 

  24. Tobacco J (1994) The genus Nicotiana illustrated. Japan Tobacco, Tokyo

    Google Scholar 

  25. Jones JDG, Dangl JL (2006) The plant immune system. Nature 444(7117):323

    CAS  Google Scholar 

  26. Kasmi FE, Nishimura MT (2016) Structural insights into plant NLR immune receptor function. Proc Natl Acad Sci 113:12619–12621

    PubMed  Google Scholar 

  27. Knapp S, Chase MW, Clarkson JJ (2004) Nomenclatural changes and a new sectional classification in Nicotiana (Solanaceae). Taxon 53:73–82

    Google Scholar 

  28. Kuang H, Woo S-S, Meyers BC, Nevo E, Michelmore RW (2004) Multiple genetic processes result in heterogeneous rates of evolution within the major cluster disease resistance genes in lettuce. Plant Cell 16:2870–2894

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Lewis RS (2019) Tobacco. In: Novak J, Bluthner, W-D (eds) Handbook of plant breeding: Vol: medicinal, aromatic, and stimulant plants. Springer, Berlin

  30. Liu Y-G, Chen Y (2007) High-efficiency thermal asymmetric interlaced PCR for amplification of unknown flanking sequences. Biotechniques 43:649–656

    CAS  PubMed  Google Scholar 

  31. Maekawa T, Cheng W, Spiridon LN, Töller A, Lukasik E, Saijo Y, Liu P, Shen Q-H, Micluta MA, Somssich IE, Takken FLW, Petrescu A-J, Chai J, Schulze-Lefert P (2011) Coiled-coil domain-dependent homodimerization of intracellular barley immune receptors defines a minimal functional module for triggering cell death. Cell Host Microbe 9:187–199

    CAS  PubMed  Google Scholar 

  32. Marubashi W, Kobayashi M (2002) Temperature-dependent apoptosis detected in hybrids between Nicotiana debneyi and N. tabacum expressing lethality. Plant Biotechnology 19:267–270

    CAS  Google Scholar 

  33. Marubashi W, Yamada Y, Niwa M (1999) Apoptosis detected in hybrids between Nicotiana glutinosa and N. repanda expressing lethality. Planta 210:168–171

    CAS  PubMed  Google Scholar 

  34. Orr HA (1996) Dobzhansky, Bateson, and the genetics of speciation. Genetics 144:1331–1335

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18:233–234

    CAS  PubMed  Google Scholar 

  36. Sierro N, Battey JN, Ouadi S, Bovet L, Goepfert S, Bakaher N, Peitsch MC, Ivanov NV (2013a) Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis. Genome Biol 14:R60

    PubMed  PubMed Central  Google Scholar 

  37. Sierro N, van Oeveren J, van Eijk MJT, Martin F, Stormo KE, Peitsch MC, Ivanov NV (2013b) Whole genome profiling physical map and ancestral annotation of tobacco Hicks Broadleaf. Plant J Cell Mol Biol 75:880–889

    CAS  Google Scholar 

  38. 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 5:3833

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Tezuka T (2012) Hybrid lethality in the genus Nicotiana. In: Botany. IntechOpen

  40. Tezuka T, Marubashi W (2004) Apoptotic cell death observed during the expression of hybrid lethality in interspecific hybrids between Nicotiana tabacum and N. suaveolens. Breed Sci 54:59–66

    CAS  Google Scholar 

  41. Tezuka T, Marubashi W (2006) Genomic factors lead to programmed cell death during hybrid lethality in interspecific hybrids between Nicotiana tabacum and N. debneyi. SABRAO J Breed Genet 38:9–81

    Google Scholar 

  42. Tezuka T, Kuboyama T, Matsuda T, Marubashi W (2010) Seven of eight species in Nicotiana section Suaveolentes have common factors leading to hybrid lethality in crosses with Nicotiana tabacum. Ann Bot 106:267–276

    CAS  PubMed  PubMed Central  Google Scholar 

  43. Tezuka T, Matsuo C, Iizuka T, Oda M, Marubashi W (2012) Identification of Nicotiana tabacum linkage group corresponding to the Q chromosome gene(s) involved in hybrid lethality. PLoS ONE 7:e37822

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Xie K, Yang Y (2013) RNA-guided genome editing in plants using a CRISPR–Cas system. Mol Plant 6:1975–1983

    CAS  Google Scholar 

  45. Yamada T, Marubashi W, Niwa M (1999) Detection of four lethality types in interspecific crosses among Nicotiana species through the use of three rescue methods for lethality. Breed Sci 49:203–210

    Google Scholar 

Download references

Author information

Affiliations

Authors

Contributions

JMM, JMN, SPK, WGH, and RSL performed the research, participated in data analyses, and reviewed the manuscript. RSL designed the research and drafted the manuscript.

Corresponding author

Correspondence to Ramsey S. Lewis.

Ethics declarations

Conflict of interest

The authors declare that they have no conflicts of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Communicated by P. Heslop-Harrison.

Electronic supplementary material

Below is the link to the electronic supplementary material.

122_2020_3641_MOESM1_ESM.pdf

Supplementary file1 (PDF 997 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Ma, J., Hancock, W.G., Nifong, J.M. et al. Identification and editing of a hybrid lethality gene expands the range of interspecific hybridization potential in Nicotiana. Theor Appl Genet 133, 2915–2925 (2020). https://doi.org/10.1007/s00122-020-03641-w

Download citation