Advertisement

Molecular Breeding

, 36:137 | Cite as

Physical mapping of NBS-coding resistance genes to the Me-gene cluster on chromosome P9 reveals markers tightly linked to the N gene for root-knot nematode resistance in pepper

  • Ibrahim Celik
  • Mehmet Ali Sogut
  • Ercan Ozkaynak
  • Sami Doganlar
  • Anne FraryEmail author
Article

Abstract

Natural root-knot nematode resistance genes are unique resources to control this major pest in pepper (Capsicum annuum). Although four genes (Me1, Me3, Me7 and N) conferring broad-spectrum resistance were mapped to a cluster in a 28-cm interval on chromosome P9, limited markers targeting this region were available. In the present study, the Me-gene cluster was structurally annotated for resistance genes to develop markers targeting the N gene. As a result, the Me-gene cluster (4.07 Mb in size) was found to contain three resistance gene hotspots. In addition, a SSR maker tightly linked to the N gene (0.8 cM away) was developed for marker-assisted selection in pepper.

Keywords

Capsicum annuum Genome annotation Meloidogyne spp. Marker-assisted selection (MAS) 

Notes

Acknowledgments

This study was supported by grant 110O675 from the Scientific and Technological Research Council of Turkey (TUBITAK).

Authors contribution

IC analyzed all data, performed all bioinformatics analysis and laboratory experiments and drafted manuscript; MAS performed all nematode tests; EO developed mapping populations; SD designed the study; AF designed the study, received funding and revised manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Human and animal rights

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

11032_2016_560_MOESM1_ESM.docx (104 kb)
Supplementary material 1 (DOCX 104 kb)

References

  1. Ameline-Torregrosa C, Wang BB, O’Bleness MS, Deshpande S, Zhu H, Roe B, Young ND, Cannon SB (2008) Identification and characterization of nucleotide-binding site-leucine-rich repeat genes in the model plant Medicago truncatula. Plant Physiol 146:5–21. doi: 10.1104/pp.107.104588 CrossRefPubMedPubMedCentralGoogle Scholar
  2. Chen R, Li H, Zhang L, Zhang J, Xiao J, Ye Z (2007) CaMi, a root-knot nematode resistance gene from hot pepper (Capsium annuum L.) confers nematode resistance in tomato. Plant Cell Rep 26(7):895–905. doi: 10.1007/s00299-007-0304-0 CrossRefPubMedGoogle Scholar
  3. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18):3674–3676. doi: 10.1093/bioinformatics/bti610 CrossRefPubMedGoogle Scholar
  4. Devran Z, Sogut MA (2009) Distribution and identification of root-knot nematodes from Turkey. J Nematol 41:128–133PubMedPubMedCentralGoogle Scholar
  5. Devran Z, Sogut MA (2011) Characterizing races of Meloidogyne incognita, M. javanica and M. arenaria in the West Mediterranean region of Turkey. Crop Prot 30:451–455. doi: 10.1016/j.cropro.2010.12.008 CrossRefGoogle Scholar
  6. Djian-Caporalino C, Pijarowski L, Januel A, Lefebvre V, Daubèze A, Palloix A, Dalmasso A, Abad P (1999) Spectrum of resistance to root-knot nematodes and inheritance of heat-stable resistance in pepper (Capsicum annuum L.). Theor Appl Genet 99:496–502. doi: 10.1007/s001220051262 CrossRefPubMedGoogle Scholar
  7. Djian-Caporalino C, Fazari A, Arguel MJ, Vernie T, VandeCasteele C, Faure I, Brunoud G, Pijarowski L, Palloix A, Lefebvre V, Abad P (2007) Root-knot nematode (Meloidogyne spp.) Me resistance genes in pepper (Capsicum annuum L.) are clustered on the P9 chromosome. Theor Appl Genet 114(3):473–486. doi: 10.1007/s00122-006-0447-3 CrossRefPubMedGoogle Scholar
  8. Fazari A, Palloix A, Wang L, Yan Hua M, Sage-Palloix AM, Zhang BX, Djian-Caporalino C (2012) The root-knot nematode resistance N-gene co-localizes in the Me-genes cluster on the pepper (Capsicum annuum L.) P9 chromosome. Plant Breed 131(5):665–673. doi: 10.1111/j.1439-0523.2012.01994.x CrossRefGoogle Scholar
  9. Grube RC, Radwanski ER, Jahn M (2000) Comparative genetics of disease resistance within the Solanaceae. Genetics 155:873–887PubMedPubMedCentralGoogle Scholar
  10. Hadisoeganda WW, Sasser JN (1982) Resistance of tomato, bean, southern pea, and garden pea cultivars to root-knot nematodes based on host suitability. Plant Dis 66:145–150. doi: 10.1094/PD-66-145 CrossRefGoogle Scholar
  11. Jupe F, Pritchard L, Etherington GJ, Mackenzie K, Cock PJ, Wright F, Sharma SK, Bolser D, Bryan GJ, Jones JD, Hein I (2012) Identification and localisation of the NB-LRR gene family within the potato genome. BMC Genomics 13:75. doi: 10.1186/1471-2164-13-75 CrossRefPubMedPubMedCentralGoogle Scholar
  12. Kim S, Park M, Yeom SI, Kim YM, Lee JM et al (2014) Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat Genet 46(3):270–278. doi: 10.1038/ng.2877 CrossRefPubMedGoogle Scholar
  13. Livingstone KD, Lackney VK, Blauth JR, van Wijk R, Jahn MK (1999) Genome mapping in Capsicum and the evolution of genome structure in the Solanaceae. Genetics 152:1183–1202PubMedPubMedCentralGoogle Scholar
  14. Mao Z, Zhu P, Liu F, Huang Y, Ling J, Chen G, Yang Y, Feng D, Xie B (2015) Cloning and functional analyses of pepper CaRKNR involved in Meloidogyne incognita resistance. Euphytica 205(3):903–913. doi: 10.1007/s10681-015-1438-8 CrossRefGoogle Scholar
  15. Mazourek M, Cirulli ET, Collier SM, Landry LG, Kang B-C, Quirin EA, Bradeen JM, Moffett P, Jahn MM (2009) The fractionated orthology of Bs2 and Rx/Gpa2 supports shared synteny of disease resistance in the Solanaceae. Genetics 182:1351–1364. doi: 10.1534/genetics.109.101022 CrossRefPubMedPubMedCentralGoogle Scholar
  16. Ooijen JW, Voorrips RE (2001) JoinMap Version 3.0: software for the calculation of genetic linkage maps. CPRO-DLO, WageningenGoogle Scholar
  17. Song R, Llaca V, Messing J (2002) Mosaic organization of orthologous sequences in grass genomes. Genome Res 12:1549–1555. doi: 10.1101/gr.268302 CrossRefPubMedPubMedCentralGoogle Scholar
  18. Tai TH, Dahlbeck D, Clark ET, Gajiwala P, Pasion R, Whalen MC, Stall RE, Staskawicz BJ (1999) Expression of the Bs2 pepper gene confers resistance to bacterial spot disease in tomato. Proc Natl Acad Sci 96(24):14153–14158CrossRefPubMedPubMedCentralGoogle Scholar
  19. Trudgill DL, Phillips MS (1997) Nematode population dynamics, threshold levels and estimation of crop losses. In: Maqbool MA (ed) Plant nematode problems and their control in the near east region (FAO Plant Production and Protection Paper, No. 144), RomeGoogle Scholar
  20. Uncu AT, Celik I, Devran Z, Ozkaynak E, Frary A, Frary A, Doganlar S (2015) Development of a SNP-based CAPS assay for the Me1 gene conferring resistance to root knot nematode in pepper. Euphytica 206(2):393–399. doi: 10.1007/s10681-015-1489-x CrossRefGoogle Scholar
  21. Van Gundy S, McKenry MV (2012) Action of nematicides. In: Horsfall JG (ed) Plant disease: an advanced treatise, 1st edn. Elsevier, pp 263–283Google Scholar
  22. Wang LH, Gu XH, Hua MY, Mao SL, Zhang ZH, Peng DL, Yun XF, Zhang BX (2009) A SCAR marker linked to the N gene for resistance to root knot nematodes (Meloidogyne spp.) in pepper (Capsicum annuum L.). Sci Hortic 122(2):318–322. doi: 10.1016/j.scienta.2009.04.011 CrossRefGoogle Scholar
  23. Williamson VM, Kumar A (2006) Nematode resistance in plants: the battle underground. Trends Genet 22(7):396–403. doi: 10.1016/j.tig.2006.05.003 CrossRefPubMedGoogle Scholar
  24. You FMN, Huo N, Gu YQ, Luo MC, Ma Y, Hane D, Lazo GR, Dvorak J, Anderson OD (2008) BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinform 9:253. doi: 10.1186/1471-2105-9-253 CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Ibrahim Celik
    • 1
  • Mehmet Ali Sogut
    • 2
  • Ercan Ozkaynak
    • 3
  • Sami Doganlar
    • 1
  • Anne Frary
    • 1
    Email author
  1. 1.Department of Molecular Biology and GeneticsIzmir Institute of TechnologyUrla, IzmirTurkey
  2. 2.Department of Plant ProtectionSuleyman Demirel UniversityIspartaTurkey
  3. 3.Yuksel Seeds Ltd.Kiziltoprak, AntalyaTurkey

Personalised recommendations