SpringerLink
Log in

Genetic and physical map** of the SH3 region that confers resistance to leaf rust in coffee tree (Coffea arabica L.)

  • Original Paper
  • Published:
Tree Genetics & Genomes Aims and scope Submit manuscript

Abstract

Resistance to coffee leaf rust is conferred by SH3, a major dominant gene that has been introgressed from a wild coffee species Coffea liberica (genome L) into the allotetraploid cultivated species, Coffea arabica (genome CaEa). As the first step toward the map-based cloning of the SH3 gene, using a bacterial artificial chromosome (BAC) library, we describe the construction of a physical map in C. arabica spanning the resistance locus. This physical map consists in two homeologous BAC-contigs of 1,170 and 1,208 kb corresponding to the subgenomes Ca and Ea, respectively. Genetic analysis was performed using a single nucleotide polymorphism detection assay based on Sanger sequencing of amplicons. The C. liberica-derived chromosome segment that carries the SH3 resistance gene appeared to be introgressed on the sub-genome Ca. The position of the SH3 locus was delimited within an interval of 550 kb on the physical map. In addition, our results indicated a sixfold reduction in recombination frequency in the introgressed SH3 region compared to the orthologous region in Coffea canephora.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price includes VAT (Germany)

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Barker CL, Donald T, Pauquet J, Ratnaparkhe MB, Bouquet A, Adam-Blondon AF, Thomas MR, Dry I (2005) Genetic and physical map** of the grapevine powdery mildew resistance gene, Run1, using a bacterial artificial chromosome library. Theor Appl Genet 111:370–377

    Article  CAS  PubMed  Google Scholar 

  • Diniz LEC, Sakiyama NS, Lashermes P, Caixeta ET, Oliviera ACB, Zambolin EM, Loureiro ME, Pereira AA, Zambolin L (2005) Analysis of AFLP markers associated to the Mex-1 locus in Icatu progenies. Crop Breed App Biotech 5:387–393

    CAS  Google Scholar 

  • Drouaud J, Camilleri C, Bourguignon PY, Canaguier A, Bérard A, Vezon D, Giancola S, Brunel D, Colot V, Prum B, Quesneville H, Mézard C (2006) Variation in crossing-over rates across chromosome 4 of Arabidopsis thaliana reveals the presence of meiotic recombination “hot spots”. Genome Res 16:106–114

    Article  CAS  PubMed  Google Scholar 

  • Eskes AB (1989) Resistance. In: Kushalappa AC, Eskes AB (eds) Coffee rust: epidemiology, resistance, and management. CRC Press, Florida, pp 171–291

    Google Scholar 

  • Etienne H, Lashermes P, Menéndez-Yuffá A, De Guglielmo-Cróquer Z, Alpizar E, Sreenath HL (2008) Coffee. In: Kole C, Hall TC (eds) A compendium of transgenic crop plants, volume 8, plantation crops, ornamentals and turf grasses. Blackwell Publishing, Oxford, UK, pp 57–84

    Google Scholar 

  • Ganal MW, Tanksley SD (1996) Recombination around the Tm2a and Mi resistance genes in different crosses of Lycopersicon peruvianum. Theor Appl Genet 92:101–108

    Article  CAS  Google Scholar 

  • Herrera JC, D’Hont A, Lashermes P (2007) Use of fluorescent in situ hybridization as a tool for introgression analysis and chromosome identification in coffee (Coffea arabica L.). Genome 50:619–626

    Article  PubMed  Google Scholar 

  • Hert DG, Fredlake CP, Barron AE (2008) Advantages and limitations of next-generation sequencing technologies: a comparison of electrophoresis and non-electrophoresis methods. Electrophoresis 29:4618–4626

    Article  CAS  PubMed  Google Scholar 

  • Kushalappa AC, Eskes AB (1989) Advances in coffee rust research. Annu Rev Phytopathol 27:503–531

    Article  Google Scholar 

  • Lander ES, Green P, Abrahamson J, Bralow A, Daly MJ, Loincoln SE, Newburg L (1987) MAP MAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181

    Article  CAS  PubMed  Google Scholar 

  • Lashermes P, Combes MC, Robert J, Trouslot P, D’hont A, Anthony F, Charrier A (1999) Molecular characterisation and origin of the Coffea arabica L. genome. Mol Gen Genet 261:259–266

    Article  CAS  PubMed  Google Scholar 

  • Lashermes P, Combes MC, Prakash NS, Trouslot P, Lorieux M, Charrier A (2001) Genetic linkage map of Coffea canephora: effect of segregation distortion and analysis of recombination rate in male and female meiosis. Genome 44:589–596

    Article  CAS  PubMed  Google Scholar 

  • Lashermes P, Combes MC, Ansaldi C, Gichuru E, Noir S (2010) Analysis of alien introgression in coffee tree (Coffea arabica L.). Mol Breed. doi:10.1007/s11032-010-9424-2, in press

    Google Scholar 

  • Mahé L, Combes MC, Lashermes P (2007) Comparison between a coffee single copy chromosomal region and Arabidopsis duplicated counterparts evidenced high level synteny between the coffee genome and the ancestral Arabidopsis genome. Plant Mol Biol 64:699–711

    Article  PubMed  CAS  Google Scholar 

  • Mahé L, Combes MC, Varzea VMP, Guilhaumon C, Lashermes P (2008) Development of sequence characterized DNA markers linked to leaf rust (Hemileia vastatrix) resistance in coffee (Coffea arabica L.). Mol Breed 21:105–113

    Article  CAS  Google Scholar 

  • Marra MA, Kucaba TA, Dietrich NL, Green ED, Brownstein B, Wilson RK, McDonald KM, Hillier L, McPherson J, Waterston R (1997) High throughput fingerprint analysis of large-insert clones. Genome Res 7:1072–1084

    CAS  PubMed  Google Scholar 

  • Martin GB, Bogdanove AJ, Sessa G (2003) Understanding the functions of plant disease resistance proteins. Annu Rev Plant Biol 54:23–61

    Article  CAS  PubMed  Google Scholar 

  • Nachman MW (2002) Variation in recombination rate across the genome: evidence and implications. Curr Opin Genet Dev 12:657–663

    Article  CAS  PubMed  Google Scholar 

  • Neu C, Stein N, Keller B (2002) Genetic map** of the Lr20–Pm1 resistance locus reveals suppressed recombination on chromosome arm 7AL in hexaploid wheat. Genome 45:737–744

    Article  CAS  PubMed  Google Scholar 

  • Noir S, Patheyron S, Combes MC, Lashermes P, Chalhoub B (2004) Construction and characterisation of a BAC library for genome analysis of the allotetraploid coffee species (Coffea arabica L.). Theor Appl Genet 109:225–230

    Article  CAS  PubMed  Google Scholar 

  • Peters JL, Cnudde F, Gerats T (2003) Forward genetics and map-based cloning approaches. Trends Plant Sci 8(10):484–491

    Article  CAS  PubMed  Google Scholar 

  • Prakash NS, Combes MC, Naveen KS, Lashermes P (2002) AFLP analysis of introgression in coffee cultivars (Coffea arabica L.) derived from a natural interspecific hybrid. Euphytica 124:265–271

    Article  Google Scholar 

  • Prakash NS, Marques DV, Varzea VMP, Silva MC, Combes MC, Lashermes P (2004) Introgression molecular analysis of a leaf rust resistance gene from Coffea liberica into Coffea arabica L. Theor Appl Genet 109:1311–1317

    Article  CAS  PubMed  Google Scholar 

  • Prakash NS, Ganesh D, Bhat SS (2005) Population dynamics of coffee leaf rust (Hemileia vastatrix) and recent advances in India. In: Zambolim L, Zambolim E, Várzea VMP (eds) Durable resistance to coffee leaf rust. Universidade Federal de Viçosa, Brasil, pp 411–442

    Google Scholar 

  • Rafalski JA (2002) Novel genetic map** tools in plants: SNPs and LD-based approaches. Plant Sci 162:329–333

    Article  CAS  Google Scholar 

  • Ramachandran M, Srinivasan CS (1979) Four generations of selection for resistance to race I of leaf rust in arabica cv. S.288 × ‘Kents’. Indian Coffee 43(6):159–161

    Google Scholar 

  • Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY

    Google Scholar 

  • Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467

    Article  CAS  PubMed  Google Scholar 

  • Srinivasan KH, Narasimhaswamy RL (1975) A review of coffee breeding work done at the Government coffee experiment station, Balehonnur. Indian coffee 34:311–321

    Google Scholar 

  • Staden R, Judge DP, Bonfield JK (2000) The Staden package, 1998. Meth Mol Biol 132:115–130

    CAS  Google Scholar 

  • Stirling B, Newcombe G, Vrebalov J, Bosdet I, Bradshaw HD (2001) Suppressed recombination around the MXC3 locus, a major gene for resistance to poplar leaf rust. Theor Appl Genet 103:1129–1137

    Article  CAS  Google Scholar 

  • Van der Vossen HAM (2001) Coffee breeding practices. In: Clarke RJ, Vitzthum OG (eds) Coffee. Recent developments – agronomy, vol 1. Blackwell Science Ltd, London, pp 184–201

    Google Scholar 

  • Várzea VMP, Marques DV (2005) Population variability of Hemileia vastatrix vs coffee durable resistance. In: Zambolim L, Zambolim E, Várzea VMP (eds) Durable resistance to coffee leaf rust. Universidade Federal de Viçosa, Brasil, pp 53–74

    Google Scholar 

  • Wei F, Gobel-Werner K, Morroll SM, Kurth J, Mao L, Wing RA, 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 153:1929–1948

    CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. IRD - Institut de Recherche pour le Développement, UMR RPB (CIRAD, IRD, Université Montpellier II), BP 64501, 34394, Montpellier Cedex 5, France

    Philippe Lashermes, Marie-Christine Combes, Alessandra Ribas, Alberto Cenci & Laetitia Mahé

  2. CIRAD–Centre de coopération internationale en recherche agronomique pour le développement, UMR RPB (CIRAD, IRD, Université Montpellier II), BP 64501, 34394, Montpellier Cedex 5, France

    Hervé Etienne

Authors
  1. Philippe Lashermes
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Marie-Christine Combes
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Alessandra Ribas
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Alberto Cenci
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Laetitia Mahé
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Hervé Etienne
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Philippe Lashermes.

Additional information

Communicated by: A. Abbott

Rights and permissions

Reprints and permissions

About this article

Cite this article

Lashermes, P., Combes, MC., Ribas, A. et al. Genetic and physical map** of the SH3 region that confers resistance to leaf rust in coffee tree (Coffea arabica L.). Tree Genetics & Genomes 6, 973–980 (2010). https://doi.org/10.1007/s11295-010-0306-x

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11295-010-0306-x

Keywords

Search

Navigation