Skip to main content
SpringerLink
Log in

Marker-assisted selection provides arabica coffee with genes from other Coffea species targeting on multiple resistance to rust and coffee berry disease

  • Published:
Molecular Breeding Aims and scope Submit manuscript

Abstract

Selecting superior genotypes is facilitated by marker-assisted selection (MAS), which is particularly suitable for transferring disease resistance alleles because it nullifies environmental effects and allows selection of resistant individuals in the absence of the pathogen or race, enabling preventive breeding. Molecular markers linked to two major genes (SH3 and SH?), conferring resistance to coffee rust, and those linked to the Ck-1 gene, conferring resistance to coffee berry disease (CBD), have previously been identified. These markers were validated and used in a progeny of crosses between Indian selections with Coffea arabica cultivars. Eleven resistant individuals homozygous for SH3 were identified by MAS. Of these, seven carry SH? from Híbrido de Timor and the gene introduced from Coffea liberica (SH3). SH? was characterized as derived from Coffea canephora. Thus, it was possible to identify C. arabica genotypes carrying important genes for rust resistance introgressed from other coffee species. MAS also allowed identification of sources of CBD resistance for use in preventive breeding for resistance to this serious disease. Using two validated molecular markers, two coffee plants carrying Ck-1 were identified: the UFV 328-60 genotype (F2) was resistant and homozygous based on both molecular markers but exhibited no markers related to SH3 and SH?, and the UFV 317-12 genotype (F1) was resistant and homozygous but resistant and heterozygous based on CBD-Sat207 and CBD-Sat235, respectively. Along with possessing Ck-1, the latter carries SH?. Overall, plants carrying different genes for resistance to rust and CBD were identified. These plants are important sources for gene pyramiding in breeding programs aimed at multiple and durable resistance.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  • Agwanda CO, Lashermes P, Trouslot P, Combes M, Charrier A (1997) Identification of RAPD markers for resistance to coffee berry disease, Colletotrichum kahawae, in arabica coffee. Euphytica 97:241–248. doi:10.1023/A:1003097913349

    Article  CAS  Google Scholar 

  • Balachiranjeevi C, Bhaskar NS, Abhilash V, Akanksha S, Viraktamath BC, Madhav MS, Hariprasad AS, Laha GS, Prasad MS, Balachandran SM, Neeraja CN, Satendra Kumar M, Senguttuvel P, Kemparaju KB, Bhadana VP, Ram T, Harika G, Mahadeva Swamy HK, Hajira SK, Yugander A (2015) Marker-assisted introgression of bacterial blight and blast resistance into DRR17B, an elite, fine-grain type maintainer line of rice. Mol Breed 35:151. doi:10.1007/s11032-015-0348-8

    Article  Google Scholar 

  • Bettencourt A, Rodrigues C (1988) Principles and practice of coffee breeding for resistance to rust and other diseases. In: Clarke R, Macrae R (eds) Coffee agronomy. Elsevier Applied Science, London, pp. 199–234

    Google Scholar 

  • Cabral PGC, Zambolim EM, Zambolim L, Lelis TP, Capucho AS, Caixeta ET (2009) Identification of a new race of Hemileia vastatrix in Brazil. Australas Plant Dis Notes 4:129–130. doi:10.1071/DN09052

    Google Scholar 

  • Cenci A, Combes M-C, Lashermes P (2012) Genome evolution in diploid and tetraploid Coffea species as revealed by comparative analysis of orthologous genome segments. Plant Mol Biol 78:135–145. doi:10.1007/s11103-011-9852-3

    Article  CAS  PubMed  Google Scholar 

  • de Brito GG, Caixeta ET, Gallina AP, Zambolim EM, Zambolim L, Diola V, Loureiro ME (2010) Inheritance of coffee leaf rust resistance and identification of AFLP markers linked to the resistance gene. Euphytica 173:255–264. doi:10.1007/s10681-010-0119-x

    Article  Google Scholar 

  • Diniz LEC, Sakiyama NS, Lashermes P, Caixeta ET, Oliveira AC, Zambolim EM, Loureiro ME, Pereira AA, Zambolim L (2005) Analysis of AFLP markers associated to the Mex-1 resistance locus in Icatu progenies. Crop Breed Appl Biotechnol 5:387–393. doi:10.12702/1984-7033.v05n04a03

    Article  CAS  Google Scholar 

  • Diola V, de Brito GG, Caixeta ET, Maciel-Zambolim E, Sakiyama NS, Loureiro ME (2011) High-density genetic mapping for coffee leaf rust resistance. Tree Genet Genomes 7:1199–1208. doi:10.1007/s11295-011-0406-2

    Article  Google Scholar 

  • Fernandez D, Tisserant E, Talhinhas P, Azinheira H, Vieira A, Petitot AS, Loureiro A, Poulain J, Da Silva C, Silva Mdo C, Duplessis S (2012) 454-pyrosequencing of Coffea arabica leaves infected by the rust fungus Hemileia vastatrix reveals in planta-expressed pathogen-secreted proteins and plant functions in a late compatible plant-rust interaction. Mol Plant Pathol 13:17–37. doi:10.1111/j.1364-3703.2011.00723.x

    Article  CAS  PubMed  Google Scholar 

  • Figueiredo A, Loureiro A, Batista D, Monteiro F, Várzea V, Pais MS, Gichuru EK, Silva MC (2013) Validation of reference genes for normalization of qPCR gene expression data from Coffea spp. hypocotyls inoculated with Colletotrichum kahawae. BMC Res Notes 6:388. doi:10.1186/1756-0500-6-388

    Article  PubMed  PubMed Central  Google Scholar 

  • Gartner GAL, McCouch SR, Moncada MDP (2013) A genetic map of an interspecific diploid pseudo testcross population of coffee. Euphytica 192:305–323. doi:10.1007/s10681-013-0926-y

    Article  CAS  Google Scholar 

  • Gichimu B, Gichuru E, Mamati G, Nyende A (2014) Occurrence of Ck-1 gene conferring resistance to coffee berry disease in Coffea arabica cv. Ruiru 11 and its parental genotypes. J Agric Crop Res 2:51–61

    Google Scholar 

  • Gichuru EK, Agwanda CO, Combes MC, Mutitu EW, Ngugi ECK, Bertrand B, Lashermes P (2008) Identification of molecular markers linked to a gene conferring resistance to coffee berry disease (Colletotrichum kahawae) in Coffea arabica. Plant Pathol 57:1117–1124. doi:10.1111/j.1365-3059.2008.01846.x

    Article  CAS  Google Scholar 

  • Kelly JD, Gepts P, Miklas PN, Coyne DP (2003) Tagging and mapping of genes and QTL and molecular marker-assisted selection for traits of economic importance in bean and cowpea. Field Crop Res 82:135–154. doi:10.1016/S0378-4290(03)00034-0

    Article  Google Scholar 

  • Kiguongo A, Omondi C, Gichuru E, Kasili R (2014) Analysis of simple sequence repeat markers linked to coffee berry disease resistance genes in a segregating population of arabica coffee (Coffea arabica L.). Int J Biotechnol Food Sci 2:156–166

    Google Scholar 

  • Mahé L, Combes MC, Várzea 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. doi:10.1007/s11032-007-9112-z

    Article  Google Scholar 

  • Maia TA, Maciel-Zambolim E, Caixeta ET, Mizubuti ESG, Zambolim L (2013) The population structure of Hemileia vastatrix in Brazil inferred from AFLP. Australas Plant Pathol 42:533–542. doi:10.1007/s13313-013-0213-3

    Article  Google Scholar 

  • Melchinger AE (1990) Use of molecular markers in breeding for oligogenic disease resistance. Plant Breed 104:1–19. doi:10.1111/j.1439-0523.1990.tb00396.x

    Article  Google Scholar 

  • Ortega F, Lopez-Vizcon C (2012) Application of molecular marker-assisted selection (MAS) for disease resistance in a practical potato breeding programme. Potato Res 55:1–13. doi:10.1007/s11540-011-9202-5

    Article  CAS  Google Scholar 

  • Prakash NS, Marques DV, Varzea VM, Silva MC, Combes MC, Lashermes P (2004) Introgression molecular analysis of a leaf rust resistance gene from Coffea liberica into C. Arabica L. Theor Appl Genet 109:1311–1317. doi:10.1007/s00122-004-1748-z

    Article  CAS  PubMed  Google Scholar 

  • Prakash NS, Muniswamy B, Hanumantha BT, Sreenath HL, Sundaresha KD, Suresh N, Santhosh P, Soumya PR, Asha BM, Bhat SS (2011) Marker assisted selection and breeding for leaf rust resistance in coffee (Coffea arabica L.)—some recent leads. Indian J Genet Plant Breed 71:185–189

    Google Scholar 

  • Ram AS (2006) Popular Indian coffee selections. Indian Coffee 70:12–18

    Google Scholar 

  • Romero G, Vásquez LM, Lashermes P, Herrera JC (2014) Identification of a major QTL for adult plant resistance to coffee leaf rust (Hemileia vastatrix) in the natural Timor hybrid (Coffea arabica x C. canephora). Plant Breed 133:121–129. doi:10.1111/pbr.12127

    Article  CAS  Google Scholar 

  • Rubio M, Ruiz D, Egea J, Martínez-Gómez P, Dicenta F (2014) Opportunities of marker-assisted selection for plum pox virus resistance in apricot breeding programs. Tree Genet Genomes 10:513–525. doi:10.1007/s11295-014-0700-x

    Article  Google Scholar 

  • Silva MC, Várzea V, Guerra-Guimarães L, Azinheira HG, Fernandez D, Petitot A, Bertrand B, Lashermes P, Nicole M (2006) Coffee resistance to the main diseases: leaf rust and coffee berry disease. Braz J Plant Physiol 18:119–147. doi:10.1590/S1677-04202006000100010

    Article  CAS  Google Scholar 

  • Singh S, Sidhu JS, Huang N, Vikal Y, Li Z, Brar DS, Dhaliwal HS, Khush GS (2001) Pyramiding three bacterial blight resistance genes (xa5, xa13 and Xa21) using marker-assisted selection into indica rice cultivar PR106. Theor Appl Genet 102:1011–1015. doi:10.1007/s001220000495

    Article  CAS  Google Scholar 

  • Van Der Vossen HAM, Walyaro DJ (1980) Breeding for resistance to coffee berry disease in Coffea arabica L. II. Inheritance of the resistance. Euphytica 29:777–791. doi:10.1007/BF00023225

    Article  Google Scholar 

  • Young N (1999) A cautiously optimistic vision for marker-assisted breeding. Mol Breed 5:505–510. doi:10.1023/A:1009684409326

    Article  Google Scholar 

Download references

Acknowledgements

This work was financially supported by the Brazilian Coffee Research and Development Consortium (Consórcio Brasileiro de Pesquisa e Desenvolvimento do Café–CBP&D/Café), by the Foundation for Research Support of the State of Minas Gerais (FAPEMIG), by the National Council of Scientific and Technological Development (CNPq), and by the National Institutes of Science and Technology of Coffee (INCT/Café).

Author information

Authors and Affiliations

  1. BIOAGRO, BioCafé, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil

    Emilly Ruas Alkimim & Tiago Vieira Sousa

  2. Empresa Brasileira de Pesquisa Agropecuária - Embrapa Café, BIOAGRO, BioCafé, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil

    Eveline Teixeira Caixeta

  3. Empresa de Pesquisa Agropecuária de Minas Gerais –Epamig, Viçosa, MG, 36570-000, Brazil

    Antônio Alves Pereira

  4. Embrapa Café, Viçosa, MG, 36570-000, Brazil

    Antonio Carlos Baião de Oliveira

  5. Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil

    Laércio Zambolim

  6. Departamento Fitotecnia, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil

    Ney Sussumu Sakiyama

Authors
  1. Emilly Ruas Alkimim
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Eveline Teixeira Caixeta
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Tiago Vieira Sousa
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Antônio Alves Pereira
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Antonio Carlos Baião de Oliveira
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Laércio Zambolim
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Ney Sussumu Sakiyama
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Eveline Teixeira Caixeta.

Electronic supplementary material

Online Resource 1

(DOCX 23 kb).

Online Resource 2

(DOCX 15 kb).

Online Resource 3

(DOCX 81 kb).

Online Resource 4

(DOCX 15 kb).

Online Resource 5

(DOCX 152 kb).

Online Resource 6

(DOCX 23 kb).

Online Resource 7

(DOCX 15 kb).

Online Resource 8

(DOCX 123 kb).

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Alkimim, E.R., Caixeta, E.T., Sousa, T.V. et al. Marker-assisted selection provides arabica coffee with genes from other Coffea species targeting on multiple resistance to rust and coffee berry disease. Mol Breeding 37, 6 (2017). https://doi.org/10.1007/s11032-016-0609-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s11032-016-0609-1

Keywords

Search

Navigation