Molecular Breeding

, 37:6 | Cite as

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

  • Emilly Ruas Alkimim
  • Eveline Teixeira Caixeta
  • Tiago Vieira Sousa
  • Antônio Alves Pereira
  • Antonio Carlos Baião de Oliveira
  • Laércio Zambolim
  • Ney Sussumu Sakiyama
Article
First Online:
Received:
Accepted:

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.

Keywords

Colletotrichum kahawae Hemileia vastatrix Preventive breeding Gene pyramiding Indian selections 
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Notes

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).

Supplementary material

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References

  1. 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 CrossRefGoogle Scholar
  2. 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 CrossRefGoogle Scholar
  3. 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. 199–234Google Scholar
  4. 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
  5. 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 CrossRefPubMedGoogle Scholar
  6. 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 CrossRefGoogle Scholar
  7. 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 CrossRefGoogle Scholar
  8. 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 CrossRefGoogle Scholar
  9. 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 CrossRefPubMedGoogle Scholar
  10. 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 CrossRefPubMedPubMedCentralGoogle Scholar
  11. 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 CrossRefGoogle Scholar
  12. 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 2:51–61Google Scholar
  13. 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 CrossRefGoogle Scholar
  14. 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 CrossRefGoogle Scholar
  15. 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 2:156–166Google Scholar
  16. 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 CrossRefGoogle Scholar
  17. 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 CrossRefGoogle Scholar
  18. 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 CrossRefGoogle Scholar
  19. 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 CrossRefGoogle Scholar
  20. 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 CrossRefPubMedGoogle Scholar
  21. 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 71:185–189Google Scholar
  22. Ram AS (2006) Popular Indian coffee selections. Indian Coffee 70:12–18Google Scholar
  23. 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 CrossRefGoogle Scholar
  24. 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 CrossRefGoogle Scholar
  25. 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 CrossRefGoogle Scholar
  26. 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 CrossRefGoogle Scholar
  27. 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 CrossRefGoogle Scholar
  28. Young N (1999) A cautiously optimistic vision for marker-assisted breeding. Mol Breed 5:505–510. doi: 10.1023/A:1009684409326 CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2017

Authors and Affiliations

  • Emilly Ruas Alkimim
    • 1
  • Eveline Teixeira Caixeta
    • 2
  • Tiago Vieira Sousa
    • 1
  • Antônio Alves Pereira
    • 3
  • Antonio Carlos Baião de Oliveira
    • 4
  • Laércio Zambolim
    • 5
  • Ney Sussumu Sakiyama
    • 6
  1. 1.BIOAGRO, BioCaféUniversidade Federal de ViçosaViçosaBrazil
  2. 2.Empresa Brasileira de Pesquisa Agropecuária - Embrapa Café, BIOAGRO, BioCaféUniversidade Federal de ViçosaViçosaBrazil
  3. 3.Empresa de Pesquisa Agropecuária de Minas Gerais –EpamigViçosaBrazil
  4. 4.Embrapa CaféViçosaBrazil
  5. 5.Departamento de FitopatologiaUniversidade Federal de ViçosaViçosaBrazil
  6. 6.Departamento FitotecniaUniversidade Federal de ViçosaViçosaBrazil

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