Genetic Resources and Crop Evolution

, Volume 65, Issue 6, pp 1615–1624 | Cite as

Exploring genetic diversity and disease response of cultivated rice accessions (Oryza spp.) against Pyricularia oryzae under rainfed upland conditions in Benin

  • Octaviano Igor YelomeEmail author
  • Kris Audenaert
  • Sofie Landschoot
  • Alexandre Dansi
  • Wouter Vanhove
  • Drissa Silue
  • Patrick Van Damme
  • Geert Haesaert
Research Article


The main goal of this study is to gain insight into the relationship between the genetic profile of cultivated rice (Oryza spp.) accessions and their resistance to rice blast. Therefore, the genetic and phenotypic variability of a set of 350 cultivated rice accessions originating from Africa (Benin, Mali and Nigeria, Ivory Coast etc.) was examined. Seventy-seven fluorescent amplified fragment polymorphism (AFLP) markers were used to gain insight into the genetic variation and to classify the germplasm collection. In addition, the rice germplasm was assessed for its resistance to blast disease caused by Pyricularia oryzae in upland field conditions. Huge differences in responses of rice accessions to P. oryzae were observed, ranging from highly susceptible to highly resistant. Twelve percent of all accessions were highly resistant to P. oryzae. Based on their AFLP marker profile these highly resistant accessions could be separated from the other accessions. Stepwise regression revealed that the best prediction of the blast resistance level was achieved with a maximum number of 13 AFLP markers. Marker CTA22 was the most important for accurate prediction of blast resistance, this marker was present in all highly resistant accessions. It can be concluded that AFLP markers are a valuable tool to screen rice accessions for their susceptibility towards blast disease and that, based on a subset of markers, it is possible to predict the resistance to rice blast.


Fluorescent-AFLP Genetic diversity Rice Blast 



Funding of this Research work by the Monsanto’s Beachell-Borlaug International Scholars Program (MBBIS) and the Flemish Fund for Scientific Research (BOF) with support of AfricaRice. Special thanks to the AfricaRice genebank for providing seed and the related information.

Authors contribution

OINY carried out the field works, the genotyping, data analysis and drafted the manuscript. KA participated in project design, genotyping, data analysis and revised the manuscript. SL participated in statistical analysis of data and revised the manuscript. DS, AD, WV, PVD, and GH participated in project design, data analysis and revised the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10722_2018_638_MOESM1_ESM.docx (39 kb)
Supplementary material 1 (DOCX 39 kb)


  1. Afouda L, Gnikpo S, Sere Y, Gumedzoe Y (2007) Prevalence des principales maladies sur des varietes de riz cultivees dans le departement de l’alibori au Nord-Benin. J de la Recherche Scientifique de l’Universite de Lome 9:1027–1988Google Scholar
  2. Baboy L, Mateso R, Sabiti K (1995) Tests de résistance au champ vis-à-vis de la pyriculariose du riz au Zaire. Tropicultura 13:93–98Google Scholar
  3. Ballini E, Morel JB, Droc G, Price A, Courtois B, Notteghem JL, Tharreau D (2008) A genome-wide meta-analysis of rice blast resistance genes and quantitative trait loci provides new insights into partial and complete resistance. Mol Plant Microbe Interact 21:859–868CrossRefPubMedGoogle Scholar
  4. Barry MB, Pham JL, Noyer JL, Billo C, Courtois B, Ahmadi N (2007) Genetic diversity of the two cultivated rice species (O. sativa & O. glaberrima) in Maritime Guinea. Evidences for inter-specific recombination. Euphytica 154:127–137CrossRefGoogle Scholar
  5. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331PubMedPubMedCentralGoogle Scholar
  6. Couch BC, Kohn LM (2002) A multilocus gene genealogy concordant with host preference indicates segregation of a new species, Magnaporthe oryzae, from M. grisea. Mycologia 94:683–693CrossRefPubMedGoogle Scholar
  7. Dai Y, Jia Y, Correll J, Wang X, Wang Y (2010) Diversification and evolution of the avirulence gene AVR-Pita1 in field isolates of Magnaporthe oryzae. Fung Genet Biol 47:973–980CrossRefGoogle Scholar
  8. Dramé KN, Sanchez I, Gregorio G, Ndjiondjop MN (2011) Suitability of a selected set of simple sequence repeats (SSR) markers for multiplexing and rapid molecular characterization of African rice (Oryza glaberrima Steud.). Afr J Biotechnol 10:6675–6685Google Scholar
  9. Futakuchi K, Sié M (2009) Better exploitation of African rice (Oryza glaberrima Steud.) in varietal development for resource-poor farmers in West and Central Africa. Agric J 4:96–102Google Scholar
  10. Hittalmani S, Parco A, Mew TV, Zeigler RS, Huang N (2000) Fine mapping and DNA marker-assisted pyramiding of the three major genes for blast resistance in rice. Theor Appl Genet 100:1121–1128CrossRefGoogle Scholar
  11. IRRI (International Rice Research Institute) (2013) Standard evaluation system for rice, 5th edn. International Rice Research Institute, ManilaGoogle Scholar
  12. Jia Y, Bryan GT, Farrall L, Valent B (2003) Natural variation at the Pi-ta rice blast resistance locus. Phytopathology 93:1452–1459CrossRefPubMedGoogle Scholar
  13. Jones MP, Dingkuhn M, Aluko GK, Semon M (1997) Interspecific Orza sativa × O.glaberrima Steud. Progenies in upland rice improvement. Euphytica 92:237–246CrossRefGoogle Scholar
  14. Jusu MS (1999) Management of genetic variability in rice (Oryza sativa L. and O. glaberrima Steud.) by breeders and farmers in Sierra Leone. PhD-thesis Wageningen University, The NetherlandsGoogle Scholar
  15. Li ZM, Zheng XM, Ge S (2011) Genetic diversity and domestication history of African rice (Oryza glaberrima) as inferred from multiple gene sequences. Theor Appl Genet 123:21–31CrossRefPubMedGoogle Scholar
  16. Linares OF (2002) African rice (Oryza glaberrima): history and future potential. Proc Natl Acad Sci USA 99:16360–16365CrossRefPubMedGoogle Scholar
  17. Mackill DJ, Bonman JM (1992) Inheritance of blast resistance in near-isogenic lines of rice. Phytopathology 82:746–749CrossRefGoogle Scholar
  18. Ming H, Fang-min X, Li-yun C, Xiang-qian Z, Jojee L, Madonna D (2010) Comparative analysis of genetic diversity and structure in rice using ILP and SSR markers. Rice Sci 17:257–268CrossRefGoogle Scholar
  19. National Research Council (1996) Lost crops of Africa. Volume 1: grains. National Academy Press, Washington, p 380Google Scholar
  20. Ndjiondjop M-N, Semagn K, Gouda AC, Kpeki SB, Dro Tia D, Sow M, Goungoulou A, Sie M, Perrier X, Ghesquiere A, Warburton ML (2017) Genetic variation and population structure of Oryza glaberrima and development of a mini-core collection using DArTseq. Front Plant Sci 8:1748. CrossRefPubMedPubMedCentralGoogle Scholar
  21. Nuijten E, van Treuren R, Struik PC, Mokuwa A, Okry F, Teeken B, Richards P (2009) Evidence for the emergence of new rice types of interspecific hybrid origin in West African farmers’ fields. PLoS ONE 4(10):e7335. CrossRefPubMedPubMedCentralGoogle Scholar
  22. Odjo T, Ahohuendo BC, Onasanya A, Akator K, Séré Y (2011) Analysis of Magnaporthe oryzae population structure in Benin. Afr J Agric Res 6:6183–6188CrossRefGoogle Scholar
  23. Pham JL (1992) Evaluation des ressources génétiques des riz cultivés en Afrique par hybridation intra et interspécifique. Thèse Docteur et sciences, Université de Paris XI ORSAY (France), p 236Google Scholar
  24. R Core Team (2017) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna.
  25. RoyChowdhury M, Jia Y, Cartwright RD (2012) Structure, function and coevolution of rice blast resistance genes. Acta Agric Sin 38:381–393CrossRefGoogle Scholar
  26. Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci 81(24):8014–8018CrossRefPubMedGoogle Scholar
  27. Salem KFM, Sallam A (2016) Analysis of population structure and genetic diversity of Egyptian and exotic rice (Oryza sativa L.) genotypes. C R Biol 339:1–9CrossRefPubMedGoogle Scholar
  28. Sano Y (1989) The direction of pollen flow between two co-occurring rice species, Oryza sativa and O. glaberrima. Heredity 63:353–357CrossRefGoogle Scholar
  29. Second G (1982) Origin of the genic diversity of cultivated rice (Oryza spp.): study of the polymorphism scored at 40 isozyme loci. Jpn J Genet 57:25–57CrossRefGoogle Scholar
  30. Semon M, Nielsen R, Jones MP, McChouch SR (2005) The population structure of African cultivated rice O. glaberrima (Steud.): evidence for elevated levels of linkage disequilibrium caused by admixture with O. sativa and ecological adaptation. Genetics 169:1639–1647CrossRefPubMedPubMedCentralGoogle Scholar
  31. Séré Y, Fargette D, Abo ME, Wydra K, Bimerew M, Onasanya A, Akator SK (2013) Managing the major diseases of rice in Africa. In: Wopereis MCS, Johnson DE, Ahmadi N, Tollens E, Jalloh A (eds) Realizing Africa’s rice promise. CABI (H ISBN 9781845938123), pp 2013–228Google Scholar
  32. Sharma T, Rai A, Gupta S, Vijayan J, Devanna B, Ray S (2012) Rice blast management through host-plant resistance: retrospect and prospects. Agric Res 1:37–52CrossRefGoogle Scholar
  33. Sié M, Ogunbayo SA, Dakouo D, Sanou I, Dembélé Y, N’dri B, Dramé KN, Sanni KA, Toulou B, Glele RK (2010) Evaluation of intra and interspecific rice varieties adapted to valley bottom conditions in Burkina Faso. Afr J Plant Sci 4:308–318Google Scholar
  34. Thakur S, Singh PK, Das A, Rathour R, Variar M, Prashanthi SK, Singh AK, Singh UD, Chand D, Singh NK, Sharma TR (2015) Extensive sequence variation in rice blast resistance gene Pi54 makes it broad spectrum in nature. Front Plant Sci 6:345. CrossRefPubMedPubMedCentralGoogle Scholar
  35. Thiémélé D, Boisnard A, Ndjiondjop M, Chéron S, Séré Y, Aké S, Ghesquière A, Albar L (2010) Identification of a second major resistance gene to Rice yellow mottle virus, RYMV2, in the African cultivated rice species, O. glaberrima. Theor Appl Genet 121:169–179CrossRefPubMedGoogle Scholar
  36. Vasudevan K, Vera Cruz CM, Gruissem W, Bhullar NK (2014) Large scale germplasm screening for identification of novel rice blast resistance sources. Plant Sci 5:1–9. CrossRefGoogle Scholar
  37. Vieira MLC, Santini L, Diniz AL, Munhoz CF (2016) Microsatellite markers: what they mean and why they are so useful. Genet Mol Biol 39:312–328CrossRefPubMedPubMedCentralGoogle Scholar
  38. Vodouhe SR, Ojegui M, Amadji F (1981) Impact of blast on rice cultivation in People’s Republic of Benin. In: Proceedings of the symposium on rice resistance to blast, Montpellier, France, 18–21 March. Service de Pathologie Végétale, Montpellier, France, pp 27–33Google Scholar
  39. Vos P, Hogers R, Bleeker M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucl Acids Res 23:4407–4414CrossRefPubMedGoogle Scholar
  40. Wambugu PW, Furtado A, Waters DL, Nyamongo DO, Henry R (2013) Conservation and utilization of African Oryza genetic resources. Rice 6:29CrossRefPubMedPubMedCentralGoogle Scholar
  41. Wang JC, Wen JW, Liu WP, Yan SR, Wang JQ, Ren JP (2010) Interaction studies between rice and Pyricularia grisea in Jilin Province, P. R. China. In: Jia, Y (ed) Proceedings of the 5th international rice blast conference, USA. USDA-DBNRRC, p 90Google Scholar
  42. Wang JC, Jia Y, Wen JW, Liu WP, Liu XM, Li L, Jiang ZY, Zhang JH, Guo XL, Ren JP (2013) Identification of rice blast resistance genes using international monogenic differentials. Crop Prot 45:109–116CrossRefGoogle Scholar
  43. Wang M, Yu Y, Haberer G, Marri PR, Fan C, Goicoechea JL, Zuccolo A, Song X, Kudrna D, Ammiraju JS, Cossu RM (2014) The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nat Genet 46:982–988CrossRefPubMedGoogle Scholar
  44. WARDA (1999) Program report 1996–1997. West Africa Rice Development Association, Bouaké, Côte d’IvoireGoogle Scholar
  45. Wisser RJ, Sun Q, Hulbert SH, Kresovich S, Nelson RJ (2005) Identification and characterization of regions of the rice genome associated with broad-spectrum, quantitative disease resistance. Genetics 169:2277–2293CrossRefPubMedPubMedCentralGoogle Scholar
  46. Zeigler RS, Tohme J, Nelson R, Levy M, Correa Victoria FJ (1994) Lineage exclusion: a proposal for linking blast population analysis to resistance breeding. In: Zeigler RS, Leong SA, Teng PS (eds) Rice blast disease. CAB International, Wallingford, pp 267–292Google Scholar

Copyright information

© Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  • Octaviano Igor Yelome
    • 1
    Email author
  • Kris Audenaert
    • 1
  • Sofie Landschoot
    • 1
    • 2
  • Alexandre Dansi
    • 3
  • Wouter Vanhove
    • 1
  • Drissa Silue
    • 4
  • Patrick Van Damme
    • 1
    • 5
  • Geert Haesaert
    • 1
  1. 1.Department of Plants and Crops, Faculty of Bioscience EngineeringGhent UniversityGhentBelgium
  2. 2.Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience EngineeringGhent UniversityGhentBelgium
  3. 3.Faculté des Sciences et Techniques de Dassa, Laboratoire de Biotechnologie, Ressources Génétiques et Amélioration des Espèces Animales et Végétales (BIORAVE)Université d’AbomeyCotonouBenin
  4. 4.AfricaRice CenterCotonouBenin
  5. 5.Faculty of Tropical AgriSciencesCzech University of Life Sciences PraguePrague 6, SuchdolCzech Republic

Personalised recommendations