Skip to main content
SpringerLink
Log in

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

  • Research Article
  • Published:
Genetic Resources and Crop Evolution Aims and scope Submit manuscript

Abstract

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.

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
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • 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 9:1027–1988

    Google Scholar 

  • Baboy L, Mateso R, Sabiti K (1995) Tests de résistance au champ vis-à-vis de la pyriculariose du riz au Zaire. Tropicultura 13:93–98

    Google Scholar 

  • 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 21:859–868

    Article  PubMed  CAS  Google Scholar 

  • 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 154:127–137

    Article  CAS  Google Scholar 

  • 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 32:314–331

    PubMed  PubMed Central  CAS  Google Scholar 

  • 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 94:683–693

    Article  PubMed  CAS  Google Scholar 

  • 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 47:973–980

    Article  CAS  Google Scholar 

  • 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 10:6675–6685

    Google Scholar 

  • 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 4:96–102

    Google Scholar 

  • 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 100:1121–1128

    Article  CAS  Google Scholar 

  • IRRI (International Rice Research Institute) (2013) Standard evaluation system for rice, 5th edn. International Rice Research Institute, Manila

    Google Scholar 

  • Jia Y, Bryan GT, Farrall L, Valent B (2003) Natural variation at the Pi-ta rice blast resistance locus. Phytopathology 93:1452–1459

    Article  PubMed  CAS  Google Scholar 

  • Jones MP, Dingkuhn M, Aluko GK, Semon M (1997) Interspecific Orza sativa × O.glaberrima Steud. Progenies in upland rice improvement. Euphytica 92:237–246

    Article  Google Scholar 

  • 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 Netherlands

  • 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 123:21–31

    Article  PubMed  Google Scholar 

  • Linares OF (2002) African rice (Oryza glaberrima): history and future potential. Proc Natl Acad Sci USA 99:16360–16365

    Article  PubMed  CAS  Google Scholar 

  • Mackill DJ, Bonman JM (1992) Inheritance of blast resistance in near-isogenic lines of rice. Phytopathology 82:746–749

    Article  Google Scholar 

  • 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 17:257–268

    Article  Google Scholar 

  • National Research Council (1996) Lost crops of Africa. Volume 1: grains. National Academy Press, Washington, p 380

  • 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. https://doi.org/10.3389/fpls.2017.01748

    Article  PubMed  PubMed Central  Google Scholar 

  • 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. https://doi.org/10.1371/journal.pone.0007335

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Odjo T, Ahohuendo BC, Onasanya A, Akator K, Séré Y (2011) Analysis of Magnaporthe oryzae population structure in Benin. Afr J Agric Res 6:6183–6188

    Article  Google Scholar 

  • 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 236

  • R Core Team (2017) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. https://www.R-project.org/

  • RoyChowdhury M, Jia Y, Cartwright RD (2012) Structure, function and coevolution of rice blast resistance genes. Acta Agric Sin 38:381–393

    Article  CAS  Google Scholar 

  • 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):8014–8018

    Article  PubMed  CAS  Google Scholar 

  • Salem KFM, Sallam A (2016) Analysis of population structure and genetic diversity of Egyptian and exotic rice (Oryza sativa L.) genotypes. C R Biol 339:1–9

    Article  PubMed  Google Scholar 

  • Sano Y (1989) The direction of pollen flow between two co-occurring rice species, Oryza sativa and O. glaberrima. Heredity 63:353–357

    Article  Google Scholar 

  • 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 57:25–57

    Article  Google Scholar 

  • 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 169:1639–1647

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • 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 2013–228

  • 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 1:37–52

    Article  Google Scholar 

  • 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 4:308–318

    Google Scholar 

  • 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. https://doi.org/10.3389/fpls.2015.00345

    Article  PubMed  PubMed Central  Google Scholar 

  • 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 121:169–179

    Article  PubMed  CAS  Google Scholar 

  • 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. https://doi.org/10.3389/fpls.2014.00505

    Article  Google Scholar 

  • Vieira MLC, Santini L, Diniz AL, Munhoz CF (2016) Microsatellite markers: what they mean and why they are so useful. Genet Mol Biol 39:312–328

    Article  PubMed  PubMed Central  Google Scholar 

  • 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 27–33

  • 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 23:4407–4414

    Article  PubMed  CAS  Google Scholar 

  • Wambugu PW, Furtado A, Waters DL, Nyamongo DO, Henry R (2013) Conservation and utilization of African Oryza genetic resources. Rice 6:29

    Article  PubMed  PubMed Central  Google Scholar 

  • 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 90

  • 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 45:109–116

    Article  CAS  Google Scholar 

  • 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 46:982–988

    Article  PubMed  CAS  Google Scholar 

  • WARDA (1999) Program report 1996–1997. West Africa Rice Development Association, Bouaké, Côte d’Ivoire

  • 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 169:2277–2293

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • 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 267–292

    Google Scholar 

Download references

Acknowledgements

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.

Author information

Author notes

  1. Drissa Silue

    Present address: AfricaRice Center, 01 B.P. 2551, Bouake 01, Côte d’Ivoire

Authors and Affiliations

  1. Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium

    Octaviano Igor Yelome, Kris Audenaert, Sofie Landschoot, Wouter Vanhove, Patrick Van Damme & Geert Haesaert

  2. Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg, 1, 9000, Ghent, Belgium

    Sofie Landschoot

  3. Faculté des Sciences et Techniques de Dassa, Laboratoire de Biotechnologie, Ressources Génétiques et Amélioration des Espèces Animales et Végétales (BIORAVE), Université d’Abomey, Cotonou, Benin

    Alexandre Dansi

  4. AfricaRice Center, 01 B.P.O. 2031, Cotonou, Benin

    Drissa Silue

  5. Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamycka 129, 165 21, Prague 6, Suchdol, Czech Republic

    Patrick Van Damme

Authors
  1. Octaviano Igor Yelome
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kris Audenaert
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sofie Landschoot
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Alexandre Dansi
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Wouter Vanhove
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Drissa Silue
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Patrick Van Damme
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Geert Haesaert
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Octaviano Igor Yelome.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 39 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Yelome, O.I., Audenaert, K., Landschoot, S. et al. Exploring genetic diversity and disease response of cultivated rice accessions (Oryza spp.) against Pyricularia oryzae under rainfed upland conditions in Benin. Genet Resour Crop Evol 65, 1615–1624 (2018). https://doi.org/10.1007/s10722-018-0638-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-018-0638-1

Keywords

Search

Navigation