Hostname: page-component-7479d7b7d-767nl Total loading time: 0 Render date: 2024-07-11T00:20:22.186Z Has data issue: false hasContentIssue false
  • English
  • Français

EST-SSR development for Digitaria exilis and its relatives D. iburua and D. longiflora from transcriptome sequences

Published online by Cambridge University Press:  21 November 2018

Katina F. Olodo ,
Mame C. Gueye ,
Caroline Calatayud ,
Baye M. Diop ,
Ndjido A. Kane ,
Ablaye Ngom ,
Valentine O. Ntui ,
Marie-Madeleine S. Barreto ,
Edak A. Uyoh  and
Salomon Abraham
...Show all authors
Katina F. Olodo*
Affiliation:
DIADE, IRD, Montpellier, France Institut Sénégalais de Recherches Agricoles (ISRA) / Centre d'Etude Régionale pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), Thiès, Sénégal Laboratoire National de Recherche sur les Productions Végétales (LNRPV), ISRA, Dakar, Sénégal Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
Mame C. Gueye
Affiliation:
Institut Sénégalais de Recherches Agricoles (ISRA) / Centre d'Etude Régionale pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), Thiès, Sénégal
Caroline Calatayud
Affiliation:
CIRAD, UMR AGAP, Montpellier, France AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
Baye M. Diop
Affiliation:
Institut Sénégalais de Recherches Agricoles (ISRA) / Centre d'Etude Régionale pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), Thiès, Sénégal Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
Ndjido A. Kane
Affiliation:
Laboratoire National de Recherche sur les Productions Végétales (LNRPV), ISRA, Dakar, Sénégal Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LMI LAPSE), Dakar, Senegal
Ablaye Ngom
Affiliation:
Laboratoire National de Recherche sur les Productions Végétales (LNRPV), ISRA, Dakar, Sénégal Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
Valentine O. Ntui
Affiliation:
International Institute of Tropical Agriculture, Nairobi, Kenya Department of Genetics and Biotechnology, University of Calabar, Calabar, Nigeria
Marie-Madeleine S. Barreto
Affiliation:
Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
Edak A. Uyoh
Affiliation:
Department of Genetics and Biotechnology, University of Calabar, Calabar, Nigeria
Salomon Abraham
Affiliation:
Department of Genetics and Biotechnology, University of Calabar, Calabar, Nigeria
Yves Vigouroux
Affiliation:
DIADE, IRD, Montpellier, France Université Montpellier, Montpellier, France
Claire Billot
Affiliation:
CIRAD, UMR AGAP, Montpellier, France AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
Adeline Barnaud
Affiliation:
DIADE, IRD, Montpellier, France Laboratoire National de Recherche sur les Productions Végétales (LNRPV), ISRA, Dakar, Sénégal Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LMI LAPSE), Dakar, Senegal Université Montpellier, Montpellier, France
*
*Corresponding author. E-mail: katina.olodo@ird.fr
Get access Rights & Permissions [Opens in a new window]

Abstract

Digitaria exilis is an important indigenous cereal in West Africa. The first fonio reference transcriptome was released and became a key tool for developing new molecular markers contributing to a better understanding of its genetic diversity. A total of 126 new putative primer pairs were successfully designed in 37,327 unigenes from the D. exilis transcriptome. Thirty-seven primer pairs were randomly selected and tested for their ability to cross-amplify to related species. Clear amplification patterns were observed on 24 primer pairs. Of these, 71, 74 and 35% showed polymorphism in three species: D. exilis, D. longiflora and D. iburua. The transferability from D. exilis was 96% to D. longiflora and 71% to D. iburua. The new SSR markers confirmed the close genetic proximity of D. exilis with D. longiflora and its stronger genetic difference of D. exilis from D. iburua. These markers will be valuable for completing future knowledge on Digitaria evolutionary history, and for testing gene flows between related species.

Keywords

cross-amplificationDigitariadiversityEST-SSRmicrosatellitePoaceae
Type
Short Communication
Information
Plant Genetic Resources , Volume 17 , Issue 3 , June 2019 , pp. 280 - 284
Copyright
Copyright © NIAB 2018 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Adoukonou-Sagbadja, H, Schubert, V, Dansi, A, Jovtchev, G, Meister, A, Pistrick, K and Friedt, W (2007) Flow cytometric analysis reveals different nuclear DNA contents in cultivated Fonio (Digitaria spp.) and some wild relatives from West-Africa. Plant Systematics and Evolution 267: 163–176.Google Scholar
Barnaud, A, Vignes, H, Risterucci, A.-M, Noyer, J.-L, Pham, J.-L, Blay, C and Billot, C (2012) Development of nuclear microsatellite markers for the fonio, Digitaria exilis (Poaceae), an understudied West African cereal. American Journal of Botany 99: e105–e107.Google Scholar
Barnaud, A, Vigouroux, Y, Diallo, MT, Saidou, SI, Piquet, M, Barry, MB, Bakasso, Y, Zekraoui, L, Rivallan, R, Kane, NA and Billot, C (2017) High selfing rate inferred for white fonio [Digitaria exilis (Kippist.) Stapf] reproductive system opens up opportunities for breeding programs. Genetic Resources and Crop Evolution 64: 1485–1490.Google Scholar
Blench, RM (2012) Vernacular names for African millets and other minor cereals and their significance for agricultural history. Archaeological and Anthropological Sciences 8: 1–8.Google Scholar
Clément, J and Leblanc, JM (1984) Prospection des Digitaria exilis (Fonio) en Afrique de l'Ouest. Marseille, France: ORSTOM.Google Scholar
Dereeper, A, Argout, X, Billot, C, Rami, JF and Ruiz, M (2007) SAT, a flexible and optimized Web application for SSR marker development. BMC Bioinformatics 8: 465–465.Google Scholar
Husson, F, Josse, J, Le, S and Mazet, J (2007) FactoMineR: Factor Analysis and Data Mining with R. R package version 1.04.Google Scholar
Jombart, T (2008) Adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics (Oxford, England) 24: 1403–1405.Google Scholar
Jombart, T, Devillard, S and Balloux, F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genetics 11: 94.Google Scholar
Kassambara, A and Mundt, F (2017) Factoextra: Extract and Visualize the Results of Multivariate Data Analyses. R package version 1.0.3 ed: https://cran.r-project.org/package=factoextraGoogle Scholar
Mariac, C, Scarcelli, N, Pouzadou, J, Barnaud, A, Billot, C, Faye, A and Couvreur, TLP (2014) Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies. Molecular Ecology Resources 14: 1103–1113.Google Scholar
Paradis, E, Claude, J and Strimmer, K (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics (Oxford, England) 20: 289–290.Google Scholar
Peakall, R and Smouse, PE (2012) Genalex 6.5: genetic analysis in Excel. Population genetic software for teaching and research – an update. Bioinformatics (Oxford, England) 28: 2537–2539.Google Scholar
R Core Team (1995–2015) The r project for statistical computing. http://r-project.orgGoogle Scholar
Roullier, C, Rossel, G, Tay, D, Mckey, D and Lebot, V (2011) Combining chloroplast and nuclear microsatellites to investigate origin and dispersal of New world sweet potato landraces. Molecular Ecology 20: 3963–3977.Google Scholar
Sarah, G, Homa, F, Pointet, S, Contreras, S, Sabot, F, Nabholz, B and Ruiz, M (2016) A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives. Molecular Ecology Resources 17: 565–558.Google Scholar
Scarcelli, N, Barnaud, A, Eiserhardt, W, Treier, UA, Seveno, M, d'Anfray, A and Vigouroux, Y (2011) A set of 100 chloroplast DNA primer pairs to study population genetics and phylogeny in monocotyledons. PLoS ONE 6: e19954.Google Scholar
Schuelke, M (2000) An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnology 18: 233.Google Scholar
Varshney, RK, Graner, A and Sorrells, ME (2005) Genic microsatellite markers in plants: features and applications. TRENDS in Biotechnology 23(1): 48–55.Google Scholar
Supplementary material: File

Olodo et al. supplementary material

Olodo et al. supplementary material 1

Download Olodo et al. supplementary material(File)
File 908.9 KB