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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
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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

Information

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

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