Identification and development of new polymorphic microsatellite markers using genome assembly for Ganoderma boninense, causal agent of oil palm basal stem rot disease

Autor: Tristan Durand-Gasselin, Sharifah Shahrul Rabiah Syed Alwee, Létizia Camus-Kulandaivelu, Frédéric Breton, Christophe Klopp, Maxime Mercière, Catherine Carasco-Lacombe, Joon Sheong Tan, Anthony Laybats
Přispěvatelé: Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Felda Global Ventures Holdings Berhad, Partenaires INRAE, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Plateforme Bio-Informatique - Génotoul, PalmElit, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Jazyk: angličtina
Rok vydání: 2015
Předmět:
Identification
Polymorphisme génétique
DIVERSITY
LOCI
Plant Science
Oilpalm
F30 - Génétique et amélioration des plantes
chemistry.chemical_compound
Molecular marker
Polymorphic Microsatellite Marker
Marqueur génétique
[MATH]Mathematics [math]
Elaeis guineensis
POPULATION
Genetics
food and beverages
SIMPLE SEQUENCE REPEATS
Agricultural and Biological Sciences (miscellaneous)
Basal stem rot
Microsatellite
Ganoderma boninense
Biologie
Séquence nucléotidique
Locus (genetics)
Biology
GENETIC-STRUCTURE
Variation génétique
[INFO]Computer Science [cs]
NULL ALLELES
Ecology
Evolution
Behavior and Systematics
Illumina dye sequencing
H20 - Maladies des plantes
Whole genome sequencing
Genetic diversity
Génome
ECOLOGISTS
Ganoderma
LUCIDUM
F.SP TRITICI
chemistry
Genetic marker
Genome sequence
FUNGAL PATHOGEN
Zdroj: Mycological Progress
Mycological Progress, Springer Verlag, 2015, 14 (11), ⟨10.1007/s11557-015-1123-2⟩
ISSN: 1617-416X
1861-8952
DOI: 10.1007/s11557-015-1123-2⟩
Popis: International audience; Ganoderma boninense is a telluric lignicolous basidiomycete and the causal agent of basal stem rot, one of the most devastating diseases of the oil palm (Elaeis guineensis). While the fight against G. boninense is of major concern in Southeast Asia, little information is available regarding the genetic diversity and evolutionary history of the fungus. In this context, the development of an informative molecular marker set to characterize the diversity of G. boninense is a key step towards understanding the biology of this pathogen. A G. boninense draft genome sequence of 63 Mbp, assembled using 454 and Illumina sequencing technology, was used to identify and develop a set of microsatellite markers (simple sequence repeats, SSRs). A total of 2487 SSRs were identified, for which 145 SSR primer pairs were designed. These SSRs are characterized by di- to hexanucleotide motifs with 5 to 34 repetitions. Ninety-seven SSR loci were successfully amplified on an initial small set of G. boninense isolates from Indonesia. A collection of 107 isolates from several regions in Southeast Asia were screened to characterize each locus for allele number, polymorphism information criterion and the presence or absence of null alleles at each locus. These results allowed us to propose an effective set of 17 SSRs for studying genetic diversity within G. boninense.
Databáze: OpenAIRE
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