Genetic variation and population structure of Oryza glaberrima and development of a mini-core collection using DArTseq

Ndjiondjop Marie-Noëlle, Semagn Kassa, Gouda Comlan Arnaud, Kpeki Sèdjro B., Tia Daniel Dro, Sow Mounirou, Goungoulou Alphonse, Sié Moussa, Perrier Xavier, Ghesquière Alain, Warburton Marilyn L.. 2017. Genetic variation and population structure of Oryza glaberrima and development of a mini-core collection using DArTseq. Frontiers in Plant Science, 8:1748, 19 p.

Journal article ; Article de recherche ; Article de revue à facteur d'impact Revue en libre accès total
Published version - Anglais
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Quartile : Q1, Sujet : PLANT SCIENCES

Abstract : The sequence variation present in accessions conserved in genebanks can best be used in plant improvement when it is properly characterized and published. Using low cost and high density single nucleotide polymorphism (SNP) assays, the genetic diversity, population structure, and relatedness between pairs of accessions can be quickly assessed. This information is relevant for different purposes, including creating core and mini-core sets that represent the maximum possible genetic variation contained in the whole collection. Here, we studied the genetic variation and population structure of 2,179 Oryza glaberrima Steud. accessions conserved at the AfricaRice genebank using 27,560 DArTseq-based SNPs. Only 14% (3,834 of 27,560) of the SNPs were polymorphic across the 2,179 accessions, which is much lower than diversity reported in other Oryza species. Genetic distance between pairs of accessions varied from 0.005 to 0.306, with 1.5% of the pairs nearly identical, 8.0% of the pairs similar, 78.1% of the pairs moderately distant, and 12.4% of the pairs very distant. The number of redundant accessions that contribute little or no new genetic variation to the O. glaberrima collection was very low. Using the maximum length sub-tree method, we propose a subset of 1,330 and 350 accessions to represent a core and mini-core collection, respectively. The core and mini-core sets accounted for ~61 and 16%, respectively, of the whole collection, and captured 97–99% of the SNP polymorphism and nearly all allele and genotype frequencies observed in the whole O. glaberrima collection available at the AfricaRice genebank. Cluster, principal component and model-based population structure analyses all divided the 2,179 accessions into five groups, based roughly on country of origin but less so on ecology. The first, third and fourth groups consisted of accessions primarily from Liberia, Nigeria, and Mali, respectively; the second group consisted primarily of accessions from Togo and Nigeria; and the fifth and smallest group was a mixture of accessions from multiple countries. Analysis of molecular variance showed between 10.8 and 28.9% of the variation among groups with the remaining 71.1–89.2% attributable to differences within groups. (Résumé d'auteur)

Mots-clés Agrovoc : Oryza glaberrima, Variation génétique, Génétique des populations, Ressource génétique végétale, Collection de matériel génétique, Banque de gènes, Phénotype, Génotype, Polymorphisme génétique, Distance génétique, Séquence d'ADN

Mots-clés géographiques Agrovoc : Afrique, Libéria, Nigéria, Mali, Togo, Côte d'Ivoire, Guinée, Sénégal, Burkina Faso

Mots-clés complémentaires : Séquencage

Mots-clés libres : African rice, Plant genetic resources, Oryza glaberrima, Core collection, Genetic differentiation, Genetic diversity, SNP

Classification Agris : F30 - Plant genetics and breeding

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

  • Ndjiondjop Marie-Noëlle, Centre du riz pour l'Afrique (CIV) - auteur correspondant
  • Semagn Kassa, University of Alberta (CAN)
  • Gouda Comlan Arnaud, Centre du riz pour l'Afrique (CIV)
  • Kpeki Sèdjro B., Centre du riz pour l'Afrique (CIV)
  • Tia Daniel Dro, Centre du riz pour l'Afrique (CIV)
  • Sow Mounirou, Centre du riz pour l'Afrique (CIV)
  • Goungoulou Alphonse, Centre du riz pour l'Afrique (CIV)
  • Sié Moussa, Centre du riz pour l'Afrique (CIV)
  • Perrier Xavier, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-0092-003X
  • Ghesquière Alain, IRD (FRA)
  • Warburton Marilyn L., ARS (USA)

Source : Cirad-Agritrop (

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