@article{fdi:010071277,
  title = {{G}enetic variation and population structure of {O}ryza glaberrima and development of a mini-core collection using {DA}r{T}seq},
  author = {{N}djiondjop, {M}. {N}. and {S}emagn, {K}. and {G}ouda, {A}. {C}. and {K}peki, {S}. {B}. and {T}ia, {D}. {D}. and {S}ow, {M}. and {G}oungoulou, {A}. and {S}ie, {M}. and {P}errier, {X}. and {G}hesqui{\`e}re, {A}lain and {W}arburton, {M}. {L}.},
  editor = {},
  language = {{ENG}},
  abstract = {{T}he sequence variation present in accessions conserved in genebanks can best be used in plant improvement when it is properly characterized and published. {U}sing 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. {T}his 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. {H}ere, we studied the genetic variation and population structure of 2,179 {O}ryza glaberrima {S}teud. accessions conserved at the {A}frica{R}ice genebank using 27,560 {DA}r{T}seq-based {SNP}s. {O}nly 14% (3,834 of 27,560) of the {SNP}s were polymorphic across the 2,179 accessions, which is much lower than diversity reported in other {O}ryza species. {G}enetic 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. {T}he number of redundant accessions that contribute little or no new genetic variation to the {O}. glaberrima collection was very low. {U}sing 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. {T}he core and mini-core sets accounted for similar to 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 {A}frica{R}ice genebank. {C}luster, 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. {T}he first, third and fourth groups consisted of accessions primarily from {L}iberia, {N}igeria, and {M}ali, respectively; the second group consisted primarily of accessions from {T}ogo and {N}igeria; and the fifth and smallest group was a mixture of accessions from multiple countries. {A}nalysis 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.},
  keywords = {{A}frican rice ; plant genetic resources ; {O}. glaberrima ; core collection ; genetic differentiation ; genetic diversity ; {SNP} ; {AFRIQUE} {DE} {L}'{OUEST}},
  booktitle = {},
  journal = {{F}rontiers in {P}lant {S}cience},
  volume = {8},
  numero = {},
  pages = {1748 [19 ]},
  ISSN = {1664-462{X}},
  year = {2017},
  DOI = {10.3389/fpls.2017.01748},
  URL = {https://www.documentation.ird.fr/hor/fdi:010071277},
}