@article{fdi:010063620,
  title = {{C}haracterization of a panel of {V}ietnamese rice varieties using {DA}r{T} and {SNP} markers for association mapping purposes},
  author = {{P}hung, {N}. {T}. {P}. and {M}ai, {C}. {D}. and {M}ournet, {P}. and {F}rouin, {J}. and {D}roc, {G}. and {T}a, {N}. {K}. and {J}ouannic, {S}tefan and {L}, {L}. {T}. and {D}o, {V}. {N}. and {G}antet, {P}ascal and {C}ourtois, {B}.},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground: {T}he development of genome-wide association studies ({GWAS}) in crops has made it possible to mine interesting alleles hidden in gene bank resources. {H}owever, only a small fraction of the rice genetic diversity of any given country has been exploited in the studies with worldwide sampling conducted to date. {T}his study presents the development of a panel of rice varieties from {V}ietnam for {GWAS} purposes. {R}esults: {T}he panel, initially composed of 270 accessions, was characterized for simple agronomic traits (maturity class, grain shape and endosperm type) commonly used to classify rice varieties. {W}e first genotyped the panel using {D}iversity {A}rray {T}echnology ({DA}r{T}) markers. {W}e analyzed the panel structure, identified two subpanels corresponding to the indica and japonica sub-species and selected 182 non-redundant accessions. {H}owever, the number of usable {DA}r{T} markers (241 for an initial library of 6444 clones) was too small for {GWAS} purposes. {T}herefore, we characterized the panel of 182 accessions with 25,971 markers using genotyping by sequencing. {T}he same indica and japonica subpanels were identified. {T}he indica subpanel was further divided into six populations ({I}1 to {I}6) using a model-based approach. {T}he japonica subpanel, which was more highly differentiated, was divided into 4 populations ({J}1 to {J}4), including a temperate type ({J}2). {P}assport data and phenotypic traits were used to characterize these populations. {S}ome populations were exclusively composed of glutinous types ({I}3 and {J}2). {S}ome of the upland rice varieties appeared to belong to indica populations, which is uncommon in this region of the world. {L}inkage disequilibrium decayed faster in the indica subpanel (r(2) below 0.2 at 101 kb) than in the japonica subpanel (r2 below 0.2 at 425 kb), likely because of the strongest differentiation of the japonica subpanel. {A} matrix adapted for {GWAS} was built by eliminating the markers with a minor allele frequency below 5% and imputing the missing data. {T}his matrix contained 21,814 markers. {A} {GWAS} was conducted on time to flowering to prove the utility of this panel. {C}onclusions: {T}his publicly available panel constitutes an important resource giving access to original allelic diversity. {I}t will be used for {GWAS} on root and panicle traits. ?},
  keywords = {{DA}r{T} markers ; {SNP} ; {G}enetic diversity ; {L}inkage disequilibrium ; {R}ice ; {V}ietnam ; {VIETNAM}},
  booktitle = {},
  journal = {{BMC} {P}lant {B}iology},
  volume = {14},
  numero = {},
  pages = {art. 371 [16 p.]},
  ISSN = {1471-2229},
  year = {2014},
  DOI = {10.1186/s12870-014-0371-7},
  URL = {https://www.documentation.ird.fr/hor/fdi:010063620},
}