@article{fdi:010066655,
  title = {{G}enome-wide association mapping for root traits in a panel of rice accessions from {V}ietnam},
  author = {{P}hung, {N}. {T}. {P}. and {M}ai, {C}. {D}. and {H}oang, {G}. {T}. and {T}ruong, {H}. {T}. {M}. and {L}avarenne, {J}{\'e}r{\'e}my and {G}onin, {M}athieu and {L}e {N}guyen, {K}hanh and {H}a, {T}. {T}. and {D}o, {V}. {N}. and {G}antet, {P}ascal and {C}ourtois, {B}.},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground: {D}espite recent sequencing efforts, local genetic resources remain underexploited, even though they carry alleles that can bring agronomic benefits. {T}aking advantage of the recent genotyping with 22,000 single-nucleotide polymorphism markers of a core collection of 180 {V}ietnamese rice varieties originating from provinces from {N}orth to {S}outh {V}ietnam and from different agrosystems characterized by contrasted water regimes, we have performed a genome-wide association study for different root parameters. {R}oots contribute to water stress avoidance and are a still underexploited target for breeding purpose due to the difficulty to observe them. {R}esults: {T}he panel of 180 rice varieties was phenotyped under greenhouse conditions for several root traits in an experimental design with 3 replicates. {T}he phenotyping system consisted of long plastic bags that were filled with sand and supplemented with fertilizer. {R}oot length, root mass in different layers, root thickness, and the number of crown roots, as well as several derived root parameters and shoot traits, were recorded. {T}he results were submitted to association mapping using a mixed model involving structure and kinship to enable the identification of significant associations. {T}he analyses were conducted successively on the whole panel and on its indica (115 accessions) and japonica (64 accessions) subcomponents. {T}he two associations with the highest significance were for root thickness on chromosome 2 and for crown root number on chromosome 11. {N}o common associations were detected between the indica and japonica subpanels, probably because of the polymorphism repartition between the subspecies. {B}ased on orthology with {A}rabidopsis, the possible candidate genes underlying the quantitative trait loci are reviewed. {C}onclusions: {S}ome of the major quantitative trait loci we detected through this genome-wide association study contain promising candidate genes encoding regulatory elements of known key regulators of root formation and development.},
  keywords = {{R}ice ; {G}enotyping by sequencing ; {R}oot development ; {A}ssociation mapping ; {S}tructure ; {VIET} {NAM}},
  booktitle = {},
  journal = {{BMC} {P}lant {B}iology},
  volume = {16},
  numero = {},
  pages = {art. 64 [19 p.]},
  ISSN = {1471-2229},
  year = {2016},
  DOI = {10.1186/s12870-016-0747-y},
  URL = {https://www.documentation.ird.fr/hor/fdi:010066655},
}