title: Genome-wide association mapping for root traits in a panel of rice accessions from Vietnam.
abstract: BACKGROUND
  Despite recent sequencing efforts, local genetic resources remain underexploited, even though they carry alleles that can bring agronomic benefits. Taking advantage of the recent genotyping with 22,000 single-nucleotide polymorphism markers of a core collection of 180 Vietnamese rice varieties originating from provinces from North to South Vietnam and from different agrosystems characterized by contrasted water regimes, we have performed a genome-wide association study for different root parameters. Roots contribute to water stress avoidance and are a still underexploited target for breeding purpose due to the difficulty to observe them.
  
  
  RESULTS
  The panel of 180 rice varieties was phenotyped under greenhouse conditions for several root traits in an experimental design with 3 replicates. The phenotyping system consisted of long plastic bags that were filled with sand and supplemented with fertilizer. Root 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. The results were submitted to association mapping using a mixed model involving structure and kinship to enable the identification of significant associations. The analyses were conducted successively on the whole panel and on its indica (115 accessions) and japonica (64 accessions) subcomponents. The two associations with the highest significance were for root thickness on chromosome 2 and for crown root number on chromosome 11. No common associations were detected between the indica and japonica subpanels, probably because of the polymorphism repartition between the subspecies. Based on orthology with Arabidopsis, the possible candidate genes underlying the quantitative trait loci are reviewed.
  
  
  CONCLUSIONS
  Some 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.
authors.affiliation: Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, 00000, Hanoi, Vietnam.
authors.forename: Nhung Thi Phuong
authors.initials: NT
authors.lastname: Phung
authors.affiliation: Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, 00000, Hanoi, Vietnam.|University of Science and Technology of Hanoi, LMI RICE, 00000, Hanoi, Vietnam.
authors.forename: Chung Duc
authors.initials: CD
authors.lastname: Mai
authors.affiliation: Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, 00000, Hanoi, Vietnam.|University of Science and Technology of Hanoi, LMI RICE, 00000, Hanoi, Vietnam.
authors.forename: Giang Thi
authors.initials: GT
authors.lastname: Hoang
authors.affiliation: Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, 00000, Hanoi, Vietnam.|University of Science and Technology of Hanoi, LMI RICE, 00000, Hanoi, Vietnam.
authors.forename: Hue Thi Minh
authors.initials: HT
authors.lastname: Truong
authors.affiliation: University of Science and Technology of Hanoi, LMI RICE, 00000, Hanoi, Vietnam.|IRD, LMI RICE, 00000, Hanoi, Vietnam.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Lavarenne
authors.affiliation: IRD, LMI RICE, 00000, Hanoi, Vietnam.
authors.forename: Mathieu
authors.initials: M
authors.lastname: Gonin
authors.affiliation: University of Science and Technology of Hanoi, LMI RICE, 00000, Hanoi, Vietnam.|IRD, LMI RICE, 00000, Hanoi, Vietnam.
authors.forename: Khanh Le
authors.initials: KL
authors.lastname: Nguyen
authors.affiliation: Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, 00000, Hanoi, Vietnam.
authors.forename: Thuy Thi
authors.initials: TT
authors.lastname: Ha
authors.affiliation: Agricultural Genetics Institute, National Key Laboratory for Plant Cell Biotechnology, LMI RICE, 00000, Hanoi, Vietnam.
authors.forename: Vinh Nang
authors.initials: VN
authors.lastname: Do
authors.affiliation: University of Science and Technology of Hanoi, LMI RICE, 00000, Hanoi, Vietnam. pascal.gantet@univ-montp2.fr.|IRD, LMI RICE, 00000, Hanoi, Vietnam. pascal.gantet@univ-montp2.fr.|Université de Montpellier, UMR DIADE, 34095, Montpellier, France. pascal.gantet@univ-montp2.fr.
authors.forename: Pascal
authors.initials: P
authors.lastname: Gantet
authors.affiliation: Cirad, UMR-AGAP, 34398, Montpellier, France.
authors.forename: Brigitte
authors.initials: B
authors.lastname: Courtois
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D005819:Genetic Markers; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D012275:Oryza / Q000235:genetics* / Q000254:growth & development; D010641:Phenotype; D018517:Plant Roots / Q000235:genetics* / Q000254:growth & development; D040641:Quantitative Trait Loci; D014744:Vietnam
chemical_list: D005819:Genetic Markers
keywords: Association mapping; Genotyping by sequencing; Rice; Root development; Structure