title: Genome-Wide Association Study for Traits Related to Plant and Grain Morphology, and Root Architecture in Temperate Rice Accessions.
abstract: In this study we carried out a genome-wide association analysis for plant and grain morphology and root architecture in a unique panel of temperate rice accessions adapted to European pedo-climatic conditions. This is the first study to assess the association of selected phenotypic traits to specific genomic regions in the narrow genetic pool of temperate japonica. A set of 391 rice accessions were GBS-genotyped yielding-after data editing-57000 polymorphic and informative SNPS, among which 54% were in genic regions.
  
  
  
  In total, 42 significant genotype-phenotype associations were detected: 21 for plant morphology traits, 11 for grain quality traits, 10 for root architecture traits. The FDR of detected associations ranged from 3 · 10-7 to 0.92 (median: 0.25). In most cases, the significant detected associations co-localised with QTLs and candidate genes controlling the phenotypic variation of single or multiple traits. The most significant associations were those for flag leaf width on chromosome 4 (FDR = 3 · 10-7) and for plant height on chromosome 6 (FDR = 0.011).
  
  
  
  We demonstrate the effectiveness and resolution of the developed platform for high-throughput phenotyping, genotyping and GWAS in detecting major QTLs for relevant traits in rice. We identified strong associations that may be used for selection in temperate irrigated rice breeding: e.g. associations for flag leaf width, plant height, root volume and length, grain length, grain width and their ratio. Our findings pave the way to successfully exploit the narrow genetic pool of European temperate rice and to pinpoint the most relevant genetic components contributing to the adaptability and high yield of this germplasm. The generated data could be of direct use in genomic-assisted breeding strategies.
authors.affiliation: PTP Science Park, 26900 Lodi, Italy.
authors.forename: Filippo
authors.identifier: 0000-0002-3901-2354
authors.initials: F
authors.lastname: Biscarini
authors.affiliation: IBBA-CNR, Lodi, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Cozzi
authors.affiliation: PTP Science Park, 26900 Lodi, Italy.
authors.forename: Laura
authors.initials: L
authors.lastname: Casella
authors.affiliation: PTP Science Park, 26900 Lodi, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Riccardi
authors.affiliation: PTP Science Park, 26900 Lodi, Italy.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Vattari
authors.affiliation: CREA-Council for Agricultural Research and Economics, Rice Research Unit, 13100 Vercelli, Italy.
authors.forename: Gabriele
authors.initials: G
authors.lastname: Orasen
authors.affiliation: CREA-Council for Agricultural Research and Economics, Rice Research Unit, 13100 Vercelli, Italy.
authors.forename: Rosaria
authors.initials: R
authors.lastname: Perrini
authors.affiliation: CREA-Council for Agricultural Research and Economics, Genomics Research Centre, 29017 Fiorenzuola d'Arda (Piacenza), Italy.
authors.forename: Gianni
authors.initials: G
authors.lastname: Tacconi
authors.affiliation: CREA-Council for Agricultural Research and Economics, Genomics Research Centre, 29017 Fiorenzuola d'Arda (Piacenza), Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Tondelli
authors.affiliation: CREA-Council for Agricultural Research and Economics, Rice Research Unit, 13100 Vercelli, Italy.
authors.forename: Chiara
authors.initials: C
authors.lastname: Biselli
authors.affiliation: CREA-Council for Agricultural Research and Economics, Genomics Research Centre, 29017 Fiorenzuola d'Arda (Piacenza), Italy.
authors.forename: Luigi
authors.initials: L
authors.lastname: Cattivelli
authors.affiliation: Department of Plant Breeding & Genetics, Cornell University, Ithaca, NY, United States of America.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Spindel
authors.affiliation: Department of Plant Breeding & Genetics, Cornell University, Ithaca, NY, United States of America.
authors.forename: Susan
authors.initials: S
authors.lastname: McCouch
authors.affiliation: PTP Science Park, 26900 Lodi, Italy.
authors.forename: Pamela
authors.initials: P
authors.lastname: Abbruscato
authors.affiliation: CREA-Council for Agricultural Research and Economics, Rice Research Unit, 13100 Vercelli, Italy.|CREA-Council for Agricultural Research and Economics, Genomics Research Centre, 29017 Fiorenzuola d'Arda (Piacenza), Italy.
authors.forename: Giampiero
authors.initials: G
authors.lastname: Valé
authors.affiliation: PTP Science Park, 26900 Lodi, Italy.
authors.forename: Pietro
authors.initials: P
authors.lastname: Piffanelli
authors.affiliation: PTP Science Park, 26900 Lodi, Italy.
authors.forename: Raffaella
authors.initials: R
authors.lastname: Greco
mesh_terms: D032461:Chromosomes, Plant / Q000235:genetics*; D055106:Genome-Wide Association Study; D005838:Genotype; D012275:Oryza / Q000235:genetics*; D018517:Plant Roots / Q000235:genetics*; D019655:Quantitative Trait, Heritable; D000067348:Whole Grains / Q000235:genetics