title: 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture.
abstract: Identification of genes that control root system architecture in crop plants requires innovations that enable high-throughput and accurate measurements of root system architecture through time. We demonstrate the ability of a semiautomated 3D in vivo imaging and digital phenotyping pipeline to interrogate the quantitative genetic basis of root system growth in a rice biparental mapping population, Bala × Azucena. We phenotyped >1,400 3D root models and >57,000 2D images for a suite of 25 traits that quantified the distribution, shape, extent of exploration, and the intrinsic size of root networks at days 12, 14, and 16 of growth in a gellan gum medium. From these data we identified 89 quantitative trait loci, some of which correspond to those found previously in soil-grown plants, and provide evidence for genetic tradeoffs in root growth allocations, such as between the extent and thoroughness of exploration. We also developed a multivariate method for generating and mapping central root architecture phenotypes and used it to identify five major quantitative trait loci (r(2) = 24-37%), two of which were not identified by our univariate analysis. Our imaging and analytical platform provides a means to identify genes with high potential for improving root traits and agronomic qualities of crops.
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708, USA.
authors.forename: Christopher N
authors.initials: CN
authors.lastname: Topp
authors.forename: Anjali S
authors.initials: AS
authors.lastname: Iyer-Pascuzzi
authors.forename: Jill T
authors.initials: JT
authors.lastname: Anderson
authors.forename: Cheng-Ruei
authors.initials: CR
authors.lastname: Lee
authors.forename: Paul R
authors.initials: PR
authors.lastname: Zurek
authors.forename: Olga
authors.initials: O
authors.lastname: Symonova
authors.forename: Ying
authors.initials: Y
authors.lastname: Zheng
authors.forename: Alexander
authors.initials: A
authors.lastname: Bucksch
authors.forename: Yuriy
authors.initials: Y
authors.lastname: Mileyko
authors.forename: Taras
authors.initials: T
authors.lastname: Galkovskyi
authors.forename: Brad T
authors.initials: BT
authors.lastname: Moore
authors.forename: John
authors.initials: J
authors.lastname: Harer
authors.forename: Herbert
authors.initials: H
authors.lastname: Edelsbrunner
authors.forename: Thomas
authors.initials: T
authors.lastname: Mitchell-Olds
authors.forename: Joshua S
authors.initials: JS
authors.lastname: Weitz
authors.forename: Philip N
authors.initials: PN
authors.lastname: Benfey
mesh_terms: D018533:Biomass; D002874:Chromosome Mapping; D003433:Crosses, Genetic; D018745:Genome, Plant / Q000235:genetics*; D021621:Imaging, Three-Dimensional; D007178:Inbreeding; D008954:Models, Biological; D015999:Multivariate Analysis; D012275:Oryza / Q000033:anatomy & histology* / Q000235:genetics* / Q000254:growth & development; D010641:Phenotype; D018517:Plant Roots / Q000033:anatomy & histology* / Q000235:genetics* / Q000254:growth & development; D025341:Principal Component Analysis; D040641:Quantitative Trait Loci / Q000235:genetics*; D019655:Quantitative Trait, Heritable; D011995:Recombination, Genetic / Q000235:genetics; D015203:Reproducibility of Results