title: Integration of genetic, genomic and transcriptomic information identifies putative regulators of adventitious root formation in Populus.
abstract: BACKGROUND
  Adventitious roots (AR) develop from tissues other than the primary root, in a process physiologically regulated by phytohormones. Adventitious roots provide structural support and contribute to water and nutrient absorption, and are critical for commercial vegetative propagation of several crops. Here we quantified the number of AR, root architectural traits and root biomass in cuttings from a pseudo-backcross population of Populus deltoides and Populus trichocarpa. Quantitative trait loci (QTL) mapping and whole-transcriptome analysis of individuals with alternative QTL alleles for AR number were used to identify putative regulators of AR development.
  
  
  RESULTS
  Parental individuals and progeny showed extensive segregation for AR developmental traits. Quantitative trait loci for number of AR mapped consistently in the same interval of linkage group (LG) II and LG XIV, explaining 7-10 % of the phenotypic variation. A time series transcriptome analysis identified 26,121 genes differentially expressed during AR development, particularly during the first 24 h after cuttings were harvested. Of those, 1929 genes were differentially regulated between individuals carrying alternative alleles for the two QTL for number of AR, in one or more time point. Eighty-one of these genes were physically located within the QTL intervals for number of AR, including putative homologs of the Arabidopsis genes SUPERROOT2 (SUR2) and TRYPTOPHAN SYNTHASE ALPHA CHAIN (TSA1), both of which are involved in the auxin indole-3-acetic acid (IAA) biosynthesis pathway.
  
  
  CONCLUSIONS
  This study suggests the involvement of two genes of the tryptophan-dependent auxin biosynthesis pathway, SUR2 and TSA1, in the regulation of a critical trait for the clonal propagation of woody species. A possible model for this regulation is that poplar individuals that have poor AR formation synthesize auxin indole-3-acetic acid (IAA) primarily through the tryptophan (Trp) pathway. Much of the Trp pathway flux appears to be directed to the synthesis of indole glucosinolates (IG), as suggested by the over-expression of SUR2. Individuals that are efficient in AR formation may utilize alternative (non-Trp) pathways to synthesize IAA, based on the observation that they down-regulate the expression of TSA1, one of the critical steps in the synthesis of tryptophan.
authors.affiliation: School of Forest Resources and Conservation, University of Florida, P.O. Box 110410, Gainesville, FL, 32611, USA.|Plant Molecular and Cellular Biology Graduate Program, University of Florida, P.O. Box 110690, Gainesville, FL, 32611, USA.|Present Address: Monsanto Company, 700 Chesterfield Pkwy W, Chesterfield, MO, 63017, USA.
authors.forename: Cintia L
authors.initials: CL
authors.lastname: Ribeiro
authors.affiliation: School of Forest Resources and Conservation, University of Florida, P.O. Box 110410, Gainesville, FL, 32611, USA.
authors.forename: Cynthia M
authors.initials: CM
authors.lastname: Silva
authors.affiliation: School of Forest Resources and Conservation, University of Florida, P.O. Box 110410, Gainesville, FL, 32611, USA.|Plant Molecular and Cellular Biology Graduate Program, University of Florida, P.O. Box 110690, Gainesville, FL, 32611, USA.|Present Address: Seminis, Inc., 37437 State Highway 16, Woodland, CA, 95695, USA.
authors.forename: Derek R
authors.initials: DR
authors.lastname: Drost
authors.affiliation: School of Forest Resources and Conservation, University of Florida, P.O. Box 110410, Gainesville, FL, 32611, USA.|Present Address: Universidade Federal de Goiás, Av. Esperança s/n°, Goiânia, GO, 74001-970, Brazil.
authors.forename: Evandro
authors.initials: E
authors.lastname: Novaes
authors.affiliation: School of Forest Resources and Conservation, University of Florida, P.O. Box 110410, Gainesville, FL, 32611, USA.|Present Address: Universidade Federal de Goiás, Av. Esperança s/n°, Goiânia, GO, 74001-970, Brazil.
authors.forename: Carolina R D B
authors.initials: CR
authors.lastname: Novaes
authors.affiliation: School of Forest Resources and Conservation, University of Florida, P.O. Box 110410, Gainesville, FL, 32611, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Dervinis
authors.affiliation: School of Forest Resources and Conservation, University of Florida, P.O. Box 110410, Gainesville, FL, 32611, USA. mkirst@ufl.edu.|Plant Molecular and Cellular Biology Graduate Program, University of Florida, P.O. Box 110690, Gainesville, FL, 32611, USA. mkirst@ufl.edu.|University of Florida Genetics Institute, University of Florida, P.O. Box 103610, Gainesville, FL, 32611, USA. mkirst@ufl.edu.
authors.forename: Matias
authors.initials: M
authors.lastname: Kirst
mesh_terms: D000483:Alleles; D001665:Binding Sites; D020869:Gene Expression Profiling; D017343:Genes, Plant; D018745:Genome, Plant; D010940:Plant Proteins / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000254:growth & development*; D032107:Populus / Q000235:genetics* / Q000254:growth & development; D040641:Quantitative Trait Loci; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors
keywords: Adventitious root; Populus; QTL; SUR2; Vegetative propagation