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Title: Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa

Authors:
; ; ;
Publication Date:
Research Org.:
Joint Genome Institute (JGI)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1153983
Resource Type:
Journal Article
Resource Relation:
Journal Name: BMC Plant Biology; Journal Volume: 7; Journal Issue: 1
Country of Publication:
United States
Language:
English

Citation Formats

Udaya C,Kalluri, Stephen P,DiFazio, Amy M,Brunner, and Gerald A,Tuskan. Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa. United States: N. p., 2007. Web. doi:10.1186/1471-2229-7-59.
Udaya C,Kalluri, Stephen P,DiFazio, Amy M,Brunner, & Gerald A,Tuskan. Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa. United States. doi:10.1186/1471-2229-7-59.
Udaya C,Kalluri, Stephen P,DiFazio, Amy M,Brunner, and Gerald A,Tuskan. Mon . "Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa". United States. doi:10.1186/1471-2229-7-59.
@article{osti_1153983,
title = {Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa},
author = {Udaya C,Kalluri and Stephen P,DiFazio and Amy M,Brunner and Gerald A,Tuskan},
abstractNote = {},
doi = {10.1186/1471-2229-7-59},
journal = {BMC Plant Biology},
number = 1,
volume = 7,
place = {United States},
year = {Mon Jan 01 00:00:00 EST 2007},
month = {Mon Jan 01 00:00:00 EST 2007}
}
  • Auxin/Indole-3-Acetic Acid (Aux/IAA) and Auxin Response Factor (ARF) transcription factors are key regulators of auxin responses in plants. A total of 35 Aux/IAA and 39 ARF genes were identified in the Populus genome. Comparative phylogenetic analysis revealed that the subgroups PoptrARF2, 6, 9 and 16 and PoptrIAA3, 16, 27 and 29 have differentially expanded in Populus relative to Arabidopsis. Activator ARFs were found to be two fold-overrepresented in the Populus genome. PoptrIAA and PoptrARF gene families appear to have expanded due to high segmental and low tandem duplication events. Furthermore, expression studies showed that genes in the expanded PoptrIAA3 subgroupmore » display differential expression. The gene-family analysis reported here will be useful in conducting future functional genomics studies to understand how the molecular roles of these large gene families translate into a diversity of biologically meaningful auxin effects.« less
  • The Auxin/indole-3-acetic acid (Aux/IAA) genes encode short-lived nuclear proteins that are known to be involved in the primary cellular responses to auxin. To date, systematic analysis of the Aux/IAA genes in potato (Solanum tuberosum) has not been conducted. In this study, a total of 26 potato Aux/IAA genes were identified (designated from StIAA1 to StIAA26), and the distribution of four conserved domains shared by the StIAAs were analyzed based on multiple sequence alignment and a motif-based sequence analysis. A phylogenetic analysis of the Aux/IAA gene families of potato and Arabidopsis was also conducted. In order to assess the roles ofmore » StIAA genes in tuber development, the results of RNA-seq studies were reformatted to analyze the expression patterns of StIAA genes, and then verified by quantitative real-time PCR. A large number of StIAA genes (12 genes) were highly expressed in stolon organs and in during the tuber initiation and expansion developmental stages, and most of these genes were responsive to indoleacetic acid treatment. Our results suggested that StIAA genes were involved in the process of tuber development and provided insights into functional roles of potato Aux/IAA genes. - Highlights: • A systematic analysis of the potato AUX/IAA gene family were performed. • StIAA genes were related to auxin perception and signal transduction. • Candidate StIAA genes likely related to tuber initiation and expansion were screened.« less
  • To uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood (Populus trichocarpa Torr. & Gray) from natural populations throughout western North America. Extensive information from large-scale trait phenotyping (with spatial and temporal replications within a common garden) and genotyping (with a 34K Populus SNP array) of all accessions were used for gene discovery in a genome-wide association study (GWAS).