Literature DB >> 19117793

Functional genomics of root growth and development in Arabidopsis.

Anjali Iyer-Pascuzzi1, June Simpson, Luis Herrera-Estrella, Philip N Benfey.   

Abstract

Roots are vital for the uptake of water and nutrients, and for anchorage in the soil. They are highly plastic, able to adapt developmentally and physiologically to changing environmental conditions. Understanding the molecular mechanisms behind this growth and development requires knowledge of root transcriptomics, proteomics, and metabolomics. Genomics approaches, including the recent publication of a root expression map, root proteome, and environment-specific root expression studies, are uncovering complex transcriptional and post-transcriptional networks underlying root development. The challenge is in further capitalizing on the information in these datasets to understand the fundamental principles of root growth and development. In this review, we highlight progress researchers have made toward this goal.

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Year:  2008        PMID: 19117793      PMCID: PMC2683257          DOI: 10.1016/j.pbi.2008.11.002

Source DB:  PubMed          Journal:  Curr Opin Plant Biol        ISSN: 1369-5266            Impact factor:   7.834


  54 in total

1.  A gene expression map of the Arabidopsis root.

Authors:  Kenneth Birnbaum; Dennis E Shasha; Jean Y Wang; Jee W Jung; Georgina M Lambert; David W Galbraith; Philip N Benfey
Journal:  Science       Date:  2003-12-12       Impact factor: 47.728

2.  The AtGenExpress hormone and chemical treatment data set: experimental design, data evaluation, model data analysis and data access.

Authors:  Hideki Goda; Eriko Sasaki; Kenji Akiyama; Akiko Maruyama-Nakashita; Kazumi Nakabayashi; Weiqiang Li; Mikihiro Ogawa; Yukika Yamauchi; Jeremy Preston; Ko Aoki; Takatoshi Kiba; Suguru Takatsuto; Shozo Fujioka; Tadao Asami; Takeshi Nakano; Hisashi Kato; Takeshi Mizuno; Hitoshi Sakakibara; Shinjiro Yamaguchi; Eiji Nambara; Yuji Kamiya; Hideki Takahashi; Masami Yokota Hirai; Tetsuya Sakurai; Kazuo Shinozaki; Kazuki Saito; Shigeo Yoshida; Yukihisa Shimada
Journal:  Plant J       Date:  2008-08       Impact factor: 6.417

3.  The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling.

Authors:  Y Helariutta; H Fukaki; J Wysocka-Diller; K Nakajima; J Jung; G Sena; M T Hauser; P N Benfey
Journal:  Cell       Date:  2000-05-26       Impact factor: 41.582

4.  Intercellular movement of the putative transcription factor SHR in root patterning.

Authors:  K Nakajima; G Sena; T Nawy; P N Benfey
Journal:  Nature       Date:  2001-09-20       Impact factor: 49.962

5.  A prominent role for the CBF cold response pathway in configuring the low-temperature metabolome of Arabidopsis.

Authors:  Daniel Cook; Sarah Fowler; Oliver Fiehn; Michael F Thomashow
Journal:  Proc Natl Acad Sci U S A       Date:  2004-09-21       Impact factor: 11.205

6.  Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana.

Authors:  Masami Yokota Hirai; Mitsuru Yano; Dayan B Goodenowe; Shigehiko Kanaya; Tomoko Kimura; Motoko Awazuhara; Masanori Arita; Toru Fujiwara; Kazuki Saito
Journal:  Proc Natl Acad Sci U S A       Date:  2004-06-15       Impact factor: 11.205

7.  Hydrogen peroxide mediates plant root cell response to nutrient deprivation.

Authors:  Ryoung Shin; Daniel P Schachtman
Journal:  Proc Natl Acad Sci U S A       Date:  2004-06-01       Impact factor: 11.205

Review 8.  Genome-wide reprogramming of primary and secondary metabolism, protein synthesis, cellular growth processes, and the regulatory infrastructure of Arabidopsis in response to nitrogen.

Authors:  Wolf-Rüdiger Scheible; Rosa Morcuende; Tomasz Czechowski; Christina Fritz; Daniel Osuna; Natalia Palacios-Rojas; Dana Schindelasch; Oliver Thimm; Michael K Udvardi; Mark Stitt
Journal:  Plant Physiol       Date:  2004-09       Impact factor: 8.340

9.  Comparative proteome analyses of phosphorus responses in maize (Zea mays L.) roots of wild-type and a low-P-tolerant mutant reveal root characteristics associated with phosphorus efficiency.

Authors:  Kunpeng Li; Changzheng Xu; Zhaoxia Li; Kewei Zhang; Aifang Yang; Juren Zhang
Journal:  Plant J       Date:  2008-05-19       Impact factor: 6.417

10.  A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies.

Authors:  Yuling Jiao; S Lori Tausta; Neeru Gandotra; Ning Sun; Tie Liu; Nicole K Clay; Teresa Ceserani; Meiqin Chen; Ligeng Ma; Matthew Holford; Hui-yong Zhang; Hongyu Zhao; Xing-Wang Deng; Timothy Nelson
Journal:  Nat Genet       Date:  2009-01-04       Impact factor: 38.330

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  16 in total

Review 1.  Integration of metabolic reactions and gene regulation.

Authors:  Chen-Hsiang Yeang
Journal:  Mol Biotechnol       Date:  2011-01       Impact factor: 2.695

2.  MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings.

Authors:  Isabel Betegón-Putze; Alejandro González; Xavier Sevillano; David Blasco-Escámez; Ana I Caño-Delgado
Journal:  Plant J       Date:  2019-04-06       Impact factor: 6.417

3.  Systems biology update: cell type-specific transcriptional regulatory networks.

Authors:  Li Pu; Siobhan Brady
Journal:  Plant Physiol       Date:  2009-12-04       Impact factor: 8.340

4.  The folylpolyglutamate synthetase plastidial isoform is required for postembryonic root development in Arabidopsis.

Authors:  Avinash C Srivastava; Perla A Ramos-Parra; Mohamed Bedair; Ana L Robledo-Hernández; Yuhong Tang; Lloyd W Sumner; Rocío I Díaz de la Garza; Elison B Blancaflor
Journal:  Plant Physiol       Date:  2011-01-13       Impact factor: 8.340

5.  Optimizing root system architecture in biofuel crops for sustainable energy production and soil carbon sequestration.

Authors:  Jennifer Pc To; Jinming Zhu; Philip N Benfey; Tedd Elich
Journal:  F1000 Biol Rep       Date:  2010-09-08

6.  Root development under control of magnesium availability.

Authors:  Yaofang Niu; Gulei Jin; Yong Song Zhang
Journal:  Plant Signal Behav       Date:  2014

7.  Chitinase-like protein CTL1 plays a role in altering root system architecture in response to multiple environmental conditions.

Authors:  Christian Hermans; Silvana Porco; Nathalie Verbruggen; Daniel R Bush
Journal:  Plant Physiol       Date:  2009-12-09       Impact factor: 8.340

Review 8.  Omics meet networks - using systems approaches to infer regulatory networks in plants.

Authors:  Miguel A Moreno-Risueno; Wolfgang Busch; Philip N Benfey
Journal:  Curr Opin Plant Biol       Date:  2009-12-28       Impact factor: 7.834

9.  Probing the roles of LRR RLK genes in Arabidopsis thaliana roots using a custom T-DNA insertion set.

Authors:  Colette A ten Hove; Zoltán Bochdanovits; Vera M A Jansweijer; Fenne G Koning; Lidija Berke; Gabino F Sanchez-Perez; Ben Scheres; Renze Heidstra
Journal:  Plant Mol Biol       Date:  2011-03-24       Impact factor: 4.076

10.  Consequences of LED Lights on Root Morphological Traits and Compounds Accumulation in Sarcandra glabra Seedlings.

Authors:  Dejin Xie; Muhammad Waqqas Khan Tarin; Lingyan Chen; Ke Ren; Deming Yang; Chengcheng Zhou; Jiayi Wan; Tianyou He; Jundong Rong; Yushan Zheng
Journal:  Int J Mol Sci       Date:  2021-07-02       Impact factor: 5.923

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