Genetic control of root development in rice, the model cereal.

Cereals possess a fibrous root system that is mainly composed of crown roots that emerge postembryonically from the nodes of the stem. Because the root system is not directly accessible and consequently difficult to study, it remains a target for breeders to improve the ability of plants to exploit the mineral and water resources of the soil. Breeding for root architecture necessitates identifying the genetic determinants of root development. This research is now underway in cereals, particularly in rice, the monocot model species. In this review, we examine recent data identifying genes that govern root development in cereals, such as ARL1/CRL1 in rice and RTCS in maize which encodes a conserved lateral organ boundary domain transcription factor involved in crown root initiation and development in response to auxin. Finally, we discuss the detection and validation of root development quantitative trait loci.

[1]  Edward S. Buckler,et al.  Dwarf8 polymorphisms associate with variation in flowering time , 2001, Nature Genetics.

[2]  H. Piepho,et al.  Assessing the importance of genotype × environment interaction for root traits in rice using a mapping population II: conventional QTL analysis , 2006, Theoretical and Applied Genetics.

[3]  M. Estelle,et al.  The F-box protein TIR1 is an auxin receptor , 2005, Nature.

[4]  Kenneth L. McNally,et al.  Evaluation of near-isogenic lines of rice introgressed with QTLs for root depth through marker-aided selection , 2001, Theoretical and Applied Genetics.

[5]  A. Price,et al.  Upland rice grown in soil-filled chambers and exposed to contrasting water-deficit regimes: II. Mapping quantitative trait loci for root morphology and distribution , 2002 .

[6]  G. Jürgens,et al.  Partial loss-of-function alleles reveal a role for GNOM in auxin transport-related, post-embryonic development of Arabidopsis , 2003, Development.

[7]  B. Courtois,et al.  Improved resolution in the position of drought-related QTLs in a single mapping population of rice by meta-analysis , 2009, BMC Genomics.

[8]  Feiyan Liu,et al.  Mapping QTLs and candidate genes for rice root traits under different water-supply conditions and comparative analysis across three populations , 2003, Theoretical and Applied Genetics.

[9]  W. R. Whalley,et al.  A bioinformatic and transcriptomic approach to identifying positional candidate genes without fine mapping: an example using rice root-growth QTLs. , 2008, Genomics.

[10]  Alain Charcosset,et al.  MetaQTL: a package of new computational methods for the meta-analysis of QTL mapping experiments , 2007, BMC Bioinformatics.

[11]  Tom Beeckman,et al.  Arabidopsis lateral root development: an emerging story. , 2009, Trends in plant science.

[12]  L. Xiong,et al.  Genetic Basis of Drought Resistance at Reproductive Stage in Rice: Separation of Drought Tolerance From Drought Avoidance , 2006, Genetics.

[13]  F. Hochholdinger,et al.  Genetic and genomic dissection of maize root development and architecture. , 2009, Current opinion in plant biology.

[14]  M. Kojima,et al.  Overexpression of a type-A response regulator alters rice morphology and cytokinin metabolism. , 2007, Plant & cell physiology.

[15]  Tom Beeckman,et al.  Cytokinins Act Directly on Lateral Root Founder Cells to Inhibit Root Initiation[W] , 2007, The Plant Cell Online.

[16]  H. Fukuda,et al.  Plant meristems: CLAVATA3/ESR-related signaling in the shoot apical meristem and the root apical meristem , 2008, Journal of Plant Research.

[17]  Haiyan Huang,et al.  Transcription Profile Analyses Identify Genes and Pathways Central to Root Cap Functions in Maize , 2006, Plant Molecular Biology.

[18]  J. Witcombe,et al.  Field evaluation of upland rice lines selected for QTLs controlling root traits , 2007 .

[19]  K. Jiang,et al.  Quiescent center formation in maize roots is associated with an auxin-regulated oxidizing environment , 2003, Development.

[20]  B. Courtois,et al.  Mapping root and shoot traits in rice: experience in UK, IRRI and WARDA , 1999 .

[21]  R. Heidstra,et al.  Who begets whom? Plant cell fate determination by asymmetric cell division. , 2008, Current opinion in plant biology.

[22]  Makoto Matsuoka,et al.  Crown rootless1, Which Is Essential for Crown Root Formation in Rice, Is a Target of an AUXIN RESPONSE FACTOR in Auxin Signalingw⃞ , 2005, The Plant Cell Online.

[23]  Wolfgang Busch,et al.  WUSCHEL controls meristem function by direct regulation of cytokinin-inducible response regulators , 2005, Nature.

[24]  P. Schnable,et al.  Transcriptomic and Proteomic Analyses of Pericycle Cells of the Maize Primary Root1[W][OA] , 2007, Plant Physiology.

[25]  A. Price,et al.  Marker-assisted selection to introgress rice QTLs controlling root traits into an Indian upland rice variety , 2006, Theoretical and Applied Genetics.

[26]  B. Goffinet,et al.  Quantitative trait loci: a meta-analysis. , 2000, Genetics.

[27]  X. Draye,et al.  Root system architecture: opportunities and constraints for genetic improvement of crops. , 2007, Trends in plant science.

[28]  M. Gore,et al.  Status and Prospects of Association Mapping in Plants , 2008 .

[29]  A. Price,et al.  A combined RFLP and AFLP linkage map of upland rice (Oryza sativa L.) used to identify QTLs for root-penetration ability , 2000, Theoretical and Applied Genetics.

[30]  Ottoline Leyser,et al.  The Arabidopsis F-box protein TIR1 is an auxin receptor , 2005, Nature.

[31]  Roberto Tuberosa,et al.  Genetic dissection of seminal root architecture in elite durum wheat germplasm , 2007 .

[32]  J. Ecker,et al.  Type-A Arabidopsis Response Regulators Are Partially Redundant Negative Regulators of Cytokinin Signaling Online version contains Web-only data. , 2004, The Plant Cell Online.

[33]  K. Jiang,et al.  Regulation of root apical meristem development. , 2005, Annual review of cell and developmental biology.

[34]  G. Slafer,et al.  Raising yield potential in wheat. , 2009, Journal of experimental botany.

[35]  S. Fukai,et al.  Yield response of rice (Oryza sativa L.) genotypes to drought under rainfed lowland: 3. Plant factors contributing to drought resistance , 2002 .

[36]  M. Matsuoka,et al.  Isolation and characterization of a rice WUSCHEL-type homeobox gene that is specifically expressed in the central cells of a quiescent center in the root apical meristem. , 2003, The Plant journal : for cell and molecular biology.

[37]  M. Soller,et al.  Advanced intercross lines, an experimental population for fine genetic mapping. , 1995, Genetics.

[38]  Eva Benková,et al.  Hormone interactions at the root apical meristem , 2009, Plant Molecular Biology.

[39]  Lu Wang,et al.  Adventitious root formation in rice requires OsGNOM1 and is mediated by the OsPINs family , 2009, Cell Research.

[40]  Y. Machida,et al.  Characterization of genes in the ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES (AS2/LOB) family in Arabidopsis thaliana, and functional and molecular comparisons between AS2 and other family members , 2009, The Plant journal : for cell and molecular biology.

[41]  Limin Huang,et al.  The WUSCHEL-Related Homeobox Gene WOX11 Is Required to Activate Shoot-Borne Crown Root Development in Rice[C][W] , 2009, The Plant Cell Online.

[42]  P. Schnable,et al.  Isolation, Characterization, and Pericycle-Specific Transcriptome Analyses of the Novel Maize Lateral and Seminal Root Initiation Mutant rum11[w] , 2005, Plant Physiology.

[43]  A. Gojon,et al.  Root uptake regulation: a central process for NPS homeostasis in plants. , 2009, Current opinion in plant biology.

[44]  B. Courtois,et al.  Rice Root Genetic Architecture: Meta-analysis from a Drought QTL Database , 2009, Rice.

[45]  Joseph R Ecker,et al.  NPH4/ARF7 and ARF19 promote leaf expansion and auxin-induced lateral root formation. , 2005, The Plant journal : for cell and molecular biology.

[46]  H. Leung,et al.  Mutant Resources in Rice for Functional Genomics of the Grasses[W] , 2009, Plant Physiology.

[47]  L. Laplaze,et al.  GAL4-GFP enhancer trap lines for genetic manipulation of lateral root development in Arabidopsis thaliana. , 2005, Journal of experimental botany.

[48]  M. McMullen,et al.  Genetic Design and Statistical Power of Nested Association Mapping in Maize , 2008, Genetics.

[49]  Takashi Aoyama,et al.  A Genetic Framework for the Control of Cell Division and Differentiation in the Root Meristem , 2008, Science.

[50]  Huanming Yang,et al.  A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica) , 2002, Science.

[51]  G. Khush.  What it will take to Feed 5.0 Billion Rice consumers in 2030 , 2005, Plant Molecular Biology.

[52]  P. Gantet,et al.  Molecular Genetics of Rice Root Development , 2009, Rice.

[53]  G. Jürgens,et al.  Coordinated polar localization of auxin efflux carrier PIN1 by GNOM ARF GEF. , 1999, Science.

[54]  Jitendra P Khurana,et al.  Transcript profiling reveals diverse roles of auxin‐responsive genes during reproductive development and abiotic stress in rice , 2009, The FEBS journal.

[55]  F. Clowes,et al.  Origin of the epidermis in root meristems. , 1994, The New phytologist.

[56]  B. Han,et al.  Genome-wide analysis of the auxin response factors (ARF) gene family in rice (Oryza sativa). , 2007, Gene.

[57]  J. Zhang,et al.  Mapping QTLs for root morphology of a rice population adapted to rainfed lowland conditions , 2002, Theoretical and Applied Genetics.

[58]  H. Kitano,et al.  Rice plant development: from zygote to spikelet. , 2005, Plant & cell physiology.

[59]  Kenneth L. McNally,et al.  Genomewide SNP variation reveals relationships among landraces and modern varieties of rice , 2009, Proceedings of the National Academy of Sciences.

[60]  B. Courtois,et al.  Mapping genes controlling root morphology and root distribution in a doubled-haploid population of rice , 1997, Theoretical and Applied Genetics.

[61]  W. Powell,et al.  From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants. , 2008, Current opinion in plant biology.

[62]  Ping Wu,et al.  ARL1, a LOB-domain protein required for adventitious root formation in rice. , 2005, The Plant journal : for cell and molecular biology.

[63]  S. Fukai,et al.  Yield response of rice (Oryza sativa L.) genotypes to drought under rainfed lowlands , 2002 .

[64]  B. Courtois,et al.  Locating QTLs controlling constitutive root traits in the rice population IAC 165 × Co39 , 2003, Euphytica.

[65]  M. Matsuoka,et al.  The SCARECROW gene's role in asymmetric cell divisions in rice plants. , 2003, The Plant journal : for cell and molecular biology.

[66]  Searching for quantitative trait loci controlling root traits in maize: a critical appraisal , 2003 .

[67]  M. Sorrells,et al.  Association Mapping of Kernel Size and Milling Quality in Wheat (Triticum aestivum L.) Cultivars , 2006, Genetics.

[68]  Kanako O. Koyanagi,et al.  Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. , 2007, Genome research.

[69]  Chao-Feng Huang,et al.  A rice mutant sensitive to Al toxicity is defective in the specification of root outer cell layers. , 2009, Plant & cell physiology.

[70]  D. Jackson,et al.  Control of phyllotaxy by the cytokinin-inducible response regulator homologue ABPHYL1 , 2004, Nature.

[71]  Roger Sylvester-Bradley,et al.  Modelling cereal root systems for water and nitrogen capture: towards an economic optimum. , 2003, Annals of botany.

[72]  A. Theologis,et al.  ARF7 and ARF19 Regulate Lateral Root Formation via Direct Activation of LBD/ASL Genes in Arabidopsis[W] , 2007, The Plant Cell Online.

[73]  R. Richards.  Genetic Opportunities to Improve Cereal Root Systems for Dryland Agriculture , 2008 .

[74]  Yoshiaki Inukai,et al.  CRL4 regulates crown root formation through auxin transport in rice , 2008 .

[75]  J. Harada,et al.  Quantitative trait loci for adventitious and lateral roots in rice , 2006 .

[76]  Teva Vernoux,et al.  An Evolutionarily Conserved Mechanism Delimiting SHR Movement Defines a Single Layer of Endodermis in Plants , 2007, Science.

[77]  M. Sauer,et al.  The maize (Zea mays L.) RTCS gene encodes a LOB domain protein that is a key regulator of embryonic seminal and post-embryonic shoot-borne root initiation. , 2007, The Plant journal : for cell and molecular biology.

[78]  Hongyu Zhao,et al.  A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies , 2009, Nature Genetics.

[79]  B. Shuai,et al.  LATERAL ORGAN BOUNDARIES defines a new family of DNA-binding transcription factors and can interact with specific bHLH proteins , 2007, Nucleic acids research.

[80]  John Draper,et al.  Brachypodium distachyon: making hay with a wild grass. , 2008, Trends in plant science.