601
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López-Arredondo D, González-Morales SI, Bello-Bello E, Alejo-Jacuinde G, Herrera L. Engineering food crops to grow in harsh environments. F1000Res 2015; 4:651. [PMID: 26380074 PMCID: PMC4560252 DOI: 10.12688/f1000research.6538.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/28/2015] [Indexed: 12/18/2022] Open
Abstract
Achieving sustainable agriculture and producing enough food for the increasing global population will require effective strategies to cope with harsh environments such as water and nutrient stress, high temperatures and compacted soils with high impedance that drastically reduce crop yield. Recent advances in the understanding of the molecular, cellular and epigenetic mechanisms that orchestrate plant responses to abiotic stress will serve as the platform to engineer improved crop plants with better designed root system architecture and optimized metabolism to enhance water and nutrients uptake and use efficiency and/or soil penetration. In this review we discuss such advances and how the generated knowledge could be used to integrate effective strategies to engineer crops by gene transfer or genome editing technologies.
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Affiliation(s)
| | - Sandra Isabel González-Morales
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, 36821, Mexico
| | - Elohim Bello-Bello
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, 36821, Mexico
| | - Gerardo Alejo-Jacuinde
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, 36821, Mexico
| | - Luis Herrera
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, 36821, Mexico
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602
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Lynch JP. Root phenes that reduce the metabolic costs of soil exploration: opportunities for 21st century agriculture. PLANT, CELL & ENVIRONMENT 2015; 38:1775-84. [PMID: 25255708 DOI: 10.1111/pce.12451] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Revised: 08/18/2014] [Accepted: 08/24/2014] [Indexed: 05/18/2023]
Abstract
Crop genotypes with reduced metabolic costs of soil exploration would have improved water and nutrient acquisition. Three strategies to achieve this goal are (1) production of the optimum number of axial roots; (2) greater biomass allocation to root classes that are less metabolically demanding; and (3) reduction of the respiratory requirement of root tissue. An example of strategy 1 is the case of reduced crown root number in maize, which is associated with greater rooting depth, N capture and yield in low N soil. An example of strategy 2 is the case of increased hypocotyl-borne rooting in bean, which decreases root cost and increases P capture from low P soil. Examples of strategy 3 are the cases of increased formation of root cortical aerenchyma, decreased cortical cell file number and increased cortical cell size in maize, which decrease specific root respiration, increase rooting depth and increase water capture and yield under water stress. Root cortical aerenchyma also increases N capture and yield under N stress. Root phenes that reduce the metabolic cost of soil exploration are promising, underexploited avenues to the climate-resilient, resource-efficient crops that are urgently needed in global agriculture.
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Affiliation(s)
- Jonathan P Lynch
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA
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603
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Kuijken RCP, van Eeuwijk FA, Marcelis LFM, Bouwmeester HJ. Root phenotyping: from component trait in the lab to breeding. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5389-401. [PMID: 26071534 DOI: 10.1093/jxb/erv239] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
In the last decade cheaper and faster sequencing methods have resulted in an enormous increase in genomic data. High throughput genotyping, genotyping by sequencing and genomic breeding are becoming a standard in plant breeding. As a result, the collection of phenotypic data is increasingly becoming a limiting factor in plant breeding. Genetic studies on root traits are being hampered by the complexity of these traits and the inaccessibility of the rhizosphere. With an increasing interest in phenotyping, breeders and scientists try to overcome these limitations, resulting in impressive developments in automated phenotyping platforms. Recently, many such platforms have been thoroughly described, yet their efficiency to increase genetic gain often remains undiscussed. This efficiency depends on the heritability of the phenotyped traits as well as the correlation of these traits with agronomically relevant breeding targets. This review provides an overview of the latest developments in root phenotyping and describes the environmental and genetic factors influencing root phenotype and heritability. It also intends to give direction to future phenotyping and breeding strategies for optimizing root system functioning. A quantitative framework to determine the efficiency of phenotyping platforms for genetic gain is described. By increasing heritability, managing effects caused by interactions between genotype and environment and by quantifying the genetic relation between traits phenotyped in platforms and ultimate breeding targets, phenotyping platforms can be utilized to their maximum potential.
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Affiliation(s)
- René C P Kuijken
- Wageningen UR, Greenhouse Horticulture, Wageningen, 6708 PB, The Netherlands Wageningen UR, Laboratory of Plant Physiology, Wageningen, 6708 PB, The Netherlands
| | | | - Leo F M Marcelis
- Wageningen UR, Horticulture and Product Physiology, Wageningen, 6708 PB, The Netherlands
| | - Harro J Bouwmeester
- Wageningen UR, Laboratory of Plant Physiology, Wageningen, 6708 PB, The Netherlands
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604
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Barboza-Barquero L, Nagel KA, Jansen M, Klasen JR, Kastenholz B, Braun S, Bleise B, Brehm T, Koornneef M, Fiorani F. Phenotype of Arabidopsis thaliana semi-dwarfs with deep roots and high growth rates under water-limiting conditions is independent of the GA5 loss-of-function alleles. ANNALS OF BOTANY 2015; 116:321-31. [PMID: 26162399 PMCID: PMC4549960 DOI: 10.1093/aob/mcv099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Revised: 04/21/2015] [Accepted: 05/19/2015] [Indexed: 05/03/2023]
Abstract
BACKGROUND AND AIMS The occurrence of Arabidopsis thaliana semi-dwarf accessions carrying inactive alleles at the gibberellin (GA) biosynthesis GA5 locus has raised the question whether there are pleiotropic effects on other traits at the root level, such as rooting depth. In addition, it is unknown whether semi-dwarfism in arabidopsis confers a growth advantage under water-limiting conditions compared with wild-type plants. The aim of this research was therefore to investigate whether semi-dwarfism has a pleiotropic effect in the root system and also whether semi-dwarfs might be more tolerant of water-limiting conditions. METHODS The root systems of different arabidopsis semi-dwarfs and GA biosynthesis mutants were phenotyped in vitro using the GROWSCREEN-ROOT image-based software. Semi-dwarfs were phenotyped together with tall, near-related accessions. In addition, root phenotypes were investigated in soil-filled rhizotrons. Rosette growth trajectories were analysed with the GROWSCREEN-FLUORO setup based on non-invasive imaging. KEY RESULTS Mutations in the early steps of the GA biosynthesis pathway led to a reduction in shoot as well as root size. Depending on the genetic background, mutations at the GA5 locus yielded phenotypes characterized by decreased root length in comparison with related wild-type ones. The semi-dwarf accession Pak-3 showed the deepest root system both in vitro and in soil cultivation experiments; this comparatively deep root system, however, was independent of the ga5 loss-of-function allele, as shown by co-segregation analysis. When the accessions were grown under water-limiting conditions, semi-dwarf accessions with high growth rates were identified. CONCLUSIONS The observed diversity in root system growth and architecture occurs independently of semi-dwarf phenotypes, and is probably linked to a genetic background effect. The results show that there are no clear advantages of semi-dwarfism at low water availability in arabidopsis.
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Affiliation(s)
- Luis Barboza-Barquero
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany, CIGRAS, Universidad de Costa Rica, San José, Costa Rica and
| | - Kerstin A Nagel
- IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Marcus Jansen
- IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Jonas R Klasen
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Bernd Kastenholz
- IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Silvia Braun
- IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Birgit Bleise
- IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Thorsten Brehm
- IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Maarten Koornneef
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Fabio Fiorani
- IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
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605
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Rellán-Álvarez R, Lobet G, Lindner H, Pradier PL, Sebastian J, Yee MC, Geng Y, Trontin C, LaRue T, Schrager-Lavelle A, Haney CH, Nieu R, Maloof J, Vogel JP, Dinneny JR. GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems. eLife 2015; 4:e07597. [PMID: 26287479 PMCID: PMC4589753 DOI: 10.7554/elife.07597] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 08/18/2015] [Indexed: 12/16/2022] Open
Abstract
Root systems develop different root types that individually sense cues from their local environment and integrate this information with systemic signals. This complex multi-dimensional amalgam of inputs enables continuous adjustment of root growth rates, direction, and metabolic activity that define a dynamic physical network. Current methods for analyzing root biology balance physiological relevance with imaging capability. To bridge this divide, we developed an integrated-imaging system called Growth and Luminescence Observatory for Roots (GLO-Roots) that uses luminescence-based reporters to enable studies of root architecture and gene expression patterns in soil-grown, light-shielded roots. We have developed image analysis algorithms that allow the spatial integration of soil properties, gene expression, and root system architecture traits. We propose GLO-Roots as a system that has great utility in presenting environmental stimuli to roots in ways that evoke natural adaptive responses and in providing tools for studying the multi-dimensional nature of such processes.
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Affiliation(s)
- Rubén Rellán-Álvarez
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | | | - Heike Lindner
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Pierre-Luc Pradier
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Jose Sebastian
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Muh-Ching Yee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Yu Geng
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
- Department of Energy, Department of Energy Joint Genome Institute, Walnut Creek, United States
| | - Charlotte Trontin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Therese LaRue
- Department of Biology, Stanford University, Stanford, United States
| | | | - Cara H Haney
- Department of Genetics, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, United States
| | - Rita Nieu
- Western Regional Research Center, United States Department of Agriculture, Albany, United States
| | - Julin Maloof
- Department of Plant Biology, University of California, Davis, Davis, United States
| | - John P Vogel
- Department of Energy, Department of Energy Joint Genome Institute, Walnut Creek, United States
| | - José R Dinneny
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
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606
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Kole C, Muthamilarasan M, Henry R, Edwards D, Sharma R, Abberton M, Batley J, Bentley A, Blakeney M, Bryant J, Cai H, Cakir M, Cseke LJ, Cockram J, de Oliveira AC, De Pace C, Dempewolf H, Ellison S, Gepts P, Greenland A, Hall A, Hori K, Hughes S, Humphreys MW, Iorizzo M, Ismail AM, Marshall A, Mayes S, Nguyen HT, Ogbonnaya FC, Ortiz R, Paterson AH, Simon PW, Tohme J, Tuberosa R, Valliyodan B, Varshney RK, Wullschleger SD, Yano M, Prasad M. Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects. FRONTIERS IN PLANT SCIENCE 2015; 6:563. [PMID: 26322050 PMCID: PMC4531421 DOI: 10.3389/fpls.2015.00563] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/08/2015] [Indexed: 05/19/2023]
Abstract
Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.
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Affiliation(s)
| | - Mehanathan Muthamilarasan
- Department of Plant Molecular Genetics and Genomics, National Institute of Plant Genome ResearchNew Delhi, India
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of QueenslandSt Lucia, QLD, Australia
| | - David Edwards
- School of Agriculture and Food Sciences, University of QueenslandBrisbane, QLD, Australia
| | - Rishu Sharma
- Department of Plant Pathology, Faculty of Agriculture, Bidhan Chandra Krishi ViswavidyalayaMohanpur, India
| | - Michael Abberton
- Genetic Resources Centre, International Institute of Tropical AgricultureIbadan, Nigeria
| | - Jacqueline Batley
- Centre for Integrated Legume Research, University of QueenslandBrisbane, QLD, Australia
| | - Alison Bentley
- The John Bingham Laboratory, National Institute of Agricultural BotanyCambridge, UK
| | | | - John Bryant
- CLES, Hatherly Laboratories, University of ExeterExeter, UK
| | - Hongwei Cai
- Forage Crop Research Institute, Japan Grassland Agriculture and Forage Seed AssociationNasushiobara, Japan
- Department of Plant Genetics and Breeding, College of Agronomy and Biotechnology, China Agricultural UniversityBeijing, China
| | - Mehmet Cakir
- Faculty of Science and Engineering, School of Biological Sciences and Biotechnology, Murdoch UniversityMurdoch, WA, Australia
| | - Leland J. Cseke
- Department of Biological Sciences, The University of Alabama in HuntsvilleHuntsville, AL, USA
| | - James Cockram
- The John Bingham Laboratory, National Institute of Agricultural BotanyCambridge, UK
| | | | - Ciro De Pace
- Department of Agriculture, Forests, Nature and Energy, University of TusciaViterbo, Italy
| | - Hannes Dempewolf
- Global Crop Diversity Trust, Platz der Vereinten NationenBonn, Germany
| | - Shelby Ellison
- Department of Horticulture, University of WisconsinMadison, WI, USA
| | - Paul Gepts
- Section of Crop and Ecosystem Sciences, Department of Plant Sciences, University of California, DavisDavis, CA, USA
| | - Andy Greenland
- The John Bingham Laboratory, National Institute of Agricultural BotanyCambridge, UK
| | - Anthony Hall
- Department of Botany and Plant Sciences, University of CaliforniaRiverside, Riverside, USA
| | - Kiyosumi Hori
- Agrogenomics Research Center, National Institute of Agrobiological SciencesTsukuba, Japan
| | | | - Mike W. Humphreys
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityWales, UK
| | - Massimo Iorizzo
- Department of Horticulture, University of WisconsinMadison, WI, USA
| | | | - Athole Marshall
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityWales, UK
| | - Sean Mayes
- Biotechnology and Crop Genetics, Crops for the FutureSemenyih, Malaysia
| | - Henry T. Nguyen
- National Center for Soybean Biotechnology and Division of Plant Science, University of MissouriColumbia, MO, USA
| | | | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural SciencesSundvagen, Sweden
| | | | - Philipp W. Simon
- Department of Horticulture, USDA-ARS, University of WisconsinMadison, WI, USA
| | - Joe Tohme
- Agrobiodiversity and Biotechnology Project, Centro International de Agricultura TropicalCali, Columbia
| | | | - Babu Valliyodan
- National Center for Soybean Biotechnology and Division of Plant Science, University of MissouriColumbia, MO, USA
| | - Rajeev K. Varshney
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Stan D. Wullschleger
- Oak Ridge National Laboratory, Environmental Sciences Division, Climate Change Science InstituteOak Ridge, TN, USA
| | - Masahiro Yano
- National Agriculture and Food Research Organization, Institute of Crop ScienceTsukuba, Japan
| | - Manoj Prasad
- Department of Plant Molecular Genetics and Genomics, National Institute of Plant Genome ResearchNew Delhi, India
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607
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Affiliation(s)
- Anthony Bishopp
- Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Jonathan P Lynch
- Department of Plant Science, Penn State University, University Park, Pennsylvania 16802, USA
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608
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Lou Q, Chen L, Mei H, Wei H, Feng F, Wang P, Xia H, Li T, Luo L. Quantitative trait locus mapping of deep rooting by linkage and association analysis in rice. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:4749-57. [PMID: 26022253 PMCID: PMC4507776 DOI: 10.1093/jxb/erv246] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Deep rooting is a very important trait for plants' drought avoidance, and it is usually represented by the ratio of deep rooting (RDR). Three sets of rice populations were used to determine the genetic base for RDR. A linkage mapping population with 180 recombinant inbred lines and an association mapping population containing 237 rice varieties were used to identify genes linked to RDR. Six quantitative trait loci (QTLs) of RDR were identified as being located on chromosomes 1, 2, 4, 7, and 10. Using 1 019 883 single-nucleotide polymorphisms (SNPs), a genome-wide association study of the RDR was performed. Forty-eight significant SNPs of the RDR were identified and formed a clear peak on the short arm of chromosome 1 in a Manhattan plot. Compared with the shallow-rooting group and the whole collection, the deep-rooting group had selective sweep regions on chromosomes 1 and 2, especially in the major QTL region on chromosome 2. Seven of the nine candidate SNPs identified by association mapping were verified in two RDR extreme groups. The findings from this study will be beneficial to rice drought-resistance research and breeding.
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Affiliation(s)
- Qiaojun Lou
- Shanghai Agrobiological Gene Center, No. 2901, Beidi Road, Minhang District, Shanghai 201106, PR China Fudan University, No. 220, Handan Road, Yangpu District, Shanghai 200433, PR China
| | - Liang Chen
- Shanghai Agrobiological Gene Center, No. 2901, Beidi Road, Minhang District, Shanghai 201106, PR China
| | - Hanwei Mei
- Shanghai Agrobiological Gene Center, No. 2901, Beidi Road, Minhang District, Shanghai 201106, PR China
| | - Haibin Wei
- Shanghai Agrobiological Gene Center, No. 2901, Beidi Road, Minhang District, Shanghai 201106, PR China
| | - Fangjun Feng
- Shanghai Agrobiological Gene Center, No. 2901, Beidi Road, Minhang District, Shanghai 201106, PR China
| | - Pei Wang
- Shanghai Agrobiological Gene Center, No. 2901, Beidi Road, Minhang District, Shanghai 201106, PR China
| | - Hui Xia
- Shanghai Agrobiological Gene Center, No. 2901, Beidi Road, Minhang District, Shanghai 201106, PR China
| | - Tiemei Li
- Shanghai Agrobiological Gene Center, No. 2901, Beidi Road, Minhang District, Shanghai 201106, PR China
| | - Lijun Luo
- Shanghai Agrobiological Gene Center, No. 2901, Beidi Road, Minhang District, Shanghai 201106, PR China
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609
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Schatz MC, Maron LG, Stein JC, Hernandez Wences A, Gurtowski J, Biggers E, Lee H, Kramer M, Antoniou E, Ghiban E, Wright MH, Chia JM, Ware D, McCouch SR, McCombie WR. Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol 2015; 15:506. [PMID: 25468217 DOI: 10.1186/preaccept-2784872521277375] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The use of high throughput genome-sequencing technologies has uncovered a large extent of structural variation in eukaryotic genomes that makes important contributions to genomic diversity and phenotypic variation. When the genomes of different strains of a given organism are compared, whole genome resequencing data are typically aligned to an established reference sequence. However, when the reference differs in significant structural ways from the individuals under study, the analysis is often incomplete or inaccurate. RESULTS Here, we use rice as a model to demonstrate how improvements in sequencing and assembly technology allow rapid and inexpensive de novo assembly of next generation sequence data into high-quality assemblies that can be directly compared using whole genome alignment to provide an unbiased assessment. Using this approach, we are able to accurately assess the "pan-genome" of three divergent rice varieties and document several megabases of each genome absent in the other two. CONCLUSIONS Many of the genome-specific loci are annotated to contain genes, reflecting the potential for new biological properties that would be missed by standard reference-mapping approaches. We further provide a detailed analysis of several loci associated with agriculturally important traits, including the S5 hybrid sterility locus, the Sub1 submergence tolerance locus, the LRK gene cluster associated with improved yield, and the Pup1 cluster associated with phosphorus deficiency, illustrating the utility of our approach for biological discovery. All of the data and software are openly available to support further breeding and functional studies of rice and other species.
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610
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De novo Transcriptome Assembly of Common Wild Rice (Oryza rufipogon Griff.) and Discovery of Drought-Response Genes in Root Tissue Based on Transcriptomic Data. PLoS One 2015; 10:e0131455. [PMID: 26134138 PMCID: PMC4489613 DOI: 10.1371/journal.pone.0131455] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 06/02/2015] [Indexed: 11/28/2022] Open
Abstract
Background The perennial O. rufipogon (common wild rice), which is considered to be the ancestor of Asian cultivated rice species, contains many useful genetic resources, including drought resistance genes. However, few studies have identified the drought resistance and tissue-specific genes in common wild rice. Results In this study, transcriptome sequencing libraries were constructed, including drought-treated roots (DR) and control leaves (CL) and roots (CR). Using Illumina sequencing technology, we generated 16.75 million bases of high-quality sequence data for common wild rice and conducted de novo assembly and annotation of genes without prior genome information. These reads were assembled into 119,332 unigenes with an average length of 715 bp. A total of 88,813 distinct sequences (74.42% of unigenes) significantly matched known genes in the NCBI NT database. Differentially expressed gene (DEG) analysis showed that 3617 genes were up-regulated and 4171 genes were down-regulated in the CR library compared with the CL library. Among the DEGs, 535 genes were expressed in roots but not in shoots. A similar comparison between the DR and CR libraries showed that 1393 genes were up-regulated and 315 genes were down-regulated in the DR library compared with the CR library. Finally, 37 genes that were specifically expressed in roots were screened after comparing the DEGs identified in the above-described analyses. Conclusion This study provides a transcriptome sequence resource for common wild rice plants and establishes a digital gene expression profile of wild rice plants under drought conditions using the assembled transcriptome data as a reference. Several tissue-specific and drought-stress-related candidate genes were identified, representing a fully characterized transcriptome and providing a valuable resource for genetic and genomic studies in plants.
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611
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Paez-Garcia A, Motes CM, Scheible WR, Chen R, Blancaflor EB, Monteros MJ. Root Traits and Phenotyping Strategies for Plant Improvement. PLANTS (BASEL, SWITZERLAND) 2015; 4:334-55. [PMID: 27135332 PMCID: PMC4844329 DOI: 10.3390/plants4020334] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 06/01/2015] [Accepted: 06/08/2015] [Indexed: 01/01/2023]
Abstract
Roots are crucial for nutrient and water acquisition and can be targeted to enhance plant productivity under a broad range of growing conditions. A current challenge for plant breeding is the limited ability to phenotype and select for desirable root characteristics due to their underground location. Plant breeding efforts aimed at modifying root traits can result in novel, more stress-tolerant crops and increased yield by enhancing the capacity of the plant for soil exploration and, thus, water and nutrient acquisition. Available approaches for root phenotyping in laboratory, greenhouse and field encompass simple agar plates to labor-intensive root digging (i.e., shovelomics) and soil boring methods, the construction of underground root observation stations and sophisticated computer-assisted root imaging. Here, we summarize root architectural traits relevant to crop productivity, survey root phenotyping strategies and describe their advantages, limitations and practical value for crop and forage breeding programs.
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Affiliation(s)
- Ana Paez-Garcia
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA.
| | - Christy M Motes
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA.
| | - Wolf-Rüdiger Scheible
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA.
| | - Rujin Chen
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA.
| | - Elison B Blancaflor
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA.
| | - Maria J Monteros
- The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA.
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612
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Li J, Han Y, Liu L, Chen Y, Du Y, Zhang J, Sun H, Zhao Q. qRT9, a quantitative trait locus controlling root thickness and root length in upland rice. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2723-32. [PMID: 25769309 DOI: 10.1093/jxb/erv076] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Breeding for strong root systems is an important strategy for improving drought avoidance in rice. To clone genes responsible for strong root traits, an upland rice introgression line IL392 with thicker and longer roots than the background parent lowland rice Yuefu was selected. A quantitative trait locus (QTL), qRT9, controlling root thickness and root length was detected under hydroponic culture using 203 F(2:3) populations derived from a cross between Yuefu and IL392. The qRT9 locus explained 32.5% and 28.1% of the variance for root thickness and root length, respectively. Using 3185 F2 plants, qRT9 was ultimately narrowed down to an 11.5 kb region by substitution mapping. One putative basic helix-loop-helix (bHLH) transcription factor gene, LOC_Os09g28210 (named OsbHLH120), is annotated in this region. Sequences of OsbHLH120 in 11 upland rice and 13 lowland rice indicated that a single nucleotide polymorphism (SNP) at position 82 and an insertion/deletion (Indel) at position 628-642 cause amino acid changes and are conserved between upland rice and lowland rice. Phenotypic analysis indicated that the two polymorphisms were significantly associated with root thickness and root length under hydroponic culture. Quantitative real-time PCR showed that OsbHLH120 was strongly induced by polyethylene glycol (PEG), salt, and abscisic acid, but higher expression was present in IL392 roots than in Yuefu under PEG and salt stress. The successfully isolated locus, qRT9, enriches our knowledge of the genetic basis for drought avoidance and provides an opportunity for breeding drought avoidance varieties by utilizing valuable genes in the upland rice germplasm.
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Affiliation(s)
- Junzhou Li
- Collaborative Innovation Center of Henan Grain Crops, Rice Engineer Center in Henan Province, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yingchun Han
- Collaborative Innovation Center of Henan Grain Crops, Rice Engineer Center in Henan Province, Henan Agricultural University, Zhengzhou, 450002, China
| | - Lei Liu
- Collaborative Innovation Center of Henan Grain Crops, Rice Engineer Center in Henan Province, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yipeng Chen
- Collaborative Innovation Center of Henan Grain Crops, Rice Engineer Center in Henan Province, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yanxiu Du
- Collaborative Innovation Center of Henan Grain Crops, Rice Engineer Center in Henan Province, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jing Zhang
- Collaborative Innovation Center of Henan Grain Crops, Rice Engineer Center in Henan Province, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hongzheng Sun
- Collaborative Innovation Center of Henan Grain Crops, Rice Engineer Center in Henan Province, Henan Agricultural University, Zhengzhou, 450002, China
| | - Quanzhi Zhao
- Collaborative Innovation Center of Henan Grain Crops, Rice Engineer Center in Henan Province, Henan Agricultural University, Zhengzhou, 450002, China
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613
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Kadam NN, Yin X, Bindraban PS, Struik PC, Jagadish KSV. Does morphological and anatomical plasticity during the vegetative stage make wheat more tolerant of water deficit stress than rice? PLANT PHYSIOLOGY 2015; 167:1389-401. [PMID: 25614066 PMCID: PMC4378155 DOI: 10.1104/pp.114.253328] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 01/16/2015] [Indexed: 05/18/2023]
Abstract
Water scarcity and the increasing severity of water deficit stress are major challenges to sustaining irrigated rice (Oryza sativa) production. Despite the technologies developed to reduce the water requirement, rice growth is seriously constrained under water deficit stress compared with other dryland cereals such as wheat (Triticum aestivum). We exposed rice cultivars with contrasting responses to water deficit stress and wheat cultivars well adapted to water-limited conditions to the same moisture stress during vegetative growth to unravel the whole-plant (shoot and root morphology) and organ/tissue (root anatomy) responses. Wheat cultivars followed a water-conserving strategy by reducing specific leaf area and developing thicker roots and moderate tillering. In contrast, rice 'IR64' and 'Apo' adopted a rapid water acquisition strategy through thinner roots under water deficit stress. Root diameter, stele and xylem diameter, and xylem number were more responsive and varied with different positions along the nodal root under water deficit stress in wheat, whereas they were relatively conserved in rice cultivars. Increased metaxylem diameter and lower metaxylem number near the root tips and exactly the opposite phenomena at the root-shoot junction facilitated the efficient use of available soil moisture in wheat. Tolerant rice 'Nagina 22' had an advantage in root morphological and anatomical attributes over cultivars IR64 and Apo but lacked plasticity, unlike wheat cultivars exposed to water deficit stress. The key traits determining the adaptation of wheat to dryland conditions have been summarized and discussed.
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Affiliation(s)
- Niteen N Kadam
- International Rice Research Institute, Los Baños, Laguna, Philippines (N.N.K., K.S.V.J.);Centre for Crop Systems Analysis, Wageningen University and Research Centre, 6700 AK Wageningen, The Netherlands (N.N.K., X.Y., P.C.S.); andVirtual Fertilizer Research Center, Washington, District of Columbia 20005 (P.S.B.)
| | - Xinyou Yin
- International Rice Research Institute, Los Baños, Laguna, Philippines (N.N.K., K.S.V.J.);Centre for Crop Systems Analysis, Wageningen University and Research Centre, 6700 AK Wageningen, The Netherlands (N.N.K., X.Y., P.C.S.); andVirtual Fertilizer Research Center, Washington, District of Columbia 20005 (P.S.B.)
| | - Prem S Bindraban
- International Rice Research Institute, Los Baños, Laguna, Philippines (N.N.K., K.S.V.J.);Centre for Crop Systems Analysis, Wageningen University and Research Centre, 6700 AK Wageningen, The Netherlands (N.N.K., X.Y., P.C.S.); andVirtual Fertilizer Research Center, Washington, District of Columbia 20005 (P.S.B.)
| | - Paul C Struik
- International Rice Research Institute, Los Baños, Laguna, Philippines (N.N.K., K.S.V.J.);Centre for Crop Systems Analysis, Wageningen University and Research Centre, 6700 AK Wageningen, The Netherlands (N.N.K., X.Y., P.C.S.); andVirtual Fertilizer Research Center, Washington, District of Columbia 20005 (P.S.B.)
| | - Krishna S V Jagadish
- International Rice Research Institute, Los Baños, Laguna, Philippines (N.N.K., K.S.V.J.);Centre for Crop Systems Analysis, Wageningen University and Research Centre, 6700 AK Wageningen, The Netherlands (N.N.K., X.Y., P.C.S.); andVirtual Fertilizer Research Center, Washington, District of Columbia 20005 (P.S.B.)
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614
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He Y, Wu J, Lv B, Li J, Gao Z, Xu W, Baluška F, Shi W, Shaw PC, Zhang J. Involvement of 14-3-3 protein GRF9 in root growth and response under polyethylene glycol-induced water stress. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2271-81. [PMID: 25873671 PMCID: PMC4986726 DOI: 10.1093/jxb/erv149] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 03/09/2015] [Accepted: 03/10/2015] [Indexed: 05/19/2023]
Abstract
Plant 14-3-3 proteins are phosphoserine-binding proteins that regulate a wide array of targets via direct protein-protein interactions. In this study, the role of a 14-3-3 protein, GRF9, in plant response to water stress was investigated. Arabidopsis wild-type, GRF9-deficient mutant (grf9), and GRF9-overexpressing (OE) plants were treated with polyethylene glycol (PEG) to induce mild water stress. OE plant showed better whole-plant growth and root growth than the wild type under normal or water stress conditions while the grf9 mutant showed worse growth. In OE plants, GRF9 favours the allocation of shoot carbon to roots. In addition, GRF9 enhanced proton extrusion, mainly in the root elongation zone and root hair zone, and maintained root growth under mild water stress. Grafting among the wild type, OE, and grf9 plants showed that when OE plants were used as the scion and GRF9 was overexpressed in the shoot, it enhanced sucrose transport into the root, and when OE plants were used as rootstock and GRF9 was overexpressed in the root, it caused more release of protons into the root surface under water stress. Taken together, the results suggest that under PEG-induced water stress, GRF9 is involved in allocating more carbon from the shoot to the root and enhancing proton secretion in the root growing zone, and this process is important for root response to mild water stress.
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Affiliation(s)
- Yuchi He
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China School of Life Sciences and State Key Laboratory of Agrobiotechnology, the Chinese University of Hong Kong, Hong Kong Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei University, Wuhan 430062, China
| | - Jingjing Wu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Bing Lv
- Yangzhou University, Yangzhou 225009, China
| | - Jia Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China Yangzhou University, Yangzhou 225009, China
| | - Zhiping Gao
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, the Chinese University of Hong Kong, Hong Kong College of Life Sciences, Nanjing Normal University, Wenyuan Road, Nanjing, China
| | - Weifeng Xu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China School of Life Sciences and State Key Laboratory of Agrobiotechnology, the Chinese University of Hong Kong, Hong Kong
| | - František Baluška
- Institute of Cellular and Molecular Botany, Universtiy of Bonn, Germany
| | - Weiming Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Pang Chui Shaw
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, the Chinese University of Hong Kong, Hong Kong
| | - Jianhua Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, the Chinese University of Hong Kong, Hong Kong
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615
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Lynch JP, Wojciechowski T. Opportunities and challenges in the subsoil: pathways to deeper rooted crops. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2199-210. [PMID: 25582451 PMCID: PMC4986715 DOI: 10.1093/jxb/eru508] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 11/04/2014] [Accepted: 11/28/2014] [Indexed: 05/18/2023]
Abstract
Greater exploitation of subsoil resources by annual crops would afford multiple benefits, including greater water and N acquisition in most agroecosystems, and greater sequestration of atmospheric C. Constraints to root growth in the subsoil include soil acidity (an edaphic stress complex consisting of toxic levels of Al, inadequate levels of P and Ca, and often toxic levels of Mn), soil compaction, hypoxia, and suboptimal temperature. Multiple root phenes under genetic control are associated with adaptation to these constraints, opening up the possibility of breeding annual crops with root traits improving subsoil exploration. Adaptation to Al toxicity, hypoxia, and P deficiency are intensively researched, adaptation to soil hardness and suboptimal temperature less so, and adaptations to Ca deficiency and Mn toxicity are poorly understood. The utility of specific phene states may vary among soil taxa and management scenarios, interactions which in general are poorly understood. These traits and issues merit research because of their potential value in developing more productive, sustainable, benign, and resilient agricultural systems.
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Affiliation(s)
- Jonathan P Lynch
- Department of Plant Science, The Pennsylvania State University, University Park, PA 16802, USA IBG2, Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich D-52445, Germany
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616
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White CA, Sylvester-Bradley R, Berry PM. Root length densities of UK wheat and oilseed rape crops with implications for water capture and yield. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2293-303. [PMID: 25750427 PMCID: PMC4986724 DOI: 10.1093/jxb/erv077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 02/06/2015] [Accepted: 02/09/2015] [Indexed: 05/18/2023]
Abstract
Root length density (RLD) was measured to 1 m depth for 17 commercial crops of winter wheat (Triticum aestivum) and 40 crops of winter oilseed rape [Brassica napus; oilseed rape (OSR)] grown in the UK between 2004 and 2013. Taking the critical RLD (cRLD) for water capture as 1cm cm(-3), RLDs appeared inadequate for full water capture on average below a depth of 0.32 m for winter wheat and below 0.45 m for OSR. These depths compare unfavourably (for wheat) with average depths of 'full capture' of 0.86 m and 0.48 m, respectively, determined for three wheat crops and one OSR crop studied in the 1970s and 1980s, and treated as references here. A simple model of water uptake and yield indicated that these shortfalls in wheat and OSR rooting compared with the reference data might be associated with shortfalls of up to 3.5 t ha(-1) and 1.2 t ha(-1), respectively, in grain yields under water-limited conditions, as increasingly occur through climate change. Coupled with decreased summer rainfall, poor rooting of modern arable crops could explain much of the yield stagnation that has been observed on UK farms since the 1990s. Methods of monitoring and improving rooting under commercial conditions are reviewed and discussed.
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Affiliation(s)
- Charlotte A White
- ADAS UK Ltd, ADAS Gleadthorpe, Meden Vale, Mansfield, Nottingham NG20 9PD, UK
| | | | - Peter M Berry
- ADAS UK Ltd, ADAS High Mowthorpe, Duggleby, Malton, North Yorkshire YO17 8BP, UK
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617
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Hollender CA, Dardick C. Molecular basis of angiosperm tree architecture. THE NEW PHYTOLOGIST 2015; 206:541-56. [PMID: 25483362 DOI: 10.1111/nph.13204] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 10/30/2014] [Indexed: 05/24/2023]
Abstract
The architecture of trees greatly impacts the productivity of orchards and forestry plantations. Amassing greater knowledge on the molecular genetics that underlie tree form can benefit these industries, as well as contribute to basic knowledge of plant developmental biology. This review describes the fundamental components of branch architecture, a prominent aspect of tree structure, as well as genetic and hormonal influences inferred from studies in model plant systems and from trees with non-standard architectures. The bulk of the molecular and genetic data described here is from studies of fruit trees and poplar, as these species have been the primary subjects of investigation in this field of science.
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Affiliation(s)
- Courtney A Hollender
- Appalachian Fruit Research Station, Agricultural Research Service, United States Department of Agriculture, 2217 Wiltshire Rd, Kearnysville, WV, 25430, USA
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618
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Kitomi Y, Kanno N, Kawai S, Mizubayashi T, Fukuoka S, Uga Y. QTLs underlying natural variation of root growth angle among rice cultivars with the same functional allele of DEEPER ROOTING 1. RICE (NEW YORK, N.Y.) 2015; 8:16. [PMID: 25844121 PMCID: PMC4385264 DOI: 10.1186/s12284-015-0049-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 02/27/2015] [Indexed: 05/17/2023]
Abstract
BACKGROUND The functional allele of the rice gene DEEPER ROOTING 1 (DRO1) increases the root growth angle (RGA). However, wide natural variation in RGA is observed among rice cultivars with the functional DRO1 allele. To elucidate genetic factors related to such variation, we quantitatively measured RGA using the basket method and analyzed quantitative trait loci (QTLs) for RGA in three F2 mapping populations derived from crosses between the large RGA-type cultivar Kinandang Patong and each of three accessions with varying RGA: Momiroman has small RGA and was used to produce the MoK-F2 population; Yumeaoba has intermediate RGA (YuK-F2 population); Tachisugata has large RGA (TaK-F2 population). All four accessions belong to the same haplotype group of functional DRO1 allele. RESULTS We detected the following statistically significant QTLs: one QTL on chromosome 4 in MoK-F2, three QTLs on chromosomes 2, 4, and 6 in YuK-F2, and one QTL on chromosome 2 in TaK-F2. Among them, the two QTLs on chromosome 4 were located near DRO2, which has been previously reported as a major QTL for RGA, whereas the two major QTLs for RGA on chromosomes 2 (DRO4) and 6 (DRO5) were novel. With the LOD threshold reduced to 3.0, several minor QTLs for RGA were also detected in each population. CONCLUSION Natural variation in RGA in rice cultivars carrying functional DRO1 alleles may be controlled by a few major QTLs and by several additional minor QTLs.
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Affiliation(s)
- Yuka Kitomi
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Noriko Kanno
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Sawako Kawai
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Tatsumi Mizubayashi
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Shuichi Fukuoka
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Yusaku Uga
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
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619
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Mickelbart MV, Hasegawa PM, Bailey-Serres J. Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability. Nat Rev Genet 2015; 16:237-51. [PMID: 25752530 DOI: 10.1038/nrg3901] [Citation(s) in RCA: 405] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Crop yield reduction as a consequence of increasingly severe climatic events threatens global food security. Genetic loci that ensure productivity in challenging environments exist within the germplasm of crops, their wild relatives and species that are adapted to extreme environments. Selective breeding for the combination of beneficial loci in germplasm has improved yields in diverse environments throughout the history of agriculture. An effective new paradigm is the targeted identification of specific genetic determinants of stress adaptation that have evolved in nature and their precise introgression into elite varieties. These loci are often associated with distinct regulation or function, duplication and/or neofunctionalization of genes that maintain plant homeostasis.
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Affiliation(s)
- Michael V Mickelbart
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Paul M Hasegawa
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907, USA
| | - Julia Bailey-Serres
- 1] Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, California 92521, USA. [2] Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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620
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Uga Y, Kitomi Y, Ishikawa S, Yano M. Genetic improvement for root growth angle to enhance crop production. BREEDING SCIENCE 2015; 65:111-9. [PMID: 26069440 PMCID: PMC4430504 DOI: 10.1270/jsbbs.65.111] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 11/09/2014] [Indexed: 05/06/2023]
Abstract
The root system is an essential organ for taking up water and nutrients and anchoring shoots to the ground. On the other hand, the root system has rarely been regarded as breeding target, possibly because it is more laborious and time-consuming to evaluate roots (which require excavation) in a large number of plants than aboveground tissues. The root growth angle (RGA), which determines the direction of root elongation in the soil, affects the area in which roots capture water and nutrients. In this review, we describe the significance of RGA as a potential trait to improve crop production, and the physiological and molecular mechanisms that regulate RGA. We discuss the prospects for breeding to improve RGA based on current knowledge of quantitative trait loci for RGA in rice.
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Affiliation(s)
- Yusaku Uga
- National Institute of Agrobiological Sciences (NIAS),
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Yuka Kitomi
- National Institute of Agrobiological Sciences (NIAS),
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Satoru Ishikawa
- National Institute of Agro-Environmental Sciences (NIAES),
Tsukuba, Ibaraki 305-8604,
Japan
| | - Masahiro Yano
- National Institute of Agrobiological Sciences (NIAS),
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
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621
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Richard CAI, Hickey LT, Fletcher S, Jennings R, Chenu K, Christopher JT. High-throughput phenotyping of seminal root traits in wheat. PLANT METHODS 2015; 11:13. [PMID: 25750658 PMCID: PMC4351910 DOI: 10.1186/s13007-015-0055-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/12/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Water availability is a major limiting factor for wheat (Triticum aestivum L.) production in rain-fed agricultural systems worldwide. Root system architecture has important functional implications for the timing and extent of soil water extraction, yet selection for root architectural traits in breeding programs has been limited by a lack of suitable phenotyping methods. The aim of this research was to develop low-cost high-throughput phenotyping methods to facilitate selection for desirable root architectural traits. Here, we report two methods, one using clear pots and the other using growth pouches, to assess the angle and the number of seminal roots in wheat seedlings- two proxy traits associated with the root architecture of mature wheat plants. RESULTS Both methods revealed genetic variation for seminal root angle and number in the panel of 24 wheat cultivars. The clear pot method provided higher heritability and higher genetic correlations across experiments compared to the growth pouch method. In addition, the clear pot method was more efficient - requiring less time, space, and labour compared to the growth pouch method. Therefore the clear pot method was considered the most suitable for large-scale and high-throughput screening of seedling root characteristics in crop improvement programs. CONCLUSIONS The clear-pot method could be easily integrated in breeding programs targeting drought tolerance to rapidly enrich breeding populations with desirable alleles. For instance, selection for narrow root angle and high number of seminal roots could lead to deeper root systems with higher branching at depth. Such root characteristics are highly desirable in wheat to cope with anticipated future climate conditions, particularly where crops rely heavily on stored soil moisture at depth, including some Australian, Indian, South American, and African cropping regions.
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Affiliation(s)
| | - Lee T Hickey
- />The University of Queensland, QAAFI, St Lucia, QLD 4072 Australia
| | - Susan Fletcher
- />Department of Agriculture, Fisheries and Forestry, Leslie Research Facility, Toowoomba, QLD 4350 Australia
| | - Raeleen Jennings
- />Department of Agriculture, Fisheries and Forestry, Leslie Research Facility, Toowoomba, QLD 4350 Australia
| | - Karine Chenu
- />The University of Queensland, QAAFI, 203 Tor Street, Toowoomba, QLD 4350 Australia
| | - Jack T Christopher
- />The University of Queensland, QAAFI, Leslie Research Facility, Toowoomba, QLD 4350 Australia
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622
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Guerra D, Crosatti C, Khoshro HH, Mastrangelo AM, Mica E, Mazzucotelli E. Post-transcriptional and post-translational regulations of drought and heat response in plants: a spider's web of mechanisms. FRONTIERS IN PLANT SCIENCE 2015; 6:57. [PMID: 25717333 PMCID: PMC4324062 DOI: 10.3389/fpls.2015.00057] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/22/2015] [Indexed: 05/14/2023]
Abstract
Drought and heat tolerance are complex quantitative traits. Moreover, the adaptive significance of some stress-related traits is more related to plant survival than to agronomic performance. A web of regulatory mechanisms fine-tunes the expression of stress-related traits and integrates both environmental and developmental signals. Both post-transcriptional and post-translational modifications contribute substantially to this network with a pivotal regulatory function of the transcriptional changes related to cellular and plant stress response. Alternative splicing and RNA-mediated silencing control the amount of specific transcripts, while ubiquitin and SUMO modify activity, sub-cellular localization and half-life of proteins. Interactions across these modification mechanisms ensure temporally and spatially appropriate patterns of downstream-gene expression. For key molecular components of these regulatory mechanisms, natural genetic diversity exists among genotypes with different behavior in terms of stress tolerance, with effects upon the expression of adaptive morphological and/or physiological target traits.
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Affiliation(s)
- Davide Guerra
- Genomics Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Fiorenzuola d’Arda, Piacenza, Italy
| | - Cristina Crosatti
- Genomics Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Fiorenzuola d’Arda, Piacenza, Italy
| | - Hamid H. Khoshro
- Department of Agronomy and Plant Breeding, Ilam University, Ilam, Iran
| | - Anna M. Mastrangelo
- Cereal Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Foggia, Italy
| | - Erica Mica
- Genomics Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Fiorenzuola d’Arda, Piacenza, Italy
| | - Elisabetta Mazzucotelli
- Genomics Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Fiorenzuola d’Arda, Piacenza, Italy
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623
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Malekpoor Mansoorkhani F, Seymour G, Swarup R, Moeiniyan Bagheri H, Ramsey R, Thompson A. Environmental, developmental, and genetic factors controlling root system architecture. Biotechnol Genet Eng Rev 2015; 30:95-112. [DOI: 10.1080/02648725.2014.995912] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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624
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Uga Y, Kitomi Y, Yamamoto E, Kanno N, Kawai S, Mizubayashi T, Fukuoka S. A QTL for root growth angle on rice chromosome 7 is involved in the genetic pathway of DEEPER ROOTING 1. RICE (NEW YORK, N.Y.) 2015; 8:8. [PMID: 25844113 PMCID: PMC4384719 DOI: 10.1186/s12284-015-0044-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 01/20/2015] [Indexed: 05/19/2023]
Abstract
BACKGROUND Root growth angle (RGA) is an important trait that influences the ability of rice to avoid drought stress. DEEPER ROOTING 1 (DRO1), which is a major quantitative trait locus (QTL) for RGA, is responsible for the difference in RGA between the shallow-rooting cultivar IR64 and the deep-rooting cultivar Kinandang Patong. However, the RGA differences between these cultivars cannot be fully explained by DRO1. The objective of this study was to identify new QTLs for RGA explaining the difference in RGA between these cultivars. RESULTS By crossing IR64 (which has a non-functional allele of DRO1) with Kinandang Patong (which has a functional allele of DRO1), we developed 26 chromosome segment substitution lines (CSSLs) that carried a particular chromosome segment from Kinandang Patong in the IR64 genetic background. Using these CSSLs, we found only one chromosomal region that was related to RGA: on chromosome 9, which includes DRO1. Using an F2 population derived from a cross between Kinandang Patong and the Dro1-NIL (near isogenic line), which had a functional DRO1 allele in the IR64 genetic background, we identified a new QTL for RGA (DRO3) on the long arm of chromosome 7. CONCLUSIONS DRO3 may only affect RGA in plants with a functional DRO1 allele, suggesting that DRO3 is involved in the DRO1 genetic pathway.
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Affiliation(s)
- Yusaku Uga
- />National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Yuka Kitomi
- />National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Eiji Yamamoto
- />National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
- />(Present address) NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie 514-2392 Japan
| | - Noriko Kanno
- />National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Sawako Kawai
- />National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Tatsumi Mizubayashi
- />National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
| | - Shuichi Fukuoka
- />National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602 Japan
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625
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Roychoudhry S, Kepinski S. Shoot and root branch growth angle control-the wonderfulness of lateralness. CURRENT OPINION IN PLANT BIOLOGY 2015; 23:124-31. [PMID: 25597285 DOI: 10.1016/j.pbi.2014.12.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 12/16/2014] [Accepted: 12/19/2014] [Indexed: 05/23/2023]
Abstract
The overall shape of plants, the space they occupy above and below ground, is determined principally by the number, length, and angle of their lateral branches. The function of these shoot and root branches is to hold leaves and other organs to the sun, and below ground, to provide anchorage and facilitate the uptake of water and nutrients. While in some respects lateral roots and shoots can be considered mere iterations of the primary root-shoot axis, in others there are fundamental differences in their biology, perhaps most conspicuously in the regulation their angle of growth. Here we discuss recent advances in the understanding of the control of branch growth angle, one of the most important but least understood components of the wonderful diversity of plant form observed throughout nature.
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Affiliation(s)
| | - Stefan Kepinski
- Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, UK.
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626
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Chen YS, Lo SF, Sun PK, Lu CA, Ho THD, Yu SM. A late embryogenesis abundant protein HVA1 regulated by an inducible promoter enhances root growth and abiotic stress tolerance in rice without yield penalty. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:105-16. [PMID: 25200982 DOI: 10.1111/pbi.12241] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 07/06/2014] [Accepted: 07/07/2014] [Indexed: 05/20/2023]
Abstract
Regulation of root architecture is essential for maintaining plant growth under adverse environment. A synthetic abscisic acid (ABA)/stress-inducible promoter was designed to control the expression of a late embryogenesis abundant protein (HVA1) in transgenic rice. The background of HVA1 is low but highly inducible by ABA, salt, dehydration and cold. HVA1 was highly accumulated in root apical meristem (RAM) and lateral root primordia (LRP) after ABA/stress treatments, leading to enhanced root system expansion. Water-use efficiency (WUE) and biomass also increased in transgenic rice, likely due to the maintenance of normal cell functions and metabolic activities conferred by HVA1 which is capable of stabilizing proteins, under osmotic stress. HVA1 promotes lateral root (LR) initiation, elongation and emergence and primary root (PR) elongation via an auxin-dependent process, particularly by intensifying asymmetrical accumulation of auxin in LRP founder cells and RAM, even under ABA/stress-suppressive conditions. We demonstrate a successful application of an inducible promoter in regulating the spatial and temporal expression of HVA1 for improving root architecture and multiple stress tolerance without yield penalty.
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Affiliation(s)
- Yi-Shih Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan; Department of Life Sciences, National Central University, Jhongli City, Taiwan
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627
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Todaka D, Shinozaki K, Yamaguchi-Shinozaki K. Recent advances in the dissection of drought-stress regulatory networks and strategies for development of drought-tolerant transgenic rice plants. FRONTIERS IN PLANT SCIENCE 2015; 6:84. [PMID: 25741357 PMCID: PMC4332304 DOI: 10.3389/fpls.2015.00084] [Citation(s) in RCA: 194] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 02/02/2015] [Indexed: 05/17/2023]
Abstract
Advances have been made in the development of drought-tolerant transgenic plants, including cereals. Rice, one of the most important cereals, is considered to be a critical target for improving drought tolerance, as present-day rice cultivation requires large quantities of water and as drought-tolerant rice plants should be able to grow in small amounts of water. Numerous transgenic rice plants showing enhanced drought tolerance have been developed to date. Such genetically engineered plants have generally been developed using genes encoding proteins that control drought regulatory networks. These proteins include transcription factors, protein kinases, receptor-like kinases, enzymes related to osmoprotectant or plant hormone synthesis, and other regulatory or functional proteins. Of the drought-tolerant transgenic rice plants described in this review, approximately one-third show decreased plant height under non-stressed conditions or in response to abscisic acid treatment. In cereal crops, plant height is a very important agronomic trait directly affecting yield, although the improvement of lodging resistance should also be taken into consideration. Understanding the regulatory mechanisms of plant growth reduction under drought stress conditions holds promise for developing transgenic plants that produce high yields under drought stress conditions. Plant growth rates are reduced more rapidly than photosynthetic activity under drought conditions, implying that plants actively reduce growth in response to drought stress. In this review, we summarize studies on molecular regulatory networks involved in response to drought stress. In a separate section, we highlight progress in the development of transgenic drought-tolerant rice plants, with special attention paid to field trial investigations.
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Affiliation(s)
- Daisuke Todaka
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, TokyoJapan
| | - Kazuo Shinozaki
- RIKEN Center for Sustainable Resource Science, YokohamaJapan
| | - Kazuko Yamaguchi-Shinozaki
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, TokyoJapan
- *Correspondence: Kazuko Yamaguchi-Shinozaki, Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan e-mail:
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628
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Fletcher RS, Mullen JL, Heiliger A, McKay JK. QTL analysis of root morphology, flowering time, and yield reveals trade-offs in response to drought in Brassica napus. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:245-56. [PMID: 25371500 PMCID: PMC4265167 DOI: 10.1093/jxb/eru423] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 08/16/2014] [Accepted: 09/15/2014] [Indexed: 05/18/2023]
Abstract
Drought escape and dehydration avoidance represent alternative strategies for drought adaptation in annual crops. The mechanisms underlying these two strategies are reported to have a negative correlation, suggesting a trade-off. We conducted a quantitative trait locus (QTL) analysis of flowering time and root mass, traits representing each strategy, in Brassica napus to understand if a trade-off exists and what the genetic basis might be. Our field experiment used a genotyped population of doubled haploid lines and included both irrigated and rainfed treatments, allowing analysis of plasticity in each trait. We found strong genetic correlations among all traits, suggesting a trade-off among traits may exist. Summing across traits and treatments we found 20 QTLs, but many of these co-localized to two major QTLs, providing evidence that the trade-off is genetically constrained. To understand the mechanistic relationship between root mass, flowering time, and QTLs, we analysed the data by conditioning upon correlated traits. Our results suggest a causal model where such QTLs affect root mass directly as well as through their impacts on flowering time. Additionally, we used draft Brassica genomes to identify orthologues of well characterized Arabidopsis thaliana flowering time genes as candidate genes. This research provides valuable clues to breeding for drought adaptation as it is the first to analyse the inheritance of the root system in B. napus in relation to drought.
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Affiliation(s)
- Richard S Fletcher
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA Cargill Specialty Seeds and Oils, Fort Collins, CO 80525, USA
| | - Jack L Mullen
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
| | - Annie Heiliger
- Cargill Specialty Seeds and Oils, Fort Collins, CO 80525, USA Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - John K McKay
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA Plant Genomics LLC, Fort Collins, CO 80524, USA
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629
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Schatz MC, Maron LG, Stein JC, Wences AH, Gurtowski J, Biggers E, Lee H, Kramer M, Antoniou E, Ghiban E, Wright MH, Chia JM, Ware D, McCouch SR, McCombie WR. Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica. Genome Biol 2014. [PMID: 25468217 PMCID: PMC4268812 DOI: 10.1186/s13059-014-0506-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background The use of high throughput genome-sequencing technologies has uncovered a large extent of structural variation in eukaryotic genomes that makes important contributions to genomic diversity and phenotypic variation. When the genomes of different strains of a given organism are compared, whole genome resequencing data are typically aligned to an established reference sequence. However, when the reference differs in significant structural ways from the individuals under study, the analysis is often incomplete or inaccurate. Results Here, we use rice as a model to demonstrate how improvements in sequencing and assembly technology allow rapid and inexpensive de novo assembly of next generation sequence data into high-quality assemblies that can be directly compared using whole genome alignment to provide an unbiased assessment. Using this approach, we are able to accurately assess the ‘pan-genome’ of three divergent rice varieties and document several megabases of each genome absent in the other two. Conclusions Many of the genome-specific loci are annotated to contain genes, reflecting the potential for new biological properties that would be missed by standard reference-mapping approaches. We further provide a detailed analysis of several loci associated with agriculturally important traits, including the S5 hybrid sterility locus, the Sub1 submergence tolerance locus, the LRK gene cluster associated with improved yield, and the Pup1 cluster associated with phosphorus deficiency, illustrating the utility of our approach for biological discovery. All of the data and software are openly available to support further breeding and functional studies of rice and other species. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0506-z) contains supplementary material, which is available to authorized users.
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630
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Mai CD, Phung NTP, To HTM, Gonin M, Hoang GT, Nguyen KL, Do VN, Courtois B, Gantet P. Genes controlling root development in rice. RICE (NEW YORK, N.Y.) 2014; 7:30. [PMID: 26224559 PMCID: PMC4884052 DOI: 10.1186/s12284-014-0030-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 10/30/2014] [Indexed: 05/20/2023]
Abstract
In this review, we report on the recent developments made using both genetics and functional genomics approaches in the discovery of genes controlling root development in rice. QTL detection in classical biparental mapping populations initially enabled the identification of a very large number of large chromosomal segments carrying root genes. Two segments with large effects have been positionally cloned, allowing the identification of two major genes. One of these genes conferred a tolerance to low phosphate content in soil, while the other conferred a tolerance to drought by controlling root gravitropism, resulting in root system expansion deep in the soil. Findings based on the higher-resolution QTL detection offered by the development of association mapping are discussed. In parallel with genetics approaches, efforts have been made to screen mutant libraries for lines presenting alterations in root development, allowing for the identification of several genes that control different steps of root development, such as crown root and lateral root initiation and emergence, meristem patterning, and the control of root growth. Some of these genes are closely phylogenetically related to Arabidopsis genes involved in the control of lateral root initiation. This close relationship stresses the conservation among plant species of an auxin responsive core gene regulatory network involved in the control of post-embryonic root initiation. In addition, we report on several genetic regulatory pathways that have been described only in rice. The complementarities and the expected convergence of the direct and reverse genetic approaches used to decipher the genetic determinants of root development in rice are discussed in regards to the high diversity characterizing this species and to the adaptations of rice root system architecture to different edaphic environments.
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Affiliation(s)
- Chung D Mai
- />Agricultural Genetic Institute, LMI RICE, Hanoi, Vietnam
- />University of Science and Technology of Hanoi, LMI RICE, Hanoi, Vietnam
| | - Nhung TP Phung
- />Agricultural Genetic Institute, LMI RICE, Hanoi, Vietnam
- />IRD, UMR DIADE, LMI RICE, Hanoi, Vietnam
- />CIRAD, UMR AGAP, Montpellier, France
| | - Huong TM To
- />University of Science and Technology of Hanoi, LMI RICE, Hanoi, Vietnam
| | | | - Giang T Hoang
- />Agricultural Genetic Institute, LMI RICE, Hanoi, Vietnam
- />University of Science and Technology of Hanoi, LMI RICE, Hanoi, Vietnam
| | - Khanh L Nguyen
- />University of Science and Technology of Hanoi, LMI RICE, Hanoi, Vietnam
- />IRD, UMR DIADE, LMI RICE, Hanoi, Vietnam
| | - Vinh N Do
- />Agricultural Genetic Institute, LMI RICE, Hanoi, Vietnam
| | | | - Pascal Gantet
- />University of Science and Technology of Hanoi, LMI RICE, Hanoi, Vietnam
- />IRD, UMR DIADE, LMI RICE, Hanoi, Vietnam
- />Université Montpellier 2, UMR DIADE, Montpellier, France
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631
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Ahmadi N, Audebert A, Bennett MJ, Bishopp A, de Oliveira AC, Courtois B, Diedhiou A, Diévart A, Gantet P, Ghesquière A, Guiderdoni E, Henry A, Inukai Y, Kochian L, Laplaze L, Lucas M, Luu DT, Manneh B, Mo X, Muthurajan R, Périn C, Price A, Robin S, Sentenac H, Sine B, Uga Y, Véry AA, Wissuwa M, Wu P, Xu J. The roots of future rice harvests. RICE (NEW YORK, N.Y.) 2014; 7:29. [PMID: 26224558 PMCID: PMC4884021 DOI: 10.1186/s12284-014-0029-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 10/12/2014] [Indexed: 05/05/2023]
Abstract
Rice production faces the challenge to be enhanced by 50% by year 2030 to meet the growth of the population in rice-eating countries. Whereas yield of cereal crops tend to reach plateaus and a yield is likely to be deeply affected by climate instability and resource scarcity in the coming decades, building rice cultivars harboring root systems that can maintain performance by capturing water and nutrient resources unevenly distributed is a major breeding target. Taking advantage of gathering a community of rice root biologists in a Global Rice Science Partnership workshop held in Montpellier, France, we present here the recent progresses accomplished in this area and focal points where an international network of laboratories should direct their efforts.
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Affiliation(s)
| | | | - Malcolm J Bennett
- />Centre for Plant Integrative Biology, University of Nottingham, Loughborough, LE12 5RD UK
| | - Anthony Bishopp
- />Centre for Plant Integrative Biology, University of Nottingham, Loughborough, LE12 5RD UK
| | | | | | - Abdala Diedhiou
- />Université Cheikh Anta Diop (UCAD), Département de Biologie Végétale, Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, Centre de Recherche de Bel Air - BP 1386, CP 18524 Dakar, Sénégal
- />Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air - BP 1386, CP 18524 Dakar, Sénégal
| | - Anne Diévart
- />CIRAD, UMR AGAP, Montpellier Cedex 5, 34398 France
| | - Pascal Gantet
- />Université Montpellier 2, UMR DIADE, Montpellier, France
- />IRD, LMI RICE, USTH, Agronomical Genetics Institute, Hanoi, Vietnam
| | | | | | | | - Yoshiaki Inukai
- />International Cooperation Center for Agricultural Education (ICCAE), Nagoya University, Furo-cho, Chikusa 464-8601 Nagoya, Japan
| | - Leon Kochian
- />Robert W. Holley Center for Agriculture and Health, USDA-ARS and Department of Plant Biology, Cornell University, Ithaca, 14853 NY USA
| | - Laurent Laplaze
- />Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air - BP 1386, CP 18524 Dakar, Sénégal
- />IRD, UMR DIADE, Montpellier, France
| | | | - Doan Trung Luu
- />Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/386 INRA/Montpellier SupAgro/Université Montpellier 2, F-34060 Montpellier Cedex 2, France
| | - Baboucarr Manneh
- />Africa Rice Center, AfricaRice Sahel Regional Station, B.P. 96, St Louis, Senegal
| | - Xiaorong Mo
- />State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, 310058 China
| | | | | | - Adam Price
- />University of Aberdeen, Aberdeen, AB24 3UU UK
| | | | - Hervé Sentenac
- />Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/386 INRA/Montpellier SupAgro/Université Montpellier 2, F-34060 Montpellier Cedex 2, France
| | - Bassirou Sine
- />Laboratoire Mixte International Adaptation des Plantes et microorganismes associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air - BP 1386, CP 18524 Dakar, Sénégal
- />ISRA, CERAAS, Thiès, Senegal
| | - Yusaku Uga
- />National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba, 305-8602 Ibaraki, Japan
| | - Anne Aliénor Véry
- />Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes, UMR 5004 CNRS/386 INRA/Montpellier SupAgro/Université Montpellier 2, F-34060 Montpellier Cedex 2, France
| | - Matthias Wissuwa
- />Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, 305-8686 Japan
| | - Ping Wu
- />State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, 310058 China
| | - Jian Xu
- />Department of Biological Sciences and NUS Centre for BioImaging Sciences, Faculty of Science, National University of Singapore, Singapore 117543 Singapore
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632
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Meister R, Rajani MS, Ruzicka D, Schachtman DP. Challenges of modifying root traits in crops for agriculture. TRENDS IN PLANT SCIENCE 2014; 19:779-88. [PMID: 25239776 DOI: 10.1016/j.tplants.2014.08.005] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 08/05/2014] [Accepted: 08/21/2014] [Indexed: 05/20/2023]
Abstract
Roots play an essential role in the acquisition of water and minerals from soils. Measuring crop root architecture and assaying for changes in function can be challenging, but examples have emerged showing that modifications to roots result in higher yield and increased stress tolerance. In this review, we focus mainly on the molecular genetic advances that have been made in altering root system architecture and function in crop plants, as well as phenotyping methods. The future for the modification of crop plant roots looks promising based on recent advances, but there are also important challenges ahead.
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Affiliation(s)
- Robert Meister
- Monsanto Company, 700 Chesterfield Parkway, Chesterfield, MO 63017, USA
| | - M S Rajani
- Monsanto Company, 700 Chesterfield Parkway, Chesterfield, MO 63017, USA
| | - Daniel Ruzicka
- Monsanto Company, 700 Chesterfield Parkway, Chesterfield, MO 63017, USA
| | - Daniel P Schachtman
- University of Nebraska Lincoln, Center for Plant Science Innovation, E243 Beadle, Lincoln, NE 68588-0660, USA.
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633
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Rogers ED, Benfey PN. Regulation of plant root system architecture: implications for crop advancement. Curr Opin Biotechnol 2014; 32:93-98. [PMID: 25448235 DOI: 10.1016/j.copbio.2014.11.015] [Citation(s) in RCA: 187] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 11/13/2014] [Indexed: 11/15/2022]
Abstract
Root system architecture (RSA) plays a major role in plant fitness, crop performance, and grain yield yet only recently has this role been appreciated. RSA describes the spatial arrangement of root tissue within the soil and is therefore crucial to nutrient and water uptake. Recent studies have identified many of the genetic and environmental factors influencing root growth that contribute to RSA. Some of the identified genes have the potential to limit crop loss caused by environmental extremes and are currently being used to confer drought tolerance. It is hypothesized that manipulating these and other genes that influence RSA will be pivotal for future crop advancements worldwide.
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Affiliation(s)
- Eric D Rogers
- Department of Biology and Duke Center for Systems Biology, Duke University, Durham, NC 27708, USA
| | - Philip N Benfey
- Department of Biology and Duke Center for Systems Biology, Duke University, Durham, NC 27708, USA; Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA.
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634
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Perego A, Sanna M, Giussani A, Chiodini ME, Fumagalli M, Pilu SR, Bindi M, Moriondo M, Acutis M. Designing a high-yielding maize ideotype for a changing climate in Lombardy plain (northern Italy). THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 499:497-509. [PMID: 24913890 DOI: 10.1016/j.scitotenv.2014.05.092] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/29/2014] [Accepted: 05/20/2014] [Indexed: 06/03/2023]
Abstract
The expected climate change will affect the maize yields in view of air temperature increase and scarce water availability. The application of biophysical models offers the chance to design a drought-resistant ideotype and to assist plant breeders and agronomists in the assessment of its suitability in future scenarios. The aim of the present work was to perform a model-based estimation of the yields of two hybrids, current vs ideotype, under future climate scenarios (2030-2060 and 2070-2100) in Lombardy (northern Italy), testing two options of irrigation (small amount at fixed dates vs optimal water supply), nitrogen (N) fertilization (300 vs 400 kg N ha(-1)), and crop cycle durations (current vs extended). For the designing of the ideotype we set several parameters of the ARMOSA process-based crop model: the root elongation rate and maximum depth, stomatal resistance, four stage-specific crop coefficients for the actual transpiration estimation, and drought tolerance factor. The work findings indicated that the current hybrid ensures good production only with high irrigation amount (245-565 mm y(-1)). With respect to the current hybrid, the ideotype will require less irrigation water (-13%, p<0.01) and it resulted in significantly higher yield under water stress condition (+15%, p<0.01) and optimal water supply (+2%, p<0.05). The elongated cycle has a positive effect on yield under any combination of options. Moreover, higher yields projected for the ideotype implicate more crop residues to be incorporated into the soil, which are positively correlated with the SOC sequestration and negatively with N leaching. The crop N uptake is expected to be adequate in view of higher rate of soil mineralization; the N fertilization rate of 400 kg N ha(-1) will involve significant increasing of grain yield, and it is expected to involve a higher rate of SOC sequestration.
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Affiliation(s)
- Alessia Perego
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milan, Via Celoria 2, 20133 Milan, Italy.
| | - Mattia Sanna
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - Andrea Giussani
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - Marcello Ermido Chiodini
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - Mattia Fumagalli
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - Salvatore Roberto Pilu
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - Marco Bindi
- Department of Plant, Soil and Environmental Science, University of Florence, Piazzale delle Cascine 18, 50144 Florence, Italy
| | - Marco Moriondo
- Department of Plant, Soil and Environmental Science, University of Florence, Piazzale delle Cascine 18, 50144 Florence, Italy
| | - Marco Acutis
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milan, Via Celoria 2, 20133 Milan, Italy
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635
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Kong X, Zhang M, De Smet I, Ding Z. Designer crops: optimal root system architecture for nutrient acquisition. Trends Biotechnol 2014; 32:597-8. [PMID: 25450041 DOI: 10.1016/j.tibtech.2014.09.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 09/09/2014] [Accepted: 09/25/2014] [Indexed: 11/27/2022]
Abstract
Plant root systems are highly plastic in response to environmental stimuli. Improved nutrient acquisition can increase fertilizer use efficiency and is critical for crop production. Recent analyses of field-grown crops highlighted the importance of root system architecture (RSA) in nutrient acquisition. This indicated that it is feasible in practice to exploit genotypes or mutations giving rise to optimal RSA for crop design in the future, especially with respect to plant breeding for infertile soils.
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Affiliation(s)
- Xiangpei Kong
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, College of Life Sciences, Shandong University, Jinan, 250100, Shandong, China
| | - Maolin Zhang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, College of Life Sciences, Shandong University, Jinan, 250100, Shandong, China
| | - Ive De Smet
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Technologiepark 927, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Genetics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium; Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Zhaojun Ding
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, College of Life Sciences, Shandong University, Jinan, 250100, Shandong, China.
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636
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Burton AL, Johnson JM, Foerster JM, Hirsch CN, Buell CR, Hanlon MT, Kaeppler SM, Brown KM, Lynch JP. QTL mapping and phenotypic variation for root architectural traits in maize (Zea mays L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:2293-311. [PMID: 25230896 DOI: 10.1007/s00122-014-2353-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 07/04/2014] [Indexed: 05/22/2023]
Abstract
QTL were identified for root architectural traits in maize. Root architectural traits, including the number, length, orientation, and branching of the principal root classes, influence plant function by determining the spatial and temporal domains of soil exploration. To characterize phenotypic patterns and their genetic control, three recombinant inbred populations of maize were grown for 28 days in solid media in a greenhouse and evaluated for 21 root architectural traits, including length, number, diameter, and branching of seminal, primary and nodal roots, dry weight of embryonic and nodal systems, and diameter of the nodal root system. Significant phenotypic variation was observed for all traits. Strong correlations were observed among traits in the same root class, particularly for the length of the main root axis and the length of lateral roots. In a principal component analysis, relationships among traits differed slightly for the three families, though vectors grouped together for traits within a given root class, indicating opportunities for more efficient phenotyping. Allometric analysis showed that trajectories of growth for specific traits differ in the three populations. In total, 15 quantitative trait loci (QTL) were identified. QTL are reported for length in multiple root classes, diameter and number of seminal roots, and dry weight of the embryonic and nodal root systems. Phenotypic variation explained by individual QTL ranged from 0.44% (number of seminal roots, NyH population) to 13.5% (shoot dry weight, OhW population). Identification of QTL for root architectural traits may be useful for developing genotypes that are better suited to specific soil environments.
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Affiliation(s)
- Amy L Burton
- Department of Plant Science, The Pennsylvania State University, 102 Tyson Building, University Park, PA, 16801, USA
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637
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Wasson AP, Rebetzke GJ, Kirkegaard JA, Christopher J, Richards RA, Watt M. Soil coring at multiple field environments can directly quantify variation in deep root traits to select wheat genotypes for breeding. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:6231-49. [PMID: 24963000 PMCID: PMC4223987 DOI: 10.1093/jxb/eru250] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We aim to incorporate deep root traits into future wheat varieties to increase access to stored soil water during grain development, which is twice as valuable for yield as water captured at younger stages. Most root phenotyping efforts have been indirect studies in the laboratory, at young plant stages, or using indirect shoot measures. Here, soil coring to 2 m depth was used across three field environments to directly phenotype deep root traits on grain development (depth, descent rate, density, length, and distribution). Shoot phenotypes at coring included canopy temperature depression, chlorophyll reflectance, and green leaf scoring, with developmental stage, biomass, and yield. Current varieties, and genotypes with breeding histories and plant architectures expected to promote deep roots, were used to maximize identification of variation due to genetics. Variation was observed for deep root traits (e.g. 111.4-178.5cm (60%) for depth; 0.09-0.22cm/°C day (144%) for descent rate) using soil coring in the field environments. There was significant variation for root traits between sites, and variation in the relative performance of genotypes between sites. However, genotypes were identified that performed consistently well or poorly at both sites. Furthermore, high-performing genotypes were statistically superior in root traits than low-performing genotypes or commercial varieties. There was a weak but significant negative correlation between green leaf score (-0.5), CTD (0.45), and rooting depth and a positive correlation for chlorophyll reflectance (0.32). Shoot phenotypes did not predict other root traits. This study suggests that field coring can directly identify variation in deep root traits to speed up selection of genotypes for breeding programmes.
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Affiliation(s)
- A P Wasson
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
| | - G J Rebetzke
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
| | - J A Kirkegaard
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
| | - J Christopher
- Queensland Alliance for Agricultural and Food Innovation, University of Queensland, Leslie Research Centre, PO Box 2282, Toowoomba Queensland 4350, Australia
| | - R A Richards
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
| | - M Watt
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
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638
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Tuberosa R, Turner NC, Cakir M. Preface: two decades of InterDrought conferences: are we bridging the genotype-to-phenotype gap? JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:6137-6139. [PMID: 25544976 DOI: 10.1093/jxb/eru407] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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639
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Ambavaram MMR, Basu S, Krishnan A, Ramegowda V, Batlang U, Rahman L, Baisakh N, Pereira A. Coordinated regulation of photosynthesis in rice increases yield and tolerance to environmental stress. Nat Commun 2014; 5:5302. [PMID: 25358745 PMCID: PMC4220491 DOI: 10.1038/ncomms6302] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 09/18/2014] [Indexed: 12/29/2022] Open
Abstract
Plants capture solar energy and atmospheric carbon dioxide (CO2) through photosynthesis, which is the primary component of crop yield, and needs to be increased considerably to meet the growing global demand for food. Environmental stresses, which are increasing with climate change, adversely affect photosynthetic carbon metabolism (PCM) and limit yield of cereals such as rice (Oryza sativa) that feeds half the world. To study the regulation of photosynthesis, we developed a rice gene regulatory network and identified a transcription factor HYR (HIGHER YIELD RICE) associated with PCM, which on expression in rice enhances photosynthesis under multiple environmental conditions, determining a morpho-physiological programme leading to higher grain yield under normal, drought and high-temperature stress conditions. We show HYR is a master regulator, directly activating photosynthesis genes, cascades of transcription factors and other downstream genes involved in PCM and yield stability under drought and high-temperature environmental stress conditions.
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Affiliation(s)
- Madana M R Ambavaram
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Supratim Basu
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Arjun Krishnan
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Venkategowda Ramegowda
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Utlwang Batlang
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Lutfor Rahman
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Niranjan Baisakh
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, Louisiana 70803, USA
| | - Andy Pereira
- 1] Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24061, USA [2] Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72701, USA
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640
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Naz AA, Arifuzzaman M, Muzammil S, Pillen K, Léon J. Wild barley introgression lines revealed novel QTL alleles for root and related shoot traits in the cultivated barley (Hordeum vulgare L.). BMC Genet 2014; 15:107. [PMID: 25286820 PMCID: PMC4200126 DOI: 10.1186/s12863-014-0107-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 09/25/2014] [Indexed: 11/17/2022] Open
Abstract
Background Root is the prime organ that sucks water and nutrients from deep layer of soil. Wild barley diversity exhibits remarkable variation in root system architecture that seems crucial in its adaptation to abiotic stresses like drought. In the present study, we performed quantitative trait locus (QTL) mapping of root and related shoot traits under control and drought conditions using a population of wild barley introgression lines (ILs). This population (S42IL) comprising of genome-wide introgressions of wild barley accession ISR42-8 in the cultivar Scarlett background. Here, we aimed to detect novel QTL alleles for improved root and related shoot features and to introduce them in modern cultivars. Results The cultivar Scarlett and wild barley accession ISR42-8 revealed significant variation of root and related shoot traits. ISR42-8 showed a higher performance in root system attributes like root dry weight (RDW), root volume (RV), root length (RL) and tiller number per plant (TIL) than Scarlett. Whereas, Scarlett exhibited erect type growth habit (GH) as compared to spreading growth habit in ISR42-8. The S42IL population revealed significant and wide range of variation for the investigated traits. Strong positive correlations were found among the root related traits whereas GH revealed negative correlation with root and shoot traits. The trait-wise comparison of phenotypic data with the ILs genetic map revealed six, eight, five, five and four QTL for RL, RDW, RV, TIL and GH, respectively. These QTL were linked to one or several traits simultaneously and localized to 15 regions across all chromosomes. Among these, beneficial QTL alleles of wild origin for RL, RDW, RV, TIL and GH, have been fixed in the cultivar Scarlett background. Conclusions The present study revealed 15 chromosomal regions where the exotic QTL alleles showed improvement for root and related shoot traits. These data suggest that wild barley accession ISR42-8 bears alleles different from those of Scarlett. Hence, the utility of genome-wide wild barley introgression lines is desirable to test the performance of individual exotic alleles in the elite gene pool as well as to transfer them in the cultivated germplasm.
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Affiliation(s)
- Ali Ahmad Naz
- Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, University of Bonn, Katzenburgweg 5, Bonn, 53115, Germany.
| | - Md Arifuzzaman
- Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, University of Bonn, Katzenburgweg 5, Bonn, 53115, Germany.
| | - Shumaila Muzammil
- Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, University of Bonn, Katzenburgweg 5, Bonn, 53115, Germany.
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, Halle, 06120, Germany.
| | - Jens Léon
- Institute of Crop Science and Resource Conservation, Crop Genetics and Biotechnology Unit, University of Bonn, Katzenburgweg 5, Bonn, 53115, Germany.
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641
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Blum A. Genomics for drought resistance - getting down to earth. FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:1191-1198. [PMID: 32481068 DOI: 10.1071/fp14018] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 03/10/2014] [Indexed: 05/20/2023]
Abstract
A meta-analysis of 520 reports published during the last 20 years on transgenic and mutant plants generated towards drought resistance revealed a total of at least 487 tested transgenic plants involving at least 100 genes claimed to be functional towards drought resistance. During this period, the rate of reported new experimental transgenic model or crop plants for drought resistance has been increasing exponentially. Despite these numbers, qualified sources of information indicate a very limited impact on global dryland agriculture, whereas the genetically modified (GM) market hardly recognises drought-resistant GM cultivars. This paper discusses possible reasons for the limited impact of genomics on the delivery of drought-resistant cultivars, which are beyond issues of regulation, propriety or commercialisation. These reasons are mainly tied to scientific and methodological problems in drought stress gene expression work and the functional genomics protocols used to identify drought resistance. Insufficient phenotyping of experimental transgenic plants for drought resistance often does not allow true conclusions about the real function of the discovered genes towards drought resistance. The discussion is concluded by proposing an outline of a minimal set of tests that might help us resolve the real function of discovered genes, thus bringing the research results down to earth.
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642
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Turner NC, Blum A, Cakir M, Steduto P, Tuberosa R, Young N. Strategies to increase the yield and yield stability of crops under drought - are we making progress? FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:1199-1206. [PMID: 32481069 DOI: 10.1071/fp14057] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 04/02/2014] [Indexed: 06/11/2023]
Abstract
The objective of the InterDrought conferences is to be a platform for debating key issues that are relevant for increasing the yield and yield stability of crops under drought via integrated approaches. InterDrought-IV, held in Perth, Australia, in September 2013, followed previous InterDrought conferences in bringing together researchers in agronomy, soil science, modelling, physiology, biochemistry, molecular biology, genetics and plant breeding. Key themes were (i) maximising water productivity; (ii) maximising dryland crop production; (iii) adaptation to water-limited environments; (iv) plant productivity under drought through effective water capture, improved transpiration efficiency, and growth and yield; and (v) breeding for water-limited environments through variety development, and trait-based genomics-assisted and transgenic approaches. This paper highlights some key issues and presents recommendations for future action. Improved agronomic interventions were recognised as being important contributors to improved dryland crop yields in water-limited environments, and new methods for exploring root architecture and water capture were highlighted. The increase in crop yields under drought through breeding and selection, the development of high-throughput phenotyping facilities for field-grown and pot-grown plants, and advances in understanding the molecular basis of plant responses and resistance to drought stress were recognised. Managed environment phenotyping facilities, a range of field environments, modelling, and genomic molecular tools are being used to select and release drought-resistant cultivars of all major crops. Delegates discussed how individuals and small teams can contribute to progress, and concluded that interdisciplinary research, linkages to international agricultural research centres, public-private partnerships and continuation of the InterDrought conferences will be instrumental for progress.
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Affiliation(s)
- Neil C Turner
- The University of Western Australia Institute of Agriculture and Centre for Plant Genetics and Breeding, M080, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | | | - Mehmet Cakir
- School of Biological Sciences and Biotechnology, Faculty of Sustainability, Environmental and Life Sciences, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Pasquale Steduto
- Food and Agriculture Organisation of the United Nations, Viale delle Terme di Caracalla, 00153 Rome, Italy
| | - Roberto Tuberosa
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Neil Young
- Rural Mail Box 232, Kojonup, WA 6395, Australia
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643
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Ober ES, Werner P, Flatman E, Angus WJ, Jack P, Smith-Reeve L, Tapsell C. Genotypic differences in deep water extraction associated with drought tolerance in wheat. FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:1078-1086. [PMID: 32481059 DOI: 10.1071/fp14094] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 06/08/2014] [Indexed: 05/24/2023]
Abstract
The ability of roots to extract soil moisture is critical for maintaining yields during drought. However, the extent of genotypic variation for rooting depth and drought tolerance in Northern European wheat (Triticum aestivum L.) germplasm is not known. The objectives of this study were to measure genotypic differences in root activity, test relationships between water use and yield, examine trade-offs between yield potential and investment of biomass in deep roots, and identify genotypes that contrast in deep root activity. A diverse set of 21 wheat genotypes was evaluated under irrigated and managed drought conditions in the field. Root activity was inferred from patterns of water extraction from the soil profile. Genotypes were equally capable of exploiting soil moisture in the upper layers, but there were significant genotypic differences in rates of water uptake after anthesis in deeper soil layers. For example, across the three years of the study, the variety Xi19 showed consistently deeper root activity than the variety Spark; Xi19 also showed greater drought tolerance than Spark. There were positive correlations between water extraction from depth and droughted yields and drought tolerance, but correlations between deep water use and yield potential were not significant or only weakly negative. With appropriate screening tools, selection for genotypes that can better mine deep soil water should improve yield stability in variable rainfall environments.
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Affiliation(s)
- Eric S Ober
- National Institute of Agricultural Botany, Huntingdon Road, Cambridge, CB3 0LE, UK
| | - Peter Werner
- KWS UK, 56 Church Street, Thriplow, Hertfordshire, SG8 7RE, UK
| | - Edward Flatman
- Limagrain, Woolpit, Bury St. Edmunds, Suffolk, IP30 9UP, UK
| | - William J Angus
- Angus Wheat Consultants, Ltd, The Pines, Rattlesden, Suffolk, IP30 0RA, UK
| | - Peter Jack
- RAGT Seeds, Grange Road, Ickleton, Essex, CB10 1TA, UK
| | | | - Chris Tapsell
- KWS UK, 56 Church Street, Thriplow, Hertfordshire, SG8 7RE, UK
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644
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Raju BR, Narayanaswamy BR, Mohankumar MV, Sumanth KK, Rajanna MP, Mohanraju B, Udayakumar M, Sheshshayee MS. Root traits and cellular level tolerance hold the key in maintaining higher spikelet fertility of rice under water limited conditions. FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:930-939. [PMID: 32481046 DOI: 10.1071/fp13291] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 03/08/2014] [Indexed: 05/16/2023]
Abstract
Reduced spikelet fertility appears to be one of the major factors responsible for the decreased rice grain yield when cultivated under semi irrigated aerobic condition. We demonstrate that genotypes with better root systems coupled with higher cellular level tolerance (CLT) can significantly improve spikelet fertility under semi-irrigated aerobic condition in the field. A set of 20 contrasting rice accessions differing in root traits and CLT with significant molecular diversity were subjected to specific soil moisture regimes during a period between five days before and 10 days after anthesis. Lowest spikelet fertility was observed among the plants grown under water limited (WL) conditions followed by the plants grown aerobically in field conditions (AF). Deep rooted genotypes generally maintained higher spikelet fertility under both WL and AF conditions. Furthermore, genotypes that had high roots biomass as well as high CLT recorded the lowest reduction in spikelet fertility under WL and AF compared with the low root and low CLT genotype. This study emphasised the relevance of combining water acquisition and CLT for improving field level tolerance of rice to water limitation. Such genotypes recorded significantly higher grain yield under stress as well as well watered conditions. The study led to the identification of promising trait donor genotypes which can be exploited in breeding to develop superior trait pyramided cultivars suitable for semi irrigated aerobic cultivation.
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Affiliation(s)
- Bheemanahalli R Raju
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bengaluru-560 065, India
| | | | | | - Kambalimath K Sumanth
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bengaluru-560 065, India
| | | | - Basavaiah Mohanraju
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bengaluru-560 065, India
| | - Makarla Udayakumar
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bengaluru-560 065, India
| | - Madavalam S Sheshshayee
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bengaluru-560 065, India
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645
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Arai-Sanoh Y, Takai T, Yoshinaga S, Nakano H, Kojima M, Sakakibara H, Kondo M, Uga Y. Deep rooting conferred by DEEPER ROOTING 1 enhances rice yield in paddy fields. Sci Rep 2014; 4:5563. [PMID: 24988911 PMCID: PMC4080195 DOI: 10.1038/srep05563] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 06/17/2014] [Indexed: 11/09/2022] Open
Abstract
To clarify the effect of deep rooting on grain yield in rice (Oryza sativa L.) in an irrigated paddy field with or without fertilizer, we used the shallow-rooting IR64 and the deep-rooting Dro1-NIL (a near-isogenic line homozygous for the Kinandang Patong allele of DEEPER ROOTING 1 (DRO1) in the IR64 genetic background). Although total root length was similar in both lines, more roots were distributed within the lower soil layer of the paddy field in Dro1-NIL than in IR64, irrespective of fertilizer treatment. At maturity, Dro1-NIL showed approximately 10% higher grain yield than IR64, irrespective of fertilizer treatment. Higher grain yield of Dro1-NIL was mainly due to the increased 1000-kernel weight and increased percentage of ripened grains, which resulted in a higher harvest index. After heading, the uptake of nitrogen from soil and leaf nitrogen concentration were higher in Dro1-NIL than in IR64. At the mid-grain-filling stage, Dro1-NIL maintained higher cytokinin fluxes from roots to shoots than IR64. These results suggest that deep rooting by DRO1 enhances nitrogen uptake and cytokinin fluxes at late stages, resulting in better grain filling in Dro1-NIL in a paddy field in this study.
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Affiliation(s)
- Yumiko Arai-Sanoh
- NARO Institute of Crop Science (NICS), 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Toshiyuki Takai
- NARO Institute of Crop Science (NICS), 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Satoshi Yoshinaga
- 1] NARO Institute of Crop Science (NICS), 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan [2] NARO Agricultural Research Center (NARO/ARC), 1-2-1 Inada, Joetsu, Niigata 943-0193, Japan
| | - Hiroshi Nakano
- NARO Institute of Crop Science (NICS), 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan
| | - Motohiko Kondo
- NARO Institute of Crop Science (NICS), 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Yusaku Uga
- National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
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646
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Tian H, De Smet I, Ding Z. Shaping a root system: regulating lateral versus primary root growth. TRENDS IN PLANT SCIENCE 2014; 19:426-31. [PMID: 24513255 DOI: 10.1016/j.tplants.2014.01.007] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 01/04/2014] [Accepted: 01/14/2014] [Indexed: 05/22/2023]
Abstract
Primary and lateral roots comprise root systems, which are vital to the growth and survival of plants. Several molecular mechanisms associated with primary and lateral root growth have been described, including some common regulatory factors for their initiation and development. However, in this opinion article, we discuss the distinct growth behavior of lateral roots in response to environmental cues, such as salinity, gravity, and nutrient availability, which are mediated via specific regulators. We propose that differential growth dynamics between primary and lateral roots are crucial for plants to adapt to the ever-changing environmental conditions.
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Affiliation(s)
- Huiyu Tian
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, Shandong 250100, PR China
| | - Ive De Smet
- Department of Plant Systems Biology, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium; Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.
| | - Zhaojun Ding
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan, Shandong 250100, PR China.
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647
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Abstract
Rajeev Varshney, Ryohei Terauchi, and Susan McCouch summarize the current and future uses of next-generation sequencing technologies, both for developing crops with improved traits and for increasing the efficiency of modern plant breeding, as a step towards meeting the challenge of feeding a growing world population. Next generation sequencing (NGS) technologies are being used to generate whole genome sequences for a wide range of crop species. When combined with precise phenotyping methods, these technologies provide a powerful and rapid tool for identifying the genetic basis of agriculturally important traits and for predicting the breeding value of individuals in a plant breeding population. Here we summarize current trends and future prospects for utilizing NGS-based technologies to develop crops with improved trait performance and increase the efficiency of modern plant breeding. It is our hope that the application of NGS technologies to plant breeding will help us to meet the challenge of feeding a growing world population.
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648
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Zhao Y, Xing L, Wang X, Hou YJ, Gao J, Wang P, Duan CG, Zhu X, Zhu JK. The ABA receptor PYL8 promotes lateral root growth by enhancing MYB77-dependent transcription of auxin-responsive genes. Sci Signal 2014; 7:ra53. [PMID: 24894996 DOI: 10.1126/scisignal.2005051] [Citation(s) in RCA: 212] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The phytohormone abscisic acid (ABA) regulates plant growth, development, and abiotic stress responses. ABA signaling is mediated by a group of receptors known as the PYR1/PYL/RCAR family, which includes the pyrabactin resistance 1-like protein PYL8. Under stress conditions, ABA signaling activates SnRK2 protein kinases to inhibit lateral root growth after emergence from the primary root. However, even in the case of persistent stress, lateral root growth eventually recovers from inhibition. We showed that PYL8 is required for the recovery of lateral root growth, following inhibition by ABA. PYL8 directly interacted with the transcription factors MYB77, MYB44, and MYB73. The interaction of PYL8 and MYB77 increased the binding of MYB77 to its target MBSI motif in the promoters of multiple auxin-responsive genes. Compared to wild-type seedlings, the lateral root growth of pyl8 mutant seedlings and myb77 mutant seedlings was more sensitive to inhibition by ABA. The recovery of lateral root growth was delayed in pyl8 mutant seedlings in the presence of ABA, and the defect was rescued by exposing pyl8 mutant seedlings to the auxin IAA (3-indoleacetic acid). Thus, PYL8 promotes lateral root growth independently of the core ABA-SnRK2 signaling pathway by enhancing the activities of MYB77 and its paralogs, MYB44 and MYB73, to augment auxin signaling.
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Affiliation(s)
- Yang Zhao
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.,Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Lu Xing
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA.,School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Xingang Wang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Yueh-Ju Hou
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Jinghui Gao
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA.,College of Animal Science and Technology, Northwest A&F University, Yangling, Shaan'xi 712100, China
| | - Pengcheng Wang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Cheng-Guo Duan
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Xiaohong Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.,Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
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649
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Nature Plants. Nat Genet 2014; 46:523. [DOI: 10.1038/ng.3005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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650
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Kissoudis C, van de Wiel C, Visser RGF, van der Linden G. Enhancing crop resilience to combined abiotic and biotic stress through the dissection of physiological and molecular crosstalk. FRONTIERS IN PLANT SCIENCE 2014; 5:207. [PMID: 24904607 PMCID: PMC4032886 DOI: 10.3389/fpls.2014.00207] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 04/28/2014] [Indexed: 05/18/2023]
Abstract
Plants growing in their natural habitats are often challenged simultaneously by multiple stress factors, both abiotic and biotic. Research has so far been limited to responses to individual stresses, and understanding of adaptation to combinatorial stress is limited, but indicative of non-additive interactions. Omics data analysis and functional characterization of individual genes has revealed a convergence of signaling pathways for abiotic and biotic stress adaptation. Taking into account that most data originate from imposition of individual stress factors, this review summarizes these findings in a physiological context, following the pathogenesis timeline and highlighting potential differential interactions occurring between abiotic and biotic stress signaling across the different cellular compartments and at the whole plant level. Potential effects of abiotic stress on resistance components such as extracellular receptor proteins, R-genes and systemic acquired resistance will be elaborated, as well as crosstalk at the levels of hormone, reactive oxygen species, and redox signaling. Breeding targets and strategies are proposed focusing on either manipulation and deployment of individual common regulators such as transcription factors or pyramiding of non- (negatively) interacting components such as R-genes with abiotic stress resistance genes. We propose that dissection of broad spectrum stress tolerance conferred by priming chemicals may provide an insight on stress cross regulation and additional candidate genes for improving crop performance under combined stress. Validation of the proposed strategies in lab and field experiments is a first step toward the goal of achieving tolerance to combinatorial stress in crops.
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