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Challenges of Crop Phenomics in the Post-genomic Era

Published on Apr 19, 2016
· DOI :10.1201/b16437-10
Vasilis C. Gegas4
Estimated H-index: 4
,
Anyela V. Camargo5
Estimated H-index: 5
,
John H. Doonan48
Estimated H-index: 48
Abstract
  • References (138)
  • Citations (4)
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References138
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#1Kenneth Haug (EMBL-EBI: European Bioinformatics Institute)H-Index: 14
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MetaboLights (http://www.ebi.ac.uk/metabolights) is the first general-purpose, open-access repository for metabolomics studies, their raw experimental data and associated metadata, maintained by one of the major open-access data providers in molecular biology. Metabolomic profiling is an important tool for research into biological functioning and into the systemic perturbations caused by diseases, diet and the environment. The effectiveness of such methods depends on the availability of public o...
352 CitationsSource
#1Christian Colmsee (Leibniz Association)H-Index: 10
#2Martin Mascher (Leibniz Association)H-Index: 26
Last. Uwe Sonnewald (FAU: University of Erlangen-Nuremberg)H-Index: 71
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Background Maize is a major crop plant, grown for human and animal nutrition, as well as a renewable resource for bioenergy. When looking at the problems of limited fossil fuels, the growth of the world’s population or the world’s climate change, it is important to find ways to increase the yield and biomass of maize and to study how it reacts to specific abiotic and biotic stress situations. Within the OPTIMAS systems biology project maize plants were grown under a large set of controlled stres...
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#1Klaus F. X. MayerH-Index: 66
#2Robbie Waugh (James Hutton Institute)H-Index: 79
Last. Nils Stein (Leibniz Association)H-Index: 60
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Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complemen...
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#1Rachel Brenchley (University of Liverpool)H-Index: 6
#2Manuel SpannaglH-Index: 27
Last. Neil Hall (University of Liverpool)H-Index: 55
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Sequencing of the hexaploid bread wheat genome shows that it is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments.
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#1Hendrik Poorter A (Forschungszentrum Jülich)H-Index: 1
#2Jonas Bühler (Forschungszentrum Jülich)H-Index: 8
Last. Johannes A. Postma (Forschungszentrum Jülich)H-Index: 16
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Themajorityofexperimentsinplantbiologyuseplantsgrowninsomekindofcontainerorpot.Weconducteda meta-analysison65studiesthatanalysedtheeffectofpotsizeongrowthandunderlyingvariables.Onaverage,adoublingof the pot size increased biomass production by 43%. Further analysis of pot size effects on the underlying components of growth suggests that reduced growth in smaller pots is caused mainly by a reduction in photosynthesis per unit leaf area, ratherthanbychangesinleafmorphologyorbiomassallocation.Theap...
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#1Kerstin Nagel (Forschungszentrum Jülich)H-Index: 15
#2Alexander Putz (Forschungszentrum Jülich)H-Index: 3
Last. Ulrich Schurr (Forschungszentrum Jülich)H-Index: 46
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Root systems play an essential role in ensuring plant productivity. Experiments conducted in controlled environments and simulation models suggest that root geometry and responses of root architecture to environmental factors should be studied as a priority. However, compared with aboveground plant organs, roots are not easily accessible by non-invasive analyses and field research is still based almost completely on manual, destructive methods. Contributing to reducing the gap between laboratory...
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#1Achim Walter (ETH Zurich)H-Index: 31
#2Bruno Studer (AU: Aarhus University)H-Index: 20
Last. Roland KöllikerH-Index: 25
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Background and Aims: Advanced phenotyping, i.e. the application of automated, high-throughput methods to characterize plant architecture and performance, has the potential to accelerate breeding progress but is far from being routinely used in current breeding approaches. In forage and turf improvement programmes, in particular, where breeding populations and cultivars are characterized by high genetic diversity and substantial genotype × environment interactions, precise and efficient phenotypi...
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#1Helen F. Downie (James Hutton Institute)H-Index: 8
#2Nicola J. Holden (James Hutton Institute)H-Index: 16
Last. Lionel X. Dupuy (James Hutton Institute)H-Index: 20
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Understanding of soil processes is essential for addressing the global issues of food security, disease transmission and climate change. However, techniques for observing soil biology are lacking. We present a heterogeneous, porous, transparent substrate for in situ 3D imaging of living plants and root-associated microorganisms using particles of the transparent polymer, Nafion, and a solution with matching optical properties. Minerals and fluorescent dyes were adsorbed onto the Nafion particles...
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#1Sonia Osorio (MPG: Max Planck Society)H-Index: 34
#2Rob AlbaH-Index: 15
Last. James J. GiovannoniH-Index: 71
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Integrative comparative analyses of transcript and metabolite levels from climacteric and nonclimacteric fruits can be employed to unravel the similarities and differences of the underlying regulatory processes. To this end, we conducted combined gas chromatography-mass spectrometry and heterologous microarray hybridization assays in tomato (Solanum lycopersicum; climacteric) and pepper (Capsicum chilense; nonclimacteric) fruits across development and ripening. Computational methods from multiva...
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A major challenge for crop research in the 21st century is how to predict crop performance as a function of genetic architecture. Advances in “next generation” DNA sequencing have greatly improved genotyping efficiency and reduced genotyping costs. Methods for characterizing plant traits (phenotypes), however, have much progressed more slowly over the past 30 years, and constraints in phenotyping capability limit our ability to dissect the genetics of quantitative traits, especially those relate...
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Cited By4
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#1Reyazul Rouf Mir (Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir)H-Index: 3
#2Mathew Reynolds (CIMMYT: International Maize and Wheat Improvement Center)H-Index: 1
Last. Mohd Ashraf Bhat (Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir)H-Index: 2
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#1Takaharu Kameoka (Mie University)H-Index: 12
#2Atsushi Hashimoto (Mie University)H-Index: 16
This paper gives an outline of key technologies necessary for science-based agriculture. In order to design future agriculture, present agriculture should be redesigned based on the context of smart agriculture that indicates the overall form of agriculture including a social system while the present precision agriculture shows a technical form of agriculture only. Wireless Sensor Network (WSN) and the various type of optical sensors are assumed to be a basic technology of smart agriculture whic...
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#1Jane L. Ward (Rothamsted Research)H-Index: 34
#2Marianna Rakszegi (MTA: Hungarian Academy of Sciences)H-Index: 8
Last. Ian MackayH-Index: 29
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Background Genomic prediction of agronomic traits as targets for selection in plant breeding programmes is increasingly common. The methods employed can also be applied to predict traits from other sources of covariates, such as metabolomics. However, prediction combining sets of covariates can be less accurate than using the best of the individual sets.
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#2Atsushi HashimotoH-Index: 16
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SUMMARY This paper gives an outline of key technologies necessary for science-based agriculture. In order to design future agriculture, present agriculture should be redesigned based on the context of smart agriculture that indicates the overall form of agriculture including a social system while the present precision agriculture shows a technical form of agriculture only. Wireless Sensor Network (WSN) and the various type of optical sensors are assumed to be a basic technology of smart agricult...