Abstract：
Background:Wheat is one of the most widely grown crop in temperate climates for food and animal feed. In order to meet the demands of the predicted population increase in an ever-changing climate, wheat production needs to dramatically increase. Spike and grain traits are critical determinants of final yield and grain uniformity a commercially desired trait, but their analysis is laborious and often requires destructive harvest. One of the current challenges is to develop an accurate, non-destructive method for spike and grain trait analysis capable of handling large populations. Results:In this study we describe the development of a robust method for the accurate extraction and measurement of spike and grain morphometric parameters from images acquired by X-ray micro-computed tomography (μCT). The image analysis pipeline developed automatically identifies plant material of interest in μCT images, performs image analysis, and extracts morphometric data. As a proof of principle, this integrated methodology was used to analyse the spikes from a population of wheat plants subjected to high temperatures under two different water regimes. Temperature has a negative effect on spike height and grain number with the middle of the spike being the most affected region. The data also confirmed that increased grain volume was correlated with the decrease in grain number under mild stress. Conclusions:Being able to quickly measure plant phenotypes in a non-destructive manner is crucial to advance our understanding of gene function and the effects of the environment. We report on the development of an image analysis pipeline capable of accurately and reliably extracting spike and grain traits from crops without the loss of positional information. This methodology was applied to the analysis of wheat spikes can be readily applied to other economically important crop species.
journal_name
Plant Methodsjournal_title
Plant methodsauthors
Hughes N,Askew K,Scotson CP,Williams K,Sauze C,Corke F,Doonan JH,Nibau Cdoi
10.1186/s13007-017-0229-8subject
Has Abstractpub_date
2017-11-01 00:00:00pages
76issn
1746-4811pii
229journal_volume
13pub_type
杂志文章相关文献
Plant Methods文献大全abstract：BACKGROUND:In silico analyses based on sequence similarities with animal channels have identified a large number of plant genes likely to encode ion channels. The attempts made to characterise such putative plant channels at the functional level have most often relied on electrophysiological analyses in classical expre...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-1-14
更新日期：2005-12-19 00:00:00
abstract：BACKGROUND:In eukaryotic cells, the proteasome maintains homeostasis by selectively degrading regulatory and misfolded proteins, and in doing so contributes to the amino acid pool. Inhibition of the proteasome in yeast and human cells decreases de novo protein synthesis. However, it is not know if proteasome inhibition...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-016-0120-z
更新日期：2016-03-16 00:00:00
abstract：BACKGROUND:Maize haploid breeding technology can be used to rapidly develop homozygous lines, significantly shorten the breeding cycle and improve breeding efficiency. Rapid and accurate sorting haploid kernels is a prerequisite for the large-scale application of this technology. At present, the automatic haploid sorti...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-020-00703-4
更新日期：2021-01-06 00:00:00
abstract：BACKGROUND:Plant metabolites are commonly functionally classified, as defense- or growth-related phytohormones, primary and specialized metabolites, and so forth. Analytical procedures for the quantifications of these metabolites are challenging because the metabolites can vary over several orders of magnitude in conce...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-016-0130-x
更新日期：2016-05-26 00:00:00
abstract：BACKGROUND:There is considerable interest in rapid assays or screening systems for assigning gene function. However, analysis of gene function in the flowers of some species is restricted due to the difficulty of producing stably transformed transgenic plants. As a result, experimental approaches based on transient gen...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-3-1
更新日期：2007-01-08 00:00:00
abstract：:Receptor-like protein kinases (RLKs) are a large and important group of plant proteins involved in numerous aspects of development and stress response. Within this family, homo-oligermization of receptors followed by autophosphorylation of the intracellular protein kinase domain appears to be a widespread mechanism to...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-9-22
更新日期：2013-06-26 00:00:00
abstract：BACKGROUND:Nectar reabsorption is a widely known phenomenon, related to the strategy of resource-recovery and also to maintain the nectar homeostasis at the nectary. The method currently performed to demonstrate nectar being reabsorbed involves the use of radioactive tracers applied to the nectary. Although this method...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-9-20
更新日期：2013-06-19 00:00:00
abstract：Background:Progress in high-throughput molecular methods accompanied by more complex experimental designs demands novel data visualisation solutions. To specifically answer the question which parts of the specifical biological system are responding in particular perturbation, integrative approach in which experimental ...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-018-0345-0
更新日期：2018-08-30 00:00:00
abstract：: Microarrays are routine tools for transcript profiling, and genomic tiling arrays such as the Arabidopsis AGRONOMICS1 arrays have been found to be highly suitable for such experiments because changes in genome annotation can be easily integrated at the data analysis level. In a transcript profiling experiment, RNA la...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-8-18
更新日期：2012-06-13 00:00:00
abstract：Background:Protein data over circadian time scale is scarce for clock transcription factors. Further work in this direction is required for refining quantitative clock models. However, gathering highly resolved dynamics of low-abundance transcription factors has been a major challenge in the field. In this work we prov...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-019-0454-4
更新日期：2019-07-08 00:00:00
abstract：:Over the last 10 years, high-density SNP arrays and DNA re-sequencing have illuminated the majority of the genotypic space for a number of organisms, including humans, maize, rice and Arabidopsis. For any researcher willing to define and score a phenotype across many individuals, Genome Wide Association Studies (GWAS)...
journal_title：Plant methods
pub_type： 杂志文章,评审
doi：10.1186/1746-4811-9-29
更新日期：2013-07-22 00:00:00
abstract：Background:Plasmopara obducens is the biotrophic oomycete responsible for impatiens downy mildew, a destructive disease of Impatiens that causes high crop loss. Currently, there are no available methods for the microscopic detection of P. obducens from leaves of impatiens, which may be contributing to the spread of the...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-018-0362-z
更新日期：2018-10-24 00:00:00
abstract：Background:The cellular morphology of plant organs is strongly related to other physical properties such as shape, size, growth, mechanical properties or chemical composition. Cell morphology often vary depending on the type of tissue, or on the distance to a specific tissue. A common challenge in quantitative plant hi...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-020-00603-7
更新日期：2020-05-06 00:00:00
abstract：Background:High throughput non-destructive phenotyping is emerging as a significant approach for phenotyping germplasm and breeding populations for the identification of superior donors, elite lines, and QTLs. Detection and counting of spikes, the grain bearing organs of wheat, is critical for phenomics of a large set ...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-020-00582-9
更新日期：2020-03-18 00:00:00
abstract：Background:Chloroplasts are critical organelles that perceive and convey metabolic and stress signals to different cellular components, while remaining the seat of photosynthesis and a metabolic factory. The proteomes of intact leaves, chloroplasts, and suborganellar fractions of plastids have been evaluated in the mod...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-020-00667-5
更新日期：2020-09-24 00:00:00
abstract：:Terahertz technology is still an evolving research field that attracts scientists with very different backgrounds working on a wide range of subjects. In the past two decades, it has been demonstrated that terahertz technology can provide a non-invasive tool for measuring and monitoring the water content of leaves and...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-015-0057-7
更新日期：2015-03-06 00:00:00
abstract：Background:Chickpea (Cicer arietinum L.), an important legume crop is one of the major source of dietary protein. Developing an efficient and reproducible transformation method is imperative to expedite functional genomics studies in this crop. Here, we present an optimized and detailed procedure for Agrobacterium rhiz...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-018-0315-6
更新日期：2018-07-06 00:00:00
abstract：UNLABELLED: BACKGROUND:Phytohormones are the key metabolites participating in the regulation of multiple functions of plant organism. Among them, jasmonates, as well as abscisic and salicylic acids are responsible for triggering and modulating plant reactions targeted against pathogens and herbivores, as well as resis...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-8-47
更新日期：2012-11-22 00:00:00
abstract：Background:Over the last years, several plant science labs have started to employ fluctuating growth light conditions to simulate natural light regimes more closely. Many plant mutants reveal quantifiable effects under fluctuating light despite being indistinguishable from wild-type plants under standard constant light...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-019-0546-1
更新日期：2019-12-23 00:00:00
abstract：BACKGROUND:Striga species are noxious root hemi-parasitic weeds that debilitate cereal production in sub-Saharan Africa (SSA). Control options for Striga are limited and developing Striga resistant crop germplasm is regarded as the best and most sustainable control measure. Efforts to improve germplasm for Striga resis...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-8-20
更新日期：2012-06-21 00:00:00
abstract：BACKGROUND:Plant breeding and genetics demand fast, exact and reproducible phenotyping. Efficient statistical evaluation of phenotyping data requires standardised data storage ensuring long-term data availability while maintaining intellectual property rights. This is state of the art at phenomics centres, which, howev...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-015-0069-3
更新日期：2015-04-07 00:00:00
abstract：BACKGROUND:Brassinosteriods (BRs) are a group of important phytohormones that have major effects on plant growth and development. To fully elucidate the function of BRs, a sensitive BR assay is required. However, most of the previously reported methods are tedious and time-consuming due to multiple pretreatment steps. ...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-10-39
更新日期：2014-11-24 00:00:00
abstract：: Three terrestrial plants are known to perform C4 photosynthesis without the dual-cell system by partitioning two distinct types of chloroplasts in separate cytoplasmic compartments. We report herein a protocol for isolating the dimorphic chloroplasts from Bienertia sinuspersici. Hypo-osmotically lysed protoplasts und...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-8-8
更新日期：2012-03-06 00:00:00
abstract：Background:Charcoal rot is a fungal disease that thrives in warm dry conditions and affects the yield of soybeans and other important agronomic crops worldwide. There is a need for robust, automatic and consistent early detection and quantification of disease symptoms which are important in breeding programs for the de...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-018-0349-9
更新日期：2018-10-03 00:00:00
abstract：Background:Nowadays, there is an increasing demand for fast and reliable plant biomolecular analyses. Conventional methods for the isolation of nucleic acids are time-consuming and require multiple and often non-automatable steps to remove cellular interferences, with consequence that sample preparation is the major bo...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-019-0408-x
更新日期：2019-03-09 00:00:00
abstract：BACKGROUND:It is well known that preparation of biological (plant and animal) tissues for Scanning Electron Microscopy (SEM) by chemical fixation and critical point drying results in shrinkage of tissues, often by up to 20-30%, depending on the tissue type and fixation protocol used. We sought to identify a protocol th...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-9-36
更新日期：2013-10-02 00:00:00
abstract：:Plants are good sources of biologically active compounds with antimicrobial activity, including polypeptides. Antimicrobial peptides (AMPs) represent one of the main barriers of plant innate immunity to environmental stress factors and are attracting much research interest. There are some extraction methods for isolat...
journal_title：Plant methods
pub_type： 杂志文章,评审
doi：10.1186/s13007-020-00687-1
更新日期：2020-10-23 00:00:00
abstract：Background:Functional genomic studies using genetics approaches of conifers are hampered by the complex and enormous genome, long vegetative growth period, and exertion in genetic transformation. Thus, the research carried out on gene function in Pinus tabuliformis is typically performed by heterologous expression base...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-020-00594-5
更新日期：2020-04-10 00:00:00
abstract：Background:Open tissue culture technique could be simplified by using different bacteriostatic agents. There is a great difference in the bacteriostatic effects of different antimicrobial agents on various explants. However, there is no report about the effective bacteriostatic agent for open tissue culture of Acacia a...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/s13007-019-0390-3
更新日期：2019-01-25 00:00:00
abstract：BACKGROUND:Protoplasts isolated from leaves are useful materials in plant research. One application, the transient expression of recombinant genes using Arabidopsis mesophyll protoplasts (TEAMP), is currently commonly used for studies of subcellular protein localization, promoter activity, and in vivo protein-protein i...
journal_title：Plant methods
pub_type： 杂志文章
doi：10.1186/1746-4811-5-16
更新日期：2009-11-24 00:00:00
