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White PJ, George TS, Gregory PJ, Bengough AG, Hallett PD, McKenzie BM. Matching roots to their environment. ANNALS OF BOTANY 2013; 112:207-22. [PMID: 23821619 PMCID: PMC3698393 DOI: 10.1093/aob/mct123] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 02/28/2013] [Indexed: 05/03/2023]
Abstract
BACKGROUND Plants form the base of the terrestrial food chain and provide medicines, fuel, fibre and industrial materials to humans. Vascular land plants rely on their roots to acquire the water and mineral elements necessary for their survival in nature or their yield and nutritional quality in agriculture. Major biogeochemical fluxes of all elements occur through plant roots, and the roots of agricultural crops have a significant role to play in soil sustainability, carbon sequestration, reducing emissions of greenhouse gasses, and in preventing the eutrophication of water bodies associated with the application of mineral fertilizers. SCOPE This article provides the context for a Special Issue of Annals of Botany on 'Matching Roots to Their Environment'. It first examines how land plants and their roots evolved, describes how the ecology of roots and their rhizospheres contributes to the acquisition of soil resources, and discusses the influence of plant roots on biogeochemical cycles. It then describes the role of roots in overcoming the constraints to crop production imposed by hostile or infertile soils, illustrates root phenotypes that improve the acquisition of mineral elements and water, and discusses high-throughput methods to screen for these traits in the laboratory, glasshouse and field. Finally, it considers whether knowledge of adaptations improving the acquisition of resources in natural environments can be used to develop root systems for sustainable agriculture in the future.
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Turner N, Kowalski GM, Leslie SJ, Risis S, Yang C, Lee-Young RS, Babb JR, Meikle PJ, Lancaster GI, Henstridge DC, White PJ, Kraegen EW, Marette A, Cooney GJ, Febbraio MA, Bruce CR. Distinct patterns of tissue-specific lipid accumulation during the induction of insulin resistance in mice by high-fat feeding. Diabetologia 2013; 56:1638-48. [PMID: 23620060 DOI: 10.1007/s00125-013-2913-1] [Citation(s) in RCA: 320] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 03/27/2013] [Indexed: 12/22/2022]
Abstract
AIMS/HYPOTHESIS While it is well known that diet-induced obesity causes insulin resistance, the precise mechanisms underpinning the initiation of insulin resistance are unclear. To determine factors that may cause insulin resistance, we have performed a detailed time-course study in mice fed a high-fat diet (HFD). METHODS C57Bl/6 mice were fed chow or an HFD from 3 days to 16 weeks and glucose tolerance and tissue-specific insulin action were determined. Tissue lipid profiles were analysed by mass spectrometry and inflammatory markers were measured in adipose tissue, liver and skeletal muscle. RESULTS Glucose intolerance developed within 3 days of the HFD and did not deteriorate further in the period to 12 weeks. Whole-body insulin resistance, measured by hyperinsulinaemic-euglycaemic clamp, was detected after 1 week of HFD and was due to hepatic insulin resistance. Adipose tissue was insulin resistant after 1 week, while skeletal muscle displayed insulin resistance at 3 weeks, coinciding with a defect in glucose disposal. Interestingly, no further deterioration in insulin sensitivity was observed in any tissue after this initial defect. Diacylglycerol content was increased in liver and muscle when insulin resistance first developed, while the onset of insulin resistance in adipose tissue was associated with increases in ceramide and sphingomyelin. Adipose tissue inflammation was only detected at 16 weeks of HFD and did not correlate with the induction of insulin resistance. CONCLUSIONS/INTERPRETATION HFD-induced whole-body insulin resistance is initiated by impaired hepatic insulin action and exacerbated by skeletal muscle insulin resistance and is associated with the accumulation of specific bioactive lipid species.
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Shi L, Shi T, Broadley MR, White PJ, Long Y, Meng J, Xu F, Hammond JP. High-throughput root phenotyping screens identify genetic loci associated with root architectural traits in Brassica napus under contrasting phosphate availabilities. ANNALS OF BOTANY 2013; 112:381-9. [PMID: 23172414 PMCID: PMC3698377 DOI: 10.1093/aob/mcs245] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 09/25/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Phosphate (Pi) deficiency in soils is a major limiting factor for crop growth worldwide. Plant growth under low Pi conditions correlates with root architectural traits and it may therefore be possible to select these traits for crop improvement. The aim of this study was to characterize root architectural traits, and to test quantitative trait loci (QTL) associated with these traits, under low Pi (LP) and high Pi (HP) availability in Brassica napus. METHODS Root architectural traits were characterized in seedlings of a double haploid (DH) mapping population (n = 190) of B. napus ['Tapidor' × 'Ningyou 7' (TNDH)] using high-throughput phenotyping methods. Primary root length (PRL), lateral root length (LRL), lateral root number (LRN), lateral root density (LRD) and biomass traits were measured 12 d post-germination in agar at LP and HP. KEY RESULTS In general, root and biomass traits were highly correlated under LP and HP conditions. 'Ningyou 7' had greater LRL, LRN and LRD than 'Tapidor', at both LP and HP availability, but smaller PRL. A cluster of highly significant QTL for LRN, LRD and biomass traits at LP availability were identified on chromosome A03; QTL for PRL were identified on chromosomes A07 and C06. CONCLUSIONS High-throughput phenotyping of Brassica can be used to identify root architectural traits which correlate with shoot biomass. It is feasible that these traits could be used in crop improvement strategies. The identification of QTL linked to root traits under LP and HP conditions provides further insights on the genetic basis of plant tolerance to P deficiency, and these QTL warrant further dissection.
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Middleton AD, Morrison TA, Fortin JK, Robbins CT, Proffitt KM, White PJ, McWhirter DE, Koel TM, Brimeyer DG, Fairbanks WS, Kauffman MJ. Grizzly bear predation links the loss of native trout to the demography of migratory elk in Yellowstone. Proc Biol Sci 2013; 280:20130870. [PMID: 23677350 DOI: 10.1098/rspb.2013.0870] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The loss of aquatic subsidies such as spawning salmonids is known to threaten a number of terrestrial predators, but the effects on alternative prey species are poorly understood. At the heart of the Greater Yellowstone ecosystem, an invasion of lake trout has driven a dramatic decline of native cutthroat trout that migrate up the shallow tributaries of Yellowstone Lake to spawn each spring. We explore whether this decline has amplified the effect of a generalist consumer, the grizzly bear, on populations of migratory elk that summer inside Yellowstone National Park (YNP). Recent studies of bear diets and elk populations indicate that the decline in cutthroat trout has contributed to increased predation by grizzly bears on the calves of migratory elk. Additionally, a demographic model that incorporates the increase in predation suggests that the magnitude of this diet shift has been sufficient to reduce elk calf recruitment (4-16%) and population growth (2-11%). The disruption of this aquatic-terrestrial linkage could permanently alter native species interactions in YNP. Although many recent ecological changes in YNP have been attributed to the recovery of large carnivores--particularly wolves--our work highlights a growing role of human impacts on the foraging behaviour of grizzly bears.
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Bengough AG, White PJ. Future roots of productivity. (Preface). JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:1179. [PMID: 23616993 DOI: 10.1093/jxb/ert033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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Broadley MR, Chilimba ADC, Joy EJM, Young SD, Black CR, Ander LE, Watts MJ, Hurst R, Fairweather-Tait SJ, White PJ, Gibson RS. Dietary requirements for magnesium, but not calcium, are likely to be met in Malawi based on national food supply data. INT J VITAM NUTR RES 2013; 82:192-9. [PMID: 23258400 DOI: 10.1024/0300-9831/a000111] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Mineral malnutrition is widespread in sub-Saharan Africa but its extent is difficult to quantify. Using Malawi as a case study, the aim of this work was to investigate the adequacy of calcium (Ca) and magnesium (Mg) nutrition by combining national food supply and food composition data with a new spatial survey of maize grain. Non-maize dietary sources of Ca and Mg were estimated using existing food supply and composition data. Calcium and Mg concentrations in maize grain were determined at 88 field sites, representing > 75 % of Malawis land area in terms of soil classification. Median maize grain concentrations from the survey were 34 and 845 mg kg(-1), representing a per capita supply of 12 and 299 mg d(-1) of Ca and Mg, respectively. Combining these data with food supply and composition data reveals that average Ca nutrition is likely to be inadequate for many individuals, whereas average Mg nutrition appears adequate. Optimal supply of Ca per capita depends critically on balanced food availability and choice. Since maize grain sourced from highly calcareous soils is still unlikely to deliver > 5 % of estimated average requirements, agronomic solutions to rectify Ca malnutrition via maize are limited, in comparison with strategies for dietary diversification.
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White PJ, George TS, Dupuy LX, Karley AJ, Valentine TA, Wiesel L, Wishart J. Root traits for infertile soils. FRONTIERS IN PLANT SCIENCE 2013; 4:193. [PMID: 23781228 PMCID: PMC3678079 DOI: 10.3389/fpls.2013.00193] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 05/24/2013] [Indexed: 05/18/2023]
Abstract
Crop production is often restricted by the availability of essential mineral elements. For example, the availability of N, P, K, and S limits low-input agriculture, the phytoavailability of Fe, Zn, and Cu limits crop production on alkaline and calcareous soils, and P, Mo, Mg, Ca, and K deficiencies, together with proton, Al and Mn toxicities, limit crop production on acid soils. Since essential mineral elements are acquired by the root system, the development of crop genotypes with root traits increasing their acquisition should increase yields on infertile soils. This paper examines root traits likely to improve the acquisition of these elements and observes that, although the efficient acquisition of a particular element requires a specific set of root traits, suites of traits can be identified that benefit the acquisition of a group of mineral elements. Elements can be divided into three Groups based on common trait requirements. Group 1 comprises N, S, K, B, and P. Group 2 comprises Fe, Zn, Cu, Mn, and Ni. Group 3 contains mineral elements that rarely affect crop production. It is argued that breeding for a limited number of distinct root ideotypes, addressing particular combinations of mineral imbalances, should be pursued.
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White PJ, Broadley MR, Thompson JA, McNicol JW, Crawley MJ, Poulton PR, Johnston AE. Testing the distinctness of shoot ionomes of angiosperm families using the Rothamsted Park Grass Continuous Hay Experiment. THE NEW PHYTOLOGIST 2012; 196:101-109. [PMID: 22803633 DOI: 10.1111/j.1469-8137.2012.04228.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
• The ionome is the elemental composition of a tissue or organism. Phylogenetic variation in the ionomes of plant shoots has been widely reported based on controlled experiments, vegetation surveys and literature meta-analyses. However, environmental effects on phylogenetic variation in shoot ionomes have not been quantified. This study tests the hypothesis that phylogenetic variation in shoot ionomes is robust to environmental perturbation and that plant families can be distinguished by their shoot ionomes. • Herbage was sampled from six subplots of the Rothamsted Park Grass Experiment. Subplots had received contrasting fertilizer treatments since 1856. Herbage was separated into its constituent species (n = 21) and concentrations of eleven mineral elements were determined in dried shoot material. • Shoot concentrations of calcium (Ca), zinc (Zn), manganese (Mn), magnesium (Mg) and sodium (Na) showed significant variation associated with plant species, and responded similarly to fertilizer treatments in diverse plant species. Species × treatment interactions were indicated for phosphorus (P), potassium (K), nickel (Ni), copper (Cu) and iron (Fe). Plant families could be distinguished by their shoot ionomes. The most informative elements for discriminant analysis were Ca > Mg > Ni > S > Na > Zn > K > Cu > Fe > Mn > P. • Whilst shoot ionomes were sensitive to fertilizer treatment, phylogenetic variation in a subset of the shoot ionome (Ca, Zn, Mn, Mg) was robust to this environmental perturbation.
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Dietrich RC, Bengough AG, Jones HG, White PJ. A new physical interpretation of plant root capacitance. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:6149-59. [PMID: 23028023 PMCID: PMC3481205 DOI: 10.1093/jxb/ers264] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Capacitance has been used as a non-destructive measure of root system size for 30 years. The equipment required is cheap and simple to apply in both field and laboratory. Good linear correlations have been reported between capacitance and root mass. A model by F. N. Dalton, predicting a linear relationship between these two variables, has become accepted widely. This model was tested for barley (Hordeum vulgare) grown hydroponically using treatments that included: raising roots out of solution, cutting roots at positions below the solution surface, and varying the distance between plant electrode and the solution surface. Although good linear correlations were found between capacitance and mass for whole root systems, when roots were raised out of solution capacitances were not linearly related to submerged root mass. Excision of roots in the solution had negligible effect on the measured capacitance. These latter observations conflict with Dalton's model. Capacitance correlated linearly with the sum of root cross-sectional areas at the solution surface and inversely with distance between plant electrode and solution surface. A new model for capacitance is proposed that is consistent with these observations.
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Veneklaas EJ, Lambers H, Bragg J, Finnegan PM, Lovelock CE, Plaxton WC, Price CA, Scheible WR, Shane MW, White PJ, Raven JA. Opportunities for improving phosphorus-use efficiency in crop plants. THE NEW PHYTOLOGIST 2012; 195:306-320. [PMID: 22691045 DOI: 10.1111/j.1469-8137.2012.04190.x] [Citation(s) in RCA: 339] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Limitation of grain crop productivity by phosphorus (P) is widespread and will probably increase in the future. Enhanced P efficiency can be achieved by improved uptake of phosphate from soil (P-acquisition efficiency) and by improved productivity per unit P taken up (P-use efficiency). This review focuses on improved P-use efficiency, which can be achieved by plants that have overall lower P concentrations, and by optimal distribution and redistribution of P in the plant allowing maximum growth and biomass allocation to harvestable plant parts. Significant decreases in plant P pools may be possible, for example, through reductions of superfluous ribosomal RNA and replacement of phospholipids by sulfolipids and galactolipids. Improvements in P distribution within the plant may be possible by increased remobilization from tissues that no longer need it (e.g. senescing leaves) and reduced partitioning of P to developing grains. Such changes would prolong and enhance the productive use of P in photosynthesis and have nutritional and environmental benefits. Research considering physiological, metabolic, molecular biological, genetic and phylogenetic aspects of P-use efficiency is urgently needed to allow significant progress to be made in our understanding of this complex trait.
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Rios JJ, Ó Lochlainn S, Devonshire J, Graham NS, Hammond JP, King GJ, White PJ, Kurup S, Broadley MR. Distribution of calcium (Ca) and magnesium (Mg) in the leaves of Brassica rapa under varying exogenous Ca and Mg supply. ANNALS OF BOTANY 2012; 109:1081-9. [PMID: 22362665 PMCID: PMC3336946 DOI: 10.1093/aob/mcs029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Accepted: 01/17/2012] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS Leafy vegetable Brassica crops are an important source of dietary calcium (Ca) and magnesium (Mg) and represent potential targets for increasing leaf Ca and Mg concentrations through agronomy or breeding. Although the internal distribution of Ca and Mg within leaves affects the accumulation of these elements, such data are not available for Brassica. The aim of this study was to characterize the internal distribution of Ca and Mg in the leaves of a vegetable Brassica and to determine the effects of altered exogenous Ca and Mg supply on this distribution. METHODS Brassica rapa ssp. trilocularis 'R-o-18' was grown at four different Ca:Mg treatments for 21 d in a controlled environment. Concentrations of Ca and Mg were determined in fully expanded leaves using inductively coupled plasma-mass spectrometry (ICP-MS). Internal distributions of Ca and Mg were determined in transverse leaf sections at the base and apex of leaves using energy-dispersive X-ray spectroscopy (EDS) with cryo-scanning electron microscopy (cryo-SEM). KEY RESULTS Leaf Ca and Mg concentrations were greatest in palisade and spongy mesophyll cells, respectively, although this was dependent on exogenous supply. Calcium accumulation in palisade mesophyll cells was enhanced slightly under high Mg supply; in contrast, Mg accumulation in spongy mesophyll cells was not affected by Ca supply. CONCLUSIONS The results are consistent with Arabidopsis thaliana and other Brassicaceae, providing phenotypic evidence that conserved mechanisms regulate leaf Ca and Mg distribution at a cellular scale. The future study of Arabidopsis gene orthologues in mutants of this reference B. rapa genotype will improve our understanding of Ca and Mg homeostasis in plants and may provide a model-to-crop translation pathway for targeted breeding.
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De Smet I, White PJ, Bengough AG, Dupuy L, Parizot B, Casimiro I, Heidstra R, Laskowski M, Lepetit M, Hochholdinger F, Draye X, Zhang H, Broadley MR, Péret B, Hammond JP, Fukaki H, Mooney S, Lynch JP, Nacry P, Schurr U, Laplaze L, Benfey P, Beeckman T, Bennett M. Analyzing lateral root development: how to move forward. THE PLANT CELL 2012; 24:15-20. [PMID: 22227890 PMCID: PMC3289553 DOI: 10.1105/tpc.111.094292] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 12/15/2011] [Accepted: 12/15/2011] [Indexed: 05/18/2023]
Abstract
Roots are important to plants for a wide variety of processes, including nutrient and water uptake, anchoring and mechanical support, storage functions, and as the major interface between the plant and various biotic and abiotic factors in the soil environment. Therefore, understanding the development and architecture of roots holds potential for the manipulation of root traits to improve the productivity and sustainability of agricultural systems and to better understand and manage natural ecosystems. While lateral root development is a traceable process along the primary root and different stages can be found along this longitudinal axis of time and development, root system architecture is complex and difficult to quantify. Here, we comment on assays to describe lateral root phenotypes and propose ways to move forward regarding the description of root system architecture, also considering crops and the environment.
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White PJ, Broadley MR. Physiological limits to zinc biofortification of edible crops. FRONTIERS IN PLANT SCIENCE 2011; 2:80. [PMID: 22645552 PMCID: PMC3355814 DOI: 10.3389/fpls.2011.00080] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 10/26/2011] [Indexed: 05/20/2023]
Abstract
It has been estimated that one-third of the world's population lack sufficient Zn for adequate nutrition. This can be alleviated by increasing dietary Zn intakes through Zn biofortification of edible crops. Biofortification strategies include the application of Zn-fertilizers and the development of crop genotypes that acquire more Zn from the soil and accumulate it in edible portions. Zinc concentrations in roots, leaves, and stems can be increased through the application of Zn-fertilizers. Root Zn concentrations of up to 500-5000 mg kg(-1) dry matter (DM), and leaf Zn concentrations of up to 100-700 mg kg(-1) DM, can be achieved without loss of yield when Zn-fertilizers are applied to the soil. It is possible that greater Zn concentrations in non-woody shoot tissues can be achieved using foliar Zn-fertilizers. By contrast, Zn concentrations in fruits, seeds, and tubers are severely limited by low Zn mobility in the phloem and Zn concentrations higher than 30-100 mg kg(-1) DM are rarely observed. However, genetically modified plants with improved abilities to translocate Zn in the phloem might be used to biofortify these phloem-fed tissues. In addition, genetically modified plants with increased tolerance to high tissue Zn concentrations could be used to increase Zn concentrations in all edible produce and, thereby, increase dietary Zn intakes.
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Hammond JP, Broadley MR, Bowen HC, Spracklen WP, Hayden RM, White PJ. Gene expression changes in phosphorus deficient potato (Solanum tuberosum L.) leaves and the potential for diagnostic gene expression markers. PLoS One 2011; 6:e24606. [PMID: 21935429 PMCID: PMC3173461 DOI: 10.1371/journal.pone.0024606] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 08/14/2011] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND There are compelling economic and environmental reasons to reduce our reliance on inorganic phosphate (Pi) fertilisers. Better management of Pi fertiliser applications is one option to improve the efficiency of Pi fertiliser use, whilst maintaining crop yields. Application rates of Pi fertilisers are traditionally determined from analyses of soil or plant tissues. Alternatively, diagnostic genes with altered expression under Pi limiting conditions that suggest a physiological requirement for Pi fertilisation, could be used to manage Pifertiliser applications, and might be more precise than indirect measurements of soil or tissue samples. RESULTS We grew potato (Solanum tuberosum L.) plants hydroponically, under glasshouse conditions, to control their nutrient status accurately. Samples of total leaf RNA taken periodically after Pi was removed from the nutrient solution were labelled and hybridised to potato oligonucleotide arrays. A total of 1,659 genes were significantly differentially expressed following Pi withdrawal. These included genes that encode proteins involved in lipid, protein, and carbohydrate metabolism, characteristic of Pi deficient leaves and included potential novel roles for genes encoding patatin like proteins in potatoes. The array data were analysed using a support vector machine algorithm to identify groups of genes that could predict the Pi status of the crop. These groups of diagnostic genes were tested using field grown potatoes that had either been fertilised or unfertilised. A group of 200 genes could correctly predict the Pi status of field grown potatoes. CONCLUSIONS This paper provides a proof-of-concept demonstration for using microarrays and class prediction tools to predict the Pi status of a field grown potato crop. There is potential to develop this technology for other biotic and abiotic stresses in field grown crops. Ultimately, a better understanding of crop stresses may improve our management of the crop, improving the sustainability of agriculture.
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Hammond JP, Mayes S, Bowen HC, Graham NS, Hayden RM, Love CG, Spracklen WP, Wang J, Welham SJ, White PJ, King GJ, Broadley MR. Regulatory hotspots are associated with plant gene expression under varying soil phosphorus supply in Brassica rapa. PLANT PHYSIOLOGY 2011; 156:1230-41. [PMID: 21527424 PMCID: PMC3135916 DOI: 10.1104/pp.111.175612] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 04/15/2011] [Indexed: 05/21/2023]
Abstract
Gene expression is a quantitative trait that can be mapped genetically in structured populations to identify expression quantitative trait loci (eQTL). Genes and regulatory networks underlying complex traits can subsequently be inferred. Using a recently released genome sequence, we have defined cis- and trans-eQTL and their environmental response to low phosphorus (P) availability within a complex plant genome and found hotspots of trans-eQTL within the genome. Interval mapping, using P supply as a covariate, revealed 18,876 eQTL. trans-eQTL hotspots occurred on chromosomes A06 and A01 within Brassica rapa; these were enriched with P metabolism-related Gene Ontology terms (A06) as well as chloroplast- and photosynthesis-related terms (A01). We have also attributed heritability components to measures of gene expression across environments, allowing the identification of novel gene expression markers and gene expression changes associated with low P availability. Informative gene expression markers were used to map eQTL and P use efficiency-related QTL. Genes responsive to P supply had large environmental and heritable variance components. Regulatory loci and genes associated with P use efficiency identified through eQTL analysis are potential targets for further characterization and may have potential for crop improvement.
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Hammond JP, White PJ. Sugar signaling in root responses to low phosphorus availability. PLANT PHYSIOLOGY 2011; 156:1033-40. [PMID: 21487049 PMCID: PMC3135921 DOI: 10.1104/pp.111.175380] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 04/10/2011] [Indexed: 05/18/2023]
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Newton AC, Flavell AJ, George TS, Leat P, Mullholland B, Ramsay L, Revoredo-Giha C, Russell J, Steffenson BJ, Swanston JS, Thomas WTB, Waugh R, White PJ, Bingham IJ. Crops that feed the world 4. Barley: a resilient crop? Strengths and weaknesses in the context of food security. Food Secur 2011. [DOI: 10.1007/s12571-011-0126-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Griffin KA, Hebblewhite M, Robinson HS, Zager P, Barber-Meyer SM, Christianson D, Creel S, Harris NC, Hurley MA, Jackson DH, Johnson BK, Myers WL, Raithel JD, Schlegel M, Smith BL, White C, White PJ. Neonatal mortality of elk driven by climate, predator phenology and predator community composition. J Anim Ecol 2011; 80:1246-57. [PMID: 21615401 DOI: 10.1111/j.1365-2656.2011.01856.x] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
1. Understanding the interaction among predators and between predation and climate is critical to understanding the mechanisms for compensatory mortality. We used data from 1999 radio-marked neonatal elk (Cervus elaphus) calves from 12 populations in the north-western United States to test for effects of predation on neonatal survival, and whether predation interacted with climate to render mortality compensatory. 2. Weibull survival models with a random effect for each population were fit as a function of the number of predator species in a community (3-5), seven indices of climatic variability, sex, birth date, birth weight, and all interactions between climate and predators. Cumulative incidence functions (CIF) were used to test whether the effects of individual species of predators were additive or compensatory. 3. Neonatal elk survival to 3 months declined following hotter previous summers and increased with higher May precipitation, especially in areas with wolves and/or grizzly bears. Mortality hazards were significantly lower in systems with only coyotes (Canis latrans), cougars (Puma concolor) and black bears (Ursus americanus) compared to higher mortality hazards experienced with gray wolves (Canis lupus) and grizzly bears (Ursus horribilis). 4. In systems with wolves and grizzly bears, mortality by cougars decreased, and predation by bears was the dominant cause of neonatal mortality. Only bear predation appeared additive and occurred earlier than other predators, which may render later mortality by other predators compensatory as calves age. Wolf predation was low and most likely a compensatory source of mortality for neonatal elk calves. 5. Functional redundancy and interspecific competition among predators may combine with the effects of climate on vulnerability to predation to drive compensatory mortality of neonatal elk calves. The exception was the evidence for additive bear predation. These results suggest that effects of predation by recovering wolves on neonatal elk survival, a contentious issue for management of elk populations, may be less important than the composition of the predator community. Future studies would benefit by synthesizing overwinter calf and adult-survival data sets, ideally from experimental studies, to test the roles of predation in annual compensatory and additive mortality of elk.
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Subramanian NK, White PJ, Broadley MR, Ramsay G. The three-dimensional distribution of minerals in potato tubers. ANNALS OF BOTANY 2011; 107:681-91. [PMID: 21289026 PMCID: PMC3064541 DOI: 10.1093/aob/mcr009] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS The three-dimensional distributions of mineral elements in potato tubers provide insight into their mechanisms of transport and deposition. Many of these minerals are essential to a healthy human diet, and characterizing their distribution within the potato tuber will guide the effective utilization of this staple foodstuff. METHODS The variation in mineral composition within the tuber was determined in three dimensions, after determining the orientation of the harvested tuber in the soil. The freeze-dried tuber samples were analysed for minerals using inductively coupled plasma-mass spectrometry (ICP-MS). Minerals measured included those of nutritional significance to the plant and to human consumers, such as iron, zinc, copper, calcium, magnesium, manganese, phosphorus, potassium and sulphur. KEY RESULTS The concentrations of most minerals were higher in the skin than in the flesh of tubers. The potato skin contained about 17 % of total tuber zinc, 34 % of calcium and 55 % of iron. On a fresh weight basis, most minerals were higher in tuber flesh at the stem end than the bud end of the tuber. Potassium, however, displayed a gradient in the opposite direction. The concentrations of phosphorus, copper and calcium decreased from the periphery towards the centre of the tuber. CONCLUSIONS The distribution of minerals varies greatly within the potato tuber. Low concentrations of some minerals relative to those in leaves may be due to their low mobility in phloem, whereas high concentrations in the skin may reflect direct uptake from the soil across the periderm. In tuber flesh, different minerals show distinct patterns of distribution in the tuber, several being consistent with phloem unloading in the tuber and limited onward movement. These findings have implications both for understanding directed transport of minerals in plants to stem-derived storage organs and for the dietary implications of different food preparation methods for potato tubers.
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Ó Lochlainn S, Bowen HC, Fray RG, Hammond JP, King GJ, White PJ, Graham NS, Broadley MR. Tandem quadruplication of HMA4 in the zinc (Zn) and cadmium (Cd) hyperaccumulator Noccaea caerulescens. PLoS One 2011; 6:e17814. [PMID: 21423774 PMCID: PMC3053397 DOI: 10.1371/journal.pone.0017814] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 02/10/2011] [Indexed: 11/19/2022] Open
Abstract
Zinc (Zn) and cadmium (Cd) hyperaccumulation may have evolved twice in the Brassicaceae, in Arabidopsis halleri and in the Noccaea genus. Tandem gene duplication and deregulated expression of the Zn transporter, HMA4, has previously been linked to Zn/Cd hyperaccumulation in A. halleri. Here, we tested the hypothesis that tandem duplication and deregulation of HMA4 expression also occurs in Noccaea.A Noccaea caerulescens genomic library was generated, containing 36,864 fosmid pCC1FOS™ clones with insert sizes ∼20-40 kbp, and screened with a PCR-generated HMA4 genomic probe. Gene copy number within the genome was estimated through DNA fingerprinting and pooled fosmid pyrosequencing. Gene copy numbers within individual clones was determined by PCR analyses with novel locus specific primers. Entire fosmids were then sequenced individually and reads equivalent to 20-fold coverage were assembled to generate complete whole contigs.Four tandem HMA4 repeats were identified in a contiguous sequence of 101,480 bp based on sequence overlap identities. These were flanked by regions syntenous with up and downstream regions of AtHMA4 in Arabidopsis thaliana. Promoter-reporter β-glucuronidase (GUS) fusion analysis of a NcHMA4 in A. thaliana revealed deregulated expression in roots and shoots, analogous to AhHMA4 promoters, but distinct from AtHMA4 expression which localised to the root vascular tissue.This remarkable consistency in tandem duplication and deregulated expression of metal transport genes between N. caerulescens and A. halleri, which last shared a common ancestor >40 mya, provides intriguing evidence that parallel evolutionary pathways may underlie Zn/Cd hyperaccumulation in Brassicaceae.
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Geremia C, White PJ, Wallen RL, Watson FGR, Treanor JJ, Borkowski J, Potter CS, Crabtree RL. Predicting bison migration out of Yellowstone National Park using bayesian models. PLoS One 2011; 6:e16848. [PMID: 21340035 PMCID: PMC3038930 DOI: 10.1371/journal.pone.0016848] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Accepted: 01/17/2011] [Indexed: 11/21/2022] Open
Abstract
Long distance migrations by ungulate species often surpass the boundaries of preservation areas where conflicts with various publics lead to management actions that can threaten populations. We chose the partially migratory bison (Bison bison) population in Yellowstone National Park as an example of integrating science into management policies to better conserve migratory ungulates. Approximately 60% of these bison have been exposed to bovine brucellosis and thousands of migrants exiting the park boundary have been culled during the past two decades to reduce the risk of disease transmission to cattle. Data were assimilated using models representing competing hypotheses of bison migration during 1990-2009 in a hierarchal bayesian framework. Migration differed at the scale of herds, but a single unifying logistic model was useful for predicting migrations by both herds. Migration beyond the northern park boundary was affected by herd size, accumulated snow water equivalent, and aboveground dried biomass. Migration beyond the western park boundary was less influenced by these predictors and process model performance suggested an important control on recent migrations was excluded. Simulations of migrations over the next decade suggest that allowing increased numbers of bison beyond park boundaries during severe climate conditions may be the only means of avoiding episodic, large-scale reductions to the Yellowstone bison population in the foreseeable future. This research is an example of how long distance migration dynamics can be incorporated into improved management policies.
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Kersten P, White PJ, Tennant A. Construct Validity of the Holistic Complementary and Alternative Medicines Questionnaire (HCAMQ)-An Investigation Using Modern Psychometric Approaches. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2011; 2011:396327. [PMID: 19793835 PMCID: PMC3135427 DOI: 10.1093/ecam/nep141] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Accepted: 08/17/2009] [Indexed: 11/23/2022]
Abstract
The scientific basis of efficacy studies of complementary medicine requires the availability of validated measures. The Holistic Complementary and Alternative Medicine Questionnaire (HCAMQ) is one such measure. This article aimed to examine its construct validity, using a modern psychometric approach. The HCAMQ was completed by 221 patients (mean age 66.8, SD 8.29, 58% females) with chronic stable pain predominantly from a single joint (hip or knee) of mechanical origin, waiting for a hip (40%) or knee (60%) joint replacement, on enrolment in a study investigating the effects of acupuncture and placebo controls. The HCAMQ contains a Holistic Health (HH) Subscale (five items) and a CAM subscale (six items). Validity of the subscales was tested using Cronbach alpha's, factor analysis, Mokken scaling and Rasch analysis, which did not support the original two-factor structure of the scale. A five-item HH subscale and a four-item CAM subscale (worded in a negative direction) fitted the Rasch model and were unidimensional (χ2 = 8.44, P = 0.39, PSI = 0.69 versus χ2 = 17.33, P = 0.03, PSI = 0.77). Two CAM items (worded in the positive direction) had significant misfit. In conclusion, we have shown that the original two-factor structure of the HCAMQ could not be supported but that two valid shortened subscales can be used, one for HH Beliefs (four-item HH), and the other for CAM Beliefs (four-item CAM). It is recommended that consideration is given to rewording the two discarded positively worded CAM questions to enhance construct validity.
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Lochlainn SO, Fray RG, Hammond JP, King GJ, White PJ, Young SD, Broadley MR. Generation of nonvernal-obligate, faster-cycling Noccaea caerulescens lines through fast neutron mutagenesis. THE NEW PHYTOLOGIST 2011; 189:409-14. [PMID: 21058953 DOI: 10.1111/j.1469-8137.2010.03554.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Noccaea caerulescens (formerly Thlaspi caerulescens) is a widely studied metal hyperaccumulator. However, molecular genetic studies are challenging in this species because of its vernal-obligate biennial life cycle of 7-9months. Here, we describe the development of genetically stable, faster cycling lines of N. caerulescens which are nonvernal-obligate. A total of 5500 M(0) seeds from Saint Laurent Le Minier (France) were subjected to fast neutron mutagenesis. Following vernalization of young plants, 79% of plants survived to maturity. In all, 80,000 M(2) lines were screened for flowering in the absence of vernalization. Floral initials were observed in 35 lines, with nine flowering in <12wk. Two lines (A2 and A7) were selfed to the M(4) generation. Floral initials were observed 66 and 87d after sowing (DAS) in A2 and A7, respectively. Silicle development occurred for all A2 and for most A7 at 92 and 123 DAS, respectively. Floral or silicle development was not observed in wild-type (WT) plants. Leaf zinc (Zn) concentration was similar in WT, A2 and A7 lines. These lines should facilitate future genetic studies of this remarkable species. Seed is publicly available through the European Arabidopsis Stock Centre (NASC).
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Lux A, Martinka M, Vaculík M, White PJ. Root responses to cadmium in the rhizosphere: a review. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:21-37. [PMID: 20855455 DOI: 10.1093/jxb/erq281] [Citation(s) in RCA: 523] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
This article reviews the responses of plant roots to elevated rhizosphere cadmium (Cd) concentrations. Cadmium enters plants from the soil solution. It traverses the root through symplasmic or apoplasmic pathways before entering the xylem and being translocated to the shoot. Leaf Cd concentrations in excess of 5-10 μg g(-1) dry matter are toxic to most plants, and plants have evolved mechanisms to limit Cd translocation to the shoot. Cadmium movement through the root symplasm is thought to be restricted by the production of phytochelatins and the sequestration of Cd-chelates in vacuoles. Apoplasmic movement of Cd to the xylem can be restricted by the development of the exodermis, endodermis, and other extracellular barriers. Increasing rhizosphere Cd concentrations increase Cd accumulation in the plant, especially in the root. The presence of Cd in the rhizosphere inhibits root elongation and influences root anatomy. Cadmium concentrations are greater in the root apoplasm than in the root symplasm, and tissue Cd concentrations decrease from peripheral to inner root tissues. This article reviews current knowledge of the proteins involved in the transport of Cd across root cell membranes and its detoxification through sequestration in root vacuoles. It describes the development of apoplastic barriers to Cd movement to the xylem and highlights recent experiments indicating that their maturation is accelerated by high Cd concentrations in their immediate locality. It concludes that accelerated maturation of the endodermis in response to local Cd availability is of functional significance in protecting the shoot from excessive Cd loads.
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White PJ, Garrott RA, Hamlin KL, Cook RC, Cook JG, Cunningham JA. Body condition and pregnancy in northern Yellowstone elk: evidence for predation risk effects? ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2011; 21:3-8. [PMID: 21516883 DOI: 10.1890/09-2123.1] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
S. Creel et al. reported a negative correlation between fecal progesterone concentrations and elk:wolf ratios in greater Yellowstone elk (Cervus elaphus) herds and interpreted this correlation as evidence that pregnancy rates of elk decreased substantially in the presence of wolves (Canis lupus). Apparently, the hypothesized mechanism is that decreased forage intake reduces body condition and either results in elk failing to conceive during the autumn rut or elk losing the fetus during winter. We tested this hypothesis by comparing age-specific body condition (percentage ingesta-free body fat) and pregnancy rates for northern Yellowstone elk, one of the herds sampled by Creel et al., before (1962-1968) and after (2000-2006) wolf restoration using indices developed and calibrated for Rocky Mountain elk. Mean age-adjusted percentage body fat of female elk was similarly high in both periods (9.0%-0.9% pre-wolf; 8.9%-0.8% post-wolf). Estimated pregnancy rates (proportion of females that were pregnant) were 0.91 pre-wolf and 0.87 post-wolf for 4-9 year-old elk (95% CI on difference = -0.15 to 0.03, P = 0.46) and 0.64 pre-wolf and 0.78 post-wolf for elk > 9 years old (95% CI on difference = -0.01 to 0.27, P = 0.06). Thus, there was little evidence in these data to support strong effects of wolf presence on elk pregnancy. We caution that multiple lines of evidence and/or strong validation should be brought to bear before relying on indirect measures of how predators affect pregnancy rates.
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