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Sigalas PP, Buchner P, Kröper A, Hawkesford MJ. The Functional Diversity of the High-Affinity Nitrate Transporter Gene Family in Hexaploid Wheat: Insights from Distinct Expression Profiles. Int J Mol Sci 2023; 25:509. [PMID: 38203680 PMCID: PMC10779101 DOI: 10.3390/ijms25010509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/22/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
High-affinity nitrate transporters (NRT) are key components for nitrogen (N) acquisition and distribution within plants. However, insights on these transporters in wheat are scarce. This study presents a comprehensive analysis of the NRT2 and NRT3 gene families, where the aim is to shed light on their functionality and to evaluate their responses to N availability. A total of 53 NRT2s and 11 NRT3s were identified in the bread wheat genome, and these were grouped into different clades and homoeologous subgroups. The transcriptional dynamics of the identified NRT2 and NRT3 genes, in response to N starvation and nitrate resupply, were examined by RT-qPCR in the roots and shoots of hydroponically grown wheat plants through a time course experiment. Additionally, the spatial expression patterns of these genes were explored within the plant. The NRT2s of clade 1, TaNRT2.1-2.6, showed a root-specific expression and significant upregulation in response to N starvation, thus emphasizing a role in N acquisition. However, most of the clade 2 NRT2s displayed reduced expression under N-starved conditions. Nitrate resupply after N starvation revealed rapid responsiveness in TaNRT2.1-2.6, while clade 2 genes exhibited gradual induction, primarily in the roots. TaNRT2.18 was highly expressed in above-ground tissues and exhibited distinct nitrate-related response patterns for roots and shoots. The TaNRT3 gene expression closely paralleled the profiles of TaNRT2.1-2.6 in response to nitrate induction. These findings enhance the understanding of NRT2 and NRT3 involvement in nitrogen uptake and utilization, and they could have practical implications for improving nitrogen use efficiency. The study also recommends a standardized nomenclature for wheat NRT2 genes, thereby addressing prior naming inconsistencies.
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Affiliation(s)
- Petros P. Sigalas
- Rothamsted Research, West Common, Harpenden AL5 2JQ, UK; (P.B.); (M.J.H.)
| | - Peter Buchner
- Rothamsted Research, West Common, Harpenden AL5 2JQ, UK; (P.B.); (M.J.H.)
| | - Alex Kröper
- Faculty of Agronomy, University of Hohenheim, 70599 Stuttgart, Germany;
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Shewry PR, Wood AJ, Hassall KL, Pellny TK, Riche A, Hussain A, Shi Z, Mosleth EF, Charlton M, Poole M, Jones S, Newton K, Penson S, Tucker G, Griffiths S, Hawkesford MJ. Identification of traits underpinning good breadmaking performance of wheat grown with reduced nitrogen fertilisation. J Sci Food Agric 2023; 103:7664-7672. [PMID: 37458104 PMCID: PMC10952534 DOI: 10.1002/jsfa.12848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/13/2023] [Accepted: 07/17/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Nitrogen fertiliser is the major input and cost for wheat production, being required to support the development of the canopy to maximise yield and for the synthesis of the gluten proteins that are necessary for breadmaking. Consequently, current high-yielding cultivars require the use of nitrogen fertilisation levels above the yield optimum to achieve the grain protein content needed for breadmaking. This study aimed to reduce this requirement by identifying traits that allow the use of lower levels of nitrogen fertiliser to produce wheat for breadmaking. RESULTS A range of commercial wheat genotypes (cultivars) were grown in multiple field trials (six sites over 3 years) in the UK with optimal (200 kg Ha-1 ) and suboptimal (150 kg Ha-1 ) application of nitrogen. Bulked grain samples from four sites per year were milled and white flours were baked using three types of breadmaking process. This identified five cultivars that consistently exhibited good breadmaking quality when grown with the lower nitrogen application. Chemical and biochemical analyses showed that the five cultivars were characterised by exhibiting grain protein deviation (GPD) and high dough elasticity. CONCLUSIONS It is possible to develop novel types of wheat that exhibit good breadmaking quality by selecting for GPD and high dough strength. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
| | | | | | | | | | - Abrar Hussain
- Rothamsted ResearchHertfordshireUK
- Department of BiosciencesCOMSATS University IslamabadSahiwalPakistan
| | | | | | | | | | | | | | - Simon Penson
- ADM Milling LimitedCorbyUK
- Campden BRIGloucestershireUK
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Cudjoe DK, Virlet N, Castle M, Riche AB, Mhada M, Waine TW, Mohareb F, Hawkesford MJ. Field phenotyping for African crops: overview and perspectives. Front Plant Sci 2023; 14:1219673. [PMID: 37860243 PMCID: PMC10582954 DOI: 10.3389/fpls.2023.1219673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/07/2023] [Indexed: 10/21/2023]
Abstract
Improvements in crop productivity are required to meet the dietary demands of the rapidly-increasing African population. The development of key staple crop cultivars that are high-yielding and resilient to biotic and abiotic stresses is essential. To contribute to this objective, high-throughput plant phenotyping approaches are important enablers for the African plant science community to measure complex quantitative phenotypes and to establish the genetic basis of agriculturally relevant traits. These advances will facilitate the screening of germplasm for optimum performance and adaptation to low-input agriculture and resource-constrained environments. Increasing the capacity to investigate plant function and structure through non-invasive technologies is an effective strategy to aid plant breeding and additionally may contribute to precision agriculture. However, despite the significant global advances in basic knowledge and sensor technology for plant phenotyping, Africa still lags behind in the development and implementation of these systems due to several practical, financial, geographical and political barriers. Currently, field phenotyping is mostly carried out by manual methods that are prone to error, costly, labor-intensive and may come with adverse economic implications. Therefore, improvements in advanced field phenotyping capabilities and appropriate implementation are key factors for success in modern breeding and agricultural monitoring. In this review, we provide an overview of the current state of field phenotyping and the challenges limiting its implementation in some African countries. We suggest that the lack of appropriate field phenotyping infrastructures is impeding the development of improved crop cultivars and will have a detrimental impact on the agricultural sector and on food security. We highlight the prospects for integrating emerging and advanced low-cost phenotyping technologies into breeding protocols and characterizing crop responses to environmental challenges in field experimentation. Finally, we explore strategies for overcoming the barriers and maximizing the full potential of emerging field phenotyping technologies in African agriculture. This review paper will open new windows and provide new perspectives for breeders and the entire plant science community in Africa.
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Affiliation(s)
- Daniel K. Cudjoe
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, United Kingdom
- School of Water, Energy and Environment, Cranfield University, Cranfield, Bedfordshire, United Kingdom
| | - Nicolas Virlet
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, United Kingdom
| | - March Castle
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, United Kingdom
| | - Andrew B. Riche
- Sustainable Soils and Crops, Rothamsted Research, Harpenden, United Kingdom
| | - Manal Mhada
- AgroBiosciences Department, Mohammed VI Polytechnic University (UM6P), Benguérir, Morocco
| | - Toby W. Waine
- School of Water, Energy and Environment, Cranfield University, Cranfield, Bedfordshire, United Kingdom
| | - Fady Mohareb
- School of Water, Energy and Environment, Cranfield University, Cranfield, Bedfordshire, United Kingdom
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4
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Waqas M, Hawkesford MJ, Geilfus CM. Feeding the world sustainably: efficient nitrogen use. Trends Plant Sci 2023; 28:505-508. [PMID: 36894361 DOI: 10.1016/j.tplants.2023.02.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 05/22/2023]
Abstract
Globally, overuse of nitrogen (N) fertilizers in croplands is causing severe environmental pollution. In this context, Gu et al. suggest environmentally friendly and cost-effective N management practices and Hamani et al. highlight the use of microbial inoculants to improve crop yields, while reducing N-associated environmental pollution and N-fertilizer use.
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Affiliation(s)
- Muhammad Waqas
- Department for Plant Nutrition and Soil Science, Hochschule Geisenheim University, 65366 Geisenheim, Germany
| | | | - Christoph-Martin Geilfus
- Department for Plant Nutrition and Soil Science, Hochschule Geisenheim University, 65366 Geisenheim, Germany.
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5
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Sigalas PP, Buchner P, Thomas SG, Jamois F, Arkoun M, Yvin JC, Bennett MJ, Hawkesford MJ. Nutritional and tissue-specific regulation of cytochrome P450 CYP711A MAX1 homologues and strigolactone biosynthesis in wheat. J Exp Bot 2023; 74:1890-1910. [PMID: 36626359 PMCID: PMC10049918 DOI: 10.1093/jxb/erad008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
Strigolactones (SLs) are a class of phytohormones regulating branching/tillering, and their biosynthesis has been associated with nutritional signals and plant adaptation to nutrient-limiting conditions. The enzymes in the SL biosynthetic pathway downstream of carlactone are of interest as they are responsible for structural diversity in SLs, particularly cytochrome P450 CYP711A subfamily members, such as MORE AXILLARY GROWTH1 (MAX1) in Arabidopsis. We identified 13 MAX1 homologues in wheat, clustering in four clades and five homoeologous subgroups. The utilization of RNA-sequencing data revealed a distinct expression pattern of MAX1 homologues in above- and below-ground tissues, providing insights into the distinct roles of MAX1 homologues in wheat. In addition, a transcriptional analysis showed that SL biosynthetic genes were systematically regulated by nitrogen supply. Nitrogen limitation led to larger transcriptional changes in the basal nodes than phosphorus limitation, which was consistent with the observed tillering suppression, as wheat showed higher sensitivity to nitrogen. The opposite was observed in roots, with phosphorus limitation leading to stronger induction of most SL biosynthetic genes compared with nitrogen limitation. The observed tissue-specific regulation of SL biosynthetic genes in response to nutritional signals is likely to reflect the dual role of SLs as rhizosphere signals and branching inhibitors.
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Affiliation(s)
| | - Peter Buchner
- Rothamsted Research, West Common, Harpenden AL5 2JQ, UK
| | | | - Frank Jamois
- Laboratoire de Physico-Chimie et Bioanalytique, Centre Mondial de l’Innovation Roullier, Timac Agro International, 18 Avenue Franklin Roosevelt, Saint-Malo, 35400, France
| | - Mustapha Arkoun
- Laboratoire de Nutrition Végétale, Centre Mondial de l’Innovation Roullier, Timac Agro International, 18 Avenue Franklin Roosevelt, Saint-Malo, 35400, France
| | - Jean-Claude Yvin
- Laboratoire de Nutrition Végétale, Centre Mondial de l’Innovation Roullier, Timac Agro International, 18 Avenue Franklin Roosevelt, Saint-Malo, 35400, France
| | - Malcolm J Bennett
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
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Li D, Bai D, Tian Y, Li YH, Zhao C, Wang Q, Guo S, Gu Y, Luan X, Wang R, Yang J, Hawkesford MJ, Schnable JC, Jin X, Qiu LJ. Time series canopy phenotyping enables the identification of genetic variants controlling dynamic phenotypes in soybean. J Integr Plant Biol 2023; 65:117-132. [PMID: 36218273 DOI: 10.1111/jipb.13380] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Advances in plant phenotyping technologies are dramatically reducing the marginal costs of collecting multiple phenotypic measurements across several time points. Yet, most current approaches and best statistical practices implemented to link genetic and phenotypic variation in plants have been developed in an era of single-time-point data. Here, we used time-series phenotypic data collected with an unmanned aircraft system for a large panel of soybean (Glycine max (L.) Merr.) varieties to identify previously uncharacterized loci. Specifically, we focused on the dissection of canopy coverage (CC) variation from this rich data set. We also inferred the speed of canopy closure, an additional dimension of CC, from the time-series data, as it may represent an important trait for weed control. Genome-wide association studies (GWASs) identified 35 loci exhibiting dynamic associations with CC across developmental stages. The time-series data enabled the identification of 10 known flowering time and plant height quantitative trait loci (QTLs) detected in previous studies of adult plants and the identification of novel QTLs influencing CC. These novel QTLs were disproportionately likely to act earlier in development, which may explain why they were missed in previous single-time-point studies. Moreover, this time-series data set contributed to the high accuracy of the GWASs, which we evaluated by permutation tests, as evidenced by the repeated identification of loci across multiple time points. Two novel loci showed evidence of adaptive selection during domestication, with different genotypes/haplotypes favored in different geographic regions. In summary, the time-series data, with soybean CC as an example, improved the accuracy and statistical power to dissect the genetic basis of traits and offered a promising opportunity for crop breeding with quantitative growth curves.
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Affiliation(s)
- Delin Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dong Bai
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yu Tian
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ying-Hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chaosen Zhao
- Crops Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Qi Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Shiyu Guo
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Yongzhe Gu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoyan Luan
- Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Ruizhen Wang
- Crops Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, 68583, USA
| | - Malcolm J Hawkesford
- Plant Sciences Department, Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, 68583, USA
| | - Xiuliang Jin
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Li-Juan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/Key Laboratory of Soybean Biology (Beijing) (MOA), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Senapati N, Semenov MA, Halford NG, Hawkesford MJ, Asseng S, Cooper M, Ewert F, van Ittersum MK, Martre P, Olesen JE, Reynolds M, Rötter RP, Webber H. Global wheat production could benefit from closing the genetic yield gap. Nat Food 2022; 3:532-541. [PMID: 37117937 DOI: 10.1038/s43016-022-00540-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 05/20/2022] [Indexed: 04/30/2023]
Abstract
Global food security requires food production to be increased in the coming decades. The closure of any existing genetic yield gap (Yig) by genetic improvement could increase crop yield potential and global production. Here we estimated present global wheat Yig, covering all wheat-growing environments and major producers, by optimizing local wheat cultivars using the wheat model Sirius. The estimated mean global Yig was 51%, implying that global wheat production could benefit greatly from exploiting the untapped global Yig through the use of optimal cultivar designs, utilization of the vast variation available in wheat genetic resources, application of modern advanced breeding tools, and continuous improvements of crop and soil management.
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Affiliation(s)
- Nimai Senapati
- Plant Sciences Department, Rothamsted Research, Harpenden, UK.
| | | | - Nigel G Halford
- Plant Sciences Department, Rothamsted Research, Harpenden, UK
| | | | - Senthold Asseng
- TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mark Cooper
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Centre for Crop Science, Brisbane, Queensland, Australia
| | - Frank Ewert
- Institute of Crop Science and Resource Conservation INRES, University of Bonn, Bonn, Germany
- Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | | | - Pierre Martre
- LEPSE, Université Montpellier, INRAE, Institut Agro Montpellier, Montpellier, France
| | - Jørgen E Olesen
- Department of Agroecology, Aarhus University, Tjele, Denmark
| | - Matthew Reynolds
- International Maize and Wheat Improvement Center, Texcoco, Mexico
| | - Reimund P Rötter
- Tropical Plant Production & Agricultural Systems Modelling (TROPAGS), University of Göttingen, Göttingen, Germany
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Göttingen, Germany
| | - Heidi Webber
- Institute of Crop Science and Resource Conservation INRES, University of Bonn, Bonn, Germany
- Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
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Wan Y, Stewart T, Amrahli M, Evans J, Sharp P, Govindan V, Hawkesford MJ, Shewry PR. Localisation of iron and zinc in grain of biofortified wheat. J Cereal Sci 2022. [DOI: 10.1016/j.jcs.2022.103470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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9
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Huber M, Armbruster L, Etherington RD, De La Torre C, Hawkesford MJ, Sticht C, Gibbs DJ, Hell R, Wirtz M. Disruption of the N α-Acetyltransferase NatB Causes Sensitivity to Reductive Stress in Arabidopsis thaliana. Front Plant Sci 2022; 12:799954. [PMID: 35046984 PMCID: PMC8761761 DOI: 10.3389/fpls.2021.799954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
In Arabidopsis thaliana, the evolutionary conserved N-terminal acetyltransferase (Nat) complexes NatA and NatB co-translationally acetylate 60% of the proteome. Both have recently been implicated in the regulation of plant stress responses. While NatA mediates drought tolerance, NatB is required for pathogen resistance and the adaptation to high salinity and high osmolarity. Salt and osmotic stress impair protein folding and result in the accumulation of misfolded proteins in the endoplasmic reticulum (ER). The ER-membrane resident E3 ubiquitin ligase DOA10 targets misfolded proteins for degradation during ER stress and is conserved among eukaryotes. In yeast, DOA10 recognizes conditional degradation signals (Ac/N-degrons) created by NatA and NatB. Assuming that this mechanism is preserved in plants, the lack of Ac/N-degrons required for efficient removal of misfolded proteins might explain the sensitivity of NatB mutants to protein harming conditions. In this study, we investigate the response of NatB mutants to dithiothreitol (DTT) and tunicamycin (TM)-induced ER stress. We report that NatB mutants are hypersensitive to DTT but not TM, suggesting that the DTT hypersensitivity is caused by an over-reduction of the cytosol rather than an accumulation of unfolded proteins in the ER. In line with this hypothesis, the cytosol of NatB depleted plants is constitutively over-reduced and a global transcriptome analysis reveals that their reductive stress response is permanently activated. Moreover, we demonstrate that doa10 mutants are susceptible to neither DTT nor TM, ruling out a substantial role of DOA10 in ER-associated protein degradation (ERAD) in plants. Contrary to previous findings in yeast, our data indicate that N-terminal acetylation (NTA) does not inhibit ER targeting of a substantial amount of proteins in plants. In summary, we provide further evidence that NatB-mediated imprinting of the proteome is vital for the response to protein harming stress and rule out DOA10 as the sole recognin for substrates in the plant ERAD pathway, leaving the role of DOA10 in plants ambiguous.
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Affiliation(s)
- Monika Huber
- Centre for Organismal Studies, Molecular Biology of Plants Group, Heidelberg University, Heidelberg, Germany
| | - Laura Armbruster
- Centre for Organismal Studies, Molecular Biology of Plants Group, Heidelberg University, Heidelberg, Germany
| | | | - Carolina De La Torre
- Institute of Clinical Chemistry, NGS Core Facility, Medical Faculty Mannheim of Heidelberg University, Heidelberg, Germany
| | | | - Carsten Sticht
- Institute of Clinical Chemistry, NGS Core Facility, Medical Faculty Mannheim of Heidelberg University, Heidelberg, Germany
| | - Daniel J. Gibbs
- School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
| | - Rüdiger Hell
- Centre for Organismal Studies, Molecular Biology of Plants Group, Heidelberg University, Heidelberg, Germany
| | - Markus Wirtz
- Centre for Organismal Studies, Molecular Biology of Plants Group, Heidelberg University, Heidelberg, Germany
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10
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Nitnavare RB, Bhattacharya J, Singh S, Kour A, Hawkesford MJ, Arora N. Next Generation dsRNA-Based Insect Control: Success So Far and Challenges. Front Plant Sci 2021; 12:673576. [PMID: 34733295 PMCID: PMC8558349 DOI: 10.3389/fpls.2021.673576] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 09/22/2021] [Indexed: 06/02/2023]
Abstract
RNA interference (RNAi) is a method of gene silencing where dsRNA is digested into small interfering RNA (siRNA) in the presence of enzymes. These siRNAs then target homologous mRNA sequences aided by the RNA-induced silencing complex (RISC). The mechanism of dsRNA uptake has been well studied and established across many living organisms including insects. In insects, RNAi is a novel and potential tool to develop future pest management means targeting various classes of insects including dipterans, coleopterans, hemipterans, lepidopterans, hymenopterans and isopterans. However, the extent of RNAi in individual class varies due to underlying mechanisms. The present review focuses on three major insect classes viz hemipterans, lepidopterans and coleopterans and the rationale behind this lies in the fact that studies pertaining to RNAi has been extensively performed in these groups. Additionally, these classes harbour major agriculturally important pest species which require due attention. Interestingly, all the three classes exhibit varying levels of RNAi efficiencies with the coleopterans exhibiting maximum response, while hemipterans are relatively inefficient. Lepidopterans on the other hand, show minimum response to RNAi. This has been attributed to many facts and few important being endosomal escape, high activity dsRNA-specific nucleases, and highly alkaline gut environment which renders the dsRNA unstable. Various methods have been established to ensure safe delivery of dsRNA into the biological system of the insect. The most common method for dsRNA administration is supplementing the diet of insects via spraying onto leaves and other commonly eaten parts of the plant. This method is environment-friendly and superior to the hazardous effects of pesticides. Another method involves submergence of root systems in dsRNA solutions and subsequent uptake by the phloem. Additionally, more recent techniques are nanoparticle- and Agrobacterium-mediated delivery systems. However, due to the novelty of these biotechnological methods and recalcitrant nature of certain crops, further optimization is required. This review emphasizes on RNAi developments in agriculturally important insect species and the major hurdles for efficient RNAi in these groups. The review also discusses in detail the development of new techniques to enhance RNAi efficiency using liposomes and nanoparticles, transplastomics, microbial-mediated delivery and chemical methods.
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Affiliation(s)
- Rahul B. Nitnavare
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, United Kingdom
- Department of Plant Science, Rothamsted Research, Harpenden, United Kingdom
| | - Joorie Bhattacharya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Satnam Singh
- Punjab Agricultural University (PAU), Regional Research Station, Faridkot, India
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Amardeep Kour
- Punjab Agricultural University (PAU), Regional Research Station, Bathinda, India
| | | | - Naveen Arora
- Department of Genetics and Plant Breeding, Punjab Agricultural University (PAU), Ludhiana, India
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11
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Wang Y, Shewry PR, Hawkesford MJ, Qi P, Wan Y. High molecular weight glutenin subunit (HMW-GS) 1Dx5 is concentrated in small protein bodies when overexpressed in wheat starchy endosperm. J Cereal Sci 2021. [DOI: 10.1016/j.jcs.2021.103291] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Zhou H, Riche AB, Hawkesford MJ, Whalley WR, Atkinson BS, Sturrock CJ, Mooney SJ. Determination of wheat spike and spikelet architecture and grain traits using X-ray Computed Tomography imaging. Plant Methods 2021; 17:26. [PMID: 33750418 PMCID: PMC7945051 DOI: 10.1186/s13007-021-00726-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/26/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND Wheat spike architecture is a key determinant of multiple grain yield components and detailed examination of spike morphometric traits is beneficial to explain wheat grain yield and the effects of differing agronomy and genetics. However, quantification of spike morphometric traits has been very limited because it relies on time-consuming manual measurements. RESULTS In this study, using X-ray Computed Tomography imaging, we proposed a method to efficiently detect the 3D architecture of wheat spikes and component spikelets by clustering grains based on their Euclidean distance and relative positions. Morphometric characteristics of wheat spikelets and grains, e.g., number, size and spatial distribution along the spike can be determined. Two commercial wheat cultivars, one old, Maris Widgeon, and one modern, Siskin, were studied as examples. The average grain volume of Maris Widgeon and Siskin did not differ, but Siskin had more grains per spike and therefore greater total grain volume per spike. The spike length and spikelet number were not statistically different between the two cultivars. However, Siskin had a higher spikelet density (number of spikelets per unit spike length), with more grains and greater grain volume per spikelet than Maris Widgeon. Spatial distribution analysis revealed the number of grains, the average grain volume and the total grain volume of individual spikelets varied along the spike. Siskin had more grains and greater grain volumes per spikelet from spikelet 6, but not spikelet 1-5, compared with Maris Widgeon. The distribution of average grain volume along the spike was similar for the two wheat cultivars. CONCLUSION The proposed method can efficiently extract spike, spikelet and grain morphometric traits of different wheat cultivars, which can contribute to a more detailed understanding of the sink of wheat grain yield.
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Affiliation(s)
- Hu Zhou
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD Leicestershire UK
| | | | | | | | - Brian S. Atkinson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD Leicestershire UK
| | - Craig J. Sturrock
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD Leicestershire UK
| | - Sacha J. Mooney
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD Leicestershire UK
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13
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Wan Y, Wang Y, Shi Z, Rentsch D, Ward JL, Hassall K, Sparks CA, Huttly AK, Buchner P, Powers S, Shewry PR, Hawkesford MJ. Wheat amino acid transporters highly expressed in grain cells regulate amino acid accumulation in grain. PLoS One 2021; 16:e0246763. [PMID: 33606697 PMCID: PMC7894817 DOI: 10.1371/journal.pone.0246763] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/25/2021] [Indexed: 11/18/2022] Open
Abstract
Amino acids are delivered into developing wheat grains to support the accumulation of storage proteins in the starchy endosperm, and transporters play important roles in regulating this process. RNA-seq, RT-qPCR, and promoter-GUS assays showed that three amino acid transporters are differentially expressed in the endosperm transfer cells (TaAAP2), starchy endosperm cells (TaAAP13), and aleurone cells and embryo of the developing grain (TaAAP21), respectively. Yeast complementation revealed that all three transporters can transport a broad spectrum of amino acids. RNAi-mediated suppression of TaAAP13 expression in the starchy endosperm did not reduce the total nitrogen content of the whole grain, but significantly altered the composition and distribution of metabolites in the starchy endosperm, with increasing concentrations of some amino acids (notably glutamine and glycine) from the outer to inner starchy endosperm cells compared with wild type. Overexpression of TaAAP13 under the endosperm-specific HMW-GS (high molecular weight glutenin subunit) promoter significantly increased grain size, grain nitrogen concentration, and thousand grain weight, indicating that the sink strength for nitrogen transport was increased by manipulation of amino acid transporters. However, the total grain number was reduced, suggesting that source nitrogen remobilized from leaves is a limiting factor for productivity. Therefore, simultaneously increasing loading of amino acids into the phloem and delivery to the spike would be required to increase protein content while maintaining grain yield.
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Affiliation(s)
- Yongfang Wan
- Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Yan Wang
- Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
- Triticeae Institute, Sichuan Agricultural University, Sichuan, P. R. China
| | - Zhiqiang Shi
- Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
- National Technology Innovation Center for Regional Wheat Production, Key Laboratory of Crop Physiology, and Ecology and Production in Southern China, Ministry of Agriculture, National Engineering and Technology Center for Information Agriculture, Nanjing Agricultural University, Nanjing, P. R. China
| | - Doris Rentsch
- University of Bern, Molecular Plant Physiology, Bern, Switzerland
| | - Jane L. Ward
- Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Kirsty Hassall
- Computational and Analytical Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Caroline A. Sparks
- Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Alison K. Huttly
- Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Peter Buchner
- Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Stephen Powers
- Computational and Analytical Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Peter R. Shewry
- Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Malcolm J. Hawkesford
- Plant Sciences Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
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14
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Zhou H, Whalley WR, Hawkesford MJ, Ashton RW, Atkinson B, Atkinson JA, Sturrock CJ, Bennett MJ, Mooney SJ. The interaction between wheat roots and soil pores in structured field soil. J Exp Bot 2021; 72:747-756. [PMID: 33064808 PMCID: PMC7853603 DOI: 10.1093/jxb/eraa475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 10/16/2020] [Indexed: 05/11/2023]
Abstract
Wheat (Triticum aestivum L.) root growth in the subsoil is usually constrained by soil strength, although roots can use macropores to elongate to deeper layers. The quantitative relationship between the elongation of wheat roots and the soil pore system, however, is still to be determined. We studied the depth distribution of roots of six wheat varieties and explored their relationship with soil macroporosity from samples with the field structure preserved. Undisturbed soil cores (to a depth of 100 cm) were collected from the field and then non-destructively imaged using X-ray computed tomography (at a spatial resolution of 90 µm) to quantify soil macropore structure and root number density (the number of roots cm-2 within a horizontal cross-section of a soil core). Soil macroporosity changed significantly with depth but not between the different wheat lines. There was no significant difference in root number density between wheat varieties. In the subsoil, wheat roots used macropores, especially biopores (i.e. former root or earthworm channels) to grow into deeper layers. Soil macroporosity explained 59% of the variance in root number density. Our data suggested that the development of the wheat root system in the field was more affected by the soil macropore system than by genotype. On this basis, management practices which enhance the porosity of the subsoil may therefore be an effective strategy to improve deep rooting of wheat.
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Affiliation(s)
- Hu Zhou
- School of Biosciences, University of Nottingham, Loughborough, Leicestershire, UK
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Sciences, Chinese Academy of Sciences, Nanjing, PR China
- Correspondence:
| | | | | | | | - Brian Atkinson
- School of Biosciences, University of Nottingham, Loughborough, Leicestershire, UK
| | - Jonathan A Atkinson
- School of Biosciences, University of Nottingham, Loughborough, Leicestershire, UK
| | - Craig J Sturrock
- School of Biosciences, University of Nottingham, Loughborough, Leicestershire, UK
| | - Malcolm J Bennett
- School of Biosciences, University of Nottingham, Loughborough, Leicestershire, UK
| | - Sacha J Mooney
- School of Biosciences, University of Nottingham, Loughborough, Leicestershire, UK
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15
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Yang W, Doonan JH, Hawkesford MJ, Pridmore T, Zhou J. Editorial: State-of-the-Art Technology and Applications in Crop Phenomics. Front Plant Sci 2021; 12:767324. [PMID: 34675958 PMCID: PMC8524054 DOI: 10.3389/fpls.2021.767324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 09/14/2021] [Indexed: 05/12/2023]
Affiliation(s)
- Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- *Correspondence: Wanneng Yang
| | - John H. Doonan
- The National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | | | - Tony Pridmore
- School of Computer Science, University of Nottingham, Nottingham, United Kingdom
| | - Ji Zhou
- Cambridge Crop Research, National Institute of Agricultural Botany, Cambridge, United Kingdom
- Academy for Advanced Interdisciplinary Studies, Jiangsu Collaborative Innovation Center for Modern Crop Production Co-sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing, China
- Ji Zhou
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16
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Mariem SB, Gámez AL, Larraya L, Fuertes-Mendizabal T, Cañameras N, Araus JL, McGrath SP, Hawkesford MJ, Murua CG, Gaudeul M, Medina L, Paton A, Cattivelli L, Fangmeier A, Bunce J, Tausz-Posch S, Macdonald AJ, Aranjuelo I. Assessing the evolution of wheat grain traits during the last 166 years using archived samples. Sci Rep 2020; 10:21828. [PMID: 33311545 PMCID: PMC7733497 DOI: 10.1038/s41598-020-78504-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/20/2020] [Indexed: 11/09/2022] Open
Abstract
The current study focuses on yield and nutritional quality changes of wheat grain over the last 166 years. It is based on wheat grain quality analyses carried out on samples collected between 1850 and 2016. Samples were obtained from the Broadbalk Continuous Wheat Experiment (UK) and from herbaria from 16 different countries around the world. Our study showed that, together with an increase in carbohydrate content, an impoverishment of mineral composition and protein content occurred. The imbalance in carbohydrate/protein content was specially marked after the 1960's, coinciding with strong increases in ambient [CO2] and temperature and the introduction of progressively shorter straw varieties. The implications of altered crop physiology are discussed.
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Affiliation(s)
- Sinda Ben Mariem
- Spanish National Research Council (CSIC)-Government of Navarre, AgroBiotechnology Institute (IdAB), Av. Pamplona 123, 31006, Mutilva, Spain
| | - Angie L Gámez
- Spanish National Research Council (CSIC)-Government of Navarre, AgroBiotechnology Institute (IdAB), Av. Pamplona 123, 31006, Mutilva, Spain
| | - Luis Larraya
- Institute for Multidisciplinary Applied Biology, Dpto. Agronomía, Biotecnología y Alimentación, Universidad Pública de Navarra, Campus Arrosadia, 31006, Pamplona, Spain
| | | | - Nuria Cañameras
- Universitat Politècnica de Catalunya, EsteveTerrades 8, Building 4, Castelldefels, Spain
| | - José L Araus
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, Barcelona, and AGROTECNIO Center, Lleida, Spain
| | - Steve P McGrath
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK
| | | | - Carmen Gonzalez Murua
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Myriam Gaudeul
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National D'Histoire Naturelle, CNRS, EPHE, UA, Sorbonne Université, 57 rue Cuvier, CP 39, 75005, Paris, France
| | - Leopoldo Medina
- Spanish National Research Council (CSIC), Real Jardín Botánico, C/ Claudio Moyano 1, Madrid, Spain
| | - Alan Paton
- Royal Botanic Gardens Kew, Kew Richmond, TW9 3AB, UK
| | - Luigi Cattivelli
- Agricultural Research Council (CREA), Centre for Genomics and Bioinformatics, Via San Protaso 302, Fiorenzuolad'Arda, Italy
| | - Andreas Fangmeier
- Institute of Landscape and Plant Ecology, University of Hohenheim, August-von-Hartmann-Str. 3, 70599, Stuttgart, Germany
| | - James Bunce
- Adaptive Cropping Systems Lab (Retired), Beltsville Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Sabine Tausz-Posch
- Department of Agriculture, Science and the Environment, School of Health, Medical and Applied Sciences, CQ University Australia, Rockhampton, QLD, Australia
| | - Andy J Macdonald
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK
| | - Iker Aranjuelo
- Spanish National Research Council (CSIC)-Government of Navarre, AgroBiotechnology Institute (IdAB), Av. Pamplona 123, 31006, Mutilva, Spain.
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17
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Mosleth EF, Lillehammer M, Pellny TK, Wood AJ, Riche AB, Hussain A, Griffiths S, Hawkesford MJ, Shewry PR. Genetic variation and heritability of grain protein deviation in European wheat genotypes. Field Crops Res 2020; 255:107896. [PMID: 32943810 PMCID: PMC7397848 DOI: 10.1016/j.fcr.2020.107896] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
There is a well-established negative relationship between the yield and the concentration of protein in the mature wheat grain. However, some wheat genotypes consistently deviate from this relationship, a phenomenon known as Grain Protein Deviation (GPD). Positive GPD is therefore of considerable interest in relation to reducing the requirement for nitrogen fertilization for producing wheat for breadmaking. We have carried out two sets of field experiments on multiple sites in South East England. The first set comprised 11 field trials of 6 cultivars grown over three years (2008-2011) and the second comprised 9 field trials of 40 genotypes grown over two years (2015-2017) and 5 field trials of 30 genotypes grown in a single year (2017-2018). All trials comprised three replicate randomized plots of each genotype and nutrient regime. These studies showed strong genetic variation in GPD, which also differed in stability between genotypes, with cultivars bred in the UK generally having higher GPD and higher stability than those bred in other European countries. The heritability of GPD was estimated as 0.44, based on data from the field trials of 30 and 40 genotypes. The largest component contributing to the genetic variance was genotype (0.30), with a smaller contribution of the interaction between genotype and year/site (0.11) and a small (but statistically significant) contribution of nitrogen level. These studies suggest that selection for GPD is a viable target for breeders.
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Affiliation(s)
| | | | - Till K Pellny
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | | | | | - Abrar Hussain
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Sahiwal, Punjab 57000, Pakistan
| | - Simon Griffiths
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | | | - Peter R. Shewry
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
- Corresponding author.
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18
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Wang H, Wan Y, Buchner P, King R, Ma H, Hawkesford MJ. Phylogeny and gene expression of the complete NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY in Triticum aestivum. J Exp Bot 2020; 71:4531-4546. [PMID: 32462194 PMCID: PMC7382379 DOI: 10.1093/jxb/eraa210] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 05/04/2020] [Indexed: 05/10/2023]
Abstract
NPF genes encode membrane transporters involved in the transport of a large variety of substrates including nitrate and peptides. The NPF gene family has been described for many plants, but the whole NPF gene family for wheat has not been completely identified. The release of the wheat reference genome has enabled the identification of the entire wheat NPF gene family. A systematic analysis of the whole wheat NPF gene family was performed, including responses of specific gene expression to development and nitrogen supply. A total of 331 NPF genes (113 homoeologous groups) have been identified in wheat. The chromosomal location of the NPF genes is unevenly distributed, with predominant occurrence in the long arms of the chromosomes. The phylogenetic analysis indicated that wheat NPF genes are closely clustered with Arabidopsis, Brachypodium, and rice orthologues, and subdivided into eight subfamilies. The expression profiles of wheat NPF genes were examined using RNA-seq data, and a subset of 44 NPF genes (homoeologous groups) with contrasting expression responses to nitrogen and/or development in different tissues were identified. The systematic identification of gene composition, chromosomal locations, evolutionary relationships, and expression profiles contributes to a better understanding of the roles of the wheat NPF genes and lays the foundation for further functional analysis in wheat.
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Affiliation(s)
- Huadun Wang
- Institute of Food Crops, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | | | - Peter Buchner
- Rothamsted Research, West Common, Harpenden, UK
- Correspondence:
| | - Robert King
- Rothamsted Research, West Common, Harpenden, UK
| | - Hongxiang Ma
- Institute of Food Crops, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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19
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Whitcomb SJ, Rakpenthai A, Brückner F, Fischer A, Parmar S, Erban A, Kopka J, Hawkesford MJ, Hoefgen R. Cysteine and Methionine Biosynthetic Enzymes Have Distinct Effects on Seed Nutritional Quality and on Molecular Phenotypes Associated With Accumulation of a Methionine-Rich Seed Storage Protein in Rice. Front Plant Sci 2020; 11:1118. [PMID: 32793268 PMCID: PMC7387578 DOI: 10.3389/fpls.2020.01118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/07/2020] [Indexed: 06/11/2023]
Abstract
Staple crops in human and livestock diets suffer from deficiencies in certain "essential" amino acids including methionine. With the goal of increasing methionine in rice seed, we generated a pair of "Push × Pull" double transgenic lines, each containing a methionine-dense seed storage protein (2S albumin from sunflower, HaSSA) and an exogenous enzyme for either methionine (feedback desensitized cystathionine gamma synthase from Arabidopsis, AtD-CGS) or cysteine (serine acetyltransferase from E. coli, EcSAT) biosynthesis. In both double transgenic lines, the total seed methionine content was approximately 50% higher than in their untransformed parental line, Oryza sativa ssp. japonica cv. Taipei 309. HaSSA-containing rice seeds were reported to display an altered seed protein profile, speculatively due to insufficient sulfur amino acid content. However, here we present data suggesting that this may result from an overloaded protein folding machinery in the endoplasmic reticulum rather than primarily from redistribution of limited methionine from endogenous seed proteins to HaSSA. We hypothesize that HaSSA-associated endoplasmic reticulum stress results in redox perturbations that negatively impact sulfate reduction to cysteine, and we speculate that this is mitigated by EcSAT-associated increased sulfur import into the seed, which facilitates additional synthesis of cysteine and glutathione. The data presented here reveal challenges associated with increasing the methionine content in rice seed, including what may be relatively low protein folding capacity in the endoplasmic reticulum and an insufficient pool of sulfate available for additional cysteine and methionine synthesis. We propose that future approaches to further improve the methionine content in rice should focus on increasing seed sulfur loading and avoiding the accumulation of unfolded proteins in the endoplasmic reticulum. Oryza sativa ssp. japonica: urn:lsid:ipni.org:names:60471378-2.
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Affiliation(s)
- Sarah J. Whitcomb
- Laboratory of Amino Acid and Sulfur Metabolism, Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Apidet Rakpenthai
- Laboratory of Amino Acid and Sulfur Metabolism, Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Franziska Brückner
- Laboratory of Amino Acid and Sulfur Metabolism, Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Axel Fischer
- Bioinformatics Infrastructure Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Saroj Parmar
- Plant Sciences Department, Rothamsted Research, Harpenden, United Kingdom
| | - Alexander Erban
- Applied Metabolome Analysis Infrastructure Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Joachim Kopka
- Applied Metabolome Analysis Infrastructure Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | | | - Rainer Hoefgen
- Laboratory of Amino Acid and Sulfur Metabolism, Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
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20
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Lyra DH, Virlet N, Sadeghi-Tehran P, Hassall KL, Wingen LU, Orford S, Griffiths S, Hawkesford MJ, Slavov GT. Functional QTL mapping and genomic prediction of canopy height in wheat measured using a robotic field phenotyping platform. J Exp Bot 2020; 71:1885-1898. [PMID: 32097472 PMCID: PMC7094083 DOI: 10.1093/jxb/erz545] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 02/19/2020] [Indexed: 05/08/2023]
Abstract
Genetic studies increasingly rely on high-throughput phenotyping, but the resulting longitudinal data pose analytical challenges. We used canopy height data from an automated field phenotyping platform to compare several approaches to scanning for quantitative trait loci (QTLs) and performing genomic prediction in a wheat recombinant inbred line mapping population based on up to 26 sampled time points (TPs). We detected four persistent QTLs (i.e. expressed for most of the growing season), with both empirical and simulation analyses demonstrating superior statistical power of detecting such QTLs through functional mapping approaches compared with conventional individual TP analyses. In contrast, even very simple individual TP approaches (e.g. interval mapping) had superior detection power for transient QTLs (i.e. expressed during very short periods). Using spline-smoothed phenotypic data resulted in improved genomic predictive abilities (5-8% higher than individual TP prediction), while the effect of including significant QTLs in prediction models was relatively minor (<1-4% improvement). Finally, although QTL detection power and predictive ability generally increased with the number of TPs analysed, gains beyond five or 10 TPs chosen based on phenological information had little practical significance. These results will inform the development of an integrated, semi-automated analytical pipeline, which will be more broadly applicable to similar data sets in wheat and other crops.
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Affiliation(s)
- Danilo H Lyra
- Department of Computational & Analytical Sciences, Rothamsted Research, Harpenden, UK
| | - Nicolas Virlet
- Department of Plant Sciences, Rothamsted Research, Harpenden, UK
| | | | - Kirsty L Hassall
- Department of Computational & Analytical Sciences, Rothamsted Research, Harpenden, UK
| | - Luzie U Wingen
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, UK
| | - Simon Orford
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, UK
| | - Simon Griffiths
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, UK
| | | | - Gancho T Slavov
- Department of Computational & Analytical Sciences, Rothamsted Research, Harpenden, UK
- Scion, Rotorua, New Zealand
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21
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Lyra DH, Virlet N, Sadeghi-Tehran P, Hassall KL, Wingen LU, Orford S, Griffiths S, Hawkesford MJ, Slavov GT. Functional QTL mapping and genomic prediction of canopy height in wheat measured using a robotic field phenotyping platform. J Exp Bot 2020. [PMID: 32097472 DOI: 10.17632/pkxpkw6j43.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Genetic studies increasingly rely on high-throughput phenotyping, but the resulting longitudinal data pose analytical challenges. We used canopy height data from an automated field phenotyping platform to compare several approaches to scanning for quantitative trait loci (QTLs) and performing genomic prediction in a wheat recombinant inbred line mapping population based on up to 26 sampled time points (TPs). We detected four persistent QTLs (i.e. expressed for most of the growing season), with both empirical and simulation analyses demonstrating superior statistical power of detecting such QTLs through functional mapping approaches compared with conventional individual TP analyses. In contrast, even very simple individual TP approaches (e.g. interval mapping) had superior detection power for transient QTLs (i.e. expressed during very short periods). Using spline-smoothed phenotypic data resulted in improved genomic predictive abilities (5-8% higher than individual TP prediction), while the effect of including significant QTLs in prediction models was relatively minor (<1-4% improvement). Finally, although QTL detection power and predictive ability generally increased with the number of TPs analysed, gains beyond five or 10 TPs chosen based on phenological information had little practical significance. These results will inform the development of an integrated, semi-automated analytical pipeline, which will be more broadly applicable to similar data sets in wheat and other crops.
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Affiliation(s)
- Danilo H Lyra
- Department of Computational & Analytical Sciences, Rothamsted Research, Harpenden, UK
| | - Nicolas Virlet
- Department of Plant Sciences, Rothamsted Research, Harpenden, UK
| | | | - Kirsty L Hassall
- Department of Computational & Analytical Sciences, Rothamsted Research, Harpenden, UK
| | - Luzie U Wingen
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, UK
| | - Simon Orford
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, UK
| | - Simon Griffiths
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, UK
| | | | - Gancho T Slavov
- Department of Computational & Analytical Sciences, Rothamsted Research, Harpenden, UK
- Scion, Rotorua, New Zealand
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22
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Zuidersma EI, Ausma T, Stuiver CEE, Prajapati DH, Hawkesford MJ, De Kok LJ. Molybdate toxicity in Chinese cabbage is not the direct consequence of changes in sulphur metabolism. Plant Biol (Stuttg) 2020; 22:331-336. [PMID: 31675464 PMCID: PMC7065239 DOI: 10.1111/plb.13065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 10/19/2019] [Indexed: 06/10/2023]
Abstract
In polluted areas, plants may be exposed to supra-optimal levels of the micronutrient molybdenum. The physiological basis of molybdenum phytotoxicity is poorly understood. Plants take up molybdenum as molybdate, which is a structural analogue of sulphate. Therefore, it is presumed that elevated molybdate concentrations may hamper the uptake and subsequent metabolism of sulphate, which may induce sulphur deficiency. In the current research, Chinese cabbage (Brassica pekinensis) seedlings were exposed to 50, 100, 150 and 200 μm Na2 MoO4 for 9 days. Leaf chlorosis and a decreased plant growth occurred at concentrations ≥100 μm. Root growth was more affected than shoot growth. At ≥100 μm Na2 MoO4 , the sulphate uptake rate and capacity were increased, although only when expressed on a root fresh weight basis. When expressed on a whole plant fresh weight basis, which corrects for the impact of molybdate on the shoot-to-root ratio, the sulphate uptake rate and capacity remained unaffected. Molybdate concentrations ≥100 μm altered the mineral nutrient composition of plant tissues, although the levels of sulphur metabolites (sulphate, water-soluble non-protein thiols and total sulphur) were not altered. Moreover, the levels of nitrogen metabolites (nitrate, amino acids, proteins and total nitrogen), which are generally strongly affected by sulphate deprivation, were not affected. The root water-soluble non-protein thiol content was increased, and the tissue nitrate levels decreased, only at 200 μm Na2 MoO4 . Evidently, molybdenum toxicity in Chinese cabbage was not due to the direct interference of molybdate with the uptake and subsequent metabolism of sulphate.
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Affiliation(s)
- E I Zuidersma
- Isotope Laboratory Life Sciences, Graduate School of Science and Engineering, University of Groningen, Groningen, The Netherlands
- Laboratory of Plant Physiology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - T Ausma
- Laboratory of Plant Physiology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - C E E Stuiver
- Laboratory of Plant Physiology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - D H Prajapati
- Laboratory of Plant Physiology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
- Department of Biotechnology, Hemchandracharya North Gujarat University, Patan, Gujarat, India
| | - M J Hawkesford
- Plant Sciences Department, Rothamsted Research, Harpenden, UK
| | - L J De Kok
- Laboratory of Plant Physiology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
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23
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Abstract
The starchy endosperm of the mature wheat grain comprises three major cell types, namely sub-aleurone cells, prismatic cells and central cells, which differ in their contents of functional components: gluten proteins, starch, cell wall polysaccharides (dietary fibre) and lipids. Gradients are established during grain development but may be modified during grain maturation and are affected by plant nutrition, particularly nitrogen application, and environmental factors. Although the molecular controls of their formation are unknown, the high content of protein and low content of starch of sub-aleurone cells, compared to the other starchy endosperm cells types, may result from differences in developmental programming related to the cells having a separate origin (from anticlinal division of the aleurone cells). The gradients within the grain may be reflected in differences in the compositions of mill streams, particularly those streams enriched in the central and outer cells of the starchy endosperm, respectively, allowing the production of specialist flours for specific end uses. The mature starchy endosperm of wheat comprises three cell types. These differ in their contents of functional components. These differences are reflected in the compositions of mill streams. These differences may affect functionality. Hence innovative milling can be used to prepare flours for special uses.
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Key Words
- A, arabinose
- AX, arabinoxylan
- AXOS, arabinoxylan oligosaccharide
- DP, degree of polymerisation
- DPA, days past anthesis
- Dietary fibre
- FTIR, Fourier transform infrared
- GL, galactolipid
- Gluten proteins
- HMW, high molecular weight
- LMW, low molecular weight
- Lipids
- NMR, nuclear magnetic resonance
- PL, phospholipid
- Polysaccharides
- SIMS, secondary ion mass spectrometry
- Starch
- Starchy endosperm
- TAG, triacylglycerol
- TDF, total dietary fibre
- WE, water-extractable
- WU, water-unextractable
- Wheat
- White flour
- X, xylose
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Affiliation(s)
- Peter R Shewry
- Plant Science Department, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK.,School of Agriculture, Policy and Development, University of Reading, Whiteknights Campus, Early Gate, RG6 6AR, Reading, UK
| | - Yongfang Wan
- Plant Science Department, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | | | - Paola Tosi
- School of Agriculture, Policy and Development, University of Reading, Whiteknights Campus, Early Gate, RG6 6AR, Reading, UK
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24
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Atkinson JA, Hawkesford MJ, Whalley WR, Zhou H, Mooney SJ. Soil strength influences wheat root interactions with soil macropores. Plant Cell Environ 2020. [PMID: 31600410 DOI: 10.1111/pce:13659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Deep rooting is critical for access to water and nutrients found in subsoil. However, damage to soil structure and the natural increase in soil strength with depth, often impedes root penetration. Evidence suggests that roots use macropores (soil cavities greater than 75 μm) to bypass strong soil layers. If roots have to exploit structures, a key trait conferring deep rooting will be the ability to locate existing pore networks; a trait called trematotropism. In this study, artificial macropores were created in repacked soil columns at bulk densities of 1.6 g cm-3 and 1.2 g cm-3 , representing compact and loose soil. Near isogenic lines of wheat, Rht-B1a and Rht-B1c, were planted and root-macropore interactions were visualized and quantified using X-ray computed tomography. In compact soil, 68.8% of root-macropore interactions resulted in pore colonization, compared with 12.5% in loose soil. Changes in root growth trajectory following pore interaction were also quantified, with 21.0% of roots changing direction (±3°) in loose soil compared with 76.0% in compact soil. These results indicate that colonization of macropores is an important strategy of wheat roots in compacted subsoil. Management practices to reduce subsoil compaction and encourage macropore formation could offer significant advantage in helping wheat roots penetrate deeper into subsoil.
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Affiliation(s)
- Jonathan A Atkinson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | | | | | - Hu Zhou
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, P.R. China
| | - Sacha J Mooney
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
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25
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Atkinson JA, Hawkesford MJ, Whalley WR, Zhou H, Mooney SJ. Soil strength influences wheat root interactions with soil macropores. Plant Cell Environ 2020; 43:235-245. [PMID: 31600410 PMCID: PMC7027857 DOI: 10.1111/pce.13659] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/19/2019] [Accepted: 09/18/2019] [Indexed: 05/24/2023]
Abstract
Deep rooting is critical for access to water and nutrients found in subsoil. However, damage to soil structure and the natural increase in soil strength with depth, often impedes root penetration. Evidence suggests that roots use macropores (soil cavities greater than 75 μm) to bypass strong soil layers. If roots have to exploit structures, a key trait conferring deep rooting will be the ability to locate existing pore networks; a trait called trematotropism. In this study, artificial macropores were created in repacked soil columns at bulk densities of 1.6 g cm-3 and 1.2 g cm-3 , representing compact and loose soil. Near isogenic lines of wheat, Rht-B1a and Rht-B1c, were planted and root-macropore interactions were visualized and quantified using X-ray computed tomography. In compact soil, 68.8% of root-macropore interactions resulted in pore colonization, compared with 12.5% in loose soil. Changes in root growth trajectory following pore interaction were also quantified, with 21.0% of roots changing direction (±3°) in loose soil compared with 76.0% in compact soil. These results indicate that colonization of macropores is an important strategy of wheat roots in compacted subsoil. Management practices to reduce subsoil compaction and encourage macropore formation could offer significant advantage in helping wheat roots penetrate deeper into subsoil.
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Affiliation(s)
- Jonathan A. Atkinson
- School of BiosciencesUniversity of Nottingham, Sutton Bonington CampusLoughboroughLE12 5RDUK
| | | | | | - Hu Zhou
- School of BiosciencesUniversity of Nottingham, Sutton Bonington CampusLoughboroughLE12 5RDUK
- State Key Laboratory of Soil and Sustainable AgricultureInstitute of Soil Science, Chinese Academy of SciencesNanjing210008P.R. China
| | - Sacha J. Mooney
- School of BiosciencesUniversity of Nottingham, Sutton Bonington CampusLoughboroughLE12 5RDUK
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26
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Zhang XX, Whalley PA, Ashton RW, Evans J, Hawkesford MJ, Griffiths S, Huang ZD, Zhou H, Mooney SJ, Whalley WR. A comparison between water uptake and root length density in winter wheat: effects of root density and rhizosphere properties. Plant Soil 2020. [PMID: 32848280 DOI: 10.1007/s11104-020-04582-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
BACKGROUND AND AIMS We aim to quantify the variation in root distribution in a set of 35 experimental wheat lines. We also compared the effect of variation in hydraulic properties of the rhizosphere on water uptake by roots. METHODS We measured the root length density and soil drying in 35 wheat lines in a field experiment. A 3D numerical model was used to predict soil drying profiles with the different root length distributions and compared with measured soil drying. The model was used to test different scenarios of the hydraulic properties of the rhizosphere. RESULTS We showed that wheat lines with no detectable differences in root length density can induce soil drying profiles with statistically significant differences. Our data confirmed that a root length density of at least 1 cm/cm3 is needed to drain all the available water in soil. In surface layers where the root length density was far greater than 1 cm/cm3 water uptake was independent of rooting density due to competition for water. However, in deeper layers where root length density was less than 1 cm/cm3, water uptake by roots was proportional to root density. CONCLUSION In a set of wheat lines with no detectable differences in the root length density we found significant differences in water uptake. This may be because small differences in root density at depth can result in larger differences in water uptake or that the hydraulic properties of the rhizosphere can greatly affect water uptake.
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Affiliation(s)
- X X Zhang
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ UK
| | - P A Whalley
- University of Oxford, Radcliffe Observatory, Andrew Wiles Building, Woodstock Rd, Oxford, OX2 6GG UK
| | - R W Ashton
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ UK
| | - J Evans
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ UK
| | - M J Hawkesford
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ UK
| | - S Griffiths
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Z D Huang
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang, 453002 Henan China
| | - H Zhou
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD UK
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Sciences, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 People's Republic of China
| | - S J Mooney
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD UK
| | - W R Whalley
- Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ UK
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27
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Rossmann A, Buchner P, Savill GP, Powers SJ, Hawkesford MJ, Mühling KH. Foliar N Application at Anthesis Stimulates Gene Expression of Grain Protein Fractions and Alters Protein Body Distribution in Winter Wheat ( Triticum aestivum L.). J Agric Food Chem 2019; 67:12709-12719. [PMID: 31697495 DOI: 10.1021/acs.jafc.9b04634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The major components of wheat storage proteins are gliadins and glutenins, and as they contribute differently to baking quality, a balanced mixture of these components is essential. The application of foliar nitrogen (N) at anthesis is a common practice to improve protein concentration and composition. The aim of this study was to investigate the effects of a foliar N application at anthesis on storage protein gene expression during grain development and on the distribution of protein concentration and protein body size within the grain. In this experiment, an additional N application at anthesis stimulated the expression of genes of the majority of storage proteins when the N supply was low. Furthermore, it led to higher protein concentrations in the subaleurone layers, while in the center of the lobes, the protein concentrations were decreased. These changes will affect the protein recovery in white flours, as proportionally more protein might be lost during milling processes.
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Affiliation(s)
- Anne Rossmann
- Institute for Plant Nutrition and Soil Science , Kiel University , Hermann-Rodewald-Str. 2 , 24118 Kiel , Germany
| | - Peter Buchner
- Plant Sciences Department , Rothamsted Research , West Common , Harpenden , AL5 2JQ , U.K
| | - George P Savill
- Plant Sciences Department , Rothamsted Research , West Common , Harpenden , AL5 2JQ , U.K
| | - Stephen J Powers
- Plant Sciences Department , Rothamsted Research , West Common , Harpenden , AL5 2JQ , U.K
| | - Malcolm J Hawkesford
- Plant Sciences Department , Rothamsted Research , West Common , Harpenden , AL5 2JQ , U.K
| | - Karl H Mühling
- Institute for Plant Nutrition and Soil Science , Kiel University , Hermann-Rodewald-Str. 2 , 24118 Kiel , Germany
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28
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Sadeghi-Tehran P, Virlet N, Ampe EM, Reyns P, Hawkesford MJ. DeepCount: In-Field Automatic Quantification of Wheat Spikes Using Simple Linear Iterative Clustering and Deep Convolutional Neural Networks. Front Plant Sci 2019; 10:1176. [PMID: 31616456 PMCID: PMC6775245 DOI: 10.3389/fpls.2019.01176] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/28/2019] [Indexed: 05/19/2023]
Abstract
Crop yield is an essential measure for breeders, researchers, and farmers and is composed of and may be calculated by the number of ears per square meter, grains per ear, and thousand grain weight. Manual wheat ear counting, required in breeding programs to evaluate crop yield potential, is labor-intensive and expensive; thus, the development of a real-time wheat head counting system would be a significant advancement. In this paper, we propose a computationally efficient system called DeepCount to automatically identify and count the number of wheat spikes in digital images taken under natural field conditions. The proposed method tackles wheat spike quantification by segmenting an image into superpixels using simple linear iterative clustering (SLIC), deriving canopy relevant features, and then constructing a rational feature model fed into the deep convolutional neural network (CNN) classification for semantic segmentation of wheat spikes. As the method is based on a deep learning model, it replaces hand-engineered features required for traditional machine learning methods with more efficient algorithms. The method is tested on digital images taken directly in the field at different stages of ear emergence/maturity (using visually different wheat varieties), with different canopy complexities (achieved through varying nitrogen inputs) and different heights above the canopy under varying environmental conditions. In addition, the proposed technique is compared with a wheat ear counting method based on a previously developed edge detection technique and morphological analysis. The proposed approach is validated with image-based ear counting and ground-based measurements. The results demonstrate that the DeepCount technique has a high level of robustness regardless of variables, such as growth stage and weather conditions, hence demonstrating the feasibility of the approach in real scenarios. The system is a leap toward a portable and smartphone-assisted wheat ear counting systems, results in reducing the labor involved, and is suitable for high-throughput analysis. It may also be adapted to work on Red; Green; Blue (RGB) images acquired from unmanned aerial vehicle (UAVs).
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Affiliation(s)
| | - Nicolas Virlet
- Plant Sciences Department, Rothamsted Research, Harpenden, United Kingdom
| | - Eva M. Ampe
- Phenotyping, Near Infrared and Research Automation Group, Limagrain Europe, Chappes, Netherlands
| | - Piet Reyns
- Phenotyping, Near Infrared and Research Automation Group, Limagrain Europe, Chappes, Netherlands
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29
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Shi Z, Wang Y, Wan Y, Hassall K, Jiang D, Shewry PR, Hawkesford MJ. Gradients of Gluten Proteins and Free Amino Acids along the Longitudinal Axis of the Developing Caryopsis of Bread Wheat. J Agric Food Chem 2019; 67:8706-8714. [PMID: 31310118 DOI: 10.1021/acs.jafc.9b02728] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Gradients in the contents and compositions of gluten proteins and free amino acids and the expression levels of gluten protein genes in developing wheat caryopses were determined by dividing the caryopsis into three longitudinal sections, namely, proximal (En1), middle (En2), and distal (En3) to embryo. The total gluten protein content was lower in En1 than in En2 and En3, with decreasing proportions of HMW-GS, LMW GS, and α/β- and γ-gliadins and increasing proportions of ω-gliadins. These differences were associated with the abundances of gluten protein transcripts. Gradients in the proportions of the gluten protein polymers which affect dough processing quality also occurred, but not in total free amino acids. Microscopy showed that the lower gluten protein content in En1 may have resulted, at least in part, from the presence of modified cells in the dorsal part of En1, but the reasons for the differences in composition are not known.
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Affiliation(s)
- Zhiqiang Shi
- National Technology Innovation Center for Regional Wheat Production, Key Laboratory of Crop Physiology, and Ecology and Production in Southern China, Ministry of Agriculture, National Engineering and Technology Center for Information Agriculture , Nanjing Agricultural University , Nanjing 210095 , P.R. China
- Plant Sciences Department , Rothamsted Research , Harpenden , Hertfordshire AL5 2JQ , U.K
| | - Yan Wang
- Plant Sciences Department , Rothamsted Research , Harpenden , Hertfordshire AL5 2JQ , U.K
| | - Yongfang Wan
- Plant Sciences Department , Rothamsted Research , Harpenden , Hertfordshire AL5 2JQ , U.K
| | - Kirsty Hassall
- Computational and Analytical Sciences Department , Rothamsted Research , Harpenden , Hertfordshire AL5 2JQ , U.K
| | - Dong Jiang
- National Technology Innovation Center for Regional Wheat Production, Key Laboratory of Crop Physiology, and Ecology and Production in Southern China, Ministry of Agriculture, National Engineering and Technology Center for Information Agriculture , Nanjing Agricultural University , Nanjing 210095 , P.R. China
| | - Peter R Shewry
- Plant Sciences Department , Rothamsted Research , Harpenden , Hertfordshire AL5 2JQ , U.K
| | - Malcolm J Hawkesford
- Plant Sciences Department , Rothamsted Research , Harpenden , Hertfordshire AL5 2JQ , U.K
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30
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Hao M, Zhang L, Zhao L, Dai S, Li A, Yang W, Xie D, Li Q, Ning S, Yan Z, Wu B, Lan X, Yuan Z, Huang L, Wang J, Zheng K, Chen W, Yu M, Chen X, Chen M, Wei Y, Zhang H, Kishii M, Hawkesford MJ, Mao L, Zheng Y, Liu D. A breeding strategy targeting the secondary gene pool of bread wheat: introgression from a synthetic hexaploid wheat. Theor Appl Genet 2019; 132:2285-2294. [PMID: 31049633 DOI: 10.1007/s00122-019-03354-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/25/2019] [Indexed: 05/15/2023]
Abstract
Introgressing one-eighth of synthetic hexaploid wheat genome through a double top-cross plus a two-phase selection is an effective strategy to develop high-yielding wheat varieties. The continued expansion of the world population and the likely onset of climate change combine to form a major crop breeding challenge. Genetic advances in most crop species to date have largely relied on recombination and reassortment within a relatively narrow gene pool. Here, we demonstrate an efficient wheat breeding strategy for improving yield potentials by introgression of multiple genomic regions of de novo synthesized wheat. The method relies on an initial double top-cross (DTC), in which one parent is synthetic hexaploid wheat (SHW), followed by a two-phase selection procedure. A genotypic analysis of three varieties (Shumai 580, Shumai 969 and Shumai 830) released from this program showed that each harbors a unique set of genomic regions inherited from the SHW parent. The first two varieties were generated from very small populations, whereas the third used a more conventional scale of selection since one of bread wheat parents was a pre-breeding material. The three varieties had remarkably enhanced yield potential compared to those developed by conventional breeding. A widely accepted consensus among crop breeders holds that introducing unadapted germplasm, such as landraces, as parents into a breeding program is a risky proposition, since the size of the breeding population required to overcome linkage drag becomes too daunting. However, the success of the proposed DTC strategy has demonstrated that novel variation harbored by SHWs can be accessed in a straightforward, effective manner. The strategy is in principle generalizable to any allopolyploid crop species where the identity of the progenitor species is known.
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Affiliation(s)
- Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, No. 211 Huiming Rd, Wenjiang District, Chengdu City, 611130, Sichuan Province, People's Republic of China.
| | - Lianquan Zhang
- Triticeae Research Institute, Sichuan Agricultural University, No. 211 Huiming Rd, Wenjiang District, Chengdu City, 611130, Sichuan Province, People's Republic of China.
| | - Laibin Zhao
- Triticeae Research Institute, Sichuan Agricultural University, No. 211 Huiming Rd, Wenjiang District, Chengdu City, 611130, Sichuan Province, People's Republic of China
| | - Shoufen Dai
- Triticeae Research Institute, Sichuan Agricultural University, No. 211 Huiming Rd, Wenjiang District, Chengdu City, 611130, Sichuan Province, People's Republic of China
| | - Aili Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Wuyun Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, People's Republic of China
| | - Die Xie
- Triticeae Research Institute, Sichuan Agricultural University, No. 211 Huiming Rd, Wenjiang District, Chengdu City, 611130, Sichuan Province, People's Republic of China
| | - Qingcheng Li
- Triticeae Research Institute, Sichuan Agricultural University, No. 211 Huiming Rd, Wenjiang District, Chengdu City, 611130, Sichuan Province, People's Republic of China
| | - Shunzong Ning
- Triticeae Research Institute, Sichuan Agricultural University, No. 211 Huiming Rd, Wenjiang District, Chengdu City, 611130, Sichuan Province, People's Republic of China
| | - Zehong Yan
- Triticeae Research Institute, Sichuan Agricultural University, No. 211 Huiming Rd, Wenjiang District, Chengdu City, 611130, Sichuan Province, People's Republic of China
| | - Bihua Wu
- Triticeae Research Institute, Sichuan Agricultural University, No. 211 Huiming Rd, Wenjiang District, Chengdu City, 611130, Sichuan Province, People's Republic of China
| | - Xiujin Lan
- Triticeae Research Institute, Sichuan Agricultural University, No. 211 Huiming Rd, Wenjiang District, Chengdu City, 611130, Sichuan Province, People's Republic of China
| | - Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University, No. 211 Huiming Rd, Wenjiang District, Chengdu City, 611130, Sichuan Province, People's Republic of China
| | - Lin Huang
- Triticeae Research Institute, Sichuan Agricultural University, No. 211 Huiming Rd, Wenjiang District, Chengdu City, 611130, Sichuan Province, People's Republic of China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, No. 211 Huiming Rd, Wenjiang District, Chengdu City, 611130, Sichuan Province, People's Republic of China
| | - Ke Zheng
- Triticeae Research Institute, Sichuan Agricultural University, No. 211 Huiming Rd, Wenjiang District, Chengdu City, 611130, Sichuan Province, People's Republic of China
| | - Wenshuai Chen
- Triticeae Research Institute, Sichuan Agricultural University, No. 211 Huiming Rd, Wenjiang District, Chengdu City, 611130, Sichuan Province, People's Republic of China
| | - Ma Yu
- Triticeae Research Institute, Sichuan Agricultural University, No. 211 Huiming Rd, Wenjiang District, Chengdu City, 611130, Sichuan Province, People's Republic of China
| | - Xuejiao Chen
- Triticeae Research Institute, Sichuan Agricultural University, No. 211 Huiming Rd, Wenjiang District, Chengdu City, 611130, Sichuan Province, People's Republic of China
| | - Mengping Chen
- Triticeae Research Institute, Sichuan Agricultural University, No. 211 Huiming Rd, Wenjiang District, Chengdu City, 611130, Sichuan Province, People's Republic of China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, No. 211 Huiming Rd, Wenjiang District, Chengdu City, 611130, Sichuan Province, People's Republic of China
| | - Huaigang Zhang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, People's Republic of China
| | - Masahiro Kishii
- International Maize and Wheat Improvement Center, 56237, Texcoco, Mexico
| | | | - Long Mao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, No. 211 Huiming Rd, Wenjiang District, Chengdu City, 611130, Sichuan Province, People's Republic of China
| | - Dengcai Liu
- Triticeae Research Institute, Sichuan Agricultural University, No. 211 Huiming Rd, Wenjiang District, Chengdu City, 611130, Sichuan Province, People's Republic of China.
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31
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Hawkesford MJ, Griffiths S. Exploiting genetic variation in nitrogen use efficiency for cereal crop improvement. Curr Opin Plant Biol 2019; 49:35-42. [PMID: 31176099 PMCID: PMC6692496 DOI: 10.1016/j.pbi.2019.05.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 05/18/2023]
Abstract
Cereals are the most important sources of calories and nutrition for the human population, and are an essential animal feed. Food security depends on adequate production and demands are predicted to rise as the global population rises. The need for increased yields will have to be coupled to the efficient use of resources including fertilisers such as nitrogen to underpin the sustainability of food production. Although optimally performing crops with high yields require a balanced mineral nutrition, nitrogen fundamentally drives growth and yield as well as requirements for other nutrients. It is estimated that globally only 33% of applied nitrogen fertiliser is recovered in the harvested grain, indicative of a huge waste of resource and potential major pollutant and is thus a major target for crop improvement. Both agronomy and breeding will contribute to improved nitrogen use efficiency (NUE) and an important component of the latter is harnessing germplasm variation. This review will consider the key traits involved in NUE, the potential to exploit genetic variation for these specific traits, and the approaches to be utilised.
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Sadeghi-Tehran P, Angelov P, Virlet N, Hawkesford MJ. Scalable Database Indexing and Fast Image Retrieval Based on Deep Learning and Hierarchically Nested Structure Applied to Remote Sensing and Plant Biology. J Imaging 2019; 5:33. [PMID: 34460461 PMCID: PMC8320911 DOI: 10.3390/jimaging5030033] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/18/2019] [Accepted: 02/18/2019] [Indexed: 11/25/2022] Open
Abstract
Digitalisation has opened a wealth of new data opportunities by revolutionizing how images are captured. Although the cost of data generation is no longer a major concern, the data management and processing have become a bottleneck. Any successful visual trait system requires automated data structuring and a data retrieval model to manage, search, and retrieve unstructured and complex image data. This paper investigates a highly scalable and computationally efficient image retrieval system for real-time content-based searching through large-scale image repositories in the domain of remote sensing and plant biology. Images are processed independently without considering any relevant context between sub-sets of images. We utilize a deep Convolutional Neural Network (CNN) model as a feature extractor to derive deep feature representations from the imaging data. In addition, we propose an effective scheme to optimize data structure that can facilitate faster querying at search time based on the hierarchically nested structure and recursive similarity measurements. A thorough series of tests were carried out for plant identification and high-resolution remote sensing data to evaluate the accuracy and the computational efficiency of the proposed approach against other content-based image retrieval (CBIR) techniques, such as the bag of visual words (BOVW) and multiple feature fusion techniques. The results demonstrate that the proposed scheme is effective and considerably faster than conventional indexing structures.
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Affiliation(s)
| | - Plamen Angelov
- School of Computing and Communications, InfoLab21, Lancaster University, Lancaster LA1 4WA, UK
| | - Nicolas Virlet
- Department of Plant Sciences, Rothamsted Research, Harpenden AL5 2JQ, UK
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Reich M, Aghajanzadeh TA, Parmar S, Hawkesford MJ, De Kok LJ. Calcium ameliorates the toxicity of sulfate salinity in Brassica rapa. J Plant Physiol 2018; 231:1-8. [PMID: 30195139 DOI: 10.1016/j.jplph.2018.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 08/13/2018] [Accepted: 08/28/2018] [Indexed: 06/08/2023]
Abstract
Salinity stress in Brassica, often only associated with osmotic effects and the toxicity of Na+, was more severe when applied as Na2SO4 than as NaCl, indicating that SO42- ions had toxic effects as well. Application of 10 mM calcium in the form of CaCl2 in the growth medium of plants only slightly ameliorated growth impairment by NaCl and KCl, but almost completely prevented negative effects of Na2SO4 and K2SO4 on plant biomass production. This effect was calcium specific, as MgCl2 ameliorated sulfate toxicity to a much lower extent. This sulfate toxicity coincided with a strong decrease in the plant content of calcium and manganese upon sulfate salinity. Application of CaCl2 largely alleviated this decrease, however, it did not prevent the higher tissue concentration of sulfate. CaCl2 prevented the increase in organic sulfur compounds presumably by reducing of relative gene expression of ATP-sulfurylase (ATPS) and adenosine 5'-phosphosulfate reductase (APR) indicating a possible regulation of sulfate assimilation by calcium. The upregulation of the genes encoding for Group 4 sulfate transporters (Sultr4;1 and 4;2) upon sulfate salinity, was absent in the presence of CaCl2. Therefore, additional calcium may facilitate an increased vacuolar capacity for sulfate accumulation.
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Affiliation(s)
- Martin Reich
- Laboratory of Plant Physiology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. Box 11103, 9700 CC Groningen, The Netherlands
| | - Tahereh A Aghajanzadeh
- Department of Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran.
| | - Saroj Parmar
- Plant Sciences Department, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
| | | | - Luit J De Kok
- Laboratory of Plant Physiology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. Box 11103, 9700 CC Groningen, The Netherlands
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Zörb C, Ludewig U, Hawkesford MJ. Perspective on Wheat Yield and Quality with Reduced Nitrogen Supply. Trends Plant Sci 2018; 23:1029-1037. [PMID: 30249481 PMCID: PMC6202697 DOI: 10.1016/j.tplants.2018.08.012] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 08/30/2018] [Accepted: 08/31/2018] [Indexed: 05/19/2023]
Abstract
Wheat is an important cereal crop with a high demand for nitrogen (N) fertilizer to enable the grain protein accumulation that is necessary for baking and processing quality. Here, perspectives for the development of improved wheat genotypes with higher yield stability, better grain quality, and improved N use efficiency to lower environmental impacts are discussed. The development of improved wheat genotypes, for example, genotypes that lack storage proteins that do not contribute to baking quality (e.g., by genome editing), in combination with appropriate N fertilizer management to prevent N losses into the environment underpins a novel approach to improving N use efficiency. This approach may be particularly applicable to wheats grown for animal feed, which have lower quality and functionality requirements.
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Affiliation(s)
- Christian Zörb
- Institute of Crop Science, Quality of Plant Products (340e), University of Hohenheim, 70593 Stuttgart, Schloss Westflügel, Germany.
| | - Uwe Ludewig
- Institute of Crop Science, Nutritional Crop Physiology (340h), University of Hohenheim, 70593 Stuttgart, Germany
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Savill GP, Michalski A, Powers SJ, Wan Y, Tosi P, Buchner P, Hawkesford MJ. Temperature and nitrogen supply interact to determine protein distribution gradients in the wheat grain endosperm. J Exp Bot 2018; 69:3117-3126. [PMID: 29660003 PMCID: PMC5972578 DOI: 10.1093/jxb/ery127] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 03/21/2018] [Indexed: 05/06/2023]
Abstract
Gradients exist in the distribution of storage proteins in the wheat (Triticum aestivum) endosperm and determine the milling properties and protein recovery rate of the grain. A novel image analysis technique was developed to quantify both the gradients in protein concentration, and the size distribution of protein bodies within the endosperm of wheat plants grown under two different (20 or 28 °C) post-anthesis temperatures, and supplied with a nutrient solution with either high or low nitrogen content. Under all treatment combinations, protein concentration was greater in the endosperm cells closest to the aleurone layer and decreased towards the centre of the two lobes of the grain, i.e. a negative gradient. This was accompanied by a decrease in size of protein bodies from the outer to the inner endosperm layers in all but one of the treatments. Elevated post-anthesis temperature had the effect of increasing the magnitude of the negative gradients in both protein concentration and protein body size, whilst limiting nitrogen supply decreased the gradients.
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Affiliation(s)
- George P Savill
- Plant Sciences Department, Rothamsted Research, West Common, Harpenden, UK
| | - Adam Michalski
- Institute of Geodesy and Geoinformatics, Wrocław University of Environmental and Life Sciences, ul. Grunwaldzka, Wrocław, Poland
| | - Stephen J Powers
- Computational and Analytical Sciences Department, Rothamsted Research, West Common, Harpenden, UK
| | - Yongfang Wan
- Plant Sciences Department, Rothamsted Research, West Common, Harpenden, UK
| | - Paola Tosi
- School of Agriculture, Policy, and Development, University of Reading, Earley, Reading, UK
| | - Peter Buchner
- Plant Sciences Department, Rothamsted Research, West Common, Harpenden, UK
| | - Malcolm J Hawkesford
- Plant Sciences Department, Rothamsted Research, West Common, Harpenden, UK
- Correspondence:
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Sadeghi-Tehran P, Virlet N, Sabermanesh K, Hawkesford MJ. Multi-feature machine learning model for automatic segmentation of green fractional vegetation cover for high-throughput field phenotyping. Plant Methods 2017; 13:103. [PMID: 29201134 PMCID: PMC5696775 DOI: 10.1186/s13007-017-0253-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 11/11/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND Accurately segmenting vegetation from the background within digital images is both a fundamental and a challenging task in phenotyping. The performance of traditional methods is satisfactory in homogeneous environments, however, performance decreases when applied to images acquired in dynamic field environments. RESULTS In this paper, a multi-feature learning method is proposed to quantify vegetation growth in outdoor field conditions. The introduced technique is compared with the state-of the-art and other learning methods on digital images. All methods are compared and evaluated with different environmental conditions and the following criteria: (1) comparison with ground-truth images, (2) variation along a day with changes in ambient illumination, (3) comparison with manual measurements and (4) an estimation of performance along the full life cycle of a wheat canopy. CONCLUSION The method described is capable of coping with the environmental challenges faced in field conditions, with high levels of adaptiveness and without the need for adjusting a threshold for each digital image. The proposed method is also an ideal candidate to process a time series of phenotypic information throughout the crop growth acquired in the field. Moreover, the introduced method has an advantage that it is not limited to growth measurements only but can be applied on other applications such as identifying weeds, diseases, stress, etc.
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Affiliation(s)
| | - Nicolas Virlet
- Plant Science Department, Rothamsted Research, Harpenden, AL5 2JQ UK
| | - Kasra Sabermanesh
- Plant Science Department, Rothamsted Research, Harpenden, AL5 2JQ UK
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Evens NP, Buchner P, Williams LE, Hawkesford MJ. The role of ZIP transporters and group F bZIP transcription factors in the Zn-deficiency response of wheat (Triticum aestivum). Plant J 2017; 92:291-304. [PMID: 28771859 PMCID: PMC5656842 DOI: 10.1111/tpj.13655] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 07/25/2017] [Accepted: 07/28/2017] [Indexed: 05/12/2023]
Abstract
Understanding the molecular basis of zinc (Zn) uptake and transport in staple cereal crops is critical for improving both Zn content and tolerance to low-Zn soils. This study demonstrates the importance of group F bZIP transcription factors and ZIP transporters in responses to Zn deficiency in wheat (Triticum aestivum). Seven group F TabZIP genes and 14 ZIPs with homeologs were identified in hexaploid wheat. Promoter analysis revealed the presence of Zn-deficiency-response elements (ZDREs) in a number of the ZIPs. Functional complementation of the zrt1/zrt2 yeast mutant by TaZIP3, -6, -7, -9 and -13 supported an ability to transport Zn. Group F TabZIPs contain the group-defining cysteine-histidine-rich motifs, which are the predicted binding site of Zn2+ in the Zn-deficiency response. Conservation of these motifs varied between the TabZIPs suggesting that individual TabZIPs may have specific roles in the wheat Zn-homeostatic network. Increased expression in response to low Zn levels was observed for several of the wheat ZIPs and bZIPs; this varied temporally and spatially suggesting specific functions in the response mechanism. The ability of the group F TabZIPs to bind to specific ZDREs in the promoters of TaZIPs indicates a conserved mechanism in monocots and dicots in responding to Zn deficiency. In support of this, TabZIPF1-7DL and TabZIPF4-7AL afforded a strong level of rescue to the Arabidopsis hypersensitive bzip19 bzip23 double mutant under Zn deficiency. These results provide a greater understanding of Zn-homeostatic mechanisms in wheat, demonstrating an expanded repertoire of group F bZIP transcription factors, adding to the complexity of Zn homeostasis.
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Affiliation(s)
- Nicholas P. Evens
- Rothamsted ResearchWest CommonHarpenden, HertfordshireAL5 2JQUK
- Biological ScienceUniversity of SouthamptonLife Sciences Building 85, Highfield CampusSouthamptonSO17 1BJUK
| | - Peter Buchner
- Rothamsted ResearchWest CommonHarpenden, HertfordshireAL5 2JQUK
| | - Lorraine E. Williams
- Biological ScienceUniversity of SouthamptonLife Sciences Building 85, Highfield CampusSouthamptonSO17 1BJUK
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Wan Y, King R, Mitchell RAC, Hassani-Pak K, Hawkesford MJ. Spatiotemporal expression patterns of wheat amino acid transporters reveal their putative roles in nitrogen transport and responses to abiotic stress. Sci Rep 2017. [PMID: 28710348 DOI: 10.1038/s41598-017-04473-4473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023] Open
Abstract
Amino acid transporters have roles in amino acid uptake from soil, long-distance transport, remobilization from vegetative tissues and accumulation in grain. Critically, the majority of wheat grain nitrogen is derived from amino acids remobilized from vegetative organs. However, no systematic analysis of wheat AAT genes has been reported to date. Here, 283 full length wheat AAT genes representing 100 distinct groups of homeologs were identified and curated by selectively consolidating IWGSC CSSv2 and TGACv1 Triticum aestivum genome assemblies and reassembling or mapping of IWGSC CSS chromosome sorted reads to fill any gaps. Gene expression profiling was performed using public RNA-seq data from root, leaf, stem, spike, grain and grain cells (transfer cell (TC), aleurone cell (AL), and starchy endosperm (SE)). AATs highly expressed in roots are good candidates for amino acid uptake from soil whilst AATs highly expressed in senescing leaves and stems may be involved in translocation to grain. AATs in TC (TaAAP2 and TaAAP19) and SE (TaAAP13) may play important roles in determining grain protein content and grain yield. The expression levels of AAT homeologs showed unequal contributions in response to abiotic stresses and development, which may aid wheat adaptation to a wide range of environments.
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Affiliation(s)
- Yongfang Wan
- Plant Sciences Department, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Robert King
- Computational and Analytical Sciences Department, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Rowan A C Mitchell
- Plant Sciences Department, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Keywan Hassani-Pak
- Computational and Analytical Sciences Department, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
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Abstract
Crop nutrient and especially nitrogen use efficiency (NUE) is both an economically and an environmentally highly desirable trait. It has been estimated that only a third of nitrogen inputs to cereal crop worldwide are recovered in grain for consumption, resulting in a huge waste of resource with major negative impacts on the environment. Most measures of NUE in wheat and other cereals are based on field assessments of crop yields at given N inputs, performance responses to added N fertilizer, or by quantifying N fertilizer recovery rates. However, NUE is a complex trait comprising two key major components, N uptake and N utilization efficiency, both also complex traits in themselves, each involving many physiological processes and biochemical pathways. A deeper understanding of the processes involved in NUE has been a target of the UK Wheat Genetic Improvement Network project (http://www.wgin.org.uk/). This has enabled the breakdown of characteristics contributing to NUE and an assessment of the variation present in those characteristics, predominantly in modern cultivars; a total of 13 years of data have been obtained to date. Significant but limited variation suggests a requirement for broader germplasm screening such as older varieties, landraces, and wild relatives.
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Affiliation(s)
- Malcolm J Hawkesford
- Rothamsted Research, Plant Sciences Department, Harpenden, Hertfordshire AL5 2JQ, UK
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40
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Sadeghi-Tehran P, Sabermanesh K, Virlet N, Hawkesford MJ. Automated Method to Determine Two Critical Growth Stages of Wheat: Heading and Flowering. Front Plant Sci 2017; 8:252. [PMID: 28289423 PMCID: PMC5326764 DOI: 10.3389/fpls.2017.00252] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 02/09/2017] [Indexed: 05/04/2023]
Abstract
Recording growth stage information is an important aspect of precision agriculture, crop breeding and phenotyping. In practice, crop growth stage is still primarily monitored by-eye, which is not only laborious and time-consuming, but also subjective and error-prone. The application of computer vision on digital images offers a high-throughput and non-invasive alternative to manual observations and its use in agriculture and high-throughput phenotyping is increasing. This paper presents an automated method to detect wheat heading and flowering stages, which uses the application of computer vision on digital images. The bag-of-visual-word technique is used to identify the growth stage during heading and flowering within digital images. Scale invariant feature transformation feature extraction technique is used for lower level feature extraction; subsequently, local linear constraint coding and spatial pyramid matching are developed in the mid-level representation stage. At the end, support vector machine classification is used to train and test the data samples. The method outperformed existing algorithms, having yielded 95.24, 97.79, 99.59% at early, medium and late stages of heading, respectively and 85.45% accuracy for flowering detection. The results also illustrate that the proposed method is robust enough to handle complex environmental changes (illumination, occlusion). Although the proposed method is applied only on identifying growth stage in wheat, there is potential for application to other crops and categorization concepts, such as disease classification.
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Forieri I, Sticht C, Reichelt M, Gretz N, Hawkesford MJ, Malagoli M, Wirtz M, Hell R. System analysis of metabolism and the transcriptome in Arabidopsis thaliana roots reveals differential co-regulation upon iron, sulfur and potassium deficiency. Plant Cell Environ 2017; 40:95-107. [PMID: 27726154 DOI: 10.1111/pce.12842] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/06/2016] [Accepted: 09/19/2016] [Indexed: 05/22/2023]
Abstract
Deprivation of mineral nutrients causes significant retardation of plant growth. This retardation is associated with nutrient-specific and general stress-induced transcriptional responses. In this study, we adjusted the external supply of iron, potassium and sulfur to cause the same retardation of shoot growth. Nevertheless, limitation by individual nutrients resulted in specific morphological adaptations and distinct shifts within the root metabolite fingerprint. The metabolic shifts affected key metabolites of primary metabolism and the stress-related phytohormones, jasmonic, salicylic and abscisic acid. These phytohormone signatures contributed to specific nutrient deficiency-induced transcriptional regulation. Limitation by the micronutrient iron caused the strongest regulation and affected 18% of the root transcriptome. Only 130 genes were regulated by all nutrients. Specific co-regulation between the iron and sulfur metabolic routes upon iron or sulfur deficiency was observed. Interestingly, iron deficiency caused regulation of a different set of genes of the sulfur assimilation pathway compared with sulfur deficiency itself, which demonstrates the presence of specific signal-transduction systems for the cross-regulation of the pathways. Combined iron and sulfur starvation experiments demonstrated that a requirement for a specific nutrient can overrule this cross-regulation. The comparative metabolomics and transcriptomics approach used dissected general stress from nutrient-specific regulation in roots of Arabidopsis.
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Affiliation(s)
- Ilaria Forieri
- Centre for Organismal Studies (COS), University of Heidelberg, 69120, Heidelberg, Germany
| | - Carsten Sticht
- Center for Medical Research, University of Mannheim, 68167, Mannheim, Germany
| | | | - Norbert Gretz
- Center for Medical Research, University of Mannheim, 68167, Mannheim, Germany
| | | | - Mario Malagoli
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padua, Italy
| | - Markus Wirtz
- Centre for Organismal Studies (COS), University of Heidelberg, 69120, Heidelberg, Germany
| | - Ruediger Hell
- Centre for Organismal Studies (COS), University of Heidelberg, 69120, Heidelberg, Germany
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Heyneke E, Watanabe M, Erban A, Duan G, Buchner P, Walther D, Kopka J, Hawkesford MJ, Hoefgen R. Characterization of the Wheat Leaf Metabolome during Grain Filling and under Varied N-Supply. Front Plant Sci 2017; 8:2048. [PMID: 29238358 PMCID: PMC5712589 DOI: 10.3389/fpls.2017.02048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/15/2017] [Indexed: 05/20/2023]
Abstract
Progress in improving crop growth is an absolute goal despite the influence multifactorial components have on crop yield and quality. An Avalon × Cadenza doubled-haploid wheat mapping population was used to study the leaf metabolome of field grown wheat at weekly intervals during the time in which the canopy contributes to grain filling, i.e., from anthesis to 5 weeks post-anthesis. Wheat was grown under four different nitrogen supplies reaching from residual soil N to a luxury over-fertilization (0, 100, 200, and 350 kg N ha-1). Four lines from a segregating doubled haploid population derived of a cross of the wheat elite cvs. Avalon and Cadenza were chosen as they showed pairwise differences in either N utilization efficiency (NUtE) or senescence timing. 108 annotated metabolites of primary metabolism and ions were determined. The analysis did not provide genotype specific markers because of a remarkable stability of the metabolome between lines. We speculate that the reason for failing to identify genotypic markers might be due to insufficient genetic diversity of the wheat parents and/or the known tendency of plants to keep metabolome homeostasis even under adverse conditions through multiple adaptations and rescue mechanism. The data, however, provided a consistent catalogue of metabolites and their respective responses to environmental and developmental factors and may bode well for future systems biology approaches, and support plant breeding and crop improvement.
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Affiliation(s)
- Elmien Heyneke
- Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Mutsumi Watanabe
- Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Alexander Erban
- Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Guangyou Duan
- Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- European Molecular Biology Laboratory, European Bioinformatics Institute, Heidelberg, Germany
| | - Peter Buchner
- Plant Sciences, Rothamsted Research, Harpenden, United Kingdom
| | - Dirk Walther
- Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Joachim Kopka
- Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | | | - Rainer Hoefgen
- Department Willmitzer, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- *Correspondence: Rainer Hoefgen
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Li W, Chen M, Wang E, Hu L, Hawkesford MJ, Zhong L, Chen Z, Xu Z, Li L, Zhou Y, Guo C, Ma Y. Genome-wide analysis of autophagy-associated genes in foxtail millet (Setaria italica L.) and characterization of the function of SiATG8a in conferring tolerance to nitrogen starvation in rice. BMC Genomics 2016; 17:797. [PMID: 27733118 PMCID: PMC5062844 DOI: 10.1186/s12864-016-3113-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 09/23/2016] [Indexed: 01/07/2023] Open
Abstract
Background Autophagy is a cellular degradation process that is highly evolutionarily-conserved in yeast, plants, and animals. In plants, autophagy plays important roles in regulating intracellular degradation and recycling of amino acids in response to nutrient starvation, senescence, and other environmental stresses. Foxtail millet (Setaria italica) has strong resistance to stresses and has been proposed as an ideal material for use in the study of the physiological mechanisms of abiotic stress tolerance in plants. Although the genome sequence of foxtail millet (Setaria italica) is available, the characteristics and functions of abiotic stress-related genes remain largely unknown for this species. Results A total of 37 putative ATG (autophagy-associated genes) genes in the foxtail millet genome were identified. Gene duplication analysis revealed that both segmental and tandem duplication events have played significant roles in the expansion of the ATG gene family in foxtail millet. Comparative synteny mapping between the genomes of foxtail millet and rice suggested that the ATG genes in both species have common ancestors, as their ATG genes were primarily located in similar syntenic regions. Gene expression analysis revealed the induced expression of 31 SiATG genes by one or more phytohormone treatments, 26 SiATG genes by drought, salt and cold, 24 SiATG genes by darkness and 25 SiATG genes by nitrogen starvation. Results of qRT-PCR showing that among 37 SiATG genes, the expression level of SiATG8a was the highest after nitrogen starvation treatment 24 h, suggesting its potential role in tolerance to nutrient starvation. Moreover, the heterologous expression of SiATG8a in rice improved nitrogen starvation tolerance. Compared to wild type rice, the transgenic rice performed better and had higher aboveground total nitrogen content when the plants were grown under nitrogen starvation conditions. Conclusions Our results deepen understanding about the characteristics and functions of ATG genes in foxtail millet and also identify promising new genetic resources that should be of use in future efforts to develop varieties of foxtail millet and other crop species that have resistance to nitrogen deficiency stress. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3113-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Weiwei Li
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, 150025, China
| | - Ming Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Erhui Wang
- College of Life Sciences, Northwest A&F University, Yangling, Shanxi, 712100, China
| | - Liqin Hu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Malcolm J Hawkesford
- Plant Biology and Crop Science Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Li Zhong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Zhu Chen
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui, 230000, China
| | - Zhaoshi Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Liancheng Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Yongbin Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China
| | - Changhong Guo
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, 150025, China.
| | - Youzhi Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China.
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Moore KL, Tosi P, Palmer R, Hawkesford MJ, Grovenor CRM, Shewry PR. The dynamics of protein body formation in developing wheat grain. Plant Biotechnol J 2016; 14:1876-82. [PMID: 26898533 PMCID: PMC4988504 DOI: 10.1111/pbi.12549] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 02/04/2016] [Accepted: 02/10/2016] [Indexed: 05/18/2023]
Abstract
Wheat is a major source of protein in the diets of humans and livestock but we know little about the mechanisms that determine the patterns of protein synthesis in the developing endosperm. We have used a combination of enrichment with (15) N glutamine and NanoSIMS imaging to establish that the substrate required for protein synthesis is transported radially from its point of entrance in the endosperm cavity across the starchy endosperm tissues, before becoming concentrated in the cells immediately below the aleurone layer. This transport occurs continuously during grain development but may be slower in the later stages. Although older starchy endosperm cells tend to contain larger protein deposits formed by the fusion of small protein bodies, small highly enriched protein bodies may also be present in the same cells. This shows a continuous process of protein body initiation, in both older and younger starchy endosperm cells and in all regions of the tissue. Immunolabeling with specific antibodies shows that the patterns of enrichment are not related to the contents of gluten proteins in the protein bodies. In addition to providing new information on the dynamics of protein deposition, the study demonstrates the wider utility of NanoSIMS and isotope labelling for studying complex developmental processes in plant tissues.
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Affiliation(s)
- Katie L Moore
- School of Materials, University of Manchester, Manchester, UK
| | - Paola Tosi
- School of Agriculture Policy and Development, Reading University, Reading, UK
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Reich M, Aghajanzadeh T, Helm J, Parmar S, Hawkesford MJ, De Kok LJ. Chloride and sulfate salinity differently affect biomass, mineral nutrient composition and expression of sulfate transport and assimilation genes in Brassica rapa. Plant Soil 2016; 411:319-332. [PMID: 32269390 PMCID: PMC7115016 DOI: 10.1007/s11104-016-3026-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/15/2016] [Indexed: 05/21/2023]
Abstract
BACKGROUND AND AIMS It remains uncertain whether a higher toxicity of either NaCl or Na2SO4 in plants is due to an altered toxicity of sodium or a different toxicity of the anions. The aim of this study was to determine the contributions of sodium and the two anions to the different toxicities of chloride and sulfate salinity. The effects of the different salts on physiological parameters, mineral nutrient composition and expression of genes of sulfate transport and assimilation were studied. METHODS Seedlings of Brassica rapa L. have been exposed to NaCl, Na2SO4, KCl and K2SO4 to assess the potential synergistic effect of the anions with the toxic cation sodium, as well as their separate toxicities if accompanied by the non-toxic cation potassium. Biomass production, stomatal resistance and Fv/fm were measured to determine differences in ionic and osmotic stress caused by the salts. Anion content (HPLC), mineral nutrient composition (ICP-AES) and gene expression of sulfate transporters and sulfur assimilatory enzymes (real-time qPCR) were analyzed. RESULTS Na2SO4 impeded growth to a higher extent than NaCl and was the only salt to decrease Fv/fm. K2SO4 reduced plant growth more than NaCl. Analysis of mineral nutrient contents of plant tissue revealed that differences in sodium accumulation could not explain the increased toxicity of sulfate over chloride salts. Shoot contents of calcium, manganese and phosphorus were decreased more strongly by exposure to Na2SO4 than by NaCl. The expression levels of genes encoding proteins for sulfate transport and assimilation were differently affected by the different salts. While gene expression of primary sulfate uptake at roots was down-regulated upon exposure to sulfate salts, presumably to prevent an excessive uptake, genes encoding for the vacuolar sulfate transporter Sultr4;1 were upregulated. Gene expression of ATP sulfurylase was hardly affected by salinity in shoot and roots, the transcript level of 5'-adenylylsulfate reductase (APR) was decreased upon exposure to sulfate salts in roots. Sulfite reductase was decreased in the shoot by all salts similarly and remained unaffected in roots. CONCLUSIONS The higher toxicity of Na2SO4 over NaCl in B. rapa seemed to be due to an increased toxicity of sulfate over chloride, as indicated by the higher toxicity of K2SO4 over KCl. Thus, toxicity of sodium was not promoted by sulfate. The observed stronger negative effect on the tissue contents of calcium, manganese and phosphorus could contribute to the increased toxicity of sulfate over chloride. The upregulation of Sultr4;1 and 4;2 under sulfate salinity might lead to a detrimental efflux of stored sulfate from the vacuole into the cytosol and the chloroplasts. It remains unclear why expression of Sultr4;1 and 4;2 was upregulated. A possible explanation is a control of the gene expression of these transporters by the sulfate gradient across the tonoplast.
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Affiliation(s)
- Martin Reich
- Laboratory of Plant Physiology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. Box 11103, 9700 CC Groningen, The Netherlands
| | - Tahereh Aghajanzadeh
- Department of Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
| | - Juliane Helm
- Plant Biodiversity Group, Institute of Systematic Botany, Friedrich Schiller University, Philosophenweg 16, D-07743 Jena, Germany
| | - Saroj Parmar
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts AL5 2JQ UK
| | - Malcolm J. Hawkesford
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts AL5 2JQ UK
| | - Luit J. De Kok
- Laboratory of Plant Physiology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, P.O. Box 11103, 9700 CC Groningen, The Netherlands
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Gao W, Hodgkinson L, Jin K, Watts CW, Ashton RW, Shen J, Ren T, Dodd IC, Binley A, Phillips AL, Hedden P, Hawkesford MJ, Whalley WR. Deep roots and soil structure. Plant Cell Environ 2016; 39:1662-8. [PMID: 26650587 PMCID: PMC4950291 DOI: 10.1111/pce.12684] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 11/10/2015] [Accepted: 11/13/2015] [Indexed: 05/18/2023]
Abstract
In this opinion article we examine the relationship between penetrometer resistance and soil depth in the field. Assuming that root growth is inhibited at penetrometer resistances > 2.5 MPa, we conclude that in most circumstances the increases in penetrometer resistance with depth are sufficiently great to confine most deep roots to elongating in existing structural pores. We suggest that deep rooting is more likely related to the interaction between root architecture and soil structure than it is to the ability of a root to deform strong soil. Although the ability of roots to deform strong soil is an important trait, we propose it is more closely related to root exploration of surface layers than deep rooting.
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Affiliation(s)
- W Gao
- China Agricultural University, Beijing, 100193, China
| | - L Hodgkinson
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - K Jin
- Huazhong Agricultural University, Hongshan District, Wuhan, 430070, China
| | - C W Watts
- Rothamsted Research, West Common, Harpenden, St. Albans, AL5 2JQ, UK
| | - R W Ashton
- Rothamsted Research, West Common, Harpenden, St. Albans, AL5 2JQ, UK
| | - J Shen
- China Agricultural University, Beijing, 100193, China
| | - T Ren
- China Agricultural University, Beijing, 100193, China
| | - I C Dodd
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - A Binley
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - A L Phillips
- Rothamsted Research, West Common, Harpenden, St. Albans, AL5 2JQ, UK
| | - P Hedden
- Rothamsted Research, West Common, Harpenden, St. Albans, AL5 2JQ, UK
| | - M J Hawkesford
- Rothamsted Research, West Common, Harpenden, St. Albans, AL5 2JQ, UK
| | - W R Whalley
- Rothamsted Research, West Common, Harpenden, St. Albans, AL5 2JQ, UK
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Reich M, Shahbaz M, Prajapati DH, Parmar S, Hawkesford MJ, De Kok LJ. Interactions of Sulfate with Other Nutrients As Revealed by H2S Fumigation of Chinese Cabbage. Front Plant Sci 2016; 7:541. [PMID: 27200018 PMCID: PMC4847332 DOI: 10.3389/fpls.2016.00541] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/05/2016] [Indexed: 05/21/2023]
Abstract
Sulfur deficiency in plants has severe impacts on both growth and nutrient composition. Fumigation with sub-lethal concentrations of H2S facilitates the supply of reduced sulfur via the leaves while sulfate is depleted from the roots. This restores growth while sulfate levels in the plant tissue remain low. In the present study this system was used to reveal interactions of sulfur with other nutrients in the plant and to ascertain whether these changes are due to the absence or presence of sulfate or rather to changes in growth and organic sulfur. There was a complex reaction of the mineral composition to sulfur deficiency, however, the changes in content of many nutrients were prevented by H2S fumigation. Under sulfur deficiency these nutrients accumulated on a fresh weight basis but were diluted on a dry weight basis, presumably due to a higher dry matter content. The pattern differed, however, between leaves and roots which led to changes in shoot to root partitioning. Only the potassium, molybdenum and zinc contents were strongly linked to the sulfate supply. Potassium was the only nutrient amongst those measured which showed a positive correlation with sulfur content in shoots, highlighting a role as a counter cation for sulfate during xylem loading and vacuolar storage in leaves. This was supported by an accumulation of potassium in roots of the sulfur-deprived plants. Molybdenum and zinc increased substantially under sulfur deficiency, which was only partly prevented by H2S fumigation. While the causes of increased molybdenum under sulfur deficiency have been previously studied, the relation between sulfate and zinc uptake needs further clarification.
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Affiliation(s)
- Martin Reich
- Laboratory of Plant Physiology, Groningen Institute for Evolutionary Life Sciences, University of GroningenGroningen, Netherlands
| | - Muhammad Shahbaz
- Department of Chemistry and Biochemistry, Worcester Polytechnic InstituteWorcester, MA, USA
| | - Dharmendra H. Prajapati
- Laboratory of Plant Physiology, Groningen Institute for Evolutionary Life Sciences, University of GroningenGroningen, Netherlands
| | - Saroj Parmar
- Plant Biology and Crop Science Department, Rothamsted ResearchHarpenden, UK
| | | | - Luit J. De Kok
- Laboratory of Plant Physiology, Groningen Institute for Evolutionary Life Sciences, University of GroningenGroningen, Netherlands
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Virlet N, Sabermanesh K, Sadeghi-Tehran P, Hawkesford MJ. Field Scanalyzer: An automated robotic field phenotyping platform for detailed crop monitoring. Funct Plant Biol 2016; 44:143-153. [PMID: 32480553 DOI: 10.1071/fp16163] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 09/02/2016] [Indexed: 05/20/2023]
Abstract
Current approaches to field phenotyping are laborious or permit the use of only a few sensors at a time. In an effort to overcome this, a fully automated robotic field phenotyping platform with a dedicated sensor array that may be accurately positioned in three dimensions and mounted on fixed rails has been established, to facilitate continual and high-throughput monitoring of crop performance. Employed sensors comprise of high-resolution visible, chlorophyll fluorescence and thermal infrared cameras, two hyperspectral imagers and dual 3D laser scanners. The sensor array facilitates specific growth measurements and identification of key growth stages with dense temporal and spectral resolution. Together, this platform produces a detailed description of canopy development across the crops entire lifecycle, with a high-degree of accuracy and reproducibility.
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Affiliation(s)
- Nicolas Virlet
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
| | - Kasra Sabermanesh
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
| | - Pouria Sadeghi-Tehran
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
| | - Malcolm J Hawkesford
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
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Abstract
In this special issue of Functional Plant Biology, we present a perspective of the current state of the art in plant phenotyping. The applications of automated and detailed recording of plant characteristics using a range of mostly non-invasive techniques are described. Papers range from tissue scale analysis through to aerial surveying of field trials and include model plant species such as Arabidopsis as well as commercial crops such as sugar beet and cereals. The common denominators are high throughput measurements, data rich analyses often utilising image based data capture, requirements for validation when proxy measurement are employed and in many instances a need to fuse datasets. The outputs are detailed descriptions of plant form and function. The papers represent technological advances and important contributions to basic plant biology, and these studies are commonly multidisciplinary, involving engineers, software specialists and plant physiologists. This is a fast moving area producing large datasets and analytical requirements are often common between very diverse platforms.
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Affiliation(s)
| | - Argelia Lorence
- Department of Chemistry and Physics and Arkansas Biosciences Institute, Arkansas State University, PO Box 639, State University, AR 72467, USA
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Reich M, van den Meerakker AN, Parmar S, Hawkesford MJ, De Kok LJ. Temperature determines size and direction of effects of elevated CO2 and nitrogen form on yield quantity and quality of Chinese cabbage. Plant Biol (Stuttg) 2016; 18 Suppl 1:63-75. [PMID: 26390257 DOI: 10.1111/plb.12396] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 09/15/2015] [Indexed: 05/26/2023]
Abstract
Rising atmospheric CO2 concentrations (e[CO2 ]) are presumed to have a significant impact on plant growth and yield and also on mineral nutrient composition, and therefore, on nutritional quality of crops and vegetables. To assess the relevance of these effects in future agroecosystems it is important to understand how e[CO2 ] interacts with other environmental factors. In the present study, we examined the interactive effects of e[CO2 ] with temperature and the form in which nitrogen is supplied (nitrate or ammonium nitrate) on growth, amino acid content and mineral nutrient composition of Chinese cabbage (Brassica pekinensis Rupr.), a crop characterised by its high nutritional value and increasing relevance for human nutrition in many developing countries. Higher temperature, ammonium nitrate and e[CO2 ] had a positive impact on net photosynthesis and growth. A stimulating effect of e[CO2 ] on growth was only observed if the temperature was high (21/18 °C, day/night), and an interaction of e[CO2 ] with N form was only observed if the temperature was ambient (15/12 °C, day/night). Mineral nutrient composition was affected in a complex manner by all three factors and their interaction. These results demonstrate how much the effect of e[CO2 ] on mineral quality of crops depends on other environmental factors. Changes in temperature, adapting N fertilisation and the oxidation state of N have the potential to counteract the mineral depletion caused by e[CO2 ].
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Affiliation(s)
- M Reich
- Laboratory of Plant Physiology, Groningen Institute of Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - A N van den Meerakker
- Laboratory of Plant Physiology, Groningen Institute of Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - S Parmar
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, UK
| | - M J Hawkesford
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, UK
| | - L J De Kok
- Laboratory of Plant Physiology, Groningen Institute of Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
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