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Resjö S, Willforss J, Large A, Siino V, Alexandersson E, Levander F, Andreasson E. Comparative proteomic analyses of potato leaves from field-grown plants grown under extremely long days. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:109032. [PMID: 39181085 DOI: 10.1016/j.plaphy.2024.109032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/08/2024] [Accepted: 08/07/2024] [Indexed: 08/27/2024]
Abstract
There are limited molecular data and few biomarkers available for studies of field-grown plants, especially for plants grown during extremely long days. In this study we present quantitative proteomics data from 3 years of field trials on potato, conducted in northern and southern Sweden and analyze over 3000 proteins per year of the study and complement the proteomic analysis with metabolomic and transcriptomic analyses. Small but consistent differences linked to the longer days (an average of four more hours of light per day) in northern Sweden (20 h light/day) compared to southern Sweden can be observed, with a high correlation between the mRNA determined by RNA-seq and protein abundances. The majority of the proteins with differential abundances between northern and southern Sweden could be divided into three groups: metabolic enzymes (especially GABA metabolism), proteins involved in redox metabolism, and hydrolytic enzymes. The observed differences in metabolic enzyme abundances corresponded well with untargeted metabolite data determined by GC and LC mass-spectrometry. We also analyzed differences in protein abundance between potato varieties that performed relatively well in northern Sweden in terms of yield with those that performed relatively less well. This comparison indicates that the proteins with higher abundance in the high-yield quotient group are more anabolic in their character, whereas the proteins with lower abundance are more catabolic. Our results create a base of information about potato "field-omics" for improved understanding of physiological and molecular processes in field-grown plants, and our data indicate that the potato plant is not generally stressed by extremely long days.
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Affiliation(s)
- Svante Resjö
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, PO Box 190, SE-234 22, Lomma, Sweden.
| | | | - Annabel Large
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, PO Box 190, SE-234 22, Lomma, Sweden
| | | | - Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, PO Box 190, SE-234 22, Lomma, Sweden
| | | | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, PO Box 190, SE-234 22, Lomma, Sweden
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2
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Samare-Najaf M, Razavinasab SA, Samareh A, Jamali N. Omics-based novel strategies in the diagnosis of endometriosis. Crit Rev Clin Lab Sci 2024; 61:205-225. [PMID: 37878077 DOI: 10.1080/10408363.2023.2270736] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 10/10/2023] [Indexed: 10/26/2023]
Abstract
Endometriosis, an enigmatic and chronic disorder, is considered a debilitating condition despite being benign. Globally, this gynecologic disorder affects up to 10% of females of reproductive age, impacting almost 190 million individuals. A variety of genetic and environmental factors are involved in endometriosis development, hence the pathophysiology and etiology of endometriosis remain unclear. The uncertainty of the etiology of the disease and its complexity along with nonspecific symptoms have led to misdiagnosis or lack of diagnosis of affected people. Biopsy and laparoscopy are referred to as the gold standard for endometriosis diagnosis. However, the invasiveness of the procedure, the unnecessary operation in disease-free women, and the dependence of the reliability of diagnosis on experience in this area are considered the most significant limitations. Therefore, continuous studies have attempted to offer a noninvasive and reliable approach. The recent advances in modern technologies have led to the generation of large-scale biological data sets, known as -omics data, resulting in the proceeding of the -omics century in biomedical sciences. Thereby, the present study critically reviews novel and noninvasive biomarkers that are based on -omics approaches from 2020 onward. The findings reveal that biomarkers identified based on genomics, epigenomics, transcriptomics, proteomics, and metabolomics are potentially able to diagnose endometriosis, predict prognosis, and stage patients, and potentially, in the near future, a multi-panel of these biomarkers will generate clinical benefits.
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Affiliation(s)
- Mohammad Samare-Najaf
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Kerman Regional Blood Transfusion Center, Kerman, Iran
- Biochemistry Department, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Ali Samareh
- Department of Clinical Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Navid Jamali
- Department of Laboratory Sciences, Sirjan School of Medical Sciences, Sirjan, Iran
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3
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Harris ZN, Pratt JE, Kovacs LG, Klein LL, Kwasniewski MT, Londo JP, Wu AS, Miller AJ. Grapevine scion gene expression is driven by rootstock and environment interaction. BMC PLANT BIOLOGY 2023; 23:211. [PMID: 37085756 PMCID: PMC10122299 DOI: 10.1186/s12870-023-04223-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Grafting is a horticultural practice used widely across woody perennial crop species to fuse together the root and shoot system of two distinct genotypes, the rootstock and the scion, combining beneficial traits from both. In grapevine, grafting is used in nearly 80% of all commercial vines to optimize fruit quality, regulate vine vigor, and enhance biotic and abiotic stress-tolerance. Rootstocks have been shown to modulate elemental composition, metabolomic profiles, and the shape of leaves in the scion, among other traits. However, it is currently unclear how rootstock genotypes influence shoot system gene expression as previous work has reported complex and often contradictory findings. RESULTS In the present study, we examine the influence of grafting on scion gene expression in leaves and reproductive tissues of grapevines growing under field conditions for three years. We show that the influence from the rootstock genotype is highly tissue and time dependent, manifesting only in leaves, primarily during a single year of our three-year study. Further, the degree of rootstock influence on scion gene expression is driven by interactions with the local environment. CONCLUSIONS Our results demonstrate that the role of rootstock genotype in modulating scion gene expression is not a consistent, unchanging effect, but rather an effect that varies over time in relation to local environmental conditions.
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Affiliation(s)
- Zachary N Harris
- Department of Biology, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO, 63103-2010, USA.
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO, 63132-2918, USA.
| | - Julia E Pratt
- Department of Biology, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO, 63103-2010, USA
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO, 63132-2918, USA
| | - Laszlo G Kovacs
- Department of Biology, Missouri State University, 901 S. National Avenue, Springfield, MO, 65897, USA
| | - Laura L Klein
- Department of Biology, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO, 63103-2010, USA
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO, 63132-2918, USA
| | - Misha T Kwasniewski
- Department of Food Science, Pennsylvania State University, 326 Rodney A. Erickson Food Science Building, University Park, PA, 16802, USA
| | - Jason P Londo
- School of Integrative Plant Science, Horticulture Section, Cornell AgriTech, 635 W. North Street, Geneva, NY, 14456, USA
| | - Angela S Wu
- Department of Computer Science, Saint Louis University, 220 N. Grand Blvd, St. Louis, MO, 63103-2010, USA
| | - Allison J Miller
- Department of Biology, Saint Louis University, 3507 Laclede Avenue, St. Louis, MO, 63103-2010, USA.
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO, 63132-2918, USA.
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4
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Nehe A, Martinsson UD, Johansson E, Chawade A. Genotype and environment interaction study shows fungal diseases and heat stress are detrimental to spring wheat production in Sweden. PLoS One 2023; 18:e0285565. [PMID: 37163567 PMCID: PMC10171613 DOI: 10.1371/journal.pone.0285565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 04/26/2023] [Indexed: 05/12/2023] Open
Abstract
Spring wheat is an economically important crop for Scandinavia and its cultivation is likely to be affected by climate change. The current study focused on wheat yield in recent years, during which climate change-related yield fluctuations have been more pronounced than previously observed. Here, effects of the environment, together with the genotype and fungicide treatment was evaluated. Spring wheat multi-location trials conducted at five locations between 2016 and 2020 were used to understand effects of the climate and fungicides on wheat yield. The results showed that the environment has a strong effect on grain yield, followed by the genotype effect. Moreover, temperature has a stronger (negative) impact than rainfall on grain yield and crop growing duration. Despite a low rainfall in the South compared to the North, the southern production region (PR) 2 had the highest yield performance, indicating the optimal environment for spring wheat production. The fungicide treatment effect was significant in 2016, 2017 and 2020. Overall, yield reduction due to fungal diseases ranged from 0.98 (2018) to 13.3% (2017) and this reduction was higher with a higher yield. Overall yield reduction due to fungal diseases was greater in the South (8.9%) than the North zone (5.3%). The genotypes with higher tolerance to diseases included G4 (KWS Alderon), G14 (WPB 09SW025-11), and G23 (SW 11360) in 2016; G24 (SW 11360), G25 (Millie), and G19 (SEC 526-07-2) in 2017; and G19 (WPB 13SW976-01), G12 (Levels), and G18 (SW 141011) in 2020. The combined best performing genotypes for disease tolerance and stable and higher yield in different locations were KWS Alderon, SEC 526-07-2, and WPB 13SW976-01 with fungicide treatment and WPB Avonmore, SEC 526-07-2, SW 131323 without fungicide treatment. We conclude that the best performing genotypes could be recommended for Scandinavian climatic conditions with or without fungicide application and that developing heat-tolerant varieties for Scandinavian countries should be prioritized.
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Affiliation(s)
- Ajit Nehe
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Eva Johansson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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5
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Malinowska M, Ruud AK, Jensen J, Svane SF, Smith AG, Bellucci A, Lenk I, Nagy I, Fois M, Didion T, Thorup-Kristensen K, Jensen CS, Asp T. Relative importance of genotype, gene expression, and DNA methylation on complex traits in perennial ryegrass. THE PLANT GENOME 2022; 15:e20253. [PMID: 35975565 DOI: 10.1002/tpg2.20253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
The growing demand for food and feed crops in the world because of growing population and more extreme weather events requires high-yielding and resilient crops. Many agriculturally important traits are polygenic, controlled by multiple regulatory layers, and with a strong interaction with the environment. In this study, 120 F2 families of perennial ryegrass (Lolium perenne L.) were grown across a water gradient in a semifield facility with subsoil irrigation. Genomic (single-nucleotide polymorphism [SNP]), transcriptomic (gene expression [GE]), and DNA methylomic (MET) data were integrated with feed quality trait data collected from control and drought sections in the semifield facility, providing a treatment effect. Deep root length (DRL) below 110 cm was assessed with convolutional neural network image analysis. Bayesian prediction models were used to partition phenotypic variance into its components and evaluated the proportion of phenotypic variance in all traits captured by different regulatory layers (SNP, GE, and MET). The spatial effects and effects of SNP, GE, MET, the interaction between GE and MET (GE × MET) and GE × treatment (GEControl and GEDrought ) interaction were investigated. Gene expression explained a substantial part of the genetic and spatial variance for all the investigated phenotypes, whereas MET explained residual variance not accounted for by SNPs or GE. For DRL, MET also contributed to explaining spatial variance. The study provides a statistically elegant analytical paradigm that integrates genomic, transcriptomic, and MET information to understand the regulatory mechanisms of polygenic effects for complex traits.
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Affiliation(s)
- Marta Malinowska
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
| | - Anja Karine Ruud
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
| | - Just Jensen
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
| | - Simon Fiil Svane
- Dep. of Plant and Environmental Sciences, Univ. of Copenhagen, Taastrup, Denmark
| | | | - Andrea Bellucci
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
| | - Ingo Lenk
- Research Division, DLF Seeds A/S, Store Heddinge, Denmark
| | - Istvan Nagy
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
| | - Mattia Fois
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
| | - Thomas Didion
- Research Division, DLF Seeds A/S, Store Heddinge, Denmark
| | | | | | - Torben Asp
- Center for Quantitative Genetics and Genomics, Aarhus Univ., Slagelse, Denmark
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6
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Roitsch T, Himanen K, Chawade A, Jaakola L, Nehe A, Alexandersson E. Functional phenomics for improved climate resilience in Nordic agriculture. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5111-5127. [PMID: 35727101 PMCID: PMC9440434 DOI: 10.1093/jxb/erac246] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 06/06/2022] [Indexed: 05/26/2023]
Abstract
The five Nordic countries span the most northern region for field cultivation in the world. This presents challenges per se, with short growing seasons, long days, and a need for frost tolerance. Climate change has additionally increased risks for micro-droughts and water logging, as well as pathogens and pests expanding northwards. Thus, Nordic agriculture demands crops that are adapted to the specific Nordic growth conditions and future climate scenarios. A focus on crop varieties and traits important to Nordic agriculture, including the unique resource of nutritious wild crops, can meet these needs. In fact, with a future longer growing season due to climate change, the region could contribute proportionally more to global agricultural production. This also applies to other northern regions, including the Arctic. To address current growth conditions, mitigate impacts of climate change, and meet market demands, the adaptive capacity of crops that both perform well in northern latitudes and are more climate resilient has to be increased, and better crop management systems need to be built. This requires functional phenomics approaches that integrate versatile high-throughput phenotyping, physiology, and bioinformatics. This review stresses key target traits, the opportunities of latitudinal studies, and infrastructure needs for phenotyping to support Nordic agriculture.
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Affiliation(s)
- Thomas Roitsch
- Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
- Department of Adaptive Biotechnologies, Global Change Research Institute, Czech Academy of Sciences, Brno, Czechia
| | - Kristiina Himanen
- National Plant Phenotyping Infrastructure, HiLIFE, University of Helsinki, Finland
- Organismal and Evolutionary Biology Research Program, Viikki Plant Science Centre, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Laura Jaakola
- Climate laboratory Holt, Department of Arctic and Marine Biology, UiT the Arctic University of Norway, Tromsø, Norway
- NIBIO, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Ajit Nehe
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
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7
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Abreha KB, Alexandersson E, Resjö S, Lankinen Å, Sueldo D, Kaschani F, Kaiser M, van der Hoorn RAL, Levander F, Andreasson E. Leaf Apoplast of Field-Grown Potato Analyzed by Quantitative Proteomics and Activity-Based Protein Profiling. Int J Mol Sci 2021; 22:12033. [PMID: 34769464 PMCID: PMC8584485 DOI: 10.3390/ijms222112033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 01/11/2023] Open
Abstract
Multiple biotic and abiotic stresses challenge plants growing in agricultural fields. Most molecular studies have aimed to understand plant responses to challenges under controlled conditions. However, studies on field-grown plants are scarce, limiting application of the findings in agricultural conditions. In this study, we investigated the composition of apoplastic proteomes of potato cultivar Bintje grown under field conditions, i.e., two field sites in June-August across two years and fungicide treated and untreated, using quantitative proteomics, as well as its activity using activity-based protein profiling (ABPP). Samples were clustered and some proteins showed significant intensity and activity differences, based on their field site and sampling time (June-August), indicating differential regulation of certain proteins in response to environmental or developmental factors. Peroxidases, class II chitinases, pectinesterases, and osmotins were among the proteins more abundant later in the growing season (July-August) as compared to early in the season (June). We did not detect significant differences between fungicide Shirlan treated and untreated field samples in two growing seasons. Using ABPP, we showed differential activity of serine hydrolases and β-glycosidases under greenhouse and field conditions and across a growing season. Furthermore, the activity of serine hydrolases and β-glycosidases, including proteins related to biotic stress tolerance, decreased as the season progressed. The generated proteomics data would facilitate further studies aiming at understanding mechanisms of molecular plant physiology in agricultural fields and help applying effective strategies to mitigate biotic and abiotic stresses.
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Affiliation(s)
- Kibrom B. Abreha
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
| | - Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
| | - Svante Resjö
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
| | - Åsa Lankinen
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
| | - Daniela Sueldo
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; (D.S.); (R.A.L.v.d.H.)
| | - Farnusch Kaschani
- Chemische Biologie, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany; (F.K.); (M.K.)
| | - Markus Kaiser
- Chemische Biologie, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany; (F.K.); (M.K.)
| | - Renier A. L. van der Hoorn
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; (D.S.); (R.A.L.v.d.H.)
| | - Fredrik Levander
- Department of Immunotechnology, Lund University, SE-221 00 Lund, Sweden;
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Lund University, SE-221 00 Lund, Sweden
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
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8
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Francesconi S, Harfouche A, Maesano M, Balestra GM. UAV-Based Thermal, RGB Imaging and Gene Expression Analysis Allowed Detection of Fusarium Head Blight and Gave New Insights Into the Physiological Responses to the Disease in Durum Wheat. FRONTIERS IN PLANT SCIENCE 2021; 12:628575. [PMID: 33868331 PMCID: PMC8047627 DOI: 10.3389/fpls.2021.628575] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/12/2021] [Indexed: 05/24/2023]
Abstract
Wheat is one of the world's most economically important cereal crop, grown on 220 million hectares. Fusarium head blight (FHB) disease is considered a major threat to durum (Triticum turgidum subsp. durum (Desfontaines) Husnache) and bread wheat (T. aestivum L.) cultivars and is mainly managed by the application of fungicides at anthesis. However, fungicides are applied when FHB symptoms are clearly visible and the spikes are almost entirely bleached (% of diseased spikelets > 80%), by when it is too late to control FHB disease. For this reason, farmers often react by performing repeated fungicide treatments that, however, due to the advanced state of the infection, cause a waste of money and pose significant risks to the environment and non-target organisms. In the present study, we used unmanned aerial vehicle (UAV)-based thermal infrared (TIR) and red-green-blue (RGB) imaging for FHB detection in T. turgidum (cv. Marco Aurelio) under natural field conditions. TIR and RGB data coupled with ground-based measurements such as spike's temperature, photosynthetic efficiency and molecular identification of FHB pathogens, detected FHB at anthesis half-way (Zadoks stage 65, ZS 65), when the percentage (%) of diseased spikelets ranged between 20% and 60%. Moreover, in greenhouse experiments the transcripts of the key genes involved in stomatal closure were mostly up-regulated in F. graminearum-inoculated plants, demonstrating that the physiological mechanism behind the spike's temperature increase and photosynthetic efficiency decrease could be attributed to the closure of the guard cells in response to F. graminearum. In addition, preliminary analysis revealed that there is differential regulation of genes between drought-stressed and F. graminearum-inoculated plants, suggesting that there might be a possibility to discriminate between water stress and FHB infection. This study shows the potential of UAV-based TIR and RGB imaging for field phenotyping of wheat and other cereal crop species in response to environmental stresses. This is anticipated to have enormous promise for the detection of FHB disease and tremendous implications for optimizing the application of fungicides, since global food crop demand is to be met with minimal environmental impacts.
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Affiliation(s)
- Sara Francesconi
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, Viterbo, Italy
| | - Antoine Harfouche
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Mauro Maesano
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
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9
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Kieu NP, Lenman M, Andreasson E. Potato as a Model for Field Trials with Modified Gene Functions in Research and Translational Experiments. Methods Mol Biol 2021; 2354:111-122. [PMID: 34448157 DOI: 10.1007/978-1-0716-1609-3_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Gene technology and editing are not only biotechnological techniques for creating new crop varieties but are also tools for researchers to discover gene functions. Field trial following laboratory experiments is an important step in order to evaluate new functions since many phenotypes, and combinations thereof, are difficult to detect in controlled environments and molecular analyses are nowadays possible to do in the field. Here we describe a standard protocol for creating new potato lines and producing seed tubers for field trials within 1 year.
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Affiliation(s)
- Nam Phuong Kieu
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Marit Lenman
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden.
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10
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Cruz DF, De Meyer S, Ampe J, Sprenger H, Herman D, Van Hautegem T, De Block J, Inzé D, Nelissen H, Maere S. Using single-plant-omics in the field to link maize genes to functions and phenotypes. Mol Syst Biol 2020; 16:e9667. [PMID: 33346944 PMCID: PMC7751767 DOI: 10.15252/msb.20209667] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/29/2020] [Accepted: 11/17/2020] [Indexed: 12/14/2022] Open
Abstract
Most of our current knowledge on plant molecular biology is based on experiments in controlled laboratory environments. However, translating this knowledge from the laboratory to the field is often not straightforward, in part because field growth conditions are very different from laboratory conditions. Here, we test a new experimental design to unravel the molecular wiring of plants and study gene-phenotype relationships directly in the field. We molecularly profiled a set of individual maize plants of the same inbred background grown in the same field and used the resulting data to predict the phenotypes of individual plants and the function of maize genes. We show that the field transcriptomes of individual plants contain as much information on maize gene function as traditional laboratory-generated transcriptomes of pooled plant samples subject to controlled perturbations. Moreover, we show that field-generated transcriptome and metabolome data can be used to quantitatively predict individual plant phenotypes. Our results show that profiling individual plants in the field is a promising experimental design that could help narrow the lab-field gap.
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Affiliation(s)
- Daniel Felipe Cruz
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Sam De Meyer
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Joke Ampe
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Heike Sprenger
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Dorota Herman
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Tom Van Hautegem
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Jolien De Block
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Dirk Inzé
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Hilde Nelissen
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Steven Maere
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
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11
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Cui J, Pottosin I, Lamade E, Tcherkez G. What is the role of putrescine accumulated under potassium deficiency? PLANT, CELL & ENVIRONMENT 2020; 43:1331-1347. [PMID: 32017122 DOI: 10.1111/pce.13740] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 01/23/2020] [Accepted: 01/25/2020] [Indexed: 05/25/2023]
Abstract
Biomarker metabolites are of increasing interest in crops since they open avenues for precision agriculture, whereby nutritional needs and stresses can be monitored optimally. Putrescine has the potential to be a useful biomarker to reveal potassium (K+ ) deficiency. In fact, although this diamine has also been observed to increase during other stresses such as drought, cold or heavy metals, respective changes are comparably low. Due to its multifaceted biochemical properties, several roles for putrescine under K+ deficiency have been suggested, such as cation balance, antioxidant, reactive oxygen species mediated signalling, osmolyte or pH regulator. However, the specific association of putrescine build-up with low K+ availability in plants remains poorly understood, and possible regulatory roles must be consistent with putrescine concentration found in plant tissues. We hypothesize that the massive increase of putrescine upon K+ starvation plays an adaptive role. A distinction of putrescine function from that of other polyamines (spermine, spermidine) may be based either on its specificity or (which is probably more relevant under K+ deficiency) on a very high attainable concentration of putrescine, which far exceeds those for spermidine and spermine. putrescine and its catabolites appear to possess a strong potential in controlling cellular K+ and Ca2+ , and mitochondria and chloroplasts bioenergetics under K+ stress.
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Affiliation(s)
- Jing Cui
- Research School of Biology, ANU Joint College of Sciences, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Igor Pottosin
- Biomedical Centre, University of Colima, Colima, Mexico
| | - Emmanuelle Lamade
- UPR34 Performance des systèmes de culture des plantes pérennes, Département PERSYST, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Montpellier, France
| | - Guillaume Tcherkez
- Research School of Biology, ANU Joint College of Sciences, Australian National University, Canberra, Australian Capital Territory, Australia
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Abstract
This article comments on:Melandri G, AbdElgawad H, Riewe D, Hageman JA, Asard H, Beemster GTS, Kadam N, Jagadish K, Altmann T, Ruyter-Spira1 C, Bouwmeester H. 2019. Biomarkers for grain yield stability in rice under drought stress. Journal of Experimental Botany 71, 669–683.
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Affiliation(s)
- Ronan Sulpice
- National University Ireland Galway, Plant Systems Biology Laboratory, Ryan Institute, School of Natural Sciences, Galway, Ireland
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13
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High-Throughput Field-Phenotyping Tools for Plant Breeding and Precision Agriculture. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9050258] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
High-throughput field phenotyping has garnered major attention in recent years leading to the development of several new protocols for recording various plant traits of interest. Phenotyping of plants for breeding and for precision agriculture have different requirements due to different sizes of the plots and fields, differing purposes and the urgency of the action required after phenotyping. While in plant breeding phenotyping is done on several thousand small plots mainly to evaluate them for various traits, in plant cultivation, phenotyping is done in large fields to detect the occurrence of plant stresses and weeds at an early stage. The aim of this review is to highlight how various high-throughput phenotyping methods are used for plant breeding and farming and the key differences in the applications of such methods. Thus, various techniques for plant phenotyping are presented together with applications of these techniques for breeding and cultivation. Several examples from the literature using these techniques are summarized and the key technical aspects are highlighted.
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Mir RR, Reynolds M, Pinto F, Khan MA, Bhat MA. High-throughput phenotyping for crop improvement in the genomics era. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 282:60-72. [PMID: 31003612 DOI: 10.1016/j.plantsci.2019.01.007] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 12/10/2018] [Accepted: 01/09/2019] [Indexed: 05/24/2023]
Abstract
Tremendous progress has been made with continually expanding genomics technologies to unravel and understand crop genomes. However, the impact of genomics data on crop improvement is still far from satisfactory, in large part due to a lack of effective phenotypic data; our capacity to collect useful high quality phenotypic data lags behind the current capacity to generate high-throughput genomics data. Thus, the research bottleneck in plant sciences is shifting from genotyping to phenotyping. This article review the current status of efforts made in the last decade to systematically collect phenotypic data to alleviate this 'phenomics bottlenecks' by recording trait data through sophisticated non-invasive imaging, spectroscopy, image analysis, robotics, high-performance computing facilities and phenomics databases. These modern phenomics platforms and tools aim to record data on traits like plant development, architecture, plant photosynthesis, growth or biomass productivity, on hundreds to thousands of plants in a single day, as a phenomics revolution. It is believed that this revolution will provide plant scientists with the knowledge and tools necessary for unlocking information coded in plant genomes. Efforts have been also made to present the advances made in the last 10 years in phenomics platforms and their use in generating phenotypic data on different traits in several major crops including rice, wheat, barley, and maize. The article also highlights the need for phenomics databases and phenotypic data sharing for crop improvement. The phenomics data generated has been used to identify genes/QTL through QTL mapping, association mapping and genome-wide association studies (GWAS) for genomics-assisted breeding (GAB) for crop improvement.
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Affiliation(s)
- Reyazul Rouf Mir
- Division of Genetics & Plant Breeding, Faculty of Agriculture (FoA), Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Wadura Campus, Sopore-193201, Kashmir, India.
| | - Mathew Reynolds
- Global Wheat Program, International Maize and Wheat Improvement Centre (CIMMYT), Mexico, D.F., Mexico
| | - Francisco Pinto
- Global Wheat Program, International Maize and Wheat Improvement Centre (CIMMYT), Mexico, D.F., Mexico
| | - Mohd Anwar Khan
- Division of Genetics & Plant Breeding, Faculty of Agriculture (FoA), Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Wadura Campus, Sopore-193201, Kashmir, India
| | - Mohd Ashraf Bhat
- Division of Genetics & Plant Breeding, Faculty of Agriculture (FoA), Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Wadura Campus, Sopore-193201, Kashmir, India
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15
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Lankinen Å, Abreha KB, Masini L, Ali A, Resjö S, Andreasson E. Plant immunity in natural populations and agricultural fields: Low presence of pathogenesis-related proteins in Solanum leaves. PLoS One 2018; 13:e0207253. [PMID: 30412603 PMCID: PMC6226184 DOI: 10.1371/journal.pone.0207253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/26/2018] [Indexed: 11/24/2022] Open
Abstract
Plant immunity has mainly been studied under controlled conditions, limiting our knowledge regarding the regulation of immunity under natural conditions where plants grow in association with multiple microorganisms. Plant pathology theory, based on laboratory data, predicts complex biochemical plant-pathogen interactions leading to coevolution of pathogen infectivity vs. plant recognition of microbes in multiple layers over time. However, plant immunity is currently not evaluated in relation to ecological time-scales and field conditions. Here we report status of immunity in plants without visible disease symptoms in wild populations of nightshades, Solanum dulcamara and Solanum nigrum, and in agricultural fields of potato, Solanum tuberosum. We analysed presence of pathogenesis-related proteins in over 500 asymptomatic leaf samples collected in the field in June, July and August over three years. Pathogenesis-related proteins were present in only one-third of the collected samples, suggesting low activity of the immune system. We could also detect an increase in pathogenesis-related proteins later in the growing season, particularly in S. tuberosum. Our findings, based on pathogenesis-related protein markers, indicate major gaps in our knowledge regarding the status and regulation of plant immunity under field conditions.
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Affiliation(s)
- Åsa Lankinen
- Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Kibrom B. Abreha
- Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Laura Masini
- Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Ashfaq Ali
- Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Svante Resjö
- Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Erik Andreasson
- Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
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16
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Fukushima A, Hikosaka S, Kobayashi M, Nishizawa T, Saito K, Goto E, Kusano M. A Systems Analysis With "Simplified Source-Sink Model" Reveals Metabolic Reprogramming in a Pair of Source-to-Sink Organs During Early Fruit Development in Tomato by LED Light Treatments. FRONTIERS IN PLANT SCIENCE 2018; 9:1439. [PMID: 30364178 PMCID: PMC6191670 DOI: 10.3389/fpls.2018.01439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 09/10/2018] [Indexed: 05/29/2023]
Abstract
Tomato (Solanum lycopersicum) is a model crop for studying development regulation and ripening in flesh fruits and vegetables. Supplementary light to maintain the optimal light environment can lead to the stable growth of tomatoes in greenhouses and areas without sufficient daily light integral. Technological advances in genome-wide molecular phenotyping have dramatically enhanced our understanding of metabolic shifts in the plant metabolism across tomato fruit development. However, comprehensive metabolic and transcriptional behaviors along the developmental process under supplementary light provided by light-emitting diodes (LEDs) remain to be fully elucidated. We present integrative omic approaches to identify the impact on the metabolism of a single tomato plant leaf exposed to monochromatic red LEDs of different intensities during the fruit development stage. Our special light delivery system, the "simplified source-sink model," involves the exposure of a single leaf below the second truss to red LED light of different intensities. We evaluated fruit-size- and fruit-shape variations elicited by different light intensities. Our findings suggest that more than high-light treatment (500 μmol m-2 s-1) with the red LED light is required to accelerate fruit growth for 2 weeks after anthesis. To investigate transcriptomic and metabolomic changes in leaf- and fruit samples we used microarray-, RNA sequencing-, and gas chromatography-mass spectrometry techniques. We found that metabolic shifts in the carbohydrate metabolism and in several key pathways contributed to fruit development, including ripening and cell-wall modification. Our findings suggest that the proposed workflow aids in the identification of key metabolites in the central metabolism that respond to monochromatic red-LED treatment and contribute to increase the fruit size of tomato plants. This study expands our understanding of systems-level responses mediated by low-, appropriate-, and high levels of red light irradiation in the fruit growth of tomato plants.
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Affiliation(s)
| | - Shoko Hikosaka
- Graduate School of Horticulture, Chiba University, Chiba, Japan
| | | | | | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Eiji Goto
- Graduate School of Horticulture, Chiba University, Chiba, Japan
| | - Miyako Kusano
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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17
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Mastronardi E, Monreal C, DeRosa MC. Personalized Medicine for Crops? Opportunities for the Application of Molecular Recognition in Agriculture. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:6457-6461. [PMID: 28985063 DOI: 10.1021/acs.jafc.7b03295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
This perspective examines the detection of rhizosphere biomarkers, namely, root exudates and microbial metabolites, using molecular recognition elements, such as molecularly imprinted polymers, antibodies, and aptamers. Tracking these compounds in the rhizosphere could provide valuable insight into the status of the crop and soil in a highly localized way. The outlook and potential impact of the combination of molecular recognition and other innovations, such as nanotechnology and precision agriculture, and the comparison to advances in personalized medicine are considered.
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Affiliation(s)
- Emily Mastronardi
- Department of Chemistry , Carleton University , 1125 Colonel By Drive , Ottawa , Ontario K1S 5B6 , Canada
| | - Carlos Monreal
- Agriculture and Agrifood Canada , 960 Carling Avenue , Neatby Building, Ottawa , Ontario K1Y 4X2 , Canada
| | - Maria C DeRosa
- Department of Chemistry , Carleton University , 1125 Colonel By Drive , Ottawa , Ontario K1S 5B6 , Canada
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18
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Billet K, Houillé B, Dugé de Bernonville T, Besseau S, Oudin A, Courdavault V, Delanoue G, Guérin L, Clastre M, Giglioli-Guivarc'h N, Lanoue A. Field-Based Metabolomics of Vitis vinifera L. Stems Provides New Insights for Genotype Discrimination and Polyphenol Metabolism Structuring. FRONTIERS IN PLANT SCIENCE 2018; 9:798. [PMID: 29977248 PMCID: PMC6021511 DOI: 10.3389/fpls.2018.00798] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/24/2018] [Indexed: 05/21/2023]
Abstract
Grape accumulates numerous polyphenols with abundant health benefit and organoleptic properties that in planta act as key components of the plant defense system against diseases. Considerable advances have been made in the chemical characterization of wine metabolites particularly volatile and polyphenolic compounds. However, the metabotyping (metabolite-phenotype characterization) of grape varieties, from polyphenolic-rich vineyard by-product is unprecedented. As this composition might result from the complex interaction between genotype, environment and viticultural practices, a field experiment was setting up with uniform pedo-climatic factors and viticultural practices of growing vines to favor the genetic determinism of polyphenol expression. As a result, UPLC-MS-based targeted metabolomic analyses of grape stems from 8 Vitis vinifera L. cultivars allowed the determination of 42 polyphenols related to phenolic acids, flavonoids, procyanidins, and stilbenoids as resveratrol oligomers (degree of oligomerization 1-4). Using a partial least-square discriminant analysis approach, grape stem chemical profiles were discriminated according to their genotypic origin showing that polyphenol profile express a varietal signature. Furthermore, hierarchical clustering highlights various degree of polyphenol similarity between grape varieties that were in agreement with the genetic distance using clustering analyses of 22 microsatellite DNA markers. Metabolite correlation network suggested that several polyphenol subclasses were differently controlled. The present polyphenol metabotyping approach coupled to multivariate statistical analyses might assist grape selection programs to improve metabolites with both health-benefit potential and plant defense traits.
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Affiliation(s)
- Kévin Billet
- EA 2106 Biomolécules et Biotechnologie Végétales, Université de Tours, Faculté des Sciences Pharmaceutiques, Tours, France
| | - Benjamin Houillé
- EA 2106 Biomolécules et Biotechnologie Végétales, Université de Tours, Faculté des Sciences Pharmaceutiques, Tours, France
| | - Thomas Dugé de Bernonville
- EA 2106 Biomolécules et Biotechnologie Végétales, Université de Tours, Faculté des Sciences Pharmaceutiques, Tours, France
| | - Sébastien Besseau
- EA 2106 Biomolécules et Biotechnologie Végétales, Université de Tours, Faculté des Sciences Pharmaceutiques, Tours, France
| | - Audrey Oudin
- EA 2106 Biomolécules et Biotechnologie Végétales, Université de Tours, Faculté des Sciences Pharmaceutiques, Tours, France
| | - Vincent Courdavault
- EA 2106 Biomolécules et Biotechnologie Végétales, Université de Tours, Faculté des Sciences Pharmaceutiques, Tours, France
| | | | | | - Marc Clastre
- EA 2106 Biomolécules et Biotechnologie Végétales, Université de Tours, Faculté des Sciences Pharmaceutiques, Tours, France
| | - Nathalie Giglioli-Guivarc'h
- EA 2106 Biomolécules et Biotechnologie Végétales, Université de Tours, Faculté des Sciences Pharmaceutiques, Tours, France
| | - Arnaud Lanoue
- EA 2106 Biomolécules et Biotechnologie Végétales, Université de Tours, Faculté des Sciences Pharmaceutiques, Tours, France
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Ichihashi Y, Kusano M, Kobayashi M, Suetsugu K, Yoshida S, Wakatake T, Kumaishi K, Shibata A, Saito K, Shirasu K. Transcriptomic and Metabolomic Reprogramming from Roots to Haustoria in the Parasitic Plant, Thesium chinense. PLANT & CELL PHYSIOLOGY 2018; 59:724-733. [PMID: 29281058 PMCID: PMC6018956 DOI: 10.1093/pcp/pcx200] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 12/07/2017] [Indexed: 05/22/2023]
Abstract
Most plants show remarkable developmental plasticity in the generation of diverse types of new organs upon external stimuli, allowing them to adapt to their environment. Haustorial formation in parasitic plants is an example of such developmental reprogramming, but its molecular mechanism is largely unknown. In this study, we performed field-omics using transcriptomics and metabolomics to profile the molecular switch occurring in haustorial formation of the root parasitic plant, Thesium chinense, collected from its natural habitat. RNA-sequencing with de novo assembly revealed that the transcripts of very long chain fatty acid (VLCFA) biosynthesis genes, auxin biosynthesis/signaling-related genes and lateral root developmental genes are highly abundant in the haustoria. Gene co-expression network analysis identified a network module linking VLCFAs and the auxin-responsive lateral root development pathway. GC-TOF-MS analysis consistently revealed a unique metabolome profile with many types of fatty acids in the T. chinense root system, including the accumulation of a 25-carbon long chain saturated fatty acid in the haustoria. Our field-omics data provide evidence supporting the hypothesis that the molecular developmental machinery used for lateral root formation in non-parasitic plants has been co-opted into the developmental reprogramming of haustorial formation in the linage of parasitic plants.
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Affiliation(s)
- Yasunori Ichihashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045 Japan
- JST, PRESTO, Kawaguchi, Saitama, 332-0012 Japan
- Corresponding authors: Y. Ichihashi, E-mail, ; K. Shirasu, E-mail,
| | - Miyako Kusano
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045 Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572 Japan
| | - Makoto Kobayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045 Japan
| | - Kenji Suetsugu
- Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501 Japan
| | - Satoko Yoshida
- Institute for Research Initiatives, Division for Research Strategy, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192 Japan
| | - Takanori Wakatake
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045 Japan
| | - Kie Kumaishi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045 Japan
| | - Arisa Shibata
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045 Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045 Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675 Japan
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045 Japan
- Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033 Japan
- Corresponding authors: Y. Ichihashi, E-mail, ; K. Shirasu, E-mail,
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Szuba A, Lorenc-Plucińska G. Field proteomics of Populus alba grown in a heavily modified environment - An example of a tannery waste landfill. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 610-611:1557-1571. [PMID: 28712470 DOI: 10.1016/j.scitotenv.2017.06.102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 06/13/2017] [Accepted: 06/13/2017] [Indexed: 05/19/2023]
Abstract
Tannery waste is highly toxic and dangerous to living organisms because of the high heavy metal content, especially chromium [Cr(III)]. This study analysed the proteomic response of the Populus alba L. clone 'Villafranca' grown for 4years on a tannery waste landfill. In this extremely hostile environment, the plants struggled with continuous stress, which inhibited growth by 54%, with a 67% decrease in tree height and diameter at breast height compared to those of the forest reference plot, respectively. The leaves and roots of the tannery landfill-grown plants produced strong proteomic stress signals for protection against reactive oxygen species (ROS) and repair to ROS-damaged proteins and DNA as well as signals for protection of the photosynthetic apparatus. The content of HSP80 was also high. However, primary metabolic pathways were generally unaffected, and signals of increased protein protection, but not turnover, were found, indicating mechanisms of adaptation to long-term stress conditions present at the landfill. A proteomic tool, two-dimensional electrophoresis coupled with tandem mass spectrometry, was successfully applied in this environmental in situ study of distant plots (280km apart).
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Affiliation(s)
- Agnieszka Szuba
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035, Kórnik, Poland.
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21
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Zargar SM, Mahajan R, Nazir M, Nagar P, Kim ST, Rai V, Masi A, Ahmad SM, Shah RA, Ganai NA, Agrawal GK, Rakwal R. Common bean proteomics: Present status and future strategies. J Proteomics 2017; 169:239-248. [DOI: 10.1016/j.jprot.2017.03.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/17/2017] [Accepted: 03/20/2017] [Indexed: 11/30/2022]
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22
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Bellucci A, Tondelli A, Fangel JU, Torp AM, Xu X, Willats WGT, Flavell A, Cattivelli L, Rasmussen SK. Genome-wide association mapping in winter barley for grain yield and culm cell wall polymer content using the high-throughput CoMPP technique. PLoS One 2017; 12:e0173313. [PMID: 28301509 PMCID: PMC5354286 DOI: 10.1371/journal.pone.0173313] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 02/17/2017] [Indexed: 12/21/2022] Open
Abstract
A collection of 112 winter barley varieties (Hordeum vulgare L.) was grown in the field for two years (2008/09 and 2009/10) in northern Italy and grain and straw yields recorded. In the first year of the trial, a severe attack of barley yellow mosaic virus (BaYMV) strongly influenced final performances with an average reduction of ~ 50% for grain and straw harvested in comparison to the second year. The genetic determination (GD) for grain yield was 0.49 and 0.70, for the two years respectively, and for straw yield GD was low in 2009 (0.09) and higher in 2010 (0.29). Cell wall polymers in culms were quantified by means of the monoclonal antibodies LM6, LM11, JIM13 and BS-400-3 and the carbohydrate-binding module CBM3a using the high-throughput CoMPP technique. Of these, LM6, which detects arabinan components, showed a relatively high GD in both years and a significantly negative correlation with grain yield (GYLD). Overall, heritability (H2) was calculated for GYLD, LM6 and JIM and resulted to be 0.42, 0.32 and 0.20, respectively. A total of 4,976 SNPs from the 9K iSelect array were used in the study for the analysis of population structure, linkage disequilibrium (LD) and genome-wide association study (GWAS). Marker-trait associations (MTA) were analyzed for grain yield and cell wall determination by LM6 and JIM13 as these were the traits showing significant correlations between the years. A single QTL for GYLD containing three MTAs was found on chromosome 3H located close to the Hv-eIF4E gene, which is known to regulate resistance to BaYMV. Subsequently the QTL was shown to be tightly linked to rym4, a locus for resistance to the virus. GWAs on arabinans quantified by LM6 resulted in the identification of major QTLs closely located on 3H and hypotheses regarding putative candidate genes were formulated through the study of gene expression levels based on bioinformatics tools.
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Affiliation(s)
- Andrea Bellucci
- Department of Plant and Environmental Sciences, Faculty of Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Alessandro Tondelli
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura e l’Analisi dell’Economia Agraria, Centro di Ricerca per la Genomica Vegetale, Fiorenzuola d’Arda, Italy
| | - Jonatan U. Fangel
- Department of Plant and Environmental Sciences, Faculty of Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Anna Maria Torp
- Department of Plant and Environmental Sciences, Faculty of Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Xin Xu
- School of Life Science, University of Dundee, Dundee, United Kingdom
| | - William G. T. Willats
- Department of Plant and Environmental Sciences, Faculty of Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Andrew Flavell
- School of Life Science, University of Dundee, Dundee, United Kingdom
| | - Luigi Cattivelli
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura e l’Analisi dell’Economia Agraria, Centro di Ricerca per la Genomica Vegetale, Fiorenzuola d’Arda, Italy
| | - Søren K. Rasmussen
- Department of Plant and Environmental Sciences, Faculty of Sciences, University of Copenhagen, Frederiksberg, Denmark
- * E-mail:
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23
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Blanco-Ulate B, Hopfer H, Figueroa-Balderas R, Ye Z, Rivero RM, Albacete A, Pérez-Alfocea F, Koyama R, Anderson MM, Smith RJ, Ebeler SE, Cantu D. Red blotch disease alters grape berry development and metabolism by interfering with the transcriptional and hormonal regulation of ripening. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1225-1238. [PMID: 28338755 PMCID: PMC5444480 DOI: 10.1093/jxb/erw506] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Grapevine red blotch-associated virus (GRBaV) is a major threat to the wine industry in the USA. GRBaV infections (aka red blotch disease) compromise crop yield and berry chemical composition, affecting the flavor and aroma properties of must and wine. In this study, we combined genome-wide transcriptional profiling with targeted metabolite analyses and biochemical assays to characterize the impact of the disease on red-skinned berry ripening and metabolism. Using naturally infected berries collected from two vineyards, we were able to identify consistent berry responses to GRBaV across different environmental and cultural conditions. Specific alterations of both primary and secondary metabolism occurred in GRBaV-infected berries during ripening. Notably, GRBaV infections of post-véraison berries resulted in the induction of primary metabolic pathways normally associated with early berry development (e.g. thylakoid electron transfer and the Calvin cycle), while inhibiting ripening-associated pathways, such as a reduced metabolic flux in the central and peripheral phenylpropanoid pathways. We show that this metabolic reprogramming correlates with perturbations at multiple regulatory levels of berry development. Red blotch caused the abnormal expression of transcription factors (e.g. NACs, MYBs, and AP2-ERFs) and elements of the post-transcriptional machinery that function during red-skinned berry ripening. Abscisic acid, ethylene, and auxin pathways, which control both the initiation of ripening and stress responses, were also compromised. We conclude that GRBaV infections disrupt normal berry development and stress responses by altering transcription factors and hormone networks, which result in the inhibition of ripening pathways involved in the generation of color, flavor, and aroma compounds.
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Affiliation(s)
- Barbara Blanco-Ulate
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
- Department of Plant Sciences, University of California Davis, Davis, CA 95616, USA
| | - Helene Hopfer
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
- Department of Food Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Zirou Ye
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Rosa M Rivero
- CEBAS-CSIC, Campus de Espinardo, 30100, Murcia, Spain
| | | | | | - Renata Koyama
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
- Department of Agronomy, Londrina State University, Celso Garcia Cid Road, Londrina, PR, 86057-970, Brazil
| | - Michael M Anderson
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Rhonda J Smith
- University of California Cooperative Extension, Sonoma County, Santa Rosa, CA 95403, USA
| | - Susan E Ebeler
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
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Abstract
The apoplast can be described as the soluble fraction of the extracellular space of plant tissue, and it plays an important role in signaling, nutrient transport, and plant-pathogen interactions. In this protocol, we describe a method where leaves are infiltrated with phosphate buffer under vacuum. The apoplast can then be extracted by centrifugation and simultaneously collected in a protease inhibitor solution. Using this protocol, typically 3 μg of apoplastic proteins can be obtained in a volume of 300 μL from five potato leaflets, with minimal contamination by non-apoplastic proteins.
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Affiliation(s)
- Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Sundsvägen 14, SE-230 53, Alnarp, Sweden
| | - Kibrom B Abreha
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Sundsvägen 14, SE-230 53, Alnarp, Sweden
| | - Svante Resjö
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Sundsvägen 14, SE-230 53, Alnarp, Sweden.
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du Plessis K, Young PR, Eyéghé-Bickong HA, Vivier MA. The Transcriptional Responses and Metabolic Consequences of Acclimation to Elevated Light Exposure in Grapevine Berries. FRONTIERS IN PLANT SCIENCE 2017; 8:1261. [PMID: 28775728 PMCID: PMC5518647 DOI: 10.3389/fpls.2017.01261] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/04/2017] [Indexed: 05/19/2023]
Abstract
An increasing number of field studies that focus on grapevine berry development and ripening implement systems biology approaches; the results are highlighting not only the intricacies of the developmental programming/reprogramming that occurs, but also the complexity of how profoundly the microclimate influences the metabolism of the berry throughout the different stages of development. In a previous study we confirmed that a leaf removal treatment to Sauvignon Blanc grapes, grown in a highly characterized vineyard, primarily affected the level of light exposure to the berries throughout their development. A full transcriptomic analysis of berries from this model vineyard details the underlying molecular responses of the berries in reaction to the exposure and show how the berries acclimated to the imposing light stress. Gene expression involved in the protection of the photosynthetic machinery through rapid protein-turnover and the expression of photoprotective flavonoid compounds were most significantly affected in green berries. Overall, the transcriptome analysis showed that the berries implemented multiple stress-mitigation strategies in parallel and metabolite analysis was used to support the main findings. Combining the transcriptome data and amino acid profiling provided evidence that amino acid catabolism probably contributed to the mitigation of a likely energetic deficit created by the upregulation of (energetically) costly stress defense mechanisms. Furthermore, the rapid turnover of essential proteins involved in the maintenance of primary metabolism and growth in the photosynthetically active grapes appeared to provide precursors for the production of protective secondary metabolites such as apocarotenoids and flavonols in the ripening stages of the berries. Taken together, these results confirmed that the green grape berries responded to light stress much like other vegetative organs and were able to acclimate to the increased exposure, managing their metabolism and energy requirements to sustain the developmental cycle toward ripening. The typical metabolic consequences of leaf removal on grape berries can therefore now be linked to increased light exposure through mechanisms of photoprotection in green berries that leads toward acclimation responses that remain intact until ripening.
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Affiliation(s)
- Kari du Plessis
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch UniversityStellenbosch, South Africa
| | - Philip R. Young
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch UniversityStellenbosch, South Africa
| | - Hans A. Eyéghé-Bickong
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch UniversityStellenbosch, South Africa
- Institute for Grape and Wine Sciences, Department of Viticulture and Oenology, Stellenbosch UniversityStellenbosch, South Africa
| | - Melané A. Vivier
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch UniversityStellenbosch, South Africa
- *Correspondence: Melané A. Vivier
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26
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Alexandersson E, Mulugeta T, Lankinen Å, Liljeroth E, Andreasson E. Plant Resistance Inducers against Pathogens in Solanaceae Species-From Molecular Mechanisms to Field Application. Int J Mol Sci 2016; 17:E1673. [PMID: 27706100 PMCID: PMC5085706 DOI: 10.3390/ijms17101673] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 09/16/2016] [Accepted: 09/21/2016] [Indexed: 12/17/2022] Open
Abstract
This review provides a current summary of plant resistance inducers (PRIs) that have been successfully used in the Solanaceae plant family to protect against pathogens by activating the plant's own defence. Solanaceous species include many important crops such as potato and tomato. We also present findings regarding the molecular processes after application of PRIs, even if the number of such studies still remains limited in this plant family. In general, there is a lack of patterns regarding the efficiency of induced resistance (IR) both between and within solanaceous species. In many cases, a hypersensitivity-like reaction needs to form in order for the PRI to be efficient. "-Omics" studies have already given insight in the complexity of responses, and can explain some of the differences seen in efficacy of PRIs between and within species as well as towards different pathogens. Finally, examples of field applications of PRIs for solanaceous crops are presented and discussed. We predict that PRIs will play a role in future plant protection strategies in Solanaceae crops if they are combined with other means of disease control in different spatial and temporal combinations.
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Affiliation(s)
- Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, P.O. Box 102, 23053 Alnarp, Sweden.
| | - Tewodros Mulugeta
- Department of Zoological Science, Addis Ababa University, 1176 Addis Ababa, Ethiopia.
| | - Åsa Lankinen
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, P.O. Box 102, 23053 Alnarp, Sweden.
| | - Erland Liljeroth
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, P.O. Box 102, 23053 Alnarp, Sweden.
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, P.O. Box 102, 23053 Alnarp, Sweden.
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Joubert C, Young PR, Eyéghé-Bickong HA, Vivier MA. Field-Grown Grapevine Berries Use Carotenoids and the Associated Xanthophyll Cycles to Acclimate to UV Exposure Differentially in High and Low Light (Shade) Conditions. FRONTIERS IN PLANT SCIENCE 2016; 7:786. [PMID: 27375645 PMCID: PMC4901986 DOI: 10.3389/fpls.2016.00786] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/22/2016] [Indexed: 05/21/2023]
Abstract
Light quantity and quality modulate grapevine development and influence berry metabolic processes. Here we studied light as an information signal for developing and ripening grape berries. A Vitis vinifera Sauvignon Blanc field experiment was used to identify the impacts of UVB on core metabolic processes in the berries under both high light (HL) and low light (LL) microclimates. The primary objective was therefore to identify UVB-specific responses on berry processes and metabolites and distinguish them from those responses elicited by variations in light incidence. Canopy manipulation at the bunch zone via early leaf removal, combined with UVB-excluding acrylic sheets installed over the bunch zones resulted in four bunch microclimates: (1) HL (control); (2) LL (control); (3) HL with UVB attenuation and (4) LL with UVB attenuation. Metabolite profiles of three berry developmental stages showed predictable changes to known UV-responsive compound classes in a typical UV acclimation (versus UV damage) response. Interestingly, the berries employed carotenoids and the associated xanthophyll cycles to acclimate to UV exposure and the berry responses differed between HL and LL conditions, particularly in the developmental stages where berries are still photosynthetically active. The developmental stage of the berries was an important factor to consider in interpreting the data. The green berries responded to the different exposure and/or UVB attenuation signals with metabolites that indicate that the berries actively managed its metabolism in relation to the exposure levels, displaying metabolic plasticity in the photosynthesis-related metabolites. Core processes such as photosynthesis, photo-inhibition and acclimation were maintained by differentially modulating metabolites under the four treatments. Ripe berries also responded metabolically to the light quality and quantity, but mostly formed compounds (volatiles and polyphenols) that have direct antioxidant and/or "sunscreening" abilities. The data presented for the green berries and those for the ripe berries conform to what is known for UVB and/or light stress in young, active leaves and older, senescing tissues respectively and provide scope for further evaluation of the sink/source status of fruits in relation to photosignalling and/or stress management.
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Affiliation(s)
- Chandré Joubert
- Department of Viticulture and Oenology, Stellenbosch UniversityStellenbosch, South Africa
| | - Philip R. Young
- Department of Viticulture and Oenology, Stellenbosch UniversityStellenbosch, South Africa
- Institute for Wine Biotechnology, Stellenbosch UniversityStellenbosch, South Africa
| | - Hans A. Eyéghé-Bickong
- Department of Viticulture and Oenology, Stellenbosch UniversityStellenbosch, South Africa
- Institute for Wine Biotechnology, Stellenbosch UniversityStellenbosch, South Africa
| | - Melané A. Vivier
- Department of Viticulture and Oenology, Stellenbosch UniversityStellenbosch, South Africa
- Institute for Wine Biotechnology, Stellenbosch UniversityStellenbosch, South Africa
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28
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Young PR, Eyeghe-Bickong HA, du Plessis K, Alexandersson E, Jacobson DA, Coetzee Z, Deloire A, Vivier MA. Grapevine Plasticity in Response to an Altered Microclimate: Sauvignon Blanc Modulates Specific Metabolites in Response to Increased Berry Exposure. PLANT PHYSIOLOGY 2016; 170:1235-54. [PMID: 26628747 PMCID: PMC4775134 DOI: 10.1104/pp.15.01775] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 12/01/2015] [Indexed: 05/19/2023]
Abstract
In this study, the metabolic and physiological impacts of an altered microclimate on quality-associated primary and secondary metabolites in grape (Vitis vinifera) 'Sauvignon Blanc' berries was determined in a high-altitude vineyard. The leaf and lateral shoot removal in the bunch zones altered the microclimate by increasing the exposure of the berries. The physical parameters (berry diameter and weight), primary metabolites (sugars and organic acids), as well as bunch temperature and leaf water potential were predominantly not affected by the treatment. The increased exposure led to higher levels of specific carotenoids and volatile terpenoids in the exposed berries, with earlier berry stages reacting distinctly from the later developmental stages. Plastic/nonplastic metabolite responses could be further classified to identify metabolites that were developmentally controlled and/or responded to the treatment in a predictable fashion (assessed over two consecutive vintages). The study demonstrates that grapevine berries exhibit a degree of plasticity within their secondary metabolites and respond physiologically to the increased exposure by increasing metabolites with potential antioxidant activity. Taken together, the data provide evidence that the underlying physiological responses relate to the maintenance of stress pathways by modulating antioxidant molecules in the berries.
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Affiliation(s)
- Philip R Young
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Hans A Eyeghe-Bickong
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Kari du Plessis
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Erik Alexandersson
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Dan A Jacobson
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Zelmari Coetzee
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Alain Deloire
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Melané A Vivier
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
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29
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Musingarabwi DM, Nieuwoudt HH, Young PR, Eyéghè-Bickong HA, Vivier MA. A rapid qualitative and quantitative evaluation of grape berries at various stages of development using Fourier-transform infrared spectroscopy and multivariate data analysis. Food Chem 2016. [DOI: 10.1016/j.foodchem.2015.05.080] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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30
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Obata T, Witt S, Lisec J, Palacios-Rojas N, Florez-Sarasa I, Yousfi S, Araus JL, Cairns JE, Fernie AR. Metabolite Profiles of Maize Leaves in Drought, Heat, and Combined Stress Field Trials Reveal the Relationship between Metabolism and Grain Yield. PLANT PHYSIOLOGY 2015; 169:2665-83. [PMID: 26424159 PMCID: PMC4677906 DOI: 10.1104/pp.15.01164] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 09/30/2015] [Indexed: 05/19/2023]
Abstract
The development of abiotic stress-resistant cultivars is of premium importance for the agriculture of developing countries. Further progress in maize (Zea mays) performance under stresses is expected by combining marker-assisted breeding with metabolite markers. In order to dissect metabolic responses and to identify promising metabolite marker candidates, metabolite profiles of maize leaves were analyzed and compared with grain yield in field trials. Plants were grown under well-watered conditions (control) or exposed to drought, heat, and both stresses simultaneously. Trials were conducted in 2010 and 2011 using 10 tropical hybrids selected to exhibit diverse abiotic stress tolerance. Drought stress evoked the accumulation of many amino acids, including isoleucine, valine, threonine, and 4-aminobutanoate, which has been commonly reported in both field and greenhouse experiments in many plant species. Two photorespiratory amino acids, glycine and serine, and myoinositol also accumulated under drought. The combination of drought and heat evoked relatively few specific responses, and most of the metabolic changes were predictable from the sum of the responses to individual stresses. Statistical analysis revealed significant correlation between levels of glycine and myoinositol and grain yield under drought. Levels of myoinositol in control conditions were also related to grain yield under drought. Furthermore, multiple linear regression models very well explained the variation of grain yield via the combination of several metabolites. These results indicate the importance of photorespiration and raffinose family oligosaccharide metabolism in grain yield under drought and suggest single or multiple metabolites as potential metabolic markers for the breeding of abiotic stress-tolerant maize.
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Affiliation(s)
- Toshihiro Obata
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (T.O., S.W., J.L., I.F.-S., A.R.F.);International Maize and Wheat Improvement Center, Kilometer 45 Carretera Mexico-Veracruz, Texcoco, Mexico 56130 (N.P.-R.);Department de Biologia Vegetal, Universitat de Barcelona, 08028 Barcelona, Spain (S.Y., J.L.A.); andInternational Maize and Wheat Improvement Center, Southern Africa Regional Office, Harare, Zimbabwe (J.E.C.)
| | - Sandra Witt
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (T.O., S.W., J.L., I.F.-S., A.R.F.);International Maize and Wheat Improvement Center, Kilometer 45 Carretera Mexico-Veracruz, Texcoco, Mexico 56130 (N.P.-R.);Department de Biologia Vegetal, Universitat de Barcelona, 08028 Barcelona, Spain (S.Y., J.L.A.); andInternational Maize and Wheat Improvement Center, Southern Africa Regional Office, Harare, Zimbabwe (J.E.C.)
| | - Jan Lisec
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (T.O., S.W., J.L., I.F.-S., A.R.F.);International Maize and Wheat Improvement Center, Kilometer 45 Carretera Mexico-Veracruz, Texcoco, Mexico 56130 (N.P.-R.);Department de Biologia Vegetal, Universitat de Barcelona, 08028 Barcelona, Spain (S.Y., J.L.A.); andInternational Maize and Wheat Improvement Center, Southern Africa Regional Office, Harare, Zimbabwe (J.E.C.)
| | - Natalia Palacios-Rojas
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (T.O., S.W., J.L., I.F.-S., A.R.F.);International Maize and Wheat Improvement Center, Kilometer 45 Carretera Mexico-Veracruz, Texcoco, Mexico 56130 (N.P.-R.);Department de Biologia Vegetal, Universitat de Barcelona, 08028 Barcelona, Spain (S.Y., J.L.A.); andInternational Maize and Wheat Improvement Center, Southern Africa Regional Office, Harare, Zimbabwe (J.E.C.)
| | - Igor Florez-Sarasa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (T.O., S.W., J.L., I.F.-S., A.R.F.);International Maize and Wheat Improvement Center, Kilometer 45 Carretera Mexico-Veracruz, Texcoco, Mexico 56130 (N.P.-R.);Department de Biologia Vegetal, Universitat de Barcelona, 08028 Barcelona, Spain (S.Y., J.L.A.); andInternational Maize and Wheat Improvement Center, Southern Africa Regional Office, Harare, Zimbabwe (J.E.C.)
| | - Salima Yousfi
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (T.O., S.W., J.L., I.F.-S., A.R.F.);International Maize and Wheat Improvement Center, Kilometer 45 Carretera Mexico-Veracruz, Texcoco, Mexico 56130 (N.P.-R.);Department de Biologia Vegetal, Universitat de Barcelona, 08028 Barcelona, Spain (S.Y., J.L.A.); andInternational Maize and Wheat Improvement Center, Southern Africa Regional Office, Harare, Zimbabwe (J.E.C.)
| | - Jose Luis Araus
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (T.O., S.W., J.L., I.F.-S., A.R.F.);International Maize and Wheat Improvement Center, Kilometer 45 Carretera Mexico-Veracruz, Texcoco, Mexico 56130 (N.P.-R.);Department de Biologia Vegetal, Universitat de Barcelona, 08028 Barcelona, Spain (S.Y., J.L.A.); andInternational Maize and Wheat Improvement Center, Southern Africa Regional Office, Harare, Zimbabwe (J.E.C.)
| | - Jill E Cairns
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (T.O., S.W., J.L., I.F.-S., A.R.F.);International Maize and Wheat Improvement Center, Kilometer 45 Carretera Mexico-Veracruz, Texcoco, Mexico 56130 (N.P.-R.);Department de Biologia Vegetal, Universitat de Barcelona, 08028 Barcelona, Spain (S.Y., J.L.A.); andInternational Maize and Wheat Improvement Center, Southern Africa Regional Office, Harare, Zimbabwe (J.E.C.)
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany (T.O., S.W., J.L., I.F.-S., A.R.F.);International Maize and Wheat Improvement Center, Kilometer 45 Carretera Mexico-Veracruz, Texcoco, Mexico 56130 (N.P.-R.);Department de Biologia Vegetal, Universitat de Barcelona, 08028 Barcelona, Spain (S.Y., J.L.A.); andInternational Maize and Wheat Improvement Center, Southern Africa Regional Office, Harare, Zimbabwe (J.E.C.)
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31
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Bellucci A, Torp AM, Bruun S, Magid J, Andersen SB, Rasmussen SK. Association Mapping in Scandinavian Winter Wheat for Yield, Plant Height, and Traits Important for Second-Generation Bioethanol Production. FRONTIERS IN PLANT SCIENCE 2015; 6:1046. [PMID: 26635859 PMCID: PMC4660856 DOI: 10.3389/fpls.2015.01046] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/09/2015] [Indexed: 05/04/2023]
Abstract
A collection of 100 wheat varieties representing more than 100 years of wheat-breeding history in Scandinavia was established in order to identify marker-trait associations for plant height (PH), grain yield (GY), and biomass potential for bioethanol production. The field-grown material showed variations in PH from 54 to 122 cm and in GY from 2 to 6.61 t ha(-1). The release of monomeric sugars was determined by high-throughput enzymatic treatment of ligno-cellulosic material and varied between 0.169 and 0.312 g/g dm for glucose (GLU) and 0.146 and 0.283 g/g dm for xylose (XYL). As expected, PH and GY showed to be highly influenced by genetic factors with repeatability (R) equal to 0.75 and 0.53, respectively, while this was reduced for GLU and XYL (R = 0.09 for both). The study of trait correlations showed how old, low-yielding, tall varieties released higher amounts of monomeric sugars after straw enzymatic hydrolysis, showing reduced recalcitrance to bioconversion compared to modern varieties. Ninety-three lines from the collection were genotyped with the DArTseq(®) genotypic platform and 5525 markers were used for genome-wide association mapping. Six quantitative trait loci (QTLs) for GY, PH, and GLU released from straw were mapped. One QTL for PH was previously reported, while the remaining QTLs constituted new genomic regions linked to trait variation. This paper is one of the first studies in wheat to identify QTLs that are important for bioethanol production based on a genome-wide association approach.
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Affiliation(s)
| | | | | | | | | | - Søren K. Rasmussen
- Plant and Soil Section, Department of Plant and Environmental Sciences, Faculty of Science, University of CopenhagenFrederiksberg, Denmark
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32
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Abstract
Systems biology represents an integrative research strategy that studies the interactions between DNA, mRNA, protein, and metabolite level in an organism, thereby including the interactions with the physical environment and other organisms. The application of metabonomics, or the quantitative study of metabolites in biological systems, in systems biology is currently an emerging area of research, which can contribute to the discovery of (disease) signatures, drug targeting and design, and the further elucidation of basic and more complex biochemical principles. This chapter covers the contribution of metabonomics in advancing our understanding in systems biology.
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Affiliation(s)
- Vicky De Preter
- Translational Research Center for Gastrointestinal Disorders (TARGID), KULeuven, Herestraat 49, 3000, Leuven, Belgium,
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33
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Singh J, Pandey P, James D, Chandrasekhar K, Achary VMM, Kaul T, Tripathy BC, Reddy MK. Enhancing C3 photosynthesis: an outlook on feasible interventions for crop improvement. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:1217-30. [PMID: 25196090 DOI: 10.1111/pbi.12246] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 07/14/2014] [Accepted: 07/20/2014] [Indexed: 05/05/2023]
Abstract
Despite the declarations and collective measures taken to eradicate hunger at World Food Summits, food security remains one of the biggest issues that we are faced with. The current scenario could worsen due to the alarming increase in world population, further compounded by adverse climatic conditions, such as increase in atmospheric temperature, unforeseen droughts and decreasing soil moisture, which will decrease crop yield even further. Furthermore, the projected increase in yields of C3 crops as a result of increasing atmospheric CO2 concentrations is much less than anticipated. Thus, there is an urgent need to increase crop productivity beyond existing yield potentials to address the challenge of food security. One of the domains of plant biology that promises hope in overcoming this problem is study of C3 photosynthesis. In this review, we have examined the potential bottlenecks of C3 photosynthesis and the strategies undertaken to overcome them. The targets considered for possible intervention include RuBisCO, RuBisCO activase, Calvin-Benson-Bassham cycle enzymes, CO2 and carbohydrate transport, and light reactions among many others. In addition, other areas which promise scope for improvement of C3 photosynthesis, such as mining natural genetic variations, mathematical modelling for identifying new targets, installing efficient carbon fixation and carbon concentrating mechanisms have been touched upon. Briefly, this review intends to shed light on the recent advances in enhancing C3 photosynthesis for crop improvement.
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Affiliation(s)
- Jitender Singh
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India; School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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