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Jin EJ, Yoon JH, Lee H, Bae EJ, Yong SH, Choi MS. Evaluation of drought stress level in Sargent's cherry ( Prunus sargentii Rehder) using photosynthesis and chlorophyll fluorescence parameters and proline content analysis. PeerJ 2023; 11:e15954. [PMID: 37842053 PMCID: PMC10576498 DOI: 10.7717/peerj.15954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 08/02/2023] [Indexed: 10/17/2023] Open
Abstract
Sargent's cherry trees (Prunus sargentiiRehder) are widely planted as an ornamental, climate change-sensing species. This study investigated changes in the soil moisture content, fresh weight, photosynthesis and chlorophyll fluorescence properties, and the chlorophyll and proline content of four-year-old P. sargentii seedlings after 30 days of drought stress. In the trees subjected to drought stress treatment, soil moisture content decreased, and the fresh weight of the aboveground part of the plant decreased. However, there was no significant difference in the root growth of the dried plants. Among the photosynthesis parameters, Pn MAX, E and gs showed a significant (p < 0.001) decrease after 15 days in dry-stressed seedlings, but there was no difference between treatments in WUE until 20 days, and there was a significant (p < 0.001) difference after 24 days. Chlorophyll fluorescence parameters, Fv/Fm, ΦPSII, Rfd, NPQ, and Pn MAX, also increased after 10 days in dry-stressed seedlings, but these changes did not reach statistical significance compared to the control treatment. These results may suggest that drought stress highly correlates with photosynthesis and chlorophyll fluorescence parameters. Chlorophyll content also significantly decreased in the seedlings under drought stress compared with the control treatment. The proline content decreased until the 10th day of drought stress treatment and increased after the 15th day, showing an increase of 10.9% on the 15th day and 57.1% on the 30th day, compared to the control treatment. These results suggest that photosynthesis, chlorophyll fluorescence parameters, and proline content can be used to evaluate drought stress in trees. The results of this study can contribute to the management of forests, such as the irrigation of trees when pore control ability and photosynthesis ability decrease.
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Affiliation(s)
- Eon Ju Jin
- Forest Biomaterials Research Center, National institute of Forest Science, Jinju, South Korea
| | - Jun-Hyuk Yoon
- Forest Biomaterials Research Center, National institute of Forest Science, Jinju, South Korea
| | - Hyeok Lee
- Forest Biomaterials Research Center, National institute of Forest Science, Jinju, South Korea
| | - Eun Ji Bae
- Forest Biomaterials Research Center, National institute of Forest Science, Jinju, South Korea
| | - Seong Hyeon Yong
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, South Korea
| | - Myung Suk Choi
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, South Korea
- Division of Environmental Forest Science, Gyeongsang National University, Jinju, South Korea
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Konrad KR, Gao S, Zurbriggen MD, Nagel G. Optogenetic Methods in Plant Biology. ANNUAL REVIEW OF PLANT BIOLOGY 2023; 74:313-339. [PMID: 37216203 DOI: 10.1146/annurev-arplant-071122-094840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Optogenetics is a technique employing natural or genetically engineered photoreceptors in transgene organisms to manipulate biological activities with light. Light can be turned on or off, and adjusting its intensity and duration allows optogenetic fine-tuning of cellular processes in a noninvasive and spatiotemporally resolved manner. Since the introduction of Channelrhodopsin-2 and phytochrome-based switches nearly 20 years ago, optogenetic tools have been applied in a variety of model organisms with enormous success, but rarely in plants. For a long time, the dependence of plant growth on light and the absence of retinal, the rhodopsin chromophore, prevented the establishment of plant optogenetics until recent progress overcame these difficulties. We summarize the recent results of work in the field to control plant growth and cellular motion via green light-gated ion channels and present successful applications to light-control gene expression with single or combined photoswitches in plants. Furthermore, we highlight the technical requirements and options for future plant optogenetic research.
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Affiliation(s)
- Kai R Konrad
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, University of Würzburg, Würzburg, Germany;
| | - Shiqiang Gao
- Department of Neurophysiology, Institute of Physiology, Biocenter, University of Würzburg, Würzburg, Germany; ,
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Düsseldorf, Germany;
| | - Georg Nagel
- Department of Neurophysiology, Institute of Physiology, Biocenter, University of Würzburg, Würzburg, Germany; ,
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Lazarević B, Carović-Stanko K, Živčak M, Vodnik D, Javornik T, Safner T. Classification of high-throughput phenotyping data for differentiation among nutrient deficiency in common bean. FRONTIERS IN PLANT SCIENCE 2022; 13:931877. [PMID: 35937354 PMCID: PMC9353735 DOI: 10.3389/fpls.2022.931877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
The development of automated, image-based, high-throughput plant phenotyping enabled the simultaneous measurement of many plant traits. Big and complex phenotypic datasets require advanced statistical methods which enable the extraction of the most valuable traits when combined with other measurements, interpretation, and understanding of their (eco)physiological background. Nutrient deficiency in plants causes specific symptoms that can be easily detected by multispectral imaging, 3D scanning, and chlorophyll fluorescence measurements. Screening of numerous image-based phenotypic traits of common bean plants grown in nutrient-deficient solutions was conducted to optimize phenotyping and select the most valuable phenotypic traits related to the specific nutrient deficit. Discriminant analysis was used to compare the efficiency of groups of traits obtained by high-throughput phenotyping techniques (chlorophyll fluorescence, multispectral traits, and morphological traits) in discrimination between nutrients [nitrogen (N), phosphorus (P), potassium (K), magnesium (Mg), and iron (Fe)] at early and prolonged deficiency. Furthermore, a recursive partitioning analysis was used to select variables within each group of traits that show the highest accuracy for assigning plants to the respective nutrient deficit treatment. Using the entire set of measured traits, the highest classification success by discriminant function was achieved using multispectral traits. In the subsequent measurements, chlorophyll fluorescence and multispectral traits achieved comparably high classification success. Recursive partitioning analysis was able to intrinsically identify variables within each group of traits and their threshold values that best separate the observations from different nutrient deficiency groups. Again, the highest success in assigning plants into their respective groups was achieved based on selected multispectral traits. Selected chlorophyll fluorescence traits also showed high accuracy for assigning plants into control, Fe, Mg, and P deficit but could not correctly assign K and N deficit plants. This study has shown the usefulness of combining high-throughput phenotyping techniques with advanced data analysis to determine and differentiate nutrient deficiency stress.
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Affiliation(s)
- Boris Lazarević
- Department of Plant Nutrition, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Zagreb, Croatia
| | - Klaudija Carović-Stanko
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Zagreb, Croatia
- Department of Seed Science and Technology, Faculty of Agriculture Zagreb, University of Zagreb, Zagreb, Croatia
| | - Marek Živčak
- Institute of Plant and Environmental Sciences, Slovak University of Agriculture, Nitra, Slovakia
| | - Dominik Vodnik
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Tomislav Javornik
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Zagreb, Croatia
- Department of Seed Science and Technology, Faculty of Agriculture Zagreb, University of Zagreb, Zagreb, Croatia
| | - Toni Safner
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Zagreb, Croatia
- Department of Plant Breeding, Genetics and Biometrics, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
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Faragó D, Zsigmond L, Benyó D, Alcazar R, Rigó G, Ayaydin F, Rabilu SA, Hunyadi‐Gulyás É, Szabados L. Small paraquat resistance proteins modulate paraquat and ABA responses and confer drought tolerance to overexpressing Arabidopsis plants. PLANT, CELL & ENVIRONMENT 2022; 45:1985-2003. [PMID: 35486392 PMCID: PMC9324991 DOI: 10.1111/pce.14338] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 03/31/2022] [Accepted: 04/03/2022] [Indexed: 05/13/2023]
Abstract
Adaptation of higher plants to extreme environmental conditions is under complex regulation. Several small peptides have recently been described to modulate responses to stress conditions. The Small Paraquat resistance protein (SPQ) of Lepidium crassifolium has previously been identified due to its capacity to confer paraquat resistance to overexpressing transgenic Arabidopsis plants. Here, we show that overexpression of the closely related Arabidopsis SPQ can also enhance resistance to paraquat, while the Arabidopsis spq1 mutant is slightly hypersensitive to this herbicide. Besides being implicated in paraquat response, overexpression of SPQs enhanced sensitivity to abscisic acid (ABA), and the knockout spq1 mutant was less sensitive to ABA. Both Lepidium- and Arabidopsis-derived SPQs could improve drought tolerance by reducing water loss, stabilizing photosynthetic electron transport and enhancing plant viability and survival in a water-limited environment. Enhanced drought tolerance of SPQ-overexpressing plants could be confirmed by characterizing various parameters of growth, morphology and photosynthesis using an automatic plant phenotyping platform with RGB and chlorophyll fluorescence imaging. Our results suggest that SPQs can be regulatory small proteins connecting ROS and ABA regulation and through that influence responses to certain stresses.
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Affiliation(s)
- Dóra Faragó
- Institute of Plant Biology, Biological Research CentreSzegedHungary
| | - Laura Zsigmond
- Institute of Plant Biology, Biological Research CentreSzegedHungary
| | - Dániel Benyó
- Institute of Plant Biology, Biological Research CentreSzegedHungary
| | - Rubén Alcazar
- Facultat de FarmàciaUniversitat de BarcelonaBarcelonaSpain
| | - Gábor Rigó
- Institute of Plant Biology, Biological Research CentreSzegedHungary
| | - Ferhan Ayaydin
- Hungarian Centre of Excellence for Molecular Medicine (HCEMM) Nonprofit Ltd.SzegedHungary
- Cellular Imaging Laboratory, Biological Research CentreSzegedHungary
| | - Sahilu Ahmad Rabilu
- Institute of Plant Biology, Biological Research CentreSzegedHungary
- Doctoral School in Biology, Faculty of Science and InformaticsUniversity of SzegedSzegedHungary
| | | | - László Szabados
- Institute of Plant Biology, Biological Research CentreSzegedHungary
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Kim HJ, Kato N, Ndathe R, Thyssen GN, Jones DC, Ratnayaka HH. Evidence for thermosensitivity of the cotton (Gossypium hirsutum L.) immature fiber (im) mutant via hypersensitive stomatal activity. PLoS One 2021; 16:e0259562. [PMID: 34898615 PMCID: PMC8668099 DOI: 10.1371/journal.pone.0259562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 10/22/2021] [Indexed: 11/18/2022] Open
Abstract
Thickness of cotton fiber, referred to as fiber maturity, is a key determinant of fiber quality, lint yield, and textile performance. The cotton immature fiber (im) mutant has been used to study fiber maturity since its fiber is thinner than the wild type near isogeneic line (NIL), Texas Marker-1 (TM-1). The im phenotype is caused by a single recessive mutation of a pentatricopeptide repeat (PPR) gene that reduces the activity of mitochondrial complex I and up-regulates stress responsive genes. However, the mechanisms altering the stress responses in im mutant are not well understood. Thus, we characterized growth and gas exchange in im and TM-1 under no stress and also investigated their stress responses by comparing gas exchange and transcriptomic profiles under high temperature. Phenotypic differences were detected between the NILs in non-fiber tissues although less pronounced than the variation in fibers. At near optimum temperature (28±3°C), im maintained the same photosynthetic performance as TM-1 by means of greater stomatal conductance. In contrast, under high temperature stress (>34°C), im leaves reduced photosynthesis by decreasing the stomatal conductance disproportionately more than TM-1. Transcriptomic analyses showed that the genes involved in heat stress responses were differentially expressed between the NIL leaves. These results indicate that the im mutant previously reported to have low activity of mitochondrial complex I displays increased thermosensitivity by impacting stomatal conductance. They also support a notion that mitochondrial complex I activity is required for maintenance of optimal photosynthetic performance and acclimation of plants to high temperature stress. These findings may be useful in the future efforts to understand how physiological mechanisms play a role in determining cotton fiber maturity and may influence stress responses in other crops.
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Affiliation(s)
- Hee Jin Kim
- USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA, United States of America
- * E-mail: (HJK); (HHR)
| | - Naohiro Kato
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States of America
| | - Ruth Ndathe
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States of America
| | - Gregory N. Thyssen
- USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA, United States of America
| | - Don C. Jones
- Cotton Incorporated, Cary, NC, United States of America
| | - Harish H. Ratnayaka
- Department of Biology, Xavier University of Louisiana, New Orleans, LA, United States of America
- * E-mail: (HJK); (HHR)
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Detection of Above-Ground Physiological Indices of an Apple Rootstock Superior Line 12-2 with Improved Apple Replant Disease (ARD) Resistance. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7100337] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
(1) Background: The cultivation of resistant rootstocks is an effective way to prevent ARD. (2) Methods: 12-2 (self-named), T337, and M26 were planted in replanted and sterilized soil. The aboveground physiological indices were determined. (3) Results: The plant heights and the stem thicknesses of T337 and M26 were significantly affected by ARD. Relative chlorophyll content (June–October), Pn (August–September), and Gs (August) of T337 and relative chlorophyll content (June–July, September), Pn (September–October), and Ci (September) of M26 were significantly affected by ARD. ARD had a significant effect on Fv/Fm (June), qP (June–July), and NPQ of T337 (June–October, except August) and Fv/Fm (June) and NPQ (June-October, except July) of M26. Additionally, ARD affected Rfd of M26 and T337 during August. SOD (August and October), POD (August–September), and CAT (July-August, October) activities and MDA (September–October) content of T338 as well as SOD (July–October), POD (June–October), and CAT (July-October) activities and MDA (July, September–October) content of M26 were significantly affected by ARD. ARD significantly reduced nitrogen (October), phosphorus (September–October), and zinc (July) contents of M26 and potassium (June) content of T337. The above physiological indices were not affected by ARD in 12-2. (4) Conclusions: 12-2 could be useful as an important rootstock to relieve ARD due to strong resistance.
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Saucedo-García M, González-Córdova CD, Ponce-Pineda IG, Cano-Ramírez D, Romero-Colín FM, Arroyo-Pérez EE, King-Díaz B, Zavafer A, Gavilanes-Ruíz M. Effects of MPK3 and MPK6 kinases on the chloroplast architecture and function induced by cold acclimation in Arabidopsis. PHOTOSYNTHESIS RESEARCH 2021; 149:201-212. [PMID: 34132948 DOI: 10.1007/s11120-021-00852-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Exposure to low, non-freezing temperatures develops freezing tolerance in many plant species. Such process is called cold acclimation. Molecular changes undergone during cold acclimation are orchestrated by signalling networks including MAP kinases. Structure and function of chloroplasts are affected by low temperatures. The aim of this work was to study how the MAP kinases MPK3 and MPK6 are involved in the chloroplast performance upon a long period of cold acclimation. We used Arabidopsis thaliana wild type and mpk3 and mpk6 mutants. Adult plants were acclimated during 7 days at 4 °C and then measurements of PSII performance and chloroplast ultrastructure were carried out. Only the mpk6 acclimated plants showed a high freezing sensitivity. No differences in the PSII function were observed in the plants from the three genotypes exposed to non-acclimated or acclimated conditions. The acclimation of wild-type plants produced severe alterations in the ultrastructure of chloroplast and thylakoids, which was more accentuated in the mpk plants. However, only the mpk6 mutant was unable to internalize the damaged chloroplasts into the vacuole. These results indicate that cold acclimation induces alterations in the chloroplast architecture leading to preserve an optimal performance of PSII. MPK3 and MPK6 are necessary to regulate these morphological changes, but besides, MPK6 is needed to the vacuolization of the damaged chloroplasts, suggesting a role in the chloroplast recycling during cold acclimation. The latter could be quite relevant, since it could explain why this mutant is the only one showing an extremely low freezing tolerance.
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Affiliation(s)
- Mariana Saucedo-García
- Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Hidalgo, México
| | - Carla D González-Córdova
- Dpto. de Bioquímica, Conjunto E. Facultad de Química, Universidad Nacional Autónoma de México, UNAM, Ciudad Universitaria Universitaria, Coyoacán, 04510, México City, México
| | - I Giordano Ponce-Pineda
- Dpto. de Bioquímica, Conjunto E. Facultad de Química, Universidad Nacional Autónoma de México, UNAM, Ciudad Universitaria Universitaria, Coyoacán, 04510, México City, México
| | - Dora Cano-Ramírez
- Dpto. de Bioquímica, Conjunto E. Facultad de Química, Universidad Nacional Autónoma de México, UNAM, Ciudad Universitaria Universitaria, Coyoacán, 04510, México City, México
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB3 0LJ, UK
| | - Fernanda M Romero-Colín
- Dpto. de Bioquímica, Conjunto E. Facultad de Química, Universidad Nacional Autónoma de México, UNAM, Ciudad Universitaria Universitaria, Coyoacán, 04510, México City, México
| | - Erik E Arroyo-Pérez
- Dpto. de Bioquímica, Conjunto E. Facultad de Química, Universidad Nacional Autónoma de México, UNAM, Ciudad Universitaria Universitaria, Coyoacán, 04510, México City, México
| | - Beatriz King-Díaz
- Dpto. de Bioquímica, Conjunto E. Facultad de Química, Universidad Nacional Autónoma de México, UNAM, Ciudad Universitaria Universitaria, Coyoacán, 04510, México City, México
| | - Alonso Zavafer
- Research School of Biology, the Australian National University, Canberra, ACT, 2600, Australia
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2001, Australia
| | - Marina Gavilanes-Ruíz
- Dpto. de Bioquímica, Conjunto E. Facultad de Química, Universidad Nacional Autónoma de México, UNAM, Ciudad Universitaria Universitaria, Coyoacán, 04510, México City, México.
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Sachdev S, Ansari SA, Ansari MI, Fujita M, Hasanuzzaman M. Abiotic Stress and Reactive Oxygen Species: Generation, Signaling, and Defense Mechanisms. Antioxidants (Basel) 2021; 10:277. [PMID: 33670123 PMCID: PMC7916865 DOI: 10.3390/antiox10020277] [Citation(s) in RCA: 270] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/19/2022] Open
Abstract
Climate change is an invisible, silent killer with calamitous effects on living organisms. As the sessile organism, plants experience a diverse array of abiotic stresses during ontogenesis. The relentless climatic changes amplify the intensity and duration of stresses, making plants dwindle to survive. Plants convert 1-2% of consumed oxygen into reactive oxygen species (ROS), in particular, singlet oxygen (1O2), superoxide radical (O2•-), hydrogen peroxide (H2O2), hydroxyl radical (•OH), etc. as a byproduct of aerobic metabolism in different cell organelles such as chloroplast, mitochondria, etc. The regulatory network comprising enzymatic and non-enzymatic antioxidant systems tends to keep the magnitude of ROS within plant cells to a non-damaging level. However, under stress conditions, the production rate of ROS increases exponentially, exceeding the potential of antioxidant scavengers instigating oxidative burst, which affects biomolecules and disturbs cellular redox homeostasis. ROS are similar to a double-edged sword; and, when present below the threshold level, mediate redox signaling pathways that actuate plant growth, development, and acclimatization against stresses. The production of ROS in plant cells displays both detrimental and beneficial effects. However, exact pathways of ROS mediated stress alleviation are yet to be fully elucidated. Therefore, the review deposits information about the status of known sites of production, signaling mechanisms/pathways, effects, and management of ROS within plant cells under stress. In addition, the role played by advancement in modern techniques such as molecular priming, systems biology, phenomics, and crop modeling in preventing oxidative stress, as well as diverting ROS into signaling pathways has been canvassed.
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Affiliation(s)
- Swati Sachdev
- Department of Environmental Science, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Rae Bareli Road, Lucknow 226 025, India;
| | | | | | - Masayuki Fujita
- Laboratory of Plant Stress Responses, Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
| | - Mirza Hasanuzzaman
- Department of Agronomy, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka 1207, Bangladesh
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Szopiński M, Sitko K, Rusinowski S, Zieleźnik-Rusinowska P, Corso M, Rostański A, Rojek-Jelonek M, Verbruggen N, Małkowski E. Different strategies of Cd tolerance and accumulation in Arabidopsis halleri and Arabidopsis arenosa. PLANT, CELL & ENVIRONMENT 2020; 43:3002-3019. [PMID: 32890409 DOI: 10.1111/pce.13883] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/18/2020] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
Pseudometallophytes are commonly used to study the evolution of metal tolerance and accumulation traits in plants. Within the Arabidopsis genus, the adaptation of Arabidopsis halleri to metalliferous soils has been widely studied, which is not the case for the closely related species Arabidopsis arenosa. We performed an in-depth physiological comparison between the A. halleri and A. arenosa populations from the same polluted site, together with the geographically close non-metallicolous (NM) populations of both species. The ionomes, growth, photosynthetic parameters and pigment content were characterized in the plants that were growing on their native site and in a hydroponic culture under Cd treatments. In situ, the metallicolous (M) populations of both species hyperaccumulated Cd and Zn. The NM population of A. halleri hyperaccumulated Cd and Zn while the NM A. arenosa did not. In the hydroponic experiments, the NM populations of both species accumulated more Cd in their shoots than the M populations. Our research suggests that the two Arabidopsis species evolved different strategies of adaptation to extreme metallic environments that involve fine regulation of metal homeostasis, adjustment of the photosynthetic apparatus and accumulation of flavonols and anthocyanins.
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Affiliation(s)
- Michał Szopiński
- Plant Ecophysiology Team, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Krzysztof Sitko
- Plant Ecophysiology Team, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | | | - Paulina Zieleźnik-Rusinowska
- Plant Ecophysiology Team, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Massimiliano Corso
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, Brussels, Belgium
| | - Adam Rostański
- Botany and Nature Protection Team, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Magdalena Rojek-Jelonek
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Nathalie Verbruggen
- Laboratory of Plant Physiology and Molecular Genetics, Université Libre de Bruxelles, Brussels, Belgium
| | - Eugeniusz Małkowski
- Plant Ecophysiology Team, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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Schmidt J, Garcia M, Brien C, Kalambettu P, Garnett T, Fleury D, Tricker PJ. Transcripts of wheat at a target locus on chromosome 6B associated with increased yield, leaf mass and chlorophyll index under combined drought and heat stress. PLoS One 2020; 15:e0241966. [PMID: 33166353 PMCID: PMC7652265 DOI: 10.1371/journal.pone.0241966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/25/2020] [Indexed: 11/18/2022] Open
Abstract
Drought and heat stress constrain wheat (Triticum aestivum L.) yields globally. To identify putative mechanisms and candidate genes associated with combined drought and heat stress tolerance, we developed bread wheat near-isogenic lines (NILs) targeting a quantitative trait locus (QTL) on chromosome 6B which was previously associated with combined drought and heat stress tolerance in a diverse panel of wheats. Genotyping-by-sequencing was used to identify additional regions that segregated in allelic pairs between the recurrent and the introduced exotic parent, genome-wide. NILs were phenotyped in a gravimetric platform with precision irrigation and exposed to either drought or to combined drought and heat stress from three days after anthesis. An increase in grain weight in NILs carrying the exotic allele at 6B locus was associated with thicker, greener leaves, higher photosynthetic capacity and increased water use index after re-watering. RNA sequencing of developing grains at early and later stages of treatment revealed 75 genes that were differentially expressed between NILs across both treatments and timepoints. Differentially expressed genes coincided with the targeted QTL on chromosome 6B and regions of genetic segregation on chromosomes 1B and 7A. Pathway enrichment analysis showed the involvement of these genes in cell and gene regulation, metabolism of amino acids and transport of carbohydrates. The majority of these genes have not been characterized previously under drought or heat stress and they might serve as candidate genes for improved abiotic stress tolerance.
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Affiliation(s)
- Jessica Schmidt
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, South Australia, Australia
| | - Melissa Garcia
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, South Australia, Australia
| | - Chris Brien
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, South Australia, Australia
- The Plant Accelerator, Australian Plant Phenomics Facility, The University of Adelaide, Adelaide, South Australia, Australia
| | - Priyanka Kalambettu
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, South Australia, Australia
| | - Trevor Garnett
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, South Australia, Australia
- The Plant Accelerator, Australian Plant Phenomics Facility, The University of Adelaide, Adelaide, South Australia, Australia
| | - Delphine Fleury
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, South Australia, Australia
| | - Penny J. Tricker
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, South Australia, Australia
- * E-mail:
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Prinzenberg AE, Campos‐Dominguez L, Kruijer W, Harbinson J, Aarts MGM. Natural variation of photosynthetic efficiency in Arabidopsis thaliana accessions under low temperature conditions. PLANT, CELL & ENVIRONMENT 2020; 43:2000-2013. [PMID: 32495939 PMCID: PMC7497054 DOI: 10.1111/pce.13811] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 03/29/2020] [Accepted: 05/18/2020] [Indexed: 05/18/2023]
Abstract
Low, but non-freezing, temperatures have negative effects on plant growth and development. Despite some molecular signalling pathways being known, the mechanisms causing different responses among genotypes are still poorly understood. Photosynthesis is one of the processes that are affected by low temperatures. Using an automated phenotyping platform for chlorophyll fluorescence imaging the steady state quantum yield of photosystem II (PSII) electron transport (ΦPSII ) was measured and used to quantify the effect of moderately low temperature on a population of Arabidopsis thaliana natural accessions. Observations were made over the course of several weeks in standard and low temperature conditions and a strong decrease in ΦPSII upon the cold treatment was found. A genome wide association study identified several quantitative trait loci (QTLs) that are associated with changes in ΦPSII in low temperature. One candidate for a cold specific QTL was validated with a mutant analysis to be one of the genes that is likely involved in the PSII response to the cold treatment. The gene encodes the PSII associated protein PSB27 which has already been implicated in the adaptation to fluctuating light.
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Affiliation(s)
- Aina E. Prinzenberg
- Horticulture and Product PhysiologyWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBThe Netherlands
- Laboratory of GeneticsWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBThe Netherlands
- Plant BreedingWageningen University and ResearchPO Box 386Wageningen6700 AJThe Netherlands
| | - Lucia Campos‐Dominguez
- Laboratory of GeneticsWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBThe Netherlands
- Royal Botanic Garden Edinburgh20A Inverleith RowEdinburghEH3 5LRUnited Kingdom
| | - Willem Kruijer
- BiometrisWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBThe Netherlands
| | - Jeremy Harbinson
- Horticulture and Product PhysiologyWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBThe Netherlands
- Laboratory of BiophysicsWageningen University and ResearchWageningenThe Netherlands
| | - Mark G. M. Aarts
- Laboratory of GeneticsWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBThe Netherlands
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12
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Adhikari ND, Simko I, Mou B. Phenomic and Physiological Analysis of Salinity Effects on Lettuce. SENSORS (BASEL, SWITZERLAND) 2019; 19:E4814. [PMID: 31694293 PMCID: PMC6864466 DOI: 10.3390/s19214814] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/23/2019] [Accepted: 11/01/2019] [Indexed: 01/08/2023]
Abstract
Salinity is a rising concern in many lettuce-growing regions. Lettuce (Lactuca sativa L.) is sensitive to salinity, which reduces plant biomass, and causes leaf burn and early senescence. We sought to identify physiological traits important in salt tolerance that allows lettuce adaptation to high salinity while maintaining its productivity. Based on previous salinity tolerance studies, one sensitive and one tolerant genotype each was selected from crisphead, butterhead, and romaine, as well as leaf types of cultivated lettuce and its wild relative, L. serriola L. Physiological parameters were measured four weeks after transplanting two-day old seedlings into 350 mL volume pots filled with sand, hydrated with Hoagland nutrient solution and grown in a growth chamber. Salinity treatment consisted of gradually increasing concentrations of NaCl and CaCl2 from 0 mM/0 mM at the time of transplanting, to 30 mM/15 mM at the beginning of week three, and maintaining it until harvest. Across the 10 genotypes, leaf area and fresh weight decreased 0-64% and 16-67%, respectively, under salinity compared to the control. Salinity stress increased the chlorophyll index by 4-26% in the cultivated genotypes, while decreasing it by 5-14% in the two wild accessions. Tolerant lines less affected by elevated salinity were characterized by high values of the chlorophyll fluorescence parameters Fv/Fm and instantaneous photosystem II quantum yield (QY), and lower leaf transpiration.
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Affiliation(s)
- Neil D. Adhikari
- Crop Improvement and Protection Research Unit, United States Department of Agriculture, Agricultural Research Service, Salinas, CA 93905, USA;
| | | | - Beiquan Mou
- Crop Improvement and Protection Research Unit, United States Department of Agriculture, Agricultural Research Service, Salinas, CA 93905, USA;
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13
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Rungrat T, Almonte AA, Cheng R, Gollan PJ, Stuart T, Aro E, Borevitz JO, Pogson B, Wilson PB. A Genome-Wide Association Study of Non-Photochemical Quenching in response to local seasonal climates in Arabidopsis thaliana. PLANT DIRECT 2019; 3:e00138. [PMID: 31276082 PMCID: PMC6603398 DOI: 10.1002/pld3.138] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 04/03/2019] [Accepted: 04/04/2019] [Indexed: 05/10/2023]
Abstract
Field-grown plants have variable exposure to sunlight as a result of shifting cloud-cover, seasonal changes, canopy shading, and other environmental factors. As a result, they need to have developed a method for dissipating excess energy obtained from periodic excessive sunlight exposure. Non-photochemical quenching (NPQ) dissipates excess energy as heat, however, the physical and molecular genetic mechanics of NPQ variation are not understood. In this study, we investigated the genetic loci involved in NPQ by first growing different Arabidopsis thaliana accessions in local and seasonal climate conditions, then measured their NPQ kinetics through development by chlorophyll fluorescence. We used genome-wide association studies (GWAS) to identify 15 significant quantitative trait loci (QTL) for a range of photosynthetic traits, including a QTL co-located with known NPQ gene PSBS (AT1G44575). We found there were large alternative regulatory segments between the PSBS promoter regions of the functional haplotypes and a significant difference in PsbS protein concentration. These findings parallel studies in rice showing recurrent regulatory evolution of this gene. The variation in the PSBS promoter and the changes underlying other QTLs could give insight to allow manipulations of NPQ in crops to improve their photosynthetic efficiency and yield.
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Affiliation(s)
- Tepsuda Rungrat
- Faculty of Agriculture, Natural resources and EnvironmentNaresuan UniversityPhitsanulokThailand
- ARC Centre of Excellence for Plant Energy BiologyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Andrew A. Almonte
- ARC Centre of Excellence for Plant Energy BiologyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Riyan Cheng
- Department of PsychiatryUniversity of California San DiegoLa JollaCalifornia
| | - Peter J. Gollan
- Faculty of Engineering and ScienceUniversity of TurkuTurkuFinland
| | - Tim Stuart
- ARC Centre of Excellence for Plant Energy BiologyUniversity of Western AustraliaPerthWestern AustraliaAustralia
| | - Eva‐Mari Aro
- Faculty of Engineering and ScienceUniversity of TurkuTurkuFinland
| | - Justin O. Borevitz
- ARC Centre of Excellence for Plant Energy BiologyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Barry Pogson
- ARC Centre of Excellence for Plant Energy BiologyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| | - Pip B. Wilson
- ARC Centre of Excellence for Plant Energy BiologyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
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14
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Bernotas G, Scorza LCT, Hansen MF, Hales IJ, Halliday KJ, Smith LN, Smith ML, McCormick AJ. A photometric stereo-based 3D imaging system using computer vision and deep learning for tracking plant growth. Gigascience 2019; 8:giz056. [PMID: 31127811 PMCID: PMC6534809 DOI: 10.1093/gigascience/giz056] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 03/25/2019] [Accepted: 04/21/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Tracking and predicting the growth performance of plants in different environments is critical for predicting the impact of global climate change. Automated approaches for image capture and analysis have allowed for substantial increases in the throughput of quantitative growth trait measurements compared with manual assessments. Recent work has focused on adopting computer vision and machine learning approaches to improve the accuracy of automated plant phenotyping. Here we present PS-Plant, a low-cost and portable 3D plant phenotyping platform based on an imaging technique novel to plant phenotyping called photometric stereo (PS). RESULTS We calibrated PS-Plant to track the model plant Arabidopsis thaliana throughout the day-night (diel) cycle and investigated growth architecture under a variety of conditions to illustrate the dramatic effect of the environment on plant phenotype. We developed bespoke computer vision algorithms and assessed available deep neural network architectures to automate the segmentation of rosettes and individual leaves, and extract basic and more advanced traits from PS-derived data, including the tracking of 3D plant growth and diel leaf hyponastic movement. Furthermore, we have produced the first PS training data set, which includes 221 manually annotated Arabidopsis rosettes that were used for training and data analysis (1,768 images in total). A full protocol is provided, including all software components and an additional test data set. CONCLUSIONS PS-Plant is a powerful new phenotyping tool for plant research that provides robust data at high temporal and spatial resolutions. The system is well-suited for small- and large-scale research and will help to accelerate bridging of the phenotype-to-genotype gap.
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Affiliation(s)
- Gytis Bernotas
- Centre for Machine Vision, Bristol Robotics Laboratory, University of the West of England, T block, Frenchay Campus, Coldharbour Lane, Bristol BS16 1QY, UK
| | - Livia C T Scorza
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, The King's Buildings, Edinburgh EH9 3BF, UK
| | - Mark F Hansen
- Centre for Machine Vision, Bristol Robotics Laboratory, University of the West of England, T block, Frenchay Campus, Coldharbour Lane, Bristol BS16 1QY, UK
| | - Ian J Hales
- Centre for Machine Vision, Bristol Robotics Laboratory, University of the West of England, T block, Frenchay Campus, Coldharbour Lane, Bristol BS16 1QY, UK
| | - Karen J Halliday
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, The King's Buildings, Edinburgh EH9 3BF, UK
| | - Lyndon N Smith
- Centre for Machine Vision, Bristol Robotics Laboratory, University of the West of England, T block, Frenchay Campus, Coldharbour Lane, Bristol BS16 1QY, UK
| | - Melvyn L Smith
- Centre for Machine Vision, Bristol Robotics Laboratory, University of the West of England, T block, Frenchay Campus, Coldharbour Lane, Bristol BS16 1QY, UK
| | - Alistair J McCormick
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, The King's Buildings, Edinburgh EH9 3BF, UK
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15
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Trinh MDL, Sato R, Masuda S. Genetic characterization of a flap1 null mutation in Arabidopsis npq4 and pgr5 plants suggests that the regulatory role of FLAP1 involves the control of proton homeostasis in chloroplasts. PHOTOSYNTHESIS RESEARCH 2019; 139:413-424. [PMID: 30390180 DOI: 10.1007/s11120-018-0575-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 08/24/2018] [Indexed: 05/21/2023]
Abstract
Precise control of the proton concentration gradient across thylakoid membranes (ΔpH) is essential for photosynthesis and its regulation because the gradient contributes to the generation of the proton motive force used for ATP synthesis and also for the fast and reversible induction of non-photochemical quenching (NPQ) to avoid photoinhibition and photodamage. However, the regulatory mechanism(s) controlling ΔpH in response to fluctuating light has not been fully elucidated. We previously described a new NPQ-regulatory chloroplastic protein, Fluctuating-Light-Acclimation Protein1 (FLAP1), which is important for plant growth and modulation of ΔpH under fluctuating light conditions. For this report, we further characterized FLAP1 activity by individually crossing an Arabidopsis flap1 mutant with npq4 and pgr5 plants; npq4 is defective in PsbS-dependent NPQ, and pgr5 is defective in induction of steady-state proton motive force (pmf) and energy-dependent quenching (qE). Both npq4 and npq4 flap1 exhibited similar NPQ kinetics and other photosynthetic parameters under constant or fluctuating actinic light. Conversely, pgr5 flap1 had recovered NPQ, photosystem II quantum yield and growth under fluctuating light, each of which was impaired in pgr5. Together with other data, we propose that FLAP1 activity controls proton homeostasis under steady-state photosynthesis to manipulate luminal acidification levels appropriately to balance photoprotection and photochemical processes.
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Affiliation(s)
- Mai Duy Luu Trinh
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Ryoichi Sato
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, 444-8585, Japan
| | - Shinji Masuda
- Center for Biological Resources & Informatics, Tokyo Institute of Technology, Yokohama, 226-8501, Japan.
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16
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van Bezouw RFHM, Keurentjes JJB, Harbinson J, Aarts MGM. Converging phenomics and genomics to study natural variation in plant photosynthetic efficiency. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:112-133. [PMID: 30548574 PMCID: PMC6850172 DOI: 10.1111/tpj.14190] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 11/27/2018] [Accepted: 11/28/2018] [Indexed: 05/18/2023]
Abstract
In recent years developments in plant phenomic approaches and facilities have gradually caught up with genomic approaches. An opportunity lies ahead to dissect complex, quantitative traits when both genotype and phenotype can be assessed at a high level of detail. This is especially true for the study of natural variation in photosynthetic efficiency, for which forward genetics studies have yielded only a little progress in our understanding of the genetic layout of the trait. High-throughput phenotyping, primarily from chlorophyll fluorescence imaging, should help to dissect the genetics of photosynthesis at the different levels of both plant physiology and development. Specific emphasis should be directed towards understanding the acclimation of the photosynthetic machinery in fluctuating environments, which may be crucial for the identification of genetic variation for relevant traits in food crops. Facilities should preferably be designed to accommodate phenotyping of photosynthesis-related traits in such environments. The use of forward genetics to study the genetic architecture of photosynthesis is likely to lead to the discovery of novel traits and/or genes that may be targeted in breeding or bio-engineering approaches to improve crop photosynthetic efficiency. In the near future, big data approaches will play a pivotal role in data processing and streamlining the phenotype-to-gene identification pipeline.
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Affiliation(s)
- Roel F. H. M. van Bezouw
- Laboratory of GeneticsWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenThe Netherlands
| | - Joost J. B. Keurentjes
- Laboratory of GeneticsWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenThe Netherlands
| | - Jeremy Harbinson
- Horticulture and Product PhysiologyWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenThe Netherlands
| | - Mark G. M. Aarts
- Laboratory of GeneticsWageningen University and ResearchDroevendaalsesteeg 16708PBWageningenThe Netherlands
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17
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Wilson PB, Streich JC, Murray KD, Eichten SR, Cheng R, Aitken NC, Spokas K, Warthmann N, Gordon SP, Vogel JP, Borevitz JO. Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate. Genetics 2019; 211:317-331. [PMID: 30446522 PMCID: PMC6325704 DOI: 10.1534/genetics.118.301589] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 11/08/2018] [Indexed: 01/29/2023] Open
Abstract
The development of model systems requires a detailed assessment of standing genetic variation across natural populations. The Brachypodium species complex has been promoted as a plant model for grass genomics with translation to small grain and biomass crops. To capture the genetic diversity within this species complex, thousands of Brachypodium accessions from around the globe were collected and genotyped by sequencing. Overall, 1897 samples were classified into two diploid or allopolyploid species, and then further grouped into distinct inbred genotypes. A core set of diverse B. distachyon diploid lines was selected for whole genome sequencing and high resolution phenotyping. Genome-wide association studies across simulated seasonal environments was used to identify candidate genes and pathways tied to key life history and agronomic traits under current and future climatic conditions. A total of 8, 22, and 47 QTL were identified for flowering time, early vigor, and energy traits, respectively. The results highlight the genomic structure of the Brachypodium species complex, and the diploid lines provided a resource that allows complex trait dissection within this grass model species.
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Affiliation(s)
- Pip B Wilson
- The ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
| | - Jared C Streich
- The ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
| | - Kevin D Murray
- The ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
| | - Steve R Eichten
- The ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
| | - Riyan Cheng
- The ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
- Department of Psychiatry, University of California San Diego, La Jolla, California 92093
| | - Nicola C Aitken
- The ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
- Ecogenomics and Bioinformatics Lab, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
| | - Kurt Spokas
- Soil and Water Management, Agricultural Research Service, United States Department of Agricutlture (USDA), St. Paul, Minnesota 55108
| | - Norman Warthmann
- The ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
| | - Sean P Gordon
- Department of Energy, Joint Genome Institute, Walnut Creek, California 94598
| | - John P Vogel
- Department of Energy, Joint Genome Institute, Walnut Creek, California 94598
| | - Justin O Borevitz
- The ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Canberra, Australian Capital Territory 200, Australia
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18
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Matsubara S. Growing plants in fluctuating environments: why bother? JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4651-4654. [PMID: 30307518 PMCID: PMC6137991 DOI: 10.1093/jxb/ery312] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Affiliation(s)
- Shizue Matsubara
- IBG-2: Plant Sciences, Forschungszentrum Jülich, D-52425 Jülich, Germany
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19
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Ganguly DR, Crisp PA, Eichten SR, Pogson BJ. Maintenance of pre-existing DNA methylation states through recurring excess-light stress. PLANT, CELL & ENVIRONMENT 2018; 41:1657-1672. [PMID: 29707792 DOI: 10.1111/pce.13324] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 04/16/2018] [Accepted: 04/17/2018] [Indexed: 05/23/2023]
Abstract
The capacity for plant stress priming and memory and the notion of this being underpinned by DNA methylation-mediated memory is an appealing hypothesis for which there is mixed evidence. We previously established a lack of drought-induced methylome variation in Arabidopsis thaliana (Arabidopsis); however, this was tied to only minor observations of physiological memory. There are numerous independent observations demonstrating that photoprotective mechanisms, induced by excess-light stress, can lead to robust programmable changes in newly developing leaf tissues. Although key signalling molecules and transcription factors are known to promote this priming signal, an untested question is the potential involvement of chromatin marks towards the maintenance of light stress acclimation, or memory. Thus, we systematically tested our previous hypothesis of a stress-resistant methylome using a recurring excess-light stress, then analysing new, emerging, and existing tissues. The DNA methylome showed negligible stress-associated variation, with the vast majority attributable to stochastic differences. Yet, photoacclimation was evident through enhanced photosystem II performance in exposed tissues, and nonphotochemical quenching and fluorescence decline ratio showed evidence of mitotic transmission. Thus, we have observed physiological acclimation in new and emerging tissues in the absence of substantive DNA methylome changes.
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Affiliation(s)
- Diep R Ganguly
- Australian Research Council Centre of Excellence in Plant Energy Biology, Division of Plant Sciences, Research School of Biology, Australian National University, Acton, ACT 2601, Australia
| | - Peter A Crisp
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Steven R Eichten
- Australian Research Council Centre of Excellence in Plant Energy Biology, Division of Plant Sciences, Research School of Biology, Australian National University, Acton, ACT 2601, Australia
| | - Barry J Pogson
- Australian Research Council Centre of Excellence in Plant Energy Biology, Division of Plant Sciences, Research School of Biology, Australian National University, Acton, ACT 2601, Australia
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20
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Faragó D, Sass L, Valkai I, Andrási N, Szabados L. PlantSize Offers an Affordable, Non-destructive Method to Measure Plant Size and Color in Vitro. FRONTIERS IN PLANT SCIENCE 2018; 9:219. [PMID: 29520290 PMCID: PMC5827667 DOI: 10.3389/fpls.2018.00219] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/05/2018] [Indexed: 05/18/2023]
Abstract
Plant size, shape and color are important parameters of plants, which have traditionally been measured by destructive and time-consuming methods. Non-destructive image analysis is an increasingly popular technology to characterize plant development in time. High throughput automatic phenotyping platforms can simultaneously analyze multiple morphological and physiological parameters of hundreds or thousands of plants. Such platforms are, however, expensive and are not affordable for many laboratories. Moreover, determination of basic parameters is sufficient for most studies. Here we describe a non-invasive method, which simultaneously measures basic morphological and physiological parameters of in vitro cultured plants. Changes of plant size, shape and color is monitored by repeated photography with a commercial digital camera using neutral white background. Images are analyzed with the MatLab-based computer application PlantSize, which simultaneously calculates several parameters including rosette size, convex area, convex ratio, chlorophyll and anthocyanin contents of all plants identified on the image. Numerical data are exported in MS Excel-compatible format. Subsequent data processing provides information on growth rates, chlorophyll and anthocyanin contents. Proof-of-concept validation of the imaging technology was demonstrated by revealing small but significant differences between wild type and transgenic Arabidopsis plants overexpressing the HSFA4A transcription factor or the hsfa4a knockout mutant, subjected to different stress conditions. While HSFA4A overexpression was associated with better growth, higher chlorophyll and lower anthocyanin content in saline conditions, the knockout hsfa4a mutant showed hypersensitivity to various stresses. Morphological differences were revealed by comparing rosette size, shape and color of wild type plants with phytochrome B (phyB-9) mutant. While the technology was developed with Arabidopsis plants, it is suitable to characterize plants of other species including crops, in a simple, affordable and fast way. PlantSize is publicly available (http://www.brc.hu/pub/psize/index.html).
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Affiliation(s)
| | | | | | | | - László Szabados
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
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21
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Großkinsky DK, Syaifullah SJ, Roitsch T. Integration of multi-omics techniques and physiological phenotyping within a holistic phenomics approach to study senescence in model and crop plants. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:825-844. [PMID: 29444308 DOI: 10.1093/jxb/erx333] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The study of senescence in plants is complicated by diverse levels of temporal and spatial dynamics as well as the impact of external biotic and abiotic factors and crop plant management. Whereas the molecular mechanisms involved in developmentally regulated leaf senescence are very well understood, in particular in the annual model plant species Arabidopsis, senescence of other organs such as the flower, fruit, and root is much less studied as well as senescence in perennials such as trees. This review addresses the need for the integration of multi-omics techniques and physiological phenotyping into holistic phenomics approaches to dissect the complex phenomenon of senescence. That became feasible through major advances in the establishment of various, complementary 'omics' technologies. Such an interdisciplinary approach will also need to consider knowledge from the animal field, in particular in relation to novel regulators such as small, non-coding RNAs, epigenetic control and telomere length. Such a characterization of phenotypes via the acquisition of high-dimensional datasets within a systems biology approach will allow us to systematically characterize the various programmes governing senescence beyond leaf senescence in Arabidopsis and to elucidate the underlying molecular processes. Such a multi-omics approach is expected to also spur the application of results from model plants to agriculture and their verification for sustainable and environmentally friendly improvement of crop plant stress resilience and productivity and contribute to improvements based on postharvest physiology for the food industry and the benefit of its customers.
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Affiliation(s)
- Dominik K Großkinsky
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Højbakkegård Allé, Taastrup, Denmark
| | - Syahnada Jaya Syaifullah
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Højbakkegård Allé, Taastrup, Denmark
| | - Thomas Roitsch
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Højbakkegård Allé, Taastrup, Denmark
- Department of Adaptive Biotechnologies, Global Change Research Institute, CAS, v.v.i., Drásov, Czech Republic
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22
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Kaiser E, Morales A, Harbinson J. Fluctuating Light Takes Crop Photosynthesis on a Rollercoaster Ride. PLANT PHYSIOLOGY 2018; 176:977-989. [PMID: 29046421 PMCID: PMC5813579 DOI: 10.1104/pp.17.01250] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/16/2017] [Indexed: 05/18/2023]
Abstract
Crops are regularly exposed to frequent irradiance fluctuations, which decrease their integrated CO2 assimilation and affect their phenotype.
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Affiliation(s)
- Elias Kaiser
- Horticulture and Product Physiology Group, Wageningen University, 6700 AA Wageningen, The Netherlands
| | - Alejandro Morales
- Centre for Crop Systems Analysis, Wageningen University, 6700 AK Wageningen, The Netherlands
| | - Jeremy Harbinson
- Horticulture and Product Physiology Group, Wageningen University, 6700 AA Wageningen, The Netherlands
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23
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Rühle T, Reiter B, Leister D. Chlorophyll Fluorescence Video Imaging: A Versatile Tool for Identifying Factors Related to Photosynthesis. FRONTIERS IN PLANT SCIENCE 2018; 9:55. [PMID: 29472935 PMCID: PMC5810273 DOI: 10.3389/fpls.2018.00055] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/10/2018] [Indexed: 05/12/2023]
Abstract
Measurements of chlorophyll fluorescence provide an elegant and non-invasive means of probing the dynamics of photosynthesis. Advances in video imaging of chlorophyll fluorescence have now made it possible to study photosynthesis at all levels from individual cells to entire crop populations. Since the technology delivers quantitative data, is easily scaled up and can be readily combined with other approaches, it has become a powerful phenotyping tool for the identification of factors relevant to photosynthesis. Here, we review genetic chlorophyll fluorescence-based screens of libraries of Arabidopsis and Chlamydomonas mutants, discuss its application to high-throughput phenotyping in quantitative genetics and highlight potential future developments.
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Affiliation(s)
- Thilo Rühle
- Plant Molecular Biology, Department of Biology, Ludwig Maximilian University of Munich, Munich, Germany
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Ganguly DR, Crisp PA, Eichten SR, Pogson BJ. The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress. PLANT PHYSIOLOGY 2017; 175:1893-1912. [PMID: 28986422 PMCID: PMC5717726 DOI: 10.1104/pp.17.00744] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 10/03/2017] [Indexed: 05/08/2023]
Abstract
Improving the responsiveness, acclimation, and memory of plants to abiotic stress holds substantive potential for improving agriculture. An unresolved question is the involvement of chromatin marks in the memory of agriculturally relevant stresses. Such potential has spurred numerous investigations yielding both promising and conflicting results. Consequently, it remains unclear to what extent robust stress-induced DNA methylation variation can underpin stress memory. Using a slow-onset water deprivation treatment in Arabidopsis (Arabidopsis thaliana), we investigated the malleability of the DNA methylome to drought stress within a generation and under repeated drought stress over five successive generations. While drought-associated epi-alleles in the methylome were detected within a generation, they did not correlate with drought-responsive gene expression. Six traits were analyzed for transgenerational stress memory, and the descendants of drought-stressed lineages showed one case of memory in the form of increased seed dormancy, and that persisted one generation removed from stress. With respect to transgenerational drought stress, there were negligible conserved differentially methylated regions in drought-exposed lineages compared with unstressed lineages. Instead, the majority of observed variation was tied to stochastic or preexisting differences in the epigenome occurring at repetitive regions of the Arabidopsis genome. Furthermore, the experience of repeated drought stress was not observed to influence transgenerational epi-allele accumulation. Our findings demonstrate that, while transgenerational memory is observed in one of six traits examined, they are not associated with causative changes in the DNA methylome, which appears relatively impervious to drought stress.
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Affiliation(s)
- Diep R Ganguly
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Peter A Crisp
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108
| | - Steven R Eichten
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton, Australian Capital Territory 2601, Australia
| | - Barry J Pogson
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University, Acton, Australian Capital Territory 2601, Australia
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High-Throughput Phenotyping in Plant Stress Response: Methods and Potential Applications to Polyamine Field. Methods Mol Biol 2017; 1694:373-388. [PMID: 29080181 DOI: 10.1007/978-1-4939-7398-9_31] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
High-throughput phenotyping has opened whole new perspectives for crop improvement and better understanding of quantitative traits in plants. Generation of loss-of-function and gain-of-function plant mutants requires processing and imaging a large number of plants in order to determine unknown gene functions and phenotypic changes generated by genetic modifications or selection of new traits. The use of phenomics for the evaluation of transgenic lines contributed significantly to the identification of plants more tolerant to biotic/abiotic stresses and furthermore, helped in the identification of unknown gene functions. In this chapter we describe the High-throughput phenotyping (HTP) platform working in our facility, drawing the general protocol and showing some examples of data obtainable from the platform. Tomato transgenic plants over-expressing the arginine decarboxylase 2 gene, which is involved in the polyamine biosynthetic pathway, were analyzed through our HTP facility for their tolerance to abiotic stress and significant differences in water content and ability to recover after drought stress where highlighted. This demonstrates the applicability of this methodology to the plant polyamine field.
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Tschiersch H, Junker A, Meyer RC, Altmann T. Establishment of integrated protocols for automated high throughput kinetic chlorophyll fluorescence analyses. PLANT METHODS 2017; 13:54. [PMID: 28690669 PMCID: PMC5496596 DOI: 10.1186/s13007-017-0204-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 06/30/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND Automated plant phenotyping has been established as a powerful new tool in studying plant growth, development and response to various types of biotic or abiotic stressors. Respective facilities mainly apply non-invasive imaging based methods, which enable the continuous quantification of the dynamics of plant growth and physiology during developmental progression. However, especially for plants of larger size, integrative, automated and high throughput measurements of complex physiological parameters such as photosystem II efficiency determined through kinetic chlorophyll fluorescence analysis remain a challenge. RESULTS We present the technical installations and the establishment of experimental procedures that allow the integrated high throughput imaging of all commonly determined PSII parameters for small and large plants using kinetic chlorophyll fluorescence imaging systems (FluorCam, PSI) integrated into automated phenotyping facilities (Scanalyzer, LemnaTec). Besides determination of the maximum PSII efficiency, we focused on implementation of high throughput amenable protocols recording PSII operating efficiency (ΦPSII). Using the presented setup, this parameter is shown to be reproducibly measured in differently sized plants despite the corresponding variation in distance between plants and light source that caused small differences in incident light intensity. Values of ΦPSII obtained with the automated chlorophyll fluorescence imaging setup correlated very well with conventionally determined data using a spot-measuring chlorophyll fluorometer. The established high throughput operating protocols enable the screening of up to 1080 small and 184 large plants per hour, respectively. The application of the implemented high throughput protocols is demonstrated in screening experiments performed with large Arabidopsis and maize populations assessing natural variation in PSII efficiency. CONCLUSIONS The incorporation of imaging systems suitable for kinetic chlorophyll fluorescence analysis leads to a substantial extension of the feature spectrum to be assessed in the presented high throughput automated plant phenotyping platforms, thus enabling the simultaneous assessment of plant architectural and biomass-related traits and their relations to physiological features such as PSII operating efficiency. The implemented high throughput protocols are applicable to a broad spectrum of model and crop plants of different sizes (up to 1.80 m height) and architectures. The deeper understanding of the relation of plant architecture, biomass formation and photosynthetic efficiency has a great potential with respect to crop and yield improvement strategies.
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Affiliation(s)
- Henning Tschiersch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, OT Gatersleben, Germany
| | - Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, OT Gatersleben, Germany
| | - Rhonda C. Meyer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, OT Gatersleben, Germany
| | - Thomas Altmann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, OT Gatersleben, Germany
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