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Kumar J, Sen Gupta D, Djalovic I, Kumar S, Siddique KHM. Root-omics for drought tolerance in cool-season grain legumes. PHYSIOLOGIA PLANTARUM 2021; 172:629-644. [PMID: 33314181 DOI: 10.1111/ppl.13313] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Root traits can be exploited to increase the physiological efficiency of crop water use under drought. Root length, root hairs, root branching, root diameter, and root proliferation rate are genetically defined traits that can help to improve the water productivity potential of crops. Recently, high-throughput phenotyping techniques/platforms have been used to screen the germplasm of major cool-season grain legumes for root traits and their impact on different physiological processes, including nutrient uptake and yield potential. Advances in omics approaches have led to the dissection of genomic, proteomic, and metabolomic structures of these traits. This knowledge facilitates breeders to improve the water productivity and nutrient uptake of cultivars under limited soil moisture conditions in major cool-season grain legumes that usually face terminal drought. This review discusses the advances in root traits and their potential for developing drought-tolerant cultivars in cool-season grain legumes.
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Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Ivica Djalovic
- Maize Department, Institute of Field and Vegetable Crops, Novi Sad, Serbia
| | - Shiv Kumar
- Biodiversity and Crop Improvement Program, International Centre for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture and School of Agriculture and Environment, The University of Western Australia, Perth, Western Australia, Australia
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Chai Y, Chen C, Luo X, Zhan S, Kim J, Luo J, Wang X, Hu Z, Ying Y, Liu X. Cohabiting Plant-Wearable Sensor In Situ Monitors Water Transport in Plant. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003642. [PMID: 34026443 PMCID: PMC8132156 DOI: 10.1002/advs.202003642] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 01/03/2021] [Indexed: 06/01/2023]
Abstract
The boom of plant phenotype highlights the need to measure the physiological characteristics of an individual plant. However, continuous real-time monitoring of a plant's internal physiological status remains challenging using traditional silicon-based sensor technology, due to the fundamental mismatch between rigid sensors and soft and curved plant surfaces. Here, the first flexible electronic sensing device is reported that can harmlessly cohabitate with the plant and continuously monitor its stem sap flow, a critical plant physiological characteristic for analyzing plant health, water consumption, and nutrient distribution. Due to a special design and the materials chosen, the realized plant-wearable sensor is thin, soft, lightweight, air/water/light-permeable, and shows excellent biocompatibility, therefore enabling the sap flow detection in a continuous and non-destructive manner. The sensor can serve as a noninvasive, high-throughput, low-cost toolbox, and holds excellent potentials in phenotyping. Furthermore, the real-time investigation on stem flow insides watermelon reveals a previously unknown day/night shift pattern of water allocation between fruit and its adjacent branch, which has not been reported before.
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Affiliation(s)
- Yangfan Chai
- College of Biosystems Engineering and Food ScienceZhejiang UniversityHangzhou310058China
| | - Chuyi Chen
- College of Biosystems Engineering and Food ScienceZhejiang UniversityHangzhou310058China
| | - Xuan Luo
- College of Biosystems Engineering and Food ScienceZhejiang UniversityHangzhou310058China
| | - Shijie Zhan
- Department of EngineeringUniversity of CambridgeCambridgeCB3 0FFUK
| | - Jongmin Kim
- Department of EngineeringUniversity of CambridgeCambridgeCB3 0FFUK
| | - Jikui Luo
- College of Information Science and Electronic EngineeringZhejiang UniversityHangzhou310058China
| | - Xiaozhi Wang
- College of Information Science and Electronic EngineeringZhejiang UniversityHangzhou310058China
| | - Zhongyuan Hu
- College of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Yibin Ying
- College of Biosystems Engineering and Food ScienceZhejiang UniversityHangzhou310058China
| | - Xiangjiang Liu
- College of Biosystems Engineering and Food ScienceZhejiang UniversityHangzhou310058China
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Root System Phenotying of Soil-Grown Plants via RGB and Hyperspectral Imaging. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2264:245-268. [PMID: 33263915 DOI: 10.1007/978-1-0716-1201-9_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Phenotyping root systems provide essential information for plant breeding, particularly aiming for better abiotic stress resistance. Rhizobox systems provide a field-near growth environment for in situ imaging of root systems in soil. A protocol for RGB and hyperspectral imaging of rhizobox-grown plants is presented that enables gathering of root structural (morphology, architecture) as well as functional (water content, decomposition) information. The protocol exemplifies the setup of a root phenotyping platform combining low-cost RGB with advanced short-wave infrared hyperspectral imaging. For both types of imaging approach, the essential steps of an image analysis pipeline are provided to retrieve biological information on breeding-relevant traits from the imaging datasets.
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Jiménez-Arias D, García-Machado FJ, Morales-Sierra S, García-García AL, Herrera AJ, Valdés F, Luis JC, Borges AA. A Beginner's Guide to Osmoprotection by Biostimulants. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10020363. [PMID: 33668668 PMCID: PMC7917748 DOI: 10.3390/plants10020363] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/08/2021] [Accepted: 02/10/2021] [Indexed: 05/04/2023]
Abstract
Water is indispensable for the life of any organism on Earth. Consequently, osmotic stress due to salinity and drought is the greatest threat to crop productivity. Ongoing climate change includes rising temperatures and less precipitation over large areas of the planet. This is leading to increased vulnerability to the drought conditions that habitually threaten food security in many countries. Such a scenario poses a daunting challenge for scientists: the search for innovative solutions to save water and cultivate under water deficit. A search for formulations including biostimulants capable of improving tolerance to this stress is a promising specific approach. This review updates the most recent state of the art in the field.
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Affiliation(s)
- David Jiménez-Arias
- Chemical Plant Defence Activators Group, Department of Agrobiology, IPNA-CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Canary Islands, Spain; (F.J.G.-M.); (A.L.G.-G.); (A.J.H.)
- Correspondence: (D.J.-A.); (A.A.B.)
| | - Francisco J. García-Machado
- Chemical Plant Defence Activators Group, Department of Agrobiology, IPNA-CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Canary Islands, Spain; (F.J.G.-M.); (A.L.G.-G.); (A.J.H.)
- Applied Plant Biology Group (GBVA), Department of Botany, Ecology and Plant Physiology–Faculty of Pharmacy, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez s/n, 38071 La Laguna, Tenerife, Canary Islands, Spain; (S.M.-S.); (F.V.); (J.C.L.)
| | - Sarai Morales-Sierra
- Applied Plant Biology Group (GBVA), Department of Botany, Ecology and Plant Physiology–Faculty of Pharmacy, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez s/n, 38071 La Laguna, Tenerife, Canary Islands, Spain; (S.M.-S.); (F.V.); (J.C.L.)
| | - Ana L. García-García
- Chemical Plant Defence Activators Group, Department of Agrobiology, IPNA-CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Canary Islands, Spain; (F.J.G.-M.); (A.L.G.-G.); (A.J.H.)
- Applied Plant Biology Group (GBVA), Department of Botany, Ecology and Plant Physiology–Faculty of Pharmacy, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez s/n, 38071 La Laguna, Tenerife, Canary Islands, Spain; (S.M.-S.); (F.V.); (J.C.L.)
| | - Antonio J. Herrera
- Chemical Plant Defence Activators Group, Department of Agrobiology, IPNA-CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Canary Islands, Spain; (F.J.G.-M.); (A.L.G.-G.); (A.J.H.)
| | - Francisco Valdés
- Applied Plant Biology Group (GBVA), Department of Botany, Ecology and Plant Physiology–Faculty of Pharmacy, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez s/n, 38071 La Laguna, Tenerife, Canary Islands, Spain; (S.M.-S.); (F.V.); (J.C.L.)
| | - Juan C. Luis
- Applied Plant Biology Group (GBVA), Department of Botany, Ecology and Plant Physiology–Faculty of Pharmacy, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez s/n, 38071 La Laguna, Tenerife, Canary Islands, Spain; (S.M.-S.); (F.V.); (J.C.L.)
| | - Andrés A. Borges
- Chemical Plant Defence Activators Group, Department of Agrobiology, IPNA-CSIC, Avda. Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Canary Islands, Spain; (F.J.G.-M.); (A.L.G.-G.); (A.J.H.)
- Correspondence: (D.J.-A.); (A.A.B.)
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Gandullo J, Ahmad S, Darwish E, Karlova R, Testerink C. Phenotyping Tomato Root Developmental Plasticity in Response to Salinity in Soil Rhizotrons. PLANT PHENOMICS (WASHINGTON, D.C.) 2021; 2021:2760532. [PMID: 33575670 PMCID: PMC7869940 DOI: 10.34133/2021/2760532] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/25/2020] [Indexed: 05/23/2023]
Abstract
Plants have developed multiple strategies to respond to salt stress. In order to identify new traits related to salt tolerance, with potential breeding application, the research focus has recently been shifted to include root system architecture (RSA) and root plasticity. Using a simple but effective root phenotyping system containing soil (rhizotrons), RSA of several tomato cultivars and their response to salinity was investigated. We observed a high level of root plasticity of tomato seedlings under salt stress. The general root architecture was substantially modified in response to salt, especially with respect to position of the lateral roots in the soil. At the soil surface, where salt accumulates, lateral root emergence was most strongly inhibited. Within the set of tomato cultivars, H1015 was the most tolerant to salinity in both developmental stages studied. A significant correlation between several root traits and aboveground growth parameters was observed, highlighting a possible role for regulation of both ion content and root architecture in salt stress resilience.
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Affiliation(s)
- Jacinto Gandullo
- Section of Plant Physiology and Plant Cell Biology, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
- Departamento de Biología Vegetal y Ecología, Área de Fisiología Vegetal, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Safarina Ahmad
- Section of Plant Physiology and Plant Cell Biology, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | - Essam Darwish
- Section of Plant Physiology and Plant Cell Biology, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
- Plant Physiology Section, Agricultural Botany Department, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Rumyana Karlova
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University and Research, 6708PB Wageningen, Netherlands
| | - Christa Testerink
- Section of Plant Physiology and Plant Cell Biology, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University and Research, 6708PB Wageningen, Netherlands
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56
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Liu H, Fiorani F, Jäck O, Colombi T, Nagel KA, Weih M. Shoot and Root Traits Underlying Genotypic Variation in Early Vigor and Nutrient Accumulation in Spring Wheat Grown in High-Latitude Light Conditions. PLANTS (BASEL, SWITZERLAND) 2021; 10:174. [PMID: 33477661 PMCID: PMC7831908 DOI: 10.3390/plants10010174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/14/2021] [Accepted: 01/14/2021] [Indexed: 06/12/2023]
Abstract
Plants with improved nutrient use efficiency are needed to maintain and enhance future crop plant production. The aim of this study was to explore candidate traits for pre-breeding to improve nutrient accumulation and early vigor of spring wheat grown at high latitudes. We quantified shoot and root traits together with nutrient accumulation in nine contrasting spring wheat genotypes grown in rhizoboxes for 20 days in a greenhouse. Whole-plant relative growth rate was here correlated with leaf area productivity and plant nitrogen productivity, but not leaf area ratio. Furthermore, the total leaf area was correlated with the accumulation of six macronutrients, and could be suggested as a candidate trait for the pre-breeding towards improved nutrient accumulation and early vigor in wheat to be grown in high-latitude environments. Depending on the nutrient of interest, different root system traits were identified as relevant for their accumulation. Accumulation of nitrogen, potassium, sulfur and calcium was correlated with lateral root length, whilst accumulation of phosphorus and magnesium was correlated with main root length. Therefore, special attention needs to be paid to specific root system traits in the breeding of wheat towards improved nutrient accumulation to counteract the suboptimal uptake of some nutrient elements.
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Affiliation(s)
- Hui Liu
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden; (O.J.); (M.W.)
| | - Fabio Fiorani
- Institute for Bio and Geosciences-2, Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; (F.F.); (K.A.N.)
| | - Ortrud Jäck
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden; (O.J.); (M.W.)
| | - Tino Colombi
- Department of Soil and Environment, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden;
| | - Kerstin A. Nagel
- Institute for Bio and Geosciences-2, Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; (F.F.); (K.A.N.)
| | - Martin Weih
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden; (O.J.); (M.W.)
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57
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Zhang Y, Zhang W, Cao Q, Zheng X, Yang J, Xue T, Sun W, Du X, Wang L, Wang J, Zhao F, Xiang F, Li S. WinRoots: A High-Throughput Cultivation and Phenotyping System for Plant Phenomics Studies Under Soil Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:794020. [PMID: 35154184 PMCID: PMC8832124 DOI: 10.3389/fpls.2021.794020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/19/2021] [Indexed: 05/12/2023]
Abstract
Soil stress, such as salinity, is a primary cause of global crop yield reduction. Existing crop phenotyping platforms cannot fully meet the specific needs of phenomics studies of plant response to soil stress in terms of throughput, environmental controllability, or root phenotypic acquisition. Here, we report the WinRoots, a low-cost and high-throughput plant soil cultivation and phenotyping system that can provide uniform, controlled soil stress conditions and accurately quantify the whole-plant phenome, including roots. Using soybean seedlings exposed to salt stress as an example, we demonstrate the uniformity and controllability of the soil environment in this system. A high-throughput multiple-phenotypic assay among 178 soybean cultivars reveals that the cotyledon character can serve as a non-destructive indicator of the whole-seedling salt tolerance. Our results demonstrate that WinRoots is an effective tool for high-throughput plant cultivation and soil stress phenomics studies.
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Affiliation(s)
- Yangyang Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Wenjing Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Qicong Cao
- Weifang Academy of Agriculture Sciences, Weifang, China
| | - Xiaojian Zheng
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Jingting Yang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Tong Xue
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Wenhao Sun
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Xinrui Du
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Lili Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Jing Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Fengying Zhao
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Fengning Xiang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
| | - Shuo Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China
- *Correspondence: Shuo Li,
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Moisan K, Raaijmakers JM, Dicke M, Lucas‐Barbosa D, Cordovez V. Volatiles from soil-borne fungi affect directional growth of roots. PLANT, CELL & ENVIRONMENT 2021; 44:339-345. [PMID: 32996612 PMCID: PMC7821104 DOI: 10.1111/pce.13890] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/08/2020] [Indexed: 05/11/2023]
Abstract
Volatiles play major roles in mediating ecological interactions between soil (micro)organisms and plants. It is well-established that microbial volatiles can increase root biomass and lateral root formation. To date, however, it is unknown whether microbial volatiles can affect directional root growth. Here, we present a novel method to study belowground volatile-mediated interactions. As proof-of-concept, we designed a root Y-tube olfactometer, and tested the effects of volatiles from four different soil-borne fungi on directional growth of Brassica rapa roots in soil. Subsequently, we compared the fungal volatile organic compounds (VOCs) previously profiled with Gas Chromatography-Mass Spectrometry (GC-MS). Using our newly designed setup, we show that directional root growth in soil is differentially affected by fungal volatiles. Roots grew more frequently toward volatiles from the root pathogen Rhizoctonia solani, whereas volatiles from the other three saprophytic fungi did not impact directional root growth. GC-MS profiling showed that six VOCs were exclusively emitted by R. solani. These findings verify that this novel method is suitable to unravel the intriguing chemical cross-talk between roots and soil-borne fungi and its impact on root growth.
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Affiliation(s)
- Kay Moisan
- Laboratory of EntomologyWageningen University and ResearchWageningenThe Netherlands
- Department of Microbial EcologyNetherlands Institute of EcologyWageningenThe Netherlands
| | - Jos M. Raaijmakers
- Department of Microbial EcologyNetherlands Institute of EcologyWageningenThe Netherlands
- Institute of BiologyLeiden UniversityLeidenThe Netherlands
| | - Marcel Dicke
- Laboratory of EntomologyWageningen University and ResearchWageningenThe Netherlands
| | - Dani Lucas‐Barbosa
- Laboratory of EntomologyWageningen University and ResearchWageningenThe Netherlands
- Present address:
Bio‐communication & EcologyETH ZürichZürichSwitzerland
| | - Viviane Cordovez
- Department of Microbial EcologyNetherlands Institute of EcologyWageningenThe Netherlands
- Institute of BiologyLeiden UniversityLeidenThe Netherlands
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Nakhforoosh A, Nagel KA, Fiorani F, Bodner G. Deep soil exploration vs. topsoil exploitation: distinctive rooting strategies between wheat landraces and wild relatives. PLANT AND SOIL 2020; 459:397-421. [PMID: 33603255 PMCID: PMC7870630 DOI: 10.1007/s11104-020-04794-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/03/2020] [Indexed: 05/27/2023]
Abstract
AIMS Diversity of root systems among genetic resources can contribute to optimize water and nutrient uptake. Topsoil exploitation vs. deep soil exploration represent two contrasting ideotypes in relation to resource use. Our study reveals how rooting patterns changed between wheat wild progenitors and landraces in regard to these ideotypes. METHODS Root (partitioning, morphology, distribution, elongation, anatomy) and shoot traits (dry-matter, leaf area, assimilation) of durum landraces, wild emmer and wild einkorn from Iran, Syria, Turkey and Lebanon were phenotyped using the GrowScreen-Rhizo platform. Distinctive rooting patterns were identified via principal component analysis and relations with collection site characteristics analyzed. RESULTS Shoot trait differentiation was strongly driven by seed weight, leading to superior early vigor of landraces. Wild progenitors formed superficial root systems with a higher contribution of lateral and early-emerging nodal axes to total root length. Durum landraces had a root system dominated by seminal axes allocated evenly over depth. Xylem anatomy was the trait most affected by the environmental influence of the collection site. CONCLUSIONS The durum landrace root system approximated a deep soil exploration ideotype which would optimize subsoil water uptake, while monococcum-type wild einkorn was most similar to a topsoil exploiting strategy with potential competitive advantages for subsistence in natural vegetation. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11104-020-04794-9.
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Affiliation(s)
- Alireza Nakhforoosh
- Division of Agronomy, Department of Crop Sciences, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz-Straße 24, A-3430 Tulln an der Donau, Austria
- Global Institute of Food Security, University of Saskatchewan, Saskatoon, SK S7N 0W9 Canada
| | - Kerstin A. Nagel
- IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Fabio Fiorani
- IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Gernot Bodner
- Division of Agronomy, Department of Crop Sciences, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz-Straße 24, A-3430 Tulln an der Donau, Austria
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60
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Li B, Chen L, Sun W, Wu D, Wang M, Yu Y, Chen G, Yang W, Lin Z, Zhang X, Duan L, Yang X. Phenomics-based GWAS analysis reveals the genetic architecture for drought resistance in cotton. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2533-2544. [PMID: 32558152 PMCID: PMC7680548 DOI: 10.1111/pbi.13431] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 02/13/2020] [Accepted: 06/05/2020] [Indexed: 05/08/2023]
Abstract
Drought resistance (DR) is a complex trait that is regulated by a variety of genes. Without comprehensive profiling of DR-related traits, the knowledge of the genetic architecture for DR in cotton remains limited. Thus, there is a need to bridge the gap between genomics and phenomics. In this study, an automatic phenotyping platform (APP) was systematically applied to examine 119 image-based digital traits (i-traits) during drought stress at the seedling stage, across a natural population of 200 representative upland cotton accessions. Some novel i-traits, as well as some traditional i-traits, were used to evaluate the DR in cotton. The phenomics data allowed us to identify 390 genetic loci by genome-wide association study (GWAS) using 56 morphological and 63 texture i-traits. DR-related genes, including GhRD2, GhNAC4, GhHAT22 and GhDREB2, were identified as candidate genes by some digital traits. Further analysis of candidate genes showed that Gh_A04G0377 and Gh_A04G0378 functioned as negative regulators for cotton drought response. Based on the combined digital phenotyping, GWAS analysis and transcriptome data, we conclude that the phenomics dataset provides an excellent resource to characterize key genetic loci with an unprecedented resolution which can inform future genome-based breeding for improved DR in cotton.
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Affiliation(s)
- Baoqi Li
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanHubeiChina
| | - Lin Chen
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanHubeiChina
| | - Weinan Sun
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanHubeiChina
| | - Di Wu
- Hubei Key Laboratory of Agricultural BioinformaticsHuazhong Agricultural UniversityWuhanHubeiChina
- College of EngineeringHuazhong Agricultural UniversityWuhanHubeiChina
| | - Maojun Wang
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanHubeiChina
| | - Yu Yu
- Cotton InstituteXinjiang Academy of Agriculture and Reclamation ScienceShiheziXinjiangChina
| | - Guoxing Chen
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze RiverHuazhong Agricultural UniversityWuhanHubeiChina
| | - Wanneng Yang
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanHubeiChina
- Hubei Key Laboratory of Agricultural BioinformaticsHuazhong Agricultural UniversityWuhanHubeiChina
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanHubeiChina
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanHubeiChina
| | - Lingfeng Duan
- Hubei Key Laboratory of Agricultural BioinformaticsHuazhong Agricultural UniversityWuhanHubeiChina
- College of EngineeringHuazhong Agricultural UniversityWuhanHubeiChina
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene Research (Wuhan)Huazhong Agricultural UniversityWuhanHubeiChina
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Abstract
A transition from qualitative to quantitative descriptors of morphology has been facilitated through the growing field of morphometrics, representing the conversion of shapes and patterns into numbers. The analysis of plant form at the macromorphological scale using morphometric approaches quantifies what is commonly referred to as a phenotype. Quantitative phenotypic analysis of individuals with contrasting genotypes in turn provides a means to establish links between genes and shapes. The path from a gene to a morphological phenotype is, however, not direct, with instructive information progressing both across multiple scales of biological complexity and through nonintuitive feedback, such as mechanical signals. In this review, we explore morphometric approaches used to perform whole-plant phenotyping and quantitative approaches in capture processes in the mesoscales, which bridge the gaps between genes and shapes in plants. Quantitative frameworks involving both the computational simulation and the discretization of data into networks provide a putative path to predicting emergent shape from underlying genetic programs.
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Affiliation(s)
- Hao Xu
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom;
| | - George W Bassel
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom;
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Tichá M, Illésová P, Hrbáčková M, Basheer J, Novák D, Hlaváčková K, Šamajová O, Niehaus K, Ovečka M, Šamaj J. Tissue culture, genetic transformation, interaction with beneficial microbes, and modern bio-imaging techniques in alfalfa research. Crit Rev Biotechnol 2020; 40:1265-1280. [PMID: 32942912 DOI: 10.1080/07388551.2020.1814689] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Current research needs to be more focused on agronomical plants to effectively utilize the knowledge obtained from model plant species. Efforts to improve legumes have long employed common breeding tools. Recently, biotechnological approaches facilitated the development of improved legumes with new traits, allowing them to withstand climatic changes and biotic stress. Owing to its multiple uses and profits, alfalfa (Medicago sativa L.) has become a prominent forage crop worldwide. This review provides a comprehensive research summary of tissue culture-based genetic transformation methods, which could be exploited for the development of transgenic alfalfa with agronomically desirable traits. Moreover, advanced bio-imaging approaches, including cutting-edge microscopy and phenotyping, are outlined here. Finally, characterization and the employment of beneficial microbes should help to produce biotechnologically improved and sustainable alfalfa cultivars.
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Affiliation(s)
- Michaela Tichá
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Petra Illésová
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Miroslava Hrbáčková
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Jasim Basheer
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Dominik Novák
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Kateřina Hlaváčková
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Olga Šamajová
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Karsten Niehaus
- Faculty of Biology, Center for Biotechnology - CeBiTec, Universität Bielefeld, Bielefeld, Germany
| | - Miroslav Ovečka
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Jozef Šamaj
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
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Bontpart T, Concha C, Giuffrida MV, Robertson I, Admkie K, Degefu T, Girma N, Tesfaye K, Haileselassie T, Fikre A, Fetene M, Tsaftaris SA, Doerner P. Affordable and robust phenotyping framework to analyse root system architecture of soil-grown plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:2330-2343. [PMID: 32530068 DOI: 10.1111/tpj.14877] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 05/15/2020] [Indexed: 06/11/2023]
Abstract
The phenotypic analysis of root system growth is important to inform efforts to enhance plant resource acquisition from soils; however, root phenotyping remains challenging because of the opacity of soil, requiring systems that facilitate root system visibility and image acquisition. Previously reported systems require costly or bespoke materials not available in most countries, where breeders need tools to select varieties best adapted to local soils and field conditions. Here, we report an affordable soil-based growth (rhizobox) and imaging system to phenotype root development in glasshouses or shelters. All components of the system are made from locally available commodity components, facilitating the adoption of this affordable technology in low-income countries. The rhizobox is large enough (approximately 6000 cm2 of visible soil) to avoid restricting vertical root system growth for most if not all of the life cycle, yet light enough (approximately 21 kg when filled with soil) for routine handling. Support structures and an imaging station, with five cameras covering the whole soil surface, complement the rhizoboxes. Images are acquired via the Phenotiki sensor interface, collected, stitched and analysed. Root system architecture (RSA) parameters are quantified without intervention. The RSAs of a dicot species (Cicer arietinum, chickpea) and a monocot species (Hordeum vulgare, barley), exhibiting contrasting root systems, were analysed. Insights into root system dynamics during vegetative and reproductive stages of the chickpea life cycle were obtained. This affordable system is relevant for efforts in Ethiopia and other low- and middle-income countries to enhance crop yields and climate resilience sustainably.
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Affiliation(s)
- Thibaut Bontpart
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, Midlothian, EH9 3BF, UK
| | - Cristobal Concha
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, Midlothian, EH9 3BF, UK
| | - Mario Valerio Giuffrida
- Institute for Digital Communications, School of Engineering, University of Edinburgh, Edinburgh, Midlothian, EH9 3FG, UK
- School of Computing, Edinburgh Napier University, Merchiston Campus, Edinburgh, EH10 5DT, UK
| | - Ingrid Robertson
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, Midlothian, EH9 3BF, UK
| | - Kassahun Admkie
- Ethiopian Institute of Agricultural Research, Debre Zeit, Oromia, PO Box 32, Ethiopia
| | - Tulu Degefu
- ICRISAT-Ethiopia, International Crops Research Institute for the Semi-Arid Tropics, c/o ILRI Campus, Addis Ababa, Addis Ababa, PO Box 5689, Ethiopia
| | - Nigusie Girma
- Ethiopian Institute of Agricultural Research, Debre Zeit, Oromia, PO Box 32, Ethiopia
| | - Kassahun Tesfaye
- College of Natural Sciences, Addis Ababa University, Addis Ababa, Addis Ababa, PO Box 1176, Ethiopia
- Ethiopian Biotechnology Institute, Addis Ababa, Addis Ababa, PO Box 5954, Ethiopia
| | | | - Asnake Fikre
- Ethiopian Institute of Agricultural Research, Debre Zeit, Oromia, PO Box 32, Ethiopia
- ICRISAT-Ethiopia, International Crops Research Institute for the Semi-Arid Tropics, c/o ILRI Campus, Addis Ababa, Addis Ababa, PO Box 5689, Ethiopia
| | - Masresha Fetene
- College of Natural Sciences, Addis Ababa University, Addis Ababa, Addis Ababa, PO Box 1176, Ethiopia
- Ethiopian Academy of Sciences, Addis Ababa, Addis Ababa, PO Box 32228, Ethiopia
| | - Sotirios A Tsaftaris
- Institute for Digital Communications, School of Engineering, University of Edinburgh, Edinburgh, Midlothian, EH9 3FG, UK
| | - Peter Doerner
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, Midlothian, EH9 3BF, UK
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64
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Korwin Krukowski P, Ellenberger J, Röhlen-Schmittgen S, Schubert A, Cardinale F. Phenotyping in Arabidopsis and Crops-Are We Addressing the Same Traits? A Case Study in Tomato. Genes (Basel) 2020; 11:E1011. [PMID: 32867311 PMCID: PMC7564427 DOI: 10.3390/genes11091011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 11/18/2022] Open
Abstract
The convenient model Arabidopsis thaliana has allowed tremendous advances in plant genetics and physiology, in spite of only being a weed. It has also unveiled the main molecular networks governing, among others, abiotic stress responses. Through the use of the latest genomic tools, Arabidopsis research is nowadays being translated to agronomically interesting crop models such as tomato, but at a lagging pace. Knowledge transfer has been hindered by invariable differences in plant architecture and behaviour, as well as the divergent direct objectives of research in Arabidopsis versus crops compromise transferability. In this sense, phenotype translation is still a very complex matter. Here, we point out the challenges of "translational phenotyping" in the case study of drought stress phenotyping in Arabidopsis and tomato. After briefly defining and describing drought stress and survival strategies, we compare drought stress protocols and phenotyping techniques most commonly used in the two species, and discuss their potential to gain insights, which are truly transferable between species. This review is intended to be a starting point for discussion about translational phenotyping approaches among plant scientists, and provides a useful compendium of methods and techniques used in modern phenotyping for this specific plant pair as a case study.
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Affiliation(s)
- Paolo Korwin Krukowski
- Plant Stress Lab, Department of Agriculture, Forestry and Food Sciences DISAFA-Turin University, 10095 Grugliasco, Italy; (A.S.); (F.C.)
| | - Jan Ellenberger
- INRES Horticultural Sciences, University of Bonn, 53121 Bonn, Germany;
| | | | - Andrea Schubert
- Plant Stress Lab, Department of Agriculture, Forestry and Food Sciences DISAFA-Turin University, 10095 Grugliasco, Italy; (A.S.); (F.C.)
| | - Francesca Cardinale
- Plant Stress Lab, Department of Agriculture, Forestry and Food Sciences DISAFA-Turin University, 10095 Grugliasco, Italy; (A.S.); (F.C.)
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65
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Plett DC, Ranathunge K, Melino VJ, Kuya N, Uga Y, Kronzucker HJ. The intersection of nitrogen nutrition and water use in plants: new paths toward improved crop productivity. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4452-4468. [PMID: 32026944 PMCID: PMC7382376 DOI: 10.1093/jxb/eraa049] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/05/2020] [Indexed: 05/19/2023]
Abstract
Water and nitrogen availability limit crop productivity globally more than most other environmental factors. Plant availability of macronutrients such as nitrate is, to a large extent, regulated by the amount of water available in the soil, and, during drought episodes, crops can become simultaneously water and nitrogen limited. In this review, we explore the intricate relationship between water and nitrogen transport in plants, from transpiration-driven mass flow in the soil to uptake by roots via membrane transporters and channels and transport to aerial organs. We discuss the roles of root architecture and of suberized hydrophobic root barriers governing apoplastic water and nitrogen movement into the vascular system. We also highlight the need to identify the signalling cascades regulating water and nitrogen transport, as well as the need for targeted physiological analyses of plant traits influencing water and nitrogen uptake. We further advocate for incorporation of new phenotyping technologies, breeding strategies, and agronomic practices to improve crop yield in water- and nitrogen-limited production systems.
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Affiliation(s)
- Darren C Plett
- School of Agriculture and Food, The University of Melbourne, Melbourne, VIC, Australia
| | - Kosala Ranathunge
- School of Biological Sciences, University of Western Australia, Crawley, Perth, Australia
| | - Vanessa J Melino
- School of Agriculture and Food, The University of Melbourne, Melbourne, VIC, Australia
| | - Noriyuki Kuya
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Yusaku Uga
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Herbert J Kronzucker
- School of Agriculture and Food, The University of Melbourne, Melbourne, VIC, Australia
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
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66
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Concha C, Doerner P. The impact of the rhizobia-legume symbiosis on host root system architecture. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3902-3921. [PMID: 32337556 PMCID: PMC7316968 DOI: 10.1093/jxb/eraa198] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 04/22/2020] [Indexed: 05/20/2023]
Abstract
Legumes form symbioses with rhizobia to fix N2 in root nodules to supplement their nitrogen (N) requirements. Many studies have shown how symbioses affect the shoot, but far less is understood about how they modify root development and root system architecture (RSA). RSA is the distribution of roots in space and over time. RSA reflects host resource allocation into below-ground organs and patterns of host resource foraging underpinning its resource acquisition capacity. Recent studies have revealed a more comprehensive relationship between hosts and symbionts: the latter can affect host resource acquisition for phosphate and iron, and the symbiont's production of plant growth regulators can enhance host resource flux and abundance. We review the current understanding of the effects of rhizobia-legume symbioses on legume root systems. We focus on resource acquisition and allocation within the host to conceptualize the effect of symbioses on RSA, and highlight opportunities for new directions of research.
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Affiliation(s)
- Cristobal Concha
- Institute for Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Peter Doerner
- Institute for Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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67
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Lopez-Cruz M, Olson E, Rovere G, Crossa J, Dreisigacker S, Mondal S, Singh R, Campos GDL. Regularized selection indices for breeding value prediction using hyper-spectral image data. Sci Rep 2020; 10:8195. [PMID: 32424224 PMCID: PMC7235263 DOI: 10.1038/s41598-020-65011-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 04/20/2020] [Indexed: 12/02/2022] Open
Abstract
High-throughput phenotyping (HTP) technologies can produce data on thousands of phenotypes per unit being monitored. These data can be used to breed for economically and environmentally relevant traits (e.g., drought tolerance); however, incorporating high-dimensional phenotypes in genetic analyses and in breeding schemes poses important statistical and computational challenges. To address this problem, we developed regularized selection indices; the methodology integrates techniques commonly used in high-dimensional phenotypic regressions (including penalization and rank-reduction approaches) into the selection index (SI) framework. Using extensive data from CIMMYT's (International Maize and Wheat Improvement Center) wheat breeding program we show that regularized SIs derived from hyper-spectral data offer consistently higher accuracy for grain yield than those achieved by standard SIs, and by vegetation indices commonly used to predict agronomic traits. Regularized SIs offer an effective approach to leverage HTP data that is routinely generated in agriculture; the methodology can also be used to conduct genetic studies using high-dimensional phenotypes that are often collected in humans and model organisms including body images and whole-genome gene expression profiles.
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Affiliation(s)
- Marco Lopez-Cruz
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Eric Olson
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Gabriel Rovere
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Jose Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
| | | | - Suchismita Mondal
- International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
| | - Ravi Singh
- International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
| | - Gustavo de Los Campos
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA.
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.
- Department of Statistics and Probability, Michigan State University, East Lansing, MI, USA.
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68
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Watt M, Fiorani F, Usadel B, Rascher U, Muller O, Schurr U. Phenotyping: New Windows into the Plant for Breeders. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:689-712. [PMID: 32097567 DOI: 10.1146/annurev-arplant-042916-041124] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Plant phenotyping enables noninvasive quantification of plant structure and function and interactions with environments. High-capacity phenotyping reaches hitherto inaccessible phenotypic characteristics. Diverse, challenging, and valuable applications of phenotyping have originated among scientists, prebreeders, and breeders as they study the phenotypic diversity of genetic resources and apply increasingly complex traits to crop improvement. Noninvasive technologies are used to analyze experimental and breeding populations. We cover the most recent research in controlled-environment and field phenotyping for seed, shoot, and root traits. Select field phenotyping technologies have become state of the art and show promise for speeding up the breeding process in early generations. We highlight the technologies behind the rapid advances in proximal and remote sensing of plants in fields. We conclude by discussing the new disciplines working with the phenotyping community: data science, to address the challenge of generating FAIR (findable, accessible, interoperable, and reusable) data, and robotics, to apply phenotyping directly on farms.
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Affiliation(s)
- Michelle Watt
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany; ,
| | - Fabio Fiorani
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany; ,
| | - Björn Usadel
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany; ,
- Institute for Botany and Molecular Genetics, BioSC, RWTH Aachen University, 52074 Aachen, Germany
| | - Uwe Rascher
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany; ,
| | - Onno Muller
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany; ,
| | - Ulrich Schurr
- IBG-2: Plant Sciences, Institute of Bio- and Geosciences, Forschungszentrum Jülich, 52425 Jülich, Germany; ,
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69
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Smith AG, Petersen J, Selvan R, Rasmussen CR. Segmentation of roots in soil with U-Net. PLANT METHODS 2020; 16:13. [PMID: 32055251 PMCID: PMC7007677 DOI: 10.1186/s13007-020-0563-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/27/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND Plant root research can provide a way to attain stress-tolerant crops that produce greater yield in a diverse array of conditions. Phenotyping roots in soil is often challenging due to the roots being difficult to access and the use of time consuming manual methods. Rhizotrons allow visual inspection of root growth through transparent surfaces. Agronomists currently manually label photographs of roots obtained from rhizotrons using a line-intersect method to obtain root length density and rooting depth measurements which are essential for their experiments. We investigate the effectiveness of an automated image segmentation method based on the U-Net Convolutional Neural Network (CNN) architecture to enable such measurements. We design a data-set of 50 annotated chicory (Cichorium intybus L.) root images which we use to train, validate and test the system and compare against a baseline built using the Frangi vesselness filter. We obtain metrics using manual annotations and line-intersect counts. RESULTS Our results on the held out data show our proposed automated segmentation system to be a viable solution for detecting and quantifying roots. We evaluate our system using 867 images for which we have obtained line-intersect counts, attaining a Spearman rank correlation of 0.9748 and an r 2 of 0.9217. We also achieve an F 1 of 0.7 when comparing the automated segmentation to the manual annotations, with our automated segmentation system producing segmentations with higher quality than the manual annotations for large portions of the image. CONCLUSION We have demonstrated the feasibility of a U-Net based CNN system for segmenting images of roots in soil and for replacing the manual line-intersect method. The success of our approach is also a demonstration of the feasibility of deep learning in practice for small research groups needing to create their own custom labelled dataset from scratch.
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Affiliation(s)
- Abraham George Smith
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegaard Allé 13, 2630 Taastrup, Denmark
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100 Copenhagen Ø, Denmark
| | - Jens Petersen
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100 Copenhagen Ø, Denmark
| | - Raghavendra Selvan
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100 Copenhagen Ø, Denmark
| | - Camilla Ruø Rasmussen
- Department of Plant and Environmental Sciences, University of Copenhagen, Højbakkegaard Allé 13, 2630 Taastrup, Denmark
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70
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Yang W, Feng H, Zhang X, Zhang J, Doonan JH, Batchelor WD, Xiong L, Yan J. Crop Phenomics and High-Throughput Phenotyping: Past Decades, Current Challenges, and Future Perspectives. MOLECULAR PLANT 2020; 13:187-214. [PMID: 31981735 DOI: 10.1016/j.molp.2020.01.008] [Citation(s) in RCA: 239] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/06/2020] [Accepted: 01/10/2020] [Indexed: 05/18/2023]
Abstract
Since whole-genome sequencing of many crops has been achieved, crop functional genomics studies have stepped into the big-data and high-throughput era. However, acquisition of large-scale phenotypic data has become one of the major bottlenecks hindering crop breeding and functional genomics studies. Nevertheless, recent technological advances provide us potential solutions to relieve this bottleneck and to explore advanced methods for large-scale phenotyping data acquisition and processing in the coming years. In this article, we review the major progress on high-throughput phenotyping in controlled environments and field conditions as well as its use for post-harvest yield and quality assessment in the past decades. We then discuss the latest multi-omics research combining high-throughput phenotyping with genetic studies. Finally, we propose some conceptual challenges and provide our perspectives on how to bridge the phenotype-genotype gap. It is no doubt that accurate high-throughput phenotyping will accelerate plant genetic improvements and promote the next green revolution in crop breeding.
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Affiliation(s)
- Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P.R. China.
| | - Hui Feng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crops Science/College of Agronomy, Henan Agricultural University, Zhengzhou 450002, P.R. China
| | - Jian Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - John H Doonan
- The National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | | | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P.R. China
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71
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Arsova B, Foster KJ, Shelden MC, Bramley H, Watt M. Dynamics in plant roots and shoots minimize stress, save energy and maintain water and nutrient uptake. THE NEW PHYTOLOGIST 2020; 225:1111-1119. [PMID: 31127613 DOI: 10.1111/nph.15955] [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: 12/21/2018] [Accepted: 04/19/2019] [Indexed: 05/12/2023]
Abstract
Plants are inherently dynamic. Dynamics minimize stress while enabling plants to flexibly acquire resources. Three examples are presented for plants tolerating saline soil: transport of sodium chloride (NaCl), water and macronutrients is nonuniform along a branched root; water and NaCl redistribute between shoot and soil at night-time; and ATP for salt exclusion is much lower in thinner branch roots than main roots, quantified using a biophysical model and geometry from anatomy. Noninvasive phenotyping and precision agriculture technologies can be used together to harness plant dynamics, but analytical methods are needed. A plant advancing in time through a soil and atmosphere space is proposed as a framework for dynamic data and their relationship to crop improvement.
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Affiliation(s)
- Borjana Arsova
- Root Dynamics Group, Institute for Bio and Geosciences-2, Plant Sciences, Forschungszentrum Juelich GmbH, Juelich, 52428, Germany
| | - Kylie J Foster
- Phenomics and Bioinformatics Research Centre, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Megan C Shelden
- Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Helen Bramley
- School of Life and Environmental Sciences, Plant Breeding Institute and Sydney Institute of Agriculture, The University of Sydney, Narrabri, NSW, 2390, Australia
| | - Michelle Watt
- Root Dynamics Group, Institute for Bio and Geosciences-2, Plant Sciences, Forschungszentrum Juelich GmbH, Juelich, 52428, Germany
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72
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Rahman G, Sohag H, Chowdhury R, Wahid KA, Dinh A, Arcand M, Vail S. SoilCam: A Fully Automated Minirhizotron using Multispectral Imaging for Root Activity Monitoring. SENSORS (BASEL, SWITZERLAND) 2020; 20:E787. [PMID: 32023975 PMCID: PMC7038518 DOI: 10.3390/s20030787] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/18/2020] [Accepted: 01/29/2020] [Indexed: 01/23/2023]
Abstract
A minirhizotron is an in situ root imaging system that captures components of root system architecture dynamics over time. Commercial minirhizotrons are expensive, limited to white-light imaging, and often need human intervention. The implementation of a minirhizotron needs to be low cost, automated, and customizable to be effective and widely adopted. We present a newly designed root imaging system called SoilCam that addresses the above mentioned limitations. The imaging system is multi-modal, i.e., it supports both conventional white-light and multispectral imaging, with fully automated operations for long-term in-situ monitoring using wireless control and access. The system is capable of taking 360° images covering the entire area surrounding the tube. The image sensor can be customized depending on the spectral imaging requirements. The maximum achievable image quality of the system is 8 MP (Mega Pixel)/picture, which is equivalent to a 2500 DPI (dots per inch) image resolution. The length of time in the field can be extended with a rechargeable battery and solar panel connectivity. Offline image-processing software, with several image enhancement algorithms to eliminate motion blur and geometric distortion and to reconstruct the 360° panoramic view, is also presented. The system is tested in the field by imaging canola roots to show the performance advantages over commercial systems.
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Affiliation(s)
- Gazi Rahman
- Department of Electrical and Computer Engineering, University of Saskatchewan, SK, S7N 5A9, Canada; (H.S.); (R.C.); (K.A.W.); (A.D.)
| | - Hanif Sohag
- Department of Electrical and Computer Engineering, University of Saskatchewan, SK, S7N 5A9, Canada; (H.S.); (R.C.); (K.A.W.); (A.D.)
| | - Rakibul Chowdhury
- Department of Electrical and Computer Engineering, University of Saskatchewan, SK, S7N 5A9, Canada; (H.S.); (R.C.); (K.A.W.); (A.D.)
| | - Khan A. Wahid
- Department of Electrical and Computer Engineering, University of Saskatchewan, SK, S7N 5A9, Canada; (H.S.); (R.C.); (K.A.W.); (A.D.)
| | - Anh Dinh
- Department of Electrical and Computer Engineering, University of Saskatchewan, SK, S7N 5A9, Canada; (H.S.); (R.C.); (K.A.W.); (A.D.)
| | - Melissa Arcand
- Department of Soil Science, University of Saskatchewan, SK, S7N 5A8, Canada;
| | - Sally Vail
- Research Scientist, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, SK S7N 0X2, Canada;
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Falk KG, Jubery TZ, Mirnezami SV, Parmley KA, Sarkar S, Singh A, Ganapathysubramanian B, Singh AK. Computer vision and machine learning enabled soybean root phenotyping pipeline. PLANT METHODS 2020; 16:5. [PMID: 31993072 PMCID: PMC6977263 DOI: 10.1186/s13007-019-0550-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 12/27/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Root system architecture (RSA) traits are of interest for breeding selection; however, measurement of these traits is difficult, resource intensive, and results in large variability. The advent of computer vision and machine learning (ML) enabled trait extraction and measurement has renewed interest in utilizing RSA traits for genetic enhancement to develop more robust and resilient crop cultivars. We developed a mobile, low-cost, and high-resolution root phenotyping system composed of an imaging platform with computer vision and ML based segmentation approach to establish a seamless end-to-end pipeline - from obtaining large quantities of root samples through image based trait processing and analysis. RESULTS This high throughput phenotyping system, which has the capacity to handle hundreds to thousands of plants, integrates time series image capture coupled with automated image processing that uses optical character recognition (OCR) to identify seedlings via barcode, followed by robust segmentation integrating convolutional auto-encoder (CAE) method prior to feature extraction. The pipeline includes an updated and customized version of the Automatic Root Imaging Analysis (ARIA) root phenotyping software. Using this system, we studied diverse soybean accessions from a wide geographical distribution and report genetic variability for RSA traits, including root shape, length, number, mass, and angle. CONCLUSIONS This system provides a high-throughput, cost effective, non-destructive methodology that delivers biologically relevant time-series data on root growth and development for phenomics, genomics, and plant breeding applications. This phenotyping platform is designed to quantify root traits and rank genotypes in a common environment thereby serving as a selection tool for use in plant breeding. Root phenotyping platforms and image based phenotyping are essential to mirror the current focus on shoot phenotyping in breeding efforts.
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Affiliation(s)
- Kevin G. Falk
- Department of Agronomy, Iowa State University, Ames, USA
| | | | | | | | - Soumik Sarkar
- Department of Mechanical Engineering, Iowa State University, Ames, USA
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, USA
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Falk KG, Jubery TZ, Mirnezami SV, Parmley KA, Sarkar S, Singh A, Ganapathysubramanian B, Singh AK. Computer vision and machine learning enabled soybean root phenotyping pipeline. PLANT METHODS 2020; 16:5. [PMID: 31993072 DOI: 10.1186/s,13007-019-0550-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 12/27/2019] [Indexed: 05/29/2023]
Abstract
BACKGROUND Root system architecture (RSA) traits are of interest for breeding selection; however, measurement of these traits is difficult, resource intensive, and results in large variability. The advent of computer vision and machine learning (ML) enabled trait extraction and measurement has renewed interest in utilizing RSA traits for genetic enhancement to develop more robust and resilient crop cultivars. We developed a mobile, low-cost, and high-resolution root phenotyping system composed of an imaging platform with computer vision and ML based segmentation approach to establish a seamless end-to-end pipeline - from obtaining large quantities of root samples through image based trait processing and analysis. RESULTS This high throughput phenotyping system, which has the capacity to handle hundreds to thousands of plants, integrates time series image capture coupled with automated image processing that uses optical character recognition (OCR) to identify seedlings via barcode, followed by robust segmentation integrating convolutional auto-encoder (CAE) method prior to feature extraction. The pipeline includes an updated and customized version of the Automatic Root Imaging Analysis (ARIA) root phenotyping software. Using this system, we studied diverse soybean accessions from a wide geographical distribution and report genetic variability for RSA traits, including root shape, length, number, mass, and angle. CONCLUSIONS This system provides a high-throughput, cost effective, non-destructive methodology that delivers biologically relevant time-series data on root growth and development for phenomics, genomics, and plant breeding applications. This phenotyping platform is designed to quantify root traits and rank genotypes in a common environment thereby serving as a selection tool for use in plant breeding. Root phenotyping platforms and image based phenotyping are essential to mirror the current focus on shoot phenotyping in breeding efforts.
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Affiliation(s)
- Kevin G Falk
- 1Department of Agronomy, Iowa State University, Ames, USA
| | - Talukder Z Jubery
- 2Department of Mechanical Engineering, Iowa State University, Ames, USA
| | - Seyed V Mirnezami
- 2Department of Mechanical Engineering, Iowa State University, Ames, USA
| | - Kyle A Parmley
- 1Department of Agronomy, Iowa State University, Ames, USA
| | - Soumik Sarkar
- 2Department of Mechanical Engineering, Iowa State University, Ames, USA
| | - Arti Singh
- 1Department of Agronomy, Iowa State University, Ames, USA
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Tracy SR, Nagel KA, Postma JA, Fassbender H, Wasson A, Watt M. Crop Improvement from Phenotyping Roots: Highlights Reveal Expanding Opportunities. TRENDS IN PLANT SCIENCE 2020; 25:105-118. [PMID: 31806535 DOI: 10.1016/j.tplants.2019.10.015] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 05/21/2023]
Abstract
Root systems determine the water and nutrients for photosynthesis and harvested products, underpinning agricultural productivity. We highlight 11 programs that integrated root traits into germplasm for breeding, relying on phenotyping. Progress was successful but slow. Today's phenotyping technologies will speed up root trait improvement. They combine multiple new alleles in germplasm for target environments, in parallel. Roots and shoots are detected simultaneously and nondestructively, seed to seed measures are automated, and field and laboratory technologies are increasingly linked. Available simulation models can aid all phenotyping decisions. This century will see a shift from single root traits to rhizosphere selections that can be managed dynamically on farms and a shift to phenotype-based improvement to accommodate the dynamic complexity of whole crop systems.
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Affiliation(s)
- Saoirse R Tracy
- School of Agriculture & Food Science, University College Dublin, Dublin, Ireland
| | - Kerstin A Nagel
- Institute for Bio and Geosciences-2, Plant Sciences, Forschungszentrum Juelich GmbH, 52428 Juelich, Germany
| | - Johannes A Postma
- Institute for Bio and Geosciences-2, Plant Sciences, Forschungszentrum Juelich GmbH, 52428 Juelich, Germany
| | - Heike Fassbender
- Institute for Bio and Geosciences-2, Plant Sciences, Forschungszentrum Juelich GmbH, 52428 Juelich, Germany
| | - Anton Wasson
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Michelle Watt
- Institute for Bio and Geosciences-2, Plant Sciences, Forschungszentrum Juelich GmbH, 52428 Juelich, Germany.
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76
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Wasson AP, Nagel KA, Tracy S, Watt M. Beyond Digging: Noninvasive Root and Rhizosphere Phenotyping. TRENDS IN PLANT SCIENCE 2020; 25:119-120. [PMID: 31791653 DOI: 10.1016/j.tplants.2019.10.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/28/2019] [Indexed: 05/24/2023]
Affiliation(s)
- Anton P Wasson
- Commonwealth Scientific and Industrial Research Organization (CSIRO) Agriculture and Food, Canberra, ACT 2601, Australia
| | - Kerstin A Nagel
- Institute for Bio- and Geosciences (IBG-2), Plant Sciences, Forschungszentrum Juelich GmbH, 52425 Juelich, Germany
| | - Saoirse Tracy
- University College Dublin (UCD) School of Agriculture and Food Science, UCD, Dublin 4, Ireland
| | - Michelle Watt
- Institute for Bio- and Geosciences (IBG-2), Plant Sciences, Forschungszentrum Juelich GmbH, 52425 Juelich, Germany.
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Robles-Aguilar AA, Grunert O, Hernandez-Sanabria E, Mysara M, Meers E, Boon N, Jablonowski ND. Effect of Applying Struvite and Organic N as Recovered Fertilizers on the Rhizosphere Dynamics and Cultivation of Lupine ( Lupinus angustifolius). FRONTIERS IN PLANT SCIENCE 2020; 11:572741. [PMID: 33329631 PMCID: PMC7717983 DOI: 10.3389/fpls.2020.572741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/19/2020] [Indexed: 05/11/2023]
Abstract
Intensive agriculture and horticulture heavily rely on the input of fertilizers to sustain food (and feed) production. However, high carbon footprint and pollution are associated with the mining processes of P and K, and the artificial nitrogen fixation for the production of synthetic fertilizers. Organic fertilizers or recovered nutrients from different waste sources can be used to reduce the environmental impact of fertilizers. We tested two recovered nutrients with slow-release patterns as promising alternatives for synthetic fertilizers: struvite and a commercially available organic fertilizer. Using these fertilizers as a nitrogen source, we conducted a rhizotron experiment to test their effect on plant performance and nutrient recovery in lupine plants. Plant performance was not affected by the fertilizer applied; however, N recovery was higher from the organic fertilizer than from struvite. As root architecture is fundamental for plant productivity, variations in root structure and length as a result of soil nutrient availability driven by plant-bacteria interactions were compared showing also no differences between fertilizers. However, fertilized plants were considerably different in the root length and morphology compared with the no fertilized plants. Since the microbial community influences plant nitrogen availability, we characterized the root-associated microbial community structure and functionality. Analyses revealed that the fertilizer applied had a significant impact on the associations and functionality of the bacteria inhabiting the growing medium used. The type of fertilizer significantly influenced the interindividual dissimilarities in the most abundant genera between treatments. This means that different plant species have a distinct effect on modulating the associated microbial community, but in the case of lupine, the fertilizer had a bigger effect than the plant itself. These novel insights on interactions between recovered fertilizers, plant, and associated microbes can contribute to developing sustainable crop production systems.
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Affiliation(s)
- Ana A. Robles-Aguilar
- Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Jülich, Germany
| | - Oliver Grunert
- Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
- Greenyard Horticulture, Ghent, Belgium
| | - Emma Hernandez-Sanabria
- Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
- Laboratory of Molecular Bacteriology, VIB – KU Leuven Center for Microbiology, Rega Institute, Leuven, Belgium
| | - Mohamed Mysara
- Unit of Microbiology, Belgian Nuclear Research Center, StudieCentrum voor Kernenergie⋅Centre d’étude de l’Energie Nucléaire (SCK⋅CEN), Mol, Belgium
- Department of Bioscience Engineering, Vrije Universiteit Brussel, Brussels, Belgium
| | - Erik Meers
- Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium
- *Correspondence: Nico Boon,
| | - Nicolai D. Jablonowski
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Jülich, Germany
- Nicolai D. Jablonowski,
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78
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Canales FJ, Nagel KA, Müller C, Rispail N, Prats E. Deciphering Root Architectural Traits Involved to Cope With Water Deficit in Oat. FRONTIERS IN PLANT SCIENCE 2019; 10:1558. [PMID: 31850037 PMCID: PMC6892839 DOI: 10.3389/fpls.2019.01558] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/07/2019] [Indexed: 05/25/2023]
Abstract
Drought tolerance is a complex phenomenon comprising many physiological, biochemical and morphological changes at both aerial and below ground levels. We aim to reveal changes on root morphology that promote drought tolerance in oat in both seedling and adult plants. To this aim, we employed two oat genotypes, previously characterized as susceptible and tolerant to drought. Root phenotyping was carried out on young plants grown either in pots or in rhizotrons under controlled environments, and on adult plants grown in big containers under field conditions. Overall, the tolerant genotype showed an increased root length, branching rate, root surface, and length of fine roots, while coarse to fine ratio decreased as compared with the susceptible genotype. We also observed a high and significant correlation between various morphological root traits within and between experiments, identifying several of them as appropriate markers to identify drought tolerant oat genotypes. Stimulation of fine root growth was one of the most prominent responses to cope with gradual soil water depletion, in both seedlings and adult plants. Although seedling experiments did not exactly match the response of adult plants, they were similarly informative for discriminating between tolerant and susceptible genotypes. This might contribute to easier and faster phenotyping of large amount of plants.
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Affiliation(s)
- Francisco J. Canales
- Institute for Sustainable Agriculture, Spanish Research Council (CSIC), Córdoba, Spain
| | - Kerstin A. Nagel
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Carmen Müller
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Nicolas Rispail
- Institute for Sustainable Agriculture, Spanish Research Council (CSIC), Córdoba, Spain
| | - Elena Prats
- Institute for Sustainable Agriculture, Spanish Research Council (CSIC), Córdoba, Spain
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79
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Bodner G, Loiskandl W, Hartl W, Erhart E, Sobotik M. Characterization of Cover Crop Rooting Types from Integration of Rhizobox Imaging and Root Atlas Information. PLANTS (BASEL, SWITZERLAND) 2019; 8:E514. [PMID: 31744188 PMCID: PMC6918168 DOI: 10.3390/plants8110514] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/06/2019] [Accepted: 11/15/2019] [Indexed: 11/24/2022]
Abstract
Plant root systems are essential for sustainable agriculture, conveying resource-efficient genotypes and species with benefits to soil ecosystem functions. Targeted selection of species/genotypes depends on available root system information. Currently there is no standardized approach for comprehensive root system characterization, suggesting the need for data integration across methods and sources. Here, we combine field measured root descriptors from the classical Root Atlas series with traits from controlled-environment root imaging for 10 cover crop species to (i) detect descriptors scaling between distant experimental methods, (ii) provide traits for species classification, and (iii) discuss implications for cover crop ecosystem functions. Results revealed relation of single axes measures from root imaging (convex hull, primary-lateral length ratio) to Root Atlas field descriptors (depth, branching order). Using composite root variables (principal components) for branching, morphology, and assimilate investment traits, cover crops were classified into species with (i) topsoil-allocated large diameter rooting type, (ii) low-branched primary/shoot-born axes-dominated rooting type, and (iii) highly branched dense rooting type, with classification trait-dependent distinction according to depth distribution. Data integration facilitated identification of root classification variables to derive root-related cover crop distinction, indicating their agro-ecological functions.
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Affiliation(s)
- Gernot Bodner
- Institute of Agronomy, Department of Crop Sciences, University of Natural Resources and Life Sciences, Konrad-Lorenz-Straße 24, A-3430 Tulln, Austria
- Austrian Society of Root Research, Muthgasse 18, A-1190 Vienna, Austria; (W.L.); (W.H.); (E.E.); (M.S.)
| | - Willibald Loiskandl
- Austrian Society of Root Research, Muthgasse 18, A-1190 Vienna, Austria; (W.L.); (W.H.); (E.E.); (M.S.)
- Institute for Soil Physics and Rural Water Management, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Wilfried Hartl
- Austrian Society of Root Research, Muthgasse 18, A-1190 Vienna, Austria; (W.L.); (W.H.); (E.E.); (M.S.)
- Bioforschung Austria, Esslinger Hauptstrasse 132-134, A-1220 Vienna, Austria
| | - Eva Erhart
- Austrian Society of Root Research, Muthgasse 18, A-1190 Vienna, Austria; (W.L.); (W.H.); (E.E.); (M.S.)
- Bioforschung Austria, Esslinger Hauptstrasse 132-134, A-1220 Vienna, Austria
| | - Monika Sobotik
- Austrian Society of Root Research, Muthgasse 18, A-1190 Vienna, Austria; (W.L.); (W.H.); (E.E.); (M.S.)
- Pflanzensoziologisches Institut, Pichlern 9, A-4822 Bad Goisern, Austria
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80
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Belachew KY, Nagel KA, Poorter H, Stoddard FL. Association of Shoot and Root Responses to Water Deficit in Young Faba Bean ( Vicia faba L.) Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:1063. [PMID: 31552067 PMCID: PMC6738164 DOI: 10.3389/fpls.2019.01063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 08/06/2019] [Indexed: 05/06/2023]
Abstract
Water deficit may occur at any stage of plant growth, with any intensity and duration. Phenotypic acclimation and the mechanism of adaptation vary with the evolutionary background of germplasm accessions and their stage of growth. Faba bean is considered sensitive to various kinds of drought. Hence, we conducted a greenhouse experiment in rhizotrons under contrasting watering regimes to explore shoot and root traits and drought avoidance mechanisms in young faba bean plants. Eight accessions were investigated for shoot and root morphological and physiological responses in two watering conditions with four replications. Pre-germinated seedlings were transplanted into rhizotron boxes filled with either air-dried or moist peat. The water-limited plants received 50-ml water at transplanting and another 50-ml water 4 days later, then no water was given until the end of the experimental period, 24 days after transplanting. The well-watered plants received 100 ml of water every 12 h throughout the experimental period. Root, stem, and leaf dry mass, their mass fractions, their dry matter contents, apparent specific root length and density, stomatal conductance, SPAD value, and Fv/Fm were recorded. Water deficit resulted in 3-4-fold reductions in shoot biomass, root biomass, and stomatal conductance along with 1.2-1.4-fold increases in leaf and stem dry matter content and SPAD values. Total dry mass and apparent root length density showed accession by treatment interactions. Accessions DS70622, DS11320, and ILB938/2 shared relatively high values of total dry mass and low values of stomatal conductance under water deficit but differed in root distribution parameters. In both treatments, DS70622 was characterized by finer roots that were distributed in both depth and width, whereas DS11320 and ILB938/2 produced less densely growing, thicker roots. French accession Mélodie/2 was susceptible to drought in the vegetative phase, in contrast to previous results from the flowering phase, showing the importance of timing of drought stress on the measured response. Syrian accession DS70622 explored the maximum root volume and maintained its dry matter production, with the difference from the other accessions being particularly large in the water-limited treatment, so it is a valuable source of traits for avoiding transient drought.
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Affiliation(s)
- Kiflemariam Y. Belachew
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
- Department of Plant Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - Kerstin A. Nagel
- IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Hendrik Poorter
- IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Frederick L. Stoddard
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
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81
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Jiang N, Floro E, Bray AL, Laws B, Duncan KE, Topp CN. Three-Dimensional Time-Lapse Analysis Reveals Multiscale Relationships in Maize Root Systems with Contrasting Architectures. THE PLANT CELL 2019; 31:1708-1722. [PMID: 31123089 DOI: 10.1101/381046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/08/2019] [Accepted: 07/01/2019] [Indexed: 05/28/2023]
Abstract
Understanding how an organism's phenotypic traits are conditioned by genetic and environmental variation is a central goal of biology. Root systems are one of the most important but poorly understood aspects of plants, largely due to the three-dimensional (3D), dynamic, and multiscale phenotyping challenge they pose. A critical gap in our knowledge is how root systems build in complexity from a single primary root to a network of thousands of roots that collectively compete for ephemeral, heterogeneous soil resources. We used time-lapse 3D imaging and mathematical modeling to assess root system architectures (RSAs) of two maize (Zea mays) inbred genotypes and their hybrid as they grew in complexity from a few to many roots. Genetically driven differences in root branching zone size and lateral branching densities along a single root, combined with differences in peak growth rate and the relative allocation of carbon resources to new versus existing roots, manifest as sharply distinct global RSAs over time. The 3D imaging of mature field-grown root crowns showed that several genetic differences in seedling architectures could persist throughout development and across environments. This approach connects individual and system-wide scales of root growth dynamics, which could eventually be used to predict genetic variation for complex RSAs and their functions.
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Affiliation(s)
- Ni Jiang
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Eric Floro
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Adam L Bray
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211
| | - Benjamin Laws
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Keith E Duncan
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
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Dodig D, Božinović S, Nikolić A, Zorić M, Vančetović J, Ignjatović-Micić D, Delić N, Weigelt-Fischer K, Junker A, Altmann T. Image-Derived Traits Related to Mid-Season Growth Performance of Maize Under Nitrogen and Water Stress. FRONTIERS IN PLANT SCIENCE 2019; 10:814. [PMID: 31297124 PMCID: PMC6607059 DOI: 10.3389/fpls.2019.00814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 06/06/2019] [Indexed: 06/09/2023]
Abstract
Phenotypic measurements under controlled cultivation conditions are essential to gain a mechanistic understanding of plant responses to environmental impacts and thus for knowledge-based improvement of their performance under natural field conditions. Twenty maize inbred lines (ILs) were phenotyped in response to two levels of water and nitrogen supply (control and stress) and combined nitrogen and water deficit. Over a course of 5 weeks (from about 4-leaf stage to the beginning of the reproductive stage), maize phenology and growth were monitored by using a high-throughput phenotyping platform for daily acquisition of images in different spectral ranges. The focus of the present study is on the measurements taken at the time of maximum water stress (for traits that reflect plant physiological properties) and at the end of the experiment (for traits that reflect plant architectural and biomass-related traits). Twenty-five phenotypic traits extracted from the digital image data that support biological interpretation of plant growth were selected for their predictive value for mid-season shoot biomass accumulation. Measured fresh and dry weights after harvest were used to calculate various indices (water-use efficiency, physiological nitrogen-use efficiency, specific plant weight) and to establish correlations with image-derived phenotypic features. Also, score indices based on dry weight were used to identify contrasting ILs in terms of productivity and tolerance to stress, and their means for image-derived and manually measured traits were compared. Color-related traits appear to be indicative of plant performance and photosystem II operating efficiency might be an importance physiological parameter of biomass accumulation, particularly under severe stress conditions. Also, genotypes showing greater leaf area may be better adapted to abiotic stress conditions.
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Affiliation(s)
- Dejan Dodig
- Department for Research and Development, Maize Research Institute Zemun Polje, Belgrade, Serbia
| | - Sofija Božinović
- Department for Research and Development, Maize Research Institute Zemun Polje, Belgrade, Serbia
| | - Ana Nikolić
- Department for Research and Development, Maize Research Institute Zemun Polje, Belgrade, Serbia
| | - Miroslav Zorić
- Department for Maize, Institute of Field and Vegetable Crops, Novi Sad, Serbia
| | - Jelena Vančetović
- Department for Research and Development, Maize Research Institute Zemun Polje, Belgrade, Serbia
| | | | - Nenad Delić
- Department for Research and Development, Maize Research Institute Zemun Polje, Belgrade, Serbia
| | - Kathleen Weigelt-Fischer
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Astrid Junker
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Thomas Altmann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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83
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Betegón‐Putze I, González A, Sevillano X, Blasco‐Escámez D, Caño‐Delgado AI. MyROOT: a method and software for the semiautomatic measurement of primary root length in Arabidopsis seedlings. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:1145-1156. [PMID: 30809923 PMCID: PMC6618301 DOI: 10.1111/tpj.14297] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 02/18/2019] [Accepted: 02/19/2019] [Indexed: 05/05/2023]
Abstract
Root analysis is essential for both academic and agricultural research. Despite the great advances in root phenotyping and imaging, calculating root length is still performed manually and involves considerable amounts of labor and time. To overcome these limitations, we developed MyROOT, a software for the semiautomatic quantification of root growth of seedlings growing directly on agar plates. Our method automatically determines the scale from the image of the plate, and subsequently measures the root length of the individual plants. To this aim, MyROOT combines a bottom-up root tracking approach with a hypocotyl detection algorithm. At the same time as providing accurate root measurements, MyROOT also significantly minimizes the user intervention required during the process. Using Arabidopsis, we tested MyROOT with seedlings from different growth stages and experimental conditions. When comparing the data obtained from this software with that of manual root measurements, we found a high correlation between both methods (R2 = 0.997). When compared with previous developed software with similar features (BRAT and EZ-Rhizo), MyROOT offered an improved accuracy for root length measurements. Therefore, MyROOT will be of great use to the plant science community by permitting high-throughput root length measurements while saving both labor and time.
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Affiliation(s)
- Isabel Betegón‐Putze
- Department of Molecular GeneticsCenter for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus UAB, Bellaterra (Cerdanyola del Vallès)08193BarcelonaSpain
| | - Alejandro González
- GTM‐ Grup de Recerca en Tecnologies Mèdia, La SalleUniversitat Ramon Llull08022BarcelonaSpain
| | - Xavier Sevillano
- GTM‐ Grup de Recerca en Tecnologies Mèdia, La SalleUniversitat Ramon Llull08022BarcelonaSpain
| | - David Blasco‐Escámez
- Department of Molecular GeneticsCenter for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus UAB, Bellaterra (Cerdanyola del Vallès)08193BarcelonaSpain
| | - Ana I. Caño‐Delgado
- Department of Molecular GeneticsCenter for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBCampus UAB, Bellaterra (Cerdanyola del Vallès)08193BarcelonaSpain
- Present address:
Department of Molecular GeneticsCentre de Recerca en Agrigenòmica (CRAG) CSIC‐IRTA‐UAB‐UBCampus UAB, Bellaterra (Cerdanyola del Vallès)E‐08193BarcelonaSpain
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Svane SF, Jensen CS, Thorup-Kristensen K. Construction of a large-scale semi-field facility to study genotypic differences in deep root growth and resources acquisition. PLANT METHODS 2019; 15:26. [PMID: 30930953 PMCID: PMC6425565 DOI: 10.1186/s13007-019-0409-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/06/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Roots are vital organs for plants, and the effective use of resources from the soil is important for yield stability. However, phenotypic variation in root traits among crop genotypes is mostly unknown and field screening of root development is costly and labour demanding. As a consequence, new methods are needed to investigate root traits of fully grown crops under field conditions, particularly roots in the deeper soil horizons. RESULTS We developed a new phenotyping facility (RadiMax) for the study of root growth and soil resource acquisition under semi-field conditions. The facility consists of 4 units each covering 400 m2 and containing 150 minirhizotrons, allowing root observation in the 0.4 m-1.8 m or 0.7 m-2.8 m soil depth interval. Roots are observed through minirhizotrons using a multispectral imaging system. Plants are grown in rows perpendicular to a water stress gradient created by a multi-depth sub-irrigation system and movable rainout shelters. The water stress gradient allows for a direct link between root observations and the development of stress response in the canopy. CONCLUSION To test the concept and technical features, selected spring barley (Hordeum vulgare L.) cultivars were grown in the system for two seasons. The system enabled genotypic differences for deep root growth to be observed, and clear aboveground physiological response was also visible along the water stress gradient. Although further technical development and field validation are ongoing, the semi-field facility concept offers novel possibilities for characterising genotypic differences in the effective use of soil resources in deeper soil layers.
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Affiliation(s)
- Simon Fiil Svane
- Department of Plant and Environmental Science, University of Copenhagen, 1871 Frederiksberg, Denmark
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85
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Abstract
Agricultural scientists face the dual challenge of breeding input-responsive, widely adoptable and climate-resilient varieties of crop plants and developing such varieties at a faster pace. Integrating the gains of genomics with modern-day phenomics will lead to increased breeding efficiency which in turn offers great promise to develop such varieties rapidly. Plant phenotyping techniques have impressively evolved during the last two decades. The low-cost, automated and semi-automated methods for data acquisition, storage and analysis are now available which allow precise quantitative analysis of plant structure and function; and genetic dissection of complex traits. Appropriate plant types can now be quickly developed that respond favorably to low input and resource-limited environments and address the challenges of subsistence agriculture. The present review focuses on the need of systematic, rapid, minimal invasive and low-cost plant phenotyping. It also discusses its evolution to modern day high throughput phenotyping (HTP), traits amenable to HTP, integration of HTP with genomics and the scope of utilizing these tools for crop improvement.
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86
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Duque LO, Villordon A. Root Branching and Nutrient Efficiency: Status and Way Forward in Root and Tuber Crops. FRONTIERS IN PLANT SCIENCE 2019; 10:237. [PMID: 30886622 PMCID: PMC6409306 DOI: 10.3389/fpls.2019.00237] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/12/2019] [Indexed: 05/08/2023]
Abstract
Plants are immobile organisms that require roots to efficiently and cost-effectively exploit their habitat for water and nutrients. Plant root systems are dynamic structures capable of altering root branching, root angle, and root growth rates determining overall architecture. This plasticity involves belowground plant-root mediated synergies coupled through a continuum of environmental interactions and endogenous developmental processes facilitating plants to adapt to favorable or adverse soil conditions. Plant root branching is paramount to ensure adequate access to soil water and nutrients. Although substantial resources have been devoted toward this goal, significant knowledge gaps exist. In well-studied systems such as rice and maize, it has become evident that root branching plays a significant role in the acquisition of nutrients and other soil-based resources. In these crop species, specific root branching traits that confer enhanced nutrient acquisition are well-characterized and are already being incorporated into breeding populations. In contrast, the understanding of root branching in root and tuber crop productivity has lagged behind. In this review article, we highlight what is known about root branching in root and tuber crops (RTCs) and mark new research directions, such as the use novel phenotyping methods, examining the changes in root morphology and anatomy under nutrient stress, and germplasm screening with enhanced root architecture for more efficient nutrient capture. These directions will permit a better understanding of the interaction between root branching and nutrient acquisition in these globally important crop species.
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Affiliation(s)
- Luis O. Duque
- Department of Plant Science, The Pennsylvania State University, University Park, PA, United States
| | - Arthur Villordon
- Sweet Potato Research Station, Louisiana State University Agricultural Center, Chase, LA, United States
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87
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Atkinson JA, Pound MP, Bennett MJ, Wells DM. Uncovering the hidden half of plants using new advances in root phenotyping. Curr Opin Biotechnol 2019; 55:1-8. [PMID: 30031961 PMCID: PMC6378649 DOI: 10.1016/j.copbio.2018.06.002] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/06/2018] [Accepted: 06/15/2018] [Indexed: 11/08/2022]
Abstract
Major increases in crop yield are required to keep pace with population growth and climate change. Improvements to the architecture of crop roots promise to deliver increases in water and nutrient use efficiency but profiling the root phenome (i.e. its structure and function) represents a major bottleneck. We describe how advances in imaging and sensor technologies are making root phenomic studies possible. However, methodological advances in acquisition, handling and processing of the resulting 'big-data' is becoming increasingly important. Advances in automated image analysis approaches such as Deep Learning promise to transform the root phenotyping landscape. Collectively, these innovations are helping drive the selection of the next-generation of crops to deliver real world impact for ongoing global food security efforts.
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Affiliation(s)
| | - Michael P Pound
- School of Biosciences, University of Nottingham, Sutton Bonington, UK; School of Computer Science, University of Nottingham, Nottingham, UK
| | - Malcolm J Bennett
- School of Biosciences, University of Nottingham, Sutton Bonington, UK.
| | - Darren M Wells
- School of Biosciences, University of Nottingham, Sutton Bonington, UK.
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88
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Neveu P, Tireau A, Hilgert N, Nègre V, Mineau‐Cesari J, Brichet N, Chapuis R, Sanchez I, Pommier C, Charnomordic B, Tardieu F, Cabrera‐Bosquet L. Dealing with multi-source and multi-scale information in plant phenomics: the ontology-driven Phenotyping Hybrid Information System. THE NEW PHYTOLOGIST 2019; 221:588-601. [PMID: 30152011 PMCID: PMC6585972 DOI: 10.1111/nph.15385] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/07/2018] [Indexed: 05/13/2023]
Abstract
Phenomic datasets need to be accessible to the scientific community. Their reanalysis requires tracing relevant information on thousands of plants, sensors and events. The open-source Phenotyping Hybrid Information System (PHIS) is proposed for plant phenotyping experiments in various categories of installations (field, glasshouse). It unambiguously identifies all objects and traits in an experiment and establishes their relations via ontologies and semantics that apply to both field and controlled conditions. For instance, the genotype is declared for a plant or plot and is associated with all objects related to it. Events such as successive plant positions, anomalies and annotations are associated with objects so they can be easily retrieved. Its ontology-driven architecture is a powerful tool for integrating and managing data from multiple experiments and platforms, for creating relationships between objects and enriching datasets with knowledge and metadata. It interoperates with external resources via web services, thereby allowing data integration into other systems; for example, modelling platforms or external databases. It has the potential for rapid diffusion because of its ability to integrate, manage and visualize multi-source and multi-scale data, but also because it is based on 10 yr of trial and error in our groups.
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Affiliation(s)
- Pascal Neveu
- MISTEA, INRA, Montpellier SupAgro, Université de MontpellierMontpellier34060France
| | - Anne Tireau
- MISTEA, INRA, Montpellier SupAgro, Université de MontpellierMontpellier34060France
| | - Nadine Hilgert
- MISTEA, INRA, Montpellier SupAgro, Université de MontpellierMontpellier34060France
| | - Vincent Nègre
- LEPSE, INRA, Montpellier SupAgro, Université de MontpellierMontpellier34060France
| | - Jonathan Mineau‐Cesari
- MISTEA, INRA, Montpellier SupAgro, Université de MontpellierMontpellier34060France
- LEPSE, INRA, Montpellier SupAgro, Université de MontpellierMontpellier34060France
| | - Nicolas Brichet
- LEPSE, INRA, Montpellier SupAgro, Université de MontpellierMontpellier34060France
| | - Romain Chapuis
- UE DIASCOPE, INRA, Montpellier SupAgro, Université de MontpellierMontpellier34060France
| | - Isabelle Sanchez
- MISTEA, INRA, Montpellier SupAgro, Université de MontpellierMontpellier34060France
| | - Cyril Pommier
- INRA, UR1164 URGI – Research Unit in Genomics‐InfoINRA de Versailles‐GrignonRoute de Saint‐CyrVersailles78026France
| | | | - François Tardieu
- LEPSE, INRA, Montpellier SupAgro, Université de MontpellierMontpellier34060France
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89
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Koch G, Rolland G, Dauzat M, Bédiée A, Baldazzi V, Bertin N, Guédon Y, Granier C. Are compound leaves more complex than simple ones? A multi-scale analysis. ANNALS OF BOTANY 2018; 122:1173-1185. [PMID: 29982438 PMCID: PMC6324747 DOI: 10.1093/aob/mcy116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 06/06/2018] [Indexed: 06/08/2023]
Abstract
Background and Aims The question of which cellular mechanisms determine the variation in leaf size has been addressed mainly in plants with simple leaves. It is addressed here in tomato taking into consideration the expected complexity added by the several lateral appendages making up the compound leaf, the leaflets. Methods Leaf and leaflet areas, epidermal cell number and areas, and endoreduplication (co-) variations were analysed in Solanum lycopersicum considering heteroblastic series in a wild type (Wva106) and an antisense mutant, the Pro35S:Slccs52AAS line, and upon drought treatments. All plants were grown in an automated phenotyping platform, PHENOPSIS, adapted to host plants grown in 7 L pots. Key Results Leaf area, leaflet area and cell number increased with leaf rank until reaching a plateau. In contrast, cell area slightly decreased and endoreduplication did not follow any trend. In the transgenic line, leaf area, leaflet areas and cell number of basal leaves were lower than in the wild type, but higher in upper leaves. Reciprocally, cell area was higher in basal leaves and lower in upper leaves. When scaled up at the whole sympodial unit, all these traits did not differ significantly between the transgenic line and the wild type. In response to drought, leaf area was reduced, with a clear dose effect that was also reported for all size-related traits, including endoreduplication. Conclusions These results provide evidence that all leaflets have the same cellular phenotypes as the leaf they belong to. Consistent with results reported for simple leaves, they show that cell number rather than cell size determines the final leaf areas and that endoreduplication can be uncoupled from leaf and cell sizes. Finally, they re-question a whole-plant control of cell division and expansion in leaves when the Wva106 and the Pro35S:Slccs52AAS lines are compared.
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Affiliation(s)
- Garance Koch
- LEPSE, Université de Montpellier, INRA, Montpellier SupAgro, Montpellier, France
- INRA, UR PSH, Avignon, France
| | - Gaëlle Rolland
- LEPSE, Université de Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Myriam Dauzat
- LEPSE, Université de Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Alexis Bédiée
- LEPSE, Université de Montpellier, INRA, Montpellier SupAgro, Montpellier, France
| | - Valentina Baldazzi
- INRA, UR PSH, Avignon, France
- ISA, INRA, CNRS, Université Côte d’Azur, France
- BIOCORE, Inria, INRA, CNRS, UPMC Université de Paris 06, Université Côte d’Azur, France
| | | | - Yann Guédon
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Christine Granier
- LEPSE, Université de Montpellier, INRA, Montpellier SupAgro, Montpellier, France
- AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
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90
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Bodner G, Nakhforoosh A, Arnold T, Leitner D. Hyperspectral imaging: a novel approach for plant root phenotyping. PLANT METHODS 2018; 14:84. [PMID: 30305838 PMCID: PMC6169016 DOI: 10.1186/s13007-018-0352-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/24/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Root phenotyping aims to characterize root system architecture because of its functional role in resource acquisition. RGB imaging and analysis procedures measure root system traits via colour contrasts between roots and growth media or artificial backgrounds. In the case of plants grown in soil-filled rhizoboxes, where the colour contrast can be poor, it is hypothesized that root imaging based on spectral signatures improves segmentation and provides additional knowledge on physico-chemical root properties. RESULTS Root systems of Triticum durum grown in soil-filled rhizoboxes were scanned in a spectral range of 1000-1700 nm with 222 narrow bands and a spatial resolution of 0.1 mm. A data processing pipeline was developed for automatic root segmentation and analysis of spectral root signatures. Spectral- and RGB-based root segmentation did not significantly differ in accuracy even for a bright soil background. Best spectral segmentation was obtained from log-linearized and asymptotic least squares corrected images via fuzzy clustering and multilevel thresholding. Root axes revealed major spectral distinction between center and border regions. Root decay was captured by an exponential function of the difference spectra between water and structural carbon absorption regions. CONCLUSIONS Fundamentals for root phenotyping using hyperspectral imaging have been established by means of an image processing pipeline for automated segmentation of soil-grown plant roots at a high spatial resolution and for the exploration of spectral signatures encoding physico-chemical root zone properties.
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Affiliation(s)
- Gernot Bodner
- Division of Agronomy, Department of Crop Sciences, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
| | - Alireza Nakhforoosh
- Division of Agronomy, Department of Crop Sciences, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
- Agriculture and Agri-Food Canada, Brandon Research and Development Centre, Brandon, MB R7A 5Y3 Canada
| | - Thomas Arnold
- Carinthian Tech Research AG, Europastraße 12, High Tech Campus Villach, 9524 Villach/St. Magdalen, Austria
| | - Daniel Leitner
- Computational Science Center, University of Vienna, Oskar-Morgenstern-Platz 1, 1090 Vienna, Austria
- Simulationswerkstatt, Ortmayrstrasse 20, 4060 Leonding, Austria
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91
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Scott GD, Baddeley JA, Watson CA, Robinson D. Demographic quantification of carbon and nitrogen dynamics associated with root turnover in white clover. PLANT, CELL & ENVIRONMENT 2018; 41:2045-2056. [PMID: 29323411 DOI: 10.1111/pce.13142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 01/04/2018] [Accepted: 01/04/2018] [Indexed: 06/07/2023]
Abstract
As well as capturing resources, roots lose resources during their lives. We quantified carbon (C) and nitrogen (N) losses associated with root turnover in white clover (Trifolium repens L.). We grew contrasting cultivars for 18 weeks in soil microcosms. Using repeated in situ observations, destructive sampling, and demographic analysis, we measured changes in C and N concentrations in dry matter of 1st- or 2nd-order (terminal) roots to derive C and N fluxes into and out of root cohorts. C and N fluxes from roots during turnover depended on cohort age and order. Ninety per cent of losses occurred from 2nd-order cohorts younger than 18 weeks. Losses were greater from roots of the larger, faster growing cultivar Alice than from the smaller lower yielding cultivar S184. C:N ratios of roots and lost material were similar within each order and between cultivars but smaller in 2nd- compared with 1st-order roots. C and N losses during root turnover could be equivalent to at least 6% of aboveground dry matter production in S184 and 12% in Alice at the field scale. C and N losses associated with root turnover will have potentially significant and previously unrecognized impacts on crop productivity, resource dynamics, and long-term soil fertility.
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Affiliation(s)
- Gavin D Scott
- Crop and Soil Systems, SRUC, Craibstone Estate, Aberdeen, AB21 9YA, UK
- Institute of Biological and Environmental Research, School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - John A Baddeley
- Crop and Soil Systems, SRUC, Craibstone Estate, Aberdeen, AB21 9YA, UK
| | | | - David Robinson
- Institute of Biological and Environmental Research, School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
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92
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Micromechanics of root development in soil. Curr Opin Genet Dev 2018; 51:18-25. [DOI: 10.1016/j.gde.2018.03.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/04/2018] [Accepted: 03/08/2018] [Indexed: 11/17/2022]
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93
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Sundgren TK, Uhlen AK, Lillemo M, Briese C, Wojciechowski T. Rapid seedling establishment and a narrow root stele promotes waterlogging tolerance in spring wheat. JOURNAL OF PLANT PHYSIOLOGY 2018; 227:45-55. [PMID: 29735176 DOI: 10.1016/j.jplph.2018.04.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/10/2018] [Accepted: 04/16/2018] [Indexed: 05/11/2023]
Abstract
Improving the waterlogging tolerance of wheat varieties could alleviate yield constraints caused by excessive rain and poor soil drainage. In this study, we investigated root and shoot growth as well as anatomical traits of six spring wheat genotypes with contrasting waterlogging tolerance properties. Our aim was to identify root traits that differentiate tolerant from sensitive genotypes. Two experiments were conducted using rhizoboxes and photography for data acquisition. In experiment one, root growth of the genotypes was studied during seedling establishment and a subsequent waterlogging treatment, starting at the 3-leaf stage and maintained for seven days. In the second experiment, root and shoot growth of previously waterlogged plants was compared between the genotypes during seven days of recovery. At harvest of experiment two, root segments were sampled to investigate genotype differences of root cross sectional area, root cortex area, stele area and percentage of aerenchyma. The results show that tolerant, in contrast to sensitive genotypes, developed seminal roots faster in the seedling establishment phase and more nodal roots during the waterlogging treatment. NK93602 and Bjarne were the best performing genotypes. Bjarne in particular had a narrower relative stele size of nodal (13.4%) and seminal roots (11.7%) compared to other genotypes (e.g. 16.3% in nodal roots and 13.9% in seminal roots of sensitive Quarna). The results from this study suggests that early vigor is an important trait for waterlogging tolerance in the field. Anatomical root traits, such as a narrow stele and aerenchyma may contribute to improving waterlogging tolerance furthermore.
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Affiliation(s)
- Tove Kristina Sundgren
- Faculty of Biosciences, Department of Plant Sciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Anne Kjersti Uhlen
- Faculty of Biosciences, Department of Plant Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Morten Lillemo
- Faculty of Biosciences, Department of Plant Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Christoph Briese
- IBG-2 (Plant Sciences), Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany
| | - Tobias Wojciechowski
- IBG-2 (Plant Sciences), Forschungszentrum Jülich, Wilhelm-Johnen-Straße, Jülich, Germany
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94
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Nabel M, Schrey SD, Poorter H, Koller R, Nagel KA, Temperton VM, Dietrich CC, Briese C, Jablonowski ND. Coming Late for Dinner: Localized Digestate Depot Fertilization for Extensive Cultivation of Marginal Soil With Sida hermaphrodita. FRONTIERS IN PLANT SCIENCE 2018; 9:1095. [PMID: 30131816 PMCID: PMC6090160 DOI: 10.3389/fpls.2018.01095] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/06/2018] [Indexed: 06/08/2023]
Abstract
Improving fertility of marginal soils for the sustainable production of biomass is a strategy for reducing land use conflicts between food and energy crops. Digestates can be used as fertilizer and for soil amelioration. In order to promote plant growth and reduce potential adverse effects on roots because of broadcast digestate fertilization, we propose to apply local digestate depots placed into the rhizosphere. We grew Sida hermaphrodita in large mesocosms outdoors for three growing seasons and in rhizotrons in the greenhouse for 3 months both filled with marginal substrate, including multiple sampling dates. We compared digestate broadcast application with digestate depot fertilization and a mineral fertilizer control. We show that depot fertilization promotes a deep reaching root system of S. hermaphrodita seedlings followed by the formation of a dense root cluster around the depot-fertilized zone, resulting in a fivefold increased biomass yield. Temporal adverse effects on root growth were linked to high initial concentrations of ammonium and nitrite in the rhizosphere in either fertilizer application, followed by a high biomass increase after its microbial conversion to nitrate. We conclude that digestate depot fertilization can contribute to an improved cultivation of perennial energy-crops on marginal soils.
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Affiliation(s)
- Moritz Nabel
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Silvia D. Schrey
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Hendrik Poorter
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Robert Koller
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Kerstin A. Nagel
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | | | - Charlotte C. Dietrich
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Christoph Briese
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Nicolai D. Jablonowski
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
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95
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Tardieu F, Cabrera-Bosquet L, Pridmore T, Bennett M. Plant Phenomics, From Sensors to Knowledge. Curr Biol 2018; 27:R770-R783. [PMID: 28787611 DOI: 10.1016/j.cub.2017.05.055] [Citation(s) in RCA: 226] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Major improvements in crop yield are needed to keep pace with population growth and climate change. While plant breeding efforts have greatly benefited from advances in genomics, profiling the crop phenome (i.e., the structure and function of plants) associated with allelic variants and environments remains a major technical bottleneck. Here, we review the conceptual and technical challenges facing plant phenomics. We first discuss how, given plants' high levels of morphological plasticity, crop phenomics presents distinct challenges compared with studies in animals. Next, we present strategies for multi-scale phenomics, and describe how major improvements in imaging, sensor technologies and data analysis are now making high-throughput root, shoot, whole-plant and canopy phenomic studies possible. We then suggest that research in this area is entering a new stage of development, in which phenomic pipelines can help researchers transform large numbers of images and sensor data into knowledge, necessitating novel methods of data handling and modelling. Collectively, these innovations are helping accelerate the selection of the next generation of crops more sustainable and resilient to climate change, and whose benefits promise to scale from physiology to breeding and to deliver real world impact for ongoing global food security efforts.
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Affiliation(s)
- François Tardieu
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, F34060, Montpellier, France.
| | - Llorenç Cabrera-Bosquet
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, F34060, Montpellier, France
| | - Tony Pridmore
- School of Computer Science, University of Nottingham, NG8 1BB, UK
| | - Malcolm Bennett
- Plant & Crop Sciences, School of Biosciences, University of Nottingham, LE12 3RD, UK.
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96
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Image-Based On-Panicle Rice [Oryza sativa L.] Grain Counting with a Prior Edge Wavelet Correction Model. AGRONOMY-BASEL 2018. [DOI: 10.3390/agronomy8060091] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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97
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Wu J, Wu Q, Pagès L, Yuan Y, Zhang X, Du M, Tian X, Li Z. RhizoChamber-Monitor: a robotic platform and software enabling characterization of root growth. PLANT METHODS 2018; 14:44. [PMID: 29930694 PMCID: PMC5991437 DOI: 10.1186/s13007-018-0316-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 06/02/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND In order to efficiently determine genotypic differences in rooting patterns of crops, novel hardware and software are needed simultaneously to characterize dynamics of root development. RESULTS We describe a prototype robotic monitoring platform-the RhizoChamber-Monitor for analyzing growth patterns of plant roots automatically. The RhizoChamber-Monitor comprises an automatic imaging system for acquiring sequential images of roots which grow on a cloth substrate in custom rhizoboxes, an automatic irrigation system and a flexible shading arrangement. A customized image processing software was developed to analyze the spatio-temporal dynamics of root growth from time-course images of multiple plants. This software can quantify overall growth of roots and extract detailed growth traits (e.g. dynamics of length and diameter) of primary roots and of individual lateral roots automatically. It can also identify local growth traits of lateral roots (pseudo-mean-length and pseudo-maximum-length) semi-automatically. Two cotton genotypes were used to test both the physical platform and the analysis software. CONCLUSIONS The combination of hardware and software is expected to facilitate quantification of root geometry and its spatio-temporal growth patterns, and therefore to provide opportunities for high-throughput root phenotyping in support of crop breeding to optimize root architecture.
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Affiliation(s)
- Jie Wu
- State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Cultivation and Farming System, Center of Crop Chemical Control, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
- Present Address: Plant Phenomics Research Center, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Qian Wu
- State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Cultivation and Farming System, Center of Crop Chemical Control, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Loïc Pagès
- INRA, UR 1115 PSH, Site Agroparc, 84914 Avignon Cedex 9, France
| | - Yeqing Yuan
- State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Cultivation and Farming System, Center of Crop Chemical Control, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Xiaolei Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Cultivation and Farming System, Center of Crop Chemical Control, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Mingwei Du
- State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Cultivation and Farming System, Center of Crop Chemical Control, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Xiaoli Tian
- State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Cultivation and Farming System, Center of Crop Chemical Control, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Zhaohu Li
- State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Cultivation and Farming System, Center of Crop Chemical Control, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
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98
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Nepolean T, Kaul J, Mukri G, Mittal S. Genomics-Enabled Next-Generation Breeding Approaches for Developing System-Specific Drought Tolerant Hybrids in Maize. FRONTIERS IN PLANT SCIENCE 2018; 9:361. [PMID: 29696027 PMCID: PMC5905169 DOI: 10.3389/fpls.2018.00361] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/05/2018] [Indexed: 05/28/2023]
Abstract
Breeding science has immensely contributed to the global food security. Several varieties and hybrids in different food crops including maize have been released through conventional breeding. The ever growing population, decreasing agricultural land, lowering water table, changing climate, and other variables pose tremendous challenge to the researchers to improve the production and productivity of food crops. Drought is one of the major problems to sustain and improve the productivity of food crops including maize in tropical and subtropical production systems. With advent of novel genomics and breeding tools, the way of doing breeding has been tremendously changed in the last two decades. Drought tolerance is a combination of several component traits with a quantitative mode of inheritance. Rapid DNA and RNA sequencing tools and high-throughput SNP genotyping techniques, trait mapping, functional characterization, genomic selection, rapid generation advancement, and other tools are now available to understand the genetics of drought tolerance and to accelerate the breeding cycle. Informatics play complementary role by managing the big-data generated from the large-scale genomics and breeding experiments. Genome editing is the latest technique to alter specific genes to improve the trait expression. Integration of novel genomics, next-generation breeding, and informatics tools will accelerate the stress breeding process and increase the genetic gain under different production systems.
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Affiliation(s)
- Thirunavukkarsau Nepolean
- Maize Research Lab, Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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99
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Tandonnet JP, Marguerit E, Cookson SJ, Ollat N. Genetic architecture of aerial and root traits in field-grown grafted grapevines is largely independent. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:903-915. [PMID: 29305700 DOI: 10.1007/s00122-017-3046-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/21/2017] [Indexed: 05/21/2023]
Abstract
QTLs were identified for traits assessed on field-grown grafted grapevines. Root number and section had the largest phenotypic variance explained. Genetic control of root and aerial traits was independent. Breeding new rootstocks for perennial crops remains challenging, mainly because of the number of desirable traits which have to be combined, these traits include good rooting ability and root development. Consequently, the present study analyzes the genetic architecture of root traits in grapevine. A segregating progeny of 138 F1 genotypes issued from an inter-specific cross between Vitis vinifera cv. Cabernet-Sauvignon × V. riparia cv. Gloire de Montpellier, used as rootstock, was phenotyped in grafted plants grown for 2 years in the field. Seven traits, related to aerial and root development, were quantified. Heritability ranged between 0.44 for aerial biomass to 0.7 for root number. Total root number was related to the number of fine roots, while root biomass was related to the number of coarse roots. Significant quantitative trait loci (QTLs) were identified for all the traits studied with some of them explaining approximately 20% of phenotypic variance. Only a single QTL co-localized for root and aerial biomass. Identified QTLs for aerial-to-root biomass ratio suggest that aerial and root traits are controlled independently. Genes known to be involved in auxin signaling pathways and phosphorus nutrition, whose orthologues were previously shown to regulate root development in Arabidopsis, were located in the confidence intervals of several QTLs. This study opens new perspectives for breeding rootstocks with improved root development capacities.
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Affiliation(s)
- Jean-Pascal Tandonnet
- EGFV, Bordeaux Sciences Agro, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France
| | - Elisa Marguerit
- EGFV, Bordeaux Sciences Agro, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France
| | - Sarah J Cookson
- EGFV, Bordeaux Sciences Agro, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France
| | - Nathalie Ollat
- EGFV, Bordeaux Sciences Agro, INRA, University of Bordeaux, 33140, Villenave d'Ornon, France.
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100
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Canto CDLF, Kalogiros DI, Ptashnyk M, George TS, Waugh R, Bengough AG, Russell J, Dupuy LX. Morphological and genetic characterisation of the root system architecture of selected barley recombinant chromosome substitution lines using an integrated phenotyping approach. J Theor Biol 2018; 447:84-97. [PMID: 29559229 DOI: 10.1016/j.jtbi.2018.03.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/12/2018] [Accepted: 03/13/2018] [Indexed: 11/27/2022]
Abstract
Discoveries on the genetics of resource acquisition efficiency are limited by the ability to measure plant roots in sufficient number and with adequate genotypic variability. This paper presents a root phenotyping study that explores ways to combine live imaging and computer algorithms for model-based extraction of root growth parameters. The study is based on a subset of barley Recombinant Chromosome Substitution Lines (RCSLs) and a combinatorial approach was designed for fast identification of the regions of the genome that contribute the most to variations in root system architecture (RSA). Results showed there was a strong genotypic variation in root growth parameters within the set of genotypes studied. The chromosomal regions associated with primary root growth differed from the regions of the genome associated with changes in lateral root growth. The concepts presented here are discussed in the context of identifying root QTL and its potential to assist breeding for novel crops with improved root systems.
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Affiliation(s)
- C De La Fuente Canto
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom ; School of Life Sciences, University of Dundee, Dundee DD2 1PP, United Kingdom
| | - D I Kalogiros
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom ; School of Science and Engineering, University of Dundee, Dundee DD2 1PP, United Kingdom
| | - M Ptashnyk
- School of Science and Engineering, University of Dundee, Dundee DD2 1PP, United Kingdom
| | - T S George
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - R Waugh
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - A G Bengough
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom ; School of Science and Engineering, University of Dundee, Dundee DD2 1PP, United Kingdom
| | - J Russell
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - L X Dupuy
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom .
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