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Wang Z, Yung WS, Gao Y, Huang C, Zhao X, Chen Y, Li MW, Lam HM. From phenotyping to genetic mapping: identifying water-stress adaptations in legume root traits. BMC PLANT BIOLOGY 2024; 24:749. [PMID: 39103780 DOI: 10.1186/s12870-024-05477-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 08/01/2024] [Indexed: 08/07/2024]
Abstract
BACKGROUND Climate change induces perturbation in the global water cycle, profoundly impacting water availability for agriculture and therefore global food security. Water stress encompasses both drought (i.e. water scarcity) that causes the drying of soil and subsequent plant desiccation, and flooding, which results in excess soil water and hypoxia for plant roots. Terrestrial plants have evolved diverse mechanisms to cope with soil water stress, with the root system serving as the first line of defense. The responses of roots to water stress can involve both structural and physiological changes, and their plasticity is a vital feature of these adaptations. Genetic methodologies have been extensively employed to identify numerous genetic loci linked to water stress-responsive root traits. This knowledge is immensely important for developing crops with optimal root systems that enhance yield and guarantee food security under water stress conditions. RESULTS This review focused on the latest insights into modifications in the root system architecture and anatomical features of legume roots in response to drought and flooding stresses. Special attention was given to recent breakthroughs in understanding the genetic underpinnings of legume root development under water stress. The review also described various root phenotyping techniques and examples of their applications in different legume species. Finally, the prevailing challenges and prospective research avenues in this dynamic field as well as the potential for using root system architecture as a breeding target are discussed. CONCLUSIONS This review integrated the latest knowledge of the genetic components governing the adaptability of legume roots to water stress, providing a reference for using root traits as the new crop breeding targets.
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Affiliation(s)
- Zhili Wang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518057, China
| | - Wai-Shing Yung
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518057, China
| | - Yamin Gao
- College of Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Cheng Huang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
- Key Laboratory of the Ministry of Education for Crop Physiology and Molecular Biology, College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Xusheng Zhao
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Yinglong Chen
- The UWA Institute of Agriculture, & School of Agriculture and Environment, The University of Western Australia, Perth, WA, 6001, Australia
| | - Man-Wah Li
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518057, China
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China.
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, 518057, China.
- Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China.
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2
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Szőke L, Tóth B, Javornik T, Lazarević B. Quantifying aluminum toxicity effects on corn phenotype using advanced imaging technologies. PLANT DIRECT 2024; 8:e623. [PMID: 39040680 PMCID: PMC11262852 DOI: 10.1002/pld3.623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/21/2024] [Accepted: 07/06/2024] [Indexed: 07/24/2024]
Abstract
Soil acidity (pH <5.5) limits agricultural production due to aluminum (Al) toxicity. The primary target of Al toxicity is the plant root. However, symptoms can be observed on the shoots. This study aims to determine the potential use of chlorophyll fluorescence imaging, multispectral imaging, and 3D multispectral scanning technology to quantify the effects of Al toxicity on corn. Corn seedlings were grown for 13 days in nutrient solutions (pH 4.0) with four Al treatments: 50, 100, 200, and 400 μM and a control (0 μM AlCl3 L-1). During the experiment, four measurements were performed: four (MT1), six (MT2), 11 (MT3), and 13 (MT4) days after the application of Al treatments. The most sensitive traits affected by Al toxicity were the reduction of plant growth and increased reflectance in the visible wavelength (affected at MT1). The reflectance of red wavelengths increased more significantly compared to near-infrared and green wavelengths, leading to a decrease in the normalized difference vegetation index and the Green Leaf Index. The most sensitive chlorophyll fluorescence traits, effective quantum yield of PSII, and photochemical quenching coefficient were affected after prolonged Al exposure (MT3). This study demonstrates the usability of selected phenotypic traits in remote sensing studies to map Al-toxic soils and in high-throughput phenotyping studies to screen Al-tolerant genotypes.
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Affiliation(s)
- Lóránt Szőke
- Department of Plant NutritionUniversity of Zagreb Faculty of AgricultureZagrebCroatia
- Institute of Food Science, Faculty of Agricultural and Food Sciences and Environmental ManagementUniversity of DebrecenDebrecenHungary
| | - Brigitta Tóth
- Institute of Food Science, Faculty of Agricultural and Food Sciences and Environmental ManagementUniversity of DebrecenDebrecenHungary
| | - Tomislav Javornik
- Centre of Excellence for Biodiversity and Molecular Plant BreedingUniversity of ZagrebZagrebCroatia
- Department of Plant BiodiversityUniversity of Zagreb Faculty of AgricultureZagrebCroatia
| | - Boris Lazarević
- Department of Plant NutritionUniversity of Zagreb Faculty of AgricultureZagrebCroatia
- Centre of Excellence for Biodiversity and Molecular Plant BreedingUniversity of ZagrebZagrebCroatia
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3
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Wang X, Cheng L, Xiong C, Whalley WR, Miller AJ, Rengel Z, Zhang F, Shen J. Understanding plant-soil interactions underpins enhanced sustainability of crop production. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00126-2. [PMID: 38897884 DOI: 10.1016/j.tplants.2024.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 05/17/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024]
Abstract
The Green Revolution transformed agriculture with high-yielding, stress-resistant varieties. However, the urgent need for more sustainable agricultural development presents new challenges: increasing crop yield, improving nutritional quality, and enhancing resource-use efficiency. Soil plays a vital role in crop-production systems and ecosystem services, providing water, nutrients, and physical anchorage for crop growth. Despite advancements in plant and soil sciences, our understanding of belowground plant-soil interactions, which impact both crop performance and soil health, remains limited. Here, we argue that a lack of understanding of these plant-soil interactions hinders sustainable crop production. We propose that targeted engineering of crops and soils can provide a fresh approach to achieve higher yields, more efficient sustainable crop production, and improved soil health.
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Affiliation(s)
- Xin Wang
- State Key Laboratory of Nutrient Use and Management, Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing 100193, China; State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lingyun Cheng
- State Key Laboratory of Nutrient Use and Management, Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing 100193, China
| | - Chuanyong Xiong
- State Key Laboratory of Nutrient Use and Management, Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing 100193, China; Horticultural Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - William R Whalley
- Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Anthony J Miller
- Biochemistry and Metabolism Department, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Zed Rengel
- Soil Science and Plant Nutrition, UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia; Institute for Adriatic Crops and Karst Reclamation, 21000 Split, Croatia
| | - Fusuo Zhang
- State Key Laboratory of Nutrient Use and Management, Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing 100193, China
| | - Jianbo Shen
- State Key Laboratory of Nutrient Use and Management, Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing 100193, China.
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4
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Xie J, Wu Q, Feng L, Li J, Zhou Y, Wu GZ, Men Y. Super-Transparent Soil for In Situ Observation of Root Phenotypes. Molecules 2024; 29:2677. [PMID: 38893550 PMCID: PMC11173578 DOI: 10.3390/molecules29112677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/06/2024] [Accepted: 05/12/2024] [Indexed: 06/21/2024] Open
Abstract
Transparent soil (TS) presents immense potential for root phenotyping due to its ability to facilitate high-resolution imaging. However, challenges related to transparency, mechanical properties, and cost hinder its development. Herein, we introduce super-transparent soil (s-TS) prepared via the droplet method using low acyl gellan gum and hydroxyethyl cellulose crosslinked with magnesium ions. The refractive index of the hydroxyethyl cellulose solution (1.345) closely aligns with that of water (1.333) and the low acyl gellan gum solution (1.340), thereby significantly enhancing the transmittance of hydrogel-based transparent soil. Optimal transmittance (98.45%) is achieved with polymer concentrations ranging from 0.8 to 1.6 wt.% and ion concentrations between 0.01 and 0.09 mol·L-1. After 60 days of plant cultivation, s-TS maintains a transmittance exceeding 89.5%, enabling the detailed visualization of root growth dynamics. Furthermore, s-TS exhibits remarkable mechanical properties, withstanding a maximum compressive stress of 477 kPa and supporting a maximum load-bearing depth of 186 cm. This innovative approach holds promising implications for advanced root phenotyping studies, fostering the investigation of root heterogeneity and the development of selective expression under controlled conditions.
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Affiliation(s)
- Jinchun Xie
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai 201620, China; (J.X.); (Q.W.); (J.L.); (Y.Z.)
| | - Qiye Wu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai 201620, China; (J.X.); (Q.W.); (J.L.); (Y.Z.)
| | - Liping Feng
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China;
| | - Junfu Li
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai 201620, China; (J.X.); (Q.W.); (J.L.); (Y.Z.)
| | - Yingjie Zhou
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai 201620, China; (J.X.); (Q.W.); (J.L.); (Y.Z.)
| | - Guo-Zhang Wu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China;
| | - Yongjun Men
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai 201620, China; (J.X.); (Q.W.); (J.L.); (Y.Z.)
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5
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Gholizadeh S, Nemati I, Vestergård M, Barnes CJ, Kudjordjie EN, Nicolaisen M. Harnessing root-soil-microbiota interactions for drought-resilient cereals. Microbiol Res 2024; 283:127698. [PMID: 38537330 DOI: 10.1016/j.micres.2024.127698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/14/2024] [Accepted: 03/17/2024] [Indexed: 04/17/2024]
Abstract
Cereal plants form complex networks with their associated microbiome in the soil environment. A complex system including variations of numerous parameters of soil properties and host traits shapes the dynamics of cereal microbiota under drought. These multifaceted interactions can greatly affect carbon and nutrient cycling in soil and offer the potential to increase plant growth and fitness under drought conditions. Despite growing recognition of the importance of plant microbiota to agroecosystem functioning, harnessing the cereal root microbiota remains a significant challenge due to interacting and synergistic effects between root traits, soil properties, agricultural practices, and drought-related features. A better mechanistic understanding of root-soil-microbiota associations could lead to the development of novel strategies to improve cereal production under drought. In this review, we discuss the root-soil-microbiota interactions for improving the soil environment and host fitness under drought and suggest a roadmap for harnessing the benefits of these interactions for drought-resilient cereals. These methods include conservative trait-based approaches for the selection and breeding of plant genetic resources and manipulation of the soil environments.
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Affiliation(s)
- Somayeh Gholizadeh
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Iman Nemati
- Department of Plant Production and Genetics Engineering, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Mette Vestergård
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Christopher James Barnes
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Enoch Narh Kudjordjie
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Mogens Nicolaisen
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark.
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Alrajhi A, Alharbi S, Beecham S, Alotaibi F. Regulation of root growth and elongation in wheat. FRONTIERS IN PLANT SCIENCE 2024; 15:1397337. [PMID: 38835859 PMCID: PMC11148372 DOI: 10.3389/fpls.2024.1397337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/06/2024] [Indexed: 06/06/2024]
Abstract
Currently, the control of rhizosphere selection on farms has been applied to achieve enhancements in phenotype, extending from improvements in single root characteristics to the dynamic nature of entire crop systems. Several specific signals, regulatory elements, and mechanisms that regulate the initiation, morphogenesis, and growth of new lateral or adventitious root species have been identified, but much more work remains. Today, phenotyping technology drives the development of root traits. Available models for simulation can support all phenotyping decisions (root trait improvement). The detection and use of markers for quantitative trait loci (QTLs) are effective for enhancing selection efficiency and increasing reproductive genetic gains. Furthermore, QTLs may help wheat breeders select the appropriate roots for efficient nutrient acquisition. Single-nucleotide polymorphisms (SNPs) or alignment of sequences can only be helpful when they are associated with phenotypic variation for root development and elongation. Here, we focus on major root development processes and detail important new insights recently generated regarding the wheat genome. The first part of this review paper discusses the root morphology, apical meristem, transcriptional control, auxin distribution, phenotyping of the root system, and simulation models. In the second part, the molecular genetics of the wheat root system, SNPs, TFs, and QTLs related to root development as well as genome editing (GE) techniques for the improvement of root traits in wheat are discussed. Finally, we address the effect of omics strategies on root biomass production and summarize existing knowledge of the main molecular mechanisms involved in wheat root development and elongation.
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Affiliation(s)
- Abdullah Alrajhi
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
- Sustainable Infrastructure and Resource Management, University of South Australia, University of South Australia Science, Technology, Engineering, and Mathematics (UniSA STEM), Mawson Lakes, SA, Australia
| | - Saif Alharbi
- The National Research and Development Center for Sustainable Agriculture (Estidamah), Riyadh, Saudi Arabia
| | - Simon Beecham
- Sustainable Infrastructure and Resource Management, University of South Australia, University of South Australia Science, Technology, Engineering, and Mathematics (UniSA STEM), Mawson Lakes, SA, Australia
| | - Fahad Alotaibi
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
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7
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Wu Q, Xie J, Li J, Men Y, Yan F. Engineering Rapeseed Germination and Root Growth with Mechanical Strength of Polysaccharide Hydrogel. ACS APPLIED BIO MATERIALS 2024; 7:3496-3505. [PMID: 38708935 DOI: 10.1021/acsabm.4c00416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Plant roots are highly sensitive to physical stress in the soil, with appropriate mechanical impedance promoting root elongation and lateral root growth. However, few studies have quantitatively explored the relationship between the mechanical impedance of the growth medium and the phenotypes of plant roots. In this study, we used a tensile machine equipped with a self-made steel needle mimicking the root tip to measure the force needed to penetrate the hydrogel medium (agar, low acyl gellan gum, and κ-carrageenan), providing insights into the force required for the rapeseed root tip to enter the medium following germination. These findings indicate that root penetration length is inversely associated with the mechanical strength of the growth medium, with variations observed in the root system adaptability across different substrates. Specifically, when the gel puncture resistance of the culture medium without adding MS reached approximately 18.4 mN, root penetration and growth were significantly hindered. With the addition of 1/2 MS medium, the polysaccharide concentration is 1.0 wt %, which is more suitable for cultivating rapeseed. This research not only offers a method for quantifying root phenotypes and medium mechanical impedance but also presents an approach for plant growth regulation and crop breeding.
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Affiliation(s)
- Qiye Wu
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai 201620, China
| | - Jinchun Xie
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai 201620, China
| | - Junfu Li
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai 201620, China
| | - Yongjun Men
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai 201620, China
| | - Feng Yan
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials, College of Materials Science and Engineering, Donghua University, Shanghai 201620, China
- Jiangsu Engineering Laboratory of Novel Functional Polymeric Materials, Jiangsu Key Laboratory of Advanced Negative Carbon Technologies College of Chemistry, Suzhou Key Laboratory of Soft Material and New Energy, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
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8
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Ru S, Sanz-Saez A, Leisner CP, Rehman T, Busby S. Review on blueberry drought tolerance from the perspective of cultivar improvement. FRONTIERS IN PLANT SCIENCE 2024; 15:1352768. [PMID: 38807786 PMCID: PMC11130474 DOI: 10.3389/fpls.2024.1352768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/22/2024] [Indexed: 05/30/2024]
Abstract
Blueberry (Vaccinium spp.) is an increasingly popular fruit around the world for their attractive taste, appearance, and most importantly their many health benefits. Global blueberry production was valued at $2.31 billion with the United States alone producing $1.02 billion of cultivated blueberries in 2021. The sustainability of blueberry production is increasingly threatened by more frequent and extreme drought events caused by climate change. Blueberry is especially prone to adverse effects from drought events due to their superficial root system and lack of root hairs, which limit blueberry's ability to intake water and nutrients from the soil especially under drought stress conditions. The goal of this paper is to review previous studies on blueberry drought tolerance focusing on physiological, biochemical, and molecular drought tolerance mechanisms, as well as genetic variability present in cultivated blueberries. We also discuss limitations of previous studies and potential directions for future efforts to develop drought-tolerant blueberry cultivars. Our review showed that the following areas are lacking in blueberry drought tolerance research: studies of root and fruit traits related to drought tolerance, large-scale cultivar screening, efforts to understand the genetic architecture of drought tolerance, tools for molecular-assisted drought tolerance improvement, and high-throughput phenotyping capability for efficient cultivar screening. Future research should be devoted to following areas: (1) drought tolerance evaluation to include a broader range of traits, such as root architecture and fruit-related performance under drought stress, to establish stronger association between physiological and molecular signals with drought tolerance mechanisms; (2) large-scale drought tolerance screening across diverse blueberry germplasm to uncover various drought tolerance mechanisms and valuable genetic resources; (3) high-throughput phenotyping tools for drought-related traits to enhance the efficiency and affordability of drought phenotyping; (4) identification of genetic architecture of drought tolerance using various mapping technologies and transcriptome analysis; (5) tools for molecular-assisted breeding for drought tolerance, such as marker-assisted selection and genomic selection, and (6) investigation of the interactions between drought and other stresses such as heat to develop stress resilient genotypes.
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Affiliation(s)
- Sushan Ru
- Department of Horticulture, Auburn University, Auburn, AL, United States
| | - Alvaro Sanz-Saez
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Courtney P. Leisner
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Tanzeel Rehman
- Department of Biosystems Engineering, Auburn University, Auburn, AL, United States
| | - Savannah Busby
- Department of Horticulture, Auburn University, Auburn, AL, United States
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Weihs BJ, Heuschele DJ, Tang Z, York LM, Zhang Z, Xu Z. The State of the Art in Root System Architecture Image Analysis Using Artificial Intelligence: A Review. PLANT PHENOMICS (WASHINGTON, D.C.) 2024; 6:0178. [PMID: 38711621 PMCID: PMC11070851 DOI: 10.34133/plantphenomics.0178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 03/27/2024] [Indexed: 05/08/2024]
Abstract
Roots are essential for acquiring water and nutrients to sustain and support plant growth and anchorage. However, they have been studied less than the aboveground traits in phenotyping and plant breeding until recent decades. In modern times, root properties such as morphology and root system architecture (RSA) have been recognized as increasingly important traits for creating more and higher quality food in the "Second Green Revolution". To address the paucity in RSA and other root research, new technologies are being investigated to fill the increasing demand to improve plants via root traits and overcome currently stagnated genetic progress in stable yields. Artificial intelligence (AI) is now a cutting-edge technology proving to be highly successful in many applications, such as crop science and genetic research to improve crop traits. A burgeoning field in crop science is the application of AI to high-resolution imagery in analyses that aim to answer questions related to crops and to better and more speedily breed desired plant traits such as RSA into new cultivars. This review is a synopsis concerning the origins, applications, challenges, and future directions of RSA research regarding image analyses using AI.
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Affiliation(s)
- Brandon J. Weihs
- United States Department of Agriculture–Agricultural Research Service–Plant Science Research, St. Paul, MN 55108, USA
- Department of Agronomy and Plant Genetics,
University of Minnesota, St. Paul, MN, 55108, USA
| | - Deborah-Jo Heuschele
- United States Department of Agriculture–Agricultural Research Service–Plant Science Research, St. Paul, MN 55108, USA
- Department of Agronomy and Plant Genetics,
University of Minnesota, St. Paul, MN, 55108, USA
| | - Zhou Tang
- Department of Crop and Soil Sciences,
Washington State University, Pullman, WA 99164, USA
| | - Larry M. York
- Biosciences Division and Center for Bioenergy Innovation,
Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences,
Washington State University, Pullman, WA 99164, USA
| | - Zhanyou Xu
- United States Department of Agriculture–Agricultural Research Service–Plant Science Research, St. Paul, MN 55108, USA
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10
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Berrigan EM, Wang L, Carrillo H, Echegoyen K, Kappes M, Torres J, Ai-Perreira A, McCoy E, Shane E, Copeland CD, Ragel L, Georgousakis C, Lee S, Reynolds D, Talgo A, Gonzalez J, Zhang L, Rajurkar AB, Ruiz M, Daniels E, Maree L, Pariyar S, Busch W, Pereira TD. Fast and Efficient Root Phenotyping via Pose Estimation. PLANT PHENOMICS (WASHINGTON, D.C.) 2024; 6:0175. [PMID: 38629082 PMCID: PMC11020144 DOI: 10.34133/plantphenomics.0175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/20/2024] [Indexed: 04/19/2024]
Abstract
Image segmentation is commonly used to estimate the location and shape of plants and their external structures. Segmentation masks are then used to localize landmarks of interest and compute other geometric features that correspond to the plant's phenotype. Despite its prevalence, segmentation-based approaches are laborious (requiring extensive annotation to train) and error-prone (derived geometric features are sensitive to instance mask integrity). Here, we present a segmentation-free approach that leverages deep learning-based landmark detection and grouping, also known as pose estimation. We use a tool originally developed for animal motion capture called SLEAP (Social LEAP Estimates Animal Poses) to automate the detection of distinct morphological landmarks on plant roots. Using a gel cylinder imaging system across multiple species, we show that our approach can reliably and efficiently recover root system topology at high accuracy, few annotated samples, and faster speed than segmentation-based approaches. In order to make use of this landmark-based representation for root phenotyping, we developed a Python library (sleap-roots) for trait extraction directly comparable to existing segmentation-based analysis software. We show that pose-derived root traits are highly accurate and can be used for common downstream tasks including genotype classification and unsupervised trait mapping. Altogether, this work establishes the validity and advantages of pose estimation-based plant phenotyping. To facilitate adoption of this easy-to-use tool and to encourage further development, we make sleap-roots, all training data, models, and trait extraction code available at: https://github.com/talmolab/sleap-roots and https://osf.io/k7j9g/.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Wolfgang Busch
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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11
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Simonetti V, Ravazzolo L, Ruperti B, Quaggiotti S, Castiello U. A system for the study of roots 3D kinematics in hydroponic culture: a study on the oscillatory features of root tip. PLANT METHODS 2024; 20:50. [PMID: 38561757 PMCID: PMC10983651 DOI: 10.1186/s13007-024-01178-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND The root of a plant is a fundamental organ for the multisensory perception of the environment. Investigating root growth dynamics as a mean of their interaction with the environment is of key importance for improving knowledge in plant behaviour, plant biology and agriculture. To date, it is difficult to study roots movements from a dynamic perspective given that available technologies for root imaging focus mostly on static characterizations, lacking temporal and three-dimensional (3D) spatial information. This paper describes a new system based on time-lapse for the 3D reconstruction and analysis of roots growing in hydroponics. RESULTS The system is based on infrared stereo-cameras acquiring time-lapse images of the roots for 3D reconstruction. The acquisition protocol guarantees the root growth in complete dark while the upper part of the plant grows in normal light conditions. The system extracts the 3D trajectory of the root tip and a set of descriptive features in both the temporal and frequency domains. The system has been used on Zea mays L. (B73) during the first week of growth and shows good inter-reliability between operators with an Intra Class Correlation Coefficient (ICC) > 0.9 for all features extracted. It also showed measurement accuracy with a median difference of < 1 mm between computed and manually measured root length. CONCLUSIONS The system and the protocol presented in this study enable accurate 3D analysis of primary root growth in hydroponics. It can serve as a valuable tool for analysing real-time root responses to environmental stimuli thus improving knowledge on the processes contributing to roots physiological and phenotypic plasticity.
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Affiliation(s)
| | - Laura Ravazzolo
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Agripolis, Italy
| | - Benedetto Ruperti
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Agripolis, Italy
| | - Silvia Quaggiotti
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Agripolis, Italy
| | - Umberto Castiello
- Department of General Psychology, University of Padova, Padova, Italy
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12
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Jayawickrama SM, Ranaweera PM, Pradeep RGGR, Jayasinghe YA, Senevirathna K, Hilmi AJ, Rajapakse RMG, Kanmodi KK, Jayasinghe RD. Developments and future prospects of personalized medicine in head and neck squamous cell carcinoma diagnoses and treatments. Cancer Rep (Hoboken) 2024; 7:e2045. [PMID: 38522008 PMCID: PMC10961052 DOI: 10.1002/cnr2.2045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 02/07/2024] [Accepted: 03/05/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND Precision healthcare has entered a new era because of the developments in personalized medicine, especially in the diagnosis and treatment of head and neck squamous cell carcinoma (HNSCC). This paper explores the dynamic landscape of personalized medicine as applied to HNSCC, encompassing both current developments and future prospects. RECENT FINDINGS The integration of personalized medicine strategies into HNSCC diagnosis is driven by the utilization of genetic data and biomarkers. Epigenetic biomarkers, which reflect modifications to DNA that can influence gene expression, have emerged as valuable indicators for early detection and risk assessment. Treatment approaches within the personalized medicine framework are equally promising. Immunotherapy, gene silencing, and editing techniques, including RNA interference and CRISPR/Cas9, offer innovative means to modulate gene expression and correct genetic aberrations driving HNSCC. The integration of stem cell research with personalized medicine presents opportunities for tailored regenerative approaches. The synergy between personalized medicine and technological advancements is exemplified by artificial intelligence (AI) and machine learning (ML) applications. These tools empower clinicians to analyze vast datasets, predict patient responses, and optimize treatment strategies with unprecedented accuracy. CONCLUSION The developments and prospects of personalized medicine in HNSCC diagnosis and treatment offer a transformative approach to managing this complex malignancy. By harnessing genetic insights, biomarkers, immunotherapy, gene editing, stem cell therapies, and advanced technologies like AI and ML, personalized medicine holds the key to enhancing patient outcomes and ushering in a new era of precision oncology.
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Affiliation(s)
| | | | | | | | - Kalpani Senevirathna
- Centre for Research in Oral Cancer, Faculty of Dental SciencesUniversity of PeradeniyaKandySri Lanka
| | | | | | - Kehinde Kazeem Kanmodi
- School of DentistryUniversity of RwandaKigaliRwanda
- Faculty of DentistryUniversity of PuthisastraPhnom PenhCambodia
- Cephas Health Research Initiative IncIbadanNigeria
- School of Health and Life SciencesTeesside UniversityMiddlesbroughUK
| | - Ruwan Duminda Jayasinghe
- Centre for Research in Oral Cancer, Faculty of Dental SciencesUniversity of PeradeniyaKandySri Lanka
- Faculty of DentistryUniversity of PuthisastraPhnom PenhCambodia
- School of Health and Life SciencesTeesside UniversityMiddlesbroughUK
- Department of Oral Medicine and Periodontology, Faculty of Dental SciencesUniversity of PeradeniyaKandySri Lanka
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13
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Sarkar S, Ganapathysubramanian B, Singh A, Fotouhi F, Kar S, Nagasubramanian K, Chowdhary G, Das SK, Kantor G, Krishnamurthy A, Merchant N, Singh AK. Cyber-agricultural systems for crop breeding and sustainable production. TRENDS IN PLANT SCIENCE 2024; 29:130-149. [PMID: 37648631 DOI: 10.1016/j.tplants.2023.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/19/2023] [Accepted: 08/03/2023] [Indexed: 09/01/2023]
Abstract
The cyber-agricultural system (CAS) represents an overarching framework of agriculture that leverages recent advances in ubiquitous sensing, artificial intelligence, smart actuators, and scalable cyberinfrastructure (CI) in both breeding and production agriculture. We discuss the recent progress and perspective of the three fundamental components of CAS - sensing, modeling, and actuation - and the emerging concept of agricultural digital twins (DTs). We also discuss how scalable CI is becoming a key enabler of smart agriculture. In this review we shed light on the significance of CAS in revolutionizing crop breeding and production by enhancing efficiency, productivity, sustainability, and resilience to changing climate. Finally, we identify underexplored and promising future directions for CAS research and development.
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Affiliation(s)
- Soumik Sarkar
- Department of Mechanical Engineering, Iowa State University, Ames, IA, USA; Department of Computer Science, Iowa State University, Ames, IA, USA.
| | - Baskar Ganapathysubramanian
- Department of Mechanical Engineering, Iowa State University, Ames, IA, USA; Department of Computer Science, Iowa State University, Ames, IA, USA
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Fateme Fotouhi
- Department of Mechanical Engineering, Iowa State University, Ames, IA, USA; Department of Computer Science, Iowa State University, Ames, IA, USA
| | | | | | - Girish Chowdhary
- Department of Agricultural and Biological Engineering and Department of Computer Science, University of Illinois at Urbana Champaign, Champaign, Urbana, IL, USA
| | - Sajal K Das
- Department of Computer Science, Missouri University of Science and Technology, Rolla, MO, USA
| | - George Kantor
- Robotics Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | | | - Nirav Merchant
- Data Science Institute, University of Arizona, Tucson, AZ, USA
| | - Asheesh K Singh
- Department of Agronomy, Iowa State University, Ames, IA, USA.
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14
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Li M, Liu Z, Jiang N, Laws B, Tiskevich C, Moose SP, Topp CN. Topological data analysis expands the genotype to phenotype map for 3D maize root system architecture. FRONTIERS IN PLANT SCIENCE 2024; 14:1260005. [PMID: 38288407 PMCID: PMC10822944 DOI: 10.3389/fpls.2023.1260005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/27/2023] [Indexed: 01/31/2024]
Abstract
A central goal of biology is to understand how genetic variation produces phenotypic variation, which has been described as a genotype to phenotype (G to P) map. The plant form is continuously shaped by intrinsic developmental and extrinsic environmental inputs, and therefore plant phenomes are highly multivariate and require comprehensive approaches to fully quantify. Yet a common assumption in plant phenotyping efforts is that a few pre-selected measurements can adequately describe the relevant phenome space. Our poor understanding of the genetic basis of root system architecture is at least partially a result of this incongruence. Root systems are complex 3D structures that are most often studied as 2D representations measured with relatively simple univariate traits. In prior work, we showed that persistent homology, a topological data analysis method that does not pre-suppose the salient features of the data, could expand the phenotypic trait space and identify new G to P relations from a commonly used 2D root phenotyping platform. Here we extend the work to entire 3D root system architectures of maize seedlings from a mapping population that was designed to understand the genetic basis of maize-nitrogen relations. Using a panel of 84 univariate traits, persistent homology methods developed for 3D branching, and multivariate vectors of the collective trait space, we found that each method captures distinct information about root system variation as evidenced by the majority of non-overlapping QTL, and hence that root phenotypic trait space is not easily exhausted. The work offers a data-driven method for assessing 3D root structure and highlights the importance of non-canonical phenotypes for more accurate representations of the G to P map.
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Affiliation(s)
- Mao Li
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Zhengbin Liu
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Ni Jiang
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Benjamin Laws
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Christine Tiskevich
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Stephen P. Moose
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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15
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Rajanala A, Taylor IW, McCaskey E, Pierce C, Ligon J, Aydin E, Hunner C, Carmichael A, Eserman L, Coffee EED, Mijar A, Shah M, Benfey PN, Goldman DI. The rhizodynamics robot: Automated imaging system for studying long-term dynamic root growth. PLoS One 2023; 18:e0295823. [PMID: 38128010 PMCID: PMC10734993 DOI: 10.1371/journal.pone.0295823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023] Open
Abstract
The study of plant root growth in real time has been difficult to achieve in an automated, high-throughput, and systematic fashion. Dynamic imaging of plant roots is important in order to discover novel root growth behaviors and to deepen our understanding of how roots interact with their environments. We designed and implemented the Generating Rhizodynamic Observations Over Time (GROOT) robot, an automated, high-throughput imaging system that enables time-lapse imaging of 90 containers of plants and their roots growing in a clear gel medium over the duration of weeks to months. The system uses low-cost, widely available materials. As a proof of concept, we employed GROOT to collect images of root growth of Oryza sativa, Hudsonia montana, and multiple species of orchids including Platanthera integrilabia over six months. Beyond imaging plant roots, our system is highly customizable and can be used to collect time- lapse image data of different container sizes and configurations regardless of what is being imaged, making it applicable to many fields that require longitudinal time-lapse recording.
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Affiliation(s)
- Aradhya Rajanala
- Department of Physics, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Isaiah W. Taylor
- Department of Biology, Duke University, Durham, NC, United States of America
| | - Erin McCaskey
- Department of Physics, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Christopher Pierce
- Department of Physics, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Jason Ligon
- Atlanta Botanical Garden, Atlanta, GA, United States of America
| | - Enes Aydin
- Department of Physics, Georgia Institute of Technology, Atlanta, GA, United States of America
| | - Carrie Hunner
- Atlanta Botanical Garden, Atlanta, GA, United States of America
| | | | - Lauren Eserman
- Atlanta Botanical Garden, Atlanta, GA, United States of America
| | | | - Anupam Mijar
- Department of Biology, Duke University, Durham, NC, United States of America
| | - Milan Shah
- Department of Biology, Duke University, Durham, NC, United States of America
| | - Philip N. Benfey
- Department of Biology, Duke University, Durham, NC, United States of America
| | - Daniel I. Goldman
- Department of Physics, Georgia Institute of Technology, Atlanta, GA, United States of America
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16
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Berrigan EM, Wang L, Carrillo H, Echegoyen K, Kappes M, Torres J, Ai-Perreira A, McCoy E, Shane E, Copeland CD, Ragel L, Georgousakis C, Lee S, Reynolds D, Talgo A, Gonzalez J, Zhang L, Rajurkar AB, Ruiz M, Daniels E, Maree L, Pariyar S, Busch W, Pereira TD. Fast and efficient root phenotyping via pose estimation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.20.567949. [PMID: 38045278 PMCID: PMC10690188 DOI: 10.1101/2023.11.20.567949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Image segmentation is commonly used to estimate the location and shape of plants and their external structures. Segmentation masks are then used to localize landmarks of interest and compute other geometric features that correspond to the plant's phenotype. Despite its prevalence, segmentation-based approaches are laborious (requiring extensive annotation to train), and error-prone (derived geometric features are sensitive to instance mask integrity). Here we present a segmentation-free approach which leverages deep learning-based landmark detection and grouping, also known as pose estimation. We use a tool originally developed for animal motion capture called SLEAP (Social LEAP Estimates Animal Poses) to automate the detection of distinct morphological landmarks on plant roots. Using a gel cylinder imaging system across multiple species, we show that our approach can reliably and efficiently recover root system topology at high accuracy, few annotated samples, and faster speed than segmentation-based approaches. In order to make use of this landmark-based representation for root phenotyping, we developed a Python library (sleap-roots) for trait extraction directly comparable to existing segmentation-based analysis software. We show that landmark-derived root traits are highly accurate and can be used for common downstream tasks including genotype classification and unsupervised trait mapping. Altogether, this work establishes the validity and advantages of pose estimation-based plant phenotyping. To facilitate adoption of this easy-to-use tool and to encourage further development, we make sleap-roots, all training data, models, and trait extraction code available at: https://github.com/talmolab/sleap-roots and https://osf.io/k7j9g/.
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Affiliation(s)
| | - Lin Wang
- Salk Institute for Biological Studies, La Jolla, CA 92037 United States of America
| | - Hannah Carrillo
- Salk Institute for Biological Studies, La Jolla, CA 92037 United States of America
| | - Kimberly Echegoyen
- Salk Institute for Biological Studies, La Jolla, CA 92037 United States of America
| | - Mikayla Kappes
- Salk Institute for Biological Studies, La Jolla, CA 92037 United States of America
| | - Jorge Torres
- Salk Institute for Biological Studies, La Jolla, CA 92037 United States of America
| | - Angel Ai-Perreira
- Salk Institute for Biological Studies, La Jolla, CA 92037 United States of America
| | - Erica McCoy
- Salk Institute for Biological Studies, La Jolla, CA 92037 United States of America
| | - Emily Shane
- Salk Institute for Biological Studies, La Jolla, CA 92037 United States of America
| | - Charles D. Copeland
- Salk Institute for Biological Studies, La Jolla, CA 92037 United States of America
| | - Lauren Ragel
- Salk Institute for Biological Studies, La Jolla, CA 92037 United States of America
| | | | - Sanghwa Lee
- Salk Institute for Biological Studies, La Jolla, CA 92037 United States of America
| | - Dawn Reynolds
- Salk Institute for Biological Studies, La Jolla, CA 92037 United States of America
| | - Avery Talgo
- Salk Institute for Biological Studies, La Jolla, CA 92037 United States of America
| | - Juan Gonzalez
- Salk Institute for Biological Studies, La Jolla, CA 92037 United States of America
| | - Ling Zhang
- Salk Institute for Biological Studies, La Jolla, CA 92037 United States of America
| | - Ashish B. Rajurkar
- Salk Institute for Biological Studies, La Jolla, CA 92037 United States of America
| | - Michel Ruiz
- Salk Institute for Biological Studies, La Jolla, CA 92037 United States of America
| | - Erin Daniels
- Salk Institute for Biological Studies, La Jolla, CA 92037 United States of America
| | - Liezl Maree
- Salk Institute for Biological Studies, La Jolla, CA 92037 United States of America
| | - Shree Pariyar
- Salk Institute for Biological Studies, La Jolla, CA 92037 United States of America
| | - Wolfgang Busch
- Salk Institute for Biological Studies, La Jolla, CA 92037 United States of America
| | - Talmo D. Pereira
- Salk Institute for Biological Studies, La Jolla, CA 92037 United States of America
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17
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Baykalov P, Bussmann B, Nair R, Smith AG, Bodner G, Hadar O, Lazarovitch N, Rewald B. Semantic segmentation of plant roots from RGB (mini-) rhizotron images-generalisation potential and false positives of established methods and advanced deep-learning models. PLANT METHODS 2023; 19:122. [PMID: 37932745 PMCID: PMC10629126 DOI: 10.1186/s13007-023-01101-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/27/2023] [Indexed: 11/08/2023]
Abstract
BACKGROUND Manual analysis of (mini-)rhizotron (MR) images is tedious. Several methods have been proposed for semantic root segmentation based on homogeneous, single-source MR datasets. Recent advances in deep learning (DL) have enabled automated feature extraction, but comparisons of segmentation accuracy, false positives and transferability are virtually lacking. Here we compare six state-of-the-art methods and propose two improved DL models for semantic root segmentation using a large MR dataset with and without augmented data. We determine the performance of the methods on a homogeneous maize dataset, and a mixed dataset of > 8 species (mixtures), 6 soil types and 4 imaging systems. The generalisation potential of the derived DL models is determined on a distinct, unseen dataset. RESULTS The best performance was achieved by the U-Net models; the more complex the encoder the better the accuracy and generalisation of the model. The heterogeneous mixed MR dataset was a particularly challenging for the non-U-Net techniques. Data augmentation enhanced model performance. We demonstrated the improved performance of deep meta-architectures and feature extractors, and a reduction in the number of false positives. CONCLUSIONS Although correction factors are still required to match human labelled root lengths, neural network architectures greatly reduce the time required to compute the root length. The more complex architectures illustrate how future improvements in root segmentation within MR images can be achieved, particularly reaching higher segmentation accuracies and model generalisation when analysing real-world datasets with artefacts-limiting the need for model retraining.
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Affiliation(s)
- Pavel Baykalov
- Institute of Forest Ecology, Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria
- Vienna Scientific Instruments GmbH, Alland, Austria
| | - Bart Bussmann
- IDLab, Department of Computer Science, University of Antwerp - Imec, Antwerp, Belgium
| | - Richard Nair
- Dept. Biogeochemical Integration, Max Planck Institute for Biogeochemistry, Jena, Germany
- Discipline of Botany, School of Natural Sciences, Trinity College, Dublin, Ireland
| | | | - Gernot Bodner
- Institute of Agronomy, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria
| | - Ofer Hadar
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Naftali Lazarovitch
- Wyler Department for Dryland Agriculture, French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Beersheba, Israel
| | - Boris Rewald
- Institute of Forest Ecology, Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria.
- Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic.
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18
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Lynch JP, Galindo-Castañeda T, Schneider HM, Sidhu JS, Rangarajan H, York LM. Root phenotypes for improved nitrogen capture. PLANT AND SOIL 2023; 502:31-85. [PMID: 39323575 PMCID: PMC11420291 DOI: 10.1007/s11104-023-06301-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2024]
Abstract
Background Suboptimal nitrogen availability is a primary constraint for crop production in low-input agroecosystems, while nitrogen fertilization is a primary contributor to the energy, economic, and environmental costs of crop production in high-input agroecosystems. In this article we consider avenues to develop crops with improved nitrogen capture and reduced requirement for nitrogen fertilizer. Scope Intraspecific variation for an array of root phenotypes has been associated with improved nitrogen capture in cereal crops, including architectural phenotypes that colocalize root foraging with nitrogen availability in the soil; anatomical phenotypes that reduce the metabolic costs of soil exploration, improve penetration of hard soil, and exploit the rhizosphere; subcellular phenotypes that reduce the nitrogen requirement of plant tissue; molecular phenotypes exhibiting optimized nitrate uptake kinetics; and rhizosphere phenotypes that optimize associations with the rhizosphere microbiome. For each of these topics we provide examples of root phenotypes which merit attention as potential selection targets for crop improvement. Several cross-cutting issues are addressed including the importance of soil hydrology and impedance, phenotypic plasticity, integrated phenotypes, in silico modeling, and breeding strategies using high throughput phenotyping for co-optimization of multiple phenes. Conclusions Substantial phenotypic variation exists in crop germplasm for an array of root phenotypes that improve nitrogen capture. Although this topic merits greater research attention than it currently receives, we have adequate understanding and tools to develop crops with improved nitrogen capture. Root phenotypes are underutilized yet attractive breeding targets for the development of the nitrogen efficient crops urgently needed in global agriculture.
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Affiliation(s)
- Jonathan P Lynch
- Department of Plant Science, The Pennsylvania State University, University Park, PA 16802 USA
| | | | - Hannah M Schneider
- Department of Plant Sciences, Wageningen University and Research, PO Box 430, 6700AK Wageningen, The Netherlands
| | - Jagdeep Singh Sidhu
- Department of Plant Science, The Pennsylvania State University, University Park, PA 16802 USA
| | - Harini Rangarajan
- Department of Plant Science, The Pennsylvania State University, University Park, PA 16802 USA
| | - Larry M York
- Biosciences Division and Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
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19
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Lärm L, Bauer FM, Hermes N, van der Kruk J, Vereecken H, Vanderborght J, Nguyen TH, Lopez G, Seidel SJ, Ewert F, Schnepf A, Klotzsche A. Multi-year belowground data of minirhizotron facilities in Selhausen. Sci Data 2023; 10:672. [PMID: 37789016 PMCID: PMC10547842 DOI: 10.1038/s41597-023-02570-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/14/2023] [Indexed: 10/05/2023] Open
Abstract
The production of crops secure the human food supply, but climate change is bringing new challenges. Dynamic plant growth and corresponding environmental data are required to uncover phenotypic crop responses to the changing environment. There are many datasets on above-ground organs of crops, but roots and the surrounding soil are rarely the subject of longer term studies. Here, we present what we believe to be the first comprehensive collection of root and soil data, obtained at two minirhizotron facilities located close together that have the same local climate but differ in soil type. Both facilities have 7m-long horizontal tubes at several depths that were used for crosshole ground-penetrating radar and minirhizotron camera systems. Soil sensors provide observations at a high temporal and spatial resolution. The ongoing measurements cover five years of maize and wheat trials, including drought stress treatments and crop mixtures. We make the processed data available for use in investigating the processes within the soil-plant continuum and the root images to develop and compare image analysis methods.
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Affiliation(s)
- Lena Lärm
- Institute of Bio-and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, 52425, Germany.
| | - Felix Maximilian Bauer
- Institute of Bio-and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, 52425, Germany.
| | - Normen Hermes
- Institute of Bio-and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
| | - Jan van der Kruk
- Institute of Bio-and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
| | - Harry Vereecken
- Institute of Bio-and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
| | - Jan Vanderborght
- Institute of Bio-and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
| | - Thuy Huu Nguyen
- Crop Science Group, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53115, Germany
| | - Gina Lopez
- Crop Science Group, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53115, Germany
| | - Sabine Julia Seidel
- Crop Science Group, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53115, Germany
| | - Frank Ewert
- Crop Science Group, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53115, Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, 15374, Germany
| | - Andrea Schnepf
- Institute of Bio-and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
| | - Anja Klotzsche
- Institute of Bio-and Geosciences, Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Jülich, 52425, Germany.
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20
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Mostafa S, Mondal D, Panjvani K, Kochian L, Stavness I. Explainable deep learning in plant phenotyping. Front Artif Intell 2023; 6:1203546. [PMID: 37795496 PMCID: PMC10546035 DOI: 10.3389/frai.2023.1203546] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 08/25/2023] [Indexed: 10/06/2023] Open
Abstract
The increasing human population and variable weather conditions, due to climate change, pose a threat to the world's food security. To improve global food security, we need to provide breeders with tools to develop crop cultivars that are more resilient to extreme weather conditions and provide growers with tools to more effectively manage biotic and abiotic stresses in their crops. Plant phenotyping, the measurement of a plant's structural and functional characteristics, has the potential to inform, improve and accelerate both breeders' selections and growers' management decisions. To improve the speed, reliability and scale of plant phenotyping procedures, many researchers have adopted deep learning methods to estimate phenotypic information from images of plants and crops. Despite the successful results of these image-based phenotyping studies, the representations learned by deep learning models remain difficult to interpret, understand, and explain. For this reason, deep learning models are still considered to be black boxes. Explainable AI (XAI) is a promising approach for opening the deep learning model's black box and providing plant scientists with image-based phenotypic information that is interpretable and trustworthy. Although various fields of study have adopted XAI to advance their understanding of deep learning models, it has yet to be well-studied in the context of plant phenotyping research. In this review article, we reviewed existing XAI studies in plant shoot phenotyping, as well as related domains, to help plant researchers understand the benefits of XAI and make it easier for them to integrate XAI into their future studies. An elucidation of the representations within a deep learning model can help researchers explain the model's decisions, relate the features detected by the model to the underlying plant physiology, and enhance the trustworthiness of image-based phenotypic information used in food production systems.
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Affiliation(s)
- Sakib Mostafa
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Debajyoti Mondal
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
| | - Karim Panjvani
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Leon Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Ian Stavness
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada
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21
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Huang L, Zhang Y, Guo J, Peng Q, Zhou Z, Duan X, Tanveer M, Guo Y. High-throughput root phenotyping of crop cultivars tolerant to low N in waterlogged soils. FRONTIERS IN PLANT SCIENCE 2023; 14:1271539. [PMID: 37780519 PMCID: PMC10533935 DOI: 10.3389/fpls.2023.1271539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 08/29/2023] [Indexed: 10/03/2023]
Affiliation(s)
- Liping Huang
- International Research Center for Environmental Membrane Biology, College of Food Science and Engineering, Foshan University, Foshan, China
- Foshan ZhiBao Ecological Technology Co. Ltd., Foshan, China
| | - Yujing Zhang
- International Research Center for Environmental Membrane Biology, College of Food Science and Engineering, Foshan University, Foshan, China
- Foshan ZhiBao Ecological Technology Co. Ltd., Foshan, China
| | - Jieru Guo
- International Research Center for Environmental Membrane Biology, College of Food Science and Engineering, Foshan University, Foshan, China
- Foshan ZhiBao Ecological Technology Co. Ltd., Foshan, China
| | - Qianlan Peng
- International Research Center for Environmental Membrane Biology, College of Food Science and Engineering, Foshan University, Foshan, China
| | - Zhaoyang Zhou
- International Research Center for Environmental Membrane Biology, College of Food Science and Engineering, Foshan University, Foshan, China
| | - Xiaosong Duan
- International Research Center for Environmental Membrane Biology, College of Food Science and Engineering, Foshan University, Foshan, China
| | - Mohsin Tanveer
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Yongjun Guo
- International Research Center for Environmental Membrane Biology, College of Food Science and Engineering, Foshan University, Foshan, China
- Foshan ZhiBao Ecological Technology Co. Ltd., Foshan, China
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22
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Bacher H, Montagu A, Herrmann I, Walia H, Schwartz N, Peleg Z. Stress-induced deeper rooting introgression enhances wheat yield under terminal drought. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4862-4874. [PMID: 36787201 DOI: 10.1093/jxb/erad059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Water scarcity is the primary environmental constraint affecting wheat growth and production and is increasingly exacerbated due to climatic fluctuation, which jeopardizes future food security. Most breeding efforts to improve wheat yields under drought have focused on above-ground traits. Root traits are closely associated with various drought adaptability mechanisms, but the genetic variation underlying these traits remains untapped, even though it holds tremendous potential for improving crop resilience. Here, we examined this potential by re-introducing ancestral alleles from wild emmer wheat (Triticum turgidum ssp. dicoccoides) and studied their impact on root architecture diversity under terminal drought stress. We applied an active sensing electrical resistivity tomography approach to compare a wild emmer introgression line (IL20) and its drought-sensitive recurrent parent (Svevo) under field conditions. IL20 exhibited greater root elongation under drought, which resulted in higher root water uptake from deeper soil layers. This advantage initiated at the pseudo-stem stage and increased during the transition to the reproductive stage. The increased water uptake promoted higher gas exchange rates and enhanced grain yield under drought. Overall, we show that this presumably 'lost' drought-induced mechanism of deeper rooting profile can serve as a breeding target to improve wheat productiveness under changing climate.
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Affiliation(s)
- Harel Bacher
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Aviad Montagu
- The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Ittai Herrmann
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Nimrod Schwartz
- The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Zvi Peleg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
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23
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Selzner T, Horn J, Landl M, Pohlmeier A, Helmrich D, Huber K, Vanderborght J, Vereecken H, Behnke S, Schnepf A. 3D U-Net Segmentation Improves Root System Reconstruction from 3D MRI Images in Automated and Manual Virtual Reality Work Flows. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0076. [PMID: 37519934 PMCID: PMC10381537 DOI: 10.34133/plantphenomics.0076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 07/10/2023] [Indexed: 08/01/2023]
Abstract
Magnetic resonance imaging (MRI) is used to image root systems grown in opaque soil. However, reconstruction of root system architecture (RSA) from 3-dimensional (3D) MRI images is challenging. Low resolution and poor contrast-to-noise ratios (CNRs) hinder automated reconstruction. Hence, manual reconstruction is still widely used. Here, we evaluate a novel 2-step work flow for automated RSA reconstruction. In the first step, a 3D U-Net segments MRI images into root and soil in super-resolution. In the second step, an automated tracing algorithm reconstructs the root systems from the segmented images. We evaluated the merits of both steps for an MRI dataset of 8 lupine root systems, by comparing the automated reconstructions to manual reconstructions of unaltered and segmented MRI images derived with a novel virtual reality system. We found that the U-Net segmentation offers profound benefits in manual reconstruction: reconstruction speed was doubled (+97%) for images with low CNR and increased by 27% for images with high CNR. Reconstructed root lengths were increased by 20% and 3%, respectively. Therefore, we propose to use U-Net segmentation as a principal image preprocessing step in manual work flows. The root length derived by the tracing algorithm was lower than in both manual reconstruction methods, but segmentation allowed automated processing of otherwise not readily usable MRI images. Nonetheless, model-based functional root traits revealed similar hydraulic behavior of automated and manual reconstructions. Future studies will aim to establish a hybrid work flow that utilizes automated reconstructions as scaffolds that can be manually corrected.
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Affiliation(s)
- Tobias Selzner
- Forschungszentrum Juelich GmbH, Agrosphere (IBG-3), Juelich, Germany
| | - Jannis Horn
- Autonomous Intelligence Systems Group,
University of Bonn, Bonn, Germany
| | - Magdalena Landl
- Forschungszentrum Juelich GmbH, Agrosphere (IBG-3), Juelich, Germany
| | - Andreas Pohlmeier
- Forschungszentrum Juelich GmbH, Agrosphere (IBG-3), Juelich, Germany
| | - Dirk Helmrich
- Forschungszentrum Juelich GmbH, Juelich Supercomputing Center, Juelich, Germany
| | - Katrin Huber
- Forschungszentrum Juelich GmbH, Agrosphere (IBG-3), Juelich, Germany
| | - Jan Vanderborght
- Forschungszentrum Juelich GmbH, Agrosphere (IBG-3), Juelich, Germany
| | - Harry Vereecken
- Forschungszentrum Juelich GmbH, Agrosphere (IBG-3), Juelich, Germany
| | - Sven Behnke
- Autonomous Intelligence Systems Group,
University of Bonn, Bonn, Germany
| | - Andrea Schnepf
- Forschungszentrum Juelich GmbH, Agrosphere (IBG-3), Juelich, Germany
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24
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Chen X, Tang Y, Duan Q, Hu J. Phenotypic quantification of root spatial distribution along circumferential direction for field paddy-wheat. PLoS One 2023; 18:e0279353. [PMID: 37418496 PMCID: PMC10328375 DOI: 10.1371/journal.pone.0279353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 12/06/2022] [Indexed: 07/09/2023] Open
Abstract
Plant roots are essential for water and nutrient absorption, anchoring, mechanical support, metabolite storage and interaction with the surrounding soil environment. A comprehensive understanding of root traits provides an opportunity to build ideal roots architectural system that provides improved stability and yield advantage in adverse target environments caused by soil quality degradation, climate change, etc. However, we hypothesize that quantitative indicators characterizing root system are still need to be supplemented. Features describing root growth and distribution, until now, belong mostly to 2D indicators or reflect changes in the root system with a depth of soil layers but are rarely considered in a spatial region along the circumferential direction. We proposed five new indicators to quantify the dynamics of the root system architecture (RSA) along its eight-part circumferential orientations with visualization technology which consists of in-situ field root samplings, RSA digitization, and reconstruction according to previous research based on field experiments that conducted on paddy-wheat cultivation land with three fertilization rates. The experimental results showed that the growth space of paddy-wheat root is mainly restricted to a cylinder with a diameter of 180 mm and height of 200 mm at the seedlings stage. There were slow fluctuating trends in growth by the mean values of five new indicators within a single volume of soil. The fluctuation of five new indicators was indicated in each sampling time, which decreased gradually with time. Furthermore, treatment of N70 and N130 could similarly impact root spatial heterogeneity. Therefore, we concluded that the five new indicators could quantify the spatial dynamics of the root system of paddy-wheat at the seedling stage of cultivation. It is of great significance to the comprehensive quantification of crop roots in targeted breeding programs and the methods innovation of field crop root research.
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Affiliation(s)
- Xinxin Chen
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, China
| | - Yongli Tang
- Nanjing Agricultural Equipment Extension Center, Nanjing, China
| | - Qingfei Duan
- College of Engineering, Nanjing Agricultural University, Nanjing, China
| | - Jianping Hu
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, China
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25
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Kaiser CF, Perilli A, Grossmann G, Meroz Y. Studying root-environment interactions in structured microdevices. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad122. [PMID: 37042515 PMCID: PMC10353529 DOI: 10.1093/jxb/erad122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Indexed: 06/19/2023]
Abstract
In negotiating with the environment, plant roots integrate sensory information over space and time, as the basis of decision making in roots under non-uniform conditions. The complexity and dynamic properties of soil across spatial and temporal scales pose a significant technical challenge for research on mechanisms that drive metabolism, growth and development in roots, as well as on inter-organismal networks in the rhizosphere. Synthetic environments, combining microscopic access and manipulation capabilities with soil-like heterogeneity, are needed to elucidate the intriguing tug-of-war that characterises subsurface ecosystems. Microdevices have provided opportunities for innovative approaches to observe, analyse and manipulate plant roots and advanced our understanding of their development, physiology and interactions with the environment. Initially conceived as perfusion platforms for root cultivation under hydroponic conditions, microdevice design has, in recent years, increasingly shifted to better reflect the complex growth conditions in soil. Heterogeneous micro-environments have been created through co-cultivation with microbes, laminar flow-based local stimulation and physical obstacles and constraints. As such, structured microdevices provide an experimental entry point to the complex network behaviour of soil communities.
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Affiliation(s)
- Christian-Frederic Kaiser
- Institute of Cell and Interaction Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
- CEPLAS - Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Alessia Perilli
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Guido Grossmann
- Institute of Cell and Interaction Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
- CEPLAS - Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Yasmine Meroz
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
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26
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Solimani F, Cardellicchio A, Nitti M, Lako A, Dimauro G, Renò V. A Systematic Review of Effective Hardware and Software Factors Affecting High-Throughput Plant Phenotyping. INFORMATION 2023. [DOI: 10.3390/info14040214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Abstract
Plant phenotyping studies the complex characteristics of plants, with the aim of evaluating and assessing their condition and finding better exemplars. Recently, a new branch emerged in the phenotyping field, namely, high-throughput phenotyping (HTP). Specifically, HTP exploits modern data sampling techniques to gather a high amount of data that can be used to improve the effectiveness of phenotyping. Hence, HTP combines the knowledge derived from the phenotyping domain with computer science, engineering, and data analysis techniques. In this scenario, machine learning (ML) and deep learning (DL) algorithms have been successfully integrated with noninvasive imaging techniques, playing a key role in automation, standardization, and quantitative data analysis. This study aims to systematically review two main areas of interest for HTP: hardware and software. For each of these areas, two influential factors were identified: for hardware, platforms and sensing equipment were analyzed; for software, the focus was on algorithms and new trends. The study was conducted following the PRISMA protocol, which allowed the refinement of the research on a wide selection of papers by extracting a meaningful dataset of 32 articles of interest. The analysis highlighted the diffusion of ground platforms, which were used in about 47% of reviewed methods, and RGB sensors, mainly due to their competitive costs, high compatibility, and versatility. Furthermore, DL-based algorithms accounted for the larger share (about 69%) of reviewed approaches, mainly due to their effectiveness and the focus posed by the scientific community over the last few years. Future research will focus on improving DL models to better handle hardware-generated data. The final aim is to create integrated, user-friendly, and scalable tools that can be directly deployed and used on the field to improve the overall crop yield.
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Affiliation(s)
- Firozeh Solimani
- Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing, National Research Council of Italy, Via Amendola 122 D/O, 70126 Bari, Italy
| | - Angelo Cardellicchio
- Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing, National Research Council of Italy, Via Amendola 122 D/O, 70126 Bari, Italy
| | - Massimiliano Nitti
- Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing, National Research Council of Italy, Via Amendola 122 D/O, 70126 Bari, Italy
| | - Alfred Lako
- Faculty of Civil Engineering, Polytechnic University of Tirana, Bulevardi Dëshmorët e Kombit Nr. 4, 1000 Tiranë, Albania
| | - Giovanni Dimauro
- Department of Computer Science, University of Bari, Via E. Orabona, 4, 70125 Bari, Italy
| | - Vito Renò
- Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing, National Research Council of Italy, Via Amendola 122 D/O, 70126 Bari, Italy
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27
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Zhang K, Rengel Z, Zhang F, White PJ, Shen J. Rhizosphere engineering for sustainable crop production: entropy-based insights. TRENDS IN PLANT SCIENCE 2023; 28:390-398. [PMID: 36470795 DOI: 10.1016/j.tplants.2022.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
There is a growing interest in exploring interactions at root-soil interface in natural and agricultural ecosystems, but an entropy-based understanding of these dynamic rhizosphere processes is lacking. We have developed a new conceptual model of rhizosphere regulation by localized nutrient supply using thermodynamic entropy. Increased nutrient-use efficiency is achieved by rhizosphere management based on self-organization and minimized entropy via equilibrium attractors comprising (i) optimized root strategies for nutrient acquisition and (ii) improved information exchange related to root-soil-microbe interactions. The cascading effects through different hierarchical levels amplify the underlying processes in plant-soil system. We propose a strategy for manipulating rhizosphere dynamics and improving nutrient-use efficiency by localized nutrient supply with minimization of entropy to underpin sustainable food/feed/fiber production.
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Affiliation(s)
- Kai Zhang
- Centre for Resources, Environment and Food Security, Department of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, China
| | - Zed Rengel
- Soil Science and Plant Nutrition, UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia; Institute for Adriatic Crops and Karst Reclamation, Split 21000, Croatia
| | - Fusuo Zhang
- Centre for Resources, Environment and Food Security, Department of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, China
| | - Philip J White
- Ecological Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Jianbo Shen
- Centre for Resources, Environment and Food Security, Department of Plant Nutrition, Key Laboratory of Plant-Soil Interactions, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, China.
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28
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Retzer K, Weckwerth W. Recent insights into metabolic and signalling events of directional root growth regulation and its implications for sustainable crop production systems. FRONTIERS IN PLANT SCIENCE 2023; 14:1154088. [PMID: 37008498 PMCID: PMC10060999 DOI: 10.3389/fpls.2023.1154088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/06/2023] [Indexed: 06/19/2023]
Abstract
Roots are sensors evolved to simultaneously respond to manifold signals, which allow the plant to survive. Root growth responses, including the modulation of directional root growth, were shown to be differently regulated when the root is exposed to a combination of exogenous stimuli compared to an individual stress trigger. Several studies pointed especially to the impact of the negative phototropic response of roots, which interferes with the adaptation of directional root growth upon additional gravitropic, halotropic or mechanical triggers. This review will provide a general overview of known cellular, molecular and signalling mechanisms involved in directional root growth regulation upon exogenous stimuli. Furthermore, we summarise recent experimental approaches to dissect which root growth responses are regulated upon which individual trigger. Finally, we provide a general overview of how to implement the knowledge gained to improve plant breeding.
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Affiliation(s)
- Katarzyna Retzer
- Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czechia
| | - Wolfram Weckwerth
- Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Molecular Systems Biology (MoSys), University of Vienna, Wien, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Wien, Austria
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29
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Shelden MC, Munns R. Crop root system plasticity for improved yields in saline soils. FRONTIERS IN PLANT SCIENCE 2023; 14:1120583. [PMID: 36909408 PMCID: PMC9999379 DOI: 10.3389/fpls.2023.1120583] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Crop yields must increase to meet the demands of a growing world population. Soil salinization is increasing due to the impacts of climate change, reducing the area of arable land for crop production. Plant root systems are plastic, and their architecture can be modulated to (1) acquire nutrients and water for growth, and (2) respond to hostile soil environments. Saline soils inhibit primary root growth and alter root system architecture (RSA) of crop plants. In this review, we explore how crop root systems respond and adapt to salinity, focusing predominately on the staple cereal crops wheat, maize, rice, and barley, that all play a major role in global food security. Cereal crops are classified as glycophytes (salt-sensitive) however salt-tolerance can differ both between species and within a species. In the past, due to the inherent difficulties associated with visualising and measuring root traits, crop breeding strategies have tended to focus on optimising shoot traits. High-resolution phenotyping techniques now make it possible to visualise and measure root traits in soil systems. A steep, deep and cheap root ideotype has been proposed for water and nitrogen capture. Changes in RSA can be an adaptive strategy to avoid saline soils whilst optimising nutrient and water acquisition. In this review we propose a new model for designing crops with a salt-tolerant root ideotype. The proposed root ideotype would exhibit root plasticity to adapt to saline soils, root anatomical changes to conserve energy and restrict sodium (Na+) uptake, and transport mechanisms to reduce the amount of Na+ transported to leaves. In the future, combining high-resolution root phenotyping with advances in crop genetics will allow us to uncover root traits in complex crop species such as wheat, that can be incorporated into crop breeding programs for yield stability in saline soils.
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Affiliation(s)
- Megan C. Shelden
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, SA, Australia
| | - Rana Munns
- Australian Research Council (ARC) Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Crawley, WA, Australia
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30
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Nair R, Strube M, Hertel M, Kolle O, Rolo V, Migliavacca M. High frequency root dynamics: sampling and interpretation using replicated robotic minirhizotrons. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:769-786. [PMID: 36273326 PMCID: PMC9899415 DOI: 10.1093/jxb/erac427] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/21/2022] [Indexed: 05/19/2023]
Abstract
Automating dynamic fine root data collection in the field is a longstanding challenge with multiple applications for co-interpretation and synthesis for ecosystem understanding. High frequency root data are only achievable with paired automated sampling and processing. However, automatic minirhizotron (root camera) instruments are still rare and data are often not collected in natural soils or analysed at high temporal resolution. Instruments must also be affordable for replication and robust under variable natural conditions. Here, we show a system built with off-the-shelf parts which samples at sub-daily resolution. We paired this with a neural network to analyse all images collected. We performed two mesocosm studies and two field trials alongside ancillary data collection (soil CO2 efflux, temperature, and moisture content, and 'PhenoCam'-derived above-ground dynamics). We produce robust and replicated daily time series of root dynamics under all conditions. Temporal root changes were a stronger driver than absolute biomass on soil CO2 efflux in the mesocosm. Proximal sensed above-ground dynamics and below-ground dynamics from minirhizotron data were not synchronized. Root properties extracted were sensitive to soil moisture and occasionally to time of day (potentially relating to soil moisture). This may only affect high frequency imagery and should be considered in interpreting such data.
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Affiliation(s)
| | - Martin Strube
- Max-Planck-Institute for Biogeochemistry, 07745 Jena, Germany
| | - Martin Hertel
- Max-Planck-Institute for Biogeochemistry, 07745 Jena, Germany
| | - Olaf Kolle
- Max-Planck-Institute for Biogeochemistry, 07745 Jena, Germany
| | - Victor Rolo
- Forest Research Group, INDEHESA, University of Extremadura, 10600, Plasencia, Spain
| | - Mirco Migliavacca
- Department for Biogeochemical Integration, Max-Planck-Institute for Biogeochemistry, 07745 Jena, Germany
- European Commission, Joint Research Centre, Ispra, Varese, Italy
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31
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Wu Q, Wu J, Hu P, Zhang W, Ma Y, Yu K, Guo Y, Cao J, Li H, Li B, Yao Y, Cao H, Zhang W. Quantification of the three-dimensional root system architecture using an automated rotating imaging system. PLANT METHODS 2023; 19:11. [PMID: 36732764 PMCID: PMC9896698 DOI: 10.1186/s13007-023-00988-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Crop breeding based on root system architecture (RSA) optimization is an essential factor for improving crop production in developing countries. Identification, evaluation, and selection of root traits of soil-grown crops require innovations that enable high-throughput and accurate quantification of three-dimensional (3D) RSA of crops over developmental time. RESULTS We proposed an automated imaging system and 3D imaging data processing pipeline to quantify the 3D RSA of soil-grown individual plants across seedlings to the mature stage. A multi-view automated imaging system composed of a rotary table and an imaging arm with 12 cameras mounted with a combination of fan-shaped and vertical distribution was developed to obtain 3D image data of roots grown on a customized root support mesh. A 3D imaging data processing pipeline was developed to quantify the 3D RSA based on the point cloud generated from multi-view images. The global architecture of root systems can be quantified automatically. Detailed analysis of the reconstructed 3D root model also allowed us to investigate the Spatio-temporal distribution of roots. A method combining horizontal slicing and iterative erosion and dilation was developed to automatically segment different root types, and identify local root traits (e.g., length, diameter of the main root, and length, diameter, initial angle, and the number of nodal roots or lateral roots). One maize (Zea mays L.) cultivar and two rapeseed (Brassica napus L.) cultivars at different growth stages were selected to test the performance of the automated imaging system and 3D imaging data processing pipeline. CONCLUSIONS The results demonstrated the capabilities of the proposed imaging and analytical system for high-throughput phenotyping of root traits for both monocotyledons and dicotyledons across growth stages. The proposed system offers a potential tool to further explore the 3D RSA for improving root traits and agronomic qualities of crops.
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Affiliation(s)
- Qian Wu
- IGRB-IAI Joint Laboratory of Germplasm Resources Innovation & Information Utilization, YuanQi-IAI Joint Laboratory for Agricultural Digital Twin, Institute of Agricultural Information, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Jie Wu
- Plant Phenomics Research Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Pengcheng Hu
- School of Agriculture and Food Sciences, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Weixin Zhang
- IGRB-IAI Joint Laboratory of Germplasm Resources Innovation & Information Utilization, YuanQi-IAI Joint Laboratory for Agricultural Digital Twin, Institute of Agricultural Information, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yuntao Ma
- College of Land Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Kun Yu
- IGRB-IAI Joint Laboratory of Germplasm Resources Innovation & Information Utilization, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Yan Guo
- College of Land Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jing Cao
- IGRB-IAI Joint Laboratory of Germplasm Resources Innovation & Information Utilization, YuanQi-IAI Joint Laboratory for Agricultural Digital Twin, Institute of Agricultural Information, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Huayong Li
- IGRB-IAI Joint Laboratory of Germplasm Resources Innovation & Information Utilization, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
| | - Baiming Li
- IGRB-IAI Joint Laboratory of Germplasm Resources Innovation & Information Utilization, YuanQi-IAI Joint Laboratory for Agricultural Digital Twin, Institute of Agricultural Information, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yuyang Yao
- College of Electronics & Information Engineering, Nanjing University of Information Science and Technology, Nanjing, 210044, Jiangsu, China
| | - Hongxin Cao
- IGRB-IAI Joint Laboratory of Germplasm Resources Innovation & Information Utilization, YuanQi-IAI Joint Laboratory for Agricultural Digital Twin, Institute of Agricultural Information, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China.
| | - Wenyu Zhang
- IGRB-IAI Joint Laboratory of Germplasm Resources Innovation & Information Utilization, YuanQi-IAI Joint Laboratory for Agricultural Digital Twin, Institute of Agricultural Information, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, Jiangsu, China.
- School of Agricultural Engineering, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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Peeples J, Xu W, Gloaguen R, Rowland D, Zare A, Brym Z. Spatial and Texture Analysis of Root System distribution with Earth mover's Distance (STARSEED). PLANT METHODS 2023; 19:2. [PMID: 36604751 PMCID: PMC9814335 DOI: 10.1186/s13007-022-00974-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
PURPOSE Root system architectures are complex and challenging to characterize effectively for agronomic and ecological discovery. METHODS We propose a new method, Spatial and Texture Analysis of Root SystEm distribution with Earth mover's Distance (STARSEED), for comparing root system distributions that incorporates spatial information through a novel application of the Earth Mover's Distance (EMD). RESULTS We illustrate that the approach captures the response of sesame root systems for different genotypes and soil moisture levels. STARSEED provides quantitative and visual insights into changes that occur in root architectures across experimental treatments. CONCLUSION STARSEED can be generalized to other plants and provides insight into root system architecture development and response to varying growth conditions not captured by existing root architecture metrics and models. The code and data for our experiments are publicly available: https://github.com/GatorSense/STARSEED .
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Affiliation(s)
- Joshua Peeples
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, 77845 USA
| | - Weihuang Xu
- Department of Electrical and Computer Engineering, University of Florida, Gainesville, 32611 USA
| | | | - Diane Rowland
- College of Natural Sciences, Forestry, and Agriculture, University of Maine, Orono, 04469 USA
| | - Alina Zare
- Department of Electrical and Computer Engineering, University of Florida, Gainesville, 32611 USA
| | - Zachary Brym
- Tropical Research and Education Center, University of Florida, Gainesville, 33031 USA
- Department of Agronomy, University of Florida, Gainesville, 32611 USA
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Genome-Wide Association Studies of Seven Root Traits in Soybean ( Glycine max L.) Landraces. Int J Mol Sci 2023; 24:ijms24010873. [PMID: 36614316 PMCID: PMC9821504 DOI: 10.3390/ijms24010873] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 01/05/2023] Open
Abstract
Soybean [Glycine max (L.) Merr.], an important oilseed crop, is a low-cost source of protein and oil. In Southeast Asia and Africa, soybeans are widely cultivated for use as traditional food and feed and industrial purposes. Given the ongoing changes in global climate, developing crops that are resistant to climatic extremes and produce viable yields under predicted climatic conditions will be essential in the coming decades. To develop such crops, it will be necessary to gain a thorough understanding of the genetic basis of agronomic and plant root traits. As plant roots generally lie beneath the soil surface, detailed observations and phenotyping throughout plant development present several challenges, and thus the associated traits have tended to be ignored in genomics studies. In this study, we phenotyped 357 soybean landraces at the early vegetative (V2) growth stages and used a 180 K single-nucleotide polymorphism (SNP) soybean array in a genome-wide association study (GWAS) conducted to determine the phenotypic relationships among root traits, elucidate the genetic bases, and identify significant SNPs associated with root trait-controlling genomic regions/loci. A total of 112 significant SNP loci/regions were detected for seven root traits, and we identified 55 putative candidate genes considered to be the most promising. Our findings in this study indicate that a combined approach based on SNP array and GWAS analyses can be applied to unravel the genetic basis of complex root traits in soybean, and may provide an alternative high-resolution marker strategy to traditional bi-parental mapping. In addition, the identified SNPs, candidate genes, and diverse variations in the root traits of soybean landraces will serve as a valuable basis for further application in genetic studies and the breeding of climate-resilient soybeans characterized by improved root traits.
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Alle J, Gruber R, Wörlein N, Uhlmann N, Claußen J, Wittenberg T, Gerth S. 3D segmentation of plant root systems using spatial pyramid pooling and locally adaptive field-of-view inference. FRONTIERS IN PLANT SCIENCE 2023; 14:1120189. [PMID: 37082341 PMCID: PMC10110838 DOI: 10.3389/fpls.2023.1120189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/13/2023] [Indexed: 05/03/2023]
Abstract
Background The non-invasive 3D-imaging and successive 3D-segmentation of plant root systems has gained interest within fundamental plant research and selectively breeding resilient crops. Currently the state of the art consists of computed tomography (CT) scans and reconstruction followed by an adequate 3D-segmentation process. Challenge Generating an exact 3D-segmentation of the roots becomes challenging due to inhomogeneous soil composition, as well as high scale variance in the root structures themselves. Approach (1) We address the challenge by combining deep convolutional neural networks (DCNNs) with a weakly supervised learning paradigm. Furthermore, (2) we apply a spatial pyramid pooling (SPP) layer to cope with the scale variance of roots. (3) We generate a fine-tuned training data set with a specialized sub-labeling technique. (4) Finally, to yield fast and high-quality segmentations, we propose a specialized iterative inference algorithm, which locally adapts the field of view (FoV) for the network. Experiments We compare our segmentation results against an analytical reference algorithm for root segmentation (RootForce) on a set of roots from Cassava plants and show qualitatively that an increased amount of root voxels and root branches can be segmented. Results Our findings show that with the proposed DCNN approach combined with the dynamic inference, much more, and especially fine, root structures can be detected than with a classical analytical reference method. Conclusion We show that the application of the proposed DCNN approach leads to better and more robust root segmentation, especially for very small and thin roots.
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Affiliation(s)
- Jonas Alle
- Fraunhofer Institut für Integrierte Schaltungen (IIS), Fraunhofer Institute for Integrated Circuits Institut für Integrierte Schaltungen (IIS), Division Development Center X-Ray Technology, Fürth, Germany
| | - Roland Gruber
- Fraunhofer Institut für Integrierte Schaltungen (IIS), Fraunhofer Institute for Integrated Circuits Institut für Integrierte Schaltungen (IIS), Division Development Center X-Ray Technology, Fürth, Germany
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Chair for Visual Computing, Erlangen, Germany
| | - Norbert Wörlein
- Fraunhofer Institut für Integrierte Schaltungen (IIS), Fraunhofer Institute for Integrated Circuits Institut für Integrierte Schaltungen (IIS), Division Development Center X-Ray Technology, Fürth, Germany
| | - Norman Uhlmann
- Fraunhofer Institut für Integrierte Schaltungen (IIS), Fraunhofer Institute for Integrated Circuits Institut für Integrierte Schaltungen (IIS), Division Development Center X-Ray Technology, Fürth, Germany
| | - Joelle Claußen
- Fraunhofer Institut für Integrierte Schaltungen (IIS), Fraunhofer Institute for Integrated Circuits Institut für Integrierte Schaltungen (IIS), Division Development Center X-Ray Technology, Fürth, Germany
| | - Thomas Wittenberg
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Chair for Visual Computing, Erlangen, Germany
- Fraunhofer Institut für Integrierte Schaltungen (IIS), Fraunhofer Institute for Integrated Circuits Institut für Integrierte Schaltungen (IIS), Division Smart Sensors and Electronics, Erlangen, Germany
| | - Stefan Gerth
- Fraunhofer Institut für Integrierte Schaltungen (IIS), Fraunhofer Institute for Integrated Circuits Institut für Integrierte Schaltungen (IIS), Division Development Center X-Ray Technology, Fürth, Germany
- *Correspondence: Stefan Gerth,
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Dowd TG, Li M, Bagnall GC, Johnston A, Topp CN. Root system architecture and environmental flux analysis in mature crops using 3D root mesocosms. FRONTIERS IN PLANT SCIENCE 2022; 13:1041404. [PMID: 36589101 PMCID: PMC9800027 DOI: 10.3389/fpls.2022.1041404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
Current methods of root sampling typically only obtain small or incomplete sections of root systems and do not capture their true complexity. To facilitate the visualization and analysis of full-sized plant root systems in 3-dimensions, we developed customized mesocosm growth containers. While highly scalable, the design presented here uses an internal volume of 45 ft3 (1.27 m3), suitable for large crop and bioenergy grass root systems to grow largely unconstrained. Furthermore, they allow for the excavation and preservation of 3-dimensional root system architecture (RSA), and facilitate the collection of time-resolved subterranean environmental data. Sensor arrays monitoring matric potential, temperature and CO2 levels are buried in a grid formation at various depths to assess environmental fluxes at regular intervals. Methods of 3D data visualization of fluxes were developed to allow for comparison with root system architectural traits. Following harvest, the recovered root system can be digitally reconstructed in 3D through photogrammetry, which is an inexpensive method requiring only an appropriate studio space and a digital camera. We developed a pipeline to extract features from the 3D point clouds, or from derived skeletons that include point cloud voxel number as a proxy for biomass, total root system length, volume, depth, convex hull volume and solidity as a function of depth. Ground-truthing these features with biomass measurements from manually dissected root systems showed a high correlation. We evaluated switchgrass, maize, and sorghum root systems to highlight the capability for species wide comparisons. We focused on two switchgrass ecotypes, upland (VS16) and lowland (WBC3), in identical environments to demonstrate widely different root system architectures that may be indicative of core differences in their rhizoeconomic foraging strategies. Finally, we imposed a strong physiological water stress and manipulated the growth medium to demonstrate whole root system plasticity in response to environmental stimuli. Hence, these new "3D Root Mesocosms" and accompanying computational analysis provides a new paradigm for study of mature crop systems and the environmental fluxes that shape them.
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Üstüner S, Schäfer P, Eichmann R. Development specifies, diversifies and empowers root immunity. EMBO Rep 2022; 23:e55631. [PMID: 36330761 PMCID: PMC9724680 DOI: 10.15252/embr.202255631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/10/2022] [Accepted: 10/13/2022] [Indexed: 08/04/2023] Open
Abstract
Roots are a highly organised plant tissue consisting of different cell types with distinct developmental functions defined by cell identity networks. Roots are the target of some of the most devastating diseases and possess a highly effective immune system. The recognition of microbe- or plant-derived molecules released in response to microbial attack is highly important in the activation of complex immunity gene networks. Development and immunity are intertwined, and immunity activation can result in growth inhibition. In turn, by connecting immunity and cell identity regulators, cell types are able to launch a cell type-specific immunity based on the developmental function of each cell type. By this strategy, fundamental developmental processes of each cell type contribute their most basic functions to drive cost-effective but highly diverse and, thus, efficient immune responses. This review highlights the interdependence of root development and immunity and how the developmental age of root cells contributes to positive and negative outcomes of development-immunity cross-talk.
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Affiliation(s)
- Sim Üstüner
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Patrick Schäfer
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Ruth Eichmann
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
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Möhl P, von Büren RS, Hiltbrunner E. Growth of alpine grassland will start and stop earlier under climate warming. Nat Commun 2022; 13:7398. [PMID: 36456572 PMCID: PMC9715633 DOI: 10.1038/s41467-022-35194-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022] Open
Abstract
Alpine plants have evolved a tight seasonal cycle of growth and senescence to cope with a short growing season. The potential growing season length (GSL) is increasing because of climate warming, possibly prolonging plant growth above- and belowground. We tested whether growth dynamics in typical alpine grassland are altered when the natural GSL (2-3 months) is experimentally advanced and thus, prolonged by 2-4 months. Additional summer months did not extend the growing period, as canopy browning started 34-41 days after the start of the season, even when GSL was more than doubled. Less than 10% of roots were produced during the added months, suggesting that root growth was as conservative as leaf growth. Few species showed a weak second greening under prolonged GSL, but not the dominant sedge. A longer growing season under future climate may therefore not extend growth in this widespread alpine community, but will foster species that follow a less strict phenology.
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Affiliation(s)
- Patrick Möhl
- Department of Environmental Sciences, University of Basel, Schönbeinstrasse 6, CH-4056, Basel, Switzerland.
| | - Raphael S von Büren
- Department of Environmental Sciences, University of Basel, Schönbeinstrasse 6, CH-4056, Basel, Switzerland
| | - Erika Hiltbrunner
- Department of Environmental Sciences, University of Basel, Schönbeinstrasse 6, CH-4056, Basel, Switzerland
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Xu Y, Zhang X, Li H, Zheng H, Zhang J, Olsen MS, Varshney RK, Prasanna BM, Qian Q. Smart breeding driven by big data, artificial intelligence, and integrated genomic-enviromic prediction. MOLECULAR PLANT 2022; 15:1664-1695. [PMID: 36081348 DOI: 10.1016/j.molp.2022.09.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 08/20/2022] [Accepted: 09/02/2022] [Indexed: 05/12/2023]
Abstract
The first paradigm of plant breeding involves direct selection-based phenotypic observation, followed by predictive breeding using statistical models for quantitative traits constructed based on genetic experimental design and, more recently, by incorporation of molecular marker genotypes. However, plant performance or phenotype (P) is determined by the combined effects of genotype (G), envirotype (E), and genotype by environment interaction (GEI). Phenotypes can be predicted more precisely by training a model using data collected from multiple sources, including spatiotemporal omics (genomics, phenomics, and enviromics across time and space). Integration of 3D information profiles (G-P-E), each with multidimensionality, provides predictive breeding with both tremendous opportunities and great challenges. Here, we first review innovative technologies for predictive breeding. We then evaluate multidimensional information profiles that can be integrated with a predictive breeding strategy, particularly envirotypic data, which have largely been neglected in data collection and are nearly untouched in model construction. We propose a smart breeding scheme, integrated genomic-enviromic prediction (iGEP), as an extension of genomic prediction, using integrated multiomics information, big data technology, and artificial intelligence (mainly focused on machine and deep learning). We discuss how to implement iGEP, including spatiotemporal models, environmental indices, factorial and spatiotemporal structure of plant breeding data, and cross-species prediction. A strategy is then proposed for prediction-based crop redesign at both the macro (individual, population, and species) and micro (gene, metabolism, and network) scales. Finally, we provide perspectives on translating smart breeding into genetic gain through integrative breeding platforms and open-source breeding initiatives. We call for coordinated efforts in smart breeding through iGEP, institutional partnerships, and innovative technological support.
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Affiliation(s)
- Yunbi Xu
- Institute of Crop Sciences, CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China; CIMMYT-China Tropical Maize Research Center, School of Food Science and Engineering, Foshan University, Foshan, Guangdong 528231, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261325, China.
| | - Xingping Zhang
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Huihui Li
- Institute of Crop Sciences, CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China
| | - Hongjian Zheng
- CIMMYT-China Specialty Maize Research Center, Shanghai Academy of Agricultural Sciences, Shanghai 201400, China
| | - Jianan Zhang
- MolBreeding Biotechnology Co., Ltd., Shijiazhuang, Hebei 050035, China
| | - Michael S Olsen
- CIMMYT (International Maize and Wheat Improvement Center), ICRAF Campus, United Nations Avenue, Nairobi, Kenya
| | - Rajeev K Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Australia
| | - Boddupalli M Prasanna
- CIMMYT (International Maize and Wheat Improvement Center), ICRAF Campus, United Nations Avenue, Nairobi, Kenya
| | - Qian Qian
- Institute of Crop Sciences, CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Abbas M, Abid MA, Meng Z, Abbas M, Wang P, Lu C, Askari M, Akram U, Ye Y, Wei Y, Wang Y, Guo S, Liang C, Zhang R. Integrating advancements in root phenotyping and genome-wide association studies to open the root genetics gateway. PHYSIOLOGIA PLANTARUM 2022; 174:e13787. [PMID: 36169590 DOI: 10.1111/ppl.13787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/12/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
Plant adaptation to challenging environmental conditions around the world has made root growth and development an important research area for plant breeders and scientists. Targeted manipulation of root system architecture (RSA) to increase water and nutrient use efficiency can minimize the adverse effects of climate change on crop production. However, phenotyping of RSA is a major bottleneck since the roots are hidden in the soil. Recently the development of 2- and 3D root imaging techniques combined with the genome-wide association studies (GWASs) have opened up new research tools to identify the genetic basis of RSA. These approaches provide a comprehensive understanding of the RSA, by accelerating the identification and characterization of genes involved in root growth and development. This review summarizes the latest developments in phenotyping techniques and GWAS for RSA, which are used to map important genes regulating various aspects of RSA under varying environmental conditions. Furthermore, we discussed about the state-of-the-art image analysis tools integrated with various phenotyping platforms for investigating and quantifying root traits with the highest phenotypic plasticity in both artificial and natural environments which were used for large scale association mapping studies, leading to the identification of RSA phenotypes and their underlying genetics with the greatest potential for RSA improvement. In addition, challenges in root phenotyping and GWAS are also highlighted, along with future research directions employing machine learning and pan-genomics approaches.
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Affiliation(s)
- Mubashir Abbas
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Ali Abid
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhigang Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Manzar Abbas
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Peilin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chao Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Askari
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Umar Akram
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yulu Ye
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunxiao Wei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sandui Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chengzhen Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rui Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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Urfan M, Hakla HR, Sharma S, Khajuria M, Satbhai SB, Vyas D, Bhougal S, Yadav NS, Pal S. Paclobutrazol improves surface water use efficiency by regulating allometric trait behavior in maize. CHEMOSPHERE 2022; 307:135958. [PMID: 35952796 DOI: 10.1016/j.chemosphere.2022.135958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/13/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
Paclobutrazol (PBZ) role in drought management of maize is least understood. In maize, root traits are linked with surface water management. Over three years, early and terminal deficit irrigation (EDI and TDI) with or without PBZ were imposed on DKC-9144 and PG-2475 maize varieties. Several allometric parameters viz. stem height, stem diameter, leaf area and root traits along with physiological processes were measured. Implication of these parameters in the management of soil surface irrigation in terms of water use efficiency (WUE) was demonstrated in maize. Increased number of lateral roots and root number density in DKC-9144 provided more surface area for water absorption for better management of EDI. Root growth rates showed a similar pattern with root length, root surface areas, and root numbers in EDI. Elevated expressions of ZmRTCL, ZmRTCS and ZmARF34 in EDI and EDI plus PBZ were associated with seminal roots and root laterals initiation. Under TDI alone or in combination with PBZ, root lengths (BRL, CRL, SRL) and root surface areas varied in DKC-9144 and PG-2475 over control. Furthermore, correlation analysis showed that decrease in WUE under TDI was significantly associated with a reduction in stem thickness and leaf surface area. For WUE_N in TDI and PBZ plus TDI, structural equation modelling proposed, brace root surface area (BRSA_N) as a positive contributor, while a negative contributor was seminal root surface area (SRSA_N). Present study explained the importance of specific root traits and their association with other allometric parameters for improving WUE in DKC-9144 variety of maize and the crop in general.
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Affiliation(s)
- Mohammad Urfan
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu, 180006, India.
| | - Haroon Rashid Hakla
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu, 180006, India.
| | - Shubham Sharma
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu, 180006, India.
| | - Manu Khajuria
- Biodiversity and Applied Botany Division, CSIR- Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India.
| | - Santosh B Satbhai
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, SAS Nagar, Punjab, 140406, India.
| | - Dhiraj Vyas
- Biodiversity and Applied Botany Division, CSIR- Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India.
| | - Sunil Bhougal
- Department of Statistics, University of Jammu, Jammu, 180006, India.
| | - Narendra Singh Yadav
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, 403587, Canada.
| | - Sikander Pal
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu, 180006, India.
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Seidenthal K, Panjvani K, Chandnani R, Kochian L, Eramian M. Iterative image segmentation of plant roots for high-throughput phenotyping. Sci Rep 2022; 12:16563. [PMID: 36195610 PMCID: PMC9532414 DOI: 10.1038/s41598-022-19754-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 09/02/2022] [Indexed: 11/24/2022] Open
Abstract
Accurate segmentation of root system architecture (RSA) from 2D images is an important step in studying phenotypic traits of root systems. Various approaches to image segmentation exist but many of them are not well suited to the thin and reticulated structures characteristic of root systems. The findings presented here describe an approach to RSA segmentation that takes advantage of the inherent structural properties of the root system, a segmentation network architecture we call ITErRoot. We have also generated a novel 2D root image dataset which utilizes an annotation tool developed for producing high quality ground truth segmentation of root systems. Our approach makes use of an iterative neural network architecture to leverage the thin and highly branched properties of root systems for accurate segmentation. Rigorous analysis of model properties was carried out to obtain a high-quality model for 2D root segmentation. Results show a significant improvement over other recent approaches to root segmentation. Validation results show that the model generalizes to plant species with fine and highly branched RSA’s, and performs particularly well in the presence of non-root objects.
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Affiliation(s)
- Kyle Seidenthal
- Department of Computer Science, University of Saskatchewan, 110 Science Place, Saskatoon, SK, S7N 5C9, Canada
| | - Karim Panjvani
- Global Institute for Food Security, University of Saskatchewan, 421 Downey Road, Saskatoon, SK, S7N 4L8, Canada
| | - Rahul Chandnani
- Global Institute for Food Security, University of Saskatchewan, 421 Downey Road, Saskatoon, SK, S7N 4L8, Canada
| | - Leon Kochian
- Global Institute for Food Security, University of Saskatchewan, 421 Downey Road, Saskatoon, SK, S7N 4L8, Canada
| | - Mark Eramian
- Department of Computer Science, University of Saskatchewan, 110 Science Place, Saskatoon, SK, S7N 5C9, Canada.
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Zhao H, Wang N, Sun H, Zhu L, Zhang K, Zhang Y, Zhu J, Li A, Bai Z, Liu X, Dong H, Liu L, Li C. RhizoPot platform: A high-throughput in situ root phenotyping platform with integrated hardware and software. FRONTIERS IN PLANT SCIENCE 2022; 13:1004904. [PMID: 36247541 PMCID: PMC9558169 DOI: 10.3389/fpls.2022.1004904] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/15/2022] [Indexed: 06/01/2023]
Abstract
Quantitative analysis of root development is becoming a preferred option in assessing the function of hidden underground roots, especially in studying resistance to abiotic stresses. It can be enhanced by acquiring non-destructive phenotypic information on roots, such as rhizotrons. However, it is challenging to develop high-throughput phenotyping equipment for acquiring and analyzing in situ root images of root development. In this study, the RhizoPot platform, a high-throughput in situ root phenotyping platform integrating plant culture, automatic in situ root image acquisition, and image segmentation, was proposed for quantitative analysis of root development. Plants (1-5) were grown in each RhizoPot, and the growth time depended on the type of plant and the experimental requirements. For example, the growth time of cotton was about 110 days. The imaging control software (RhizoAuto) could automatically and non-destructively image the roots of RhizoPot-cultured plants based on the set time and resolution (50-4800 dpi) and obtain high-resolution (>1200 dpi) images in batches. The improved DeepLabv3+ tool was used for batch processing of root images. The roots were automatically segmented and extracted from the background for analysis of information on radical features using conventional root software (WinRhizo and RhizoVision Explorer). Root morphology, root growth rate, and lifespan analysis were conducted using in situ root images and segmented images. The platform illustrated the dynamic response characteristics of root phenotypes in cotton. In conclusion, the RhizoPot platform has the characteristics of low cost, high-efficiency, and high-throughput, and thus it can effectively monitor the development of plant roots and realize the quantitative analysis of root phenotypes in situ.
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Affiliation(s)
- Hongjuan Zhao
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Nan Wang
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
- College of Mechanical and Electrical Engineering, Hebei Agricultural University, Baoding, China
| | - Hongchun Sun
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Lingxiao Zhu
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Ke Zhang
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Yongjiang Zhang
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Jijie Zhu
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Anchang Li
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Zhiying Bai
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Xiaoqing Liu
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Hezhong Dong
- Cotton Research Center, Shandong Key Lab for Cotton Culture and Physiology, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Liantao Liu
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Cundong Li
- State Key Laboratory of North China Crop Improvement and Regulation/Key Laboratory of Crop Growth Regulation of Hebei Province/College of Agronomy, Hebei Agricultural University, Baoding, China
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Herrero-Huerta M, Raumonen P, Gonzalez-Aguilera D. 4DRoot: Root phenotyping software for temporal 3D scans by X-ray computed tomography. FRONTIERS IN PLANT SCIENCE 2022; 13:986856. [PMID: 36212319 PMCID: PMC9539560 DOI: 10.3389/fpls.2022.986856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Currently, plant phenomics is considered the key to reducing the genotype-to-phenotype knowledge gap in plant breeding. In this context, breakthrough imaging technologies have demonstrated high accuracy and reliability. The X-ray computed tomography (CT) technology can noninvasively scan roots in 3D; however, it is urgently required to implement high-throughput phenotyping procedures and analyses to increase the amount of data to measure more complex root phenotypic traits. We have developed a spatial-temporal root architectural modeling software tool based on 4D data from temporal X-ray CT scans. Through a cylinder fitting, we automatically extract significant root architectural traits, distribution, and hierarchy. The open-source software tool is named 4DRoot and implemented in MATLAB. The source code is freely available at https://github.com/TIDOP-USAL/4DRoot. In this research, 3D root scans from the black walnut tree were analyzed, a punctual scan for the spatial study and a weekly time-slot series for the temporal one. 4DRoot provides breeders and root biologists an objective and useful tool to quantify carbon sequestration throw trait extraction. In addition, 4DRoot could help plant breeders to improve plants to meet the food, fuel, and fiber demands in the future, in order to increase crop yield while reducing farming inputs.
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Affiliation(s)
- Monica Herrero-Huerta
- Department of Cartographic and Land Engineering, Higher Polytechnic School of Ávila, Universidad de Salamanca, Ávila, Spain
| | - Pasi Raumonen
- Department of Computing Sciences, Tampere University, Tampere, Finland
| | - Diego Gonzalez-Aguilera
- Department of Cartographic and Land Engineering, Higher Polytechnic School of Ávila, Universidad de Salamanca, Ávila, Spain
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Dutilleul P, Mudalige N, Rivest LP. Learning how a tree branches out: A statistical modeling approach. PLoS One 2022; 17:e0274168. [PMID: 36129851 PMCID: PMC9491565 DOI: 10.1371/journal.pone.0274168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/23/2022] [Indexed: 11/18/2022] Open
Abstract
The increasingly large size of the graphical and numerical data sets collected with modern technologies requires constant update and upgrade of the statistical models, methods and procedures to be used for their analysis in order to optimize learning and maximize knowledge and understanding. This is the case for plant CT scanning (CT: computed tomography), including applications aimed at studying leaf canopies and the structural complexity of the branching patterns that support them in trees. Therefore, we first show after a brief review, how the CT scanning data can be leveraged by constructing an analytical representation of a tree branching structure where each branch is represented by a line segment in 3D and classified in a level of a hierarchy, starting with the trunk (level 1). Each segment, or branch, is characterized by four variables: (i) the position on its parent, (ii) its orientation, a unit vector in 3D, (iii) its length, and (iv) the number of offspring that it bears. The branching structure of a tree can then be investigated by calculating descriptive statistics on these four variables. A deeper analysis, based on statistical models aiming to explain how the characteristics of a branch are associated with those of its parents, is also presented. The branching patterns of three miniature trees that were CT scanned are used to showcase the statistical modeling framework, and the differences in their structural complexity are reflected in the results. Overall, the most important determinant of a tree structure appears to be the length of the branches attached to the trunk. This variable impacts the characteristics of all the other branches of the tree.
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Affiliation(s)
- Pierre Dutilleul
- Department of Plant Science, McGill University, Montréal, Québec, Canada
| | - Nishan Mudalige
- Department of Mathematics and Statistics, Université Laval, Québec City, Québec, Canada
| | - Louis-Paul Rivest
- Department of Mathematics and Statistics, Université Laval, Québec City, Québec, Canada
- * E-mail:
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Ahmad N, Ibrahim S, Tian Z, Kuang L, Wang X, Wang H, Dun X. Quantitative trait loci mapping reveals important genomic regions controlling root architecture and shoot biomass under nitrogen, phosphorus, and potassium stress in rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2022; 13:994666. [PMID: 36172562 PMCID: PMC9511887 DOI: 10.3389/fpls.2022.994666] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Plants rely on root systems for nutrient uptake from soils. Marker-assisted selection helps breeders to select desirable root traits for effective nutrient uptake. Here, 12 root and biomass traits were investigated at the seedling stage under low nitrogen (LN), low phosphorus (LP), and low potassium (LK) conditions, respectively, in a recombinant inbred line (RIL) population, which was generated from Brassica napus L. Zhongshuang11 and 4D122 with significant differences in root traits and nutrient efficiency. Significant differences for all the investigated traits were observed among RILs, with high heritabilities (0.43-0.74) and high correlations between the different treatments. Quantitative trait loci (QTL) mapping identified 57, 27, and 36 loci, explaining 4.1-10.9, 4.6-10.8, and 4.9-17.4% phenotypic variances under LN, LP, and LK, respectively. Through QTL-meta analysis, these loci were integrated into 18 significant QTL clusters. Four major QTL clusters involved 25 QTLs that could be repeatedly detected and explained more than 10% phenotypic variances, including two NPK-common and two specific QTL clusters (K and NK-specific), indicating their critical role in cooperative nutrients uptake of N, P, and K. Moreover, 264 genes within the four major QTL clusters having high expressions in roots and SNP/InDel variations between two parents were identified as potential candidate genes. Thirty-eight of them have been reported to be associated with root growth and development and/or nutrient stress tolerance. These key loci and candidate genes lay the foundation for deeper dissection of the NPK starvation response mechanisms in B. napus.
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Affiliation(s)
- Nazir Ahmad
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
| | - Sani Ibrahim
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
| | - Ze Tian
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
| | - Lieqiong Kuang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
| | - Xinfa Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Hanzhong Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xiaoling Dun
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Wuhan, China
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Langan P, Bernád V, Walsh J, Henchy J, Khodaeiaminjan M, Mangina E, Negrão S. Phenotyping for waterlogging tolerance in crops: current trends and future prospects. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5149-5169. [PMID: 35642593 PMCID: PMC9440438 DOI: 10.1093/jxb/erac243] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Yield losses to waterlogging are expected to become an increasingly costly and frequent issue in some regions of the world. Despite the extensive work that has been carried out examining the molecular and physiological responses to waterlogging, phenotyping for waterlogging tolerance has proven difficult. This difficulty is largely due to the high variability of waterlogging conditions such as duration, temperature, soil type, and growth stage of the crop. In this review, we highlight use of phenotyping to assess and improve waterlogging tolerance in temperate crop species. We start by outlining the experimental methods that have been utilized to impose waterlogging stress, ranging from highly controlled conditions of hydroponic systems to large-scale screenings in the field. We also describe the phenotyping traits used to assess tolerance ranging from survival rates and visual scoring to precise photosynthetic measurements. Finally, we present an overview of the challenges faced in attempting to improve waterlogging tolerance, the trade-offs associated with phenotyping in controlled conditions, limitations of classic phenotyping methods, and future trends using plant-imaging methods. If effectively utilized to increase crop resilience to changing climates, crop phenotyping has a major role to play in global food security.
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Affiliation(s)
- Patrick Langan
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Villő Bernád
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Jason Walsh
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- School of Computer Science and UCD Energy Institute, University College Dublin, Dublin, Ireland
| | - Joey Henchy
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | | | - Eleni Mangina
- School of Computer Science and UCD Energy Institute, University College Dublin, Dublin, Ireland
| | - Sónia Negrão
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
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Sandhu KS, Shiv A, Kaur G, Meena MR, Raja AK, Vengavasi K, Mall AK, Kumar S, Singh PK, Singh J, Hemaprabha G, Pathak AD, Krishnappa G, Kumar S. Integrated Approach in Genomic Selection to Accelerate Genetic Gain in Sugarcane. PLANTS 2022; 11:plants11162139. [PMID: 36015442 PMCID: PMC9412483 DOI: 10.3390/plants11162139] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/08/2022] [Accepted: 08/08/2022] [Indexed: 11/30/2022]
Abstract
Marker-assisted selection (MAS) has been widely used in the last few decades in plant breeding programs for the mapping and introgression of genes for economically important traits, which has enabled the development of a number of superior cultivars in different crops. In sugarcane, which is the most important source for sugar and bioethanol, marker development work was initiated long ago; however, marker-assisted breeding in sugarcane has been lagging, mainly due to its large complex genome, high levels of polyploidy and heterozygosity, varied number of chromosomes, and use of low/medium-density markers. Genomic selection (GS) is a proven technology in animal breeding and has recently been incorporated in plant breeding programs. GS is a potential tool for the rapid selection of superior genotypes and accelerating breeding cycle. However, its full potential could be realized by an integrated approach combining high-throughput phenotyping, genotyping, machine learning, and speed breeding with genomic selection. For better understanding of GS integration, we comprehensively discuss the concept of genetic gain through the breeder’s equation, GS methodology, prediction models, current status of GS in sugarcane, challenges of prediction accuracy, challenges of GS in sugarcane, integrated GS, high-throughput phenotyping (HTP), high-throughput genotyping (HTG), machine learning, and speed breeding followed by its prospective applications in sugarcane improvement.
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Affiliation(s)
- Karansher Singh Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA
| | - Aalok Shiv
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Gurleen Kaur
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Mintu Ram Meena
- Regional Center, ICAR-Sugarcane Breeding Institute, Karnal 132001, India
| | - Arun Kumar Raja
- Division of Crop Production, ICAR-Sugarcane Breeding Institute, Coimbatore 641007, India
| | - Krishnapriya Vengavasi
- Division of Crop Production, ICAR-Sugarcane Breeding Institute, Coimbatore 641007, India
| | - Ashutosh Kumar Mall
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Sanjeev Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Praveen Kumar Singh
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Jyotsnendra Singh
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Govind Hemaprabha
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore 641007, India
| | - Ashwini Dutt Pathak
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
| | - Gopalareddy Krishnappa
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore 641007, India
- Correspondence: (G.K.); (S.K.)
| | - Sanjeev Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Sugarcane Research, Lucknow 226002, India
- Correspondence: (G.K.); (S.K.)
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Kim SH, Subramanian P, Hahn BS, Ha BK. High-Throughput Phenotypic Characterization and Diversity Analysis of Soybean Roots (Glycine max L.). PLANTS 2022; 11:plants11152017. [PMID: 35956495 PMCID: PMC9370148 DOI: 10.3390/plants11152017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/21/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022]
Abstract
Soybean (Glycine max L.) is a crop native to Northeast Asia, including China, Korea, and Japan, but currently cultivated all over the world. The National Agrobiodiversity Center in Korea at the Rural Development Administration (RDA) conserves approximately 26,000 accessions and conducts characterizations of its accessions, to accumulate new information. Roots are essential organs of a plant, providing mechanical support, as well as aiding water and nutrient acquisition. Currently, not much information is available in international gene banks regarding root characterization. We studied the root phenotype of 374 soybean accessions, using a high-throughput method. Eight root morphological traits (RMT) were studied and we observed that the surface area (SA), number of forks (NF), and number of tips (NT) had a positive correlation with total length (LENGTH), and that link average length (LAL) and other traits all had a negative correlation. Additionally, the correlation between seed traits (height, width, and 100-seed weight) and root traits was confirmed for the first time in this experiment. The germplasms were divided into three clusters by k-means clustering, and orthogonal projections to latent structures discriminant analysis (OPLS-DA) was used to compare clusters. The most distinctive characteristics between clusters were total lateral average length (LAD) and total lateral average length (DIAM). Cluster 3 had the highest LENGTH, SA, NF, and NF, whereas cluster 1 had the smallest LENGTH, SA, and NF. We selected the top 10 accessions for each RMT, and IT208321, IT216313, and IT216137 were nominated as the best germplasms. These accessions can be recommended to breeders as materials for breeding programs. This is a preliminary report on the characterization of the root phenotype at an international gene bank and will open up the possibility of improving the available information on accessions in gene banks worldwide.
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Affiliation(s)
- Seong-Hoon Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju 5487, Korea;
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Korea
- Correspondence: (S.-H.K.); (B.-S.H.); (B.-K.H.)
| | - Parthiban Subramanian
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju 5487, Korea;
- PG & Research Department of Biotechnology and Microbiology, National College (Autonomous), Tiruchirapalli 620001, Tamilnadu, India
| | - Bum-Soo Hahn
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju 5487, Korea;
- Correspondence: (S.-H.K.); (B.-S.H.); (B.-K.H.)
| | - Bo-Keun Ha
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Korea
- Correspondence: (S.-H.K.); (B.-S.H.); (B.-K.H.)
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49
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Bello-Bello E, López-Arredondo D, Rico-Chambrón TY, Herrera-Estrella L. Conquering compacted soils: uncovering the molecular components of root soil penetration. TRENDS IN PLANT SCIENCE 2022; 27:814-827. [PMID: 35525799 DOI: 10.1016/j.tplants.2022.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 03/28/2022] [Accepted: 04/04/2022] [Indexed: 06/14/2023]
Abstract
Global agriculture and food security face paramount challenges due to climate change and land degradation. Human-induced soil compaction severely affects soil fertility, impairing root system development and crop yield. There is a need to design compaction-resilient crops that can thrive in degraded soils and maintain high yields. To address plausible solutions to this challenging scenario, we discuss current knowledge on plant root penetration ability and delineate potential approaches based on root-targeted genetic engineering (RGE) and genomics-assisted breeding (GAB) for developing crops with enhanced root system penetrability (RSP) into compacted soils. Such approaches could lead to crops with improved resilience to climate change and marginal soils, which can help to boost CO2 sequestration and storage in deeper soil strata.
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Affiliation(s)
- Elohim Bello-Bello
- Unidad de Genómica Avanzada/LANGEBIO, Centro de Investigación y de Estudios Avanzados, Irapuato, México
| | - Damar López-Arredondo
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA
| | - Thelma Y Rico-Chambrón
- Unidad de Genómica Avanzada/LANGEBIO, Centro de Investigación y de Estudios Avanzados, Irapuato, México
| | - Luis Herrera-Estrella
- Unidad de Genómica Avanzada/LANGEBIO, Centro de Investigación y de Estudios Avanzados, Irapuato, México; Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA.
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50
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Sánchez-Bermúdez M, del Pozo JC, Pernas M. Effects of Combined Abiotic Stresses Related to Climate Change on Root Growth in Crops. FRONTIERS IN PLANT SCIENCE 2022; 13:918537. [PMID: 35845642 PMCID: PMC9284278 DOI: 10.3389/fpls.2022.918537] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Climate change is a major threat to crop productivity that negatively affects food security worldwide. Increase in global temperatures are usually accompanied by drought, flooding and changes in soil nutrients composition that dramatically reduced crop yields. Against the backdrop of climate change, human population increase and subsequent rise in food demand, finding new solutions for crop adaptation to environmental stresses is essential. The effects of single abiotic stress on crops have been widely studied, but in the field abiotic stresses tend to occur in combination rather than individually. Physiological, metabolic and molecular responses of crops to combined abiotic stresses seem to be significantly different to individual stresses. Although in recent years an increasing number of studies have addressed the effects of abiotic stress combinations, the information related to the root system response is still scarce. Roots are the underground organs that directly contact with the soil and sense many of these abiotic stresses. Understanding the effects of abiotic stress combinations in the root system would help to find new breeding tools to develop more resilient crops. This review will summarize the current knowledge regarding the effects of combined abiotic stress in the root system in crops. First, we will provide a general overview of root responses to particular abiotic stresses. Then, we will describe how these root responses are integrated when crops are challenged to the combination of different abiotic stress. We will focus on the main changes on root system architecture (RSA) and physiology influencing crop productivity and yield and convey the latest information on the key molecular, hormonal and genetic regulatory pathways underlying root responses to these combinatorial stresses. Finally, we will discuss possible directions for future research and the main challenges needed to be tackled to translate this knowledge into useful tools to enhance crop tolerance.
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