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Jiang N, Zhu XG. Modern phenomics to empower holistic crop science, agronomy, and breeding research. J Genet Genomics 2024; 51:790-800. [PMID: 38734136 DOI: 10.1016/j.jgg.2024.04.016] [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: 12/29/2023] [Revised: 04/25/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
Crop phenomics enables the collection of diverse plant traits for a large number of samples along different time scales, representing a greater data collection throughput compared with traditional measurements. Most modern crop phenomics use different sensors to collect reflective, emitted, and fluorescence signals, etc., from plant organs at different spatial and temporal resolutions. Such multi-modal, high-dimensional data not only accelerates basic research on crop physiology, genetics, and whole plant systems modeling, but also supports the optimization of field agronomic practices, internal environments of plant factories, and ultimately crop breeding. Major challenges and opportunities facing the current crop phenomics research community include developing community consensus or standards for data collection, management, sharing, and processing, developing capabilities to measure physiological parameters, and enabling farmers and breeders to effectively use phenomics in the field to directly support agricultural production.
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Affiliation(s)
- Ni Jiang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xin-Guang Zhu
- Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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2
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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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3
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Ning J, Yamauchi T, Takahashi H, Omori F, Mano Y, Nakazono M. Asymmetric auxin distribution establishes a contrasting pattern of aerenchyma formation in the nodal roots of Zea nicaraguensis during gravistimulation. FRONTIERS IN PLANT SCIENCE 2023; 14:1133009. [PMID: 37152158 PMCID: PMC10154625 DOI: 10.3389/fpls.2023.1133009] [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: 12/28/2022] [Accepted: 03/28/2023] [Indexed: 05/09/2023]
Abstract
Auxin distribution is essential for determining root developmental patterns. The formation of lateral roots and constitutive aerenchyma, which is a gas space developed through cell death, is regulated by auxin in rice (Oryza sativa). However, it is unclear whether the involvement of auxin in constitutive aerenchyma formation is conserved in other species. In this study, we found that constitutive aerenchyma formation was regulated by auxin in the nodal roots of Zea nicaraguensis, a wild relative of maize (Zea mays ssp. mays) grown naturally on frequently flooded coastal plains. Subsequent gravistimulation (root rotation) experiments showed opposite patterns of aerenchyma and lateral root formation. Lateral root formation on the convex side of rotated roots is known to be stimulated by a transient increase in auxin level in the pericycle. We found that aerenchyma formation was accelerated in the cortex on the concave side of the rotated nodal roots of Z. nicaraguensis. A cortex-specific expression analysis of auxin-responsive genes suggested that the auxin level was higher on the concave side than on the convex side. These results suggest that asymmetric auxin distribution underlies the regulation of aerenchyma and lateral root formation in the nodal roots of Z. nicaraguensis. As aerenchyma reduces the respiratory cost of the roots, constitutive aerenchyma on the concave side of the nodal root may balance resource allocation, thereby contributing to the uptake of water and nutrients by newly formed lateral roots. Our study provides insights into auxin-dependent asymmetric root patterning such as that of gravistimulation and hydropatterning response.
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Affiliation(s)
- Jiayang Ning
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Takaki Yamauchi
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi, Japan
| | - Hirokazu Takahashi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
| | - Fumie Omori
- Division of Feed and Livestock Research, National Agriculture and Food Research Organization (NARO) Institute of Livestock and Grassland Science, Nasushiobara, Tochigi, Japan
| | - Yoshiro Mano
- Division of Feed and Livestock Research, National Agriculture and Food Research Organization (NARO) Institute of Livestock and Grassland Science, Nasushiobara, Tochigi, Japan
| | - Mikio Nakazono
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
- The University of Western Australia (UWA) School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
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4
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Glass NT, Yun K, Dias de Oliveira EA, Zare A, Matamala R, Kim SH, Gonzalez-Meler M. Perennial grass root system specializes for multiple resource acquisitions with differential elongation and branching patterns. FRONTIERS IN PLANT SCIENCE 2023; 14:1146681. [PMID: 37008471 PMCID: PMC10064013 DOI: 10.3389/fpls.2023.1146681] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/24/2023] [Indexed: 06/19/2023]
Abstract
Roots optimize the acquisition of limited soil resources, but relationships between root forms and functions have often been assumed rather than demonstrated. Furthermore, how root systems co-specialize for multiple resource acquisitions is unclear. Theory suggests that trade-offs exist for the acquisition of different resource types, such as water and certain nutrients. Measurements used to describe the acquisition of different resources should then account for differential root responses within a single system. To demonstrate this, we grew Panicum virgatum in split-root systems that vertically partitioned high water availability from nutrient availability so that root systems must absorb the resources separately to fully meet plant demands. We evaluated root elongation, surface area, and branching, and we characterized traits using an order-based classification scheme. Plants allocated approximately 3/4th of primary root length towards water acquisition, whereas lateral branches were progressively allocated towards nutrients. However, root elongation rates, specific root length, and mass fraction were similar. Our results support the existence of differential root functioning within perennial grasses. Similar responses have been recorded in many plant functional types suggesting a fundamental relationship. Root responses to resource availability can be incorporated into root growth models via maximum root length and branching interval parameters.
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Affiliation(s)
- Nicholas T. Glass
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
| | - Kyungdahm Yun
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA, United States
| | | | - Alina Zare
- Department of Electrical & Computer Engineering, University of Florida, Gainesville, FL, United States
| | - Roser Matamala
- Environmental Science Division, Argonne National Laboratory, Lemont, IL, United States
| | - Soo-Hyung Kim
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA, United States
| | - Miquel Gonzalez-Meler
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, United States
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5
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Huang C, Butterly CR, Moody D, Pourkheirandish M. Mini review: Targeting below-ground plant performance to improve nitrogen use efficiency (NUE) in barley. Front Genet 2023; 13:1060304. [PMID: 36935938 PMCID: PMC10017981 DOI: 10.3389/fgene.2022.1060304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/19/2022] [Indexed: 03/06/2023] Open
Abstract
Nitrogen (N) fertilizer is one of the major inputs for grain crops including barley and its usage is increasing globally. However, N use efficiency (NUE) is low in cereal crops, leading to higher production costs, unfulfilled grain yield potential and environmental hazards. N uptake is initiated from plant root tips but a very limited number of studies have been conducted on roots relevant to NUE specifically. In this review, we used barley, the fourth most important cereal crop, as the primary study plant to investigate this topic. We first highlighted the recent progress and study gaps in genetic analysis results, primarily, the genome-wide association study (GWAS) regarding both biological and statistical considerations. In addition, different factors contributing to NUE are discussed in terms of root morphological and anatomical traits, as well as physiological mechanisms such as N transporter activities and hormonal regulation.
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Affiliation(s)
- Claire Huang
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Clayton R. Butterly
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
| | - David Moody
- InterGrain Pty Ltd., Bibra Lake, WA, Australia
| | - Mohammad Pourkheirandish
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
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Yu Q, Tang H, Zhu L, Zhang W, Liu L, Wang N. A method of cotton root segmentation based on edge devices. FRONTIERS IN PLANT SCIENCE 2023; 14:1122833. [PMID: 36875594 PMCID: PMC9982017 DOI: 10.3389/fpls.2023.1122833] [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: 12/13/2022] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
The root is an important organ for plants to absorb water and nutrients. In situ root research method is an intuitive method to explore root phenotype and its change dynamics. At present, in situ root research, roots can be accurately extracted from in situ root images, but there are still problems such as low analysis efficiency, high acquisition cost, and difficult deployment of image acquisition devices outdoors. Therefore, this study designed a precise extraction method of in situ roots based on semantic segmentation model and edge device deployment. It initially proposes two data expansion methods, pixel by pixel and equal proportion, expand 100 original images to 1600 and 53193 respectively. It then presents an improved DeeplabV3+ root segmentation model based on CBAM and ASPP in series is designed, and the segmentation accuracy is 93.01%. The root phenotype parameters were verified through the Rhizo Vision Explorers platform, and the root length error was 0.669%, and the root diameter error was 1.003%. It afterwards designs a time-saving Fast prediction strategy. Compared with the Normal prediction strategy, the time consumption is reduced by 22.71% on GPU and 36.85% in raspberry pie. It ultimately deploys the model to Raspberry Pie, realizing the low-cost and portable root image acquisition and segmentation, which is conducive to outdoor deployment. In addition, the cost accounting is only $247. It takes 8 hours to perform image acquisition and segmentation tasks, and the power consumption is as low as 0.051kWh. In conclusion, the method proposed in this study has good performance in model accuracy, economic cost, energy consumption, etc. This paper realizes low-cost and high-precision segmentation of in-situ root based on edge equipment, which provides new insights for high-throughput field research and application of in-situ root.
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Affiliation(s)
- Qiushi Yu
- College of Mechanical and Electrical Engineering, Hebei Agricultural University, Baoding, China
| | - Hui Tang
- College of Mechanical and Electrical Engineering, Hebei Agricultural University, Baoding, China
| | - Lingxiao Zhu
- College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Wenjie Zhang
- College of Modern Science And Technology, Hebei Agricultural University, Baoding, China
| | - Liantao Liu
- College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Nan Wang
- College of Mechanical and Electrical Engineering, Hebei Agricultural University, Baoding, China
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Rossi R, Bitella G, Bochicchio R, Labella R, Angerame F, Urbano M, Amato M. Root and Shoot Growth of a Modern and an Old Tall Durum Wheat ( Triticum durum Desf.) Variety under Dual-Purpose Management. PLANTS (BASEL, SWITZERLAND) 2023; 12:588. [PMID: 36771671 PMCID: PMC9921935 DOI: 10.3390/plants12030588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/10/2023] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
In dual-purpose cereal systems, the co-production of fodder and grain can increase farm profitability and reduce farming risks. Our work evaluated shoot and root growth in durum wheat (Triticum durum Desf.) under dual-purpose management in a medium-high rainfall area of southern Italy. We compared a modern variety (Core) with a tall ancient variety (Saragolle lucana) under traditional (NDP) and dual-purpose (DP) management and tested the hypothesis that clipping plants during the vegetative stage would reduce root growth and dewatering before anthesis, which is advantageous in drought-prone environments. Experiments were conducted in Bella (PZ), Basilicata region, southern Italy (40°42' N, 15°32' E) on a clay loam soil in 2021 in a split-plot design on 2 × 2 main plots and 1 × 2 split-plots with 6 replicates. The DP treatment consisted of simulated grazing by clipping plants at 5 cm from the ground 3 months after sowing (at first hollow stem). Forage Biomass was not different at p = 0.05 between varieties, with an average of 0.58 t ha-1 DM. Grain yield was not penalized by clipping (p = 0.05) and did not differ significantly between varieties. SPAD was always lower in the Saragolle variety and lowered by clipping. Defoliation delayed phenology in both cultivars but did not reduce the final number of spikes per square meter. Stomatal conductance was correlated to temperature, did not differ between cultivars, and was not influenced by clipping. Soil water depletion was monitored in modern wheat from the booting stage to the beginning of grain filling. Clipping did not result in a reduction in pre-anthesis water depletion, possibly due to evaporative losses. Root density was markedly reduced by clipping in core variety between 0.20 and 0.60 m and much less in Saragolle. Unclipped Saragolle produced thicker roots and higher root masses compared to clipped plants. Defoliated Saragolle shifted to finer roots, reducing root mass more than length. This may have reduced the metabolic cost of soil exploration, thereby increasing root foraging efficiency.
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Affiliation(s)
- Roberta Rossi
- Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture (CREA-ZA), 85051 Bella-Muro (Potenza), Italy
| | - Giovanni Bitella
- School of Agriculture, Forestry, Food and Environmental Sciences, University of Basilicata, 85100 Potenza, Italy
| | - Rocco Bochicchio
- School of Agriculture, Forestry, Food and Environmental Sciences, University of Basilicata, 85100 Potenza, Italy
| | - Rosanna Labella
- School of Agriculture, Forestry, Food and Environmental Sciences, University of Basilicata, 85100 Potenza, Italy
| | - Francesco Angerame
- Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture (CREA-ZA), 85051 Bella-Muro (Potenza), Italy
| | - Marcella Urbano
- Institute of Biosciences and Bioresources, CNR (National Research Council), 70126 Bari, Italy
| | - Mariana Amato
- School of Agriculture, Forestry, Food and Environmental Sciences, University of Basilicata, 85100 Potenza, Italy
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8
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Si Z, Delhaize E, Hendriks PW, Li X. Differences in Root Morphologies of Contrasting Wheat ( Triticum aestivum) Genotypes Are Robust of a Drought Treatment. PLANTS (BASEL, SWITZERLAND) 2023; 12:275. [PMID: 36678988 PMCID: PMC9863919 DOI: 10.3390/plants12020275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/21/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
We aimed to assess the effect of water deprivation on root traits and to establish if the wheat cultivars Spica and Maringa would be useful as parental germplasm for a genetic analysis of root traits. Plants were grown in two markedly different soils under well-watered and water-limited treatments in controlled environment growth cabinets. The drought treatment was imposed as a gradual depletion of water over 28 days as seedlings grew from a defined starting moisture content. The root traits analyzed included length, nodal root number, thickness and nodal root angle. The relative differences in traits between genotypes generally proved to be robust in terms of water treatment and soil type. Maringa had a shallower nodal root angle than Spica, which was driven by the nodal roots. By contrast, the seminal roots of Maringa were found to be similar to or even steeper than those of Spica. We conclude that the differences in root traits between Spica and Maringa were robust to the drought treatment and soil types. Phenotyping on well-watered soil is relevant for identifying traits potentially involved in conferring water use efficiency. Furthermore, Spica and Maringa are suitable parental germplasm for developing populations to determine the genetics of key root traits.
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Affiliation(s)
- Zhuanyun Si
- Key Laboratory of Crop Water Use and Regulation, Ministry of Agriculture and Rural Affairs/Institute of Farmland Irrigation, Chinese Academy of Agricultural Sciences, Xinxiang 453002, China
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Emmanuel Delhaize
- Australian Plant Phenomics Facility, Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
| | - Pieter-Willem Hendriks
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
- Faculty of Agriculture and Life Sciences, Lincoln University, 85084 Ellesmere Junction Road, Lincoln 7647, New Zealand
| | - Xiaoqing Li
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
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9
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Schneider HM. Functional implications of multiseriate cortical sclerenchyma for soil resource capture and crop improvement. AOB PLANTS 2022; 14:plac050. [PMID: 36545297 PMCID: PMC9762723 DOI: 10.1093/aobpla/plac050] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/17/2022] [Indexed: 06/09/2023]
Abstract
Suboptimal nutrient and water availability are primary constraints to crop growth. Global agriculture requires crops with greater nutrient and water efficiency. Multiseriate cortical sclerenchyma (MCS), a root anatomical trait characterized by small cells with thick cell walls encrusted with lignin in the outer cortex, has been shown to be an important trait for adaptation in maize and wheat in mechanically impeded soils. However, MCS has the potential to improve edaphic stress tolerance in a number of different crop taxa and in a number of different environments. This review explores the functional implications of MCS as an adaptive trait for water and nutrient acquisition and discusses future research perspectives on this trait for incorporation into crop breeding programs. For example, MCS may influence water and nutrient uptake, resistance to pests, symbiotic interactions, microbial interactions in the rhizosphere and soil carbon deposition. Root anatomical phenotypes are underutilized; however, important breeding targets for the development of efficient, productive and resilient crops urgently needed in global agriculture.
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10
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Clément C, Schneider HM, Dresbøll DB, Lynch JP, Thorup-Kristensen K. Root and xylem anatomy varies with root length, root order, soil depth and environment in intermediate wheatgrass (Kernza®) and alfalfa. ANNALS OF BOTANY 2022; 130:367-382. [PMID: 35468194 PMCID: PMC9486898 DOI: 10.1093/aob/mcac058] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/25/2022] [Indexed: 06/08/2023]
Abstract
BACKGROUND AND AIMS Deep roots (i.e. >1 m depth) are important for crops to access water when the topsoil is dry. Root anatomy and hydraulic conductance play important roles in the uptake of soil water, particularly water located deep in the soil. We investigated whether root and xylem anatomy vary as a function of root type, order and length, or with soil depth in roots of two deep-rooted perennial crops: intermediate wheatgrass [Thinopyrum intermedium (Kernza®)] and alfalfa (Medicago sativa). We linked the expression of these anatomical traits to the plants' capacity to take up water from deep soil layers. METHODS Using laser ablation tomography, we compared the roots of the two crops for cortical area, number and size of metaxylem vessels, and their estimated root axial hydraulic conductance (ERAHCe). The deepest roots investigated were located at soil depths of 2.25 and at 3.5 m in the field and in rhizoboxes, respectively. Anatomical differences were characterized along 1-m-long individual roots, among root types and orders, as well as between environmental conditions. KEY RESULTS For both crops, a decrease in the number and diameter, or both, of metaxylem vessels along individual root segments and with soil depth in the field resulted in a decrease in ERAHCe. Alfalfa, with a greater number of metaxylem vessels per root throughout the soil profile and, on average, a 4-fold greater ERAHCe, took up more water from the deep soil layers than intermediate wheatgrass. Root anatomical traits were significantly different across root types, classes and growth conditions. CONCLUSIONS Root anatomical traits are important tools for the selection of crops with enhanced exploitation of deep soil water. The development and breeding of perennial crops for improved subsoil exploitation will be aided by greater understanding of root phenotypes linked to deep root growth and activity.
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Affiliation(s)
| | - Hannah M Schneider
- Department of Plant Science, Pennsylvania State University, University Park, PA 16802, USA
| | - Dorte Bodin Dresbøll
- Department of Plant and Environmental Science, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Jonathan P Lynch
- Department of Plant Science, Pennsylvania State University, University Park, PA 16802, USA
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11
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Ndoye MS, Burridge J, Bhosale R, Grondin A, Laplaze L. Root traits for low input agroecosystems in Africa: Lessons from three case studies. PLANT, CELL & ENVIRONMENT 2022; 45:637-649. [PMID: 35037274 DOI: 10.1111/pce.14256] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
In many regions across Africa, agriculture is largely based on low-input and small-holder farming systems that use little inorganic fertilisers and have limited access to irrigation and mechanisation. Improving agricultural practices and developing new cultivars adapted to these environments, where production already suffers from climate change, is a major priority for food security. Here, we illustrate how breeding for specific root traits could improve crop resilience in Africa using three case studies covering very contrasting low-input agroecosystems. We first review how greater basal root whorl number and longer and denser root hairs increased P acquisition efficiency and yield in common bean in South East Africa. We then discuss how water-saving strategies, root hair density and deep root growth could be targeted to improve sorghum and pearl millet yield in West Africa. Finally, we evaluate how breeding for denser root systems in the topsoil and interactions with arbuscular mycorrhizal fungi could be mobilised to optimise water-saving alternate wetting and drying practices in West African rice agroecosystems. We conclude with a discussion on how to evaluate the utility of root traits and how to make root trait selection feasible for breeders so that improved varieties can be made available to farmers through participatory approaches.
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Affiliation(s)
- Mame S Ndoye
- CERAAS, Thies Escale, Thies, Senegal
- LMI LAPSE, Centre de Recherche ISRA/IRD de Bel Air, Dakar, Senegal
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - James Burridge
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Rahul Bhosale
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, Nottingham, UK
| | - Alexandre Grondin
- CERAAS, Thies Escale, Thies, Senegal
- LMI LAPSE, Centre de Recherche ISRA/IRD de Bel Air, Dakar, Senegal
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Laurent Laplaze
- LMI LAPSE, Centre de Recherche ISRA/IRD de Bel Air, Dakar, Senegal
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
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12
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G. Viana W, Scharwies JD, Dinneny JR. Deconstructing the root system of grasses through an exploration of development, anatomy and function. PLANT, CELL & ENVIRONMENT 2022; 45:602-619. [PMID: 35092025 PMCID: PMC9303260 DOI: 10.1111/pce.14270] [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: 01/21/2022] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 05/16/2023]
Abstract
Well-adapted root systems allow plants to grow under resource-limiting environmental conditions and are important determinants of yield in agricultural systems. Important staple crops such as rice and maize belong to the family of grasses, which develop a complex root system that consists of an embryonic root system that emerges from the seed, and a postembryonic nodal root system that emerges from basal regions of the shoot after germination. While early seedling establishment is dependent on the embryonic root system, the nodal root system, and its associated branches, gains in importance as the plant matures and will ultimately constitute the bulk of below-ground growth. In this review, we aim to give an overview of the different root types that develop in cereal grass root systems, explore the different physiological roles they play by defining their anatomical features, and outline the genetic networks that control their development. Through this deconstructed view of grass root system function, we provide a parts-list of elements that function together in an integrated root system to promote survival and crop productivity.
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Affiliation(s)
| | | | - José R. Dinneny
- Department of BiologyStanford UniversityStanfordCaliforniaUSA
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13
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Strock CF, Rangarajan H, Black CK, Schäfer ED, Lynch JP. Theoretical evidence that root penetration ability interacts with soil compaction regimes to affect nitrate capture. ANNALS OF BOTANY 2022; 129:315-330. [PMID: 34850823 PMCID: PMC8835659 DOI: 10.1093/aob/mcab144] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/26/2021] [Indexed: 05/14/2023]
Abstract
BACKGROUND AND AIMS Although root penetration of strong soils has been intensively studied at the scale of individual root axes, interactions between soil physical properties and soil foraging by whole plants are less clear. Here we investigate how variation in the penetration ability of distinct root classes and bulk density profiles common to real-world soils interact to affect soil foraging strategies. METHODS We utilize the functional-structural plant model 'OpenSimRoot' to simulate the growth of maize (Zea mays) root systems with variable penetration ability of axial and lateral roots in soils with (1) uniform bulk density, (2) plow pans and (3) increasing bulk density with depth. We also modify the availability and leaching of nitrate to uncover reciprocal interactions between these factors and the capture of mobile resources. KEY RESULTS Soils with plow pans and bulk density gradients affected overall size, distribution and carbon costs of the root system. Soils with high bulk density at depth impeded rooting depth and reduced leaching of nitrate, thereby improving the coincidence of nitrogen and root length. While increasing penetration ability of either axial or lateral root classes produced root systems of comparable net length, improved penetration of axial roots increased allocation of root length in deeper soil, thereby amplifying N acquisition and shoot biomass. Although enhanced penetration ability of both root classes was associated with greater root system carbon costs, the benefit to plant fitness from improved soil exploration and resource capture offset these. CONCLUSIONS While lateral roots comprise the bulk of root length, axial roots function as a scaffold determining the distribution of these laterals. In soils with high soil strength and leaching, root systems with enhanced penetration ability of axial roots have greater distribution of root length at depth, thereby improving capture of mobile resources.
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Affiliation(s)
- Christopher F Strock
- 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
| | - Christopher K Black
- Department of Plant Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - Ernst D Schäfer
- Department of Plant Science, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jonathan P Lynch
- Department of Plant Science, The Pennsylvania State University, University Park, PA 16802, USA
- For correspondence. E-mail
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Burridge JD, Grondin A, Vadez V. Optimizing Crop Water Use for Drought and Climate Change Adaptation Requires a Multi-Scale Approach. FRONTIERS IN PLANT SCIENCE 2022; 13:824720. [PMID: 35574091 PMCID: PMC9100818 DOI: 10.3389/fpls.2022.824720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/11/2022] [Indexed: 05/09/2023]
Abstract
Selection criteria that co-optimize water use efficiency and yield are needed to promote plant productivity in increasingly challenging and variable drought scenarios, particularly dryland cereals in the semi-arid tropics. Optimizing water use efficiency and yield fundamentally involves transpiration dynamics, where restriction of maximum transpiration rate helps to avoid early crop failure, while maximizing grain filling. Transpiration restriction can be regulated by multiple mechanisms and involves cross-organ coordination. This coordination involves complex feedbacks and feedforwards over time scales ranging from minutes to weeks, and from spatial scales ranging from cell membrane to crop canopy. Aquaporins have direct effect but various compensation and coordination pathways involve phenology, relative root and shoot growth, shoot architecture, root length distribution profile, as well as other architectural and anatomical aspects of plant form and function. We propose gravimetric phenotyping as an integrative, cross-scale solution to understand the dynamic, interwoven, and context-dependent coordination of transpiration regulation. The most fruitful breeding strategy is likely to be that which maintains focus on the phene of interest, namely, daily and season level transpiration dynamics. This direct selection approach is more precise than yield-based selection but sufficiently integrative to capture attenuating and complementary factors.
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Affiliation(s)
- James D. Burridge
- DIADE Group, Cereal Root Systems, Institute de Recherche pour le Développement/Université de Montpellier, Montpellier, France
- *Correspondence: James D. Burridge,
| | - Alexandre Grondin
- DIADE Group, Cereal Root Systems, Institute de Recherche pour le Développement/Université de Montpellier, Montpellier, France
- Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux, Laboratoire Mixte International, Dakar, Senegal
- Centre d’Étude Régional pour l’Amélioration de l’Adaptation à la Sécheresse, Thiès, Senegal
| | - Vincent Vadez
- DIADE Group, Cereal Root Systems, Institute de Recherche pour le Développement/Université de Montpellier, Montpellier, France
- Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux, Laboratoire Mixte International, Dakar, Senegal
- Centre d’Étude Régional pour l’Amélioration de l’Adaptation à la Sécheresse, Thiès, Senegal
- International Crops Research Institute for Semi-Arid Tropics (ICRISAT), Patancheru, India
- Vincent Vadez,
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Schneider HM, Yang JT, Brown KM, Lynch JP. Nodal root diameter and node number in maize ( Zea mays L.) interact to influence plant growth under nitrogen stress. PLANT DIRECT 2021; 5:e00310. [PMID: 33748655 PMCID: PMC7963125 DOI: 10.1002/pld3.310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 01/23/2021] [Accepted: 01/25/2021] [Indexed: 05/11/2023]
Abstract
Under nitrogen limitation, plants increase resource allocation to root growth relative to shoot growth. The utility of various root architectural and anatomical phenotypes for nitrogen acquisition are not well understood. Nodal root number and root cross-sectional area were evaluated in maize in field and greenhouse environments. Nodal root number and root cross-sectional area were inversely correlated under both high and low nitrogen conditions. Attenuated emergence of root nodes, as opposed to differences in the number of axial roots per node, was associated with substantially reduced root number. Greater root cross-sectional area was associated with a greater stele area and number of cortical cell files. Genotypes that produced few, thick nodal roots rather than many, thin nodal roots had deeper rooting and better shoot growth in low nitrogen environments. Fewer nodal roots offset the respiratory and nitrogen costs of thicker diameter roots, since total nodal root respiration and nitrogen content was similar for genotypes with many, thin and few, thick nodal roots. We propose that few, thick nodal roots may enable greater capture of deep soil nitrogen and improve plant performance under nitrogen stress. Synergistic interactions between an architectural and anatomical trait may be an important strategy for nitrogen acquisition. Understanding trait interactions among different root nodes has important implications in for improving crop nutrient uptake and stress tolerance.
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Affiliation(s)
- Hannah M. Schneider
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPAUSA
| | - Jennifer T. Yang
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPAUSA
- Present address:
Wellesley CollegeWellesleyMAUSA
| | - Kathleen M. Brown
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPAUSA
| | - Jonathan P. Lynch
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPAUSA
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