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Zhang Y, Gu S, Du J, Huang G, Shi J, Lu X, Wang J, Yang W, Guo X, Zhao C. Plant microphenotype: from innovative imaging to computational analysis. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:802-818. [PMID: 38217351 PMCID: PMC10955502 DOI: 10.1111/pbi.14244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 01/15/2024]
Abstract
The microphenotype plays a key role in bridging the gap between the genotype and the complex macro phenotype. In this article, we review the advances in data acquisition and the intelligent analysis of plant microphenotyping and present applications of microphenotyping in plant science over the past two decades. We then point out several challenges in this field and suggest that cross-scale image acquisition strategies, powerful artificial intelligence algorithms, advanced genetic analysis, and computational phenotyping need to be established and performed to better understand interactions among genotype, environment, and management. Microphenotyping has entered the era of Microphenotyping 3.0 and will largely advance functional genomics and plant science.
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Affiliation(s)
- Ying Zhang
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shenghao Gu
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jianjun Du
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Guanmin Huang
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jiawei Shi
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xianju Lu
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jinglu Wang
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Xinyu Guo
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chunjiang Zhao
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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Kopeć P. Climate Change-The Rise of Climate-Resilient Crops. PLANTS (BASEL, SWITZERLAND) 2024; 13:490. [PMID: 38498432 PMCID: PMC10891513 DOI: 10.3390/plants13040490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/31/2024] [Accepted: 02/06/2024] [Indexed: 03/20/2024]
Abstract
Climate change disrupts food production in many regions of the world. The accompanying extreme weather events, such as droughts, floods, heat waves, and cold snaps, pose threats to crops. The concentration of carbon dioxide also increases in the atmosphere. The United Nations is implementing the climate-smart agriculture initiative to ensure food security. An element of this project involves the breeding of climate-resilient crops or plant cultivars with enhanced resistance to unfavorable environmental conditions. Modern agriculture, which is currently homogeneous, needs to diversify the species and cultivars of cultivated plants. Plant breeding programs should extensively incorporate new molecular technologies, supported by the development of field phenotyping techniques. Breeders should closely cooperate with scientists from various fields of science.
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Affiliation(s)
- Przemysław Kopeć
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239 Kraków, Poland
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Wang W, Hu C, Chang Y, Wang L, Bi Q, Lu X, Zheng Z, Zheng X, Wu D, Niu B. Differentiated responses of the phyllosphere bacterial community of the yellowhorn tree to precipitation and temperature regimes across Northern China. FRONTIERS IN PLANT SCIENCE 2023; 14:1265362. [PMID: 37954985 PMCID: PMC10634255 DOI: 10.3389/fpls.2023.1265362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 10/10/2023] [Indexed: 11/14/2023]
Abstract
Introduction As an ephemeral and oligotrophic environment, the phyllosphere harbors many highly diverse microorganisms. Importantly, it is known that their colonization of plant leaf surfaces is considerably influenced by a few abiotic factors related to climatic conditions. Yet how the dynamics of phyllosphere bacterial community assembly are shaped by detailed climatological elements, such as various bioclimatic variables, remains poorly understood. Methods Using high-throughput 16S rRNA gene amplicon sequencing technology, we analyzed the bacterial communities inhabiting the leaf surfaces of an oilseed tree, yellowhorn (Xanthoceras sorbifolium), grown at four sites (Yinchuan, Otogqianqi, Tongliao, and Zhangwu) whose climatic status differs in northern China. Results and Discussion We found that the yellowhorn phyllosphere's bacterial community was generally dominated by four phyla: Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Nevertheless, bacterial community composition differed significantly among the four sampled site regions, indicating the possible impact of climatological factors upon the phyllosphere microbiome. Interestingly, we also noted that the α-diversities of phyllosphere microbiota showed strong positive or negative correlation with 13 bioclimatic factors (including 7 precipitation factors and 6 temperature factors). Furthermore, the relative abundances of 55 amplicon sequence variants (ASVs), including three ASVs representing two keystone taxa (the genera Curtobacterium and Streptomyces), exhibited significant yet contrary responses to the precipitation and temperature climatic variables. That pattern was consistent with all ASVs' trends of possessing opposite correlations to those two parameter classes. In addition, the total number of links and nodes, which conveys community network complexity, increased with rising values of most temperature variables. Besides that, remarkably positive relevance was found between average clustering coefficient and most precipitation variables. Altogether, these results suggest the yellowhorn phyllosphere bacterial community is capable of responding to variation in rainfall and temperature regimes in distinctive ways.
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Affiliation(s)
- Weixiong Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Congcong Hu
- Department of Mathematics, Shanghai Normal University, Shanghai, China
| | - Yu Chang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Libing Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Quanxin Bi
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xin Lu
- Chifeng Research Institute of Forestry Science, Chifeng, China
- National Forestry and Grassland Shiny-Leaved Yellowhorn Engineering and Technology Research Center, Chifeng, China
| | - Zhimin Zheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
| | - Xiaoqi Zheng
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Di Wu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Ben Niu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
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Zhang P, Huang J, Ma Y, Wang X, Kang M, Song Y. Crop/Plant Modeling Supports Plant Breeding: II. Guidance of Functional Plant Phenotyping for Trait Discovery. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0091. [PMID: 37780969 PMCID: PMC10538623 DOI: 10.34133/plantphenomics.0091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/26/2023] [Indexed: 10/03/2023]
Abstract
Observable morphological traits are widely employed in plant phenotyping for breeding use, which are often the external phenotypes driven by a chain of functional actions in plants. Identifying and phenotyping inherently functional traits for crop improvement toward high yields or adaptation to harsh environments remains a major challenge. Prediction of whole-plant performance in functional-structural plant models (FSPMs) is driven by plant growth algorithms based on organ scale wrapped up with micro-environments. In particular, the models are flexible for scaling down or up through specific functions at the organ nexus, allowing the prediction of crop system behaviors from the genome to the field. As such, by virtue of FSPMs, model parameters that determine organogenesis, development, biomass production, allocation, and morphogenesis from a molecular to the whole plant level can be profiled systematically and made readily available for phenotyping. FSPMs can provide rich functional traits representing biological regulatory mechanisms at various scales in a dynamic system, e.g., Rubisco carboxylation rate, mesophyll conductance, specific leaf nitrogen, radiation use efficiency, and source-sink ratio apart from morphological traits. High-throughput phenotyping such traits is also discussed, which provides an unprecedented opportunity to evolve FSPMs. This will accelerate the co-evolution of FSPMs and plant phenomics, and thus improving breeding efficiency. To expand the great promise of FSPMs in crop science, FSPMs still need more effort in multiscale, mechanistic, reproductive organ, and root system modeling. In summary, this study demonstrates that FSPMs are invaluable tools in guiding functional trait phenotyping at various scales and can thus provide abundant functional targets for phenotyping toward crop improvement.
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Affiliation(s)
- Pengpeng Zhang
- School of Agronomy, Anhui Agricultural University, Hefei, Anhui Province 230036, China
| | - Jingyao Huang
- School of Agronomy, Anhui Agricultural University, Hefei, Anhui Province 230036, China
| | - Yuntao Ma
- College of Land Science and Technology, China Agricultural University, Beijing 100094, China
| | - Xiujuan Wang
- The State Key Laboratory for Management and Control of Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
| | - Mengzhen Kang
- The State Key Laboratory for Management and Control of Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
| | - Youhong Song
- School of Agronomy, Anhui Agricultural University, Hefei, Anhui Province 230036, China
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4350, Australia
- Centre for Crop Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4350, Australia
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Nehe A, Martinsson UD, Johansson E, Chawade A. Genotype and environment interaction study shows fungal diseases and heat stress are detrimental to spring wheat production in Sweden. PLoS One 2023; 18:e0285565. [PMID: 37163567 PMCID: PMC10171613 DOI: 10.1371/journal.pone.0285565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 04/26/2023] [Indexed: 05/12/2023] Open
Abstract
Spring wheat is an economically important crop for Scandinavia and its cultivation is likely to be affected by climate change. The current study focused on wheat yield in recent years, during which climate change-related yield fluctuations have been more pronounced than previously observed. Here, effects of the environment, together with the genotype and fungicide treatment was evaluated. Spring wheat multi-location trials conducted at five locations between 2016 and 2020 were used to understand effects of the climate and fungicides on wheat yield. The results showed that the environment has a strong effect on grain yield, followed by the genotype effect. Moreover, temperature has a stronger (negative) impact than rainfall on grain yield and crop growing duration. Despite a low rainfall in the South compared to the North, the southern production region (PR) 2 had the highest yield performance, indicating the optimal environment for spring wheat production. The fungicide treatment effect was significant in 2016, 2017 and 2020. Overall, yield reduction due to fungal diseases ranged from 0.98 (2018) to 13.3% (2017) and this reduction was higher with a higher yield. Overall yield reduction due to fungal diseases was greater in the South (8.9%) than the North zone (5.3%). The genotypes with higher tolerance to diseases included G4 (KWS Alderon), G14 (WPB 09SW025-11), and G23 (SW 11360) in 2016; G24 (SW 11360), G25 (Millie), and G19 (SEC 526-07-2) in 2017; and G19 (WPB 13SW976-01), G12 (Levels), and G18 (SW 141011) in 2020. The combined best performing genotypes for disease tolerance and stable and higher yield in different locations were KWS Alderon, SEC 526-07-2, and WPB 13SW976-01 with fungicide treatment and WPB Avonmore, SEC 526-07-2, SW 131323 without fungicide treatment. We conclude that the best performing genotypes could be recommended for Scandinavian climatic conditions with or without fungicide application and that developing heat-tolerant varieties for Scandinavian countries should be prioritized.
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Affiliation(s)
- Ajit Nehe
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Eva Johansson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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Janni M, Pieruschka R. Plant phenotyping for a sustainable future. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5085-5088. [PMID: 36056763 DOI: 10.1093/jxb/erac286] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Affiliation(s)
- Michela Janni
- Institute of Materials for Electronics and Magnetism (IMEM), National Research Council (CNR), Parco Area delle Scienze 37/A, 43124 Parma, Italy
| | - Roland Pieruschka
- IBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, Germany
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