1
|
Bhoite R, Han Y, Chaitanya AK, Varshney RK, Sharma DL. Genomic approaches to enhance adaptive plasticity to cope with soil constraints amidst climate change in wheat. THE PLANT GENOME 2024; 17:e20358. [PMID: 37265088 DOI: 10.1002/tpg2.20358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/09/2023] [Accepted: 05/09/2023] [Indexed: 06/03/2023]
Abstract
Climate change is varying the availability of resources, soil physicochemical properties, and rainfall events, which collectively determines soil physical and chemical properties. Soil constraints-acidity (pH < 6), salinity (pH ≤ 8.5), sodicity, and dispersion (pH > 8.5)-are major causes of wheat yield loss in arid and semiarid cropping systems. To cope with changing environments, plants employ adaptive strategies such as phenotypic plasticity, a key multifaceted trait, to promote shifts in phenotypes. Adaptive strategies for constrained soils are complex, determined by key functional traits and genotype × environment × management interactions. The understanding of the molecular basis of stress tolerance is particularly challenging for plasticity traits. Advances in sequencing and high-throughput genomics technologies have identified functional alleles in gene-rich regions, haplotypes, candidate genes, mechanisms, and in silico gene expression profiles at various growth developmental stages. Our review focuses on favorable alleles for enhanced gene expression, quantitative trait loci, and epigenetic regulation of plant responses to soil constraints, including heavy metal stress and nutrient limitations. A strategy is then described for quantitative traits in wheat by investigating significant alleles and functional characterization of variants, followed by gene validation using advanced genomic tools, and marker development for molecular breeding and genome editing. Moreover, the review highlights the progress of gene editing in wheat, multiplex gene editing, and novel alleles for smart control of gene expression. Application of these advanced genomic technologies to enhance plasticity traits along with soil management practices will be an effective tool to build yield, stability, and sustainability on constrained soils in the face of climate change.
Collapse
Affiliation(s)
- Roopali Bhoite
- Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia, Australia
| | - Yong Han
- Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Perth, Western Australia, Australia
| | - Alamuru Krishna Chaitanya
- Grains Genetics Portfolio, University of Southern Queensland, Centre for Crop Health, Toowoomba, Queensland, Australia
| | - Rajeev K Varshney
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Perth, Western Australia, Australia
| | - Darshan Lal Sharma
- Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Perth, Western Australia, Australia
| |
Collapse
|
2
|
Ginzburg DN, Cox JA, Rhee SY. Non-destructive, whole-plant phenotyping reveals dynamic changes in water use efficiency, photosynthesis, and rhizosphere acidification of sorghum accessions under osmotic stress. PLANT DIRECT 2024; 8:e571. [PMID: 38464685 PMCID: PMC10918709 DOI: 10.1002/pld3.571] [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: 12/05/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 03/12/2024]
Abstract
Noninvasive phenotyping can quantify dynamic plant growth processes at higher temporal resolution than destructive phenotyping and can reveal phenomena that would be missed by end-point analysis alone. Additionally, whole-plant phenotyping can identify growth conditions that are optimal for both above- and below-ground tissues. However, noninvasive, whole-plant phenotyping approaches available today are generally expensive, complex, and non-modular. We developed a low-cost and versatile approach to noninvasively measure whole-plant physiology over time by growing plants in isolated hydroponic chambers. We demonstrate the versatility of our approach by measuring whole-plant biomass accumulation, water use, and water use efficiency every two days on unstressed and osmotically stressed sorghum accessions. We identified relationships between root zone acidification and photosynthesis on whole-plant water use efficiency over time. Our system can be implemented using cheap, basic components, requires no specific technical expertise, and should be suitable for any non-aquatic vascular plant species.
Collapse
Affiliation(s)
- Daniel N. Ginzburg
- Department of Plant BiologyCarnegie Institution for ScienceStanfordCaliforniaUSA
- Present address:
Department of Plant SciencesUniversity of CambridgeCambridgeUK
| | - Jack A. Cox
- Department of Plant BiologyCarnegie Institution for ScienceStanfordCaliforniaUSA
| | - Seung Y. Rhee
- Department of Plant BiologyCarnegie Institution for ScienceStanfordCaliforniaUSA
- Present address:
Plant Resilience Institute, Departments of Biochemistry and Molecular Biology, Plant Biology, and Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
- Present address:
Water and Life Interface InstituteEast LansingMichigan48824USA
| |
Collapse
|
3
|
Wang Y, Shang B, Génard M, Hilbert-Masson G, Delrot S, Gomès E, Poni S, Keller M, Renaud C, Kong J, Chen J, Liang Z, Dai Z. Model-assisted analysis for tuning anthocyanin composition in grape berries. ANNALS OF BOTANY 2023; 132:1033-1050. [PMID: 37850481 PMCID: PMC10808033 DOI: 10.1093/aob/mcad165] [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: 09/06/2023] [Accepted: 10/17/2023] [Indexed: 10/19/2023]
Abstract
Anthocyanin composition is responsible for the red colour of grape berries and wines, and contributes to their organoleptic quality. However, anthocyanin biosynthesis is under genetic, developmental and environmental regulation, making its targeted fine-tuning challenging. We constructed a mechanistic model to simulate the dynamics of anthocyanin composition throughout grape ripening in Vitis vinifera, employing a consensus anthocyanin biosynthesis pathway. The model was calibrated and validated using six datasets from eight cultivars and 37 growth conditions. Tuning the transformation and degradation parameters allowed us to accurately simulate the accumulation process of each individual anthocyanin under different environmental conditions. The model parameters were robust across environments for each genotype. The coefficients of determination (R2) for the simulated versus observed values for the six datasets ranged from 0.92 to 0.99, while the relative root mean square errors (RRMSEs) were between 16.8 and 42.1 %. The leave-one-out cross-validation for three datasets showed R2 values of 0.99, 0.96 and 0.91, and RRMSE values of 28.8, 32.9 and 26.4 %, respectively, suggesting a high prediction quality of the model. Model analysis showed that the anthocyanin profiles of diverse genotypes are relatively stable in response to parameter perturbations. Virtual experiments further suggested that targeted anthocyanin profiles may be reached by manipulating a minimum of three parameters, in a genotype-dependent manner. This model presents a promising methodology for characterizing the temporal progression of anthocyanin composition, while also offering a logical foundation for bioengineering endeavours focused on precisely adjusting the anthocyanin composition of grapes.
Collapse
Affiliation(s)
- Yongjian Wang
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Boxing Shang
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Michel Génard
- INRAE, UR1115, Unité Plantes et Systèmes de Culture Horticoles, Avignon, France
| | | | - Serge Delrot
- EGFV, University of Bordeaux, Bordeaux-Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Eric Gomès
- EGFV, University of Bordeaux, Bordeaux-Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Stefano Poni
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Markus Keller
- Department of Viticulture and Enology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, USA
| | - Christel Renaud
- EGFV, University of Bordeaux, Bordeaux-Sciences Agro, INRAE, ISVV, Villenave d’Ornon, France
| | - Junhua Kong
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Jinliang Chen
- Center for Agricultural Water Research in China, China Agricultural University, Beijing, 100083, China
| | - Zhenchang Liang
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhanwu Dai
- State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Gracia-Romero A, Vatter T, Kefauver SC, Rezzouk FZ, Segarra J, Nieto-Taladriz MT, Aparicio N, Araus JL. Defining durum wheat ideotypes adapted to Mediterranean environments through remote sensing traits. FRONTIERS IN PLANT SCIENCE 2023; 14:1254301. [PMID: 37731983 PMCID: PMC10508639 DOI: 10.3389/fpls.2023.1254301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/03/2023] [Indexed: 09/22/2023]
Abstract
An acceleration of the genetic advances of durum wheat, as a major crop for the Mediterranean region, is required, but phenotyping still represents a bottleneck for breeding. This study aims to define durum wheat ideotypes under Mediterranean conditions by selecting the most suitable phenotypic remote sensing traits among different ones informing on characteristics related with leaf pigments/photosynthetic status, crop water status, and crop growth/green biomass. A set of 24 post-green revolution durum wheat cultivars were assessed in a wide set of 19 environments, accounted as the specific combinations of a range of latitudes in Spain, under different management conditions (water regimes and planting dates), through 3 consecutive years. Thus, red-green-blue and multispectral derived vegetation indices and canopy temperature were evaluated at anthesis and grain filling. The potential of the assessed remote sensing parameters alone and all combined as grain yield (GY) predictors was evaluated through random forest regression models performed for each environment and phenological stage. Biomass and plot greenness indicators consistently proved to be reliable GY predictors in all of the environments tested for both phenological stages. For the lowest-yielding environment, the contribution of water status measurements was higher during anthesis, whereas, for the highest-yielding environments, better predictions were reported during grain filling. Remote sensing traits measured during the grain filling and informing on pigment content and photosynthetic capacity were highlighted under the environments with warmer conditions, as the late-planting treatments. Overall, canopy greenness indicators were reported as the highest correlated traits for most of the environments and regardless of the phenological moment assessed. The addition of carbon isotope composition of mature kernels was attempted to increase the accuracies, but only a few were slightly benefited, as differences in water status among cultivars were already accounted by the measurement of canopy temperature.
Collapse
Affiliation(s)
- Adrian Gracia-Romero
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, Barcelona, Spain and AGROTECNIO (Center for Research in Agrotechnology), Lleida, Spain
| | - Thomas Vatter
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, Barcelona, Spain and AGROTECNIO (Center for Research in Agrotechnology), Lleida, Spain
| | - Shawn C. Kefauver
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, Barcelona, Spain and AGROTECNIO (Center for Research in Agrotechnology), Lleida, Spain
| | - Fatima Zahra Rezzouk
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, Barcelona, Spain and AGROTECNIO (Center for Research in Agrotechnology), Lleida, Spain
| | - Joel Segarra
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, Barcelona, Spain and AGROTECNIO (Center for Research in Agrotechnology), Lleida, Spain
| | | | - Nieves Aparicio
- Agro-technological Institute of Castilla y León (ITACyL), Valladolid, Spain
| | - José Luis Araus
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, Barcelona, Spain and AGROTECNIO (Center for Research in Agrotechnology), Lleida, Spain
| |
Collapse
|
6
|
Echarte L, Alfonso CS, González H, Hernández MD, Lewczuk NA, Nagore L, Echarte MM. Influence of management practices on water-related grain yield determinants. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4825-4846. [PMID: 37490359 DOI: 10.1093/jxb/erad269] [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: 02/24/2023] [Accepted: 07/24/2023] [Indexed: 07/27/2023]
Abstract
Adequate management of N supply, plant density, row spacing, and soil cover has proved useful for increasing grain yields and/or grain yield stability of rainfed crops over the years. We review the impact of these management practices on grain yield water-related determinants: seasonal crop evapotranspiration (ET) and water use efficiency for grain production per unit of evapotranspired water during the growing season (WUEG,ET,s). We highlight a large number of conflicting results for the impact of management on ET and expose the complexity of the ET response to environmental factors. We analyse the influence of management practices on WUEG,ET,s in terms of the three main processes controlling it: (i) the proportion of transpiration in ET (T/ET), (ii) transpiration efficiency for shoot biomass production (TEB), and (iii) the harvest index. We directly relate the impact of management practices on T/ET to their effect on crop light interception and provide evidence that management practices significantly influence TEB. To optimize WUEG,ET,s, management practices should favor soil water availability during critical periods for seed set, thereby improving the harvest index. The need to improve the performance of existing crop growth models for the prediction of water-related grain yield determinants under different management practices is also discussed.
Collapse
Affiliation(s)
- Laura Echarte
- IPADS (INTA-CONICET), Ruta 226 Km 73.5, Balcarce, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Ruta 226 Km 73.5, Balcarce, Argentina
| | - Carla S Alfonso
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Ruta 226 Km 73.5, Balcarce, Argentina
| | - Hugo González
- IPADS (INTA-CONICET), Ruta 226 Km 73.5, Balcarce, Argentina
| | - Mariano D Hernández
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Ruta 226 Km 73.5, Balcarce, Argentina
| | | | - Luján Nagore
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Ruta 226 Km 73.5, Balcarce, Argentina
| | | |
Collapse
|
7
|
Tirfessa A, McLean G, Baker P, Mortlock M, Hammer G, van Oosterom E. Differences in temperature responses among phenological processes in diverse Ethiopian sorghum germplasm can affect their specific adaptation to environmental conditions. ANNALS OF BOTANY 2023; 131:601-611. [PMID: 36661105 PMCID: PMC10147321 DOI: 10.1093/aob/mcad011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/12/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Main shoot total leaf number (TLN) is a key determinant of plant leaf area and crop adaptation. Environmental factors other than photoperiod can affect TLN in sorghum, implying that leaf appearance rate (LAR) and development rate can differ in response to temperature. The objectives of this study were to determine (1) if temperature effects on TLN can be explained as a consequence of differences in temperature responses across phenological processes and (2) if genotypic differences in these responses can be linked to agroecological adaptation. METHODS Nineteen sorghum genotypes were sown on 12 dates at two locations in Ethiopia with contrasting altitude, creating temperature differences independent of photoperiod. TLN and temperature were recorded in all experiments and LAR for six sowing dates. KEY RESULTS Eleven of the genotypes showed a temperature effect on TLN, which was associated with a significantly higher base temperature (Tbase) for LAR than for pre-anthesis development rate (DR). In contrast, genotypes with no effect of temperature on TLN had similar Tbase for LAR and DR. Across genotypes, Tbase for LAR and DR were highly correlated, but genotypes with low Tbase had the greatest difference in Tbase between the two processes. Genotypic differences were associated with racial grouping. CONCLUSIONS Genotypic and racial differences in responses of phenological processes to temperature, in particular in Tbase, can affect specific adaptation to agroecological zones, as these differences can affect TLN in response to temperature and hence canopy size and the duration of the pre-anthesis period. These can both affect the amount of water used and radiation intercepted pre-anthesis. A multi-disciplinary approach is required to identify genotype × environment × management combinations that can best capture the ensuing specific adaptation.
Collapse
Affiliation(s)
- Alemu Tirfessa
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St Lucia, QLD 4072, Australia
- Ethiopian Institute of Agricultural Research (EIAR), Melkassa Agricultural Research Center, PO Box 436, Adama, Ethiopia
| | - Greg McLean
- Agri-Science Queensland, Department of Agriculture and Fisheries, Toowoomba, QLD 4350, Australia
| | - Peter Baker
- The University of Queensland, School of Public Health, St Lucia, QLD 4072, Australia
| | - Miranda Mortlock
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St Lucia, QLD 4072, Australia
- Queensland University of Technology, Brisbane City, QLD 4000, Australia
| | - Graeme Hammer
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St Lucia, QLD 4072, Australia
| | | |
Collapse
|
8
|
Li Y, Tao F, Hao Y, Tong J, Xiao Y, Zhang H, He Z, Reynolds M. Linking genetic markers with an eco-physiological model to pyramid favourable alleles and design wheat ideotypes. PLANT, CELL & ENVIRONMENT 2023; 46:780-795. [PMID: 36517924 DOI: 10.1111/pce.14518] [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: 08/14/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Genetic markers can be linked with eco-physiological crop models to accurately predict genotype performance and individual markers' contributions in target environments, exploring interactions between genotype and environment. Here, wheat (Triticum aestivum L.) yield was dissected into seven traits corresponding to cultivar genetic coefficients in an eco-physiological model. Loci for these traits were discovered through the genome-wide association studies (GWAS). The cultivar genetic coefficients were derived from the loci using multiple linear regression or random forest, building a marker-based eco-physiological model. It is then applied to simulate wheat yields and design virtual ideotypes. The results indicated that the loci identified through GWAS explained 46%-75% variations in cultivar genetic coefficients. Using the marker-based model, the normalized root mean square error (nRMSE) between the simulated yield and observed yield was 13.95% by multiple linear regression and 13.62% by random forest. The nRMSE between the simulated and observed maturity dates was 1.24% by multiple linear regression and 1.11% by random forest, respectively. Structural equation modelling indicated that variations in grain yield could be well explained by cultivar genetic coefficients and phenological data. In addition, 24 pleiotropic loci in this study were detected on 15 chromosomes. More significant loci were detected by the model-based dissection method than considering yield per se. Ideotypes were identified by higher yield and more favourable alleles of cultivar genetic traits. This study proposes a genotype-to-phenotype approach and demonstrates novel ideas and tools to support the effective breeding of new cultivars with high yield through pyramiding favourable alleles and designing crop ideotypes.
Collapse
Affiliation(s)
- Yibo Li
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fulu Tao
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jingyang Tong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yonggui Xiao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - He Zhang
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Matthew Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| |
Collapse
|
9
|
Bowerman AF, Byrt CS, Roy SJ, Whitney SM, Mortimer JC, Ankeny RA, Gilliham M, Zhang D, Millar AA, Rebetzke GJ, Pogson BJ. Potential abiotic stress targets for modern genetic manipulation. THE PLANT CELL 2023; 35:139-161. [PMID: 36377770 PMCID: PMC9806601 DOI: 10.1093/plcell/koac327] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/03/2022] [Indexed: 05/06/2023]
Abstract
Research into crop yield and resilience has underpinned global food security, evident in yields tripling in the past 5 decades. The challenges that global agriculture now faces are not just to feed 10+ billion people within a generation, but to do so under a harsher, more variable, and less predictable climate, and in many cases with less water, more expensive inputs, and declining soil quality. The challenges of climate change are not simply to breed for a "hotter drier climate," but to enable resilience to floods and droughts and frosts and heat waves, possibly even within a single growing season. How well we prepare for the coming decades of climate variability will depend on our ability to modify current practices, innovate with novel breeding methods, and communicate and work with farming communities to ensure viability and profitability. Here we define how future climates will impact farming systems and growing seasons, thereby identifying the traits and practices needed and including exemplars being implemented and developed. Critically, this review will also consider societal perspectives and public engagement about emerging technologies for climate resilience, with participatory approaches presented as the best approach.
Collapse
Affiliation(s)
- Andrew F Bowerman
- ARC Training Centre for Accelerated Future Crops Development, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Caitlin S Byrt
- ARC Training Centre for Accelerated Future Crops Development, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Stuart John Roy
- ARC Training Centre for Accelerated Future Crops Development, University of Adelaide, South Australia, Australia
- School of Agriculture, Food and Wine & Waite Research Institute, University of Adelaide, Glen Osmond, South Australia, Australia
| | - Spencer M Whitney
- ARC Training Centre for Accelerated Future Crops Development, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jenny C Mortimer
- ARC Training Centre for Accelerated Future Crops Development, University of Adelaide, South Australia, Australia
- School of Agriculture, Food and Wine & Waite Research Institute, University of Adelaide, Glen Osmond, South Australia, Australia
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Rachel A Ankeny
- ARC Training Centre for Accelerated Future Crops Development, University of Adelaide, South Australia, Australia
- School of Humanities, University of Adelaide, North Terrace, South Australia, Australia
| | - Matthew Gilliham
- ARC Training Centre for Accelerated Future Crops Development, University of Adelaide, South Australia, Australia
- School of Agriculture, Food and Wine & Waite Research Institute, University of Adelaide, Glen Osmond, South Australia, Australia
| | - Dabing Zhang
- ARC Training Centre for Accelerated Future Crops Development, University of Adelaide, South Australia, Australia
- School of Agriculture, Food and Wine & Waite Research Institute, University of Adelaide, Glen Osmond, South Australia, Australia
| | - Anthony A Millar
- ARC Training Centre for Accelerated Future Crops Development, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Greg J Rebetzke
- CSIRO Agriculture & Food, Canberra, Australian Capital Territory, Australia
| | - Barry J Pogson
- ARC Training Centre for Accelerated Future Crops Development, The Australian National University, Canberra, Australian Capital Territory, Australia
| |
Collapse
|
10
|
Tefera AT, O’Leary GJ, Thayalakumaran T, Rao S, Silva-Perez V, Shunmugam ASK, Armstrong R, Rosewarne GM. Identification of agro-physiological traits of lentil that reduce risks of drought. FRONTIERS IN PLANT SCIENCE 2022; 13:1019491. [PMID: 36352869 PMCID: PMC9637959 DOI: 10.3389/fpls.2022.1019491] [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: 08/15/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Ideotype breeding is an essential approach for selection of desired combination of plant traits for testing in crop growth model for potential yield gain in specific environments and management practices. Here we parameterized plant traits for untested lentil cultivars for the APSIM-lentil model in phenology, biomass, and seed yield. We then tested these against independent data and applied the model in an extrapolated analysis (i) to assess the impact of drought on productivity across different rainfall environments; (ii) to identify impactful plant traits and (iii) to design new lentil ideotypes with a combination of desirable traits that mitigate the impact of drought, in the context of various agronomic practices across a wide range of production environments. Desirable phenological and physiological traits related to yield were identified with RUE having the greatest effect on yield followed by HI rate. Leaf size significantly affected seed yield (p< 0.05) more than phenological phases. The physiological traits were integrated into four ideotype designs applied to two baseline cultivars (PBA Hallmark XT and PBA Jumbo2) providing eight ideotypes. We identified a combination of genetic traits that promises a yield advantage of around 10% against our current cultivars PBA Hallmark XT and PBA Jumbo2. Under drought conditions, our ideotypes achieved 5 to 25% yield advantages without stubble and 20 to 40% yield advantages with stubble residues. This shows the importance of genetic screening under realistic production conditions (e.g., stubble retention in particular environments). Such screening is aided by the employment of biophysical models that incorporate both genetic and agronomic variables that focus on successful traits in combination, to reduce the impact of drought in the development of new cultivars for various environments. Stubble retention was found to be a major agronomic contributor to high yield in water-limiting environments and this contribution declined with increasing growing season rainfall. In mid- and high-rainfall environments, the key drivers of yield were time of sowing, physiological traits and soil type. Overall, the agronomic practices, namely, early sowing, residue retention and narrow row spacing deceased the impact of drought when combined with improved physiological traits of the ideotypes based on long term climate data.
Collapse
Affiliation(s)
| | - Garry J. O’Leary
- Agriculture Victoria Research, Grain Innovation Park, Horsham, VIC, Australia
- Centre for Agricultural Innovation, The University of Melbourne, Parkville, VIC, Australia
| | - Thabo Thayalakumaran
- Agriculture Victoria Research, Centre for Agri Bioscience, Melbourne, VIC, Australia
| | - Shiwangni Rao
- Agriculture Victoria Research, Grain Innovation Park, Horsham, VIC, Australia
| | | | | | - Roger Armstrong
- Agriculture Victoria Research, Grain Innovation Park, Horsham, VIC, Australia
- Department of Animal, Plant and Soil Sciences, La Trobe University, Melbourne, VIC, Australia
| | - Garry M. Rosewarne
- Agriculture Victoria Research, Grain Innovation Park, Horsham, VIC, Australia
- Centre for Agricultural Innovation, The University of Melbourne, Parkville, VIC, Australia
| |
Collapse
|
11
|
Zhi X, Hammer G, Borrell A, Tao Y, Wu A, Hunt C, van Oosterom E, Massey-Reed SR, Cruickshank A, Potgieter AB, Jordan D, Mace E, George-Jaeggli B. Genetic basis of sorghum leaf width and its potential as a surrogate for transpiration efficiency. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3057-3071. [PMID: 35933636 PMCID: PMC9482571 DOI: 10.1007/s00122-022-04167-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 06/27/2022] [Indexed: 06/08/2023]
Abstract
Leaf width was correlated with plant-level transpiration efficiency and associated with 19 QTL in sorghum, suggesting it could be a surrogate for transpiration efficiency in large breeding program. Enhancing plant transpiration efficiency (TE) by reducing transpiration without compromising photosynthesis and yield is a desirable selection target in crop improvement programs. While narrow individual leaf width has been correlated with greater intrinsic water use efficiency in C4 species, the extent to which this translates to greater plant TE has not been investigated. The aims of this study were to evaluate the correlation of leaf width with TE at the whole-plant scale and investigate the genetic control of leaf width in sorghum. Two lysimetry experiments using 16 genotypes varying for stomatal conductance and three field trials using a large sorghum diversity panel (n = 701 lines) were conducted. Negative associations of leaf width with plant TE were found in the lysimetry experiments, suggesting narrow leaves may result in reduced plant transpiration without trade-offs in biomass accumulation. A wide range in width of the largest leaf was found in the sorghum diversity panel with consistent ranking among sorghum races, suggesting that environmental adaptation may have a role in modifying leaf width. Nineteen QTL were identified by genome-wide association studies on leaf width adjusted for flowering time. The QTL identified showed high levels of correspondence with those in maize and rice, suggesting similarities in the genetic control of leaf width across cereals. Three a priori candidate genes for leaf width, previously found to regulate dorsoventrality, were identified based on a 1-cM threshold. This study provides useful physiological and genetic insights for potential manipulation of leaf width to improve plant adaptation to diverse environments.
Collapse
Affiliation(s)
- Xiaoyu Zhi
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Crop Science, The University of Queensland, Warwick, QLD, Australia.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Henan, China.
| | - Graeme Hammer
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Crop Science, The University of Queensland, St Lucia, QLD, Australia
| | - Andrew Borrell
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Crop Science, The University of Queensland, Warwick, QLD, Australia
| | - Yongfu Tao
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Crop Science, The University of Queensland, Warwick, QLD, Australia
| | - Alex Wu
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Crop Science, The University of Queensland, St Lucia, QLD, Australia
| | - Colleen Hunt
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Crop Science, The University of Queensland, Warwick, QLD, Australia
- Department of Agriculture and Fisheries (DAF), Hermitage Research Facility, Agri-Science Queensland, Warwick, QLD, Australia
| | - Erik van Oosterom
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Crop Science, The University of Queensland, St Lucia, QLD, Australia
| | - Sean Reynolds Massey-Reed
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Crop Science, The University of Queensland, Warwick, QLD, Australia
| | - Alan Cruickshank
- Department of Agriculture and Fisheries (DAF), Hermitage Research Facility, Agri-Science Queensland, Warwick, QLD, Australia
| | - Andries B Potgieter
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Crop Science, The University of Queensland, Gatton, QLD, Australia
| | - David Jordan
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Crop Science, The University of Queensland, Warwick, QLD, Australia.
- Department of Agriculture and Fisheries (DAF), Hermitage Research Facility, Agri-Science Queensland, Warwick, QLD, Australia.
| | - Emma Mace
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Crop Science, The University of Queensland, Warwick, QLD, Australia.
- Department of Agriculture and Fisheries (DAF), Hermitage Research Facility, Agri-Science Queensland, Warwick, QLD, Australia.
| | - Barbara George-Jaeggli
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Crop Science, The University of Queensland, Warwick, QLD, Australia.
- Department of Agriculture and Fisheries (DAF), Hermitage Research Facility, Agri-Science Queensland, Warwick, QLD, Australia.
| |
Collapse
|
12
|
Langstroff A, Heuermann MC, Stahl A, Junker A. Opportunities and limits of controlled-environment plant phenotyping for climate response traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1-16. [PMID: 34302493 PMCID: PMC8741719 DOI: 10.1007/s00122-021-03892-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 06/17/2021] [Indexed: 05/19/2023]
Abstract
Rising temperatures and changing precipitation patterns will affect agricultural production substantially, exposing crops to extended and more intense periods of stress. Therefore, breeding of varieties adapted to the constantly changing conditions is pivotal to enable a quantitatively and qualitatively adequate crop production despite the negative effects of climate change. As it is not yet possible to select for adaptation to future climate scenarios in the field, simulations of future conditions in controlled-environment (CE) phenotyping facilities contribute to the understanding of the plant response to special stress conditions and help breeders to select ideal genotypes which cope with future conditions. CE phenotyping facilities enable the collection of traits that are not easy to measure under field conditions and the assessment of a plant's phenotype under repeatable, clearly defined environmental conditions using automated, non-invasive, high-throughput methods. However, extrapolation and translation of results obtained under controlled environments to field environments is ambiguous. This review outlines the opportunities and challenges of phenotyping approaches under controlled environments complementary to conventional field trials. It gives an overview on general principles and introduces existing phenotyping facilities that take up the challenge of obtaining reliable and robust phenotypic data on climate response traits to support breeding of climate-adapted crops.
Collapse
Affiliation(s)
- Anna Langstroff
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich Buff-Ring 26, 35392, Giessen, Germany
| | - Marc C Heuermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, OT Gatersleben, 06466, Seeland, Germany
| | - Andreas Stahl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich Buff-Ring 26, 35392, Giessen, Germany
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kühn-Institut (JKI), Erwin-Baur-Strasse 27, 06484, Quedlinburg, Germany
| | - Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, OT Gatersleben, 06466, Seeland, Germany.
| |
Collapse
|
13
|
El Haddad N, Choukri H, Ghanem ME, Smouni A, Mentag R, Rajendran K, Hejjaoui K, Maalouf F, Kumar S. High-Temperature and Drought Stress Effects on Growth, Yield and Nutritional Quality with Transpiration Response to Vapor Pressure Deficit in Lentil. PLANTS (BASEL, SWITZERLAND) 2021; 11:95. [PMID: 35009098 PMCID: PMC8747359 DOI: 10.3390/plants11010095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/20/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
High temperature and water deficit are among the major limitations reducing lentil (Lens culinaris Medik.) yield in many growing regions. In addition, increasing atmospheric vapor pressure deficit (VPD) due to global warming causes a severe challenge by influencing the water balance of the plants, thus also affecting growth and yield. In the present study, we evaluated 20 lentil genotypes under field conditions and controlled environments with the following objectives: (i) to investigate the impact of temperature stress and combined temperature-drought stress on traits related to phenology, grain yield, nutritional quality, and canopy temperature under field conditions, and (ii) to examine the genotypic variability for limited transpiration (TRlim) trait in response to increased VPD under controlled conditions. The field experiment results revealed that high-temperature stress significantly affected all parameters compared to normal conditions. The protein content ranged from 23.4 to 31.9%, while the range of grain zinc and iron content varied from 33.1 to 64.4 and 62.3 to 99.3 mg kg-1, respectively, under normal conditions. The grain protein content, zinc and iron decreased significantly by 15, 14 and 15% under high-temperature stress, respectively. However, the impact was more severe under combined temperature-drought stress with a reduction of 53% in protein content, 18% in zinc and 20% in iron. Grain yield declined significantly by 43% in temperature stress and by 49% in the combined temperature-drought stress. The results from the controlled conditions showed a wide variation in TR among studied lentil genotypes. Nine genotypes displayed TRlim at 2.76 to 3.51 kPa, with the genotypes ILL 7833 and ILL 7835 exhibiting the lowest breakpoint. Genotypes with low breakpoints had the ability to conserve water, allowing it to be used at later stages for increased yield. Our results identified promising genotypes including ILL 7835, ILL 7814 and ILL 4605 (Bakria) that could be of great interest in breeding for high yields, protein and micronutrient contents under high-temperature and drought stress. In addition, it was found that the TRlim trait has the potential to select for increased lentil yields under field water-deficit environments.
Collapse
Affiliation(s)
- Noureddine El Haddad
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat 10112, Morocco; (H.C.); (K.H.)
- Laboratoire de Biotechnologie et de Physiologie Végétales, Centre de Recherche BioBio, Faculté des Sciences, Mohammed V University Rabat, Rabat 10112, Morocco;
| | - Hasnae Choukri
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat 10112, Morocco; (H.C.); (K.H.)
- Laboratoire de Biotechnologie et de Physiologie Végétales, Centre de Recherche BioBio, Faculté des Sciences, Mohammed V University Rabat, Rabat 10112, Morocco;
| | - Michel Edmond Ghanem
- AgroBioSciences (AgBS) Research Division, Mohammed VI Polytechnic University, Lot 660 Hay Moulay Rachid, Ben Guerir 43150, Morocco;
| | - Abdelaziz Smouni
- Laboratoire de Biotechnologie et de Physiologie Végétales, Centre de Recherche BioBio, Faculté des Sciences, Mohammed V University Rabat, Rabat 10112, Morocco;
| | - Rachid Mentag
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research (INRA), Rabat 10090, Morocco;
| | - Karthika Rajendran
- Vellore Institute of Technology (VIT), VIT School of Agricultural Innovations and Advanced Learning (VAIAL), Vellore 632014, Tamil Nadu, India;
| | - Kamal Hejjaoui
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat 10112, Morocco; (H.C.); (K.H.)
| | - Fouad Maalouf
- International Center for Agricultural Research in the Dry Areas (ICARDA), Beirut 1108 2010, Lebanon;
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat 10112, Morocco; (H.C.); (K.H.)
| |
Collapse
|
14
|
Liu F, Song Q, Zhao J, Mao L, Bu H, Hu Y, Zhu XG. Canopy occupation volume as an indicator of canopy photosynthetic capacity. THE NEW PHYTOLOGIST 2021; 232:941-956. [PMID: 34245568 DOI: 10.1111/nph.17611] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/03/2021] [Indexed: 06/13/2023]
Abstract
Leaf angle and leaf area index together influence canopy light interception and canopy photosynthesis. However, so far, there is no effective method to identify the optimal combination of these two parameters for canopy photosynthesis. In this study, first a robust high-throughput method for accurate segmentation of maize organs based on 3D point clouds data was developed, then the segmented plant organs were used to generate new 3D point clouds for the canopy of altered architectures. With this, we simulated the synergistic effect of leaf area and leaf angle on canopy photosynthesis. The results show that, compared to the traditional parameters describing the canopy photosynthesis including leaf area index, facet angle and canopy coverage, a new parameter - the canopy occupation volume (COV) - can better explain the variations of canopy photosynthetic capacity. Specifically, COV can explain > 79% variations of canopy photosynthesis generated by changing leaf angle and > 84% variations of canopy photosynthesis generated by changing leaf area. As COV can be calculated in a high-throughput manner based on the canopy point clouds, it can be used to evaluate canopy architecture in breeding and agronomic research.
Collapse
Affiliation(s)
- Fusang Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qingfeng Song
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jinke Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Linxiong Mao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongyi Bu
- Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai, 200083, China
| | - Yong Hu
- Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai, 200083, China
| | - Xin-Guang Zhu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200031, China
| |
Collapse
|
15
|
Snowdon RJ, Wittkop B, Chen TW, Stahl A. Crop adaptation to climate change as a consequence of long-term breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1613-1623. [PMID: 33221941 PMCID: PMC8205907 DOI: 10.1007/s00122-020-03729-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/11/2020] [Indexed: 05/09/2023]
Abstract
Major global crops in high-yielding, temperate cropping regions are facing increasing threats from the impact of climate change, particularly from drought and heat at critical developmental timepoints during the crop lifecycle. Research to address this concern is frequently focused on attempts to identify exotic genetic diversity showing pronounced stress tolerance or avoidance, to elucidate and introgress the responsible genetic factors or to discover underlying genes as a basis for targeted genetic modification. Although such approaches are occasionally successful in imparting a positive effect on performance in specific stress environments, for example through modulation of root depth, major-gene modifications of plant architecture or function tend to be highly context-dependent. In contrast, long-term genetic gain through conventional breeding has incrementally increased yields of modern crops through accumulation of beneficial, small-effect variants which also confer yield stability via stress adaptation. Here we reflect on retrospective breeding progress in major crops and the impact of long-term, conventional breeding on climate adaptation and yield stability under abiotic stress constraints. Looking forward, we outline how new approaches might complement conventional breeding to maintain and accelerate breeding progress, despite the challenges of climate change, as a prerequisite to sustainable future crop productivity.
Collapse
Affiliation(s)
- Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392, Giessen, Germany.
| | - Benjamin Wittkop
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392, Giessen, Germany
| | - Tsu-Wei Chen
- Albrecht Daniel Thaer Institute of Agricultural and Horticultural Sciences, Humboldt University Berlin, Lentzeallee 75, 14195, Berlin, Germany
| | - Andreas Stahl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392, Giessen, Germany
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kühn-Institut (JKI), Erwin-Baur-Strasse 27, 06484, Quedlinburg, Germany
| |
Collapse
|
16
|
Thermal Stresses in Maize: Effects and Management Strategies. PLANTS 2021; 10:plants10020293. [PMID: 33557079 PMCID: PMC7913793 DOI: 10.3390/plants10020293] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 01/30/2021] [Accepted: 02/01/2021] [Indexed: 01/03/2023]
Abstract
Climate change can decrease the global maize productivity and grain quality. Maize crop requires an optimal temperature for better harvest productivity. A suboptimal temperature at any critical stage for a prolonged duration can negatively affect the growth and yield formation processes. This review discusses the negative impact of temperature extremes (high and low temperatures) on the morpho-physiological, biochemical, and nutritional traits of the maize crop. High temperature stress limits pollen viability and silks receptivity, leading to a significant reduction in seed setting and grain yield. Likewise, severe alterations in growth rate, photosynthesis, dry matter accumulation, cellular membranes, and antioxidant enzyme activities under low temperature collectively limit maize productivity. We also discussed various strategies with practical examples to cope with temperature stresses, including cultural practices, exogenous protectants, breeding climate-smart crops, and molecular genomics approaches. We reviewed that identified quantitative trait loci (QTLs) and genes controlling high- and low temperature stress tolerance in maize could be introgressed into otherwise elite cultivars to develop stress-tolerant cultivars. Genome editing has become a key tool for developing climate-resilient crops. Moreover, challenges to maize crop improvement such as lack of adequate resources for breeding in poor countries, poor communication among the scientists of developing and developed countries, problems in germplasm exchange, and high cost of advanced high-throughput phenotyping systems are discussed. In the end, future perspectives for maize improvement are discussed, which briefly include new breeding technologies such as transgene-free clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas)-mediated genome editing for thermo-stress tolerance in maize.
Collapse
|
17
|
Nogales A, Ribeiro H, Nogales-Bueno J, Hansen LD, Gonçalves EF, Coito JL, Rato AE, Peixe A, Viegas W, Cardoso H. Response of Mycorrhizal 'Touriga Nacional' Variety Grapevines to High Temperatures Measured by Calorespirometry and Near-Infrared Spectroscopy. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1499. [PMID: 33167584 PMCID: PMC7694551 DOI: 10.3390/plants9111499] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 12/24/2022]
Abstract
Heat stress negatively affects several physiological and biochemical processes in grapevine plants. In this work, two new methods, calorespirometry, which has been used to determine temperature adaptation in plants, and near-infrared (NIR) spectroscopy, which has been used to determine several grapevine-related traits and to discriminate among varieties, were tested to evaluate grapevine response to high temperatures. 'Touriga Nacional' variety grapevines, inoculated or not with Rhizoglomus irregulare or Funneliformis mosseae, were used in this study. Calorespirometric parameters and NIR spectra, as well as other parameters commonly used to assess heat injury in plants, were measured before and after high temperature exposure. Growth rate and substrate carbon conversion efficiency, calculated from calorespirometric measurements, and stomatal conductance, were the most sensitive parameters for discriminating among high temperature responses of control and inoculated grapevines. The results revealed that, although this vine variety can adapt its physiology to temperatures up to 40 °C, inoculation with R. irregulare could additionally help to sustain its growth, especially after heat shocks. Therefore, the combination of calorespirometry together with gas exchange measurements is a promising strategy for screening grapevine heat tolerance under controlled conditions and has high potential to be implemented in initial phases of plant breeding programs.
Collapse
Affiliation(s)
- Amaia Nogales
- LEAF—Linking Landscape, Environment, Agriculture and Food. Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal; (E.F.G.); (J.L.C.); (W.V.)
| | - Hugo Ribeiro
- Departamento de Fitotecnia, MED-Instituto Mediterrâneo para a Agricultura, Ambiente e Desenvolvimento, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal; (H.R.); (J.N.-B.); (A.E.R.); (A.P.)
| | - Julio Nogales-Bueno
- Departamento de Fitotecnia, MED-Instituto Mediterrâneo para a Agricultura, Ambiente e Desenvolvimento, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal; (H.R.); (J.N.-B.); (A.E.R.); (A.P.)
- Food Colour and Quality Laboratory, Department of Nutrition and Food Science, Facultad de Farmacia, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Lee D. Hansen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA;
| | - Elsa F. Gonçalves
- LEAF—Linking Landscape, Environment, Agriculture and Food. Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal; (E.F.G.); (J.L.C.); (W.V.)
| | - João Lucas Coito
- LEAF—Linking Landscape, Environment, Agriculture and Food. Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal; (E.F.G.); (J.L.C.); (W.V.)
| | - Ana Elisa Rato
- Departamento de Fitotecnia, MED-Instituto Mediterrâneo para a Agricultura, Ambiente e Desenvolvimento, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal; (H.R.); (J.N.-B.); (A.E.R.); (A.P.)
| | - Augusto Peixe
- Departamento de Fitotecnia, MED-Instituto Mediterrâneo para a Agricultura, Ambiente e Desenvolvimento, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal; (H.R.); (J.N.-B.); (A.E.R.); (A.P.)
| | - Wanda Viegas
- LEAF—Linking Landscape, Environment, Agriculture and Food. Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal; (E.F.G.); (J.L.C.); (W.V.)
| | - Hélia Cardoso
- MED-Instituto Mediterrâneo para a Agricultura, Ambiente e Desenvolvimento, Instituto de Investigação e Formação Avançada, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal;
| |
Collapse
|
18
|
Kar S, Tanaka R, Korbu LB, Kholová J, Iwata H, Durbha SS, Adinarayana J, Vadez V. Automated discretization of 'transpiration restriction to increasing VPD' features from outdoors high-throughput phenotyping data. PLANT METHODS 2020; 16:140. [PMID: 33072176 PMCID: PMC7565372 DOI: 10.1186/s13007-020-00680-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/05/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Restricting transpiration under high vapor pressure deficit (VPD) is a promising water-saving trait for drought adaptation. However, it is often measured under controlled conditions and at very low throughput, unsuitable for breeding. A few high-throughput phenotyping (HTP) studies exist, and have considered only maximum transpiration rate in analyzing genotypic differences in this trait. Further, no study has precisely identified the VPD breakpoints where genotypes restrict transpiration under natural conditions. Therefore, outdoors HTP data (15 min frequency) of a chickpea population were used to automate the generation of smooth transpiration profiles, extract informative features of the transpiration response to VPD for optimal genotypic discretization, identify VPD breakpoints, and compare genotypes. RESULTS Fifteen biologically relevant features were extracted from the transpiration rate profiles derived from load cells data. Genotypes were clustered (C1, C2, C3) and 6 most important features (with heritability > 0.5) were selected using unsupervised Random Forest. All the wild relatives were found in C1, while C2 and C3 mostly comprised high TE and low TE lines, respectively. Assessment of the distinct p-value groups within each selected feature revealed highest genotypic variation for the feature representing transpiration response to high VPD condition. Sensitivity analysis on a multi-output neural network model (with R of 0.931, 0.944, 0.953 for C1, C2, C3, respectively) found C1 with the highest water saving ability, that restricted transpiration at relatively low VPD levels, 56% (i.e. 3.52 kPa) or 62% (i.e. 3.90 kPa), depending whether the influence of other environmental variables was minimum or maximum. Also, VPD appeared to have the most striking influence on the transpiration response independently of other environment variable, whereas light, temperature, and relative humidity alone had little/no effect. CONCLUSION Through this study, we present a novel approach to identifying genotypes with drought-tolerance potential, which overcomes the challenges in HTP of the water-saving trait. The six selected features served as proxy phenotypes for reliable genotypic discretization. The wild chickpeas were found to limit water-loss faster than the water-profligate cultivated ones. Such an analytic approach can be directly used for prescriptive breeding applications, applied to other traits, and help expedite maximized information extraction from HTP data.
Collapse
Affiliation(s)
- Soumyashree Kar
- Centre of Studies in Resources Engineering, Indian Institute of Technology Bombay, Mumbai, India 400076
| | - Ryokei Tanaka
- Laboratory of Biometrics and Bioinformatics, University of Tokyo, Tokyo, Japan
| | - Lijalem Balcha Korbu
- Debre Zeit Research Center, Ethiopian Institute of Agricultural Research (EIAR), Debre Zeit, Ethiopia
| | - Jana Kholová
- International Crop Research Institute for Semi-Arid Tropics, Hyderabad, India 502319
| | - Hiroyoshi Iwata
- Laboratory of Biometrics and Bioinformatics, University of Tokyo, Tokyo, Japan
| | - Surya S. Durbha
- Centre of Studies in Resources Engineering, Indian Institute of Technology Bombay, Mumbai, India 400076
| | - J. Adinarayana
- Centre of Studies in Resources Engineering, Indian Institute of Technology Bombay, Mumbai, India 400076
| | - Vincent Vadez
- International Crop Research Institute for Semi-Arid Tropics, Hyderabad, India 502319
- Institut de Recherche Pour Le Développement (IRD), Université de Montpellier—UMR DIADE, 911 Avenue Agropolis, BP 64501, 34394 Montpellier cedex 5, France
| |
Collapse
|
19
|
Low JW, Ortiz R, Vandamme E, Andrade M, Biazin B, Grüneberg WJ. Nutrient-Dense Orange-Fleshed Sweetpotato: Advances in Drought-Tolerance Breeding and Understanding of Management Practices for Sustainable Next-Generation Cropping Systems in Sub-Saharan Africa. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.00050] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
|
20
|
Stahl A, Wittkop B, Snowdon RJ. High-resolution digital phenotyping of water uptake and transpiration efficiency. TRENDS IN PLANT SCIENCE 2020; 25:429-433. [PMID: 32304656 DOI: 10.1016/j.tplants.2020.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/28/2020] [Accepted: 02/04/2020] [Indexed: 05/16/2023]
Abstract
Despite innovations in phenotyping, dissecting impacts of water uptake, transpiration efficiency and harvest index on crop yield under defined drought stress scenarios remains challenging. Here, we highlight benefits of concepts enabling plant growth in extra-large containers accompanied by continuous tracking of transpiration, nondestructive plant growth monitoring, and subsequent yield evaluation.
Collapse
Affiliation(s)
- Andreas Stahl
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich Buff-Ring 26, 35392 Giessen, Germany. @agrar.uni-giessen.de
| | - Benjamin Wittkop
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich Buff-Ring 26, 35392 Giessen, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich Buff-Ring 26, 35392 Giessen, Germany
| |
Collapse
|
21
|
Condon AG. Drying times: plant traits to improve crop water use efficiency and yield. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2239-2252. [PMID: 31912130 DOI: 10.1093/jxb/eraa002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/07/2020] [Indexed: 05/13/2023]
Abstract
Crop water use efficiency (WUE) has come into sharp focus as population growth and climate change place increasing strain on the water used in cropping. Rainfed crops are being challenged by an upward trend in evaporative demand as average temperatures rise and, in many regions, there is an increased irregularity and a downward trend in rainfall. In addition, irrigated cropping faces declining water availability and increased competition from other users. Crop WUE would be improved by, first, ensuring that as much water as possible is actually transpired by the crop rather than being wasted. Deeper roots and greater early crop vigour are two traits that should help achieve this. Crop WUE would also be improved by achieving greater biomass per unit water transpired. A host of traits has been proposed to address this outcome. Restricting crop transpiration through lower stomatal conductance is assessed as having limited utility compared with traits that improve carbon gain, such as enhancements to photosynthetic biochemistry and responsiveness, or greater mesophyll conductance. Ultimately, the most useful outcomes for improved crop WUE will probably be achieved by combining traits to achieve synergistic benefit. The potential utility of trait combinations is supported by the results of crop simulation modelling.
Collapse
|
22
|
Bustos-Korts D, Malosetti M, Chenu K, Chapman S, Boer MP, Zheng B, van Eeuwijk FA. From QTLs to Adaptation Landscapes: Using Genotype-To-Phenotype Models to Characterize G×E Over Time. FRONTIERS IN PLANT SCIENCE 2019; 10:1540. [PMID: 31867027 PMCID: PMC6904366 DOI: 10.3389/fpls.2019.01540] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/04/2019] [Indexed: 05/18/2023]
Abstract
Genotype by environment interaction (G×E) for the target trait, e.g. yield, is an emerging property of agricultural systems and results from the interplay between a hierarchy of secondary traits involving the capture and allocation of environmental resources during the growing season. This hierarchy of secondary traits ranges from basic traits that correspond to response mechanisms/sensitivities, to intermediate traits that integrate a larger number of processes over time and therefore show a larger amount of G×E. Traits underlying yield differ in their contribution to adaptation across environmental conditions and have different levels of G×E. Here, we provide a framework to study the performance of genotype to phenotype (G2P) modeling approaches. We generate and analyze response surfaces, or adaptation landscapes, for yield and yield related traits, emphasizing the organization of the traits in a hierarchy and their development and interactions over time. We use the crop growth model APSIM-wheat with genotype-dependent parameters as a tool to simulate non-linear trait responses over time with complex trait dependencies and apply it to wheat crops in Australia. For biological realism, APSIM parameters were given a genetic basis of 300 QTLs sampled from a gamma distribution whose shape and rate parameters were estimated from real wheat data. In the simulations, the hierarchical organization of the traits and their interactions over time cause G×E for yield even when underlying traits do not show G×E. Insight into how G×E arises during growth and development helps to improve the accuracy of phenotype predictions within and across environments and to optimize trial networks. We produced a tangible simulated adaptation landscape for yield that we first investigated for its biological credibility by statistical models for G×E that incorporate genotypic and environmental covariables. Subsequently, the simulated trait data were used to evaluate statistical genotype-to-phenotype models for multiple traits and environments and to characterize relationships between traits over time and across environments, as a way to identify traits that could be useful to select for specific adaptation. Designed appropriately, these types of simulated landscapes might also serve as a basis to train other, more deep learning methodologies in order to transfer such network models to real-world situations.
Collapse
Affiliation(s)
| | - Marcos Malosetti
- Biometris, Wageningen University and Research Centre, Wageningen, Netherlands
| | - Karine Chenu
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Toowoomba, QLD, Australia
| | - Scott Chapman
- Agriculture and Food, CSIRO, Queensland Bioscience Precinct, St Lucia, QLD, Australia
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD, Australia
| | - Martin P. Boer
- Biometris, Wageningen University and Research Centre, Wageningen, Netherlands
| | - Bangyou Zheng
- Agriculture and Food, CSIRO, Queensland Bioscience Precinct, St Lucia, QLD, Australia
| | - Fred A. van Eeuwijk
- Biometris, Wageningen University and Research Centre, Wageningen, Netherlands
| |
Collapse
|
23
|
Geetika G, van Oosterom EJ, George-Jaeggli B, Mortlock MY, Deifel KS, McLean G, Hammer GL. Genotypic variation in whole-plant transpiration efficiency in sorghum only partly aligns with variation in stomatal conductance. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:1072-1089. [PMID: 31615621 DOI: 10.1071/fp18177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 07/01/2019] [Indexed: 05/13/2023]
Abstract
Water scarcity can limit sorghum (Sorghum bicolor (L.) Moench) production in dryland agriculture, but increased whole-plant transpiration efficiency (TEwp, biomass production per unit of water transpired) can enhance grain yield in such conditions. The objectives of this study were to quantify variation in TEwp for 27 sorghum genotypes and explore the linkages of this variation to responses of the underpinning leaf-level processes to environmental conditions. Individual plants were grown in large lysimeters in two well-watered experiments. Whole-plant transpiration per unit of green leaf area (TGLA) was monitored continuously and stomatal conductance and maximum photosynthetic capacity were measured during sunny conditions on recently expanded leaves. Leaf chlorophyll measurements of the upper five leaves of the main shoot were conducted during early grain filling. TEwp was determined at harvest. The results showed that diurnal patterns in TGLA were determined by vapour pressure deficit (VPD) and by the response of whole-plant conductance to radiation and VPD. Significant genotypic variation in the response of TGLA to VPD occurred and was related to genotypic differences in stomatal conductance. However, variation in TGLA explained only part of the variation in TEwp, with some of the residual variation explained by leaf chlorophyll readings, which were a reflection of photosynthetic capacity. Genotypes with different genetic background often differed in TEwp, TGLA and leaf chlorophyll, indicating potential differences in photosynthetic capacity among these groups. Observed differences in TEwp and its component traits can affect adaptation to drought stress.
Collapse
Affiliation(s)
- Geetika Geetika
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St Lucia, Qld 4072, Australia; and Corresponding author.
| | - Erik J van Oosterom
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St Lucia, Qld 4072, Australia
| | - Barbara George-Jaeggli
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Hermitage Research Facility, Warwick, Qld 4370, Australia; and Agri-Science Queensland, Department of Agriculture and Fisheries, Warwick, Qld 4370, Australia
| | - Miranda Y Mortlock
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St Lucia, Qld 4072, Australia
| | - Kurt S Deifel
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St Lucia, Qld 4072, Australia
| | - Greg McLean
- Agri-Science Queensland, Department of Agriculture and Fisheries, Toowoomba, Qld 4350, Australia
| | - Graeme L Hammer
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St Lucia, Qld 4072, Australia
| |
Collapse
|
24
|
Costa JM, Marques da Silva J, Pinheiro C, Barón M, Mylona P, Centritto M, Haworth M, Loreto F, Uzilday B, Turkan I, Oliveira MM. Opportunities and Limitations of Crop Phenotyping in Southern European Countries. FRONTIERS IN PLANT SCIENCE 2019; 10:1125. [PMID: 31608085 PMCID: PMC6774291 DOI: 10.3389/fpls.2019.01125] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 08/15/2019] [Indexed: 05/31/2023]
Abstract
The Mediterranean climate is characterized by hot dry summers and frequent droughts. Mediterranean crops are frequently subjected to high evapotranspiration demands, soil water deficits, high temperatures, and photo-oxidative stress. These conditions will become more severe due to global warming which poses major challenges to the sustainability of the agricultural sector in Mediterranean countries. Selection of crop varieties adapted to future climatic conditions and more tolerant to extreme climatic events is urgently required. Plant phenotyping is a crucial approach to address these challenges. High-throughput plant phenotyping (HTPP) helps to monitor the performance of improved genotypes and is one of the most effective strategies to improve the sustainability of agricultural production. In spite of the remarkable progress in basic knowledge and technology of plant phenotyping, there are still several practical, financial, and political constraints to implement HTPP approaches in field and controlled conditions across the Mediterranean. The European panorama of phenotyping is heterogeneous and integration of phenotyping data across different scales and translation of "phytotron research" to the field, and from model species to crops, remain major challenges. Moreover, solutions specifically tailored to Mediterranean agriculture (e.g., crops and environmental stresses) are in high demand, as the region is vulnerable to climate change and to desertification processes. The specific phenotyping requirements of Mediterranean crops have not yet been fully identified. The high cost of HTPP infrastructures is a major limiting factor, though the limited availability of skilled personnel may also impair its implementation in Mediterranean countries. We propose that the lack of suitable phenotyping infrastructures is hindering the development of new Mediterranean agricultural varieties and will negatively affect future competitiveness of the agricultural sector. We provide an overview of the heterogeneous panorama of phenotyping within Mediterranean countries, describing the state of the art of agricultural production, breeding initiatives, and phenotyping capabilities in five countries: Italy, Greece, Portugal, Spain, and Turkey. We characterize some of the main impediments for development of plant phenotyping in those countries and identify strategies to overcome barriers and maximize the benefits of phenotyping and modeling approaches to Mediterranean agriculture and related sustainability.
Collapse
Affiliation(s)
| | - Jorge Marques da Silva
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, Universidade de Lisboa, Lisbon, Portugal
| | - Carla Pinheiro
- FCT NOVA, Universidade Nova de Lisboa, Monte da Caparica, Portugal
- ITQB NOVA, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Matilde Barón
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Photini Mylona
- HAO-DEMETER, Institute of Plant Breeding and Genetic Resources, Thermi, Greece
| | - Mauro Centritto
- Institute for Sustainable Plant Protection, Italian National Research Council (IPSP-CNR), Sesto Fiorentino, Italy
| | | | - Francesco Loreto
- Department of Biology, Agriculture and Food Sciences, CNR, Rome, Italy
| | - Baris Uzilday
- Department of Biology, Faculty of Science, Ege University, I˙zmir, Turkey
| | - Ismail Turkan
- Department of Biology, Faculty of Science, Ege University, I˙zmir, Turkey
| | | |
Collapse
|
25
|
Gosa SC, Lupo Y, Moshelion M. Quantitative and comparative analysis of whole-plant performance for functional physiological traits phenotyping: New tools to support pre-breeding and plant stress physiology studies. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 282:49-59. [PMID: 31003611 DOI: 10.1016/j.plantsci.2018.05.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 04/14/2018] [Accepted: 05/14/2018] [Indexed: 05/18/2023]
Abstract
Plants are autotrophic organisms in which there are linear relationships between the rate at which organic biomass is accumulated and many ambient parameters such as water, nutrients, CO2 and solar radiation. These linear relationships are the result of good feedback regulation between a plants sensing of the environment and the optimization of its performance response. In this review, we suggest that continuous monitoring of the plant physiological profile in response to changing ambient conditions could be a useful new phenotyping tool, allowing the characterization and comparison of different levels of functional phenotypes and productivity. This functional physiological phenotyping (FPP) approach can be integrated into breeding programs, which are facing difficulties in selecting plants that perform well under abiotic stress. Moreover, high-throughput FPP will increase the efficiency of the selection of traits that are closely related to environmental interactions (such as plant water status, water-use efficiency, stomatal conductance, etc.) thanks to its high resolution and dynamic measurements. One of the important advantages of FPP is, its simplicity and effectiveness and compatibility with experimental methods that use load-cell lysimeters and ambient sensors. In the future, this platform could help with phenotyping of complex physiological traits, beneficial for yield gain to enhance functional breeding approaches and guide in crop modeling.
Collapse
Affiliation(s)
- Sanbon Chaka Gosa
- The Robert H Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Yaniv Lupo
- The Robert H Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Menachem Moshelion
- The Robert H Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel.
| |
Collapse
|
26
|
Leakey ADB, Ferguson JN, Pignon CP, Wu A, Jin Z, Hammer GL, Lobell DB. Water Use Efficiency as a Constraint and Target for Improving the Resilience and Productivity of C 3 and C 4 Crops. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:781-808. [PMID: 31035829 DOI: 10.1146/annurev-arplant-042817-040305] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The ratio of plant carbon gain to water use, known as water use efficiency (WUE), has long been recognized as a key constraint on crop production and an important target for crop improvement. WUE is a physiologically and genetically complex trait that can be defined at a range of scales. Many component traits directly influence WUE, including photosynthesis, stomatal and mesophyll conductances, and canopy structure. Interactions of carbon and water relations with diverse aspects of the environment and crop development also modulate WUE. As a consequence, enhancing WUE by breeding or biotechnology has proven challenging but not impossible. This review aims to synthesize new knowledge of WUE arising from advances in phenotyping, modeling, physiology, genetics, and molecular biology in the context of classical theoretical principles. In addition, we discuss how rising atmospheric CO2 concentration has created and will continue to create opportunities for enhancing WUE by modifying the trade-off between photosynthesis and transpiration.
Collapse
Affiliation(s)
- Andrew D B Leakey
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA;
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - John N Ferguson
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Charles P Pignon
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA;
| | - Alex Wu
- Centre for Crop Science and Centre of Excellence for Translational Photosynthesis, University of Queensland, St. Lucia, Queensland 4069, Australia
| | - Zhenong Jin
- Department of Earth System Science and Center for Food Security and Environment, Stanford University, Stanford, California 94305, USA
| | - Graeme L Hammer
- Centre for Crop Science and Centre of Excellence for Translational Photosynthesis, University of Queensland, St. Lucia, Queensland 4069, Australia
| | - David B Lobell
- Department of Earth System Science and Center for Food Security and Environment, Stanford University, Stanford, California 94305, USA
| |
Collapse
|
27
|
Zardilis A, Hume A, Millar AJ. A multi-model framework for the Arabidopsis life cycle. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2463-2477. [PMID: 31091320 PMCID: PMC6487595 DOI: 10.1093/jxb/ery394] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 11/20/2018] [Indexed: 05/04/2023]
Abstract
Linking our understanding of biological processes at different scales is a major conceptual challenge in biology and aggravated by differences in research methods. Modelling can be a useful approach to consolidating our understanding across traditional research domains. The laboratory model species Arabidopsis is very widely used to study plant growth processes and has also been tested more recently in ecophysiology and population genetics. However, approaches from crop modelling that might link these domains are rarely applied to Arabidopsis. Here, we combine plant growth models with phenology models from ecophysiology, using the agent-based modelling language Chromar. We introduce a simpler Framework Model of vegetative growth for Arabidopsis, FM-lite. By extending this model to include inflorescence and fruit growth and seed dormancy, we present a whole-life-cycle, multi-model FM-life, which allows us to simulate at the population level in various genotype × environment scenarios. Environmental effects on plant growth distinguish between the simulated life history strategies that were compatible with previously described Arabidopsis phenology. Our results simulate reproductive success that is founded on the broad range of physiological processes familiar from crop models and suggest an approach to simulating evolution directly in future.
Collapse
Affiliation(s)
- Argyris Zardilis
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Alastair Hume
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- EPCC, University of Edinburgh, Edinburgh, UK
| | - Andrew J Millar
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
28
|
Fletcher A, Christopher J, Hunter M, Rebetzke G, Chenu K. A low-cost method to rapidly and accurately screen for transpiration efficiency in wheat. PLANT METHODS 2018; 14:77. [PMID: 30181766 PMCID: PMC6116455 DOI: 10.1186/s13007-018-0339-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/14/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND Wheat (Triticum aestivum L.) productivity is commonly limited by the availability of water. Increasing transpiration efficiency (biomass produced per unit of water used, TE) can potentially lead to increased grain yield in water-limited environments ('more crop per drop'). Currently, the ability to screen large populations for TE is limited by slow, low-throughput and/or expensive screening procedures. Here, we propose a low-cost, low-technology, rapid, and scalable method to screen for TE. The method uses a Pot-in-Bucket system that allows continuous watering of the pots and frequent monitoring of water use. To investigate the robustness of the method across environments, and to determine the shortest trial duration required to get accurate and repeatable TE estimates in wheat, plants from 11 genotypes varying in phenology were sown at three dates and grown for different durations in a polyhouse with partial environmental control. RESULTS The method revealed significant genotypic variations in TE among the 11 studied wheat genotypes. Genotype rankings for TE were consistent when plants were harvested the same day, at the flag-leaf stage or later. For these harvests, genotype rankings were consistent across experiments despite changes in environmental conditions, such as evaporative demand. CONCLUSIONS These results indicate that (1) the Pot-In-Bucket system is suitable to screen TE for breeding purposes in populations with varying phenology, (2) multiple short trials can be carried out within a season to allow increased throughput of genotypes for TE screening, and (3) root biomass measurement is not required to screen for TE, as whole-plant TE and shoot-only TE are highly correlated, at least in wheat. The method is particularly relevant in developing countries where low-cost and relatively high labour input may be most applicable.
Collapse
Affiliation(s)
- Andrew Fletcher
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, 203 Tor Street, Toowoomba, QLD 4350 Australia
| | - Jack Christopher
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, 13 Holberton Street, Toowoomba, QLD 4350 Australia
| | - Mal Hunter
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, 4072 Australia
| | - Greg Rebetzke
- CSIRO Plant Industry, PO Box 1600, Canberra, ACT 2601 Australia
| | - Karine Chenu
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, 203 Tor Street, Toowoomba, QLD 4350 Australia
| |
Collapse
|
29
|
Varshney RK, Tuberosa R, Tardieu F. Progress in understanding drought tolerance: from alleles to cropping systems. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3175-3179. [PMID: 29878257 PMCID: PMC5991209 DOI: 10.1093/jxb/ery187] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Affiliation(s)
- Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, Italy
| | | |
Collapse
|