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Park B, Wi S, Chung H, Lee H. Chlorophyll Fluorescence Imaging for Environmental Stress Diagnosis in Crops. SENSORS (BASEL, SWITZERLAND) 2024; 24:1442. [PMID: 38474977 DOI: 10.3390/s24051442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024]
Abstract
The field of plant phenotype is used to analyze the shape and physiological characteristics of crops in multiple dimensions. Imaging, using non-destructive optical characteristics of plants, analyzes growth characteristics through spectral data. Among these, fluorescence imaging technology is a method of evaluating the physiological characteristics of crops by inducing plant excitation using a specific light source. Through this, we investigate how fluorescence imaging responds sensitively to environmental stress in garlic and can provide important information on future stress management. In this study, near UV LED (405 nm) was used to induce the fluorescence phenomenon of garlic, and fluorescence images were obtained to classify and evaluate crops exposed to abiotic environmental stress. Physiological characteristics related to environmental stress were developed from fluorescence sample images using the Chlorophyll ratio method, and classification performance was evaluated by developing a classification model based on partial least squares discrimination analysis from the image spectrum for stress identification. The environmental stress classification performance identified from the Chlorophyll ratio was 14.9% in F673/F717, 25.6% in F685/F730, and 0.209% in F690/F735. The spectrum-developed PLS-DA showed classification accuracy of 39.6%, 56.2% and 70.7% in Smoothing, MSV, and SNV, respectively. Spectrum pretreatment-based PLS-DA showed higher discrimination performance than the existing image-based Chlorophyll ratio.
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Affiliation(s)
- Beomjin Park
- Department of Biosystems Engineering, College of Agriculture, Life & Environment Science, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju-si 28644, Republic of Korea
| | - Seunghwan Wi
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Wanju 55365, Republic of Korea
| | - Hwanjo Chung
- Department of Biosystems Engineering, College of Agriculture, Life & Environment Science, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju-si 28644, Republic of Korea
| | - Hoonsoo Lee
- Department of Biosystems Engineering, College of Agriculture, Life & Environment Science, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Cheongju-si 28644, Republic of Korea
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Farooqi MQU, Nawaz G, Wani SH, Choudhary JR, Rana M, Sah RP, Afzal M, Zahra Z, Ganie SA, Razzaq A, Reyes VP, Mahmoud EA, Elansary HO, El-Abedin TKZ, Siddique KHM. Recent developments in multi-omics and breeding strategies for abiotic stress tolerance in maize ( Zea mays L.). FRONTIERS IN PLANT SCIENCE 2022; 13:965878. [PMID: 36212378 PMCID: PMC9538355 DOI: 10.3389/fpls.2022.965878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/23/2022] [Indexed: 06/12/2023]
Abstract
High-throughput sequencing technologies (HSTs) have revolutionized crop breeding. The advent of these technologies has enabled the identification of beneficial quantitative trait loci (QTL), genes, and alleles for crop improvement. Climate change have made a significant effect on the global maize yield. To date, the well-known omic approaches such as genomics, transcriptomics, proteomics, and metabolomics are being incorporated in maize breeding studies. These approaches have identified novel biological markers that are being utilized for maize improvement against various abiotic stresses. This review discusses the current information on the morpho-physiological and molecular mechanism of abiotic stress tolerance in maize. The utilization of omics approaches to improve abiotic stress tolerance in maize is highlighted. As compared to single approach, the integration of multi-omics offers a great potential in addressing the challenges of abiotic stresses of maize productivity.
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Affiliation(s)
| | - Ghazala Nawaz
- Department of Botanical and Environmental Sciences, Kohat University of Science and Technology, Kohat, Pakistan
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Jeet Ram Choudhary
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Maneet Rana
- Division of Crop Improvement, ICAR-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Rameswar Prasad Sah
- Division of Crop Improvement, ICAR-National Rice Research Institute, Cuttack, India
| | - Muhammad Afzal
- College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Zahra Zahra
- Department of Civil and Environmental Engineering, University of California, Irvine, Irvine, CA, United States
| | | | - Ali Razzaq
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | | | - Eman A. Mahmoud
- Department of Food Industries, Faculty of Agriculture, Damietta University, Damietta, Egypt
| | - Hosam O. Elansary
- Plant Production Department, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
- Floriculture, Ornamental Horticulture, and Garden Design Department, Faculty of Agriculture (El-Shatby), Alexandria University, Alexandria, Egypt
- Department of Geography, Environmental Management, and Energy Studies, University of Johannesburg, Johannesburg, South Africa
| | - Tarek K. Zin El-Abedin
- Department of Agriculture & Biosystems Engineering, Faculty of Agriculture (El-Shatby), Alexandria University, Alexandria, Egypt
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Galić V, Mlinarić S, Marelja M, Zdunić Z, Brkić A, Mazur M, Begović L, Šimić D. Contrasting Water Withholding Responses of Young Maize Plants Reveal Link Between Lipid Peroxidation and Osmotic Regulation Corroborated by Genetic Analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:804630. [PMID: 35873985 PMCID: PMC9296821 DOI: 10.3389/fpls.2022.804630] [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: 10/29/2021] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Linking biochemistry and genetics of tolerance to osmotic stress is of interest for understanding plant adaptations to unfavorable conditions. The aims of this study were to investigate the variability in responses of panel of elite maize inbred lines to water withholding for stress-related traits through association study and to identify pathways linked to detected associations for better understanding of maize stress responses. Densely genotyped public and expired Plant Variety Protection Certificate (ex-PVP) inbred lines were planted in controlled conditions (16-h/8-h day/night, 25°C, 50% RH) in control (CO) and exposed to 10-day water withholding (WW). Traits analyzed were guaiacol peroxidase activity (GPOD), total protein content (PROT), lipid peroxidation (TBARS), hydrogen peroxide accumulation (H2O2), proline accumulation (proline), and current water content (CWC). Proline accumulation was found to be influenced by H2O2 and TBARS signaling pathways acting as an accumulation-switching mechanism. Most of the associations detected were for proline (29.4%) and TBARS (44.1%). Gene ontology (GO) enrichment analysis showed significant enrichment in regulation of integral membrane parts and peroxisomes along with regulation of transcription and polysaccharide catabolism. Dynamic studies involving inbreds with extreme phenotypes are needed to elucidate the role of this signaling mechanism in regulation of response to water deficit.
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Affiliation(s)
- Vlatko Galić
- Department of Maize Breeding and Genetics, Agricultural Institute Osijek, Osijek, Croatia
| | - Selma Mlinarić
- Department of Biology, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Matea Marelja
- Department of Biology, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Zvonimir Zdunić
- Department of Maize Breeding and Genetics, Agricultural Institute Osijek, Osijek, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), Zagreb, Croatia
| | - Andrija Brkić
- Department of Maize Breeding and Genetics, Agricultural Institute Osijek, Osijek, Croatia
| | - Maja Mazur
- Department of Maize Breeding and Genetics, Agricultural Institute Osijek, Osijek, Croatia
| | - Lidija Begović
- Department of Biology, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Domagoj Šimić
- Department of Maize Breeding and Genetics, Agricultural Institute Osijek, Osijek, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), Zagreb, Croatia
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Zhao Z, Liu Z, Zhou Y, Wang J, Zhang Y, Yu X, Wu R, Guo C, Qin A, Bawa G, Sun X. Creation of cotton mutant library based on linear electron accelerator radiation mutation. Biochem Biophys Rep 2022; 30:101228. [PMID: 35243011 PMCID: PMC8867050 DOI: 10.1016/j.bbrep.2022.101228] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/29/2022] [Accepted: 01/31/2022] [Indexed: 11/21/2022] Open
Abstract
Cotton (Gossypium spp.) is one of the most important cash crops worldwide. At present, new cotton varieties are mainly produced through conventional cross breeding, which is limited by available germplasm. Although the genome of cotton has been fully sequenced, research on the function of specific genes lags behind due to the lack of sufficient genetic material. Therefore, it is very important to create a cotton mutant library to create new, higher-quality varieties and identify genes associated with the regulation of key traits. Traditional mutagenic strategies, such as physical, chemical, and site-directed mutagenesis, are relatively costly, inefficient, and difficult to perform. In this study, we used a radiation mutation method based on linear electron acceleration to mutate cotton variety 'TM-1', for which a whole-genome sequence has previously been performed, to create a high throughput cotton mutant library. Abundant phenotypic variation was observed in the progeny population for three consecutive generations, including cotton fiber color variation, plant dwarfing, significant improvement of yield traits, and increased sensitivity to Verticillium wilt. These results show that radiation mutagenesis is an effective and feasible method to create plant mutant libraries.
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Affiliation(s)
| | | | - Yaping Zhou
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Jiajing Wang
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Yixin Zhang
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Xiaole Yu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Rui Wu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Chenxi Guo
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Aizhi Qin
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - George Bawa
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Xuwu Sun
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
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Machine Learning in the Analysis of Multispectral Reads in Maize Canopies Responding to Increased Temperatures and Water Deficit. REMOTE SENSING 2022. [DOI: 10.3390/rs14112596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Real-time monitoring of crop responses to environmental deviations represents a new avenue for applications of remote and proximal sensing. Combining the high-throughput devices with novel machine learning (ML) approaches shows promise in the monitoring of agricultural production. The 3 × 2 multispectral arrays with responses at 610 and 680 nm (red), 730 and 760 nm (red-edge) and 810 and 860 nm (infrared) spectra were used to assess the occurrence of leaf rolling (LR) in 545 experimental maize plots measured four times for calibration dataset (n = 2180) and 145 plots measured once for external validation. Multispectral reads were used to calculate 15 simple normalized vegetation indices. Four ML algorithms were assessed: single and multilayer perceptron (SLP and MLP), convolutional neural network (CNN) and support vector machines (SVM) in three validation procedures, which were stratified cross-validation, random subset validation and validation with external dataset. Leaf rolling occurrence caused visible changes in spectral responses and calculated vegetation indexes. All algorithms showed good performance metrics in stratified cross-validation (accuracy >80%). SLP was the least efficient in predictions with external datasets, while MLP, CNN and SVM showed comparable performance. Combining ML with multispectral sensing shows promise in transition towards agriculture based on data-driven decisions especially considering the novel Internet of Things (IoT) avenues.
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Liang F, Zhan W, Hu G, Liu H, Xing Y, Li Z, Han Z. Five plants per RIL for phenotyping traits of high or moderate heritability ensure the power of QTL mapping in a rice MAGIC population. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:28. [PMID: 37309531 PMCID: PMC10248629 DOI: 10.1007/s11032-022-01299-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/20/2022] [Indexed: 06/14/2023]
Abstract
Currently, the power of QTL mapping is mainly dependent on the quality of phenotypic data in a given population, regardless of the statistical method, as the quality of genotypic data is easily guaranteed in the laboratory. Increasing the sample size per line used for phenotyping is a good way to improve the quality of phenotypic data. However, accommodating a large-scale mapping population takes a large area of rice field, which frequently results in high costs and extra environmental noises. To acquire a reasonable small sample size without a penalty in mapping power, we conducted three experiments with a 4-way MAGIC population and measured phenotypes of 5, 10, and 20 plants per RIL. Three traits including heading date, plant height, and tillers per plant were focused. With SNP- and bin-based QTL mapping, 3 major and 3 minor QTLs for heading date with high heritability and 2 major QTLs for plant height with moderate heritability were commonly detected across the three experiments, but no QTL for tillers per plant with low heritability were commonly identified. In addition, bin-based QTL mapping was more powerful than SNP-based mapping and able to rank the genetic effects of parental alleles. Thus, 5 plants per RIL for phenotyping ensure the power of QTL mapping for traits of high or moderate heritability, and bin-based QTL mapping is recommended for multiparent populations.
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Affiliation(s)
- Famao Liang
- College of Agriculture, Yangtze University, Jingzhou, 434000 China
| | - Wei Zhan
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, South-Central University for Nationalities, Wuhan, 430074 China
| | - Gang Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070 China
| | - Hua Liu
- College of Agriculture, Yangtze University, Jingzhou, 434000 China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070 China
| | - Zhixin Li
- College of Agriculture, Yangtze University, Jingzhou, 434000 China
| | - Zhongmin Han
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 150081 Harbin, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan, 430070 China
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7
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Assessing Phytosanitary Application Efficiency of a Boom Sprayer Machine Using RGB Sensor in Grassy Fields. SUSTAINABILITY 2022. [DOI: 10.3390/su14063666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The systematic use of plant protection products is now being called into question with the growing awareness of the risks they can represent for the environment and human health. The application of precision agriculture technologies helps to improve agricultural production but also to rationalize input costs and improve ecological footprints. Here we present a study on fungicide application efficiency and its impact on the grass quality of a golf course green using the free open-source image analysis software FIJI (Image J) to analyze ground RGB (high-resolution digital cameras) and multispectral aerial imagery in combination with experimental data of spray pressure and hydraulic slot nozzle size of a boom sprayer machine. The multivariate regression model best explained variance in the normalized green-red difference index (NGRDI) as a relevant indicator of healthy turfgrass fields from the aerial, ground, and machine data set.
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Metabolic Insight into Cold Stress Response in Two Contrasting Maize Lines. Life (Basel) 2022; 12:life12020282. [PMID: 35207570 PMCID: PMC8875087 DOI: 10.3390/life12020282] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 02/04/2023] Open
Abstract
Maize (Zea mays L.) is sensitive to a minor decrease in temperature at early growth stages, resulting in deteriorated growth at later stages. Although there are significant variations in maize germplasm in response to cold stress, the metabolic responses as stress tolerance mechanisms are largely unknown. Therefore, this study aimed at providing insight into the metabolic responses under cold stress at the early growth stages of maize. Two inbred lines, tolerant (B144) and susceptible (Q319), were subjected to cold stress at the seedling stage, and their corresponding metabolic profiles were explored. The study identified differentially accumulated metabolites in both cultivars in response to induced cold stress with nine core conserved cold-responsive metabolites. Guanosine 3′,5′-cyclic monophosphate was detected as a potential biomarker metabolite to differentiate cold tolerant and sensitive maize genotypes. Furthermore, Quercetin-3-O-(2″′-p-coumaroyl)sophoroside-7-O-glucoside, Phloretin, Phloretin-2′-O-glucoside, Naringenin-7-O-Rutinoside, L-Lysine, L-phenylalanine, L-Glutamine, Sinapyl alcohol, and Feruloyltartaric acid were regulated explicitly in B144 and could be important cold-tolerance metabolites. These results increase our understanding of cold-mediated metabolic responses in maize that can be further utilized to enhance cold tolerance in this significant crop.
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Park SI, Kwon HJ, Cho MH, Song JS, Kim BG, Baek J, Kim SL, Ji H, Kwon TR, Kim KH, Yoon IS. The OsERF115/AP2EREBP110 Transcription Factor Is Involved in the Multiple Stress Tolerance to Heat and Drought in Rice Plants. Int J Mol Sci 2021; 22:ijms22137181. [PMID: 34281241 PMCID: PMC8269390 DOI: 10.3390/ijms22137181] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/17/2021] [Accepted: 06/24/2021] [Indexed: 01/26/2023] Open
Abstract
The AP2/EREBP family transcription factors play important roles in a wide range of stress tolerance and hormone signaling. In this study, a heat-inducible rice ERF gene was isolated and functionally characterized. The OsERF115/AP2EREBP110 was categorized to Group-IIIc of the rice AP2/EREBP family and strongly induced by heat and drought treatment. The OsERF115/AP2EREBP110 protein targeted to nuclei and suppressed the ABA-induced transcriptional activation of Rab16A promoter in rice protoplasts. Overexpression of OsERF115/AP2EREBP110 enhanced thermotolerance of seeds and vegetative growth stage plants. The OsERF115/AP2EREBP110 overexpressing (OE) plants exhibited higher proline level and increased expression of a proline biosynthesis P5CS1 gene. Phenotyping of water use dynamics of the individual plant indicates that the OsERF115/AP2EREBP110-OE plant exhibited better water saving traits under heat and drought combined stress. Our combined results suggest the potential use of OsERF115/AP2EREBP110 as a candidate gene for genetic engineering approaches to develop heat and drought stress-tolerant crops.
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Affiliation(s)
- Seong-Im Park
- Gene Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (S.-I.P.); (H.J.K.); (M.H.C.); (J.S.S.); (J.B.); (S.L.K.); (H.J.); (T.-R.K.); (K.-H.K.)
| | - Hyeok Jin Kwon
- Gene Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (S.-I.P.); (H.J.K.); (M.H.C.); (J.S.S.); (J.B.); (S.L.K.); (H.J.); (T.-R.K.); (K.-H.K.)
| | - Mi Hyeon Cho
- Gene Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (S.-I.P.); (H.J.K.); (M.H.C.); (J.S.S.); (J.B.); (S.L.K.); (H.J.); (T.-R.K.); (K.-H.K.)
| | - Ji Sun Song
- Gene Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (S.-I.P.); (H.J.K.); (M.H.C.); (J.S.S.); (J.B.); (S.L.K.); (H.J.); (T.-R.K.); (K.-H.K.)
| | - Beom-Gi Kim
- Metabolic Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea;
| | - JeongHo Baek
- Gene Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (S.-I.P.); (H.J.K.); (M.H.C.); (J.S.S.); (J.B.); (S.L.K.); (H.J.); (T.-R.K.); (K.-H.K.)
| | - Song Lim Kim
- Gene Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (S.-I.P.); (H.J.K.); (M.H.C.); (J.S.S.); (J.B.); (S.L.K.); (H.J.); (T.-R.K.); (K.-H.K.)
| | - HyeonSo Ji
- Gene Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (S.-I.P.); (H.J.K.); (M.H.C.); (J.S.S.); (J.B.); (S.L.K.); (H.J.); (T.-R.K.); (K.-H.K.)
| | - Taek-Ryoun Kwon
- Gene Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (S.-I.P.); (H.J.K.); (M.H.C.); (J.S.S.); (J.B.); (S.L.K.); (H.J.); (T.-R.K.); (K.-H.K.)
| | - Kyung-Hwan Kim
- Gene Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (S.-I.P.); (H.J.K.); (M.H.C.); (J.S.S.); (J.B.); (S.L.K.); (H.J.); (T.-R.K.); (K.-H.K.)
| | - In Sun Yoon
- Gene Engineering Division, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (S.-I.P.); (H.J.K.); (M.H.C.); (J.S.S.); (J.B.); (S.L.K.); (H.J.); (T.-R.K.); (K.-H.K.)
- Correspondence:
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Guimarães PHR, de Lima IP, de Castro AP, Lanna AC, Guimarães Santos Melo P, de Raïssac M. Phenotyping Root Systems in a Set of Japonica Rice Accessions: Can Structural Traits Predict the Response to Drought? RICE (NEW YORK, N.Y.) 2020; 13:67. [PMID: 32930888 PMCID: PMC7492358 DOI: 10.1186/s12284-020-00404-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 06/23/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND The root system plays a major role in plant growth and development and root system architecture is reported to be the main trait related to plant adaptation to drought. However, phenotyping root systems in situ is not suited to high-throughput methods, leading to the development of non-destructive methods for evaluations in more or less controlled root environments. This study used a root phenotyping platform with a panel of 20 japonica rice accessions in order to: (i) assess their genetic diversity for a set of structural and morphological root traits and classify the different types; (ii) analyze the plastic response of their root system to a water deficit at reproductive phase and (iii) explore the ability of the platform for high-throughput phenotyping of root structure and morphology. RESULTS High variability for the studied root traits was found in the reduced set of accessions. Using eight selected traits under irrigated conditions, five root clusters were found that differed in root thickness, branching index and the pattern of fine and thick root distribution along the profile. When water deficit occurred at reproductive phase, some accessions significantly reduced root growth compared to the irrigated treatment, while others stimulated it. It was found that root cluster, as defined under irrigated conditions, could not predict the plastic response of roots under drought. CONCLUSIONS This study revealed the possibility of reconstructing the structure of root systems from scanned images. It was thus possible to significantly class root systems according to simple structural traits, opening up the way for using such a platform for medium to high-throughput phenotyping. The study also highlighted the uncoupling between root structures under non-limiting water conditions and their response to drought.
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Affiliation(s)
| | - Isabela Pereira de Lima
- Universidade Federal de Lavras, Departamento de Agricultura, Campus Universitário, Lavras, MG, 37200-000, Brazil
| | | | - Anna Cristina Lanna
- Embrapa Arroz e Feijão, Rodovia GO-462, km 12, Santo Antônio de Goiás, GO, 75375-000, Brazil
| | | | - Marcel de Raïssac
- Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, AGAP, Montpellier, France.
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Adjusting for Spatial Effects in Genomic Prediction. JOURNAL OF AGRICULTURAL, BIOLOGICAL AND ENVIRONMENTAL STATISTICS 2020. [DOI: 10.1007/s13253-020-00396-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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12
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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
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Lv Y, Hu F, Zhou Y, Wu F, Gaut BS. Maize transposable elements contribute to long non-coding RNAs that are regulatory hubs for abiotic stress response. BMC Genomics 2019; 20:864. [PMID: 31729949 PMCID: PMC6858665 DOI: 10.1186/s12864-019-6245-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/30/2019] [Indexed: 02/07/2023] Open
Abstract
Background Several studies have mined short-read RNA sequencing datasets to identify long non-coding RNAs (lncRNAs), and others have focused on the function of individual lncRNAs in abiotic stress response. However, our understanding of the complement, function and origin of lncRNAs – and especially transposon derived lncRNAs (TE-lncRNAs) - in response to abiotic stress is still in its infancy. Results We utilized a dataset of 127 RNA sequencing samples that included total RNA datasets and PacBio fl-cDNA data to discover lncRNAs in maize. Overall, we identified 23,309 candidate lncRNAs from polyA+ and total RNA samples, with a strong discovery bias within total RNA. The majority (65%) of the 23,309 lncRNAs had sequence similarity to transposable elements (TEs). Most had similarity to long-terminal-repeat retrotransposons from the Copia and Gypsy superfamilies, reflecting a high proportion of these elements in the genome. However, DNA transposons were enriched for lncRNAs relative to their genomic representation by ~ 2-fold. By assessing the fraction of lncRNAs that respond to abiotic stresses like heat, cold, salt and drought, we identified 1077 differentially expressed lncRNA transcripts, including 509 TE-lncRNAs. In general, the expression of these lncRNAs was significantly correlated with their nearest gene. By inferring co-expression networks across our large dataset, we found that 39 lncRNAs are as major hubs in co-expression networks that respond to abiotic stress, and 18 appear to be derived from TEs. Conclusions Our results show that lncRNAs are enriched in total RNA samples, that most (65%) are derived from TEs, that at least 1077 are differentially expressed during abiotic stress, and that 39 are hubs in co-expression networks, including a small number that are evolutionary conserved. These results suggest that lncRNAs, including TE-lncRNAs, may play key regulatory roles in moderating abiotic responses.
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Affiliation(s)
- Yuanda Lv
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China.,Department of Ecology and Evolutionary, Biology, UC Irvine, Irvine, CA, USA
| | - Fengqin Hu
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yongfeng Zhou
- Department of Ecology and Evolutionary, Biology, UC Irvine, Irvine, CA, USA
| | - Feilong Wu
- Department of Civil and Environmental, Engineering, UC Irvine, Irvine, CA, USA
| | - Brandon S Gaut
- Department of Ecology and Evolutionary, Biology, UC Irvine, Irvine, CA, USA.
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Casari RACN, Paiva DS, Silva VNB, Ferreira TMM, Souza Junior MT, Oliveira NG, Kobayashi AK, Molinari HBC, Santos TT, Gomide RL, Magalhães PC, Sousa CAF. Using Thermography to Confirm Genotypic Variation for Drought Response in Maize. Int J Mol Sci 2019; 20:E2273. [PMID: 31071964 PMCID: PMC6540190 DOI: 10.3390/ijms20092273] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/31/2019] [Accepted: 04/03/2019] [Indexed: 11/20/2022] Open
Abstract
The feasibility of thermography as a technique for plant screening aiming at drought-tolerance has been proven by its relationship with gas exchange, biomass, and yield. In this study, unlike most of the previous, thermography was applied for phenotyping contrasting maize genotypes whose classification for drought tolerance had already been established in the field. Our objective was to determine whether thermography-based classification would discriminate the maize genotypes in a similar way as the field selection in which just grain yield was taken into account as a criterion. We evaluated gas exchange, daily water consumption, leaf relative water content, aboveground biomass, and grain yield. Indeed, the screening of maize genotypes based on canopy temperature showed similar results to traditional methods. Nevertheless, canopy temperature only partially reflected gas exchange rates and daily water consumption in plants under drought. Part of the explanation may lie in the changes that drought had caused in plant leaves and canopy structure, altering absorption and dissipation of energy, photosynthesis, transpiration, and partitioning rates. Accordingly, although there was a negative relationship between grain yield and plant canopy temperature, it does not necessarily mean that plants whose canopies were maintained cooler under drought achieved the highest yield.
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Affiliation(s)
- Raphael A C N Casari
- Embrapa Agroenergia, Parque Estação Biológica (PqEB), Avenida W3 Norte (Final), Brasília 70.770-901, DF, Brazil.
| | - Dayane S Paiva
- Embrapa Agroenergia, Parque Estação Biológica (PqEB), Avenida W3 Norte (Final), Brasília 70.770-901, DF, Brazil.
| | - Vivianny N B Silva
- Embrapa Agroenergia, Parque Estação Biológica (PqEB), Avenida W3 Norte (Final), Brasília 70.770-901, DF, Brazil.
- Universidade Federal de Lavras, Campus Universitário, Lavras 37.200-000, MG, Brazil.
| | - Thalita M M Ferreira
- Embrapa Agroenergia, Parque Estação Biológica (PqEB), Avenida W3 Norte (Final), Brasília 70.770-901, DF, Brazil.
- Universidade Federal de Lavras, Campus Universitário, Lavras 37.200-000, MG, Brazil.
| | - Manoel T Souza Junior
- Embrapa Agroenergia, Parque Estação Biológica (PqEB), Avenida W3 Norte (Final), Brasília 70.770-901, DF, Brazil.
- Universidade Federal de Lavras, Campus Universitário, Lavras 37.200-000, MG, Brazil.
| | - Nelson G Oliveira
- Embrapa Agroenergia, Parque Estação Biológica (PqEB), Avenida W3 Norte (Final), Brasília 70.770-901, DF, Brazil.
| | - Adilson K Kobayashi
- Embrapa Agroenergia, Parque Estação Biológica (PqEB), Avenida W3 Norte (Final), Brasília 70.770-901, DF, Brazil.
| | - Hugo B C Molinari
- Embrapa Agroenergia, Parque Estação Biológica (PqEB), Avenida W3 Norte (Final), Brasília 70.770-901, DF, Brazil.
| | - Thiago T Santos
- Embrapa Informática, Av. Dr. André Tosello, 209 - Cidade Universitária, Campinas 13.083-886, SP, Brazil.
| | - Reinaldo L Gomide
- Embrapa Milho e Sorgo, Rod. MG 424 km 45, Zona Rural, Sete Lagoas 35.701-970, MG, Brazil.
| | - Paulo C Magalhães
- Embrapa Milho e Sorgo, Rod. MG 424 km 45, Zona Rural, Sete Lagoas 35.701-970, MG, Brazil.
| | - Carlos A F Sousa
- Embrapa Agroenergia, Parque Estação Biológica (PqEB), Avenida W3 Norte (Final), Brasília 70.770-901, DF, Brazil.
- Embrapa Meio-Norte, Av. Duque de Caxias 5650, Teresina 64.006-245, PI, Brazil.
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15
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Mir RR, Reynolds M, Pinto F, Khan MA, Bhat MA. High-throughput phenotyping for crop improvement in the genomics era. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 282:60-72. [PMID: 31003612 DOI: 10.1016/j.plantsci.2019.01.007] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 12/10/2018] [Accepted: 01/09/2019] [Indexed: 05/24/2023]
Abstract
Tremendous progress has been made with continually expanding genomics technologies to unravel and understand crop genomes. However, the impact of genomics data on crop improvement is still far from satisfactory, in large part due to a lack of effective phenotypic data; our capacity to collect useful high quality phenotypic data lags behind the current capacity to generate high-throughput genomics data. Thus, the research bottleneck in plant sciences is shifting from genotyping to phenotyping. This article review the current status of efforts made in the last decade to systematically collect phenotypic data to alleviate this 'phenomics bottlenecks' by recording trait data through sophisticated non-invasive imaging, spectroscopy, image analysis, robotics, high-performance computing facilities and phenomics databases. These modern phenomics platforms and tools aim to record data on traits like plant development, architecture, plant photosynthesis, growth or biomass productivity, on hundreds to thousands of plants in a single day, as a phenomics revolution. It is believed that this revolution will provide plant scientists with the knowledge and tools necessary for unlocking information coded in plant genomes. Efforts have been also made to present the advances made in the last 10 years in phenomics platforms and their use in generating phenotypic data on different traits in several major crops including rice, wheat, barley, and maize. The article also highlights the need for phenomics databases and phenotypic data sharing for crop improvement. The phenomics data generated has been used to identify genes/QTL through QTL mapping, association mapping and genome-wide association studies (GWAS) for genomics-assisted breeding (GAB) for crop improvement.
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Affiliation(s)
- Reyazul Rouf Mir
- Division of Genetics & Plant Breeding, Faculty of Agriculture (FoA), Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Wadura Campus, Sopore-193201, Kashmir, India.
| | - Mathew Reynolds
- Global Wheat Program, International Maize and Wheat Improvement Centre (CIMMYT), Mexico, D.F., Mexico
| | - Francisco Pinto
- Global Wheat Program, International Maize and Wheat Improvement Centre (CIMMYT), Mexico, D.F., Mexico
| | - Mohd Anwar Khan
- Division of Genetics & Plant Breeding, Faculty of Agriculture (FoA), Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Wadura Campus, Sopore-193201, Kashmir, India
| | - Mohd Ashraf Bhat
- Division of Genetics & Plant Breeding, Faculty of Agriculture (FoA), Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Wadura Campus, Sopore-193201, Kashmir, India
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16
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Buchaillot ML, Gracia-Romero A, Vergara-Diaz O, Zaman-Allah MA, Tarekegne A, Cairns JE, Prasanna BM, Araus JL, Kefauver SC. Evaluating Maize Genotype Performance under Low Nitrogen Conditions Using RGB UAV Phenotyping Techniques. SENSORS (BASEL, SWITZERLAND) 2019; 19:E1815. [PMID: 30995754 PMCID: PMC6514658 DOI: 10.3390/s19081815] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/01/2019] [Accepted: 04/08/2019] [Indexed: 11/29/2022]
Abstract
Maize is the most cultivated cereal in Africa in terms of land area and production, but low soil nitrogen availability often constrains yields. Developing new maize varieties with high and reliable yields using traditional crop breeding techniques in field conditions can be slow and costly. Remote sensing has become an important tool in the modernization of field-based high-throughput plant phenotyping (HTPP), providing faster gains towards the improvement of yield potential and adaptation to abiotic and biotic limiting conditions. We evaluated the performance of a set of remote sensing indices derived from red-green-blue (RGB) images along with field-based multispectral normalized difference vegetation index (NDVI) and leaf chlorophyll content (SPAD values) as phenotypic traits for assessing maize performance under managed low-nitrogen conditions. HTPP measurements were conducted from the ground and from an unmanned aerial vehicle (UAV). For the ground-level RGB indices, the strongest correlations to yield were observed with hue, greener green area (GGA), and a newly developed RGB HTPP index, NDLab (normalized difference Commission Internationale de I´Edairage (CIE)Lab index), while GGA and crop senescence index (CSI) correlated better with grain yield from the UAV. Regarding ground sensors, SPAD exhibited the closest correlation with grain yield, notably increasing in its correlation when measured in the vegetative stage. Additionally, we evaluated how different HTPP indices contributed to the explanation of yield in combination with agronomic data, such as anthesis silking interval (ASI), anthesis date (AD), and plant height (PH). Multivariate regression models, including RGB indices (R2 > 0.60), outperformed other models using only agronomic parameters or field sensors (R2 > 0.50), reinforcing RGB HTPP's potential to improve yield assessments. Finally, we compared the low-N results to the same panel of 64 maize genotypes grown under optimal conditions, noting that only 11% of the total genotypes appeared in the highest yield producing quartile for both trials. Furthermore, we calculated the grain yield loss index (GYLI) for each genotype, which showed a large range of variability, suggesting that low-N performance is not necessarily exclusive of high productivity in optimal conditions.
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Affiliation(s)
- Ma Luisa Buchaillot
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain.
- AGROTECNIO (Center for Research in Agrotechnology), Av. Rovira Roure 191, 25198 Lleida, Spain.
| | - Adrian Gracia-Romero
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain.
- AGROTECNIO (Center for Research in Agrotechnology), Av. Rovira Roure 191, 25198 Lleida, Spain.
| | - Omar Vergara-Diaz
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain.
- AGROTECNIO (Center for Research in Agrotechnology), Av. Rovira Roure 191, 25198 Lleida, Spain.
| | - Mainassara A Zaman-Allah
- International Maize and Wheat Improvement Center, CIMMYT Southern Africa Regional Office, P.O. Box MP163 Harare, Zimbabwe.
| | - Amsal Tarekegne
- International Maize and Wheat Improvement Center, CIMMYT Southern Africa Regional Office, P.O. Box MP163 Harare, Zimbabwe.
| | - Jill E Cairns
- International Maize and Wheat Improvement Center, CIMMYT Southern Africa Regional Office, P.O. Box MP163 Harare, Zimbabwe.
| | - Boddupalli M Prasanna
- International Maize and Wheat Improvement Center (CIMMYT), P.O. Box 1041 Nairobi, Kenya.
| | - Jose Luis Araus
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain.
- AGROTECNIO (Center for Research in Agrotechnology), Av. Rovira Roure 191, 25198 Lleida, Spain.
| | - Shawn C Kefauver
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain.
- AGROTECNIO (Center for Research in Agrotechnology), Av. Rovira Roure 191, 25198 Lleida, Spain.
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17
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Das B, Atlin GN, Olsen M, Burgueño J, Tarekegne A, Babu R, Ndou EN, Mashingaidze K, Moremoholo L, Ligeyo D, Matemba-Mutasa R, Zaman-Allah M, San Vicente F, Prasanna BM, Cairns JE. Identification of donors for low-nitrogen stress with maize lethal necrosis (MLN) tolerance for maize breeding in sub-Saharan Africa. EUPHYTICA: NETHERLANDS JOURNAL OF PLANT BREEDING 2019; 215:80. [PMID: 31057179 PMCID: PMC6445404 DOI: 10.1007/s10681-019-2406-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 03/21/2019] [Indexed: 05/30/2023]
Abstract
After drought, a major challenge to smallholder farmers in sub-Saharan Africa is low-fertility soils with poor nitrogen (N)-supplying capacity. Many challenges in this region need to be overcome to create a viable fertilizer market. An intermediate solution is the development of maize varieties with an enhanced ability to take up or utilize N in severely depleted soils, and to more efficiently use the small amounts of N that farmers can supply to their crops. Over 400 elite inbred lines from seven maize breeding programs were screened to identify new sources of tolerance to low-N stress and maize lethal necrosis (MLN) for introgression into Africa-adapted elite germplasm. Lines with high levels of tolerance to both stresses were identified. Lines previously considered to be tolerant to low-N stress ranked in the bottom 10% under low-N confirming the need to replace these lines with new donors identified in this study. The lines that performed best under low-N yielded about 0. 5 Mg ha-1 (20%) more in testcross combinations than some widely used commercial parent lines such as CML442 and CML395. This is the first large scale study to identify maize inbred lines with tolerance to low-N stress and MLN in eastern and southern Africa.
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Affiliation(s)
- Biswanath Das
- International Maize and Wheat Improvement Center (CIMMYT), United Nations Avenue, Gigiri, Village Market, PO Box 1041, Nairobi, 00621 Kenya
| | - Gary N. Atlin
- Bill & Melinda Gates Foundation, PO Box 23350, Seattle, WA 98102 USA
| | - Michael Olsen
- International Maize and Wheat Improvement Center (CIMMYT), United Nations Avenue, Gigiri, Village Market, PO Box 1041, Nairobi, 00621 Kenya
| | - Juan Burgueño
- CIMMYT, km. 35 Carr. Mexico-Veracruz, Texcoco, Edo. de Mexico, DF Mexico
| | | | | | - Eric N. Ndou
- Agricultural Research Council-Grain Crop Institute, Private Bag X1251, Potchestroom, South Africa
| | - Kingstone Mashingaidze
- Agricultural Research Council-Grain Crop Institute, Private Bag X1251, Potchestroom, South Africa
| | - Lieketso Moremoholo
- Agricultural Research Council-Grain Crop Institute, Private Bag X1251, Potchestroom, South Africa
| | - Dickson Ligeyo
- Kenya Agriculture and Livestock Research Organization, Kitale, Kenya
| | | | | | - Felix San Vicente
- CIMMYT, km. 35 Carr. Mexico-Veracruz, Texcoco, Edo. de Mexico, DF Mexico
| | - B. M. Prasanna
- International Maize and Wheat Improvement Center (CIMMYT), United Nations Avenue, Gigiri, Village Market, PO Box 1041, Nairobi, 00621 Kenya
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18
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Abstract
Agricultural scientists face the dual challenge of breeding input-responsive, widely adoptable and climate-resilient varieties of crop plants and developing such varieties at a faster pace. Integrating the gains of genomics with modern-day phenomics will lead to increased breeding efficiency which in turn offers great promise to develop such varieties rapidly. Plant phenotyping techniques have impressively evolved during the last two decades. The low-cost, automated and semi-automated methods for data acquisition, storage and analysis are now available which allow precise quantitative analysis of plant structure and function; and genetic dissection of complex traits. Appropriate plant types can now be quickly developed that respond favorably to low input and resource-limited environments and address the challenges of subsistence agriculture. The present review focuses on the need of systematic, rapid, minimal invasive and low-cost plant phenotyping. It also discusses its evolution to modern day high throughput phenotyping (HTP), traits amenable to HTP, integration of HTP with genomics and the scope of utilizing these tools for crop improvement.
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19
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Identification and Classification of Maize Drought Stress Using Deep Convolutional Neural Network. Symmetry (Basel) 2019. [DOI: 10.3390/sym11020256] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Drought stress seriously affects crop growth, development, and grain production. Existing machine learning methods have achieved great progress in drought stress detection and diagnosis. However, such methods are based on a hand-crafted feature extraction process, and the accuracy has much room to improve. In this paper, we propose the use of a deep convolutional neural network (DCNN) to identify and classify maize drought stress. Field drought stress experiments were conducted in 2014. The experiment was divided into three treatments: optimum moisture, light drought, and moderate drought stress. Maize images were obtained every two hours throughout the whole day by digital cameras. In order to compare the accuracy of DCNN, a comparative experiment was conducted using traditional machine learning on the same dataset. The experimental results demonstrated an impressive performance of the proposed method. For the total dataset, the accuracy of the identification and classification of drought stress was 98.14% and 95.95%, respectively. High accuracy was also achieved on the sub-datasets of the seedling and jointing stages. The identification and classification accuracy levels of the color images were higher than those of the gray images. Furthermore, the comparison experiments on the same dataset demonstrated that DCNN achieved a better performance than the traditional machine learning method (Gradient Boosting Decision Tree GBDT). Overall, our proposed deep learning-based approach is a very promising method for field maize drought identification and classification based on digital images.
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20
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Peirone LS, Pereyra Irujo GA, Bolton A, Erreguerena I, Aguirrezábal LAN. Assessing the Efficiency of Phenotyping Early Traits in a Greenhouse Automated Platform for Predicting Drought Tolerance of Soybean in the Field. FRONTIERS IN PLANT SCIENCE 2018; 9:587. [PMID: 29774042 PMCID: PMC5943574 DOI: 10.3389/fpls.2018.00587] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/16/2018] [Indexed: 05/14/2023]
Abstract
Conventional field phenotyping for drought tolerance, the most important factor limiting yield at a global scale, is labor-intensive and time-consuming. Automated greenhouse platforms can increase the precision and throughput of plant phenotyping and contribute to a faster release of drought tolerant varieties. The aim of this work was to establish a framework of analysis to identify early traits which could be efficiently measured in a greenhouse automated phenotyping platform, for predicting the drought tolerance of field grown soybean genotypes. A group of genotypes was evaluated, which showed variation in their drought susceptibility index (DSI) for final biomass and leaf area. A large number of traits were measured before and after the onset of a water deficit treatment, which were analyzed under several criteria: the significance of the regression with the DSI, phenotyping cost, earliness, and repeatability. The most efficient trait was found to be transpiration efficiency measured at 13 days after emergence. This trait was further tested in a second experiment with different water deficit intensities, and validated using a different set of genotypes against field data from a trial network in a third experiment. The framework applied in this work for assessing traits under different criteria could be helpful for selecting those most efficient for automated phenotyping.
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Affiliation(s)
- Laura S. Peirone
- Laboratorio de Fisiología Vegetal, Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Gustavo A. Pereyra Irujo
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- Agronomy Department, Instituto Nacional de Tecnología Agropecuaria, Balcarce, Argentina
| | - Alejandro Bolton
- Laboratorio de Fisiología Vegetal, Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
- Agronomy Department, Instituto Nacional de Tecnología Agropecuaria, Balcarce, Argentina
| | - Ignacio Erreguerena
- Agronomy Department, Instituto Nacional de Tecnología Agropecuaria, Balcarce, Argentina
| | - Luis A. N. Aguirrezábal
- Laboratorio de Fisiología Vegetal, Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- *Correspondence: Luis A. N. Aguirrezábal
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Gracia-Romero A, Kefauver SC, Vergara-Díaz O, Zaman-Allah MA, Prasanna BM, Cairns JE, Araus JL. Comparative Performance of Ground vs. Aerially Assessed RGB and Multispectral Indices for Early-Growth Evaluation of Maize Performance under Phosphorus Fertilization. FRONTIERS IN PLANT SCIENCE 2017; 8:2004. [PMID: 29230230 PMCID: PMC5711853 DOI: 10.3389/fpls.2017.02004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/10/2017] [Indexed: 05/25/2023]
Abstract
Low soil fertility is one of the factors most limiting agricultural production, with phosphorus deficiency being among the main factors, particularly in developing countries. To deal with such environmental constraints, remote sensing measurements can be used to rapidly assess crop performance and to phenotype a large number of plots in a rapid and cost-effective way. We evaluated the performance of a set of remote sensing indices derived from Red-Green-Blue (RGB) images and multispectral (visible and infrared) data as phenotypic traits and crop monitoring tools for early assessment of maize performance under phosphorus fertilization. Thus, a set of 26 maize hybrids grown under field conditions in Zimbabwe was assayed under contrasting phosphorus fertilization conditions. Remote sensing measurements were conducted in seedlings at two different levels: at the ground and from an aerial platform. Within a particular phosphorus level, some of the RGB indices strongly correlated with grain yield. In general, RGB indices assessed at both ground and aerial levels correlated in a comparable way with grain yield except for indices a* and u*, which correlated better when assessed at the aerial level than at ground level and Greener Area (GGA) which had the opposite correlation. The Normalized Difference Vegetation Index (NDVI) evaluated at ground level with an active sensor also correlated better with grain yield than the NDVI derived from the multispectral camera mounted in the aerial platform. Other multispectral indices like the Soil Adjusted Vegetation Index (SAVI) performed very similarly to NDVI assessed at the aerial level but overall, they correlated in a weaker manner with grain yield than the best RGB indices. This study clearly illustrates the advantage of RGB-derived indices over the more costly and time-consuming multispectral indices. Moreover, the indices best correlated with GY were in general those best correlated with leaf phosphorous content. However, these correlations were clearly weaker than against grain yield and only under low phosphorous conditions. This work reinforces the effectiveness of canopy remote sensing for plant phenotyping and crop management of maize under different phosphorus nutrient conditions and suggests that the RGB indices are the best option.
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Affiliation(s)
- Adrian Gracia-Romero
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Shawn C. Kefauver
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Omar Vergara-Díaz
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Mainassara A. Zaman-Allah
- International Maize and Wheat Improvement Center, CIMMYT Southern Africa Regional Office, Harare, Zimbabwe
| | - Boddupalli M. Prasanna
- International Maize and Wheat Improvement Center, CIMMYT Southern Africa Regional Office, Harare, Zimbabwe
| | - Jill E. Cairns
- International Maize and Wheat Improvement Center, CIMMYT Southern Africa Regional Office, Harare, Zimbabwe
| | - José L. Araus
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, Barcelona, Spain
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22
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Velázquez L, Alberdi I, Paz C, Aguirrezábal L, Pereyra Irujo G. Biomass Allocation Patterns Are Linked to Genotypic Differences in Whole-Plant Transpiration Efficiency in Sunflower. FRONTIERS IN PLANT SCIENCE 2017; 8:1976. [PMID: 29204153 PMCID: PMC5698287 DOI: 10.3389/fpls.2017.01976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 11/02/2017] [Indexed: 05/08/2023]
Abstract
Increased transpiration efficiency (the ratio of biomass to water transpired, TE) could lead to increased drought tolerance under some water deficit scenarios. Intrinsic (i.e., leaf-level) TE is usually considered as the primary source of variation in whole-plant TE, but empirical data usually contradict this assumption. Sunflower has a significant variability in TE, but a better knowledge of the effect of leaf and plant-level traits could be helpful to obtain more efficient genotypes for water use. The objective of this study was, therefore, to assess if genotypic variation in whole-plant TE is better related to leaf- or plant-level traits. Three experiments were conducted, aimed at verifying the existence of variability in whole-plant TE and whole-plant and leaf-level traits, and to assess their correlation. Sunflower public inbred lines and a segregating population of recombinant inbred lines were grown under controlled conditions and subjected to well-watered and water-deficit treatments. Significant genotypic variation was found for TE and related traits. These differences in whole-plant transpiration efficiency, both between genotypes and between plants within each genotype, showed no association to leaf-level traits, but were significantly and negatively correlated to biomass allocation to leaves and to the ratio of leaf area to total biomass. These associations are likely of a physiological origin, and not only a consequence of genetic linkage in the studied population. These results suggest that genotypic variation for biomass allocation could be potentially exploited as a source for increased transpiration efficiency in sunflower breeding programmes. It is also suggested that phenotyping for TE in this species should not be restricted to leaf-level measurements, but also include measurements of plant-level traits, especially those related to biomass allocation between photosynthetic and non-photosynthetic organs.
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Affiliation(s)
- Luciano Velázquez
- Laboratorio de Fisiología Vegetal, Unidad Integrada Balcarce, Instituto Nacional de Tecnología Agropecuaria - Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Ignacio Alberdi
- Laboratorio de Fisiología Vegetal, Unidad Integrada Balcarce, Instituto Nacional de Tecnología Agropecuaria - Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Cosme Paz
- Laboratorio de Fisiología Vegetal, Unidad Integrada Balcarce, Instituto Nacional de Tecnología Agropecuaria - Universidad Nacional de Mar del Plata, Balcarce, Argentina
| | - Luis Aguirrezábal
- Laboratorio de Fisiología Vegetal, Unidad Integrada Balcarce, Instituto Nacional de Tecnología Agropecuaria - Universidad Nacional de Mar del Plata, Balcarce, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Gustavo Pereyra Irujo
- Laboratorio de Fisiología Vegetal, Unidad Integrada Balcarce, Instituto Nacional de Tecnología Agropecuaria - Universidad Nacional de Mar del Plata, Balcarce, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
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Ertiro BT, Beyene Y, Das B, Mugo S, Olsen M, Oikeh S, Juma C, Labuschagne M, Prasanna BM. Combining ability and testcross performance of drought-tolerant maize inbred lines under stress and non-stress environments in Kenya. PLANT BREEDING = ZEITSCHRIFT FUR PFLANZENZUCHTUNG 2017; 136:197-205. [PMID: 28781399 PMCID: PMC5518761 DOI: 10.1111/pbr.12464] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 01/04/2017] [Indexed: 05/24/2023]
Abstract
Drought and poor soil fertility are among the major abiotic stresses affecting maize productivity in sub-Saharan Africa. Maize breeding efforts at the International Maize and Wheat Improvement Center (CIMMYT) have focused on incorporating drought stress tolerance and nitrogen-use efficiency (NUE) into tropical maize germplasm. The objectives of this study were to estimate the general combining ability (GCA) and specific combining ability (SCA) of selected maize inbred lines under drought stress (DS), low-nitrogen (LN) and optimum moisture and nitrogen (optimum) conditions, and to assess the yield potential and stability of experimental hybrids under these management conditions. Forty-nine experimental three-way cross hybrids, generated from a 7 × 7 line by tester crosses, and six commercial checks were evaluated across 11 optimum, DS and LN sites in Kenya in 2014 using an alpha lattice design with two replicates per entry at each site. DS reduced both grain yield (GY) and plant height (PH), while anthesis-silking interval (ASI) increased under both DS and LN. Hybrids 'L4/T2' and 'L4/T1' were found to be superior and stable, while inbreds 'L4' and 'L6' were good combiners for GY and other secondary traits across sites. Additive variance played a greater role for most traits under the three management conditions, suggesting that further progress in the improvement of these traits should be possible. GY under optimum conditions was positively correlated with GY under both DS and LN conditions, but GY under DS and LN was not correlated. Our results suggest the feasibility for simultaneous improvement in grain yield performance of genotypes under optimum, DS and LN conditions.
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Affiliation(s)
- Berhanu T. Ertiro
- Ethiopian Institute of Agricultural Research (EIAR)Bako National Maize Research CenterP.O.Box 03BakoWest ShoaOromiaEthiopia
| | - Yoseph Beyene
- International Maize and Wheat Improvement Center (CIMMYT)P.O. Box 1041‐00621NairobiKenya
| | - Biswanath Das
- International Maize and Wheat Improvement Center (CIMMYT)P.O. Box 1041‐00621NairobiKenya
| | - Stephen Mugo
- International Maize and Wheat Improvement Center (CIMMYT)P.O. Box 1041‐00621NairobiKenya
| | - Michael Olsen
- International Maize and Wheat Improvement Center (CIMMYT)P.O. Box 1041‐00621NairobiKenya
| | - Sylvester Oikeh
- African Agricultural Technology Foundation (AATF)P.O. Box 30709‐00100NairobiKenya
| | - Collins Juma
- International Maize and Wheat Improvement Center (CIMMYT)P.O. Box 1041‐00621NairobiKenya
| | - Maryke Labuschagne
- Department of Plant SciencesUniversity of the Free StateP.O. Box 339Bloemfontein9300Republic of South Africa
| | - Boddupalli M. Prasanna
- International Maize and Wheat Improvement Center (CIMMYT)P.O. Box 1041‐00621NairobiKenya
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Kyratzis AC, Skarlatos DP, Menexes GC, Vamvakousis VF, Katsiotis A. Assessment of Vegetation Indices Derived by UAV Imagery for Durum Wheat Phenotyping under a Water Limited and Heat Stressed Mediterranean Environment. FRONTIERS IN PLANT SCIENCE 2017; 8:1114. [PMID: 28694819 PMCID: PMC5483459 DOI: 10.3389/fpls.2017.01114] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/08/2017] [Indexed: 05/06/2023]
Abstract
There is growing interest for using Spectral Vegetation Indices (SVI) derived by Unmanned Aerial Vehicle (UAV) imagery as a fast and cost-efficient tool for plant phenotyping. The development of such tools is of paramount importance to continue progress through plant breeding, especially in the Mediterranean basin, where climate change is expected to further increase yield uncertainty. In the present study, Normalized Difference Vegetation Index (NDVI), Simple Ratio (SR) and Green Normalized Difference Vegetation Index (GNDVI) derived from UAV imagery were calculated for two consecutive years in a set of twenty durum wheat varieties grown under a water limited and heat stressed environment. Statistically significant differences between genotypes were observed for SVIs. GNDVI explained more variability than NDVI and SR, when recorded at booting. GNDVI was significantly correlated with grain yield when recorded at booting and anthesis during the 1st and 2nd year, respectively, while NDVI was correlated to grain yield when recorded at booting, but only for the 1st year. These results suggest that GNDVI has a better discriminating efficiency and can be a better predictor of yield when recorded at early reproductive stages. The predictive ability of SVIs was affected by plant phenology. Correlations of grain yield with SVIs were stronger as the correlations of SVIs with heading were weaker or not significant. NDVIs recorded at the experimental site were significantly correlated with grain yield of the same set of genotypes grown in other environments. Both positive and negative correlations were observed indicating that the environmental conditions during grain filling can affect the sign of the correlations. These findings highlight the potential use of SVIs derived by UAV imagery for durum wheat phenotyping under low yielding Mediterranean conditions.
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Affiliation(s)
- Angelos C. Kyratzis
- Department of Vegetable Crops, Agricultural Research InstituteNicosia, Cyprus
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of TechnologyLimassol, Cyprus
- *Correspondence: Andreas Katsiotis, Angelos C. Kyratzis,
| | - Dimitrios P. Skarlatos
- Department of Civil Engineering and Geomatics, Cyprus University of TechnologyLimassol, Cyprus
| | - George C. Menexes
- Laboratory of Agronomy, School of Agriculture, Aristotle University of ThessalonikiThessaloniki, Greece
| | | | - Andreas Katsiotis
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of TechnologyLimassol, Cyprus
- *Correspondence: Andreas Katsiotis, Angelos C. Kyratzis,
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25
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Vergara-Díaz O, Zaman-Allah MA, Masuka B, Hornero A, Zarco-Tejada P, Prasanna BM, Cairns JE, Araus JL. A Novel Remote Sensing Approach for Prediction of Maize Yield Under Different Conditions of Nitrogen Fertilization. FRONTIERS IN PLANT SCIENCE 2016; 7:666. [PMID: 27242867 PMCID: PMC4870241 DOI: 10.3389/fpls.2016.00666] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 05/01/2016] [Indexed: 05/19/2023]
Abstract
Maize crop production is constrained worldwide by nitrogen (N) availability and particularly in poor tropical and subtropical soils. The development of affordable high-throughput crop monitoring and phenotyping techniques is key to improving maize cultivation under low-N fertilization. In this study several vegetation indices (VIs) derived from Red-Green-Blue (RGB) digital images at the leaf and canopy levels are proposed as low-cost tools for plant breeding and fertilization management. They were compared with the performance of the normalized difference vegetation index (NDVI) measured at ground level and from an aerial platform, as well as with leaf chlorophyll content (LCC) and other leaf composition and structural parameters at flowering stage. A set of 10 hybrids grown under five different nitrogen regimes and adequate water conditions were tested at the CIMMYT station of Harare (Zimbabwe). Grain yield and leaf N concentration across N fertilization levels were strongly predicted by most of these RGB indices (with R (2)~ 0.7), outperforming the prediction power of the NDVI and LCC. RGB indices also outperformed the NDVI when assessing genotypic differences in grain yield and leaf N concentration within a given level of N fertilization. The best predictor of leaf N concentration across the five N regimes was LCC but its performance within N treatments was inefficient. The leaf traits evaluated also seemed inefficient as phenotyping parameters. It is concluded that the adoption of RGB-based phenotyping techniques may significantly contribute to the progress of plant breeding and the appropriate management of fertilization.
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Affiliation(s)
- Omar Vergara-Díaz
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of BarcelonaBarcelona, Spain
| | - Mainassara A. Zaman-Allah
- International Maize and Wheat Improvement Center, CIMMYT Southern Africa Regional OfficeHarare, Zimbabwe
| | - Benhildah Masuka
- International Maize and Wheat Improvement Center, CIMMYT Southern Africa Regional OfficeHarare, Zimbabwe
| | - Alberto Hornero
- Laboratory for Research Methods in Quantitative Remote Sensing, QuantaLab, Institute for Sustainable Agriculture, National Research CouncilCordoba, Spain
| | - Pablo Zarco-Tejada
- Laboratory for Research Methods in Quantitative Remote Sensing, QuantaLab, Institute for Sustainable Agriculture, National Research CouncilCordoba, Spain
| | - Boddupalli M. Prasanna
- International Maize and Wheat Improvement Center, CIMMYT Southern Africa Regional OfficeHarare, Zimbabwe
| | - Jill E. Cairns
- International Maize and Wheat Improvement Center, CIMMYT Southern Africa Regional OfficeHarare, Zimbabwe
| | - José L. Araus
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of BarcelonaBarcelona, Spain
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26
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Xu Y. Envirotyping for deciphering environmental impacts on crop plants. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:653-673. [PMID: 26932121 PMCID: PMC4799247 DOI: 10.1007/s00122-016-2691-5] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 02/08/2016] [Indexed: 05/17/2023]
Abstract
Global climate change imposes increasing impacts on our environments and crop production. To decipher environmental impacts on crop plants, the concept "envirotyping" is proposed, as a third "typing" technology, complementing with genotyping and phenotyping. Environmental factors can be collected through multiple environmental trials, geographic and soil information systems, measurement of soil and canopy properties, and evaluation of companion organisms. Envirotyping contributes to crop modeling and phenotype prediction through its functional components, including genotype-by-environment interaction (GEI), genes responsive to environmental signals, biotic and abiotic stresses, and integrative phenotyping. Envirotyping, driven by information and support systems, has a wide range of applications, including environmental characterization, GEI analysis, phenotype prediction, near-iso-environment construction, agronomic genomics, precision agriculture and breeding, and development of a four-dimensional profile of crop science involving genotype (G), phenotype (P), envirotype (E) and time (T) (developmental stage). In the future, envirotyping needs to zoom into specific experimental plots and individual plants, along with the development of high-throughput and precision envirotyping platforms, to integrate genotypic, phenotypic and envirotypic information for establishing a high-efficient precision breeding and sustainable crop production system based on deciphered environmental impacts.
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Affiliation(s)
- Yunbi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, CP 56130, Mexico.
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27
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DETERMINATION OF THE GENETICALLY VALUABLE CORN SAMPLES AT THE CREATION OF THE SOURCE MATERIAL FOR THE CORN SELECTION. EUREKA: LIFE SCIENCES 2016. [DOI: 10.21303/2504-5695.2016.00108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
For selection of the lines of new generation were used the donors of tolerance to the disease exciters and introduced the modified methods of artificial infection and selection that allowed create the new source material of corn. There were received 302 lines of UKC (Ukraine, Kharkiv, Chernobay) tolerant to the bubble smut that are characterized with valuable agricultural signs. Among them were separated 21 lines with the high productivity and valuable agricultural signs: UKC 85-2, UKC 80-3, UKC 80-2, UKC 135-2,
UKC 155-2, UKC 96, UKC 86, UKC 142, UKC 83, UKC 96-2, UKC 129-2, UKC 164,UKC 83-2, UKC 88-2, UKC 131, UKC 147, UKC 144-2, UKC 167,UKC 164-2, UKC 90-2, UKC 163-2; were created lines with the complex tolerance to the bubble smut and crop moth with the high productivity: UKC 144-2, UKC 167, UKC 164-2, UKC 90-2, UKC 163-2. The UKC lined were included into selection work in the laboratory of selection and seeding of the corn of the Institute of crop production of V. Y. Yuriev, NAAS of Ukraine.
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28
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Nuccio ML, Wu J, Mowers R, Zhou HP, Meghji M, Primavesi LF, Paul MJ, Chen X, Gao Y, Haque E, Basu SS, Lagrimini LM. Expression of trehalose-6-phosphate phosphatase in maize ears improves yield in well-watered and drought conditions. Nat Biotechnol 2016; 33:862-9. [PMID: 26473199 DOI: 10.1038/nbt.3277] [Citation(s) in RCA: 246] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Maize, the highest-yielding cereal crop worldwide, is particularly susceptible to drought during its 2- to 3-week flowering period. Many genetic engineering strategies for drought tolerance impinge on plant development, reduce maximum yield potential or do not translate from laboratory conditions to the field. We overexpressed a gene encoding a rice trehalose-6-phosphate phosphatase (TPP) in developing maize ears using a floral promoter. This reduced the concentration of trehalose-6-phosphate (T6P), a sugar signal that regulates growth and development, and increased the concentration of sucrose in ear spikelets. Overexpression of TPP increased both kernel set and harvest index. Field data at several sites and over multiple seasons showed that the engineered trait improved yields from 9% to 49% under non-drought or mild drought conditions, and from 31% to 123% under more severe drought conditions, relative to yields from nontransgenic controls.
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29
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Fita A, Rodríguez-Burruezo A, Boscaiu M, Prohens J, Vicente O. Breeding and Domesticating Crops Adapted to Drought and Salinity: A New Paradigm for Increasing Food Production. FRONTIERS IN PLANT SCIENCE 2015; 6:978. [PMID: 26617620 PMCID: PMC4641906 DOI: 10.3389/fpls.2015.00978] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/26/2015] [Indexed: 05/17/2023]
Abstract
World population is expected to reach 9.2 × 10(9) people by 2050. Feeding them will require a boost in crop productivity using innovative approaches. Current agricultural production is very dependent on large amounts of inputs and water availability is a major limiting factor. In addition, the loss of genetic diversity and the threat of climate change make a change of paradigm in plant breeding and agricultural practices necessary. Average yields in all major crops are only a small fraction of record yields, and drought and soil salinity are the main factors responsible for yield reduction. Therefore there is the need to enhance crop productivity by improving crop adaptation. Here we review the present situation and propose the development of crops tolerant to drought and salt stress for addressing the challenge of dramatically increasing food production in the near future. The success in the development of crops adapted to drought and salt depends on the efficient and combined use of genetic engineering and traditional breeding tools. Moreover, we propose the domestication of new halophilic crops to create a 'saline agriculture' which will not compete in terms of resources with conventional agriculture.
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Affiliation(s)
- Ana Fita
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
| | - Adrián Rodríguez-Burruezo
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
| | - Monica Boscaiu
- Mediterranean Agroforestal Institute, Universitat Politècnica de ValènciaValencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de ValènciaValencia, Spain
| | - Oscar Vicente
- Institute of Plant Molecular and Cellular Biology, Universitat Politècnica de València – Consejo Superior de Investigaciones CientíficasValencia, Spain
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30
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Zaman-Allah M, Vergara O, Araus JL, Tarekegne A, Magorokosho C, Zarco-Tejada PJ, Hornero A, Albà AH, Das B, Craufurd P, Olsen M, Prasanna BM, Cairns J. Unmanned aerial platform-based multi-spectral imaging for field phenotyping of maize. PLANT METHODS 2015; 11:35. [PMID: 26106438 PMCID: PMC4477614 DOI: 10.1186/s13007-015-0078-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 06/09/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Recent developments in unmanned aerial platforms (UAP) have provided research opportunities in assessing land allocation and crop physiological traits, including response to abiotic and biotic stresses. UAP-based remote sensing can be used to rapidly and cost-effectively phenotype large numbers of plots and field trials in a dynamic way using time series. This is anticipated to have tremendous implications for progress in crop genetic improvement. RESULTS We present the use of a UAP equipped with sensors for multispectral imaging in spatial field variability assessment and phenotyping for low-nitrogen (low-N) stress tolerance in maize. Multispectral aerial images were used to (1) characterize experimental fields for spatial soil-nitrogen variability and (2) derive indices for crop performance under low-N stress. Overall, results showed that the aerial platform enables to effectively characterize spatial field variation and assess crop performance under low-N stress. The Normalized Difference Vegetation Index (NDVI) data derived from spectral imaging presented a strong correlation with ground-measured NDVI, crop senescence index and grain yield. CONCLUSION This work suggests that the aerial sensing platform designed for phenotyping studies has the potential to effectively assist in crop genetic improvement against abiotic stresses like low-N provided that sensors have enough resolution for plot level data collection. Limitations and future potential uses are also discussed.
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Affiliation(s)
- M Zaman-Allah
- />International Maize and Wheat Improvement Center (CIMMYT), PO Box MP163, Peg Mazowe Rd, Mt Pleasant, Harare, Zimbabwe
| | - O Vergara
- />Plant Physiology Unit, Department of Plant Biology, University of Barcelona, 08028 Barcelona, Spain
| | - J L Araus
- />Plant Physiology Unit, Department of Plant Biology, University of Barcelona, 08028 Barcelona, Spain
| | - A Tarekegne
- />International Maize and Wheat Improvement Center (CIMMYT), PO Box MP163, Peg Mazowe Rd, Mt Pleasant, Harare, Zimbabwe
| | - C Magorokosho
- />International Maize and Wheat Improvement Center (CIMMYT), PO Box MP163, Peg Mazowe Rd, Mt Pleasant, Harare, Zimbabwe
| | - P J Zarco-Tejada
- />Laboratory for Research Methods in Quantitative Remote Sensing (Quantalab IAS-CSIC), Cordoba, Spain
| | - A Hornero
- />Laboratory for Research Methods in Quantitative Remote Sensing (Quantalab IAS-CSIC), Cordoba, Spain
| | | | - B Das
- />International Maize and Wheat Improvement Center (CIMMYT), PO Box 1041, Nairobi, Kenya
| | - P Craufurd
- />International Maize and Wheat Improvement Center (CIMMYT), PO Box 1041, Nairobi, Kenya
| | - M Olsen
- />International Maize and Wheat Improvement Center (CIMMYT), PO Box 1041, Nairobi, Kenya
| | - B M Prasanna
- />International Maize and Wheat Improvement Center (CIMMYT), PO Box 1041, Nairobi, Kenya
| | - J Cairns
- />International Maize and Wheat Improvement Center (CIMMYT), PO Box MP163, Peg Mazowe Rd, Mt Pleasant, Harare, Zimbabwe
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31
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Dolferus R. To grow or not to grow: a stressful decision for plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 229:247-261. [PMID: 25443851 DOI: 10.1016/j.plantsci.2014.10.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/06/2014] [Accepted: 10/09/2014] [Indexed: 05/18/2023]
Abstract
Progress in improving abiotic stress tolerance of crop plants using classic breeding and selection approaches has been slow. This has generally been blamed on the lack of reliable traits and phenotyping methods for stress tolerance. In crops, abiotic stress tolerance is most often measured in terms of yield-capacity under adverse weather conditions. "Yield" is a complex trait and is determined by growth and developmental processes which are controlled by environmental signals throughout the life cycle of the plant. The use of model systems has allowed us to gradually unravel how plants grow and develop, but our understanding of the flexibility and opportunistic nature of plant development and its capacity to adapt growth to environmental cues is still evolving. There is genetic variability for the capacity to maintain yield and productivity under abiotic stress conditions in crop plants such as cereals. Technological progress in various domains has made it increasingly possible to mine that genetic variability and develop a better understanding about the basic mechanism of plant growth and abiotic stress tolerance. The aim of this paper is not to give a detailed account of all current research progress, but instead to highlight some of the current research trends that may ultimately lead to strategies for stress-proofing crop species. The focus will be on abiotic stresses that are most often associated with climate change (drought, heat and cold) and those crops that are most important for human nutrition, the cereals.
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Affiliation(s)
- Rudy Dolferus
- CSIRO, Agriculture Flagship, GPO Box 1600, Canberra, ACT 2601, Australia.
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32
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Blum A. Genomics for drought resistance - getting down to earth. FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:1191-1198. [PMID: 32481068 DOI: 10.1071/fp14018] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 03/10/2014] [Indexed: 05/20/2023]
Abstract
A meta-analysis of 520 reports published during the last 20 years on transgenic and mutant plants generated towards drought resistance revealed a total of at least 487 tested transgenic plants involving at least 100 genes claimed to be functional towards drought resistance. During this period, the rate of reported new experimental transgenic model or crop plants for drought resistance has been increasing exponentially. Despite these numbers, qualified sources of information indicate a very limited impact on global dryland agriculture, whereas the genetically modified (GM) market hardly recognises drought-resistant GM cultivars. This paper discusses possible reasons for the limited impact of genomics on the delivery of drought-resistant cultivars, which are beyond issues of regulation, propriety or commercialisation. These reasons are mainly tied to scientific and methodological problems in drought stress gene expression work and the functional genomics protocols used to identify drought resistance. Insufficient phenotyping of experimental transgenic plants for drought resistance often does not allow true conclusions about the real function of the discovered genes towards drought resistance. The discussion is concluded by proposing an outline of a minimal set of tests that might help us resolve the real function of discovered genes, thus bringing the research results down to earth.
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33
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Turner NC, Blum A, Cakir M, Steduto P, Tuberosa R, Young N. Strategies to increase the yield and yield stability of crops under drought - are we making progress? FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:1199-1206. [PMID: 32481069 DOI: 10.1071/fp14057] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 04/02/2014] [Indexed: 06/11/2023]
Abstract
The objective of the InterDrought conferences is to be a platform for debating key issues that are relevant for increasing the yield and yield stability of crops under drought via integrated approaches. InterDrought-IV, held in Perth, Australia, in September 2013, followed previous InterDrought conferences in bringing together researchers in agronomy, soil science, modelling, physiology, biochemistry, molecular biology, genetics and plant breeding. Key themes were (i) maximising water productivity; (ii) maximising dryland crop production; (iii) adaptation to water-limited environments; (iv) plant productivity under drought through effective water capture, improved transpiration efficiency, and growth and yield; and (v) breeding for water-limited environments through variety development, and trait-based genomics-assisted and transgenic approaches. This paper highlights some key issues and presents recommendations for future action. Improved agronomic interventions were recognised as being important contributors to improved dryland crop yields in water-limited environments, and new methods for exploring root architecture and water capture were highlighted. The increase in crop yields under drought through breeding and selection, the development of high-throughput phenotyping facilities for field-grown and pot-grown plants, and advances in understanding the molecular basis of plant responses and resistance to drought stress were recognised. Managed environment phenotyping facilities, a range of field environments, modelling, and genomic molecular tools are being used to select and release drought-resistant cultivars of all major crops. Delegates discussed how individuals and small teams can contribute to progress, and concluded that interdisciplinary research, linkages to international agricultural research centres, public-private partnerships and continuation of the InterDrought conferences will be instrumental for progress.
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Affiliation(s)
- Neil C Turner
- The University of Western Australia Institute of Agriculture and Centre for Plant Genetics and Breeding, M080, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | | | - Mehmet Cakir
- School of Biological Sciences and Biotechnology, Faculty of Sustainability, Environmental and Life Sciences, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Pasquale Steduto
- Food and Agriculture Organisation of the United Nations, Viale delle Terme di Caracalla, 00153 Rome, Italy
| | - Roberto Tuberosa
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Neil Young
- Rural Mail Box 232, Kojonup, WA 6395, Australia
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Virlet N, Lebourgeois V, Martinez S, Costes E, Labbé S, Regnard JL. Stress indicators based on airborne thermal imagery for field phenotyping a heterogeneous tree population for response to water constraints. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5429-42. [PMID: 25080086 PMCID: PMC4157722 DOI: 10.1093/jxb/eru309] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 02/05/2014] [Accepted: 06/15/2014] [Indexed: 05/18/2023]
Abstract
As field phenotyping of plant response to water constraints constitutes a bottleneck for breeding programmes, airborne thermal imagery can contribute to assessing the water status of a wide range of individuals simultaneously. However, the presence of mixed soil-plant pixels in heterogeneous plant cover complicates the interpretation of canopy temperature. Moran's Water Deficit Index (WDI = 1-ETact/ETmax), which was designed to overcome this difficulty, was compared with surface minus air temperature (T s-T a) as a water stress indicator. As parameterization of the theoretical equations for WDI computation is difficult, particularly when applied to genotypes with large architectural variability, a simplified procedure based on quantile regression was proposed to delineate the Vegetation Index-Temperature (VIT) scatterplot. The sensitivity of WDI to variations in wet and dry references was assessed by applying more or less stringent quantile levels. The different stress indicators tested on a series of airborne multispectral images (RGB, near-infrared, and thermal infrared) of a population of 122 apple hybrids, under two irrigation regimes, significantly discriminated the tree water statuses. For each acquisition date, the statistical method efficiently delineated the VIT scatterplot, while the limits obtained using the theoretical approach overlapped it, leading to inconsistent WDI values. Once water constraint was established, the different stress indicators were linearly correlated to the stem water potential among a tree subset. T s-T a showed a strong sensitivity to evaporative demand, which limited its relevancy for temporal comparisons. Finally, the statistical approach of WDI appeared the most suitable for high-throughput phenotyping.
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Affiliation(s)
- Nicolas Virlet
- Montpellier SupAgro, UMR 1334 Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales, TA-A-108/03, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Valentine Lebourgeois
- CIRAD, UMR Territoires, Environnement, Télédétection et Information Spatiale, Station Ligne-Paradis, 7 Chemin de l'IRAT, 97410 Saint-Pierre, France
| | - Sébastien Martinez
- INRA, UMR 1334 AGAP, TA-A-108/03, Avenue Agropolis, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Evelyne Costes
- INRA, UMR 1334 AGAP, TA-A-108/03, Avenue Agropolis, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Sylvain Labbé
- IRSTEA, UMR TETIS, Remote Sensing Centre, 500 rue J. F. Breton, 34093 Montpellier Cedex 5, France
| | - Jean-Luc Regnard
- Montpellier SupAgro, UMR 1334 Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales, TA-A-108/03, Avenue Agropolis, 34398 Montpellier Cedex 5, France
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Silvestre S, Araújo SDS, Vaz Patto MC, Marques da Silva J. Performance index: An expeditious tool to screen for improved drought resistance in the Lathyrus genus. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:610-21. [PMID: 25126659 DOI: 10.1111/jipb.12186] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Some species of the Lathyrus genus are among the most promising crops for marginal lands, with high resilience to drought, flood, and fungal diseases, combined with high yields and seed nutritional value. However, lack of knowledge on the mechanisms underlying its outstanding performance and methodologies to identify elite genotypes has hampered its proper use in breeding. Chlorophyll a fast fluorescence transient (JIP test), was used to evaluate water deficit (WD) resistance in Lathyrus genus. Our results reveal unaltered photochemical values for all studied genotypes showing resistance to mild WD. Under severe WD, two Lathyrus sativus genotypes showed remarkable resilience maintaining the photochemical efficiency, contrary to other genotypes studied. Performance index (PIABS) is the best parameter to screen genotypes with improved performance and grain production under WD. Moreover, we found that JIP indices are good indicators of genotypic grain production under WD. Quantum yield of electron transport (ϕEo) and efficiency with which trapped excitons can move electrons further than QA (ψ0) revealed as important traits related to improved photosynthetic performance and should be exploited in future Lathyrus germplasm improvements. The JIP test herein described showed to be an expeditious tool to screen and to identify elite genotypes with improved drought resistance.
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Araus JL, Li J, Parry MAJ, Wang J. Phenotyping and other breeding approaches for a New Green Revolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:422-4. [PMID: 24703237 DOI: 10.1111/jipb.12202] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
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Nelissen H, Moloney M, Inzé D. Translational research: from pot to plot. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:277-85. [PMID: 24646295 DOI: 10.1111/pbi.12176] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 01/02/2014] [Accepted: 01/27/2014] [Indexed: 05/08/2023]
Abstract
Plant molecular biology has been the key driver to elucidate molecular pathways underlying plant growth, development and stress responses during the past decades. Although this has led to a plethora of available data, the translation to crop improvement is lagging behind. Here, we argue that plant scientists should become more involved in converting basic knowledge into applications in crops to sustainably support food security and agriculture. As the translatability from model species to crops is rather poor, this kind of translational research requires diligence and a thorough knowledge of the investigated trait in the crop. In addition, the robustness of a trait depends on the genotype and environmental conditions, demanding a holistic approach, which cannot always be evaluated under growth chamber and greenhouse conditions. To date, the improved resolution of many genome-wide technologies and the emerging expertise in canopy imaging, plant phenotyping and field monitoring make it very timely to move from the pathway specifics to important agronomical realizations, thus from pot to plot. Despite the availability of scientific know-how and expertise, the translation of new traits to applications using a transgene approach is in some regions of the world, such as Europe, seriously hampered by heavy and nontranslucent legislation for biotech crops. Nevertheless, progress in crop improvement will remain highly dependent on our ability to evaluate improved varieties in field conditions. Here, we plead for a network of protected sites for field trials across the different European climates to test improved biotech traits directly in crops.
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Affiliation(s)
- Hilde Nelissen
- Department of Plant Systems Biology, VIB, Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
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Almeida GD, Nair S, Borém A, Cairns J, Trachsel S, Ribaut JM, Bänziger M, Prasanna BM, Crossa J, Babu R. Molecular mapping across three populations reveals a QTL hotspot region on chromosome 3 for secondary traits associated with drought tolerance in tropical maize. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2014; 34:701-715. [PMID: 25076840 PMCID: PMC4092235 DOI: 10.1007/s11032-014-0068-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 03/05/2014] [Indexed: 05/18/2023]
Abstract
Identifying quantitative trait loci (QTL) of sizeable effects that are expressed in diverse genetic backgrounds across contrasting water regimes particularly for secondary traits can significantly complement the conventional drought tolerance breeding efforts. We evaluated three tropical maize biparental populations under water-stressed and well-watered regimes for drought-related morpho-physiological traits, such as anthesis-silking interval (ASI), ears per plant (EPP), stay-green (SG) and plant-to-ear height ratio (PEH). In general, drought stress reduced the genetic variance of grain yield (GY), while that of morpho-physiological traits remained stable or even increased under drought conditions. We detected consistent genomic regions across different genetic backgrounds that could be target regions for marker-assisted introgression for drought tolerance in maize. A total of 203 QTL for ASI, EPP, SG and PEH were identified under both the water regimes. Meta-QTL analysis across the three populations identified six constitutive genomic regions with a minimum of two overlapping traits. Clusters of QTL were observed on chromosomes 1.06, 3.06, 4.09, 5.05, 7.03 and 10.04/06. Interestingly, a ~8-Mb region delimited in 3.06 harboured QTL for most of the morpho-physiological traits considered in the current study. This region contained two important candidate genes viz., zmm16 (MADS-domain transcription factor) and psbs1 (photosystem II unit) that are responsible for reproductive organ development and photosynthate accumulation, respectively. The genomic regions identified in this study partially explained the association of secondary traits with GY. Flanking single nucleotide polymorphism markers reported herein may be useful in marker-assisted introgression of drought tolerance in tropical maize.
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Affiliation(s)
- Gustavo Dias Almeida
- Universidade Federal de Viçosa (UFV), CEP: 36.570-000 Viçosa, Minas Gerais State Brazil
- Monsanto Company, CEP: 38.405-232 Uberlândia, Minas Gerais Brazil
| | - Sudha Nair
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico, DF Mexico
| | - Aluízio Borém
- Universidade Federal de Viçosa (UFV), CEP: 36.570-000 Viçosa, Minas Gerais State Brazil
| | - Jill Cairns
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico, DF Mexico
| | - Samuel Trachsel
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico, DF Mexico
| | - Jean-Marcel Ribaut
- Generation Challenge Program, Hosted by CIMMYT, Apdo. Postal 6-641, Mexico, DF Mexico
| | - Marianne Bänziger
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico, DF Mexico
| | | | - Jose Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico, DF Mexico
| | - Raman Babu
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico, DF Mexico
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Araus JL, Cairns JE. Field high-throughput phenotyping: the new crop breeding frontier. TRENDS IN PLANT SCIENCE 2014; 19:52-61. [PMID: 24139902 DOI: 10.1016/j.tplants.2013.09.008] [Citation(s) in RCA: 600] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 09/16/2013] [Accepted: 09/18/2013] [Indexed: 05/18/2023]
Abstract
Constraints in field phenotyping capability limit our ability to dissect the genetics of quantitative traits, particularly those related to yield and stress tolerance (e.g., yield potential as well as increased drought, heat tolerance, and nutrient efficiency, etc.). The development of effective field-based high-throughput phenotyping platforms (HTPPs) remains a bottleneck for future breeding advances. However, progress in sensors, aeronautics, and high-performance computing are paving the way. Here, we review recent advances in field HTPPs, which should combine at an affordable cost, high capacity for data recording, scoring and processing, and non-invasive remote sensing methods, together with automated environmental data collection. Laboratory analyses of key plant parts may complement direct phenotyping under field conditions. Improvements in user-friendly data management together with a more powerful interpretation of results should increase the use of field HTPPs, therefore increasing the efficiency of crop genetic improvement to meet the needs of future generations.
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Affiliation(s)
- José Luis Araus
- Department of Plant Biology, Unit of Plant Physiology, University of Barcelona, 08028 Barcelona, Spain.
| | - Jill E Cairns
- CIMMYT Southern Africa Regional Office, Harare, Zimbabwe
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Lado B, Matus I, Rodríguez A, Inostroza L, Poland J, Belzile F, del Pozo A, Quincke M, Castro M, von Zitzewitz J. Increased genomic prediction accuracy in wheat breeding through spatial adjustment of field trial data. G3 (BETHESDA, MD.) 2013; 3:2105-14. [PMID: 24082033 PMCID: PMC3852373 DOI: 10.1534/g3.113.007807] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 09/18/2013] [Indexed: 01/09/2023]
Abstract
In crop breeding, the interest of predicting the performance of candidate cultivars in the field has increased due to recent advances in molecular breeding technologies. However, the complexity of the wheat genome presents some challenges for applying new technologies in molecular marker identification with next-generation sequencing. We applied genotyping-by-sequencing, a recently developed method to identify single-nucleotide polymorphisms, in the genomes of 384 wheat (Triticum aestivum) genotypes that were field tested under three different water regimes in Mediterranean climatic conditions: rain-fed only, mild water stress, and fully irrigated. We identified 102,324 single-nucleotide polymorphisms in these genotypes, and the phenotypic data were used to train and test genomic selection models intended to predict yield, thousand-kernel weight, number of kernels per spike, and heading date. Phenotypic data showed marked spatial variation. Therefore, different models were tested to correct the trends observed in the field. A mixed-model using moving-means as a covariate was found to best fit the data. When we applied the genomic selection models, the accuracy of predicted traits increased with spatial adjustment. Multiple genomic selection models were tested, and a Gaussian kernel model was determined to give the highest accuracy. The best predictions between environments were obtained when data from different years were used to train the model. Our results confirm that genotyping-by-sequencing is an effective tool to obtain genome-wide information for crops with complex genomes, that these data are efficient for predicting traits, and that correction of spatial variation is a crucial ingredient to increase prediction accuracy in genomic selection models.
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Affiliation(s)
- Bettina Lado
- Programa Nacional de Investigación Cultivos de Secano, Instituto Nacional de Investigación Agropecuaria, Est. Exp. La Estanzuela, Colonia 70000, Uruguay
| | - Ivan Matus
- Instituto de Investigaciones Agropecuarias, Centro Regional de Investigación Quilamapu, Casilla 426, Chillán, Chile
| | - Alejandra Rodríguez
- Instituto de Investigaciones Agropecuarias, Centro Regional de Investigación Quilamapu, Casilla 426, Chillán, Chile
| | - Luis Inostroza
- Instituto de Investigaciones Agropecuarias, Centro Regional de Investigación Quilamapu, Casilla 426, Chillán, Chile
| | - Jesse Poland
- United States Department of Agriculture, Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas 66506
- Department of Agronomy, Kansas State University, Manhattan, Kansas
| | - François Belzile
- Département de Phytologie and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC G1V 0A6, Canada
| | - Alejandro del Pozo
- Universidad de Talca, Facultad de Ciencias Agrarias, Casilla 747, Talca, Chile
| | - Martín Quincke
- Programa Nacional de Investigación Cultivos de Secano, Instituto Nacional de Investigación Agropecuaria, Est. Exp. La Estanzuela, Colonia 70000, Uruguay
| | - Marina Castro
- Programa Nacional de Investigación Cultivos de Secano, Instituto Nacional de Investigación Agropecuaria, Est. Exp. La Estanzuela, Colonia 70000, Uruguay
| | - Jarislav von Zitzewitz
- Programa Nacional de Investigación Cultivos de Secano, Instituto Nacional de Investigación Agropecuaria, Est. Exp. La Estanzuela, Colonia 70000, Uruguay
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Pujar A, Menda N, Bombarely A, Edwards JD, Strickler SR, Mueller LA. From manual curation to visualization of gene families and networks across Solanaceae plant species. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2013; 2013:bat028. [PMID: 23681907 PMCID: PMC3655285 DOI: 10.1093/database/bat028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
High-quality manual annotation methods and practices need to be scaled to the increased rate of genomic data production. Curation based on gene families and gene networks is one approach that can significantly increase both curation efficiency and quality. The Sol Genomics Network (SGN; http://solgenomics.net) is a comparative genomics platform, with genetic, genomic and phenotypic information of the Solanaceae family and its closely related species that incorporates a community-based gene and phenotype curation system. In this article, we describe a manual curation system for gene families aimed at facilitating curation, querying and visualization of gene interaction patterns underlying complex biological processes, including an interface for efficiently capturing information from experiments with large data sets reported in the literature. Well-annotated multigene families are useful for further exploration of genome organization and gene evolution across species. As an example, we illustrate the system with the multigene transcription factor families, WRKY and Small Auxin Up-regulated RNA (SAUR), which both play important roles in responding to abiotic stresses in plants. Database URL:http://solgenomics.net/
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Affiliation(s)
- Anuradha Pujar
- Boyce Thompson Institute for Plant Research, 533, Tower Road, Ithaca, NY 14853, USA
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Cobb JN, DeClerck G, Greenberg A, Clark R, McCouch S. Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype-phenotype relationships and its relevance to crop improvement. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:867-87. [PMID: 23471459 PMCID: PMC3607725 DOI: 10.1007/s00122-013-2066-0] [Citation(s) in RCA: 238] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 02/08/2013] [Indexed: 05/19/2023]
Abstract
More accurate and precise phenotyping strategies are necessary to empower high-resolution linkage mapping and genome-wide association studies and for training genomic selection models in plant improvement. Within this framework, the objective of modern phenotyping is to increase the accuracy, precision and throughput of phenotypic estimation at all levels of biological organization while reducing costs and minimizing labor through automation, remote sensing, improved data integration and experimental design. Much like the efforts to optimize genotyping during the 1980s and 1990s, designing effective phenotyping initiatives today requires multi-faceted collaborations between biologists, computer scientists, statisticians and engineers. Robust phenotyping systems are needed to characterize the full suite of genetic factors that contribute to quantitative phenotypic variation across cells, organs and tissues, developmental stages, years, environments, species and research programs. Next-generation phenotyping generates significantly more data than previously and requires novel data management, access and storage systems, increased use of ontologies to facilitate data integration, and new statistical tools for enhancing experimental design and extracting biologically meaningful signal from environmental and experimental noise. To ensure relevance, the implementation of efficient and informative phenotyping experiments also requires familiarity with diverse germplasm resources, population structures, and target populations of environments. Today, phenotyping is quickly emerging as the major operational bottleneck limiting the power of genetic analysis and genomic prediction. The challenge for the next generation of quantitative geneticists and plant breeders is not only to understand the genetic basis of complex trait variation, but also to use that knowledge to efficiently synthesize twenty-first century crop varieties.
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Affiliation(s)
- Joshua N. Cobb
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853 USA
- United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853 USA
| | - Genevieve DeClerck
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853 USA
| | - Anthony Greenberg
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853 USA
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853 USA
| | - Randy Clark
- United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853 USA
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853 USA
| | - Susan McCouch
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853 USA
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Almeida GD, Makumbi D, Magorokosho C, Nair S, Borém A, Ribaut JM, Bänziger M, Prasanna BM, Crossa J, Babu R. QTL mapping in three tropical maize populations reveals a set of constitutive and adaptive genomic regions for drought tolerance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:583-600. [PMID: 23124431 PMCID: PMC3579412 DOI: 10.1007/s00122-012-2003-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Accepted: 10/06/2012] [Indexed: 05/18/2023]
Abstract
Despite numerous published reports of quantitative trait loci (QTL) for drought-related traits, practical applications of such QTL in maize improvement are scarce. Identifying QTL of sizeable effects that express more or less uniformly in diverse genetic backgrounds across contrasting water regimes could significantly complement conventional breeding efforts to improve drought tolerance. We evaluated three tropical bi-parental populations under water-stress (WS) and well-watered (WW) regimes in Mexico, Kenya and Zimbabwe to identify genomic regions responsible for grain yield (GY) and anthesis-silking interval (ASI) across multiple environments and diverse genetic backgrounds. Across the three populations, on average, drought stress reduced GY by more than 50 % and increased ASI by 3.2 days. We identified a total of 83 and 62 QTL through individual environment analyses for GY and ASI, respectively. In each population, most QTL consistently showed up in each water regime. Across the three populations, the phenotypic variance explained by various individual QTL ranged from 2.6 to 17.8 % for GY and 1.7 to 17.8 % for ASI under WS environments and from 5 to 19.5 % for GY under WW environments. Meta-QTL (mQTL) analysis across the three populations and multiple environments identified seven genomic regions for GY and one for ASI, of which six mQTL on chr.1, 4, 5 and 10 for GY were constitutively expressed across WS and WW environments. One mQTL on chr.7 for GY and one on chr.3 for ASI were found to be 'adaptive' to WS conditions. High throughput assays were developed for SNPs that delimit the physical intervals of these mQTL. At most of the QTL, almost equal number of favorable alleles was donated by either of the parents within each cross, thereby demonstrating the potential of drought tolerant × drought tolerant crosses to identify QTL under contrasting water regimes.
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Affiliation(s)
- Gustavo Dias Almeida
- Universidade Federal de Viçosa (UFV), CEP 36.570-000 Viçosa, Minas Gerais Brazil
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico, DF Mexico
| | - Dan Makumbi
- CIMMYT, ICRAF House, United Nations Avenue, Gigiri, Nairobi, 00621 Kenya
| | | | - Sudha Nair
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico, DF Mexico
| | - Aluízio Borém
- Universidade Federal de Viçosa (UFV), CEP 36.570-000 Viçosa, Minas Gerais Brazil
| | - Jean-Marcel Ribaut
- Generation Challenge Program, hosted By CIMMYT, Apdo. Postal 6-641, Mexico, DF Mexico
| | - Marianne Bänziger
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico, DF Mexico
| | | | - Jose Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico, DF Mexico
| | - Raman Babu
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, Mexico, DF Mexico
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Cairns JE, Sanchez C, Vargas M, Ordoñez R, Araus JL. Dissecting maize productivity: ideotypes associated with grain yield under drought stress and well-watered conditions. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2012; 54:1007-20. [PMID: 22925524 DOI: 10.1111/j.1744-7909.2012.01156.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
To increase maize (Zea mays L.) yields in drought-prone environments and offset predicted maize yield losses under future climates, the development of improved breeding pipelines using a multi-disciplinary approach is essential. Elucidating key growth processes will provide opportunities to improve drought breeding progress through the identification of key phenotypic traits, ideotypes, and donors. In this study, we tested a large set of tropical and subtropical maize inbreds and single cross hybrids under reproductive stage drought stress and well-watered conditions. Patterns of biomass production, senescence, and plant water status were measured throughout the crop cycle. Under drought stress, early biomass production prior to anthesis was important for inbred yield, while delayed senescence was important for hybrid yield. Under well-watered conditions, the ability to maintain a high biomass throughout the growing cycle was crucial for inbred yield, while a stay-green pattern was important for hybrid yield. While new quantitative phenotyping tools such as spectral reflectance (Normalized Difference Vegetation Index, NDVI) allowed for the characterization of growth and senescence patterns as well as yield, qualitative measurements of canopy senescence were also found to be associated with grain yield.
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Affiliation(s)
- Jill E Cairns
- Global Maize Program, International Maize and Wheat Improvement Center-CIMMYT, Mexico D.F., Mexico.
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Passioura JB. Phenotyping for drought tolerance in grain crops: when is it useful to breeders? FUNCTIONAL PLANT BIOLOGY : FPB 2012; 39:851-859. [PMID: 32480835 DOI: 10.1071/fp12079] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 09/05/2012] [Indexed: 05/24/2023]
Abstract
Breeding for drought tolerance in grain crops is not a generic issue. Periods of drought vary in length, timing and intensity and different traits are important with different types of drought. The search for generic drought tolerance using single-gene transformations has been disappointing. It has typically concentrated on survival of plants suffering from severe water stress, which is rarely an important trait in crops. More promising approaches that target complex traits tailored to specific requirements at the different main stages of the life of a crop, during: establishment, vegetative development, floral development and grain growth are outlined. The challenge is to devise inexpensive and effective ways of identifying promising phenotypes with the aim of aligning them with genomic information to identify molecular markers useful to breeders. Controlled environments offer the stability to search for attractive phenotypes or genotypes in a specific type of drought. The recent availability of robots for measuring large number of plants means that large numbers of genotypes can be readily phenotyped. However, controlled environments differ greatly from those in the field. Devising pot experiments that cater for important yield-determining processes in the field is difficult, especially when water is limiting. Thus, breeders are unlikely to take much notice of research in controlled environments unless the worth of specific traits has been demonstrated in the field. An essential link in translating laboratory research to the field is the development of novel genotypes that incorporate gene(s) expressing a promising trait into breeding lines that are adapted to target field environments. Only if the novel genotypes perform well in the field are they likely to gain the interest of breeders. High throughput phenotyping will play a pivotal role in this process.
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Araus JL, Serret MD, Edmeades GO. Phenotyping maize for adaptation to drought. Front Physiol 2012; 3:305. [PMID: 22934056 PMCID: PMC3429076 DOI: 10.3389/fphys.2012.00305] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Accepted: 07/12/2012] [Indexed: 01/08/2023] Open
Abstract
The need of a better adaptation of crops to drought is an issue of increasing urgency. However, enhancing the tolerance of maize has, therefore, proved to be somewhat elusive in terms of plant breeding. In that context, proper phenotyping remains as one of the main factors limiting breeding advance. Topics covered by this review include the conceptual framework for identifying secondary traits associated with yield response to drought and how to measure these secondary traits in practice.
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Affiliation(s)
- Jose L Araus
- Facultat de Biologia, Unitat de Fisiologia Vegetal, Departament de Biologia Vegetal, Universitat de Barcelona Barcelona, Catalonia, Spain
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Cabrera-Bosquet L, Crossa J, von Zitzewitz J, Serret MD, Araus JL. High-throughput phenotyping and genomic selection: the frontiers of crop breeding converge. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2012; 54:312-20. [PMID: 22420640 DOI: 10.1111/j.1744-7909.2012.01116.x] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Genomic selection (GS) and high-throughput phenotyping have recently been captivating the interest of the crop breeding community from both the public and private sectors world-wide. Both approaches promise to revolutionize the prediction of complex traits, including growth, yield and adaptation to stress. Whereas high-throughput phenotyping may help to improve understanding of crop physiology, most powerful techniques for high-throughput field phenotyping are empirical rather than analytical and comparable to genomic selection. Despite the fact that the two methodological approaches represent the extremes of what is understood as the breeding process (phenotype versus genome), they both consider the targeted traits (e.g. grain yield, growth, phenology, plant adaptation to stress) as a black box instead of dissecting them as a set of secondary traits (i.e. physiological) putatively related to the target trait. Both GS and high-throughput phenotyping have in common their empirical approach enabling breeders to use genome profile or phenotype without understanding the underlying biology. This short review discusses the main aspects of both approaches and focuses on the case of genomic selection of maize flowering traits and near-infrared spectroscopy (NIRS) and plant spectral reflectance as high-throughput field phenotyping methods for complex traits such as crop growth and yield.
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Affiliation(s)
- Llorenç Cabrera-Bosquet
- French National Institute for Agricultural Research (INRA, UMR759), Ecophysiology Laboratory of Plants under Environmental Stress, Montpellier F-34060, France
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Parry MAJ, Wang J, Araus JL. New technologies, tools and approaches for improving crop breeding. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2012; 54:210-214. [PMID: 22409541 DOI: 10.1111/j.1744-7909.2012.01114.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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