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Falcioni R, Gonçalves JVF, de Oliveira KM, de Oliveira CA, Demattê JAM, Antunes WC, Nanni MR. Enhancing Pigment Phenotyping and Classification in Lettuce through the Integration of Reflectance Spectroscopy and AI Algorithms. PLANTS (BASEL, SWITZERLAND) 2023; 12:1333. [PMID: 36987021 PMCID: PMC10059284 DOI: 10.3390/plants12061333] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/03/2023] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
In this study, we investigated the use of artificial intelligence algorithms (AIAs) in combination with VIS-NIR-SWIR hyperspectroscopy for the classification of eleven lettuce plant varieties. For this purpose, a spectroradiometer was utilized to collect hyperspectral data in the VIS-NIR-SWIR range, and 17 AIAs were applied to classify lettuce plants. The results showed that the highest accuracy and precision were achieved using the full hyperspectral curves or the specific spectral ranges of 400-700 nm, 700-1300 nm, and 1300-2400 nm. Four models, AdB, CN2, G-Boo, and NN, demonstrated exceptional R2 and ROC values, exceeding 0.99, when compared between all models and confirming the hypothesis and highlighting the potential of AIAs and hyperspectral fingerprints for efficient, precise classification and pigment phenotyping in agriculture. The findings of this study have important implications for the development of efficient methods for phenotyping and classification in agriculture and the potential of AIAs in combination with hyperspectral technology. To advance our understanding of the capabilities of hyperspectroscopy and AIs in precision agriculture and contribute to the development of more effective and sustainable agriculture practices, further research is needed to explore the full potential of these technologies in different crop species and environments.
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Affiliation(s)
- Renan Falcioni
- Graduate Program in Agronomy, Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Paraná, Brazil; (J.V.F.G.); (K.M.d.O.); (C.A.d.O.); (W.C.A.); (M.R.N.)
| | - João Vitor Ferreira Gonçalves
- Graduate Program in Agronomy, Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Paraná, Brazil; (J.V.F.G.); (K.M.d.O.); (C.A.d.O.); (W.C.A.); (M.R.N.)
| | - Karym Mayara de Oliveira
- Graduate Program in Agronomy, Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Paraná, Brazil; (J.V.F.G.); (K.M.d.O.); (C.A.d.O.); (W.C.A.); (M.R.N.)
| | - Caio Almeida de Oliveira
- Graduate Program in Agronomy, Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Paraná, Brazil; (J.V.F.G.); (K.M.d.O.); (C.A.d.O.); (W.C.A.); (M.R.N.)
| | - José A. M. Demattê
- Department of Soil Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Av. Pádua Dias, 11, Piracicaba 13418-260, São Paulo, Brazil;
| | - Werner Camargos Antunes
- Graduate Program in Agronomy, Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Paraná, Brazil; (J.V.F.G.); (K.M.d.O.); (C.A.d.O.); (W.C.A.); (M.R.N.)
| | - Marcos Rafael Nanni
- Graduate Program in Agronomy, Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Paraná, Brazil; (J.V.F.G.); (K.M.d.O.); (C.A.d.O.); (W.C.A.); (M.R.N.)
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Yang J, Ma C, Jia R, Zhang H, Zhao Y, Yue H, Li H, Jiang X. Different responses of two maize cultivars to Spodoptera frugiperda (Lepidoptera: Noctuidae) larvae infestation provide insights into their differences in resistance. FRONTIERS IN PLANT SCIENCE 2023; 14:1065891. [PMID: 36844097 PMCID: PMC9950569 DOI: 10.3389/fpls.2023.1065891] [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: 10/10/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Spodoptera frugiperda (Lepidoptera: Noctuidae), a pest with an amazing appetite, damages many crops and causes great losses, especially maize. Understanding the differences in different maize cultivars' responses to S. frugiperda infestation is very important for revealing the mechanisms involved in the resistance of maize plants to S. frugiperda. In this study, a comparative analysis of two maize cultivars, the common cultivar 'ZD958' and the sweet cultivar 'JG218', was used to investigate their physico-biochemical responses to S. frugiperda infestation by a pot experiment. The results showed that the enzymatic and non-enzymatic defense responses of maize seedlings were rapidly induced by S. frugiperda. Frist, the hydrogen peroxide (H2O2) and malondialdehyde (MDA) contents of infested maize leaves were significantly increased and then decreased to the level of the control. Furthermore, compared with the control leaves, the puncture force values and the total phenolics, total flavonoids, and 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one contents of infested leaves were significantly increased within a certain time. The superoxide dismutase and peroxidase activities of infested leaves were significantly increased in a certain period of time, while the catalase activities decreased significantly and then increased to the control level. The jasmonic acid (JA) levels of infested leaves were significantly improved, whereas the salicylic acid and abscisic acid levels changed less. Signaling genes associated with phytohormones and defensive substances including PAL4, CHS6, BX12, LOX1, and NCED9 were significantly induced at certain time points, especially LOX1. Most of these parameters changed greater in JG218 than in ZD958. Moreover, the larvae bioassay showed that S. frugiperda larvae weighed more on JG218 leaves than those on ZD958 leaves. These results suggested that JG218 was more susceptible to S. frugiperda than ZD958. Our findings will make it easier to develop strategies for controlling S. frugiperda for sustainable maize production and breeding of new maize cultivars with increased resistance to herbivores.
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Affiliation(s)
- Jinwen Yang
- College of Agronomy, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Changlu Ma
- College of Agronomy, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Ru Jia
- College of Agronomy, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Haiyan Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Yanming Zhao
- College of Agronomy, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Haiwang Yue
- Dryland Farming Institute, Hebei Academy of Agriculture and Forestry Sciences, Hengshui, China
| | - Heqin Li
- College of Agronomy, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Xuwen Jiang
- College of Agronomy, Qingdao Agricultural University, Qingdao, Shandong, China
- Department of Biological Sciences, Royal Holloway University of London, Egham, United Kingdom
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Falcioni R, Moriwaki T, Gibin MS, Vollmann A, Pattaro MC, Giacomelli ME, Sato F, Nanni MR, Antunes WC. Classification and Prediction by Pigment Content in Lettuce ( Lactuca sativa L.) Varieties Using Machine Learning and ATR-FTIR Spectroscopy. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11243413. [PMID: 36559526 PMCID: PMC9783279 DOI: 10.3390/plants11243413] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/01/2022] [Accepted: 12/06/2022] [Indexed: 05/14/2023]
Abstract
Green or purple lettuce varieties produce many secondary metabolites, such as chlorophylls, carotenoids, anthocyanins, flavonoids, and phenolic compounds, which is an emergent search in the field of biomolecule research. The main objective of this study was to use multivariate and machine learning algorithms on Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy (ATR-FTIR)-based spectra to classify, predict, and categorize chemometric attributes. The cluster heatmap showed the highest efficiency in grouping similar lettuce varieties based on pigment profiles. The relationship among pigments was more significant than the absolute contents. Other results allow classification based on ATR-FTIR fingerprints of inflections associated with structural and chemical components present in lettuce, obtaining high accuracy and precision (>97%) by using principal component analysis and discriminant analysis (PCA-LDA)-associated linear LDA and SVM machine learning algorithms. In addition, PLSR models were capable of predicting Chla, Chlb, Chla+b, Car, AnC, Flv, and Phe contents, with R2P and RPDP values considered very good (0.81−0.88) for Car, Anc, and Flv and excellent (0.91−0.93) for Phe. According to the RPDP metric, the models were considered excellent (>2.10) for all variables estimated. Thus, this research shows the potential of machine learning solutions for ATR-FTIR spectroscopy analysis to classify, estimate, and characterize the biomolecules associated with secondary metabolites in lettuce.
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Affiliation(s)
- Renan Falcioni
- Plant Ecophysiology Laboratory, Graduate Program in Agronomy, Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Brazil
- Correspondence: ; Tel.: +55-44-3011-8940
| | - Thaise Moriwaki
- Plant Ecophysiology Laboratory, Graduate Program in Agronomy, Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Brazil
| | - Mariana Sversut Gibin
- Optical Spectroscopy and Thermophysical Properties Research Group, Graduate Program in Physics, Department of Physics, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Brazil
| | - Alessandra Vollmann
- Plant Ecophysiology Laboratory, Graduate Program in Agronomy, Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Brazil
| | - Mariana Carmona Pattaro
- Plant Ecophysiology Laboratory, Graduate Program in Agronomy, Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Brazil
| | - Marina Ellen Giacomelli
- Plant Ecophysiology Laboratory, Graduate Program in Agronomy, Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Brazil
| | - Francielle Sato
- Optical Spectroscopy and Thermophysical Properties Research Group, Graduate Program in Physics, Department of Physics, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Brazil
| | - Marcos Rafael Nanni
- Plant Ecophysiology Laboratory, Graduate Program in Agronomy, Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Brazil
| | - Werner Camargos Antunes
- Plant Ecophysiology Laboratory, Graduate Program in Agronomy, Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, Brazil
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Malhotra EV, Jain R, Tyagi S, Venkat Raman K, Bansal S, Pattanayak D. Identification of dynamic microRNA associated with systemic defence against Helicoverpa armigera infestation in Cajanus scarabaeoides. PEST MANAGEMENT SCIENCE 2022; 78:3144-3154. [PMID: 35452179 DOI: 10.1002/ps.6941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 04/07/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Helicoverpa armigera is a major insect pest of several crop plants, including pigeonpea. Resistant gene sources are not available in the cultivated gene pool, but resistance has been observed in its crop wild relative, Cajanus scarabaeoides. Gene regulatory mechanisms governing the systemic immune response of this plant to pod borer infestation have not yet been deciphered. MicroRNA (miRNA) profiles of H. armigera-infested and undamaged adjacent leaves of C. scarabaeoides were compared to gain an insight into the plant-insect interactions and to identify dynamic miRNA molecules potentially acting as mediators of systemic defence responses. RESULTS A total of 211 conserved, temporally dynamic miRNA were identified in the unfed adjacent leaves, out of which 98 were found to be differentially expressed in comparison to control leaves. On further analysis, most of the miRNA detected in the adjacent leaves was found to target genes involved in the defence pathways and plant immune response. An overlap of the differentially expressing miRNAs was observed between insect-fed and adjacent unfed leaves, indicating the transmission of signal from the site of infestation to the undamaged parts of the plant, indicative of induction of a systemic defence response. CONCLUSION The miRNA response in the unfed leaves had the signatures of induced changes in metabolism and signal transduction for induction of defence pathway genes. This study reveals the participation of miRNAs in imparting pod borer resistance and mounting a systemic defence response against pod borer infestation in C. scarabaeoides. © 2022 Society of Chemical Industry.
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Affiliation(s)
| | - Rishu Jain
- ICAR - National Bureau of Plant Genetic Resources, New Delhi, India
| | - Saurabh Tyagi
- ICAR - National Institute for Plant Biotechnology, New Delhi, India
| | - K Venkat Raman
- ICAR - National Institute for Plant Biotechnology, New Delhi, India
| | - Sangita Bansal
- ICAR - National Bureau of Plant Genetic Resources, New Delhi, India
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Falcioni R, Moriwaki T, Furlanetto RH, Nanni MR, Antunes WC. Simple, Fast and Efficient Methods for Analysing the Structural, Ultrastructural and Cellular Components of the Cell Wall. PLANTS 2022; 11:plants11070995. [PMID: 35406975 PMCID: PMC9003262 DOI: 10.3390/plants11070995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 10/30/2021] [Accepted: 11/13/2021] [Indexed: 12/17/2022]
Abstract
Plant cell walls are a fundamental component of plant biology and play an essential role in plant growth and development. The metabolic components of the cell wall can be investigated in a fast, simple, and highly efficient manner using various and distinct microscopy techniques. Here, we report implementing a flowchart to analyse tobacco plants’ structural, ultrastructural, and metabolic components supplemented with far-red light. In addition, biochemical components, such as lignin, cellulose, phenolic compounds, and reducing sugars, present in the plant cell walls were quantified using light, fluorescence, and electron microscopy. Our data were generated from samples prepared via tissue fixation, incorporation in resins, and slicing using microtomes. Moreover, we have used routine staining and contrast techniques to characterise plant cell walls. Here, we describe several protocols that use classic and modern techniques as well as qualitative and quantitative analytical methods to study cell walls, enabling the plant research community to understand and select the most suitable methods for the microscopic analysis of metabolic components. Finally, we discuss specific ideas aimed at new students of plant anatomy and microscopy. This research not only described the structural, ultrastructural, and metabolic components of the plant cell wall, but also explained the strategies for understanding cellular development.
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Affiliation(s)
- Renan Falcioni
- Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, PR, Brazil or (T.M.); (R.H.F.); (M.R.N.); (W.C.A.)
- Department of Biology, Paraná Federal Institute of Education, Science and Technology, Avenida Bento Munhoz da Rocha, PRT 280, s/n°, Trevo Codapar, Palmas 85555-000, PR, Brazil
- Correspondence: or ; Tel.: +55-463-262-1274
| | - Thaise Moriwaki
- Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, PR, Brazil or (T.M.); (R.H.F.); (M.R.N.); (W.C.A.)
| | - Renato Herrig Furlanetto
- Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, PR, Brazil or (T.M.); (R.H.F.); (M.R.N.); (W.C.A.)
| | - Marcos Rafael Nanni
- Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, PR, Brazil or (T.M.); (R.H.F.); (M.R.N.); (W.C.A.)
| | - Werner Camargos Antunes
- Department of Agronomy, State University of Maringá, Av. Colombo, 5790, Maringá 87020-900, PR, Brazil or (T.M.); (R.H.F.); (M.R.N.); (W.C.A.)
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Malhotra EV, Jain R, Tyagi S, Raman KV, Bansal S, Aminedi R, Pattanayak D. Comparative analysis of herbivory responsive miRNAs to delineate pod borer (Helicoverpa armigera) resistance mechanisms in Cajanus cajan and its wild relative Cajanus scarabaeoides. PLANT CELL REPORTS 2022; 41:1147-1161. [PMID: 35366099 DOI: 10.1007/s00299-022-02842-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Comparative analysis of herbivory responsive miRNAs between pod borer susceptible C. cajan and its resistant Crop Wild Relative (CWR) C. scarabaeoides revealed miRNA-based regulation of defense genes and plant-insect interactions. Gram pod borer (Helicoverpa armigera) is one of most devastating pests of pigeon pea (Cajanus cajan) worldwide, responsible for huge losses in crop productivity. The lack of genes conferring resistance to pod borer in pigeon pea has proven to be a bottleneck for its improvement. One of its CWR, C. scarabaeoides has demonstrated resistance to this pest and can be exploited for developing pest resistant crop varieties. Differences in expression patterns of herbivory responsive microRNAs in the susceptible C. cajan and resistant C. scarabaeoides after different time duration of pod borer infestation (2 h, 8 h and 18 h) were identified, characterized and functionally validated to understand their role in insect defense response. A total of 462 conserved and 449 novel miRNAs and 273 conserved and 185 novel miRNAs, were identified in C. cajan and C. scarabaeoides, respectively. Among the identified miRNAs, 65, 68 and 65 miRNAs were found to be differentially expressing between the C. scarabaeoides and C. cajan libraries 2 h, 8 h and 18 h post infestation, respectively. These miRNAs were found to target genes involved in a number of pathways contributing to defense and acquired resistance in C. scarabaeoides against pod borer, indicating miRNA-based regulation of defense pathways. Expression patterns of eight of these miRNAs were validated by qRT-PCR. This study provides novel insights into the miRNA-mediated plant-insect interactions and the mechanisms of regulatory pathways involved in insect defense. These findings can be utilized for further exploring the mechanism of herbivore defense in plant systems.
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Affiliation(s)
| | - Rishu Jain
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Saurabh Tyagi
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - K Venkat Raman
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Sangita Bansal
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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Plant Cell and Organism Development 2.0. Int J Mol Sci 2022; 23:ijms23031885. [PMID: 35163807 PMCID: PMC8836925 DOI: 10.3390/ijms23031885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 01/31/2022] [Accepted: 02/02/2022] [Indexed: 12/10/2022] Open
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Ngugi-Dawit A, Njaci I, Higgins TJV, Williams B, Ghimire SR, Mundree SG, Hoang LTM. Comparative TMT Proteomic Analysis Unveils Unique Insights into Helicoverpa armigera (Hübner) Resistance in Cajanus scarabaeoides (L.) Thouars. Int J Mol Sci 2021; 22:ijms22115941. [PMID: 34073052 PMCID: PMC8198728 DOI: 10.3390/ijms22115941] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 11/21/2022] Open
Abstract
Pigeonpea [Cajanus cajan (L.) Millspaugh] is an economically important legume playing a crucial role in the semi-arid tropics. Pigeonpea is susceptible to Helicoverpa armigera (Hübner), which causes devastating yield losses. This pest is developing resistance to many commercially available insecticides. Therefore, crop wild relatives of pigeonpea, are being considered as potential sources of genes to expand the genetic base of cultivated pigeonpea to improve traits such as host plant resistance to pests and pathogens. Quantitative proteomic analysis was conducted using the tandem mass tag platform to identify differentially abundant proteins between IBS 3471 and ICPL 87 tolerant accession and susceptible variety to H. armigera, respectively. Leaf proteome were analysed at the vegetative and flowering/podding growth stages. H. armigera tolerance in IBS 3471 appeared to be related to enhanced defence responses, such as changes in secondary metabolite precursors, antioxidants, and the phenylpropanoid pathway. The development of larvae fed on an artificial diet with IBS 3471 lyophilised leaves showed similar inhibition with those fed on an artificial diet with quercetin concentrations with 32 mg/25 g of artificial diet. DAB staining (3,3′-diaminobenzidine) revealed a rapid accumulation of reactive oxygen species in IBS 3471. We conclude that IBS 3471 is an ideal candidate for improving the genetic base of cultivated pigeonpea, including traits for host plant resistance.
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Affiliation(s)
- Abigail Ngugi-Dawit
- Centre for Agriculture and the Bioeconomy (CAB), Queensland University of Technology (QUT), Brisbane 4001, Australia;
- Correspondence: (A.N.-D.); (S.G.M.); (L.T.M.H.); Tel.: +61-731-388-386 (S.G.M.)
| | - Isaac Njaci
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, P.O. 30709, Nairobi 00100, Kenya; (I.N.); (S.R.G.)
| | - Thomas J. V. Higgins
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Agriculture and Food, Canberra 2601, Australia;
| | - Brett Williams
- Centre for Agriculture and the Bioeconomy (CAB), Queensland University of Technology (QUT), Brisbane 4001, Australia;
| | - Sita R. Ghimire
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, P.O. 30709, Nairobi 00100, Kenya; (I.N.); (S.R.G.)
| | - Sagadevan G. Mundree
- Centre for Agriculture and the Bioeconomy (CAB), Queensland University of Technology (QUT), Brisbane 4001, Australia;
- Correspondence: (A.N.-D.); (S.G.M.); (L.T.M.H.); Tel.: +61-731-388-386 (S.G.M.)
| | - Linh Thi My Hoang
- Centre for Agriculture and the Bioeconomy (CAB), Queensland University of Technology (QUT), Brisbane 4001, Australia;
- Correspondence: (A.N.-D.); (S.G.M.); (L.T.M.H.); Tel.: +61-731-388-386 (S.G.M.)
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