1
|
Aviles Toledo C, Crawford MM, Tuinstra MR. Integrating multi-modal remote sensing, deep learning, and attention mechanisms for yield prediction in plant breeding experiments. FRONTIERS IN PLANT SCIENCE 2024; 15:1408047. [PMID: 39119495 PMCID: PMC11306015 DOI: 10.3389/fpls.2024.1408047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 07/04/2024] [Indexed: 08/10/2024]
Abstract
In both plant breeding and crop management, interpretability plays a crucial role in instilling trust in AI-driven approaches and enabling the provision of actionable insights. The primary objective of this research is to explore and evaluate the potential contributions of deep learning network architectures that employ stacked LSTM for end-of-season maize grain yield prediction. A secondary aim is to expand the capabilities of these networks by adapting them to better accommodate and leverage the multi-modality properties of remote sensing data. In this study, a multi-modal deep learning architecture that assimilates inputs from heterogeneous data streams, including high-resolution hyperspectral imagery, LiDAR point clouds, and environmental data, is proposed to forecast maize crop yields. The architecture includes attention mechanisms that assign varying levels of importance to different modalities and temporal features that, reflect the dynamics of plant growth and environmental interactions. The interpretability of the attention weights is investigated in multi-modal networks that seek to both improve predictions and attribute crop yield outcomes to genetic and environmental variables. This approach also contributes to increased interpretability of the model's predictions. The temporal attention weight distributions highlighted relevant factors and critical growth stages that contribute to the predictions. The results of this study affirm that the attention weights are consistent with recognized biological growth stages, thereby substantiating the network's capability to learn biologically interpretable features. Accuracies of the model's predictions of yield ranged from 0.82-0.93 R2 ref in this genetics-focused study, further highlighting the potential of attention-based models. Further, this research facilitates understanding of how multi-modality remote sensing aligns with the physiological stages of maize. The proposed architecture shows promise in improving predictions and offering interpretable insights into the factors affecting maize crop yields, while demonstrating the impact of data collection by different modalities through the growing season. By identifying relevant factors and critical growth stages, the model's attention weights provide valuable information that can be used in both plant breeding and crop management. The consistency of attention weights with biological growth stages reinforces the potential of deep learning networks in agricultural applications, particularly in leveraging remote sensing data for yield prediction. To the best of our knowledge, this is the first study that investigates the use of hyperspectral and LiDAR UAV time series data for explaining/interpreting plant growth stages within deep learning networks and forecasting plot-level maize grain yield using late fusion modalities with attention mechanisms.
Collapse
Affiliation(s)
- Claudia Aviles Toledo
- Lyles School of Civil Engineering, Purdue University, West Lafayette, IN, United States
| | - Melba M. Crawford
- Lyles School of Civil Engineering, Purdue University, West Lafayette, IN, United States
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | | |
Collapse
|
2
|
Dwivedi SL, Heslop-Harrison P, Amas J, Ortiz R, Edwards D. Epistasis and pleiotropy-induced variation for plant breeding. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38875130 DOI: 10.1111/pbi.14405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 05/07/2024] [Accepted: 05/24/2024] [Indexed: 06/16/2024]
Abstract
Epistasis refers to nonallelic interaction between genes that cause bias in estimates of genetic parameters for a phenotype with interactions of two or more genes affecting the same trait. Partitioning of epistatic effects allows true estimation of the genetic parameters affecting phenotypes. Multigenic variation plays a central role in the evolution of complex characteristics, among which pleiotropy, where a single gene affects several phenotypic characters, has a large influence. While pleiotropic interactions provide functional specificity, they increase the challenge of gene discovery and functional analysis. Overcoming pleiotropy-based phenotypic trade-offs offers potential for assisting breeding for complex traits. Modelling higher order nonallelic epistatic interaction, pleiotropy and non-pleiotropy-induced variation, and genotype × environment interaction in genomic selection may provide new paths to increase the productivity and stress tolerance for next generation of crop cultivars. Advances in statistical models, software and algorithm developments, and genomic research have facilitated dissecting the nature and extent of pleiotropy and epistasis. We overview emerging approaches to exploit positive (and avoid negative) epistatic and pleiotropic interactions in a plant breeding context, including developing avenues of artificial intelligence, novel exploitation of large-scale genomics and phenomics data, and involvement of genes with minor effects to analyse epistatic interactions and pleiotropic quantitative trait loci, including missing heritability.
Collapse
Affiliation(s)
| | - Pat Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, UK
| | - Junrey Amas
- Centre for Applied Bioinformatics, School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - David Edwards
- Centre for Applied Bioinformatics, School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| |
Collapse
|
3
|
Montesinos-López A, Crespo-Herrera L, Dreisigacker S, Gerard G, Vitale P, Saint Pierre C, Govindan V, Tarekegn ZT, Flores MC, Pérez-Rodríguez P, Ramos-Pulido S, Lillemo M, Li H, Montesinos-López OA, Crossa J. Deep learning methods improve genomic prediction of wheat breeding. FRONTIERS IN PLANT SCIENCE 2024; 15:1324090. [PMID: 38504889 PMCID: PMC10949530 DOI: 10.3389/fpls.2024.1324090] [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: 10/18/2023] [Accepted: 02/19/2024] [Indexed: 03/21/2024]
Abstract
In the field of plant breeding, various machine learning models have been developed and studied to evaluate the genomic prediction (GP) accuracy of unseen phenotypes. Deep learning has shown promise. However, most studies on deep learning in plant breeding have been limited to small datasets, and only a few have explored its application in moderate-sized datasets. In this study, we aimed to address this limitation by utilizing a moderately large dataset. We examined the performance of a deep learning (DL) model and compared it with the widely used and powerful best linear unbiased prediction (GBLUP) model. The goal was to assess the GP accuracy in the context of a five-fold cross-validation strategy and when predicting complete environments using the DL model. The results revealed the DL model outperformed the GBLUP model in terms of GP accuracy for two out of the five included traits in the five-fold cross-validation strategy, with similar results in the other traits. This indicates the superiority of the DL model in predicting these specific traits. Furthermore, when predicting complete environments using the leave-one-environment-out (LOEO) approach, the DL model demonstrated competitive performance. It is worth noting that the DL model employed in this study extends a previously proposed multi-modal DL model, which had been primarily applied to image data but with small datasets. By utilizing a moderately large dataset, we were able to evaluate the performance and potential of the DL model in a context with more information and challenging scenario in plant breeding.
Collapse
Affiliation(s)
- Abelardo Montesinos-López
- Departamento de Matemáticas, Centro Universitario de Ciencias Exactas e Ingenierías (CUCEI), Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Leonardo Crespo-Herrera
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Estado. de México, Mexico
| | - Susanna Dreisigacker
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Estado. de México, Mexico
| | - Guillermo Gerard
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Estado. de México, Mexico
| | - Paolo Vitale
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Estado. de México, Mexico
| | - Carolina Saint Pierre
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Estado. de México, Mexico
| | - Velu Govindan
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Estado. de México, Mexico
| | | | - Moisés Chavira Flores
- Instituto de Investigaciones en Matemáticas Aplicadas y Sistemas (IIMAS), Universidad Nacional Autónoma de México (UNAM), Ciudad Universitaria, Ciudad de México, Mexico
| | - Paulino Pérez-Rodríguez
- Estudios del Desarrollo Rural, Economía, Estadística y Cómputo Aplicado, Colegio de Postgraduados, Texcoco, Estado de México, Mexico
| | - Sofía Ramos-Pulido
- Departamento de Matemáticas, Centro Universitario de Ciencias Exactas e Ingenierías (CUCEI), Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Morten Lillemo
- Department of Plant Science, Norwegian University of Life Science (NMBU), Ås, Norway
| | - Huihui Li
- 6State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences and CIMMYT China Office, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | | | - Jose Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Estado. de México, Mexico
- Estudios del Desarrollo Rural, Economía, Estadística y Cómputo Aplicado, Colegio de Postgraduados, Texcoco, Estado de México, Mexico
| |
Collapse
|
4
|
Hu H, Scheben A, Wang J, Li F, Li C, Edwards D, Zhao J. Unravelling inversions: Technological advances, challenges, and potential impact on crop breeding. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:544-554. [PMID: 37961986 PMCID: PMC10893937 DOI: 10.1111/pbi.14224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/11/2023] [Accepted: 10/22/2023] [Indexed: 11/15/2023]
Abstract
Inversions, a type of chromosomal structural variation, significantly influence plant adaptation and gene functions by impacting gene expression and recombination rates. However, compared with other structural variations, their roles in functional biology and crop improvement remain largely unexplored. In this review, we highlight technological and methodological advancements that have allowed a comprehensive understanding of inversion variants through the pangenome framework and machine learning algorithms. Genome editing is an efficient method for inducing or reversing inversion mutations in plants, providing an effective mechanism to modify local recombination rates. Given the potential of inversions in crop breeding, we anticipate increasing attention on inversions from the scientific community in future research and breeding applications.
Collapse
Affiliation(s)
- Haifei Hu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering LaboratoryGuangzhouChina
| | - Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor LaboratoryCold Spring HarborNew YorkUSA
| | - Jian Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering LaboratoryGuangzhouChina
| | - Fangping Li
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
| | - Chengdao Li
- Western Crop Genetics Alliance, Centre for Crop & Food Innovation, Food Futures Institute, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - David Edwards
- School of Biological SciencesUniversity of Western AustraliaPerthWestern AustraliaAustralia
- Australia & Centre for Applied BioinformaticsUniversity of Western AustraliaPerthWestern AustraliaAustralia
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering LaboratoryGuangzhouChina
| |
Collapse
|
5
|
Song B, Ning W, Wei D, Jiang M, Zhu K, Wang X, Edwards D, Odeny DA, Cheng S. Plant genome resequencing and population genomics: Current status and future prospects. MOLECULAR PLANT 2023; 16:1252-1268. [PMID: 37501370 DOI: 10.1016/j.molp.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 05/30/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
Abstract
Advances in DNA sequencing technology have sparked a genomics revolution, driving breakthroughs in plant genetics and crop breeding. Recently, the focus has shifted from cataloging genetic diversity in plants to exploring their functional significance and delivering beneficial alleles for crop improvement. This transformation has been facilitated by the increasing adoption of whole-genome resequencing. In this review, we summarize the current progress of population-based genome resequencing studies and how these studies affect crop breeding. A total of 187 land plants from 163 countries have been resequenced, comprising 54 413 accessions. As part of resequencing efforts 367 traits have been surveyed and 86 genome-wide association studies have been conducted. Economically important crops, particularly cereals, vegetables, and legumes, have dominated the resequencing efforts, leaving a gap in 49 orders, including Lycopodiales, Liliales, Acorales, Austrobaileyales, and Commelinales. The resequenced germplasm is distributed across diverse geographic locations, providing a global perspective on plant genomics. We highlight genes that have been selected during domestication, or associated with agronomic traits, and form a repository of candidate genes for future research and application. Despite the opportunities for cross-species comparative genomics, many population genomic datasets are not accessible, impeding secondary analyses. We call for a more open and collaborative approach to population genomics that promotes data sharing and encourages contribution-based credit policy. The number of plant genome resequencing studies will continue to rise with the decreasing DNA sequencing costs, coupled with advances in analysis and computational technologies. This expansion, in terms of both scale and quality, holds promise for deeper insights into plant trait genetics and breeding design.
Collapse
Affiliation(s)
- Bo Song
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Weidong Ning
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Huazhong Agricultural University, College of Informatics, Hubei Key Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, China
| | - Di Wei
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 53007, China
| | - Mengyun Jiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Kun Zhu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Xingwei Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, Nairobi, Kenya
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
| |
Collapse
|
6
|
Montesinos-López A, Rivera C, Pinto F, Piñera F, Gonzalez D, Reynolds M, Pérez-Rodríguez P, Li H, Montesinos-López OA, Crossa J. Multimodal deep learning methods enhance genomic prediction of wheat breeding. G3 (BETHESDA, MD.) 2023; 13:jkad045. [PMID: 36869747 PMCID: PMC10151399 DOI: 10.1093/g3journal/jkad045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/05/2023]
Abstract
While several statistical machine learning methods have been developed and studied for assessing the genomic prediction (GP) accuracy of unobserved phenotypes in plant breeding research, few methods have linked genomics and phenomics (imaging). Deep learning (DL) neural networks have been developed to increase the GP accuracy of unobserved phenotypes while simultaneously accounting for the complexity of genotype-environment interaction (GE); however, unlike conventional GP models, DL has not been investigated for when genomics is linked with phenomics. In this study we used 2 wheat data sets (DS1 and DS2) to compare a novel DL method with conventional GP models. Models fitted for DS1 were GBLUP, gradient boosting machine (GBM), support vector regression (SVR) and the DL method. Results indicated that for 1 year, DL provided better GP accuracy than results obtained by the other models. However, GP accuracy obtained for other years indicated that the GBLUP model was slightly superior to the DL. DS2 is comprised only of genomic data from wheat lines tested for 3 years, 2 environments (drought and irrigated) and 2-4 traits. DS2 results showed that when predicting the irrigated environment with the drought environment, DL had higher accuracy than the GBLUP model in all analyzed traits and years. When predicting drought environment with information on the irrigated environment, the DL model and GBLUP model had similar accuracy. The DL method used in this study is novel and presents a strong degree of generalization as several modules can potentially be incorporated and concatenated to produce an output for a multi-input data structure.
Collapse
Affiliation(s)
- Abelardo Montesinos-López
- Departamento de Matemáticas, Centro Universitario de Ciencias Exactas e Ingenierías (CUCEI), Universidad de Guadalajara, 44430, Guadalajara, Jalisco, Mexico
| | - Carolina Rivera
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México- Veracruz Km. 45, El Batán, CP 56237, Texcoco, Edo. de México, Mexico
| | - Francisco Pinto
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México- Veracruz Km. 45, El Batán, CP 56237, Texcoco, Edo. de México, Mexico
| | - Francisco Piñera
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México- Veracruz Km. 45, El Batán, CP 56237, Texcoco, Edo. de México, Mexico
| | - David Gonzalez
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México- Veracruz Km. 45, El Batán, CP 56237, Texcoco, Edo. de México, Mexico
| | - Mathew Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México- Veracruz Km. 45, El Batán, CP 56237, Texcoco, Edo. de México, Mexico
| | | | - Huihui Li
- Institute of Crop Sciences, The National Key Facility for Crop Gene Resources and Genetic Improvement and CIMMYT China office, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | | | - Jose Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México- Veracruz Km. 45, El Batán, CP 56237, Texcoco, Edo. de México, Mexico
- Colegio de Postgraduados, Montecillos, Edo. de México, CP 56230, Mexico
| |
Collapse
|
7
|
Neik TX, Siddique KHM, Mayes S, Edwards D, Batley J, Mabhaudhi T, Song BK, Massawe F. Diversifying agrifood systems to ensure global food security following the Russia–Ukraine crisis. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2023. [DOI: 10.3389/fsufs.2023.1124640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023] Open
Abstract
The recent Russia–Ukraine conflict has raised significant concerns about global food security, leaving many countries with restricted access to imported staple food crops, particularly wheat and sunflower oil, sending food prices soaring with other adverse consequences in the food supply chain. This detrimental effect is particularly prominent for low-income countries relying on grain imports, with record-high food prices and inflation affecting their livelihoods. This review discusses the role of Russia and Ukraine in the global food system and the impact of the Russia–Ukraine conflict on food security. It also highlights how diversifying four areas of agrifood systems—markets, production, crops, and technology can contribute to achieving food supply chain resilience for future food security and sustainability.
Collapse
|
8
|
Monitoring of Paddy and Maize Fields Using Sentinel-1 SAR Data and NGB Images: A Case Study in Papua, Indonesia. Processes (Basel) 2023. [DOI: 10.3390/pr11030647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
This study addresses the question of how to evaluate the growth stage of food crops, for instance, paddy (Oryza sativa) and maize (Zea mays), from two different sensors in selected developed areas of Papua Province of Indonesia. Level-1 Ground Range Detected (L1 GRD) images from Sentinel-1 Synthetic Aperture Radar (SAR) data were used to investigate the growth of paddy and maize crops. An NGB camera was then used to obtain the Green Normalized Difference Vegetation Index (GNDVI), and the Enhanced Normalized Difference Vegetation Index (ENDVI) as in situ measurement. Afterwards, the results were analyzed based on the Radar Vegetation Index (RVI) and the Vertical-Vertical (VV) and Vertical Horizontal (VH) band backscatters at incidence angles of 30.55°–45.88°, and 30.59°–46.16° in 2021 and 2022, respectively. The findings showed that Sigma0_VV_db and sigma0_VH_db had a strong correlation (R2 above 0.900); however, polarization modification is required, specifically in the maize field. The RVI calculated and backscatter changes in this study were comparable to the in situ measurements, specifically those of paddy fields, in 2022. Even though the results of this study were not able to prove the RVI values from the two relative orbits (orbit31 and orbit155) due to the different angle incidences and the availability of the Sentinel-1 SAR data set over the study area, the division of SAR image data based on each relative orbit adequately represents the development of crops in our study areas. The significance of this study is expected to support food crop security and the implementation of development plans that contribute to the local government’s goals and settings.
Collapse
|
9
|
Abstract
Over the past decade, advances in plant genotyping have been critical in enabling the identification of genetic diversity, in understanding evolution, and in dissecting important traits in both crops and native plants. The widespread popularity of single-nucleotide polymorphisms (SNPs) has prompted significant improvements to SNP-based genotyping, including SNP arrays, genotyping by sequencing, and whole-genome resequencing. More recent approaches, including genotyping structural variants, utilizing pangenomes to capture species-wide genetic diversity and exploiting machine learning to analyze genotypic data sets, are pushing the boundaries of what plant genotyping can offer. In this chapter, we highlight these innovations and discuss how they will accelerate and advance future genotyping efforts.
Collapse
|
10
|
Ren Y, Li Q, Du X, Zhang Y, Wang H, Shi G, Wei M. Analysis of Corn Yield Prediction Potential at Various Growth Phases Using a Process-Based Model and Deep Learning. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12030446. [PMID: 36771530 PMCID: PMC9920366 DOI: 10.3390/plants12030446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/05/2023] [Accepted: 01/16/2023] [Indexed: 05/26/2023]
Abstract
Early and accurate prediction of grain yield is of great significance for ensuring food security and formulating food policy. The exploration of key growth phases and features is beneficial to improving the efficiency and accuracy of yield prediction. In this study, a hybrid approach using the WOFOST model and deep learning was developed to forecast corn yield, which analysed yield prediction potential at different growth phases and features. The World Food Studies (WOFOST) model was used to build a comprehensive simulated dataset by inputting meteorological, soil, crop and management data. Different feature combinations at various growth phases were designed to forecast yield using machine learning and deep learning methods. The results show that the key features of corn's vegetative growth stage and reproductive growth stage were growth state features and water-related features, respectively. With the continuous advancement of the crop growth stage, the ability to predict yield continued to improve. Especially after entering the reproductive growth stage, corn kernels begin to form, and the yield prediction performance is significantly improved. The performance of the optimal yield prediction model in flowering (R2 = 0.53, RMSE = 554.84 kg/ha, MRE = 8.27%), in milk maturity (R2 = 0.89, RMSE = 268.76 kg/ha, MRE = 4.01%), and in maturity (R2 = 0.98, RMSE = 102.65 kg/ha, MRE = 1.53%) were given. Thus, our method improves the accuracy of yield prediction, and provides reliable analysis results for predicting yield at various growth phases, which is helpful for farmers and governments in agricultural decision making. This can also be applied to yield prediction for other crops, which is of great value to guide agricultural production.
Collapse
Affiliation(s)
- Yiting Ren
- Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100094, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Qiangzi Li
- Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100094, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Xin Du
- Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100094, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Yuan Zhang
- Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100094, China
| | - Hongyan Wang
- Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100094, China
| | - Guanwei Shi
- Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100094, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Mengfan Wei
- Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100094, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| |
Collapse
|
11
|
Chatterjee S, Adak A, Wilde S, Nakasagga S, Murray SC. Cumulative temporal vegetation indices from unoccupied aerial systems allow maize (Zea mays L.) hybrid yield to be estimated across environments with fewer flights. PLoS One 2023; 18:e0277804. [PMID: 36701283 PMCID: PMC9879521 DOI: 10.1371/journal.pone.0277804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 11/03/2022] [Indexed: 01/27/2023] Open
Abstract
Unoccupied aerial systems (UAS) based high throughput phenotyping studies require further investigation to combine different environments and planting times into one model. Here 100 elite breeding hybrids of maize (Zea mays L.) were evaluated in two environment trials-one with optimal planting and irrigation (IHOT), and one dryland with delayed planting (DHOT). RGB (Red-Green-Blue) based canopy height measurement (CHM) and vegetation indices (VIs) were estimated from a UAS platform. Time series and cumulative VIs, by both summation (ΣVI-SUMs) and area under the curve (ΣVI-AUCs), were fit via machine learning regression modeling (random forest, linear, ridge, lasso, elastic net regressions) to estimate grain yield. VIs were more valuable predictors of yield to combine different environments than CHM. Time series VIs and CHM produced high accuracies (~68-72%), but inconsistent models. A little sacrifice in accuracy (~60-65%) produced consistent models using ΣVI-SUMs and CHM during pre-reproductive vegetative growth. Absence of VIs produced poorer accuracies (by about ~5-10%). Normalized difference type VIs produced maximum accuracies, and flowering times were the best times for UAS data acquisition. This study suggests that the best yielding varieties can be accurately predicted in new environments at or before flowering when combining multiple temporal flights and predictors.
Collapse
Affiliation(s)
- Sumantra Chatterjee
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States of America
| | - Alper Adak
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States of America
| | - Scott Wilde
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States of America
| | - Shakirah Nakasagga
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States of America
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Seth C. Murray
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States of America
- * E-mail:
| |
Collapse
|
12
|
Tirnaz S, Zandberg J, Thomas WJW, Marsh J, Edwards D, Batley J. Application of crop wild relatives in modern breeding: An overview of resources, experimental and computational methodologies. FRONTIERS IN PLANT SCIENCE 2022; 13:1008904. [PMID: 36466237 PMCID: PMC9712971 DOI: 10.3389/fpls.2022.1008904] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/25/2022] [Indexed: 06/01/2023]
Abstract
Global agricultural industries are under pressure to meet the future food demand; however, the existing crop genetic diversity might not be sufficient to meet this expectation. Advances in genome sequencing technologies and availability of reference genomes for over 300 plant species reveals the hidden genetic diversity in crop wild relatives (CWRs), which could have significant impacts in crop improvement. There are many ex-situ and in-situ resources around the world holding rare and valuable wild species, of which many carry agronomically important traits and it is crucial for users to be aware of their availability. Here we aim to explore the available ex-/in- situ resources such as genebanks, botanical gardens, national parks, conservation hotspots and inventories holding CWR accessions. In addition we highlight the advances in availability and use of CWR genomic resources, such as their contribution in pangenome construction and introducing novel genes into crops. We also discuss the potential and challenges of modern breeding experimental approaches (e.g. de novo domestication, genome editing and speed breeding) used in CWRs and the use of computational (e.g. machine learning) approaches that could speed up utilization of CWR species in breeding programs towards crop adaptability and yield improvement.
Collapse
|
13
|
Zandberg JD, Fernandez CT, Danilevicz MF, Thomas WJW, Edwards D, Batley J. The Global Assessment of Oilseed Brassica Crop Species Yield, Yield Stability and the Underlying Genetics. PLANTS (BASEL, SWITZERLAND) 2022; 11:2740. [PMID: 36297764 PMCID: PMC9610009 DOI: 10.3390/plants11202740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/08/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
The global demand for oilseeds is increasing along with the human population. The family of Brassicaceae crops are no exception, typically harvested as a valuable source of oil, rich in beneficial molecules important for human health. The global capacity for improving Brassica yield has steadily risen over the last 50 years, with the major crop Brassica napus (rapeseed, canola) production increasing to ~72 Gt in 2020. In contrast, the production of Brassica mustard crops has fluctuated, rarely improving in farming efficiency. The drastic increase in global yield of B. napus is largely due to the demand for a stable source of cooking oil. Furthermore, with the adoption of highly efficient farming techniques, yield enhancement programs, breeding programs, the integration of high-throughput phenotyping technology and establishing the underlying genetics, B. napus yields have increased by >450 fold since 1978. Yield stability has been improved with new management strategies targeting diseases and pests, as well as by understanding the complex interaction of environment, phenotype and genotype. This review assesses the global yield and yield stability of agriculturally important oilseed Brassica species and discusses how contemporary farming and genetic techniques have driven improvements.
Collapse
Affiliation(s)
- Jaco D. Zandberg
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | | | - Monica F. Danilevicz
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - William J. W. Thomas
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - David Edwards
- Center for Applied Bioinformatics, School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia
| |
Collapse
|
14
|
Estimation of Maize Yield and Flowering Time Using Multi-Temporal UAV-Based Hyperspectral Data. REMOTE SENSING 2022. [DOI: 10.3390/rs14133052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Maize (Zea mays L.) is one of the most consumed grains in the world. Within the context of continuous climate change and the reduced availability of arable land, it is urgent to breed new maize varieties and screen for the desired traits, e.g., high yield and strong stress tolerance. Traditional phenotyping methods relying on manual assessment are time-consuming and prone to human errors. Recently, the application of uncrewed aerial vehicles (UAVs) has gained increasing attention in plant phenotyping due to their efficiency in data collection. Moreover, hyperspectral sensors integrated with UAVs can offer data streams with high spectral and spatial resolutions, which are valuable for estimating plant traits. In this study, we collected UAV hyperspectral imagery over a maize breeding field biweekly across the growing season, resulting in 11 data collections in total. Multiple machine learning models were developed to estimate the grain yield and flowering time of the maize breeding lines using the hyperspectral imagery. The performance of the machine learning models and the efficacy of different hyperspectral features were evaluated. The results showed that the models with the multi-temporal imagery outperformed those with imagery from single data collections, and the ridge regression using the full band reflectance achieved the best estimation accuracies, with the correlation coefficients (r) between the estimates and ground truth of 0.54 for grain yield, 0.91 for days to silking, and 0.92 for days to anthesis. In addition, we assessed the estimation performance with data acquired at different growth stages to identify the good periods for the UAV survey. The best estimation results were achieved using the data collected around the tasseling stage (VT) for the grain yield estimation and around the reproductive stages (R1 or R4) for the flowering time estimation. Our results showed that the robust phenotyping framework proposed in this study has great potential to help breeders efficiently estimate key agronomic traits at early growth stages.
Collapse
|
15
|
Mohd Saad NS, Neik TX, Thomas WJW, Amas JC, Cantila AY, Craig RJ, Edwards D, Batley J. Advancing designer crops for climate resilience through an integrated genomics approach. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102220. [PMID: 35489163 DOI: 10.1016/j.pbi.2022.102220] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 03/15/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Climate change and exponential population growth are exposing an immediate need for developing future crops that are highly resilient and adaptable to changing environments to maintain global food security in the next decade. Rigorous selection from long domestication history has rendered cultivated crops genetically disadvantaged, raising concerns in their ability to adapt to these new challenges and limiting their usefulness in breeding programmes. As a result, future crop improvement efforts must rely on integrating various genomic strategies ranging from high-throughput sequencing to machine learning, in order to exploit germplasm diversity and overcome bottlenecks created by domestication, expansive multi-dimensional phenotypes, arduous breeding processes, complex traits and big data.
Collapse
Affiliation(s)
- Nur Shuhadah Mohd Saad
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Ting Xiang Neik
- Sunway College Kuala Lumpur, Bandar Sunway, 47500, Selangor, Malaysia
| | - William J W Thomas
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Junrey C Amas
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Aldrin Y Cantila
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Ryan J Craig
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - David Edwards
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Jacqueline Batley
- UWA School of Biological Sciences and the UWA Institute of Agriculture, University of Western Australia, Crawley, WA, Australia.
| |
Collapse
|
16
|
DeSalvio AJ, Adak A, Murray SC, Wilde SC, Isakeit T. Phenomic data-facilitated rust and senescence prediction in maize using machine learning algorithms. Sci Rep 2022; 12:7571. [PMID: 35534655 PMCID: PMC9085875 DOI: 10.1038/s41598-022-11591-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/19/2022] [Indexed: 11/09/2022] Open
Abstract
Current methods in measuring maize (Zea mays L.) southern rust (Puccinia polyspora Underw.) and subsequent crop senescence require expert observation and are resource-intensive and prone to subjectivity. In this study, unoccupied aerial system (UAS) field-based high-throughput phenotyping (HTP) was employed to collect high-resolution aerial imagery of elite maize hybrids planted in the 2020 and 2021 growing seasons, with 13 UAS flights obtained from 2020 and 17 from 2021. In total, 36 vegetation indices (VIs) were extracted from mosaicked aerial images that served as temporal phenomic predictors for southern rust scored in the field and senescence as scored using UAS-acquired mosaic images. Temporal best linear unbiased predictors (TBLUPs) were calculated using a nested model that treated hybrid performance as nested within flights in terms of rust and senescence. All eight machine learning regressions tested (ridge, lasso, elastic net, random forest, support vector machine with radial and linear kernels, partial least squares, and k-nearest neighbors) outperformed a general linear model with both higher prediction accuracies (92-98%) and lower root mean squared error (RMSE) for rust and senescence scores (linear model RMSE ranged from 65.8 to 2396.5 across all traits, machine learning regressions RMSE ranged from 0.3 to 17.0). UAS-acquired VIs enabled the discovery of novel early quantitative phenotypic indicators of maize senescence and southern rust before being detectable by expert annotation and revealed positive correlations between grain filling time and yield (0.22 and 0.44 in 2020 and 2021), with practical implications for precision agricultural practices.
Collapse
Affiliation(s)
- Aaron J DeSalvio
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
| | - Alper Adak
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843-2474, USA
| | - Seth C Murray
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843-2474, USA.
| | - Scott C Wilde
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843-2474, USA
| | - Thomas Isakeit
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843-2474, USA
| |
Collapse
|
17
|
A Systematic Literature Review on Crop Yield Prediction with Deep Learning and Remote Sensing. REMOTE SENSING 2022. [DOI: 10.3390/rs14091990] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Deep learning has emerged as a potential tool for crop yield prediction, allowing the model to automatically extract features and learn from the datasets. Meanwhile, smart farming technology enables the farmers to achieve maximum crop yield by extracting essential parameters of crop growth. This systematic literature review highlights the existing research gaps in a particular area of deep learning methodologies and guides us in analyzing the impact of vegetation indices and environmental factors on crop yield. To achieve the aims of this study, prior studies from 2012 to 2022 from various databases are collected and analyzed. The study focuses on the advantages of using deep learning in crop yield prediction, the suitable remote sensing technology based on the data acquisition requirements, and the various features that influence crop yield prediction. This study finds that Long Short-Term Memory (LSTM) and Convolutional Neural Networks (CNN) are the most widely used deep learning approaches for crop yield prediction. The commonly used remote sensing technology is satellite remote sensing technology—in particular, the use of the Moderate-Resolution Imaging Spectroradiometer (MODIS). Findings show that vegetation indices are the most used feature for crop yield prediction. However, it is also observed that the most used features in the literature do not always work for all the approaches. The main challenges of using deep learning approaches and remote sensing for crop yield prediction are how to improve the working model for better accuracy, the practical implication of the model for providing accurate information about crop yield to agriculturalists, growers, and policymakers, and the issue with the black box property.
Collapse
|
18
|
Al-Adhaileh MH, Aldhyani TH. Artificial intelligence framework for modeling and predicting crop yield to enhance food security in Saudi Arabia. PeerJ Comput Sci 2022; 8:e1104. [PMID: 36262130 PMCID: PMC9575863 DOI: 10.7717/peerj-cs.1104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/24/2022] [Indexed: 05/17/2023]
Abstract
Predicting crop yields is a critical issue in agricultural production optimization and intensification research. Accurate foresights of natural circumstances a year in advance can have a considerable impact on management decisions regarding crop selection, rotational location in crop rotations, agrotechnical methods employed, and long-term land use planning. One of the most important aspects of precision farming is sustainability. The novelty of this study is to evidence the effective of the temperature, pesticides, and rainfall environment parameters in the influence sustainable agriculture and economic efficiency at the farm level in Saudi Arabia. Furthermore, predicting the future values of main crop yield in Saudi Arabia. The use of artificial intelligence (AI) to estimate the impact of environment factors and agrotechnical parameters on agricultural crop yields and to anticipate yields is examined in this study. Using artificial neural networks (ANNs), a highly effective multilayer perceptron (MLP) model was built to accurately predict the crop yield, temperature, insecticides, and rainfall based on environmental data. The dataset is collected from different Saudi Arabia regions from 1994 to 2016, including the temperature, insecticides, rainfall, and crop yields for potatoes, rice, sorghum, and wheat. For this study, we relied on five different statistical evaluation metrics: the mean square error (MSE), the root-mean-square error (RMSE), normalized root mean square error (NRMSE), Pearson's correlation coefficient (R%), and the determination coefficient (R 2). Analyses of datasets for crop yields, temperature, and insecticides led to the development of the MLP models. The datasets are randomly divided into separate samples, 70% for training and 30% for testing. The best-performing MLP model is characterized by values of (R = 100%) and (R 2 = 96.33) for predicting insecticides in the testing process. The temperature, insecticides, and rainfall were examined with different crop yields to confirm the effectiveness of these parameters for increasing product crop yields in Saudi Arabia; we found that these items had highest relationships. The average values are R = 98.20%, 96.50, and 99.14% with for the temperature, insecticides, and rainfall, respectively. Based on these findings, it appeared that each of the parameter categories that are considered (temperature, pesticides, and rainfall) had a similar contribution to the accuracy of anticipated yield projection.
Collapse
Affiliation(s)
- Mosleh Hmoud Al-Adhaileh
- Al Bilad Bank Scholarly Chair for Food Security in Saudi Arabia, The Deanship of Scientific Research, The Vice Presidency for Graduate Studies and Scientific Research, King Faisal University, Al Ahsa, Saudi Arabia
- Deanship of E-learning and Distance Education, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Theyazn H.H. Aldhyani
- Al Bilad Bank Scholarly Chair for Food Security in Saudi Arabia, The Deanship of Scientific Research, The Vice Presidency for Graduate Studies and Scientific Research, King Faisal University, Al Ahsa, Saudi Arabia
- Applied college in Abqaiq, King Faisal University, Al-Ahsa, Saudi Arabia
| |
Collapse
|