Applications of artificial intelligence, machine learning, and deep learning in plant breeding

Book excerpt: Artificial Intelligence (AI) is an extensive concept that can be interpreted as a concentration on designing computer programs to train machines to accomplish functions like or better than hu-mans. An important subset of AI is Machine Learning (ML), in which a computer is provided with the capacity to learn its own patterns instead of the patterns and restrictions set by a human programmer, thus improving from experience. Deep Learning (DL), as a class of ML techniques, employs multilayered neural networks. The application of AI to plant science research is new and has grown significantly in recent years due to developments in calculation power, proficien-cies of hardware, and software progress. AI algorithms try to provide classifications and predic-tions. As applied to plant breeding, particularly omics data, ML as a given AI algorithm tries to translate omics data, which are intricate and include nonlinear interactions, into precise plant breeding. The applications of AI are extending rapidly and enhancing intensely in sophistication owing to the capability of rapid processing of huge and heterogeneous data. The conversion of AI techniques into accurate plant breeding is of great importance and will play a key role in the new era of plant breeding techniques in the coming years, particularly multi-omics data analysis. Advancements in plant breeding mainly depend upon developing statistical methods that harness the complicated data provided by analytical technologies identifying and quantifying genes, transcripts, proteins, metabolites, etc. The systems biology approach used in plant breeding, which integrates genomics, transcriptomics, proteomics, metabolomics, and other omics data, provides a massive amount of information. It is essential to perform accurate statistical analyses and AI methods such as ML and DL as well as optimization techniques to not only achieve an understanding of networks regulation and plant cell functions but develop high-precision models to predict the reaction of new Genetically Modified (GM) plants in special conditions. The constructed models will be of great economic importance, significantly reducing the time, labor, and instrument costs when finding optimized conditions for the bio-exploitation of plants. This Research Topic covers a wide range of studies on artificial intelligence-assisted plant breeding techniques, which contribute to plant biology and plant omics research. The relevant sub-topics include, but are not restricted to, the following: • AI-assisted plant breeding using omics and multi-omics approaches • Applying AI techniques along with multi-omics to recognize novel biomarkers associated with plant biological activities • Constructing up-to-date ML modeling and analyzing methods for dealing with omics data related to different plant growth processes • AI-assisted omics techniques in the plant defense process • Combining AI-assisted omics and multi-omics techniques using plant system biology approaches • Combining bioinformatics tools with AI approaches to analyze plant omics data • Designing cutting-edge workflow and developing innovative AI biology methods for omics data analysis