An Integrated Multi-Omics and Artificial Intelligence Framework for Advance Plant Phenotyping in Horticulture

Abstract

This review discusses the transformative potential of integrating multi-omics data and artificial intelligence (AI) in advancing horticultural research, specifically plant phenotyping. The traditional methods of plant phenotyping, while valuable, are limited in their ability to capture the complexity of plant biology. The advent of (meta-)genomics, (meta-)transcriptomics, proteomics, and metabolomics has provided an opportunity for a more comprehensive analysis. AI and machine learning (ML) techniques can effectively handle the complexity and volume of multi-omics data, providing meaningful interpretations and predictions. Reflecting the multidisciplinary nature of this area of research, in this review, readers will find a collection of state-of-the-art solutions that are key to the integration of multi-omics data and AI for phenotyping experiments in horticulture, including experimental design considerations with several technical and non-technical challenges, which are discussed along with potential solutions. The future prospects of this integration include precision horticulture, predictive breeding, improved disease and stress response management, sustainable crop management, and exploration of plant biodiversity. The integration of multi-omics and AI holds immense promise for revolutionizing horticultural research and applications, heralding a new era in plant phenotyping.

The role of priming and memory in rice environmental stress adaptation: Current knowledge and perspectives

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“…Recent advancements involve the incorporation of genomics, transcriptomics, proteomics, and metabolomics, leading to improved biotechnological production of valuable natural products ( Dai and Shen, 2022 ). Additionally, omics technologies are increasingly paired with machine learning and artificial intelligence to further enhance bioprospecting objectives ( Cembrowska-Lech et al, 2023 ).…”

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“…This integration yields more refined phenotype predictions by considering the intricate interactions between the genotype, envirotype, and genotype-environment (GxE) interactions, which are crucial for successful plant breeding [66]. Furthermore, AI's capacity to manage and interpret the inherent complexity of multi-omics data has been demonstrated, leading to significant advancements in plant phenotyping [67]. This integration promises to revolutionize the field by enabling more comprehensive analyses, improved prediction, and enhance the management of plant diseases and stress responses.…”