Accelerating Climate Resilience in Vegetables: The Synergistic Role of Genomics and Phenomics

Abstract

Vegetable crops are the backbone of global food and nutritional security, yet they remain among the most vulnerable agricultural commodities to climate change. Heat, drought, salinity, flooding and escalating biotic pressures now represent existential threats to vegetable productivity, quality and accessibility, particularly in developing nations. This review examines how the synergistic deployment of genomics and phenomics can accelerate the development of climate-resilient vegetable cultivars. The objective is to critically synthesize current advances in genomic tools—including next-generation sequencing (NGS), genome-wide association studies (GWAS), CRISPR/Cas9 genome editing and genomic selection—alongside high-throughput phenotyping (HTP) technologies such as multispectral imaging, thermal sensors and drone-based platforms, and to evaluate their integration as a strategic framework for vegetable breeding. Key findings demonstrate that the integration of genomics and phenomics enables high-resolution genotype-to-phenotype (G→P) mapping, significantly reduces breeding cycle duration and improves selection accuracy for complex, multigenic stress-adaptive traits across major vegetable crops including tomato, pepper, cucumber, lettuce, spinach and Brassica species. Specific discoveries include the identification of heat-tolerance QTL in tomato via GWAS-phenomics integration, CRISPR-mediated improvement of drought signaling in pepper and genomic selection models achieving prediction accuracies of 0.65 for heat stress indices in lettuce. The review also identifies critical limitations including high phenotyping costs, data integration challenges, lack of standardized protocols, regulatory hurdles for genome-edited cultivars and limited capacity in low-income countries. These findings have direct policy implications: so in order to unlock the transformative potential of genomics-phenomics integration, smallholder farmers in climate-vulnerable regions will not have access to improved cultivars. Instead, national agricultural research programs and international funding bodies should prioritize investment in affordable phenotyping infrastructure, open-access pan-genome databases, harmonized data ontologies, and regulatory frameworks that facilitate the deployment of genome-edited vegetables.

Plant phenotyping relevance

植物フェノタイピング技術（マルチスペクトル画像、熱センサー、ドローンプラットフォーム等）をゲノミクスとの統合という観点から批判的にレビューしており、方法論が中心的である。

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