Genomics-Driven Optimization of Horticultural Crops: From Discovery to Potential Application

1. Introduction

Horticultural crops play a vital role in global food security, medicine, ornamental decoration, and environmental sustainability. As a primary source of essential nutrients, bioactive compounds, and ecosystem services, these crops significantly contribute to human well-being and ecological balance [1]. Given the increasing demands of a growing population and the challenges posed by climate change, horticultural scientists are tasked with enhancing the productivity, resilience, and nutritional quality of these crops through advanced breeding and biotechnological approaches.

Modern plant breeding requires a comprehensive understanding of plant genetics and physiology, supported by cutting-edge molecular techniques that generate high-throughput omics data (genomics, transcriptomics, proteomics, and metabolomics). Functional genomics has been instrumental in unraveling the regulatory networks that govern plant growth, development, and stress responses, particularly in model species [2]. These insights are now being translated to horticultural crops, enabling the precise manipulation of desirable traits.

The rapid advancement of omics technologies has revolutionized crop improvement by allowing researchers to identify the key genes, metabolic pathways, and molecular markers associated with agronomically important traits [3]. By integrating these tools with traditional breeding methods, horticultural scientists can accelerate the development of superior cultivars with enhanced adaptability and performance. This multidisciplinary approach holds great promise for addressing current and future challenges in horticulture, ensuring sustainable production systems in the face of environmental and socio-economic pressures.

2. Overview of Published Articles

The seven research articles published in this Special Issue highlight contributions from diverse fields, employing interdisciplinary approaches to advance plant breeding strategies.

Zhang et al. (2024) (Contribution 1) investigated pollen development in the medicinal and edible plant Lycium barbarum using transcriptomics and phylogenomics. Their findings provide valuable insights into sterility genes, which could be harnessed to improve crop yields through controlled pollen abortion.

Cheng et al. (2023) (Contribution 2) conducted genome-wide analyses and gene expression quantification to explore the plant-specific RAV (RELATED to ABI3/VP1) transcription factor family in Chrysanthemum seticuspe. They identified and characterized key RAV genes, offering a foundation for future research on chrysanthemum breeding. Another study in this Special Issue (Ma et al., 2023; Contribution 4) further underscores the horticultural significance of chrysanthemums by examining the morphological differences and potential molecular mechanisms underlying the ecological adaptation of two Chrysanthemum species to extreme environments.

A comparative genomic study by Gladysheva-Azgari et al. (2023) (Contribution 3) revealed significant structural rearrangements in the chloroplast genomes of kiwifruit (Actinidia spp.). Given the recent advances in chloroplast genetic engineering (plastid transformation) [4], understanding chloroplast genome diversification could open new avenues for breeding strategies.

Olive trees (Olea europaea L.) represent a vital food and economic resource with extensive morphological diversity. Sarwar et al. (2023) (Contribution 5) characterized key morphological traits across eight olive cultivars, linking them to genetic diversity and geographical origins.

Xiong et al. (2022) (Contribution 6) performed a genome-wide comparative analysis of Golden2-like (GLK) transcription factors in sweet orange (Citrus sinensis), which are critical for chloroplast development. Notably, specific GLK family members showed a strong positive correlation with the chlorophyll (and precursor) content, highlighting their potential for future crop improvement.

Finally, Rodriguez Melo et al. (2022) (Contribution 7) explored the LysM-RLK-mediated perception of rhizobial lipo-chitooligosaccharides (LCOs/Nod factors) in wild and domesticated peanut (Arachis hypogaea L.). Their phylogenomic and transcriptomic analyses provide novel insights into the molecular basis of legume–microbe interactions, with implications for enhancing this globally important oil and food crop.

3. Conclusions

The studies presented in this Special Issue underscore the transformative potential of integrating omics technologies with traditional breeding to advance horticultural crop improvement. These contributions highlight the power of interdisciplinary research in addressing pressing agricultural challenges. As climate change and population growth intensify, leveraging functional genomics, comparative transcriptomics, and phylogenomics will be crucial for developing resilient, high-yielding, and nutritionally enhanced cultivars. By bridging fundamental discoveries with applied breeding strategies, horticultural scientists can pave the way for sustainable production systems that ensure food security, economic stability, and ecological balance in the decades to come.