Molecular regulatory mechanisms play a crucial role in efficient and precise breeding of horticultural crops, including vegetables, fruits, and flowers. These mechanisms regulate key traits such as disease resistance, stress tolerance, plant growth and development, flowering time, fruit formation, yield, and quality through various transcription factors, non-coding RNAs, epigenetic modifications, and diverse signaling pathways. The identification of genomic loci (QTL) and the development of candidate gene linked DNA markers support genomic selection through marker-assisted selection (MAS), accelerating breeding by linking DNA markers to specific phenotypes. Advances in genome editing tools, such as CRISPR/Cas, enable precise manipulation of genes responsible for desirable traits. Gene regulatory networks also assist breeders in predicting crop performance. Understanding complex molecular pathways allows the development of improved cultivars on diverse aspects.

In this research topic we aim to compile recent advancement of molecular breeding in horticultural crops and understand the gap for future breeding. Therefore, we highlight unmet needs to guide future breeding strategies, spanning QTL mapping, GWAS, transcriptomics (coding and non-coding RNAs), gene mining, gene editing, and epigenomics across vegetables, fruits, flowers, and other horticultural species.

In this Research Topic, we welcome original research, reviews, protocols, or perspectives published by Frontiers in Plant Science that dissect the use of advanced breeding technologies in horticultural crops especially those that focus on:

• Genomic loci identification (QTL-mapping, QTL-seq, MutMap, GWAS)

• Approaches for candidate gene identifications

• Functional validations of candidate genes (e.g., CRISPR-Cas9, RNAi)

• OMICS studies for breeding (genomics, transcriptomics, and epigenomics)

• Molecular regulatory mechanisms for breeding in horticultural crops

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From Molecular Regulation to Breeding Applications in Horticultural Crops