Horticultural Functional Genomics and Breeding

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: 20 September 2026 | Viewed by 232

Editor


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Guest Editor
Horticulture Department, Northwest A&F University, Yangling 712100, China
Interests: cucumber molecular genetics; genomics; cucumber breeding
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Horticultural crops, including vegetables, fruits, and ornamentals, play a crucial role in global food security and human nutrition. With the rapid development of genomics, multi-omics integration, and genome editing technologies, functional genomics has become a central driving force in accelerating trait dissection and precision breeding in horticulture.

This Special Issue aims to highlight recent advances in gene discovery, regulatory mechanisms, and molecular breeding strategies in horticultural species. Particular attention will be paid to forward and reverse genetics, GWAS- and BSA-based gene mapping, transcriptional and epigenetic regulation, hormone signaling pathways, genome editing technologies, and marker-assisted or genomic selection approaches.

Recent breakthroughs in high-throughput sequencing, phenotyping platforms, and CRISPR-based editing have greatly enhanced our capacity to bridge gene function with agronomic improvement. We welcome original research articles and reviews that integrate functional genomics with breeding applications, especially studies addressing yield, quality traits, stress tolerance, and developmental regulation in horticultural crops.

Dr. Hanqiang Liu
Guest Editor

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Keywords

  • functional genomics
  • multi-omics integration
  • epigenetic regulation
  • gene regulatory networks
  • forward genetics
  • GWAS
  • genome engineering
  • molecular breeding
  • precision breeding
  • trait dissection

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Published Papers (1 paper)

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Research

18 pages, 21057 KB  
Article
Developmental Transcriptome Profiling and WGCNA Identify Candidate Genes Associated with Sugar Accumulation and Fruit Enlargement in Lycium ruthenicum
by Yunzhang Xu, Xin Wu, Zhanwen Ma, Yu-E Ma, Zhenzhong Wu, Hengxia Yin, Shaoshan Zhang, Wenbing Li and Huachun Sheng
Genes 2026, 17(9), 986; https://doi.org/10.3390/genes17090986 (registering DOI) - 23 Aug 2026
Abstract
Background: Lycium ruthenicum, commonly known as Black goji berry, is a shrub species native to western China and is rich in bioactive compounds that contribute to its nutritional and health-promoting effects. However, the transcriptional dynamics associated with fruit development and quality [...] Read more.
Background: Lycium ruthenicum, commonly known as Black goji berry, is a shrub species native to western China and is rich in bioactive compounds that contribute to its nutritional and health-promoting effects. However, the transcriptional dynamics associated with fruit development and quality formation in black goji berry remain incompletely understood. This study aimed to investigate transcriptional dynamics during fruit development and identify candidate genes associated with sugar accumulation and fruit enlargement. Methods: Fruits were sampled at five developmental stages (S1–S5), and RNA-seq was performed to investigate the alterations in gene expression. Differential expression analysis, temporal expression-pattern analysis, functional enrichment analysis, and weighted gene co-expression network analysis (WGCNA) were performed, followed by the integration of differential expression, temporal expression patterns, co-expression relationships, and functional annotation. Results: Fruit diameter, fresh weight, and total soluble sugar content increased markedly during the later developmental stages. Differential expression analysis revealed extensive transcriptional changes across successive developmental transitions, while temporal expression-pattern analysis identified distinct increasing and decreasing gene clusters. Functional enrichment analysis showed that the DEGs were mainly associated with carbohydrate metabolism, sugar transport, hormone-related processes, photosynthesis, and cell-wall modification. WGCNA identified 13 co-expression modules, among which MEyellow and MEbrown showed strong but opposite associations with developmental stage, total soluble sugar content, fruit diameter, and fruit fresh weight. The integrated analysis highlighted several candidate genes associated with sugar metabolism and transport during late fruit development. Conclusions: These findings provide a transcriptomic perspective on the coordinated changes in sugar accumulation and fruit enlargement during L. ruthenicum fruit development. Full article
(This article belongs to the Special Issue Horticultural Functional Genomics and Breeding)
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