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Horticulturae
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Precision Breeding in Vegetables: The Mining and Utilization of Key...
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Precision Breeding in Vegetables: The Mining and Utilization of Key Genes Regulating Important Agronomic Traits

A special issue of Horticulturae (ISSN 2311-7524). This special issue belongs to the section "Vegetable Production Systems".

Deadline for manuscript submissions: 25 January 2027 | Viewed by 3013

Special Issue Editors

Dr. Jia Shen

E-Mail Website
Guest Editor
Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
Interests: horticulture; vegetable; cucurbitaceae; vegetable breeding; molecular biology
Dr. Xiaoguang Sheng

E-Mail Website
Guest Editor
Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
Interests: horticulture; gene editing; vegetable breeding; molecular biology
Dr. Xinyi Wu

E-Mail Website
Guest Editor
Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
Interests: horticulture; gene mapping; leguminosae; vegetable breeding; molecular biology

Special Issue Information

Dear Colleagues,

Vegetables are indispensable components of global food systems, supplying essential nutrients and contributing significantly to human health and agricultural economies. However, traditional breeding approaches often struggle to efficiently improve complex agronomic traits, owing to the intricate genetic backgrounds and considerable heterogeneity in population structure characteristic of many vegetable species. Recent advances in genomics and biotechnology have catalyzed a shift toward precision breeding, allowing researchers to unravel the genetic architecture of key traits with unprecedented resolution.

This Special Issue, “Precision Breeding in Vegetables: The Mining and Utilization of Key Genes Regulating Important Agronomic Traits”, aims to present cutting-edge strategies and technological innovations that are transforming vegetable breeding. It encompasses topics ranging from the development of populations for high-resolution genetic mapping to the deployment of gene editing tools for precise trait enhancement. We also welcome studies that deepen our understanding of vegetable biology or provide genetic resources and molecular tools conducive to designing future crops with improved yield, quality, and resilience to changing environmental conditions.

Dr. Jia Shen
Dr. Xiaoguang Sheng
Dr. Xinyi Wu
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Horticulturae is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2200 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • gene mining
  • molecular markers
  • vegetable genetics
  • precision breeding

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Published Papers (3 papers)

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Research

20 pages, 6238 KB  
Article
Comparative Transcriptomics Reveals the Transcriptional Regulation of Anthocyanin Spatial Distribution in Brassica juncea (L.) Czern
by Dong Li, Qizan Hu, Xuena Yu, Longda Wang, Jiaxin Li, Bo Sun, Yanting Zhao and Meilan Li
Horticulturae 2026, 12(5), 537; https://doi.org/10.3390/horticulturae12050537 - 29 Apr 2026
Viewed by 769
Abstract
Brassica juncea exhibits diverse foliar pigmentation patterns caused by anthocyanin accumulation, but the molecular basis of margin-specific pigmentation remains unclear. Here, we combined anthocyanin measurement, comparative transcriptomics, and functional analysis of BjMYB113 to investigate anthocyanin spatial distribution in mustard. The data showed that [...] Read more.
Brassica juncea exhibits diverse foliar pigmentation patterns caused by anthocyanin accumulation, but the molecular basis of margin-specific pigmentation remains unclear. Here, we combined anthocyanin measurement, comparative transcriptomics, and functional analysis of BjMYB113 to investigate anthocyanin spatial distribution in mustard. The data showed that anthocyanin content was significantly higher in the leaf margin (LM) than in the leaf interior (LI) of the bicolored accession ZD30. Transcriptome analysis identified 618 DEGs between LM and LI in ZD30, compared with only 134 DEGs in the uniformly purple accession JCS53. Enrichment analyses indicated that ZD30-specific DEGs were mainly involved in flavonoid metabolism, anthocyanin biosynthesis, and secondary metabolism. Expression profiles of genes involved in anthocyanin biosynthesis indicated that BjMYB113 and BjTT8 were more highly expressed in the pigmented margin of ZD30, together with key late biosynthetic genes (DFR, ANS, and UFGT) and GSTF. In addition, transient overexpression of BjMYB113 promoted anthocyanin accumulation in leaves, suggesting that BjMYB113 acts as a positive regulator of anthocyanin accumulation and supporting a putative model in which localized activation of anthocyanin-related genes contributes to margin-specific pigmentation in B. juncea. This study provides insight into the transcriptional regulation of anthocyanin spatial distribution in mustard. Full article
(This article belongs to the Special Issue Precision Breeding in Vegetables: The Mining and Utilization of Key Genes Regulating Important Agronomic Traits)
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20 pages, 3547 KB  
Article
Integrated Metabolomic and Transcriptomic Analysis Uncovers the Roles of Fructose and Mannose Metabolism-Related Metabolites and Genes in Regulating Bitter Gourd Flesh Thickness and Exogenous Sugar Responses
by Boyin Qiu, Qianrong Zhang, Hui Lin, Jianting Liu, Zuliang Li, Changhui Bai, Qingfang Wen, Dazhong Li and Haisheng Zhu
Horticulturae 2026, 12(5), 518; https://doi.org/10.3390/horticulturae12050518 - 23 Apr 2026
Viewed by 1007
Abstract
Fruit flesh thickness is one of the key factors affecting the yield and quality of bitter melon, and its regulatory mechanisms remain unclear. One thick-flesh germplasm (KF) and one thin-flesh germplasm (NF) with significantly different flesh thicknesses were screened from 70 bitter melon [...] Read more.
Fruit flesh thickness is one of the key factors affecting the yield and quality of bitter melon, and its regulatory mechanisms remain unclear. One thick-flesh germplasm (KF) and one thin-flesh germplasm (NF) with significantly different flesh thicknesses were screened from 70 bitter melon germplasms. Through phenotypic surveys, combined metabolomic and transcriptomic analyses, and exogenous sugar treatments, the regulatory mechanisms on flesh thickness were preliminary investigated. The results showed that flesh thickness of the two germplasms remained stable during different years and seasons. Metabolomic and transcriptomic analyses revealed that fructose and mannose metabolism pathway significantly enriched in both omics datasets. The expression of key enzyme encoding genes from this pathway exhibited various expression patterns. In KF, most genes showed significantly higher expression levels than NF, with synergistic expression predominating among genes. Soluble sugar content was positively correlated with gene expression, while HXK, SDH, and TPI activities were negatively correlated with most genes, and FBP activity was positively correlated with most genes. Genes affect carbon source metabolic flux distribution by promoting sugar synthesis and inhibiting sugar respiration consumption. Exogenous sugar treatment exhibited germplasm-specific and concentration-dependent influence of gene expression, with KF primarily showing negative feedback and NF predominantly activating expression. Fruit flesh thickness was significantly positively correlated with the synergistic high expression of sugar metabolism genes and soluble sugar accumulation. This study provides a theoretical basis for molecular improvement of bitter melon fruit flesh thickness. Full article
(This article belongs to the Special Issue Precision Breeding in Vegetables: The Mining and Utilization of Key Genes Regulating Important Agronomic Traits)
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14 pages, 1227 KB  
Article
Cytokinin–Ethylene Crosstalk Mediates Bottle Gourd Rootstock-Induced Vigor in Grafted Melon
by Wen Han, Mei Ai, Sishi Song, Xinyang Xu, Yanjun He, Weisong Shou, Jia Shen and Zhe Wu
Horticulturae 2026, 12(1), 82; https://doi.org/10.3390/horticulturae12010082 - 10 Jan 2026
Viewed by 786
Abstract
Grafting is a pivotal horticultural technique for enhancing vegetable crop productivity; however, the specific molecular mechanisms governing rootstock-induced vigor remain insufficiently elucidated. This study deciphers how bottle gourd rootstock augments growth in melon scions through an integrated approach combining physiology, transcriptomics, phytohormone profiling, [...] Read more.
Grafting is a pivotal horticultural technique for enhancing vegetable crop productivity; however, the specific molecular mechanisms governing rootstock-induced vigor remain insufficiently elucidated. This study deciphers how bottle gourd rootstock augments growth in melon scions through an integrated approach combining physiology, transcriptomics, phytohormone profiling, and functional genetics. Phenotypic analysis confirmed a significant increase in plant height, fresh weight, and stem diameter in heterografted scions compared to controls. Transcriptome sequencing of scion apices identified 663 core differentially expressed genes (DEGs) specifically modulated by the bottle gourd rootstock. These DEGs were prominently enriched in carbohydrate metabolism and plant hormone signal transduction pathways. Consistent with this, hormonal assays revealed a specific elevation in cytokinin and ethylene levels in the scion, accompanied by the upregulation of key pathway genes, including MELO3C016881 (LOG) and MELO3C007769 (ERF060). Crucially, virus-induced gene silencing of either gene completely abolished the rootstock-conferred growth advantage. Our findings preliminarily unveil the secret behind scion vigor, providing a foundational mechanistic framework for how rootstocks reprogram scion development. The identified genes, MELO3C016881 and MELO3C007769, offer direct molecular targets for the precision breeding of superior scions in melon. Full article
(This article belongs to the Special Issue Precision Breeding in Vegetables: The Mining and Utilization of Key Genes Regulating Important Agronomic Traits)
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