Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
5.5
2.8
Journals
Genes
Special Issues
Genetic and Breeding Improvement of Horticultural Crops
share announcement

Genetic and Breeding Improvement of Horticultural Crops

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

Deadline for manuscript submissions: 25 May 2026 | Viewed by 3520

Special Issue Editors

Prof. Dr. Zhiqiang Wu

E-Mail Website
Guest Editor
Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
Interests: horticultural species; floral genomes; functional traits; molecular breeding; phylogenetics; population genomics; organellar genome
Special Issues, Collections and Topics in MDPI journals
Dr. Xiaoni Zhang

E-Mail Website
Guest Editor
College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China
Interests: ornamental traits; molecular mechanisms; floral genomes; variation maps; key regulatory sites; genetic improvement

Special Issue Information

Dear Colleagues,

Horticultural crops represent an essential group of plant species that provide food, nutrition, and economic value worldwide. Despite their importance, significant variation exists in yield, quality, and stress resilience among different species and cultivars. These differences arise from diverse genetic backgrounds, environmental conditions, and cultivation practices. Such variability emphasizes the need to strengthen genomic research and breeding innovation to accelerate the improvement of horticultural crops.

This Special Issue, titled “Genetic and Breeding Improvement of Horticultural Crops,” aims to showcase cutting-edge studies, approaches, and technologies that deepen our understanding of horticultural crop genetics, their evolution, and functional biology. Topics of interest include, but are not limited to, the following: chloroplast, mitochondrial, and nuclear genome analyses; gene family evolution and functional diversification; gene function studies using multi-omics and genome editing; molecular mechanisms underlying development, metabolism, and stress adaptation; and advanced breeding strategies such as molecular breeding, marker-assisted selection, and genomic selection for the creation of high-yielding, high-quality, and stress-tolerant horticultural cultivars.

Prof. Dr. Zhiqiang Wu
Dr. Xiaoni Zhang
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

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. Genes 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 2600 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

  • chloroplast genome
  • mitochondrial genome
  • nuclear genome
  • gene family evolution
  • functional genomics
  • genome editing
  • molecular breeding
  • horticultural crops

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (5 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

Jump to: Review

14 pages, 4667 KB  
Article
QTL Mapping of SPAD Values Associated with Leaf Color in Bunching Onion
by Tetsuya Nakajima, Kouei Fujii, Kenji Watanabe, Yoichi Mizukami, Masaru Bamba, Shusei Sato and Masayoshi Shigyo
Genes 2026, 17(5), 534; https://doi.org/10.3390/genes17050534 - 30 Apr 2026
Viewed by 267
Abstract
Background/Objectives: The dark green leaf color trait in bunching onion (Allium fistulosum L.) is an important agronomic trait closely associated with market value; however, its genetic basis remains poorly understood. This study aimed to identify quantitative trait loci (QTLs) associated with [...] Read more.
Background/Objectives: The dark green leaf color trait in bunching onion (Allium fistulosum L.) is an important agronomic trait closely associated with market value; however, its genetic basis remains poorly understood. This study aimed to identify quantitative trait loci (QTLs) associated with leaf color using SPAD values as a phenotypic indicator. Methods: An F2 population derived from a cross between the dark green line YSG1go and the light green line Asagikei-KUJYO was used. A linkage map was constructed based on RNA-seq-derived SNP markers, and SPAD values were measured for QTL analysis. Results: The linkage map consisted of eight linkage groups with a total length of 2103.0 cM and 765 mapped markers. SPAD values showed significant differences between the parental lines, with high broad-sense heritability (H2 = 0.76), indicating a strong genetic contribution to this trait. Multiple significant QTLs were detected on chromosomes 4 and 5, each explaining 27.4–38.1% of the phenotypic variance. The direction of allelic effects differed among QTLs, suggesting that favorable alleles are distributed between the parental lines. In addition, genes related to chloroplast protein translation were identified within the QTL regions. Conclusions: SPAD values are a suitable indicator for genetic analysis of leaf color in bunching onion, and the QTLs identified in this study provide valuable information for molecular breeding aimed at improving dark green leaf color. Full article
(This article belongs to the Special Issue Genetic and Breeding Improvement of Horticultural Crops)
►▼ Show Figures

Graphical abstract

15 pages, 4641 KB  
Article
The Mitochondrial Genome of Curcuma longa: A Large and Structurally Complex Genome with Extensive Intracellular DNA Transfer
by Bing Xu, Minlong Jia, Jiali Kong, Liyun Nie, Jie Wang, Luke R. Tembrock, Zhiqiang Wu, Sen Li and Xuezhu Liao
Genes 2026, 17(2), 243; https://doi.org/10.3390/genes17020243 - 19 Feb 2026
Cited by 1 | Viewed by 612
Abstract
Background: Plant mitochondrial genomes exhibit extreme variation in size and structure while maintaining a conserved set of core protein-coding genes. This combination of structural diversity and functional conservation provides valuable insights into evolutionary processes such as genome expansion, rearrangement, and intracellular DNA [...] Read more.
Background: Plant mitochondrial genomes exhibit extreme variation in size and structure while maintaining a conserved set of core protein-coding genes. This combination of structural diversity and functional conservation provides valuable insights into evolutionary processes such as genome expansion, rearrangement, and intracellular DNA transfer. Curcuma longa, an economically and medicinally important species in the genus Curcuma (Zingiberaceae), has not yet been studied in terms of the organization and evolution of its mitochondrial genome. Methods: In this study, we assembled and annotated the mitochondrial and plastid genomes of C. longa using third-generation HiFi sequencing data, systematically analyzing their genomic structure, repetitive sequence content, and features of sequence transfer between nuclear and organellar genomes. Results: The mitochondrial genome of C. longa was assembled as a complex, network-like structure consisting of 12 contigs with a total length of approximately 7.7 Mb, making it one of the largest mitochondrial genomes reported in monocots to date. Comparative analysis revealed significant differences in repeat types, abundance, and length distribution between the two organellar genomes. Additionally, extensive intracellular DNA transfer events were identified among the nuclear, mitochondrial, and plastid genomes. Conclusions: Overall, this study provides the first comprehensive report on the giant mitochondrial genome of C. longa, detailing its structural organization, repeat content, and intergenomic transfers. These findings lay a foundation for understanding mitochondrial genome evolution in Curcuma and offer broader insights into the mechanisms driving extreme mitochondrial genome expansion in angiosperms and monocots specifically. Full article
(This article belongs to the Special Issue Genetic and Breeding Improvement of Horticultural Crops)
►▼ Show Figures

Figure 1

18 pages, 3248 KB  
Article
Variation in Fruit Quality and Aroma Biosynthesis of ‘Summer Black’ Grape in Southern China
by Rong Wang, Meng Yan, Wenting Chen, Shumin Lei, Jun Tan, Yanshuai Xu and Guoshun Yang
Genes 2026, 17(2), 172; https://doi.org/10.3390/genes17020172 - 31 Jan 2026
Viewed by 599
Abstract
Objectives: The aroma profile is a key determinant of fruit quality. Methods: In this study, mature ‘Summer Black’ grape berries were collected from 36 major producing areas in southern China to evaluate regional differences in fruit quality, volatile compounds were analyzed by via [...] Read more.
Objectives: The aroma profile is a key determinant of fruit quality. Methods: In this study, mature ‘Summer Black’ grape berries were collected from 36 major producing areas in southern China to evaluate regional differences in fruit quality, volatile compounds were analyzed by via GC-MS, and a representative volatile profile was established. Furthermore, transcriptome sequencing was employed to identify key genes involved in the phenylpropanoid biosynthesis pathway related to aroma formation. Results: The results showed the following: (1) Samples from CD-2 exhibited the highest soluble solid content and the largest TSS/TA ratio. (2) A total of 20 volatile compounds were selected as indicators for the aroma fingerprint. MS-1 samples contained the most diverse aroma compounds (19 types), while CS-2 had the fewest (12 types). (3) Eight aroma compounds were consistently detected across all regions: hexanal, trans-2-hexenal, n-hexanol, β-citronellol, geraniol, nerol, benzyl alcohol, and phenethyl alcohol. Among these, hexanal and trans-2-hexenal were the most abundant; phenylethyl alcohol exhibited the most significant variation in percentage content across all samples, and was determined to be the representative and dominant volatile compound in ‘Summer Black’ grapes. (4) A transcriptome analysis of six representative regions identified 15 differentially expressed genes associated with phenylpropanoid biosynthesis and metabolism. Among them, PAO (Vitvi04g01467) was significantly correlated with phenethyl alcohol content. Conclusions: These findings provide a basis for evaluating the aroma quality of ‘Summer Black’ grapes and offer insights for regional cultivation selection. Full article
(This article belongs to the Special Issue Genetic and Breeding Improvement of Horticultural Crops)
►▼ Show Figures

Figure 1

15 pages, 5525 KB  
Article
Multi-Omics Analysis Identifies the Key Defence Pathways in Chinese Cabbage Responding to Black Spot Disease
by Wenyuan Yan, Hong Zhang, Weiqiang Fan, Xiaohui Liu, Zhiyin Huang, Yong Wang, Yerong Zhu, Chaonan Wang and Bin Zhang
Genes 2026, 17(1), 115; https://doi.org/10.3390/genes17010115 - 21 Jan 2026
Viewed by 570
Abstract
Background: Black spot disease severely constrains Chinese cabbage production. Methods: To elucidate the defence mechanisms underlying this response, transcriptomic and metabolomic profiles were analysed in leaves of the Chinese cabbage line 904B at 24 h post-inoculation (hpi) with Alternaria brassicicola. In parallel, [...] Read more.
Background: Black spot disease severely constrains Chinese cabbage production. Methods: To elucidate the defence mechanisms underlying this response, transcriptomic and metabolomic profiles were analysed in leaves of the Chinese cabbage line 904B at 24 h post-inoculation (hpi) with Alternaria brassicicola. In parallel, gene silencing and overexpression were conducted for BraPBL, an RLCK family member in Chinese cabbage. Results: The Chinese cabbage line 904B exhibited marked suppression of cytokinin and auxin signalling, coupled with enhanced expression of genes involved in ethylene and jasmonic acid signalling. Multiple secondary metabolites exhibited differential changes, specifically the sterol compound 4,4-dimethyl-5alpha-cholest-7-en-3beta-ol was significantly upregulated in the treatment group. These metabolites were primarily enriched in the indole alkaloid metabolism and glycerolipid metabolism pathways. Concurrently, BraPBL exhibits increasing expression with prolonged infection. BraPBL overexpression enhances resistance to black spot disease, whereas silencing reduces resistance. Subcellular localization confirmed BraPBL at the plasma membrane. Overexpression of BraPBL upregulates the reactive oxygen species-related gene RBOH and the signal transduction-related gene MEKK1, whilst simultaneously activating the JA pathway. Conclusions: Overall, 904B activates defence-related hormones while suppressing growth and development-related hormones during early infection. Secondary metabolites, particularly the sterol compound 4,4-dimethyl-5alpha-cholest-7-en-3beta-ol, play key roles in defence, and BraPBL functions as a black spot disease–related defence gene in Chinese cabbage. Full article
(This article belongs to the Special Issue Genetic and Breeding Improvement of Horticultural Crops)
►▼ Show Figures

Figure 1

Review

Jump to: Research

21 pages, 1921 KB  
Review
From High-Density Genomic Mapping to Precision Molecular Breeding: A Comprehensive Review of Capsicum Genomic Resources
by Luyao Wang, Junhu Kan, Weiting Zhong, Shuo Zhang, Yanghe Zhao, Yingke Hou, Luke R. Tembrock, Xiaolin Gu and Yan Cheng
Genes 2026, 17(3), 298; https://doi.org/10.3390/genes17030298 - 28 Feb 2026
Viewed by 902
Abstract
The genus Capsicum comprises several species that are vital vegetable and spice crops cultivated worldwide, possessing significant economic, nutritional, and ornamental value due to their diverse fruit morphologies, colors, spiciness levels, and stress resistance. Historically, the large genome size (approximately 3 Gb) and [...] Read more.
The genus Capsicum comprises several species that are vital vegetable and spice crops cultivated worldwide, possessing significant economic, nutritional, and ornamental value due to their diverse fruit morphologies, colors, spiciness levels, and stress resistance. Historically, the large genome size (approximately 3 Gb) and high proportion of repetitive sequences (over 80% transposable elements) have constrained in-depth analysis of structural variations and functional genes within Capsicum species. However, recent advances in long-read sequencing, Hi-C scaffolding, and genome assembly have enabled the production of multiple high-quality and telomere-to-telomere (T2T) Capsicum genomes, which have ushered in a new era of research at the nuclear, organellar, and pan-genome levels. The publication of these omics resources has greatly expanded our understanding of the evolution of agronomically and environmentally relevant traits in peppers and their wild relatives. This review systematically summarizes recent progress in reference genomes, pan-genomes, and organellar genomes of the genus Capsicum, highlighting the enhancement of key breeding trait analyses through omics data, and outlines future integrated breeding strategies to provide theoretical and methodological references for genetic improvement and molecular breeding in pepper. Full article
(This article belongs to the Special Issue Genetic and Breeding Improvement of Horticultural Crops)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-5
Back to TopTop