Horticultural Plant Genomics and Quantitative Genetics

A special issue of Horticulturae (ISSN 2311-7524). This special issue belongs to the section "Genetics, Genomics, Breeding, and Biotechnology (G2B2)".

Deadline for manuscript submissions: 5 February 2026 | Viewed by 1435

Special Issue Editors


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Guest Editor
Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
Interests: plant molecular biology; plant genomics; quantitative genetics; plant breeding
College of Smart Agriculture (Institute of Special Plant Research), Chongqing University of Arts and Sciences, Chongqing 402160, China
Interests: angiosperm phylogenomics; evo-devo of key innovations; integrative evolutionary mechanisms analysis
Special Issues, Collections and Topics in MDPI journals
Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
Interests: agronomic trait genetic architecture; plant specialized metabolism; molecular regulation of plant development

Special Issue Information

Dear Colleagues,

Horticultural and specialty economic crops are crucial for global agriculture, providing both nutritional security and high-value commodities for pharmaceutical, ornamental, and industrial sectors. Recent advances in genomics and quantitative genetics have revolutionized our ability to decode complex agronomic traits, accelerating precision breeding for yield, stress resilience, and quality enhancement.

Amid escalating challenges such as climate volatility, pathogen evolution, and resource use efficiency demands, integrating multi-omics data with cutting-edge computational tools is critical. This synergy enables us to identify causal genes/networks underlying key traits, optimize genomic selection models, and bridge the gap between genetic discovery and field application.

This Special Issue seeks high-quality contributions that address (but are not limited to) the following:

  • Pan-genome/transcriptome construction for capturing species diversity;
  • Forward/reverse genetics approaches (GWAS, QTL mapping, and CRISPR-based validation);
  • Multi-omics data integration strategies (genomics, phenomics, and metabolomics);
  • Machine learning-driven prediction models for trait dissection and breeding;
  • Database development for germplasm genotype–phenotype associations;
  • Field-to-lab translational studies applying genomic selection in real-world breeding programs.

We particularly welcome submissions that demonstrate interdisciplinary methodologies that connect molecular insights with scalable breeding solutions for understudied specialty crops.

Prof. Dr. Yanjun Zan
Dr. Honglei Li
Dr. Huan Si
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. 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

  • horticultural crop pan-genomes
  • genomics-assisted breeding
  • multi-omics data integration
  • machine learning-driven phenomics
  • genomic selection models
  • germplasm genotype–phenotype databases

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Published Papers (2 papers)

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Research

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18 pages, 7685 KB  
Article
Complete Chloroplast Genome of Hygrophila polysperma (Acanthaceae): Insights into Its Genetic Features and Phylogenetic Relationships
by Li-Xuan Chin, Qiurui Huang, Qinglang Fan, Haibo Tan, Yuping Li, Caixia Peng, Yunfei Deng and Yongqing Li
Horticulturae 2025, 11(10), 1240; https://doi.org/10.3390/horticulturae11101240 - 14 Oct 2025
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Abstract
Hygrophila polysperma is a type of amphibious plant that originates from Acanthaceae. Here, we report its first complete chloroplast (cp) genome. The complete cp genome is 146,675 bp in length with 38.3% of GC content. There are 130 genes including 86 protein coding [...] Read more.
Hygrophila polysperma is a type of amphibious plant that originates from Acanthaceae. Here, we report its first complete chloroplast (cp) genome. The complete cp genome is 146,675 bp in length with 38.3% of GC content. There are 130 genes including 86 protein coding genes, 36 tRNA genes, and 8 rRNA genes in this genome. Simple short sequence (SSR) analysis found 30 SSRs, 24 of which are located in a large single-copy region. Nucleotide diversity identified six most divergent sequences (trns-GCU, psaA-pafI, psaI-pafII, ycf2, rpl32, and ycf1) among 3 close-related species, H. polysperma, H. ringens, and Asteracantha longifolia. A phylogenetic tree among H. polysperma and another 30 related species was constructed based on the common coding sequence of the cp genome and showed that H. polysperma is most closely related to H. ringens (both belong to subtribe Hygrophilinae) and, together, they form a clade that is sister to A. longifolia. This study provides a basis for systemic and evolution studies as well as the development of molecular markers for species identification and genetic breeding. Full article
(This article belongs to the Special Issue Horticultural Plant Genomics and Quantitative Genetics)
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Review

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26 pages, 456 KB  
Review
Tree Fruit and Nut Crops at the Dawn of the Pangenomic Era
by June Labbancz and Amit Dhingra
Horticulturae 2025, 11(12), 1537; https://doi.org/10.3390/horticulturae11121537 - 18 Dec 2025
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Abstract
Tree fruit and nut crops are a critical component of the global economy, producing at least 400 million tonnes of produce in 2022 and nourishing a growing population of approximately 8 billion humans every year. Improved cultivars and growing practices depend upon an [...] Read more.
Tree fruit and nut crops are a critical component of the global economy, producing at least 400 million tonnes of produce in 2022 and nourishing a growing population of approximately 8 billion humans every year. Improved cultivars and growing practices depend upon an understanding of the molecular basis of tree traits and physiology. Over the past 20 years, the proliferation of reference genomes for tree fruit and nut crop species has transformed the study of genetics in these crops, providing a platform for resequencing analyses of large populations, enabling comparative genomic analyses between distant plant species, and allowing the development of molecular markers for use in breeding. However, reference bias and poor transferability of markers limit widespread applicability in many instances. As third-generation sequencing has become more accurate and accessible, a greater number of reference genomes have become available, enabling higher-quality assemblies and wider sampling of genomic diversity. To facilitate the effective use of multiple closely related genomes to create a reference and comparative genomics platform, tools have been developed for the creation of pangenome graphs, a data structure using nodes connected by edges to represent multiple genomes and their sequence variations. Pangenome graphs allow for singular representations of diversity within a species or even a wider genus. Pangenomic analyses at the genus-scale (e.g., Malus, Citrus) have been conducted for Malus and Citrus, and more tree fruit and nut species are likely to follow. As the number of genome sequences and pangenome resources increases, the importance of generating great quantities of transcriptomic and phenomic data will increase as well. This data is essential in the drive to connect genes to traits and overcome traditional breeding bottlenecks, which is needed to develop improved tree fruit and nut crops, which can satisfy global demand. Full article
(This article belongs to the Special Issue Horticultural Plant Genomics and Quantitative Genetics)
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