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Horticulturae
Special Issues
New Insights into Breeding and Genetic Improvement of Fruit Crops
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New Insights into Breeding and Genetic Improvement of Fruit Crops

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: 15 March 2026 | Viewed by 2257

Special Issue Editors

Prof. Dr. Xiaobiao Xu

E-Mail Website
Guest Editor
College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China
Interests: fruit tree germplasm resources; molecular biology
Prof. Dr. Yuepeng Han

E-Mail Website
Guest Editor
Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
Interests: fruit tree genomics; particularly in genetic basis and molecular mechanisms of fruit quality in peach and apple
Dr. Songtao Jiu

E-Mail Website
Guest Editor
Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
Interests: horticultural genetic resources; genomics; molecular breeding; phytohormone; molecular biology
Special Issues, Collections and Topics in MDPI journals
Dr. Guanglian Liao

E-Mail Website
Guest Editor
School of Agricultural Sciences, Jiangxi Agricultural University, Nanchang 330029, China
Interests: fruit quality; genetic; Genome; kiwifruit; postharvest biotechnology
Special Issues, Collections and Topics in MDPI journals
Dr. Dongfeng Jia

E-Mail Website
Guest Editor
College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China
Interests: molecular mechanisms of fruit quality and response to abiotic stress in fruit trees

Special Issue Information

Dear Colleagues,

Fruit tree breeding and genetic improvements are critical for enhancing the yield, quality, and stress resistance to meet the growing demands of sustainable horticulture. With advances in molecular biology, genomics, and biotechnology, modern breeding strategies such as marker-assisted selection, genome editing, polyploidy breeding, and functional genomics have significantly accelerated the development of improved cultivars.

This Special Issue aims to highlight the latest research on innovative breeding approaches, genetic diversity, and germplasm enhancement. We welcome studies exploring molecular mechanisms underlying key agronomic traits, strategies for improving fruit quality and stress tolerance, and the integration of multi-omics technologies in breeding programs. Research focusing on novel genetic and biotechnological tools, as well as their practical applications in fruit tree breeding, is particularly encouraged.

We invite original research articles and reviews that provide new insights into the genetic basis of fruit tree traits and contribute to the advancement of efficient and sustainable breeding strategies for the future of horticultural science.

Prof. Dr. Xiaobiao Xu
Prof. Dr. Yuepeng Han
Dr. Songtao Jiu
Prof. Dr. Guanglian Liao
Dr. Dongfeng Jia
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 100 words) can be sent to the Editorial Office for announcement on this website.

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

  • fruit breeding
  • genetic improvement
  • molecular breeding
  • germplasm innovation
  • marker-assisted selection
  • genome editing
  • polyploidy breeding
  • stress resistance
  • fruit quality enhancement

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

Published Papers (4 papers)

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Research

30 pages, 10676 KiB  
Article
Domestication Has Reshaped Gene Families, Gene Expressions and Flavonoid Metabolites in Green Jujube (Ziziphus mauritiana Lam.) Fruit
by Fan Jiang, Xudong Zhu, Miaohong Wu, Pengyan Chang, Huini Wu and Haiming Li
Horticulturae 2025, 11(8), 974; https://doi.org/10.3390/horticulturae11080974 - 17 Aug 2025
Viewed by 275
Abstract
Domestication has been proven to significantly impact the biosynthesis of plant secondary metabolites. Cultivated green jujube (Ziziphus mauritiana Lam.), as an important autotetraploid fruit crop widely planted in tropical regions, exhibits differential physicochemical traits compared with its wild progenitor. To assess the [...] Read more.
Domestication has been proven to significantly impact the biosynthesis of plant secondary metabolites. Cultivated green jujube (Ziziphus mauritiana Lam.), as an important autotetraploid fruit crop widely planted in tropical regions, exhibits differential physicochemical traits compared with its wild progenitor. To assess the traits lost in cultivated green jujube during domestication, the study performed comprehensive genomic, transcriptomic and metabolomic investigations of flavonoid pathways in wild and cultivated green jujube. Based on the four haplotype genomes of wild and cultivated green jujube, for the first time, the study bulk-identified 16 key gene families associated with flavonoid biosynthesis. Collinearity analysis revealed that tandem duplication was the predominant event in flavonoid-related genes rather than WGD. Through the expression profiles in different tissues, the distinct member of these gene families was classified as “redundant” or “functional”. Transcriptomic analyses illustrated the significant differential expressions (p < 0.05) of 13 flavonoid-related gene families in fruits of six cultivated and three wild green jujube accessions, except for FLS, LAR and PPO. The wild green jujube fruits accumulated more abundance of flavonoid metabolites than in cultivated fruits (p < 0.0001), as evidenced by upregulated chalcones, dihydroflavonol, isoflavones and flavonoid carbonoside. Gene–metabolite co-expression modules further validated the potential transcription regulators, such as BBX21, WRI1 and bZIP44. Together, the study suggested a genomic, transcriptomic and metabolic perspective for domestication regarding fruit flavonoid pathways in green jujube, which provides a valuable genetic resource for fruit quality improvement in cultivated green jujube. Full article
(This article belongs to the Special Issue New Insights into Breeding and Genetic Improvement of Fruit Crops)
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13 pages, 1211 KiB  
Article
Collection, Evaluation, and New Cultivar Breeding of Actinidia chinensis var. chinensis in Wudang Mountains, China
by Tao Xiao, Tianjiao Jia, Wei Wu, Jiaqing Peng, Liang Pan, Xianbo Zhu, Tao Liu, Junhuan Cheng, Hualing Wang, Lili Xiao, Hailei Huang, Guangming Hu and Shuaiyu Zou
Horticulturae 2025, 11(7), 739; https://doi.org/10.3390/horticulturae11070739 - 26 Jun 2025
Viewed by 480
Abstract
To develop new kiwifruit cultivars (Actinidia chinensis var. chinensis) with desirable traits, we conducted wild resource surveys in the Wudang Mountains region of China. Seven promising accessions were identified through preliminary screening, exhibiting fruit weights ranging from 50.46 g to 75.06 [...] Read more.
To develop new kiwifruit cultivars (Actinidia chinensis var. chinensis) with desirable traits, we conducted wild resource surveys in the Wudang Mountains region of China. Seven promising accessions were identified through preliminary screening, exhibiting fruit weights ranging from 50.46 g to 75.06 g and a soluble solids content (SSC) between 14.33% and 16.32%. The accession ‘WD-03-1’ stood out by meeting the dual selection criteria of fruit weight exceeding 70 g and a SSC above 15%. After a decade-long evaluation, this elite genotype was officially certified as a superior cultivar by the Hubei Provincial Variety Committee for Forestry in 2016, receiving the registered name ‘Wudang 1’. Distinguished as a rare green-fleshed variety in the A. chinensis var. chinensis, ‘Wudang 1’ produces uniform elliptical fruits (shape index of 1.34) with an average weight of 83.22 g. Its flesh combines sweet and tart flavors with exceptional nutritional parameters: 16.33% SSC, 15.28% dry matter, 12.10% soluble sugars, 1.24% titratable acidity, 132.10 mg/100 g vitamin C, and 7.77 mg/g amino acids. Comparative analysis with established cultivars ‘Jinnong’ and ‘Cuiyu’ revealed that ‘Wudang 1’ matures earlier and demonstrates superior performance in three key quality metrics (SSC, dry matter, and vitamin C). Further analysis of aromatic profiles during the prime consumption stage identified 41 volatile compounds, predominantly comprising aldehydes, esters, alcohols, and ketones, which collectively contribute to its distinctive fragrance. Full article
(This article belongs to the Special Issue New Insights into Breeding and Genetic Improvement of Fruit Crops)
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19 pages, 3126 KiB  
Article
Characterization and Expression Analysis of PUB Gene Family Involved in Drought Stress Response in Trifoliate Orange (Poncirus trifoliata)
by Bobo Song, Sanpeng Jin, Xuchen Gong, Yong Liu, Dechun Liu, Li Yang, Wei Hu, Liuqing Kuang and Jie Song
Horticulturae 2025, 11(6), 604; https://doi.org/10.3390/horticulturae11060604 - 29 May 2025
Viewed by 473
Abstract
The U-box E3 ubiquitin ligase (PUB) gene family plays an important role in regulating plant responses to abiotic stress. Poncirus trifoliata (trifoliate orange), a citrus rootstock with notable cold, drought, and salt tolerance, serves as an excellent model for studying stress-responsive genes. In [...] Read more.
The U-box E3 ubiquitin ligase (PUB) gene family plays an important role in regulating plant responses to abiotic stress. Poncirus trifoliata (trifoliate orange), a citrus rootstock with notable cold, drought, and salt tolerance, serves as an excellent model for studying stress-responsive genes. In this study, a total of 47 PUB genes (PtrPUBs) were identified in the trifoliate orange genome. Chromosomal distribution analysis indicated that PtrPUB genes were unevenly distributed across nine trifoliate orange chromosomes. Phylogenetic tree analysis indicated that 170 PUB proteins from trifoliate orange, Arabidopsis thaliana, and tomato were clustered into five subfamilies. Gene structure, conserved domain, and motif analyses revealed diverse exon–intron and motif organizations of PtrPUB genes, suggesting potential functional differentiation among PtrPUBs. Cis-acting analysis indicated that the promoters of PtrPUB genes harbor elements related to hormone signaling (ABA, MeJA), drought stress, and low-temperature responses. Transcriptomic data and qRT-PCR results suggested that PtrPUB genes are responsive to ABA and dehydration treatments. This study provides a foundation for understanding the functional roles of PUB genes in trifoliate orange and offers insights for improving stress tolerance in citrus breeding programs. Full article
(This article belongs to the Special Issue New Insights into Breeding and Genetic Improvement of Fruit Crops)
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17 pages, 3048 KiB  
Article
Genome-Wide Association Studies Provide Molecular Insights into the Genetic Determination of the Fruit Shape-Related Traits of Actinidia eriantha
by Lu Chen, Dongfeng Jia, Yansong Liu, Huan Gao, Jipeng Mao and Xiaobiao Xu
Horticulturae 2025, 11(5), 538; https://doi.org/10.3390/horticulturae11050538 - 15 May 2025
Viewed by 633
Abstract
In the selection of new horticultural crops varieties, fruit shape and size are key agronomic traits targeted by breeders, as well as critical criteria for commercial evaluation and grading. Wild germplasm resources typically exhibit greater genetic diversity in fruit morphology compared to cultivated [...] Read more.
In the selection of new horticultural crops varieties, fruit shape and size are key agronomic traits targeted by breeders, as well as critical criteria for commercial evaluation and grading. Wild germplasm resources typically exhibit greater genetic diversity in fruit morphology compared to cultivated varieties. The study analyzed fruit shape-related traits of 216 Actinidia eriantha plants from a wild population in Jiangxi Province, China, and identified significant associated single nucleotide polymorphisms (SNPs) and candidate genes for the target traits using genome-wide association analysis (GWAS). The results revealed substantial phenotypic variation in fruit shape- and size-related traits. A total of 115 SNPs and 349 putative coding genes were significantly associated with 7 fruit shape-related traits. Within the candidate genomic regions, we identified several key genes linked to specific morphological features, including F-box and MADS4, previously reported to influence fruit shape; WOX, F-box, and OVATE, associated with fruit shape index; RING-type E3 ubiquitin transferase, correlated with transverse diameter; and PLATZ, COL, and Aux/IAA, implicated in fruit weight regulation. These findings facilitate the precise identification of genes or quantitative trait loci (QTLs) governing fruit morphology. Furthermore, the associated SNP markers provide valuable tools for marker-assisted breeding, enabling the development of elite cultivars with desirable fruit characteristics. Full article
(This article belongs to the Special Issue New Insights into Breeding and Genetic Improvement of Fruit Crops)
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