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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 7507

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Special Issue Editors

Prof. Dr. Xiaobiao Xu

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Guest Editor

College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China
Interests: fruit tree germplasm resources; molecular biology

Prof. Dr. Yuepeng Han

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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

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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
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Dr. Guanglian Liao

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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

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Guest Editor

College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China
Interests: horticulture; abiotic stress; drought; salt stress
Special Issues, Collections and Topics in MDPI journals

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

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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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Published Papers (8 papers)

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Research

21 pages, 3143 KB

Open AccessArticle

Effects of Basal Fertilization Supplemented with Graphene and/or Microbial Inoculants on Growth and Fruit Quality of Winter Jujube Based on Metabolomics Analysis

by Bingxin Chen, Dengyang Lu, Hengzhou Yuan, Xiaofeng Zhou, Yan Wang and Cuiyun Wu

Horticulturae 2026, 12(2), 133; https://doi.org/10.3390/horticulturae12020133 - 25 Jan 2026

Viewed by 207

Abstract

Winter jujube is highly favored by consumers, and improving both the fruit quality and yield during cultivation is a key issue in horticultural research. Fertilization is a critical measure regulating growth. This study aimed to evaluate the effects of basal fertilizer combined with two novel synergistic additives—graphene and microbial inoculants—on the growth, fruit quality, and metabolic profiles of winter jujube, providing new fertilization strategies. The selected doses of graphene (0.38 g/plant) and microbial inoculant (0.26 g/plant) were based on the previous literature to balance efficacy, cost, and environmental safety. The graphene used was functionalized graphene oxide provided by Shanxi Datong University, chosen for its enhanced dispersibility and plant compatibility. Although this study focused on physiological and metabolic responses, the economic feasibility and potential environmental implications of these additives are discussed in the context of sustainable jujube production. Six-year-old winter jujube trees were treated with four fertilization regimes: basal fertilizer + graphene (T1), basal fertilizer + microbial fertilizer (T2), basal fertilizer + graphene + microbial fertilizer (T3), and basal fertilizer only (CK). Growth indices, mineral element contents in different organs, and fruit quality traits were measured. Widely targeted metabolomics was used to analyze metabolic variations among treatments. Compared with CK, all three synergistic fertilizer treatments tended to promote growth, increasing leaf area, chlorophyll content, and jujube bearing shoot length; contributed to the accumulation of P, K, Ca, Mg, and other minerals in various organs; and helped improve fruit quality by increasing the total sugars and flavonoids. T1 and T3 exhibited relatively better overall performance. Metabolomic analysis revealed significant differences in the metabolite profiles of winter jujube fruits across different treatments. Phenolic acids and flavonoids were closely associated with the improvement in fruit quality; further screening identified seven differential metabolites, predominantly belonging to phenolic acids. Basal fertilizer combined with graphene alone or with microbial inoculants may effectively promote growth and improve fruit quality by optimizing mineral uptake and regulating metabolic processes. These findings provide potential theoretical and practical support for high-quality, high-yield fertilization strategies for winter jujube. Full article

(This article belongs to the Special Issue New Insights into Breeding and Genetic Improvement of Fruit Crops)

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15 pages, 6445 KB

Open AccessArticle

Comparative Analysis of the Cuticular Wax Morphology, Composition and Biosynthesis in Two Kumquat Cultivars During Fruit Development

by Yingjie Huang, Li Qiu, Dechun Liu, Wei Hu, Zhonghua Xiong, Liuqing Kuang, Jie Song, Li Yang and Yong Liu

Horticulturae 2025, 11(12), 1516; https://doi.org/10.3390/horticulturae11121516 - 15 Dec 2025

Viewed by 454

Abstract

Cuticular wax plays an important role in the quality of kumquat (Fortunella crassifolia Swingle) fruit. In this study, the wax morphology, compositional profile of epi- and intracuticular wax, and crucial gene expression in ‘Rongan’ kumquat (RAK) and ‘Huapi’ kumquat (HPK) were analyzed during fruit development. The results showed that the surfaces of two kumquat fruits were covered with an amorphous wax layer containing a small number of platelets. Compared to RAK, HPK contained more abundant and larger wax crystals during fruit development. In two kumquat fruits, the epicuticular wax and its major compositions consistently displayed significantly higher levels than the intracuticular wax. Additionally, their main wax composition shifted from alkanes in the early developmental stages to triterpenoids at harvest in both layers, while aldehydes were specifically enriched in the epicuticular wax. During the fruit development from 90 to 180 DAF, HPK fruit exhibited significantly higher levels of epicuticular wax and its majority fractions than RAK fruit. Meanwhile, the intracuticular wax contents of HPK from 90 DAF to 150 DAF were significantly higher than those in RAK, with triterpenoids accounting for the largest proportion of this increase. qRT-PCR results indicated that the up-regulation of wax-related genes in HPK was linked to its increased epicuticular wax deposition during the development. Overall, this study provided a comprehensive overview of the morphology, composition, and biosynthesis of cuticular wax in kumquat fruit during development. 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, 3759 KB

Open AccessArticle

Genome-Wide Identification of SWEET Genes and Expression Dynamics of MrSWEET15 During Fruit Ripening in Chinese Bayberry (Morella rubra)

by Jianfeng Liang, Wenjie Chen, Junjie Tao, Keyuan Duan, Jida Zhou, Zhiyu Yin, Jie Song, Zhongshan Gao, Chunhui Huang and Huimin Jia

Horticulturae 2025, 11(11), 1343; https://doi.org/10.3390/horticulturae11111343 - 8 Nov 2025

Viewed by 633

Abstract

Sugar transporters of the SWEET family play a crucial role in sugar partitioning and fruit quality, yet their functions remain uncharacterized in Chinese bayberry (Morella rubra). In this study, we present the first genome-wide identification and characterization of the SWEET gene family in species, revealing 15 MrSWEET genes distributed across eight chromosomes. Phylogenetic analysis classified these genes into four conserved clades with distinct tissue-specific expression patterns. During fruit ripening, transcripts of MrSWEET1, 2b, 4, and 15 accumulated progressively, with MrSWEET15 showing the strongest increase. Weighted gene co-expression network analysis (WGCNA) identified a “lightcyan” module that correlates strongly with fruit sugar content (r > 0.8) and contains MrSWEET15, three additional MrSWEET genes, and 47 transcription factors (Dof, MYB, NAC, ERF, MADS, WRKY). Promoter analysis of MrSWEET15 revealed the presence of light- and hormone-responsive cis-elements (MYB, MYC, HY5, bZIP, and Dof), and MYB1, HY5, and Dof1.5 expression profiles are synchronized with MrSWEET15, suggesting potential regulatory relationships. These findings establish MrSWEET15 as a priority candidate for sugar transport in Chinese bayberry and our understanding of the molecular basis of sugar transport and fruit quality formation. 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, 3829 KB

Open AccessArticle

Physiological Mechanisms of Drought-Induced Creasing in Citrus unshiu Marc: Roles of Antioxidant Dysregulation, Hormonal Imbalance, Cell Wall Degradation, and Mineral Redistribution

by Wei Hu, Woxing Fu, Dechun Liu, Zhonghua Xiong, Li Yang, Liuqing Kuang, Jie Song, Jingheng Xie and Yong Liu

Horticulturae 2025, 11(10), 1197; https://doi.org/10.3390/horticulturae11101197 - 3 Oct 2025

Viewed by 854

Abstract

Citrus creasing is a physiological rind disorder. Satsuma mandarin (Citrus unshiu Marc.) is the most widely cultivated mandarin variety worldwide and exhibits a high susceptibility to creasing. To investigate the physiological mechanisms underlying creasing, satsuma mandarin trees were treated with different drought stress during fruit expansion, then the relationship between the soil water content and creasing incidence was analyzed, while also examining the rind morphology, oil gland distribution in the flavedo, antioxidant enzyme activities, hormone concentrations, cell wall components, mineral content of creasing fruit, and the impact of creasing on fruit quality. Results showed that severe water stress (35% SRWC) increased the creasing incidence rate by 28% compared to well-irrigated treatments (80% SRWC). The creasing fruit oil gland diameter reduced by 35.7% and the density increased by 149.7% compared to healthy fruits. Simultaneously, the content of H₂O₂ and proline elevated by 47.1% and 8.3% respectively, and the activities of SOD, POD, and CAT of the creasing rind were enhanced significantly. Additionally, the content of IAA, ZR, and MeJA decreased by 17.2%, 7.8%, and 50.2%, respectively. Cell wall components such as cellulose, hemicellulose, and protopectin content reduced by 44.6%, 31.7%, and 33.1%, while soluble pectin increased by 36.3%. Significant alterations were observed in several minerals (Al, Fe, Na, Ni, V, Ga, Zn, Ba, Sn, Hg, Sc, Y, and La). However, fruit quality remained unaffected by creasing. These results demonstrate that drought is a key factor inducing creasing. Increased oil gland density, the degradation of cell wall components, elevated oxidative stress, reductions in phytohormones, and altered mineral element content work together to contribute to rind cells’ structural instability and lead to creasing in the satsuma mandarin. Full article

(This article belongs to the Special Issue New Insights into Breeding and Genetic Improvement of Fruit Crops)

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30 pages, 10676 KB

Open AccessArticle

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 1151

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 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 KB

Open AccessArticle

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

Cited by 2 | Viewed by 1406

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 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 KB

Open AccessArticle

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 958

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 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 KB

Open AccessArticle

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

Cited by 1 | Viewed by 1120

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 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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