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Agronomy
Special Issues
Fruit Tree Germplasm Innovation Driven by Molecular Breeding and Genomics
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Fruit Tree Germplasm Innovation Driven by Molecular Breeding and Genomics

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Horticultural and Floricultural Crops".

Deadline for manuscript submissions: 20 November 2026 | Viewed by 3241

Special Issue Editors

Dr. Runze Wang

E-Mail Website
Guest Editor
School of Horticulture, Anhui Agricultural University, Hefei 230036, China
Interests: fruit tree quality traits; QTL mapping; multi-omics analysis; regulation network; molecular breeding marker
Prof. Dr. Yue Huang

E-Mail Website
Guest Editor
School of Horticulture, Anhui Agricultural University, Hefei 230036, China
Interests: fruit tree functional genomics; bioinformatics; disease-resistant breeding of kiwifruit
Prof. Dr. Xia Wang

E-Mail Website
Guest Editor
National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
Interests: citrus functional genomics; intelligent design breeding of citrus; somatic genetics of horticultural plants

Special Issue Information

Dear Colleagues,

Fruit crops are indispensable pillars of global food security, providing essential nutrients and economic value to people worldwide. However, escalating multifaceted challenges—including climate change-induced environmental stressors, soil degradation, water resource constraints, and emerging pathogens—threaten the sustainability of fruit production systems. The genetic complexity of perennial crops (e.g., high heterozygosity, polyploidy, and extended juvenile phases) further complicates traditional breeding efforts. Addressing these systemic bottlenecks necessitates a paradigm shift toward molecular breeding integrated with genomic innovation, leveraging cutting-edge technologies to unlock the genetic potential of fruit germplasm. Recent breakthroughs in plant genomics, CRISPR-based gene editing platforms, and multi-omics approaches (genomics, transcriptomics, proteomics, and metabolomics) have revolutionized our capacity to dissect complex agronomic traits and accelerate precision breeding. This Special Issue aims to bridge the gap between fundamental research and practical applications, fostering interdisciplinary translational studies that address critical challenges in fruit crop improvement.

Titled "Fruit Tree Germplasm Innovation Driven by Molecular Breeding and Genomics", this Special Issue seeks original research articles and comprehensive reviews that push the boundaries of fruit crop biology. Submissions may address molecular mechanisms controlling fruit quality traits, abiotic/biotic stress tolerance, hormone signalling pathways, postharvest biology, and self-incompatibility systems, as well as novel methods—including databases, bioinformatics pipelines, and phenotyping platforms—that address translational challenges in fruit crop improvement.

Dr. Runze Wang
Prof. Dr. Yue Huang
Prof. Dr. Xia Wang
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. Agronomy is an international peer-reviewed open access semimonthly 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

  • multi-omics
  • gene editing
  • fruit quality traits
  • stress
  • databases

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Published Papers (3 papers)

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Research

13 pages, 2374 KB  
Article
Transcription Factor AcMYB5 Activates Flavonoid Biosynthesis and Enhances Resistance of Kiwifruit to Bacterial Canker
by Shunyuan Wu, Rundong Dai, Wenli Yue, Ge Guo, Jiawei Liu, Yue Huang and Pu Liu
Agronomy 2025, 15(11), 2598; https://doi.org/10.3390/agronomy15112598 - 12 Nov 2025
Viewed by 777
Abstract
Bacterial canker of kiwifruit, caused by Pseudomonas syringae pv. actinidiae (Psa), poses a serious threat to the global kiwifruit industry. Although flavonoids are widely recognized as natural antibacterial compounds, the transcriptional regulatory networks controlling their synthesis in kiwifruit and their relationship [...] Read more.
Bacterial canker of kiwifruit, caused by Pseudomonas syringae pv. actinidiae (Psa), poses a serious threat to the global kiwifruit industry. Although flavonoids are widely recognized as natural antibacterial compounds, the transcriptional regulatory networks controlling their synthesis in kiwifruit and their relationship with production of downstream antibacterial metabolites remain poorly understood. In this study, we identified the transcription factor AcMYB5 as a key mediator of salicylic acid (SA) signaling that activates flavonoid biosynthesis and enhances resistance to Psa. Comparative analysis between the resistant cultivar ‘Jinkui’ and the susceptible cultivar ‘Hongyang’ revealed that Psa infection induced a rapid accumulation of endogenous SA, accompanied by a decrease in jasmonic acid (JA) levels in ‘Jinkui’. From a pool of SA-induced candidate genes, we identified AcMYB5, which is rapidly up-regulated by SA and encodes a nuclear localization protein. Overexpression of AcMYB5 in susceptible kiwifruit significantly enhanced resistance to Psa. Mechanistically, AcMYB5 directly binds to and activates the promoter of the chalcone isomerase (AcCHI), a key structural gene in the flavonoid pathway, leading to a marked increase in total flavonoid content. Notably, AcMYB5 did not activate any other genes in the flavonoid synthesis pathway in our assays, underscoring its target specificity. Our findings reveals a novel AcMYB5-AcCHI module that finely tunes flavonoid-mediated defense responses, offering valuable genetic targets and strategic insights for kiwifruit-resistant breeding. Full article
(This article belongs to the Special Issue Fruit Tree Germplasm Innovation Driven by Molecular Breeding and Genomics)
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21 pages, 15552 KB  
Article
Multi-Omics Dissection of Gene–Metabolite Networks Underlying Lenticel Spot Formation via Cell-Wall Deposition in Pear Peel
by Na Ma, Ziwen Xiao, Liqing Lu, Haiqi Zhang, Chunyan Liu, Yiliu Xu, Yongjie Qi and Zhenghui Gao
Agronomy 2025, 15(11), 2564; https://doi.org/10.3390/agronomy15112564 - 6 Nov 2025
Viewed by 976
Abstract
Lenticel spots (fruit dots) on pear peel strongly influence consumer preference and market price, yet the regulatory networks underlying their lignin/cellulose deposition remain elusive. Here, we integrated electron microscopy, metabolomics, and RNA-seq across three developmental stages (30, 40, and 60 d after full [...] Read more.
Lenticel spots (fruit dots) on pear peel strongly influence consumer preference and market price, yet the regulatory networks underlying their lignin/cellulose deposition remain elusive. Here, we integrated electron microscopy, metabolomics, and RNA-seq across three developmental stages (30, 40, and 60 d after full bloom, DAFB) in the pear cultivar ‘Dangshansuli’ (SL) and its bud-sport ‘Dangshanxisu’ (XS). XS exhibited fewer lenticel spots and lower lignin, cellulose, and hemicellulose contents than SL, with the critical onset of lignin and cellulose accumulation detected between 40 and 60 DAFB. Metabolome-wide analysis detected five differentially accumulated lignin monomers, while transcriptome profiling revealed 79 differentially expressed genes (padj ≤ 0.05, |log2FC| ≥ 1) enriched in phenylpropanoid and cellulose-synthase pathways. Weighted gene co-expression network analysis (WGCNA) uncovered two modules (|r| > 0.8, p < 0.05) positively correlated with lignin and cellulose content, harboring 11 structural genes (4CL, F5H, CCR, COMT, PRX/POD and CESA isoforms) and five transcription-factor families (MYB, NAC, AP2/ERF, WRKY, bHLH). RT-qPCR validated the coordinated down-regulation of these genes in XS relative to SL. Our results decipher the gene–metabolite circuitry driving lenticel lignification in pear, providing molecular targets for breeding peel-perfect cultivars and for cultural practices that minimize superficial blemishes. Full article
(This article belongs to the Special Issue Fruit Tree Germplasm Innovation Driven by Molecular Breeding and Genomics)
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15 pages, 5094 KB  
Article
Genome-Wide Identification and Functional Characterization Under Abiotic Stress of Melatonin Biosynthesis Enzyme Family Genes in Poncirus trifoliata
by Jian Zhu, Ligang He, Fang Song, Zhijing Wang, Xiaofang Ma, Cui Xiao, Xin Song, Yanjie Fan, Ce Wang, Yun Xie, Yingchun Jiang, Liming Wu and Yu Zhang
Agronomy 2025, 15(10), 2246; https://doi.org/10.3390/agronomy15102246 - 23 Sep 2025
Viewed by 985
Abstract
Plant melatonin is widely recognized as a pleiotropic regulator. As a growth-regulating hormone, it extensively participates in various growth and developmental processes and has significant functions in stress responses and disease resistance. Plant melatonin is synthesized primarily through the catalytic actions of five [...] Read more.
Plant melatonin is widely recognized as a pleiotropic regulator. As a growth-regulating hormone, it extensively participates in various growth and developmental processes and has significant functions in stress responses and disease resistance. Plant melatonin is synthesized primarily through the catalytic actions of five enzymes: TDC (tryptophan decarboxylase), T5H (tryptamine-5-hydroxylase), SNAT (serotonin N-acetyltransferase), ASMT (N-acetylserotonin methyltransferase), and COMT (caffeic acid-O-methyltransferase). There are multiple genes for each of these five enzymes in citrus genomes, however, with the exception of COMT5—whose function has recently been elucidated—and SNAT, which has only been preliminarily identified, the remaining genes have not been unequivocally characterized or functionally annotated. Hence, we carried out a genome-wide analysis of melatonin biosynthesis enzyme-related gene families in trifoliate orange (Poncirus trifoliata), one of the most common citrus rootstock varieties. Through bioinformatics approaches, we identified 96 gene family members encoding melatonin biosynthetic enzymes and characterized their protein sequence properties, phylogenetic relationships, gene structures, chromosomal distributions, and promoter cis-acting elements. Furthermore, by analyzing expression patterns in different tissues and under various stresses, we identified multiple stress-responsive melatonin synthase genes. These genes likely participate in melatonin synthesis under adverse conditions, thereby enhancing stress adaptation. Specifically, PtCOMT5, PtASMT11, and PtTDC9 were significantly induced by low temperature; PtSNAT1, PtSNAT14, PtSNAT18, and PtTDC10 were markedly responsive to drought; and PtASMT15, PtSNAT15, PtASMT16, and PtSNAT3 were strongly induced by ABA. Among them, PtASMT23 expression was induced up to 120-fold under low temperature, while PtSNAT18 showed over 100-fold upregulation under dehydration treatment. These findings strongly suggest that PtASMT23 and PtSNAT18 play critical roles in regulating melatonin biosynthesis in response to cold and drought stress, respectively. Collectively, these findings pinpoint novel genetic targets for enhancing stress resilience in citrus breeding programs and lay the foundation for the functional characterization of specific melatonin biosynthesis pathway gene family members in citrus and other horticultural crop species. Full article
(This article belongs to the Special Issue Fruit Tree Germplasm Innovation Driven by Molecular Breeding and Genomics)
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