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Horticulturae
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Advances in Developmental Biology in Tree Fruit and Nut Crops—2nd...
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Advances in Developmental Biology in Tree Fruit and Nut Crops—2nd Edition

A special issue of Horticulturae (ISSN 2311-7524). This special issue belongs to the section "Developmental Physiology, Biochemistry, and Molecular Biology".

Deadline for manuscript submissions: 28 February 2026 | Viewed by 1599

Special Issue Editors

Prof. Dr. Zhaohe Yuan

E-Mail Website
Guest Editor
College of Forestry, Nanjing Forestry University, Nanjing 210037, China
Interests: tree fruit and nut crops; pomegranate; developmental biology; flower and fruit development; germplasm; genetics and genomics
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Bo Li

E-Mail Website
Guest Editor
Shandong Academy of Grape, Jinan 250199, China
Interests: grape physiology; grape germplasm; developmental biology; environmental influences on development; adaptation and evolutionary aspects; biotic and abiotic stress responses
Special Issues, Collections and Topics in MDPI journals
Dr. Yujie Zhao

E-Mail Website
Guest Editor
College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
Interests: tree fruit; flower and fruit development; reproductive biology; genomics; transcriptomics and proteomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Following the tremendous success of the first edition of the Special Issue ‘Advances in Developmental Biology in Tree Fruit and Nut Crops’ (https://www.mdpi.com/journal/horticulturae/special_issues/2YE02K1N11), a second edition is being launched.

Developmental biology is a field of biological science that explores the processes through which organisms grow, develop, and ultimately mature. In the context of tree fruit and nut crops, developmental biology investigates the intricate mechanisms governing the growth, differentiation, and reproduction of these plants. Understanding the developmental processes in tree fruit and nut crops is crucial for improving crop yield, quality, and resistance to various environmental stressors, pests, and diseases. This Special Issue aims to showcase cutting-edge research on developmental biology in tree fruit and nut crops, providing a platform for researchers to disseminate their findings and foster collaboration within the scientific community.

Potential topics include, but are not limited to:

  1. Genetic regulation of fruit and nut development: Investigating the genetic factors and regulatory networks controlling the development of fruits and nuts in trees.
  2. Molecular mechanisms of seed and fruit development: Exploring the molecular processes involved in seed development, fruit ripening, and maturation in tree crops.
  3. Environmental influences on development: Studying the impact of environmental factors such as temperature, light, and water availability on the developmental processes of tree fruit and nut crops.
  4. Nutrient and hormonal regulation: Analyzing the role of nutrients and hormones in shaping the growth and development of fruits and nuts in trees.
  5. Reproductive biology: Examining the reproductive structures, mechanisms of pollination, and fertilization in tree fruit and nut crops.
  6. Adaptation and evolutionary aspects: Investigating the evolutionary history and adaptive traits related to developmental biology in tree fruit and nut species.
  7. Biotic and abiotic stress responses: Understanding how tree fruit and nut crops respond to biotic stresses such as pests and diseases, as well as abiotic stresses including drought, salinity, and climate change.
  8. Biotechnological advances in developmental biology: Highlighting innovative biotechnological approaches and tools used in the study and manipulation of developmental processes in tree fruit and nut crops.

Submission Guidelines:

Researchers are encouraged to submit original research articles and reviews that contribute significantly to the understanding of developmental biology in tree fruit and nut crops. All submissions will undergo a rigorous peer review process to ensure the highest scientific quality and relevance to the theme of the Special Issue.

We invite researchers, academicians, and practitioners to contribute to this Special Issue and share their valuable insights, discoveries, and innovations in the field of developmental biology in tree fruit and nut crops. By bringing together diverse perspectives and expertise, this Special Issue aims to advance our knowledge and contribute to the sustainable development of tree fruit and nut crop industries worldwide.

Prof. Dr. Zhaohe Yuan
Prof. Dr. Bo Li
Dr. Yujie Zhao
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

  • developmental biology
  • tree fruit crops
  • nut crops
  • genetic regulation
  • molecular mechanisms
  • seed and fruit development
  • flower development
  • environmental influences on development
  • nutrient and hormonal regulation
  • reproductive biology
  • adaptation and evolutionary aspects
  • biotic and abiotic stress responses
  • biotechnology
  • genetics
  • genomics, transcriptomics, and proteomics

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  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
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  • 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 (3 papers)

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Research

16 pages, 4138 KB  
Article
Clonal Micropropagation of Promising Genotypes of Amygdalus communis L. for Population Restoration and Gene Pool Conservation
by Timur Turdiyev, Kumissay Duisenova, Irina Kovalchuk, Aigul Madenova, Saule Baizhumanova, Kamila Yemesheva, Natalya Mikhailenko and Zakir Tuigunov
Horticulturae 2025, 11(9), 999; https://doi.org/10.3390/horticulturae11090999 - 22 Aug 2025
Viewed by 236
Abstract
The southern region of Kazakhstan represents the northernmost boundary of the natural habitat of five wild almond species, among which Amygdalus communis L. is of particular interest due to a range of favorable traits for use in breeding programs and cultivation in the [...] Read more.
The southern region of Kazakhstan represents the northernmost boundary of the natural habitat of five wild almond species, among which Amygdalus communis L. is of particular interest due to a range of favorable traits for use in breeding programs and cultivation in the region. The current distribution range of common almond growth was clarified using GPS to determine precise coordinates, and a schematic map was developed. Monitoring revealed a significant reduction in population size. In the surveyed areas, 54 trees were selected and described. Seed material was collected from 34 genotypes and characterized according to a descriptor. Genotypes A3, A8, and A15 were identified as having favorable trait combinations. To restore populations and preserve the gene pool of Amygdalus communis L., a method of clonal micropropagation was employed. The composition of the nutrient medium was optimized for establishment, multiplication, and rhizogenesis. It was determined that Murashige and Skoog (MS) medium without phytohormones is effective for in vitro establishment (70% regeneration rate). For multiplication, MS medium with 0.5 mg/L BAP (6-benzylaminopurine) was used (with a multiplication rate of 3.5 per explant). For rhizogenesis, MS medium with 0.5 mg/L BAP, 0.02 mg/L gibberellic acid (GA), and 0.1 mg/L IBA (indole-3-butyric acid) was used. A total of 340 clonal Amygdalus communis L. plants with closed root systems were grown for field collection. The research results can be applied for the restoration, propagation, and conservation of populations both in vitro and in situ, as well as for the inclusion of selected high-performing genotypes in breeding programs. Full article
(This article belongs to the Special Issue Advances in Developmental Biology in Tree Fruit and Nut Crops—2nd Edition)
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16 pages, 3152 KB  
Article
Transcriptome Analysis Reveals Potential Mechanism of Regulating Fruit Shape of ‘Laiyang Cili’ Pear with Calyx Excision Treatment
by Huijun Jiao, Yaojun Chang, Qiming Chen, Chaoran Xu, Qiuzhu Guan and Shuwei Wei
Horticulturae 2025, 11(8), 939; https://doi.org/10.3390/horticulturae11080939 - 8 Aug 2025
Viewed by 338
Abstract
Fruit shape is an important quality and yield trait of pear, and the fruit shape of ‘Laiyang Cili’ presents a spindle shape which seriously affects its commercial value. Calyx excision treatment could change the fruit shape, while the underlying genes and their regulatory [...] Read more.
Fruit shape is an important quality and yield trait of pear, and the fruit shape of ‘Laiyang Cili’ presents a spindle shape which seriously affects its commercial value. Calyx excision treatment could change the fruit shape, while the underlying genes and their regulatory mechanism remain poorly understood. In this study, we constructed RNA-seq libraries of pear treated with calyx excision to explore underlying regulatory mechanisms. At the early stage of the calyx excision treatment, the numbers of differentially expressed genes (DEGs) between each comparison group were relatively high and gradually decreased along with fruit development. The expression pattern of the DEGs ranked in the top 30 of the six groups had obvious divergence, and DEGs were mainly distributed in the “after calyx excision treatment (0 days)” (AC0d) and AC2d groups. The DEGs were mainly enriched in plant hormone signal transduction and plant defense response. We identified 17 candidate genes related to fruit shape and tested their expression patterns along with fruit development. Among them, nine candidate genes expression trends were consistent with fragments per kilobase of exon model per million mapped fragment (FPKM) values, including MYB62, outer envelope pore protein 62 (OEP62), auxin response factor 3 (ARF3), auxin-responsive protein 50 (SAUR50), protein phosphatase 2C 51 (PP2C 51), major allergen Pyr c 1 (PYRC1), aquaporin TIP1-3 (TIP1-3), transcription factor TGA4 (TGA4) and auxin-responsive protein 17 (IAA17). And then, weighted gene co-expression network analysis (WGCNA) analysis revealed that the OVATE family protein (OFP) and SUN domain-containing protein (SUN) were divided into the MEblue model, which had a positive correlation with calyx excision treatment, and the expression trend of LOC103960706 (OFP8) appeared cohesive with FPKM values. Pbr014104.1 and Pbr016952.1, which were the ortholog genes of LOC103960706, were further identified from the pear genome, and were found to be highly expressed in pear fruit through RT-PCR analysis. Taken together, the key stage determining the development of fruit shape was in the early stage after calyx excision treatment, and fruit shape regulation and development were co-regulated by multiple genes. Full article
(This article belongs to the Special Issue Advances in Developmental Biology in Tree Fruit and Nut Crops—2nd Edition)
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24 pages, 27138 KB  
Article
Comprehensive Genome-Wide Characterization of the GRAS Gene Family and Their Role in Salt Stress Tolerance in Punica granatum L.
by Jingyi Huang, Hongfang Ren, Fan Cheng, Yingfen Teng, Xueqing Zhao and Zhaohe Yuan
Horticulturae 2025, 11(5), 504; https://doi.org/10.3390/horticulturae11050504 - 7 May 2025
Cited by 1 | Viewed by 523
Abstract
The GRAS gene family is broadly distributed in plants and plays key regulatory roles in development, signal transduction, and the adaptation to adverse environments. Pomegranate (Punica granatum L.)—a high-value fruit tree with ecological, economic, health, and ornamental importance—exhibits notable salt tolerance. While [...] Read more.
The GRAS gene family is broadly distributed in plants and plays key regulatory roles in development, signal transduction, and the adaptation to adverse environments. Pomegranate (Punica granatum L.)—a high-value fruit tree with ecological, economic, health, and ornamental importance—exhibits notable salt tolerance. While GRAS genes have been characterized in various species, their functional roles in pomegranate remain underexplored. In this study, 54 GRAS genes (PgGRAS) were identified in the pomegranate genome and were found to be unevenly distributed across eight chromosomes. Phylogenetic analysis grouped these genes into eight subfamilies, revealing highly similar conserved motifs, functional domains, and gene structures within each group. Notably, the DELLA subfamily is distinguished by a unique DELLA domain. Our findings indicate that the expansion of GRAS genes in pomegranate may be linked to fragment duplication events, and many PgGRAS genes contain both phytohormone- and stress-responsive cis-elements. Under 200 mM NaCl treatment, the expression of two DELLA genes was markedly upregulated. Therefore, PgGRAS24 was selected as a candidate gene for stable expression in Arabidopsis to further verify the role of DELLA family members in plant salt tolerance. Overall, this study provides new insights into the molecular functions of the GRAS gene family in pomegranate, gives insights into their role in salt stress tolerance, and lays a theoretical foundation for developing salt-tolerant pomegranate varieties. Full article
(This article belongs to the Special Issue Advances in Developmental Biology in Tree Fruit and Nut Crops—2nd Edition)
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