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Horticulturae
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Fruit Tree Physiology and Molecular Biology
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Fruit Tree Physiology and Molecular Biology

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: 5 August 2025 | Viewed by 5840

Special Issue Editors

Prof. Dr. Dajiang Wang

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Guest Editor
Research Institute of Pomology, Chinese Academy of Agricultural Sciences (CAAS), Key Laboratory of Horticulture Crops Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, No. 98 Xinghai South Street, Xingcheng 125100, China
Interests: fruit gremplasm resources; fruit tree; apple; rootstock
Prof. Dr. Yuan Gao

E-Mail Website
Guest Editor
Research Institute of Pomology, Chinese Academy of Agricultural Sciences (CAAS), Key Laboratory of Horticulture Crops Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs of the People’s Republic of China, No. 98 Xinghai South Street, Xingcheng 125100, China
Interests: fruit gremplasm resources; fruit tree; apple; genetic breeding

Special Issue Information

Dear Colleagues,

In fruit trees, physiological changes such as flower bud differentiation, fruit and seed development, fruit sugar and acid quality formation, color formation and regulation, the influence of rootstock on tree and fruit quality, and response to stress are the keys to guiding fruit tree production. The analysis of molecular biological mechanisms related to these changes has always been the focus of scientific research, and the successful analysis of molecular biological mechanisms can promote production guidance.

The purpose of this Special Issue “Fruit Tree Physiology and Molecular Biology” is to present the latest research about fruit tree physiology and molecular biology by researchers worldwide. Innovative studies about fruit tree physiology and molecular biology (growth and development, fruit quality formation, stress response physiology and molecular biology, etc.) are welcome in this Special Issue.

Prof. Dr. Dajiang Wang
Prof. Dr. Yuan Gao
Guest Editors

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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 tree physiology
  • molecular biology
  • fruit germplasm resources
  • stress response
  • rootstock

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Published Papers (8 papers)

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Research

21 pages, 9041 KiB  
Article
De Novo Assembly and Comparative Analysis of the Mitochondrial Genomes for Six Rubus Species
by Yujie Shi, Zhen Chen, Jingyong Jiang, Qianfan Li and Wei Zeng
Horticulturae 2025, 11(5), 559; https://doi.org/10.3390/horticulturae11050559 - 21 May 2025
Viewed by 126
Abstract
Rubus is a genus of small berry-producing shrubs, valued for their medicinal properties and as a food source. This genus is a large, globally distributed group that includes over 700 species. Despite numerous plastid and nuclear genomes having been reported for Rubus, [...] Read more.
Rubus is a genus of small berry-producing shrubs, valued for their medicinal properties and as a food source. This genus is a large, globally distributed group that includes over 700 species. Despite numerous plastid and nuclear genomes having been reported for Rubus, there is a notable lack of research on its mitogenomes. We utilized PMAT to assemble the mitogenomes of six Rubus species according to long-read HiFi reads and annotated them through homologous alignment. Subsequently, we compared their characteristic differences within Rubus mitogenomes. The complete mitogenomes of R. parviflorus, R. spectabilis, R. idaeus, R. armeniacus, and R. caesius all exhibit master circle structures, with lengths ranging from 360,869 bp to 447,754 bp. However, R. chamaemorus displays a double-circle structure composed of two small circular molecules, spanning 392,134 bp. These mitogenomes encode a total of 54–61 genes, including 33–34 PCGs, 17–24 tRNAs, and 3 rRNA genes. Compared to the other five Rubus species, R. chamaemorus has fewer sequence repeats. These six species exhibit similar codon usage patterns. A large number of gene transfers were detected between organellar genomes of six Rubus species. Additionally, two phylogenetic trees were constructed using 31 mitogenomes and 94 chloroplast genomes, revealing a minor conflict within Rubus. Overall, this study clarifies the mitogenome characteristics of Rubus and provides valuable insights into the evolution of the genus. Full article
(This article belongs to the Special Issue Fruit Tree Physiology and Molecular Biology)
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24 pages, 11670 KiB  
Article
Efficient Identification and Classification of Pear Varieties Based on Leaf Appearance with YOLOv10 Model
by Niman Li, Yongqing Wu, Zhengyu Jiang, Yulu Mou, Xiaohao Ji, Hongliang Huo and Xingguang Dong
Horticulturae 2025, 11(5), 489; https://doi.org/10.3390/horticulturae11050489 - 30 Apr 2025
Viewed by 157
Abstract
The accurate and efficient identification of pear varieties is paramount to the intelligent advancement of the pear industry. This study introduces a novel approach to classifying pear varieties by recognizing their leaves. We collected leaf images of 33 pear varieties against natural backgrounds, [...] Read more.
The accurate and efficient identification of pear varieties is paramount to the intelligent advancement of the pear industry. This study introduces a novel approach to classifying pear varieties by recognizing their leaves. We collected leaf images of 33 pear varieties against natural backgrounds, including 5 main cultivation species and inter-species selection varieties. Images were collected at different times of the day to cover changes in natural lighting and ensure model robustness. From these, a representative dataset containing 17,656 pear leaf images was self-made. YOLOv10 based on the PyTorch framework was applied to train the leaf dataset, and construct a pear leaf identification and classification model. The efficacy of the YOLOv10 method was validated by assessing important metrics such as precision, recall, F1-score, and mAP value, which yielded results of 99.6%, 99.4%, 0.99, and 99.5%, respectively. Among them, the precision rate of nine varieties reached 100%. Compared with existing recognition networks and target detection algorithms such as YOLOv7, ResNet50, VGG16, and Swin Transformer, YOLOv10 performs the best in pear leaf recognition in natural scenes. To address the issue of low recognition precision in Yuluxiang, the Spatial and Channel reconstruction Convolution (SCConv) module is introduced on the basis of YOLOv10 to improve the model. The result shows that the model precision can reach 99.71%, and Yuluxiang’s recognition and classification precision increased from 96.4% to 98.3%. Consequently, the model established in this study can realize automatic recognition and detection of pear varieties, and has room for improvement, providing a reference for the conservation, utilization, and classification research of pear resources, as well as for the identification of other varietal identification of other crops. Full article
(This article belongs to the Special Issue Fruit Tree Physiology and Molecular Biology)
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18 pages, 6449 KiB  
Article
Identification and Evaluation of Flesh Texture of Crisp Pear Fruit Based on Penetration Test Using Texture Analyzer
by Yulu Mou, Xingguang Dong, Ying Zhang, Luming Tian, Hongliang Huo, Dan Qi, Jiayu Xu, Chao Liu, Niman Li, Chen Yin and Xiang Yang
Horticulturae 2025, 11(4), 359; https://doi.org/10.3390/horticulturae11040359 - 27 Mar 2025
Viewed by 368
Abstract
Flesh texture is an important quality trait and is related to people’s preference for fruit, especially for crisp pears. Puncture tests were carried out on 156 crisp pear fruit germplasm samples to analyze the diversity level of texture traits, to clarify the correlation [...] Read more.
Flesh texture is an important quality trait and is related to people’s preference for fruit, especially for crisp pears. Puncture tests were carried out on 156 crisp pear fruit germplasm samples to analyze the diversity level of texture traits, to clarify the correlation between sensory description evaluation and instrumental traits, and to explore the effects of fruit ripening, size, and shelf life on the change in flesh texture. The results showed that puncture parameters were significantly different between crisp pear cultivars, and the work associated with the flesh limit compression force had the highest coefficient of variation (0.281). There was a significant correlation between puncture parameters and sensory evaluation scores. The correlation between sensory score and flesh firmness was the highest, with a correlation coefficient of 0.708, indicating that hardness can significantly influence the sensory evaluation of texture. Cluster analysis based on sensory evaluation and puncture determination could divide the germplasm resources of crisp pear into five texture categories: loosen, crunchy, crisp, tight–crisp, and dense. A comprehensive texture score model, constructed by principal component analysis, showed consistency with sensory evaluation scores and proved that the combination of a puncture test and sensory evaluation is the best way to identify and evaluate the texture of crisp pear. Further analysis of the influencing factors of flesh texture showed that fruit maturity and shelf life had significant effects on flesh quality. This study provides an important reference for the standardization, evaluation, and utilization of crisp pear variety resources. Full article
(This article belongs to the Special Issue Fruit Tree Physiology and Molecular Biology)
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16 pages, 3910 KiB  
Article
Impact of Aerated Irrigation Duration on the Growth of Greenhouse Grape Seedlings and Rhizosphere Soil Microorganisms
by Yinchi Liang, Wei Wang, Jinshan Xi, Shiqiang Zhao, Yufan Zhou, Huanhuan Zhang, Kun Yu, Zhong Zheng and Fengyun Zhao
Horticulturae 2024, 10(12), 1351; https://doi.org/10.3390/horticulturae10121351 - 16 Dec 2024
Viewed by 916
Abstract
This study investigates the effects of varying durations of aerated irrigation, administered at a consistent frequency, on the growth of greenhouse grape seedlings and the structure of the rhizosphere soil microbial community. Using two-year-old ‘Flame Seedless’ grape seedlings as the test material, we [...] Read more.
This study investigates the effects of varying durations of aerated irrigation, administered at a consistent frequency, on the growth of greenhouse grape seedlings and the structure of the rhizosphere soil microbial community. Using two-year-old ‘Flame Seedless’ grape seedlings as the test material, we established a control group with no aeration (CK) and three treatment groups with aeration durations of 10 min (T1), 20 min (T2), and 30 min (T3), respectively. We determined grape seedling growth under different aerating durations. Additionally, changes in the rhizosphere soil microbial community of the plants were analyzed using 16S and ITS high-throughput genome sequencing to further explore the correlation between microbial diversity and plant growth. The results revealed that: (1) Aerated irrigation significantly enhanced plant growth, with the T2 treatment yielding superior increases in plant height, above-ground dry weight, below-ground dry weight, total root length, and root volume compared to T1 and T3 treatments. (2) Aeration treatments notably elevated the Shannon and Chao1 indices of the rhizosphere soil fungal community, with the T2 treatment exhibiting the most substantial effects, and the Shannon index of the bacterial community was also significantly higher under the T2 treatment. (3) The T2 treatment significantly increased the relative abundance of beneficial aerobic bacterial genera such as Flavobacterium, Ellin6067, and Coniochaeta, while decreasing the relative abundance of detrimental fungal genera like Fusarium and Gibberella. In conclusion, a 20 min aeration duration can effectively promote grape seedling growth, enhance the diversity of rhizosphere soil microbial communities, increase beneficial aerobic microorganisms, and reduce harmful ones. This study provides a theoretical basis for optimizing aerated irrigation practices in facility grape cultivation. Full article
(This article belongs to the Special Issue Fruit Tree Physiology and Molecular Biology)
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16 pages, 4390 KiB  
Article
Effects of Different Tree Shapes on Canopy Characteristics of Zaosu Pear (Pyrus ssp. Va.) in the Northwest Arid Zone
by Mingxin Zhao, Mingze Ma, Wei Wang, Sufang Cao, Gang Cao and Hongxu Li
Horticulturae 2024, 10(12), 1254; https://doi.org/10.3390/horticulturae10121254 - 26 Nov 2024
Viewed by 671
Abstract
Zaosu pear (Pyrus ssp. Va., Zaosu) is the main variety of pear cultivated in Gansu Province. Tree shape selection is important in pear cultivation: reasonable tree shapes affect the growth and development of fruit trees and fruit quality, which, in turn, affect [...] Read more.
Zaosu pear (Pyrus ssp. Va., Zaosu) is the main variety of pear cultivated in Gansu Province. Tree shape selection is important in pear cultivation: reasonable tree shapes affect the growth and development of fruit trees and fruit quality, which, in turn, affect the economic benefits of orchards. In this study, Zaosu pear was used as a test material, and five different tree shapes—Y, trunk, single-arm, double-arm, and spindle shapes—were studied regarding three aspects, namely, branching and leafing parameters, light radiation parameters, and root distribution, in order to provide a theoretical basis for the selection of pear tree shapes in arid areas. The results showed that the single-arm and double-arm shapes had the highest fruit weight per fruit values, reaching 280.06 g and 278.27 g, respectively, and the difference in soluble solids—12.42 mg·g−1 and 12.91 mg·g−1, respectively—was not significant; the mu yield of the single-arm shape was 3282 kg; and the yield of a single tree was 39.54 kg, which was the highest for the five tree shapes. The trees mainly had short fruiting branches when they entered the fruiting stage, and the double-arm shape had the highest number of short fruiting branches, which was significantly higher than those of the other tree shapes. Correlation analysis revealed that the number of long fruiting branches was significantly and positively correlated with axillary flower buds. The distribution of light intensity for all five tree shapes showed a gradual increase from bottom to top and from inside to outside, and the single-arm and double-arm shapes had a uniform distribution of light intensity, which translated into better growth and fruiting potential. The trunk shape had the largest leaf area index, resulting in too much depression within the canopy and reducing light, while the single-arm and double-arm shapes had the smallest leaf area indexes, resulting in the light being evenly distributed inside and outside the canopy, and the percentage of light intensity was greater than 50% in all cases, reaching up to 80%. The double-arm form had the highest chlorophyll a content of 24.55 mg·g−1, implying the ability to convert more light energy into chemical energy, and the content of chlorophyll a + b was highest in the single-arm form and the double-arm form, with values of 31.13 mg·g−1 and 33.65 mg·g−1. The total length of the root system and the total surface area of the root system for the single-arm shape were the largest, i.e., 558,550.64 cm and 79,252.32 cm2, respectively, indicating that it has stronger adaptability and resource acquisition ability compared to the other tree shapes. In conclusion, the single-arm form is more suitable for planting in arid areas. Full article
(This article belongs to the Special Issue Fruit Tree Physiology and Molecular Biology)
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16 pages, 6842 KiB  
Article
Isolation and Identification of Pear Ring Rot Fungus and Resistance Evaluation of Different Pear Varieties
by Chen Wang, Yanjie Zhang, Chunqing Ou, Fei Wang, Li Ma, Caihong Wang and Shuling Jiang
Horticulturae 2024, 10(11), 1152; https://doi.org/10.3390/horticulturae10111152 - 30 Oct 2024
Viewed by 799
Abstract
Botryosphaeria dothidea is a significant plant pathogen responsible for causing ulcers, wilt, and fruit decay across a wide range of host plants. One notable fungal disease attributed to B. dothidea is pear tree ring rot, which currently ranks among the most severe diseases [...] Read more.
Botryosphaeria dothidea is a significant plant pathogen responsible for causing ulcers, wilt, and fruit decay across a wide range of host plants. One notable fungal disease attributed to B. dothidea is pear tree ring rot, which currently ranks among the most severe diseases affecting pear trees in China. This pathogen primarily targets branches and fruits, occasionally impacting leaves as well, leading to tree weakening, fruit rot, and leaf drop. The annual repercussions of this disease severely affect both the yield and quality of pear fruits, thereby impeding the healthy development of the pear industry. Recent studies have indicated that other species within the B. dothidea complex can also induce pear ring rot; however, specific physiological strains of B. dothidea remain unreported. Consequently, this study collected tissues from pear trees infected with ring rot from orchards located in Liaoning, Hebei, Shandong, and other regions throughout China. Through morphological characterization combined with pathogenicity assessments and DNA sequence comparisons involving partial internal transcribed spacer (ITS), translation elongation factor (TEF), and β-tubulin (TUB) genes, 21 strains belonging to the Botryosphaeria spp. were identified. These 21 strains served as research subjects for inoculating dormant annual branches from 30 germplasm resources of pear trees in vitro. The results demonstrated that all tested strains could induce lesions on the branches which were characterized by dark brown spots. Furthermore, inoculation experiments involving these 21 strains were conducted to evaluate the resistance levels of various pear varieties against ring rot disease. The resistance was assessed by inoculating different isolates onto distinct pear varieties; this approach established the criteria for evaluating resistance while minimizing identification errors stemming from the variable responses exhibited by certain varieties towards individual strains. Ultimately, this study aims to provide a theoretical foundation for effective prevention and treatment strategies against pear ring rot. Full article
(This article belongs to the Special Issue Fruit Tree Physiology and Molecular Biology)
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17 pages, 1524 KiB  
Article
Dynamic Changes in Polyphenols in Fruit Development of Red Flesh Apple ‘Hongxun 2’
by Dajiang Wang, Guangyi Wang, Xiang Lu, Zhao Liu, Simiao Sun, Hanxin Guo, Wen Tian, Zichen Li, Lin Wang, Lianwen Li, Yuan Gao and Kun Wang
Horticulturae 2024, 10(11), 1125; https://doi.org/10.3390/horticulturae10111125 - 22 Oct 2024
Viewed by 990
Abstract
In this study, fruits of the red flesh Malus plant ‘Hongxun 2’ (Malus neidzwetzkyana (Dieck) Langenf.) and green flesh Malus plant ‘Xinye 13-11’ (Malus sieversii (Led.) Roem.) were used as experimental materials. Both of them came from Xinjiang, China, and Malus [...] Read more.
In this study, fruits of the red flesh Malus plant ‘Hongxun 2’ (Malus neidzwetzkyana (Dieck) Langenf.) and green flesh Malus plant ‘Xinye 13-11’ (Malus sieversii (Led.) Roem.) were used as experimental materials. Both of them came from Xinjiang, China, and Malus neidzwetzkyana (Dieck) Langenf. is believed to be a variant of Malus sieversii (Led.) Roem. The components and contents of polyphenols in the peel and pulp of the two kinds of fruit during the development period were detected, and the dynamic changes and differences in the polyphenols between the two kinds of fruit were discussed. The results showed that the total polyphenol content of ‘Xinye 13-11’ was higher in the peel and pulp than that of ‘Hongxun 2’, and the content of peel was higher than that of pulp in the two kinds of fruit. An analysis of five types of polyphenols showed that anthocyanins were only contained in the peel and pulp of ‘Hongxun-2’, and the peel had a higher content than the pulp. Cyanidin 3-O-galactoside was the main anthocyanin component. Four other types of substances, except hydroxycinnamics, were higher in ‘Hongxun-2’ than ‘Xinye 13-11’, while the contents of other substances in ‘Xinye 13-11’ were higher than those of ‘Hongxun 2’. The accumulation of major polyphenol components in the peel and flesh of ‘Hongxun 2’ and ‘Xinye 13-11’ apples was significant in the period before and after 65 days after flowering, and the contents of procyanidin B1 and procyanidin C1 were the highest in this period. In addition to the difference in anthocyanin content between ‘Hongxun 2’ and ‘Xinye 13-11’, the chlorogenic acid content in the peel and pulp of ‘Hongxun 2’ was significantly higher than that of ‘Xinye 13-11’, and the contents of other components were lower than those of ‘Xinye 13-11’. Moreover, based on the components and contents of polyphenol components, this paper supports the viewpoint that Malus neidzwetzkyana (Dieck) Langenf is a separate species to Malus sieversii (Led.) Roem. Full article
(This article belongs to the Special Issue Fruit Tree Physiology and Molecular Biology)
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14 pages, 5175 KiB  
Article
Comparative Transcriptome Analysis of Mature Leaves of Dimocarpus longan cv. ‘Sijimi’ Provides Insight into Its Continuous-Flowering Trait
by Shilian Huang, Xinmin Lv, Junbin Wei, Dongmei Han, Jianguang Li and Dongliang Guo
Horticulturae 2024, 10(9), 974; https://doi.org/10.3390/horticulturae10090974 - 14 Sep 2024
Cited by 1 | Viewed by 846
Abstract
Longan (Dimocarpus longan Lour.) is an important tropical and subtropical fruit, and most of its cultivars bloom once a year (once-flowering, OF). Dimocarpus longan cv. ‘Sijimi’ (SJ) is a tropical ecotype variety that blooms several times a year (continuous-flowering, CF) without the [...] Read more.
Longan (Dimocarpus longan Lour.) is an important tropical and subtropical fruit, and most of its cultivars bloom once a year (once-flowering, OF). Dimocarpus longan cv. ‘Sijimi’ (SJ) is a tropical ecotype variety that blooms several times a year (continuous-flowering, CF) without the need for low-temperature induction. Several studies have focused on the mechanism of continuous flowering in SJ longan; however, none used leaves as research material. As leaves are a key organ in sensing floral-induction signals, we compared gene-expression differences between mature leaves of CF (SJ) and OF (D. longan cv. ‘Shixia’ (SX) and D. longan cv. ‘Chuliang’ (CL)) longan by transcriptome sequencing. An average of 47,982,637, 43,833,340 and 54,441,291 clean reads were obtained for SJ, SX and CL respectively, and a total of 6745 differentially expressed genes (DEGs) were detected. Following Metabolic pathways, Plant-pathogen interaction and Biosynthesis of secondary metabolites, most of the other genes were assigned to the KEGG classifications of MAPK signaling pathway- plant, Plant hormone signal transduction, Amino sugar and nucleotide sugar metabolism and Starch and sucrose metabolism. WGCNA analysis clustered genes into 27 modules, among which bisque4 and darkorange2 module genes specifically were expressed at low and high levels in SJ, respectively. Different gene-expression patterns were detected between CF and OF longan in bisque4 and darkorange2 modules, especially the high levels of transcription factor (TF) expression and the large number of gibberellic acid (GA)-signaling-pathway-specific genes expressed at high levels in CF longan (SJ). Floral-induction-gene expression levels in CF longan, such as levels of GA-signaling-related and FT genes, were always high. In CF longan, after vegetative-growth accumulation, flowers could be directly induced, thereby eliminating the need for low-temperature induction. Full article
(This article belongs to the Special Issue Fruit Tree Physiology and Molecular Biology)
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