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Gene Expressions in Response to Diseases, Abiotic Stresses and Pest Damage of Horticultural Products

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A special issue of Horticulturae (ISSN 2311-7524). This special issue belongs to the section "Biotic and Abiotic Stress".

Deadline for manuscript submissions: closed (25 February 2025) | Viewed by 20911

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Dr. Giuliana Maddalena

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Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy
Interests: grapevine downy mildew; disease resistance; disease control strategy; host-pathogen interaction

Dr. Annamaria Mincuzzi

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Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
Interests: postharvest pathology; alternative control means; plant extracts; polyphenolic compounds; pomegranates; seaweeds; disease control; fungi; postharvest diseases; ozone; electrolyzed water; chitosan; latent infections; wound infection; identification; coniella; alternaria; penicillium; botrytis; colletotrichum; cytospora; aspergillus; beneficial microrganisms; aureobasidium; bacillus

Dr. Francesca Garganese

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Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, University of Bari Aldo Moro, Via Amendola 165/A, 70126, Bari, Italy
Interests: insect-borne plant pathogen; olive and citrus pest; microbiome insect, insect/plant interaction; environmental ipm; vector pest damage; insect bionomics

Prof. Dr. Antonio Ippolito

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Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70126 Bari, Italy
Interests: postharvest pathology; molecular biology; alternative control means; grape; citrus; pomegranate
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Special Issue Information

Dear Colleagues,

The international open access journal Horticulturae (SCIE-indexed, Q1-ranked in Horticulture, and is 2.331 IF in 2020) is pleased to announce a new Special Issue titled “Gene Expressions in Response to Diseases, Abiotic Stresses and Pest Damage of Horticultural Products”. We would like to invite you to be part of this Special Issue by submitting a paper.

Horticultural crops encompass a wide range of plant species worldwide. Many of these crops represent important sources of food, feed and raw substances, providing a broad spectrum of nutrients and bioactive compounds that play an essential role in resisting plant and human diseases, in accordance with the One Health approach.

It must also be pointed out that horticultural crops represent a key resource in the economy of several countries. Unfortunately, crops are continuously exposed to a broad spectrum of pathogens (viruses, bacteria and fungi), pests and abiotic damages responsible for significant yield and economic losses along the supply chain, starting in the field and up to the point of sale. In addition, the increasingly restrictive European regulations for plant protection products encourage studies on innovative tools for disease and pest control programs, such as genetic modification and analysis of alternative control means. However, over time, plants have evolved sophisticated defense mechanisms to face both pathogen and insect attacks and respond to abiotic stresses. The identification of genes involved in the defense response and stress tolerance is essential for choosing more resistant or less susceptible crops that could allow for the more sustainable management of diseases and damage.

The proposed Special Issue welcomes original and explorative articles that investigate pathways and expressed genes involved in resistance mechanisms to pests and pathogens and abiotic stress tolerance, thus opening new horizons for preserving and increasing crop production.

In the hope that this invitation receives your favorable consideration, we look forward to our future collaboration.

Dr. Giuliana Maddalena
Dr. Annamaria Mincuzzi
Dr. Francesca Garganese
Prof. Dr. Antonio Ippolito
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

disease resistance
IPM
horticultural products
host–pathogen interactions
resistance genes
NGS
alternative control means
biostimulants
infection and vector biocontrol
abiotic damage
stress tolerance
environmental conditions

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Published Papers (9 papers)

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Research

20 pages, 6044 KiB

Open AccessArticle

Coordinated Regulation of Iron-Acquisition Genes and Citrate Biosynthesis Drives Seasonal Iron Deficiency Adaptation in ‘Yali’ Pears (Pyrus bretschneideri Rehd.)

by Shuilin Liu, Ming Zhang, Huiying Wang, Yue Xu, Chaodie Wen, Jianguang Zhang, Yuxing Zhang and Haiyan Shi

Horticulturae 2025, 11(5), 460; https://doi.org/10.3390/horticulturae11050460 - 25 Apr 2025

Viewed by 241

Abstract

Iron deficiency chlorosis severely limits the productivity of ‘Yali’ pears in alkaline soils. This study systematically investigated the physiological and molecular responses of ‘Yali’ pears to varying degrees of iron deficiency, focusing on the roles of PbFRO2 (Pyrus bretschneideri Ferric Reductase Oxidase 2), PbIRT1 (Pyrus bretschneideri Iron-Regulated Transporter 1), and PbCS2 (Pyrus bretschneideri Citrate Synthase 2) in iron uptake and homeostasis. Based on field observations, pear trees were categorized into normal, moderately chlorotic, and severely chlorotic groups. Results demonstrated that moderate iron deficiency upregulated PbFRO2 (2.86–7.09-fold), enhanced root ferric reductase (FCR) activity, and promoted Fe³⁺ reduction and Fe²⁺ transport. In contrast, severe deficiency suppressed the expression of these genes and reduced photosynthetic efficiency. Leaf citrate content significantly increased with chlorosis severity, while root citrate content exhibited seasonal fluctuations, peaking in July. Multivariate analyses (PCA and PLS-DA) revealed distinct physiological clustering: normal and moderately chlorotic groups overlapped, whereas the severely chlorotic group formed a separate cluster, reflecting a transition from compensatory activation to metabolic collapse. PbFRO2 emerged as a central regulator, driving root iron storage in spring and redistribution in summer. These findings elucidate a biphasic adaptation strategy, where moderate deficiency triggers gene-mediated iron mobilization, whereas severe stress disrupts homeostasis. This study provides critical insights into iron metabolism dynamics and proposes PbFRO2 as a molecular target for breeding iron-efficient pear cultivars. Full article

(This article belongs to the Special Issue Gene Expressions in Response to Diseases, Abiotic Stresses and Pest Damage of Horticultural Products)

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18 pages, 5388 KiB

Open AccessArticle

Transcriptome and Physiological Analyses of Resistant and Susceptible Pepper (Capsicum annuum) to Verticillium dahliae Inoculum

by Xinmin Huang, Liming He, Huimin Tan, Jiayi Liu, Qiucheng Qiu, Qidi Sun, Lejun Ouyang, Hanbing Han and Qinqin He

Horticulturae 2024, 10(11), 1160; https://doi.org/10.3390/horticulturae10111160 - 31 Oct 2024

Viewed by 1077

Abstract

Pepper (Capsicum annuum) is a globally important vegetable, and Verticillium wilt is an important disease affecting peppers and is caused by Verticillium dahliae, which can severely reduce yields. However, the molecular mechanisms underlying the responses of pepper to infection by V. dahliae are largely unknown. We performed physiological and transcriptome analysis using resistant and susceptible pepper cultivars inoculated with V. dahliae. Compared to the susceptible cultivar MS66, the resistant cultivar MS72 retained higher chlorophyll content and lower malondialdehyde content after inoculation. At 3 days after inoculation (DAI), compared with MS66, 534 differentially expressed genes (DEGs) were identified in MS72. At 5 DAI, 2392 DEGs were identified in MS72 compared with MS66. The DEGs in MS72 were mainly enriched in the cell wall and photosynthesis-related Gene Ontology terms, as well as in pathways such as cutin, suberin, wax biosynthesis, phenylpropanoid biosynthesis, and photosynthesis. Using weighted gene co-expression network analysis, 36 hub genes involved in the resistance response were identified, including the transcription factor bHLH93 (Capana04g000815), defense-like protein 1 (MSTRG.5904), and miraculin-like (Capana10g002167). Our findings contribute to a more comprehensive understanding of the response mechanism of pepper to V. dahliae inoculation, providing new avenues for improving pepper resistance through breeding programs. Full article

(This article belongs to the Special Issue Gene Expressions in Response to Diseases, Abiotic Stresses and Pest Damage of Horticultural Products)

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14 pages, 4565 KiB

Open AccessFeature PaperArticle

Virus-Induced Silencing of a Sequence Coding for Loricrin-like Protein in Phytophthora infestans upon Infection of a Recombinant Vector Based on Tobacco Mosaic Virus

by Rossella Labarile, Annamaria Mincuzzi, Roberta Spanò and Tiziana Mascia

Horticulturae 2023, 9(3), 360; https://doi.org/10.3390/horticulturae9030360 - 9 Mar 2023

Viewed by 2654

Abstract

Phytophthora infestans is the oomycete responsible for late blight disease of Solanaceae that causes both yield and economic losses. With the aim of reducing plant wilt and high management costs mainly due to wide fungicide applications, alternative eco-sustainable control strategies are needed. RNA interference (RNAi) is a powerful tool for gene function studies that can be accomplished by constitutive transformation or transient expression such as virus-induced gene silencing (VIGS) experiments. VIGS makes use of viruses to deliver sequences homologous to a target gene fragment and trigger RNAi. Indeed, a P. infestans ortholog of plant loricrin-like protein (LLP), named PiLLP, has been silenced using the direct infection of a recombinant vector based on the plant virus tobacco mosaic virus (TMV-PiLLP-1056), aiming to reduce the oomycete sexual reproduction. For this purpose, the gene coding for the green fluorescent protein (GFP) present in the TMV-GFP-1056 vector has been replaced with an antisense construct obtained by fusion PCR of the PiLLP 5′-UTR and 3′-UTR sequences. Here, we show that RNAi can be expressed in the A1 mating type of P. infestans strain 96.9.5.1 by VIGS using the direct infection of TMV-PiLLP-1056. We provide evidence that the recombinant vector can enter, replicate, and persist in mycelia of P. infestans where it induces the partial downregulation of the PiLLP transcript. Compared with the wild-type, the PiLLP-silenced A1 mating type had slower colony growth and a diminished virulence in detached tomato leaflets. This seems to be the first evidence of a constitutive gene downregulation of P. infestans using a recombinant vector based on a plus-sense RNA plant virus. Full article

(This article belongs to the Special Issue Gene Expressions in Response to Diseases, Abiotic Stresses and Pest Damage of Horticultural Products)

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16 pages, 5371 KiB

Open AccessArticle

Physiological and Transcriptomic Analyses Reveal the Response of Medicinal Plant Bletilla striata (Thunb. ex A. Murray) Rchb. f. via Regulating Genes Involved in the ABA Signaling Pathway, Photosynthesis, and ROS Scavenging under Drought Stress

by Hai Liu, Kaizhang Chen, Lin Yang, Xue Han, Mingkai Wu and Zhijun Shen

Horticulturae 2023, 9(3), 307; https://doi.org/10.3390/horticulturae9030307 - 23 Feb 2023

Cited by 3 | Viewed by 2127

Abstract

Bletilla striata is a valuable Chinese herbal medicinal plant widely used in various fields. To meet the market demand for this herb, the tissue culture technology of B. striata was developed. However, drought stress has been a significant threat to the survival of cultivated B. striata. To further understand the underlying mechanisms of B. striata under drought stress, its response was investigated at the physiological and transcriptional levels. Our photosynthesis results show that the decline of the net photosynthesis rate (Pn) in B. striata leaves was mainly caused by nonstomatal limitation factors. Using transcriptomic analysis 2398, differentially expressed genes (DEGs) were identified. KEGG enrichment analysis showed that DEGs involved in plant hormone signal transduction (ko04075) were significantly altered, especially the abscisic-acid signaling pathway. The up-regulations of the serine/threonine protein kinase (SnRK2) and S-type anion (SLAH2) channels might lead to stomatal closure, which is the reason for decline of photosynthesis. Moreover, the downregulation of cytochrome b6 and photosystem I reaction center subunit III/IV might be the major reason for nonstomatal limitation. In addition, B. striata enhanced the ability of ROS scavenging via activating the gene expression of superoxide dismutase, catalase, and peroxidase in response to drought stress. Our study enhanced the understanding of B. striata in response to drought stress. Full article

(This article belongs to the Special Issue Gene Expressions in Response to Diseases, Abiotic Stresses and Pest Damage of Horticultural Products)

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16 pages, 3165 KiB

Open AccessArticle

Stepwise Optimization of the RT-qPCR Protocol and the Evaluation of Housekeeping Genes in Pears (Pyrus bretschneideri) under Various Hormone Treatments and Stresses

by Peng Zhou, Linlin Huang, Yingtao Wang, Xiao Li, Xinxin Feng and Liulin Li

Horticulturae 2023, 9(2), 275; https://doi.org/10.3390/horticulturae9020275 - 17 Feb 2023

Cited by 5 | Viewed by 2639

Abstract

Real-time quantitative PCR (RT-qPCR) has become a widely used method for exploring plant gene expression level. The method requires using some stably expressed genes as a reference to accurately normalize the RT-qPCR data. However, under various stresses and hormone treatments, the levels of most reference genes vary. Environmental variations also influence their expression levels. The lack of validated, stably expressed reference genes can mislead the study of gene function in pears. “Huangguan” pears have recently become the focus of research on stress resistance mechanisms, such as high resistance. Therefore, the aim of this study was to select the optimal reference genes in Huangguan pears, and we analyzed the expression of the genes EF1α, ACT, SKD1, YLS8, UBQ, GAPDH, TUB, and WDP in a series of pear leaf sets under various stresses and hormone treatments. Using different statistical algorithms, we found that under various treatments, the WDP gene had more stable expression, ACT was the most stable under MeJA treatment, YLS8 was the most valuable reference gene under ABA hormone and heat stress conditions, and GAPDH showed worst results compared to other housekeeping genes, except under heat stress. These results will supply valuable and updated information for the selection of housekeeping genes in pears under biotic and abiotic stresses in the future. Full article

(This article belongs to the Special Issue Gene Expressions in Response to Diseases, Abiotic Stresses and Pest Damage of Horticultural Products)

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6 pages, 886 KiB

Open AccessCommunication

Touch-Induced Transcriptional Changes in Flower Buds of a Non-Model Horticultural Plant Dianthus hybrida

by Ryo Nishijima, Alvin Sanjaya, Harue Shinoyama and Yusuke Kazama

Horticulturae 2022, 8(10), 918; https://doi.org/10.3390/horticulturae8100918 - 7 Oct 2022

Cited by 1 | Viewed by 2038

Abstract

Touch stimulus responses are common in plants. Some flowering plants sense the arrival of their pollinators and secrete nectar or release pollen sacs, facilitating successful pollination. Molecular mechanisms for mechanical stimulus responses in plants are well characterized in Arabidopsis leaves, but not in non-model plants or other organs such as flowers. Here, we performed RNA-seq analysis of touched flower buds of Dianthus hybrida, a major ornamental plant. Upon touch treatment, 931 and 132 genes were upregulated and downregulated, respectively. GO enrichment analysis revealed that genes encoding serine/threonine protein kinases were significantly abundant among the upregulated genes, which is consistent with previous studies that demonstrated the pivotal role of protein phosphorylation in the touch stimulus response of Arabidopsis leaves. In comparison with the gene expression profile of touched Arabidopsis leaves, the same families but different homologs of the representative touch-induced genes encoding protein kinases were upregulated, showing that phosphorelay signaling was the common mechanism for touch stimulus response in flowers and leaves, but the players of the phosphorelay signaling were different. These results will contribute to further studies on the mechanical stimulus responses of ornamental flowers and the utilization of this mechanism for breeding programs. Full article

(This article belongs to the Special Issue Gene Expressions in Response to Diseases, Abiotic Stresses and Pest Damage of Horticultural Products)

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19 pages, 3012 KiB

Open AccessArticle

The Genes Associated with Jasmonic Acid and Salicylic Acid Are Induced in Tropical Chili Pepper against Ralstonia solanacearum by Applying Arbuscular Mycorrhizal Fungi

by Erlina Ambarwati, Triwidodo Arwiyanto, Jaka Widada, Taufan Alam, Ignatius Putra Andika and Taryono

Horticulturae 2022, 8(10), 876; https://doi.org/10.3390/horticulturae8100876 - 23 Sep 2022

Cited by 6 | Viewed by 2866

Abstract

Controlling soil-borne pathogens is a significant problem in agriculture. Arbuscular mycorrhizae have a potential role in controlling soil-borne pathogens by increasing plant phytohormone contents. However, the mechanism of resistance by mycorrhizae has not been fully elucidated, particularly against bacterial wilt disease in Solanaceae. This study examined the role of mycorrhizae in expressing genes involved in the signaling pathways mediated by jasmonic acid (JA) and salicylic acid (SA) in tropical chili pepper against the bacterium Ralstonia solanacearum. Seedlings from ten genotypes of chili pepper were inoculated with a consortium of five mycorrhizal species and/or inoculated with a mixture of nine isolates of R. solanacearum. The leaves of 10-week-old plants after the treatment were sampled for real-time polymerase chain reaction analysis. The results showed that the mycorrhizae strengthened the immune system of tropical chili pepper by increasing the relative gene expression levels of JA and SA in genotypes with high and low responsiveness to the mycorrhizae. The relative gene expression level of JA was related to the percentage colonization of mycorrhizae and the resistance of the tropical chili pepper genotypes to R. solanacearum. The relative gene expression level of SA was associated with the resistance of tropical chili pepper to R. solanacearum. Full article

(This article belongs to the Special Issue Gene Expressions in Response to Diseases, Abiotic Stresses and Pest Damage of Horticultural Products)

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19 pages, 7008 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of Eggplant DIR Gene Family in Response to Biotic and Abiotic Stresses

by Kaijing Zhang, Wujun Xing, Suao Sheng, Dekun Yang, Fengxian Zhen, Haikun Jiang, Congsheng Yan and Li Jia

Horticulturae 2022, 8(8), 732; https://doi.org/10.3390/horticulturae8080732 - 14 Aug 2022

Cited by 10 | Viewed by 2826

Abstract

Dirigent proteins (DIR) play important roles in the biosynthesis of lignins and lignans, defensive responses, secondary metabolism, and disease resistance in plants. The DIR gene family has been identified and studied in many plants. However, the identification of DIR gene family in eggplant has not been conducted yet. Therefore, in this study, based on the available genome information of eggplant, the DIR family genes in eggplant were identified with bioinformatics methods. The expression pattern analyses of eggplant DIR family genes in different organs and stresses were also conducted to understand their biological functions. The results showed that a total of 24 DIR genes were identified in the eggplant, which were divided into three subfamilies (DIR-a, DIR-b/d, and DIR-e). Synteny analysis of DIR genes among eggplant, Arabidopsis, and rice showed that 15 eggplant DIR genes were colinear with 18 Arabidopsis DIR genes, and 16 eggplant DIR genes were colinear with 15 rice DIR genes. Phylogenetic tree analysis showed that 19 pairs of orthologous genes were identified between eggplant and pepper. The cis-acting elements analysis implied that the eggplant DIR genes contained a lot of cis-elements associated with stress and hormone response. The organ-specific expression analysis of eggplant DIR family genes revealed that only the SmDIR3 gene was highly expressed in all the 19 organs of eggplant. Some SmDIR genes, including SmDIR7, SmDIR8, SmDIR11, SmDIR14, SmDIR18, SmDIR19, SmDIR20, and SmDIR23, were not or were lowly expressed in the eggplant organs, while the other eggplant DIR family genes showed an organ-specific expression pattern. Furthermore, 19 of 24 SmDIR genes were differentially expressed in response to abiotic and biotic stresses. 5 SmDIR genes, including SmDIR3, SmDIR5, SmDIR6, SmDIR12, and SmDIR22, were differentially expressed under multiple types of abiotic and biotic stresses. Especially notable, the SmDIR22 gene was differentially expressed under three types of abiotic stresses and two types of biotic stresses, which indicated that the SmDIR22 gene plays an important role in the response to abiotic and biotic stresses. These results provide valuable evidence for a better understanding of the biological role of DIR genes in eggplant. Full article

(This article belongs to the Special Issue Gene Expressions in Response to Diseases, Abiotic Stresses and Pest Damage of Horticultural Products)

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14 pages, 3090 KiB

Open AccessArticle

Molecular Cloning, Characterization, and Expression Analysis of SIMILAR TO RCD-ONE (SRO) Family Genes Responding to Abiotic and Biotic Stress in Cucumber

by Lingdi Xiao, Zixian Zhou, Chuxia Zhu, Jindong Zhao, Zhaoyang Hu, Shiqiang Liu and Yong Zhou

Horticulturae 2022, 8(7), 634; https://doi.org/10.3390/horticulturae8070634 - 13 Jul 2022

Cited by 1 | Viewed by 2229

Abstract

SIMILAR TO RCD-ONE (SRO) is a plant-specific small protein family that controls many biological processes including physiological development and stress responses. The SRO gene family has been studied in several plant species, but no detailed characterization and expression profiles of this important gene family were performed in cucumber. In this study, we characterize the SRO genes in cucumber, and determined their transcript levels in various tissues and under exposure to diverse biotic and abiotic stressors. Four SRO genes (named as CsSRO1–CsSRO4) were identified and isolated, which were distributed on three different chromosomes. Gene duplication analysis showed that only one pair of segmental duplication event was identified, but no tandem duplication events were detected. All CsSROs consist of the PARP domain and a C-terminal RST domain, while the N-terminal WWE domain was only present in CsSRO2 and CsSRO4. SROs from 15 plant species are divided into two groups (I and II), and group I can be further divided into four subgroups (Ia to Id) according to the phylogenetic tree. The conserved motif and gene structure analyses showed that SROs within the same branch of the phylogenetic tree have analogous conserved motifs configuration and gene structures. However, SRO genes possessed variable numbers of introns in different subgroups, which may affect the evolution of new family members. RNA-Seq data and qRT-PCR results showed that the four CsSRO genes have distinct expression pattern in various tissues and under diverse stresses, suggesting their multiple functions in plant growth and stress responses. The findings provide a basis for further research aiming at functional characterization of the regulatory mechanism to reveal the roles of CsSRO genes in developmental and stress-related processes of cucumber. Full article

(This article belongs to the Special Issue Gene Expressions in Response to Diseases, Abiotic Stresses and Pest Damage of Horticultural Products)

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