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Gene Regulation of Ripening, Senescence and Stress Resistance in Horticultural...
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Gene Regulation of Ripening, Senescence and Stress Resistance in Horticultural Crops

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (20 February 2025) | Viewed by 8040

Special Issue Editor

Prof. Dr. Shaolan Yang

E-Mail Website
Guest Editor
College of Horticulture, Qingdao Agricultural University, Qingdao, China
Interests: horticultural crops; fruits; genetics; breeding; genome; genomics; gene regulation

Special Issue Information

Dear Colleagues,

Horticultural crops' ripening, senescence and stress resistance affect the postharvest life, quality, and commercial value. So, how may we maintain and extend the shelf-life most effectively to increase product values? Ripening and senescence are complex processes, which include cell wall softening, sugar accumulation, color changes, the production of aroma and volatiles and increased pathogen invasion. The progress was related to gene expression coordination, cell–cell signaling, and various biochemical pathways. Genes involved in regulating fruit ripening, senescence and stress resistance are being studied in great demand, which provides the theoretical basis for elucidating the mechanism of such progress. In this Special Issue, we encourage the submission of manuscripts of original papers and review articles focusing on the gene regulation of ripening, senescence and stress resistance in horticultural crops, including fruit, vegetables, flowers, tea and nuts. Manuscripts reporting novel fundamentals and innovations in research techniques are encouraged.

Prof. Dr. Shaolan Yang
Guest Editor

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Keywords

  • horticultural crops
  • fruits
  • flowers
  • tea
  • nuts
  • ripening
  • senescence
  • stress resistance gene regulation
  • genetics
  • transcriptomics

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Published Papers (5 papers)

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Research

19 pages, 3638 KiB  
Article
Systematic Analysis of Stay-Green Genes in Six Ipomoea Species Reveals the Evolutionary Dynamics, Carotenoid and Anthocyanin Accumulation, and Stress Responses of Sweet Potato
by Zhidan Zuo, Huihui Ma, Longteng Li, Jialin Qian, Minghui Zhang, Xiang Li, Yeshun Sheng and Yuxin Wang
Genes 2025, 16(3), 266; https://doi.org/10.3390/genes16030266 - 24 Feb 2025
Viewed by 438
Abstract
Background/Objectives: Stay-green proteins (SGRs) play a vital role in regulating plant chlorophyll degradation and senescence. However, this gene family has not been explored in Ipomoea species and sweet potato. Methods: A total of 19 SGR family genes (SGRs) were identified using [...] Read more.
Background/Objectives: Stay-green proteins (SGRs) play a vital role in regulating plant chlorophyll degradation and senescence. However, this gene family has not been explored in Ipomoea species and sweet potato. Methods: A total of 19 SGR family genes (SGRs) were identified using Basic Local Alignment Search Tool (BLAST) methods. The proteins’ physiological properties, evolutionary and phylogenetic relationships, conserved domain and motifs, gene structures, collinearity, and promoter cis-elements were systematically analyzed. Moreover, expression patterns and protein interaction network analyses were performed for sweet potato. Results: In this study, we identified 19 SGRs in six Ipomoea species. These SGRs were divided into four subgroups according to their phylogenetic relationships. Domian analysis revealed that SGRs had the conserved “stay-green” domain. Gene structure analysis showed that SGRs had similar structures. The collinearity analysis revealed that the SGRs originated from two genes, with one gene undergoing duplication during evolution history; moreover, the SGRs experienced rearrangement throughout the evolutionary process in the Ipomoea species. Cis-elements related to pigment biosynthesis and hormone and stress responses were found. In addition, expression pattern analysis showed that IbSGRs, especially IbSGR1, IbSGR2, and IbSGR3, might play an important role in pigment accumulation. The SGRs could also respond to stress responses (i.e., cold, drought, and salt) and take part in hormone crosstalk (i.e., abscisic acid (ABA), methyl jasmonate (MeJA), salicylic acid (SA)). Conclusions: Taken together, the findings of this study provide new insights for further understanding the functions of SGRs and candidate genes for pigment accumulation and stress tolerance in sweet potatoes. Full article
(This article belongs to the Special Issue Gene Regulation of Ripening, Senescence and Stress Resistance in Horticultural Crops)
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13 pages, 2981 KiB  
Article
Transcriptome Analysis of Ethylene-Related Genes in Chlorine Dioxide-Treated Fresh-Cut Cauliflower
by Weiwei Jin, Qiaojun Jiang, Haijun Zhao, Fengxian Su, Yan Li and Shaolan Yang
Genes 2024, 15(8), 1102; https://doi.org/10.3390/genes15081102 - 21 Aug 2024
Cited by 2 | Viewed by 1114
Abstract
Chlorine dioxide (ClO2) is widely used for the quality preservation of postharvest horticultural plants. However, the molecular mechanism of how ClO2 works is not clear. The purpose of this study was to understand ethylene-related molecular signaling in ClO2-treated [...] Read more.
Chlorine dioxide (ClO2) is widely used for the quality preservation of postharvest horticultural plants. However, the molecular mechanism of how ClO2 works is not clear. The purpose of this study was to understand ethylene-related molecular signaling in ClO2-treated fresh-cut cauliflower florets. Transcriptome analysis was used to investigate ethylene-related gene regulation. A total of 182.83 Gb clean data were acquired, and the reads of each sample to the unique mapped position of the reference genome could reach more than 85.51%. A sum of 2875, 3500, 4582 and 1906 differential expressed genes (DEGs) were identified at 0 d, 4 d, 8 d and 16 d between the control group and ClO2-treated group, respectively. DEGs were enriched in functions such as ‘response to oxygen-containing compounds’ and ‘phosphorylation’, as well as MAPK signaling pathway, plant hormone transduction pathway and so on. Genes, including OXI1, MPK3, WRKY22 and ERF1, which are located at the junction of wounding, pathogen attack, pathogen infection or ethylene signal transduction pathways, were up-regulated in response to stress. ETR and CTR1 (both up-regulated), as well as three down-regulated genes, including BolC5t34953H (a probable NAC), BolC1t05767H (a probable NAC) and BolC2t06548H (a probable ERF13), might work as negative regulators for ethylene signal transduction. In conclusion, ethylene-related genes and pathways are involved in ClO2 treatment, which might enhance stress resistance and have a negative feedback mechanism. Full article
(This article belongs to the Special Issue Gene Regulation of Ripening, Senescence and Stress Resistance in Horticultural Crops)
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17 pages, 5866 KiB  
Article
Transcriptomic Analysis of Alternative Splicing Events during Different Fruit Ripening Stages of Coffea arabica L.
by Haohao Yu, Xiaofei Bi, Zhongxian Li, Xingfei Fu, Yanan Li, Yaqi Li, Yang Yang, Dexin Liu, Guiping Li, Wenjiang Dong and Faguang Hu
Genes 2024, 15(4), 459; https://doi.org/10.3390/genes15040459 - 5 Apr 2024
Cited by 1 | Viewed by 1640
Abstract
To date, genomic and transcriptomic data on Coffea arabica L. in public databases are very limited, and there has been no comprehensive integrated investigation conducted on alternative splicing (AS). Previously, we have constructed and sequenced eighteen RNA-seq libraries of C. arabica at different [...] Read more.
To date, genomic and transcriptomic data on Coffea arabica L. in public databases are very limited, and there has been no comprehensive integrated investigation conducted on alternative splicing (AS). Previously, we have constructed and sequenced eighteen RNA-seq libraries of C. arabica at different ripening stages of fruit development. From this dataset, a total of 3824, 2445, 2564, 2990, and 3162 DSGs were identified in a comparison of different fruit ripening stages. The largest proportion of DSGs, approximately 65%, were of the skipped exon (SE) type. Biologically, 9 and 29 differentially expressed DSGs in the spliceosome pathway and carbon metabolism pathway, respectively, were identified. These DSGs exhibited significant variations, primarily in S1 vs. S2 and S5 vs. S6, and they involve many aspects of organ development, hormone transduction, and the synthesis of flavor components. Through the examination of research findings regarding the biological functions and biochemical pathways associated with DSGs and DEGs, it was observed that six DSGs significantly enriched in ABC transporters, namely, LOC113712394, LOC113726618, LOC113739972, LOC113725240, LOC113730214, and LOC113707447, were continually down-regulated at the fruit ripening stage. In contrast, a total of four genes, which were LOC113732777, LOC113727880, LOC113690566, and LOC113711936, including those enriched in the cysteine and methionine metabolism, were continually up-regulated. Collectively, our findings may contribute to the exploration of alternative splicing mechanisms for focused investigations of potential genes associated with the ripening of fruits in C. arabica. Full article
(This article belongs to the Special Issue Gene Regulation of Ripening, Senescence and Stress Resistance in Horticultural Crops)
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14 pages, 7588 KiB  
Article
Genome-Wide Investigation of the PLD Gene Family in Tomato: Identification, Analysis, and Expression
by Xudong Guo, Wenying Zhu, Fu Wang and Hui Wang
Genes 2024, 15(3), 326; https://doi.org/10.3390/genes15030326 - 2 Mar 2024
Cited by 3 | Viewed by 2153
Abstract
Phospholipase Ds (PLDs) are important phospholipid hydrolases in plants that play crucial roles in the regulation of plant growth, development, and stress tolerance. In this study, 14 PLD genes were identified in the tomato genome and were localized on eight chromosomes, and one [...] Read more.
Phospholipase Ds (PLDs) are important phospholipid hydrolases in plants that play crucial roles in the regulation of plant growth, development, and stress tolerance. In this study, 14 PLD genes were identified in the tomato genome and were localized on eight chromosomes, and one tandem-duplicated gene pair was identified. According to a phylogenetic analysis, the genes were categorized into four subtypes: SlPLDα, β, and δ belonged to the C2-PLD subfamily, while SlPLDζ belonged to the PXPH-PLD subfamily. The gene structure and protein physicochemical properties were highly conserved within the same subtype. The promoter of all the SlPLD genes contained hormone-, light-, and stress-responsive cis-acting regulatory elements, but no significant correlation between the number, distribution, and type of cis-acting elements was observed among the members of the same subtype. Transcriptome data showed that the expression of the SlPLD genes was different in multiple tissues. A quantitative RT-PCR analysis revealed that the SlPLD genes responded positively to cold, salt, drought, and abscisic acid treatments, particularly to salt stress. Different expression patterns were observed for different genes under the same stress, and for the same gene under different stresses. The results provide important insights into the functions of SlPLD genes and lay a foundation for further studies of the response of SlPLD genes to abiotic stresses. Full article
(This article belongs to the Special Issue Gene Regulation of Ripening, Senescence and Stress Resistance in Horticultural Crops)
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16 pages, 7572 KiB  
Article
CaCP15 Gene Negatively Regulates Salt and Osmotic Stress Responses in Capsicum annuum L.
by Luyao Zhou, Sizhen Yang, Chunlin Chen, Meng Li, Qingjie Du, Jiqing Wang, Yanxu Yin and Huaijuan Xiao
Genes 2023, 14(7), 1409; https://doi.org/10.3390/genes14071409 - 7 Jul 2023
Cited by 3 | Viewed by 1932
Abstract
Salt and osmotic stress seriously restrict the growth, development, and productivity of horticultural crops in the greenhouse. The papain-like cysteine proteases (PLCPs) participate in multi-stress responses in plants. We previously demonstrated that salt and osmotic stress affect cysteine protease 15 of pepper ( [...] Read more.
Salt and osmotic stress seriously restrict the growth, development, and productivity of horticultural crops in the greenhouse. The papain-like cysteine proteases (PLCPs) participate in multi-stress responses in plants. We previously demonstrated that salt and osmotic stress affect cysteine protease 15 of pepper (Capsicum annuum L.) (CaCP15); however, the role of CaCP15 in salt and osmotic stress responses is unknown. Here, the function of CaCP15 in regulating pepper salt and osmotic stress resistance was explored. Pepper plants were subjected to abiotic (sodium chloride, mannitol, salicylic acid, ethrel, methyl jasmonate, etc.) and biotic stress (Phytophthora capsici inoculation). The CaCP15 was silenced through the virus-induced gene silencing (VIGS) and transiently overexpressed in pepper plants. The full-length CaCP15 fragment is 1568 bp, with an open reading frame of 1032 bp, encoding a 343 amino acid protein. CaCP15 is a senescence-associated gene 12 (SAG12) subfamily member containing two highly conserved domains, Inhibitor 129 and Peptidase_C1. CaCP15 expression was the highest in the stems of pepper plants. The expression was induced by salicylic acid, ethrel, methyl jasmonate, and was infected by Phytophthora capsici inoculation. Furthermore, CaCP15 was upregulated under salt and osmotic stress, and CaCP15 silencing in pepper enhanced salt and mannitol stress resistance. Conversely, transient overexpression of CaCP15 increased the sensitivity to salt and osmotic stress by reducing the antioxidant enzyme activities and negatively regulating the stress-related genes. This study indicates that CaCP15 negatively regulates salt and osmotic stress resistance in pepper via the ROS-scavenging. Full article
(This article belongs to the Special Issue Gene Regulation of Ripening, Senescence and Stress Resistance in Horticultural Crops)
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