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Keywords = auxin signal transduction

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25 pages, 16017 KB  
Article
Identification of Key Regulatory Genes Associated with Double-Petaled Phenotype in Lycoris longituba via Transcriptome Profiling
by Zhong Wang, Xiaoxiao Xu, Chuanqi Liu, Fengjiao Zhang, Xiaochun Shu and Ning Wang
Horticulturae 2025, 11(10), 1156; https://doi.org/10.3390/horticulturae11101156 - 26 Sep 2025
Viewed by 285
Abstract
Lycoris longituba produces a single flower bearing six tepals. The double-petaled phenotype of L. longituba has gained significant interest in China due to its ornamental and commercial value in tourism industries. This double-petal phenotype, characterized by stamen petalization, shows improved esthetic characteristics compared [...] Read more.
Lycoris longituba produces a single flower bearing six tepals. The double-petaled phenotype of L. longituba has gained significant interest in China due to its ornamental and commercial value in tourism industries. This double-petal phenotype, characterized by stamen petalization, shows improved esthetic characteristics compared with conventional single-petal form. However, the molecular mechanisms underlying this floral trait remain largely undefined. In this study, RNA-based comparative transcriptomic analysis was performed between single- and double-petaled flowers of L. longituba at the fully opened flower stage. Approximately 13,848 differentially expressed genes (DEGs) were identified (6528 upregulated and 7320 downregulated genes). Functional annotation through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed several DEGs potentially involved in double-petal development. Six candidate genes, including the hub genes LlbHLH49, LlNAC1, LlSEP, LlTIFY, and LlAGL11, were identified based on DEG functional annotation and weighted gene co-expression network analysis (WGCNA). Transcription factors responsive to phytohormonal signaling were found to play a pivotal role in modulating double-petal development. Specifically, 123 DEGs were involved in phytohormone biosynthesis and signal transduction pathways, including those associated with auxin, cytokinin, gibberellin, ethylene, brassinosteroid, and jasmonic acid. Moreover, 521 transcription factors (TFs) were identified, including members of the MYB, WRKY, AP2/ERF, and MADS-box families. These results improve the current understanding of the genetic regulation of the double tepal trait in L. longituba and offer a base for future molecular breeding strategies to enhance ornamental characteristics. Full article
(This article belongs to the Topic Genetic Breeding and Biotechnology of Garden Plants)
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21 pages, 8141 KB  
Article
Comprehensive Histological, Endogenous Hormone, and Transcriptome Analysis to Reveal the Mechanism of Hormone Regulation Mediating Pepper (Capsicum annum L.) Fruit Size
by Sijie Tang, Zekui Ou, Xiaowen Fan, Qijian Ning, Wei Liu, Xin Liu, Xingtian Long, Jiahao Zhou and Yuhua Liu
Horticulturae 2025, 11(10), 1150; https://doi.org/10.3390/horticulturae11101150 - 25 Sep 2025
Viewed by 349
Abstract
As the only harvest organ of pepper, fruit size is an important yield determinant. To elucidate the molecular mechanisms underlying pepper fruit size, we performed histological, physiological, and transcriptomic analyses on the pepper varieties QB6 (large fruit) and CXJ82 (small fruit). High contents [...] Read more.
As the only harvest organ of pepper, fruit size is an important yield determinant. To elucidate the molecular mechanisms underlying pepper fruit size, we performed histological, physiological, and transcriptomic analyses on the pepper varieties QB6 (large fruit) and CXJ82 (small fruit). High contents of auxin and cytokinin in the early stage of fruit development promoted the rapid division of fruit cells in both varieties, which provided sufficient cells for subsequent fruit enlargement. High gibberellin accumulation induced the elongation and expansion of QB6 pericarp cells. Transcriptome analysis showed that genes related to cell division, cell wall polysaccharide degradation, and photosynthesis were highly expressed in QB6 fruit, likely contributing to its larger size. In the hormone–signal transduction factor–gene interaction network, GID6, GID1, IAA12, MYC30, and SAUR36 exhibited high correlations with numerous genes related to cell division, the cell wall, and photosynthesis, emerging as key signal transduction factors for the hormone-mediated regulation of pepper fruit size. Weighted gene co-expression network analysis identified the transcription factors OFP20, HD-ZIP6, and HD-ZIP13 as fundamental for pepper fruit size regulation. Our results expand the understanding of hormone regulation of pepper fruit size, providing a foundation for the breeding and improvement of excellent pepper varieties. Full article
(This article belongs to the Special Issue Genomics and Genetic Diversity in Vegetable Crops)
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21 pages, 2296 KB  
Article
Integrated Transcriptomic and Metabolomic Analyses of Seed-Filling Disorders in Soybeans Under Different Ecological Conditions
by Junxia Huang, Wei Zheng, Zicong Liang, Zhenghao Zhang, Jiayi Li, Huijun Zhang, Haiying Wang, Xue Ao, Xingdong Yao and Futi Xie
Agronomy 2025, 15(10), 2266; https://doi.org/10.3390/agronomy15102266 - 24 Sep 2025
Viewed by 262
Abstract
Disorders in soybean seed-filling can lead to wrinkled seeds, affecting yield and quality. Previous studies have demonstrated that some soybean cultivars from Jiamusi, Heilongjiang Province (cold-temperate continental monsoon, ~3.5 °C mean annual temperature, ~530 mm precipitation) exhibit seed-filling disorders when cultivated in Shenyang, [...] Read more.
Disorders in soybean seed-filling can lead to wrinkled seeds, affecting yield and quality. Previous studies have demonstrated that some soybean cultivars from Jiamusi, Heilongjiang Province (cold-temperate continental monsoon, ~3.5 °C mean annual temperature, ~530 mm precipitation) exhibit seed-filling disorders when cultivated in Shenyang, Liaoning Province (mid-temperate semi-humid continental monsoon, ~8.3 °C, ~610 mm). However, the causes and regulatory mechanisms remain unclear. In this study, Henong 76 (a soybean cultivar with seeds less prone to wrinkling) and Heihe 43 (a soybean cultivar with seeds prone to wrinkling) were used as experimental materials. They were sown simultaneously in Jiamusi and Shenyang, respectively, to explore the causes of seed-filling disorders in Heihe 43. The results indicated that there were significant differences in the contents of soluble sugars and starch, as well as in the activities of sucrose synthase and invertase, between the seeds of Henong 76 and Heihe 43 grown in Shenyang. However, no significant differences were found between them in Jiamusi. Transcriptomic and metabolomic analyses suggested that genes related to controlling starch hydrolysis (isoamylase, α-amylase, and glycogen phosphorylase) and sucrose synthesis and decomposition (sucrose synthase, invertase, glucose-6-phosphate isomerase, and phosphoglucomutase) in Heihe 43 were upregulated in Shenyang. In contrast, genes regulating plant hormone signal transduction (auxin, gibberellin, abscisic acid, and cytokinin) were generally downregulated. These changes led to differences in metabolites, resulting in the occurrence of seed-filling disorders. Furthermore, we analyzed the climatic conditions of the two cultivars during the soybean seed-filling period. The results indicated that high temperature might be the primary meteorological factor contributing to the occurrence of seed-filling disorders. All results indicated that the insufficient accumulation of sugars in seeds due to exposure to high temperatures during the seed-filling period is the primary cause of the prone-to-wrinkling phenomenon of the Heihe 43 cultivar under the ecological conditions of Shenyang. Full article
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27 pages, 14478 KB  
Article
rolB Promotes Adventitious Root Development in Pyrus betulaefolia by Modulating Endogenous Hormones and Gene Expression
by Ting Xie, Weimin Wang, Kuozhen Nie, Zijuan He, Jiaojiao He, Yuxing Zhang, Na Liu and Yingli Li
Agronomy 2025, 15(9), 2165; https://doi.org/10.3390/agronomy15092165 - 11 Sep 2025
Viewed by 347
Abstract
We investigated the effect of Agrobacterium rhizogenes-mediated transformation mof rolB on adventitious root development and endogenous hormones in ‘duli’ (Pyrus betulaefolia) via transcriptomic analysis of wild-type (WT) and rolB-transformed plants. The formation of root primordia occurred earlier [...] Read more.
We investigated the effect of Agrobacterium rhizogenes-mediated transformation mof rolB on adventitious root development and endogenous hormones in ‘duli’ (Pyrus betulaefolia) via transcriptomic analysis of wild-type (WT) and rolB-transformed plants. The formation of root primordia occurred earlier in transgenic ‘duli’ than in the WT plants. At seven days, 57% of the transgenic seedlings had formed root primordia, whereas root primordia first appeared at seven days in WT ‘duli’. The rooting rate of transgenic ‘duli’ and WT plants was 90% and 77.14%, respectively. rolB significantly promoted the formation of secondary roots. Within 20 days, auxin (IAA), gibberellic acid (GA3), and zeatin riboside (ZR) were higher and abscisic acid (ABA) was lower in transgenic ‘duli’ than in WT plants. Gene Ontology analysis revealed high enrichment in signaling pathways and ADP binding, and Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that several differentially expressed genes were enriched in flavonoid and carotenoid-related pathways and plant hormone signal transduction. rolB induced changes in the expression patterns of several genes involved in hormone biosynthesis, metabolism, and signal transduction pathways in ‘duli’. Weighted gene co-expression network analysis identified the DEGs associated with endogenous hormone levels and indicated that the central genes of modules most strongly correlated with ABA, ZR, IAA, and GA3 regulate protein synthesis, signaling, and root tissue meristem activity. Protein–protein interaction analysis yielded a co-expression network of physiological and transcriptomic data during rooting and identified key genes at the network core. These findings provide valuable insights into the regulatory mechanisms of rolB and its influence on root development in ‘duli’. Full article
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29 pages, 22431 KB  
Article
Transcriptomic Analysis of Resistant and Susceptible Eggplant Genotypes (Solanum melongena L.) Provides Insights into Phytophthora capsici Infection Defense Mechanisms
by Hesbon Ochieng Obel, Xiaohui Zhou, Songyu Liu, Yan Yang, Jun Liu and Yong Zhuang
Horticulturae 2025, 11(9), 1026; https://doi.org/10.3390/horticulturae11091026 - 1 Sep 2025
Viewed by 540
Abstract
Phytophthora fruit rot caused by Phytophthora capsici is a devastating disease in many solanaceous vegetables, resulting in tremendous yield and economic losses. However, the underlying resistance or susceptibility to P. capsici in eggplant remains obscure. In this study, the transcriptomic analysis was performed [...] Read more.
Phytophthora fruit rot caused by Phytophthora capsici is a devastating disease in many solanaceous vegetables, resulting in tremendous yield and economic losses. However, the underlying resistance or susceptibility to P. capsici in eggplant remains obscure. In this study, the transcriptomic analysis was performed between the resistant (G42) and susceptible (EP28) eggplant genotypes at 0, 1, 3 and 5 days post-inoculation (dpi). Taking 0 dpi as the control, a total of 4111, 7496 and 7325 DEGs were expressed at 1, 3 and 5 dpi, respectively, in G42 and 5316, 12675 and 12048 DEGs were identified at 1, 3 and 5 dpi, respectively, in EP28. P. capsici infection induced substantial transcriptional changes in the inoculated fruits. The analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) identified defense-related pathways including ‘plant-pathogen interactions’, ‘mitogen-activated protein kinase (MAPK)’ and ‘hormone biosynthesis and signal transduction’. The hormone-related genes encompassing ethylene, abscisic acid, auxins and gibberellins showed differential expression between G42 and EP28 eggplant genotypes, signifying their important roles in plant disease resistance. P. capsici infection induced the expression of major transcription factors such as MYB, NAC/NAM, bHLH, WRK, HSF, HD-ZIPAP2/ERF and Mad-box. qRT-PCR validation of the selected genes corroborates with RNA-seq, depicting the precision and consistency of the transcriptomic data. According to qRT-PCR and RNA-seq analyses, the expression of the pathogenesis-related gene transcriptional activator, SmPTI6 (Smechr0603020), is upregulated in G42 and downregulated in EP28. This differential expression suggests a potential role in the resistance to P. capsici. Functional analysis via a virus-induced gene silencing (VIGS) system found that silencing SmPTI6 in G42 enhanced infection by P. capsici, indicating that SmPTI6 performs a critical role in response to pathogen attack. The comprehensive results obtained in this study provide a valuable resource for understanding the molecular mechanisms underlying eggplant resistance to P. capsici and for establishing breeding resistant eggplant genotypes to P. capsici. Full article
(This article belongs to the Special Issue Vegetable Genomics and Breeding Research)
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17 pages, 2681 KB  
Article
Transcriptome Analysis Reveals Key Genes Involved in Fruit Length Trait Formation in Pepper (Capsicum annuum L.)
by Jie Zeng, Peiru Li, Jingwei Duan, Fei Huang, Jinqi Hou, Xuexiao Zou, Lijun Ou, Zhoubin Liu and Sha Yang
Horticulturae 2025, 11(9), 1025; https://doi.org/10.3390/horticulturae11091025 - 1 Sep 2025
Cited by 1 | Viewed by 615
Abstract
Pepper is a major horticultural crop cultivated extensively worldwide. Among its various agronomic characteristics, fruit length is a key trait influencing both yield and visual quality. Despite its importance, the genetic mechanisms regulating fruit length in Capsicum remain insufficiently characterized, hindering the development [...] Read more.
Pepper is a major horticultural crop cultivated extensively worldwide. Among its various agronomic characteristics, fruit length is a key trait influencing both yield and visual quality. Despite its importance, the genetic mechanisms regulating fruit length in Capsicum remain insufficiently characterized, hindering the development of high-yielding and aesthetically desirable cultivars. In this study, fruits at three developmental stages (0, 15, and 30 days after flowering) were sampled from the long-fruit mutant fe1 and its wild-type progenitor LY0. Phenotypic characterization and transcriptomic sequencing were conducted to identify candidate genes associated with fruit length regulation. Morphological analysis revealed that the most pronounced difference in fruit length occurred at 30 days after flowering. RNA-seq analysis identified 41,194 genes, including 13,512 differentially expressed genes (DEGs). Enrichment analysis highlighted key pathways, such as plant–pathogen interaction, plant hormone signal transduction, and the MAPK signaling pathway. DEG classification suggested that several downregulated genes related to early auxin responses may contribute to the regulation of fruit elongation. Notably, the gibberellin signaling gene SCL13 (Caz12g26660), transcription factors MYB48 (Caz11g07190) and ERF3-like (Caz10g00810), and the cell-wall-modifying gene XTH15-like (Caz07g19100) showed significantly elevated expression in 30-day-old fruits of fe1. Weighted gene co-expression network analysis (WGCNA) further revealed a strong positive correlation among these genes. Quantitative RT-PCR analysis of eight selected DEGs confirmed the RNA-seq results. This study provides a foundational framework for dissecting the molecular regulatory network of fruit length in Capsicum, offering valuable insights for breeding programs. Full article
(This article belongs to the Special Issue Genomics and Genetic Diversity in Vegetable Crops)
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22 pages, 4499 KB  
Article
Genome-Wide Analysis and Expression Profiles of Auxin Response Factors in Ginger (Zingiber officinale Roscoe)
by Yuanyuan Tong, Sujuan Xu, Jiayu Shi, Yi He, Hong-Lei Li, Tian Yu, Sinian Zhang and Hai-Tao Xing
Int. J. Mol. Sci. 2025, 26(17), 8412; https://doi.org/10.3390/ijms26178412 - 29 Aug 2025
Viewed by 501
Abstract
Ginger, an economically important crop, fulfills multifunctional roles as a spice, vegetable, and raw material for medicinal and chemical products. The family of Auxin Response Factors (ARFs) plays an essential role in facilitating auxin signal transduction and regulating plant growth and development. However, [...] Read more.
Ginger, an economically important crop, fulfills multifunctional roles as a spice, vegetable, and raw material for medicinal and chemical products. The family of Auxin Response Factors (ARFs) plays an essential role in facilitating auxin signal transduction and regulating plant growth and development. However, the role of ARF genes in ginger, a crop of considerable economic importance, remains elucidated. In this study, a total of 26 ZoARF genes were identified in the ginger genome, which were further categorized into four subfamilies (I–IV) and displayed a non-uniform distribution across 11 chromosomes. The proteins are predominantly localized to the nucleus. Promoter regions contained numerous cis-elements linked to light signaling, phytohormones, growth, development, and stress responses. Collinearity analysis revealed 9 pairs of fragment duplication events in ZoARFs, all uniformly distributed across their related chromosomes. In addition, the expression profiles of ZoARFs in ginger were analyzed during development and under several stress conditions like ABA, cold, drought, heat, and salt, employing RNA-seq data and qRT-PCR analysis. Notably, expression profiling revealed tissue-specific functions, with ZoARF#04/05/12/22 associated with flower development and ZoARF#06/13/14/23 implicated in root growth. This work provides an in-depth insight into the ARF family and establishes a foundation for future investigations of ZoARF gene functions in ginger growth, development, and abiotic stress tolerance. Full article
(This article belongs to the Special Issue Plant Tolerance to Stress)
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16 pages, 1891 KB  
Article
Transcriptomic and Metabolomic Analyses Reveal Differing Phytohormone Regulation in Rhododendron Cultivars in Response to Azalea Lace Bug (Stephanitis pyrioides)
by Bei He, Yu Peng, Jun Tong, Dongyun Xu, Yanfang Dong, Yuan Zhou, Yanping Tang, Si Zhang, Linchuan Fang and Jing Mao
Horticulturae 2025, 11(9), 1005; https://doi.org/10.3390/horticulturae11091005 - 24 Aug 2025
Viewed by 681
Abstract
Rhododendron spp., valuable ornamental plants, frequently suffer from infestations of the azalea lace bug (Stephanitis pyrioides Scott, ALB). However, the hormonal regulatory mechanisms underlying Rhododendron defense against ALB are not well understood. In this study, integrated transcriptomic and metabolomic analyses were performed [...] Read more.
Rhododendron spp., valuable ornamental plants, frequently suffer from infestations of the azalea lace bug (Stephanitis pyrioides Scott, ALB). However, the hormonal regulatory mechanisms underlying Rhododendron defense against ALB are not well understood. In this study, integrated transcriptomic and metabolomic analyses were performed to investigate the phytohormone responses under ALB stress in two Rhododendron cultivars with distinct insect susceptibility: the resistant ‘Taile’ (TL), and the susceptible ‘Yanzhimi’ (YZM). Transcriptomic sequencing identified 10,052 and 3113 differentially expressed genes (DEGs) in ‘TL’ and ‘YZM’, respectively, after ALB infestation. KEGG pathway enrichment analysis revealed that the DEGs in ‘TL’ were significantly enriched in hormone signal transduction pathways, including gibberellin (GA), jasmonic acid (JA), salicylic acid (SA), and ethylene (ETH), with 21 out of 25 hormone-related DEGs being upregulated. In contrast, ‘YZM’ exhibited 18 upregulated and 13 downregulated DEGs and suppressed auxin and cytokinin signaling. Non-targeted metabolomic analysis detected increased indole-3-acetic acid (IAA), abscisic acid (ABA), and jasmonoyl–isoleucine (JA-Ile) levels in both cultivars. ‘TL’ also showed elevated levels of SA precursor (benzoic acid) and ethylene precursor (1-aminocyclopropane-1-carboxylate, ACC). These findings indicate that ALB infestation induces endogenous hormone signaling-related genes in Rhododendron leaves and regulates hormones such as SA and JA to counteract insect stress. This study provides theoretical insights into the molecular mechanisms of Rhododendron defense against insect herbivory and lays the foundation for breeding resistant cultivars. Full article
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24 pages, 3694 KB  
Article
JA Signaling Inhibitor JAZ Is Involved in Regulation of AM Symbiosis with Cassava, Including Symbiosis Establishment and Cassava Growth
by Yu Gao, Siyuan Huang, Jingling Zhang, Lin Zhu, Baocan Zhan, Xiaohui Yu and Yinhua Chen
J. Fungi 2025, 11(8), 601; https://doi.org/10.3390/jof11080601 - 19 Aug 2025
Viewed by 681
Abstract
Mutualism between plants and arbuscular mycorrhizal fungi (AMF) is imperative for sustainable agricultural production. Jasmonic acid (JA) signal transduction has been demonstrated to play an important role in AMF symbiosis with the host. In this study, SC9 cassava was selected as the research [...] Read more.
Mutualism between plants and arbuscular mycorrhizal fungi (AMF) is imperative for sustainable agricultural production. Jasmonic acid (JA) signal transduction has been demonstrated to play an important role in AMF symbiosis with the host. In this study, SC9 cassava was selected as the research object to investigate the effect of the jasmonic acid signaling pathway on symbiosis establishment and cassava growth in AMF and cassava symbiosis. It was first found that the symbiosis of cassava and mycorrhizal fungi could increase the biomass of both the aboveground and belowground parts of cassava. Secondly, JA content increased significantly in the early stage of AMF inoculation and auxin content increased significantly in the late stage of AMF inoculation, suggesting that JA signal transduction played an important role in the symbiosis between cassava and mycorrhizal fungi. Transcriptome data were used to analyze the expression differences of genes related to JA synthesis and signal transduction in cassava. The MeJAZ gene positively responded to symbiosis between cassava and mycorrhizal fungi. The analysis of MeJAZ gene family expression and its promoter supported this result. Spraying different concentrations of MeJA on leaves could affect the colonization rate and root biomass of cassava, indicating that JA was an active regulator of mycorrhizal formation. PPI prediction and qPCR analysis suggested that the MeJAZ7 gene might be a key transcriptional regulator responding to jasmonic acid signals and regulating mycorrhizal influence on cassava growth and development. Full article
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16 pages, 5010 KB  
Article
Auxin Responds to Flowing Nutrient Solution to Accelerate the Root Growth of Lettuce in Hydroponic Culture
by Yue Xiang, Jie Peng, Yang Shao, Jung Eek Son, Kotaro Tagawa, Satoshi Yamada, Mina Yamada, Bateer Baiyin and Qichang Yang
Int. J. Mol. Sci. 2025, 26(16), 7742; https://doi.org/10.3390/ijms26167742 - 11 Aug 2025
Viewed by 583
Abstract
Traditional soil cultivation of lettuce faces challenges; hydroponic technology offers solutions to improve lettuce production. However, the interrelationships among the root phenotype of lettuce, auxin synthesis and signal transduction, and nutrient solution flow, and their effects on hydroponic lettuce growth remain unclear. We [...] Read more.
Traditional soil cultivation of lettuce faces challenges; hydroponic technology offers solutions to improve lettuce production. However, the interrelationships among the root phenotype of lettuce, auxin synthesis and signal transduction, and nutrient solution flow, and their effects on hydroponic lettuce growth remain unclear. We investigated the effects of nutrient solution flow state on lettuce’s early growth, transcriptomic changes, and auxin-related gene expression. Growth indicators were measured 2, 4, and 6 days after transplanting. The shoot and root fresh weights, total root length, and root surface area were significantly higher under the flow treatment than under the non-flow condition. The shoot fresh weight increased by 29, 64, and 31%, respectively, at the three growth stages. A clear distinction was observed between the samples from different treatment groups. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways that were commonly enriched included “Plant hormone signal transduction (auxin)”. Moreover, the significantly enriched Gene Ontology (GO) terms varied across different time points, which vividly reflected the dynamic characteristics of the plant’s response. Genes related to auxin biosynthesis—such as AL3F1, YUC5, and AMI4G—exhibited higher expression levels under the flow treatment. Overall, these results indicate that nutrient solution flow can promote auxin synthesis and signal transduction in early roots of lettuce. Full article
(This article belongs to the Section Molecular Plant Sciences)
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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 488
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
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31 pages, 6501 KB  
Review
From Hormones to Harvests: A Pathway to Strengthening Plant Resilience for Achieving Sustainable Development Goals
by Dipayan Das, Hamdy Kashtoh, Jibanjyoti Panda, Sarvesh Rustagi, Yugal Kishore Mohanta, Niraj Singh and Kwang-Hyun Baek
Plants 2025, 14(15), 2322; https://doi.org/10.3390/plants14152322 - 27 Jul 2025
Viewed by 2376
Abstract
The worldwide agriculture industry is facing increasing problems due to rapid population increase and increasingly unfavorable weather patterns. In order to reach the projected food production targets, which are essential for guaranteeing global food security, innovative and sustainable agricultural methods must be adopted. [...] Read more.
The worldwide agriculture industry is facing increasing problems due to rapid population increase and increasingly unfavorable weather patterns. In order to reach the projected food production targets, which are essential for guaranteeing global food security, innovative and sustainable agricultural methods must be adopted. Conventional approaches, including traditional breeding procedures, often cannot handle the complex and simultaneous effects of biotic pressures such as pest infestations, disease attacks, and nutritional imbalances, as well as abiotic stresses including heat, salt, drought, and heavy metal toxicity. Applying phytohormonal approaches, particularly those involving hormonal crosstalk, presents a viable way to increase crop resilience in this context. Abscisic acid (ABA), gibberellins (GAs), auxin, cytokinins, salicylic acid (SA), jasmonic acid (JA), ethylene, and GA are among the plant hormones that control plant stress responses. In order to precisely respond to a range of environmental stimuli, these hormones allow plants to control gene expression, signal transduction, and physiological adaptation through intricate networks of antagonistic and constructive interactions. This review focuses on how the principal hormonal signaling pathways (in particular, ABA-ET, ABA-JA, JA-SA, and ABA-auxin) intricately interact and how they affect the plant stress response. For example, ABA-driven drought tolerance controls immunological responses and stomatal behavior through antagonistic interactions with ET and SA, while using SnRK2 kinases to activate genes that react to stress. Similarly, the transcription factor MYC2 is an essential node in ABA–JA crosstalk and mediates the integration of defense and drought signals. Plants’ complex hormonal crosstalk networks are an example of a precisely calibrated regulatory system that strikes a balance between growth and abiotic stress adaptation. ABA, JA, SA, ethylene, auxin, cytokinin, GA, and BR are examples of central nodes that interact dynamically and context-specifically to modify signal transduction, rewire gene expression, and change physiological outcomes. To engineer stress-resilient crops in the face of shifting environmental challenges, a systems-level view of these pathways is provided by a combination of enrichment analyses and STRING-based interaction mapping. These hormonal interactions are directly related to the United Nations Sustainable Development Goals (SDGs), particularly SDGs 2 (Zero Hunger), 12 (Responsible Consumption and Production), and 13 (Climate Action). This review emphasizes the potential of biotechnologies to use hormone signaling to improve agricultural performance and sustainability by uncovering the molecular foundations of hormonal crosstalk. Increasing our understanding of these pathways presents a strategic opportunity to increase crop resilience, reduce environmental degradation, and secure food systems in the face of increasing climate unpredictability. Full article
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20 pages, 4054 KB  
Article
Identification of Auxin-Associated Genes in Wheat Through Comparative Transcriptome Analysis and Validation of the Candidate Receptor-like Kinase Gene TaPBL7-2B in Arabidopsis
by Mengjie Zhang, Guangzhu Chen, Jie Cai, Yongjie Ji, Linrun Xiang, Xinhong Chen and Jun Wang
Plants 2025, 14(15), 2277; https://doi.org/10.3390/plants14152277 - 24 Jul 2025
Viewed by 647
Abstract
Auxin (IAA), a key natural signaling molecule, plays a pivotal role in regulating plant growth, development, and stress responses. Understanding its signal transduction mechanisms is crucial for improving crop yields. In this study, we conducted a comparative transcriptome analysis of wheat leaf and [...] Read more.
Auxin (IAA), a key natural signaling molecule, plays a pivotal role in regulating plant growth, development, and stress responses. Understanding its signal transduction mechanisms is crucial for improving crop yields. In this study, we conducted a comparative transcriptome analysis of wheat leaf and root tissues treated with different concentrations of IAA (0, 1, and 50 μM). Functional enrichment analysis revealed that differentially expressed genes (DEGs) exhibited tissue-specific regulatory patterns in response to auxin. Weighted Gene Co-expression Network Analysis (WGCNA) identified receptor-like kinase genes within the MEgreen module as highly correlated with auxin response, suggesting their involvement in both root and leaf regulation. Among them, TaPBL7-2B, a receptor-like kinase gene significantly upregulated under 50 μM IAA treatment, was selected for functional validation. Ectopic overexpression of TaPBL7-2B in Arabidopsis thaliana (Col-0) enhanced auxin sensitivity and inhibited plant growth by suppressing root development and leaf expansion. In contrast, knockout of the Arabidopsis homolog AtPBL7 reduced auxin sensitivity and promoted both root and leaf growth. Transcriptome analysis of Col-0, the TaPBL7-2B overexpression line, and the pbl7 mutant indicated that TaPBL7-2B primarily functions through the MAPK signaling pathway and plant hormone signal transduction pathway. Furthermore, qRT-PCR analysis of wheat varieties with differing auxin sensitivities confirmed a positive correlation between TaPBL7-2B expression and auxin response. In conclusion, TaPBL7-2B acts as a negative regulator of plant growth, affecting root development and leaf expansion in both Arabidopsis and wheat. These findings enhance our understanding of auxin signaling and provide new insights for optimizing crop architecture and productivity. Full article
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15 pages, 2281 KB  
Article
Transcriptome and Anthocyanin Profile Analysis Reveals That Exogenous Ethylene Regulates Anthocyanin Biosynthesis in Grape Berries
by Min Liu, Boyuan Fan, Le Li, Jinmei Hao, Ruteng Wei, Hua Luo, Fei Shi, Zhiyuan Ren and Jun Wang
Foods 2025, 14(14), 2551; https://doi.org/10.3390/foods14142551 - 21 Jul 2025
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Abstract
Anthocyanins are important phenolic compounds in grape skins, affecting the color, oxidation resistance, and aging ability of red wine. In recent years, global warming has had a negative effect on anthocyanin biosynthesis in grape berries. Ethylene serves as a crucial phytohormone regulating the [...] Read more.
Anthocyanins are important phenolic compounds in grape skins, affecting the color, oxidation resistance, and aging ability of red wine. In recent years, global warming has had a negative effect on anthocyanin biosynthesis in grape berries. Ethylene serves as a crucial phytohormone regulating the development and ripening processes of fruit; however, the specific molecular mechanism and the regulatory network between ethylene signaling and the anthocyanin biosynthesis pathway remain incompletely understood. In this study, 400 mg/L ethephon (ETH) solution was sprayed onto the surface of grape berries at the lag phase (EL-34), and the changes in anthocyanin-related genes and metabolites were explored through transcriptomic and metabolomic analysis. The results showed that ETH treatment increased Brix and pH in mature berries. In total, 35 individual anthocyanins were detected, in which 21 individual anthocyanins were enhanced by ETH treatment. However, the anthocyanin profile was not affected by exogenous ethylene. Transcriptomics analysis showed that there were a total of 825 and 1399 differentially expressed genes (DEGs) 12 h and 24 h after treatment. Moreover, key structural genes in the anthocyanin synthesis pathway were strongly induced, including VvPAL, VvCHS, VvF3H, VvF3′5′H, VvDFR and VvUFGT. At the maturity stage (EL-38), the expression levels of these genes were still higher in EHT-treated berries than in the control. ETH treatment also influenced the expression of genes related to hormone biosynthesis and signal transduction. The ethylene biosynthesis gene (VvACO), ethylene receptor genes (VvETR2, VvERS1 and VvEIN4), ABA biosynthesis gene (VvNCED2), and ABA receptor gene (VvPYL4) were up-regulated by ETH treatment, while the auxin biosynthesis gene (VvTAA3) and seven genes of the auxin-responsive protein were inhibited by exogenous ethylene. Meanwhile, ETH treatment promoted the expression of the sugar transporter gene (VvEDL16) and two sucrose synthase genes (VvSUS2 and VvSUS6). In EHT-treated berries, 19 MYB and 23 ERF genes were expressed differently compared with the control (p < 0.05). This study provides the theoretical foundation and technical support for the regulation of anthocyanin synthesis in non-climacteric fruit. Full article
(This article belongs to the Section Food Physics and (Bio)Chemistry)
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Article
Hormone Fluctuation and Gene Expression During Early Stages of the Hickory Grafting Process
by Qiaoyu Huang, Haixia Liu, Qinyuan Shen, Huwei Yuan, Fuqiang Cui, Daoliang Yan, Wona Ding, Xiaofei Wang and Bingsong Zheng
Plants 2025, 14(14), 2229; https://doi.org/10.3390/plants14142229 - 18 Jul 2025
Cited by 1 | Viewed by 578
Abstract
Grafting involves complex hormonal interactions at graft interfaces that are not yet fully understood. In this study, we analyzed hormone fluctuations and gene expression during callus proliferation and vascular tissue differentiation in hickory (Carya cathayensis Sarg.) grafts. Cytokinin and ethylene precursor ACC [...] Read more.
Grafting involves complex hormonal interactions at graft interfaces that are not yet fully understood. In this study, we analyzed hormone fluctuations and gene expression during callus proliferation and vascular tissue differentiation in hickory (Carya cathayensis Sarg.) grafts. Cytokinin and ethylene precursor ACC levels steadily increased after grafting. The biosynthetic genes for these hormones (IPT3, ACS1, ACO1, and ACO5) exhibited heightened expression. Genes related to cytokinin signaling (RR3, ARR4, and ZFP5) and ethylene signaling (MKK9, ESE1, and ESE3) were similarly upregulated. Conversely, genes associated with jasmonic acid, abscisic acid, and strigolactone pathways were downregulated, including synthesis genes (AOC4 and AOS) and those involved in signal transduction (NAC3, WRKY51, and SMAX1). Correspondingly, JA-Ile and 5-deoxystrigol levels significantly decreased. Indole-3-acetic acid (IAA) levels also dropped during the early stages of graft union formation. These results suggest that low auxin concentrations may be essential in the initial stages after grafting to encourage callus proliferation, followed by an increase at later stages to facilitate vascular bundle differentiation. These findings imply that maintaining a balance between low auxin levels and elevated cytokinin and ethylene levels may be critical to support cell division and callus formation during the initial proliferation phase. Later, during the vascular differentiation phase, a gradual rise in auxin levels, accompanied by elevated ethylene, may facilitate the differentiation of vascular bundles in hickory grafts. Full article
(This article belongs to the Section Plant Development and Morphogenesis)
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