Horticultural Plant Journal最新文献

{"title":"Multi-omics analysis reveals the epitranscriptomic and proteomic regulation network of tomato in low-temperature stress response","authors":"Na Wang, Yanting Li, Tianli Guo, Libo Jiang","doi":"10.1016/j.hpj.2024.03.017","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.03.017","url":null,"abstract":"Tomato (<ce:italic>Solanum lycopersicum</ce:italic>) is an extensively cultivated vegetable, and its growth and fruit quality can be significantly impaired by low temperatures. The widespread presence of N<ce:sup loc=\"post\">6</ce:sup>-methyladenosine (m<ce:sup loc=\"post\">6</ce:sup>A) modification on RNA is involved in a diverse range of stress response processes. There is a significant knowledge gap regarding the precise roles of m<ce:sup loc=\"post\">6</ce:sup>A modification in tomato, particularly for cold stress response. Here, we assessed the m<ce:sup loc=\"post\">6</ce:sup>A modification landscape of <ce:italic>S. lycopersicum</ce:italic> ‘Micro-Tom’ leaves in response to low-temperature stress. Furthermore, we investigated the potential relationship among m<ce:sup loc=\"post\">6</ce:sup>A modification, transcriptional regulation, alternative polyadenylation events, and protein translation via MeRIP-seq, RNA-seq, and protein mass spectrometry. After omic date analysis, 11 378 and 10 735 significant m<ce:sup loc=\"post\">6</ce:sup>A peak associated genes were identified in the control and cold treatment tomato leaves, respectively. Additionally, we observed a UGUACAK (<ce:italic>K</ce:italic> = G/U) motif under both conditions. Differential m<ce:sup loc=\"post\">6</ce:sup>A site associated genes most likely play roles in protein translation regulatory pathway. Besides directly altering gene expression levels, m<ce:sup loc=\"post\">6</ce:sup>A also leads to differential poly(A) site usage under low-temperature. Finally, 24 important candidate genes associated with cold stress were identified by system-level multi-omic analysis. Among them, m<ce:sup loc=\"post\">6</ce:sup>A modification levels were increased in SBPase (Sedoheptulose-1,7-bisphosphatase, <ce:italic>Solyc05g052600.4</ce:italic>) mRNA, causing distal poly(A) site usage, downregulation of mRNA expression level, and increased protein abundance. Through these, tomato leaves try to maintain normal photosynthetic carbon assimilation and nitrogen metabolism under low-temperature condition. The comprehensive investigation of the m<ce:sup loc=\"post\">6</ce:sup>A modification landscape and multi-omics analysis provide valuable insights into the epigenetic regulatory mechanisms in tomato cold stress response.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"18 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142790171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The telomere-to-telomere gap-free genome assembly of Juglans sigillata","authors":"Delu Ning, Tao Wu, Wenlong Lei, Shengcheng Zhang, Ting Ma, Li Pan, Liangjun Xiao, Noor ul-Ain, Xingtan Zhang, Fuliang Cao","doi":"10.1016/j.hpj.2024.06.010","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.06.010","url":null,"abstract":"<ce:italic>Juglans sigillata</ce:italic> is an economically valuable nut crop renowned for its nutritional richness, including essential nutrients, antioxidants, and healthy fats, which boost human cardial, brain and gut health. Despite its importance, the lack of a complete genome assembly has been a stumbling block in its biological breeding process. Therefore, we generated deep coverage ultralong Oxford Nanopore Technology (ONT) and PacBio HiFi reads to construct a telomere-to-telomere (T2T) genome assembly. The final assembly spans 537.27 Mb with no gaps, demonstrating a remarkable completeness of 98.1 %. We utilized a combination of transcriptome data and homologous proteins to annotate the genome, identifying 36 018 protein-coding genes. Furthermore, we profiled global cytosine DNA methylations using ONT sequencing data. Global methylome analysis revealed high methylation levels in transposable element (TE)-rich chromosomal regions juxtaposed with comparatively lower methylation in gene-rich areas. By integrating a detailed multi-omics data analysis, we obtained valuable insights into the mechanism underlying endopleura coloration. This investigation led to the identification of eight candidate genes (e.g. <ce:italic>ANR</ce:italic>) involved in anthocyanin biosynthesis pathways, which are crucial for the development of color in plants. The comprehensive genome assembly and the understanding of the genetic basis of important traits like endopleura coloration will open avenues for more efficient breeding programs and improved crop quality.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"37 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142790173","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genes associated with pale green leaves in Chinese cabbage and cabbage translocation line lrlc","authors":"Guanghuan Li, Ziyang Zhang, Wei Ma, Hao Liang, Zengfeng Wang, Tiantian Zhao, Xing Li, Ruixin Qin, Yan Li, Yanhua Wang, Shuxin Xuan, Shuxing Shen, Jianjun Zhao, Aixia Gu","doi":"10.1016/j.hpj.2024.04.013","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.04.013","url":null,"abstract":"","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"2 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142790202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Physiology, transcriptomics, and metabolomics reveal the regulation of calcium distribution in tomato under reduced vapor pressure deficit and increased calcium fertilizer","authors":"Xuemei Yu, Luqi Niu, Yuxin Liu, Yuhui Zhang, Jianming Li, Shuhui Zhang","doi":"10.1016/j.hpj.2024.03.015","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.03.015","url":null,"abstract":"High atmospheric vapor pressure deficit (VPD) reduces the calcium (Ca) distribution in tomato (<ce:italic>Solanum lycopersicum</ce:italic> L.) fruits, severely reducing fruit mass. Reducing the VPD or increasing Ca fertilizer is an important measure to improve Ca distribution in fruits. However, the mechanism through which VPD and Ca regulate fruit Ca distribution remains unclear. This study investigated the effects of high and low VPD and Ca levels on Ca distribution and fruit mass based on carbon fixation, water transport dynamics, and pectin and Ca content and identified key differential genes and metabolites through transcriptome and metabolome analyses. The results showed that both reducing VPD under low Ca and increasing Ca under high VPD increased water and Ca transport to fruits. The increased Ca combined with pectin to form Ca pectinate, which effectively stabilized the cell wall and enhanced the fruit mass. Reduced VPD under low Ca increased the distribution of Ca to fruits but decreased the distribution of Ca to leaves. Lower Ca distribution in leaves increased their absorption of other nutrients, such as potassium, magnesium, copper, and zinc, which increased the stomatal size and density, thereby improving plant carbon absorption and assimilation efficiency. However, transcriptomic and metabolomic data indicated that carbohydrates, as important regulatory factors under drought stress, increased significantly under high VPD, thereby reducing the fruit water potential while improving fruit water and Ca absorption. Therefore, the carbon assimilation efficiency, water transport capacity, and differential genes and metabolites regulated Ca distribution. This work provides a theoretical basis for environmental and fertilizer management in greenhouse tomato production.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"131 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142756145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of three novel R2R3-MYB transcription factors PrMYBi(1–3) repressing the anthocyanin biosynthesis in tree peony","authors":"Jin Zhu, Yizhou Wang, Xian Zhou, Hechen Zhang, Shanshan Li, Liangsheng Wang","doi":"10.1016/j.hpj.2024.08.005","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.08.005","url":null,"abstract":"Petal blotch is a prevalent pigmentation pattern observed in the Xibei tree peony (<ce:italic>Paeonia rockii</ce:italic>), possessing significant aesthetic value and playing a crucial role in the species' reproduction and fitness. Despite years of research, deciphering the molecular mechanisms underlying blotch formation remains challenging. As is well known, floral pigmentation is frequently associated with the familiar R2R3-MYB transcription factors. The key MYB anthocyanin activators of <ce:italic>P. rockii</ce:italic> ‘Shu Sheng Peng Mo’ were previously reported in our preceding study. In this study, we identified and characterized three R2R3-MYBs, PrMYBi1, PrMYBi2, and PrMYBi3, which belong to subgroup 4 (SG4) and play repressor roles in anthocyanin biosynthesis. A quantitative real-time PCR (qRT-PCR) assay indicated that the expression of <ce:italic>PrMYBi1</ce:italic> and <ce:italic>PrMYBi3</ce:italic> gradually increased during flowering development and was substantially up-regulated in non-blotch compared to blotch. Yeast one-hybrid and dual-luciferase assays demonstrated that PrMYBi(1–3) directly target the anthocyanin structural genes and repress their transcription. The genetic transformation of tobacco demonstrated that the overexpression of <ce:italic>PrMYBi(1–3)</ce:italic> decreased anthocyanin accumulation in flowers, with PrMYBi1 serving as the most effective repressor. Our results revealed that SG4 R2R3-MYBs negatively regulate the anthocyanin pathway in <ce:italic>P. rockii</ce:italic> conservatively, and we provide the definite members. These findings will advance future research to unravel the mystery of blotch pattern formation.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"17 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142756232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"BSA-seq and transcriptomic analyses identify Chinese cabbage NB-LRR-encoding genes conferring resistance to soft rot disease","authors":"Yunjia Ge, Kaiyun Zhao, Ni Wang, Han Song, Xudong Wang, Hao Liang, Xiaomeng Zhang, Yin Lu, Yanhua Wang, Wei Ma, Jianjun Zhao, Lisong Ma, Mengyang Liu","doi":"10.1016/j.hpj.2024.02.016","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.02.016","url":null,"abstract":"","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"64 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142756146","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"stu-miR159a negatively regulates anthocyanin-specific MYB transcription factor to mediate drought stress tolerance in potato","authors":"Yurong Deng, Jiangwei Yang, Jingjing Wei, Shengyan Liu, Liang Yang, Xiaofeng Wang, Ning Zhang, Huaijun Si","doi":"10.1016/j.hpj.2024.03.016","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.03.016","url":null,"abstract":"MicroRNAs (miRNAs) are a class of small endogenous non-coding RNAs that direct post-transcriptional gene silencing. In plants, numerous miRNAs have been demonstrated to be regulated under drought-induced stress. However, the role of miRNAs in drought regulation remains unclear in potato. In this work, the function of stu-miR159a was investigated in responding to drought stress in potato. Upon examination, <ce:italic>StGAMyb-like1</ce:italic> was identified as the target gene for stu-miR159a. Overexpression of stu-miR159a (stu-miR159a OE plants) increased sensitivity to drought, interference with stu-miR159a activity by target mimics (stu-miR159a ST plants) resulted in drought resistance. During drought treatment, the target gene <ce:italic>StGAMyb-like1</ce:italic> showed increased activation in stu-miR159a ST plants compared to non-transgenic plants. In contrast, drought stress induced weaker activation of the target gene in stu-miR159a OE plants. In stu-miR159a ST plants, the expression of critical genes in the anthocyanin biosynthesis pathway (<ce:italic>StF3′5′H, StF3′H</ce:italic> and <ce:italic>StCHS2</ce:italic>) was increased by decreasing stu-miR159a activity and simultaneously increasing that of <ce:italic>StGAMyb-like1</ce:italic>. Meanwhile, with drought treatment, stu-miR159a ST plants exhibited higher anthocyanin accumulation than non-transgenic ones, indicating enhanced antioxidant capacity and improved drought tolerance. The above data support that stu-miR159a is a negative regulator of drought stress and provide new insights into the stu-miR159a-mediated regulation of the anthocyanin biosynthesis pathway in controlling drought tolerance in potato.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"66 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142756151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mining candidate genes for grape seed traits based on a genome-wide association study","authors":"Chuan Zhang, Yameng Yang, Songlin Zhang, Vivek Yadav, Haixia Zhong, Fuchun Zhang, Xiaoming Zhou, Xinyu Wu, Xue Cao, Liwen Cui","doi":"10.1016/j.hpj.2024.02.015","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.02.015","url":null,"abstract":"Seedlessness has always been a valuable quality characteristic of edible grape varieties. Although the production of seedless grapes has been ongoing for decades, the genetic complexity of seedless grapes is not yet fully understood. Therefore, determining the genetic mechanisms and key regulatory genes of seedless grapes is of great significance for seedless grape breeding and meeting market demands. The emergence of high-throughput analysis software offers greater possibilities for mining genes related to plant organ development. Specifically, to mine a greater number of candidate genes related to grape seed traits, this study used the seed trait parameters analyzed by Tomato Analyzer as the target trait and then used a genome-wide association study (GWAS) to mine candidate genes. In the two-year analysis using principal component analysis (PCA), we extracted five principal components with a cumulative contribution rate of 96.586 %. The cumulative contribution rate for component 1 reached 87.352 %. Correlation analysis revealed correlation coefficients ranging from 0.54 to 0.98 among the seven basic traits. The GWAS results indicated that 370 SNP loci were significantly correlated with seed traits. These SNP loci were distributed on 18 chromosomes, except for chromosome 4, with most SNP loci distributed on chromosome 18. Based on the physical location of single nucleotide polymorphism (SNP) markers significantly associated with seed-related traits in the grape reference genome, candidate genes are screened within the range of linkage disequilibrium (LD) attenuation distance, both upstream and downstream of the significant SNP loci. These candidate genes were mainly transcription factor-related genes (<ce:italic>VvMADS4</ce:italic> and <ce:italic>VvMADS5</ce:italic>), ubiquitin ligase-related genes (<ce:italic>E3 ubiquitin ligase BIG BROTHER</ce:italic>), serine/threonine protein kinase-related genes, and carbohydrate metabolism-related genes (<ce:italic>Sucrose Synthase 2</ce:italic>) and simultaneously controlled multiple (at least two or more) seed traits. These results indicate that seed traits are jointly regulated by some genes involved in seed morphology regulation. In this work, we identified new gene loci related to grape seed traits. Identifying molecular markers closely related to these seed traits is of great significance for breeding seedless grape varieties.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"26 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142756132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome-based analysis reveals a role for PpCDF5 in the promotion of anthocyanin accumulation at a low nighttime temperature","authors":"Shulin Yang, Duanni Wang, Yuhao Gao, Jiaxin Zhang, Xuan Luo, Junbei Ni, Yuanwen Teng, Jun Su, Songling Bai","doi":"10.1016/j.hpj.2024.08.003","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.08.003","url":null,"abstract":"For red pear, the anthocyanin content is a crucial factor determining the fruit skin color, which affects consumer preferences. Low overnight temperatures promote anthocyanin accumulation, but the molecular mechanism responsible is unclear. In this study, ‘Hongzaosu’ pear (<ce:italic>Pyrus pyrifolia</ce:italic> × <ce:italic>Pyrus communis</ce:italic>) fruit were treated with a low nighttime temperature (LNT, 16 °C) or a warm nighttime temperature (WNT, 26 °C), with sampling conducted within two diurnal cycles. The results showed that LNT promoted anthocyanin accumulation in the fruit skin. The structural anthocyanin biosynthetic genes <ce:italic>PpCHS</ce:italic>, <ce:italic>PpF3H</ce:italic>, and <ce:italic>PpUFGT</ce:italic> exhibited a rhythmic increase in expression at night under LNT. To examine the underlying mechanism, RNA sequencing was conducted using pear calli exposed to LNT and WNT for different durations (24, 48, 72, or 96 h). Transcriptome analysis revealed 285 differentially expressed genes (DEGs) common to all pairwise comparisons of LNT- and WNT-treated calli of ‘Clapp's Favorite’ (<ce:italic>P. communis)</ce:italic> at the sampling time points. KEGG pathway and gene ontology enrichment analyses indicated that the common DEGs were enriched in secondary metabolic processes and phenylpropanoid metabolic processes, which are associated with anthocyanin biosynthesis. The transcription factor PpCDF5, which was responsive to LNT, was selected for further study. Dual-luciferase assays showed that PpCDF5 activated the transcription of anthocyanin biosynthetic genes <ce:italic>PpMYB10</ce:italic>, <ce:italic>PpCHS</ce:italic>, <ce:italic>PpF3H</ce:italic>, <ce:italic>PpDFR</ce:italic>, <ce:italic>PpANS</ce:italic>, and <ce:italic>PpUFGT</ce:italic>. The yeast one-hybrid and EMSA assays demonstrated that PpCDF5 directly binds to the <ce:italic>PpF3H</ce:italic> promoter, which contains an AAAG motif. Overexpression of <ce:italic>PpCDF</ce:italic>5 in pear calli and transient overexpression in pear fruit both increased anthocyanin accumulation. The results indicate that PpCDF5 is involved in LNT-induced anthocyanin biosynthesis in pear fruit and provide insights into the molecular regulation of commercial fruit coloration.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"131 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142756183","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Knockdown of SlEMS1 causes male sterility in tomato","authors":"Yu He, Juan Wang, Jingang Hu, Jinhui Zheng, Ziyi Guo, Qinghui Yu, Qinghua Shi, Yan Zhang","doi":"10.1016/j.hpj.2024.01.015","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.01.015","url":null,"abstract":"","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"184 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142696404","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}