Horticulture Research最新文献

{"title":"The SEP homologous gene TEMARY regulates inflorescence phenotypes in H. macrophylla","authors":"K Nashima, T Uemachi, K Shirasawa, A Shimizu, T Takeuchi, T Obata, S Isobe, M Azuma, M Akutsu, Y Nakazawa, M Kodama, K Namai, T Kurokura, T Suyama","doi":"10.1093/hr/uhae332","DOIUrl":"https://doi.org/10.1093/hr/uhae332","url":null,"abstract":"Most Hydrangea species have inflorescences composed of two types of flowers: decorative flowers with showy sepals, and plain non-decorative flowers. In wild plants of H. macrophylla, the decorative flowers are located at the periphery of the corymb, resulting in the lacecap phenotype. However, after the discovery of the mophead phenotype, in which decorative flowers are borne not only at the periphery but also on the entire inflorescence, it developed remarkably as a garden plant. In this study, we aimed to identify the gene controlling the inflorescence type and the mutations causing the mophead phenotype. Linkage analyses identified a SEPALLATA (SEP) homologous gene as a candidate gene, named TEMARY. We analyzed the genome sequences of TEMARY using several cultivars. The results revealed that the H. macrophylla cultivars had three types of loss-of-function alleles, and that the locus of the mophead cultivars consisted of only loss-of-function alleles. The phenotypes of 27 mophead cultivars could be explained by three types of loss-of-function TEMARY alleles. RNA-seq analysis and qRT-PCR analysis using two bud sport mutant lines related to the inflorescence type revealed that mophead mutants did not express TEMARY normally. These results suggest that TEMARY controls the inflorescence type and that mutations in this gene cause the mophead phenotype.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"1 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142718169","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 shade-tolerance gene network in soybean revealed by forward integrated reverse genetic studies","authors":"Yanzhu Su, Yongpeng Pan, Weiying Zeng, Zhenguang Lai, Pengfei Guo, Xiaoshuai Hao, Shengyu Gu, Zhipeng Zhang, Lei Sun, Ning Li, Jianbo He, Wubin Wang, Guangnan Xing, Jiaoping Zhang, Zudong Sun, Junyi Gai","doi":"10.1093/hr/uhae333","DOIUrl":"https://doi.org/10.1093/hr/uhae333","url":null,"abstract":"Shade-tolerance is a key trait for cultivars in inter/relay-cropped soybeans in maize field. Our previous genome-wide association study (GWAS) results on southern China soybean germplasm revealed that the shade-tolerance was conferred by a complex of genes with multiple alleles. To complete our understanding on shade-tolerance gene system, the GWAS with gene-allele sequences as markers (designated GASM-RTM-GWAS) was conducted in a recombinant inbred lines (RILs) population between two extreme parents using shade-tolerance index (STI) and relative pith-cell length (RCL) as indicators. Altogether, 211 genes, including 99 and 119 genes (seven shared) for STI and RCL, respectively, were identified and then annotated into a similar set of five biological categories. Furthermore, transcriptome analysis detected 7,837 differentially expressed genes (DEGs), indicating plentiful DEGs involved in the expression of regulatory/causal GWAS-genes. The protein-protein interaction (PPI) analysis and gene functional analysis for both GWAS-genes and DEGs showed a group of interrelated causal genes and a group of interrelated DEGs with that of the former including in the latter and their functions interconnected as a gene network. For further understanding of the response of soybean to shade stress in a sequential connection, six chronological gene modules were grouped as Signal-activation and transport, Signal-transduction, Signal-amplification, Gene expression, Regulated metabolites, and Material transport. From the modules, 12 key genes were selected as entry-points for further analysis. Our study characterizes with overview of shade tolerance gene network as a new insight into the complex trait genetic system, rather than the usual way starting from a handpicked single gene.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"8 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142718343","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":"SlKNUCKLES regulates floral meristem activity and controls fruit size in Solanum lycopersicum","authors":"Dongbao Li, Wen Yang, Zhiyue Wu, Yonghua Yang, Zhongling Wen, Bo Sun","doi":"10.1093/hr/uhae331","DOIUrl":"https://doi.org/10.1093/hr/uhae331","url":null,"abstract":"Timed termination of floral meristem (FM) is crucial for proper development of floral organs and fruits. In Solanum lycopersicum, CLAVATA3 (CLV3)-WUSCHEL (WUS) feedback regulation maintains FM homeostasis in early stage of floral buds. It is known that the zinc finger protein SlKNUCKLES (SlKNU) functions to promote FM determinacy by directly repressing the stem cell identity gene SlWUS. However, how the robust FM activity is suppressed to secure fruit development is not fully understood in tomato. Here, we demonstrate that SlKNU also directly represses the stem cell marker gene SlCLV3 and the receptor gene SlCLV1 for FM determinacy control. Besides, loss-of-function mutants of SlKNU generated by CRISPR-Cas9 show increased fruit size of tomato. Moreover, overexpression of SlKNU attenuates the activities of the shoot apical meristem (SAM) and FM in Arabidopsis, but normal carpel development is still maintained. Hence, although the function of KNU in tomato and Arabidopsis may diverge during evolution, the role of KNU for FM determinacy and fruit size control is conserved and may potentially be useful for enhancing fruit yield of tomato.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"181 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142684242","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":"Phytop: A tool for visualizing and recognizing signals of incomplete lineage sorting and hybridization using species trees output from ASTRAL","authors":"Hong-Yun Shang, Kai-Hua Jia, Nai-Wei Li, Min-Jie Zhou, Hao Yang, Xiao-Ling Tian, Yong-Peng Ma, Ren-Gang Zhang","doi":"10.1093/hr/uhae330","DOIUrl":"https://doi.org/10.1093/hr/uhae330","url":null,"abstract":"Incomplete lineage sorting (ILS) and introgression/hybridization (IH) are prevalent in nature and thus frequently result in discrepancies within phylogenetic tree topologies, leading to misinterpretation of phylogenomic data. Despite the availability of numerous tools for detecting ILS and IH among species, many of these tools lack effective visualization, or are time-consuming, or require prior predetermination. Here, we addressed these shortcomings by developing a fast-running, user-friendly tool called Phytop. By defining ILS and IH indices to quantify ILS and IH, this tool can detect the extent of ILS and IH among lineages with high reliability, and can visualize them based on the gene tree topology patterns constructed using ASTRAL. We tested Phytop extensively using both simulated and real data, and found that it enables users to quickly and conveniently estimate the extent of ILS and IH, thus clarifying the phylogenetic uncertainty. Phytop is available at https://github.com/zhangrengang/phytop and is expected to contribute to the intuitive and convenient inference of genetic relationships among lineages in future research.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"198 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142684241","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 genus Paris: a fascinating resource for medicinal and botanical studies","authors":"Xiao Ye, Yang Tao, Xiu-Lan Pu, Hong Hu, Jing Chen, Chun-Lin Tan, Xin Tan, Sheng-Hong Li, Yan Liu","doi":"10.1093/hr/uhae327","DOIUrl":"https://doi.org/10.1093/hr/uhae327","url":null,"abstract":"The genus Paris, comprising a series of distinctive medicinal plants, has been utilized globally for its therapeutic properties over centuries. Modern pharmacological studies have demonstrated that secondary metabolites from Paris species exhibit significant pharmacological activities, including anticancer, hemostatic, anti-inflammatory, antimicrobial and other effects. Additionally, the unique morphological traits and large genome size of Paris species have continuously captivated the interest of botanists and horticulturalists. Nonetheless, the conservation of wild Paris populations is threatened due to the lengthy reproductive cycle and overexploitation, posing considerable challenges to their development and sustainable use. This review provides a comprehensive overview of the botanical characteristics, historical medicinal uses, pharmacological effects and toxicity evaluation of secondary metabolites in Paris species. It also covers the molecular biological research conducted on the genus Paris and proposes key research questions and important directions for future solutions. We advocate for the expansion and implementation of multi-omics approaches, as well as molecular and genetic technologies recently advanced in model plant research, to intensively study Paris species. This will facilitate the comprehensive understanding of gene function and molecular mechanisms underlying specialized metabolite formation in Paris.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"71 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142684243","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":"Tomato HAIRY MERISTEM4, expressed in the phloem, is required for proper shoot and fruit development","authors":"Jackson Khedia, Abhay Pratap Vishwakarma, Ortal Galsurker, Shira Corem, Suresh Kumar Gupta, Tzahi Arazi","doi":"10.1093/hr/uhae325","DOIUrl":"https://doi.org/10.1093/hr/uhae325","url":null,"abstract":"The HAIRY MERISTEM (HAM) gene family encodes Type I and II GRAS domain transcriptional regulators in plants. Type II HAMs, predominantly expressed in meristems and regulated by microRNA171, are essential for maintaining undifferentiated meristems, a role conserved across various species. Conversely, the functions of Type I HAMs have been less characterized. In this study, we investigated the role of SlHAM4, a Type I HAM in tomato. CRISPR-induced SlHAM4 loss-of-function mutations (slham4CR) resulted in shoot and fruit abnormalities, which were fully reversed by reintroducing SlHAM4, driven by its native promoter, into the mutant background. Mutant abnormalities included simpler leaves and increased anthocyanin pigmentation in the leaf and sepal primordia, reminiscent of phenotypes observed in certain Arabidopsis mutants with compromised phloem. In addition, slham4CR plants produced significantly smaller fruits with a subset developing catface-like scars, attributed to tears that occurred in the pericarp of setting fruits. Using a GUS reporter gene driven by the native SlHAM4 promoter, we found that SlHAM4 is predominantly expressed in phloem tissues. Consistent with this, transcriptome analysis of mutant anthesis ovaries revealed specific downregulation of genes implicated in phloem development and function, particularly those expressed in companion cells. However, histological analysis showed no obvious abnormalities in phloem vasculature. Taken together, our data suggest that SlHAM4 plays a role in shoot and fruit development likely by regulating genes essential for phloem function.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"13 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142684244","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":"SoNAC72-SoMYB44/SobHLH130 module contributes to flower color fading via regulating anthocyanin biosynthesis by directly binding to the SoUFGT1 promoter in lilac (Syringa oblata)","authors":"Jinxuan Wang, Xin Wang, Bo Ma, Pingsheng Leng, Jing Wu, Zenghui Hu","doi":"10.1093/hr/uhae326","DOIUrl":"https://doi.org/10.1093/hr/uhae326","url":null,"abstract":"The fading of flower color is caused by changes of anthocyanin content during flower development in many plants, including lilac (Syringa oblata). However, the molecular regulatory mechanism of this phenomenon is still poorly understood. UDP-glucose: flavonoid 3-O-glucosyltransferase (UFGT) has a pivotal role in the formation of stable anthocyanins. Here, SoUFGT1 and three transcription factors, SoMYB44, SobHLH130, and SoNAC72, were identified and verified to participate in anthocyanin production in lilac. Overexpressing SoMYB44 promoted SoUFGT1 expression in lilac petals. The yeast one-hybrid (Y1H) and dual-luciferase (Dual-LUC) assays demonstrated that SoMYB44 activated SoUFGT1, thereby bolstering anthocyanin accumulation. The overexpression and silencing of SoNAC72 in petals revealed that it facilitated anthocyanin accumulation. The Y1H and Dual-LUC assays verified that SoNAC72 was capable of directly binding to the SoMYB44 promoter to activate the latter’s expression. In addition, SobHLH130 was also displayed to mediate anthocyanin accumulation in petals. By using yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays, the interaction between SoMYB44 and SobHLH130 was confirmed. These results corroborated that SoNAC72 regulates SoMYB44 expression, and SoMYB44 interacts with SobHLH130 to trigger SoUFGT1 expression in lilac, which then contributes to their anthocyanin accumulation. In sum, along with lilac flower development, the lower expression of SoNAC72 and SobHLH130 reduces SoMYB44 transcripts and depresses transcriptional regulation of SoUFGT1, thus diminishing anthocyanin biosynthesis, leading to the fading of petal color. These study’s findings provide valuable new insight for understanding the formation and regulatory mechanisms of flower color in lilac.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"19 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142684245","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":"Integrative multi-environmental genomic prediction in apple","authors":"Michaela Jung, Carles Quesada-Traver, Morgane Roth, Maria José Aranzana, Hélène Muranty, Marijn Rymenants, Walter Guerra, Elias Holzknecht, Nicole Pradas, Lidia Lozano, Frédérique Didelot, François Laurens, Steven Yates, Bruno Studer, Giovanni A L Broggini, Andrea Patocchi","doi":"10.1093/hr/uhae319","DOIUrl":"https://doi.org/10.1093/hr/uhae319","url":null,"abstract":"Genomic prediction for multiple environments can aid the selection of genotypes suited to specific soil and climate conditions. Methodological advances allow effective integration of phenotypic, genomic (additive, non-additive), and large-scale environmental (enviromic) data into multi-environmental genomic prediction models. These models can also account for genotype-by-environment interaction, utilize alternative relationship matrices (kernels), or substitute statistical approaches with deep learning. However, the application of multi-environmental genomic prediction in apple remained limited, likely due to the challenge of building multi-environmental datasets and structurally complex models. Here, we applied efficient statistical and deep learning models for multi-environmental genomic prediction of eleven apple traits with contrasting genetic architectures by integrating genomic- and enviromic-based model components. Incorporating genotype-by-environment interaction effects into statistical models improved predictive ability by up to 0.08 for nine traits compared to the benchmark model. This outcome, based on Gaussian and Deep kernels, shows these alternatives can effectively substitute the standard G-BLUP. Including non-additive and enviromic-based effects resulted in a predictive ability very similar to the benchmark model. The deep learning approach achieved the highest predictive ability for three traits with oligogenic genetic architectures, outperforming the benchmark by up to 0.10. Our results demonstrate that the tested statistical models capture genotype-by-environment interactions particularly well, and the deep learning models efficiently integrate data from diverse sources. This study will foster the adoption of multi-environmental genomic prediction to select apple cultivars adapted to diverse environmental conditions, providing an opportunity to address climate change impacts.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"16 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142679062","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":"Gibberellin promotes theanine synthesis by relieving the inhibition of CsWRKY71 on CsTSI in tea plant (Camellia sinensis)","authors":"Fen Xiang, Yi Su, Lingyun Zhou, Cuiting Dai, Xuan Jin, Hongyan Liu, Weigui Luo, Wenbo Yang, Wei Li","doi":"10.1093/hr/uhae317","DOIUrl":"https://doi.org/10.1093/hr/uhae317","url":null,"abstract":"Theanine is a crucial indicator of tea quality, its significance is closely tied to the economic value of tea. There were many reports on the regulation mechanism of theanine synthesis and accumulation, but the mechanism of gibberellin regulates theanine synthesis in tea plants is poorly understood. Previous studies have shown that the content of theanine experiences significant changed in the growth stages of tea shoots, displayed a strong correlation with gibberellin. This study confirmed that gibberellin significantly promoted the expression of the major gene of theanine synthesis, known as CsTSI. Additionally, the study identified CsWRKY71, a transcription factor mediated the regulation of gibberellin on theanine synthesis in tea plants. CsWRKY71 was localized in the nucleus and had a typical WRKY domain. It was a member of class IIC sub- and its expression was significantly suppressed following exogenous GA3 treatment. Further assay such as EMSA, dual luciferase and asODN interfering demonstrated that CsWRKY71 significantly interacted with the promoter of CsTSI, which inhibited theanine synthesis by binding to the cis-acting element (C/T)TGAC(T/C) of CsTSI promoter. Overall, the addition of exogenous gibberellin alleviated the inhibition of CsTSI by down-regulating the expression of CsWRKY71, ultimately facilitated the rapid biosynthesis of theanine. This study elucidated the molecular mechanism of CsWRKY71 mediated gibberellin regulation of theanine synthesis in tea plant. The findings not only enhance our understanding of the regulatory processes involved in theanine synthesis in tea plants, but also provide important references for maintaining the characteristics of high theanine in tea plant.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"11 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142670689","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":"Transcription factors MdEIL1 and MdHY5 integrate ethylene and light signaling to promote chlorophyll degradation in mature apple peels","authors":"Li-Xian Li, San-Kui Yang, Yue Fang, Zhi-Meng Wu, Hua-Ying Ma, Shuo Wang, Dan Li, Shou-Qian Feng","doi":"10.1093/hr/uhae324","DOIUrl":"https://doi.org/10.1093/hr/uhae324","url":null,"abstract":"Although it is well-established that ethylene and light stimulate the process of chlorophyll degradation in mature apple peels, there is still a need for further exploration of the molecular mechanisms that regulate this process. This study identified MdEIL1 and MdHY5 as promoters of the chlorophyll degradation pathway in apple peels, activated by ethylene and light. Physiological and molecular tests demonstrated that MdEIL1 and MdHY5 are responsible for activating the expression of genes associated with chlorophyll degradation, including MdERF17, MdNYC1, MdPPH and MdPAO. Furthermore, the interaction between MdEIL1 and MdHY5 proteins enhances their regulatory activity on the target gene MdERF17. Moreover, MdEIL1 binds to the promoter of MdHY5, resulting in the upregulation of its expression, which is further enhanced in the presence of the MdEIL1-MdHY5 protein complex. These findings indicate that MdEIL1-MdHY5 module acts as positive regulator mediating ethylene and light signals that promote chlorophyll degradation in apple peels.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"8 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142684294","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}