Shengyan Liu, Jiangwei Yang, Ning Zhang, Huaijun Si
Tuber dormancy and sprouting are significant for potato cultivation, storage, and processing. Although the substantial role of miRNAs in some biological processes has been recognized, the critical role of miRNA in breaking potato tuber dormancy is not well understood to date. In this investigation, we expand research on miRNA-mediated gene regulation in tuber dormancy release. In this work, 204 known and 192 novel miRNAs were identified. 136 differentially expressed miRNAs (DE-miRNAs) were also screened out, of which 56 DE-miRNAs were regulated by temperature during tuber dormancy release. Additionally, degradome sequencing revealed that 821 target genes for 202 miRNAs were discovered. Among them, 63 target genes and 48 miRNAs were predicted to be involved in plant hormone signaling pathways. This study used degradome sequencing, tobacco co-transformation system, and GUS staining technology to confirm that stu-miR319c can target StTCP26 and StTCP27 and effectively suppress their expression. The transgenic approach exhibited that stu-miR319c overexpressed tubers sprouted in advance, while silent expression of stu-miR319c showed delayed sprouting. Treatment of wild-type tubers with exogenous MeJA revealed that 1 mg/L MeJA significantly broke dormancy and enhanced potato sprouting ability. Furthermore, transgenic tubers revealed variance in JA content and relative expression of genes associated with JA synthesis pathway, including StAOC, StLOX2, and StLOX4, suggesting that the miR319c may participate in the JA pathway to regulate tuber dormancy release. In summary, our research offers evidence that miRNA regulates potato dormancy release and supports the idea that stu-miR319c is a unique epigenetic regulator for dormancy-sprouting transition in potatoes.
{"title":"Genome-wide analysis of non-coding RNA reveals the role of a novel miR319c for tuber dormancy release process in potato","authors":"Shengyan Liu, Jiangwei Yang, Ning Zhang, Huaijun Si","doi":"10.1093/hr/uhae303","DOIUrl":"https://doi.org/10.1093/hr/uhae303","url":null,"abstract":"Tuber dormancy and sprouting are significant for potato cultivation, storage, and processing. Although the substantial role of miRNAs in some biological processes has been recognized, the critical role of miRNA in breaking potato tuber dormancy is not well understood to date. In this investigation, we expand research on miRNA-mediated gene regulation in tuber dormancy release. In this work, 204 known and 192 novel miRNAs were identified. 136 differentially expressed miRNAs (DE-miRNAs) were also screened out, of which 56 DE-miRNAs were regulated by temperature during tuber dormancy release. Additionally, degradome sequencing revealed that 821 target genes for 202 miRNAs were discovered. Among them, 63 target genes and 48 miRNAs were predicted to be involved in plant hormone signaling pathways. This study used degradome sequencing, tobacco co-transformation system, and GUS staining technology to confirm that stu-miR319c can target StTCP26 and StTCP27 and effectively suppress their expression. The transgenic approach exhibited that stu-miR319c overexpressed tubers sprouted in advance, while silent expression of stu-miR319c showed delayed sprouting. Treatment of wild-type tubers with exogenous MeJA revealed that 1 mg/L MeJA significantly broke dormancy and enhanced potato sprouting ability. Furthermore, transgenic tubers revealed variance in JA content and relative expression of genes associated with JA synthesis pathway, including StAOC, StLOX2, and StLOX4, suggesting that the miR319c may participate in the JA pathway to regulate tuber dormancy release. In summary, our research offers evidence that miRNA regulates potato dormancy release and supports the idea that stu-miR319c is a unique epigenetic regulator for dormancy-sprouting transition in potatoes.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"240 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142561878","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}
The genus Brassica includes six species and over 15 types of vegetables that are widely cultivated and consumed globally. This group of vegetables is rich in bioactive compounds, including glucosinolates, vitamins (such as vitamin C, folate, tocopherol, and phylloquinone), carotenoids, phenols, and minerals, which are crucial for enriching diets and maintaining human health. However, the full extent of these phytonutrients and their significant health benefits remain to be fully elucidated. This review highlights the nutrient compositions and health advantages of Brassica vegetables and discusses the impacts of various processing methods on their nutritional value. Additionally, we discuss potential strategies for enhancing the nutrition of Brassica crops through agronomic biofortification, conventional breeding, and biotechnological or metabolic engineering approaches. This review lays the foundation for the nutritional improvement of Brassica crops.
{"title":"Brassica Vegetables - An Undervalued Nutritional Goldmine","authors":"Xiaomeng Zhang, Qiong Jia, Xin Jia, Jie Li, Xiaoxue Sun, Leiguo Min, Zhaokun Liu, Wei Ma, Jianjun Zhao","doi":"10.1093/hr/uhae302","DOIUrl":"https://doi.org/10.1093/hr/uhae302","url":null,"abstract":"The genus Brassica includes six species and over 15 types of vegetables that are widely cultivated and consumed globally. This group of vegetables is rich in bioactive compounds, including glucosinolates, vitamins (such as vitamin C, folate, tocopherol, and phylloquinone), carotenoids, phenols, and minerals, which are crucial for enriching diets and maintaining human health. However, the full extent of these phytonutrients and their significant health benefits remain to be fully elucidated. This review highlights the nutrient compositions and health advantages of Brassica vegetables and discusses the impacts of various processing methods on their nutritional value. Additionally, we discuss potential strategies for enhancing the nutrition of Brassica crops through agronomic biofortification, conventional breeding, and biotechnological or metabolic engineering approaches. This review lays the foundation for the nutritional improvement of Brassica crops.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"131 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142555819","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}
Najla Ksouri, María Ángeles Moreno, Bruno Contreras-Moreira, Yolanda Gogorcena
Next-generation sequencing has fueled significant advancement in plant breeding tools, such as genome-wide association studies (GWAS) and single-nucleotide polymorphism (SNP) analysis. In this dynamic landscape, plant databases housing SNP markers have evolved into hubs facilitating breeding initiatives and genomic research. PrunusMap, accessible at https://prunusmap.eead.csic.es is an open-source Web application tailored for the Prunus community. Featuring a user-friendly interface, PrunusMap empowers users to seamlessly align and locate markers across multiple genome versions of Prunus species and cultivars, supporting different queries and formats. Beyond locating marker positions, it provides a comprehensive list of annotated nearby genes and proteins. This streamlined process, driven by four intuitive features “Find markers”, “Align sequences”, “Align proteins” and “Locate by position”, significantly reduces workload and boosts efficiency, particularly for users with limited bioinformatics expertise. Moreover, PrunusMap's versatility is underscored by its commitment to incorporate additional Prunus genome sequences, annotations, and markers upon user request.
{"title":"Mapping the genomic landscape of Prunus spp. with PrunusMap","authors":"Najla Ksouri, María Ángeles Moreno, Bruno Contreras-Moreira, Yolanda Gogorcena","doi":"10.1093/hr/uhae301","DOIUrl":"https://doi.org/10.1093/hr/uhae301","url":null,"abstract":"Next-generation sequencing has fueled significant advancement in plant breeding tools, such as genome-wide association studies (GWAS) and single-nucleotide polymorphism (SNP) analysis. In this dynamic landscape, plant databases housing SNP markers have evolved into hubs facilitating breeding initiatives and genomic research. PrunusMap, accessible at https://prunusmap.eead.csic.es is an open-source Web application tailored for the Prunus community. Featuring a user-friendly interface, PrunusMap empowers users to seamlessly align and locate markers across multiple genome versions of Prunus species and cultivars, supporting different queries and formats. Beyond locating marker positions, it provides a comprehensive list of annotated nearby genes and proteins. This streamlined process, driven by four intuitive features “Find markers”, “Align sequences”, “Align proteins” and “Locate by position”, significantly reduces workload and boosts efficiency, particularly for users with limited bioinformatics expertise. Moreover, PrunusMap's versatility is underscored by its commitment to incorporate additional Prunus genome sequences, annotations, and markers upon user request.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"236 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142489638","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}
Tien Van Vu, Ngan Thi Nguyen, Jihae Kim, Minh Huy Vu, Young Jong Song, Mil Thi Tran, Yeon Woo Sung, Jae-Yean Kim
The CRISPR-Cas-based gene targeting (GT) method has enabled precise modifications of genomic DNA ranging from single base to several kilobase scales through homologous recombination (HR). In plant somatic cells, canonical nonhomologous end-joining (cNHEJ) is the predominant mechanism for repairing double-stranded breaks (DSBs), thus limiting the HR-mediated GT. In this study, we implemented an approach to shift the repair pathway preference toward HR by using a dominant-negative ku80 mutant protein (KUDN) to disrupt the initiation of cNHEJ. The employment of KUDN conferred a 1.71- to 3.55-fold improvement in GT efficiency at the callus stage. When we screened transformants, there was a more remarkable increase in GT efficiency, ranging from 1.62- to 9.84-fold, at two specific tomato loci, SlHKT1;2 and SlEPSPS1. With practical levels of efficiency, this enhanced KUDN-based GT tool successfully facilitated a 9-bp addition at an additional locus, SlCAB13. These findings provide another promising method for more efficient and precise plant breeding.
{"title":"Enhancing CRISPR-Cas-based gene targeting in tomato using a dominant-negative ku80","authors":"Tien Van Vu, Ngan Thi Nguyen, Jihae Kim, Minh Huy Vu, Young Jong Song, Mil Thi Tran, Yeon Woo Sung, Jae-Yean Kim","doi":"10.1093/hr/uhae294","DOIUrl":"https://doi.org/10.1093/hr/uhae294","url":null,"abstract":"The CRISPR-Cas-based gene targeting (GT) method has enabled precise modifications of genomic DNA ranging from single base to several kilobase scales through homologous recombination (HR). In plant somatic cells, canonical nonhomologous end-joining (cNHEJ) is the predominant mechanism for repairing double-stranded breaks (DSBs), thus limiting the HR-mediated GT. In this study, we implemented an approach to shift the repair pathway preference toward HR by using a dominant-negative ku80 mutant protein (KUDN) to disrupt the initiation of cNHEJ. The employment of KUDN conferred a 1.71- to 3.55-fold improvement in GT efficiency at the callus stage. When we screened transformants, there was a more remarkable increase in GT efficiency, ranging from 1.62- to 9.84-fold, at two specific tomato loci, SlHKT1;2 and SlEPSPS1. With practical levels of efficiency, this enhanced KUDN-based GT tool successfully facilitated a 9-bp addition at an additional locus, SlCAB13. These findings provide another promising method for more efficient and precise plant breeding.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"13 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142488747","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}
Pre-fertilization hybridization barriers are the main causes of inter-subgeneric hybridization challenges in water lily. However, the mechanism underlying low compatibility between pollen and stigma of water lily remains unclear. This study demonstrates that CBL-interacting protein kinase 6 (CIPK6) responded to the signaling exchange between incompatible pollen and stigma through interactions with SNF1-related kinase 1 (SnRK1) and promotes the accumulation of SnRK1 protein. Activated SnRK1 interacted with 9-cis-epoxycarotenoid dioxygenase 2 (NCED2) to promote its degradation, thereby inhibiting abscisic acid (ABA) synthesis. A decrease in ABA content in the stigma impaired the ABA-mediated removal of reactive oxygen species (ROS), ultimately resulting in the rejection of the incompatible pollen by the stigma. Our results highlight the essential role of the NpCIPK6–NpSnRK1–NpNCED2 module in conferring inter-subgeneric hybridization barriers in water lily by interfering with ABA synthesis and promoting ROS accumulation. This study offers valuable mechanistic insights into cellular signaling and reproductive barriers in water lily as well as across other biological contexts.
受精前杂交障碍是睡莲亚属间杂交难题的主要原因。然而，睡莲花粉与柱头之间低相容性的机制仍不清楚。本研究表明，CBL-互作蛋白激酶6（CIPK6）通过与SNF1相关激酶1（SnRK1）相互作用，对不相容花粉和柱头之间的信号交换做出反应，并促进SnRK1蛋白的积累。活化的 SnRK1 与 9-顺式环氧类胡萝卜素二氧酶 2（NCED2）相互作用，促进其降解，从而抑制脱落酸（ABA）的合成。柱头中 ABA 含量的减少损害了 ABA 介导的活性氧（ROS）清除，最终导致不相容花粉被柱头排斥。我们的研究结果突出表明，NpCIPK6-NpSnRK1-NpNCED2 模块通过干扰 ABA 合成和促进 ROS 积累，在赋予睡莲亚属间杂交障碍方面起着至关重要的作用。这项研究为睡莲以及其他生物环境中的细胞信号传导和繁殖障碍提供了宝贵的机理见解。
{"title":"NpCIPK6–NpSnRK1 module facilitates inter-subgeneric hybridization barriers in water lily (nymphaea) by reducing abscisic acid content","authors":"Ping Zhou, Jingwen Li, Huiyan Jiang, Zhijuan Yang, Chunqing Sun, Hongyan Wang, Qun Su, Qijiang Jin, Yanjie Wang, Yingchun Xu","doi":"10.1093/hr/uhae289","DOIUrl":"https://doi.org/10.1093/hr/uhae289","url":null,"abstract":"Pre-fertilization hybridization barriers are the main causes of inter-subgeneric hybridization challenges in water lily. However, the mechanism underlying low compatibility between pollen and stigma of water lily remains unclear. This study demonstrates that CBL-interacting protein kinase 6 (CIPK6) responded to the signaling exchange between incompatible pollen and stigma through interactions with SNF1-related kinase 1 (SnRK1) and promotes the accumulation of SnRK1 protein. Activated SnRK1 interacted with 9-cis-epoxycarotenoid dioxygenase 2 (NCED2) to promote its degradation, thereby inhibiting abscisic acid (ABA) synthesis. A decrease in ABA content in the stigma impaired the ABA-mediated removal of reactive oxygen species (ROS), ultimately resulting in the rejection of the incompatible pollen by the stigma. Our results highlight the essential role of the NpCIPK6–NpSnRK1–NpNCED2 module in conferring inter-subgeneric hybridization barriers in water lily by interfering with ABA synthesis and promoting ROS accumulation. This study offers valuable mechanistic insights into cellular signaling and reproductive barriers in water lily as well as across other biological contexts.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"235 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142488742","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}
Alberto Rodriguez-Izquierdo, David Carrasco, Luis Valledor, Josefina Bota, Cristina López-Hidalgo, Maria A Revilla, Rosa Arroyo-Garcia
The large diversity of grapevine cultivars includes genotypes more tolerant to water deficit than others. Widely distributed cultivars, like Merlot, are more sensitive to water deprivation than local cultivars like Callet, which are more adapted to water deficit due to their Mediterranean origin. Despite their tolerance, adaptation to water deficit influenced by grafting in rootstocks like 110 Richter is key to facing drought in vineyards, defining the scion/rootstock relationship. To understand these differences, we explored transcriptomic, metabolic, hormonal and physiological responses under three levels of water deficit (mild, high and extreme), using 110 Richter as the rootstock in both cultivars. Results revealed that sensitivity to ABA is essential for water deficit tolerance in the aerial part, guiding root responses. Callet/110 Richter activates more gene expression patterns in response to ABA, reducing water loss compared to Merlot/110 Richter in both aerial and root parts. This modulation in Callet/110 Richter involves regulating metabolic pathways to increase cell turgor, reducing photosynthesis, and producing molecules like polyphenols or flavonoids to respond to oxidative stress. In contrast, Merlot/110 Richter shows a lack of specific response, especially in the roots, indicating less resilience to water stress. Therefore, selecting genotypes more sensitive to ABA and their interaction with rootstocks is key for managing vineyards in future climate change scenarios.
葡萄栽培品种种类繁多，其中包括比其他品种更耐缺水的基因型。分布广泛的栽培品种，如美乐，比当地的栽培品种，如卡莱，对缺水更为敏感。尽管它们具有耐受性，但对缺水的适应性受砧木（如 110 Richter）嫁接的影响，是葡萄园应对干旱的关键，也决定了接穗与砧木之间的关系。为了了解这些差异，我们以 110 Richter 作为两个栽培品种的砧木，探讨了三种程度（轻度、高度和极端）的水分亏缺下的转录组、代谢、激素和生理反应。结果表明，对 ABA 的敏感性是气生部分耐受水分亏缺的必要条件，并能指导根系的反应。与 Merlot/110 Richter 相比，Callet/110 Richter 对 ABA 的反应激活了更多的基因表达模式，减少了气生部分和根部的水分损失。Callet/110 Richter 的这种调节包括调节新陈代谢途径以增加细胞张力、减少光合作用以及产生多酚或类黄酮等分子以应对氧化应激。相比之下，Merlot/110 Richter 缺乏特异性反应，尤其是在根部，这表明其对水分胁迫的恢复能力较弱。因此，选择对 ABA 更为敏感的基因型及其与砧木的相互作用是在未来气候变化情况下管理葡萄园的关键。
{"title":"The scion-driven transcriptomic changes guide the resilience of grafted near-isohydric grapevines under water deficit","authors":"Alberto Rodriguez-Izquierdo, David Carrasco, Luis Valledor, Josefina Bota, Cristina López-Hidalgo, Maria A Revilla, Rosa Arroyo-Garcia","doi":"10.1093/hr/uhae291","DOIUrl":"https://doi.org/10.1093/hr/uhae291","url":null,"abstract":"The large diversity of grapevine cultivars includes genotypes more tolerant to water deficit than others. Widely distributed cultivars, like Merlot, are more sensitive to water deprivation than local cultivars like Callet, which are more adapted to water deficit due to their Mediterranean origin. Despite their tolerance, adaptation to water deficit influenced by grafting in rootstocks like 110 Richter is key to facing drought in vineyards, defining the scion/rootstock relationship. To understand these differences, we explored transcriptomic, metabolic, hormonal and physiological responses under three levels of water deficit (mild, high and extreme), using 110 Richter as the rootstock in both cultivars. Results revealed that sensitivity to ABA is essential for water deficit tolerance in the aerial part, guiding root responses. Callet/110 Richter activates more gene expression patterns in response to ABA, reducing water loss compared to Merlot/110 Richter in both aerial and root parts. This modulation in Callet/110 Richter involves regulating metabolic pathways to increase cell turgor, reducing photosynthesis, and producing molecules like polyphenols or flavonoids to respond to oxidative stress. In contrast, Merlot/110 Richter shows a lack of specific response, especially in the roots, indicating less resilience to water stress. Therefore, selecting genotypes more sensitive to ABA and their interaction with rootstocks is key for managing vineyards in future climate change scenarios.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"19 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142488743","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}
Cold stress seriously affects the plant growth and development. The ubiquitination system plays an important role by degrading and modifying substrates at the protein level. In this study, the U-box type ubiquitin ligase VviPUB19 gene was induced by low temperature (4°C) in grapevine. In Arabidopsis thaliana, the pub19 mutant, a homologous mutation of VviPUB19, exhibited enhanced cold tolerance, and the resistance phenotype of the mutant could be attenuated by VviPUB19. VviPUB19 overexpressing grape lines exhibited lower cold tolerance. Furthermore, it was revealed that VviPUB19 interacted with the cold-related transcription factors VviICE1, 2 and 3 and VviCBF1 and 2, and was involved in the degradation of them. This is the first time that an E3 ligase (VviPUB19) that interacts with CBFs and affects its protein stability has been identified. It was also shown that VviICE1, 2 and 3 positively regulated VviPUB19 promoter activity. Therefore, our results suggest that VviPUB19 reduces grape cold tolerance via participating in the CBF-dependent pathway.
{"title":"The ubiquitin ligase VviPUB19 negatively regulates grape cold tolerance by affecting the stability of ICEs and CBFs","authors":"Ling Wang, Mengyu Zhao, Xue Zhang, Ting Zhao, Congbo Huang, Yujin Tang, Yan Li, Chaohong Zhang","doi":"10.1093/hr/uhae297","DOIUrl":"https://doi.org/10.1093/hr/uhae297","url":null,"abstract":"Cold stress seriously affects the plant growth and development. The ubiquitination system plays an important role by degrading and modifying substrates at the protein level. In this study, the U-box type ubiquitin ligase VviPUB19 gene was induced by low temperature (4°C) in grapevine. In Arabidopsis thaliana, the pub19 mutant, a homologous mutation of VviPUB19, exhibited enhanced cold tolerance, and the resistance phenotype of the mutant could be attenuated by VviPUB19. VviPUB19 overexpressing grape lines exhibited lower cold tolerance. Furthermore, it was revealed that VviPUB19 interacted with the cold-related transcription factors VviICE1, 2 and 3 and VviCBF1 and 2, and was involved in the degradation of them. This is the first time that an E3 ligase (VviPUB19) that interacts with CBFs and affects its protein stability has been identified. It was also shown that VviICE1, 2 and 3 positively regulated VviPUB19 promoter activity. Therefore, our results suggest that VviPUB19 reduces grape cold tolerance via participating in the CBF-dependent pathway.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"4 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142488744","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}
Black wolfberry (Lycium ruthenicum Murr.) is an important plant for ecological preservation. In addition, its fruits are rich in anthocyanins and have important edible and medicinal value. However, a high quality chromosome-level genome for this species is not yet available, and the regulatory mechanisms involved in the biosynthesis of anthocyanins are unclear. In this study, haploid material was used to assemble a high-quality chromosome-level reference genome of Lycium ruthenicum, resulting in a genome size of 2,272 Mb with contig N50 of 92.64 Mb, and 38,993 annotated gene models. In addition, the evolution of this genome and large-scale variations compared with the Ningxia wolfberry Lycium barbarum were determined. Importantly, homology annotation identified 86 genes involved in the regulatory pathway of anthocyanin biosynthesis, five of which [LrCHS1 (evm.TU.Chr05.295), LrCHS2 (evm.TU.Chr09.488), LrAOMT (evm.TU.Chr09.809), LrF3'5'H (evm.TU.Chr06.177) and LrAN2.1 (evm.TU.Chr05.2618)] were screened by differential expression analysis and correlation analysis using a combination of transcriptome and metabolome testing. Overexpression of these genes could significantly up- or downregulate anthocyanin-related metabolites. These results will help accelerate the functional genomic research of L. ruthenicum, and the elucidation of the genes involved in anthocyanin synthesis will be beneficial for breeding new varieties and further exploring its ecological conservation potential.
{"title":"High-quality genome of black wolfberry (Lycium ruthenicum Murr.) provides insights into the genetics of anthocyanin biosynthesis regulation","authors":"Yuhui Xu, Haoxia Li, Tongwei Shi, Qing Luo, Yuchao Chen, Shenghu Guo, Weiwei Tian, Wei An, Jian Zhao, Yue Yin, Jun He, Rui Zheng, Xiaojie Liang, Yajun Wang, Xiyan Zhang, Zhigang Shi, Linyuan Duan, Xiaoya Qin, Ting Huang, Bo Zhang, Ru Wan, Yanlong Li, Youlong Cao, Hui Liu, Sheng Shu, Aisheng Xiong, Jianhua Zhao","doi":"10.1093/hr/uhae298","DOIUrl":"https://doi.org/10.1093/hr/uhae298","url":null,"abstract":"Black wolfberry (Lycium ruthenicum Murr.) is an important plant for ecological preservation. In addition, its fruits are rich in anthocyanins and have important edible and medicinal value. However, a high quality chromosome-level genome for this species is not yet available, and the regulatory mechanisms involved in the biosynthesis of anthocyanins are unclear. In this study, haploid material was used to assemble a high-quality chromosome-level reference genome of Lycium ruthenicum, resulting in a genome size of 2,272 Mb with contig N50 of 92.64 Mb, and 38,993 annotated gene models. In addition, the evolution of this genome and large-scale variations compared with the Ningxia wolfberry Lycium barbarum were determined. Importantly, homology annotation identified 86 genes involved in the regulatory pathway of anthocyanin biosynthesis, five of which [LrCHS1 (evm.TU.Chr05.295), LrCHS2 (evm.TU.Chr09.488), LrAOMT (evm.TU.Chr09.809), LrF3'5'H (evm.TU.Chr06.177) and LrAN2.1 (evm.TU.Chr05.2618)] were screened by differential expression analysis and correlation analysis using a combination of transcriptome and metabolome testing. Overexpression of these genes could significantly up- or downregulate anthocyanin-related metabolites. These results will help accelerate the functional genomic research of L. ruthenicum, and the elucidation of the genes involved in anthocyanin synthesis will be beneficial for breeding new varieties and further exploring its ecological conservation potential.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"25 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142488745","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}
GRAS, termed after GAI (gibberellic acid insensitive), RGA (repressor of GA1), and SCR (scarecrow), is a plant-specific transcription factor crucial for plant development and stress response. However, understanding of the functions played by the GRAS members and their target genes in citrus is limited. In this study, we identified a cold stress-responsive GRAS gene from Poncirus trifoliate, designated as PtrPAT1, by yeast one-hybrid library screening using the promoter of PtrBADH-l, a betaine aldehyde dehydrogenase (BADH)-like gene. PtrPAT1, belonging to the PAT1 subfamily, was localized in the nucleus and plasma membrane, exhibited transactivation activity and showed a remarkable upregulation under cold stress. Overexpression of PtrPAT1 elevated BADH activity, increased glycine betaine (GB) accumulation and conferred enhanced cold tolerance in transgenic tobacco plants compared with wild type, while downregulation in trifoliate orange by virus-induced gene silencing (VIGS) resulted in opposite trends. Furthermore, the activities of two antioxidant enzymes, including peroxidase (POD) and superoxide dismutase (SOD), were significantly increased in the overexpression plants, but remarkably decreased in the VIGS line, consistent with accumulation patterns of the reactive oxygen species (ROS). PtrPAT1 was demonstrated to interact with and activate the PtrBADH-l promoter through the putative PAT1-binding motif with the core sequence of TTTCATGT, indicating that PtrBADH-l is a target gene of PtrPAT1. Taken together, these results demonstrate that PtrPAT1 positively affects cold tolerance through the regulation of GB biosynthesis by modulating PtrBADH-l expression.
{"title":"The GRAS transcription factor PtrPAT1 of Poncirus trifoliata functions in cold tolerance and modulates glycine betaine content by regulating the BADH-like gene","authors":"Ruhong Ming, Tian Fang, Wei Ling, Jingjing Geng, Jing Qu, Yu Zhang, Jianhua Chen, Shaochang Yao, Liangbo Li, Ding Huang, Ji-Hong Liu","doi":"10.1093/hr/uhae296","DOIUrl":"https://doi.org/10.1093/hr/uhae296","url":null,"abstract":"GRAS, termed after GAI (gibberellic acid insensitive), RGA (repressor of GA1), and SCR (scarecrow), is a plant-specific transcription factor crucial for plant development and stress response. However, understanding of the functions played by the GRAS members and their target genes in citrus is limited. In this study, we identified a cold stress-responsive GRAS gene from Poncirus trifoliate, designated as PtrPAT1, by yeast one-hybrid library screening using the promoter of PtrBADH-l, a betaine aldehyde dehydrogenase (BADH)-like gene. PtrPAT1, belonging to the PAT1 subfamily, was localized in the nucleus and plasma membrane, exhibited transactivation activity and showed a remarkable upregulation under cold stress. Overexpression of PtrPAT1 elevated BADH activity, increased glycine betaine (GB) accumulation and conferred enhanced cold tolerance in transgenic tobacco plants compared with wild type, while downregulation in trifoliate orange by virus-induced gene silencing (VIGS) resulted in opposite trends. Furthermore, the activities of two antioxidant enzymes, including peroxidase (POD) and superoxide dismutase (SOD), were significantly increased in the overexpression plants, but remarkably decreased in the VIGS line, consistent with accumulation patterns of the reactive oxygen species (ROS). PtrPAT1 was demonstrated to interact with and activate the PtrBADH-l promoter through the putative PAT1-binding motif with the core sequence of TTTCATGT, indicating that PtrBADH-l is a target gene of PtrPAT1. Taken together, these results demonstrate that PtrPAT1 positively affects cold tolerance through the regulation of GB biosynthesis by modulating PtrBADH-l expression.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"12 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142488746","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}
Flowering Chinese cabbage is a type of leafy vegetable that belongs to the Brassica genus. Originally native to South China, it is now widely cultivated and consumed across the globe, particularly in Asian countries. The recent cultivation and regional expansion of flowering Chinese cabbage provides a valuable opportunity to elucidate the genomic basis underlying environmental adaptation and desired traits during a short-term artificial selection process. Here, we investigate the genetic variation, population structure, and diversity of a diverse germplasm collection of 403 flowering Chinese cabbage accessions. Our investigation seeks to elucidate the genomic basis that guide the selection of adaptability, yield, and pivotal agronomic traits. We further investigated breeding improvement associated with stem development by integrating transcriptome data. Genome-wide association analysis identified 642 loci and corresponding candidate genes associated with 11 essential agronomic traits, including plant architecture and yield. Furthermore, we uncovered a significant disparity in the allele frequency distribution of non-synonymous mutations in these candidate genes throughout the improvement stages. Our results shed light on the genetic basis of improvement and crucial agronomic traits in flowering Chinese cabbage, offering invaluable resources for upcoming genomics-assisted breeding endeavors.
{"title":"Genomic selection and genetic architecture of agronomic traits during modern flowering Chinese cabbage breeding","authors":"Yahui Zhao, Guangguang Li, Zhangsheng Zhu, Ming Hu, Ding Jiang, Muxi Chen, Juantao Wang, Kexin Zhang, Yansong Zheng, Yi Liao, Changming Chen","doi":"10.1093/hr/uhae299","DOIUrl":"https://doi.org/10.1093/hr/uhae299","url":null,"abstract":"Flowering Chinese cabbage is a type of leafy vegetable that belongs to the Brassica genus. Originally native to South China, it is now widely cultivated and consumed across the globe, particularly in Asian countries. The recent cultivation and regional expansion of flowering Chinese cabbage provides a valuable opportunity to elucidate the genomic basis underlying environmental adaptation and desired traits during a short-term artificial selection process. Here, we investigate the genetic variation, population structure, and diversity of a diverse germplasm collection of 403 flowering Chinese cabbage accessions. Our investigation seeks to elucidate the genomic basis that guide the selection of adaptability, yield, and pivotal agronomic traits. We further investigated breeding improvement associated with stem development by integrating transcriptome data. Genome-wide association analysis identified 642 loci and corresponding candidate genes associated with 11 essential agronomic traits, including plant architecture and yield. Furthermore, we uncovered a significant disparity in the allele frequency distribution of non-synonymous mutations in these candidate genes throughout the improvement stages. Our results shed light on the genetic basis of improvement and crucial agronomic traits in flowering Chinese cabbage, offering invaluable resources for upcoming genomics-assisted breeding endeavors.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"55 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142448348","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}
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