Pub Date : 2024-12-18DOI: 10.1016/j.hpj.2024.09.003
Xinjie Yuan, Kunhua Zhou, Yueqin Huang, Gang Lei, Gege Li, Yu Fang, Yuanyuan Xie, Xuejun Chen, Rong Fang
Phytophthora capsici Leonian is a destructive pathogen that affects pepper production worldwide. Resistance breeding has been proposed as the most efficient and eco-friendly management strategy for controlling this pathogen. This study aimed to characterize the genetic architecture of P. capsici resistance in pepper to support its resistance breeding. In this study, a panel of 220 accessions of Capsicum annuum were evaluated for resistance to P. capsici under controlled conditions. The panel was genotyped via genotyping-by-sequencing (GBS), and the resulting 955 772 high-quality variations were used for the population stratification analysis and the identification of chromosome regions associated with resistance against P. capsici. Strong association signals were detected mainly on chromosomes 5 (CaRPc5.1) and 10 (CaRPc10.1). The associated single nucleotide polymorphisms (SNPs) explained 5.61–11.71 % of the phenotypic variation. The 220 accessions were divided into four genetic clusters, including an ancestral cluster, a transition cluster, and two recently emerged clusters. P. capsici resistance of the four clusters unveiled compromised resistance to P. capsici during modern domestication, which was hypothesized to be a trade-off for desirable horticultural traits. Using bulked sergeant analysis (BSA) and whole-genome resequencing (WGR), a major locus in an F4:5 population, derived from a cross between the P. capsici-resistant parent A204 and the susceptible parent A198, was mapped to a 1.81 Mb region on chromosome 10, which coincided with the CaRPc10.1 locus. This locus was further fine-mapped into a 32.36 kb region based on two derived F5:6 populations consisting of 2 713 individuals. The Capann_59Chr10g029350 gene, a likely allelic variation of the Pvr4 gene in this interval, was proposed as a strong candidate gene for Phytophthora capsisi resistance. Our results provide molecular perspectives into the P. capsici-resistance mechanism and molecular markers for the improvement of P. capsici resistance in pepper and pave the way for cloning the resistance gene underlying CaRPc10.1.
{"title":"Genetic dissection of Phytophthora capsici resistance in Capsicum annuum by genome-wide association mapping and fine mapping","authors":"Xinjie Yuan, Kunhua Zhou, Yueqin Huang, Gang Lei, Gege Li, Yu Fang, Yuanyuan Xie, Xuejun Chen, Rong Fang","doi":"10.1016/j.hpj.2024.09.003","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.09.003","url":null,"abstract":"<ce:italic>Phytophthora capsici</ce:italic> Leonian is a destructive pathogen that affects pepper production worldwide. Resistance breeding has been proposed as the most efficient and eco-friendly management strategy for controlling this pathogen. This study aimed to characterize the genetic architecture of <ce:italic>P</ce:italic>. <ce:italic>capsici</ce:italic> resistance in pepper to support its resistance breeding. In this study, a panel of 220 accessions of <ce:italic>Capsicum annuum</ce:italic> were evaluated for resistance to <ce:italic>P</ce:italic>. <ce:italic>capsici</ce:italic> under controlled conditions. The panel was genotyped via genotyping-by-sequencing (GBS), and the resulting 955 772 high-quality variations were used for the population stratification analysis and the identification of chromosome regions associated with resistance against <ce:italic>P</ce:italic>. <ce:italic>capsici</ce:italic>. Strong association signals were detected mainly on chromosomes 5 (<ce:italic>CaRPc5</ce:italic>.<ce:italic>1</ce:italic>) and 10 (<ce:italic>CaRPc10</ce:italic>.<ce:italic>1</ce:italic>). The associated single nucleotide polymorphisms (SNPs) explained 5.61–11.71 % of the phenotypic variation. The 220 accessions were divided into four genetic clusters, including an ancestral cluster, a transition cluster, and two recently emerged clusters. <ce:italic>P. capsici</ce:italic> resistance of the four clusters unveiled compromised resistance to <ce:italic>P</ce:italic>. <ce:italic>capsici</ce:italic> during modern domestication, which was hypothesized to be a trade-off for desirable horticultural traits. Using bulked sergeant analysis (BSA) and whole-genome resequencing (WGR), a major locus in an F<ce:inf loc=\"post\">4:5</ce:inf> population, derived from a cross between the <ce:italic>P</ce:italic>. <ce:italic>capsici</ce:italic>-resistant parent A204 and the susceptible parent A198, was mapped to a 1.81 Mb region on chromosome 10, which coincided with the <ce:italic>CaRPc10</ce:italic>.<ce:italic>1</ce:italic> locus. This locus was further fine-mapped into a 32.36 kb region based on two derived F<ce:inf loc=\"post\">5:6</ce:inf> populations consisting of 2 713 individuals. The <ce:italic>Capann_59Chr10g029350</ce:italic> gene, a likely allelic variation of the <ce:italic>Pvr4</ce:italic> gene in this interval, was proposed as a strong candidate gene for <ce:italic>Phytophthora capsisi</ce:italic> resistance. Our results provide molecular perspectives into the <ce:italic>P</ce:italic>. <ce:italic>capsici</ce:italic>-resistance mechanism and molecular markers for the improvement of <ce:italic>P</ce:italic>. <ce:italic>capsici</ce:italic> resistance in pepper and pave the way for cloning the resistance gene underlying <ce:italic>CaRPc10</ce:italic>.<ce:italic>1</ce:italic>.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"279 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142874079","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}
Pub Date : 2024-12-17DOI: 10.1016/j.hpj.2024.01.016
Nan Liu, Yupan Zou, Zhouqian Jiang, Lichan Tu, Xiaoyi Wu, Dan Li, Jiadian Wang, Luqi Huang, Cao Xu, Wei Gao
Safflower is an important oilseed crop that has been used in traditional Chinese medicine for thousands of years because of the clinically valuable flavonoid glycosides in its flower petals. However, the biosynthesis and molecular regulation of these compounds are still elusive due to the lack of a high-quality reference genome and scarce identification of key biosynthetic pathway genes in a medicinal safflower variety. Here we leveraged an integrative multi-omics strategy by combining genomic, comparative genomics, and tissue-specific transcriptome profiling with biochemical analysis to identify uridine diphosphate glycosyltransferases (UGTs) for flavonoid glycoside biosynthesis in safflower. We assembled and annotated a high-quality reference genome of a medicinal safflower variety, ‘Yunhong3’. A comprehensive comparative genomic analysis indicated that an evolutionary whole-genome triplication event occurring in safflower contributed to gene amplification of the flavonoid biosynthetic pathway. By combining comparative transcriptome profiling with enzymatic reactions, we identified 11 novel UGTs that could catalyze the conversion of naringenin chalcone and phloretin to the corresponding O-glycosides. Moreover, we outlined the molecular pathway of hydroxysafflor yellow A (HSYA) biosynthesis featured by 17 newly identified UGTs with promising catalytic activity, laying the foundation for the synthetic production of HSYA. Our study reports systemic genome and gene expression information for flavonoid glycoside biosynthesis in medicinal safflower and provides insights into mechanisms regulating HSYA biosynthesis, which would facilitate the genetic improvement and synthetic bioengineering design for producing clinically valuable flavonoid glycosides in safflower.
红花是一种重要的油籽作物，几千年来一直被用于中药中，因为它的花瓣中含有有临床价值的黄酮类苷。然而，由于缺乏高质量的参考基因组和对药用红花中关键生物合成途径基因的鉴定，这些化合物的生物合成和分子调控仍然是难以捉摸的。在这里，我们利用综合多组学策略，将基因组学、比较基因组学和组织特异性转录组分析与生化分析相结合，确定了红花中用于类黄酮苷生物合成的尿苷二磷酸糖基转移酶（UGTs）。我们组装并注释了药用红花品种“云红3号”的高质量参考基因组。综合比较基因组分析表明，发生在红花中的一个进化的全基因组三复制事件促进了黄酮类化合物生物合成途径的基因扩增。通过比较转录组分析和酶促反应相结合，我们鉴定出了11个新的ugt，它们可以催化柚皮素、查尔酮和根皮素转化为相应的o -糖苷。此外，我们还概述了17个新发现的具有良好催化活性的ugt的羟基afflor yellow A （HSYA）生物合成的分子途径，为HSYA的合成生产奠定了基础。本研究报告了药用红花黄酮类苷生物合成的系统基因组和基因表达信息，为HSYA生物合成的调控机制提供了新的思路，为生产具有临床应用价值的红花黄酮类苷提供遗传改良和合成生物工程设计。
{"title":"Multiomics driven identification of glycosyltransferases in flavonoid glycoside biosynthesis in safflower","authors":"Nan Liu, Yupan Zou, Zhouqian Jiang, Lichan Tu, Xiaoyi Wu, Dan Li, Jiadian Wang, Luqi Huang, Cao Xu, Wei Gao","doi":"10.1016/j.hpj.2024.01.016","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.01.016","url":null,"abstract":"Safflower is an important oilseed crop that has been used in traditional Chinese medicine for thousands of years because of the clinically valuable flavonoid glycosides in its flower petals. However, the biosynthesis and molecular regulation of these compounds are still elusive due to the lack of a high-quality reference genome and scarce identification of key biosynthetic pathway genes in a medicinal safflower variety. Here we leveraged an integrative multi-omics strategy by combining genomic, comparative genomics, and tissue-specific transcriptome profiling with biochemical analysis to identify uridine diphosphate glycosyltransferases (UGTs) for flavonoid glycoside biosynthesis in safflower. We assembled and annotated a high-quality reference genome of a medicinal safflower variety, ‘Yunhong3’. A comprehensive comparative genomic analysis indicated that an evolutionary whole-genome triplication event occurring in safflower contributed to gene amplification of the flavonoid biosynthetic pathway. By combining comparative transcriptome profiling with enzymatic reactions, we identified 11 novel UGTs that could catalyze the conversion of naringenin chalcone and phloretin to the corresponding O-glycosides. Moreover, we outlined the molecular pathway of hydroxysafflor yellow A (HSYA) biosynthesis featured by 17 newly identified UGTs with promising catalytic activity, laying the foundation for the synthetic production of HSYA. Our study reports systemic genome and gene expression information for flavonoid glycoside biosynthesis in medicinal safflower and provides insights into mechanisms regulating HSYA biosynthesis, which would facilitate the genetic improvement and synthetic bioengineering design for producing clinically valuable flavonoid glycosides in safflower.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"13 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142874154","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}
Potato (Solanum tuberosum) is a globally important staple crop. However, cultivated potato varieties are highly sensitive to low temperatures. The molecular mechanisms underlying freezing resistance in potatoes remain poorly understood. Through comparative metabolome and transcriptome analyses of freezing-tolerant (CM,Solanum commersonii) and freezing-sensitive (DM, DM1-3 516R44) varieties, we identified a cold-induced UDP-glycosyltransferase gene, ScUGT73B4, which is associated with the accumulation of glycosylated flavonoids in wild CM varieties. Overexpression of ScUGT73B4 led to increased accumulation of glycosylated flavonoids and enhanced antioxidant capacity, resulting in improved freezing tolerance in potato plantlets. These findings reveal a UDP-glycosyltransferase in the flavonoid pathway and offer a potential valuable genetic resource for breeding potatoes with improved freezing tolerance.
{"title":"A freezing responsive UDP-glycosyltransferase improves potato freezing tolerance via modifying flavonoid metabolism","authors":"Huihui Bao, Li Yuan, Yongchao Luo, Xinyu Jing, Zhenjie Zhang, Jinglei Wang, Guangtao Zhu","doi":"10.1016/j.hpj.2024.09.002","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.09.002","url":null,"abstract":"Potato (<ce:italic>Solanum tuberosum</ce:italic>) is a globally important staple crop. However, cultivated potato varieties are highly sensitive to low temperatures. The molecular mechanisms underlying freezing resistance in potatoes remain poorly understood. Through comparative metabolome and transcriptome analyses of freezing-tolerant (CM<ce:bold>,</ce:bold><ce:italic>Solanum commersonii</ce:italic>) and freezing-sensitive (DM, DM1-3 516R44) varieties, we identified a cold-induced UDP-glycosyltransferase gene, <ce:italic>ScUGT73B4</ce:italic>, which is associated with the accumulation of glycosylated flavonoids in wild CM varieties. Overexpression of <ce:italic>ScUGT73B4</ce:italic> led to increased accumulation of glycosylated flavonoids and enhanced antioxidant capacity, resulting in improved freezing tolerance in potato plantlets. These findings reveal a UDP-glycosyltransferase in the flavonoid pathway and offer a potential valuable genetic resource for breeding potatoes with improved freezing tolerance.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"20 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142874076","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}
Horticultural crops suffer massive production losses due to abiotic stress, which is a key limiting factor worldwide. The ability of these crops to withstand such stress has been linked to melatonin, a biomolecule with significant roles in both physiological and molecular defense responses. Melatonin is pivotal in enhancing the resilience of horticultural crops to abiotic stress, making it a critical component in their survival strategies. The application of exogenous melatonin improves abiotic stress tolerance by preserving membrane integrity, maintaining redox equilibrium, scavenging reactive oxygen species effectively, activating antioxidant defense mechanisms, and elevating gene expression related to stress responses. Furthermore, the integrated management of melatonin with other phytohormones demonstrates its potential relevance in addressing various stresses across a wide range of horticultural crops. Therefore, it is crucial to elucidate the physiological and molecular processes involving melatonin in abiotic stress in these crops. Here, we discuss current studies on the use of melatonin in horticultural crops in response to abiotic stresses, and explores future research directions and potential applications to enhance the productivity and abiotic stress tolerance of horticulture crops.
{"title":"Melatonin-mediated physiological and molecular responses to abiotic stress in horticultural crops","authors":"Xinyi Hao, Binghui Sun, Yaxiao Song, Junxia Zhang, Jieping Wu, Ningbo Zhang, Xiuming Zhang, Wenkong Yao, Weirong Xu","doi":"10.1016/j.hpj.2024.08.006","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.08.006","url":null,"abstract":"Horticultural crops suffer massive production losses due to abiotic stress, which is a key limiting factor worldwide. The ability of these crops to withstand such stress has been linked to melatonin, a biomolecule with significant roles in both physiological and molecular defense responses. Melatonin is pivotal in enhancing the resilience of horticultural crops to abiotic stress, making it a critical component in their survival strategies. The application of exogenous melatonin improves abiotic stress tolerance by preserving membrane integrity, maintaining redox equilibrium, scavenging reactive oxygen species effectively, activating antioxidant defense mechanisms, and elevating gene expression related to stress responses. Furthermore, the integrated management of melatonin with other phytohormones demonstrates its potential relevance in addressing various stresses across a wide range of horticultural crops. Therefore, it is crucial to elucidate the physiological and molecular processes involving melatonin in abiotic stress in these crops. Here, we discuss current studies on the use of melatonin in horticultural crops in response to abiotic stresses, and explores future research directions and potential applications to enhance the productivity and abiotic stress tolerance of horticulture crops.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"142 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823234","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}
Pub Date : 2024-12-09DOI: 10.1016/j.hpj.2024.07.007
Riya Johnson, Joy M. Joel, K.S. Anjitha, Szilvia Z. Tóth, Jos T. Puthur
Ascorbate (Asc), commonly known as vitamin C, is a vital molecule for plant growth, development, and stress resilience. It is also known to play a crucial role in various physiological processes, including photosynthesis, cell division, and differentiation. This article thoroughly explores the processes governing the metabolism of Asc in plants and its roles in physiological functions. It lays down a robust theoretical groundwork for delving into Asc production, transportation, functions, and its potential applications in stress alleviation and horticulture. Furthermore, recent studies indicate that Asc plays a role in regulating fruit development and affecting postharvest storage characteristics, thereby influencing fruit ripening and resilience to stress. Hence, there is a growing importance in studying the synthesis and utilization of Asc in plants. Although the critical role of Asc in controlling plant redox signals has been extensively studied, the precise mechanisms by which it manages cellular redox homeostasis to maintain the equilibrium between reactive oxygen scavenging and cell redox signaling remain elusive. This gap in knowledge presents fresh opportunities to explore how the production of Asc in plants is regulated and how plants react to environmental stressors. Furthermore, this article delves into the potential for a comprehensive investigation into the essential function of Asc in fruits, the development of Asc-rich fruits, and the enhancement of postharvest storage properties.
{"title":"Ascorbate, as a versatile regulator of plant development: Practical implications for enhancing crop productivity, quality, and postharvest storage","authors":"Riya Johnson, Joy M. Joel, K.S. Anjitha, Szilvia Z. Tóth, Jos T. Puthur","doi":"10.1016/j.hpj.2024.07.007","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.07.007","url":null,"abstract":"Ascorbate (Asc), commonly known as vitamin C, is a vital molecule for plant growth, development, and stress resilience. It is also known to play a crucial role in various physiological processes, including photosynthesis, cell division, and differentiation. This article thoroughly explores the processes governing the metabolism of Asc in plants and its roles in physiological functions. It lays down a robust theoretical groundwork for delving into Asc production, transportation, functions, and its potential applications in stress alleviation and horticulture. Furthermore, recent studies indicate that Asc plays a role in regulating fruit development and affecting postharvest storage characteristics, thereby influencing fruit ripening and resilience to stress. Hence, there is a growing importance in studying the synthesis and utilization of Asc in plants. Although the critical role of Asc in controlling plant redox signals has been extensively studied, the precise mechanisms by which it manages cellular redox homeostasis to maintain the equilibrium between reactive oxygen scavenging and cell redox signaling remain elusive. This gap in knowledge presents fresh opportunities to explore how the production of Asc in plants is regulated and how plants react to environmental stressors. Furthermore, this article delves into the potential for a comprehensive investigation into the essential function of Asc in fruits, the development of Asc-rich fruits, and the enhancement of postharvest storage properties.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"14 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823235","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}
Pub Date : 2024-12-07DOI: 10.1016/j.hpj.2024.07.006
Ying Ye, Yanrong Hu, Yuan Liu, Cheng Yu, Kun Zhou, Fengwang Ma, Xiaoqing Gong
UGT (UDP-dependent glycosyltransferase) family members are mainly involved in the modification of secondary metabolites, as well as plant stress responses. Previously, we identified the UGT gene MdUGT88F4 from Malus spp. In order to verify whether it had biological function in apple plants, we generated transgenic apple plants overexpressed MdUGT88F4 and treated them with salt stress. The results showed that it conferred enhanced salt stress tolerance in transgenic ‘GL-3’ apple (Malus domestica) plants. The expression of MdUGT88F4 was induced by salt stress, and overexpression of this gene alleviated the inhibitory effects of salt stress on the growth of apple plants. After 15 days of salt stress treatment (100 mmol·L−1 NaCl), necrotic spots were present on the leaves of wild-type (WT) plants, and none were observed on the leaves of transgenic plants overexpressing MdUGT88F4 (OX). The relative electrolyte leakage and malondialdehyde content were lower and the total chlorophyll content and the relative water content were higher in OX plants than in WT plants. The photosynthetic efficiency was higher in OX plants than in WT plants under salt stress, which was consistent with their larger stomatal aperture; this might stem from a reduction in the content of abscisic acid. The production of reactive oxygen species was lower and the activities of antioxidant enzymes were higher in OX plants than in WT plants. In addition, OX plants accumulated less Na+ but more K+ than WT plants, and the expression of several genes involved in Na + transport was upregulated in OX plants. MdUGT88F4 failed to promote the accumulation of isosalipurposide in vivo, and it was involved in isosalipurposide synthesis. Most of the flavonoid metabolites accumulated to a greater degree in OX plants than in WT plants. In summary, our results show that MdUGT88F4 positively regulates the salt stress response in apple plants, possibly by affecting stomatal movement, as well as the accumulation of ions and flavonoids. Our findings enhance our understanding of the metabolic mechanisms by which UGT proteins ameliorate the effects of salt stress in plants.
{"title":"MdUGT88F4 involved in the synthesis of isosalipurposide positively regulates the salt stress response of apple plants","authors":"Ying Ye, Yanrong Hu, Yuan Liu, Cheng Yu, Kun Zhou, Fengwang Ma, Xiaoqing Gong","doi":"10.1016/j.hpj.2024.07.006","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.07.006","url":null,"abstract":"UGT (UDP-dependent glycosyltransferase) family members are mainly involved in the modification of secondary metabolites, as well as plant stress responses. Previously, we identified the UGT gene <ce:italic>MdUGT88F4</ce:italic> from <ce:italic>Malus</ce:italic> spp. In order to verify whether it had biological function in apple plants, we generated transgenic apple plants overexpressed <ce:italic>MdUGT88F4</ce:italic> and treated them with salt stress. The results showed that it conferred enhanced salt stress tolerance in transgenic ‘GL-3’ apple (<ce:italic>Malus domestica</ce:italic>) plants. The expression of <ce:italic>MdUGT88F4</ce:italic> was induced by salt stress, and overexpression of this gene alleviated the inhibitory effects of salt stress on the growth of apple plants. After 15 days of salt stress treatment (100 mmol·L<ce:sup loc=\"post\">−1</ce:sup> NaCl), necrotic spots were present on the leaves of wild-type (WT) plants, and none were observed on the leaves of transgenic plants overexpressing <ce:italic>MdUGT88F4</ce:italic> (OX). The relative electrolyte leakage and malondialdehyde content were lower and the total chlorophyll content and the relative water content were higher in OX plants than in WT plants. The photosynthetic efficiency was higher in OX plants than in WT plants under salt stress, which was consistent with their larger stomatal aperture; this might stem from a reduction in the content of abscisic acid. The production of reactive oxygen species was lower and the activities of antioxidant enzymes were higher in OX plants than in WT plants. In addition, OX plants accumulated less Na<ce:sup loc=\"post\">+</ce:sup> but more K<ce:sup loc=\"post\">+</ce:sup> than WT plants, and the expression of several genes involved in Na <ce:sup loc=\"post\">+</ce:sup> transport was upregulated in OX plants. <ce:italic>MdUGT88F4</ce:italic> failed to promote the accumulation of isosalipurposide <ce:italic>in vivo</ce:italic>, and it was involved in isosalipurposide synthesis. Most of the flavonoid metabolites accumulated to a greater degree in OX plants than in WT plants. In summary, our results show that <ce:italic>MdUGT88F4</ce:italic> positively regulates the salt stress response in apple plants, possibly by affecting stomatal movement, as well as the accumulation of ions and flavonoids. Our findings enhance our understanding of the metabolic mechanisms by which UGT proteins ameliorate the effects of salt stress in plants.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"29 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823236","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}
Pub Date : 2024-12-07DOI: 10.1016/j.hpj.2024.07.005
Guiling Liu, Huijun Liu, Gongfa Shi, Nuo Xu, Zhaoqian Niu, Lei Wang, Ruiyang Zhao, Ling Wang, Lijuan Fan
Iris sanguinea Donn ex Horn. is a common perennial ornamental herb in Northeast China due to its strong cold-resistance capacity. In this study, integrative analyses of metabolomics and transcriptomics data were performed on five cultivars of I. sanguinea with varying petal colors to elucidate the molecular basis underlying petal pigmentation. The metabolomics data revealed that a total of five major anthocyanins were responsible for petal pigmentation in I. sanguinea. While two delphinidin-3-O-glucoside derivatives contributed to blue coloration in petals, two petunidin-3-O-glucoside and cyanidin-3-O-rutinoside derivatives exhibited significantly higher abundances in the deep pink petals. In addition, transcriptomics revealed a gradual increase in the expression of a large set of genes involved in flavonoid and anthocyanin biosynthesis pathways, corresponding to the varying levels of anthocyanin content among cultivar petals. Integrated metabolomics and transcriptomics analysis further led to the discovery of molecular modules controlling petal pigmentation, in which an R2R3 MYB transcription factor IsMYBL1 was found to be associated with the accumulation of key anthocyanin derivatives, it localized to the nucleus. The regulatory role of IsMYBL1 in anthocyanin accumulation has been validated through overexpressing in tobacco and knockdown in I. sanguinea using an improved virus-induced gene silencing (VIGS) approach. Finally, BiFC and Y2H showed that IsMYBL1 interacts with IsEGL3 and IsTTG1 to activate the expression of genes involved in anthocyanin biosynthesis, Yeast one-hybrid, dual-luciferase assays, showed that IsMYBL1 significantly increased anthocyanin contents in I. sanguinea by promoting the expression of IsANS, thereby promoting anthocyanin accumulation. Taken together, our study has provided a comprehensive molecular profiling of petal coloration in I. sanguinea and revealed key gene/metabolite networks that determine petal pigmentation.
鸢尾花（鸢尾花）是东北地区常见的多年生观赏草本植物，抗寒能力强。在本研究中，对5个不同花瓣颜色的血地兰品种进行了代谢组学和转录组学的综合分析，以阐明花瓣色素沉着的分子基础。代谢组学分析结果表明，血地菊花瓣色素沉着主要由5种主要花青素组成。虽然两种飞燕草苷-3- o -葡萄糖苷衍生物对花瓣的蓝色有贡献，但两种牵牛花苷-3- o -葡萄糖苷和花青素-3- o -芦丁苷衍生物在深粉红色花瓣中的丰度明显更高。此外，转录组学结果显示，黄酮类和花青素生物合成途径中大量基因的表达逐渐增加，这与不同品种花瓣中花青素含量的不同水平相对应。综合代谢组学和转录组学分析进一步发现了控制花瓣色素沉着的分子模块，其中发现R2R3 MYB转录因子IsMYBL1与关键花青素衍生物的积累有关，它定位于细胞核。IsMYBL1在花青素积累中的调控作用已经通过在烟草中过表达和使用改进的病毒诱导基因沉默（VIGS）方法在血地菊中敲低得到验证。最后，BiFC和Y2H研究表明，IsMYBL1与IsEGL3和IsTTG1相互作用，激活花青素生物合成相关基因的表达，酵母单杂交、双荧光素酶实验表明，IsMYBL1通过促进IsANS的表达，显著增加了血地花中花青素的含量，从而促进花青素的积累。综上所述，我们的研究提供了一个全面的分子图谱，血地兰花瓣的颜色，并揭示了关键的基因/代谢物网络决定花瓣的颜色。
{"title":"Multi-omics analysis of Iris sanguinea with distinctive flower colors provides insights into petal coloration","authors":"Guiling Liu, Huijun Liu, Gongfa Shi, Nuo Xu, Zhaoqian Niu, Lei Wang, Ruiyang Zhao, Ling Wang, Lijuan Fan","doi":"10.1016/j.hpj.2024.07.005","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.07.005","url":null,"abstract":"<ce:italic>Iris sanguinea</ce:italic> Donn ex Horn. is a common perennial ornamental herb in Northeast China due to its strong cold-resistance capacity. In this study, integrative analyses of metabolomics and transcriptomics data were performed on five cultivars of <ce:italic>I. sanguinea</ce:italic> with varying petal colors to elucidate the molecular basis underlying petal pigmentation. The metabolomics data revealed that a total of five major anthocyanins were responsible for petal pigmentation in <ce:italic>I. sanguinea</ce:italic>. While two delphinidin-3-<ce:italic>O</ce:italic>-glucoside derivatives contributed to blue coloration in petals, two petunidin-3-<ce:italic>O</ce:italic>-glucoside and cyanidin-3-<ce:italic>O</ce:italic>-rutinoside derivatives exhibited significantly higher abundances in the deep pink petals. In addition, transcriptomics revealed a gradual increase in the expression of a large set of genes involved in flavonoid and anthocyanin biosynthesis pathways, corresponding to the varying levels of anthocyanin content among cultivar petals. Integrated metabolomics and transcriptomics analysis further led to the discovery of molecular modules controlling petal pigmentation, in which an R2R3 MYB transcription factor <ce:italic>IsMYBL1</ce:italic> was found to be associated with the accumulation of key anthocyanin derivatives, it localized to the nucleus. The regulatory role of <ce:italic>IsMYBL1</ce:italic> in anthocyanin accumulation has been validated through overexpressing in tobacco and knockdown in <ce:italic>I. sanguinea</ce:italic> using an improved virus-induced gene silencing (VIGS) approach. Finally, BiFC and Y2H showed that <ce:italic>IsMYBL1</ce:italic> interacts with <ce:italic>IsEGL3</ce:italic> and <ce:italic>IsTTG1</ce:italic> to activate the expression of genes involved in anthocyanin biosynthesis, Yeast one-hybrid, dual-luciferase assays, showed that <ce:italic>IsMYBL1</ce:italic> significantly increased anthocyanin contents in <ce:italic>I. sanguinea</ce:italic> by promoting the expression of <ce:italic>IsANS</ce:italic>, thereby promoting anthocyanin accumulation. Taken together, our study has provided a comprehensive molecular profiling of petal coloration in <ce:italic>I. sanguinea</ce:italic> and revealed key gene/metabolite networks that determine petal pigmentation.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"200 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823294","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}
Pub Date : 2024-12-02DOI: 10.1016/j.hpj.2024.03.017
Na Wang, Yanting Li, Tianli Guo, Libo Jiang
Tomato (Solanum lycopersicum) is an extensively cultivated vegetable, and its growth and fruit quality can be significantly impaired by low temperatures. The widespread presence of N6-methyladenosine (m6A) modification on RNA is involved in a diverse range of stress response processes. There is a significant knowledge gap regarding the precise roles of m6A modification in tomato, particularly for cold stress response. Here, we assessed the m6A modification landscape of S. lycopersicum ‘Micro-Tom’ leaves in response to low-temperature stress. Furthermore, we investigated the potential relationship among m6A 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 m6A peak associated genes were identified in the control and cold treatment tomato leaves, respectively. Additionally, we observed a UGUACAK (K = G/U) motif under both conditions. Differential m6A site associated genes most likely play roles in protein translation regulatory pathway. Besides directly altering gene expression levels, m6A 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, m6A modification levels were increased in SBPase (Sedoheptulose-1,7-bisphosphatase, Solyc05g052600.4) 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 m6A modification landscape and multi-omics analysis provide valuable insights into the epigenetic regulatory mechanisms in tomato cold stress response.
{"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}
Pub Date : 2024-11-29DOI: 10.1016/j.hpj.2024.06.010
Delu Ning, Tao Wu, Wenlong Lei, Shengcheng Zhang, Ting Ma, Li Pan, Liangjun Xiao, Noor ul-Ain, Xingtan Zhang, Fuliang Cao
Juglans sigillata 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. ANR) 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.
{"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}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：