Nodes are a distinct feature of bamboo plants, categorized into three main types: culm, shoot, and rhizome nodes. However, the latter two are often overlooked due to their underground growth, resulting in a limited understanding of their structure and function. In this study, we examined the structure and mineral elements deposition in the nodes of Moso bamboo (Phyllostachys edulis). Our findings indicate that all three node types possess a complex yet well-organized vascular bundle system, with notable differences. Culm nodes feature enlarged vascular bundles with distinct xylem and phloem regions, whereas shoot and rhizome nodes have less-developed phloem regions. The rhizome node contains a vascular structure of crown root and coronary shoot bud, which is absent in culm and shoot nodes. In culm node, iron accumulation decreases gradually from the bottom to the top, primarily localizing in cells near the enlarged and small vascular bundles. Zinc is deposited in both the enlarged and small vascular bundles in the lower part of the node. In contrast, calcium accumulates predominantly in the upper part, particularly in cells adjacent to enlarged and small vascular bundles including diffuse and parenchyma cells. Potassium is distributed throughout most cells but is less abundant in the pith cavity and xylem transfer cells. In shoot and rhizome nodes, iron, zinc, calcium, and potassium exhibit specific regional and cellular deposition patterns. Overall, the vascular structure and mineral element deposition patterns suggest that bamboo nodes function not only as tissue junctions but also as critical hubs for mineral element deposition and distribution.
{"title":"Linking the structure of vascular bundles and mineral element deposition reveals the hub role of nodes in bamboo","authors":"Xianyu Pan, Ji Feng Shao","doi":"10.1093/hr/uhaf113","DOIUrl":"https://doi.org/10.1093/hr/uhaf113","url":null,"abstract":"Nodes are a distinct feature of bamboo plants, categorized into three main types: culm, shoot, and rhizome nodes. However, the latter two are often overlooked due to their underground growth, resulting in a limited understanding of their structure and function. In this study, we examined the structure and mineral elements deposition in the nodes of Moso bamboo (Phyllostachys edulis). Our findings indicate that all three node types possess a complex yet well-organized vascular bundle system, with notable differences. Culm nodes feature enlarged vascular bundles with distinct xylem and phloem regions, whereas shoot and rhizome nodes have less-developed phloem regions. The rhizome node contains a vascular structure of crown root and coronary shoot bud, which is absent in culm and shoot nodes. In culm node, iron accumulation decreases gradually from the bottom to the top, primarily localizing in cells near the enlarged and small vascular bundles. Zinc is deposited in both the enlarged and small vascular bundles in the lower part of the node. In contrast, calcium accumulates predominantly in the upper part, particularly in cells adjacent to enlarged and small vascular bundles including diffuse and parenchyma cells. Potassium is distributed throughout most cells but is less abundant in the pith cavity and xylem transfer cells. In shoot and rhizome nodes, iron, zinc, calcium, and potassium exhibit specific regional and cellular deposition patterns. Overall, the vascular structure and mineral element deposition patterns suggest that bamboo nodes function not only as tissue junctions but also as critical hubs for mineral element deposition and distribution.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"7 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143866395","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}
Xiaoying Liu, Yachen Li, Xianzhi Zhang, Xiaodong Xie, Abu Naim Md Muzahid, Jing Tu, Lansha Luo, Gudeta Chalchisa, Haiyan Lv, Hua Tian, Sean M Bulley, Dawei Li, Caihong Zhong
Consumers value highly the nutritional content and flavor of fresh fruits, which are influenced by endogenous plant hormones. However, the molecular mechanisms governing the hormonal regulation of essential nutrients such as ascorbic acid (AsA) in fruit are still unclear. This study investigates the regulation of AsA synthesis in kiwifruit by the transcription factor AcABI5a, which is involved in mediating the abscisic acid (ABA) signal. A negative correlation between AcABI5a expression and AsA levels across different developmental stages of kiwifruit was observed. Furthermore, AcABI5a was found to bind both the AcMYBS1 promoter, repressing its transcriptional activity, and its own promoter, fostering expression and maintaining active repression of AcMYBS1. AcMYBS1 activates the expression of AcGGP3, which encodes an enzymatic step in AsA biosynthesis that is highly regulated both transcriptionally and translationally. In-depth interaction studies utilizing yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC), firefly luciferase complementation (NC-LUC), and pull-down assays unveiled that AcABI5a also physically interacts with AcMYBS1, further impeding its activation of AcGGP3. Results from knock-out by gene editing and overexpression of AcABI5a support the role of AcABI5a in mediating the ABA inhibitory effect on AsA synthesis by repressing the expression of AcMYBS1 and thus AcGGP3. Overall, our findings highlight AcABI5a’s negative regulatory role in AsA synthesis by integrating ABA signaling during fruit development, providing new insights into the regulation of AsA synthesis by phytohormones.
{"title":"AcABI5a integrates abscisic acid signaling to developmentally modulate fruit ascorbic acid biosynthesis in kiwifruit","authors":"Xiaoying Liu, Yachen Li, Xianzhi Zhang, Xiaodong Xie, Abu Naim Md Muzahid, Jing Tu, Lansha Luo, Gudeta Chalchisa, Haiyan Lv, Hua Tian, Sean M Bulley, Dawei Li, Caihong Zhong","doi":"10.1093/hr/uhaf111","DOIUrl":"https://doi.org/10.1093/hr/uhaf111","url":null,"abstract":"Consumers value highly the nutritional content and flavor of fresh fruits, which are influenced by endogenous plant hormones. However, the molecular mechanisms governing the hormonal regulation of essential nutrients such as ascorbic acid (AsA) in fruit are still unclear. This study investigates the regulation of AsA synthesis in kiwifruit by the transcription factor AcABI5a, which is involved in mediating the abscisic acid (ABA) signal. A negative correlation between AcABI5a expression and AsA levels across different developmental stages of kiwifruit was observed. Furthermore, AcABI5a was found to bind both the AcMYBS1 promoter, repressing its transcriptional activity, and its own promoter, fostering expression and maintaining active repression of AcMYBS1. AcMYBS1 activates the expression of AcGGP3, which encodes an enzymatic step in AsA biosynthesis that is highly regulated both transcriptionally and translationally. In-depth interaction studies utilizing yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC), firefly luciferase complementation (NC-LUC), and pull-down assays unveiled that AcABI5a also physically interacts with AcMYBS1, further impeding its activation of AcGGP3. Results from knock-out by gene editing and overexpression of AcABI5a support the role of AcABI5a in mediating the ABA inhibitory effect on AsA synthesis by repressing the expression of AcMYBS1 and thus AcGGP3. Overall, our findings highlight AcABI5a’s negative regulatory role in AsA synthesis by integrating ABA signaling during fruit development, providing new insights into the regulation of AsA synthesis by phytohormones.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"2 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143872673","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}
Xiongfang Liu, Youming Wan, Jihua Wang, Fu Gao, Zihuan Wu, Zhenghong Li, Yao Zhang, Yongpeng Ma, Hong Ma
Photoperiod-dependent flowering is a critical trait in breeding for flowering time in woody ornamental plants. Circadian clocks are vital for the regulation of photoperiodic flowering in plants, but their molecular regulation pathways in woody perennials remain poorly explored. Here, we identified two circadian clock components LgPSEUDO-RESPONSE REGULATOR 7 (LgPRR7) and LgFLAVIN-BINDING KELCH REPEAT F-BOX 1 (LgFKF1) as key repressors of flowering in Luculia gratissima, a short-day woody ornamental plant with commercial potential. Levels of LgPRR7 and LgFKF1 transcripts exhibited photoperiodic responses and diurnal patterns. Ectopic overexpression of LgPRR7 or LgFKF1 in Arabidopsis thaliana accelerated flowering, whereas silencing LgPRR7 or LgFKF1 in L. gratissima accelerated flowering. Crucially, LgPRR7 directly interacts with LgFKF1, forming a self-reinforcing regulatory module LgPRR7-LgFKF1 to repress flowering in L. gratissima. Furthermore, the observed physical interactions among LgFKF1, LgCONSTANS-LIKE 12 (LgCOL12), and LgREPRESSOR OF ga1-3-LIKE 2 (LgRGL2) implied that they possibly formed a protein complex LgFKF1-LgCOL12-LgRGL2, bridging the circadian clock, photoperiod, and gibberellin signaling pathways to suppress downstream floral integrators. Intriguingly, silencing LgPRR7 and LgFKF1 extended the duration of L. gratissima flowering, a trait of horticultural significance. These results suggest the integration of multi-layered environmental and endogenous signals in the regulation of flowering time. The LgPRR7-LgFKF1 module provides novel targets for molecular improvement to manipulate flowering time and duration in L. gratissima and other economically valuable woody ornamental plants. Our results also support the mediation of flowering convergence in short-day plants through the action of circadian clock genes.
{"title":"The circadian clock module LgPRR7-LgFKF1 negatively regulates flowering time in Luculia gratissima, a woody ornamental plant","authors":"Xiongfang Liu, Youming Wan, Jihua Wang, Fu Gao, Zihuan Wu, Zhenghong Li, Yao Zhang, Yongpeng Ma, Hong Ma","doi":"10.1093/hr/uhaf110","DOIUrl":"https://doi.org/10.1093/hr/uhaf110","url":null,"abstract":"Photoperiod-dependent flowering is a critical trait in breeding for flowering time in woody ornamental plants. Circadian clocks are vital for the regulation of photoperiodic flowering in plants, but their molecular regulation pathways in woody perennials remain poorly explored. Here, we identified two circadian clock components LgPSEUDO-RESPONSE REGULATOR 7 (LgPRR7) and LgFLAVIN-BINDING KELCH REPEAT F-BOX 1 (LgFKF1) as key repressors of flowering in Luculia gratissima, a short-day woody ornamental plant with commercial potential. Levels of LgPRR7 and LgFKF1 transcripts exhibited photoperiodic responses and diurnal patterns. Ectopic overexpression of LgPRR7 or LgFKF1 in Arabidopsis thaliana accelerated flowering, whereas silencing LgPRR7 or LgFKF1 in L. gratissima accelerated flowering. Crucially, LgPRR7 directly interacts with LgFKF1, forming a self-reinforcing regulatory module LgPRR7-LgFKF1 to repress flowering in L. gratissima. Furthermore, the observed physical interactions among LgFKF1, LgCONSTANS-LIKE 12 (LgCOL12), and LgREPRESSOR OF ga1-3-LIKE 2 (LgRGL2) implied that they possibly formed a protein complex LgFKF1-LgCOL12-LgRGL2, bridging the circadian clock, photoperiod, and gibberellin signaling pathways to suppress downstream floral integrators. Intriguingly, silencing LgPRR7 and LgFKF1 extended the duration of L. gratissima flowering, a trait of horticultural significance. These results suggest the integration of multi-layered environmental and endogenous signals in the regulation of flowering time. The LgPRR7-LgFKF1 module provides novel targets for molecular improvement to manipulate flowering time and duration in L. gratissima and other economically valuable woody ornamental plants. Our results also support the mediation of flowering convergence in short-day plants through the action of circadian clock genes.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"68 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143866398","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}
Mannan Zhang, Huaiqian Tang, Qin Xu, Zhihao Xiao, Chengxuan Zhou, Yuxiao Qian, Ruyue Gong, Huating Zhao, Jiaying Wang, Zijing Xing, Taotao Wang, Bo Ouyang, Yuyang Zhang, Junhong Zhang, Zhibiao Ye, Jie Ye
Plant growth is inseparable from the presence of mineral nutrients such as nitrogen, phosphorus and potassium, but the mechanism by which horticultural plants such as tomatoes respond to mineral elements is poorly understood. Here, we collected 28 phenotypic datasets, including 5 agronomic traits and 4 pigment accumulation traits, under full nutrition and nitrogen/phosphorus/potassium deficiency conditions, most of which showed abundant variation. Phenotyping analysis suggested that the yellowing of leaves under low-nitrogen treatment was caused by an increase in the carotenoid content and a decrease in the chlorophyll b content. A genome-wide association study identified a total of 138 suggestive loci (including 23 significant loci) corresponding to 116 loci, including many reported and new candidate genes related to mineral element response and absorption. Transcriptome analysis of tomato seedlings under full nutrient and N/P/K deficiency conditions revealed 1,108 and 1,507 common differentially expressed genes in above-ground and below-ground tissues, respectively, with 103 overlapping genes. GO term enrichment analysis revealed that tomato plants resist low nutrient stress by increasing photosynthesis in the above-ground parts and ion transport capacity in the below-ground parts. Through the combined analysis of GWAS and RNA-Seq, we identified 28 mineral element response genes with high confidence, corresponding to 17 loci, which may be closely related to the response and utilization of N, P, and K in tomato. Two candidate genes, auxin-repressed protein (Solyc02g077880), which responds to carotenoid and chlorophyll b accumulation, and guanine nucleotide exchange factor-like protein (Solyc04g005560), which responds to low-phosphorus conditions, were further validated via haplotype analysis. This study provides new insights into the nitrogen, phosphorus, and potassium response mechanisms of tomato and offers valuable genetic resources for future improvements in tomato breeding.
{"title":"Integration of GWAS and transcriptome approaches for the identification of nitrogen-, phosphorus-, and potassium-responsive genes in tomato","authors":"Mannan Zhang, Huaiqian Tang, Qin Xu, Zhihao Xiao, Chengxuan Zhou, Yuxiao Qian, Ruyue Gong, Huating Zhao, Jiaying Wang, Zijing Xing, Taotao Wang, Bo Ouyang, Yuyang Zhang, Junhong Zhang, Zhibiao Ye, Jie Ye","doi":"10.1093/hr/uhaf112","DOIUrl":"https://doi.org/10.1093/hr/uhaf112","url":null,"abstract":"Plant growth is inseparable from the presence of mineral nutrients such as nitrogen, phosphorus and potassium, but the mechanism by which horticultural plants such as tomatoes respond to mineral elements is poorly understood. Here, we collected 28 phenotypic datasets, including 5 agronomic traits and 4 pigment accumulation traits, under full nutrition and nitrogen/phosphorus/potassium deficiency conditions, most of which showed abundant variation. Phenotyping analysis suggested that the yellowing of leaves under low-nitrogen treatment was caused by an increase in the carotenoid content and a decrease in the chlorophyll b content. A genome-wide association study identified a total of 138 suggestive loci (including 23 significant loci) corresponding to 116 loci, including many reported and new candidate genes related to mineral element response and absorption. Transcriptome analysis of tomato seedlings under full nutrient and N/P/K deficiency conditions revealed 1,108 and 1,507 common differentially expressed genes in above-ground and below-ground tissues, respectively, with 103 overlapping genes. GO term enrichment analysis revealed that tomato plants resist low nutrient stress by increasing photosynthesis in the above-ground parts and ion transport capacity in the below-ground parts. Through the combined analysis of GWAS and RNA-Seq, we identified 28 mineral element response genes with high confidence, corresponding to 17 loci, which may be closely related to the response and utilization of N, P, and K in tomato. Two candidate genes, auxin-repressed protein (Solyc02g077880), which responds to carotenoid and chlorophyll b accumulation, and guanine nucleotide exchange factor-like protein (Solyc04g005560), which responds to low-phosphorus conditions, were further validated via haplotype analysis. This study provides new insights into the nitrogen, phosphorus, and potassium response mechanisms of tomato and offers valuable genetic resources for future improvements in tomato breeding.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"17 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143872670","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}
Breeding for improved immunity is essential to achieve sustainable fruit production, yet requiring to account for genotype-by-environment interactions (GxE), which still represent a major challenge. To tackle this issue, we conducted a comprehensive study to identify genetic markers with main and environment-specific effects on pest and disease response in peach (P. persica) and apricot (P. armeniaca). Leveraging multi-environment trials (MET), we assessed the genetic architecture of resistance and tolerance to 7 major pests and diseases through visual scoring of symptoms in naturally infected core-collections, repeated within and between years and sites. We applied a series of genome-wide association models (GWAS) to both maximum of symptom severity and kinetic disease progression. These analyzes lead to the identification of environment-shared QTLs, environment-specific QTLs, and interactive QTLs with antagonist or differential effects across environments. We mapped 60 high confidence QTLs encompassing a total of 87 candidate genes involved in both basal and host-specific responses, mostly consisting in Leucine-Rich Repeat Containing Receptors (LRR-CRs) gene family. The most promising disease resistance candidate genes were found for peach leaf curl on LG4 and for apricot and peach rust on LG2 and LG4. These findings underscore the critical role of GxE in shaping the phenotypic response to biotic pressure, especially for blossom blight. Last, models including dominance effects revealed 123 specific QTLs, emphasizing the significance of non-additive genetic effects, therefore warrant further investigation. These insights will support the development of marker-assisted selection to improve the immunity of Prunus varieties in diverse environmental conditions.
{"title":"Multi-environment GWAS uncovers markers associated to biotic stress response and genotype-by-environment interactions in stone fruit trees","authors":"Marie Serrie, Vincent Segura, Alain Blanc, Laurent Brun, Naïma Dlalah, Frédéric Gilles, Laure Heurtevin, Mathilde Le-Pans, Véronique Signoret, Sabrina Viret, Jean-Marc Audergon, Bénédicte Quilot, Morgane Roth","doi":"10.1093/hr/uhaf088","DOIUrl":"https://doi.org/10.1093/hr/uhaf088","url":null,"abstract":"Breeding for improved immunity is essential to achieve sustainable fruit production, yet requiring to account for genotype-by-environment interactions (GxE), which still represent a major challenge. To tackle this issue, we conducted a comprehensive study to identify genetic markers with main and environment-specific effects on pest and disease response in peach (P. persica) and apricot (P. armeniaca). Leveraging multi-environment trials (MET), we assessed the genetic architecture of resistance and tolerance to 7 major pests and diseases through visual scoring of symptoms in naturally infected core-collections, repeated within and between years and sites. We applied a series of genome-wide association models (GWAS) to both maximum of symptom severity and kinetic disease progression. These analyzes lead to the identification of environment-shared QTLs, environment-specific QTLs, and interactive QTLs with antagonist or differential effects across environments. We mapped 60 high confidence QTLs encompassing a total of 87 candidate genes involved in both basal and host-specific responses, mostly consisting in Leucine-Rich Repeat Containing Receptors (LRR-CRs) gene family. The most promising disease resistance candidate genes were found for peach leaf curl on LG4 and for apricot and peach rust on LG2 and LG4. These findings underscore the critical role of GxE in shaping the phenotypic response to biotic pressure, especially for blossom blight. Last, models including dominance effects revealed 123 specific QTLs, emphasizing the significance of non-additive genetic effects, therefore warrant further investigation. These insights will support the development of marker-assisted selection to improve the immunity of Prunus varieties in diverse environmental conditions.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"17 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143863051","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}
Huaye Xiong, Bin Hu, Jie Wang, Xing-zheng Fu, Yueqiang Zhang, Xiaojun Shi, Heinz Rennenberg
Seasonal nitrogen (N) storage and remobilization are critical for tree growth. Deciduous trees primarily store N in bark, evergreen trees utilize both mature leaves and bark. Citrus is an evergreen species, leaf N storage and remobilization are well studied, but inner bark remains poorly understood. This study used pot experiments with three N supply rates (low, moderate and high) to examine seasonal (winter, early, and late spring) N storage and remobilization between mature leaves (developed in autumn) and bark (from the main stem). Bark contains 15-35 kDa vegetative storage proteins (VSPs), which are highly abundant and accumulate seasonally, while mature leaves contain 45-55 kDa VSPs. Proteomic analysis revealed the oxygen-evolving enhancer protein as a key bark VSP, with Rubisco and others predominant in leaves. Under high N supply, bark total N decreased by 1.30 times from winter to early spring, while leaf N decreased only 1.01 times. Under high N supply, bark arginine decreased significantly by 2.66 times in early spring, whereas mature leaf arginine remained unchanged. Under low N supply, mature leaf proline decreased by 17.52 times in late spring, while proline in bark decreased by 5.50 times. Thus, under high N, bark is the primary early spring arginine source, whereas under low N, leaves supply more proline later. Bioinformatics indicate that ribosomal proteins may be involved in N remobilization in bark under high N and in both bark and leaves under low N. These results demonstrate that bark and mature leaves exhibit different seasonal N remobilization patterns.
{"title":"Evergreen citrus trees exhibit distinct seasonal nitrogen remobilization patterns between mature leaves and bark","authors":"Huaye Xiong, Bin Hu, Jie Wang, Xing-zheng Fu, Yueqiang Zhang, Xiaojun Shi, Heinz Rennenberg","doi":"10.1093/hr/uhaf103","DOIUrl":"https://doi.org/10.1093/hr/uhaf103","url":null,"abstract":"Seasonal nitrogen (N) storage and remobilization are critical for tree growth. Deciduous trees primarily store N in bark, evergreen trees utilize both mature leaves and bark. Citrus is an evergreen species, leaf N storage and remobilization are well studied, but inner bark remains poorly understood. This study used pot experiments with three N supply rates (low, moderate and high) to examine seasonal (winter, early, and late spring) N storage and remobilization between mature leaves (developed in autumn) and bark (from the main stem). Bark contains 15-35 kDa vegetative storage proteins (VSPs), which are highly abundant and accumulate seasonally, while mature leaves contain 45-55 kDa VSPs. Proteomic analysis revealed the oxygen-evolving enhancer protein as a key bark VSP, with Rubisco and others predominant in leaves. Under high N supply, bark total N decreased by 1.30 times from winter to early spring, while leaf N decreased only 1.01 times. Under high N supply, bark arginine decreased significantly by 2.66 times in early spring, whereas mature leaf arginine remained unchanged. Under low N supply, mature leaf proline decreased by 17.52 times in late spring, while proline in bark decreased by 5.50 times. Thus, under high N, bark is the primary early spring arginine source, whereas under low N, leaves supply more proline later. Bioinformatics indicate that ribosomal proteins may be involved in N remobilization in bark under high N and in both bark and leaves under low N. These results demonstrate that bark and mature leaves exhibit different seasonal N remobilization patterns.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"11 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143853366","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}
Shangxiang Lai, Yunshuai Huang, Yumei Liu, Fengqing Han, Mu Zhuang, Xia Cui, Zhansheng Li
Clubroot, caused by Plasmodiophora brassicae (P. brassicae), poses a serious threat to cruciferous crop production worldwide. Breeding resistant varieties remains the most cost-effective strategy to mitigate yield losses, yet achieving durable, stable, and broad-spectrum resistance continues to be a formidable challenge. Recent advances in genetic and genomic technologies have improved the understanding of complex host–pathogen interactions, leading to the identification of key resistance loci, including dominant resistance genes such as CRa and Crr1, as well as quantitative trait loci (QTLs). This review discusses the genetic mechanisms governing clubroot resistance and highlights applications in breeding, such as marker-assisted selection (MAS) and CRISPR/Cas9-based genome editing, which are accelerating the development of resistant germplasm. Furthermore, integrated management strategies—encompassing resistant cultivars, crop rotation, biocontrol agents, and soil amendments—are emphasized as critical components for sustainable disease. This review summarizes the major resistance genes against clubroot and discusses potential strategies to address the persistent threat posed by the disease.
{"title":"Clubroot Resistant in Cruciferous Crops: Recent Advances in Genes and QTLs Identification and Utilization","authors":"Shangxiang Lai, Yunshuai Huang, Yumei Liu, Fengqing Han, Mu Zhuang, Xia Cui, Zhansheng Li","doi":"10.1093/hr/uhaf105","DOIUrl":"https://doi.org/10.1093/hr/uhaf105","url":null,"abstract":"Clubroot, caused by Plasmodiophora brassicae (P. brassicae), poses a serious threat to cruciferous crop production worldwide. Breeding resistant varieties remains the most cost-effective strategy to mitigate yield losses, yet achieving durable, stable, and broad-spectrum resistance continues to be a formidable challenge. Recent advances in genetic and genomic technologies have improved the understanding of complex host–pathogen interactions, leading to the identification of key resistance loci, including dominant resistance genes such as CRa and Crr1, as well as quantitative trait loci (QTLs). This review discusses the genetic mechanisms governing clubroot resistance and highlights applications in breeding, such as marker-assisted selection (MAS) and CRISPR/Cas9-based genome editing, which are accelerating the development of resistant germplasm. Furthermore, integrated management strategies—encompassing resistant cultivars, crop rotation, biocontrol agents, and soil amendments—are emphasized as critical components for sustainable disease. This review summarizes the major resistance genes against clubroot and discusses potential strategies to address the persistent threat posed by the disease.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"15 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143841743","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}
Xue Cui, Yuxin Liu, Miao Sun, Qiyue Zhao, Yicheng Huang, Jianwei Zhang, Qiulin Yao, Hang Yin, Huixin Zhang, Fulei Mo, Hongbin Zhong, Yang Liu, Xiuling Chen, Yao Zhang, Jiayin Liu, Youwen Qiu, Mingfang Feng, Xu Chen, Hossein Ghanizadeh, Yao Zhou, Aoxue Wang
Structural variations (SVs) in repetitive sequences could only be detected within a broad region due to imprecise breakpoints, leading to classification errors and inaccurate trait analysis. Through manual inspection at 4,532 variant regions identified by integrating 14 detection pipelines between two tomato genomes, we generated an SV benchmark at base-pair resolution. Evaluation of all pipelines yielded F1-scores below 53.77% with this benchmark, underscoring the urgent need for advanced detection algorithms in plant genomics. Analyzing the alignment features of the repetitive sequences in each region, we summarized four patterns of SV breakpoints and revealed that deviations in breakpoint identification were primarily due to copy misalignment. According to the similarities among copies, we identified 1,635 bona fide SVs with precise breakpoints, including substitutions (223), which should be taken as a fundamental SV type, alongside insertions (780), deletions (619), and inversions (13), all showing preferences for SV occurrence within AT-repeat regions of regulatory loci. This precise resolution of complex SVs will foster genome analysis and crop improvement.
{"title":"The nature of complex structural variations in tomatoes","authors":"Xue Cui, Yuxin Liu, Miao Sun, Qiyue Zhao, Yicheng Huang, Jianwei Zhang, Qiulin Yao, Hang Yin, Huixin Zhang, Fulei Mo, Hongbin Zhong, Yang Liu, Xiuling Chen, Yao Zhang, Jiayin Liu, Youwen Qiu, Mingfang Feng, Xu Chen, Hossein Ghanizadeh, Yao Zhou, Aoxue Wang","doi":"10.1093/hr/uhaf107","DOIUrl":"https://doi.org/10.1093/hr/uhaf107","url":null,"abstract":"Structural variations (SVs) in repetitive sequences could only be detected within a broad region due to imprecise breakpoints, leading to classification errors and inaccurate trait analysis. Through manual inspection at 4,532 variant regions identified by integrating 14 detection pipelines between two tomato genomes, we generated an SV benchmark at base-pair resolution. Evaluation of all pipelines yielded F1-scores below 53.77% with this benchmark, underscoring the urgent need for advanced detection algorithms in plant genomics. Analyzing the alignment features of the repetitive sequences in each region, we summarized four patterns of SV breakpoints and revealed that deviations in breakpoint identification were primarily due to copy misalignment. According to the similarities among copies, we identified 1,635 bona fide SVs with precise breakpoints, including substitutions (223), which should be taken as a fundamental SV type, alongside insertions (780), deletions (619), and inversions (13), all showing preferences for SV occurrence within AT-repeat regions of regulatory loci. This precise resolution of complex SVs will foster genome analysis and crop improvement.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"218 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143836983","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}
Andrea R Kohler, Courtney A Hollender, Doug Raines, Mark Demuth, Lisa Tang, Macarena Farcuh, Chris Dardick
Controlling branch orientation is a central challenge in tree fruit production, as it impacts light interception, pesticide use, fruit quality, yield, and labor costs. To modify branch orientation, growers use many different management practices, including tying branches to wires or applying growth regulator sprays. However, these practices are often costly and ineffective. In contrast, altering the expression of genes that control branch angles and orientations would permanently optimize tree architecture and reduce management requirements. One gene implicated in branch angle control, LAZY1, has potential for such applications as it is a key modulator of upward branch orientations in response to gravity. Here we describe the phenotypes of transgenic plum (Prunus domestica) trees containing an antisense vector to silence LAZY1. We found that LAZY1 silencing significantly increased branch and petiole angles. LAZY1-antisense lines also displayed “wandering” or weeping branch trajectories. These phenotypes were not associated with decreases in branch strength or stiffness. We evaluated the utility of LAZY1-antisense trees for use in two planar orchard systems by training them according to super slender axe and espalier methods. We found that the LAZY1-antisense trees had more open canopies and were easier to constrain to the trellis height. This work illustrates the power of manipulating gene expression to optimize plant architecture for specific horticultural applications
{"title":"Working smarter, not harder: silencing LAZY1 in Prunus domestica causes outward, wandering branch orientations with commercial and ornamental applications","authors":"Andrea R Kohler, Courtney A Hollender, Doug Raines, Mark Demuth, Lisa Tang, Macarena Farcuh, Chris Dardick","doi":"10.1093/hr/uhaf106","DOIUrl":"https://doi.org/10.1093/hr/uhaf106","url":null,"abstract":"Controlling branch orientation is a central challenge in tree fruit production, as it impacts light interception, pesticide use, fruit quality, yield, and labor costs. To modify branch orientation, growers use many different management practices, including tying branches to wires or applying growth regulator sprays. However, these practices are often costly and ineffective. In contrast, altering the expression of genes that control branch angles and orientations would permanently optimize tree architecture and reduce management requirements. One gene implicated in branch angle control, LAZY1, has potential for such applications as it is a key modulator of upward branch orientations in response to gravity. Here we describe the phenotypes of transgenic plum (Prunus domestica) trees containing an antisense vector to silence LAZY1. We found that LAZY1 silencing significantly increased branch and petiole angles. LAZY1-antisense lines also displayed “wandering” or weeping branch trajectories. These phenotypes were not associated with decreases in branch strength or stiffness. We evaluated the utility of LAZY1-antisense trees for use in two planar orchard systems by training them according to super slender axe and espalier methods. We found that the LAZY1-antisense trees had more open canopies and were easier to constrain to the trellis height. This work illustrates the power of manipulating gene expression to optimize plant architecture for specific horticultural applications","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"19 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143841748","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}
Lei Gong, Li Zhang, Haiwen Zhang, Fengjie Nie, Zhenning Liu, Xuan Liu, Miaoquan Fang, Wenjing Yang, Yu Zhang, Guohui Zhang, Zhiqian Guo, Hongxia Zhang
As an important non-cereal food crop grown worldwide, the genetic improvement of potato in tuber yield and quality is largely constrained due to the lacking of a high-quality reference genome and understanding of the regulatory mechanism underlying the formation of superior alleles. Here, a chromosome-scale haplotype-resolved genome assembled from an anther-cultured progeny of ‘Ningshu 15’, a tetraploid variety featured by its high starch content and drought resistance, was presented. The assembled genome size was 1.653 Gb, with a contig N50 of approximately 1.4 Mb and a scaffold N50 of 61 Mb. The long terminal repeat (LTR) assembly index (LAI) score of the two identified haplotypes of ‘Ningshu 15’ was 11.62 and 11.94, respectively. Comparative genomic analysis revealed that positive selection occurred in gene families related to starch, sucrose, fructose and mannose metabolism, and carotenoid biosynthesis. Further genome-wide association study (GWAS) in 141 accessions identified a total number of 53 quantitative trait loci (QTL) related to fructose, glucose and sucrose content. Among them, a tonoplast sugar transporter encoding gene, StTST2, closely associated with glucose content was identified. Constitutive expression of StTST2 in potato and Arabidopsis increased the photosynthetic rate, chlorophyll and sugar content, biomass tuber and seed production in transgenic plants. In addition, co-immunoprecipitation (Co-IP) assays demonstrated that StTST2 directly interacted with SUT2. Our study provides a high-quality genome assembly and new genetic locus of potato for molecular breeding.
{"title":"Haplotype-resolved genome assembly and genome-wide association study identifies the candidate gene closely related to sugar content and tuber yield in Solanum tuberosum","authors":"Lei Gong, Li Zhang, Haiwen Zhang, Fengjie Nie, Zhenning Liu, Xuan Liu, Miaoquan Fang, Wenjing Yang, Yu Zhang, Guohui Zhang, Zhiqian Guo, Hongxia Zhang","doi":"10.1093/hr/uhaf075","DOIUrl":"https://doi.org/10.1093/hr/uhaf075","url":null,"abstract":"As an important non-cereal food crop grown worldwide, the genetic improvement of potato in tuber yield and quality is largely constrained due to the lacking of a high-quality reference genome and understanding of the regulatory mechanism underlying the formation of superior alleles. Here, a chromosome-scale haplotype-resolved genome assembled from an anther-cultured progeny of ‘Ningshu 15’, a tetraploid variety featured by its high starch content and drought resistance, was presented. The assembled genome size was 1.653 Gb, with a contig N50 of approximately 1.4 Mb and a scaffold N50 of 61 Mb. The long terminal repeat (LTR) assembly index (LAI) score of the two identified haplotypes of ‘Ningshu 15’ was 11.62 and 11.94, respectively. Comparative genomic analysis revealed that positive selection occurred in gene families related to starch, sucrose, fructose and mannose metabolism, and carotenoid biosynthesis. Further genome-wide association study (GWAS) in 141 accessions identified a total number of 53 quantitative trait loci (QTL) related to fructose, glucose and sucrose content. Among them, a tonoplast sugar transporter encoding gene, StTST2, closely associated with glucose content was identified. Constitutive expression of StTST2 in potato and Arabidopsis increased the photosynthetic rate, chlorophyll and sugar content, biomass tuber and seed production in transgenic plants. In addition, co-immunoprecipitation (Co-IP) assays demonstrated that StTST2 directly interacted with SUT2. Our study provides a high-quality genome assembly and new genetic locus of potato for molecular breeding.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"4 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143819032","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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