Eye depth is an important agronomic trait affecting tubers' appearance, quality, and processing suitability. Hence, cultivating varieties with uniform shapes and shallow eye depth are important goals for potato breeding. In this study, based on the primary mapping of the tuber eye-depth locus using a small primary-segregating population, a large secondary-segregating population with 2,100 individuals was used to map the eye-depth locus further. A major quantitative trait locus for eye-depth on chromosome 10 was identified (designated ) using BSA-seq and traditional QTL mapping method. The could explain 55.0% of the eye depth phenotypic variation and was further narrowed to a 309.10 kb interval using recombinant analysis. To predict candidate genes, tissue sectioning and RNA-seq of the specific tuber tissues were performed. Genes encoding members of the peroxidase superfamily with likely roles in indole acetic acid regulation were considered the most promising candidates. These results will facilitate marker-assisted selection for the shallow-eye trait in potato breeding and provide a solid basis for eye-depth gene cloning and the analysis of tuber eye-depth regulatory mechanisms.
{"title":"Fine-mapping and candidate gene analysis of tuber eye depth in potato","authors":"Guiyan Fan, Shaoguang Duan, Yuting Yang, Yanfeng Duan, Yinqiao Jian, Jun Hu, Zhiyuan Liu, Yang-dong Guo, Liping Jin, Jianfei Xu, Guangcun Li","doi":"10.1016/j.hpj.2024.03.006","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.03.006","url":null,"abstract":"Eye depth is an important agronomic trait affecting tubers' appearance, quality, and processing suitability. Hence, cultivating varieties with uniform shapes and shallow eye depth are important goals for potato breeding. In this study, based on the primary mapping of the tuber eye-depth locus using a small primary-segregating population, a large secondary-segregating population with 2,100 individuals was used to map the eye-depth locus further. A major quantitative trait locus for eye-depth on chromosome 10 was identified (designated ) using BSA-seq and traditional QTL mapping method. The could explain 55.0% of the eye depth phenotypic variation and was further narrowed to a 309.10 kb interval using recombinant analysis. To predict candidate genes, tissue sectioning and RNA-seq of the specific tuber tissues were performed. Genes encoding members of the peroxidase superfamily with likely roles in indole acetic acid regulation were considered the most promising candidates. These results will facilitate marker-assisted selection for the shallow-eye trait in potato breeding and provide a solid basis for eye-depth gene cloning and the analysis of tuber eye-depth regulatory mechanisms.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"18 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141588672","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 : 2024-06-28DOI: 10.1016/j.hpj.2024.06.001
Xiaoxiao Yu, Jintai Yu, Yin Lu, Wenjing Li, Guanzhong Huo, Jun Zhang, Yan Li, Jianjun Zhao, Jun Li
Protoplast-based transient gene expression system has been widely used in plant genome editing because of its simple operation and less time-consuming. In order to establish a universal protoplast-based transient transfection system for verifying activities of genome editing vectors containing targets in Brassica, we systematically optimized factors affecting protoplast isolation and transient gene expression. We established an efficient protoplast-based transient gene expression system (PTGE) in Chinese cabbage, achieving high protoplast yield of 4.9 × 10 g FW, viability over 95%, and transfection efficiency of 76%. We showed for the first time that pretreatment of protoplasts with a hypotonic MMG could significantly enhance the transfection efficiency. Furthermore, protoplasts incubated at 37 °C for 6 min improved the transfection efficiency to 86%. We also demonstrated that PTGE worked well (more than 50% transfection efficiency) in multiple Brassica species including cabbage, Pak Choi, Chinese kale, and turnip. Finally, PTGE was used for validating the activities of CRISPR/Cas9 vectors containing targets in Chinese cabbage, cabbage, and pak choi, demonstrating the broad applicability of the established PTGE for genome editing in crops.
{"title":"An efficient and universal protoplast-based transient gene expression system for genome editing in Brassica crops","authors":"Xiaoxiao Yu, Jintai Yu, Yin Lu, Wenjing Li, Guanzhong Huo, Jun Zhang, Yan Li, Jianjun Zhao, Jun Li","doi":"10.1016/j.hpj.2024.06.001","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.06.001","url":null,"abstract":"Protoplast-based transient gene expression system has been widely used in plant genome editing because of its simple operation and less time-consuming. In order to establish a universal protoplast-based transient transfection system for verifying activities of genome editing vectors containing targets in Brassica, we systematically optimized factors affecting protoplast isolation and transient gene expression. We established an efficient protoplast-based transient gene expression system (PTGE) in Chinese cabbage, achieving high protoplast yield of 4.9 × 10 g FW, viability over 95%, and transfection efficiency of 76%. We showed for the first time that pretreatment of protoplasts with a hypotonic MMG could significantly enhance the transfection efficiency. Furthermore, protoplasts incubated at 37 °C for 6 min improved the transfection efficiency to 86%. We also demonstrated that PTGE worked well (more than 50% transfection efficiency) in multiple Brassica species including cabbage, Pak Choi, Chinese kale, and turnip. Finally, PTGE was used for validating the activities of CRISPR/Cas9 vectors containing targets in Chinese cabbage, cabbage, and pak choi, demonstrating the broad applicability of the established PTGE for genome editing in crops.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"43 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141521580","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}
Bamboo was one of the first plants to be cultivated in China and is widely used in industry and daily life. The study of gene function has become an important part of bamboo breeding, whereas quantitative real-time PCR (qRT-PCR) is a powerful tool for gene expression analysis. The accuracy of qRT-PCR results largely depends on suitable reference genes. In this study, a transcriptome-wide identification of reference genes was conducted based on 447 transcriptome datasets, comprising 200 tissue samples, 107 treated samples, and 140 samples from various moso bamboo () forms. A total of 3444, 1013, and 3962 stably expressed genes were identified from these three groups, respectively. Functional enrichment analysis revealed significant enrichment of these genes in pathways, including the spliceosome, proteasome, and oxidative phosphorylation. Eight candidate genes (, , , , , , , and ), were selected for qRT-PCR validation using 112 samples. To assess their stability, five statistical methods (geNorm, NormFinder, BestKeeper, Delta-Ct, and RefFinder) were employed. The most suitable reference genes were and for different tissues, and for different treatments, and and for various moso bamboo forms. Overall, and were the most stable reference genes across all conditions, while and were the least stable reference genes. In addition, a significant negative correlation was found between the Ct values of RT-qPCR and the logTPM values from the transcriptome data (Ct = −1.534x + 37.221), providing a potential method for estimating gene expression levels. The identified reference genes, particularly and , provide a robust set of references for gene expression studies in moso bamboo.
{"title":"Systematic identification and validation of the reference genes from 447 transcriptome datasets of moso bamboo (Phyllostachys edulis)","authors":"Yan Liu, Chenglei Zhu, Zeming Lin, Hui Li, Xiaolin Di, Xianghua Yue, Zhimin Gao","doi":"10.1016/j.hpj.2023.11.007","DOIUrl":"https://doi.org/10.1016/j.hpj.2023.11.007","url":null,"abstract":"Bamboo was one of the first plants to be cultivated in China and is widely used in industry and daily life. The study of gene function has become an important part of bamboo breeding, whereas quantitative real-time PCR (qRT-PCR) is a powerful tool for gene expression analysis. The accuracy of qRT-PCR results largely depends on suitable reference genes. In this study, a transcriptome-wide identification of reference genes was conducted based on 447 transcriptome datasets, comprising 200 tissue samples, 107 treated samples, and 140 samples from various moso bamboo () forms. A total of 3444, 1013, and 3962 stably expressed genes were identified from these three groups, respectively. Functional enrichment analysis revealed significant enrichment of these genes in pathways, including the spliceosome, proteasome, and oxidative phosphorylation. Eight candidate genes (, , , , , , , and ), were selected for qRT-PCR validation using 112 samples. To assess their stability, five statistical methods (geNorm, NormFinder, BestKeeper, Delta-Ct, and RefFinder) were employed. The most suitable reference genes were and for different tissues, and for different treatments, and and for various moso bamboo forms. Overall, and were the most stable reference genes across all conditions, while and were the least stable reference genes. In addition, a significant negative correlation was found between the Ct values of RT-qPCR and the logTPM values from the transcriptome data (Ct = −1.534x + 37.221), providing a potential method for estimating gene expression levels. The identified reference genes, particularly and , provide a robust set of references for gene expression studies in moso bamboo.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"203 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141521581","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 : 2024-06-23DOI: 10.1016/j.hpj.2024.01.009
Yan Li, Yu Tao, Aimei Bai, Haibin Wang, Zhanghong Yu, Tongkun Liu, Xilin Hou, Ying Li
The nuclear factor Y (NF–Y) is a class of heterotrimeric transcription factors comprising three subunits: NF-YA, NF-YB, and NF-YC. These transcription factors participate in many plant bioprocesses, including the regulation of flowering time. Although the gene family has been systematically studied in many species, little is known about its role in the non-heading Chinese cabbage (NHCC) [ (syn) ssp. ]. In this study, we identified 57 NF–Y members in the genome of NHCC using BLASTP, including 20 , 24 , and 13 . These genes are randomly distributed on the 10 chromosomes of NHCC. The results of yeast two hybrid experiments indicated that among some members of the three subunits of BcNF-Ys, the members of the NF-YA and NF-YC subunits interact with each other, a third of the members of the NF-YB and NF-YC subunits interact with each other, while no interaction was observed between the members of the NF-YA and NF-YB subunits. Subcellular localization experiments in tobacco showed that BcNF-YA2 and BcNF-YA8 were expressed in the nucleus; BcNF-YB18 and BcNF-YB23 were located in the cell membrane and cytoplasm; and BcNF-YC6 and BcNF-YC7 were expressed in the nucleus, cytoplasm, and cell membrane. We analyzed the -acting elements in the promoter of genes and found that the ABA response element is the most distributed hormone response element, which is regulated by ABA signals triggered by environmental stimuli. Accordingly, we treated three-week-old NHCC leaves with 100 μmol L ABA and analyzed the expression profile of s through RNA-seq. The results showed that except for six undetected , the remaining 51 showed varying degrees of response to ABA signals. Among these, was positively regulated by ABA signals, with the highest upregulation amplitude. Subsequently, the function of was extensively studied, which demonstrated that its expression promotes plant flowering. This result enriches our understanding of the potential molecular mechanism by which ABA positively regulates NHCC flowering.
{"title":"Genome-wide analysis of the NF–Y gene family in non-heading Chinese cabbage and the involvement of BcNF-YA8 in ABA-mediated flowering regulation","authors":"Yan Li, Yu Tao, Aimei Bai, Haibin Wang, Zhanghong Yu, Tongkun Liu, Xilin Hou, Ying Li","doi":"10.1016/j.hpj.2024.01.009","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.01.009","url":null,"abstract":"The nuclear factor Y (NF–Y) is a class of heterotrimeric transcription factors comprising three subunits: NF-YA, NF-YB, and NF-YC. These transcription factors participate in many plant bioprocesses, including the regulation of flowering time. Although the gene family has been systematically studied in many species, little is known about its role in the non-heading Chinese cabbage (NHCC) [ (syn) ssp. ]. In this study, we identified 57 NF–Y members in the genome of NHCC using BLASTP, including 20 , 24 , and 13 . These genes are randomly distributed on the 10 chromosomes of NHCC. The results of yeast two hybrid experiments indicated that among some members of the three subunits of BcNF-Ys, the members of the NF-YA and NF-YC subunits interact with each other, a third of the members of the NF-YB and NF-YC subunits interact with each other, while no interaction was observed between the members of the NF-YA and NF-YB subunits. Subcellular localization experiments in tobacco showed that BcNF-YA2 and BcNF-YA8 were expressed in the nucleus; BcNF-YB18 and BcNF-YB23 were located in the cell membrane and cytoplasm; and BcNF-YC6 and BcNF-YC7 were expressed in the nucleus, cytoplasm, and cell membrane. We analyzed the -acting elements in the promoter of genes and found that the ABA response element is the most distributed hormone response element, which is regulated by ABA signals triggered by environmental stimuli. Accordingly, we treated three-week-old NHCC leaves with 100 μmol L ABA and analyzed the expression profile of s through RNA-seq. The results showed that except for six undetected , the remaining 51 showed varying degrees of response to ABA signals. Among these, was positively regulated by ABA signals, with the highest upregulation amplitude. Subsequently, the function of was extensively studied, which demonstrated that its expression promotes plant flowering. This result enriches our understanding of the potential molecular mechanism by which ABA positively regulates NHCC flowering.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"111 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141521582","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}
Turnip mosaic virus (TuMV) constitutes one of the primary diseases affecting , severely impacting its production and resulting in crop failures in various regions worldwide. Recent research has demonstrated the significance of plant translation initiation factors, specifically the and family genes, as essential recessive disease resistance genes. In our study, we conducted evolutionary and gene expression studies, leading us to identify as a potential TuMV-resistant gene. Leveraging CRISPR/Cas9 technology, we obtained mutant plants with edited gene. We confirmed confers resistance against TuMV through phenotypic observations and virus content evaluations. Furthermore, we employed ribosome profiling assays on mutant seedlings to unravel the translation landscape in response to TuMV. Interestingly, we observed a moderate correlation between the fold changes in gene expression at the transcriptional and translational levels ( = 0.729). Comparative analysis of ribosome profiling and RNA-seq data revealed that plant–pathogen interaction, and MAPK signaling pathway–plant pathways were involved in -mediated TuMV resistance. Further analysis revealed that sequence features, coding sequence length, and normalized minimal free energy, influenced the translation efficiency of genes. Our study highlights that the loss of can result in a highly intricate translation mechanism, acting synergistically with transcription to confer resistance against TuMV.
{"title":"Editing of eIF(iso)4E.c confers resistance against Turnip mosaic virus in Brassica rapa","authors":"Yujia Liu, Xiaoyun Xin, Peirong Li, Weihong Wang, Yangjun Yu, Xiuyun Zhao, Deshuang Zhang, Jiao Wang, Fenglan Zhang, Shujiang Zhang, Shuancang Yu, Tongbing Su","doi":"10.1016/j.hpj.2024.05.001","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.05.001","url":null,"abstract":"Turnip mosaic virus (TuMV) constitutes one of the primary diseases affecting , severely impacting its production and resulting in crop failures in various regions worldwide. Recent research has demonstrated the significance of plant translation initiation factors, specifically the and family genes, as essential recessive disease resistance genes. In our study, we conducted evolutionary and gene expression studies, leading us to identify as a potential TuMV-resistant gene. Leveraging CRISPR/Cas9 technology, we obtained mutant plants with edited gene. We confirmed confers resistance against TuMV through phenotypic observations and virus content evaluations. Furthermore, we employed ribosome profiling assays on mutant seedlings to unravel the translation landscape in response to TuMV. Interestingly, we observed a moderate correlation between the fold changes in gene expression at the transcriptional and translational levels ( = 0.729). Comparative analysis of ribosome profiling and RNA-seq data revealed that plant–pathogen interaction, and MAPK signaling pathway–plant pathways were involved in -mediated TuMV resistance. Further analysis revealed that sequence features, coding sequence length, and normalized minimal free energy, influenced the translation efficiency of genes. Our study highlights that the loss of can result in a highly intricate translation mechanism, acting synergistically with transcription to confer resistance against TuMV.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"54 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141588701","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}
Cruciferous sprout is a new form of vegetable product rich in bioactive compounds, especially glucosinolates. Previous studies have focused on increasing the accumulation of glucosinolates in cruciferous sprouts by applying different chemical regulators, with a particular focus on their contribution to nutritional quality and health benefits. Nevertheless, the effects of melatonin and UV-B irradiation on glucosinolate biosynthesis remain unclear. In this study, it was found that changes in melatonin concentrations significantly affected the contents of individual as well as total aliphatic and indolic glucosinolates. The 5 μmol L melatonin was decided as the optimum concentration that could increase the content of beneficial glucosinolates including glucoraphanin and 4-methoxy glucobrassicin in Chinese kale sprouts. Notably, the enhancement of glucosinolate accumulation by melatonin treatment could be further amplified by UV-B irradiation. Furthermore, our results showed that R2R3-MYB transcription factor BoaMYB28 and BoaMYB51, which are central regulators of aliphatic and indolic glucosinolate biosynthesis respectively, were both involved in the regulation of glucosinolate biosynthesis by melatonin and UV-B irradiation. Additionally, the expression of glucosinolate biosynthetic genes, including , , , , , , and participated in the formation of core structures and , , , and involved in the side-chain modification of aliphatic and indolic glucosinolate, was regulated by melatonin or UV-B irradiation. Taken together, these findings provide a potential strategy for improving the nutritional quality and resistance of Chinese kale sprouts.
{"title":"UV-B irradiation enhances the accumulation of beneficial glucosinolates induced by melatonin in Chinese kale sprout","authors":"Mengyu Wang, Jiansheng Wang, Yuhe Yang, Zhiqing Li, Ghazala Mustafa, Yubo Li, Lihong Liu, Zuofa Zhang, Qiaomei Wang","doi":"10.1016/j.hpj.2024.05.003","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.05.003","url":null,"abstract":"Cruciferous sprout is a new form of vegetable product rich in bioactive compounds, especially glucosinolates. Previous studies have focused on increasing the accumulation of glucosinolates in cruciferous sprouts by applying different chemical regulators, with a particular focus on their contribution to nutritional quality and health benefits. Nevertheless, the effects of melatonin and UV-B irradiation on glucosinolate biosynthesis remain unclear. In this study, it was found that changes in melatonin concentrations significantly affected the contents of individual as well as total aliphatic and indolic glucosinolates. The 5 μmol L melatonin was decided as the optimum concentration that could increase the content of beneficial glucosinolates including glucoraphanin and 4-methoxy glucobrassicin in Chinese kale sprouts. Notably, the enhancement of glucosinolate accumulation by melatonin treatment could be further amplified by UV-B irradiation. Furthermore, our results showed that R2R3-MYB transcription factor BoaMYB28 and BoaMYB51, which are central regulators of aliphatic and indolic glucosinolate biosynthesis respectively, were both involved in the regulation of glucosinolate biosynthesis by melatonin and UV-B irradiation. Additionally, the expression of glucosinolate biosynthetic genes, including , , , , , , and participated in the formation of core structures and , , , and involved in the side-chain modification of aliphatic and indolic glucosinolate, was regulated by melatonin or UV-B irradiation. Taken together, these findings provide a potential strategy for improving the nutritional quality and resistance of Chinese kale sprouts.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"66 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141461863","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 : 2024-06-20DOI: 10.1016/j.hpj.2023.08.004
Liyong Sun, Yao Chen, Tangjie Nie, Xiaoxia Wan, Xuan Zou, Zheng Jiang, Huilin Zhu, Qiang Wei, Yaling Wang, Shuxian Li, Zengfang Yin
In angiosperms, floral architecture diversity reflects its significance in exploring plant evolution. , an endemic and ancient species in China, possesses a unique multi-tepal trait. Notably, the origin and formation of these multi-tepals are poorly understood. In this study, we investigated the origin and formation of multi-tepals from the inner floral whorl and elucidated the underlying molecular regulatory mechanisms by combining phenotypic analysis, sequencing, and molecular experiments. We found that the multi-tepals exhibited morpho-anatomical characteristics similar to normal tepals but differed from petaloid and normal stamens. The temporal dynamics of a large number of differentially expressed genes (DEGs) involved in multiple signaling (transduction) pathways contributed to multi-tepal primordia initiation during early floral differentiation. In particular, the dynamic expression of , , , and might be responsible for floral meristem activation and maintenance, while and potentially regulated floral organ initiation. Floral homeotic genes, such as , contributed to subsequent organ identity specialization. We further isolated a nucleus-localized APETALA3 homolog from , terming it the () gene, which was expressed in almost all vegetative and reproductive tissues. Ectopically expressing in resulted in altered phenotypes of rosette leaves, inflorescences, and florets, particularly generating extra petals instead of undergoing homeotic organ conversion. This discovery revealed an additional function of in regulating organ initiation in addition to its conserved B-function in floral architecture plasticity. In summary, the multi-tepals of originated from the early tepal primordia initiation event rather than stamen petalody. The formation of the multi-tepal trait was attributed to the coordinated regulation of several vital DEGs, with the gene playing an important role. These results provide additional insight into the regulation underlying the floral architecture formation in ancient species and suggest that manipulating the gene may hold promising potential for genetic breeding in ornamental plants.
在被子植物中，花结构的多样性反映了其在探索植物进化中的重要意义。中国特有的一个古老物种--榆叶梅，具有独特的多花被特征。值得注意的是，人们对这些多花被片的起源和形成知之甚少。在这项研究中，我们通过表型分析、测序和分子实验，研究了多花被片的起源和形成，并阐明了其背后的分子调控机制。我们发现，多花被片的形态解剖特征与正常花被片相似，但与瓣状雄蕊和正常雄蕊不同。在早期花分化过程中，涉及多种信号（传导）途径的大量差异表达基因（DEGs）的时间动态促进了多花被片原基的形成。其中，、、和的动态表达可能对花分生组织的激活和维持负责，而和则可能调控花器官的萌发。花的同源基因，如 、 和 ，有助于随后的器官特征特化。我们进一步从Ⅳ中分离出一个细胞核定位的APETALA3同源基因，称其为（）基因，该基因在几乎所有无性和生殖组织中都有表达。异位表达in基因会导致莲座叶、花序和小花的表型发生改变，尤其是产生额外的花瓣，而不是进行同源器官转换。这一发现揭示了 in 除了在花卉结构可塑性中保守的 B 功能外，还具有调控器官萌发的其他功能。总之，多花被片起源于早期的花被片原基萌发，而不是雄蕊花瓣。多花被性状的形成归因于几个重要的 DEGs 的协调调控，其中该基因发挥了重要作用。这些结果进一步揭示了古老物种花卉结构形成的内在调控机制，并表明操纵该基因有可能为观赏植物的遗传育种带来希望。
{"title":"B-class floral homeotic gene MapoAPETALA3 may play an important role in the origin and formation of multi-tepals in Magnolia polytepala","authors":"Liyong Sun, Yao Chen, Tangjie Nie, Xiaoxia Wan, Xuan Zou, Zheng Jiang, Huilin Zhu, Qiang Wei, Yaling Wang, Shuxian Li, Zengfang Yin","doi":"10.1016/j.hpj.2023.08.004","DOIUrl":"https://doi.org/10.1016/j.hpj.2023.08.004","url":null,"abstract":"In angiosperms, floral architecture diversity reflects its significance in exploring plant evolution. , an endemic and ancient species in China, possesses a unique multi-tepal trait. Notably, the origin and formation of these multi-tepals are poorly understood. In this study, we investigated the origin and formation of multi-tepals from the inner floral whorl and elucidated the underlying molecular regulatory mechanisms by combining phenotypic analysis, sequencing, and molecular experiments. We found that the multi-tepals exhibited morpho-anatomical characteristics similar to normal tepals but differed from petaloid and normal stamens. The temporal dynamics of a large number of differentially expressed genes (DEGs) involved in multiple signaling (transduction) pathways contributed to multi-tepal primordia initiation during early floral differentiation. In particular, the dynamic expression of , , , and might be responsible for floral meristem activation and maintenance, while and potentially regulated floral organ initiation. Floral homeotic genes, such as , contributed to subsequent organ identity specialization. We further isolated a nucleus-localized APETALA3 homolog from , terming it the () gene, which was expressed in almost all vegetative and reproductive tissues. Ectopically expressing in resulted in altered phenotypes of rosette leaves, inflorescences, and florets, particularly generating extra petals instead of undergoing homeotic organ conversion. This discovery revealed an additional function of in regulating organ initiation in addition to its conserved B-function in floral architecture plasticity. In summary, the multi-tepals of originated from the early tepal primordia initiation event rather than stamen petalody. The formation of the multi-tepal trait was attributed to the coordinated regulation of several vital DEGs, with the gene playing an important role. These results provide additional insight into the regulation underlying the floral architecture formation in ancient species and suggest that manipulating the gene may hold promising potential for genetic breeding in ornamental plants.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"237 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141521583","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}
Many economically important crops and vegetables belonging to the cruciferous family are heavily endangered by clubroot disease caused by infection. Breeding of clubroot resistant cultivars based on mapping and cloning of resistant genes is commonly regarded as the most cost-effective and efficient way to fight against this disease. The traditional way of R gene functional validation requires stable transformation that is both time- and labor-consuming. In this study, a rapid and efficient hairy-root transgenic protocol mediated by was developed. The transformation positive rate was over 80% in showed by GUS reporter gene and this transformation only took 1/6 of the time compared with stable transformation. The system was applicable to different varieties and other cruciferous crops including and . In particular, two known CR genes, and were used respectively, as example to show that the system works well for CR gene study combined with subsequent infection in . Most importantly, it works both in over-expression that led to disease resistance, as well as in RNAi which led to disease susceptible phenotype. Therefore, this system can be used in batch-wise identification of CR genes, and also offered the possibility of manipulating key genes within the genome that could improve our knowledge on host–pathogen interaction.
{"title":"Development of a rapid and efficient system for CR genes identification based on hairy root transformation in Brassicaceae","authors":"Wenlin Yu, Lu Yang, Yuanyuan Xiang, Rongde Li, Xueqing Zhou, Longcai Gan, Xianyu Xiang, Yunyun Zhang, Lei Yuan, Yanqing Luo, Genze Li, Youning Wang, Yinhua Chen, Peng Chen, Chunyu Zhang","doi":"10.1016/j.hpj.2024.05.002","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.05.002","url":null,"abstract":"Many economically important crops and vegetables belonging to the cruciferous family are heavily endangered by clubroot disease caused by infection. Breeding of clubroot resistant cultivars based on mapping and cloning of resistant genes is commonly regarded as the most cost-effective and efficient way to fight against this disease. The traditional way of R gene functional validation requires stable transformation that is both time- and labor-consuming. In this study, a rapid and efficient hairy-root transgenic protocol mediated by was developed. The transformation positive rate was over 80% in showed by GUS reporter gene and this transformation only took 1/6 of the time compared with stable transformation. The system was applicable to different varieties and other cruciferous crops including and . In particular, two known CR genes, and were used respectively, as example to show that the system works well for CR gene study combined with subsequent infection in . Most importantly, it works both in over-expression that led to disease resistance, as well as in RNAi which led to disease susceptible phenotype. Therefore, this system can be used in batch-wise identification of CR genes, and also offered the possibility of manipulating key genes within the genome that could improve our knowledge on host–pathogen interaction.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"5 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141461871","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 : 2024-06-19DOI: 10.1016/j.hpj.2024.02.006
Yi Zhang, Shaoyun Dong, Jiantao Guan, Xiaoping Liu, Xuewen Xie, Karin Albornoz, Jianan Han, Zaizhan Wang, Xingfang Gu, Shengping Zhang, Han Miao
Bacterial soft rot (BSR) caused by subsp. () is a serious bacterial disease which negatively impact yield and quality in cucumber. However, the genetic mechanism of BSR resistance in cucumber has not been reported. Here, we investigated the BSR resistance of 119 cucumber core germplasm worldwide at the seedling stage and identified 26 accessions highly resistant to BSR. A total of 1 642 740 single-nucleotide polymorphisms (SNPs) were used to conduct GWAS, and five loci associated with BSR resistance were detected on four chromosomes: , , , and . Based on haplotype analysis, sequence polymorphisms, functional annotation and qRT-PCR analysis, six candidate genes were identified within the five loci. , , , , , and each had nonsynonymous SNPs, and were significantly up-regulated in the resistant genotypes after inoculation. And in the susceptible genotype was significantly up-regulated after inoculation. The identification of these candidate genes lays a foundation for understanding the genetic mechanism of BSR resistance in cucumber. Generally, our study mined genes associated with BSR resistance in cucumber seedlings and will assist the breeding of BSR-resistant cucumber cultivars.
{"title":"Genome-wide association study identifies candidate genes for bacterial soft rot resistance in cucumber seedlings","authors":"Yi Zhang, Shaoyun Dong, Jiantao Guan, Xiaoping Liu, Xuewen Xie, Karin Albornoz, Jianan Han, Zaizhan Wang, Xingfang Gu, Shengping Zhang, Han Miao","doi":"10.1016/j.hpj.2024.02.006","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.02.006","url":null,"abstract":"Bacterial soft rot (BSR) caused by subsp. () is a serious bacterial disease which negatively impact yield and quality in cucumber. However, the genetic mechanism of BSR resistance in cucumber has not been reported. Here, we investigated the BSR resistance of 119 cucumber core germplasm worldwide at the seedling stage and identified 26 accessions highly resistant to BSR. A total of 1 642 740 single-nucleotide polymorphisms (SNPs) were used to conduct GWAS, and five loci associated with BSR resistance were detected on four chromosomes: , , , and . Based on haplotype analysis, sequence polymorphisms, functional annotation and qRT-PCR analysis, six candidate genes were identified within the five loci. , , , , , and each had nonsynonymous SNPs, and were significantly up-regulated in the resistant genotypes after inoculation. And in the susceptible genotype was significantly up-regulated after inoculation. The identification of these candidate genes lays a foundation for understanding the genetic mechanism of BSR resistance in cucumber. Generally, our study mined genes associated with BSR resistance in cucumber seedlings and will assist the breeding of BSR-resistant cucumber cultivars.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"66 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141461958","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 : 2024-06-19DOI: 10.1016/j.hpj.2024.03.005
Yinqing Yang, Lei Zhang, Qi Tang, Lingkui Zhang, Xing Li, Shumin Chen, Kang Zhang, Ying Li, Xilin Hou, Feng Cheng
has been developed into many important crops, including cabbage, kale, cauliflower, broccoli and so on. The genome and gene annotation of cabbage (cultivar JZS), a representative morphotype of , has been widely used as a common reference in biological research. Although its genome assembly has been updated twice, the current gene annotation still lacks information on untranslated regions (UTRs) and alternative splicing (AS). Here, we constructed a high-quality gene annotation (JZSv3) using a full-length transcriptome acquired by nanopore sequencing, yielding a total of 59 452 genes and 75 684 transcripts. Additionally, we re-analyzed the previously reported transcriptome data related to the development of different tissues and cold response using JZSv3 as a reference, and found that 3843 out of 11 908 differentially expressed genes (DEGs) underwent AS during the development of different tissues and 309 out of 903 cold-related genes underwent AS in response to cold stress. Meanwhile, we also identified many AS genes, including and , that displayed distinct expression patterns within variant transcripts of the same gene, highlighting the importance of JZSv3 as a pivotal reference for AS analysis. Overall, JZSv3 provides a valuable resource for exploring gene function, especially for obtaining a deeper understanding of AS regulation mechanisms.
{"title":"Improved genome annotation of Brassica oleracea highlights the importance of alternative splicing","authors":"Yinqing Yang, Lei Zhang, Qi Tang, Lingkui Zhang, Xing Li, Shumin Chen, Kang Zhang, Ying Li, Xilin Hou, Feng Cheng","doi":"10.1016/j.hpj.2024.03.005","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.03.005","url":null,"abstract":"has been developed into many important crops, including cabbage, kale, cauliflower, broccoli and so on. The genome and gene annotation of cabbage (cultivar JZS), a representative morphotype of , has been widely used as a common reference in biological research. Although its genome assembly has been updated twice, the current gene annotation still lacks information on untranslated regions (UTRs) and alternative splicing (AS). Here, we constructed a high-quality gene annotation (JZSv3) using a full-length transcriptome acquired by nanopore sequencing, yielding a total of 59 452 genes and 75 684 transcripts. Additionally, we re-analyzed the previously reported transcriptome data related to the development of different tissues and cold response using JZSv3 as a reference, and found that 3843 out of 11 908 differentially expressed genes (DEGs) underwent AS during the development of different tissues and 309 out of 903 cold-related genes underwent AS in response to cold stress. Meanwhile, we also identified many AS genes, including and , that displayed distinct expression patterns within variant transcripts of the same gene, highlighting the importance of JZSv3 as a pivotal reference for AS analysis. Overall, JZSv3 provides a valuable resource for exploring gene function, especially for obtaining a deeper understanding of AS regulation mechanisms.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"1 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141461862","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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