Horticulture Research最新文献_第2页

A comprehensive overview of omics-based approaches to enhance biotic and abiotic stress tolerance in sweet potato 全面概述基于组学的提高甘薯生物和非生物胁迫耐受性的方法

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2024-01-12 DOI: 10.1093/hr/uhae014

Sulaiman Ahmed, Muhammad Saad Shoaib Khan, Songlei Xue, Faisal Islam, Aziz Ul Ikram, Muhammad Abdullah, Shan Liu, Piengtawan Tappiban, Jian Chen

{"title":"A comprehensive overview of omics-based approaches to enhance biotic and abiotic stress tolerance in sweet potato","authors":"Sulaiman Ahmed, Muhammad Saad Shoaib Khan, Songlei Xue, Faisal Islam, Aziz Ul Ikram, Muhammad Abdullah, Shan Liu, Piengtawan Tappiban, Jian Chen","doi":"10.1093/hr/uhae014","DOIUrl":"https://doi.org/10.1093/hr/uhae014","url":null,"abstract":"Biotic and abiotic stresses negatively affect the yield and overall plant developmental process, thus causing substantial losses in global sweet potato production. To cope with stresses, sweet potato has evolved numerous strategies to tackle ever-changing surroundings and biological and environmental conditions. The invention of modern sequencing technology and the latest data processing and analysis instruments has paved the way to integrate biological information from different approaches and helps to understand plant system biology more precisely. The advancement in omics technologies has accumulated and provided a great source of information at all levels (genome, transcript, protein, and metabolite) under stressful conditions. These latest molecular tools facilitate us to understand better the plant's responses to stress signaling and help to process/integrate the biological information encoded within the biological system of plants. This review briefly addresses utilizing the latest omics strategies for deciphering the adaptive mechanisms for sweet potatoes' biotic and abiotic stress tolerance via functional genomics, transcriptomics, proteomics, and metabolomics. This information also provides a powerful reference to understand the complex, well-coordinated stress signaling genetic regulatory networks and better comprehend the plant phenotypic responses at the cellular/molecular level under various environmental stimuli, thus accelerating the design of stress-resilient sweet potato via the latest genetic engineering approaches.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"4 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139435478","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}

引用次数: 0

Chloroplast C-to-U editing, regulated by a PPR protein BoYgl-2, is important for chlorophyll biosynthesis in cabbage 受 PPR 蛋白 BoYgl-2 调节的叶绿体 C 到 U 编辑对卷心菜的叶绿素生物合成非常重要

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2024-01-11 DOI: 10.1093/hr/uhae006

Bin Zhang, Yuankang Wu, Shoufan Li, Wenjing Ren, Limei Yang, Mu Zhuang, Honghao Lv, Yong Wang, Jialei Ji, Xilin Hou, Yangyong Zhang

{"title":"Chloroplast C-to-U editing, regulated by a PPR protein BoYgl-2, is important for chlorophyll biosynthesis in cabbage","authors":"Bin Zhang, Yuankang Wu, Shoufan Li, Wenjing Ren, Limei Yang, Mu Zhuang, Honghao Lv, Yong Wang, Jialei Ji, Xilin Hou, Yangyong Zhang","doi":"10.1093/hr/uhae006","DOIUrl":"https://doi.org/10.1093/hr/uhae006","url":null,"abstract":"Leaf color is an important agronomic trait in cabbage (Brassica oleracea L. var. capitata), but the detailed mechanism underlying leaf color formation remains unclear. In this study, we characterized a Brassica oleracea yellow-green leaf 2 (BoYgl-2) mutant 4036Y, which has significantly reduced chlorophyll content and abnormal chloroplasts during early leaf development. Genetic analysis revealed that the yellow-green leaf trait is controlled by a single recessive gene. Map-based cloning revealed that BoYgl-2 encodes a novel nuclear-targeted P-type PPR protein, which is absent in the 4036Y mutant. Functional complementation showed that BoYgl-2 from the normal-green leaf 4036G can rescue the yellow-green leaf phenotype of 4036Y. The C-to-U editing efficiency and expression levels of atpF, rps14, petL and ndhD were significantly reduced in 4036Y than that in 4036G, and significantly increased in BoYgl-2 overexpression lines than that in 4036Y. The expression levels of many plastid- and nuclear-encoded genes associated with chloroplast development in BoYgl-2 mutant were also significantly altered. These results suggest that BoYgl-2 participates in chloroplast C-to-U editing and development, which provides rare insight into the molecular mechanism underlying leaf color formation in cabbage.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"94 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139431283","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}

引用次数: 0

DNA methylome analysis reveals novel insights into active hypomethylated regulatory mechanisms of temperature-dependent flower opening in Osmanthus fragrans DNA 甲基组分析揭示了桂花随温度开放的活性低甲基化调控机制的新见解

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2024-01-11 DOI: 10.1093/hr/uhae010

Shiwei Zhong, Huijun Zhu, Wenle Li, Dan Wu, Yunfeng Miao, Bin Dong, Yiguang Wang, Zhen Xiao, Qiu Fang, Jinping Deng, Hongbo Zhao

{"title":"DNA methylome analysis reveals novel insights into active hypomethylated regulatory mechanisms of temperature-dependent flower opening in Osmanthus fragrans","authors":"Shiwei Zhong, Huijun Zhu, Wenle Li, Dan Wu, Yunfeng Miao, Bin Dong, Yiguang Wang, Zhen Xiao, Qiu Fang, Jinping Deng, Hongbo Zhao","doi":"10.1093/hr/uhae010","DOIUrl":"https://doi.org/10.1093/hr/uhae010","url":null,"abstract":"s Short-term ambient low temperature (ALT) stimulation is necessary for Osmanthus fragrans to facilitate continued flower opening after floral bud development reaches maturity. DNA methylation, a vital epigenetic modification, regulates various biological processes in response to temperature fluctuations. However, its role in temperature-driven flower opening remains elusive. In this study, we identified the pivotal timeframe during which O. fragrans promptly detected temperature cues. Using whole-genome bisulfite sequencing (WGBS), we explored global DNA hypomethylation during this phase, with the most significant changes occurring in CHH sequence contexts. Auxin transport inhibitor (TIBA) application revealed that ALT-induced endogenous auxin accumulation promoted peduncle elongation. In our mRNA-seq analysis, we discovered the differentially expressed genes (DEGs) with hypo-differentially methylated regions (hypo-DMRs) were mainly enriched in auxin and temperature response, RNA processing, carbohydrate and lipid metabolism. The transcripts of three DNA demethylase genes (OfROS1a, OfDML3, OfDME) showed upregulation. Furthermore, all DNA methylase genes, except for OfCMT2b, also displayed increased expression, specifically with two of them, OfCMT3a and OfCMT1, being associated with hypo-DMRs. Promoter assays showed that OfROS1a, with promoters containing low temperature and auxin responsive elements, were activated by ALT and exogenous IAA at low concentrations but inhibited at high concentrations. Overexpression OfROS1 reduced endogenous auxin levels but enhanced the expression of genes related to auxin response and spliceosome in petunia. Furthermore, OfROS1 promoted sucrose synthesis in petunia corollas. Our data characterized the rapid response of active DNA hypomethylation to ALT and suggested a possible epiregulation of temperature-dependent flower opening in O. fragrans.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"54 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139431383","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}

引用次数: 0

EasyDAM_V4: Guided-GAN based cross-species data labeling for fruit detection with significant shape difference EasyDAM_V4：基于引导式聚类分析（GAN）的跨物种数据标注，用于具有显著形状差异的水果检测

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2024-01-11 DOI: 10.1093/hr/uhae007

Wenli Zhang, Yuxin Liu, Chenhuizi Wang, Chao Zheng, Guoqiang Cui, Wei Guo

{"title":"EasyDAM_V4: Guided-GAN based cross-species data labeling for fruit detection with significant shape difference","authors":"Wenli Zhang, Yuxin Liu, Chenhuizi Wang, Chao Zheng, Guoqiang Cui, Wei Guo","doi":"10.1093/hr/uhae007","DOIUrl":"https://doi.org/10.1093/hr/uhae007","url":null,"abstract":"Traditional agriculture is gradually being combined with artificial intelligence technology. High-performance fruit detection technology is an important basic technology in the practical application of modern smart orchards and has great application value. At this stage, fruit detection models need to rely on a large number of labeled datasets to support the training and learning of detection models, resulting in higher manual labeling costs. Our previous work uses a generative adversarial network to translate the source domain to the target fruit images. Thus, automatic labeling is performed on the actual dataset in the target domain. However, the method still does not achieve satisfactory results for translating fruits with significant shape variance. Therefore, this study proposes an improved fruit automatic labeling method EasyDAM_V4, which introduced Across-CycleGAN fruit translation model to achieve spanning translation between phenotypic features such as fruit shape, texture, and color to reduce domain differences effectively. We validated the proposed method using pear fruit as the source domain and three fruits with large phenotypic differences, namely pitaya, eggplant and cucumber, as the target domain. The results show that the EasyDAM_V4 method achieves substantial cross-fruit shape translation, and the average accuracy of labeling reached 87.8%, 87.0% and 80.7% for the three types of target domain datasets, respectively. Therefore, this research method can improve the applicability of the automatic labeling process even if a significant shape variance exists between the source and target domain.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"35 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139431257","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}

引用次数: 0

Genome and GWAS analysis identified genes significantly related to phenotypic state of rhododendron bark 基因组和 GWAS 分析确定了与杜鹃花树皮表型状态显著相关的基因

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2024-01-11 DOI: 10.1093/hr/uhae008

Qiannan Ye, Lu Zhang, Qing Li, Yaliang Ji, Yanli Zhou, Zhenzhen Wu, Yanting Hu, Yongpeng Ma, Jihua Wang, Chengjun Zhang

{"title":"Genome and GWAS analysis identified genes significantly related to phenotypic state of rhododendron bark","authors":"Qiannan Ye, Lu Zhang, Qing Li, Yaliang Ji, Yanli Zhou, Zhenzhen Wu, Yanting Hu, Yongpeng Ma, Jihua Wang, Chengjun Zhang","doi":"10.1093/hr/uhae008","DOIUrl":"https://doi.org/10.1093/hr/uhae008","url":null,"abstract":"As an important horticultural plant, Rhododendron is often used in urban greening and landscape design. However, factors such as the high rate of genetic recombination, frequent outcrossing in the wild, weak linkage disequilibrium, and the susceptibility of gene expression to environmental factors limit further exploration of functional genes related to important horticultural traits, and making the breeding of new varieties require longer time. Therefore, we choose bark as the target trait which is not easily affected by environmental factors, but also has ornamental properties. Genome-wide association study (GWAS) of Rhododendron delavayi (30 samples), Rhododendron irroratum (30 samples) and their F1 generation Rhododendron agastum (200 samples) was conducted on the roughness of bark phenotypes. Finally, we obtained 2416.31 Gbp of clean data and identified 5,328,800 high-quality SNPs. According to the P-value and the degree of linkage disequilibrium of SNPs, we further identified 4 genes out of 11 candidate genes that affect bark roughness. The results of gene differential expression analysis further indicated that the expression levels of Rhdel02G0243600 and Rhdel08G0220700 in different bark phenotypes were significantly different. Our study identified functional genes that influence important horticultural traits of Rhododendron, and illustrated the powerful utility and great potential of GWAS in understanding and exploiting wild germplasm genetic resources of Rhododendron.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"87 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139431287","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}

引用次数: 0

Towards the completion of Koch’s postulates for the citrus huanglongbing bacterium, Candidatus Liberibacter asiaticus 努力完成柑橘黄龙病菌亚洲自由杆菌的科赫假设

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2024-01-11 DOI: 10.1093/hr/uhae011

Desen Zheng, Cheryl Armstrong, Wei Yao, Bo Wu, Weiqi Luo, Charles Powell, Wayne Hunter, Feng Luo, Dean Gabriel, Yongping Duan

{"title":"Towards the completion of Koch’s postulates for the citrus huanglongbing bacterium, Candidatus Liberibacter asiaticus","authors":"Desen Zheng, Cheryl Armstrong, Wei Yao, Bo Wu, Weiqi Luo, Charles Powell, Wayne Hunter, Feng Luo, Dean Gabriel, Yongping Duan","doi":"10.1093/hr/uhae011","DOIUrl":"https://doi.org/10.1093/hr/uhae011","url":null,"abstract":"Candidatus Liberibacter asiaticus (Las) is one of the causal agents of huanglongbing (HLB), the most devastating disease of citrus worldwide. Due to the intracellular lifestyle and significant genome reduction, culturing Las in vitro has proven to be extremely challenging. In this study, we optimized growth conditions and developed a semi-selective medium based on the results of nutritional and antibiotic screening assays. Using these optimized conditions, we were able to grow Las in the LG liquid medium with ca.100-1000-fold increase, which peaked after 4-6 weeks and were estimated to contain 106-107 cells/ml. The cultured Las bacteria remained in a dynamic state of growth for over 20 months and displayed limited growth in subcultures. The survival and growth of Las was confirmed by fluorescence in situ hybridization with Las-specific probes and expression of its metabolic genes. Growth of Las in the optimized medium relied on the presence of a helper bacterium, Stenotrophomonas maltophilia FLMAT-1 that is multi-drug resistant and dominant in the Las co-culture system. To recapitulate the disease, the co-cultured Las was inoculated back to citrus seedlings via psyllid feeding. Although the Las-positive rate of the fed psyllids and inoculated plants were relatively low, this is the first demonstration of partial fulfillment of Koch’s postulates with significant growth of Las in vitro and a successful inoculation of cultured Las back to psyllids and citrus plants that resulted in HLB symptoms. These results provide new insights into Las growth in vitro and a system for improvement towards axenic culture and anti-Las compound screening.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"8 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139431229","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}

引用次数: 0

Phenotyping, genetics and ‘-omics’ approaches to unravel and introgress enhanced resistance against apple scab (Venturia inaequalis) in apple cultivars (Malus × domestica) 用表型分析、遗传学和 "组学 "方法揭示和导入苹果栽培品种（Malus × domestica）对苹果疮痂病（Venturia inaequalis）的增强抗性

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2024-01-11 DOI: 10.1093/hr/uhae002

Anže Švara, Nico De Storme, Sebastien Carpentier, Wannes Keulemans, Barbara De Coninck

{"title":"Phenotyping, genetics and ‘-omics’ approaches to unravel and introgress enhanced resistance against apple scab (Venturia inaequalis) in apple cultivars (Malus × domestica)","authors":"Anže Švara, Nico De Storme, Sebastien Carpentier, Wannes Keulemans, Barbara De Coninck","doi":"10.1093/hr/uhae002","DOIUrl":"https://doi.org/10.1093/hr/uhae002","url":null,"abstract":"Apple scab disease, caused by the fungus Venturia inaequalis, endangers commercial apple production globally. It is predominantly managed by frequent fungicide sprays that can harm the environment and promote the development of fungicide-resistant strains. Cultivation of scab-resistant cultivars harboring diverse qualitative Rvi resistance loci and quantitative trait loci associated with scab resistance could reduce the chemical footprint. A comprehensive understanding of the host-pathogen interaction is, however, needed to efficiently breed cultivars with enhanced resistance against a variety of pathogenic strains. Breeding efforts should not only encompass pyramiding of Rvi loci and their corresponding resistance alleles that directly or indirectly recognize pathogen effectors, but should also integrate genes that contribute to effective downstream defense mechanisms. This review provides an overview of the phenotypic and genetic aspects of apple scab resistance, and currently known corresponding defense mechanisms. Implementation of recent ‘-omics’ approaches has provided insights into the complex network of physiological, molecular and signaling processes that occur before and upon scab infection, thereby revealing the importance of both constitutive and induced defense mechanisms. Based on the current knowledge, we outline advances towards more efficient introgression of enhanced scab resistance into novel apple cultivars by conventional breeding or genetic modification techniques. However, additional studies integrating different ‘-omics’ approaches combined with functional studies will be necessary to unravel effective defense mechanisms as well as key regulatory genes underpinning scab resistance in apple. This crucial information will set the stage for successful knowledge-based breeding for enhanced scab resistance.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"18 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139431382","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}

引用次数: 0

CsMYB73 negatively regulates theanine accumulation mediated by CsGGT2 and CsGGT4 in tea shoots (Camellia sinensis) CsMYB73 负向调节茶芽中由 CsGGT2 和 CsGGT4 介导的茶氨酸积累

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2024-01-11 DOI: 10.1093/hr/uhae012

Manman Chang, Ying Sun, Kangzhi Fang, Maoyin Fu, Jingyu Ma, Yang Gao, Qi Chen, Linlin Liu, Zhaoliang Zhang, Xiaochun Wan, Jun Sun

{"title":"CsMYB73 negatively regulates theanine accumulation mediated by CsGGT2 and CsGGT4 in tea shoots (Camellia sinensis)","authors":"Manman Chang, Ying Sun, Kangzhi Fang, Maoyin Fu, Jingyu Ma, Yang Gao, Qi Chen, Linlin Liu, Zhaoliang Zhang, Xiaochun Wan, Jun Sun","doi":"10.1093/hr/uhae012","DOIUrl":"https://doi.org/10.1093/hr/uhae012","url":null,"abstract":"Theanine metabolism is a necessary biological process during the planting and production of tea that determines tea quality. There is currently little knowledge about the transcriptional regulation of theanine metabolism in tea plants. This study, we demonstrated that γ-glutamyl-transpeptidase CsGGT4, as a homologous protein of the theanine hydrolase CsGGT2, exhibited a higher theanine synthesis catalytic efficiency. Homology modeling and molecular docking showed that differential protein structures between CsGGT2 and CsGGT4 implied their different biological functions in tea plants. Theanine content correlated significantly with the expression of CsGGT2, CsGGT4 and the transcription factor CsMYB73 in tea shoots from different seasons. Additionally, CsMYB73 was confirmed to act as a nucleus-localized transcription factor (TF), directly interacts with the CsGGT2 and CsGGT4 promoters, serving as an activator of CsGGT2 and a suppressor of CsGGT4. Consequently, this leads to a negative association with theanine accumulation in tea shoots. Furthermore, the continuous increase in CsMYB73 produced a significantly increase in CsGGT2 expression and inhibited CsGGT4 expression. The present study reveals that the degradation of theanine has been observed to increase, concomitantly with the inhibition of theanine synthesis, resulting in a significant decline in the accumulation of theanine in tea shoots during the process of seasonal greening in 'Huangkui' leaves. This study contributes to the broader comprehension of the intricate transcriptional regulatory hierarchy that governs the metabolism of theanine in tea shoots, offering novel approaches for managing tea plantations and enhancing tea quality.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"19 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139431275","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}

引用次数: 0

Leaf variegation caused by plastome structural variation: an example from Dianella tasmanica 由质体结构变异引起的叶片变色：以塔斯马尼亚石竹（Dianella tasmanica）为例

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2024-01-11 DOI: 10.1093/hr/uhae009

Shuaixi Zhou, Kainan Ma, Jeffrey P Mower, Ying Liu, Renchao Zhou

{"title":"Leaf variegation caused by plastome structural variation: an example from Dianella tasmanica","authors":"Shuaixi Zhou, Kainan Ma, Jeffrey P Mower, Ying Liu, Renchao Zhou","doi":"10.1093/hr/uhae009","DOIUrl":"https://doi.org/10.1093/hr/uhae009","url":null,"abstract":"Summary Variegated plants often exhibit plastomic heteroplasmy due to single nucleotide mutations or small insertions/deletions in their albino sectors. Here, however, we identified a plastome structural variation in albino sectors of the variegated plant Dianella tasmanica (Asphodelaceae), a perennial herbaceous plant widely cultivated as an ornamental in tropical Asia. This structural variation, caused by intermolecular recombination mediated by an 11-bp inverted repeat flanking a 92 bp segment in the large single copy region (LSC), generates a giant plastome (228,878 bp) with the largest inverted repeat (IR) of 105,226 bp and the smallest LSC of 92 bp known in land plants. It also generates a ~7 kb deletion on the boundary of LSC, which eliminates three protein coding genes (psbA, matK and rps16) and one tRNA gene (trnK). Albino sectors exhibit dramatic changes in expression of many plastid genes, including negligible expression of psbA, matK and rps16, reduced expression of photosynthesis-related genes, and increased expression of genes related to the translational apparatus. Microscopic and ultrastructure observations showed that albino tissues were present in both green and albino sectors of the variegated individuals, and chloroplasts were poorly developed in the mesophyll cells of the albino tissues of the variegated individuals. These poorly developed chloroplasts likely carry the large and rearranged plastome, which is likely responsible for the loss of photosynthesis and albinism in the leaf margins. Considering that short repeats are relatively common in plant plastomes, and that photosynthesis is not necessary for albino sectors, structural variation of this kind may not be rare in the plastomes of variegated plants.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"65 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139431277","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}

引用次数: 0

Flowering genes identification, network analysis and database construction for 837 plants 837 种植物的开花基因鉴定、网络分析和数据库构建

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2024-01-11 DOI: 10.1093/hr/uhae013

Tong Wu, Zhuo Liu, Tong Yu, Rong Zhou, Qihang Yang, Rui Cao, Fulei Nie, Xiao Ma, Yun Bai, Xiaoming Song

{"title":"Flowering genes identification, network analysis and database construction for 837 plants","authors":"Tong Wu, Zhuo Liu, Tong Yu, Rong Zhou, Qihang Yang, Rui Cao, Fulei Nie, Xiao Ma, Yun Bai, Xiaoming Song","doi":"10.1093/hr/uhae013","DOIUrl":"https://doi.org/10.1093/hr/uhae013","url":null,"abstract":"Flowering is one of the most important biological phenomena in the plant kingdom, which not only has important ecological significance, but also has substantial horticultural ornamental value. In this study, we undertook an exhaustive review of the advancements in our understanding of plant flowering genes. We delved into the identification and conducted comparative analyses of flowering genes across virtually all sequenced angiosperm plant genomes. Furthermore, we established an extensive angiosperm flowering atlas, encompassing a staggering 183,720 genes across eight pathways, along with 10,155 ABCDE mode genes, which play a pivotal role in plant flowering regulation. Through the examination of expression patterns, we unveiled the specificities of these flowering genes. An interaction network between flowering genes of the ABCDE model and their corresponding upstream genes offered a blueprint for comprehending their regulatory mechanisms. Moreover, we predicted the miRNA and target genes linked to the flowering processes of each species. To culminate our efforts, we have built a user-friendly web interface, named the 'Plant Flowering-time Gene Database' (PFGD), accessible at http://pfgd.bio2db.com/. We firmly believe that this database will serve as a cornerstone in the global research community, facilitating the in-depth exploration of flowering genes in the plant kingdom. In summation, this pioneering endeavor represents the first comprehensive collection and comparative analysis of flowering genes in plants, offering valuable resources for the study of plant flowering genetics.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"97 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139431371","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}

引用次数: 0