aBIOTECH最新文献

{"title":"The evolution of China’s regulation of agricultural biotechnology","authors":"Jingang Liang,&nbsp;Xiaowei Yang,&nbsp;Yue Jiao,&nbsp;Danxia Wang,&nbsp;Qiang Zhao,&nbsp;Yu Sun,&nbsp;Yunhe Li,&nbsp;Kongming Wu","doi":"10.1007/s42994-022-00086-1","DOIUrl":"10.1007/s42994-022-00086-1","url":null,"abstract":"<div><p>To ensure safe use of genetically modified organisms (GMOs), since 1993, China has made great efforts to establish and improve the safety regulatory system for GMOs. Here, we summarize and analyze the regulatory framework of agricultural GMOs, and the progress in regulatory approval of GM crops in China. In general, the development of GMO safety regulations underwent four stages: exploration (1993–2000), development (2001–2010), improvement (2011–2020) and current (2021-present) stage. The first formal regulation was promulgated in 1993, which provided a basis for further development of the regulations, during the exploration stage, when insect-resistant GM cotton, expressing genes from <i>Bacillus thuringiensis</i> (<i>Bt</i>), was approved for cultivation. During the development stage, the Chinese government issued a series of administrative measures, which covered almost all the fields relative to GMO safety when the basic regulatory system was established. Along with the controversy over GMO safety, the regulations have been further, and greatly improved, during improvement stage. From 2021, a few additional revisions have been made, and meanwhile, the new regulation on gene-edited crops was introduced with the development of biotechnology, forming a relative complete regulation and law system for China. The well-developed GMO regulations establishes a firm basis for safe use of GM crops in China. Currently, GM cotton and GM papaya have been widely grown on a large scale in China that have brought great economic and ecological benefits. In addition, 12 corn events, 3 soybean events, and 2 rice events have also obtained biosafety certification, but presently, these lines have yet to enter commercial production. However, several GM soybean and corn events have entered pilot industrialization, and can soon be expected to be commercially grown in China. In addition to planting, six GM crops, including soybean, corn, cotton, canola, papaya and sugar beet, with a total of 64 events, have been approved for import as processing material in China.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"3 4","pages":"237 - 249"},"PeriodicalIF":3.6,"publicationDate":"2022-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-022-00086-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10406498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"G2-LIKE CAROTENOID REGULATOR (SlGCR) is a positive regulator of lutein biosynthesis in tomato","authors":"Siyan Ren,&nbsp;Yong Yuan,&nbsp;Hsihua Wang,&nbsp;Yang Zhang","doi":"10.1007/s42994-022-00088-z","DOIUrl":"10.1007/s42994-022-00088-z","url":null,"abstract":"<div><p>Lutein is an oxygen-containing carotenoid synthesized in plant chloroplasts and chromoplasts. It plays an indispensable role in promoting plant growth and maintaining eye health in humans. The rate-limiting step of lutein biosynthesis is catalyzed by the lycopene ε-cyclase enzyme (LCYE). Although great progress has been made in the identification of transcription factors involved in the lutein biosynthetic pathway, many systematic molecular mechanisms remain to be elucidated. Here, using co-expression analysis, we identified a gene, <i>G2-LIKE CAROTENOID REGULATOR</i> (<i>SlGCR</i>), encoding a GARP G2-like transcription factor, as the potential regulator of <i>SlLCYE</i> in tomato. Silencing of <i>SlGCR</i> reduced the expression of carotenoid biosynthetic genes and the accumulation of carotenoids in tomato leaves. By contrast, overexpression of <i>SlGCR</i> in tomato fruit significantly increased the expression of relevant genes and enhanced the accumulation of carotenoids. SlGCR can directly bind to the <i>SlLCYE</i> promoter and activate its expression. In addition, we also discovered that expression of <i>SlGCR</i> was negatively regulated by the master regulator SlRIN, thereby inhibiting lutein synthesis during tomato fruit ripening. Taken together, we identified SlGCR as a novel regulator involved in tomato lutein biosynthesis, elucidated the regulatory mechanism, and provided a potential tool for tomato lutein metabolic engineering.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"3 4","pages":"267 - 280"},"PeriodicalIF":3.6,"publicationDate":"2022-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-022-00088-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9235746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcription factor CsESE3 positively modulates both jasmonic acid and wax biosynthesis in citrus","authors":"Haoliang Wan,&nbsp;Haiji Qiu,&nbsp;Zhuoran Li,&nbsp;Xiaoliang Zhang,&nbsp;Jingyu Zhang,&nbsp;Deyuan Jiang,&nbsp;Alisdair R. Fernie,&nbsp;Yi Lyu,&nbsp;Yunjiang Cheng,&nbsp;Weiwei Wen","doi":"10.1007/s42994-022-00085-2","DOIUrl":"10.1007/s42994-022-00085-2","url":null,"abstract":"<div><p>PLIP lipases can initiate jasmonic acid (JA) biosynthesis. However, little is known about the transcriptional regulation of this process. In this study, an ERF transcription factor (<i>CsESE3</i>) was found to be co-expressed with all necessary genes for JA biosynthesis and several key genes for wax biosynthesis in transcriptomes of ‘Newhall’ navel orange. <i>CsESE3</i> shows partial sequence similarity to the well-known wax regulator SHINEs (SHNs), but lacks a complete MM protein domain. Ectopic overexpression of <i>CsESE3</i> in tomato (OE) resulted in reduction of fruit surface brightness and dwarf phenotype compared to the wild type. The OE tomato lines also showed significant increases in the content of wax and JA and the expression of key genes related to their biosynthesis. Overexpression of <i>CsESE3</i> in citrus callus and fruit enhanced the JA content and the expression of JA biosynthetic genes. Furthermore, <i>CsESE3</i> could bind to and activate the promoters of two phospholipases from the PLIP gene family to initiate JA biosynthesis. Overall, this study indicated that <i>CsESE3</i> could mediate JA biosynthesis by activating <i>PLIP</i> genes and positively modulate wax biosynthesis. The findings provide important insights into the coordinated control of two defense strategies of plants represented by wax and JA biosynthesis.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"3 4","pages":"250 - 266"},"PeriodicalIF":3.6,"publicationDate":"2022-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-022-00085-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50505950","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Solanaceae pangenomes are coming of graphical age to bring heritability back","authors":"Björn Usadel","doi":"10.1007/s42994-022-00087-0","DOIUrl":"10.1007/s42994-022-00087-0","url":null,"abstract":"<div><p>Two recent articles describe a pangenome of potato and a graph-based pangenome for tomato, respectively. The latter improves our understanding of the tomato genomics architecture even further and the use of this graph-based pangenome versus a single reference dramatically improves heritability in tomato.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"3 4","pages":"233 - 236"},"PeriodicalIF":3.6,"publicationDate":"2022-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-022-00087-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50481745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The genomic and bulked segregant analysis of Curcuma alismatifolia revealed its diverse bract pigmentation","authors":"Xuezhu Liao,&nbsp;Yuanjun Ye,&nbsp;Xiaoni Zhang,&nbsp;Dan Peng,&nbsp;Mengmeng Hou,&nbsp;Gaofei Fu,&nbsp;Jianjun Tan,&nbsp;Jianli Zhao,&nbsp;Rihong Jiang,&nbsp;Yechun Xu,&nbsp;Jinmei Liu,&nbsp;Jinliang Yang,&nbsp;Wusheng Liu,&nbsp;Luke R. Tembrock,&nbsp;Genfa Zhu,&nbsp;Zhiqiang Wu","doi":"10.1007/s42994-022-00081-6","DOIUrl":"10.1007/s42994-022-00081-6","url":null,"abstract":"<div><p>Compared with most flowers where the showy part comprises specialized leaves (petals) directly subtending the reproductive structures, most Zingiberaceae species produce showy “flowers” through modifications of leaves (bracts) subtending the true flowers throughout an inflorescence. <i>Curcuma alismatifolia</i>, belonging to the Zingiberaceae family, a plant species originating from Southeast Asia, has become increasingly popular in the flower market worldwide because of its varied and esthetically pleasing bracts produced in different cultivars. Here, we present the chromosome-scale genome assembly of <i>C. alismatifolia</i> “Chiang Mai Pink” and explore the underlying mechanisms of bract pigmentation. Comparative genomic analysis revealed <i>C. alismatifolia</i> contains a residual signal of whole-genome duplication. Duplicated genes, including pigment-related genes, exhibit functional and structural differentiation resulting in diverse bract colors among <i>C. alismatifolia</i> cultivars. In addition, we identified the key genes that produce different colored bracts in <i>C. alismatifolia</i>, such as <i>F3′5'H</i>, <i>DFR</i>, <i>ANS</i> and several transcription factors for anthocyanin synthesis, as well as <i>chlH</i> and <i>CAO</i> in the chlorophyll synthesis pathway by conducting transcriptomic analysis, bulked segregant analysis using both DNA and RNA data, and population genomic analysis. This work provides data for understanding the mechanism of bract pigmentation and will accelerate breeding in developing novel cultivars with richly colored bracts in <i>C. alismatifolia</i> and related species. It is also important to understand the variation in the evolution of the Zingiberaceae family.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"3 3","pages":"178 - 196"},"PeriodicalIF":3.6,"publicationDate":"2022-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-022-00081-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50457351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"LncPheDB: a genome-wide lncRNAs regulated phenotypes database in plants","authors":"Danjing Lou,&nbsp;Fei Li,&nbsp;Jinyue Ge,&nbsp;Weiya Fan,&nbsp;Ziran Liu,&nbsp;Yanyan Wang,&nbsp;Jingfen Huang,&nbsp;Meng Xing,&nbsp;Wenlong Guo,&nbsp;Shizhuang Wang,&nbsp;Weihua Qiao,&nbsp;Zhenyun Han,&nbsp;Qian Qian,&nbsp;Qingwen Yang,&nbsp;Xiaoming Zheng","doi":"10.1007/s42994-022-00084-3","DOIUrl":"10.1007/s42994-022-00084-3","url":null,"abstract":"<div><p>LncPheDB (https://www.lncphedb.com/) is a systematic resource of genome-wide long non-coding RNAs (lncRNAs)-phenotypes associations for multiple species. It was established to display the genome-wide lncRNA annotations, target genes prediction, variant-trait associations, gene-phenotype correlations, lncRNA-phenotype correlations, and the similar non-coding regions of the queried sequence in multiple species. LncPheDB sorted out a total of 203,391 lncRNA sequences, 2000 phenotypes, and 120,271 variants of nine species (<i>Zea mays</i> L., <i>Gossypium barbadense</i> L., <i>Triticum aestivum</i> L., <i>Lycopersicon esculentum</i> Mille, <i>Oryza sativa</i> L., <i>Hordeum vulgare</i> L., <i>Sorghum bicolor</i> L., <i>Glycine max</i> L., and <i>Cucumis sativus</i> L.). By exploring the relationship between lncRNAs and the genomic position of variants in genome-wide association analysis, a total of 68,862 lncRNAs were found to be related to the diversity of agronomic traits. More importantly, to facilitate the study of the functions of lncRNAs, we analyzed the possible target genes of lncRNAs, constructed a blast tool for performing similar fragmentation studies in all species, linked the pages of phenotypic studies related to lncRNAs that possess similar fragments and constructed their regulatory networks. In addition, LncPheDB also provides a user-friendly interface, a genome visualization platform, and multi-level and multi-modal convenient data search engine. We believe that LncPheDB plays a crucial role in mining lncRNA-related plant data.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"3 3","pages":"169 - 177"},"PeriodicalIF":3.6,"publicationDate":"2022-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-022-00084-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9462831","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advances in plastid transformation for metabolic engineering in higher plants","authors":"Sheng Yang,&nbsp;Yi Deng,&nbsp;Shengchun Li","doi":"10.1007/s42994-022-00083-4","DOIUrl":"10.1007/s42994-022-00083-4","url":null,"abstract":"<div><p>The plastid (chloroplast) genome of higher plants is an appealing target for metabolic engineering via genetic transformation. Although the bacterial-type plastid genome is small compared with the nuclear genome, it can accommodate large quantities of foreign genes that precisely integrate through homologous recombination. Engineering complex metabolic pathways in plants often requires simultaneous and concerted expression of multiple transgenes, the possibility of stacking several transgenes in synthetic operons makes the transplastomic approach amazing. The potential for extraordinarily high-level transgene expression, absence of epigenetic gene silencing and transgene containment due to the exclusion of plastids from pollen transmission in most angiosperm species further add to the attractiveness of plastid transformation technology. This minireview describes recent advances in expanding the toolboxes for plastid genome engineering, and highlights selected high-value metabolites produced using transplastomic plants, including artemisinin, astaxanthin and paclitaxel.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"3 3","pages":"224 - 232"},"PeriodicalIF":3.6,"publicationDate":"2022-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9590572/pdf/42994_2022_Article_83.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10506680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Fundamental and practical approaches for single-cell ATAC-seq analysis","authors":"Peiyu Shi,&nbsp;Yage Nie,&nbsp;Jiawen Yang,&nbsp;Weixing Zhang,&nbsp;Zhongjie Tang,&nbsp;Jin Xu","doi":"10.1007/s42994-022-00082-5","DOIUrl":"10.1007/s42994-022-00082-5","url":null,"abstract":"<div><p>Assays for transposase-accessible chromatin through high-throughput sequencing (ATAC-seq) are effective tools in the study of genome-wide chromatin accessibility landscapes. With the rapid development of single-cell technology, open chromatin regions that play essential roles in epigenetic regulation have been measured at the single-cell level using single-cell ATAC-seq approaches. The application of scATAC-seq has become as popular as that of scRNA-seq. However, owing to the nature of scATAC-seq data, which are sparse and noisy, processing the data requires different methodologies and empirical experience. This review presents a practical guide for processing scATAC-seq data, from quality evaluation to downstream analysis, for various applications. In addition to the epigenomic profiling from scATAC-seq, we also discuss recent studies in which the function of non-coding variants has been investigated based on cell type-specific cis-regulatory elements and how to use the by-product genetic information obtained from scATAC-seq to infer single-cell copy number variants and trace cell lineage. We anticipate that this review will assist researchers in designing and implementing scATAC-seq assays to facilitate research in diverse fields.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"3 3","pages":"212 - 223"},"PeriodicalIF":3.6,"publicationDate":"2022-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9590475/pdf/42994_2022_Article_82.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10506674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The global integrative network: integration of signaling and metabolic pathways","authors":"Yuying Lin,&nbsp;Shen Yan,&nbsp;Xiao Chang,&nbsp;Xiaoquan Qi,&nbsp;Xu Chi","doi":"10.1007/s42994-022-00078-1","DOIUrl":"10.1007/s42994-022-00078-1","url":null,"abstract":"<div><p>The crosstalk between signaling and metabolic pathways has been known to play key roles in human diseases and plant biological processes. The integration of signaling and metabolic pathways can provide an essential reference framework for crosstalk analysis. However, current databases use distinct structures to present signaling and metabolic pathways, which leads to the chaos in the integrated networks. Moreover, for the metabolic pathways, the metabolic enzymes and the reactions are disconnected by the current widely accepted layout of edges and nodes, which hinders the topological analysis of the integrated networks. Here, we propose a novel “meta-pathway” structure, which uses the uniformed structure to display the signaling and metabolic pathways, and resolves the difficulty in linking the metabolic enzymes to the reactions topologically. We compiled a comprehensive collection of global integrative networks (GINs) by merging the meta-pathways of 7077 species. We demonstrated the assembly of the signaling and metabolic pathways using the GINs of four species—human, mouse, <i>Arabidopsis</i>, and rice. Almost all of the nodes were assembled into one major network for each of the four species, which provided opportunities for robust crosstalk and topological analysis, and knowledge graph construction.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"3 4","pages":"281 - 291"},"PeriodicalIF":3.6,"publicationDate":"2022-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-022-00078-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9096669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Construction of homozygous diploid potato through maternal haploid induction","authors":"Jinzhe Zhang,&nbsp;Jian Yin,&nbsp;Jiayi Luo,&nbsp;Die Tang,&nbsp;Xijian Zhu,&nbsp;Jie Wang,&nbsp;Zhihong Liu,&nbsp;Pei Wang,&nbsp;Yu Zhong,&nbsp;Chenxu Liu,&nbsp;Canhui Li,&nbsp;Shaojiang Chen,&nbsp;Sanwen Huang","doi":"10.1007/s42994-022-00080-7","DOIUrl":"10.1007/s42994-022-00080-7","url":null,"abstract":"<div><p>Reinventing the tetraploid potato into a seed-propagated, diploid, hybrid potato would significantly accelerate potato breeding. In this regard, the development of highly homozygous inbred lines is a prerequisite for breeding hybrid potatoes, but self-incompatibility and inbreeding depression present challenges for developing pure inbred lines. To resolve this impediment, we developed a doubled haploid (DH) technology, based on mutagenesis of the potato <i>DOMAIN OF UNKNOWN FUNCTION 679 membrane protein</i> (<i>StDMP</i>) gene. Here, we show that a deficiency in <i>StDMP</i> allows the generation of maternal haploids for generating diploid potato lines. An exercisable protocol, involving hybridization, fluorescent marker screening, molecular and flow cytometric identification, and doubling with colchicine generates nearly 100% homozygous diploid potato lines. This <i>dmp</i>-triggered haploid induction (HI) system greatly shortens the breeding process and offers a robust method for generating diploid potato inbred lines with high purity.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"3 3","pages":"163 - 168"},"PeriodicalIF":3.6,"publicationDate":"2022-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-022-00080-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9446913","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}