aBIOTECH最新文献

{"title":"Weed genomics: yielding insights into the genetics of weedy traits for crop improvement","authors":"Yujie Huang,&nbsp;Dongya Wu,&nbsp;Zhaofeng Huang,&nbsp;Xiangyu Li,&nbsp;Aldo Merotto Jr,&nbsp;Lianyang Bai,&nbsp;Longjiang Fan","doi":"10.1007/s42994-022-00090-5","DOIUrl":"10.1007/s42994-022-00090-5","url":null,"abstract":"<div><p>Weeds cause tremendous economic and ecological damage worldwide. The number of genomes established for weed species has sharply increased during the recent decade, with some 26 weed species having been sequenced and de novo genomes assembled. These genomes range from 270 Mb (<i>Barbarea vulgaris</i>) to almost 4.4 Gb (<i>Aegilops tauschii</i>). Importantly, chromosome-level assemblies are now available for 17 of these 26 species, and genomic investigations on weed populations have been conducted in at least 12 species. The resulting genomic data have greatly facilitated studies of weed management and biology, especially origin and evolution. Available weed genomes have indeed revealed valuable weed-derived genetic materials for crop improvement. In this review, we summarize the recent progress made in weed genomics and provide a perspective for further exploitation in this emerging field.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"4 1","pages":"20 - 30"},"PeriodicalIF":3.6,"publicationDate":"2023-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-022-00090-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9515722","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":"Genetic architecture and molecular regulation of sorghum domestication","authors":"Fengyong Ge,&nbsp;Peng Xie,&nbsp;Yaorong Wu,&nbsp;Qi Xie","doi":"10.1007/s42994-022-00089-y","DOIUrl":"10.1007/s42994-022-00089-y","url":null,"abstract":"<div><p>Over time, wild crops have been domesticated by humans, and the knowledge gained from parallel selection and convergent domestication-related studies in cereals has contributed to current techniques used in molecular plant breeding. Sorghum (<i>Sorghum bicolor</i> (L.) Moench) is the world’s fifth-most popular cereal crop and was one of the first crops cultivated by ancient farmers. In recent years, genetic and genomic studies have provided a better understanding of sorghum domestication and improvements. Here, we discuss the origin, diversification, and domestication processes of sorghum based on archeological discoveries and genomic analyses. This review also comprehensively summarized the genetic basis of key genes related to sorghum domestication and outlined their molecular mechanisms. It highlights that the absence of a domestication bottleneck in sorghum is the result of both evolution and human selection. Additionally, understanding beneficial alleles and their molecular interactions will allow us to quickly design new varieties by further de novo domestication.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"4 1","pages":"57 - 71"},"PeriodicalIF":3.6,"publicationDate":"2022-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-022-00089-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9515725","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 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":"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}

{"title":"Current overview on the genetic basis of key genes involved in soybean domestication","authors":"Sijia Lu,&nbsp;Chao Fang,&nbsp;Jun Abe,&nbsp;Fanjiang Kong,&nbsp;Baohui Liu","doi":"10.1007/s42994-022-00074-5","DOIUrl":"10.1007/s42994-022-00074-5","url":null,"abstract":"<div><p>Modern crops were created through the domestication and genetic introgression of wild relatives and adaptive differentiation in new environments. Identifying the domestication-related genes and unveiling their molecular diversity provide clues for understanding how the domesticated variants were selected by ancient people, elucidating how and where these crops were domesticated. Molecular genetics and genomics have explored some domestication-related genes in soybean (<i>Glycine max</i>). Here, we summarize recent studies about the quantitative trait locus (QTL) and genes involved in the domestication traits, introduce the functions of these genes, clarify which alleles of domesticated genes were selected during domestication. A deeper understanding of soybean domestication could help to break the bottleneck of modern breeding by highlighting unused genetic diversity not selected in the original domestication process, as well as highlighting promising new avenues for the identification and research of important agronomic traits among different crop species.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"3 2","pages":"126 - 139"},"PeriodicalIF":3.6,"publicationDate":"2022-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9590488/pdf/42994_2022_Article_74.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9549837","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}