aBIOTECH最新文献_第3页

Plant metabolomics: applications and challenges in the era of multi-omics big data 植物代谢组学：多组学大数据时代的应用与挑战

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2025-01-23 DOI: 10.1007/s42994-024-00194-0

Yingchen Hao, Zhonghui Zhang, Enxi Luo, Jun Yang, Shouchuang Wang

{"title":"Plant metabolomics: applications and challenges in the era of multi-omics big data","authors":"Yingchen Hao, Zhonghui Zhang, Enxi Luo, Jun Yang, Shouchuang Wang","doi":"10.1007/s42994-024-00194-0","DOIUrl":"10.1007/s42994-024-00194-0","url":null,"abstract":"<div>Plant metabolites are crucial for the growth, development, environmental adaptation, and nutritional quality of plants. Plant metabolomics, a key branch of systems biology, involves the comprehensive analysis and interpretation of the composition, variation, and functions of these metabolites. Advances in technology have transformed plant metabolomics into a sophisticated process involving sample collection, metabolite extraction, high-throughput analysis, data processing, and multidimensional statistical analysis. In today’s era of big data, the field is witnessing an explosion in data acquisition, offering insight into the complexity and dynamics of plant metabolism. Moreover, multiple omics strategies can be integrated to reveal interactions and regulatory networks across different molecular levels, deepening our understanding of plant biological processes. In this review, we highlight recent advances and challenges in plant metabolomics, emphasizing the roles for this technique in improving crop varieties, enhancing nutritional value, and increasing stress resistance. We also explore the scientific foundations of plant metabolomics and its applications in medicine, and ecological conservation.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 1","pages":"116 - 132"},"PeriodicalIF":4.6,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-024-00194-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564475","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}

引用次数: 0

A 6.49-Mb inversion associated with the purple embryo spot trait in potato 马铃薯紫色胚斑性状的6.49 mb反转

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2025-01-18 DOI: 10.1007/s42994-025-00197-5

Pei Wang, Lin Cheng, Jun Pan, Lianlian Ma, Xiaojing Hu, Zhong Zhang, Dawei Li, Yanhui Zhu, Shiwei Chang, Pingping Yuan, Philip Kear, Ludivine Lassois, Guangtao Zhu, Sanwen Huang, Hui Du, Chunzhi Zhang

{"title":"A 6.49-Mb inversion associated with the purple embryo spot trait in potato","authors":"Pei Wang, Lin Cheng, Jun Pan, Lianlian Ma, Xiaojing Hu, Zhong Zhang, Dawei Li, Yanhui Zhu, Shiwei Chang, Pingping Yuan, Philip Kear, Ludivine Lassois, Guangtao Zhu, Sanwen Huang, Hui Du, Chunzhi Zhang","doi":"10.1007/s42994-025-00197-5","DOIUrl":"10.1007/s42994-025-00197-5","url":null,"abstract":"<div>The embryo spot trait leads to a deep purple or reddish coloration at the base of the cotyledons of the embryo, visible on both sides of flat potato (Solanum tuberosum) seeds. This trait has long been used by potato researchers and breeders as a morphological marker during dihaploid induction. The formation of embryo spots reflects the accumulation of anthocyanins, but the genetic basis of this trait remains unclear. In this study, we mapped the embryo spot trait to a 6.78-Mb region at the end of chromosome 10 using an F2 population derived from a cross between spotted and spotless plants. The recombination rate in the candidate region is severely suppressed, posing challenges for the map-based cloning of the underlying gene and suggesting large-scale rearrangements in this region. A de novo genome assembly of the spotted individual and a comparative genomic analysis to the reference genome of spotless potato revealed a 6.49-Mb inversion present in the spotted plant genome. The left breakpoint of this inversion occurred in the promoter region of an R2R3 MYB transcription factor gene that is highly expressed in the cotyledon base of spotted embryos but is not expressed in that of spotless embryos. This study elucidated the genetic basis for embryo spot formation in potato and provides a foundation for future cloning of the causative gene.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 1","pages":"22 - 32"},"PeriodicalIF":4.6,"publicationDate":"2025-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00197-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564437","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}

引用次数: 0

Enacting partner specificity in legume-rhizobia symbioses. 豆科植物与根瘤菌共生的伴侣特异性研究。

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2024-12-23 eCollection Date: 2025-06-01 DOI: 10.1007/s42994-024-00193-1

Xiaocheng Yu, Hongyan Zhu

{"title":"Enacting partner specificity in legume-rhizobia symbioses.","authors":"Xiaocheng Yu, Hongyan Zhu","doi":"10.1007/s42994-024-00193-1","DOIUrl":"10.1007/s42994-024-00193-1","url":null,"abstract":"Legumes, such as peas, beans, and alfalfa, have evolved a remarkable ability to establish root nodule symbioses with nitrogen-fixing soil bacteria to fulfill their nitrogen needs. This partnership is characterized by a high degree of specificity, occurring both within and between host and bacterial species. Consequently, nodulation capacity and nitrogen-fixing efficiency vary significantly among different plant-bacteria pairs. The genetic and molecular mechanisms regulating symbiotic specificity are diverse, involving a wide array of host and bacterial genes and signals with various modes of action. Understanding the genetic basis of symbiotic specificity could enable the development of strategies to enhance nodulation capacity and nitrogen fixation efficiency. This knowledge will also help overcome the host range barrier, which is a critical step toward extending root nodule symbiosis to non-leguminous plants. In this review, we provide an update on our current understanding of the genetics and evolution of recognition specificity in root nodule symbioses, providing more comprehensive insights into the molecular signaling in plant-bacterial interactions.","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 2","pages":"311-327"},"PeriodicalIF":4.6,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12237847/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144610298","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}

引用次数: 0

LEAFY1 and 2 are required for floral organ development in soybean 大豆花器官发育需要LEAFY1和2

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2024-12-22 DOI: 10.1007/s42994-024-00192-2

Lingshuang Wang, Huan Liu, Lei Chen, Tong Su, Shichen Li, Chao Fang, Sijia Lu, Baohui Liu, Hui Yang, Fanjiang Kong

{"title":"LEAFY1 and 2 are required for floral organ development in soybean","authors":"Lingshuang Wang, Huan Liu, Lei Chen, Tong Su, Shichen Li, Chao Fang, Sijia Lu, Baohui Liu, Hui Yang, Fanjiang Kong","doi":"10.1007/s42994-024-00192-2","DOIUrl":"10.1007/s42994-024-00192-2","url":null,"abstract":"<div>The transition from vegetative to reproductive growth is a vital step for the reproductive success of plants. In Arabidopsis thaliana, LEAFY (LFY) plays crucial roles in inflorescence primordium and floral organ development, but little is known about the roles of its homologs in crop plants such as soybean (Glycine max). Here, we investigated the expression patterns and functions of the two LFY genes (LFY1 and LFY2) in soybean. Both genes were predominantly expressed in unopened flowers and the shoot apical meristem, with LFY2 having the higher transcript abundance. In an in situ hybridization assay, LFY genes produced strong signals in the floral meristem. We next generated lfy1 and lfy2 knockout lines. The lfy2 mutants showed obvious changes in floral organ morphology, but the lfy1 mutants showed no obvious changes in floral organ morphology or pod development. The lfy1 lfy2 double mutants displayed more serious defects in floral organ development than lfy2, resulting in complete sterility. Gene expression analysis revealed differences in expression of the A-class APETALA (AP) genes AP1a and AP1b in the double mutant lines. These results suggest that LFY2 plays an important role in floral organ formation in soybean by regulating the expression of homeotic genes. Our findings increase the understanding of floral development, which could be useful for flower designs during hybrid soybean breeding.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 1","pages":"12 - 21"},"PeriodicalIF":4.6,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-024-00192-2.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564472","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}

引用次数: 0

Correction: Inference and prioritization of tissue-specific regulons in Arabidopsis and Oryza 更正：拟南芥和稻谷中组织特异性调控的推断和优先排序

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2024-12-19 DOI: 10.1007/s42994-024-00191-3

Honggang Dai, Yaxin Fan, Yichao Mei, Ling-Ling Chen, Junxiang Gao

引用次数: 0

Applying conventional and cell-type-specific CRISPR/Cas9 genome editing in legume plants. 在豆科植物中应用常规和细胞类型特异性CRISPR/Cas9基因组编辑

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2024-12-16 eCollection Date: 2025-06-01 DOI: 10.1007/s42994-024-00190-4

Jin-Peng Gao, Yangyang Su, Suyu Jiang, Wenjie Liang, Zhijun Lou, Florian Frugier, Ping Xu, Jeremy D Murray

{"title":"Applying conventional and cell-type-specific CRISPR/Cas9 genome editing in legume plants.","authors":"Jin-Peng Gao, Yangyang Su, Suyu Jiang, Wenjie Liang, Zhijun Lou, Florian Frugier, Ping Xu, Jeremy D Murray","doi":"10.1007/s42994-024-00190-4","DOIUrl":"10.1007/s42994-024-00190-4","url":null,"abstract":"The advent of genome editing technologies, particularly CRISPR/Cas9, has significantly advanced the generation of legume mutants for reverse genetic studies and understanding the mechanics of the rhizobial symbiosis. The legume-rhizobia symbiosis is crucial for sustainable agriculture, enhancing nitrogen fixation and improving soil fertility. Numerous genes with a symbiosis-specific expression have been identified, sometimes exclusively expressed in cells forming infection threads or in nitrogen-fixing nodule cells. Typically, mutations in these genes do not affect plant growth. However, in some instances, germline homozygous mutations can be lethal or result in complex pleiotropic phenotypes that are challenging to interpret. To address this issue, a rhizobia-inducible and cell-type-specific CRISPR/Cas9 strategy was developed to knock-out genes in specific legume transgenic root tissues. In this review, we discuss recent advancements in legume genome editing, highlighting the cell-type-specific CRISPR system and its crucial applications in symbiotic nitrogen fixation and beyond.","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 2","pages":"346-360"},"PeriodicalIF":4.6,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12238430/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144610294","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}

引用次数: 0

MHZ3: a key regulator of ethylene signaling in rice MHZ3：水稻乙烯信号的关键调控因子

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2024-12-06 DOI: 10.1007/s42994-024-00189-x

Arif Ali Khattak, Yingshan Huang, Muhammad Afzal, Xiaolin Wang

引用次数: 0

Stable plastid transformation in kiwifruit (Actinidia chinensis) 猕猴桃稳定质体转化的研究

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2024-11-28 DOI: 10.1007/s42994-024-00186-0

Qiqi Chen, Yuyong Wu, Yanchang Wang, Jiang Zhang, Shengchun Li

引用次数: 0

Development of an RNA virus vector for non-transgenic genome editing in tobacco and generation of berberine bridge enzyme-like mutants with reduced nicotine content 烟草非转基因基因组编辑RNA病毒载体的研制和尼古丁含量降低的小檗碱桥酶样突变体的产生

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2024-11-22 DOI: 10.1007/s42994-024-00188-y

Haiying Xiang, Binhuan Chen, Shuo Wang, Wanli Zeng, Jiarui Jiang, Weisong Kong, Haitao Huang, Qili Mi, Shuang Ni, Qian Gao, Zhenghe Li

{"title":"Development of an RNA virus vector for non-transgenic genome editing in tobacco and generation of berberine bridge enzyme-like mutants with reduced nicotine content","authors":"Haiying Xiang, Binhuan Chen, Shuo Wang, Wanli Zeng, Jiarui Jiang, Weisong Kong, Haitao Huang, Qili Mi, Shuang Ni, Qian Gao, Zhenghe Li","doi":"10.1007/s42994-024-00188-y","DOIUrl":"10.1007/s42994-024-00188-y","url":null,"abstract":"<div>Tobacco (Nicotiana tabacum) plants synthesize the psychoactive pyridine alkaloid nicotine, which has sparked growing interest in reducing nicotine levels through genome editing aiming at inactivating key biosynthetic genes. Although stable transformation-mediated genome editing is effective in tobacco, its polyploid nature complicates the complete knockout of genes and the segregation of transgenes from edited plants. In this study, we developed a non-transgenic genome editing method in tobacco by delivering the CRISPR/Cas machinery via an engineered negative-strand RNA rhabdovirus vector, followed by the regeneration of mutant plants through tissue culture. Using this method, we targeted six berberine bridge enzyme-like protein (BBL) family genes for mutagenesis, which are implicated in the last steps of pyridine alkaloid biosynthesis, in the commercial tobacco cultivar Hongda. We generated a panel of 16 mutant lines that were homozygous for mutations in various combinations of BBL genes. Alkaloid profiling revealed that lines homozygous for BBLa and BBLb mutations exhibited drastically reduced nicotine levels, while other BBL members played a minor role in nicotine synthesis. The decline of nicotine content in these lines was accompanied by reductions in anatabine and cotinine levels but increases in nornicotine and its derivative myosmine. Preliminary agronomic evaluation identified two low-nicotine lines with growth phenotypes comparable to those of wild-type plants under greenhouse and field conditions. Our work provides potentially valuable genetic materials for breeding low-nicotine tobacco and enhances our understanding of alkaloid biosynthesis.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"5 4","pages":"449 - 464"},"PeriodicalIF":4.6,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-024-00188-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142789188","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}

引用次数: 0

Developing a pipeline for identification, characterization and molecular editing of cis-regulatory elements: a case study in potato 开发顺式调控元件的鉴定、表征和分子编辑管道：以马铃薯为例

IF 4.6 4区农林科学

aBIOTECH Pub Date : 2024-10-30 DOI: 10.1007/s42994-024-00185-1

Min Wan, Handan Xie, Hongwei Guo, Shenglin Jing, Deying Zeng, Bing Li, Bo Zhu, Zixian Zeng

{"title":"Developing a pipeline for identification, characterization and molecular editing of cis-regulatory elements: a case study in potato","authors":"Min Wan, Handan Xie, Hongwei Guo, Shenglin Jing, Deying Zeng, Bing Li, Bo Zhu, Zixian Zeng","doi":"10.1007/s42994-024-00185-1","DOIUrl":"10.1007/s42994-024-00185-1","url":null,"abstract":"<div>Crop breeding requires a balance of tradeoffs among key agronomic traits caused by gene pleiotropy. The molecular manipulation of genes can effectively improve target traits, but this may not reduce gene pleiotropy, potentially leading to undesirable traits or even lethal conditions. However, molecular editing of cis-regulatory elements (CREs) of target genes may facilitate the dissection of gene pleiotropy to fine-tune gene expression. In this study, we developed a pipeline, in potato, which employs open chromatin to predict candidate CREs, along with both transient and genetic assays to validate the function of CREs and CRISPR/Cas9 to edit candidate CREs. We used StCDF1 as an example, a key gene for potato tuberization and identified a 288 bp-core promoter region, which showed photoperiodic inducibility. A homozygous CRISPR/Cas9-editing line was established, with two deletions in the core promoter, which displayed a reduced expression level, resulting in late tuberization under both long-day and short-day conditions. This pipeline provides an alternative pathway to improve a specific trait with limited downside on other phenotypes.</div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 1","pages":"91 - 96"},"PeriodicalIF":4.6,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-024-00185-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143564560","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}

引用次数: 0