aBIOTECH最新文献

{"title":"Multi-trait improvement of sorghum: co-expression of <i>bar</i>, <i>mcry1Ab</i>, and <i>mvip3A</i> enhances herbicide tolerance and pest resistance.","authors":"Xuan Liu, JiangTao Yang, Yuxin Cui, Xiaochun Zhang, Xujing Wang, Zhixing Wang","doi":"10.1016/j.abiote.2025.100013","DOIUrl":"10.1016/j.abiote.2025.100013","url":null,"abstract":"<p><p>Sorghum (<i>Sorghum bicolor</i>) has held significant historical importance and economic value for centuries. As consumer demands have diversified in recent years, the need for sorghum in industrial sectors such as brewing and food processing has grown substantially. However, competition from weeds and damage caused by lepidopteran pests greatly limit the yield and quality of sorghum. Developing genetically modified sorghum varieties that are both herbicide tolerant and insect resistant is an effective approach to address these challenges. In this study, we stably co-expressed codon-optimized versions of the insect resistance genes <i>mcry1Ab</i> and <i>mvip3A</i> and the <i>bar</i> gene in sorghum using <i>Agrobacterium</i>-mediated genetic transformation. The genetically modified sorghum line can withstand treatment with the herbicide glufosinate at doses up to four times higher than the recommended field level and demonstrated strong resistance to lepidopteran pests such as <i>Ostrinia furnacalis</i>, <i>Mythimna separata</i>, and <i>Spodoptera frugiperda</i>. This new transgenic sorghum germplasm, which has enhanced resistance to both herbicides and insects, offers valuable genetic material for sorghum breeding and could help boost the competitiveness of the sorghum industry.</p>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"7 1","pages":"100013"},"PeriodicalIF":8.5,"publicationDate":"2025-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12973393/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624736","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":"quota_Anchor: a strand and whole genome duplication-aware collinear gene identification tool.","authors":"Xiaodong Li, Yan Zhang, Rui Zhang, Zhiyu Liu, Jiquan Xue, Baoxing Song","doi":"10.1016/j.abiote.2025.100008","DOIUrl":"10.1016/j.abiote.2025.100008","url":null,"abstract":"<p><p>Whole-genome duplication (WGD) events have occurred in numerous branches of the tree of life and are particularly prominent within plant lineages. The significant disparity in the frequency of WGD events across different species imposes specific technical requirements on collinearity alignment tools. Here we present quota_Anchor, a tool for conducting strand- and WGD-aware collinear gene identification. This tool was designed to strictly control the alignment depth and directionality of adjacent gene pairs when searching collinear blocks. We explored the ability of quota_Anchor to position WGD events and classify homologous genes based on different gene duplication modes. User-friendly modules were employed for generating high-quality plots, which revealed that relatively inverted gene pairs tend to exhibit less similar expression patterns than non-relatively inverted gene pairs. Notably, we determined that WGD-derived genes are more frequently associated with plant growth and developmental processes, while genes derived from tandem duplication and proximal duplication are often enriched in stress response and defense-related functions. The accuracy and flexibility of quota_Anchor make it a powerful toolkit for comparative genomics research.</p>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"7 1","pages":"100008"},"PeriodicalIF":8.5,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12973394/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624705","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":"BacPhase: Long-insert paired-end sequencing for bin marker construction and genome phasing.","authors":"Yinqiao Jian, Xiao Guo, Yangyang Shang, Yu Yang, Daofeng Dong, Xiaohui Yang, Guangcun Li","doi":"10.1016/j.abiote.2025.100012","DOIUrl":"10.1016/j.abiote.2025.100012","url":null,"abstract":"<p><p>In genome sequence analysis, phasing, i.e., determining which genetic variants reside on the same chromosome, is essential for assembling genomic sequences into scaffolds. However, phasing remains challenging for plant species with autopolyploid genomes such as potato (<i>Solanum tuberosum</i> L.) due to the high sequence similarity among homologous and homoeologous chromosomes. Bin marker is a DNA tag for a chromosome segment, helping create genetic maps and find trait-related genes. Traditional bacterial artificial chromosome (BAC)-based methods use end-sequencing of BAC clones to provide information on phasing; however, they need for labor-intensive library construction and selection of single colonies limits these methods. Here, we present BacPhase, an innovative sequence-based approach in which constructed BACs are digested with a restriction enzyme and self-ligated to produce small inserts that can be amplified by PCR and sequenced, thus removing the need for selecting single colonies. The restriction enzyme used affects the evenness and spacing of markers and we evaluated 14 restriction enzymes to select optimal restriction enzymes in multiple crop species. Using PacBio HiFi long-read sequencing to span repetitive regions, we generated 39,484 high-confidence, high-resolution bin markers in potato. Unlike Hi-C, which relies on chromatin interactions, BacPhase uses sequence polymorphisms directly, enabling precise haplotype resolution. Indeed, BacPhase anchored 59.58 ​% of scaffolds to the chromosomes in the autotetraploid potato cultivar C88, substantially improving contiguity without requiring physical maps or Hi-C data. The BacPhase method could facilitate trait mapping, genomic selection, and accelerated breeding in polyploid crops such as potato, sugarcane (<i>Saccharum officinarum</i>), and alfalfa (<i>Medicago sativa</i>).</p>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"7 1","pages":"100012"},"PeriodicalIF":8.5,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12973386/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624753","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 regulation of rice minor vein patterning by the OsIDD14/12/13 protein complex.","authors":"Haoshu Li, Liying Zhang, Jingke Wang, Huanglei Tang, Zhiguo Zhang, Tiegang Lu, Xuehui Sun","doi":"10.1016/j.abiote.2025.100010","DOIUrl":"10.1016/j.abiote.2025.100010","url":null,"abstract":"<p><p>INDETERMINATE DOMAIN (IDD) transcription factors play important and diverse roles in plant growth, development, and stress responses. For example, OsIDD12 and OsIDD13 associate with SHORT ROOT transcription factors to mediate the expression of the auxin influx transporter gene <i>OsPIN5c</i> in rice (<i>Oryza sativa</i>), thereby regulating minor vein differentiation. However, the underlying mechanism is unclear. In this study, we demonstrate that OsIDD14 associates with OsIDD12 and OsIDD13 to regulate minor vein patterning in rice. <i>In situ</i> hybridization and GUS reporter assays revealed that <i>OsIDD14</i> expression is restricted to the rice vasculature. The <i>osidd12 osidd13 osidd14</i> triple mutant exhibited a minor vein pattern similar to that of C₄ grasses. We demonstrate that OsIDD14 forms a heterogeneous protein complex with OsIDD12 and OsIDD13 that suppresses <i>OsPIN5c</i> expression and inhibits minor vein formation. Ectopic expression of <i>OsIDD14</i> rescued the phenotypes of the <i>osidd12 osidd13</i> double mutant, revealing the functional redundancy of rice IDD12, 13, and 14. In summary, these study reveals that OsIDD14 plays a pivotal role in minor vein patterning and has pleiotropic functions in rice, and laying the foundation for developing rice with high vein density.</p>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"7 1","pages":"100010"},"PeriodicalIF":8.5,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12973406/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624751","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":"<i>GmWOX1</i> regulates the mediolateral polarity of compound leaves in soybean.","authors":"Xuan Zhou, Dan Wang, Dongfa Wang, Mingzhu Sun, Shuifen Huang, Jing Yang, Xiaomin Ji, Weiyue Zhao, Jianghua Chen","doi":"10.1016/j.abiote.2025.100011","DOIUrl":"10.1016/j.abiote.2025.100011","url":null,"abstract":"<p><p>The morphology of soybean (<i>Glycine max</i>) leaves is a key agricultural trait that determines the planting density and photosynthetic efficiency. In soybean-producing regions of Northern China, narrow-leaf varieties carrying loss-of-function mutations in the ​<i>Ln</i> ​gene are widely cultivated and have been incorporated into breeding programs, as the narrow-leaf trait enhances light-use efficiency under high-density planting conditions. However, the molecular mechanism underlying mediolateral axis development of soybean leaf is largely unknown. The WUSCHEL-RELATED HOMEOBOX transcription factor WOX1 plays a key role in mediolateral leaf development. Here, we identified four <i>WOX1</i> homologs in soybean and determined that <i>GmWOX1a</i> and <i>GmWOX1b</i> are specifically and highly expressed in the middle domain of the leaf primordium. Heterologous expression of <i>GmWOX1a</i> fully complemented the leaf defects of the <i>Nicotiana sylvestris lam1</i> mutant. <i>Gmwox1acd</i> and <i>Gmwox1bcd</i> triple mutant produced by gene editing exhibited narrow leaves and developmental abnormalities. However, <i>Gmwox1a, Gmwox1b,</i> and <i>Gmwox1cd</i> displayed no visibly altered phenotypes, suggesting functional redundancy among the <i>WOX1</i> homologs. These findings demonstrate that the four <i>WOX1</i> homologs redundantly regulate mediolateral axis development in soybean leaves, providing a basis for future studies on leaf morphology and soybean breeding.</p>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"7 1","pages":"100011"},"PeriodicalIF":8.5,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12973388/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624678","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":"High levels of ADAR overexpression induce abundant and stochastic off-target RNA editing in rice protoplasts.","authors":"Shuai Yin, Shumin Li, Yang Yuan, Kabin Xie","doi":"10.1016/j.abiote.2025.100007","DOIUrl":"10.1016/j.abiote.2025.100007","url":null,"abstract":"<p><p>Adenosine deaminase acting on RNA (ADAR) mediates adenosine-to-inosine (A-to-I) conversions, with its deaminase domain (ADARdd) acting as a core component of targeted RNA editing. However, the off-target effects of ADARdd remain poorly characterized in plants. Here, we demonstrate that high-level overexpression of ADARdd induces widespread off-target editing in rice protoplasts, an effect not observed in stable transgenic lines. From six biological replicates of ADARdd-overexpressing protoplasts, we identified 2794 off-target editing sites (OFTEs). These OFTEs exhibited stochastic distribution across mRNAs and low editing efficiency (20-40 %), contrasting sharply with the high-confidence editing sites in OsDRB1-ADARdd stable lines. We further identify risky endogenous promoters and establish an empirical expression threshold for ADARdd to minimize off-target editing. Our findings highlight that controlled ADARdd expression is essential for reliable RNA editing in plants, providing valuable guidance for enhancing the precision of plant RNA editing experiments.</p>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"7 1","pages":"100007"},"PeriodicalIF":8.5,"publicationDate":"2025-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12973391/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624744","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":"Correction: FHBDSR-Net: automated measurement of diseased spikelet rate of Fusarium Head Blight on wheat spikes","authors":"Ze Wu,&nbsp;Haowei Zhao,&nbsp;Zeyu Chen,&nbsp;Yongqiang Suo,&nbsp;Seena Joseph,&nbsp;Xiaohui Yuan,&nbsp;Caixia Lan,&nbsp;Weizhen Liu","doi":"10.1007/s42994-025-00250-3","DOIUrl":"10.1007/s42994-025-00250-3","url":null,"abstract":"","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 4","pages":"831 - 831"},"PeriodicalIF":5.0,"publicationDate":"2025-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00250-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145595209","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":"APTES: a high-throughput deep learning–based Arabidopsis phenotypic trait estimation system for individual leaves and siliques","authors":"Ruifang Zhai,&nbsp;Ning Tang,&nbsp;Zhi Liu,&nbsp;Sha Tao,&nbsp;Yupu Huang,&nbsp;Xue Jiang,&nbsp;Aobo Du,&nbsp;Jiashi Wang,&nbsp;Tao Luo,&nbsp;Jinbao Liu,&nbsp;Gina A. Garzon-Martınez,&nbsp;Fiona M. K. Corke,&nbsp;John H. Doonan,&nbsp;Wanneng Yang","doi":"10.1007/s42994-025-00239-y","DOIUrl":"10.1007/s42994-025-00239-y","url":null,"abstract":"<div><p>High-throughput phenotyping of growth kinetics and organ size in the model plant <i>Arabidopsis thaliana</i> requires rapid and precise methods for trait estimation. To address this need, we developed the Arabidopsis Phenotypic Trait Estimation System, APTES, an open-access, high-throughput program that uses computer vision and deep learning to extract 64 leaf traits and 64 silique traits from photographs. The enhanced segmentation model Cascade Mask Region-based Convolutional Neural Network (Mask R-CNN) achieved precision (measure of positive prediction accuracy), recall (sensitivity in detection), and F1 score values (harmonic mean of precision and recall) of 0.965, 0.958, and 0.961, respectively, for individual leaf segmentation. These metrics demonstrated a consistent improvement of approximately 1 percentage point over the baseline model. For silique segmentation, our enhanced DetectoRS model for silique segmentation attained precision, recall, and F1 scores of 0.954, 0.930, and 0.942, respectively. Notably, precision increased by 1%, while the F1 score improved by 2 percentage points. Trait parameters were automatically calculated with coefficient of determination values for leaf and silique traits ranging from 0.776 to 0.976 and mean absolute percentage error values from 1.89% to 7.90%. We phenotyped 166 Arabidopsis accessions, using APTES, and subjected the resulting values to a genome-wide association study (GWAS), revealing 1,042 single-nucleotide polymorphisms (SNPs) as being significantly associated with 18 leaf and silique traits, and one significant SNP on chromosome 3 linked to silique number. Furthermore, we validated APTES across other public Arabidopsis databases and other plant species, with segmentation results demonstrating its applicability across diverse datasets. In conclusion, APTES is a valuable automated tool for leaf and silique segmentation and trait estimation, which should offer benefits to the broader plant science community.</p></div>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"6 4","pages":"744 - 762"},"PeriodicalIF":5.0,"publicationDate":"2025-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s42994-025-00239-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145595152","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":"Co-transcriptional gene regulation in plants.","authors":"Mengshi Wu, Danling Zhu, Zhe Wu","doi":"10.1016/j.abiote.2025.100006","DOIUrl":"10.1016/j.abiote.2025.100006","url":null,"abstract":"<p><p>The essence of life lies in the precise regulation of genetic information flow, namely, the central dogma, with gene transcription playing a pivotal role as the starting point. For a living cell, it is not only essential via transcription to synthesize the RNA but also to ensure its timely processing, packaging, and sorting, thereby determining its distinct fate, such as nuclear retention, export, translation, or degradation. Initially observed in yeast and animals, and more recently in plants, a large amount of evidence indicates that RNA processing and protein-RNA packaging occur largely concomitantly with transcription, a phenomenon known as co-transcriptional gene regulation. Increasing evidence suggests that this mechanism provides extensive regulatory potential for gene expression. It not only ensures timely RNA processing, thus determining the fate of RNA, but may also influence the transcription dynamics of RNA polymerase II (Pol II) and the chromatin environment. In this review, we highlight recent advances in understanding co-transcriptional gene regulation in the model plant <i>Arabidopsis thaliana</i>, focusing on Pol II dynamics post-initiation and their interplay with RNA-processing events such as capping, splicing, 3' end processing, protein-RNA interactions, and RNA fate determination. By comparing these findings with progress in other model systems, we discuss the unique characteristics of co-transcriptional gene regulation in plants and its potential biological significance. Additionally, we introduce recent key discoveries at the <i>FLOWERING LOCUS C</i> (<i>FLC</i>) gene under warm conditions, which exemplify how co-transcriptional RNA processing influences the chromatin environment and leads to long-term regulatory impacts. Finally, we provide perspectives on yet-unanswered key questions related to co-transcriptional gene regulation in plants.</p>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"7 1","pages":"100006"},"PeriodicalIF":8.5,"publicationDate":"2025-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12973403/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624659","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":"Plant base editing: a decade of progress and future applications.","authors":"Ruixiang Zhang, Zhiye Zheng, Guangzhou Li, Xinglei Zheng, Liying Su, Xudong Yuan, Tie Li, Jiantao Tan, Dongchang Zeng, Shaocun Zhang, Jialin Liu, Haochun Shen, Nan Chai, Yao-Guang Liu, Qinlong Zhu","doi":"10.1016/j.abiote.2025.100003","DOIUrl":"10.1016/j.abiote.2025.100003","url":null,"abstract":"<p><p>Base editors derived from clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) systems are widely used for genomic studies in both plants and animals. The broad applicability and safety of base-editing approaches have garnered considerable attention from the research community, and there could be ways to further enhance targeting efficiency and target window range. However, the complex classification and diverse functionalities of base editors pose challenges to their effective utilization and improvement. In this review, we discuss technical principles characterizing various types of base editors, including cytosine base editors (CBEs), adenine base editors (ABEs), dual base editors (DBEs), thymine base editors (TBEs), and guanine base editors (GBEs), among others, which employ distinct mechanisms and DNA repair pathways. We also describe current optimization strategies to assist researchers in improving the deployment of these tools under specific conditions. Finally, we comprehensively analyze the practical applications and advantages of base editors, offering a clear view of their development, their previous and potential applications, and how to select the appropriate tools for specific purposes.</p>","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"7 1","pages":"100003"},"PeriodicalIF":8.5,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12973408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624727","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}