IF 5 4区农林科学

aBIOTECH Pub Date : 2025-12-13 eCollection Date: 2026-03-01 DOI: 10.1016/j.abiote.2025.100018

Muhammad Salman Iqbal, Revocatus Bahitwa, Abdul Ali Azam, Hui Xu, Hai Wang

{"title":"Deep learning-driven protein binder design for crop improvement.","authors":"Muhammad Salman Iqbal, Revocatus Bahitwa, Abdul Ali Azam, Hui Xu, Hai Wang","doi":"10.1016/j.abiote.2025.100018","DOIUrl":"https://doi.org/10.1016/j.abiote.2025.100018","url":null,"abstract":"Deep learning (DL) now enables the end-to-end design of protein binders-proteins that bind to specific targets-to precisely modulate protein-protein interactions (PPIs). Models and tools such as BindCraft, AlphaFold, RoseTTAFold, RFdiffusion, and ProteinMPNN predict the structures of these binders and their targets, generate binder sequences, and refine their binding interfaces with increasing accuracy. Most progress so far has been in the therapeutics field, where de novo protein binders are now common targets for design and testing. In plant biology, however, applications remain early and scattered, and clear, crop-focused guidance that links design choices to practical testing is limited. This review explores the potential of protein binders by outlining an end-to-end pipeline for DL-driven protein binder design in plants. The pipeline covers target selection in key pathways for disease resistance, stress tolerance, and plant development; protein binder generation using current DL tools; and tiered in silico screening of the best binders using interface quality and stability metrics. We connect these steps to laboratory practice, including initial binding assays, production in suitable systems, and early in planta evaluation before stable transformation. Current constraints are also discussed, including uncertainty in affinity prediction and the limited structural information available for many plant proteins, as well as practical approaches to mitigate risk during target selection. Together, this plant-focused synthesis illustrates how DL-driven protein binder design can be applied to crop engineering and highlights the work still required to move from early demonstrations of success cases to robust agricultural use.","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"7 1","pages":"100018"},"PeriodicalIF":5.0,"publicationDate":"2025-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12973395/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624731","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

Improved efficiency of genetic transformation for the development of elite germplasm using CRISPR/Cas12i3 in maize. 利用CRISPR/Cas12i3提高玉米优质种质的遗传转化效率

IF 5 4区农林科学

aBIOTECH Pub Date : 2025-12-12 eCollection Date: 2026-03-01 DOI: 10.1016/j.abiote.2025.100017

Yao Wang, Lu Zhang, Mengyuan Liu, Miaoyi Zhou, Xinxiang Liu, Ziheng Song, Xiaoxu Li, Yue Fu, Hao Chen, Ya Liu, Ronghuan Wang, Jiuran Zhao

{"title":"Improved efficiency of genetic transformation for the development of elite germplasm using CRISPR/Cas12i3 in maize.","authors":"Yao Wang, Lu Zhang, Mengyuan Liu, Miaoyi Zhou, Xinxiang Liu, Ziheng Song, Xiaoxu Li, Yue Fu, Hao Chen, Ya Liu, Ronghuan Wang, Jiuran Zhao","doi":"10.1016/j.abiote.2025.100017","DOIUrl":"https://doi.org/10.1016/j.abiote.2025.100017","url":null,"abstract":"Genetic transformation and gene-editing technologies have driven progress in molecular design breeding. Jing 724, an elite founder inbred line from the X heterotic group in maize, was previously recalcitrant to genetic transformation owing to genotype-dependent restrictions. Here, we established a stable and efficient genetic transformation system for Jing 724 using the morphogenic genes Baby boom (Bbm) and Wuschel (Wus2) and the selection marker 6-phosphomannose isomerase (PMI). Under identical Bbm/Wus2-regulation conditions, the efficiencies of callus induction, regeneration, and transformation were significantly higher (30 %) with PMI (mannose) selection than with bar (bialaphos) selection. By optimizing callus induction and regeneration time, we reduced the transformation period for Jing 724 from 90 days to 60 days and increased the transformation efficiency by 20 %. We then combined this transformation system with the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease 12i3 (Cas12i3) system to edit the Sugary1 (Su1) and Waxy (Wx) genes, thereby developing elite germplasms with common sweet, waxy, and combined sweet-waxy traits in the Jing 724 background. We obtained mutation efficiencies of 29.41 % (homozygous), 41.18 % (heterozygous), and 35.29 % (simultaneous). Additionally, concentrations of sucrose, water-soluble polysaccharides, and starch in the endosperms of T1 homozygous kernels were confirmed to differ significantly from those in wild-type kernels. Thus, we have established a highly efficient molecular breeding system that integrates genetic transformation, gene editing, and germplasm development.","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"7 1","pages":"100017"},"PeriodicalIF":5.0,"publicationDate":"2025-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12973389/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624709","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

Double-fluorescent proteins enable robust maternal haploid identification in wheat. 双荧光蛋白使小麦母系单倍体的识别更加可靠。

IF 5 4区农林科学

aBIOTECH Pub Date : 2025-12-11 eCollection Date: 2026-03-01 DOI: 10.1016/j.abiote.2025.100016

Yang Li, Le Dong, Shaoshuai Liu, Guoliang Sun, Zhongyin Deng, Yuqing Che, Dada Cui, Guoliang Chen, Xinyu Zou, Wanxin Xu, Xingchen Kong, Jianhui Ma, Long Mao, Aili Li, Chuanxiao Xie, Shuaifeng Geng

{"title":"Double-fluorescent proteins enable robust maternal haploid identification in wheat.","authors":"Yang Li, Le Dong, Shaoshuai Liu, Guoliang Sun, Zhongyin Deng, Yuqing Che, Dada Cui, Guoliang Chen, Xinyu Zou, Wanxin Xu, Xingchen Kong, Jianhui Ma, Long Mao, Aili Li, Chuanxiao Xie, Shuaifeng Geng","doi":"10.1016/j.abiote.2025.100016","DOIUrl":"https://doi.org/10.1016/j.abiote.2025.100016","url":null,"abstract":"Doubled haploid (DH) technology is crucial for accelerating crop breeding. While the functional conservation of MATRILINEAL (MTL) in cereals enables haploid induction (HI) in wheat (Triticum aestivum), distinguishing haploid from diploid seeds remains a major bottleneck. Here, we developed an efficient haploid identification (HID) system for wheat by seamlessly integrating a two-fluorescent protein-based HID toolbox with an MTL mutant HI wheat line. This system enables efficient HI and utilizes dual-fluorescence screening, offering high accuracy while being independent of the genetic background of the recipient material. Our work demonstrates that engineered intraspecific HI is achievable in self-pollinating crops such as wheat, paving the way for applications that shorten the breeding cycle, facilitate quantitative genetic studies, and accelerate the fixation of desirable alleles. With further optimization and development, this system holds promise as a commercially viable pipeline for haploid production to facilitate wheat breeding.","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"7 1","pages":"100016"},"PeriodicalIF":5.0,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12973401/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624726","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

The root's hidden ally: How the rhizosheath microbiome fortifies crops against drought. 根的隐藏盟友：根鞘微生物群如何加强作物抵御干旱。

IF 5 4区农林科学

aBIOTECH Pub Date : 2025-12-07 eCollection Date: 2026-03-01 DOI: 10.1016/j.abiote.2025.100015

Hassan Etesami, Amir Hosein Yadegari, Umarov Otabek, Bafayeva Zahro, Nafetdinov Shavakatullo, Avezov Tolqinjon

{"title":"The root's hidden ally: How the rhizosheath microbiome fortifies crops against drought.","authors":"Hassan Etesami, Amir Hosein Yadegari, Umarov Otabek, Bafayeva Zahro, Nafetdinov Shavakatullo, Avezov Tolqinjon","doi":"10.1016/j.abiote.2025.100015","DOIUrl":"https://doi.org/10.1016/j.abiote.2025.100015","url":null,"abstract":"Drought stress poses a significant threat to global agriculture, necessitating innovative strategies to enhance plant resilience. This review highlights the rhizosheath-the soil layer tightly bound to roots by mucilage and microbial biofilms-as a critical but underexplored microbial niche for sustainable drought mitigation. Unlike the vulnerable rhizosphere, the rhizosheath has a cohesive structure that acts as a protective \"mini-oasis,\" preserving moisture and sustaining microbial activity when water is scarce. We synthesize evidence showing that resident rhizosheath bacteria, including genera such as Bacillus, Pseudomonas, and Azospirillum, enhance plant drought tolerance through multiple mechanisms: improving soil structure and water retention, modulating phytohormone levels, facilitating nutrient acquisition, and activating antioxidant and genetic defense pathways in the plant. Despite promising laboratory findings, there has been little field-scale validation of these effects. Here, we critically assess translational challenges and outline future research priorities, such as understanding plant-microbe specificity and optimizing synthetic microbial consortia. Addressing these questions will enable manipulation of the rhizosheath microbiome for development of climate-resilient crops and securing food production in water-limited environments.","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"7 1","pages":"100015"},"PeriodicalIF":5.0,"publicationDate":"2025-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12973410/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624745","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

Artificial intelligence-driven discovery of bioactive peptides: Computational approaches and future perspectives. 人工智能驱动的生物活性肽发现：计算方法和未来展望。

IF 5 4区农林科学

aBIOTECH Pub Date : 2025-12-03 eCollection Date: 2026-03-01 DOI: 10.1016/j.abiote.2025.100014

Xu Liu, Feifei Guan, Huiying Luo, Bin Yao, Jian Tian

{"title":"Artificial intelligence-driven discovery of bioactive peptides: Computational approaches and future perspectives.","authors":"Xu Liu, Feifei Guan, Huiying Luo, Bin Yao, Jian Tian","doi":"10.1016/j.abiote.2025.100014","DOIUrl":"https://doi.org/10.1016/j.abiote.2025.100014","url":null,"abstract":"Bioactive peptides, defined as amino acid chains exhibiting diverse biological functions such as antimicrobial, antioxidant, and anti-inflammatory activities, are primarily generated through protein digestion methods including enzymatic hydrolysis, physical processing techniques and controlled microbial fermentation. Conventional discovery techniques that rely on multi-stage separation processes, such as enzymatic digestion, ultrafiltration, ion-exchange chromatography, gel filtration chromatography, and reverse-phase high-performance liquid chromatography (RP-HPLC) inherently demand substantial laboratory resources and extended timeframes. To address these limitations, artificial intelligence (AI)-driven approaches have emerged as transformative discovery platforms. These computational pipelines systematically execute six critical phases: comprehensive data acquisition and curation, advanced feature engineering utilizing physicochemical descriptors, machine learning model construction using algorithms, iterative model training incorporating hyperparameter optimization, rigorous validation against benchmark datasets, and high-throughput bioactive peptide prediction. This comprehensive review critically evaluates recent AI applications across four key bioactive peptide categories including antimicrobial peptides, antioxidant peptides, anti-inflammatory peptides, and multifunctional variants. Furthermore, it proposes integrated enhancement strategies such as classifying peptides via their functional mechanism or using database-independent modeling approaches. Additionally, based on AI methods, scenario-specific peptide customization and prediction of bioactivity in digested proteomes are anticipated to be achieved in the future.","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"7 1","pages":"100014"},"PeriodicalIF":5.0,"publicationDate":"2025-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12973402/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624717","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

Deciphering the dynamics of active autonomous terminal inverted repeat transposons in the plant kingdom 解析植物界主动自主末端倒置重复转座子的动力学

4区农林科学

aBIOTECH Pub Date : 2025-12-02 DOI: 10.1016/j.abiote.2025.100009

Ziye Huang, Bicong Shi, Li Huang, Damon Lisch, Xinyan Zhang

{"title":"Deciphering the dynamics of active autonomous terminal inverted repeat transposons in the plant kingdom","authors":"Ziye Huang, Bicong Shi, Li Huang, Damon Lisch, Xinyan Zhang","doi":"10.1016/j.abiote.2025.100009","DOIUrl":"https://doi.org/10.1016/j.abiote.2025.100009","url":null,"abstract":"Terminal inverted repeat (TIR) transposons are powerful drivers of genome evolution. However, a comprehensive understanding of their recent, lineage-specific activity across the plant kingdom has remained elusive. In this study, we developed a data-distillation pipeline to systematically identify recently active autonomous TIR transposons in 1007 plant genomes. Our analysis identified 3203 active clusters. The vast majority (93.3 %) of these clusters are maintained at low copy numbers, which suggests that robust host-mediated regulation restricts excessive proliferation. These TIR transposons exhibit striking heterogeneity and predominantly lineage-restricted diversification, with functional extinction being a common fate of TIR transposons across the plant kingdom. Among the identified active clusters, the Mutator-like element ( MULE ) superfamily was the most prevalent, accounting for 57.6 % of all TIR clusters. Furthermore, we uncovered extensive, previously uncharacterized intraspecific diversity through a genome analysis of four crop species, suggesting that single reference genomes substantially underestimate transposon dynamics. When we examined the molecular innovations that enable transposon success, we observed that MULE -encoded transposases possessed hypervariable termini that interact with accessory proteins. Using the hyperactive maize ( Zea mays ) MuDR element as a model, we obtained direct in vivo and in vitro evidence of an interaction between the transposase MURA and the accessory protein MURB, mapping the critical binding site to the N terminus of MURA. This atlas offers critical insights into transposon–host coevolution and provides a rich, species-specific toolkit for plant biotechnology.","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"7 1","pages":"100009-100009"},"PeriodicalIF":0.0,"publicationDate":"2025-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147330337","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

Multi-trait improvement of sorghum: co-expression of bar, mcry1Ab, and mvip3A enhances herbicide tolerance and pest resistance. 高粱多性状改良：bar、mcry1Ab和mvip3A共表达增强抗除草剂和抗虫能力

IF 5 4区农林科学

aBIOTECH Pub Date : 2025-11-21 eCollection Date: 2026-03-01 DOI: 10.1016/j.abiote.2025.100013

Xuan Liu, JiangTao Yang, Yuxin Cui, Xiaochun Zhang, Xujing Wang, Zhixing Wang

{"title":"Multi-trait improvement of sorghum: co-expression of bar, mcry1Ab, and mvip3A 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":"https://doi.org/10.1016/j.abiote.2025.100013","url":null,"abstract":"Sorghum (Sorghum bicolor) 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 mcry1Ab and mvip3A and the bar gene in sorghum using Agrobacterium-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 Ostrinia furnacalis, Mythimna separata, and Spodoptera frugiperda. 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.","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"7 1","pages":"100013"},"PeriodicalIF":5.0,"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}

引用次数: 0

quota_Anchor: a strand and whole genome duplication-aware collinear gene identification tool. quota_Anchor：一个链和全基因组复制感知共线基因鉴定工具。

IF 5 4区农林科学

aBIOTECH Pub Date : 2025-11-17 eCollection Date: 2026-03-01 DOI: 10.1016/j.abiote.2025.100008

Xiaodong Li, Yan Zhang, Rui Zhang, Zhiyu Liu, Jiquan Xue, Baoxing Song

{"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":"https://doi.org/10.1016/j.abiote.2025.100008","url":null,"abstract":"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.","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"7 1","pages":"100008"},"PeriodicalIF":5.0,"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}

引用次数: 0

BacPhase: Long-insert paired-end sequencing for bin marker construction and genome phasing. BacPhase：用于bin标记构建和基因组分期的长插入对端测序。

IF 5 4区农林科学

aBIOTECH Pub Date : 2025-11-17 eCollection Date: 2026-03-01 DOI: 10.1016/j.abiote.2025.100012

Yinqiao Jian, Xiao Guo, Yangyang Shang, Yu Yang, Daofeng Dong, Xiaohui Yang, Guangcun Li

{"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":"https://doi.org/10.1016/j.abiote.2025.100012","url":null,"abstract":"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 (Solanum tuberosum 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 (Saccharum officinarum), and alfalfa (Medicago sativa).","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"7 1","pages":"100012"},"PeriodicalIF":5.0,"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}

引用次数: 0

Genetic regulation of rice minor vein patterning by the OsIDD14/12/13 protein complex. OsIDD14/12/13蛋白复合物对水稻小叶脉形成的遗传调控。

IF 5 4区农林科学

aBIOTECH Pub Date : 2025-11-17 eCollection Date: 2026-03-01 DOI: 10.1016/j.abiote.2025.100010

Haoshu Li, Liying Zhang, Jingke Wang, Huanglei Tang, Zhiguo Zhang, Tiegang Lu, Xuehui Sun

{"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":"https://doi.org/10.1016/j.abiote.2025.100010","url":null,"abstract":"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 OsPIN5c in rice (Oryza sativa), 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. In situ hybridization and GUS reporter assays revealed that OsIDD14 expression is restricted to the rice vasculature. The osidd12 osidd13 osidd14 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 OsPIN5c expression and inhibits minor vein formation. Ectopic expression of OsIDD14 rescued the phenotypes of the osidd12 osidd13 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.","PeriodicalId":53135,"journal":{"name":"aBIOTECH","volume":"7 1","pages":"100010"},"PeriodicalIF":5.0,"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}

引用次数: 0

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