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[学术文献 ] Advances in haplotype phasing and genotype imputation 进入全文
Nature Reviews Genetics
Haplotype phasing — to determine which genetic variants reside on the same chromosome — and genotype imputation — to infer unobserved genotypes — have become indispensable steps to improve genome coverage for genomic analyses such as genome-wide association studies. Several tools exist for haplotype phasing and genotype imputation, all of which have continuously evolved to accommodate the increasing sample sizes of genomic studies and rapidly improving sequencing technologies. To fully leverage these recent advances, researchers must deliberate several practical considerations, including tool choice, quality control filters, data privacy concerns and reference panel choice. Looking ahead, long-read sequencing technologies are poised to bring novel opportunities to this field and drive methodological development.
[学术文献 ] Non-model bacteria as platforms for endogenous gene expression in synthetic biology 进入全文
Nature Reviews Bioengineering
Microbial synthetic biology seeks to engineer bacterial genomes for industrial and biomedical applications, typically by applying heterologous gene expression in well-characterized model organisms, such as Escherichia coli. However, heterologous gene expression might cause metabolic disruptions, thereby impacting production efficiency and yield. In this Review, we highlight non-model organisms, such as Lacticaseibacillus and pseudomonads, for endogenous compound production, taking advantage of their evolutionary optimization for the production of certain metabolites and proteins. We first outline key limitations of heterologous production and then examine endogenous production pathways in non-model organisms for biotechnological and therapeutic applications. In particular, multi-omics approaches enable the discovery and characterization of these organisms, and phage-based genome refactoring enhances genome engineering capabilities. Finally, we outline key bottlenecks in the application of non-model organisms in biotechnology, including scale-up, costs and safety.
[前沿资讯 ] Spuds of the future: Buba AI’s role in transforming potato breeding for sustainability 进入全文
PotatoNewsToday
一款名为 Buba AI 的智能平台正在以数据驱动方式重塑马铃薯育种流程，目标是提升品种在气候变化与病害压力下的适应性与可持续性。该项目源自 CIP（国际马铃薯中心）2024 AI-griculture Challenge Hackathon，并于 2025年5月23日 获得“作物改良”赛道优胜。报道指出，传统马铃薯育种需要多年表型鉴定、杂交与多季田间试验，周期长、成本高。Buba AI 通过引入预测建模与数据驱动决策，在早期即识别潜力组合，用以减少试错并提高选择效率；文章称该平台有望将新品种育成时间缩短约30%—50%。在技术路径上，Buba AI 围绕性状优化引擎、气候适应建模、病害抗性预测与情景化性能仿真四大能力展开：一方面利用遗传数据、环境变量与历史育种结果优化目标性状组合；另一方面结合未来气候情景与病原数据（如晚疫病、普通疮痂）进行抗性与稳产性评估，并对不同农生态区进行产量与适应性模拟。报道还提到，该平台提供可视化界面与潜在API对接，支持与 CIP 数据库联通，便于低资源环境的育种团队协同使用。文章进一步提到，Buba AI 的设计思路与黑客松“增强种质选择”任务相关，可能通过 NLP 补全研究文献与报告中的性状缺失条目，以改善数据完整性；并展望后续与 CIP 基因库请求系统集成、在合作国家开展试点，以及纳入无人机影像、基因组测序等数据源以提升预测精度。据报道，Buba 团队成员包括 Shadrack Odikara 与 Meshak Emakunat，其开发与落地将得到 CIP 网络的合作与支持。文章将该平台定位为将“经验艺术”转化为“数据科学”的代表性工具，期望在保障粮食安全与小农减投入方面发挥作用。
[前沿资讯 ] Record-breaking edition PotatoEurope Netherlands 2025: The international potato industry comes together in Lelystad 进入全文
Potatoworld magazine
PotatoEurope 2025于2025年9月3–4日在荷兰莱利斯塔德WUR Open Crops举办，吸引17,268名参观者、覆盖107个国家，创历届之最，现场成为全球马铃薯产业链交流与技术展示的中心。活动设置25公顷示范田（品种 Alegria），在理想收获条件下完成从 收获—装箱—光学分选 的全流程演示，其中 现场光学分选 为首次加入的亮点，试验区还集中展示了 品种、施肥与植保 等方面的实用创新。开幕由国王专员 Arjen Gerritsen、Janine Luten（NAO）、Richard Harrison（WUR） 与主办方 Kuno Jacobs（DLG Benelux）共同主持。创新奖评选结果：一等奖授予Croptimal — Croptiscan 9000（田间选择机器人，搭载相机与 AI，可在田间识别Y病毒、卷叶病毒及细菌性病害，预计2026年交付）；二等奖为BioScout（与 WUR 合作的 实时晚疫病孢子监测 智能捕捉系统）；三等奖为Maxstim Furrow Treatment（沟施型生物刺激剂）。同期会议聚焦产业前沿：WUR 大会 “Integrated Crop Management – The future of potato farming”深入讨论作物多样性、品种选择、土壤管理、靶向植保；商务会议 “The Position of Europe in a Changing Potato World” 关注欧洲在变局中的地位。整场活动实现从 机械制造—种植—育种—加工—政策 的全链条参与，Case IH 作为演示拖拉机赞助方。下一届PotatoEurope将于2026年9月9–10日 在德国举办。
[学术文献 ] Constructing synthetic nuclear architectures via transcriptional condensates in a DNA protonucleus 进入全文
Nature Communications
Nuclear biomolecular condensates are essential sub-compartments within the cell nucleus and play key roles in transcription and RNA processing. Bottom-up construction of nuclear architectures in synthetic settings is non-trivial but vital for understanding the mechanisms of condensates in real cellular systems. Here, we present a facile and versatile synthetic DNA protonucleus (PN) platform that facilitates localized transcription of branched RNA motifs with kissing loops (KLs) for subsequent condensation into complex condensate architectures. We identify salinity, monomer feeding, and KL-PN interactions as key parameters to control co-transcriptional condensation of these KLs into diverse artificial nuclear patterns, including single and multiple condensates, interface condensates, and biphasic condensates. Over time, KL transcripts co-condense with the PN matrix, with the final architecture determined by their interactions, which can be precisely modulated using a short DNA invader strand that outcompetes these interactions. Our findings deepen the understanding of RNA condensation in nuclear environments and provide strategies for designing functional nucleus-mimetic systems with precise architectural control.
[科研项目 ] "Deutschlands größtes Kartoffelforschungsprojekt gestartet: POMORROW – Potatoes for tomorrow" 进入全文
Gemeinschaft zur Förderung von Pflanzeninnovation e.V.德国植物促进创新学会
POMORROW—“Potatoes for tomorrow”项目于2025年5月启动，周期4年（至2029年5月），被称为德国最大的马铃薯研究项目。项目由联邦层面资助，总额约470万欧元，由Projektträger Jülich管理，隶属“面向气候与立地条件的现代育种研究”计划。项目旨在提升马铃薯的气候适应性与生产性能。核心任务包括：对位于Groß Lüsewitz、由IPK管理的德国外源基因库（北部分藏）材料实施全量基因分型；对遗传上独特的材料进行高通量测序并纳入国际马铃薯泛基因组；据此建立600份核心种质，其中300份进入表型鉴定，重点性状涵盖抗旱、养分利用效率、主要病虫害（晚疫病、病毒、叶蝉类）抗性以及块茎营养品质（如蛋白质含量）。在遗传解析与育种导入方面，项目利用关联遗传学定位目标性状位点，供企业通过杂交与选择导入育种流程；并针对德国新发/再现问题（如Schilf-Glasflügelzikade与马铃薯卷叶病毒）寻找抗性供体。技术创新侧重两点：一是CRISPR基因组编辑，在无需繁琐回交的前提下向优势（精英）品种定点导入新性状；二是基因组预测（Genomic Prediction），使小效应遗传信息也能高效转化为育种增益。参与机构包括JKI、IPK、明斯特大学IBBP、马普分子植物生理研究所、盖森海姆大学等科研单位；SaKa（总体协调：Dr. Vanessa Prigge）、Europlant、Norika及GFPi等产业伙伴参与；科学协调为Prof. Dr. Benjamin Stich（JKI）。
