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Brachypodium distachyon has emerged as a pivotal model system for deciphering the complex agronomic traits of temperate grasses, owing to its compact genome, short life cycle, and high phylogenetic affinity with Triticeae crops. This article systematically reviews the core advances in Brachypodium functional genomics over the past years and their applications in cereal breeding. First, we elucidate the evolution from a single reference genome to a pangenome atlas, alongside innovations in efficient genetic transformation and multiplex CRISPR/Cas9 genome editing toolkits. These breakthroughs have laid a robust foundation for high-throughput gene function analysis. Second, we highlight key mechanistic discoveries in three core areas: (1)dissecting the ferulic acid cross-linking network of the unique grass Type II cell wall to guide biomass energy improvement; (2)revealing the CBF-dependent cold acclimation and ABA-mediated drought signaling pathways to elucidate the environmental adaptation mechanisms of “cool-season” grasses; and (3)serving as a plant pathology model to decipher defense networks against fungal diseases such as wheat rust and Fusarium head blight. Finally, we discuss the potential and pathways for utilizing Brachypodium as a “rapid prototyping platform” to accelerate precision design breeding in crops like wheat and barley, in the context of integrating synthetic biology and artificial intelligence.

, authors=Meiting Du^{1, 2}, Huize Chen^{1, 2}, authorsList=Meiting Du, Huize Chen, authorCompany=null, correspAuthors=Huize Chen, authorNote=null, correspAuthorsNote=null, copyrightStatement=null, copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=null, magXml=null, pdfUrl=null, pdf=null, pdfFileSize=null, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=null, mapNumber=null, fund=null), CN=ArticleExt(id=1319244646673396617, articleId=1319244646249771911, tenantId=1146029695717560320, journalId=1303687221787852879, language=CN, title=二穗短柄草功能基因组学研究进展及育种应用, columnId=1305133119284212678, journalTitle=麦类作物学报, columnName=遗传育种, runingTitle=null, highlight=null, articleAbstract=

二穗短柄草凭借其基因组精简、生命周期短及与麦类作物高度的亲缘关系，已成为解析温带禾本科植物复杂农艺性状的模式植物。本文系统综述了近年来二穗短柄草功能基因组学的核心进展及其在麦类育种中的应用。首先，阐述了该物种从单一参考基因组向泛基因组图谱的演进，以及高效遗传转化与多靶点CRISPR/Cas9基因编辑工具集的革新，这些突破为高通量基因功能解析奠定了坚实基础。其次，重点总结了二穗短柄草三大核心领域的发现：一是解析禾本科特有的II型细胞壁阿魏酸交联网络；二是揭示CBF依赖的冷驯化与ABA介导的抗旱信号通路，阐明“冷季型”草类的环境适应机制；三是作为病理学模型，解析麦类锈病、赤霉病等真菌病害的防御网络。最后，展望了在合成生物学与人工智能融合背景下，利用二穗短柄草作为“快速原型平台”加速小麦、大麦等作物精准设计育种的潜力与路径。

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