Scientia Agricultura Sinica ›› 2026, Vol. 59 ›› Issue (21): 4697-4709.doi: 10.3864/j.issn.0578-1752.2026.21.001

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Progress and Prospects of Crop Precision Breeding Based on uORF Editing

YU BuKa1(), TAN YuanYuan3, SHU QingYao1,2()   

  1. 1 College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058
    2 Hainan Institute of Zhejiang University, Sanya 572025, Hainan
    3 The New Countryside Development Institute of Zhejiang University, Hangzhou 310058
  • Received:2026-03-08 Accepted:2026-05-01 Online:2026-11-01 Published:2026-11-06
  • Contact: SHU QingYao

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Abstract:

Upstream open reading frames (uORFs) are key cis-acting elements in the 5′ untranslated region (5′UTR) of eukaryotic mRNAs, which play important roles in regulation of gene translation and ultimately phenotypes. uORFs mainly block scanning ribosomes through mechanisms like leaky scanning, translation reinitiation, ribosome stalling, or nonsense-mediated mRNA decay (NMD), which consequently inhibits the translation of the downstream main open reading frame (mORF). The strength of such inhibition depends heavily on specific uORF structural features, such as the sequence around its start codon and RNA secondary structures. The uORF-based translation regulation allows plants to quickly respond to environmental signals without changing transcription levels, playing a unique role in balancing normal growth with stress adaptation. Evolutionary analysis shows that beneficial uORFs are often kept by natural selection and highly conserved. Moreover, natural uORF sequence variations in plant populations can finely adjust the translation efficiency of target genes. This provides an important genetic basis for the diversity of stress responses and agronomic traits in crops. With the development of high-throughput omics technologies, the translation profiles of many functional uORFs have been accurately mapped, providing a solid data foundation for targeted editing. Compared to editing other regions like promoters or 3′UTRs, targeting uORFs has major advantages: lower pleiotropy, higher predictability, and no need to introduce foreign sequences. Various engineering strategies—such as changing uORF length, modifying Kozak sequences, and using environment-responsive uORFs—can be achieved using genome editing technologies like CRISPR/Cas9 and prime editing (PE). These fine-tuning strategies avoid the negative side effects often caused by traditional overexpression with strong promoters, allowing for a moderate increase in target gene expression. Precisely adjusting endogenous protein levels through uORF editing has great potential for crop improvement. This includes improving broad-spectrum disease resistance and stress tolerance, optimizing traits like the growth period, and increasing nutritional quality, such as vitamin content. To help establish an efficient precision crop breeding system based on uORF editing, this review explains the main characteristics and molecular mechanisms of uORFs, summarized current uORF editing strategies and progress in trait improvement. Also discussed are t future applications and challenges of uORF editing in precision crop breeding, and the prospect of using deep learning models to improve the efficiency and predictability of uORF editing.

Key words: uORF, translational regulation, gene editing, precision breeding, 5′UTR

Fig. 1

Classification of uORFs A: Classified based on the positional relationship between uORF and mORF; B: Classified based on whether the polypeptide encoded by uORF functions or not"

Fig. 2

The model of eukaryotic cap-dependent translation initiation and ribosome recycling The protein translation process can be divided into nine steps. (2) TC Formation: The eukaryotic translation initiation factor eIF2 binds with GTP and the initiator methionyl-tRNA (Met-tRNAi) to form the ternary complex (TC). (3) 43S PIC Formation: The TC recruits additional factors, including eIF1, eIF1A, eIF3, and eIF5, and binds to the 40S small subunit to assemble the 43S pre-initiation complex (43S PIC). (4)-(5) mRNA Activation & Attachment: The eIF4F complex (comprising the cap-binding protein eIF4E, the scaffold protein eIF4G, and the helicase eIF4A) recognizes and binds to the 5′cap structure of the mRNA. Facilitated by eIF4B and driven by ATP hydrolysis, the secondary structure at the 5′end of the mRNA is unwound, followed by the recruitment and attachment of the 43S PIC. (6) Scanning: The 43S PIC scans along the 5′untranslated region (5′UTR) of the mRNA in search of the start codon. (7) AUG Recognition & 48S Formation: Upon recognition of the start codon, the anticodon of the Met-tRNAi base-pairs with the AUG codon. This interaction triggers a conformational change and the release of eIF1, resulting in the formation of a stable 48S initiation complex. (8)-(9) Subunit Joining & 80S Formation: Mediated by eIF5B, the 60S large subunit joins the complex, facilitating the release of eIF2-GDP and other initiation factors. The process concludes with the assembly of a translationally competent 80S ribosome, which then proceeds to the elongation phase. (1) Termination and Recycling: When translation reaches the stop codon on the mRNA, the nascent peptide chain is released through the coordinated action of release factors (eRFs) and ABCE1. The 80S ribosome subsequently dissociates into 40S and 60S subunits, preparing for the next round of the translation cycle"

Fig. 3

Translation regulation of mORF by uORF A: Ribosome scanning on mRNA without a uORF; B: Ribosome scanning modes on mRNA with a uORF. (1): The ribosome skips the uORF, and the mORF is translated normally; (2)-(3): The ribosome successfully recognizes the uORF, leading to repressed mORF translation (2) or no mORF translation (3)"

Fig. 4

Key sequence features affecting uORF translational efficiency The schematic illustrates the regulation of ribosome scanning and translation initiation by uORFs and surrounding cis-acting elements within 5′UTR. Ribosomes enter at the 5′cap structure (m7G) and scan downstream. Key factors influencing uORF function and downstream mORF translation efficiency include: (1) the distance between the 5′cap and the uORF start site; (2) the number of uORFs; (3) the length of the uORF; (4) RNA secondary structures (e.g., hairpins) near the start site; (5) the strength of the Kozak context surrounding the uORF start codon; (6) the charge properties of the uORF-encoded nascent peptide (potentially causing ribosome stalling); (7) the presence of rare codons; (8) the strength of the stop codon; and (9) the intercistronic distance between the uORF stop site and the mORF start site. Collectively, these factors determine whether the ribosome translates the uORF, stalls at the uORF, triggers NMD, or successfully re-initiates translation at the downstream mORF"

Table 1

Comparison of uORF editing with other regulatory strategies"

调控策略
Regulatory strategy		 作用区域
Target region		 调控水平
Regulatory level		 作用机制
Mechanism of action		 参考文献
References
uORF编辑
uORF editing		 5′UTR 翻译水平
Translational		 消除uORF对下游mORF翻译抑制，增加核糖体对mORF的翻译
Eliminating uORF-mediated translational inhibition of the downstream mORF, thereby increasing ribosome recruitment and translation of the mORF		 [11]
启动子编辑
Promoter editing		 启动子
Promoter		 转录水平
Transcriptional		 破坏转录抑制因子结合位点，提高转录效率
Disrupting transcriptional repressor binding sites to enhance transcription efficiency		 [40]
3′UTR编辑
3′UTR editing		 3′UTR 转录后水平
Post-transcriptional		 敲除3′UTR负调控区域（通常包含 miRNA特异性识别的顺式元件或形成比较稳定RNA二级结构的区域）
Knocking out negative regulatory regions in the 3′UTR (typically containing cis-elements for specific miRNA recognition or regions forming stable RNA secondary structures)		 [41]
染色体结构重排
Chromosomal rearrangement		 基因组大片段
Large genomic segments		 转录水平
Transcriptional		 通过染色体的倒置或重复，让同一条染色体上的强启动子去驱动弱表达的基因
Leveraging chromosomal inversions or duplications to allow a strong promoter on the same chromosome to drive the expression of a weakly expressed target gene		 [42]

Fig. 5

Workflow of CRISPR/Cas9-based functional identification and editing of plant uORFs for breeding"

Table 2

Current main uORF databases and identification tools"

类别
Category		 数据库名称
Name of the database		 适用物种、输入数据
Applicable species or input data		 主要功能与特色
Main functions and features		 参考文献
References
鉴定工具
Identification tool		 ORFfinder 序列
Sequence		 NCBI的经典工具。常用于对5′UTR序列进行初步的ORF识别
A classic tool of NCBI. It is often used for the initial ORF scanning of 5′UTR sequences		 [49]
uORF-seqr Ribo-seq数据、RNA-seq数据、基因组注释文件
Ribo-seq data, RNA-seq data, genomic annotation files		 高效鉴定非AUG起始的近同密码子uORF，并给出每个uORF的显著性评估值
Efficiently identify near-similar codon uORFs that do not start with AUG, and provide a significance evaluation value for each uORF		 [50]
uORF4u 序列
Sequence		 支持原核生物预测其核糖体结合位点
Support the prediction of ribosome binding sites for prokaryotes		 [51]
数据库
Database		 uORFlight 拟南芥、水稻等
Arabidopsis thaliana, Oryza sativa, etc.		 可在种群尺度评估uORF出现频率，通过数据库挖掘，找出单核苷酸多态性或插入/缺失
By mining the database, it enables the evaluation of uORF occurrence frequencies at the population level and the identification of SNPs or InDels		 [52]
PsORF 拟南芥、棉花、水稻、玉米等
Arabidopsis thaliana, Gossypium spp., Oryza sativa, Zea mays, etc.		 植物小ORF库，包含uORF、dORF等共5类小ORF
Plant small ORF library. It includes five types of small ORFs such as uORF and dORF		 [53]
uORFdb 人、拟南芥等
Homo sapiens, Arabidopsis thaliana, etc.		 计算预测、试验文献与群体变异数据深度融合
The deep integration of computational prediction, experimental literature and population variation data		 [54]

Table 3

Main Engineering Strategies of uORF in crop breeding"

方法
Method		 物种
Species		 基因
Gene		 突变体性状
Mutant trait		 参考文献
References
缺失uORF
Delete uORF		 水稻O. sativa Hd2 延迟开花Delay flowering [46]
水稻O. sativa GLW7 改善粒型Improve grain shape [45]
水稻
O. sativa		 GW7 增加粒长和长宽比
Increased grain length and length/width ratio		 [45]
大麦H. vulgare Mla13 加快免疫应答Accelerate immune response [57]
生菜L. sativa GGP2 增加维生素C含量Increase vitamin C content [11]
拟南芥
A. thaliana		 bZIP11 消除蔗糖的抑制效应
Eliminate the inhibitory effect of sucrose		 [58]
生成uORF
Generate uORF		 水稻O. sativa Waxy 降低直链淀粉含量Reduce amylose content [59]
水稻O. sativa DLT 降低株高和分蘖数Reduce plant height and tiller numbers [60]
改变uORF长度
Change uORF length		 水稻O. sativa Hd2 延迟开花Delay flowering [46]
生菜L. sativa GGP1 增加维生素C含量Increase vitamin C content [11]
转换uORF种类
Switch uORF types		 水稻O. sativa GS2 增强抗病性Enhance disease resistance [61]
番茄Solanum lycopersicum RabGAP22 增强耐盐性Enhance salt tolerance [62]
改变uORF起始密码子上下文序列
Mutant uORF initiation codon context		 水稻O. sativa Waxy 降低直链淀粉含量Reduce amylose content [63]
番茄S. lycopersicum GGP1 增加维生素C含量Increase vitamin C content [64]
偶联环境响应型 uORF
Coupled environment-responsive uORF		 水稻O. sativa NPR1 抗病但正常生长Resistance but minimal fitness costs [55]
拟南芥A. thaliana snc1 抗病但正常生长Resistance but minimal fitness costs [55]
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