Molecular Plant最新文献_第8页

Graph-based pangenome provides insights into structural variations and genetic basis of metabolic traits in potato. 基于图谱的泛基因组为马铃薯代谢性状的结构变异和遗传基础提供了新的思路。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-04-07 Epub Date: 2025-01-27 DOI: 10.1016/j.molp.2025.01.017

Xiaoling Zhu, Rui Yang, Qiqi Liang, Yuye Yu, Tingting Wang, Li Meng, Ping Wang, Shaoyang Wang, Xianping Li, Qiongfen Yang, Huachun Guo, Qijun Sui, Qiang Wang, Hai Du, Qin Chen, Zhe Liang, Xuewei Wu, Qian Zeng, Binquan Huang

{"title":"Graph-based pangenome provides insights into structural variations and genetic basis of metabolic traits in potato.","authors":"Xiaoling Zhu, Rui Yang, Qiqi Liang, Yuye Yu, Tingting Wang, Li Meng, Ping Wang, Shaoyang Wang, Xianping Li, Qiongfen Yang, Huachun Guo, Qijun Sui, Qiang Wang, Hai Du, Qin Chen, Zhe Liang, Xuewei Wu, Qian Zeng, Binquan Huang","doi":"10.1016/j.molp.2025.01.017","DOIUrl":"10.1016/j.molp.2025.01.017","url":null,"abstract":"Potato is the world's most important nongrain crop. In this study, to assess genetic diversity within the Petota section, 29 genomes from Petota and Etuberosum sections were newly de novo assembled and 248 accessions of wild potatoes, landraces, and modern cultivars were re-sequenced at >25× depth. Subsequently, a graph-based pangenome was constructed using DM8.1 as the backbone, integrating194,330 nonredundant structural variants. To characterize the metabolome of tubers and illuminate the genomic basis of metabolic traits, LC-MS/MS was employed to obtain the metabolome of 157 accessions, and 9,321 structural variants (SVs) were detected to be significantly associated with 1,258 distinct metabolites via PAV (presence and absence variations)-based metabolomics-GWAS analysis, including metabolites of flavonoids, phenolic acids, and phospholipids. To facilitate the utilization of pangenome resources, a comprehensive platform, the Potato Pangenome Database (PPDB), was developed. Our study provides a comprehensive genomic resource for dissecting the genomic basis of agronomic and metabolic traits in potato, which will accelerate functional genomics studies and genetic improvements in potato.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"590-602"},"PeriodicalIF":17.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143052868","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

SuperDecode: An integrated toolkit for analyzing mutations induced by genome editing. SuperDecode：一个用于分析基因组编辑引起的突变的集成工具包。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-04-07 Epub Date: 2025-03-04 DOI: 10.1016/j.molp.2025.03.002

Fuquan Li, Xiyu Tan, Shengting Li, Shaotong Chen, Lin Liu, Jingjing Huang, Gufeng Li, Zijun Lu, Jinwen Wu, Dongchang Zeng, Yanqiu Luo, Xiaoou Dong, Xingliang Ma, Qinlong Zhu, Letian Chen, Yao-Guang Liu, Chengjie Chen, Xianrong Xie

{"title":"SuperDecode: An integrated toolkit for analyzing mutations induced by genome editing.","authors":"Fuquan Li, Xiyu Tan, Shengting Li, Shaotong Chen, Lin Liu, Jingjing Huang, Gufeng Li, Zijun Lu, Jinwen Wu, Dongchang Zeng, Yanqiu Luo, Xiaoou Dong, Xingliang Ma, Qinlong Zhu, Letian Chen, Yao-Guang Liu, Chengjie Chen, Xianrong Xie","doi":"10.1016/j.molp.2025.03.002","DOIUrl":"10.1016/j.molp.2025.03.002","url":null,"abstract":"Genome editing using CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) or other systems has become a cornerstone of numerous biological and applied research fields. However, detecting the resulting mutations by analyzing sequencing data remains time consuming and inefficient. In response to this issue, we designed SuperDecode, an integrated software toolkit for analyzing editing outcomes using a range of sequencing strategies. SuperDecode comprises three modules, DSDecodeMS, HiDecode, and LaDecode, each designed to automatically decode mutations from Sanger, high-throughput short-read, and long-read sequencing data, respectively, from targeted PCR amplicons. By leveraging specific strategies for constructing sequencing libraries of pooled multiple amplicons, HiDecode and LaDecode facilitate large-scale identification of mutations induced by single or multiplex target-site editing in a cost-effective manner. We demonstrate the efficacy of SuperDecode by analyzing mutations produced using different genome editing tools (CRISPR/Cas, base editing, and prime editing) in different materials (diploid and tetraploid rice and protoplasts), underscoring its versatility in decoding genome editing outcomes across different applications. Furthermore, this toolkit can be used to analyze other genetic variations, as exemplified by its ability to estimate the C-to-U editing rate of the cellular RNA of a mitochondrial gene. SuperDecode offers both a standalone software package and a web-based version, ensuring its easy access and broad compatibility across diverse computer systems. Thus, SuperDecode provides a comprehensive platform for analyzing a wide array of mutations, advancing the utility of genome editing for scientific research and genetic engineering.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"690-702"},"PeriodicalIF":17.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143567749","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A genomic variation map provides insights into potato evolution and key agronomic traits. 基因组变异图提供了对马铃薯进化和关键农艺性状的深入了解。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-04-07 Epub Date: 2025-01-23 DOI: 10.1016/j.molp.2025.01.016

Qun Lian, Yingying Zhang, Jinzhe Zhang, Zhen Peng, Weilun Wang, Miru Du, Hongbo Li, Xinyan Zhang, Lin Cheng, Ran Du, Zijian Zhou, Zhenqiang Yang, Guohui Xin, Yuanyuan Pu, Zhiwen Feng, Qian Wu, Guochao Xuanyuan, Shunbuer Bai, Rong Hu, Sónia Negrão, Glenn J Bryan, Christian W B Bachem, Yongfeng Zhou, Ruofang Zhang, Yi Shang, Sanwen Huang, Tao Lin, Jianjian Qi

{"title":"A genomic variation map provides insights into potato evolution and key agronomic traits.","authors":"Qun Lian, Yingying Zhang, Jinzhe Zhang, Zhen Peng, Weilun Wang, Miru Du, Hongbo Li, Xinyan Zhang, Lin Cheng, Ran Du, Zijian Zhou, Zhenqiang Yang, Guohui Xin, Yuanyuan Pu, Zhiwen Feng, Qian Wu, Guochao Xuanyuan, Shunbuer Bai, Rong Hu, Sónia Negrão, Glenn J Bryan, Christian W B Bachem, Yongfeng Zhou, Ruofang Zhang, Yi Shang, Sanwen Huang, Tao Lin, Jianjian Qi","doi":"10.1016/j.molp.2025.01.016","DOIUrl":"10.1016/j.molp.2025.01.016","url":null,"abstract":"Hybrid potato breeding based on diploid inbred lines is transforming the way of genetic improvement of this staple food crop, which requires a deep understanding of potato domestication and differentiation. In the present study, we resequenced 314 diploid wild and landrace accessions to generate a variome map of 47,203,407 variants. Using the variome map, we discovered the reshaping of tuber transcriptome during potato domestication, characterized genome-wide differentiation between landrace groups Stenotomum and Phureja. We identified a jasmonic acid biosynthetic gene possibly affecting the tuber dormancy period. Genome-wide association studies revealed a UDP-glycosyltransferase gene for the biosynthesis of anti-nutritional steroidal glycoalkaloids (SGAs), and a Dehydration Responsive Element Binding (DREB) transcription factor conferring increased average tuber weight. In addition, genome similarity and group-specific SNP analyses indicated that tetraploid potatoes originated from the diploid Solanum tuberosum group Stenotomum. These findings shed light on the evolutionary trajectory of potato domestication and improvement, providing a solid foundation for advancing hybrid potato-breeding practices.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"570-589"},"PeriodicalIF":17.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143040156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

NTRC's novel role: Bridging chloroplast redox oscillations and nuclear circadian clock. NTRC的新作用：连接叶绿体氧化还原振荡和核生物钟。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-04-07 Epub Date: 2025-03-03 DOI: 10.1016/j.molp.2025.03.003

Francisco Javier Cejudo

引用次数: 0

A comprehensive omics resource and genetic tools for functional genomics research and genetic improvement of sorghum. 高粱功能基因组学研究和遗传改良的综合组学资源和遗传工具。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-04-07 Epub Date: 2025-03-07 DOI: 10.1016/j.molp.2025.03.005

Chengxuan Chen, Fengyong Ge, Huilong Du, Yuanchang Sun, Yi Sui, Sanyuan Tang, Zhengwei Shen, Xuefeng Li, Huili Zhang, Cuo Mei, Peng Xie, Chao Li, Sen Yang, Huimin Wei, Jiayang Shi, Dan Zhang, Kangxu Zhao, Dekai Yang, Yi Qiao, Zuyong Luo, Li Zhang, Aimal Khan, Baye Wodajo, Yaorong Wu, Ran Xia, Chuanyin Wu, Chengzhi Liang, Qi Xie, Feifei Yu

{"title":"A comprehensive omics resource and genetic tools for functional genomics research and genetic improvement of sorghum.","authors":"Chengxuan Chen, Fengyong Ge, Huilong Du, Yuanchang Sun, Yi Sui, Sanyuan Tang, Zhengwei Shen, Xuefeng Li, Huili Zhang, Cuo Mei, Peng Xie, Chao Li, Sen Yang, Huimin Wei, Jiayang Shi, Dan Zhang, Kangxu Zhao, Dekai Yang, Yi Qiao, Zuyong Luo, Li Zhang, Aimal Khan, Baye Wodajo, Yaorong Wu, Ran Xia, Chuanyin Wu, Chengzhi Liang, Qi Xie, Feifei Yu","doi":"10.1016/j.molp.2025.03.005","DOIUrl":"10.1016/j.molp.2025.03.005","url":null,"abstract":"Sorghum, the fifth most important food crop globally, is a source of silage forage, fiber, syrup, and biofuel. Moreover, it is widely recognized as an ideal model crop for studying stress biology becaused of its ability to tolerate multiple abiotic stresses, including high salt-alkali conditions, drought, and heat. However, functional genomics studies on sorghum have been challenging, primarily due to the limited availability of genetic resources and effective genetic transformation techniques. In this study, we developed the Sorghum Genomics and Mutation Database (SGMD), aiming to advance the genetic understanding of sorghum. Our effort encompassed a telomere-to-telomere genome assembly of an inbred sorghum line, E048, yielding 729.46 Mb of sequence data representing the complete genome. Alongside the high-quality sequence data, a gene expression atlas covering 13 distinct tissues was developed. We constructed a saturated ethyl methane sulfonate mutant library comprising 13,226 independent mutants. Causal genes in chlorosis and leafy mutants from the library were easily identified by leveraging the MutMap and MutMap+ methodologies, demonstrating the powerful application of this library for identifying functional genes. To facilitate sorghum research, we performed whole-genome sequencing of 179 M2 mutant lines, resulting in 2,291,074 mutations that covered 97.54% of all genes. In addition, an Agrobacterium-mediated sorghum transformation platform was established for gene function studies. In summary, this work establishes a comprehensive platform and provides valuable resources for functional genomics investigations and genetic improvement of sorghum.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"703-719"},"PeriodicalIF":17.1,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

DNA damage triggers heritable alterations in DNA methylation patterns in Arabidopsis. DNA损伤引发拟南芥DNA甲基化模式的遗传改变

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-03 Epub Date: 2025-01-24 DOI: 10.1016/j.molp.2025.01.019

Jinchao Li, Wenjie Liang, Xin-Qiang He, Weiqiang Qian

{"title":"DNA damage triggers heritable alterations in DNA methylation patterns in Arabidopsis.","authors":"Jinchao Li, Wenjie Liang, Xin-Qiang He, Weiqiang Qian","doi":"10.1016/j.molp.2025.01.019","DOIUrl":"10.1016/j.molp.2025.01.019","url":null,"abstract":"It has been hypothesized that DNA damage has the potential to induce DNA hypermethylation, contributing to carcinogenesis in mammals. However, there is no sufficient evidence to support that DNA damage can cause genome-wide DNA hypermethylation. In this study, we demonstrated that DNA single-strand breaks with 3' blocked ends (DNA 3' blocks) not only can reinforce DNA methylation at normally methylated loci but also can induce DNA methylation at normally nonmethylated loci in plants. The CG and CHG hypermethylation tend to localize within gene bodies, with a significant proportion being de novo generated. In contrast, the CHH hypermethylation is concentrated in centromeric and pericentromeric regions, primarily being reinforced methylation. Mechanistically, DNA 3' blocks regulate the DREAM complex to induce CG and CHG methylation. Moreover, they utilize the RdDM pathway to induce CHH hypermethylation. Intriguingly, repair of DNA damage or blocking the DNA damage response can fully abolish CHH hypermethylation and partially rescue CHG hypermethylation but rarely alter CG hypermethylation, indicating that DNA damage-induced symmetric DNA methylation can serve as a form of genetic imprinting. Collectively, these results suggest that DNA damage is an important force driving the emergence and evolution of genomic DNA methylation levels and patterns in plants.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"501-512"},"PeriodicalIF":17.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143040166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The plant retromer components SNXs bind to ATG8 and CLASP to mediate autophagosome movement along microtubules. 植物逆转录成分SNXs与ATG8和CLASP结合介导自噬体沿微管运动。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-03 Epub Date: 2024-12-24 DOI: 10.1016/j.molp.2024.12.013

Yanglan Liao, Xibao Li, Wenlong Ma, Xinyi Lin, Jiayi Kuang, Xuanang Zheng, Zien Li, Fanfan Qiao, Chuanliang Liu, Jun Zhou, Faqiang Li, Ruixi Li, Byung-Ho Kang, Hongbo Li, Caiji Gao

{"title":"The plant retromer components SNXs bind to ATG8 and CLASP to mediate autophagosome movement along microtubules.","authors":"Yanglan Liao, Xibao Li, Wenlong Ma, Xinyi Lin, Jiayi Kuang, Xuanang Zheng, Zien Li, Fanfan Qiao, Chuanliang Liu, Jun Zhou, Faqiang Li, Ruixi Li, Byung-Ho Kang, Hongbo Li, Caiji Gao","doi":"10.1016/j.molp.2024.12.013","DOIUrl":"10.1016/j.molp.2024.12.013","url":null,"abstract":"In eukaryotic cells, autophagosomes are double-membrane vesicles that are highly mobile and traffic along cytoskeletal tracks. While core autophagy-related proteins (ATGs) and other regulators involved in autophagosome biogenesis in plants have been extensively studied, the specific components regulating plant autophagosome motility remain elusive. In this study, using TurboID-based proximity labeling, we identify the retromer subcomplex comprising sorting nexin 1 (SNX1), SNX2a, and SNX2b as interacting partners of ATG8. Remarkably, SNX proteins decorate ATG8-labeled autophagosomes and facilitate their coordinated movement along microtubules. Depletion of SNX proteins restricts the motility of autophagosomes in the cytoplasm, resulting in decreased autophagic flux. Furthermore, we show that the microtubule-associated protein CLASP is a bridge, connecting the SNX-ATG8-decorated autophagosomes to the microtubules. Genetically, the clasp-1 mutant phenotype resembles that of plants with disrupted SNXs or microtubule networks, displaying diminished autophagosome motility and reduced autophagic flux. Collectively, our study unveils a hitherto unanticipated role of the SNXs subcomplex in connecting autophagosomes with microtubules to promote autophagosome mobility in Arabidopsis.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"416-436"},"PeriodicalIF":17.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142885951","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Reevaluating statistical methods in metabolomic studies: A case for Spearman's correlation. 代谢组学研究中统计方法的重新评估：一个Spearman相关的案例。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-03 Epub Date: 2024-12-24 DOI: 10.1016/j.molp.2024.12.014

Yoshiyasu Takefuji

引用次数: 0

Activation and memory of the heat shock response is mediated by prion-like domains of sensory HSFs in Arabidopsis. 拟南芥热休克反应的激活和记忆是由感觉hsf的朊蛋白样结构域介导的。

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-03 Epub Date: 2025-01-09 DOI: 10.1016/j.molp.2025.01.007

Maolin Peng, Katja E Jaeger, Yunlong Lu, Zhuping Fan, Wei Zeng, Arun Sampathkumar, Philip A Wigge

{"title":"Activation and memory of the heat shock response is mediated by prion-like domains of sensory HSFs in Arabidopsis.","authors":"Maolin Peng, Katja E Jaeger, Yunlong Lu, Zhuping Fan, Wei Zeng, Arun Sampathkumar, Philip A Wigge","doi":"10.1016/j.molp.2025.01.007","DOIUrl":"10.1016/j.molp.2025.01.007","url":null,"abstract":"Plants are able to sense and remember heat stress. An initial priming heat stress enables plants to acclimate so that they are able to survive a subsequent higher temperature. The heat shock transcription factors (HSFs) play a crucial role in this process, but the mechanisms by which plants sense heat stress are not well understood. By comprehensively analyzing the binding targets of all the HSFs, we found that HSFs act in a network, with upstream sensory HSFs acting in a transcriptional cascade to activate downstream HSFs and protective proteins. The upstream sensory HSFs are activated by heat at the protein level via a modular prion-like domain (PrD) structure. PrD1 enables HSF sequestration via chaperone binding, allowing release under heat shock. Activated HSFs are recruited into transcriptionally active foci via PrD2, enabling the formation of DNA loops between heat-responsive promoters and enhancer motifs, boosting gene expression days after a priming heat stress. The ability of HSFs to respond rapidly to heat via a protein phase-change response is likely a conserved mechanism in eukaryotes.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"457-467"},"PeriodicalIF":17.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142952128","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

GEFormer: A genotype-environment interaction-based genomic prediction method that integrates the gating multilayer perceptron and linear attention mechanisms. 整合门控机制MLP和线性注意机制的玉米基因型-环境互作基因组预测方法GEFormer

IF 17.1 1区生物学

Molecular Plant Pub Date : 2025-03-03 Epub Date: 2025-01-28 DOI: 10.1016/j.molp.2025.01.020

Zhou Yao, Mengting Yao, Chuang Wang, Ke Li, Junhao Guo, Yingjie Xiao, Jianbing Yan, Jianxiao Liu

{"title":"GEFormer: A genotype-environment interaction-based genomic prediction method that integrates the gating multilayer perceptron and linear attention mechanisms.","authors":"Zhou Yao, Mengting Yao, Chuang Wang, Ke Li, Junhao Guo, Yingjie Xiao, Jianbing Yan, Jianxiao Liu","doi":"10.1016/j.molp.2025.01.020","DOIUrl":"10.1016/j.molp.2025.01.020","url":null,"abstract":"The integration of genotypic and environmental data can enhance genomic prediction accuracy for crop field traits. Existing genomic prediction methods fail to consider environmental factors and the real growth environments of crops, resulting in low genomic prediction accuracy. In this work, we developed GEFormer, a genotype-environment interaction genomic prediction method that integrates gating multilayer perceptron (gMLP) and linear attention mechanisms. First, GEFormer uses gMLP to extract local and global features among SNPs. Then, Omni-dimensional Dynamic Convolution is used to extract the dynamic and comprehensive features of multiple environmental factors within each day, taking into consideration the real growth pattern of crops. A linear attention mechanism is used to capture the temporal features of environmental changes. Finally, GEFormer uses a gating mechanism to effectively fuse the genomic and environmental features. We examined the accuracy of GEFormer for predicting important agronomic traits of maize, rice, and wheat under three experimental scenarios: untested genotypes in tested environments, tested genotypes in untested environments, and untested genotypes in untested environments. The results showed that GEFormer outperforms six cutting-edge statistical learning methods and four machine learning methods, especially with great advantages under the scenario of untested genotypes in untested environments. In addition, we used GEFormer for three real-world breeding applications: phenotype prediction in unknown environments, hybrid phenotype prediction using an inbred population, and cross-population phenotype prediction. The results showed that GEFormer had better prediction performance in actual breeding scenarios and could be used to assist in crop breeding.","PeriodicalId":19012,"journal":{"name":"Molecular Plant","volume":" ","pages":"527-549"},"PeriodicalIF":17.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066845","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0