数字农科院2.0

Large DNA and protein language models enhance discovery of deleterious mutations in maize

文献类型： 外文期刊

作者： Yiru Wang; Cheng He; Qiqi Wang; Rui Li; Yang Qin; Hongwu Wang; Mingyue Gou; Xuebin Zhang; Huiyong Li; Quansheng Huang; Xinfang Liu; Jinliang Yang; Frank F. White; Junjie Fu; Sanzhen Liu; Jun Zheng

关键词： Zea mays; Genome assembly; Mutation; EMS

期刊名称： GENOME BIOLOGY

ISSN： 1474-760X

年卷期： 2025 年

页码：

收录情况： SCIE（2025版）

摘要： Background The maize inbred line Chang7-2 and derived lines are important male donors for hybrid production, contributing significantly to the development of high-yield and stress-tolerant hybrids. Additionally, Chang7-2 serves as a valuable model inbred line for genetic and genomic studies, facilitating the discovery of genes underlying hybrid vigor and other agronomic traits. Results Here, a reference genome assembly and a chemical-induced mutant population (N = 1,716) through ethyl methyl sulfonate (EMS) treatments are generated using Chang7-2. Each EMS line is whole genome sequenced and compared to the Chang7-2 genome, identifying 2,586,769 mutations with 4,939 mutations causing premature stop codons or altered splicing sites. The effect estimation of mutations using two large language artificial intelligence (AI) models, namely the protein language model ESM1b and the DNA language model PlantCaduceus, reveals 15,264 and 18,326 deleterious mutations, respectively. Mutation effects estimated with AI models accelerate revelation of four causal mutations underlying phenotypes of albino leaf, reduced cuticular wax, altered seed color, and male sterility. In addition, allelic expression quantification of genic mutations in 13 EMS M1 lines and their M2 heterozygous progeny, which contain both wildtype and mutant alleles, shows that mutant alleles are overall accumulated at a lower level compared to wildtype. Such allelic disparity is observed for some synonymous mutations, indicating they may not be biologically inconsequential. Conclusions AI-based estimation of mutation effects offers cross-species evidence for functional impacts of mutations. Our study demonstrates its application in revealing deleterious EMS mutations and identifying causal mutations responsible for mutant phenotypes.

分类号：

  • 相关文献

[1]Generation And Characterization Of A F.oxtail Millet (Setaria Italica) M utant Library. Zhang, Zhiguo,Chen, Zhenhua,Chen, Bing,Lu, Tiegang,Cui, Xuean,Ngoc Sinh Luu,Sun, Jing,Wu, Jinxia. 2019

[2]Construction of a high-density mutant population of Chinese cabbage facilitates the genetic dissection of agronomic traits. Xiaoxue Sun1,3, Xing Li2,3, Yin Lu1,3, Shan Wang1,3, Xiaomeng Zhang1,3, Kang Zhang2,3, Xiangjie Su1, Mengyang Liu1, Daling Feng1, Shuangxia Luo1, Aixia Gu1, Yu Fu2, Xueping Chen1, Shuxin Xuan1, Yanhua Wang1, Donghui Xu2, Shumin Chen2, Wei Ma1,*, Shuxing Shen1,*, Feng Cheng2,* and Jianjun Zhao1,*. 2022

[3]An Ems Mutant Library For C.ucumber. Chen, C, Cui, QZ, Huang, SW, Wang, SH, Liu, XH, Lu, XY, Chen, HM, Tian, Y. 2018

[4]Fast Construction Of A Reference G.enome: Challenges And Opportunities U sing 'Royal Gala' Apple As A Case Study. Cong, P.,Chagne, D.,Deng, C. H.,Zhang, C.,Bus, V.,Yao, J. -L.,Sullivan, S.,Tian, Y.,Liachko, I.,Gardiner, S. E.,Gleave, A.. 2018

[5]The Complete Chloroplast Genome Of B.iondia Insignis Tsiang (Apocynaceae). Zhang, Rui,Guan, Min. 2019

[6]Genome Assembly and Transcriptome Analysis of the Fungus Coniella diplodiella During Infection on Grapevine (Vitis vinifera L.). Ruitao Liu,Yiming Wang,Peng Li,Lei Sun,Jianfu Jiang,Xiucai Fan,Chonghuai Liu,Ying Zhang. 2021

[7]Chromosome-Level Genome Assembly Of Aldrichina Grahami, A Forensically Important Blowfly. Meng, FM, Liu, ZY, Han, H, Finkelbergs, D, Jiang, YS, Zhu, MF, Wang, Y, Sun, ZY, Chen, C, Guo, YD, Cai, JF. 2020

[8]Structural Variation During Dog Domestication: I.nsights From Gray Wolf A nd Dhole Genomes. Zhang, Shao-Jie,Zhang, Ya-Ping,Zhang, Ya-Ping,Zhao, Wenming,Zhang, Shao-Jie,Zhang, Bing,Yin, Ting-Ting,Yin, Ting-Ting,Wang, Zechong,Wang, Xuan,Wang, Xuan,Wang, Xiaobo,Wang, Lu,Wang, Junlong,Wang, Junlong,Wang, Guo-Dong,Wang, Guo-Dong,Shao, Xiu-Juan,Ruan, Jue,Cao, Xue,Liu, Yan-Hu,Liu, Yan-Hu,Wang, Lu,Bai, Bing,Bai, Bing,Lu, Yan. 2019

[9]De Novo Genome Assembly And C.omparative Genomics Of The B arley Leaf Rust Pathogen Puccinia Hordei Identifies Candidates For Three Avirulence Genes. Dodds, Peter,Upadhyaya, Narayana M.,Zhou, Qian,Dong, Chongmei,Zhang, Peng,Park, Robert F.,Chen, Jiapeng,Wu, Jingqin. 2019

[10]Chromosome‐level reference genome assembly provides insights into aroma biosynthesis in passion fruit ( Passiflora edulis ). Dongna Ma,Shanshan Dong,Shengcheng Zhang,Xiuqing Wei,Qingjun Xie,Qiansu Ding,Rui Xia,Xingtan Zhang. 2021

[11]Genus-Wide Characterization of Bumblebee Genomes Provides Insights into Their Evolution and Variation in Ecological and Behavioral Traits. Cheng Sun,Jiaxing Huang,Yun Wang,Xiaomeng Zhao,Long Su,Gregg W C Thomas,Mengya Zhao,Xingtan Zhang,Irwin Jungreis,Manolis Kellis,Saverio Vicario,Igor V Sharakhov,Semen M Bondarenko,Martin Hasselmann,Chang N Kim,Benedict Paten,Luca Penso-Dolfin,Li Wang,Yuxiao Chang,Qiang Gao,Ling Ma,Lina Ma,Zhang Zhang,Hongbo Zhang,Huahao Zhang,Livio Ruzzante,Hugh M Robertson,Yihui Zhu,Yanjie Liu,Huipeng Yang,Lele Ding,Quangui Wang,Dongna Ma,Weilin Xu,Cheng Liang,Michael W Itgen,Lauren Mee,Gang Cao,Ze Zhang,Ben M Sadd,Matthew W Hahn,Sarah Schaack,Seth M Barribeau,Paul H Williams,Robert M Waterhouse,Rachel Lockridge Mueller. 2021

[12]A chromosome-scale genome and transcriptomic analysis of the endangered tropical tree Vatica mangachapoi (Dipterocarpaceae). Liang Tang,Xuezhu Liao,Luke R Tembrock,Song Ge,Zhiqiang Wu. 2022

[13]Integrating genome assembly, structural variation map construction and GWAS reveal the impact of SVs on agronomic traits of Brassica napus. Nian Wang,Xianshuai Song,Lieqiong Kuang,Ze Tian,Kaifeng Wang,Keqi Li,Lan Ge,Yu Wu,Xinfa Wang,Xiaoling Dun,Hanzhong Wang. 2025

[14]Structural variation in Heinong 531 soybean genome underlies yield and resistance traits. Yu Tian,Jia You,Zihao Zheng,Hao Zhang,Shiyu Guo,Xueqing Wang,Jinrong Li,Lichun Huang,Jiajun Wang,Ying-hui Li,Li-juan Qiu. 2025

[15]Nicosulfuron-Resistant Amaranthus Retroflexus L. In N.ortheast China. Wei, Shouhui,Chen, Jinyi,Zhang, Chaoxian,Huang, Zhaofeng,Huang, Hongjuan,Chen, Jingchao. 2019

[16]Identification Of Substitutions And Small I.nsertion-Deletions Induced By Carbon-Ion B eam Irradiation In Arabidopsis Thaliana. Luo, Wenlong,Mu, Jinhu,Du, Yan,Cui, Tao,Cui, Tao,Luo, Shanwei,Li, Wenjian,Luo, Shanwei,Mu, Jinhu,Li, Xin,Zhou, Libin,Chen, Xia,Yu, Lixia,Yang, Jiangyan,Shu, Qingyao,Feng, Hui,Guo, Tao,Feng, Hui,Chen, Xia,Chen, Yuze. 2017

[17]Isolation And Characteristics Of The A.rkansas-Type Infectious Bronchitis Virus I n China. Han, ZX, Jiang, L, Zhao, WJ, Chen, YQ, Xu, LW, Sun, JF, Zhao, Y, Liu, SW. 2018

[18]Topoisomerase Mutations Are Associated With H.igh-Level Ciprofloxacin Resistance In S taphylococcus Saprophyticus, Enterococcus Faecalis And Escherichia Coli Isolated From Ducks. Ji, G, Chen, QW, Gong, XW, Zheng, FY, Li, SD, Liu, YS. 2018

[19]Two Residues In Nsp9 Contribute T.o The Enhanced Replication A nd Pathogenicity Of Highly Pathogenic Porcine Reproductive And Respiratory Syndrome Virus. Zhao, K, Gao, JC, Xiong, JY, Guo, JC, Yang, YB, Jiang, CG, Tang, YD, Tian, ZJ, Cai, XH, Tong, GZ, An, TQ. 2018

[20]First report of molecular basis of resistance to imazethapyr in common lambsquarters (Chenopodium album). Zhaofeng Huang, Xinxin Zhou, Chaoxian Zhang, Cuilan Jiang, Hongjuan Huang, Shouhui Wei. 2020

作者其他论文 更多>>