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Dual-extraction modeling:A multi-modal deeplearning architecture for phenotypic prediction and functional gene mining of complex traits

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Plant Communications 2024年第9期5卷 54-71页

作者： Yanlin Ren Chenhua Wu He Zhou Xiaona Hu Zhenyan Miao State Key Laboratory for Crop Stress Resistance and High-Efficiency Production Center of BioinformaticsCollege of Life SciencesNorthwest A&F UniversityYanglingShaanxi 712100China College of Chemistry&Pharmacy Northwest A&F UniversityYanglingShaanxi 712100China Key Laboratory of Biology and genetics Improvement of Maize in Arid Area of Northwest Region Ministry of AgricultureNorthwest A&F UniversityYanglingShaanxi 712100China

Despite considerable advances in extracting crucial insights from bio-omics data to unravel the intricate mechanisms underlying complex traits,the absence of a universal multi-modal computational tool with robust interpretability for accurate phenotype prediction and identification of trait-associated genes remains a *** study introduces the dual-extraction modeling(DEM)approach,a multi-modal deep-learning architecture designed to extract representative features from heterogeneous omics datasets,enabling the prediction of complex trait *** comprehensive benchmarking experiments,we demonstrate the efficacy of DEM in classification and regression prediction of complex *** consistently exhibits superior accuracy,robustness,generalizability,and ***,we establish its effectiveness in predicting pleiotropic genes that influence both flowering time and rosette leaf number,underscoring its commendable *** addition,we have developed user-friendly software to facilitate seamless utilization of DEM’s *** summary,this study presents a state-of-the-art approach with the ability to effectively predict qualitative and quantitative traits and identify functional genes,confirming its potential as a valuable tool for exploring the genetic basis of complex traits.

关键词： deep learning complex traits multi-omics phenotypic prediction gene mining

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genetic Resources,Breeding Programs in China,and gene mining of Peach:A Review

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Horticultural Plant Journal 2020年第4期6卷 205-215页

作者： Yong Li Lirong Wang Zhengzhou Fruit Research Institute Chinese Academy of Agricultural SciencesZhengzhou450009China

Research on peach genetic resources and breeding has achieved remarkable progress in recent decades,especially in *** this review,we first described the geographic distribution,ecology,phenotypes,and genetic diversity of peach landraces and wild relatives in *** also discussed the ***,breeding programs of peaches in China are summarized,including breeding history,breeding targets,breeding institutes,elite breeding materials,breeding solutions,and domestically bred representative ***,we reviewed the genes or loci that have been mined using both linkage mapping and genome wide association study(GWAS)as well as the evolutionary genetics and domestication history of the ***,we gave our perspectives and suggestions for future breeding in terms of breeding material selection and breeding technology innovation.

关键词： peach genetic resources landrace wild relatives breeding gene mining GWAS

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Enzyme annotation for orphan reactions and its applications in biomanufacturing

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Green Chemical Engineering 2023年第2期4卷 137-145页

作者： Zhen Zhang Chun Li Key Lab for Industrial Biocatalysis Ministry of EducationDepartment of Chemical EngineeringTsinghua UniversityBeijing100084China Center for Synthetic&Systems Biology Department of Chemical EngineeringTsinghua UniversityBeijing100084China

There are lots of biochemical reactions in the biosynthetic pathway without associated *** predicted by retro-biosynthetic tools are not assigned gene ***,non-natural reactions designed with novel functions also lack suitable *** these reactions can be categorized as orphan *** absence of protein-encoding genes in these orphan reactions limits their direct experimental *** tools have been developed to find candidate enzymes for these orphan ***,we discuss recent advances in these computational tools,including reaction similarity-based methods for calculating the substructural similarity between orphan reactions and known enzymatic reactions;sequence-based tools combine metabolic knowledge base and phenotypic information with genomic,transcriptomic,and metabolomic data to mine appropriate enzymes for orphan reactions;and approaches based on the creation of enzyme variants for orphan reactions as enzyme engineering modifications and de novo design of *** believe that our review will greatly facilitate the design of microbial cell factories and contribute to the development of the biomanufacturing field.

关键词： Enzyme annotation Orphan reactions Reaction similarity gene mining Computational enzyme design

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The design of aided software for osmotic stress responding genes mining in plant genome

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Journal of Northeast Agricultural University(English Edition) 2007年第3期14卷 256-259页

作者： LU Yanmin MENG Fanjiang LI Yong LIU Bei Engineering College Northeast Agricultural University Harbin 150030 China

A software and algorithm which based on random sequence model uses osmotic stress responding cis elements from existing information sources of biology was designed. It can infer the genic downstream function of Arabidopsis thaliana through analyzing its promoter region, and can offer effective aided analysis to mine osmotic stress responding genes in Arabidopsis thatiana genome. The practical application proves that this software can aid to analyze vast genic data and offer important data evidence.

关键词： plant genome bioinformatics gene mining P value

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Development and function analysis of SSR molecular markers in Glycyrrhiza inflata transcriptome

Development and function analysis of SSR molecular markers i...

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中国植物学会第十六次全国会员代表大会暨85周年学术年会

作者： Qian Xin Jiahui Lu Yue Wang Wenqing Cheng College of Life Sciences Shihezi University Key Laboratory of Xinjiang Phytomedicine Resources and Utilization Ministy of EducationShihezi University Institute of Licorice Shihezi University

Glycyrrhiza inflata *** most salt tolerance among three authentic medicinal licorices in *** mainly distributed arid,semi-arid and desert regions in Xinjiang and Gansu *** this study,a total of 7.31 Gb clean data and a total of 35,717 Unigenes including 1,272 novel transcripts were obtained from transcriptome sequencing on the Illumina HiSeqTM sequencing platform.A total of 7,660（30.06%） SSR-containing sequences and 10,738 simple sequence repeats（SSR） were identified from transcriptome ***（47.51%） and trinucleotidetype（47.6%） among them were the dominant ***,the dominant repeat types were AG/CT,GA/TC and GAA/*** distribution frequencies were 35.11%,31.77% and 9.98%.7,120 SSR-containing sequences were annotated by BLASTX.A total of 2813（36.72%） the annotated genes were mapped onto 117 pathway using the Kyoto Encyclopedia of genes（KEGG） *** representatives pathways were the metabolic pathways,biosynthesis of secondary metabolites,phytohormone signal transduction,carbon metabolism,and amino acid ***,74 primer pairs designed and synthesized were successfully amplified and 41 primer pairs were polymorphic in 14 samples from 4 species of *** to their high level of polymorphism and transferability,the SSR markers in the transcriptome of *** are valuable tools for the gene mining and germplasm conservation and phylogenetic study of Glycyrrhiza.

关键词： Glycyrrhiza inflata Bat transcriptome simple sequence repeat (SSR) function analysis gene mining phylogenetic

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