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Forensic Sciences Research 2022年第2期7卷 189-195页

作者： Jing Liu Ziwei Ye Zheng Wang Xing Zou Guanglin He Mengge Wang Shouyu Wang Yiping Hou Institute of Forensic Medicine West China School of Basic Medical Sciences&Forensic MedicineSichuan UniversityChengduChina

With the characteristics of low mutation rate,length variation and short amplicon size,insertion/deletion polymorphisms(indels)have the advantages of both short tandem repeats(STRs)and single nucleotide polymorphisms(SNPs).Herein,people of two ethnicities from Hainan Island were genotyped for the first time using the Investigator DIPplex kit.We investigated the forensic parameters of the 30 indels and the phylogenetic relationships among different populations.The accumulated powers of discrimination and powers of exclusion were 0.9999999999646 and 0.9897 in the Hainan Han population and 0.9999999999292 and 0.9861 in the Hainan Li population,respectively.Additionally,population comparisons among geographically,ethnically and linguistically diverse populations via cluster heatmap,multidimensional scaling,principal component analysis,phylogenetic tree and STRUCTURE analyses demonstrated that the Hainan Han population had genetic similarities to the other Han,She and Tujia populations,while the Hainan Li population had close genetic relationships to the Zhuang and Miao groups;both populations had a high degree of genetic differentiation from most Turkic-speaking populations.Aforementioned results suggested that the 30 autosomal indels are highly polymorphic and informative,which are suitable for human identification and population genetics.

关键词： Forensic sciences forensic genetics indels Investigator DIPplex kit Hainan Han Hainan Li

Research Progress of Genomic Variation in Psoriasis

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International Journal of Dermatology and Venereology 2022年第4期5卷 207-212页

作者： Liang-Dan Sun Department of Dermatology No.1 HospitalAnhui Medical UniversityHefeiAnhui 230022China Institute of Dermatology Anhui Medical UniversityHefeiAnhui 230032China Key Laboratory of Dermatology Anhui Medical UniversityMinistry of EducationHefeiAnhui 230032China.

As a typical representative of global complex diseases,psoriasis has attracted widespread attention because of its high heritability,heterogeneity,and incidence.Environmentally induced activation of the inflammatory-immune axis in patients with psoriasis relies on genetic regulation of genomic variation.The heritability of psoriasis exceeds 80%,and research of genomic variation in psoriasis is of great significance to the interpretation of the biological pathogenesis of the disease.The development of genome-wide association studies(GWASs)has provided a powerful means for the capture of psoriasis susceptibility genes.More than 100 psoriasis susceptibility loci have been captured,enabling humans to gain a breakthrough understanding of the genetics and traits of psoriasis.With the advancement of research methods,increasingly more genetic methodologies are being used to capture the locations and types of variants outside the scope of GWAS scanning,making up for the inclinations and deficiencies of traditional GWAS capture of gene loci in a more detailed manner.This review covers several decades of research on genomic variation in psoriasis,including GWASs in psoriasis,the capture of functional gene variant types,and the translation of genomic variation into precision medicine;summarizes the research progress of genomic variation in psoriasis;and provides a theoretical reference for future genetic-based research of the mechanisms underlying psoriasis.

关键词： psoriasis genomic variation functional structural variation indels precision medicine

Developing Exon-Primed Intron-Crossing （EPIC） markers for population genetic studies in three Aedes disease vectors

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Insect Science 2015年第3期22卷 409-423页

作者： Vanessa Linley White Nancy Margaret Endersby Janice Chan Ary Anthony Hoffmann Andrew Raymond Weeks Department of Genetics Bio21 Institute the University of Melbourne Victoria 3010 Australia

Aedes aegypti, Aedes notoscriptus, and Aedes albopictus are important vectors of many arboviruses implicated in human disease such as dengue fever. Genetic markers applied across vector species can provide important information on population structure, gene flow, insecticide resistance, and taxonomy, however, robust microsatellite markers have proven difficult to develop in these species and mosquitoes generally. Here we consider the utility and transferability of 15 Ribosome protein （Rp） Exon-Primed Intron- Crossing （EPIC） markers for population genetic studies in these 3 Aedes species. Rp EPIC markers designed for Ae. aegypti also successfully amplified populations of the sister species, Ae. albopictus, as well as the distantly related species, Ae. notoscriptus. High SNP and good indel diversity in sequenced alleles plus support for amplification of the same regions across populations and species were additional benefits of these markers. These findings point to the general value of EPIC markers in mosquito population studies.

关键词： Aedes aegypti Aedes albopictus Aedes notoscriptus Exon-Primed Intron- Crossing （EPIC） indels Ribosome protein （Rp） SNPs

基于38-plex indels的青海地区三个族群遗传推断

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中国法医学杂志 2021年第1期36卷 47-51页

作者：王庆国韩俊萍唐广峰张金科谢何鑫赵慧李唐松黄有为孙文平赵蕾山东第一医科大学山东济南250000 公安部物证鉴定中心法医遗传学公安部重点实验室北京市现场物证检验工程技术研究中心现场物证溯源技术国家工程实验室北京100038 北京市公安局朝阳分局刑事侦查支队北京100025 泰安市公安局刑事科学技术研究所山东泰安271000

目的基于38-plex indels族群推断体系研究青海地区汉族、回族及撒拉族的族群成分与遗传结构。方法使用38-plex indels复合扩增体系检测3个族群的220份样本并获取indels位点分型,利用主成分分析、STRUCTURE聚类分析及系统发育树综合分析... 详细信息

目的基于38-plex indels族群推断体系研究青海地区汉族、回族及撒拉族的族群成分与遗传结构。方法使用38-plex indels复合扩增体系检测3个族群的220份样本并获取indels位点分型,利用主成分分析、STRUCTURE聚类分析及系统发育树综合分析族群之间的遗传关系,使用族群推断软件DAA v1.0(DNA Ancestry Analyzer,DAA)对220份样本的族群来源进行分析,并与已知样本信息来源对比,计算体系推断结果的准确性。结果主成分分析和STRUCTURE聚类分析结果显示青海地区汉族、回族及撒拉族主要族群成分为东亚(占90%以上);系统发育树显示青海地区汉族、回族及撒拉族与其他东亚族群的亲缘关系较近,聚为一支;除4份样本祖先来源被归为欧亚混合族群外,其余样本祖先来源均为东亚或不排除东亚,推断准确率达95.24%以上。结论青海地区汉族、回族及撒拉族均为东亚族群,且青海地区回族和撒拉族相较青海地区汉族有着更近的遗传关系,使用38-plex indels族群推断体系对青海地区汉族、回族及撒拉族进行遗传推断,结果可靠。

关键词：法医物证学 indels 族群来源推断 DAA族群推断软件

同羊尾脂相关基因indels检测及其与尾脂和生长性状的关联分析

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同羊尾脂相关基因InDels检测及其与尾脂和生长性状的关联分析

作者：袁婷婷西北农林科技大学

学位级别：硕士

同羊是一种脂尾型绵羊品种,通过尾部脂肪沉积以满足其在恶劣环境下的正常生长发育。近年来,随着饲养条件的改善,脂尾型绵羊尾部沉积过量的脂肪对自身已无太大意义,还会造成自身的饲料转化率低、肉品质低下等。因此,脂尾型绵羊的瘦尾化... 详细信息

同羊是一种脂尾型绵羊品种,通过尾部脂肪沉积以满足其在恶劣环境下的正常生长发育。近年来,随着饲养条件的改善,脂尾型绵羊尾部沉积过量的脂肪对自身已无太大意义,还会造成自身的饲料转化率低、肉品质低下等。因此,脂尾型绵羊的瘦尾化改良已成为养殖户的迫切需求。随着基因组研究水平和动物分子育种技术的提升,为同羊肥尾改良及分子育种过程提供相关理论依据。Adipocytokine（脂肪细胞因子）信号通路中的瘦素受体（Leptinreceptor,LEPR）与过氧化物酶体增殖物激活受体辅激活因子1A（promoter of peroxisome proliferators-activated receptor-γcoactivator 1A,PPARGC1A）和PPAR信号通路中的脂肪和肥胖相关基因（fat mass and obesity associated gene,FTO）、血小板衍生生长因子D（Recombinant Platelet Derived Growth Factor D,PDGFD）、脂滴包被蛋白（perilipin1,PLIN1）、解偶联蛋白2（Uncoupling protein 2,UCP2）和肿瘤相关抗原1（Ewing tumor-associated antigen 1,ETAA1）等基因与绵羊尾部脂肪沉积有一定相关性,均直接或间接地参与了绵羊尾部脂肪的分解代谢过程。为了验证上述基因的多态与同羊尾脂及生长性状之间的关系,本研究以同羊（166只）为研究对象,通过Ensemble数据库筛选LEPR、PPARGC1A、FTO、PDGFD、PLIN1、UCP2和ETAA1等基因的插入/缺失（indels）位点,根据筛选的多态位点设计相应的引物,利用PCR扩增、琼脂糖凝胶电泳和测序等技术进行indels位点验证,对存在的indels位点进行个体分型,并将分型结果与同羊尾脂及生长性状进行关联分析。旨在研究上述基因多态与同羊尾脂及生长性状之间的相关性,为绵羊尾脂相关基因在同羊分子育种中的应用提供理论依据,进而为同羊尾型选育及品种改良提供重要参考。研究结果如下:1.同羊LEPR基因检测到1个InDel位点,该InDel位点II基因型的母羊腰角宽显著高于DD基因型（P＜0.05）;DD基因型的公羊体高和背高显著大于II基因型（P＜0.05）,DD基因型的公羊荐高和胸深显著高于ID基因型（P＜0.05）。2.同羊PPARGC1A基因验证出1个InDel位点,该位点DD基因型的母羊体高和背高显著高于II基因型（P＜0.05）,II和ID基因型的公羊臀端高显著大于DD基因型（P＜0.05）。3.同羊PLIN1基因存在1个InDel位点,该位点II基因型的母羊背高显著高于ID和DD基因型（P＜0.05）。4.同羊UCP2基因验证出2个indels位点,存在4种单倍型。该基因indels位点对同羊尾脂及生长性状均无显著影响（P＞0.05）。5.同羊ETAA1基因存在1个InDel位点,该InDel位点处II基因型的公羊臀端宽显著高于DD基因型（P＜0.05）。6.同羊PDGFD基因共验证出3个indels位点,其中InDel-1位点ID基因型的母羊尾长相较于II基因型显著增加（P＜0.05）,InDel-3位点DD基因型的母羊尾长显著大于ID基因型（P＜0.05）;InDel-2位点ID基因型的母羊体高和体长相较于DD基因型显著增加（P＜0.05）,ID基因型的母羊胸深显著高于II和DD基因型（P＜0.05）;公羊InDel-2位点中,II和ID基因型个体的体高、胸深、背高和头长相较于DD基因型显著增加（P＜0.05）,在公羊的荐高性状上,ID基因型相较于DD基因型表现为优势基因型（P＜0.05）。7.同羊FTO基因共验证出了10个indels位点,其中InDel-5位点中DD基因型的母羊尾宽相较于ID基因型显著增加（P＜0.05）,ID基因型的公羊尾长显著高于DD基因型（P＜0.05）;InDel-4位点II和DD基因型的公羊尾长均显著大于ID基因型（P＜0.05）;InDel-6位点II基因型的公羊尾宽显著高于DD基因型（P＜0.05）;InDel-9位点ID基因型的母羊尾宽相较于II基因型显著增大（P＜0.05）,DD基因型的公羊尾宽显著高于ID和II基因型（P＜0.05）。FTO基因多态位点与同羊生长性状关联分析结果表明,同羊FTO基因InDel-1多态位点、InDel-2多态位点、InDel-3多态位点、InDel-4多态位点、InDel-5多态位点、InDel-6多态位点、InDel-8多态位点等对同羊的生长性状均具有显著的影响（P＜0.05）。综上所述,同羊FTO和PDGFD两个基因共6个多态位点对同羊尾脂均具有显著的影响（P＜0.05）,可作为同羊肥尾改良及分子育种过程中的重要候选基因。此外,FTO、PDGFD、PLIN

关键词：同羊 indels 尾脂生长性状关联分析

Active motif finder-a bio-tool based on mutational structures in DNA sequences

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The Journal of Biomedical Research 2011年第6期25卷 444-448页

作者： Mani Udayakumar Palaniyandi Shanmuga-priya Kamalakannan Hemavathi Rengasamy Seenivasagam Department of Bioinformatics School of Chemical and Biotechnology Shanmugha Arts Science Technology & Research Academy (SASTRA University) Tanjore Tamilnadu 613402 India Division of Drug Discovery and Development Centre of Molecular and Computational Biology Department of Botany St. Joseph College Bangalore Karnataka 560027 India

Active Motif Finder （AMF） is a novel algorithmic tool, designed based on mutations in DNA sequences. Tools available at present for finding motifs are based on matching a given motif in the query sequence. AMF describes a new algorithm that identifies the occurrences of patterns which possess all kinds of mutations like insertion, deletion and mismatch. The algorithm is mainly based on the Alignment Score Matrix （ASM） computation by com paring input motif with full length sequence. Much of the effort in bioinformatics is directed to identify these motifs in the sequences of newly discovered genes. The proposed bio-tool serves as an open resource for analysis and useful for studying polymorphisms in DNA sequences. AMF can be searched via a user-friendly interface. This tool is intended to serve the scientific community working in the areas of chemical and structural biology, and is freely available to all users, at http：//www.***.edu/scbt/amf/.

关键词： mutations alignment score matrix back track indels pattern occurrence DNA sequences.

Genomic variation in size is major due to indels in chloroplast genomes in Gossypium

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Genomic variation in size is major due to indels in chloropl...

Completed chloroplast genome sequences of five Gossypium species:genomic variation in size is mainly due to indels

第十四届全国植物基因组学大会

作者： Zhiwen Chen Pengbo Li Qin Xu Jinping Hua Department of Plant Genetics and Breeding College of Agronomy and BiotechnologyKey Laboratory of Crop Heterosis and Utilization of Ministry of EducationBeijing Key Laboratory of Crop Genetic ImprovementChina Agricultural University Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau of Ministry of Agriculture Institute of Cotton ResearchShanxi Academy of Agricultural Sciences

Cotton(Gossypium spp.) is a model system for evolution analysis in which consists of 8 diploid sub-genome groups A,B,C,D,E,F,G,K and a tetraploid sub-genome group AD.Plant chloroplast genomes offer irreplaceable molec... 详细信息

关键词： cotton chloroplast genome sizes indels

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Completed chloroplast genome sequences of five Gossypium spe...

Gene editing for corneal disease management

第十四届全国植物基因组学大会

作者： Pengbo Li Zhiwen Chen Jinping Hua Department of Plant Genetics and Breeding College of Agronomy and BiotechnologyKey Laboratory of Crop Heterosis and Utilization of Ministry of EducationBeijing Key Laboratory of Crop Genetic ImprovementChina Agricultural University

Cotton(Gossypium spp.) is a model system for analysis of plant chloroplast genomes size,owning 8 different genome groups,A,B,C,D,E,F,G,K.To better understand the molecular basis of Gossypium chloroplast genome sizes from different groups,we characterized 5 completed cotton diploid chloroplast(cp) genome sequences,G. capitis-viridis,G.robinsonii,G.somalense,G.areysianum,G.incanum,obtained from

关键词： cotton chloroplast genome sizes indels

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World Journal of Translational Medicine 2016年第1期5卷 1-13页

作者： Sudhanshu P Raikwar Apoorva S Raikwar Shyam S Chaurasia Rajiv R Mohan Department of Veterinary Medicine and Surgery College of Veterinary MedicineUniversity of Missouri Harry S.Truman Memorial Veterans’ Hospital Department of Microbiology Roy J.and Lucille A.Carver College of MedicineUniversity of Iowa Mason Eye Institute School of MedicineUniversity of Missouri Ophthalmology and Molecular Medicine One-health One-Medicine Ophthalmology and Vision ResearchUniversity of Missouri

Gene editing has recently emerged as a promising technology to engineer genetic modifications precisely in the genome to achieve long-term relief from corneal disorders.Recent advances in the molecular biology leading to the development of clustered regularly interspaced short palindromic repeats(CRISPRs) and CRISPR-associated systems,zinc finger nucleases and transcription activator like effector nucleases have ushered in a new era for high throughput in vitro and in vivo genome engineering.Genome editing can be successfully used to decipher complex molecular mechanisms underlying disease pathophysiology,develop innovative next generation gene therapy,stem cell-based regenerative therapy,and personalized medicine for corneal and other ocular diseases.In this review we describe latest developments in the field of genome editing,current challenges,and future prospects for the development of personalized genebased medicine for corneal diseases.The gene editing approach is expected to revolutionize current diagnostic and treatment practices for curing blindness.

关键词： Adeno-associated virus Clustered Regularly-Interspaced Short Palindromic Repeats associated protein 9 Cornea Clustered regularly interspaced short palindromic repeat Double strand breaks Gene editing sgRNA Gene targeting Homology directed repair Homologous recombination indels Lentiviral vector Protospacer-adjacent motif Transcription activator like effector nucleases Zinc finger nucleases

Genetic Analysis of Selected Mutants of Cowpea (<i>Vigna unguiculata</i>[L.] Walp) Using Simple Sequence Repeat and <i>rcb</i>L Markers

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American Journal of Plant Sciences 2018年第13期9卷 2728-2756页

作者： Festus Olakunle Olasupo Christopher Olumuyiwa Ilori Esther Adekemi Stanley Temitope Esther Owoeye David Okeh Igwe Department of Crop Protection and Environmental Biology University of Ibadan Ibadan Nigeria Plant Breeding Section Cocoa Research Institute of Nigeria Ibadan Nigeria Bioscience Centre International Institute of Tropical Agriculture Ibadan Nigeria Department of Genomics and Bioinformatics BIODEC National Biotechnology Development Agency Abuja Nigeria Department of Biotechnology Ebonyi State University Abakaliki Nigeria Department of Natural Sciences Bowie State University Bowie MD USA

Genetic diversity evaluation of mutant lines is essential to facilitate their conservation and utility in breeding programs. Characterization of plant genotypes using morphological markers has limitations which make the procedure inefficient. Application of molecular tools for characterization and diversity assessment has been found useful to complement phenotypic evaluation of plant population. Therefore genetic diversity of some cowpea mutant lines was studied using simple sequence repeats (SSR) markers. DNA barcoding marker, ribulose-1,5-bisphosphate carboxylase(rbcL) of the chloroplast DNA (cpDNA) was also used for characterization and identification of the mutants to species level. The mean polymorphic information content (0.51) obtained from the microsatellites showed high polymorphism in accessing wide genetic diversity among the mutants and their parents. Dendrogram generated revealed 8 groups with most mutants clustered separately from their parents. Sequence analysis revealed insertions/deletions (indels) and base substitutions as the two main classes of mutations induced in the plastid DNA of the mutants studied. The nucleotide frequencies were 26.95% (A), 34.43% (T), 24.09% (C) and 14.53% (G). A total of 61.38% AT rich region was identified, while GC rich region was found to be 38.62%. Highest rate of mutations were observed in region 3 - 4 indicating that the region is less conserved in cowpea rbcL gene. The present study proved that SSR markers are useful for the genetic diversity assessment of cowpea mutants. It also proved the efficiency of rbcL markers in mutants’ identification. The results indicate that the mutants are valuable genetic resources that have been developed to widen cowpea genetic base.

关键词： Cowpea Mutants Genetic Diversity rbcL Gene Sequence Analysis indels Point Mutation