Short tandem repeats(STRs)modulate gene expression and contribute to trait variation.However,a systematic evaluation of the genomic characteristics of STRs has not been conducted,and their influence on gene expression...Short tandem repeats(STRs)modulate gene expression and contribute to trait variation.However,a systematic evaluation of the genomic characteristics of STRs has not been conducted,and their influence on gene expression in rice remains unclear.Here,we construct a map of 137,629 polymorphic STRs in the rice(Oryza sativa L.)genome using a population-scale resequencing dataset.A genome-wide survey encompassing 4726 accessions shows that the occurrence frequency,mutational patterns,chromosomal distribution,and functional properties of STRs are correlated with the sequences and lengths of repeat motifs.Leveraging a transcriptome dataset from 127 rice accessions,we identify 44,672 expression STRs(eSTRs)by modeling gene expression in response to the length variation of STRs.These eSTRs are notably enriched in the regulatory regions of genes with active transcriptional signatures.Population analysis identifies numerous STRs that have undergone genetic divergence among different rice groups and 1726 tagged STRs that may be associated with agronomic traits.By editing the(ACT)_(7) STR in OsFD1 promoter,we further experimentally validate its role in regulating gene expression and phenotype.Our study highlights the contribution of STRs to transcriptional regulation in plants and establishes the foundation for their potential use as alternative targets for genetic improvement.展开更多
为了评估内蒙古自治区呼和浩特汉族群体38个Y染色体短串联重复序列(Y-chromosomal short tandem repeat,Y-STR)的遗传多态性,探索其法医学应用价值及与国内其他群体的遗传关系,应用38个Y染色体遗传标记构成的复合扩增系统对随机选取的...为了评估内蒙古自治区呼和浩特汉族群体38个Y染色体短串联重复序列(Y-chromosomal short tandem repeat,Y-STR)的遗传多态性,探索其法医学应用价值及与国内其他群体的遗传关系,应用38个Y染色体遗传标记构成的复合扩增系统对随机选取的呼和浩特市272个无关汉族男性个体样本进行扩增,统计38个Y-STR基因座的等位基因频率和法医遗传学参数;基于Y染色体短串联重复序列单倍型数据库(Y-chromosomal short tandem repeat haplotype reference database,YHRD)纳入的国内各群体单倍型数据计算群体间的遗传距离(pairwise genetic distance,Rst),并在此基础上进行多维尺度分析(multidimensional scaling,MDS)。38个Y-STR基因座共检出333个等位基因,基因多样性值(gene diversity,GD)为0.0434~0.9675。共检出269种单倍型,其中3种单倍型出现2次。单倍型多样性(haplotype diversity,HD)和单倍型识别率(discrimination power,DC)分别为0.9999和0.9890。群体比较结果显示,呼和浩特汉族与陕西汉族等同一种族或地理位置毗邻的群体的遗传距离较小,即遗传关系较近,反之则遗传关系较远。研究选取的包含38个YSTR基因座的复合检测体系具有较高的遗传多态性,适合呼和浩特汉族群体的法医学分析和群体遗传学研究。展开更多
目的探讨低深度全基因组拷贝数变异测序(copy number variation sequencing,CNV-seq)联合短串联重复序列(short tandem repeat,STR)分型技术在早期稽留流产组织遗传学分析中的应用价值,明确流产病因,为优生优育提供指导。方法选取2023年...目的探讨低深度全基因组拷贝数变异测序(copy number variation sequencing,CNV-seq)联合短串联重复序列(short tandem repeat,STR)分型技术在早期稽留流产组织遗传学分析中的应用价值,明确流产病因,为优生优育提供指导。方法选取2023年9月至2025年4月在汕头大学医学院附属粤北人民医院确诊的155例早期稽留流产患者,采用CNV-seq与STR分型技术对流产组织进行遗传学检测,分析染色体异常类型及其与流产次数的相关性。结果染色体异常检出率:155例样本中检出染色体异常89例(57.4%),其中数目异常67例(75.3%),包括非整倍体58例(以16-三体最常见)、三倍体4例及嵌合体5例;染色体结构异常(>5Mb)致病性1例(1.1%);微缺失/微重复21例(23.6%),其中致病性拷贝数变异(pathogenic copy number variation,pCNV)3例和临床意义不明拷贝数变异(variant of uncertain significance copy number variation,VUS-CNV)18例。流产次数:流产次数≥2次组与<2次组的胚胎染色体数目异常率(44.9%比43.7%)及拷贝数变异率(25.6%比28.6%)均无统计学差异(P>0.05)。结论染色体异常是早期稽留流产的主要遗传学病因。CNV-seq联合STR分型技术可全面解析流产组织的遗传学异常,为临床遗传咨询及再生育决策提供精准依据。展开更多
基金supported by the National Natural Science Foundation of China(32172010)the Major Program of Guangdong Basic and Applied Basic Research(2019B030302006).
文摘Short tandem repeats(STRs)modulate gene expression and contribute to trait variation.However,a systematic evaluation of the genomic characteristics of STRs has not been conducted,and their influence on gene expression in rice remains unclear.Here,we construct a map of 137,629 polymorphic STRs in the rice(Oryza sativa L.)genome using a population-scale resequencing dataset.A genome-wide survey encompassing 4726 accessions shows that the occurrence frequency,mutational patterns,chromosomal distribution,and functional properties of STRs are correlated with the sequences and lengths of repeat motifs.Leveraging a transcriptome dataset from 127 rice accessions,we identify 44,672 expression STRs(eSTRs)by modeling gene expression in response to the length variation of STRs.These eSTRs are notably enriched in the regulatory regions of genes with active transcriptional signatures.Population analysis identifies numerous STRs that have undergone genetic divergence among different rice groups and 1726 tagged STRs that may be associated with agronomic traits.By editing the(ACT)_(7) STR in OsFD1 promoter,we further experimentally validate its role in regulating gene expression and phenotype.Our study highlights the contribution of STRs to transcriptional regulation in plants and establishes the foundation for their potential use as alternative targets for genetic improvement.
文摘为了评估内蒙古自治区呼和浩特汉族群体38个Y染色体短串联重复序列(Y-chromosomal short tandem repeat,Y-STR)的遗传多态性,探索其法医学应用价值及与国内其他群体的遗传关系,应用38个Y染色体遗传标记构成的复合扩增系统对随机选取的呼和浩特市272个无关汉族男性个体样本进行扩增,统计38个Y-STR基因座的等位基因频率和法医遗传学参数;基于Y染色体短串联重复序列单倍型数据库(Y-chromosomal short tandem repeat haplotype reference database,YHRD)纳入的国内各群体单倍型数据计算群体间的遗传距离(pairwise genetic distance,Rst),并在此基础上进行多维尺度分析(multidimensional scaling,MDS)。38个Y-STR基因座共检出333个等位基因,基因多样性值(gene diversity,GD)为0.0434~0.9675。共检出269种单倍型,其中3种单倍型出现2次。单倍型多样性(haplotype diversity,HD)和单倍型识别率(discrimination power,DC)分别为0.9999和0.9890。群体比较结果显示,呼和浩特汉族与陕西汉族等同一种族或地理位置毗邻的群体的遗传距离较小,即遗传关系较近,反之则遗传关系较远。研究选取的包含38个YSTR基因座的复合检测体系具有较高的遗传多态性,适合呼和浩特汉族群体的法医学分析和群体遗传学研究。
文摘目的探讨低深度全基因组拷贝数变异测序(copy number variation sequencing,CNV-seq)联合短串联重复序列(short tandem repeat,STR)分型技术在早期稽留流产组织遗传学分析中的应用价值,明确流产病因,为优生优育提供指导。方法选取2023年9月至2025年4月在汕头大学医学院附属粤北人民医院确诊的155例早期稽留流产患者,采用CNV-seq与STR分型技术对流产组织进行遗传学检测,分析染色体异常类型及其与流产次数的相关性。结果染色体异常检出率:155例样本中检出染色体异常89例(57.4%),其中数目异常67例(75.3%),包括非整倍体58例(以16-三体最常见)、三倍体4例及嵌合体5例;染色体结构异常(>5Mb)致病性1例(1.1%);微缺失/微重复21例(23.6%),其中致病性拷贝数变异(pathogenic copy number variation,pCNV)3例和临床意义不明拷贝数变异(variant of uncertain significance copy number variation,VUS-CNV)18例。流产次数:流产次数≥2次组与<2次组的胚胎染色体数目异常率(44.9%比43.7%)及拷贝数变异率(25.6%比28.6%)均无统计学差异(P>0.05)。结论染色体异常是早期稽留流产的主要遗传学病因。CNV-seq联合STR分型技术可全面解析流产组织的遗传学异常,为临床遗传咨询及再生育决策提供精准依据。
