旨在揭示拜城油鸡、和田鸡和吐鲁番鸡等3种新疆地方鸡相互之间的遗传关系和基因组差异,从而在基因组层面为新疆地方鸡遗传资源的保护与开发提供科学依据。本研究以65份鸡的全基因组重测序数据为对象,借助Rstudio、Plink、Pedstats等软...旨在揭示拜城油鸡、和田鸡和吐鲁番鸡等3种新疆地方鸡相互之间的遗传关系和基因组差异,从而在基因组层面为新疆地方鸡遗传资源的保护与开发提供科学依据。本研究以65份鸡的全基因组重测序数据为对象,借助Rstudio、Plink、Pedstats等软件对数据实施过滤处理;通过状态同源(identical by state,IBS)多维标度分析不同鸡种的群体遗传结构,利用Treemix及Dsuite开展基因渗入(gene introgression)分析,采用群体间单倍体扩增纯合性检测(cross population extended haplotype homozygosity,XP-EHH)及跨群体的符合似然比检验(cross population composite likelihood radio test,XP-CLR)挖掘选择信号。数据质控后,10228705个常染色体的单核苷酸多态位点(single nucleotide polymorphism,SNP)用于基因渗入和选择信号的研究,4657217个最小等位基因频率(minor allele frequency,MAF)≥0.2的常染色体SNPs则被用来进行遗传关系分析。群体遗传关系分析显示,拜城油鸡和吐鲁番鸡的遗传距离最远,遗传分化系数达到(genetic differentiation coefficient,FST)0.0777,和田鸡与拜城油鸡及吐鲁番鸡的遗传距离较近,FST分别为0.0535和0.0563。且和田鸡与吐鲁番鸡之间存在一次基因渗入,渗入信号最强的区域位于4号染色体,该区域包含ABLIM2等与耐热性能相关的基因。而在拜城油鸡与吐鲁番鸡的选择信号分析中,共筛选出70个参与关键生物学进程的候选基因。其中,CLCN6、ACTA2、CRIM1、IARS2等基因可能与耐热性能相关;BNIP2、DTNA、RAB3GAP2等基因可能涉及肌肉生长调控;AGMO、TSNARE1等基因则可能与斗鸡攻击性行为的形成有关。研究清晰地揭示了新疆3种地方鸡种之间存在的遗传关系,发现了和田鸡与吐鲁番鸡之间存在的基因组渗入区域及相关基因,鉴定了拜城油鸡和吐鲁番鸡之间的基因组选择区域及其中包括的与耐热性、肌肉生长、斗鸡攻击性行为等特色性状相关的候选基因,从而为新疆地方鸡种特色性状的保护和利用提供分子依据。展开更多
The development of skeletal muscle are complicated processes involving genes responsible for proper muscle morphology,contractility,cell proliferation,differentiation,interactions,migration,and death.The three-dimensi...The development of skeletal muscle are complicated processes involving genes responsible for proper muscle morphology,contractility,cell proliferation,differentiation,interactions,migration,and death.The three-dimensional chromatin architecture of skeletal muscle development has not been studied intensively although dynamic transcriptional regulation during differentiation of muscle cells is one of the most deeply studied processes.The RNA-seq was used to analyze the transcriptome pattern during chicken muscle development across 12 stages.Hi-C was used to build chromatin architectures during four representative stages.Ch IP-seq was conducted to identify enhancers and promoters in these four stages,which are occupied by histone H3K27ac and H3K4me3 peaks.Results show that large-scale genome architecture changes are mostly unidirectional,and coupled by complex on/off dynamic patterns of gene expression.Specifically,we observed 258.30 Mb of the genome undergoing A/B compartment switching.Notable alterations(316.57 Mb)of interaction frequencies within TADs were observed.Substantial aging-associated genes exhibited ascending connectivity with the compartment transition from repressive to active status during muscle development.Some muscle-related gene promoters that interacted with active enhancers during development,and some myopathy/aging-associated genes that were activated in aging muscle were founded.These results provide key insights into skeletal muscle development in vivo,and offer a valuable resource that allows in-depth functional characterization of candidate genes.展开更多
文摘旨在揭示拜城油鸡、和田鸡和吐鲁番鸡等3种新疆地方鸡相互之间的遗传关系和基因组差异,从而在基因组层面为新疆地方鸡遗传资源的保护与开发提供科学依据。本研究以65份鸡的全基因组重测序数据为对象,借助Rstudio、Plink、Pedstats等软件对数据实施过滤处理;通过状态同源(identical by state,IBS)多维标度分析不同鸡种的群体遗传结构,利用Treemix及Dsuite开展基因渗入(gene introgression)分析,采用群体间单倍体扩增纯合性检测(cross population extended haplotype homozygosity,XP-EHH)及跨群体的符合似然比检验(cross population composite likelihood radio test,XP-CLR)挖掘选择信号。数据质控后,10228705个常染色体的单核苷酸多态位点(single nucleotide polymorphism,SNP)用于基因渗入和选择信号的研究,4657217个最小等位基因频率(minor allele frequency,MAF)≥0.2的常染色体SNPs则被用来进行遗传关系分析。群体遗传关系分析显示,拜城油鸡和吐鲁番鸡的遗传距离最远,遗传分化系数达到(genetic differentiation coefficient,FST)0.0777,和田鸡与拜城油鸡及吐鲁番鸡的遗传距离较近,FST分别为0.0535和0.0563。且和田鸡与吐鲁番鸡之间存在一次基因渗入,渗入信号最强的区域位于4号染色体,该区域包含ABLIM2等与耐热性能相关的基因。而在拜城油鸡与吐鲁番鸡的选择信号分析中,共筛选出70个参与关键生物学进程的候选基因。其中,CLCN6、ACTA2、CRIM1、IARS2等基因可能与耐热性能相关;BNIP2、DTNA、RAB3GAP2等基因可能涉及肌肉生长调控;AGMO、TSNARE1等基因则可能与斗鸡攻击性行为的形成有关。研究清晰地揭示了新疆3种地方鸡种之间存在的遗传关系,发现了和田鸡与吐鲁番鸡之间存在的基因组渗入区域及相关基因,鉴定了拜城油鸡和吐鲁番鸡之间的基因组选择区域及其中包括的与耐热性、肌肉生长、斗鸡攻击性行为等特色性状相关的候选基因,从而为新疆地方鸡种特色性状的保护和利用提供分子依据。
基金supported by the National Key R&D Program of China(2023YFD1300040 and 2022YFF1000100)the Sichuan Science and Technology Program,China(2022NSFSC0132,2021YFYZ0009 and 2022JDJQ0054)the National Natural Science Foundation of China(32225046)。
文摘The development of skeletal muscle are complicated processes involving genes responsible for proper muscle morphology,contractility,cell proliferation,differentiation,interactions,migration,and death.The three-dimensional chromatin architecture of skeletal muscle development has not been studied intensively although dynamic transcriptional regulation during differentiation of muscle cells is one of the most deeply studied processes.The RNA-seq was used to analyze the transcriptome pattern during chicken muscle development across 12 stages.Hi-C was used to build chromatin architectures during four representative stages.Ch IP-seq was conducted to identify enhancers and promoters in these four stages,which are occupied by histone H3K27ac and H3K4me3 peaks.Results show that large-scale genome architecture changes are mostly unidirectional,and coupled by complex on/off dynamic patterns of gene expression.Specifically,we observed 258.30 Mb of the genome undergoing A/B compartment switching.Notable alterations(316.57 Mb)of interaction frequencies within TADs were observed.Substantial aging-associated genes exhibited ascending connectivity with the compartment transition from repressive to active status during muscle development.Some muscle-related gene promoters that interacted with active enhancers during development,and some myopathy/aging-associated genes that were activated in aging muscle were founded.These results provide key insights into skeletal muscle development in vivo,and offer a valuable resource that allows in-depth functional characterization of candidate genes.
