The Bama Xiang pig （BMX） Chinese indigenous breed is a famous early-maturing with a two-end black coat To uncover the genetic basis of the BMX phenotype, we conducted comparative genomic analyses between BMX and Eas...The Bama Xiang pig （BMX） Chinese indigenous breed is a famous early-maturing with a two-end black coat To uncover the genetic basis of the BMX phenotype, we conducted comparative genomic analyses between BMX and East Asian wild boars and Laiwu pigs, respectively. Genes under positive selection were enriched in pathways associated with gonadal hormone and melanin synthesis, consistent with the phenotypic changes observed during development in BMX pigs. We also performed differentially expressed gene analysis based on RNA-seq data from pituitary tissues of BMX and Large White pigs. The CTTNBP2NL, FRS2, KANK4, and KATNAL1 genes were under selection and exhibited expressional changes in the pituitary tissue, which may affect BMX pig puberty. Our study demonstrated the positive selection of early maturity in the development of BMX pigs and advances our knowledge on the role of regulatory elements in puberty evolution in pigs.展开更多
The gastrointestinal tract is essential for food digestion,nutrient absorption,waste elimination,and microbial defense.Single-cell transcriptome profiling of the intestinal tract has greatly enriched our understanding...The gastrointestinal tract is essential for food digestion,nutrient absorption,waste elimination,and microbial defense.Single-cell transcriptome profiling of the intestinal tract has greatly enriched our understanding of cellular diversity,functional heterogeneity,and their importance in intestinal tract development and disease.Although such profiling has been extensively conducted in humans and mice,the single-cell gene expression landscape of the pig cecum remains unexplored.Here,single-cell RNA sequencing was performed on 45572 cells obtained from seven cecal samples in pigs at four different developmental stages(days(D)30,42,150,and 730).Analysis revealed 12 major cell types and 38 subtypes,as well as their distinctive genes,transcription factors,and regulons,many of which were conserved in humans.An increase in the relative proportions of CD8^(+)T and Granzyme A(low expression)natural killer T cells(GZMA^(low)NKT)cells and a decrease in the relative proportions of epithelial stem cells,Tregs,RHEX^(+)T cells,and plasmacytoid dendritic cells(pDCs)were noted across the developmental stages.Moreover,the post-weaning period exhibited an up-regulation in mitochondrial genes,COX2 and ND2,as well as genes involved in immune activation in multiple cell types.Cell-cell crosstalk analysis indicated that IBP6^(+)fibroblasts were the main signal senders at D30,whereas IBP6^(−)fibroblasts assumed this role at the other stages.NKT cells established interactions with epithelial cells and IBP6^(+)fibroblasts in the D730 cecum through mediation of GZMA-F2RL1/F2RL2 pairs.This study provides valuable insights into cellular heterogeneity and function in the pig cecum at different development stages.展开更多
旨在探究 TAS1 R3基因通过mTOR对从江香猪自噬相关基因表达的影响。本试验选择30日龄健康雄性从江香猪3头,采集睾丸组织并培养出睾丸间质细胞。将构建成功的干扰载体和空载体转染至细胞中,利用qRT-PCR检测其对 TAS 1R3基因表达影响,运用...旨在探究 TAS1 R3基因通过mTOR对从江香猪自噬相关基因表达的影响。本试验选择30日龄健康雄性从江香猪3头,采集睾丸组织并培养出睾丸间质细胞。将构建成功的干扰载体和空载体转染至细胞中,利用qRT-PCR检测其对 TAS 1R3基因表达影响,运用qRT-PCR和Western blot检测 TAS1 R3基因干扰后对味觉受体第一家族一号受体(TAS1R1)、细胞外信号调节激酶1(ERK1 ) 、细胞外信号调节激酶2(ERK2)、雷帕霉素靶蛋白(mTOR)、 BECN1 和微管相关蛋白1轻链3β(MAP1LC3B)表达的影响。结果表明,当 TAS 1R3基因被干扰后,相较于shRNA-NC对照组, TAS 1R1、 ERK 1、 ERK 2、 mTOR 基因mRNA表达量均极显著降低( P <0.01),自噬因子 BECN1 和 MAP 1LC3B表达量极显著升高( P <0.01)。Western blot结果表明当 TAS 1R3基因被干扰后,与 shRNA-NC 对照组相比,蛋白T1R3、T1R1、p-mTOR、p-S6K1、p-ERK12均极显著降低( P <0.01),而自噬蛋白 Beclin 1 表达量极显著升高( P <0.01)。本试验通过将 TAS 1R3基因干扰载体转染至睾丸间质细胞,发现当 TAS 1R3基因被干扰后可通过影响 mTOR 基因的表达,调控其下游自噬因子的表达,提示 TAS 1R3基因与睾丸间质细胞的自噬密切相关,这为进一步研究 TAS 1R3基因通过调节自噬影响香猪生殖活动提供了借鉴。展开更多
【目的】探究猪特有的细胞色素P450超家族3A亚族成员29(cytochrome P4503A 29,CYP3A29)基因3′-UTR区核苷酸结构变异(structural variation,SV)对该基因表达的影响,解析该结构变异与香猪肉质性状形成的关系。【方法】以香猪、大白猪为...【目的】探究猪特有的细胞色素P450超家族3A亚族成员29(cytochrome P4503A 29,CYP3A29)基因3′-UTR区核苷酸结构变异(structural variation,SV)对该基因表达的影响,解析该结构变异与香猪肉质性状形成的关系。【方法】以香猪、大白猪为研究对象,应用UCSC、miRBase、PITA、RBPsuite等软件预测CYP 3 A 29基因3′-UTR区结构变异区间所包含的重复元件、miRNA和RBP结合位点;采用PCR方法对结构变异位点进行基因分型;计算群体基因型频率、基因频率及Hardy-Weinberg平衡状态;采用实时荧光定量PCR检测该变异对CYP 3 A 29基因表达的影响;利用ELISA法检测香猪肌肉组织中CYP3A29蛋白含量和雄激素(T、DHT)水平,并使用SPSS 17.0软件对T、DHT含量与不同基因型进行Pearson相关性分析。【结果】生物信息学分析显示,CYP 3 A 29基因3′-UTR的结构变异区全长303 bp,该变异区存在1个长为241 bp的短散在元件(short interspersed element,SINE),属于Pre0_SStRNA家族,位于Chr3:6819917―6820161,含有33个miRNAs和13个RBPs结合位点。基因分型显示,该结构变异在香猪、大白猪群体中呈现出丰富的多态性,表现为II基因型(插入型)、ID基因型(杂合型)、DD基因型(双缺失)。基因型群体分布频率显示,香猪中的D等位基因频率高于大白猪,该结构变异在香猪中处于Hardy-Weinberg平衡状态(P>0.05),在大白猪中处于Hardy-Weinberg不平衡状态(P<0.05)。实时荧光定量PCR和ELISA结果显示,CYP 3 A 29基因ID基因型个体mRNA表达量和蛋白含量均显著高于II和DD基因型(P<0.05)。相关性分析结果显示,香猪不同基因型个体CYP3A29基因含量与肌肉组织中T浓度呈显著相关(P<0.05),与DHT浓度不相关(P>0.05)。香猪ID基因型个体T浓度显著高于DD和II基因型(P<0.05),DD基因型个体DHT浓度显著高于ID和II基因型(P<0.05)。【结论】CYP 3 A 29基因3′-UTR区长度为303 bp的结构变异在香猪群体中具有多态性,以缺失型D等位基因为主,即该结构变异在香猪中缺失SINE元件,导致CYP 3 A 29基因表达上调,进而影响香猪肌肉组织中T浓度。CYP 3 A 29基因3′-UTR结构变异与香猪肉质性状具有相关性。展开更多
基金supported by grants from the National Natural Science Foundation of China(31472000)National 973 Program of China(2013CB835203)Animal Branch of the Germplasm Bank of Wild Species,Chinese Academy of Sciences(Large Research Infrastructure Funding)
文摘The Bama Xiang pig （BMX） Chinese indigenous breed is a famous early-maturing with a two-end black coat To uncover the genetic basis of the BMX phenotype, we conducted comparative genomic analyses between BMX and East Asian wild boars and Laiwu pigs, respectively. Genes under positive selection were enriched in pathways associated with gonadal hormone and melanin synthesis, consistent with the phenotypic changes observed during development in BMX pigs. We also performed differentially expressed gene analysis based on RNA-seq data from pituitary tissues of BMX and Large White pigs. The CTTNBP2NL, FRS2, KANK4, and KATNAL1 genes were under selection and exhibited expressional changes in the pituitary tissue, which may affect BMX pig puberty. Our study demonstrated the positive selection of early maturity in the development of BMX pigs and advances our knowledge on the role of regulatory elements in puberty evolution in pigs.
基金supported by the National Natural Science Foundation of China(31790410,32160781)。
文摘The gastrointestinal tract is essential for food digestion,nutrient absorption,waste elimination,and microbial defense.Single-cell transcriptome profiling of the intestinal tract has greatly enriched our understanding of cellular diversity,functional heterogeneity,and their importance in intestinal tract development and disease.Although such profiling has been extensively conducted in humans and mice,the single-cell gene expression landscape of the pig cecum remains unexplored.Here,single-cell RNA sequencing was performed on 45572 cells obtained from seven cecal samples in pigs at four different developmental stages(days(D)30,42,150,and 730).Analysis revealed 12 major cell types and 38 subtypes,as well as their distinctive genes,transcription factors,and regulons,many of which were conserved in humans.An increase in the relative proportions of CD8^(+)T and Granzyme A(low expression)natural killer T cells(GZMA^(low)NKT)cells and a decrease in the relative proportions of epithelial stem cells,Tregs,RHEX^(+)T cells,and plasmacytoid dendritic cells(pDCs)were noted across the developmental stages.Moreover,the post-weaning period exhibited an up-regulation in mitochondrial genes,COX2 and ND2,as well as genes involved in immune activation in multiple cell types.Cell-cell crosstalk analysis indicated that IBP6^(+)fibroblasts were the main signal senders at D30,whereas IBP6^(−)fibroblasts assumed this role at the other stages.NKT cells established interactions with epithelial cells and IBP6^(+)fibroblasts in the D730 cecum through mediation of GZMA-F2RL1/F2RL2 pairs.This study provides valuable insights into cellular heterogeneity and function in the pig cecum at different development stages.
文摘旨在探究 TAS1 R3基因通过mTOR对从江香猪自噬相关基因表达的影响。本试验选择30日龄健康雄性从江香猪3头,采集睾丸组织并培养出睾丸间质细胞。将构建成功的干扰载体和空载体转染至细胞中,利用qRT-PCR检测其对 TAS 1R3基因表达影响,运用qRT-PCR和Western blot检测 TAS1 R3基因干扰后对味觉受体第一家族一号受体(TAS1R1)、细胞外信号调节激酶1(ERK1 ) 、细胞外信号调节激酶2(ERK2)、雷帕霉素靶蛋白(mTOR)、 BECN1 和微管相关蛋白1轻链3β(MAP1LC3B)表达的影响。结果表明,当 TAS 1R3基因被干扰后,相较于shRNA-NC对照组, TAS 1R1、 ERK 1、 ERK 2、 mTOR 基因mRNA表达量均极显著降低( P <0.01),自噬因子 BECN1 和 MAP 1LC3B表达量极显著升高( P <0.01)。Western blot结果表明当 TAS 1R3基因被干扰后,与 shRNA-NC 对照组相比,蛋白T1R3、T1R1、p-mTOR、p-S6K1、p-ERK12均极显著降低( P <0.01),而自噬蛋白 Beclin 1 表达量极显著升高( P <0.01)。本试验通过将 TAS 1R3基因干扰载体转染至睾丸间质细胞,发现当 TAS 1R3基因被干扰后可通过影响 mTOR 基因的表达,调控其下游自噬因子的表达,提示 TAS 1R3基因与睾丸间质细胞的自噬密切相关,这为进一步研究 TAS 1R3基因通过调节自噬影响香猪生殖活动提供了借鉴。
基金National Natural Science Foundation of China(31960641,31672390)Guizhou Province Science and Technology Innovation Team Building Special(QKHPTRC[2019]5615)+2 种基金Guizhou Province“Hundred”Innovative Talents Project(2016-4012)Guizhou Agriculture Research program(QKHZC[2017]2585,QKHZC[2017]2587,QKHNY[2013]3073)National High Technology Research and Development Program of China(2013AA102503)。
文摘【目的】探究猪特有的细胞色素P450超家族3A亚族成员29(cytochrome P4503A 29,CYP3A29)基因3′-UTR区核苷酸结构变异(structural variation,SV)对该基因表达的影响,解析该结构变异与香猪肉质性状形成的关系。【方法】以香猪、大白猪为研究对象,应用UCSC、miRBase、PITA、RBPsuite等软件预测CYP 3 A 29基因3′-UTR区结构变异区间所包含的重复元件、miRNA和RBP结合位点;采用PCR方法对结构变异位点进行基因分型;计算群体基因型频率、基因频率及Hardy-Weinberg平衡状态;采用实时荧光定量PCR检测该变异对CYP 3 A 29基因表达的影响;利用ELISA法检测香猪肌肉组织中CYP3A29蛋白含量和雄激素(T、DHT)水平,并使用SPSS 17.0软件对T、DHT含量与不同基因型进行Pearson相关性分析。【结果】生物信息学分析显示,CYP 3 A 29基因3′-UTR的结构变异区全长303 bp,该变异区存在1个长为241 bp的短散在元件(short interspersed element,SINE),属于Pre0_SStRNA家族,位于Chr3:6819917―6820161,含有33个miRNAs和13个RBPs结合位点。基因分型显示,该结构变异在香猪、大白猪群体中呈现出丰富的多态性,表现为II基因型(插入型)、ID基因型(杂合型)、DD基因型(双缺失)。基因型群体分布频率显示,香猪中的D等位基因频率高于大白猪,该结构变异在香猪中处于Hardy-Weinberg平衡状态(P>0.05),在大白猪中处于Hardy-Weinberg不平衡状态(P<0.05)。实时荧光定量PCR和ELISA结果显示,CYP 3 A 29基因ID基因型个体mRNA表达量和蛋白含量均显著高于II和DD基因型(P<0.05)。相关性分析结果显示,香猪不同基因型个体CYP3A29基因含量与肌肉组织中T浓度呈显著相关(P<0.05),与DHT浓度不相关(P>0.05)。香猪ID基因型个体T浓度显著高于DD和II基因型(P<0.05),DD基因型个体DHT浓度显著高于ID和II基因型(P<0.05)。【结论】CYP 3 A 29基因3′-UTR区长度为303 bp的结构变异在香猪群体中具有多态性,以缺失型D等位基因为主,即该结构变异在香猪中缺失SINE元件,导致CYP 3 A 29基因表达上调,进而影响香猪肌肉组织中T浓度。CYP 3 A 29基因3′-UTR结构变异与香猪肉质性状具有相关性。
