Background:Genotyping by sequencing(GBS)still has problems with missing genotypes.Imputation is important for using GBS for genomic predictions,especially for low depths,due to the large number of missing genotypes.Mi...Background:Genotyping by sequencing(GBS)still has problems with missing genotypes.Imputation is important for using GBS for genomic predictions,especially for low depths,due to the large number of missing genotypes.Minor allele frequency(MAF)is widely used as a marker data editing criteria for genomic predictions.In this study,three imputation methods(Beagle,IMPUTE2 and FImpute software)based on four MAF editing criteria were investigated with regard to imputation accuracy of missing genotypes and accuracy of genomic predictions,based on simulated data of livestock population.Results:Four MAFs(no MAF limit,MAF≥0.001,MAF≥0.01 and MAF≥0.03)were used for editing marker data before imputation.Beagle,IMPUTE2 and FImpute software were applied to impute the original GBS.Additionally,IMPUTE2 also imputed the expected genotype dosage after genotype correction(GcIM).The reliability of genomic predictions was calculated using GBS and imputed GBS data.The results showed that imputation accuracies were the same for the three imputation methods,except for the data of sequencing read depth(depth)=2,where FImpute had a slightly lower imputation accuracy than Beagle and IMPUTE2.GcIM was observed to be the best for all of the imputations at depth=4,5 and 10,but the worst for depth=2.For genomic prediction,retaining more SNPs with no MAF limit resulted in higher reliability.As the depth increased to 10,the prediction reliabilities approached those using true genotypes in the GBS loci.Beagle and IMPUTE2 had the largest increases in prediction reliability of 5 percentage points,and FImpute gained 3 percentage points at depth=2.The best prediction was observed at depth=4,5 and 10 using GcIM,but the worst prediction was also observed using GcIM at depth=2.Conclusions:The current study showed that imputation accuracies were relatively low for GBS with low depths and high for GBS with high depths.Imputation resulted in larger gains in the reliability of genomic predictions for GBS with lower depths.These results suggest that the application of IMPUTE2,based on a corrected GBS(GcIM)to improve genomic predictions for higher depths,and FImpute software could be a good alternative for routine imputation.展开更多
Background: MicroRNAs act as post-transcriptional regulators that repress translation or degrade mRNA transcripts.Each microRNA has many mRNA targets and each mRNA may be targeted by several microRNAs. Skeletal muscle...Background: MicroRNAs act as post-transcriptional regulators that repress translation or degrade mRNA transcripts.Each microRNA has many mRNA targets and each mRNA may be targeted by several microRNAs. Skeletal muscles express a plethora of microRNA genes that regulate muscle development and function by controlling the expression of protein-coding target genes. To expand our understanding of the role of microRNA, specifically btamiR-365-3 p, in muscle biology, we investigated its functions in regulating primary bovine myoblast proliferation and differentiation.Results: Firstly, we found that bta-miR-365-3 p was predominantly expressed in skeletal muscle and heart tissue in Chinese Qinchuan beef cattle. Quantitative PCR and western blotting results showed that overexpression of btamiR-365-3 p significantly reduced the expression levels of cyclin D1(CCND1), cyclin dependent kinase 2(CDK2) and proliferating cell nuclear antigen(PCNA) but stimulated the expression levels of muscle differentiation markers, i.e.,MYOD1, MYOG at both mRNA and protein level. Moreover, downregulation of bta-miR-365-3 p increased the expression of CCND1, CDK2 and PCNA but decreased the expression of MYOD1 and MYOG at both mRNA and protein levels. Furthermore, flow cytometry, EdU proliferation assays and immunostaining results showed that increased levels of bta-miR-365-3 p suppressed cell proliferation but promoted myotube formation, whereas decreased levels of bta-miR-365-3 p resulted in the opposite consequences. Finally, we identified that activin A receptor type I(ACVR1) could be a direct target of bta-miR-365-3 p. It was demonstrated that bta-miR-365-3 p can bind to the 3'UTR of ACVR1 gene to regulate its expression based on dual luciferase gene reporter assays.Consistently, knock-down of ACVR1 was associated with decreased expressions of CDK2, CCND1 and PCNA but increased expression of MYOG and MYOD1 both at mRNA and protein level.Conclusion: Collectively, these data suggested that bta-miR-365-3 p represses proliferation but promotes differentiation of bovine myoblasts through several biological mechanisms involving downregulation of ACVR1.展开更多
基金This study was funded by the Genomic Selection in Animals and Plants(GenSAP)research project financed by the Danish Council of Strategic Research(Aarhus,Denmark).Xiao Wang received Ph.D.stipends from the Technical University of Denmark(DTU Bioinformatics and DTU Compute),Denmark,and the China Scholarship Council,China.
文摘Background:Genotyping by sequencing(GBS)still has problems with missing genotypes.Imputation is important for using GBS for genomic predictions,especially for low depths,due to the large number of missing genotypes.Minor allele frequency(MAF)is widely used as a marker data editing criteria for genomic predictions.In this study,three imputation methods(Beagle,IMPUTE2 and FImpute software)based on four MAF editing criteria were investigated with regard to imputation accuracy of missing genotypes and accuracy of genomic predictions,based on simulated data of livestock population.Results:Four MAFs(no MAF limit,MAF≥0.001,MAF≥0.01 and MAF≥0.03)were used for editing marker data before imputation.Beagle,IMPUTE2 and FImpute software were applied to impute the original GBS.Additionally,IMPUTE2 also imputed the expected genotype dosage after genotype correction(GcIM).The reliability of genomic predictions was calculated using GBS and imputed GBS data.The results showed that imputation accuracies were the same for the three imputation methods,except for the data of sequencing read depth(depth)=2,where FImpute had a slightly lower imputation accuracy than Beagle and IMPUTE2.GcIM was observed to be the best for all of the imputations at depth=4,5 and 10,but the worst for depth=2.For genomic prediction,retaining more SNPs with no MAF limit resulted in higher reliability.As the depth increased to 10,the prediction reliabilities approached those using true genotypes in the GBS loci.Beagle and IMPUTE2 had the largest increases in prediction reliability of 5 percentage points,and FImpute gained 3 percentage points at depth=2.The best prediction was observed at depth=4,5 and 10 using GcIM,but the worst prediction was also observed using GcIM at depth=2.Conclusions:The current study showed that imputation accuracies were relatively low for GBS with low depths and high for GBS with high depths.Imputation resulted in larger gains in the reliability of genomic predictions for GBS with lower depths.These results suggest that the application of IMPUTE2,based on a corrected GBS(GcIM)to improve genomic predictions for higher depths,and FImpute software could be a good alternative for routine imputation.
基金supported by the National Natural Science Foundation of China (No.31772574)the Program of National Beef Cattle and Yak Industrial Technology System (CARS-37)the scholarship from the China Scholarship Council (CSC),China。
文摘Background: MicroRNAs act as post-transcriptional regulators that repress translation or degrade mRNA transcripts.Each microRNA has many mRNA targets and each mRNA may be targeted by several microRNAs. Skeletal muscles express a plethora of microRNA genes that regulate muscle development and function by controlling the expression of protein-coding target genes. To expand our understanding of the role of microRNA, specifically btamiR-365-3 p, in muscle biology, we investigated its functions in regulating primary bovine myoblast proliferation and differentiation.Results: Firstly, we found that bta-miR-365-3 p was predominantly expressed in skeletal muscle and heart tissue in Chinese Qinchuan beef cattle. Quantitative PCR and western blotting results showed that overexpression of btamiR-365-3 p significantly reduced the expression levels of cyclin D1(CCND1), cyclin dependent kinase 2(CDK2) and proliferating cell nuclear antigen(PCNA) but stimulated the expression levels of muscle differentiation markers, i.e.,MYOD1, MYOG at both mRNA and protein level. Moreover, downregulation of bta-miR-365-3 p increased the expression of CCND1, CDK2 and PCNA but decreased the expression of MYOD1 and MYOG at both mRNA and protein levels. Furthermore, flow cytometry, EdU proliferation assays and immunostaining results showed that increased levels of bta-miR-365-3 p suppressed cell proliferation but promoted myotube formation, whereas decreased levels of bta-miR-365-3 p resulted in the opposite consequences. Finally, we identified that activin A receptor type I(ACVR1) could be a direct target of bta-miR-365-3 p. It was demonstrated that bta-miR-365-3 p can bind to the 3'UTR of ACVR1 gene to regulate its expression based on dual luciferase gene reporter assays.Consistently, knock-down of ACVR1 was associated with decreased expressions of CDK2, CCND1 and PCNA but increased expression of MYOG and MYOD1 both at mRNA and protein level.Conclusion: Collectively, these data suggested that bta-miR-365-3 p represses proliferation but promotes differentiation of bovine myoblasts through several biological mechanisms involving downregulation of ACVR1.
