Background MicroRNAs(miRNAs)are presented in the uterine lumen of many mammals,and in vitro experiments have determined that several miRNAs are important for the regulation of endometrial and trophoblast functions.Our...Background MicroRNAs(miRNAs)are presented in the uterine lumen of many mammals,and in vitro experiments have determined that several miRNAs are important for the regulation of endometrial and trophoblast functions.Our aim was to identify and contrast the miRNAs present in extracellular vesicles(EVs)in the uterine lumen fluid(ULF)at the onset of attachment in cattle pregnancies(gestation d 18)initiated by artificial insemination(AI)or by the trans-fer of an in vitro-produced blastocyst(IVP-ET).A third group had no conceptus after the transfer of an IVP embryo.Results The abundance of 263 annotated miRNAs was quantified in the EVs collected from ULF.There was an increase in the transcript abundance of 20 miRNAs in the ULF EVs from the AI pregnant group,while 4 miRNAs had a lower abundance relative to the group not containing a conceptus.Additionally,4 miRNAs were more abun-dant in ULF EVs in the AI pregnant group relative to IVP-ET group(bta-mir-17,bta-mir-7-3,MIR7-1,MIR18A).Specific miRNAs in the ULF EVs were co-expressed with messenger RNAs expressed in extra-embryonic tissues and endome-trium,including genes that are known to be their targets.Conclusions The results provide biological insights into the participation of miRNAs in the regulation of trophoblast proliferation and differentiation,as well as in endometrium receptivity.The knowledge that in vitro cultured embryos can contribute to the altered abundance of specific miRNAs in the uterine lumen can lead to the development of cor-rective approaches to reduce conceptus losses during the first month of pregnancy in cattle.展开更多
Background:Artificial insemination is a preferred breeding method for beef heifers as it advances the genetic background,produces a predictive and profitable calving season,and extends the heifer’s reproductive life ...Background:Artificial insemination is a preferred breeding method for beef heifers as it advances the genetic background,produces a predictive and profitable calving season,and extends the heifer’s reproductive life span.As reproductive efficiency in heifers is key for the success of beef cattle production systems,following artificial insemination,heifers are exposed to a bull for the remainder of the breeding season.Altogether,up to 95%of heifers might become pregnant in their first breeding season.Heifers that do not become pregnant at the end of the breeding season represent an irreparable economical loss.Additionally,heifers conceiving late in the breeding season to natural service,although acceptable,poses serious losses to producers.To minimize losses due to reproductive failure,different phenotypic parameters can be assessed and utilized as selection tools.Here,we tested the hypothesis that in a group of pre-selected heifers,records of weaning weight,age at weaning,age at artificial insemination,and age of dam differ among heifers of varied reproductive outcomes during the first breeding season.Results:None of the parameters tested presented predictive ability to discriminate the heifers based on the response variable(‘pregnant to artificial insemination’,‘pregnant to natural service’,‘not pregnant’).Heifers categorized with body condition score=6 and reproductive tract score≥4 had the greatest proportion of pregnancy to artificial insemination(49%and 44%,respectively).Furthermore,it was notable that heifers presenting body condition score=6 and reproductive tract score=5 presented the greatest pregnancy rate at end of the breeding season(89%).Heifers younger than 368 d at the start of the breeding season did not become pregnant to artificial insemination.Those young heifers had 12.5%chance to become pregnant in their first breeding season,compared to 87.5%if the heifers were older than 368 days.Conclusion:Our results suggest that beef heifers with body condition score=6 and reproductive tract score≥4 are more likely to become pregnant to artificial insemination.Careful assessment should be undertaken when developing replacement heifers that will not reach 12 months of age by the beginning of the breeding season.展开更多
Background A gap currently exists between genetic variants and the underlying cell and tissue biology of a trait,and expression quantitative trait loci(eQTL)studies provide important information to help close that gap...Background A gap currently exists between genetic variants and the underlying cell and tissue biology of a trait,and expression quantitative trait loci(eQTL)studies provide important information to help close that gap.However,two concerns that arise with eQTL analyses using RNA-sequencing data are normalization of data across samples and the data not following a normal distribution.Multiple pipelines have been suggested to address this.For instance,the most recent analysis of the human and farm Genotype-Tissue Expression(GTEx)project proposes using trimmed means of M-values(TMM)to normalize the data followed by an inverse normal transformation.Results In this study,we reasoned that eQTL analysis could be carried out using the same framework used for dif-ferential gene expression(DGE),which uses a negative binomial model,a statistical test feasible for count data.Using the GTEx framework,we identified 35 significant eQTLs(P<5×10^(–8))following the ANOVA model and 39 significant eQTLs(P<5×10^(–8))following the additive model.Using a differential gene expression framework,we identified 930 and six significant eQTLs(P<5×10^(–8))following an analytical framework equivalent to the ANOVA and additive model,respectively.When we compared the two approaches,there was no overlap of significant eQTLs between the two frameworks.Because we defined specific contrasts,we identified trans eQTLs that more closely resembled what we expect from genetic variants showing complete dominance between alleles.Yet,these were not identified by the GTEx framework.Conclusions Our results show that transforming RNA-sequencing data to fit a normal distribution prior to eQTL analysis is not required when the DGE framework is employed.Our proposed approach detected biologically relevant variants that otherwise would not have been identified due to data transformation to fit a normal distribution.展开更多
The development of replacement heifers is at the core of cow-calf beef production systems. In 2020, the USDA,National Agricultural Statistics Service reported 5.771 million beef heifers, 500 pounds and over, are under...The development of replacement heifers is at the core of cow-calf beef production systems. In 2020, the USDA,National Agricultural Statistics Service reported 5.771 million beef heifers, 500 pounds and over, are under development for cow replacement. A compilation of data from several studies indicate that between 85% and 95% of these heifers will become pregnant in their first breeding season. Several thousands of heifers being raised for replacement may not deliver a calf on their first breeding season and result in economic losses to cow-calf producers. Many management procedures have been developed to maximize the reproductive potential of beef heifers. Such approaches include, but are not limited to the following: nutritional management for controlled weight gain, identification of reproductive maturity by physiological and morphological indicators, and the implementation of an estrous synchronization program.The implementation of management strategies has important positive impact(s) on the reproductive efficiency of heifers.There are limitations, however, because some heifers deemed ready to enter their first breeding season do not become pregnant. In parallel, genetic selection for fertility-related traits in beef heifers have not promoted major genetic gains on this particular area, most likely due to low heritability of female fertility traits in cattle. Technologies such as antral follicle counting, DNA genotyping and RNA profiling are being investigated as a means to aid in the identification of heifers of low fertility potential. To date, many polymorphisms have been associated with heifer fertility, but no DNA markers have been identified across herds. Antral follicle count is an indication of the ovarian reserve and is an indicator of the reproductive health of a heifer. We have been working on the identification of transcriptome profiles in heifers associated with pregnancy outcome. Our current investigations integrating protein-coding transcript abundance and artificial intelligence have identified the potential for bloodborne transcript abundance to be used as indicators of fertility potential in beef heifers. In summary, there is an ongoing pressure for reducing costs and increasing efficiency in cow-calf production systems, and new technologies can help reduce the long-standing limitations in beef heifer fertility.展开更多
基金Agriculture and Food Research Initiative Competitive Grant no.2018-67015-31936 from the USDA National Institute of Food and Agriculture.
文摘Background MicroRNAs(miRNAs)are presented in the uterine lumen of many mammals,and in vitro experiments have determined that several miRNAs are important for the regulation of endometrial and trophoblast functions.Our aim was to identify and contrast the miRNAs present in extracellular vesicles(EVs)in the uterine lumen fluid(ULF)at the onset of attachment in cattle pregnancies(gestation d 18)initiated by artificial insemination(AI)or by the trans-fer of an in vitro-produced blastocyst(IVP-ET).A third group had no conceptus after the transfer of an IVP embryo.Results The abundance of 263 annotated miRNAs was quantified in the EVs collected from ULF.There was an increase in the transcript abundance of 20 miRNAs in the ULF EVs from the AI pregnant group,while 4 miRNAs had a lower abundance relative to the group not containing a conceptus.Additionally,4 miRNAs were more abun-dant in ULF EVs in the AI pregnant group relative to IVP-ET group(bta-mir-17,bta-mir-7-3,MIR7-1,MIR18A).Specific miRNAs in the ULF EVs were co-expressed with messenger RNAs expressed in extra-embryonic tissues and endome-trium,including genes that are known to be their targets.Conclusions The results provide biological insights into the participation of miRNAs in the regulation of trophoblast proliferation and differentiation,as well as in endometrium receptivity.The knowledge that in vitro cultured embryos can contribute to the altered abundance of specific miRNAs in the uterine lumen can lead to the development of cor-rective approaches to reduce conceptus losses during the first month of pregnancy in cattle.
基金partially funded by the Alabama Agricultural Experiment Stationthe Hatch program of the National Institute of Food and Agriculture,U.S.Department of Agriculture
文摘Background:Artificial insemination is a preferred breeding method for beef heifers as it advances the genetic background,produces a predictive and profitable calving season,and extends the heifer’s reproductive life span.As reproductive efficiency in heifers is key for the success of beef cattle production systems,following artificial insemination,heifers are exposed to a bull for the remainder of the breeding season.Altogether,up to 95%of heifers might become pregnant in their first breeding season.Heifers that do not become pregnant at the end of the breeding season represent an irreparable economical loss.Additionally,heifers conceiving late in the breeding season to natural service,although acceptable,poses serious losses to producers.To minimize losses due to reproductive failure,different phenotypic parameters can be assessed and utilized as selection tools.Here,we tested the hypothesis that in a group of pre-selected heifers,records of weaning weight,age at weaning,age at artificial insemination,and age of dam differ among heifers of varied reproductive outcomes during the first breeding season.Results:None of the parameters tested presented predictive ability to discriminate the heifers based on the response variable(‘pregnant to artificial insemination’,‘pregnant to natural service’,‘not pregnant’).Heifers categorized with body condition score=6 and reproductive tract score≥4 had the greatest proportion of pregnancy to artificial insemination(49%and 44%,respectively).Furthermore,it was notable that heifers presenting body condition score=6 and reproductive tract score=5 presented the greatest pregnancy rate at end of the breeding season(89%).Heifers younger than 368 d at the start of the breeding season did not become pregnant to artificial insemination.Those young heifers had 12.5%chance to become pregnant in their first breeding season,compared to 87.5%if the heifers were older than 368 days.Conclusion:Our results suggest that beef heifers with body condition score=6 and reproductive tract score≥4 are more likely to become pregnant to artificial insemination.Careful assessment should be undertaken when developing replacement heifers that will not reach 12 months of age by the beginning of the breeding season.
基金partially funded by the Virginia Cattle Industry Board and the Virginia Agriculture CouncilVT Open Access Subvention Fund for the partial support of the publication fees
文摘Background A gap currently exists between genetic variants and the underlying cell and tissue biology of a trait,and expression quantitative trait loci(eQTL)studies provide important information to help close that gap.However,two concerns that arise with eQTL analyses using RNA-sequencing data are normalization of data across samples and the data not following a normal distribution.Multiple pipelines have been suggested to address this.For instance,the most recent analysis of the human and farm Genotype-Tissue Expression(GTEx)project proposes using trimmed means of M-values(TMM)to normalize the data followed by an inverse normal transformation.Results In this study,we reasoned that eQTL analysis could be carried out using the same framework used for dif-ferential gene expression(DGE),which uses a negative binomial model,a statistical test feasible for count data.Using the GTEx framework,we identified 35 significant eQTLs(P<5×10^(–8))following the ANOVA model and 39 significant eQTLs(P<5×10^(–8))following the additive model.Using a differential gene expression framework,we identified 930 and six significant eQTLs(P<5×10^(–8))following an analytical framework equivalent to the ANOVA and additive model,respectively.When we compared the two approaches,there was no overlap of significant eQTLs between the two frameworks.Because we defined specific contrasts,we identified trans eQTLs that more closely resembled what we expect from genetic variants showing complete dominance between alleles.Yet,these were not identified by the GTEx framework.Conclusions Our results show that transforming RNA-sequencing data to fit a normal distribution prior to eQTL analysis is not required when the DGE framework is employed.Our proposed approach detected biologically relevant variants that otherwise would not have been identified due to data transformation to fit a normal distribution.
基金The Virginia Tech Open Access Subvention Fund contributed to the fee for article-processing charges。
文摘The development of replacement heifers is at the core of cow-calf beef production systems. In 2020, the USDA,National Agricultural Statistics Service reported 5.771 million beef heifers, 500 pounds and over, are under development for cow replacement. A compilation of data from several studies indicate that between 85% and 95% of these heifers will become pregnant in their first breeding season. Several thousands of heifers being raised for replacement may not deliver a calf on their first breeding season and result in economic losses to cow-calf producers. Many management procedures have been developed to maximize the reproductive potential of beef heifers. Such approaches include, but are not limited to the following: nutritional management for controlled weight gain, identification of reproductive maturity by physiological and morphological indicators, and the implementation of an estrous synchronization program.The implementation of management strategies has important positive impact(s) on the reproductive efficiency of heifers.There are limitations, however, because some heifers deemed ready to enter their first breeding season do not become pregnant. In parallel, genetic selection for fertility-related traits in beef heifers have not promoted major genetic gains on this particular area, most likely due to low heritability of female fertility traits in cattle. Technologies such as antral follicle counting, DNA genotyping and RNA profiling are being investigated as a means to aid in the identification of heifers of low fertility potential. To date, many polymorphisms have been associated with heifer fertility, but no DNA markers have been identified across herds. Antral follicle count is an indication of the ovarian reserve and is an indicator of the reproductive health of a heifer. We have been working on the identification of transcriptome profiles in heifers associated with pregnancy outcome. Our current investigations integrating protein-coding transcript abundance and artificial intelligence have identified the potential for bloodborne transcript abundance to be used as indicators of fertility potential in beef heifers. In summary, there is an ongoing pressure for reducing costs and increasing efficiency in cow-calf production systems, and new technologies can help reduce the long-standing limitations in beef heifer fertility.
