Background Pork quality can directly affect customer purchase tendency and meat quality traits have become valu-able in modern pork production.However,genetic improvement has been slow due to high phenotyping costs.In...Background Pork quality can directly affect customer purchase tendency and meat quality traits have become valu-able in modern pork production.However,genetic improvement has been slow due to high phenotyping costs.In this study,whole genome sequence(WGS)data was used to evaluate the prediction accuracy of genomic best linear unbiased prediction(GBLUP)for meat quality in large-scale crossbred commercial pigs.Results We produced WGS data(18,695,907 SNPs and 2,106,902 INDELs exceed quality control)from 1,469 sequenced Duroc×(Landrace×Yorkshire)pigs and developed a reference panel for meat quality including meat color score,marbling score,L*(lightness),a*(redness),and b*(yellowness)of genomic prediction.The prediction accuracy was defined as the Pearson correlation coefficient between adjusted phenotypes and genomic estimated breeding values in the validation population.Using different marker density panels derived from WGS data,accuracy differed substantially among meat quality traits,varied from 0.08 to 0.47.Results showed that MultiBLUP outperform GBLUP and yielded accuracy increases ranging from 17.39%to 75%.We optimized the marker density and found medium-and high-density marker panels are beneficial for the estimation of heritability for meat quality.Moreover,we conducted genotype imputation from 50K chip to WGS level in the same population and found average concord-ance rate to exceed 95%and r^(2)=0.81.Conclusions Overall,estimation of heritability for meat quality traits can benefit from the use of WGS data.This study showed the superiority of using WGS data to genetically improve pork quality in genomic prediction.展开更多
Sterol o-acyltransferase1(SOAT1)is an enzyme that regulates lipid metabolism.Nevertheless,the predictive value of SOAT1 regarding immune responses in cancer is not fully understood.Herein,we aimed to expound the predi...Sterol o-acyltransferase1(SOAT1)is an enzyme that regulates lipid metabolism.Nevertheless,the predictive value of SOAT1 regarding immune responses in cancer is not fully understood.Herein,we aimed to expound the predictive value and the potential biological functions of SOAT1 in pan-cancer.Raw data related to SOAT1 expression in 33 different types of cancer were acquired from The Cancer Genome Atlas(TCGA)and Genotype-Tissue Expression(GTEx)databases.SOAT1 expression was significantly increased in most cancers and showed a distinct correlation with prognosis.This enhanced expression of the SOAT1 gene was confirmed by evaluating SOAT1 protein expression using tissue microarrays.In addition,we found significant positive associations between SOAT1 expression levels and infiltrating immune cells,including T cells,neutrophils,and macrophages.Moreover,the co-expression analysis between SOAT1 and immune genes showed that many immune-related genes were increased with enhanced SOAT1 expression.A gene set enrichment analysis(GSEA)revealed that the expression of SOAT1 correlated with the tumor microenvironment,adaptive immune response,interferon signaling,and cytokine signaling.These findings indicate that SOAT1 is a potential candidate marker for predicting prognosis and a promising target for tumor immunotherapy in cancers.展开更多
The effects of ultrasonic vibration assisted(UVA) treatment on the microstructures and mechanical properties of MB3/AZ31 dissimilar magnesium(Mg) alloy joints were studied by microstructural characterization, micr...The effects of ultrasonic vibration assisted(UVA) treatment on the microstructures and mechanical properties of MB3/AZ31 dissimilar magnesium(Mg) alloy joints were studied by microstructural characterization, micro-hardness testing and tensile testing. Results indicate that the welding pores are eliminated and coarse a-Mg grains of fusion zone are refined to 26 μm, owing to the acoustic streaming effect and cavitation effect induced by the UVA treatment with an optimal ultrasonic power of 1.0 kW.In addition, Mg;Al;precipitation phases are fine and uniformly distributed in the whole fusion zone of weldment. Micro-hardness of fusion zone of the Mg alloy joints increases to 53.5 HV after UVA process,and the maximum tensile strength with optimized UVA treatment increases to 263 MPa, which leads to fracture occurrence in the Mg alloy base plate. Eventually, it is experimentally demonstrated that robust MB3/AZ31 Mg alloy joints can be obtained by UVA process.展开更多
Intramuscular fat(IMF) is a major meat-quality trait in pigs. The content of IMF is directly associated with the taste and flavor of pork. As a complex trait, there could be multiple genes affecting IMF content in por...Intramuscular fat(IMF) is a major meat-quality trait in pigs. The content of IMF is directly associated with the taste and flavor of pork. As a complex trait, there could be multiple genes affecting IMF content in pork. Genomewide association study is a powerful tool to detect genomic regions associated with phenotypic variations. The objectives of the present study were to identify or refine the positions of genomic regions affecting IMF, and to characterize candidate genes and pathways that may influence this trait. Of note, we identified a significant region in longissium dorsi muscle in a Duroc pig population for IMF content with Porcine SNP60 v2 Bead Chip. This region spans 1.24 Mb on chromosome 8 and had been identified as a quantitative trait locus for IMF in Pietrain, Large White, Landrace, and Leicoma pigs. In this region, eight SNPs were significantly associated with IMF content. Three genes proximal to these significant SNPs were considered candidate genes, including ZDHHC16, LOC102162218 and PCDH7. Our results confirm several previous findings and highlight several genes that may contribute to IMF variation in Duroc pigs.展开更多
基金supported by a Technical Innovation of Crossbred in Swine and Breed High Fertility Lines Project(2022B0202090002)a Local Innovative and Research Teams Project of Guangdong Province(2019BT02N630)+1 种基金a Natural Science Foundation of Guangdong Province project(2018B030313011)Innovative Teams of Modern Agriculture and Industry Technology System of Guangdong Province(2022KJ26).
文摘Background Pork quality can directly affect customer purchase tendency and meat quality traits have become valu-able in modern pork production.However,genetic improvement has been slow due to high phenotyping costs.In this study,whole genome sequence(WGS)data was used to evaluate the prediction accuracy of genomic best linear unbiased prediction(GBLUP)for meat quality in large-scale crossbred commercial pigs.Results We produced WGS data(18,695,907 SNPs and 2,106,902 INDELs exceed quality control)from 1,469 sequenced Duroc×(Landrace×Yorkshire)pigs and developed a reference panel for meat quality including meat color score,marbling score,L*(lightness),a*(redness),and b*(yellowness)of genomic prediction.The prediction accuracy was defined as the Pearson correlation coefficient between adjusted phenotypes and genomic estimated breeding values in the validation population.Using different marker density panels derived from WGS data,accuracy differed substantially among meat quality traits,varied from 0.08 to 0.47.Results showed that MultiBLUP outperform GBLUP and yielded accuracy increases ranging from 17.39%to 75%.We optimized the marker density and found medium-and high-density marker panels are beneficial for the estimation of heritability for meat quality.Moreover,we conducted genotype imputation from 50K chip to WGS level in the same population and found average concord-ance rate to exceed 95%and r^(2)=0.81.Conclusions Overall,estimation of heritability for meat quality traits can benefit from the use of WGS data.This study showed the superiority of using WGS data to genetically improve pork quality in genomic prediction.
基金This work was mainly supported by the Science and Technology Innovation Fund Project of Shanghai Jinshan District Science and Technology Commission(No.2021-3-55)All sponsors or funders played no roles in the study design,data collection and analysis,decision to publish,or preparation of the manuscript.
文摘Sterol o-acyltransferase1(SOAT1)is an enzyme that regulates lipid metabolism.Nevertheless,the predictive value of SOAT1 regarding immune responses in cancer is not fully understood.Herein,we aimed to expound the predictive value and the potential biological functions of SOAT1 in pan-cancer.Raw data related to SOAT1 expression in 33 different types of cancer were acquired from The Cancer Genome Atlas(TCGA)and Genotype-Tissue Expression(GTEx)databases.SOAT1 expression was significantly increased in most cancers and showed a distinct correlation with prognosis.This enhanced expression of the SOAT1 gene was confirmed by evaluating SOAT1 protein expression using tissue microarrays.In addition,we found significant positive associations between SOAT1 expression levels and infiltrating immune cells,including T cells,neutrophils,and macrophages.Moreover,the co-expression analysis between SOAT1 and immune genes showed that many immune-related genes were increased with enhanced SOAT1 expression.A gene set enrichment analysis(GSEA)revealed that the expression of SOAT1 correlated with the tumor microenvironment,adaptive immune response,interferon signaling,and cytokine signaling.These findings indicate that SOAT1 is a potential candidate marker for predicting prognosis and a promising target for tumor immunotherapy in cancers.
基金the financial support by the National Natural Science Foundation of China(No.51575067)the Major and Special Project by Ministry of Science and Technology(No.2012ZX04010-081)
文摘The effects of ultrasonic vibration assisted(UVA) treatment on the microstructures and mechanical properties of MB3/AZ31 dissimilar magnesium(Mg) alloy joints were studied by microstructural characterization, micro-hardness testing and tensile testing. Results indicate that the welding pores are eliminated and coarse a-Mg grains of fusion zone are refined to 26 μm, owing to the acoustic streaming effect and cavitation effect induced by the UVA treatment with an optimal ultrasonic power of 1.0 kW.In addition, Mg;Al;precipitation phases are fine and uniformly distributed in the whole fusion zone of weldment. Micro-hardness of fusion zone of the Mg alloy joints increases to 53.5 HV after UVA process,and the maximum tensile strength with optimized UVA treatment increases to 263 MPa, which leads to fracture occurrence in the Mg alloy base plate. Eventually, it is experimentally demonstrated that robust MB3/AZ31 Mg alloy joints can be obtained by UVA process.
基金financial support from the National Natural Science Foundation of China (31601912)the Natural Science Foundation of Guangdong Province (2016A030310447)the Applied Science and Technology Research and Development of Special Funds of Guangdong Province (2015B020231010)
文摘Intramuscular fat(IMF) is a major meat-quality trait in pigs. The content of IMF is directly associated with the taste and flavor of pork. As a complex trait, there could be multiple genes affecting IMF content in pork. Genomewide association study is a powerful tool to detect genomic regions associated with phenotypic variations. The objectives of the present study were to identify or refine the positions of genomic regions affecting IMF, and to characterize candidate genes and pathways that may influence this trait. Of note, we identified a significant region in longissium dorsi muscle in a Duroc pig population for IMF content with Porcine SNP60 v2 Bead Chip. This region spans 1.24 Mb on chromosome 8 and had been identified as a quantitative trait locus for IMF in Pietrain, Large White, Landrace, and Leicoma pigs. In this region, eight SNPs were significantly associated with IMF content. Three genes proximal to these significant SNPs were considered candidate genes, including ZDHHC16, LOC102162218 and PCDH7. Our results confirm several previous findings and highlight several genes that may contribute to IMF variation in Duroc pigs.