Improving the accuracy of genomic prediction for meat quality traits using whole genome sequence data in pigs

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.

A pan-cancer analysis identifies SOAT1 as an immunological and prognostic biomarker

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.

Ultrasonic vibration assisted tungsten inert gas welding of dissimilar magnesium alloys

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.

杂种优势形成机制和预测方法及其在猪生产中的应用与展望

杂种优势是指杂种后代的性能优于双亲群体的现象。杂交能有效提高后代的生长发育性能、繁殖性能和抗病性,因此被广泛应用于动植物生产。研究人员利用杂交育种技术培育了超优千号杂交水稻、小偃6号杂交小麦、杜蒙羊、山下黑猪等优秀的农牧新品系和配套系。然而当前的杂种优势研究仍存在一些亟待解决的问题:现有杂种优势理论只能部分解释动植物杂种优势现象,动物杂种优势理论研究较少,且现有的杂种优势预测方法准确性有限。我国是世界上最大的猪肉生产消费国,杂种优势能够有效提高生猪生产性能,在生猪产业的应用方面具有重要的经济和研究价值。但目前有关猪杂交生产研究还处于起步阶段,亟待进一步深入。本文综述了现有的杂种优势理论、杂种优势预测方法,及其在猪生产中的应用研究,以期为杂种优势在生猪育种中的应用提供借鉴与参考。

Genome-wide association analysis reveals genetic loci and candidate genes associated with intramuscular fat in Duroc pigs

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.