Construction of a transposase accessible chromatin landscape reveals chromatin state of repeat elements and potential causal variant for complex traits in pigs

Background:A comprehensive landscape of chromatin states for multiple mammalian tissues is essential for elucidating the molecular mechanism underlying regulatory variants on complex traits.However,the genome-wide chromatin accessibility has been only reported in limited tissue types in pigs.Results:Here we report a genome-wide landscape of chromatin accessibility of 20 tissues in two female pigs at ages of 6 months using ATAC-seq,and identified 557,273 merged peaks,which greatly expanded the pig regulatory ele-ment repository.We revealed tissue-specific regulatory elements which were associated with tissue-relevant biologi-cal functions.We identified both positive and negative significant correlations between the regulatory elements and gene transcripts,which showed distinct distributions in terms of their strength and distances from corresponding genes.We investigated the presence of transposable elements(TEs)in open chromatin regions across all tissues,these included identifications of porcine endogenous retroviruses(PERVs)exhibiting high accessibility in liver and homology of porcine specific virus sequences to universally accessible transposable elements.Furthermore,we prior-itized a potential causal variant for polyunsaturated fatty acid in the muscle.Conclusions:Our data provides a novel multi-tissues accessible chromatin landscape that serve as an important resource for interpreting regulatory sequences in tissue-specific and conserved biological functions,as well as regula-tory variants of loci associated with complex traits in pigs.

Evaluation of Young's Modulus and Residual Stress of NiFe Film by Microbridge Testing

Microbridge testing was used to measure the Young＇s modulus and residual stress of metallic films. Samples of freestanding NiFe film microbridge were fabricated by microelectromechanical systems. Special ceramic shaft structure was designed to solve the problem of getting the load-deflection curve of NiFe film microbridge by the Nanoindenter XP system with normal Berkovich probe. Theoretical analysis of load-deflection curves of the microbridges was proposed to evaluate the Young＇s modulus and residual stress of the films simultaneously. The calculated results based on experimental measurements show that the average Young＇s modulus and residual stress for the electroplated NiFe films are 203.2 GPa and 333.0 MPa, respectively, while the Young＇s modulus measured by the Nano-hardness method is 209.6：1：11.8 GPa for the thick NiFe film with silicon substrate.

Mapping short tandem repeats for liver gene expression traits helps prioritize potential causal variants for complex traits in pigs

Background:Short tandem repeats(STRs)were recently found to have significant impacts on gene expression and diseases in humans,but their roles on gene expression and complex traits in pigs remain unexplored.This study investigates the effects of STRs on gene expression in liver tissues based on the whole-genome sequences and RNA-Seq data of a discovery cohort of 260 F6 individuals and a validation population of 296 F7 individuals from a heterogeneous population generated from crosses among eight pig breeds.Results:We identified 5203 and 5868 significantly expression STRs(eSTRs,FDR<1%)in the F6 and F7 populations,respectively,most of which could be reciprocally validated(π1=0.92).The eSTRs explained 27.5%of the cisheritability of gene expression traits on average.We further identified 235 and 298 fine-mapped STRs through the Bayesian fine-mapping approach in the F6 and F7 pigs,respectively,which were significantly enriched in intron,ATAC peak,compartment A and H3K4me3 regions.We identified 20 fine-mapped STRs located in 100 kb windows upstream and downstream of published complex trait-associated SNPs,which colocalized with epigenetic markers such as H3K27ac and ATAC peaks.These included eSTR of the CLPB,PGLS,PSMD6 and DHDH genes,which are linked with genome-wide association study(GWAS)SNPs for blood-related traits,leg conformation,growth-related traits,and meat quality traits,respectively.Conclusions:This study provides insights into the effects of STRs on gene expression traits.The identified eSTRs are valuable resources for prioritizing causal STRs for complex traits in pigs.

Photometric Redshifts and Galaxy Clusters for DES DR2, DESI DR9, and HSC-SSP PDR3 Data

Photometric redshift(photoz)is a fundamental parameter for multi-wavelength photometric surveys,while galaxy clusters are important cosmological probes and ideal objects for exploring the dense environmental impact on galaxy evolution.We extend our previous work on estimating photoz and detecting galaxy clusters to the latest data releases of the Dark Energy Spectroscopic Instrument(DESI)imaging surveys,Dark Energy Survey(DES)and Hyper Suprime-Cam Subaru Strategic Program(HSC-SSP)imaging surveys and make corresponding catalogs publicly available for more extensive scientific applications.The photoz catalogs include accurate measurements of photoz and stellar mass for about 320,293and 134 million galaxies with r<23,i<24 and i<25 in DESI DR9,DES DR2 and HSC-SSP PDR3 data,respectively.The photoz accuracy is about 0.017,0.024 and 0.029 and the general redshift coverage is z<1,z<1.2 and z<1.6,respectively for those three surveys.The uncertainty of the logarithmic stellar mass that is inferred from stellar population synthesis fitting is about 0.2 dex.With the above photoz catalogs,galaxy clusters are detected using a fast cluster-finding algorithm.A total of 532,810,86,963 and 36,566 galaxy clusters with the number of members larger than 10 is discovered for DESI,DES and HSC-SSP,respectively.Their photoz accuracy is at the level of 0.01.The total mass of our clusters is also estimated by using the calibration relations between the optical richness and the mass measurement from X-ray and radio observations.The photoz and cluster catalogs are available at Science DB(https://www.doi.org/10.11922/sciencedb.o00069.00003)and Paper Data Repository(https://doi.org/10.12149/101089).

Microstructural Evolution of 6061 Alloy during Isothermal Heat Treatment

The semi-solid billet of 6061 aluminum alloy was prepared by the near-liquidus semi-continuous casting（LSC） with rosette or near-spheroide grains.The pre-deformation processing was applied before partial remelting to further improve the microstructure and properties of the semi-solid alloy.The effects of different processing parameters,such as holding temperature and holding time,on the semisolid microstructures during partial remelting have been investigated.It was found that the optimal partial remelting parameters should be 630℃ and 10-15 min for 6061 alloy cold rolled with 60% reduction in height of pre-deformation.The coarsening rates were anasysed by Lifshitz-Slyozov-Wagner（LSW） theory.The pre-deformed 6061 alloy exhibits lower coarsening rate constants than that of the as-cast one,and also lower than other alloys processed by different method found in previous literature.It is because the coarsening rate is associated with the initial microstructure and composition of the alloy.The secondary phases in the alloy inhibit the migration of the liquid film grain boundaries.The microstructure obtained by using the combination of near-liquidus semicontinuous casting and pre-deformation treatment is better than that without pre-deformation processing,which demonstrates that the used method is promising for fabricating high quality semi-solid alloys.

Mapping and analysis of a spatiotemporal H3K27ac and gene expression spectrum in pigs

The limited knowledge of genomic noncoding and regulatory regions has restricted our ability to decipher the genetic mechanisms underlying complex traits in pigs. In this study, we characterized the spatiotemporal landscape of putative enhancers and promoters and their target genes by combining H3K27ac-targeted Ch IP-Seq and RNA-Seq in fetal(prenatal days 74–75) and adult(postnatal days 132–150) tissues(brain, liver, heart, muscle and small intestine) sampled from Asian aboriginal Bama Xiang and European highly selected Large White pigs of both sexes. We identified 101,290 H3K27ac peaks, marking 18,521promoters and 82,769 enhancers, including peaks that were active across all tissues and developmental stages(which could indicate safe harbor locus for exogenous gene insertion) and tissue-and developmental stage-specific peaks(which regulate gene pathways matching tissue-and developmental stage-specific physiological functions). We found that H3K27ac and DNA methylation in the promoter region of the XIST gene may be involved in X chromosome inactivation and demonstrated the utility of the present resource for revealing the regulatory patterns of known causal genes and prioritizing candidate causal variants for complex traits in pigs. In addition, we identified an average of 1,124 super-enhancers per sample and found that they were more likely to show tissue-specific activity than ordinary peaks. We have developed a web browser to improve the accessibility of the results(http://segtp.jxau.edu.cn/pencode/?genome=sus Scr11).

Whole-genome sequence-based association study for immune cells in an eight-breed pig heterogeneous population

Pigs are an important domestic animal for meat production and animal models for biomedical research such as research on infectious diseases(Meurens et al.,2012).Immune cells,including T cells,B cells,monocytes,and macrophages,are among the major indicators of immune status in health and disease.Revealing the genetic basis of immune cell phenotypes would be helpful for improving the immunity of pigs genetically and reducing the disease occurrence,antibiotic usage.