80 results on '"Xinhua Hou"'
Search Results
2. Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs
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Wencheng Zong, Jinbu Wang, Runze Zhao, Naiqi Niu, Yanfang Su, Ziping Hu, Xin Liu, Xinhua Hou, Ligang Wang, Lixian Wang, and Longchao Zhang
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Body size ,GWAS ,Pig ,Skeleton ,Structural variations ,Animal culture ,SF1-1100 ,Veterinary medicine ,SF600-1100 - Abstract
Abstract Background During approximately 10,000 years of domestication and selection, a large number of structural variations (SVs) have emerged in the genome of pig breeds, profoundly influencing their phenotypes and the ability to adapt to the local environment. SVs (≥ 50 bp) are widely distributed in the genome, mainly in the form of insertion (INS), mobile element insertion (MEI), deletion (DEL), duplication (DUP), inversion (INV), and translocation (TRA). While studies have investigated the SVs in pig genomes, genome-wide association studies (GWAS)-based on SVs have been rarely conducted. Results Here, we obtained a high-quality SV map containing 123,151 SVs from 15 Large White and 15 Min pigs through integrating the power of several SV tools, with 53.95% of the SVs being reported for the first time. These high-quality SVs were used to recover the population genetic structure, confirming the accuracy of genotyping. Potential functional SV loci were then identified based on positional effects and breed stratification. Finally, GWAS were performed for 36 traits by genotyping the screened potential causal loci in the F2 population according to their corresponding genomic positions. We identified a large number of loci involved in 8 carcass traits and 6 skeletal traits on chromosome 7, with FKBP5 containing the most significant SV locus for almost all traits. In addition, we found several significant loci in intramuscular fat, abdominal circumference, heart weight, and liver weight, etc. Conclusions We constructed a high-quality SV map using high-coverage sequencing data and then analyzed them by performing GWAS for 25 carcass traits, 7 skeletal traits, and 4 meat quality traits to determine that SVs may affect body size between European and Chinese pig breeds.
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- 2023
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3. Identifying long non-coding RNAs and characterizing their functional roles in swine mammary gland from colostrogenesis to lactogenesis
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Lijun Shi, Longchao Zhang, Ligang Wang, Xin Liu, Hongmei Gao, Xinhua Hou, Fuping Zhao, Hua Yan, Wentao Cai, and Lixian Wang
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colostrum ,lncrna ,mammary gland ,pig ,weighted gene co-expression network analysis (wgcna) ,Zoology ,QL1-991 - Abstract
Objective This study was conducted to identify the functional long non-coding RNAs (lncRNAs) for swine lactation by RNA-seq data of mammary gland. Methods According to the RNA-seq data of swine mammary gland, we screened lncRNAs, performed differential expression analysis, and confirmed the functional lncRNAs for swine lactation by validation of genome wide association study (GWAS) signals, functional annotation and weighted gene co-expression network analysis (WGCNA). Results We totally identified 286 differentially expressed (DE) lncRNAs in mammary gland at different stages from 14 days prior to (-) parturition to day 1 after (+) parturition, and the expressions of most of lncRNAs were strongly changed from day −2 to day +1. Further, the GWAS signals of sow milk ability trait were significantly enriched in DE lncRNAs. Functional annotation revealed that these DE lncRNAs were mainly involved in mammary gland and lactation developing, milk composition metabolism and colostrum function. By performing weighted WGCNA, we identified 7 out of 12 lncRNA-mRNA modules that were highly associated with the mammary gland at day −14, day −2, and day +1, in which, 35 lncRNAs and 319 mRNAs were involved. Conclusion This study suggested that 18 lncRNAs and their 20 target genes were promising candidates for swine parturition and colostrum occurrence processes. Our research provided new insights into lncRNA profiles and their regulating mechanisms from colostrogenesis to lactogenesis in swine.
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- 2022
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4. A strategy for accurately and sensitively quantifying free and esterified fatty acids using liquid chromatography mass spectrometry
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Xiaohui Feng, Juan Wang, Zhonghai Tang, Bingyao Chen, Xinhua Hou, Jing Li, Shengnan Feng, Peng Li, and Qingshi Meng
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fatty acids ,isotopic-based derivatization ,chemical derivatization ,quantification ,meat processing ,Nutrition. Foods and food supply ,TX341-641 - Abstract
Fatty acid (FA) composition of foods dictates a diversity of aspects regarding food quality, ranging from product shelf life, sensory properties to nutrition. There is a challenge to quantitate FAs using liquid chromatography-mass spectrometry due to poor ionization efficiency and matrix effects. Here, an isotopic-tagged derivatization strategy was established to accurately and sensitively quantify free and esterified FAs. After derivatization reaction, the detection sensitivity of FAs was remarkably improved and the limit of quantitation was lower than 100 ng/L. The quantitative errors caused by matrix effects were diminished benefiting from isotope-derivatized internal standards. The established quantitation strategy was successfully applied to verify both free and esterified FA contents in meat after different post-harvest procedures, finding that free polyunsaturated FAs increased significantly during freezing process.
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- 2022
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5. The landscape of chromatin accessibility in skeletal muscle during embryonic development in pigs
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Jingwei Yue, Xinhua Hou, Xin Liu, Ligang Wang, Hongmei Gao, Fuping Zhao, Lijun Shi, Liangyu Shi, Hua Yan, Tianyu Deng, Jianfei Gong, Lixian Wang, and Longchao Zhang
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Chromatin accessibility ,Embryo ,Pig ,Skeletal muscle ,Transcriptome ,Animal culture ,SF1-1100 ,Veterinary medicine ,SF600-1100 - Abstract
Abstract Background The development of skeletal muscle in pigs during the embryonic stage is precisely regulated by transcriptional mechanisms, which depend on chromatin accessibility. However, how chromatin accessibility plays a regulatory role during embryonic skeletal muscle development in pigs has not been reported. To gain insight into the landscape of chromatin accessibility and the associated genome-wide transcriptome during embryonic muscle development, we performed ATAC-seq and RNA-seq analyses of skeletal muscle from pig embryos at 45, 70 and 100 days post coitus (dpc). Results In total, 21,638, 35,447 and 60,181 unique regions (or peaks) were found across the embryos at 45 dpc (LW45), 70 dpc (LW70) and 100 dpc (LW100), respectively. More than 91% of the peaks were annotated within − 1 kb to 100 bp of transcription start sites (TSSs). First, widespread increases in specific accessible chromatin regions (ACRs) from embryos at 45 to 100 dpc suggested that the regulatory mechanisms became increasingly complicated during embryonic development. Second, the findings from integrated ATAC-seq and RNA-seq analyses showed that not only the numbers but also the intensities of ACRs could control the expression of associated genes. Moreover, the motif screening of stage-specific ACRs revealed some transcription factors that regulate muscle development-related genes, such as MyoG, Mef2c, and Mef2d. Several potential transcriptional repressors, including E2F6, OTX2 and CTCF, were identified among the genes that exhibited different regulation trends between the ATAC-seq and RNA-seq data. Conclusions This work indicates that chromatin accessibility plays an important regulatory role in the embryonic muscle development of pigs and regulates the temporal and spatial expression patterns of key genes in muscle development by influencing the binding of transcription factors. Our results contribute to a better understanding of the regulatory dynamics of genes involved in pig embryonic skeletal muscle development.
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- 2021
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6. Optimizing the Construction and Update Strategies for the Genomic Selection of Pig Reference and Candidate Populations in China
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Xia Wei, Tian Zhang, Ligang Wang, Longchao Zhang, Xinhua Hou, Hua Yan, and Lixian Wang
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genomic selection ,optimizing strategies ,reference population ,candidate population ,breeding scheme ,Genetics ,QH426-470 - Abstract
Optimizing the construction and update strategies for reference and candidate populations is the basis of the application of genomic selection (GS). In this study, we first simulated1200-purebred-pigs population that have been popular in China for 20 generations to study the effects of different population sizes and the relationship between individuals of the reference and candidate populations. The results showed that the accuracy was positively correlated with the size of the reference population within the same generation (r = 0.9366, p < 0.05), while was negatively correlated with the number of generation intervals between the reference and candidate populations (r = −0.9267, p < 0.01). When the reference population accumulated more than seven generations, the accuracy began to decline. We then simulated the population structure of 1200 purebred pigs for five generations and studied the effects of different heritabilities (0.1, 0.3, and 0.5), genotyping proportions (20, 30, and 50%), and sex ratios on the accuracy of the genomic estimate breeding value (GEBV) and genetic progress. The results showed that if the proportion of genotyping individuals accounts for 20% of the candidate population, the traits with different heritabilities can be genotyped according to the sex ratio of 1:1male to female. If the proportion is 30% and the traits are of low heritability (0.1), the sex ratio of 1:1 male to female is the best. If the traits are of medium or high heritability, the male-to-female ratio is 1:1, 1:2, or 2:1, which may achieve higher genetic progress. If the genotyping proportion is up to 50%, for low heritability traits (0.1), the proportion of sows from all genotyping individuals should not be less than 25%, and for the medium and high heritability traits, the optimal choice for the male-to-female ratio is 1:1, which may obtain the greatest genetic progress. This study provides a reference for determining a construction and update plan for the reference population of breeding pigs.
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- 2022
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7. IRLnc: a novel functional noncoding RNA contributes to intramuscular fat deposition
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Ligang Wang, Zhong-Yin Zhou, Tian Zhang, Longchao Zhang, Xinhua Hou, Hua Yan, and Lixian Wang
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Intramuscular fat ,Long non-coding RNA ,Insulin resistance ,Pig ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Intramuscular fat (IMF) is associated with meat quality and insulin resistance in animals. Research on genetic mechanism of IMF decomposition has positive meaning to pork quality and diseases such as obesity and type 2 diabetes treatment. In this study, an IMF trait segregation population was used to perform RNA sequencing and to analyze the joint or independent effects of genes and long intergenic non-coding RNAs (lincRNAs) on IMF. Results A total of 26 genes including six lincRNA genes show significantly different expression between high- and low-IMF pigs. Interesting, one lincRNA gene, named IMF related lincRNA (IRLnc) not only has a 292-bp conserved region in 100 vertebrates but also has conserved up and down stream genes (
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- 2021
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8. Metabolite and Proteomic Profiling of Serum Reveals the Differences in Molecular Immunity between Min and Large White Pig Breeds
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Liyu Yang, Xin Liu, Xiaoyu Huang, Longchao Zhang, Hua Yan, Xinhua Hou, Lixian Wang, and Ligang Wang
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Min pigs ,Large White pigs ,metabolomic ,proteomics ,biomarker ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Pig diseases seriously threaten the health of pigs and the benefits of pig production. Previous research has indicated that Chinese native pigs, such as the Min (M) pig, has a better disease resistance ability than Large White (LW) pigs. However, the molecular mechanism of this resistance is still unclear. In our study, we used serum untargeted metabolomics and proteomics, interrogated to characterize differences in the molecular immunities between six resistant and six susceptible pigs raised in the same environment. A total of 62 metabolites were identified as being significantly exhibited in M and LW pigs. Ensemble feature selection (EFS) machine learning methods were used to predict biomarkers of metabolites and proteins, and the top 30 were selected and retained. Weighted gene co-expression network analysis (WGCNA) confirmed that four key metabolites, PC (18:1 (11 Z)/20:0), PC (14:0/P-18: 0), PC (18:3 (6 Z, 9 Z, 12 Z)/16:0), and PC (16:1 (9 Z)/22:2 (13 Z, 16 Z)), were significantly associated with phenotypes, such as cytokines, and different pig breeds. Correlation network analysis showed that 15 proteins were significantly correlated with the expression of both cytokines and unsaturated fatty acid metabolites. Quantitative trait locus (QTL) co-location analysis results showed that 13 of 15 proteins co-localized with immune or polyunsaturated fatty acid (PUFA)-related QTL. Moreover, seven of them co-localized with both immune and PUFA QTLs, including proteasome 20S subunit beta 8 (PSMB8), mannose binding lectin 1 (MBL1), and interleukin-1 receptor accessory protein (IL1RAP). These proteins may play important roles in regulating the production or metabolism of unsaturated fatty acids and immune factors. Most of the proteins could be validated with parallel reaction monitoring, which suggests that these proteins may play an essential role in producing or regulating unsaturated fatty acids and immune factors to cope with the adaptive immunity of different pig breeds. Our study provides a basis for further clarifying the disease resistance mechanism of pigs.
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- 2023
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9. Integrative Analysis of Nanopore and Illumina Sequencing Reveals Alternative Splicing Complexity in Pig Longissimus Dorsi Muscle
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Ze Shu, Ligang Wang, Jinbu Wang, Longchao Zhang, Xinhua Hou, Hua Yan, and Lixian Wang
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alternative splicing ,pig ,intramuscular fat ,nanopore sequencing ,RNA-seq ,Genetics ,QH426-470 - Abstract
Alternative splicing (AS) is a key step in the post-transcriptional regulation of gene expression that can affect intramuscular fat (IMF). In this study, longissimus dorsi muscles from 30 pigs in high- and low- IMF groups were used to perform Oxford Nanopore Technologies (ONT) full-length sequencing and Illumina strand-specific RNA-seq. A total of 43,688 full-length transcripts were identified, with 4,322 novel genes and 30,795 novel transcripts. Using AStalavista, a total of 14,728 AS events were detected in the longissimus dorsi muscle. About 17.79% of the genes produced splicing isoforms, in which exon skipping was the most frequent AS event. By analyzing the expression differences of mRNAs and splicing isoforms, we found that differentially expressed mRNAs with splicing isoforms could participate in skeletal muscle development and fatty acid metabolism, which might determine muscle-related traits. SERBP1, MYL1, TNNT3, and TNNT1 were identified with multiple splicing isoforms, with significant differences in expression. AS events occurring in IFI6 and GADD45G may cause significant differences in gene expression. Other AS events, such as ONT.15153.3, may regulate the function of ART1 by regulating the expression of different transcripts. Moreover, co-expression and protein-protein interaction (PPI) analysis indicated that several genes (MRPL27, AAR2, PYGM, PSMD4, SCNM1, and HNRNPDL) may be related to intramuscular fat. The splicing isoforms investigated in our research provide a reference for the study of alternative splicing regulation of intramuscular fat deposition.
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- 2022
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10. Liver transcriptome profiling and functional analysis of intrauterine growth restriction (IUGR) piglets reveals a genetic correction and sexual-dimorphic gene expression during postnatal development
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Hongmei Gao, Longchao Zhang, Ligang Wang, Xin Liu, Xinhua Hou, Fuping Zhao, Hua Yan, and Lixian Wang
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Intrauterine growth restriction (IUGR) ,Piglets ,Liver ,Transcriptome ,Sexual dimorphism ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Intrauterine growth restriction (IUGR) remains a major problem associated with swine production. Thus, understanding the physiological changes of postnatal IUGR piglets would aid in improving growth performance. Moreover, liver metabolism plays an important role in the growth and survival of neonatal piglets. Results By profiling the transcriptome of liver samples on postnatal Days 1, 7, and 28, our study focused on characterizing the growth, function, and metabolism in the liver of IUGR neonatal piglets. Our study demonstrates that the livers of IUGR piglets were associated with a series of complications, including inflammatory stress and immune dysregulation; cytoskeleton and membrane structure disorganization; dysregulated transcription events; and abnormal glucocorticoid metabolism. In addition, the abnormal liver function index in the serum [alanine aminotransferase (ALT), aspartate aminotransferase (AST), and total protein (TP)], coupled with hepatic pathological and ultrastructural morphological changes are indicative of liver damage and dysfunction in IUGR piglets. Moreover, these results reveal the sex-biased developmental dynamics between male and female IUGR piglets, and that male IUGR piglets may be more sensitive to disrupted metabolic homeostasis. Conclusions These observations provide a detailed reference for understanding the mechanisms and characterizations of IUGR liver functions, and suggest that the potential strategies for improving the survival and growth performance of IUGR offspring should consider the balance between postnatal catch-up growth and adverse metabolic consequences. In particular, sex-specific intervention strategies should be considered for both female and male IUGR piglets.
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- 2020
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11. Estimation of inbreeding and identification of regions under heavy selection based on runs of homozygosity in a Large White pig population
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Liangyu Shi, Ligang Wang, Jiaxin Liu, Tianyu Deng, Hua Yan, Longchao Zhang, Xin Liu, Hongmei Gao, Xinhua Hou, Lixian Wang, and Fuping Zhao
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Candidate genes ,Inbreeding coefficients ,Runs of homozygosity ,Sus scrofa ,Animal culture ,SF1-1100 ,Veterinary medicine ,SF600-1100 - Abstract
Abstract Background Runs of homozygosity (ROHs) are homozygous segments of the genome where the two haplotypes inherited from the parents are identical. The current availability of genotypes for a very large number of single nucleotide polymorphisms (SNPs) is leading to more accurate characterization of ROHs in the whole genome. Here, we investigated the occurrence and distribution of ROHs in 3,692 Large White pigs and compared estimates of inbreeding coefficients calculated based on ROHs (F ROH), homozygosity (F HOM), genomic relationship matrix (F GRM) and pedigree (F PED). Furthermore, we identified genomic regions with high ROH frequencies and annotated their candidate genes. Results In total, 176,182 ROHs were identified from 3,569 animals, and all individuals displayed at least one ROH longer than 1 Mb. The ROHs identified were unevenly distributed on the autosomes. The highest and lowest coverages of Sus scrofa chromosomes (SSC) by ROH were on SSC14 and SSC13, respectively. The highest pairwise correlation among the different inbreeding coefficient estimates was 0.95 between F ROH_total and F HOM, while the lowest was − 0.083 between F GRM and F PED. The correlations between F PED and F ROH using four classes of ROH lengths ranged from 0.18 to 0.37 and increased with increasing ROH length, except for ROH > 10 Mb. Twelve ROH islands were located on four chromosomes (SSC1, 4, 6 and 14). These ROH islands harboured genes associated with reproduction, muscular development, fat deposition and adaptation, such as SIRT1, MYPN, SETDB1 and PSMD4. Conclusion F ROH can be used to accurately assess individual inbreeding levels compared to other inbreeding coefficient estimators. In the absence of pedigree records, F ROH can provide an alternative to inbreeding estimates. Our findings can be used not only to effectively increase the response to selection by appropriately managing the rate of inbreeding and minimizing the negative effects of inbreeding depression but also to help detect genomic regions with an effect on traits under selection.
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- 2020
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12. Integrated Proteotranscriptomics Reveals Differences in Molecular Immunity between Min and Large White Pig Breeds
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Liyu Yang, Xin Liu, Xiaoyu Huang, Na Li, Longchao Zhang, Hua Yan, Xinhua Hou, Lixian Wang, and Ligang Wang
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transcriptome ,proteome ,cytokines ,min pigs ,disease resistance ,Biology (General) ,QH301-705.5 - Abstract
Long-term selection or evolution is an important factor governing the development of disease resistance in pigs. To better clarify the molecular mechanisms underlying different levels of disease resistance, we used transcriptomics and proteomics analysis to characterize differences in the immunities between six resistant (Min pig) and six susceptible (Large White, LW) pigs which were raised in the same environment. A total of 135 proteins and 791 genes were identified as being differentially expressed between the Large White and Min pig groups. Protein expression clustering and functional analysis revealed that proteins related to immune system process, humoral immune response, the B cell receptor signaling pathway, lymphocyte-mediated immunity, and innate immune responses were more highly expressed in Min pigs. Transcriptome gene set enrichment analysis was used to reveal that pathways of cell adhesion molecules and antigen processing and presentation are significantly enriched in Min pigs. Integrated proteomics and transcriptomics data analysis identified 16 genes that are differentially expressed at both the mRNA and protein levels. In addition, 13 out of these 16 genes were related to the quantitative trait loci of immune diseases, including neural EGFL-like 2 (NELL2) and lactate dehydrogenase B (LDHB), which are involved in innate immunity. Correlation analysis between the genes/proteins and cytokines shows upregulated proteins in LW pigs in association with immunosuppressive/pro-inflammatory cytokines, such as interleukin (IL) 10, IL6, and tumor necrosis factor alpha. This was further validated using parallel reaction monitoring analysis. In summary, we discovered several potential candidate pathways and key genes/proteins involved in determining differences in disease resistance between the two studied pig breeds, which could provide new insights into the breeding of pigs for disease resistance.
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- 2022
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13. Integrating Genome-Wide Association Study with RNA-Sequencing Reveals HDAC9 as a Candidate Gene Influencing Loin Muscle Area in Beijing Black Pigs
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Renda Hou, Li Chen, Xiance Liu, Hai Liu, Guohua Shi, Xinhua Hou, Run Zhang, Man Yang, Naiqi Niu, Lixian Wang, and Longchao Zhang
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Beijing Black pig ,HDAC9 ,genome-wide association study ,loin muscle area ,transcriptome ,Biology (General) ,QH301-705.5 - Abstract
Loin muscle area (LMA) is an important meat production trait and plays a key role in determining carcass leanness. Genome-wide association study (GWAS) and RNA sequencing (RNA-seq) analysis were used to identify candidate LMA genes in Beijing Black pigs, a popular breed among consumers in northern China. Ten single nucleotide polymorphisms (SNPs) in sus scrofa chromosome (SSC) 9 were significantly associated with LMA. These SNPs were mapped to a 2.90 Mb (84.94–87.84 Mb) region. A total of 11 annotated genes were mapped on this region, namely MEOX2, CRPPA, SOSTDC1, LRRC72, ANKMY2, BZW2, TSPAN13, AGR2, AHR, SNX13, and HDAC9. In addition, RNA-seq analysis was performed between the high- and low-LMA groups, and 329 differentially expressed genes (DEGs) were identified. Further, Kyoto Encyclopedia of Genes and Genomes analysis based on DEGs revealed that the JAK/STAT signaling pathway and oxytocin signaling pathway may be responsible for LMA. Both GWAS and RNA-seq analysis identified the HDAC9 gene, indicating that it may be an important candidate gene affecting LMA in Beijing Black pigs. The findings provide valuable molecular insights into the mechanisms that influence LMA content in pigs, which can be utilized in targeted approaches to enhance meat quality and commercial profitability.
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- 2022
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14. Identification of SNPs and Candidate Genes for Milk Production Ability in Yorkshire Pigs
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Lijun Shi, Yang Li, Qian Liu, Longchao Zhang, Ligang Wang, Xin Liu, Hongmei Gao, Xinhua Hou, Fuping Zhao, Hua Yan, and Lixian Wang
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Yorkshire pig ,litter weight gain ,GWAS ,SNP ,candidate gene ,Genetics ,QH426-470 - Abstract
Sow milk production ability is an important limiting factor impacting suboptimal growth and the survival of piglets. Through pig genetic improvement, litter sizes have been increased. Larger litters need more suckling mammary glands, which results in increased milk from the lactating sow. Hence, there is much significance to exploring sow lactation performance. For milk production ability, it is not practical to directly measure the milk yield, we used litter weight gain (LWG) throughout sow lactation as an indicator. In this study, we estimated the heritability of LWG, namely, 0.18 ± 0.07. We then performed a GWAS, and detected seven significant SNPs, namely, Sus scrofa Chromosome (SSC) 2: ASGA0010040 (p = 7.73E-11); SSC2:MARC0029355 (p = 1.30E-08), SSC6: WU_10.2_6_65751151 (p = 1.32E-10), SSC7: MARC0058875 (p = 4.99E-09), SSC10: WU_10.2_10_49571394 (p = 6.79E-08), SSC11: M1GA0014659 (p = 1.19E-07), and SSC15: MARC0042106 (p = 1.16E-07). We performed the distribution of phenotypes corresponding to the genotypes of seven significant SNPs and showed that ASGA0010040, MARC0029355, MARC0058875, WU_10.2_10_49571394, M1GA0014659, and MARC0042106 had extreme phenotypic values that corresponded to the homozygous genotypes, while the intermediate values corresponded to the heterozygous genotypes. We screened for flanking regions ± 200 kb nearby the seven significant SNPs, and identified 38 genes in total. Among them, 28 of the candidates were involved in lactose metabolism, colostrum immunity, milk protein, and milk fat by functional enrichment analysis. Through the combined analysis between 28 candidate genes and transcriptome data of the sow mammary gland, we found nine commons (ANO3, MUC15, DISP3, FBXO6, CLCN6, HLA-DRA, SLA-DRB1, SLA-DQB1, and SLA-DQA1). Furthermore, by comparing the chromosome positions of the candidate genes with the quantitative trait locus (QTLs) as previously reported, a total of 17 genes were found to be within 0.86–94.02 Mb of the reported QTLs for sow milk production ability, in which, NAV2 was found to be located with 0.86 Mb of the QTL region ssc2: 40936355. In conclusion, we identified seven significant SNPs located on SSC2, 6, 7, 10, 11, and 15, and propose 28 candidate genes for the ability to produce milk in Yorkshire pigs, 10 of which were key candidates.
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- 2021
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15. Genome-wide identification of RNA editing in seven porcine tissues by matched DNA and RNA high-throughput sequencing
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Yuebo Zhang, Longchao Zhang, Jingwei Yue, Xia Wei, Ligang Wang, Xin Liu, Hongmei Gao, Xinhua Hou, Fuping Zhao, Hua Yan, and Lixian Wang
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ADAR ,A-to-G ,High-throughput sequencing ,RNA editing ,Swine ,Animal culture ,SF1-1100 ,Veterinary medicine ,SF600-1100 - Abstract
Abstract Background RNA editing is a co/posttranscriptional modification mechanism that increases the diversity of transcripts, with potential functional consequences. The advent of next-generation sequencing technologies has enabled the identification of RNA edits at unprecedented throughput and resolution. However, our knowledge of RNA editing in swine is still limited. Results Here, we utilized RES-Scanner to identify RNA editing sites in the brain, subcutaneous fat, heart, liver, muscle, lung and ovary in three 180-day-old Large White gilts based on matched strand-specific RNA sequencing and whole-genome resequencing datasets. In total, we identified 74863 editing sites, and 92.1% of these sites caused adenosine-to-guanosine (A-to-G) conversion. Most A-to-G sites were located in noncoding regions and generally had low editing levels. In total, 151 A-to-G sites were detected in coding regions (CDS), including 94 sites that could lead to nonsynonymous amino acid changes. We provide further evidence supporting a previous observation that pig transcriptomes are highly editable at PRE-1 elements. The number of A-to-G editing sites ranged from 4155 (muscle) to 25001 (brain) across the seven tissues. The expression levels of the ADAR enzymes could explain some but not all of this variation across tissues. The functional analysis of the genes with tissue-specific editing sites in each tissue revealed that RNA editing might play important roles in tissue function. Specifically, more pathways showed significant enrichment in the fat and liver than in other tissues, while no pathway was enriched in the muscle. Conclusions This study identified a total of 74863 nonredundant RNA editing sites in seven tissues and revealed the potential importance of RNA editing in tissue function. Our findings largely extend the porcine editome and enhance our understanding of RNA editing in swine.
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- 2019
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16. Copy Number Variations Contribute to Intramuscular Fat Content Differences by Affecting the Expression of PELP1 Alternative Splices in Pigs
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Xia Wei, Ze Shu, Ligang Wang, Tian Zhang, Longchao Zhang, Xinhua Hou, Hua Yan, and Lixian Wang
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intramuscular fat ,copy number variations ,alternative splicing ,PELP1 ,pig ,Veterinary medicine ,SF600-1100 ,Zoology ,QL1-991 - Abstract
Intramuscular fat (IMF) is a key meat quality trait. Research on the genetic mechanisms of IMF decomposition is valuable for both pork quality improvement and the treatment of obesity and type 2 diabetes. Copy number variations (CNVs) are a type of variant that may influence meat quality. In this study, a total of 1185 CNV regions (CNVRs) including 393 duplicated CNVRs, 432 deleted CNVRs, and 361 CNVRs with both duplicated and deleted status were identified in a pig F2 resource population using next-generation sequencing data. A genome-wide association study (GWAS) was then performed between CNVs and IMF, and a total of 19 CNVRs were found to be significantly associated with IMF. QTL colocation analysis indicated that 3 of the 19 CNVRs overlapped with known QTLs. RNA-seq and qPCR validation results indicated that CNV150, which is located on the 3′UTR end of the proline, as well as glutamate and the leucine rich protein 1 (PELP1) gene may affect the expression of PELP1 alternative splices. Sequence alignment and Alphafold2 structure prediction results indicated that the two alternative splices of PELP1 have a 23 AA sequence variation and a helix-fold structure variation. This region is located in the region of interaction between PELP1 and other proteins which have been reported to be significantly associated with fat deposition or insulin resistance. We infer that the CNVR may influence IMF content by regulating the alternative splicing of the PELP1 gene and ultimately affects the structure of the PELP1 protein. In conclusion, we found some CNVRs, especially CNV150, located in PELP1 that affect IMF. These findings suggest a novel mechanistic approach for meat quality improvement in animals and the potential treatment of insulin resistance in human beings.
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- 2022
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17. Genome-Wide Expression Profiling of mRNAs, lncRNAs and circRNAs in Skeletal Muscle of Two Different Pig Breeds
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Xinhua Hou, Ligang Wang, Fuping Zhao, Xin Liu, Hongmei Gao, Lijun Shi, Hua Yan, Lixian Wang, and Longchao Zhang
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pigs ,RNA-seq ,skeletal muscle ,mRNAs ,lncRNAs ,circRNAs ,Veterinary medicine ,SF600-1100 ,Zoology ,QL1-991 - Abstract
RNA-Seq technology is widely used to analyze global changes in the transcriptome and investigate the influence on relevant phenotypic traits. Beijing Black pigs show differences in growth rate and meat quality compared to western pig breeds. However, the molecular mechanisms responsible for such phenotypic differences remain unknown. In this study, longissimus dorsi muscles from Beijing Black and Yorkshire pigs were used to construct RNA libraries and perform RNA-seq. Significantly different expressions were observed in 1051 mRNAs, 322 lncRNAs, and 82 circRNAs. GO and KEGG pathway annotation showed that differentially expressed mRNAs participated in skeletal muscle development and fatty acid metabolism, which determined the muscle-related traits. To explore the regulatory role of lncRNAs, the cis and trans-target genes were predicted and these lncRNAswere involved in the biological processes related to skeletal muscle development and fatty acid metabolismvia their target genes. CircRNAs play a ceRNA role by binding to miRNAs. Therefore, the potential miRNAs of differentially expressed circRNAs were predicted and interaction networks among circRNAs, miRNAs, and key regulatory mRNAs were constructed to illustrate the function of circRNAs underlying skeletal muscle development and fatty acid metabolism. This study provides new clues for elucidating muscle phenotypic variation in pigs.
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- 2021
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18. A Comparison of the Behavior, Physiology, and Offspring Resilience of Gestating Sows When Raised in a Group Housing System and Individual Stalls
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Xin Liu, Pengkang Song, Hua Yan, Longchao Zhang, Ligang Wang, Fuping Zhao, Hongmei Gao, Xinhua Hou, Lijun Shi, Bugao Li, and Lixian Wang
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group housing system ,individual stall ,behavior ,stress hormone ,offspring ,gestating sows ,Veterinary medicine ,SF600-1100 ,Zoology ,QL1-991 - Abstract
Being in a confined environment causes chronic stress in gestating sows, which is detrimental for sow health, welfare and, consequently, offspring physiology. This study assessed the health and welfare of gestating sows housed in a group housing system compared to individual gestation stalls. After pregnancy was confirmed, experimental sows were divided randomly into two groups: the group housing system (GS), with the electronic sow feeding (ESF) system; or individual stall (IS). The behavior of sows housed in the GS or IS was then compared; throughout pregnancy, GS sows displayed more exploratory behavior, less vacuum chewing, and less sitting behavior (p < 0.05). IS sows showed higher stress hormone levels than GS sows. In particular, at 41 days of gestation, the concentration of the adrenocorticotropic hormone (ACTH) and adrenaline (A) in IS sows was significantly higher than that of GS sows, and the A level of IS sows remained significantly higher at 71 days of gestation (p < 0.01). The lipopolysaccharide (LPS) test was carried out in the weaned piglets of the studied sows. Compared with the offspring of gestating sows housed in GS (PG) or IS (PS), PG experienced a shorter period of high temperature and showed a quicker return to the normal state (p < 0.05). Additionally, their lower levels of stress hormone (p < 0.01) suggest that PG did not suffer from as much stress as PS. These findings suggested that gestating sows housed in GS were more able to carry out their natural behaviors and, therefore, had lower levels of stress and improved welfare. In addition, PG also showed better disease resistance and resilience. These results will provide a research basis for the welfare and breeding of gestating sows.
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- 2021
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19. Genome-Wide Association Analysis Identified BMPR1A as a Novel Candidate Gene Affecting the Number of Thoracic Vertebrae in a Large White × Minzhu Intercross Pig Population
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Qian Liu, Jingwei Yue, Naiqi Niu, Xin Liu, Hua Yan, Fuping Zhao, Xinhua Hou, Hongmei Gao, Lijun Shi, Lixian Wang, Ligang Wang, and Longchao Zhang
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BMPR1A ,FOS ,genome-wide association study ,number of thoracic vertebrae ,pig ,Veterinary medicine ,SF600-1100 ,Zoology ,QL1-991 - Abstract
The number of vertebrae (NV), especially the number of thoracic vertebrae (NTV), varies among pig breeds. The NTV is controlled by vertebral segmentation and the number of somites during embryonic development. Although there is a high correlation between the NTV and NV, studies on a fixed NV have mainly considered the absolute numbers of thoracic vertebrae instead of vertebral segmentation. Therefore, this study aimed to discover variants associated with the NTV by considering the effect of the NV in pigs. The NTV and NV of 542 F2 individuals from a Large White × Minzhu pig crossbreed were recorded. All animals were genotyped for VRTN g.19034 A > C, LTBP2 c.4481A > C, and 37 missense or splice variants previously reported in a 951-kb interval on SSC7 and 147 single nucleotide polymorphisms (SNPs) on SSC14. To identify NTV-associated SNPs, we firstly performed a genome-wide association study (GWAS) using the Q + K (population structure + kinship matrix) model in TASSEL. With the NV as a covariate, the obtained data were used to identify the SNPs with the most significant genome-wide association with the NTV by performing a GWAS on a PorcineSNP60K Genotyping BeadChip. Finally, a conditional GWAS was performed by fixing this SNP. The GWAS showed that 31 SNPs on SSC7 have significant genome-wide associations with the NTV. No missense or splice variants were found to be associated with the NTV significantly. A linkage disequilibrium analysis suggested the existence of quantitative trait loci (QTL) in a 479-Kb region on SSC7, which contained a critical candidate gene FOS for the NTV in pigs. Subsequently, a conditional GWAS was performed by fixing M1GA0010658, the most significant of these SNPs. Two SNPs in BMPR1A were found to have significant genome-wide associations and a significant dominant effect. The leading SNP, S14_87859370, accounted for 3.86% of the phenotypic variance. Our study uncovered that regulation variants in FOS on SSC7 and in BMPR1A on SSC14 might play important roles in controlling the NTV, and thus these genetic factors may be harnessed for increasing the NTV in pigs.
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- 2020
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20. Genome-Wide Identification of RNA Editing Sites Affecting Intramuscular Fat in Pigs
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Ligang Wang, Jingna Li, Xinhua Hou, Hua Yan, Longchao Zhang, Xin Liu, Hongmei Gao, Fuping Zhao, and Lixian Wang
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high-throughput sequencing ,RNA editing ,muscle growth ,intramuscular fat ,swine ,Veterinary medicine ,SF600-1100 ,Zoology ,QL1-991 - Abstract
Intramuscular fat (IMF) is essential for improving the palatability and flavor of meat, and it is strongly associated with human insulin resistance. RNA editing is a widespread regulating event in different tissues. Here, we investigated the global RNA editing difference of two groups of pig with different IMF contents to find the potential editing sites affecting IMF. In this research, RES-Scanner and REDItools were used to identify RNA editing sites based on the whole genome and transcriptome sequencing data of the high and low groups composed of three full-sib pairs with opposite IMF phenotypes. A total of 295 RNA editing sites were investigated in the longissimus dorsi muscle, and 90.17% of these sites caused A to G conversion. After annotation, most editing sites were located in noncoding regions (including five sites located on the 3′ UTR regions). Five editing sites (including two sites that could lead to nonsynonymous amino acid changes) were located in the exons of genes. A total of 36 intergroup (high and low IMF) differential RNA editing sites were found in 33 genes. Some candidate editing sites, such as sites in acyl-coenzymeA: cholesterol acyltransferase 1 (ACAT1), coatomer protein, subunit alpha (COPA), and nuclear receptor coactivator 3 (NCOA3), were selected as candidate RNA editing sites associated with IMF. One site located on the 3′ UTR region of growth hormone secretagogue receptor (GHSR) may regulate GHSR expression by affecting the interaction of miRNA and mRNA. In conclusion, we identified a total of 36 nonredundant RNA editing sites in the longissimus dorsi muscle, which may reveal the potential importance of RNA editing in IMF. Four were selected as candidate sites associated with IMF. Our findings provide some new insights of RNA editing function in pig longissimus dorsi muscle which useful for pig IMF breeding or human insulin resistances research.
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- 2020
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21. NTN1 Affects Porcine Intramuscular Fat Content by Affecting the Expression of Myogenic Regulatory Factors
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Ligang Wang, Lingling Zhao, Longchao Zhang, Xin Liu, Xinhua Hou, Hongmei Gao, Hua Yan, Fuping Zhao, and Lixian Wang
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copy number variation ,intramuscular fat content ,NTN1 ,swine ,Veterinary medicine ,SF600-1100 ,Zoology ,QL1-991 - Abstract
Intramuscular fat (IMF) content is an important economic trait for pork quality. Our previous results regarding the genome-wide association between IMF content and copy number variations (CNVs) indicated that the CNV within Netrin-1(NTN1-CNV) was significantly associated with IMF. In order to validate the effect of NTN1-CNV, we detected the Netrin-1 (NTN1) gene dose and protein expression content in the longissimus dorsi of different IMF content pigs using Western blotting and investigated the expression of NTN1 RNA in different tissues using real-time quantitative polymerase chain reaction (qPCR). The knock-down of the NTN1 gene in C2C12 and 3T3-L1 cells and over-expression in C2C12 cells during the proliferation and differentiation stage were also investigated to explore the possible pathway of action of NTN1. The results showed that in individuals with IMF content differences, the gene dose of NTN1 and the expression of NTN1 protein were also significantly different, which indicated that NTN1-CNV may directly affect IMF by its coding protein. NTN1 had the highest expression in pig longissimus dorsi and backfat tissues, which indicates that NTN1 may play an important role in muscle and fat tissues. The in vitro validation assay indicated that NTN1 silencing could promote the proliferation and inhibit the differentiation of C2C12 cells, with no effect on 3T3-L1 cells. Additionally, NTN1 over-expression could inhibit the proliferation and promote the differentiation of C2C12 cells. Combined with previous research, we conclude that NTN1-CNV may affect IMF by its gene dose, and the expression of NTN1 may affect the proliferation and differentiation of muscle cells by the AMP-activated protein kinase (AMPK) pathway and finally influence the IMF.
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- 2019
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22. Genome-Wide Profiling of the Microrna Transcriptome Regulatory Network to Identify Putative Candidate Genes Associated with Backfat Deposition in Pigs
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Xin Liu, Jianfei Gong, Ligang Wang, Xinhua Hou, Hongmei Gao, Hua Yan, Fuping Zhao, Longchao Zhang, and Lixian Wang
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backfat deposition ,candidate gene ,expression profile ,pig ,regulatory network ,Veterinary medicine ,SF600-1100 ,Zoology ,QL1-991 - Abstract
Backfat deposition is strongly related to carcass traits, growth rate, feed conversion rate, and reproductive performance in pig production. To understand the molecular mechanisms underlying porcine backfat thickness phenotypes, transcriptome and miRNA profiling of backfat from high-backfat thickness and low-backfat thickness pigs were performed by RNA sequencing. Twenty genes encoding for miRNAs and 126 genes encoding for protein-coding genes were found to be differentially expressed between the two libraries. After integrative analysis of DEMs targets and DEGs, a total of 33 mRNA‒miRNA interaction pairs were identified, and the regulatory networks of these pairs were determined. Among these genes, five (AQP9, DKK3, GLYCTK, GLIPR1, and DUSP2) related to fat deposition were found to be strong candidate genes, and mir-31-5p/AQP9 and mir-31-5p/GLIPR1 may play important roles in fat deposition. Additionally, potential adipogenesis-related genes and miRNAs were identified. These findings improve the current understanding of the molecular genetic mechanisms of subcutaneous fat deposition in pigs and provide a foundation for further studies.
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- 2019
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23. New results on periodic solutions of delayed Nicholson's blowflies models
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Xinhua Hou and Lian Duan
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nicholson's blowflies model ,positive periodic solution ,coincidence degree ,nonlinear density-dependent mortality term ,Mathematics ,QA1-939 - Abstract
This paper is concerned with a class of Nicholson's blowflies models with a nonlinear density-dependent mortality term. We use coincidence degree theory and give several sufficient conditions which guarantee the existence of positive periodic solutions of the model. Moreover, we give an example to illustrate our main results.
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- 2012
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24. MicroRNA-21 Regulates PI3K/Akt/mTOR Signaling by Targeting TGFβI during Skeletal Muscle Development in Pigs.
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Lijing Bai, Ruyi Liang, Yalan Yang, Xinhua Hou, Zishuai Wang, Shiyun Zhu, Chuduan Wang, Zhonglin Tang, and Kui Li
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Medicine ,Science - Abstract
MicroRNAs (miRNAs), which are short (22-24 base pairs), non-coding RNAs, play critical roles in myogenesis. Using Solexa deep sequencing, we detected the expression levels of 229 and 209 miRNAs in swine skeletal muscle at 90 days post-coitus (E90) and 100 days postnatal (D100), respectively. A total of 138 miRNAs were up-regulated on E90, and 31 were up-regulated on D100. Of these, 9 miRNAs were selected for the validation of the small RNA libraries by quantitative RT-PCR (RT-qPCR). We found that miRNA-21 was down-regulated by 17-fold on D100 (P
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- 2015
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25. Discovery of MicroRNAs associated with myogenesis by deep sequencing of serial developmental skeletal muscles in pigs.
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Xinhua Hou, Zhonglin Tang, Honglin Liu, Ning Wang, Huiming Ju, and Kui Li
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Medicine ,Science - Abstract
MicroRNAs (miRNAs) are short, single-stranded non-coding RNAs that repress their target genes by binding their 3' UTRs. These RNAs play critical roles in myogenesis. To gain knowledge about miRNAs involved in the regulation of myogenesis, porcine longissimus muscles were collected from 18 developmental stages (33-, 40-, 45-, 50-, 55-, 60-, 65-, 70-, 75-, 80-, 85-, 90-, 95-, 100- and 105-day post-gestation fetuses, 0 and 10-day postnatal piglets and adult pigs) to identify miRNAs using Solexa sequencing technology. We detected 197 known miRNAs and 78 novel miRNAs according to comparison with known miRNAs in the miRBase (release 17.0) database. Moreover, variations in sequence length and single nucleotide polymorphisms were also observed in 110 known miRNAs. Expression analysis of the 11 most abundant miRNAs were conducted using quantitative PCR (qPCR) in eleven tissues (longissimus muscles, leg muscles, heart, liver, spleen, lung, kidney, stomach, small intestine and colon), and the results revealed that ssc-miR-378, ssc-miR-1 and ssc-miR-206 were abundantly expressed in skeletal muscles. During skeletal muscle development, the expression level of ssc-miR-378 was low at 33 days post-coitus (dpc), increased at 65 and 90 dpc, peaked at postnatal day 0, and finally declined and maintained a comparatively stable level. This expression profile suggested that ssc-miR-378 was a new candidate miRNA for myogenesis and participated in skeletal muscle development in pigs. Target prediction and KEGG pathway analysis suggested that bone morphogenetic protein 2 (BMP2) and mitogen-activated protein kinase 1 (MAPK1), both of which were relevant to proliferation and differentiation, might be the potential targets of miR-378. Luciferase activities of report vectors containing the 3'UTR of porcine BMP2 or MAPK1 were downregulated by miR-378, which suggested that miR-378 probably regulated myogenesis though the regulation of these two genes.
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- 2012
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26. Integrating genome‐wide association study with <scp>RNA</scp> ‐seq revealed <scp> DBI </scp> as a good candidate gene for intramuscular fat content in Beijing black pigs
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Man Yang, Run Zhang, Xiance Liu, Guohua Shi, Hai Liu, Ligang Wang, Xinhua Hou, Lijun Shi, Lixian Wang, and Longchao Zhang
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Genetics ,Animal Science and Zoology ,General Medicine - Abstract
Increasing intramuscular fat (IMF) content can enhance the sensory quality of meat, including tenderness, juiciness, flavor, and color. Genome-wide association study and RNA-sequencing (RNA-seq) analysis were used to identify candidate IMF genes in Beijing Black pigs, a popular species among consumers in northern China. Two and three single nucleotide polymorphisms were significantly associated with IMF in SSC13 and SSC15 respectively. Solute carrier family 4 member 7 (SLC4A7) on SSC13 and insulin induced gene 2 (INSIG2), coiled-coil domain containing 93 (CCDC93), and diazepam binding inhibitor acyl-CoA binding protein (DBI) on SSC15 are good candidate genes in this population. Furthermore, RNA-seq analysis was performed between high and low IMF groups, and 534 differentially expressed genes were identified. In addition, based on differentially expressed genes, Kyoto Encyclopedia of Genes and Genomes analysis revealed that peroxisome proliferator-activated receptors and FoxO signaling pathway pathways might contribute to IMF. Moreover, the DBI gene was identified as a candidate for IMF both by genome-wide association study and RNA-seq analysis, suggesting that it might be a crucial candidate gene for influencing IMF in Beijing Black pigs.
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- 2022
27. Genome‐wide association study revealed <scp> ABCD4 </scp> on <scp>SSC7</scp> and <scp> GREB1L </scp> and <scp> MIB1 </scp> on <scp>SSC6</scp> as crucial candidate genes for rib number in Beijing Black pigs
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Naiqi Niu, Qian Liu, Xinhua Hou, Xin Liu, Ligang Wang, Fuping Zhao, Hongmei Gao, Lijun Shi, Lixian Wang, and Longchao Zhang
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Genetics ,Animal Science and Zoology ,General Medicine - Published
- 2022
28. Identification of imprinted genes in the skeletal muscle of newborn piglets by high‐throughput sequencing
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Xinhua Hou, Zishuai Wang, Liangyu Shi, Ligang Wang, Fuping Zhao, Xin Liu, Hongmei Gao, Lijun Shi, Hua Yan, Lixian Wang, and Longchao Zhang
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Mammals ,Genomic Imprinting ,Animals, Newborn ,Nucleotides ,Swine ,Genetics ,Animals ,High-Throughput Nucleotide Sequencing ,Animal Science and Zoology ,DNA ,General Medicine ,DNA Methylation ,Muscle, Skeletal - Abstract
Imprinted genes - exhibiting parent-specific transcription - play essential roles in the process of mammalian development and growth. Skeletal muscle growth is crucial for meat production. To further understand the role of imprinted genes during the porcine skeletal muscle growth, DNA-seq and RNA-seq were used to explore the characteristics of imprinted genes from porcine reciprocal crosses. A total of 584 545 single-nucleotide variations were discovered in the DNA-seq data of F0 parents, heterozygous in two pig breeds (Yorkshire and Min pigs) but homozygous in each breed. These single-nucleotide variations were used to determine the allelic-specific expression in F1 individuals. Finally, eight paternal expression sites and three maternal expression sites were detected, whereas two paternally expressed imprinted genes (NDN and IGF2) and one maternally expressed imprinted gene (H1-3) were validated by Sanger sequencing. DNA methylation regulates the expression of imprinted genes, and all of the identified imprinted genes in this study were predicted to possess CpG islands. PBX1 and YY1 binding motifs were discovered in the promoter regions of all three imprinted genes, which were candidate elements regulating the transcription of imprinted genes. For these identified imprinted genes, IGF2 and NDN promoted muscle growth whereas H1-3 inhibited cell proliferation, corroborating the 'parental conflict' theory that paternally expressed imprinted genes assisted descendants' growth whereas maternally expressed imprinted genes inhibited it. This study discovered porcine imprinted genes in skeletal muscle and was the first to reveal that H1-3 was expressed by the maternal allele to our knowledge. Our findings provided valuable resources for the potential utilization of imprinted genes in pig breeding.
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- 2022
29. Genome-wide association study revealed ABCD4 on SSC7 and GREB1L and MIB1 on SSC6 as crucial candidate genes for rib number in Beijing Black pigs
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Naiqi, Niu, Qian, Liu, Xinhua, Hou, Xin, Liu, Ligang, Wang, Fuping, Zhao, Hongmei, Gao, Lijun, Shi, Lixian, Wang, and Longchao, Zhang
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Mice ,Swine ,Beijing ,Quantitative Trait Loci ,Sus scrofa ,Animals ,Ribs ,Polymorphism, Single Nucleotide ,Genome-Wide Association Study - Abstract
As one of the few animals with variation in the number of rib pairs (RIB), the pig is a good model to study the mechanism of RIB regulation. Quantitative trait loci (QTL) for porcine RIB are present on Sus scrofa chromosome 7 (SSC7). Although several candidate genes exist in this QTL region on SSC7, the causal gene has yet to be verified. Beijing Black pig with 14-17 RIB is a good population for candidate gene mining and 1104 individuals were genotyped using the Illumina Porcine 50K BeadChip. A total of 14 SNPs from 95.49 to 97.78 Mb on SSC7 showed genome-wide significant association with RIB. On SSC7, a locuszoom plot using pairwise linkage disequilibrium displayed the narrowest linkage region encompassing only two genes, ABCD4 and VRTN. In mice, a transcriptome expression profile was obtained using three embryos at E9.5 (the critical period for rib formation). ABCD4 was highly expressed, but no expression of VRTN was detected. On SSC6, there were four genome-wide significant SNPs from 106.42 to 106.92 Mb associated with RIB. GREB1L and MIB1, in this region, were regarded as novel candidate genes. These results revealed a crucial candidate causal gene on SSC7 and novel genes on SSC6 for rib number and provided interesting new insights into its genetic basis.
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- 2022
30. IRLnc: a novel functional noncoding RNA contributes to intramuscular fat deposition
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Lixian Wang, Tian Zhang, Zhong-Yin Zhou, Xinhua Hou, Ligang Wang, Hua Yan, and Longchao Zhang
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Meat ,RNA, Untranslated ,lcsh:QH426-470 ,Swine ,lcsh:Biotechnology ,Population ,Biology ,03 medical and health sciences ,0302 clinical medicine ,lcsh:TP248.13-248.65 ,Genetics ,Animals ,Gene silencing ,education ,Gene ,030304 developmental biology ,0303 health sciences ,education.field_of_study ,Pig ,Sequence Analysis, RNA ,RNA ,Intramuscular fat ,Insulin resistance ,Non-coding RNA ,Long non-coding RNA ,lcsh:Genetics ,Diabetes Mellitus, Type 2 ,030220 oncology & carcinogenesis ,RNA, Long Noncoding ,DNA microarray ,Research Article ,Biotechnology - Abstract
Background Intramuscular fat (IMF) is associated with meat quality and insulin resistance in animals. Research on genetic mechanism of IMF decomposition has positive meaning to pork quality and diseases such as obesity and type 2 diabetes treatment. In this study, an IMF trait segregation population was used to perform RNA sequencing and to analyze the joint or independent effects of genes and long intergenic non-coding RNAs (lincRNAs) on IMF. Results A total of 26 genes including six lincRNA genes show significantly different expression between high- and low-IMF pigs. Interesting, one lincRNA gene, named IMF related lincRNA (IRLnc) not only has a 292-bp conserved region in 100 vertebrates but also has conserved up and down stream genes (NR4A3) which located at the downstream of IRLnc has similar expression pattern with IRLnc. RNAi-mediated loss of function screens identified that IRLnc silencing could inhibit both of the RNA and protein expression of NR4A3. And the in-situ hybridization co-expression experiment indicates that IRLnc may directly binding to NR4A3. As the NR4A3 could regulate the catecholamine catabolism, which could affect insulin sensitivity, we inferred that IRLnc influence IMF decomposition by regulating the expression of NR4A3. Conclusions In conclusion, a novel functional noncoding variation named IRLnc has been found contribute to IMF by regulating the expression of NR4A3. These findings suggest novel mechanistic approach for treatment of insulin resistance in human beings and meat quality improvement in animal.
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- 2021
31. Metabolomics and lipidomics profiles related to intramuscular fat content and flavor precursors between Laiwu and Yorkshire pigs
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Xinhua Hou, Run Zhang, Man Yang, Naiqi Niu, Junchao Wu, Ze Shu, Pengfei Zhang, Lijun Shi, Fuping Zhao, Ligang Wang, Lixian Wang, and Longchao Zhang
- Subjects
Fumarates ,Swine ,Lipidomics ,Pork Meat ,Animals ,Metabolomics ,General Medicine ,Triglycerides ,Food Science ,Analytical Chemistry - Abstract
Chinese indigenous pig breeds have higher intramuscular fat content (IMF) and better meat quality than Western commercial pigs. The differential metabolites and lipids in the skeletal muscle associated with IMF contents and meat flavor in Laiwu and Yorkshire pigs were investigated in this study. As a result, 113 differential metabolites and 54 differential lipids were discovered. Lipidomics revealed that the Laiwu pig had a fast lipid droplet formation and contained more triglyceride than the Yorkshire pig, which was corresponded to its high IMF contents. Both the lipidomics and metabolomics results indicated that the Laiwu pig had a higher mitochondrial content and aerobic respiration, due to its larger percentage of oxidative fibers. In addition, differential metabolites, such as oxoglutaric acid, fumarate, and l-aspartate, were thought to be important flavor precursors contributing to the Laiwu pig's improved pork taste.
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- 2023
32. Transcriptome Analysis of Skeletal Muscle in Pigs with Divergent Residual Feed Intake Phenotypes
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Xin Liu, Yuebo Zhang, Hongmei Gao, Longchao Zhang, Jingwei Yue, Ligang Wang, Jinshan Zhang, Hua Yan, Xinhua Hou, Lixian Wang, and Lei Pu
- Subjects
0301 basic medicine ,Swine ,Biology ,Transcriptome ,03 medical and health sciences ,0302 clinical medicine ,Genetics ,medicine ,Animals ,RNA, Messenger ,Muscle, Skeletal ,Molecular Biology ,Illumina dye sequencing ,Cell growth ,Skeletal muscle ,Lipid metabolism ,Cell Biology ,General Medicine ,Phenotype ,Cell biology ,030104 developmental biology ,medicine.anatomical_structure ,030220 oncology & carcinogenesis ,Animal Nutritional Physiological Phenomena ,RNA, Long Noncoding ,Residual feed intake ,Energy Metabolism ,Extracellular matrix organization - Abstract
Residual feed intake (RFI) is defined as the difference between the observed and expected feed intake for maintenance and growth requirements. In this study, the expression profiles of mRNAs and long noncoding RNAs (lncRNAs) from skeletal muscle in Duroc pigs with divergent RFI phenotypes were investigated by Illumina sequencing. Finally, a total of 2195 annotated lncRNAs and 1976 novel lncRNAs were obtained. About 210 mRNAs and 43 lncRNAs were differentially expressed among high and low RFI pigs. The differentially expressed mRNAs were potentially involved in the biological processes of lipid metabolism, extracellular matrix organization, cell proliferation, and cell adhesion. The lipolysis in skeletal muscle was increased in high RFI pigs, suggesting that high RFI pigs might need more energy than low RFI pigs. However, skeletal muscle development was increased in low RFI pigs. These results suggested that low RFI pigs might be more efficient in energy utilization during skeletal muscle growth. The function of lncRNA was also analyzed by target prediction. Nine lncRNAs might be candidate lncRNAs for the determination of RFI phenotype, by the regulation of the biological processes of lipid metabolism, cell proliferation, and cell adhesion. This study should facilitate a further understanding of the molecular mechanism for the determination of RFI phenotype in pigs.
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- 2020
33. Genome-Wide Expression Profiling of mRNAs, lncRNAs and circRNAs in Skeletal Muscle of Two Different Pig Breeds
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Longchao Zhang, Lijun Shi, Xinhua Hou, Fuping Zhao, Xin Liu, Lixian Wang, Ligang Wang, Hua Yan, and Hongmei Gao
- Subjects
Genetics ,General Veterinary ,Competing endogenous RNA ,Veterinary medicine ,mRNAs ,lncRNAs ,Skeletal muscle ,pigs ,RNA-Seq ,Biology ,Phenotype ,Article ,Transcriptome ,medicine.anatomical_structure ,QL1-991 ,microRNA ,SF600-1100 ,medicine ,Animal Science and Zoology ,RNA-seq ,skeletal muscle ,circRNAs ,Gene ,Zoology ,Function (biology) - Abstract
Simple Summary Variation exists in muscle-related traits, such as muscle growth and meat quality, between obese and lean pigs. In this study, the transcriptome profiles of skeletal muscle between Beijing Blackand Yorkshire pigs were characterized to explore the molecular mechanism underlying skeletal muscle-relatedtraits. Gene Ontology (GO) and KEGG pathway enrichment analyses showed that differentially expressed mRNAs, lncRNAs, and circRNAs involved in skeletal muscle development and fatty acid metabolism played a key role in the determination of muscle-related traits between different pig breeds. These results provide candidate genes responsible for muscle phenotypic variation and are valuable for pig breeding. Abstract RNA-Seq technology is widely used to analyze global changes in the transcriptome and investigate the influence on relevant phenotypic traits. Beijing Black pigs show differences in growth rate and meat quality compared to western pig breeds. However, the molecular mechanisms responsible for such phenotypic differences remain unknown. In this study, longissimus dorsi muscles from Beijing Black and Yorkshire pigs were used to construct RNA libraries and perform RNA-seq. Significantly different expressions were observed in 1051 mRNAs, 322 lncRNAs, and 82 circRNAs. GO and KEGG pathway annotation showed that differentially expressed mRNAs participated in skeletal muscle development and fatty acid metabolism, which determined the muscle-related traits. To explore the regulatory role of lncRNAs, the cis and trans-target genes were predicted and these lncRNAswere involved in the biological processes related to skeletal muscle development and fatty acid metabolismvia their target genes. CircRNAs play a ceRNA role by binding to miRNAs. Therefore, the potential miRNAs of differentially expressed circRNAs were predicted and interaction networks among circRNAs, miRNAs, and key regulatory mRNAs were constructed to illustrate the function of circRNAs underlying skeletal muscle development and fatty acid metabolism. This study provides new clues for elucidating muscle phenotypic variation in pigs.
- Published
- 2021
34. Characterization and difference of lipids and metabolites from Jianhe White Xiang and Large White pork by high-performance liquid chromatography–tandem mass spectrometry
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Run, Zhang, Man, Yang, Xinhua, Hou, Renda, Hou, Ligang, Wang, Lijun, Shi, Fuping, Zhao, Xin, Liu, Qingshi, Meng, Lixian, Wang, and Longchao, Zhang
- Subjects
Red Meat ,Swine ,Tandem Mass Spectrometry ,Carnitine ,Lecithins ,Pork Meat ,Animals ,Sugars ,Chromatography, High Pressure Liquid ,Triglycerides ,Food Science - Abstract
The quality of pork, such as intramuscular fat (IMF) content and flavor, can affect the acceptance of the consumer. Many studies have reported on the pork quality of Chinese local and commercial pigs (for example Large White (LW) pigs). The Jianhe White Xiang (JWX) pig, one of the Chinese Xiang pigs, is known for its high IMF and pork flavor. However, studies investigating the characterization and difference of lipids and metabolites between the JWX and LW pork are limited. Herein, we performed metabolomic and lipidomic profiling of JWX and LW pork by high-performance liquid chromatography-tandem mass spectrometry. The IMF and meat redness (a*) of the JWX pork were significantly higher than those of the LW pork. Metabolomic profiling revealed that 118 out of 501 polar metabolites, such as carnitine, amino acids, sugar, and dipeptide, were significantly different between the two types of pork. Additionally, the screened metabolites were mainly related to carnitine synthesis, phospholipid metabolism, sugar metabolism, and amino acid metabolism. Lipidomic profiling identified 100 of 376 lipids, which contained carnitine, diglyceride, triglyceride (TG), sphingomyelin, cardiolipin, fatty acid, phosphatidylcholine (PC), and phosphatidylethanolamine (PE), which were significantly different between the two types of pork under the positive and negative ion modes (variable importance in projection (VIP) 1, p 0.05, and fold change (FC) 2 or FC 0.5). All of the different TG substances were up-regulated in the JWX pork, and their carbon chain length was longer than that of the residual TGs. In addition, the JWX pork had more double bonds of PC and PE substances than LW pork. Thus, our findings provide comprehensive metabolomic and lipidomic profiles between the JWX and LW pork and a basic understanding on increasing the pork quality.
- Published
- 2022
35. Copy Number Variations Contribute to Intramuscular Fat Content Differences By Affecting The Expression of PELP1 Alternative Splices in Pig
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Longchao Zhang, Tian Zhang, Ligang Wang, Lixian Wang, Li Na, Xinhua Hou, and Hua Yan
- Subjects
Andrology ,Copy-number variation ,Intramuscular fat ,Biology - Abstract
Background Intramuscular fat (IMF) is a key meat quality trait. Research on the genetic mechanisms of IMF decomposition is valuable for both pork quality improvement and the treatment of obesity and type 2 diabetes. Copy number variations (CNVs) are a type of variant that may influence meat quality.ResultsIn this study, a total of 1185 CNV regions (CNVRs) including 393 duplicated CNVRs, 432 deleted CNVRs, and 361 CNVRs with both duplicated and deleted status were identified in a pig F2 resource population using next-generation sequencing data. A genome-wide association study (GWAS) was then performed between CNVs and IMF, and a total of 19 CNVRs were found to be significantly associated with IMF. QTL colocation analysis indicated that 3 of the 19 CNVRs overlapped with known QTLs. RNA-seq and qPCR validation results indicated that CNV150, which is located on the 3’UTR end of the proline, glutamate, and leucine rich protein 1 (PELP1) gene, may affect the expression of PELP1 alternative splices. Sequence alignment and Alphafold2 structure prediction results indicated that the two alternative splices of PELP1 have a 23 AA sequence variation and a helix-fold structure variation. This region is located in the region of interaction between PELP1 and other proteins which have been reported to be significantly associated with fat deposition or insulin resistance. We infer that the CNVR may influence IMF content by regulating the alternative splicing of the PELP1 gene and ultimately affecting the structure of the PELP1 protein. ConclusionsIn conclusion, we found some CNVRs, especially CNV150, located in PELP1 that affect IMF. These findings suggest a novel mechanistic approach for meat quality improvement in animals and potential treatment of insulin resistance in human beings.
- Published
- 2021
36. A Comparison of the Behavior, Physiology, and Offspring Resilience of Gestating Sows When Raised in a Group Housing System and Individual Stalls
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Pengkang Song, Hongmei Gao, Ligang Wang, Xinhua Hou, Longchao Zhang, Lixian Wang, Lijun Shi, Li Bugao, Hua Yan, Xin Liu, and Fuping Zhao
- Subjects
Offspring ,Veterinary medicine ,animal diseases ,Physiology ,group housing system ,Adrenocorticotropic hormone ,Normal state ,Biology ,Article ,Weaned piglets ,SF600-1100 ,medicine ,0501 psychology and cognitive sciences ,Chronic stress ,050102 behavioral science & comparative psychology ,Pregnancy ,General Veterinary ,offspring ,behavior ,05 social sciences ,0402 animal and dairy science ,food and beverages ,04 agricultural and veterinary sciences ,medicine.disease ,040201 dairy & animal science ,Stress hormone ,QL1-991 ,individual stall ,stress hormone ,Gestation ,gestating sows ,Animal Science and Zoology ,Zoology - Abstract
Being in a confined environment causes chronic stress in gestating sows, which is detrimental for sow health, welfare and, consequently, offspring physiology. This study assessed the health and welfare of gestating sows housed in a group housing system compared to individual gestation stalls. After pregnancy was confirmed, experimental sows were divided randomly into two groups: the group housing system (GS), with the electronic sow feeding (ESF) system, or individual stall (IS). The behavior of sows housed in the GS or IS was then compared, throughout pregnancy, GS sows displayed more exploratory behavior, less vacuum chewing, and less sitting behavior (p <, 0.05). IS sows showed higher stress hormone levels than GS sows. In particular, at 41 days of gestation, the concentration of the adrenocorticotropic hormone (ACTH) and adrenaline (A) in IS sows was significantly higher than that of GS sows, and the A level of IS sows remained significantly higher at 71 days of gestation (p <, 0.01). The lipopolysaccharide (LPS) test was carried out in the weaned piglets of the studied sows. Compared with the offspring of gestating sows housed in GS (PG) or IS (PS), PG experienced a shorter period of high temperature and showed a quicker return to the normal state (p <, 0.05). Additionally, their lower levels of stress hormone (p <, 0.01) suggest that PG did not suffer from as much stress as PS. These findings suggested that gestating sows housed in GS were more able to carry out their natural behaviors and, therefore, had lower levels of stress and improved welfare. In addition, PG also showed better disease resistance and resilience. These results will provide a research basis for the welfare and breeding of gestating sows.
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- 2021
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37. Identification of SNPs and Candidate Genes for Milk Production Ability in Yorkshire Pigs
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Ligang Wang, Lijun Shi, Hua Yan, Xinhua Hou, Fuping Zhao, Lixian Wang, Yang Li, Xin Liu, Hongmei Gao, Qian Liu, and Longchao Zhang
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Litter (animal) ,Candidate gene ,Mammary gland ,food and beverages ,SNP ,candidate gene ,Single-nucleotide polymorphism ,Quantitative trait locus ,Heritability ,Biology ,QH426-470 ,medicine.anatomical_structure ,Animal science ,Lactation ,medicine ,Genetics ,Yorkshire pig ,Colostrum ,Molecular Medicine ,GWAS ,Genetics (clinical) ,Original Research ,litter weight gain - Abstract
Sow milk production ability is an important limiting factor impacting suboptimal growth and the survival of piglets. Through pig genetic improvement, litter sizes have been increased. Larger litters need more suckling mammary glands, which results in increased milk from the lactating sow. Hence, there is much significance to exploring sow lactation performance. For milk production ability, it is not practical to directly measure the milk yield, we used litter weight gain (LWG) throughout sow lactation as an indicator. In this study, we estimated the heritability of LWG, namely, 0.18 ± 0.07. We then performed a GWAS, and detected seven significant SNPs, namely, Sus scrofa Chromosome (SSC) 2: ASGA0010040 (p = 7.73E-11); SSC2:MARC0029355 (p = 1.30E-08), SSC6: WU_10.2_6_65751151 (p = 1.32E-10), SSC7: MARC0058875 (p = 4.99E-09), SSC10: WU_10.2_10_49571394 (p = 6.79E-08), SSC11: M1GA0014659 (p = 1.19E-07), and SSC15: MARC0042106 (p = 1.16E-07). We performed the distribution of phenotypes corresponding to the genotypes of seven significant SNPs and showed that ASGA0010040, MARC0029355, MARC0058875, WU_10.2_10_49571394, M1GA0014659, and MARC0042106 had extreme phenotypic values that corresponded to the homozygous genotypes, while the intermediate values corresponded to the heterozygous genotypes. We screened for flanking regions ± 200 kb nearby the seven significant SNPs, and identified 38 genes in total. Among them, 28 of the candidates were involved in lactose metabolism, colostrum immunity, milk protein, and milk fat by functional enrichment analysis. Through the combined analysis between 28 candidate genes and transcriptome data of the sow mammary gland, we found nine commons (ANO3, MUC15, DISP3, FBXO6, CLCN6, HLA-DRA, SLA-DRB1, SLA-DQB1, and SLA-DQA1). Furthermore, by comparing the chromosome positions of the candidate genes with the quantitative trait locus (QTLs) as previously reported, a total of 17 genes were found to be within 0.86–94.02 Mb of the reported QTLs for sow milk production ability, in which, NAV2 was found to be located with 0.86 Mb of the QTL region ssc2: 40936355. In conclusion, we identified seven significant SNPs located on SSC2, 6, 7, 10, 11, and 15, and propose 28 candidate genes for the ability to produce milk in Yorkshire pigs, 10 of which were key candidates.
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- 2021
38. The landscape of chromatin accessibility in skeletal muscle during embryonic development in pigs
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Liangyu Shi, Hua Yan, Ligang Wang, Jingwei Yue, Tianyu Deng, Xinhua Hou, Jianfei Gong, Hongmei Gao, Xin Liu, Longchao Zhang, Lijun Shi, Lixian Wang, and Fuping Zhao
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0301 basic medicine ,Veterinary medicine ,Skeletal muscle ,Biology ,Biochemistry ,SF1-1100 ,Transcriptome ,03 medical and health sciences ,0302 clinical medicine ,SF600-1100 ,medicine ,MEF2C ,Gene ,Transcription factor ,Chromatin accessibility ,Pig ,Research ,Embryonic Stage ,Chromatin ,Cell biology ,Animal culture ,030104 developmental biology ,medicine.anatomical_structure ,CTCF ,Embryo ,Animal Science and Zoology ,030217 neurology & neurosurgery ,Food Science ,Biotechnology - Abstract
BackgroundThe development of skeletal muscle in pigs during the embryonic stage is precisely regulated by transcriptional mechanisms, which depend on chromatin accessibility. However, how chromatin accessibility plays a regulatory role during embryonic skeletal muscle development in pigs has not been reported. To gain insight into the landscape of chromatin accessibility and the associated genome-wide transcriptome during embryonic muscle development, we performed ATAC-seq and RNA-seq analyses of skeletal muscle from pig embryos at 45, 70 and 100 days post coitus (dpc).ResultsIn total, 21,638, 35,447 and 60,181 unique regions (or peaks) were found across the embryos at 45 dpc (LW45), 70 dpc (LW70) and 100 dpc (LW100), respectively. More than 91% of the peaks were annotated within − 1 kb to 100 bp of transcription start sites (TSSs). First, widespread increases in specific accessible chromatin regions (ACRs) from embryos at 45 to 100 dpc suggested that the regulatory mechanisms became increasingly complicated during embryonic development. Second, the findings from integrated ATAC-seq and RNA-seq analyses showed that not only the numbers but also the intensities of ACRs could control the expression of associated genes. Moreover, the motif screening of stage-specific ACRs revealed some transcription factors that regulate muscle development-related genes, such as MyoG, Mef2c, and Mef2d. Several potential transcriptional repressors, including E2F6, OTX2 and CTCF, were identified among the genes that exhibited different regulation trends between the ATAC-seq and RNA-seq data.ConclusionsThis work indicates that chromatin accessibility plays an important regulatory role in the embryonic muscle development of pigs and regulates the temporal and spatial expression patterns of key genes in muscle development by influencing the binding of transcription factors. Our results contribute to a better understanding of the regulatory dynamics of genes involved in pig embryonic skeletal muscle development.
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- 2021
39. Porous nano-silicon/TiO2/rGO@carbon architecture with 1000-cycling lifespan as superior durable anodes for lithium-ion batteries
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Xinhua Hou, Peng Zhang, Lingzhi Zhao, Yuqing Gao, Shejun Hu, Honglin Yan, Qiang Ru, and Fuming Chen
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Materials science ,General Chemical Engineering ,General Engineering ,General Physics and Astronomy ,chemistry.chemical_element ,02 engineering and technology ,010402 general chemistry ,021001 nanoscience & nanotechnology ,Electrochemistry ,01 natural sciences ,Energy storage ,0104 chemical sciences ,Anode ,Chemical engineering ,chemistry ,Electrical resistivity and conductivity ,General Materials Science ,Lithium ,0210 nano-technology ,Porosity ,Carbon ,Current density - Abstract
Novel porous nano-silicon/TiO2/rGO@carbon anodes with superior lifespan and desirable cycling stability are prepared by a step-wise synthetic procedure. The hybrid exhibits a high specific capacity of 1073.43 mAh g−1 at a current density of 500 mA g−1. Additionally, it delivers a reversible capacity of 724.08 mAh g−1 at 1000 mA g−1 even after 1000 long-term cycles. Simultaneously, a large average capacity is reinstated after cycling at high rates, such as 994.76, 743.33, and 599.70 mAh g−1 at 1000, 2000, and 3000 mA g−1, respectively. The greatly ameliorative electrochemical characteristics could be attributed to the abundant buffering space of hierarchical architecture, good separation of mechanically robust anatase-TiO2, sustainable confinement of elastic carbon skeletons, as well as improved electrical conductivity of rGO, which could suppress drastic volume variations and promote multiple Li+/electron transport without distinct pulverization.
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- 2019
40. Identifying long non-coding RNAs and characterizing their functional roles in swine mammary gland from colostrogenesis to lactogenesis
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Lixian Wang, Ligang Wang, Wentao Cai, Xinhua Hou, Hua Yan, Xin Liu, Fuping Zhao, Hongmei Gao, Longchao Zhang, and Lijun Shi
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Differential expression analysis ,General Veterinary ,Physiology ,Mammary gland ,Genome-wide association study ,Computational biology ,Biology ,Mammary gland development ,Cell biology ,medicine.anatomical_structure ,Functional annotation ,Expression pattern ,Lactation ,Genetics ,medicine ,Colostrum ,Animal Science and Zoology ,Gene ,Function (biology) ,Food Science - Abstract
Long non-coding RNAs (lncRNAs) play important regulatory roles in milk biological processes. While, little is known about the identification and function of swine lncRNAs in response to mammary gland development. Here, we identified 286 differentially expressed (DE) lncRNAs in mammary gland at different stages from 14 days prior to (-) parturition to day 1 after (+) parturition using the published RNA-seq data. The expression pattern of these DE lncRNAs was examined, and most of lncRNAs expressions were strongly changed from Day −2 to Day +1. Functional annotation revealed that the DE lncRNAs were mainly involved in the mammary gland developing, lactation developing, milk composition metabolism and colostrum function. By performing the weighted gene co-expression network analysis (WGCNA), we identified 7 out of 12 lncRNA-mRNA modules, including 35 lncRNAs and 319 mRNAs, which were highly associated with the mammary gland at Day −14, Day −2 and Day +1. Integrated analysis of the DE lncRNAs expression pattern examination, targets prediction, function annotation and WGCNA suggested that 18 lncRNAs (such as, XLOC_020627, ENSSSCG00000051193, XLOC_025150, ENSSSCG00000042618, XLOC_963181, ENSSSCG00000051701, XLOC_018030, and XLOC_025146) and their 20 target genes (such as, ACTN4, ADCY1, CSN3, SMO, CSN2, PRKAG2, FIBCD1, and GALNT7), were considered as the promising candidates for swine parturition and colostrum occurrence processes. Our research provided the insights into lncRNA profiles and their regulating mechanisms from colostrogenesis to lactogenesis in swine.
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- 2021
41. Additional file 1 of IRLnc: a novel functional noncoding RNA contributes to intramuscular fat deposition
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Ligang Wang, Zhong-Yin Zhou, Zhang, Tian, Longchao Zhang, Xinhua Hou, Yan, Hua, and Wang, Lixian
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Additional file 1: Table S1. cn- stream genes. Table S2. Primers of DE si-RNA of IRLnc.
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- 2021
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42. Additional file 2 of The landscape of chromatin accessibility in skeletal muscle during embryonic development in pigs
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Jingwei Yue, Xinhua Hou, Liu, Xin, Ligang Wang, Hongmei Gao, Fuping Zhao, Lijun Shi, Liangyu Shi, Yan, Hua, Tianyu Deng, Jianfei Gong, Lixian Wang, and Zhang, Longchao
- Abstract
Additional file 2: Fig. S1. Insertion size distribution of all libraries. A, B and C show the insertion sizes of the LW45, LW70 and LW100 libraries, respectively. Fig. S2. Heatmap of the peak signals across the gene body in each library. A, B and C show the results for the LW45, LW70 and LW100 libraries, respectively. Fig. S3. Heatmap of all genes at all stages. Fig. S4. Percentages of ACR-associated gene expression levels in different groups. The genes contained multiple ACRs in the proximal promoter regions were grouped according to the total peak length and were then divided into three equal groups (the top, middle and bottom groups). The expression levels of the genes were divided into five groups based on the FPKM values: 0–2, 2–5, 5–10, 10–30, and 30-more. Fig. S5. The landscape of stage-specific ACRs related genes and DPIs related genes. (a) Heatmap of all expressed genes contained stage-specific ACRs at the LW45, LW70 and LW100 stages. The red color indicates high expression level; whereas the green color indicates low expression level. (b) The distribution of the pearson correlation coefficient between the peak intensity and expression level of each DPI-related gene. Fig. S6. Enrichment of known TF motifs identified in the proximal promoter regions of cluster 3 genes with specific ACRs at the LW45 stage. Fig. S7. Enrichment of known TF motifs identified in the proximal promoter regions of cluster 3 genes with specific ACRs at the LW70 stage. Fig. S8. Enrichment of known TF motifs identified in the proximal promoter regions of cluster 2 genes with specific ACRs at the LW100 stage. Fig. S9. Enrichment of known TF motifs identified in the proximal promoter regions of cluster 5 genes with specific ACRs at the LW100 stage. Fig. S10. Enrichment of known TF motifs identified from the common ACRs showing DPIs in the LW70 vs LW45 comparison. Fig. S11. Enrichment of known TF motifs identified from the common ACRs showing DPIs in the LW100 vs LW70 comparison. Fig. S12. Enrichment of known TF motifs identified from the common ACRs showing DPIs in the LW100 vs LW45 comparison.
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- 2021
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43. Genome-Wide Association Analysis Identified BMPR1A as a Novel Candidate Gene Affecting the Number of Thoracic Vertebrae in a Large White × Minzhu Intercross Pig Population
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Xin Liu, Qian Liu, Lijun Shi, Fuping Zhao, Hongmei Gao, Ligang Wang, Longchao Zhang, Jingwei Yue, Naiqi Niu, Xinhua Hou, Lixian Wang, and Hua Yan
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pig ,Linkage disequilibrium ,Candidate gene ,Population ,Single-nucleotide polymorphism ,Genome-wide association study ,Quantitative trait locus ,Biology ,Article ,BMPR1A ,03 medical and health sciences ,0302 clinical medicine ,lcsh:Zoology ,SNP ,lcsh:QL1-991 ,education ,Genotyping ,030304 developmental biology ,Genetics ,0303 health sciences ,education.field_of_study ,lcsh:Veterinary medicine ,genome-wide association study ,General Veterinary ,FOS ,number of thoracic vertebrae ,030220 oncology & carcinogenesis ,lcsh:SF600-1100 ,Animal Science and Zoology - Abstract
The number of vertebrae (NV), especially the number of thoracic vertebrae (NTV), varies among pig breeds. The NTV is controlled by vertebral segmentation and the number of somites during embryonic development. Although there is a high correlation between the NTV and NV, studies on a fixed NV have mainly considered the absolute numbers of thoracic vertebrae instead of vertebral segmentation. Therefore, this study aimed to discover variants associated with the NTV by considering the effect of the NV in pigs. The NTV and NV of 542 F2 individuals from a Large White ×, Minzhu pig crossbreed were recorded. All animals were genotyped for VRTN g.19034 A >, C, LTBP2 c.4481A >, C, and 37 missense or splice variants previously reported in a 951-kb interval on SSC7 and 147 single nucleotide polymorphisms (SNPs) on SSC14. To identify NTV-associated SNPs, we firstly performed a genome-wide association study (GWAS) using the Q + K (population structure + kinship matrix) model in TASSEL. With the NV as a covariate, the obtained data were used to identify the SNPs with the most significant genome-wide association with the NTV by performing a GWAS on a PorcineSNP60K Genotyping BeadChip. Finally, a conditional GWAS was performed by fixing this SNP. The GWAS showed that 31 SNPs on SSC7 have significant genome-wide associations with the NTV. No missense or splice variants were found to be associated with the NTV significantly. A linkage disequilibrium analysis suggested the existence of quantitative trait loci (QTL) in a 479-Kb region on SSC7, which contained a critical candidate gene FOS for the NTV in pigs. Subsequently, a conditional GWAS was performed by fixing M1GA0010658, the most significant of these SNPs. Two SNPs in BMPR1A were found to have significant genome-wide associations and a significant dominant effect. The leading SNP, S14_87859370, accounted for 3.86% of the phenotypic variance. Our study uncovered that regulation variants in FOS on SSC7 and in BMPR1A on SSC14 might play important roles in controlling the NTV, and thus these genetic factors may be harnessed for increasing the NTV in pigs.
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- 2020
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44. Identification of porcine imprinted genes involved in skeletal muscle development by high-throughput sequencing
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Xinhua Hou, Zishuai Wang, Ligang Wang, Fuping Zhao, Xin Liu, Hongmei Gao, Lijun Shi, Hua Yan, Longchao Zhang, and Lixian Wang
- Abstract
Background Imprinted genes—exhibiting parent-specific transcription—play essential roles in the process of mammalian development and growth. To further understand the imprinted genes involved in skeletal muscle development, DNA-seq and RNA-seq were used to explore the characteristics of imprinted genes involved in skeletal muscle development from porcine reciprocal crosses. Results A total of 211 paternally and 417 maternally imprinted genes were obtained in this study. Of the candidate imprinted genes, 50 paternally and 112 maternally imprinted genes possessed cytosine and guanine dinucleotide (CpG) islands in their promoters that may have regulated the imprinted gene expression. Imprint-related motifs were predicted and PBX1 motifs may mediate the expression of imprinted genes in the process of skeletal-muscle development. Functional analysis showed that a maternally imprinted gene of EPHB1 was involved in skeletal muscle cell proliferation. Imprinted genes involved in the biological processes of cell proliferation, differentiation and fusion were also analyzed. More maternally imprinted genes, including ADRA1D, E2F1, FBXO40, GHRH and WNT5A, were involved in skeletal muscle development than paternally imprinted genes. Conclusions Skeletal muscle development is crucial for meat production. This study identified 628 porcine imprinted genes in skeletal muscle and revealed their functional role in skeletal muscle development. Our findings should further assist with the potential use of imprinted genes in pig breeding.
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- 2020
45. Estimation of inbreeding and identification of regions under heavy selection based on runs of homozygosity in a Large White pig population
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Fuping Zhao, Liangyu Shi, Longchao Zhang, Lixian Wang, Xin Liu, Xinhua Hou, Jiaxin Liu, Ligang Wang, Hongmei Gao, Tianyu Deng, and Hua Yan
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0301 basic medicine ,Population ,Sus scrofa ,Single-nucleotide polymorphism ,Runs of Homozygosity ,Biology ,Runs of homozygosity ,Biochemistry ,Candidate genes ,03 medical and health sciences ,Inbreeding depression ,education ,Selection (genetic algorithm) ,lcsh:SF1-1100 ,Genetics ,education.field_of_study ,Autosome ,lcsh:Veterinary medicine ,Inbreeding coefficients ,Research ,Haplotype ,0402 animal and dairy science ,04 agricultural and veterinary sciences ,040201 dairy & animal science ,030104 developmental biology ,lcsh:SF600-1100 ,Animal Science and Zoology ,lcsh:Animal culture ,Inbreeding ,Food Science ,Biotechnology - Abstract
Background Runs of homozygosity (ROHs) are homozygous segments of the genome where the two haplotypes inherited from the parents are identical. The current availability of genotypes for a very large number of single nucleotide polymorphisms (SNPs) is leading to more accurate characterization of ROHs in the whole genome. Here, we investigated the occurrence and distribution of ROHs in 3,692 Large White pigs and compared estimates of inbreeding coefficients calculated based on ROHs (FROH), homozygosity (FHOM), genomic relationship matrix (FGRM) and pedigree (FPED). Furthermore, we identified genomic regions with high ROH frequencies and annotated their candidate genes. Results In total, 176,182 ROHs were identified from 3,569 animals, and all individuals displayed at least one ROH longer than 1 Mb. The ROHs identified were unevenly distributed on the autosomes. The highest and lowest coverages of Sus scrofa chromosomes (SSC) by ROH were on SSC14 and SSC13, respectively. The highest pairwise correlation among the different inbreeding coefficient estimates was 0.95 between FROH_total and FHOM, while the lowest was − 0.083 between FGRM and FPED. The correlations between FPED and FROH using four classes of ROH lengths ranged from 0.18 to 0.37 and increased with increasing ROH length, except for ROH > 10 Mb. Twelve ROH islands were located on four chromosomes (SSC1, 4, 6 and 14). These ROH islands harboured genes associated with reproduction, muscular development, fat deposition and adaptation, such as SIRT1, MYPN, SETDB1 and PSMD4. Conclusion FROH can be used to accurately assess individual inbreeding levels compared to other inbreeding coefficient estimators. In the absence of pedigree records, FROH can provide an alternative to inbreeding estimates. Our findings can be used not only to effectively increase the response to selection by appropriately managing the rate of inbreeding and minimizing the negative effects of inbreeding depression but also to help detect genomic regions with an effect on traits under selection.
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- 2020
46. Liver transcriptome profiling and functional analysis of intrauterine growth restriction (IUGR) piglets reveals a genetic correction and sexual-dimorphic gene expression during postnatal development
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Xinhua Hou, Hua Yan, Longchao Zhang, Ligang Wang, Fuping Zhao, Xin Liu, Lixian Wang, and Hongmei Gao
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Male ,medicine.medical_specialty ,congenital, hereditary, and neonatal diseases and abnormalities ,lcsh:QH426-470 ,Offspring ,Swine ,lcsh:Biotechnology ,animal diseases ,Intrauterine growth restriction ,Biology ,medicine.disease_cause ,Transcriptome ,03 medical and health sciences ,Sexual dimorphism ,Sex Factors ,Pregnancy ,Internal medicine ,lcsh:TP248.13-248.65 ,Gene expression ,Genetics ,medicine ,Animals ,Pathological ,reproductive and urinary physiology ,030304 developmental biology ,0303 health sciences ,Fetal Growth Retardation ,Gene Expression Profiling ,0402 animal and dairy science ,Intrauterine growth restriction (IUGR) ,Gene Expression Regulation, Developmental ,04 agricultural and veterinary sciences ,Metabolism ,Immune dysregulation ,medicine.disease ,040201 dairy & animal science ,female genital diseases and pregnancy complications ,lcsh:Genetics ,Endocrinology ,Piglets ,Animals, Newborn ,Liver ,Female ,Biotechnology ,Research Article - Abstract
BackgroundIntrauterine growth restriction (IUGR) remains a major problem associated with swine production. Thus, understanding the physiological changes of postnatal IUGR piglets would aid in improving growth performance. Moreover, liver metabolism plays an important role in the growth and survival of neonatal piglets.ResultsBy profiling the transcriptome of liver samples on postnatal Days 1, 7, and 28, our study focused on characterizing the growth, function, and metabolism in the liver of IUGR neonatal piglets. Our study demonstrates that the livers of IUGR piglets were associated with a series of complications, including inflammatory stress and immune dysregulation; cytoskeleton and membrane structure disorganization; dysregulated transcription events; and abnormal glucocorticoid metabolism. In addition, the abnormal liver function index in the serum [alanine aminotransferase (ALT), aspartate aminotransferase (AST), and total protein (TP)], coupled with hepatic pathological and ultrastructural morphological changes are indicative of liver damage and dysfunction in IUGR piglets. Moreover, these results reveal the sex-biased developmental dynamics between male and female IUGR piglets, and that male IUGR piglets may be more sensitive to disrupted metabolic homeostasis.ConclusionsThese observations provide a detailed reference for understanding the mechanisms and characterizations of IUGR liver functions, and suggest that the potential strategies for improving the survival and growth performance of IUGR offspring should consider the balance between postnatal catch-up growth and adverse metabolic consequences. In particular, sex-specific intervention strategies should be considered for both female and male IUGR piglets.
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- 2020
47. Additional file 2 of Estimation of inbreeding and identification of regions under heavy selection based on runs of homozygosity in a Large White pig population
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Liangyu Shi, Ligang Wang, Jiaxin Liu, Tianyu Deng, Yan, Hua, Longchao Zhang, Liu, Xin, Hongmei Gao, Xinhua Hou, Lixian Wang, and Fuping Zhao
- Abstract
Additional file 2: Table S2 GO terms and KEGG pathways enriched (P
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- 2020
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48. Additional file 1 of Estimation of inbreeding and identification of regions under heavy selection based on runs of homozygosity in a Large White pig population
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Liangyu Shi, Ligang Wang, Jiaxin Liu, Tianyu Deng, Yan, Hua, Longchao Zhang, Liu, Xin, Hongmei Gao, Xinhua Hou, Lixian Wang, and Fuping Zhao
- Abstract
Additional file 1: Table S1. Gene content inside run-of-homozygosity islands.
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- 2020
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49. TMT-based quantitative proteomic analysis of porcine muscle associated with postmortem meat quality
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Qingshi Meng, Qiufeng Liu, Xinhua Hou, Ligang Wang, Lixian Wang, Longchao Zhang, and Hua Yan
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Proteomics ,Swine ,Porcine muscle ,Meat Proteins ,Apoptosis ,Tandem mass tag ,medicine.disease_cause ,01 natural sciences ,Analytical Chemistry ,Decreased Glycogenolysis ,chemistry.chemical_compound ,0404 agricultural biotechnology ,Tandem Mass Spectrometry ,medicine ,Food Quality ,Animals ,Glycolysis ,Food science ,Muscle, Skeletal ,Longissimus dorsi ,Glycogen ,010401 analytical chemistry ,food and beverages ,04 agricultural and veterinary sciences ,General Medicine ,040401 food science ,0104 chemical sciences ,Oxidative Stress ,Red Meat ,chemistry ,Proteome ,Autopsy ,Oxidative stress ,Food Science - Abstract
To explore the molecular mechanisms of meat quality, four high-quality (HQ) samples and four low-quality (LQ) samples from longissimus dorsi muscles were chosen, and tandem mass tag (TMT) labeling combined with mass spectrometry (MS) were performed to find associations between meat quality and proteome profiles. The LQ meats had lower pH, lighter color, and higher drip loss compared to the HQ meats. About 140 differentially expressed proteins were identified. Functional analysis results of differentially expressed proteins showed that decreased release of Ca2+, lower contents of type II fibers, lower contents of glycogen, and decreased glycogenolysis in HQ meats indicated a lower degree of glycolysis in HQ as compared to LQ meats. Meanwhile, some differentially expressed proteins suggested that the levels of oxidative stress and apoptosis were lower in HQ meats than in LQ meats. This study reveals physiological changes between HQ and LQ meats according to the proteome profiles.
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- 2019
50. NTN1 Affects Porcine Intramuscular Fat Content by Affecting the Expression of Myogenic Regulatory Factors
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Lingling Zhao, Hua Yan, Xinhua Hou, Ligang Wang, Lixian Wang, Longchao Zhang, Xin Liu, Fuping Zhao, and Hongmei Gao
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NTN1 ,Biology ,Article ,Andrology ,03 medical and health sciences ,0302 clinical medicine ,lcsh:Zoology ,Myocyte ,Gene silencing ,lcsh:QL1-991 ,intramuscular fat content ,Protein kinase A ,Gene ,030304 developmental biology ,0303 health sciences ,lcsh:Veterinary medicine ,General Veterinary ,copy number variation ,swine ,Real-time polymerase chain reaction ,030220 oncology & carcinogenesis ,Myogenic regulatory factors ,lcsh:SF600-1100 ,Animal Science and Zoology ,Intramuscular fat ,C2C12 - Abstract
Simple Summary Intramuscular fat (IMF) is a key meat quality trait in the pork industry. In this study, we validated the effect of the copy number of Netrin-1 (NTN1-CNV) on Netrin-1 (NTN1) protein expression and explored the possible affective mechanism of NTN1 on IMF. The results indicated that NTN1-CNV may affect the expression of NTN1 protein by its gene dose, and the expression of NTN1 may affect the proliferation and differentiation of muscle cells by the AMP-activated protein kinase (AMPK) pathway and finally influence the IMF content. Abstract Intramuscular fat (IMF) content is an important economic trait for pork quality. Our previous results regarding the genome-wide association between IMF content and copy number variations (CNVs) indicated that the CNV within Netrin-1(NTN1-CNV) was significantly associated with IMF. In order to validate the effect of NTN1-CNV, we detected the Netrin-1 (NTN1) gene dose and protein expression content in the longissimus dorsi of different IMF content pigs using Western blotting and investigated the expression of NTN1 RNA in different tissues using real-time quantitative polymerase chain reaction (qPCR). The knock-down of the NTN1 gene in C2C12 and 3T3-L1 cells and over-expression in C2C12 cells during the proliferation and differentiation stage were also investigated to explore the possible pathway of action of NTN1. The results showed that in individuals with IMF content differences, the gene dose of NTN1 and the expression of NTN1 protein were also significantly different, which indicated that NTN1-CNV may directly affect IMF by its coding protein. NTN1 had the highest expression in pig longissimus dorsi and backfat tissues, which indicates that NTN1 may play an important role in muscle and fat tissues. The in vitro validation assay indicated that NTN1 silencing could promote the proliferation and inhibit the differentiation of C2C12 cells, with no effect on 3T3-L1 cells. Additionally, NTN1 over-expression could inhibit the proliferation and promote the differentiation of C2C12 cells. Combined with previous research, we conclude that NTN1-CNV may affect IMF by its gene dose, and the expression of NTN1 may affect the proliferation and differentiation of muscle cells by the AMP-activated protein kinase (AMPK) pathway and finally influence the IMF.
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- 2019
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