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  • 1
    In: BMC Genomics, Springer Science and Business Media LLC, Vol. 22, No. 1 ( 2021-12)
    Abstract: In the process of pig breeding, the average daily gain (ADG), days to 100 kg (AGE), and backfat thickness (BFT) are directly related to growth rate and fatness. However, the genetic mechanisms involved are not well understood. Copy number variation (CNV), an important source of genetic diversity, can affect a variety of complex traits and diseases and has gradually been thrust into the limelight. In this study, we reported the genome-wide CNVs of Duroc pigs using SNP genotyping data from 6627 animals. We also performed a copy number variation region (CNVR)-based genome-wide association studies (GWAS) for growth and fatness traits in two Duroc populations. Results Our study identified 953 nonredundant CNVRs in U.S. and Canadian Duroc pigs, covering 246.89 Mb (~ 10.90%) of the pig autosomal genome. Of these, 802 CNVRs were in U.S. Duroc pigs with 499 CNVRs were in Canadian Duroc pigs, indicating 348 CNVRs were shared by the two populations. Experimentally, 77.8% of nine randomly selected CNVRs were validated through quantitative PCR (qPCR). We also identified 35 CNVRs with significant association with growth and fatness traits using CNVR-based GWAS. Ten of these CNVRs were associated with both ADG and AGE traits in U.S. Duroc pigs. Notably, four CNVRs showed significant associations with ADG, AGE, and BFT, indicating that these CNVRs may play a pleiotropic role in regulating pig growth and fat deposition. In Canadian Duroc pigs, nine CNVRs were significantly associated with both ADG and AGE traits. Further bioinformatic analysis identified a subset of potential candidate genes, including PDGFA , GPER1 , PNPLA2 and BSCL2 . Conclusions The present study provides a necessary supplement to the CNV map of the Duroc genome through large-scale population genotyping. In addition, the CNVR-based GWAS results provide a meaningful way to elucidate the genetic mechanisms underlying complex traits. The identified CNVRs can be used as molecular markers for genetic improvement in the molecular-guided breeding of modern commercial pigs.
    Type of Medium: Online Resource
    ISSN: 1471-2164
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2041499-7
    SSG: 12
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  • 2
    In: Frontiers in Veterinary Science, Frontiers Media SA, Vol. 7 ( 2020-8-5)
    Type of Medium: Online Resource
    ISSN: 2297-1769
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2020
    detail.hit.zdb_id: 2834243-4
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  • 3
    Online Resource
    Online Resource
    Frontiers Media SA ; 2020
    In:  Frontiers in Veterinary Science Vol. 7 ( 2020-11-11)
    In: Frontiers in Veterinary Science, Frontiers Media SA, Vol. 7 ( 2020-11-11)
    Type of Medium: Online Resource
    ISSN: 2297-1769
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2020
    detail.hit.zdb_id: 2834243-4
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  • 4
    In: Animals, MDPI AG, Vol. 13, No. 15 ( 2023-07-26), p. 2414-
    Abstract: Body conformation is the most direct production index, which can fully reflect pig growth status and is closely related to critical economic traits. In this study, we conducted a genome-wide association study (GWAS) on body conformation traits in a population of 1518 Duroc × (Landrace × Yorkshire) commercial pigs. These traits included body length (BL), body height (BH), chest circumference (CC), abdominal circumference (AC), and waist circumference (WC). Both the mixed linear model (MLM) and fixed and random model circulating probability unification (FarmCPU) approaches were employed for the analysis. Our findings revealed 60 significant single nucleotide polymorphisms (SNPs) associated with these body conformation traits in the crossbred pig population. Specifically, sixteen SNPs were significantly associated with BL, three SNPs with BH, thirteen SNPs with CC, twelve SNPs with AC, and sixteen SNPs with WC. Moreover, we identified several promising candidate genes located within the genomic regions associated with body conformation traits. These candidate genes include INTS10, KIRREL3, SOX21, BMP2, MAP4K3, SOD3, FAM160B1, ATL2, SPRED2, SEC16B, and RASAL2. Furthermore, our analysis revealed a novel significant quantitative trait locus (QTL) on SSC7 specifically associated with waist circumference, spanning an 84 kb interval. Overall, the identification of these significant SNPs and potential candidate genes in crossbred commercial pigs enhances our understanding of the genetic basis underlying body conformation traits. Additionally, these findings provide valuable genetic resources for pig breeding programs.
    Type of Medium: Online Resource
    ISSN: 2076-2615
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 2606558-7
    SSG: 23
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  • 5
    In: Nephron, S. Karger AG, Vol. 145, No. 4 ( 2021), p. 353-362
    Abstract: 〈 b 〉 〈 i 〉 Objectives: 〈 /i 〉 〈 /b 〉 The determinants leading to different renal outcomes in community-acquired acute kidney injury (CA-AKI) and the influence of renal histological damage on the prognosis and recovery of CA-AKI are scarcely reported. 〈 b 〉 〈 i 〉 Methods: 〈 /i 〉 〈 /b 〉 Adult patients with CA-AKI admitted to Shanghai Changzheng Hospital with renal biopsy profiles from January 1, 2010, to December 31, 2018, were enrolled in our cohort. After 3 months of follow-up, clinical outcomes, including patient survival, dialysis requirement during hospitalization and at 3 months, CKD stage 3–5, and renal functional recovery at 3 months, were analyzed, and risk factors were identified. 〈 b 〉 〈 i 〉 Results: 〈 /i 〉 〈 /b 〉 A total of 294 patients with CA-AKI with renal pathology were identified for this cohort. Among 282 patients who survived 3 months after AKI, 59.6% completely recovered, 21.3% partially recovered, 21.3% progressed to stage 3–5 CKD without dialysis, and 17.7% maintained dialysis. Moreover, 70.4% of patients in the cohort presented with de novo intrinsic renal disease, except acute tubular necrosis or acute interstitial nephritis, on renal biopsy. In the multivariate analyses, clinical factors were more related to short-term outcomes and severity of CA-AKI, represented by mortality, in-hospital dialysis, and CRRT requirement, while pathological elements were more involved with CKD progression, including dialysis-dependent or stage 3–5 CKD, and renal function recovery at the 3-month follow-up. The detrimental influence of glomerular and arterial lesions on renal prognosis of CA-AKI was as critical as tubular and interstitial lesions. 〈 b 〉 〈 i 〉 Conclusions: 〈 /i 〉 〈 /b 〉 Clinical and pathological parameters both contribute to patient and renal outcomes after CA-AKI. The value of renal biopsy should be recognized in prognostic prediction.
    Type of Medium: Online Resource
    ISSN: 1660-8151 , 2235-3186
    Language: English
    Publisher: S. Karger AG
    Publication Date: 2021
    detail.hit.zdb_id: 2810853-X
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  • 6
    In: International Journal of Molecular Sciences, MDPI AG, Vol. 23, No. 15 ( 2022-07-24), p. 8157-
    Abstract: Litter size is an important indicator to measure the production capacity of commercial pigs. Spontaneous embryo loss is an essential factor in determining sow litter size. In early pregnancy, spontaneous embryo loss in porcine is as high as 20–30% during embryo implantation. However, the specific molecular mechanism underlying spontaneous embryo loss at the end of embryo implantation remains unknown. Therefore, we comprehensively used small RNA sequencing technology, bioinformatics analysis, and molecular experiments to determine the microRNA (miRNA) expression profile in the healthy and arresting embryo implantation site of porcine endometrium on day of gestation (DG) 28. A total of 464 miRNAs were identified in arresting endometrium (AE) and healthy endometrium (HE), and 139 differentially expressed miRNAs (DEMs) were screened. We combined the mRNA sequencing dataset from the SRA database to predict the target genes of these miRNAs. A quantitative real-time PCR assay identified the expression levels of miRNAs and mRNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed on differentially expressed target genes of DEMs, mainly enriched in epithelial development and amino acids metabolism-related pathways. We performed fluorescence in situ hybridization (FISH) and the dual-luciferase report gene assay to confirm miRNA and predicted target gene binding. miR-205 may inhibit its expression by combining 3′-untranslated regions (3′ UTR) of tubulointerstitial nephritis antigen-like 1 (TINAGL1). The resulting inhibition of angiogenesis in the maternal endometrium ultimately leads to the formation of arresting embryos during the implantation period. This study provides a reference for the effect of miRNA on the successful implantation of pig embryos in early gestation.
    Type of Medium: Online Resource
    ISSN: 1422-0067
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2019364-6
    SSG: 12
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  • 7
    In: mSystems, American Society for Microbiology, Vol. 8, No. 2 ( 2023-04-27)
    Abstract: Extensive research has explored the causes of embryo losses during early pregnancy by analyzing interaction mechanisms in sows’ uterus, ignoring the importance of the lower reproductive tract in pregnancy development regulation. Despite recent progress in understanding the diversity of vaginal microbes under different physiological states, the dynamic of sows’ vaginal microbiotas during pregnancy and the interaction between vaginal microbes and the host are poorly understood. Here, we performed a comprehensive analysis of sows’ vaginal microbial communities in early pregnancy coupled with overall patterns of vaginal mucosal epithelium gene expression. The vaginal microbiota was analyzed by 16s rRNA or metagenome sequencing, and the vaginal mucosal epithelium transcriptome was analyzed by RNA sequencing, followed by integration of the data layers. We found that the sows’ vaginal microbiotas in early pregnancy develop dynamically, and there is a homeostasis balance of Firmicutes and Proteobacteria . Subsequently, we identified two pregnancy-specific communities, which play diverse roles. The microbes in the vagina stimulate the epithelial cells, while vaginal epithelium changes its structure and functions in response to stimulation. These changes produce specific inflammation responses to promote pregnancy development. Our findings demonstrate the interaction between microbes and host in the sow vagina in early pregnancy to promote pregnancy development, meanwhile providing a reference data set for the study of targeted therapies of microbial homeostasis dysregulation in the female reproductive tract. IMPORTANCE This work sheds light on the dynamics of the sow vaginal microbiotas in early pregnancy and its roles in pregnancy development. Furthermore, this study provides insight into the functional mechanisms of reproductive tract microbes by outlining vaginal microbe-host interactions, which might identify new research and intervention targets for improving pregnancy development by modulating lower reproductive tract microbiota.
    Type of Medium: Online Resource
    ISSN: 2379-5077
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2023
    detail.hit.zdb_id: 2844333-0
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  • 8
    Online Resource
    Online Resource
    Asian Australasian Association of Animal Production Societies ; 2023
    In:  Animal Bioscience Vol. 36, No. 6 ( 2023-06-01), p. 861-868
    In: Animal Bioscience, Asian Australasian Association of Animal Production Societies, Vol. 36, No. 6 ( 2023-06-01), p. 861-868
    Abstract: Objective: Loin muscle area (LMA) is an important target trait of pig breeding. This study aimed to identify single nucleotide polymorphisms (SNPs) and genes associated with LMA in the Duroc×(Landrace×Yorkshire) crossbred pigs (DLY).Methods: A genome-wide association study was performed using the Illumina 50K chip to map the genetic marker and genes associated with LMA in 511 DLY pigs (255 boars and 256 sows).Results: After quality control, we detected 35,426 SNPs, including six SNPs significantly associated with LMA in pigs, with MARC0094338 and ASGA0072817 being the two key SNPs responsible for 1.77% and 2.48% of the phenotypic variance of LMA, respectively. Based on previous research, we determined two candidate genes (growth hormone receptor [ 〈 i 〉 GHR 〈 /i 〉 ] and 3-oxoacid Co A-transferase 1 [ 〈 i 〉 OXCT1 〈 /i 〉 ]) that are associated with fat deposition and muscle growth and found further additional genes ( 〈 i 〉 MYOCD 〈 /i 〉 , 〈 i 〉 ARHGAP44 〈 /i 〉 , 〈 i 〉 ELAC2 〈 /i 〉 , 〈 i 〉 MAP2K4 〈 /i 〉 , 〈 i 〉 FBXO4 〈 /i 〉 , 〈 i 〉 FBLL1 〈 /i 〉 , 〈 i 〉 RARS1 〈 /i 〉 , 〈 i 〉 SLIT3 〈 /i 〉 , and 〈 i 〉 RANK3 〈 /i 〉 ) that are presumed to have an effect on LMA.Conclusion: This study contributes to the identification of the mutation that underlies quantitative trait loci associated with LMA and to future pig breeding programs based on marker-assisted selection. Further studies are needed to elucidate the role of the identified candidate genes in the physiological processes involved in LMA regulation.
    Type of Medium: Online Resource
    ISSN: 2765-0189 , 2765-0235
    Language: English
    Publisher: Asian Australasian Association of Animal Production Societies
    Publication Date: 2023
    detail.hit.zdb_id: 3055169-9
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  • 9
    In: Biochemical Pharmacology, Elsevier BV, Vol. 221 ( 2024-03), p. 116039-
    Type of Medium: Online Resource
    ISSN: 0006-2952
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2024
    detail.hit.zdb_id: 1496199-4
    SSG: 15,3
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  • 10
    Online Resource
    Online Resource
    Frontiers Media SA ; 2020
    In:  Frontiers in Genetics Vol. 11 ( 2020-5-26)
    In: Frontiers in Genetics, Frontiers Media SA, Vol. 11 ( 2020-5-26)
    Type of Medium: Online Resource
    ISSN: 1664-8021
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2020
    detail.hit.zdb_id: 2606823-0
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