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Wang H, Wang X, Yang Y, Zhu Y, Wang S, Chen Q, Yan D, Dong X, Li M, Lu S. Genome-wide identification of quantitative trait loci and candidate genes for seven carcass traits in a four-way intercross porcine population. BMC Genomics 2024; 25:582. [PMID: 38858624 PMCID: PMC11165779 DOI: 10.1186/s12864-024-10484-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 05/30/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Carcass traits are essential economic traits in the commercial pig industry. However, the genetic mechanism of carcass traits is still unclear. In this study, we performed a genome-wide association study (GWAS) based on the specific-locus amplified fragment sequencing (SLAF-seq) to study seven carcass traits on 223 four-way intercross pigs, including dressing percentage (DP), number of ribs (RIB), skin thinkness (ST), carcass straight length (CSL), carcass diagonal length (CDL), loin eye width (LEW), and loin eye thickness (LET). RESULTS A total of 227,921 high-quality single nucleotide polymorphisms (SNPs) were detected to perform GWAS. A total of 30 SNPs were identified for seven carcass traits using the mixed linear model (MLM) (p < 1.0 × 10- 5), of which 9 SNPs were located in previously reported quantitative trait loci (QTL) regions. The phenotypic variation explained (PVE) by the significant SNPs was from 2.43 to 16.32%. Furthermore, 11 candidate genes (LYPLAL1, EPC1, MATN2, ZFAT, ZBTB10, ZNF704, INHBA, SMYD3, PAK1, SPTBN2, and ACTN3) were found for carcass traits in pigs. CONCLUSIONS The GWAS results will improve our understanding of the genetic basis of carcass traits. We hypothesized that the candidate genes associated with these discovered SNPs would offer a biological basis for enhancing the carcass quality of pigs in swine breeding.
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Affiliation(s)
- Huiyu Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- Faculty of Animal Science, Xichang University, Xichang, Sichuan, 615000, China
| | - Xiaoyi Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Yongli Yang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Yixuan Zhu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Shuyan Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Qiang Chen
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Dawei Yan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Xinxing Dong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Mingli Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
| | - Shaoxiong Lu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China.
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Curtis D. Multiple Linear Regression Allows Weighted Burden Analysis of Rare Coding Variants in an Ethnically Heterogeneous Population. Hum Hered 2021; 85:1-10. [PMID: 33412546 DOI: 10.1159/000512576] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/20/2020] [Indexed: 11/19/2022] Open
Abstract
Weighted burden analysis has been used in exome-sequenced case-control studies to identify genes in which there is an excess of rare and/or functional variants associated with phenotype. Implementation in a ridge regression framework allows simultaneous analysis of all variants along with relevant covariates, such as population principal components. In order to apply the approach to a quantitative phenotype, a weighted burden score is derived for each subject and included in a linear regression analysis. The weighting scheme is adjusted in order to apply differential weights to rare and very rare variants and a score is derived based on both the frequency and predicted effect of each variant. When applied to an ethnically heterogeneous dataset consisting of 49,790 exome-sequenced UK Biobank subjects and using body mass index as the phenotype, the method produces a very inflated test statistic. However, this is almost completely corrected by including 20 population principal components as covariates. When this is done, the top 30 genes include a few which are quite plausibly associated with the phenotype, including LYPLAL1 and NSDHL. This approach offers a way to carry out gene-based analyses of rare variants identified by exome sequencing in heterogeneous datasets without requiring that data from ethnic minority subjects be discarded. This research has been conducted using the UK Biobank Resource.
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Affiliation(s)
- David Curtis
- UCL Genetics Institute, University College London, London, United Kingdom, .,Centre for Psychiatry, Queen Mary University of London, London, United Kingdom,
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Discovery of small-molecule enzyme activators by activity-based protein profiling. Nat Chem Biol 2020; 16:997-1005. [PMID: 32514184 PMCID: PMC7442688 DOI: 10.1038/s41589-020-0555-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 04/23/2020] [Indexed: 12/17/2022]
Abstract
Activity-based protein profiling (ABPP) has been used extensively to discover and optimize selective inhibitors of enzymes. Here, we show that ABPP can also be implemented to identify the converse – small-molecule enzyme activators. Using a kinetically controlled, fluorescence polarization-ABPP assay, we identify compounds that stimulate the activity of LYPLAL1 – a poorly characterized serine hydrolase with complex genetic links to human metabolic traits. We apply ABPP-guided medicinal chemistry to advance a lead into a selective LYPLAL1 activator suitable for use in vivo. Structural simulations coupled to mutational, biochemical, and biophysical analyses indicate that this compound increases LYPLAL1’s catalytic activity likely by enhancing the efficiency of the catalytic triad charge-relay system. Treatment with this LYPLAL1 activator confers beneficial effects in a mouse model of diet-induced obesity. These findings reveal a new mode of pharmacological regulation for this large enzyme family and suggest that ABPP may aid discovery of activators for additional enzyme classes.
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Norheim F, Hasin-Brumshtein Y, Vergnes L, Chella Krishnan K, Pan C, Seldin MM, Hui ST, Mehrabian M, Zhou Z, Gupta S, Parks BW, Walch A, Reue K, Hofmann SM, Arnold AP, Lusis AJ. Gene-by-Sex Interactions in Mitochondrial Functions and Cardio-Metabolic Traits. Cell Metab 2019; 29:932-949.e4. [PMID: 30639359 PMCID: PMC6447452 DOI: 10.1016/j.cmet.2018.12.013] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/29/2018] [Accepted: 12/17/2018] [Indexed: 12/20/2022]
Abstract
We studied sex differences in over 50 cardio-metabolic traits in a panel of 100 diverse inbred strains of mice. The results clearly showed that the effects of sex on both clinical phenotypes and gene expression depend on the genetic background. In support of this, genetic loci associated with the traits frequently showed sex specificity. For example, Lyplal1, a gene implicated in human obesity, was shown to underlie a sex-specific locus for diet-induced obesity. Global gene expression analyses of tissues across the panel implicated adipose tissue "beiging" and mitochondrial functions in the sex differences. Isolated mitochondria showed gene-by-sex interactions in oxidative functions, such that some strains (C57BL/6J) showed similar function between sexes, whereas others (DBA/2J and A/J) showed increased function in females. Reduced adipose mitochondrial function in males as compared to females was associated with increased susceptibility to obesity and insulin resistance. Gonadectomy studies indicated that gonadal hormones acting in a tissue-specific manner were responsible in part for the sex differences.
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Affiliation(s)
- Frode Norheim
- Department of Medicine/Division of Cardiology and Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Yehudit Hasin-Brumshtein
- Department of Medicine/Division of Cardiology and Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Laurent Vergnes
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Karthickeyan Chella Krishnan
- Department of Medicine/Division of Cardiology and Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Calvin Pan
- Department of Medicine/Division of Cardiology and Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Marcus M Seldin
- Department of Medicine/Division of Cardiology and Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Simon T Hui
- Department of Medicine/Division of Cardiology and Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Margarete Mehrabian
- Department of Medicine/Division of Cardiology and Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Zhiqiang Zhou
- Department of Medicine/Division of Cardiology and Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sonul Gupta
- Department of Medicine/Division of Cardiology and Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Brian W Parks
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Axel Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Karen Reue
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Susanna M Hofmann
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health (GmbH), Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, München 80336, Germany; Medizinische Klinik und Poliklinik IV, Klinikum der Ludwig Maximilian Universität (LMU), Munich, Germany
| | - Arthur P Arnold
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Aldons J Lusis
- Department of Medicine/Division of Cardiology and Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
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Loos RJ. The genetics of adiposity. Curr Opin Genet Dev 2018; 50:86-95. [PMID: 29529423 PMCID: PMC6089650 DOI: 10.1016/j.gde.2018.02.009] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 02/09/2018] [Accepted: 02/14/2018] [Indexed: 02/08/2023]
Abstract
Genome-wide discovery efforts have identified more than 500 genetic loci associated with adiposity traits. The vast majority of these loci were found through large-scale meta-analyses for body mass index (BMI) and waist-to-hip ratio (WHR), and in European ancestry populations. However, alternative approaches, focusing on non-European ancestry populations, more refined adiposity measures, and low-frequency (minor allele frequency (MAF)<5%) coding variants, identified additional novel loci that had not been identified before. Loci associated with overall obesity implicate pathways that act in the brain, whereas loci associated with fat distribution point to pathways involved in adipocyte biology. Pinpointing the causal gene within each locus remains challenging, but is a critical step towards translation of genome-wide association study (GWAS) loci into new biology. Ultimately, new genes may provide pharmacological targets for the development of weight loss drugs.
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Affiliation(s)
- Ruth Jf Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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