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Xu W, Wang Z, Tao Z, Li K, Lu L. Discover QTLs for the level of blood components in Shaoxing duck using GWAS and haplotype sharing analysis. Anim Biotechnol 2024; 35:2390940. [PMID: 39137276 DOI: 10.1080/10495398.2024.2390940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/06/2024] [Indexed: 08/15/2024]
Abstract
Blood composition is indicative of health-related traits such as immunity and metabolism. The use of molecular genetics to investigate alterations in these attributes in laying ducks is a novel approach. Our objective was to employ genome - wide association studies (GWAS) and haplotype - sharing analysis to identify genomic regions and potential genes associated with 11 blood components in Shaoxing ducks. Our findings revealed 35 SNPs and 1 SNP associated with low-density lipoprotein cholesterol (LDL) and globulin (GLB), respectively. We identified 36 putative candidate genes for the LDL trait in close proximity to major QTLs and key loci. Based on their biochemical and physiological properties, TRA2A, NPY, ARHGEF26, DHX36, and AADAC are the strongest putative candidate genes. Through linkage disequilibrium analysis and haplotype sharing analysis, we identified three haplotypes and one haplotype, respectively, that were significantly linked with LDL and GLB. These haplotypes could be selected as potential candidate haplotypes for molecular breeding of Shaoxing ducks. Additionally, we utilized a bootstrap test to verify the reliability of GWAS with small experimental samples. The test can be accessed at https://github.com/xuwenwu24/Bootstrap-test.
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Affiliation(s)
- Wenwu Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Science, Hangzhou, China
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhenzhen Wang
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zeng Tao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Science, Hangzhou, China
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Kui Li
- Zhejiang Animal Husbandry Technology Extension and Breeding Livestock & Poultry Testing Station, Hangzhou, Zhejiang, China
| | - Lizhi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Science, Hangzhou, China
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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2
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Yang Y, Gan M, Liu C, Xie Z, Wang M, Zhou C, Cheng W, Chen L, Zhang S, Zhao Y, Niu L, Wang Y, Wang J, Shen L, Zhu L. Analysis of genetic evolutionary differences among four Tibetan pig populations in China. Genomics 2024; 116:110950. [PMID: 39393592 DOI: 10.1016/j.ygeno.2024.110950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 09/02/2024] [Accepted: 10/07/2024] [Indexed: 10/13/2024]
Abstract
Tibetan pigs are a locally bred domestic pig breed originating from the Tibetan Plateau in China. They can be categorized into four distinct groups based on their geographical locations: Sichuan Tibetan pigs, Tibetan pigs from Tibet, Yunnan Tibetan pigs, and Gansu Tibetan pigs. This study aimed to explore population diversity, genetic structure and selection signals among Tibetan pigs in four Chinese national nature reserves. The results show that there is different observed heterozygosity among Tibetan pig populations (0.1957-0.1978). Ratio of runs of homozygosity (Froh) calculation of four Tibetan pig populations by runs of homozygosity (ROH) revealed the presence of inbreeding within the population (0.0336-0.0378). Analysis of the genetic structure demonstrated distinct population stratification among the four Tibetan pig populations, with each showing relatively independent evolutionary directions. Furthermore, Five methods (FST, Piratio, ROD, Tajima's D, XP-CLR) were used to artificially select evolutionary trajectories. The results mainly involved processes such as DNA repair, immune regulation, muscle fat deposition and adaptation to hypoxia. In conclusion, this study enhances our understanding of the genetic characteristics of Tibetan pig populations and provides a theoretical reference for the conservation of resources across different populations of Tibetan pigs.
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Affiliation(s)
- Yiting Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Mailin Gan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Chengming Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhongwei Xie
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Meng Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Chengpeng Zhou
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Wenqiang Cheng
- National Animal Husbandry Service, Beijing 100125, China
| | - Lei Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Shunhua Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Ye Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Lili Niu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jingyong Wang
- Chongqing Academy of Animal Science, Chongqing 402460, China
| | - Linyuan Shen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Li Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu 611130, China.
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3
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Zhuang Z, Li K, Yang K, Gao G, Li Z, Zhu X, Zhao Y. Genome-Wide Association Study Reveals Novel Candidate Genes Influencing Semen Traits in Landrace Pigs. Animals (Basel) 2024; 14:1839. [PMID: 38997951 PMCID: PMC11240458 DOI: 10.3390/ani14131839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/04/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
Artificial insemination plays a crucial role in pig production, particularly in enhancing the genetic potential of elite boars. To accelerate genetic progress for semen traits in pigs, it is vital to understand and identify the underlying genetic markers associated with desirable traits. Herein, we genotyped 1238 Landrace boars with GeneSeek Porcine SNP50 K Bead chip and conducted genome-wide association studies to identify genetic regions and candidate genes associated with 12 semen traits. Our study identified 38 SNPs associated with the analyzed 12 semen traits. Furthermore, we identified several promising candidate genes, including HIBADH, DLG1, MED1, APAF1, MGST3, MTG2, and ZP4. These candidate genes have the potential function to facilitate the breeding of boars with improved semen traits. By further investigating and understanding the roles of these genes, we can develop more effective breeding strategies that contribute to the overall enhancement of pig production. The results of our study provide valuable insights for the pig-breeding industry and support ongoing research efforts to optimize genetic selection for superior semen traits.
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Affiliation(s)
- Zhanwei Zhuang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Kebiao Li
- School of Life Sciences and Engineering, Foshan University, Foshan 528231, China
| | - Kai Yang
- School of Life Sciences and Engineering, Foshan University, Foshan 528231, China
| | - Guangxiong Gao
- School of Life Sciences and Engineering, Foshan University, Foshan 528231, China
| | - Zhili Li
- School of Life Sciences and Engineering, Foshan University, Foshan 528231, China
| | - Xiaoping Zhu
- School of Life Sciences and Engineering, Foshan University, Foshan 528231, China
| | - Yunxiang Zhao
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
- Guangxi Yangxiang Co., Ltd., Guigang 537100, China
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Bolner M, Bertolini F, Bovo S, Schiavo G, Fontanesi L. Investigation of ABO Gene Variants across More Than 60 Pig Breeds and Populations and Other Suidae Species Using Whole-Genome Sequencing Datasets. Animals (Basel) 2023; 14:5. [PMID: 38200737 PMCID: PMC10778222 DOI: 10.3390/ani14010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/04/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Polymorphisms in the human ABO gene determine the major blood classification system based on the three well-known forms: A; B; and O. In pigs that carry only two main alleles in this gene (A and O), we still need to obtain a more comprehensive distribution of variants, which could also impact its function. In this study, we mined more than 500 whole-genome sequencing datasets to obtain information on the ABO gene in different Suidae species, pig breeds, and populations and provide (i) a comprehensive distribution of the A and O alleles, (ii) evolutionary relationships of ABO gene sequences across Suidae species, and (iii) an exploratory evaluation of the effect of the different ABO gene variants on production traits and blood-related parameters in Italian Large White pigs. We confirmed that allele O is likely under balancing selection, present in all Sus species investigated, without being fixed in any of them. We reported a novel structural variant in perfect linkage disequilibrium with allele O that made it possible to estimate the evolutionary time window of occurrence of this functional allele. We also identified two single nucleotide polymorphisms that were suggestively associated with plasma magnesium levels in pigs. Other studies can also be constructed over our results to further evaluate the effect of this gene on economically relevant traits and basic biological functions.
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Affiliation(s)
| | | | | | | | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Giuseppe Fanin 46, 40127 Bologna, Italy; (M.B.); (S.B.); (G.S.)
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5
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Bordonaro S, Chessari G, Mastrangelo S, Senczuk G, Chessa S, Castiglioni B, Tumino S, Marletta D, Criscione A. Genome-wide population structure, homozygosity, and heterozygosity patterns of Nero Siciliano pig in the framework of Italian and cosmopolitan breeds. Anim Genet 2023; 54:591-605. [PMID: 37381662 DOI: 10.1111/age.13344] [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: 06/13/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/30/2023]
Abstract
Analysis of genomic data is becoming more and more common for the effective management of livestock breeding programmes, even in the case of local populations. In this work, the genome-wide data of Nero Siciliano pig breed were compared to that of wild boar, Italian local and cosmopolitan breeds to investigate its genetic structure, and runs of homozygosity (ROH) and heterozygosity patterns. The Nero Siciliano has been reported to have the highest rate of genetic diversity among the Italian breeds, and a genetic variability comparable to that of the cosmopolitan breeds. Analyses of genomic structure and relationships underlined its proximity to wild boar, and an internal substructure probably linked to different family lines. The breed showed a low value of inbreeding estimated from ROH, and the highest diversity index among the Italian breeds, even if lower than that of the cosmopolitans. Four ROH islands in three chromosomes (SSC8, SSC11, and SSC14) and one heterozygosity-rich region (SSC1) were identified in Nero Siciliano, highlighting genomic regions related to productive QTL. Across breeds, SSC8 and SSC14 were the chromosomes with most ROH islands, with Mora Romagnola and wild boar showing the highest level of autozygosity. Chromosomes SSC2, SSC6, SSC8 and SSC13 showed the majority of runs of heterozygosity regions, mainly found in the cosmopolitan pig breeds, which reported several genes associated with health-related QTL. The outlined results can help to better identify the genomic profile of this local breed in order to plan matings, maintain adequate internal diversity and exploit the production system.
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Affiliation(s)
- Salvatore Bordonaro
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Giorgio Chessari
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, Università del Molise, Campobasso, Italy
| | - Stefania Chessa
- Dipartimento di Scienze Veterinarie, Università di Torino, Torino, Italy
| | - Bianca Castiglioni
- Istituto di Biologia e Biotecnologia Agraria, National Research Council, Lodi, Italy
| | - Serena Tumino
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Donata Marletta
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
| | - Andrea Criscione
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università di Catania, Catania, Italy
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6
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Bovo S, Ballan M, Schiavo G, Gallo M, Dall'Olio S, Fontanesi L. Haplotype-based genome-wide association studies reveal new loci for haematological and clinical-biochemical parameters in Large White pigs. Anim Genet 2020; 51:601-606. [PMID: 32511786 DOI: 10.1111/age.12959] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 02/24/2020] [Accepted: 05/02/2020] [Indexed: 01/21/2023]
Abstract
We report haplotype-based GWASs for 33 blood parameters measured in 843 Italian Large White pigs. In the single-trait analysis, a total of 30 QTL for number of basophils, six erythrocyte traits (haemoglobin, haematocrit, mean corpuscular haemoglobin, mean corpuscular haemoglobin concentration, mean corpuscular volume and red blood cell count) and two clinical-biochemical traits (alkaline phosphatase and Ca2+ contents) were identified. In the multiple-trait analysis, a total of five QTL affected three different clusters of traits. Only four of these QTL were already reported in the single-marker and multi-marker GWASs we previously carried out on the same pig population. QTL on SSC11 and SSC17 showed effects on multiple traits. These results further dissected the genetic architecture of parameters that could be used as proxies in breeding programmes for more complex traits. In addition, these results might help to better define the pig as an animal model for several blood-related biological functions.
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Affiliation(s)
- S Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, Bologna, 40127, Italy
| | - M Ballan
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, Bologna, 40127, Italy
| | - G Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, Bologna, 40127, Italy
| | - M Gallo
- Associazione Nazionale Allevatori Suini, Via Nizza 53, Roma, 00198, Italy
| | - S Dall'Olio
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, Bologna, 40127, Italy
| | - L Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, Bologna, 40127, Italy
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7
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Gan QF, Li YR, Lund M, Su GS, Liang XW. Genome‐wide association study identifies loci linked to serum electrolyte traits in Chinese Holstein cattle. Anim Genet 2019; 50:744-748. [DOI: 10.1111/age.12851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Q. F. Gan
- College of Animal Science Fujian Agriculture and Forestry University Fuzhou 350002China
| | - Y. R. Li
- College of Animal Science Fujian Agriculture and Forestry University Fuzhou 350002China
| | - M. Lund
- Department of Molecular Biology and Genetics Center for Quantitative Genetics and Genomics Aarhus University Aarhus 8000Denmark
| | - G. S. Su
- Department of Molecular Biology and Genetics Center for Quantitative Genetics and Genomics Aarhus University Aarhus 8000Denmark
| | - X. W. Liang
- College of Animal Science Fujian Agriculture and Forestry University Fuzhou 350002China
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Reyer H, Oster M, Wittenburg D, Murani E, Ponsuksili S, Wimmers K. Genetic Contribution to Variation in Blood Calcium, Phosphorus, and Alkaline Phosphatase Activity in Pigs. Front Genet 2019; 10:590. [PMID: 31316547 PMCID: PMC6610066 DOI: 10.3389/fgene.2019.00590] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 06/04/2019] [Indexed: 12/18/2022] Open
Abstract
Blood values of calcium (Ca), inorganic phosphorus (IP), and alkaline phosphatase activity (ALP) are valuable indicators for mineral status and bone mineralization. The mineral homeostasis is maintained by absorption, retention, and excretion processes employing a number of known and unknown sensing and regulating factors with implications on immunity. Due to the high inter-individual variation of Ca and P levels in the blood of pigs and to clarify molecular contributions to this variation, the genetics of hematological traits related to the Ca and P balance were investigated in a German Landrace population, integrating both single-locus and multi-locus genome-wide association study (GWAS) approaches. Genomic heritability estimates suggest a moderate genetic contribution to the variation of hematological Ca (N = 456), IP (N = 1049), ALP (N = 439), and the Ca/P ratio (N = 455), with values ranging from 0.27 to 0.54. The genome-wide analysis of markers adds a number of genomic regions to the list of quantitative trait loci, some of which overlap with previous results. Despite the gaps in knowledge of genes involved in Ca and P metabolism, genes like THBS2, SHH, PTPRT, PTGS1, and FRAS1 with reported connections to bone metabolism were derived from the significantly associated genomic regions. Additionally, genomic regions included TRAFD1 and genes coding for phosphate transporters (SLC17A1-SLC17A4), which are linked to Ca and P homeostasis. The study calls for improved functional annotation of the proposed candidate genes to derive features involved in maintaining Ca and P balance. This gene information can be exploited to diagnose and predict characteristics of micronutrient utilization, bone development, and a well-functioning musculoskeletal system in pig husbandry and breeding.
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Affiliation(s)
- Henry Reyer
- Genomics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Michael Oster
- Genomics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Dörte Wittenburg
- Biomathematics and Bioinformatics Unit, Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Eduard Murani
- Genomics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Siriluck Ponsuksili
- Functional Genome Analysis Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Klaus Wimmers
- Genomics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.,Department of Animal Breeding and Genetics, Faculty of Agricultural and Environmental Sciences, University of Rostock, Rostock, Germany
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9
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Bovo S, Mazzoni G, Bertolini F, Schiavo G, Galimberti G, Gallo M, Dall'Olio S, Fontanesi L. Genome-wide association studies for 30 haematological and blood clinical-biochemical traits in Large White pigs reveal genomic regions affecting intermediate phenotypes. Sci Rep 2019; 9:7003. [PMID: 31065004 PMCID: PMC6504931 DOI: 10.1038/s41598-019-43297-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 04/16/2019] [Indexed: 12/20/2022] Open
Abstract
Haematological and clinical-biochemical parameters are considered indicators of the physiological/health status of animals and might serve as intermediate phenotypes to link physiological aspects to production and disease resistance traits. The dissection of the genetic variability affecting these phenotypes might be useful to describe the resilience of the animals and to support the usefulness of the pig as animal model. Here, we analysed 15 haematological and 15 clinical-biochemical traits in 843 Italian Large White pigs, via three genome-wide association scan approaches (single-trait, multi-trait and Bayesian). We identified 52 quantitative trait loci (QTLs) associated with 29 out of 30 analysed blood parameters, with the most significant QTL identified on porcine chromosome 14 for basophil count. Some QTL regions harbour genes that may be the obvious candidates: QTLs for cholesterol parameters identified genes (ADCY8, APOB, ATG5, CDKAL1, PCSK5, PRL and SOX6) that are directly involved in cholesterol metabolism; other QTLs highlighted genes encoding the enzymes being measured [ALT (known also as GPT) and AST (known also as GOT)]. Moreover, the multivariate approach strengthened the association results for several candidate genes. The obtained results can contribute to define new measurable phenotypes that could be applied in breeding programs as proxies for more complex traits.
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Affiliation(s)
- Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - Gianluca Mazzoni
- Department of Health Technology, Technical University of Denmark (DTU), Lyngby, 2800, Denmark
| | - Francesca Bertolini
- National Institute of Aquatic Resources, Technical University of Denmark (DTU), Lyngby, 2800, Denmark
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - Giuliano Galimberti
- Department of Statistical Sciences "Paolo Fortunati", University of Bologna, Via delle Belle Arti 41, 40126, Bologna, Italy
| | - Maurizio Gallo
- Associazione Nazionale Allevatori Suini (ANAS), Via Nizza 53, 00198, Roma, Italy
| | - Stefania Dall'Olio
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy.
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10
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Geraci C, Varzandi AR, Schiavo G, Bovo S, Ribani A, Utzeri VJ, Galimberti G, Buttazzoni L, Ovilo C, Gallo M, Dall'Olio S, Fontanesi L. Genetic markers associated with resistance to infectious diseases have no effects on production traits and haematological parameters in Italian Large White pigs. Livest Sci 2019. [DOI: 10.1016/j.livsci.2019.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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11
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Zhu F, Cui QQ, Yang YZ, Hao JP, Yang FX, Hou ZC. Genome-wide association study of the level of blood components in Pekin ducks. Genomics 2019; 112:379-387. [PMID: 30818062 DOI: 10.1016/j.ygeno.2019.02.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/12/2019] [Accepted: 02/22/2019] [Indexed: 12/29/2022]
Abstract
Blood components are considered to reflect nutrient metabolism and immune activity in both humans and animals. In this study, we measured 12 blood components in Pekin ducks and performed genome-wide association analysis to identify the QTLs (quantitative trait locus) using a genotyping-by-sequencing strategy. A total of 54 QTLs were identified for blood components. One genome-wide significant QTL for alkaline phosphatase was identified within the intron-region of the OTOG gene (P = 1.31E-07). Moreover, 21 genome-wide significant SNPs for the level of serum cholinesterase were identified on six different scaffolds. In addition, for serum calcium, one genome-wide significant QTL was identified in the upstream region of gene RAB11B. These results provide new markers for functional studies in Pekin ducks, and several candidate genes were identified, which may provide additional insights into specific mechanisms for blood metabolism in ducks and their potential application for duck breeding programs.
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Affiliation(s)
- Feng Zhu
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Qian-Qian Cui
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Yu-Ze Yang
- Beijing General Station of Animal Husbandry, Beijing 100107, China
| | | | | | - Zhuo-Cheng Hou
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China.
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12
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A comparative analysis of label-free liquid chromatography-mass spectrometry liver proteomic profiles highlights metabolic differences between pig breeds. PLoS One 2018; 13:e0199649. [PMID: 30208024 PMCID: PMC6135354 DOI: 10.1371/journal.pone.0199649] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 08/28/2018] [Indexed: 02/01/2023] Open
Abstract
The liver is a complex organ governing several physiological processes that define biological mechanisms affecting growth, feed efficiency and performance traits in all livestock species, including pig. Proteomics may contribute to a better understanding of the relationship between liver functions and complex production traits in pigs and to characterize this species as biomedical model. This study applied, for the first time, a label‐free liquid chromatography-mass spectrometry (LC‐MS) proteomic approach to compare the liver proteome profiles of two important heavy pig breeds, Italian Duroc and Italian Large White. Liver specimens were collected (after slaughtering) from performance tested pigs of these two breeds, raised in standard conditions. The label‐free LC‐MS method captured a total of 501 proteins of which 200 were subsequently considered in the between breeds comparison. A statistical pipeline based on the sparse Partial Least Squares Discriminant Analysis (sPLS-DA), coupled with stability and significance tests, was applied for the identification of up or down regulated proteins between breeds. This analysis revealed a total of 25 proteins clearly separating Italian Duroc and Italian Large White pigs. Among the top proteins differentiating the two breeds, 3-ketoacyl-CoA thiolase, mitochondrial (ACAA2) and histone H2B type 2-F (HIST2H2BF) were up-regulated in Italian Duroc pigs and carboxylesterase 3 (CES3) and ketohexokinase (KHK) were up-regulated in Italian Large White pigs. Fatty acid synthase (FASN), involved in fatty acid metabolism and encoded by a gene located in a QTL region for fatty acid composition, was up-regulated in Italian Large White pigs. The in silico protein interaction analysis showed that 16 of these proteins were connected in one big module. Bioinformatic functional analysis indicated that differentially expressed proteins were involved in several biological processes related to the metabolism of lipids, amino-acids, carbohydrates, cofactors and antibiotics/drugs, suggesting that these functions might distinguish Italian Duroc and Italian Large White pigs. This pilot comparative proteomic analysis of the porcine liver highlighted several biological factors that could determine the peculiar production potentials of these two heavy pig breeds, derived by their different genetic backgrounds.
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Just F, Reyer H, Muráni E, Ponsuksili S, Oster M, Wimmers K. Genetic variants of major genes contributing to phosphate and calcium homeostasis and their association with serum parameters in pigs. J Appl Genet 2018; 59:325-333. [PMID: 29931419 PMCID: PMC6061000 DOI: 10.1007/s13353-018-0449-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 04/12/2018] [Accepted: 06/08/2018] [Indexed: 12/29/2022]
Abstract
Calcium and phosphorus are irreplaceable components of life. Tracking the fate of calcium and phosphorus in organisms deserves high attention due to their relevance in bone metabolism and subsequently animal health. Indeed, bone serves as reservoir for calcium and phosphorus, whose formation and resorption follow specific molecular routes including hormones, receptors, and transcription factors. The objective of the study was to analyze the genetic variation of major components driving mineral utilization such as calcitonin receptor, calcium sensing receptor, fibroblast growth factor 23 (FGF23), parathyroid hormone receptor, osteopontin, stanniocalcin 1, RAF-type zinc finger domain containing 1 (TRAFD1), and vitamin D receptor. A German Landrace pig population (n = 360) was used to perform an association analysis between selected single nucleotide polymorphisms (SNP) and relevant serum parameters (calcium, phosphorus, calcium/phosphorus ratio, alkaline phosphatase). Analyzed SNPs in FGF23 (rs710498025) and TRAFD1 (rs345195312) were significantly (p ≤ 0.05) associated with the serum calcium/phosphorus ratio and serum phosphorus levels, respectively. This might represent a modulation of the homeostatic balance between calcium and phosphorus. Furthermore, TRAFD1 is known to be involved in skeletal disorders which emphasize its link to phosphorus utilization and immune system. However, none of the analyzed genetic variants of these major regulators of phosphate and calcium homeostasis showed significant associations after correction for multiple testing (q value > 0.05). Thus, minor contributors as well as unknown and yet to be elucidated regulators of mineral homeostasis need to be characterized towards the implementation of improved phosphorus efficiency in pig breeding programs.
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Affiliation(s)
- Franziska Just
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Henry Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Eduard Muráni
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Siriluck Ponsuksili
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Michael Oster
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Klaus Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany. .,Faculty of Agricultural and Environmental Sciences, University Rostock, 18059, Rostock, Germany.
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Bridging Gaps in the Agricultural Phosphorus Cycle from an Animal Husbandry Perspective—The Case of Pigs and Poultry. SUSTAINABILITY 2018. [DOI: 10.3390/su10061825] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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