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Zhang W, Liu L, Zhou M, Su S, Dong L, Meng X, Li X, Wang C. Assessing Population Structure and Signatures of Selection in Wanbei Pigs Using Whole Genome Resequencing Data. Animals (Basel) 2022; 13:ani13010013. [PMID: 36611624 PMCID: PMC9817800 DOI: 10.3390/ani13010013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/10/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022] Open
Abstract
Wanbei pig (WBP) is one of the indigenous pig resources in China and has many germplasm characteristics. However, research on its genome is lacking. To assess the genomic variation, population structure, and selection signatures, we resequenced 18 WBP for the first time and performed a comprehensive analysis with resequenced data of 10 Asian wild boars. In total, 590.03 Gb of data and approximately 41 million variants were obtained. Polymorphism level (θπ) ratio and genetic differentiation (fixation index)-based cross approaches were applied, and 539 regions, which harbored 176 genes, were selected. Functional analysis of the selected genes revealed that they were associated with lipid metabolism (SCP2, APOA1, APOA4, APOC3, CD36, BCL6, ADCY8), backfat thickness (PLAG1, CACNA2D1), muscle (MYOG), and reproduction (CABS1). Overall, our results provide a valuable resource for characterizing the uniqueness of WBP and a basis for future breeding.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Pig Molecular Quantitative Genetics, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei 230031, China
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Linqing Liu
- Key Laboratory of Pig Molecular Quantitative Genetics, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei 230031, China
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Mei Zhou
- Key Laboratory of Pig Molecular Quantitative Genetics, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei 230031, China
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Shiguang Su
- Key Laboratory of Pig Molecular Quantitative Genetics, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei 230031, China
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Lin Dong
- Key Laboratory of Pig Molecular Quantitative Genetics, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xinxin Meng
- Key Laboratory of Pig Molecular Quantitative Genetics, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Xueting Li
- Key Laboratory of Pig Molecular Quantitative Genetics, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Chonglong Wang
- Key Laboratory of Pig Molecular Quantitative Genetics, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei 230031, China
- Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Correspondence:
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Salavati M, Woolley SA, Cortés Araya Y, Halstead MM, Stenhouse C, Johnsson M, Ashworth CJ, Archibald AL, Donadeu FX, Hassan MA, Clark EL. Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions. G3 (BETHESDA, MD.) 2022; 12:6460335. [PMID: 34897420 PMCID: PMC9210303 DOI: 10.1093/g3journal/jkab424] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
There is very little information about how the genome is regulated in domestic pigs (Sus scrofa). This lack of knowledge hinders efforts to define and predict the effects of genetic variants in pig breeding programs. To address this knowledge gap, we need to identify regulatory sequences in the pig genome starting with regions of open chromatin. We used the "Improved Protocol for the Assay for Transposase-Accessible Chromatin (Omni-ATAC-Seq)" to identify putative regulatory regions in flash-frozen semitendinosus muscle from 24 male piglets. We collected samples from the smallest-, average-, and largest-sized male piglets from each litter through five developmental time points. Of the 4661 ATAC-Seq peaks identified that represent regions of open chromatin, >50% were within 1 kb of known transcription start sites. Differential read count analysis revealed 377 ATAC-Seq defined genomic regions where chromatin accessibility differed significantly across developmental time points. We found regions of open chromatin associated with downregulation of genes involved in muscle development that were present in small-sized fetal piglets but absent in large-sized fetal piglets at day 90 of gestation. The dataset that we have generated provides a resource for studies of genome regulation in pigs and contributes valuable functional annotation information to filter genetic variants for use in genomic selection in pig breeding programs.
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Affiliation(s)
- Mazdak Salavati
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Shernae A Woolley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Yennifer Cortés Araya
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Michelle M Halstead
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA
| | - Claire Stenhouse
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Department of Animal Science, Texas A&M University, College Station, TX 77843, USA
| | - Martin Johnsson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala 750 07, Sweden
| | - Cheryl J Ashworth
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Alan L Archibald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Francesc X Donadeu
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Musa A Hassan
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Emily L Clark
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
- Centre for Tropical Livestock Genetics and Health (CTLGH), Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
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Li C, Duan D, Xue Y, Han X, Wang K, Qiao R, Li XL, Li XJ. An association study on imputed whole-genome resequencing from high-throughput sequencing data for body traits in crossbred pigs. Anim Genet 2022; 53:212-219. [PMID: 35026054 DOI: 10.1111/age.13170] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 10/20/2021] [Accepted: 12/24/2021] [Indexed: 12/12/2022]
Abstract
Body traits are important economic factors in the pig industry. Genome-wide association studies (GWASs) have been widely applied using high-density genotype data to detect QTL in pigs. The aim of the present study was to detect the genetic variants significantly associated with body traits in crossbred pigs using the Illumina Porcine SNP50 BeadChip and imputed whole-genome sequence data. A set of seven body traits - body length, body height, chest circumference, cannon bone circumference, leg buttock circumference, back fat thickness and loin muscle depth - were measured. Moderate to high heritabilities were obtained for most traits (from 0.14 to 0.46), and significant genetic and phenotypic correlations among them were observed. GWAS identified 714 significantly associated SNPs located at 39 regions on all autosomes for body traits, and a total of seven functionally related candidate genes: PIK3CD, HOXA, PCGF2, CHST11, COL2A1, BMI1 and OSR2. Functional enrichment analysis revealed that candidate genes were enriched in the estrogen signaling pathway, embryonic skeletal system morphogenesis and embryonic skeletal system development. These results aim to uncover the genetic mechanisms underlying body development and marker-assisted selection programs focusing on body traits in pigs.
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Affiliation(s)
- Cong Li
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Dongdong Duan
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yahui Xue
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xuelei Han
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Kejun Wang
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Ruimin Qiao
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xiu-Ling Li
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xin-Jian Li
- College of Animal Sciences and Technology, Henan Agricultural University, Zhengzhou, Henan, China
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Fabbri MC, Dadousis C, Tiezzi F, Maltecca C, Lozada-Soto E, Biffani S, Bozzi R. Genetic diversity and population history of eight Italian beef cattle breeds using measures of autozygosity. PLoS One 2021; 16:e0248087. [PMID: 34695128 PMCID: PMC8544844 DOI: 10.1371/journal.pone.0248087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 10/06/2021] [Indexed: 11/18/2022] Open
Abstract
In the present study, GeneSeek GGP-LDv4 33k single nucleotide polymorphism chip was used to detect runs of homozygosity (ROH) in eight Italian beef cattle breeds, six breeds with distribution limited to Tuscany (Calvana, Mucca Pisana, Pontremolese) or Sardinia (Sarda, Sardo Bruna and Sardo Modicana) and two cosmopolitan breeds (Charolais and Limousine). ROH detection analyses were used to estimate autozygosity and inbreeding and to identify genomic regions with high frequency of ROH, which might reflect selection signatures. Comparative analysis among breeds revealed differences in length and distribution of ROH and inbreeding levels. The Charolais, Limousine, Sarda, and Sardo Bruna breeds were found to have a high frequency of short ROH (~ 15.000); Calvana and Mucca Pisana presented also runs longer than 16 Mbp. The highest level of average genomic inbreeding was observed in Tuscan breeds, around 0.3, while Sardinian and cosmopolitan breeds showed values around 0.2. The population structure and genetic distances were analyzed through principal component and multidimensional scaling analyses, and resulted in a clear separation among the breeds, with clusters related to productive purposes. The frequency of ROH occurrence revealed eight breed-specific genomic regions where genes of potential selective and conservative interest are located (e.g. MYOG, CHI3L1, CHIT1 (BTA16), TIMELESS, APOF, OR10P1, OR6C4, OR2AP1, OR6C2, OR6C68, CACNG2 (BTA5), COL5A2 and COL3A1 (BTA2)). In all breeds, we found the largest proportion of homozygous by descent segments to be those that represent inbreeding events that occurred around 32 generations ago, with Tuscan breeds also having a significant proportion of segments relating to more recent inbreeding.
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Affiliation(s)
- Maria Chiara Fabbri
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy
- * E-mail:
| | - Christos Dadousis
- Dipartimento di Scienze Medico‐Veterinarie, Università di Parma, Parma, Italy
| | - Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, NC, United States of America
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, United States of America
| | - Emmanuel Lozada-Soto
- Department of Animal Science, North Carolina State University, Raleigh, NC, United States of America
| | - Stefano Biffani
- Institute of Agricultural Biology and Biotechnology (CNR), Milano, Italy
| | - Riccardo Bozzi
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy
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Zhang X, Zhang D, Wang L, Liu D. Molecular cloning and functional characterization of myogenin promoter in Min pig. ACTA AGR SCAND A-AN 2017. [DOI: 10.1080/09064702.2017.1334811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- X. Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, People’s Republic of China
| | - D. Zhang
- Heilongjiang Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - L. Wang
- Heilongjiang Academy of Agricultural Sciences, Harbin, People’s Republic of China
| | - D. Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, People’s Republic of China
- Heilongjiang Academy of Agricultural Sciences, Harbin, People’s Republic of China
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Fernández AI, Pérez-Montarelo D, Barragán C, Ramayo-Caldas Y, Ibáñez-Escriche N, Castelló A, Noguera JL, Silió L, Folch JM, Rodríguez MC. Genome-wide linkage analysis of QTL for growth and body composition employing the PorcineSNP60 BeadChip. BMC Genet 2012; 13:41. [PMID: 22607048 PMCID: PMC3432624 DOI: 10.1186/1471-2156-13-41] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 04/30/2012] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The traditional strategy to map QTL is to use linkage analysis employing a limited number of markers. These analyses report wide QTL confidence intervals, making very difficult to identify the gene and polymorphisms underlying the QTL effects. The arrival of genome-wide panels of SNPs makes available thousands of markers increasing the information content and therefore the likelihood of detecting and fine mapping QTL regions. The aims of the current study are to confirm previous QTL regions for growth and body composition traits in different generations of an Iberian x Landrace intercross (IBMAP) and especially identify new ones with narrow confidence intervals by employing the PorcineSNP60 BeadChip in linkage analyses. RESULTS Three generations (F3, Backcross 1 and Backcross 2) of the IBMAP and their related animals were genotyped with PorcineSNP60 BeadChip. A total of 8,417 SNPs equidistantly distributed across autosomes were selected after filtering by quality, position and frequency to perform the QTL scan. The joint and separate analyses of the different IBMAP generations allowed confirming QTL regions previously identified in chromosomes 4 and 6 as well as new ones mainly for backfat thickness in chromosomes 4, 5, 11, 14 and 17 and shoulder weight in chromosomes 1, 2, 9 and 13; and many other to the chromosome-wide signification level. In addition, most of the detected QTLs displayed narrow confidence intervals, making easier the selection of positional candidate genes. CONCLUSIONS The use of higher density of markers has allowed to confirm results obtained in previous QTL scans carried out with microsatellites. Moreover several new QTL regions have been now identified in regions probably not covered by markers in previous scans, most of these QTLs displayed narrow confidence intervals. Finally, prominent putative biological and positional candidate genes underlying those QTL effects are listed based on recent porcine genome annotation.
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Affiliation(s)
- Ana I Fernández
- Departamento de Mejora Genética Animal, INIA, Ctra, De la Coruña km, 7, Madrid, 28040, Spain.
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