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Liu X, Hu F, Wang W, Chen X, Niu X, Huang S, Wang Z, Wang J, Ran X. Genome-wide identification of copy number variations in wrinkled skin cases of Xiang pigs. Sci Rep 2024; 14:19695. [PMID: 39181933 PMCID: PMC11344843 DOI: 10.1038/s41598-024-70732-9] [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: 02/17/2024] [Accepted: 08/20/2024] [Indexed: 08/27/2024] Open
Abstract
Copy number variation (CNV) tends to occur in genetically enriched regions and is likely associated with a number of complex diseases such as skin aging. In this study, we investigated the genome-wide CNVs in 20 wrinkled skin cases (WSC) of Xiang pigs and 63 controls, and identified 7893 copy number variable regions (CNVRs). We estimated the F-statistic (Fst) at each locus and identified that 93 case-controls stratified CNVRs (Fst > = 0.15) overlapped with 87 known genes. Functional enrichment analysis showed that most of these genes were predominantly enriched in pathways and terms related to the extracellular matrix. Finally, we found that some CNVs were predicted to have high effects on genes such as VCAN, TIMP1 and FOXO1 through transcriptional amplification, transcript ablation and so on. Most of the genes overlapped with those CNVRs have been reported to be related to aging in human or animals. The copy numbers presented the positive correlations with the transcript level of the genes in skins between the cases and controls. Our results suggested that those 22 CNVRs, including 19 CNV losses and 3 CNV gains, were putatively associated with the skin wrinkle of Xiang pigs.
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Affiliation(s)
- Xiaoli Liu
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, College of Life Science, College of Animal Science, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Fenbin Hu
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, College of Life Science, College of Animal Science, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Wei Wang
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, College of Life Science, College of Animal Science, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Xia Chen
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, College of Life Science, College of Animal Science, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Xi Niu
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, College of Life Science, College of Animal Science, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Shihui Huang
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, College of Life Science, College of Animal Science, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Zhou Wang
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, College of Life Science, College of Animal Science, Guizhou University, Guiyang, 550025, Guizhou, China
| | - Jiafu Wang
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, College of Life Science, College of Animal Science, Guizhou University, Guiyang, 550025, Guizhou, China.
| | - Xueqin Ran
- Institute of Agro-Bioengineering/Key Laboratory of Plant Resource Conservative and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, College of Life Science, College of Animal Science, Guizhou University, Guiyang, 550025, Guizhou, China.
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Yuan H, Wei W, Zhang Y, Li C, Zhao S, Chao Z, Xia C, Quan J, Gao C. Unveiling the Influence of Copy Number Variations on Genetic Diversity and Adaptive Evolution in China's Native Pig Breeds via Whole-Genome Resequencing. Int J Mol Sci 2024; 25:5843. [PMID: 38892031 PMCID: PMC11172908 DOI: 10.3390/ijms25115843] [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: 04/10/2024] [Revised: 05/22/2024] [Accepted: 05/25/2024] [Indexed: 06/21/2024] Open
Abstract
Copy number variations (CNVs) critically influence individual genetic diversity and phenotypic traits. In this study, we employed whole-genome resequencing technology to conduct an in-depth analysis of 50 pigs from five local swine populations [Rongchang pig (RC), Wuzhishan pig (WZS), Tibetan pig (T), Yorkshire (YL) and Landrace (LR)], aiming to assess their genetic potential and explore their prospects in the field of animal model applications. We identified a total of 96,466 CNVs, which were subsequently integrated into 7112 non-redundant CNVRs, encompassing 1.3% of the swine genome. Functional enrichment analysis of the genes within these CNVRs revealed significant associations with sensory perception, energy metabolism, and neural-related pathways. Further selective scan analyses of the local pig breeds RC, T, WZS, along with YL and LR, uncovered that for the RC variety, the genes PLA2G10 and ABCA8 were found to be closely related to fat metabolism and cardiovascular health. In the T breed, the genes NCF2 and CSGALNACT1 were associated with immune response and connective tissue characteristics. As for the WZS breed, the genes PLIN4 and CPB2 were primarily linked to fat storage and anti-inflammatory responses. In summary, this research underscores the pivotal role of CNVs in fostering the diversity and adaptive evolution of pig breeds while also offering valuable insights for further exploration of the advantageous genetic traits inherent to China's local pig breeds. This facilitates the creation of experimental animal models tailored to the specific characteristics of these breeds, contributing to the advancement of livestock and biomedical research.
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Affiliation(s)
- Haonan Yuan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730030, China; (H.Y.); (W.W.); (Y.Z.); (S.Z.)
| | - Wenjing Wei
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730030, China; (H.Y.); (W.W.); (Y.Z.); (S.Z.)
| | - Yue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730030, China; (H.Y.); (W.W.); (Y.Z.); (S.Z.)
| | - Changwen Li
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin 150069, China; (C.L.); (C.X.)
| | - Shengguo Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730030, China; (H.Y.); (W.W.); (Y.Z.); (S.Z.)
| | - Zhe Chao
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Key Laboratory of Tropical Animal Breeding and Disease Research, Haikou 571100, China;
| | - Changyou Xia
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin 150069, China; (C.L.); (C.X.)
| | - Jinqiang Quan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730030, China; (H.Y.); (W.W.); (Y.Z.); (S.Z.)
| | - Caixia Gao
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin 150069, China; (C.L.); (C.X.)
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Romanets E, Bakoev S, Romanets T, Kolosova M, Kolosov A, Bakoev F, Tretiakova O, Usatov A, Getmantseva L. Evaluation of genetic differentiation and search for candidate genes for reproductive traits in pigs. Anim Biosci 2024; 37:832-838. [PMID: 38271973 PMCID: PMC11065708 DOI: 10.5713/ab.23.0297] [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: 08/11/2023] [Revised: 10/03/2023] [Accepted: 11/22/2023] [Indexed: 01/27/2024] Open
Abstract
OBJECTIVE The use of molecular genetic methods in pig breeding can significantly increase the efficiency of breeding and breeding work. We applied the Fst (fixsacion index) method, the main focus of the work was on the search for common options related to the number of born piglets and the weight of born piglets, since today the urgent task is to prevent a decrease in the weight of piglets at birth while maintaining high fertility of sows. METHODS One approach is to scan the genome, followed by an assessment of Fst and identification of selectively selected regions. We chose Large White sows (n = 237) with the same conditions of keeping and feeding. The data were collected from the sows across three farrowing. For genotyping, we used GeneSeek GGP Porcine HD Genomic Profiler v1, which included 68,516 single nucleotide polymorphisms evenly distributed with an average spacing of 25 kb (Illumina Inc, San Diego, CA, USA). RESULTS Based on the results of the Fst analysis, 724 variants representing selection signals for the signs BALWT, BALWT1, NBA, and TNB (weight of piglets born alive, average weight of the 1st piglets born alive, total number born alive, total number born). At the same time, 18 common variants have been identified that are potential markers for both the number of piglets at birth and the weight of piglets at birth, which is extremely important for breeding work to improve reproductive characteristics in sows. CONCLUSION Оur work resulted in identification of variants associated with the reproductive characteristics of pigs. Moreover, we identified, variants which are potential markers for both the number of piglets at birth and the weight of piglets at birth, which is extremely important for breeding work to improve reproductive performance in sows.
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Affiliation(s)
- Elena Romanets
- Faculty of Biotechnology, Don State Agrarian University, 346493, Rostov region, Oktyabrsky district,
Russia
| | - Siroj Bakoev
- Faculty of Biotechnology, Don State Agrarian University, 346493, Rostov region, Oktyabrsky district,
Russia
- Academy of Biology and Biotechnology named after. DI. Ivanovsky, Southern Federal University, 344090, Rostov region, Rostov-on-Don,
Russia
| | - Timofey Romanets
- Faculty of Biotechnology, Don State Agrarian University, 346493, Rostov region, Oktyabrsky district,
Russia
| | - Maria Kolosova
- Faculty of Biotechnology, Don State Agrarian University, 346493, Rostov region, Oktyabrsky district,
Russia
| | - Anatoly Kolosov
- Faculty of Biotechnology, Don State Agrarian University, 346493, Rostov region, Oktyabrsky district,
Russia
| | - Faridun Bakoev
- Faculty of Biotechnology, Don State Agrarian University, 346493, Rostov region, Oktyabrsky district,
Russia
| | - Olga Tretiakova
- Faculty of Biotechnology, Don State Agrarian University, 346493, Rostov region, Oktyabrsky district,
Russia
| | - Alexander Usatov
- Academy of Biology and Biotechnology named after. DI. Ivanovsky, Southern Federal University, 344090, Rostov region, Rostov-on-Don,
Russia
| | - Lyubov Getmantseva
- Faculty of Biotechnology, Don State Agrarian University, 346493, Rostov region, Oktyabrsky district,
Russia
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A V, Kumar A, Mahala S, Chandra Janga S, Chauhan A, Mehrotra A, Kumar De A, Ranjan Sahu A, Firdous Ahmad S, Vempadapu V, Dutt T. Revelation of genetic diversity and genomic footprints of adaptation in Indian pig breeds. Gene 2024; 893:147950. [PMID: 37918549 DOI: 10.1016/j.gene.2023.147950] [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: 08/04/2023] [Revised: 10/16/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
In the present study, the genetic diversity measures among four Indian domestic breeds of pig namely Agonda Goan, Ghurrah, Ghungroo, and Nicobari, of different agro-climatic regions of country were explored and compared with European commercial breeds, European wild boar and Chinese domestic breeds. The double digest restriction site-associated DNA sequencing (ddRADseq) data of Indian pigs (102) and Landrace (10 animals) were generated and whole genome sequencing data of exotic pigs (60 animals) from public data repository were used in the study. The principal component analysis (PCA), admixture analysis and phylogenetic analysis revealed that Indian breeds were closer in ancestry to Chinese breeds than European breeds. European breeds exhibited highest genetic diversity measures among all the considered breeds. Among Indian breeds, Agonda Goan and Ghurrah were found to be more genetically diverse than Nicobari and Ghungroo. The selection signature regions in Indian pigs were explored using iHS and XP-EHH, and during iHS analysis, it was observed that genes related to growth, reproduction, health, meat quality, sensory perception and behavior were found to be under selection pressure in Indian pig breeds. Strong selection signatures were recorded in 24.25-25.25 Mb region of SSC18, 123.25-124 Mb region of SSC15 and 118.75-119.5 Mb region of SSC2 in most of the Indian breeds upon pairwise comparison with European commercial breeds using XP-EHH. These regions were harboring some important genes such as EPHA4 for thermotolerance, TAS2R16, FEZF1, CADPS2 and PTPRZ1 for adaptability to scavenging system of rearing, TRIM36 and PGGT1B for disease resistance and CCDC112, PIAS1, FEM1B and ITGA11 for reproduction.
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Affiliation(s)
- Vani A
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Amit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India.
| | - Sudarshan Mahala
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Sarath Chandra Janga
- Luddy School of Informatics, Computing, and Engineering, Indiana University, IUPUI, Indianapolis, IN, USA
| | - Anuj Chauhan
- Livestock Production and Management, Indian Veterinary Research Institute, Bareilly, UP, India
| | | | - Arun Kumar De
- Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Amiya Ranjan Sahu
- Central Coastal Agricultural Research Institute, Old Goa, Goa, India
| | - Sheikh Firdous Ahmad
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Varshini Vempadapu
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Triveni Dutt
- Livestock Production and Management, Indian Veterinary Research Institute, Bareilly, UP, India
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Davoudi P, Do DN, Colombo S, Rathgeber B, Sargolzaei M, Plastow G, Wang Z, Hu G, Valipour S, Miar Y. Genome-wide association studies for economically important traits in mink using copy number variation. Sci Rep 2024; 14:24. [PMID: 38167844 PMCID: PMC10762091 DOI: 10.1038/s41598-023-50497-3] [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: 10/04/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024] Open
Abstract
Copy number variations (CNVs) are structural variants consisting of duplications and deletions of DNA segments, which are known to play important roles in the genetics of complex traits in livestock species. However, CNV-based genome-wide association studies (GWAS) have remained unexplored in American mink. Therefore, the purpose of the current study was to investigate the association between CNVs and complex traits in American mink. A CNV-based GWAS was performed with the ParseCNV2 software program using deregressed estimated breeding values of 27 traits as pseudophenotypes, categorized into traits of growth and feed efficiency, reproduction, pelt quality, and Aleutian disease tests. The study identified a total of 10,137 CNVs (6968 duplications and 3169 deletions) using the Affymetrix Mink 70K single nucleotide polymorphism (SNP) array in 2986 American mink. The association analyses identified 250 CNV regions (CNVRs) associated with at least one of the studied traits. These CNVRs overlapped with a total of 320 potential candidate genes, and among them, several genes have been known to be related to the traits such as ARID1B, APPL1, TOX, and GPC5 (growth and feed efficiency traits); GRM1, RNASE10, WNT3, WNT3A, and WNT9B (reproduction traits); MYO10, and LIMS1 (pelt quality traits); and IFNGR2, APEX1, UBE3A, and STX11 (Aleutian disease tests). Overall, the results of the study provide potential candidate genes that may regulate economically important traits and therefore may be used as genetic markers in mink genomic breeding programs.
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Affiliation(s)
- Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Duy Ngoc Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Stefanie Colombo
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Bruce Rathgeber
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
- Select Sires Inc., Plain City, OH, USA
| | - Graham Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Zhiquan Wang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Guoyu Hu
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Shafagh Valipour
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada.
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Li L, Quan J, Liu H, Yu H, Chen H, Xia C, Zhao S, Gao C. Identification of the genetic characteristics of copy number variations in experimental specific pathogen-free ducks using whole-genome resequencing. BMC Genomics 2024; 25:17. [PMID: 38166615 PMCID: PMC10759622 DOI: 10.1186/s12864-023-09928-8] [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: 08/31/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Specific pathogen-free ducks are a valuable laboratory resource for waterfowl disease research and poultry vaccine development. High throughput sequencing allows the systematic identification of structural variants in genomes. Copy number variation (CNV) can explain the variation of important duck genetic traits. Herein, the genome-wide CNVs of the three experimental duck species in China (Jinding ducks (JD), Shaoxing ducks (SX), and Fujian Shanma ducks (SM)) were characterized using resequencing to determine their genetic characteristics and selection signatures. RESULTS We obtained 4,810 CNV regions (CNVRs) by merging 73,012 CNVs, covering 4.2% of the duck genome. Functional analysis revealed that the shared CNVR-harbored genes were significantly enriched for 31 gene ontology terms and 16 Kyoto Encyclopedia of Genes and Genomes pathways (e.g., olfactory transduction and immune system). Based on the genome-wide fixation index for each CNVR, growth (SPAG17 and PTH1R), disease resistance (CATHL3 and DMBT1), and thermoregulation (TRPC4 and SLIT3) candidate genes were identified in strongly selected signatures specific to JD, SM, and SX, respectively. CONCLUSIONS In conclusion, we investigated the genome-wide distribution of experimental duck CNVs, providing a reference to establish the genetic basis of different phenotypic traits, thus contributing to the management of experimental animal genetic resources.
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Affiliation(s)
- Lanlan Li
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, 730070, P.R. China
- College of Animal Science & Technology, Ningxia University, Yinchuan, 750021, P.R. China
| | - Jinqiang Quan
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, 730070, P.R. China.
| | - Hongyi Liu
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China
| | - Haibo Yu
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China
| | - Hongyan Chen
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China
| | - Changyou Xia
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China
| | - Shengguo Zhao
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, 730070, P.R. China
| | - Caixia Gao
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China.
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Getmantseva L, Kolosova M, Fede K, Korobeinikova A, Kolosov A, Romanets E, Bakoev F, Romanets T, Yudin V, Keskinov A, Bakoev S. Finding Predictors of Leg Defects in Pigs Using CNV-GWAS. Genes (Basel) 2023; 14:2054. [PMID: 38002997 PMCID: PMC10671522 DOI: 10.3390/genes14112054] [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: 10/08/2023] [Revised: 11/04/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
One of the most important areas of modern genome research is the search for meaningful relationships between genetic variants and phenotypes. In the livestock field, there has been research demonstrating the influence of copy number variants (CNVs) on phenotypic variation. Despite the wide range in the number and size of detected CNVs, a significant proportion differ between breeds and their functional effects are underestimated in the pig industry. In this work, we focused on the problem of leg defects in pigs (lumps/growths in the area of the hock joint on the hind legs) and focused on searching for molecular genetic predictors associated with this trait for the selection of breeding stock. The study was conducted on Large White pigs using three CNV calling tools (PennCNV, QuantiSNP and R-GADA) and the CNVRanger association analysis tool (CNV-GWAS). As a result, the analysis identified three candidate CNVRs associated with the formation of limb defects. Subsequent functional analysis suggested that all identified CNVs may act as potential predictors of the hock joint phenotype of pigs. It should be noted that the results obtained indicate that all significant regions are localized in genes (CTH, SRSF11, MAN1A1 and LPIN1) responsible for the metabolism of amino acids, fatty acids, glycerolipids and glycerophospholipids, thereby related to the immune response, liver functions, content intramuscular fat and animal fatness. These results are consistent with previously published studies, according to which a predisposition to the formation of leg defects can be realized through genetic variants associated with the functions of the liver, kidneys and hematological characteristics.
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Affiliation(s)
- Lyubov Getmantseva
- Federal State Budgetary Educational Institution of Higher Education, Don State Agrarian University, 346493 Persianovsky, Russia; (L.G.); (A.K.)
- Federal State Budgetary Institution, “Center for Strategic Planning and Management of Medical and Biological Health Risks” of the Federal Medical and Biological Agency, 10/1 Pogodinskaya St., 119121 Moscow, Russia; (K.F.); (A.K.)
| | - Maria Kolosova
- Federal State Budgetary Educational Institution of Higher Education, Don State Agrarian University, 346493 Persianovsky, Russia; (L.G.); (A.K.)
| | - Kseniia Fede
- Federal State Budgetary Institution, “Center for Strategic Planning and Management of Medical and Biological Health Risks” of the Federal Medical and Biological Agency, 10/1 Pogodinskaya St., 119121 Moscow, Russia; (K.F.); (A.K.)
| | - Anna Korobeinikova
- Federal State Budgetary Institution, “Center for Strategic Planning and Management of Medical and Biological Health Risks” of the Federal Medical and Biological Agency, 10/1 Pogodinskaya St., 119121 Moscow, Russia; (K.F.); (A.K.)
| | - Anatoly Kolosov
- Federal State Budgetary Educational Institution of Higher Education, Don State Agrarian University, 346493 Persianovsky, Russia; (L.G.); (A.K.)
| | - Elena Romanets
- Federal State Budgetary Educational Institution of Higher Education, Don State Agrarian University, 346493 Persianovsky, Russia; (L.G.); (A.K.)
| | - Faridun Bakoev
- Federal State Budgetary Educational Institution of Higher Education, Don State Agrarian University, 346493 Persianovsky, Russia; (L.G.); (A.K.)
| | - Timofey Romanets
- Federal State Budgetary Educational Institution of Higher Education, Don State Agrarian University, 346493 Persianovsky, Russia; (L.G.); (A.K.)
| | - Vladimir Yudin
- Federal State Budgetary Institution, “Center for Strategic Planning and Management of Medical and Biological Health Risks” of the Federal Medical and Biological Agency, 10/1 Pogodinskaya St., 119121 Moscow, Russia; (K.F.); (A.K.)
| | - Anton Keskinov
- Federal State Budgetary Institution, “Center for Strategic Planning and Management of Medical and Biological Health Risks” of the Federal Medical and Biological Agency, 10/1 Pogodinskaya St., 119121 Moscow, Russia; (K.F.); (A.K.)
| | - Siroj Bakoev
- Federal State Budgetary Institution, “Center for Strategic Planning and Management of Medical and Biological Health Risks” of the Federal Medical and Biological Agency, 10/1 Pogodinskaya St., 119121 Moscow, Russia; (K.F.); (A.K.)
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Wu J, Wu T, Xie X, Niu Q, Zhao Z, Zhu B, Chen Y, Zhang L, Gao X, Niu X, Gao H, Li J, Xu L. Genetic Association Analysis of Copy Number Variations for Meat Quality in Beef Cattle. Foods 2023; 12:3986. [PMID: 37959106 PMCID: PMC10647706 DOI: 10.3390/foods12213986] [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: 09/17/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Meat quality is an economically important trait for global food production. Copy number variations (CNVs) have been previously implicated in elucidating the genetic basis of complex traits. In this article, we detected a total of 112,198 CNVs and 10,102 CNV regions (CNVRs) based on the Bovine HD SNP array. Next, we performed a CNV-based genome-wide association analysis (GWAS) of six meat quality traits and identified 12 significant CNV segments corresponding to eight candidate genes, including PCDH15, CSMD3, etc. Using region-based association analysis, we further identified six CNV segments relevant to meat quality in beef cattle. Among these, TRIM77 and TRIM64 within CNVR4 on BTA29 were detected as candidate genes for backfat thickness (BFT). Notably, we identified a 34 kb duplication for meat color (MC) which was supported by read-depth signals, and this duplication was embedded within the keratin gene family including KRT4, KRT78, and KRT79. Our findings will help to dissect the genetic architecture of meat quality traits from the aspects of CNVs, and subsequently improve the selection process in breeding programs.
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Affiliation(s)
- Jiayuan Wu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Tianyi Wu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Xueyuan Xie
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Qunhao Niu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Zhida Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Bo Zhu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Yan Chen
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Lupei Zhang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Xue Gao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Xiaoyan Niu
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Huijiang Gao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Junya Li
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Lingyang Xu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
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9
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Desire S, Johnsson M, Ros-Freixedes R, Chen CY, Holl JW, Herring WO, Gorjanc G, Mellanby RJ, Hickey JM, Jungnickel MK. A genome-wide association study for loin depth and muscle pH in pigs from intensely selected purebred lines. Genet Sel Evol 2023; 55:42. [PMID: 37322449 DOI: 10.1186/s12711-023-00815-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 05/26/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) aim at identifying genomic regions involved in phenotype expression, but identifying causative variants is difficult. Pig Combined Annotation Dependent Depletion (pCADD) scores provide a measure of the predicted consequences of genetic variants. Incorporating pCADD into the GWAS pipeline may help their identification. Our objective was to identify genomic regions associated with loin depth and muscle pH, and identify regions of interest for fine-mapping and further experimental work. Genotypes for ~ 40,000 single nucleotide morphisms (SNPs) were used to perform GWAS for these two traits, using de-regressed breeding values (dEBV) for 329,964 pigs from four commercial lines. Imputed sequence data was used to identify SNPs in strong ([Formula: see text] 0.80) linkage disequilibrium with lead GWAS SNPs with the highest pCADD scores. RESULTS Fifteen distinct regions were associated with loin depth and one with loin pH at genome-wide significance. Regions on chromosomes 1, 2, 5, 7, and 16, explained between 0.06 and 3.55% of the additive genetic variance and were strongly associated with loin depth. Only a small part of the additive genetic variance in muscle pH was attributed to SNPs. The results of our pCADD analysis suggests that high-scoring pCADD variants are enriched for missense mutations. Two close but distinct regions on SSC1 were associated with loin depth, and pCADD identified the previously identified missense variant within the MC4R gene for one of the lines. For loin pH, pCADD identified a synonymous variant in the RNF25 gene (SSC15) as the most likely candidate for the muscle pH association. The missense mutation in the PRKAG3 gene known to affect glycogen content was not prioritised by pCADD for loin pH. CONCLUSIONS For loin depth, we identified several strong candidate regions for further statistical fine-mapping that are supported in the literature, and two novel regions. For loin muscle pH, we identified one previously identified associated region. We found mixed evidence for the utility of pCADD as an extension of heuristic fine-mapping. The next step is to perform more sophisticated fine-mapping and expression quantitative trait loci (eQTL) analysis, and then interrogate candidate variants in vitro by perturbation-CRISPR assays.
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Affiliation(s)
- Suzanne Desire
- The Roslin Institute, The University of Edinburgh, Midlothian, UK.
| | - Martin Johnsson
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Roger Ros-Freixedes
- Departament de Ciència Animal, Universitat de Lleida-Agrotecnio-CERCA Center, Lleida, Spain
| | - Ching-Yi Chen
- The Pig Improvement Company, Genus Plc, Hendersonville, TN, USA
| | - Justin W Holl
- The Pig Improvement Company, Genus Plc, Hendersonville, TN, USA
| | | | - Gregor Gorjanc
- The Roslin Institute, The University of Edinburgh, Midlothian, UK
| | - Richard J Mellanby
- The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - John M Hickey
- The Roslin Institute, The University of Edinburgh, Midlothian, UK
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10
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Arias KD, Pablo Gutiérrez J, Fernandez I, Menéndez-Arias NA, Álvarez I, Goyache F. Segregation patterns and inheritance rate of copy number variations regions assessed in a Gochu Asturcelta pig pedigree. Gene X 2023; 854:147111. [PMID: 36509293 DOI: 10.1016/j.gene.2022.147111] [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: 09/22/2022] [Revised: 11/30/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Copy Number Variation Regions (CNVR) were subjected to pedigree analysis to contribute to the understanding of their segregation patterns. Up to 492 Gochu Asturcelta pig individuals forming 478 different parents-offspring trios (61 different families) were genotyped using the Axiom_PigHDv1 Array (658,692 SNPs). CNVR calling, performed using two different platforms (PennCNV and QuantiSNP), allowed to identify a total of 344 candidate CNVR on the 18 porcine autosomes covering about 106.8 Mb of the pig genome. Sixty-nine CNVR were identified, to some extent, in both the parents and the offspring and were classified as segregating CNVR. The other candidate CNVR were called in one or more progeny but in neither parent and classified either as singleton or recurrent de novo CNVR. Segregating CNVR were, on average, larger and more frequent than the recurrent de novo CNVR (444.8 kb vs 287.9 kb long and 34 vs 5 individuals, respectively). In any case, segregating CNVR did not conform to strict Mendelian inheritance patterns: estimates of average paternal and maternal transmission rates ranged from 11.0 % to 13.4 % and mean inheritance rate was below 21 %. This issue should be carefully considered when interpreting the results of CNV studies. Segregating CNVR, present across generations, are unlikely to be artifacts or false positives and can be hypothesized to be important at the population level.
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Affiliation(s)
| | - Juan Pablo Gutiérrez
- Departamento de Producción Animal, Universidad Complutense de Madrid, Avda. Puerta de Hierro s/n, 28040 Madrid, Spain
| | | | | | | | - Félix Goyache
- SERIDA-Deva, Camino de Rioseco 1225, 33394-Gijón, Spain.
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11
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Cis-eQTL Analysis and Functional Validation of Candidate Genes for Carcass Yield Traits in Beef Cattle. Int J Mol Sci 2022; 23:ijms232315055. [PMID: 36499383 PMCID: PMC9736101 DOI: 10.3390/ijms232315055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 12/04/2022] Open
Abstract
Carcass yield traits are of considerable economic importance for farm animals, which act as a major contributor to the world’s food supply. Genome-wide association studies (GWASs) have identified many genetic variants associated with carcass yield traits in beef cattle. However, their functions are not effectively illustrated. In this study, we performed an integrative analysis of gene-based GWAS with expression quantitative trait locus (eQTL) analysis to detect candidate genes for carcass yield traits and validate their effects on bovine skeletal muscle satellite cells (BSCs). The gene-based GWAS and cis-eQTL analysis revealed 1780 GWAS and 1538 cis-expression genes. Among them, we identified 153 shared genes that may play important roles in carcass yield traits. Notably, the identified cis-eQTLs of PON3 and PRIM2 were significantly (p < 0.001) enriched in previous GWAS loci for carcass traits. Furthermore, overexpression of PON3 and PRIM2 promoted the BSCs’ proliferation, increased the expression of MYOD and downregulated the expression of MYOG, which indicated that these genes may inhibit myogenic differentiation. In contrast, PON3 and PRIM2 were significantly downregulated during the differentiation of BSCs. These findings suggested that PON3 and PRIM2 may promote the proliferation of BSCs and inhibit them in the pre-differentiation stage. Our results further contribute to the understanding of the molecular mechanisms of carcass yield traits in beef cattle.
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12
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Zhukorskyi ОМ, Tsereniuk ОМ, Vashchenko PА, Khokhlov AM, Chereuta YV, Akimov ОV, Kryhina NV. The effect of the ryanodine receptor gene on the reproductive traits of Welsh sows. REGULATORY MECHANISMS IN BIOSYSTEMS 2022. [DOI: 10.15421/022248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
Abstract
The reproductive performance of sows largely determines the efficiency of the entire pig farming industry. The purpose of our work is the evaluation of polymorphism of the ryanodine receptor gene and its impact on the reproductive traits of sows of the Welsh breed of pigs. For this study, 148 pigs of the Welsh breed were used. The reproductive traits of sows were evaluated in two adjacent generations. We conducted a comprehensive assessment of the reproductive ability of sows using the SIRQS (selection index of reproductive qualities of sows), determined phenotypic consolidation coefficients and assessed the genetic potential of the animals’ productivity. The polymorphism of the RYR1 gene was determined using polymerase chain reaction-restriction fragment length polymorphism analysis (PCR-RFLP). Data processing was performed using single-factor analysis of variance (ANOVA). Polymorphism of the ryanodine receptor gene in sows of the Welsh pig breed was evaluated. 8.0% of the animals were identified as carriers of the mutant allele of the RYR1 gene. However, no homozygous RYR1-nn animals were found. Pigs of the maternal generation carrying the homozygous NN genotype had better reproductive performance in all indicators. Sows that were carriers of the mutant allele were characterized by lower values of the genetic productivity potential compared with the entire estimated population for all productive traits. Sows which were free of the mutant allele of the RYR1 gene were characterized by large values of the SIRQS index. The values of the coefficients of phenotypic consolidation of the number of live born piglets in sows without the mutant allele were lower than in sows with the mutant allele n. Better performance of sows free of the mutant allele of the RYR1 gene was established over sows carrying it in all evaluated traits of reproductive capacity (for different traits P ranged from 0.021 to 1.0*10–4), except for number of piglets born alive per sow in the daughter generation. Sows with the NN genotype had better selection index values by 15.7% in the maternal generation and by 10.2% in the daughter generation. In order to increase the reproductive ability of sows in the studied population of Welsh pigs and achieve similar results in other herds of this breed, animals free from the mutant allele of the RYR1 gene should be selected for further reproduction in the process of breeding, while on the contrary, carriers of this gene should be gradually eliminated from the herd. To carry out breeding work, further research is needed on the entire population of Welsh pigs for the RYR1 gene.
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