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Roth K, Pröll-Cornelissen MJ, Henne H, Appel AK, Schellander K, Tholen E, Große-Brinkhaus C. Multivariate genome-wide associations for immune traits in two maternal pig lines. BMC Genomics 2023; 24:492. [PMID: 37641029 PMCID: PMC10463314 DOI: 10.1186/s12864-023-09594-w] [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: 02/01/2023] [Accepted: 08/16/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Immune traits are considered to serve as potential biomarkers for pig's health. Medium to high heritabilities have been observed for some of the immune traits suggesting genetic variability of these phenotypes. Consideration of previously established genetic correlations between immune traits can be used to identify pleiotropic genetic markers. Therefore, genome-wide association study (GWAS) approaches are required to explore the joint genetic foundation for health biomarkers. Usually, GWAS explores phenotypes in a univariate (uv), trait-by-trait manner. Besides two uv GWAS methods, four multivariate (mv) GWAS approaches were applied on combinations out of 22 immune traits for Landrace (LR) and Large White (LW) pig lines. RESULTS In total 433 (LR: 351, LW: 82) associations were identified with the uv approach implemented in PLINK and a Bayesian linear regression uv approach (BIMBAM) software. Single Nucleotide Polymorphisms (SNPs) that were identified with both uv approaches (n = 32) were mostly associated with immune traits such as haptoglobin, red blood cell characteristics and cytokines, and were located in protein-coding genes. Mv GWAS approaches detected 647 associations for different mv immune trait combinations which were summarized to 133 Quantitative Trait Loci (QTL). SNPs for different trait combinations (n = 66) were detected with more than one mv method. Most of these SNPs are associated with red blood cell related immune trait combinations. Functional annotation of these QTL revealed 453 immune-relevant protein-coding genes. With uv methods shared markers were not observed between the breeds, whereas mv approaches were able to detect two conjoint SNPs for LR and LW. Due to unmapped positions for these markers, their functional annotation was not clarified. CONCLUSIONS This study evaluated the joint genetic background of immune traits in LR and LW piglets through the application of various uv and mv GWAS approaches. In comparison to uv methods, mv methodologies identified more significant associations, which might reflect the pleiotropic background of the immune system more accurately. In genetic research of complex traits, the SNP effects are generally small. Furthermore, one genetic variant can affect several correlated immune traits at the same time, termed pleiotropy. As mv GWAS methods consider strong dependencies among traits, the power to detect SNPs can be boosted. Both methods revealed immune-relevant potential candidate genes. Our results indicate that one single test is not able to detect all the different types of genetic effects in the most powerful manner and therefore, the methods should be applied complementary.
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Affiliation(s)
- Katharina Roth
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany
| | | | - Hubert Henne
- BHZP GmbH, An der Wassermühle 8, 21368, Dahlenburg-Ellringen, Germany
| | | | - Karl Schellander
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany
| | - Ernst Tholen
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115, Bonn, Germany
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2
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Zhang Y, Zhang X, Li F, Lin C, Zhang D, Duan B, Zhao Y, Li X, Xu D, Cheng J, Zhao L, Wang J, Wang W. Expression profiles of the CD274 and PLEKHH2 gene and association of its polymorphism with hematologic parameters in sheep. Vet Immunol Immunopathol 2023; 259:110597. [PMID: 37094535 DOI: 10.1016/j.vetimm.2023.110597] [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: 11/28/2022] [Revised: 04/10/2023] [Accepted: 04/20/2023] [Indexed: 04/26/2023]
Abstract
CD274 and PLEKHH2 genes have been identified as immune- and multiple diseases-related genes, and have recently garnered significant interest. However, their role in regulating immune functions in sheep remains largely unexplored. In this study, we aimed to investigate the effects of polymorphisms in CD274 and PLEKHH2 on hematologic parameters in 915 sheep. Our results showed that the CD274 and PLEKHH2 genes were most highly expressed in the spleen and tail fat, respectively, as determined by qRT-PCR. We also identified a G to A mutation (g 0.11858 G > A) in the exon 4 region of CD274, and a C to G mutation (g 0.38384 C > G) in the intron 8 region of PLEKH2. Association analysis revealed that CD274 g 0.11858 G > A was significantly associated with RBC, HCT, MCHC, and MCV (P < 0.05), while PLEKHH2 g 0.38384 C > G was significantly associated with HCT, MPV, MCHC, and MCV (P < 0.05). These results suggest that CD274 and PLEKHH2 genes may play a role in regulating blood physiological indicators and could be potential functional candidates for influencing immune traits in sheep breeding programs.
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Affiliation(s)
- Yukun Zhang
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou 730020, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Fadi Li
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou 730020, China
| | - Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Deyin Zhang
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou 730020, China
| | - Benzhen Duan
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai 200433, China; Key Laboratory of Medical Molecular Virology, MOE & NHC, School of Basic Medical Sciences, Fudan University, Shanghai 200433, China
| | - Yuan Zhao
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou 730020, China
| | - Xiaolong Li
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou 730020, China
| | - Dan Xu
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou 730020, China
| | - Jiangbo Cheng
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou 730020, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Weimin Wang
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China; State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou 730020, China.
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Van Goor A, Pasternak A, Walugembe M, Chehab N, Hamonic G, Dekkers JCM, Harding JCS, Lunney JK. Genome wide association study of thyroid hormone levels following challenge with porcine reproductive and respiratory syndrome virus. Front Genet 2023; 14:1110463. [PMID: 36845393 PMCID: PMC9947478 DOI: 10.3389/fgene.2023.1110463] [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: 11/28/2022] [Accepted: 01/25/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction: Porcine reproductive and respiratory syndrome virus (PRRSV) causes respiratory disease in piglets and reproductive disease in sows. Piglet and fetal serum thyroid hormone (i.e., T3 and T4) levels decrease rapidly in response to Porcine reproductive and respiratory syndrome virus infection. However, the genetic control of T3 and T4 levels during infection is not completely understood. Our objective was to estimate genetic parameters and identify quantitative trait loci (QTL) for absolute T3 and/or T4 levels of piglets and fetuses challenged with Porcine reproductive and respiratory syndrome virus. Methods: Sera from 5-week-old pigs (N = 1792) at 11 days post inoculation (DPI) with Porcine reproductive and respiratory syndrome virus were assayed for T3 levels (piglet_T3). Sera from fetuses (N = 1,267) at 12 or 21 days post maternal inoculation (DPMI) with Porcine reproductive and respiratory syndrome virus of sows (N = 145) in late gestation were assayed for T3 (fetal_T3) and T4 (fetal_T4) levels. Animals were genotyped using 60 K Illumina or 650 K Affymetrix single nucleotide polymorphism (SNP) panels. Heritabilities, phenotypic correlations, and genetic correlations were estimated using ASREML; genome wide association studies were performed for each trait separately using Julia for Whole-genome Analysis Software (JWAS). Results: All three traits were low to moderately heritable (10%-16%). Phenotypic and genetic correlations of piglet_T3 levels with weight gain (0-42 DPI) were 0.26 ± 0.03 and 0.67 ± 0.14, respectively. Nine significant quantitative trait loci were identified for piglet_T3, on Sus scrofa chromosomes (SSC) 3, 4, 5, 6, 7, 14, 15, and 17, and collectively explaining 30% of the genetic variation (GV), with the largest quantitative trait loci identified on SSC5, explaining 15% of the genetic variation. Three significant quantitative trait loci were identified for fetal_T3 on SSC1 and SSC4, which collectively explained 10% of the genetic variation. Five significant quantitative trait loci were identified for fetal_T4 on SSC1, 6, 10, 13, and 15, which collectively explained 14% of the genetic variation. Several putative immune-related candidate genes were identified, including CD247, IRF8, and MAPK8. Discussion: Thyroid hormone levels following Porcine reproductive and respiratory syndrome virus infection were heritable and had positive genetic correlations with growth rate. Multiple quantitative trait loci with moderate effects were identified for T3 and T4 levels during challenge with Porcine reproductive and respiratory syndrome virus and candidate genes were identified, including several immune-related genes. These results advance our understanding of growth effects of both piglet and fetal response to Porcine reproductive and respiratory syndrome virus infection, revealing factors associated with genomic control of host resilience.
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Affiliation(s)
- Angelica Van Goor
- Animal Parasitic Diseases Laboratory, United States Department of Agriculture, Agricultural Research Services, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Alex Pasternak
- Department of Animal Science, Purdue University, West Lafayette, IN, United States
| | - Muhammed Walugembe
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Nadya Chehab
- Animal Parasitic Diseases Laboratory, United States Department of Agriculture, Agricultural Research Services, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Glenn Hamonic
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jack C. M. Dekkers
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - John C. S. Harding
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Joan K. Lunney
- Animal Parasitic Diseases Laboratory, United States Department of Agriculture, Agricultural Research Services, Beltsville Agricultural Research Center, Beltsville, MD, United States,*Correspondence: Joan K. Lunney,
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Jung J, Bugenyi AW, Lee MR, Choi YJ, Song KD, Lee HK, Son YO, Lee DS, Lee SC, Son YJ, Heo J. High-quality metagenome-assembled genomes from proximal colonic microbiomes of synbiotic-treated korean native black pigs reveal changes in functional capacity. Sci Rep 2022; 12:14595. [PMID: 36109557 PMCID: PMC9478101 DOI: 10.1038/s41598-022-18503-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/12/2022] [Indexed: 11/22/2022] Open
Abstract
Synbiotics are feed supplements with the potential to promote health and productivity in pigs partly, through modulation of the intestinal microbiome. Our study used shotgun sequencing and 16S rRNA gene sequencing techniques to characterize the effect of a synbiotic containing three Lactobacillus species and a fructo-oligosaccharide on the proximal colonic microbiome of 4- to 7-month-old Korean native black gilts. With shotgun sequencing we constructed unique metagenome-assembled genomes of gut microbiota in Native Black Pig for the first time, which we then used for downstream analysis. Results showed that synbiotic treatment did not alter microbial diversity and evenness within the proximal colons, but altered composition of some members of the Lactobacillaceae, Enterococcaceae and Streptococcaceae families. Functional analysis of the shotgun sequence data revealed 8 clusters of orthologous groups (COGs) that were differentially represented in the proximal colonic microbiomes of synbiotic-treated Jeju black pigs relative to controls. In conclusion, our results show that administering this synbiotic causes changes in the functional capacity of the proximal colonic microbiome of the Korean native black pig. This study improves our understanding of the potential impact of synbiotics on the colonic microbiome of Korean native black pigs.
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Affiliation(s)
- Jaehoon Jung
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-742, Republic of Korea
- eGnome, 26 Beobwon-ro, Songpa-gu, Seoul, 05836, Republic of Korea
| | - Andrew W Bugenyi
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, 54896, Republic of Korea
- National Agricultural Research Organization, Mbarara, Uganda
| | - Ma-Ro Lee
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Yeon-Jae Choi
- International Agricultural Development and Cooperation Center, Jeonbuk National University, Jeonju, 54896, Korea
| | - Ki-Duk Song
- The Animal Molecular Genetics and Breeding Center, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Hak-Kyo Lee
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, 54896, Republic of Korea
- International Agricultural Development and Cooperation Center, Jeonbuk National University, Jeonju, 54896, Korea
- The Animal Molecular Genetics and Breeding Center, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Young-Ok Son
- Department of Animal Biotechnology, Faculty of Biotechnology, College of Applied Life Sciences and Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, Jeju, 63243, Republic of Korea
- Jeju Microbiome Research Center, Jeju National University, Jeju, Jeju Special Self-Governing Province, 63243, Republic of Korea
| | - Dong-Sun Lee
- Faculty of Biotechnology, College of Applied Life Sciences and Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, Jeju, 63243, Republic of Korea
- Jeju Microbiome Research Center, Jeju National University, Jeju, Jeju Special Self-Governing Province, 63243, Republic of Korea
| | | | | | - Jaeyoung Heo
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, 54896, Republic of Korea.
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Lee JB, Kang YJ, Kim SG, Woo JH, Shin MC, Park NG, Yang BC, Han SH, Han KM, Lim HT, Ryu YC, Park HB, Cho IC. GWAS and Post-GWAS High-Resolution Mapping Analyses Identify Strong Novel Candidate Genes Influencing the Fatty Acid Composition of the Longissimus dorsi Muscle in Pigs. Genes (Basel) 2021; 12:1323. [PMID: 34573305 PMCID: PMC8468772 DOI: 10.3390/genes12091323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 12/02/2022] Open
Abstract
Fatty acid (FA) composition is one of the most important parameters for the assessment of meat quality in pigs. The FA composition in pork can also affect human health. Our aim was to identify quantitative trait loci (QTLs) and positional candidate genes affecting the FA profile of the longissimus dorsi muscle in a large F2 intercross between Landrace and Korean native pigs comprising 1105 F2 progeny by genome-wide association studies (GWAS) and post-GWAS high-resolution mapping analyses. We performed GWAS using the PorcineSNP60K BeadChip and a linear mixed model. Four genome-wide significant QTL regions in SSC8, SSC12, SSC14, and SSC16 were detected (p < 2.53 × 10-7). Several co-localizations of QTLs in SSC12 for oleic acid, linoleic acid, arachidonic acid, monounsaturated FAs, polyunsaturated FAs, and the polyunsaturated/saturated FA ratio were observed. To refine the QTL region in SSC12, a linkage and linkage disequilibrium analysis was applied and could narrow down the critical region to a 0.749 Mb region. Of the genes in this region, GAS7, MYH2, and MYH3 were identified as strong novel candidate genes based on further conditional association analyses. These findings provide a novel insight into the genetic basis of FA composition in pork and could contribute to the improvement of pork quality.
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Affiliation(s)
- Jae-Bong Lee
- Korea Zoonosis Research Institute, Jeonbuk National University, Iksan 54531, Korea;
| | - Yong-Jun Kang
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju 63242, Korea; (Y.-J.K.); (S.-G.K.); (J.-H.W.); (M.-C.S.); (N.-G.P.); (B.-C.Y.)
| | - Sang-Geum Kim
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju 63242, Korea; (Y.-J.K.); (S.-G.K.); (J.-H.W.); (M.-C.S.); (N.-G.P.); (B.-C.Y.)
| | - Jae-Hoon Woo
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju 63242, Korea; (Y.-J.K.); (S.-G.K.); (J.-H.W.); (M.-C.S.); (N.-G.P.); (B.-C.Y.)
| | - Moon-Cheol Shin
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju 63242, Korea; (Y.-J.K.); (S.-G.K.); (J.-H.W.); (M.-C.S.); (N.-G.P.); (B.-C.Y.)
| | - Nam-Geon Park
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju 63242, Korea; (Y.-J.K.); (S.-G.K.); (J.-H.W.); (M.-C.S.); (N.-G.P.); (B.-C.Y.)
| | - Byoung-Chul Yang
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju 63242, Korea; (Y.-J.K.); (S.-G.K.); (J.-H.W.); (M.-C.S.); (N.-G.P.); (B.-C.Y.)
| | - Sang-Hyun Han
- Species Restoration Technology Institute, Korea National Park Service, Yeongju 36015, Korea;
| | - Kang-Min Han
- Department of Pathology, Dongguk University Ilsan Hospital, Goyang 10326, Korea;
| | - Hyun-Tae Lim
- Department of Animal Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Korea;
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Youn-Chul Ryu
- Division of Biotechnology, Jeju National University, SARI, Jeju 63243, Korea;
| | - Hee-Bok Park
- Department of Animal Resources Science, Kongju National University, Yesan 32439, Korea
| | - In-Cheol Cho
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju 63242, Korea; (Y.-J.K.); (S.-G.K.); (J.-H.W.); (M.-C.S.); (N.-G.P.); (B.-C.Y.)
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Sodhi SS, Sharma N, Ghosh M, Sethi RS, Jeong DK, Lee SJ. Differential expression patterns of myogenic regulatory factors in the postnatal longissimus dorsi muscle of Jeju Native Pig and Berkshire breeds along with their co-expression with Pax7. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2021.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Kim K, Kim D, Min Y, Jeong D, Son YO, Do K. Myogenic regulatory factors are key players in determining muscle mass and meat quality in Jeju native and Berkshire pigs. Vet Med Sci 2020; 7:735-745. [PMID: 33372732 PMCID: PMC8136949 DOI: 10.1002/vms3.418] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/30/2020] [Accepted: 12/09/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Meat from Jeju native pigs (JNPs) is highly popular among Korean consumers; however, the production efficiency is limited due to the low adult body weight. In contrast, the Berkshire breed, which has a genetic background closely related to Asian native pigs, gains weight more efficiently. OBJECTIVES This study focused on the differential expression of genes related to muscle growth in postnatal myogenesis between Berkshire and JNPs, specifically the myogenic regulatory factor (MRF) genes (MyoD, Pax7, Myf5, Myf6 and MyBPH). The MRF family is primarily involved in the proliferation and development of muscle. METHODS Qualitative reverse transcription-polymerase chain reaction and western blot analyses revealed that expression of MyoD and Pax7 was significantly higher in Berkshire pigs than in JNPs. In addition, co-expression of MyoD and Pax7 was observed in myotubes formed in cultured C2C12 cells. ToppCluster was used to elucidate the relationship between biological processes of the MRFs and muscle-related signalling pathways. RESULTS MyoD and Pax7 are factors essential for the activation of satellite cell during myogenesis. However, the mRNA and protein levels of MyBPH (which is responsible for meat quality, e.g. water content, colour and tenderness) are significantly higher in both 1-day-old piglets and adult JNPs than in Berkshire pigs. CONCLUSIONS This study provides a genetic understanding of myogenesis in the postnatal and adult stages of Berkshire pigs and JNPs. Moreover, these results will help identify marker genes related to muscle mass, growth performance and meat quality in indigenous Korean pig breeds.
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Affiliation(s)
- Kyoungho Kim
- Department of Animal Biotechnology, Faculty of Biotechnology, College of Applied Life Sciences, Jeju National University, Jeju-si, Jeju Special Self-Governing Province, Republic of Korea.,Livestock Division, Jeju-si, Jeju Special Self-Governing Province, Republic of Korea
| | - Dahye Kim
- Department of Animal Biotechnology, Faculty of Biotechnology, College of Applied Life Sciences, Jeju National University, Jeju-si, Jeju Special Self-Governing Province, Republic of Korea.,Practical Translational Research Center, Jeju National University, Jeju-si, Jeju Special Self-Governing Province, Republic of Korea
| | - Yunhui Min
- Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, Jeju-si, Jeju Special Self-Governing Province, Republic of Korea
| | - DongKee Jeong
- Department of Animal Biotechnology, Faculty of Biotechnology, College of Applied Life Sciences, Jeju National University, Jeju-si, Jeju Special Self-Governing Province, Republic of Korea
| | - Young-Ok Son
- Department of Animal Biotechnology, Faculty of Biotechnology, College of Applied Life Sciences, Jeju National University, Jeju-si, Jeju Special Self-Governing Province, Republic of Korea.,Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, Jeju-si, Jeju Special Self-Governing Province, Republic of Korea.,Bio-Health Materials Core-Facility Center, Jeju National University, Jeju-si, Jeju Special Self-Governing Province, Republic of Korea.,Practical Translational Research Center, Jeju National University, Jeju-si, Jeju Special Self-Governing Province, Republic of Korea
| | - Kyoungtag Do
- Department of Animal Biotechnology, Faculty of Biotechnology, College of Applied Life Sciences, Jeju National University, Jeju-si, Jeju Special Self-Governing Province, Republic of Korea
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Genetic parameters and associated genomic regions for global immunocompetence and other health-related traits in pigs. Sci Rep 2020; 10:18462. [PMID: 33116177 PMCID: PMC7595139 DOI: 10.1038/s41598-020-75417-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/15/2020] [Indexed: 12/16/2022] Open
Abstract
The inclusion of health-related traits, or functionally associated genetic markers, in pig breeding programs could contribute to produce more robust and disease resistant animals. The aim of the present work was to study the genetic determinism and genomic regions associated to global immunocompetence and health in a Duroc pig population. For this purpose, a set of 30 health-related traits covering immune (mainly innate), haematological, and stress parameters were measured in 432 healthy Duroc piglets aged 8 weeks. Moderate to high heritabilities were obtained for most traits and significant genetic correlations among them were observed. A genome wide association study pointed out 31 significantly associated SNPs at whole-genome level, located in six chromosomal regions on pig chromosomes SSC4, SSC6, SSC17 and SSCX, for IgG, γδ T-cells, C-reactive protein, lymphocytes phagocytic capacity, total number of lymphocytes, mean corpuscular volume and mean corpuscular haemoglobin. A total of 16 promising functionally-related candidate genes, including CRP, NFATC2, PRDX1, SLA, ST3GAL1, and VPS4A, have been proposed to explain the variation of immune and haematological traits. Our results enhance the knowledge of the genetic control of traits related with immunity and support the possibility of applying effective selection programs to improve immunocompetence in pigs.
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Cho IC, Park HB, Ahn JS, Han SH, Lee JB, Lim HT, Yoo CK, Jung EJ, Kim DH, Sun WS, Ramayo-Caldas Y, Kim SG, Kang YJ, Kim YK, Shin HS, Seong PN, Hwang IS, Park BY, Hwang S, Lee SS, Ryu YC, Lee JH, Ko MS, Lee K, Andersson G, Pérez-Enciso M, Lee JW. A functional regulatory variant of MYH3 influences muscle fiber-type composition and intramuscular fat content in pigs. PLoS Genet 2019; 15:e1008279. [PMID: 31603892 PMCID: PMC6788688 DOI: 10.1371/journal.pgen.1008279] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 07/01/2019] [Indexed: 11/18/2022] Open
Abstract
Muscle development and lipid accumulation in muscle critically affect meat quality of livestock. However, the genetic factors underlying myofiber-type specification and intramuscular fat (IMF) accumulation remain to be elucidated. Using two independent intercrosses between Western commercial breeds and Korean native pigs (KNPs) and a joint linkage-linkage disequilibrium analysis, we identified a 488.1-kb region on porcine chromosome 12 that affects both reddish meat color (a*) and IMF. In this critical region, only the MYH3 gene, encoding myosin heavy chain 3, was found to be preferentially overexpressed in the skeletal muscle of KNPs. Subsequently, MYH3-transgenic mice demonstrated that this gene controls both myofiber-type specification and adipogenesis in skeletal muscle. We discovered a structural variant in the promotor/regulatory region of MYH3 for which Q allele carriers exhibited significantly higher values of a* and IMF than q allele carriers. Furthermore, chromatin immunoprecipitation and cotransfection assays showed that the structural variant in the 5'-flanking region of MYH3 abrogated the binding of the myogenic regulatory factors (MYF5, MYOD, MYOG, and MRF4). The allele distribution of MYH3 among pig populations worldwide indicated that the MYH3 Q allele is of Asian origin and likely predates domestication. In conclusion, we identified a functional regulatory sequence variant in porcine MYH3 that provides novel insights into the genetic basis of the regulation of myofiber type ratios and associated changes in IMF in pigs. The MYH3 variant can play an important role in improving pork quality in current breeding programs.
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Affiliation(s)
- In-Cheol Cho
- National Institute of Animal Science, Rural Development Administration, Jeju, Republic of Korea
- * E-mail: (I-CC); (J-WL)
| | - Hee-Bok Park
- Department of Animal Resources Science, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Jin Seop Ahn
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Sang-Hyun Han
- Educational Science Research Institute, Jeju National University, Jeju, Republic of Korea
| | - Jae-Bong Lee
- Korea Zoonosis Research Institute, Chonbuk National University, Iksan, Republic of Korea
| | - Hyun-Tae Lim
- Department of Animal Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, Republic of Korea
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Chae-Kyoung Yoo
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Eun-Ji Jung
- Bio-Medical Science Co., Ltd., Gimpo, Republic of Korea
| | - Dong-Hwan Kim
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea
| | - Wu-Sheng Sun
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Yuliaxis Ramayo-Caldas
- Génétique Animale et Biologie Intégrative (GABI), INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, Caldes de Montbui, Spain
| | - Sang-Geum Kim
- National Institute of Animal Science, Rural Development Administration, Jeju, Republic of Korea
| | - Yong-Jun Kang
- National Institute of Animal Science, Rural Development Administration, Jeju, Republic of Korea
| | - Yoo-Kyung Kim
- Educational Science Research Institute, Jeju National University, Jeju, Republic of Korea
| | - Hyun-Sook Shin
- National Institute of Animal Science, Rural Development Administration, Jeju, Republic of Korea
| | - Pil-Nam Seong
- National Institute of Animal Science, Rural Development Administration, Jeju, Republic of Korea
| | - In-Sul Hwang
- National Institute of Animal Science, Rural Development Administration, Wanju, Republic of Korea
| | - Beom-Young Park
- National Institute of Animal Science, Rural Development Administration, Wanju, Republic of Korea
| | - Seongsoo Hwang
- National Institute of Animal Science, Rural Development Administration, Wanju, Republic of Korea
| | - Sung-Soo Lee
- National Institute of Animal Science, Rural Development Administration, Namwon, Republic of Korea
| | - Youn-Chul Ryu
- Division of Biotechnology, SARI, Jeju National University, Jeju, Republic of Korea
| | - Jun-Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, Deajeon, Republic of Korea
| | - Moon-Suck Ko
- National Institute of Animal Science, Rural Development Administration, Jeju, Republic of Korea
| | - Kichoon Lee
- Department of Animal Sciences, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Columbus, OH, United States of America
| | - Göran Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Miguel Pérez-Enciso
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Barcelona, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Barcelona, Spain
- ICREA, Carrer de Lluís Companys, Barcelona, Spain
| | - Jeong-Woong Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea
- * E-mail: (I-CC); (J-WL)
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10
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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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11
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The first comprehensive description of the expression profile of genes involved in differential body growth and the immune system of the Jeju Native Pig and miniature pig. Amino Acids 2018; 51:495-511. [PMID: 30519757 DOI: 10.1007/s00726-018-2685-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 11/29/2018] [Indexed: 12/12/2022]
Abstract
Sus scrofa provides a major source of animal protein for humans as well as being an excellent biomedical model. This study was carried out to understand, in detail, the genetic and functional variants of Jeju Native Pigs and miniature pigs through differential expression profiling of the genes controlling their immune response, growth performance, and meat quality. The Illumina HiSeq 2000 platform was used for generating 1.3 billion 90 bp paired-end reads, which were mapped to the S. scrofa genome using TopHat2. A total of 2481 and 2768 genes were differentially expressed with 8-log changes in muscle and liver samples, respectively. Five hundred forty-eight genes in muscle and 642 genes in liver samples had BLAST matches within the non-redundant database. GO process and pathway analyses showed enhanced biological processes related to the extracellular structural organization and skeletal muscle cell differentiation in muscle tissue, whereas the liver tissue shares functions related to the inflammatory response. Herein, we identify inflammatory regulatory genes in miniature pigs and growth response genes in Jeju Native Pigs, information which can provide a stronger base for the selection of breeding stock and facilitate further in vitro and in vivo studies for therapeutic purposes.
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12
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Joint linkage and linkage disequilibrium mapping reveals association of BRMS1L with total teat number in a large intercross between Landrace and Korean native pigs. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.09.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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13
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Zhang Z, Zhang Q, Xiao Q, Sun H, Gao H, Yang Y, Chen J, Li Z, Xue M, Ma P, Yang H, Xu N, Wang Q, Pan Y. Distribution of runs of homozygosity in Chinese and Western pig breeds evaluated by reduced-representation sequencing data. Anim Genet 2018; 49:579-591. [DOI: 10.1111/age.12730] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2018] [Indexed: 02/02/2023]
Affiliation(s)
- Zhe Zhang
- Department of Animal Science; School of Agriculture and Biology; Shanghai Jiao Tong University; Shanghai 200240 China
- Shanghai Key Laboratory of Veterinary Biotechnology; Shanghai 200240 China
| | - Qianqian Zhang
- Animal Genetics, Bioinformatics and Breeding; University of Copenhagen; Frederiksberg 1870 Denmark
| | - Qian Xiao
- Department of Animal Science; School of Agriculture and Biology; Shanghai Jiao Tong University; Shanghai 200240 China
- Shanghai Key Laboratory of Veterinary Biotechnology; Shanghai 200240 China
| | - Hao Sun
- Department of Animal Science; School of Agriculture and Biology; Shanghai Jiao Tong University; Shanghai 200240 China
- Shanghai Key Laboratory of Veterinary Biotechnology; Shanghai 200240 China
| | - Hongding Gao
- Center for Quantitative Genetics and Genomics; Department of Molecular Biology and Genetics; Aarhus University; 8830 Tjele Denmark
| | - Yumei Yang
- Department of Animal Science; School of Agriculture and Biology; Shanghai Jiao Tong University; Shanghai 200240 China
- Shanghai Key Laboratory of Veterinary Biotechnology; Shanghai 200240 China
| | - Jiucheng Chen
- College of Animal Sciences; Zhejiang University; Hangzhou 310058 China
| | - Zhengcao Li
- College of Animal Sciences; Zhejiang University; Hangzhou 310058 China
| | - Ming Xue
- National Station of Animal Husbandry; Beijing 100125 China
| | - Peipei Ma
- Department of Animal Science; School of Agriculture and Biology; Shanghai Jiao Tong University; Shanghai 200240 China
- Shanghai Key Laboratory of Veterinary Biotechnology; Shanghai 200240 China
| | - Hongjie Yang
- National Station of Animal Husbandry; Beijing 100125 China
| | - Ningying Xu
- College of Animal Sciences; Zhejiang University; Hangzhou 310058 China
| | - Qishan Wang
- Department of Animal Science; School of Agriculture and Biology; Shanghai Jiao Tong University; Shanghai 200240 China
- Shanghai Key Laboratory of Veterinary Biotechnology; Shanghai 200240 China
| | - Yuchun Pan
- Department of Animal Science; School of Agriculture and Biology; Shanghai Jiao Tong University; Shanghai 200240 China
- Shanghai Key Laboratory of Veterinary Biotechnology; Shanghai 200240 China
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14
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Park HB, Han SH, Lee JB, Cho IC. Rapid Communication: High-resolution quantitative trait loci analysis identifies LTBP2 encoding latent transforming growth factor beta binding protein 2 associated with thoracic vertebrae number in a large F2 intercross between Landrace and Korean native pigs. J Anim Sci 2018; 95:1957-1962. [PMID: 28727023 DOI: 10.2527/jas.2017.1390] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Number of vertebrae is associated with body size and meat productivity in pigs. The aim of this study was to identify QTL and associated positional candidate genes affecting the number of thoracic vertebrae (THO). A genomewide association study was conducted in a large resource population derived from an F intercross between Landrace and Korean native pigs using the Porcine SNP 60K BeadChip and the genomewide complex trait analysis (GCTA) program based on a linear mixed-effects model. A total of 38,385 SNP markers from 1,105 F progeny were analyzed for the THO trait after filtering for quality control. A total of 90 genomewide significant SNP markers ( < 1.30 × 10) on SSC 7 covering a 20-Mb region were identified for THO in this study. Several previous studies also mapped QTL for vertebral numbers in this region. The strongest association signals were detected at ASGA0035500 (-value = 4.46 × 10; 103,574,383 bp) and DIAS0000795 (-value = 4.46 × 10; 103,594,753 bp). The QTL region on SSC 7 for THO encompasses and , which are previously described candidate genes for vertebral number variation. To refine the QTL region, a haplotype-based linkage and linkage disequilibrium (LALD) analysis using the DualPHASE program was applied because subsequent conditional association and haplotype block analyses could not resolve the region that contains the 2 loci. The LALD analysis refined the critical region to a 533.9-kb region including ; was located outside the critical region. The gene encoding latent transforming growth factor beta binding protein 2 is involved in bone metabolisms. Based on these data, we propose as a positional candidate gene for THO in pigs. After further functional studies and verification of the association in other independent populations, these results could be useful for optimizing breeding programs that improve THO and other economically important traits in pigs.
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15
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Waide EH, Tuggle CK, Serão NVL, Schroyen M, Hess A, Rowland RRR, Lunney JK, Plastow G, Dekkers JCM. Genomewide association of piglet responses to infection with one of two porcine reproductive and respiratory syndrome virus isolates. J Anim Sci 2017; 95:16-38. [PMID: 28177360 DOI: 10.2527/jas.2016.0874] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Porcine reproductive and respiratory syndrome (PRRS) is a devastating disease in the swine industry. Identification of host genetic factors that enable selection for improved performance during PRRS virus (PRRSV) infection would reduce the impact of this disease on animal welfare and production efficiency. We conducted genomewide association study (GWAS) analyses of data from 13 trials of approximately 200 commercial crossbred nursery-age piglets that were experimentally infected with 1 of 2 type 2 isolates of PRRSV (NVSL 97-7985 [NVSL] and KS2006-72109 [KS06]). Phenotypes analyzed were viral load (VL) in blood during the first 21 d after infection (dpi) and weight gain (WG) from 0 to 42 dpi. We accounted for the previously identified QTL in the region on SSC4 in our models to increase power to identify additional regions. Many regions identified by single-SNP analyses were not identified using Bayes-B, but both analyses identified the same regions on SSC3 and SSC5 to be associated with VL in the KS06 trials and on SSC6 in the NVSL trials ( < 5 × 10); for WG, regions on SSC5 and SSC17 were associated in the NVSL trials ( < 3 × 10). No regions were identified with either method for WG in the KS06 trials. Except for the region on SSC4, which was associated with VL for both isolates (but only with WG for NVSL), identified regions did not overlap between the 2 PRRSV isolate data sets, despite high estimates of the genetic correlation between isolates for traits based on these data. We also identified genomic regions whose associations with VL or WG interacted with either PRRSV isolate or with genotype at the SSC4 QTL. Gene ontology (GO) annotation terms for genes located near moderately associated SNP ( < 0.003) were enriched for multiple immunologically (VL) and metabolism- (WG) related GO terms. The biological relevance of these regions suggests that, although it may increase the number of false positives, the use of single-SNP analyses and a relaxed threshold also increased the identification of true positives. In conclusion, although only the SSC4 QTL was associated with response to both PRRSV isolates, genes near associated SNP were enriched for the same GO terms across PRRSV isolates, suggesting that host responses to these 2 isolates are affected by the actions of many genes that function together in similar biological processes.
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16
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Taye M, Kim J, Yoon SH, Lee W, Hanotte O, Dessie T, Kemp S, Mwai OA, Caetano-Anolles K, Cho S, Oh SJ, Lee HK, Kim H. Whole genome scan reveals the genetic signature of African Ankole cattle breed and potential for higher quality beef. BMC Genet 2017; 18:11. [PMID: 28183280 PMCID: PMC5301378 DOI: 10.1186/s12863-016-0467-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 12/20/2016] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Africa is home to numerous cattle breeds whose diversity has been shaped by subtle combinations of human and natural selection. African Sanga cattle are an intermediate type of cattle resulting from interbreeding between Bos taurus and Bos indicus subspecies. Recently, research has asserted the potential of Sanga breeds for commercial beef production with better meat quality as compared to Bos indicus breeds. Here, we identified meat quality related gene regions that are positively selected in Ankole (Sanga) cattle breeds as compared to indicus (Boran, Ogaden, and Kenana) breeds using cross-population (XP-EHH and XP-CLR) statistical methods. RESULTS We identified 238 (XP-EHH) and 213 (XP-CLR) positively selected genes, of which 97 were detected from both statistics. Among the genes obtained, we primarily reported those involved in different biological process and pathways associated with meat quality traits. Genes (CAPZB, COL9A2, PDGFRA, MAP3K5, ZNF410, and PKM2) involved in muscle structure and metabolism affect meat tenderness. Genes (PLA2G2A, PARK2, ZNF410, MAP2K3, PLCD3, PLCD1, and ROCK1) related to intramuscular fat (IMF) are involved in adipose metabolism and adipogenesis. MB and SLC48A1 affect meat color. In addition, we identified genes (TIMP2, PKM2, PRKG1, MAP3K5, and ATP8A1) related to feeding efficiency. Among the enriched Gene Ontology Biological Process (GO BP) terms, actin cytoskeleton organization, actin filament-based process, and protein ubiquitination are associated with meat tenderness whereas cellular component organization, negative regulation of actin filament depolymerization and negative regulation of protein complex disassembly are involved in adipocyte regulation. The MAPK pathway is responsible for cell proliferation and plays an important role in hyperplastic growth, which has a positive effect on meat tenderness. CONCLUSION Results revealed several candidate genes positively selected in Ankole cattle in relation to meat quality characteristics. The genes identified are involved in muscle structure and metabolism, and adipose metabolism and adipogenesis. These genes help in the understanding of the biological mechanisms controlling beef quality characteristics in African Ankole cattle. These results provide a basis for further research on the genomic characteristics of Ankole and other Sanga cattle breeds for quality beef.
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Affiliation(s)
- Mengistie Taye
- Department of Agricultural Biotechnology, Animal Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
- Bahir Dar University, College of Agriculture and Environmental Sciences, PO Box 79, Bahir Dar, Ethiopia
| | - Jaemin Kim
- National Human Genome Research Institute, National Institutes of Health, 50 South Drive, Building 50 Room 5351, Bethesda, MD, 20892, USA
| | - Sook Hee Yoon
- Department of Agricultural Biotechnology, Animal Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
| | - Wonseok Lee
- Department of Agricultural Biotechnology, Animal Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea
| | - Olivier Hanotte
- The University of Nottingham, School of Life Sciences, Nottingham, NG7 2RD, UK
- International Livestock Research Institute (ILRI), PO Box 5689, Addis Ababa, Ethiopia
| | - Tadelle Dessie
- International Livestock Research Institute (ILRI), PO Box 5689, Addis Ababa, Ethiopia
| | - Stephen Kemp
- International Livestock Research Institute (ILRI), PO Box 30709-00100, Nairobi, Kenya
- The Centre for Tropical Livestock Genetics and Health, The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, Scotland
| | - Okeyo Ally Mwai
- International Livestock Research Institute (ILRI), PO Box 30709-00100, Nairobi, Kenya
| | | | - Seoae Cho
- C&K genomics, Main Bldg. #514, SNU Research Park, Seoul, 151-919, Republic of Korea
| | - Sung Jong Oh
- National Institute of Animal Science, RDA, Wanju, Republic of Korea
| | - Hak-Kyo Lee
- The Animal Molecular Genetics & Breeding Center, Department of Animal Biotechnology, Chonbuk National University, Jeonju, 561-756, Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology, Animal Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea.
- C&K genomics, Main Bldg. #514, SNU Research Park, Seoul, 151-919, Republic of Korea.
- Institute for Biomedical Sciences, Shinshu University, Nagano, Japan.
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17
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Park HB, Han SH, Yoo CK, Lee JB, Kim JH, Baek KS, Son JK, Shin SM, Lim HT, Cho IC. Genome scan linkage analysis identifies a major quantitative trait loci for fatty acid composition in longissimus dorsi muscle in an F 2 intercross between Landrace and Korean native pigs. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2017; 30:1061-1065. [PMID: 28111443 PMCID: PMC5494477 DOI: 10.5713/ajas.16.0562] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/25/2016] [Accepted: 12/29/2016] [Indexed: 11/27/2022]
Abstract
OBJECTIVE This study was conducted to locate quantitative trait loci (QTL) influencing fatty acid (FA) composition in a large F2 intercross between Landrace and Korean native pigs. METHODS Eighteen FA composition traits were measured in more than 960 F2 progeny. All experimental animals were genotyped with 165 microsatellite markers located throughout the pig autosomes. RESULTS We detected 112 QTLs for the FA composition; Forty seven QTLs reached the genome-wide significant threshold. In particular, we identified a cluster of highly significant QTLs for FA composition on SSC12. QTL for polyunsaturated fatty acid on pig chromosome 12 (F-value = 97.2 under additive and dominance model, nominal p-value 3.6×10-39) accounted for 16.9% of phenotypic variance. In addition, four more QTLs for C18:1, C18:2, C20:4, and monounsaturated fatty acids on the similar position explained more than 10% of phenotypic variance. CONCLUSION Our findings of a major QTL for FA composition presented here could provide helpful information to locate causative variants to improve meat quality traits in pigs.
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Affiliation(s)
- Hee-Bok Park
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju 63242, Korea
| | - Sang-Hyun Han
- Educational Science Research Institute, Jeju National University, Jeju 63243, Korea
| | - Chae-Kyoung Yoo
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Korea
| | - Jae-Bong Lee
- Korea Zoonosis Research Institute, Chonbuk National University, Iksan 54531, Korea
| | - Ji-Hyang Kim
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju 63242, Korea
| | - Kwang-Soo Baek
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju 63242, Korea
| | - Jun-Kyu Son
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju 63242, Korea
| | - Sang-Min Shin
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju 63242, Korea
| | - Hyun-Tae Lim
- Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Korea.,Department of Animal Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju 52828, Korea
| | - In-Cheol Cho
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju 63242, Korea
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18
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Lee JB, Park HB, Yoo CK, Kim HS, Cho IC, Lim HT. Association of a missense mutation in the positional candidate gene glutamate receptor-interacting protein 1 with backfat thickness traits in pigs. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 30:1081-1085. [PMID: 28111449 PMCID: PMC5494480 DOI: 10.5713/ajas.16.0414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 10/10/2016] [Accepted: 12/16/2016] [Indexed: 11/27/2022]
Abstract
OBJECTIVE Previously, we reported quantitative trait loci (QTLs) affecting backfat thickness (BFT) traits on pig chromosome 5 (SW1482-SW963) in an F2 intercross population between Landrace and Korean native pigs. The aim of this study was to evaluate glutamate receptor-interacting protein 1 (GRIP1) as a positional candidate gene underlying the QTL affecting BFT traits. METHODS Genotype and phenotype analyses were performed using the 1,105 F2 progeny. A mixed-effect linear model was used to access association between these single nucleotide polymorphism (SNP) markers and the BFT traits in the F2 intercross population. RESULTS Highly significant associations of two informative SNPs (c.2442 T>C, c.3316 C>G [R1106G]) in GRIP1 with BFT traits were detected. In addition, the two SNPs were used to construct haplotypes that were also highly associated with the BFT traits. CONCLUSION The SNPs and haplotypes of the GRIP1 gene determined in this study can contribute to understand the genetic structure of BFT traits in pigs.
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Affiliation(s)
- Jae-Bong Lee
- Korea Zoonosis Research Institute (KoZRI), Chonbuk National University, Iksan 54531, Korea
| | - Hee-Bok Park
- Subtropical Livestock Research Institute, National Institute of Animal Science, Jeju 63242, Korea
| | - Chae-Kyoung Yoo
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Hee-Sung Kim
- Division of Applied Life Science (BK21 plus), Gyeongsang National University, Jinju 52828, Korea
| | - In-Cheol Cho
- Subtropical Livestock Research Institute, National Institute of Animal Science, Jeju 63242, Korea
| | - Hyun-Tae Lim
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Korea.,Division of Applied Life Science (BK21 plus), Gyeongsang National University, Jinju 52828, Korea
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Lee JB, Yoo CK, Park HB, Cho IC, Lim HT. Association of the Single Nucleotide Polymorphisms in RUNX1, DYRK1A, and KCNJ15 with Blood Related Traits in Pigs. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 29:1675-1681. [PMID: 27492348 PMCID: PMC5088413 DOI: 10.5713/ajas.16.0348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/26/2016] [Accepted: 08/03/2016] [Indexed: 11/27/2022]
Abstract
The aim of this study was to detect positional candidate genes located within the support interval (SI) regions based on the results of red blood cell, mean corpuscular volume (MCV), and mean corpuscular hemoglobin quantitative trait locus (QTL) in Sus scrofa chromosome 13, and to verify the correlation between specific single-nucleotide polymorphisms (SNPs) located in the exonic region of the positional candidate gene and the three genetic traits. The flanking markers of the three QTL SI regions are SW38 and S0215. Within the QTL SI regions, 44 genes were located, and runt-related transcription factor 1, dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A (DYRK1A), and potassium inwardly-rectifying channel, subfamily J, member 15 KCNJ15-which are reported to be related to the hematological traits and clinical features of Down syndrome-were selected as positional candidate genes. The ten SNPs located in the exonic region of the three genes were detected by next generation sequencing. A total of 1,232 pigs of an F2 resource population between Landrace and Korean native pigs were genotyped. To investigate the effects of the three genes on each genotype, a mixed-effect model which is the considering family structure model was used to evaluate the associations between the SNPs and three genetic traits in the F2 intercross population. Among them, the MCV level was highly significant (nominal p = 9.8×10-9) in association with the DYRK1A-SNP1 (c.2989 G<A), and explained 4.9% of the phenotypic variance. However, since linkage disequilibrium is quite extensive in an F2 intercross, our approach has limited power to distinguish one particular positional candidate gene from a QTL region.
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Affiliation(s)
- Jae-Bong Lee
- Korea Zoonosis Research Institute (KoZRI), Chonbuk National University, Iksan 54531, Korea
| | - Chae-Kyoung Yoo
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Hee-Bok Park
- National Institute of Animal Science, Rural Development Administration, Jeju 63242, Korea
| | - In-Cheol Cho
- National Institute of Animal Science, Rural Development Administration, Jeju 63242, Korea
| | - Hyun-Tae Lim
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Korea.,Division of Applied Life Science (BK21 plus), Graduate School of Gyeongsang National University, Jinju 52828, Korea
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Ponsuksili S, Reyer H, Trakooljul N, Murani E, Wimmers K. Single- and Bayesian Multi-Marker Genome-Wide Association for Haematological Parameters in Pigs. PLoS One 2016; 11:e0159212. [PMID: 27434032 PMCID: PMC4951017 DOI: 10.1371/journal.pone.0159212] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/28/2016] [Indexed: 12/15/2022] Open
Abstract
Haematological traits are important traits that show associations with immune and metabolic status, as well as diseases in humans and animals. Mapping genome regions that affect the blood cell traits can contribute to the identification of genomic features useable as biomarkers for immune, disease and metabolic status. A genome-wide association study (GWAS) was conducted using PorcineSNP60 BeadChips. Single-marker and Bayesian multi-marker approaches were integrated to identify genomic regions and corresponding genes overlapping for both methods. GWAS was performed for haematological traits of 591 German Landrace pig. Heritability estimates for haematological traits were medium to high. In total 252 single SNPs associated with 12 haematological traits were identified (NegLog10 of p-value > 5). The Bayesian multi-marker approach revealed 102 QTL regions across the genome, indicated by 1-Mb windows with contribution to additive genetic variance above 0.5%. The integration of both methods resulted in 24 overlapping QTL regions. This study identified overlapping QTL regions from single- and multi-marker approaches for haematological traits. Identifying candidate genes that affect blood cell traits provides the first step towards the understanding of the molecular basis of haematological phenotypes.
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Affiliation(s)
- Siriluck Ponsuksili
- Research Unit ‘Functional Genome Analyses’, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany
| | - Henry Reyer
- Research Unit ‘Genomics’, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany
| | - Nares Trakooljul
- Research Unit ‘Genomics’, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany
| | - Eduard Murani
- Research Unit ‘Genomics’, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany
| | - Klaus Wimmers
- Research Unit ‘Genomics’, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany
- * E-mail:
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21
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Ghosh M, Sodhi SS, Sharma N, Mongre RK, Kim N, Singh AK, Lee SJ, Kim DC, Kim SW, Lee HK, Song KD, Jeong DK. An integrated in silico approach for functional and structural impact of non- synonymous SNPs in the MYH1 gene in Jeju Native Pigs. BMC Genet 2016; 17:35. [PMID: 26847462 PMCID: PMC4741023 DOI: 10.1186/s12863-016-0341-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 01/25/2016] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND This study was performed to identify the non- synonymous polymorphisms in the myosin heavy chain 1 gene (MYH1) association with skeletal muscle development in economically important Jeju Native Pig (JNP) and Berkshire breeds. Herein, we present an in silico analysis, with a focus on (a) in silico approaches to predict the functional effect of non-synonymous SNP (nsSNP) in MYH1 on growth, and (b) molecular docking and dynamic simulation of MYH1 to predict the effects of those nsSNP on protein-protein association. RESULTS The NextGENe (V 2.3.4.) tool was used to identify the variants in MYH1 from JNP and Berkshire using RNA seq. Gene ontology analysis of MYH1 revealed significant association with muscle contraction and muscle organ development. The 95 % confidence intervals clearly indicate that the mRNA expression of MYH1 is significantly higher in the Berkshire longissimus dorsi muscle samples than JNP breed. Concordant in silico analysis of MYH1, the open-source software tools identified 4 potential nsSNP (L884T, K972C, N981G, and Q1285C) in JNP and 1 nsSNP (H973G) in Berkshire pigs. Moreover, protein-protein interactions were studied to investigate the effect of MYH1 mutations on association with hub proteins, and MYH1 was found to be closely associated with the protein myosin light chain, phosphorylatable, fast skeletal muscle MYLPF. The results of molecular docking studies on MYH1 (native and 4 mutants) and MYLFP demonstrated that the native complex showed higher electrostatic energy (-466.5 Kcal mol(-1)), van der Walls energy (-87.3 Kcal mol(-1)), and interaction energy (-835.7 Kcal mol(-1)) than the mutant complexes. Furthermore, the molecular dynamic simulation revealed that the native complex yielded a higher root-mean-square deviation (0.2-0.55 nm) and lower root-mean-square fluctuation (approximately 0.08-0.3 nm) as compared to the mutant complexes. CONCLUSIONS The results suggest that the variants at L884T, K972C, N981G, and Q1285C in MYH1 in JNP might represent a cause for the poor growth performance for this breed. This study is a pioneering in-depth in silico analysis of polymorphic MYH1 and will serve as a valuable resource for further targeted molecular diagnosis and population-based studies conducted for improving the growth performance of JNP.
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Affiliation(s)
- Mrinmoy Ghosh
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju-Do, 690-756, Republic of Korea.
| | - Simrinder Singh Sodhi
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju-Do, 690-756, Republic of Korea.
| | - Neelesh Sharma
- Sher-e-Kashmir University of Agricultural Sciences and Technology, R.S. Pura, Jammu, India.
| | - Raj Kumar Mongre
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju-Do, 690-756, Republic of Korea.
| | - Nameun Kim
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju-Do, 690-756, Republic of Korea.
| | - Amit Kumar Singh
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju-Do, 690-756, Republic of Korea.
| | - Sung Jin Lee
- Department of Animal Biotechnology, College of Animal Bioscience and Technology, Kangwon National University, Chuncheon, 200-701, Republic of Korea.
| | - Dae Cheol Kim
- Livestock Promotion Institute, Jeju Special Self-governing Province, Jeju-Do, 690-756, Republic of Korea.
| | - Sung Woo Kim
- Animal Genetic Resources Station, National Institute of Animal Science, Rural Administration, Namwon, Republic of Korea.
| | - Hak Kyo Lee
- Department of Animal Biotechnology, Chonbuk National University, Jeonju, 561-756, Republic of Korea.
| | - Ki-Duk Song
- Department of Animal Biotechnology, Chonbuk National University, Jeonju, 561-756, Republic of Korea.
| | - Dong Kee Jeong
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju-Do, 690-756, Republic of Korea.
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22
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Ghosh M, Sodhi SS, Song KD, Kim JH, Mongre RK, Sharma N, Singh NK, Kim SW, Lee HK, Jeong DK. Evaluation of body growth and immunity-related differentially expressed genes through deep RNA sequencing in the piglets of Jeju native pig and Berkshire. Anim Genet 2015; 46:255-64. [PMID: 25752324 DOI: 10.1111/age.12281] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2015] [Indexed: 01/12/2023]
Abstract
This study was carried out with the objective to investigate the differentially expressed genes (DEGs) between Jeju native pig (JNP) and Berkshire piglets. The RNA-Seq technique was used to investigate the transcriptomes in the fat, liver and longissimus dorsi muscle from these two breeds. Paired-end reads of the sequences that passed the quality filters were aligned to the Sus scrofa genome using tophat2 (v2.0.2). In this study, 65% of muscle, 20% of fat and 54% of liver genes showed higher expression in the piglets of JNP than in Berkshire. Gene Ontology and signaling pathways showed that immune response and lipid metabolisms were commonly enriched pathways in all three tissues. It was found that the genes pertaining to body growth and immune system are significantly (P < 0.01) more highly expressed in Berkshire piglets. DEGs explored between the piglets of the two breeds might influence the identification of the genetic markers for further breed improvement programs. Our findings provide a new perspective for understanding and identifying candidate genes that are involved in various biological functions. Moreover, transcriptome analysis makes it easier to understand the differences between genetic mechanisms of breeds.
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Affiliation(s)
- M Ghosh
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju, 690-756, Korea
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23
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Cho IC, Yoo CK, Lee JB, Jung EJ, Han SH, Lee SS, Ko MS, Lim HT, Park HB. Genome-wide QTL analysis of meat quality-related traits in a large F2 intercross between Landrace and Korean native pigs. Genet Sel Evol 2015; 47:7. [PMID: 25888076 PMCID: PMC4336478 DOI: 10.1186/s12711-014-0080-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 11/20/2014] [Indexed: 11/21/2022] Open
Abstract
Background We conducted a genome-wide linkage analysis to identify quantitative trait loci (QTL) that influence meat quality-related traits in a large F2 intercross between Landrace and Korean native pigs. Thirteen meat quality-related traits of the m. longissimus lumborum et thoracis were measured in more than 830 F2 progeny. All these animals were genotyped with 173 microsatellite markers located throughout the pig genome, and the GridQTL program based on the least squares regression model was used to perform the QTL analysis. Results We identified 23 genome-wide significant QTL in eight chromosome regions (SSC1, 2, 6, 7, 9, 12, 13, and 16) (SSC for Sus Scrofa) and detected 51 suggestive QTL in the 17 chromosome regions. QTL that affect 10 meat quality traits were detected on SSC12 and were highly significant at the genome-wide level. In particular, the QTL with the largest effect affected crude fat percentage and explained 22.5% of the phenotypic variance (F-ratio = 278.0 under the additive model, nominal P = 5.5 × 10−55). Interestingly, the QTL on SSC12 that influenced meat quality traits showed an obvious trend for co-localization. Conclusions Our results confirm several previously reported QTL. In addition, we identified novel QTL for meat quality traits, which together with the associated positional candidate genes improve the knowledge on the genetic structure that underlies genetic variation for meat quality traits in pigs. Electronic supplementary material The online version of this article (doi:10.1186/s12711-014-0080-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- In-Cheol Cho
- Subtropical Animal Experiment Station, National Institute of Animal Science, Rural Development Administration, Jeju, 690-150, Korea.
| | - Chae-Kyoung Yoo
- Department of Animal Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 660-701, Korea. .,Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, 660-701, Korea.
| | - Jae-Bong Lee
- Department of Animal Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 660-701, Korea. .,Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, 660-701, Korea.
| | - Eun-Ji Jung
- Department of Animal Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 660-701, Korea. .,Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, 660-701, Korea.
| | - Sang-Hyun Han
- Subtropical Animal Experiment Station, National Institute of Animal Science, Rural Development Administration, Jeju, 690-150, Korea.
| | - Sung-Soo Lee
- Subtropical Animal Experiment Station, National Institute of Animal Science, Rural Development Administration, Jeju, 690-150, Korea.
| | - Moon-Suck Ko
- Subtropical Animal Experiment Station, National Institute of Animal Science, Rural Development Administration, Jeju, 690-150, Korea.
| | - Hyun-Tae Lim
- Department of Animal Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 660-701, Korea. .,Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, 660-701, Korea.
| | - Hee-Bok Park
- Department of Animal Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 660-701, Korea. .,Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, 660-701, Korea. .,Department of Animal Science and Biotechnology (BK21 plus program), College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 305-764, Korea.
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24
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Kim J, Cho S, Caetano-Anolles K, Kim H, Ryu YC. Genome-wide detection and characterization of positive selection in Korean Native Black Pig from Jeju Island. BMC Genet 2015; 16:3. [PMID: 25634476 PMCID: PMC4314801 DOI: 10.1186/s12863-014-0160-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 12/30/2014] [Indexed: 01/01/2023] Open
Abstract
Background In the 1980s, Korean native black pigs from Jeju Island (Jeju black pigs) served as representative sample of Korean native black pigs, and efforts were made to help the species rebound from the brink of extinction, which occurred as a result of the introduction of Western pig breeds. Geographical separation of Jeju Island from the Korean peninsula has allowed Jeju black pigs not only to acquire unique characteristics but also to retain merits of rare Korean native black pigs. Results To further analyze the Jeju black pig genome, we performed whole-genome re-sequencing (average read depth of 14×) of 8 Jeju black pig and 6 Korean pigs (which live on the Korean peninsula) to compare and identify putative signatures of positive selection in Jeju black pig, the true and pure Korean native black pigs. The candidate genes potentially under positive selection in Jeju black pig support previous reports of high marbling score, rare occurrence of pale, soft, exudative (PSE) meat, but low growth rate and carcass weight compared to Western breeds. Conclusions Several candidate genes potentially under positive selection were involved in fatty acid transport and may have contributed to the unique characteristics of meat quality in JBP. Jeju black pigs can offer a unique opportunity to investigate the true genetic resource of once endangered Korean native black pigs. Further genome-wide analyses of Jeju black pigs on a larger population scale are required in order to define a conservation strategy and improvement of native pig resources. Electronic supplementary material The online version of this article (doi:10.1186/s12863-014-0160-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jaemin Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-742, Korea.
| | - Seoae Cho
- CHO&KIM genomics, Main Bldg. #514, SNU Research Park, Seoul National University Mt.4-2, NakSeoungDae, Gwanakgu, Seoul, 151-919, Republic of Korea.
| | | | - Heebal Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-742, Korea. .,CHO&KIM genomics, Main Bldg. #514, SNU Research Park, Seoul National University Mt.4-2, NakSeoungDae, Gwanakgu, Seoul, 151-919, Republic of Korea. .,Department of Agricultural Biotechnology and Research Institute of Population Genomics, Seoul National University, Seoul, 151-742, Republic of Korea.
| | - Youn-Chul Ryu
- Division of Biotechnology, The Research Institute for Subtropical Agriculture and Biotechnology, Jeju National University, Jeju, 690-756, Republic of Korea.
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25
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Lee JB, Jung EJ, Park HB, Jin S, Seo DW, Ko MS, Cho IC, Lee JH, Lim HT. Genome-wide association analysis to identify SNP markers affecting teat numbers in an F2 intercross population between Landrace and Korean native pigs. Mol Biol Rep 2014; 41:7167-73. [PMID: 25055975 DOI: 10.1007/s11033-014-3599-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 07/07/2014] [Indexed: 11/28/2022]
Abstract
Most reproductive traits have low heritability and are greatly affected by environmental factors. Teat number and litter size are traits related to the reproduction ability of pigs. To identify quantitative trait loci (QTLs) for teat number traits, a genome-wide association study (GWAS) was conducted using an F2 intercross between Landrace and Korean native pigs. Genotype analysis was performed using the porcine SNP 60 K beadchip. The GWAS was performed using a mixed-effects model and linear regression approach. When a genome-wide threshold was determined using the Bonferroni method (P = 1.61 × 10(-6)), 38 single nucleotide polymorphism (SNP) markers in pig chromosome 7 (SSC7) were significantly associated with three teat number traits (total teat number, left teat number, and right teat number). Among these, SNPs in 5 genes (HDDC3, LOC100156276, LOC100155863, ANPEP, SCAMP2) were selected for further study based primarily on their statistical significance. A significant association was detected in SCAMP2 g.25280 G>A for total teat number (P = 2.0 × 10(-12)), HDDC3 g.1319 G>A SNP for left teat number (P = 2.3 × 10(-7)), and SCAMP2 g.14198 G>A for right teat number (P = 4.7 × 10(-12)). These results provide valuable information about the selective breeding for desirable teat numbers in pigs.
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Affiliation(s)
- Jae-Bong Lee
- Division of Applied Life Science, Graduate School of Gyeongsang National University, Jinju, 660-701, Korea,
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26
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Jin S, Lee JB, Kang K, Yoo CK, Kim BM, Park HB, Lim HT, Cho IC, Maharani D, Lee JH. The Possibility of TBC1D21 as a Candidate Gene for Teat Numbers in Pigs. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 26:1374-8. [PMID: 25049720 PMCID: PMC4093071 DOI: 10.5713/ajas.2013.13140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 06/24/2013] [Accepted: 05/29/2013] [Indexed: 12/02/2022]
Abstract
Based on a quantitative traits locus (QTL) study using a F2 intercross between Landrace and Korean native pigs, a significant QTL affecting teat numbers in SSC7 was identified. The strong positional candidate gene, TBC1D21, was selected due to its biological function for epithelial mesenchymal cell development. Sequence analysis revealed six single nucleotide polymorphisms (SNPs) in the TBC1D21 gene. Among these, two SNP markers, one silent mutation (SNP01) for g.13,050A>G and one missense mutation (SNP04) for c.829A>T (S277C), were genotyped and they showed significant associations with teat number traits (p value = 6.38E-05 for SNP01 and p value = 1.06E-07 for SNP04 with total teat numbers). Further functional validation of these SNPs could give valuable information for understanding the teat number variation in pigs.
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Affiliation(s)
- S Jin
- Department of Animal Science and Biotechnology, Chungnam National University, Deajeon 305-764, Korea
| | - J B Lee
- Department of Animal Science and Biotechnology, Chungnam National University, Deajeon 305-764, Korea
| | - K Kang
- Department of Animal Science and Biotechnology, Chungnam National University, Deajeon 305-764, Korea
| | - C K Yoo
- Department of Animal Science and Biotechnology, Chungnam National University, Deajeon 305-764, Korea
| | - B M Kim
- Department of Animal Science and Biotechnology, Chungnam National University, Deajeon 305-764, Korea
| | - H B Park
- Department of Animal Science and Biotechnology, Chungnam National University, Deajeon 305-764, Korea
| | - H T Lim
- Department of Animal Science and Biotechnology, Chungnam National University, Deajeon 305-764, Korea
| | - I C Cho
- Department of Animal Science and Biotechnology, Chungnam National University, Deajeon 305-764, Korea
| | - D Maharani
- Department of Animal Science and Biotechnology, Chungnam National University, Deajeon 305-764, Korea
| | - J H Lee
- Department of Animal Science and Biotechnology, Chungnam National University, Deajeon 305-764, Korea
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27
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Lee YM, Alam M, Choi BH, Kim KS, Kim JJ. A Whole Genome Association Study to Detect Single Nucleotide Polymorphisms for Blood Components (Immunity) in a Cross between Korean Native Pig and Yorkshire. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 25:1674-80. [PMID: 25049532 PMCID: PMC4094150 DOI: 10.5713/ajas.2012.12503] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 09/20/2012] [Accepted: 09/19/2012] [Indexed: 01/06/2023]
Abstract
The purpose of this study was to detect significant SNPs for blood components that were related to immunity using high single nucleotide polymorphism (SNP) density panels in a Korean native pig (KNP)×Yorkshire (YK) cross population. A reciprocal design of KNP×YK produced 249 F2 individuals that were genotyped for a total of 46,865 available SNPs in the Illumina porcine 60K beadchip. To perform whole genome association analysis (WGA), phenotypes were regressed on each SNP under a simple linear regression model after adjustment for sex and slaughter age. To set up a significance threshold, 0.1% point-wise p value from F distribution was used for each SNP test. Among the significant SNPs for a trait, the best set of SNP markers were determined using a stepwise regression procedure with the rates of inclusion and exclusion of each SNP out of the model at 0.001 level. A total of 54 SNPs were detected; 10, 6, 4, 4, 5, 4, 5, 10, and 6 SNPs for neutrophil, lymphocyte, monocyte, eosinophil, basophil, atypical lymph, immunoglobulin, insulin, and insulin-like growth factor-I, respectively. Each set of significant SNPs per trait explained 24 to 42% of phenotypic variance. Several pleiotropic SNPs were detected on SSCs 4, 13, 14 and 15.
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Affiliation(s)
- Y-M Lee
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Suwon, Korea
| | - M Alam
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Suwon, Korea
| | - B H Choi
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Suwon, Korea
| | - K-S Kim
- Department of Animal Science, Chungbuk National University, Cheongju, Korea
| | - J-J Kim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Suwon, Korea
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28
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Comparative transcriptomic analysis to identify differentially expressed genes in fat tissue of adult Berkshire and Jeju Native Pig using RNA-seq. Mol Biol Rep 2014; 41:6305-15. [PMID: 25008993 DOI: 10.1007/s11033-014-3513-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 06/19/2014] [Indexed: 10/25/2022]
Abstract
Pork is a major source of animal protein for humans. The subcutaneous, intermuscular and the intramuscular fat are the factors responsible for meat quality. RNA-seq is rapidly adopted for the profiling of the transcriptomes in the studies related to gene regulation. The discovery of differentially expressed genes (DEGs) between adult animals of Jeju Native Pig (JNP) and Berkshire breeds are of particular interest for the current study. RNA-seq was used to investigate the transcriptome profiling in the fat tissue. Sequence reads were obtained from Ilumina HiSeq2000 and mapped to the pig genome using Tophat2. Total 153 DEGs were identified and 71 among the annotated genes, have BLAST matches in the non- redundant database. Metabolic, immune response and protein binding are enriched pathways in the fat tissue. In our study, biological adhesion, cellular, developmental and multicellular organismal processes in fat were up-regulated in JNP as compare to Berkshire. Multicellular organismal process, developmental process, embryonic morphogenesis and skeletal system development were the most significantly enriched terms in fat of JNP and Berkshire breeds (p = 1.17E-04, 0.044, 3.47E-04 and 4.48E-04 respectively). COL10A1, COL11A2, PDK4 and PNPLA3 genes responsible for skeletal system morphogenesis and body growth were down regulated in JNP. This study is the first statistical analysis for the detection of DEGs from RNA-seq data generated from fat tissue sample. This analysis can be used as stepping stone to understand the difference in the genetic mechanisms that might influence the identification of novel transcripts, sequence polymorphisms, isoforms and noncoding RNAs.
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29
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Sodhi SS, Song KD, Ghosh M, Sharma N, Lee SJ, Kim JH, Kim N, Mongre RK, Adhikari P, Kim JY, Hong SP, Oh SJ, Jeong DK. Comparative transcriptomic analysis by RNA-seq to discern differential expression of genes in liver and muscle tissues of adult Berkshire and Jeju Native Pig. Gene 2014; 546:233-42. [PMID: 24910116 DOI: 10.1016/j.gene.2014.06.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 05/29/2014] [Accepted: 06/04/2014] [Indexed: 12/16/2022]
Abstract
RNA-seq is being rapidly adopted for the profiling of the transcriptomes in different areas of biology, especially in the studies related to gene regulation. The discovery of differentially expressed genes (DEGs) between adult animals of Jeju Native Pig (JNP) and Berkshire breeds of Sus scrofa, is of particular interest for the current study. For the better understanding of the gene expression profiles of the liver and longissimus dorsi muscle, DEGs were identified via RNA-seq. Sequence reads were obtained from Illumina HiSeq2000 and mapped to the pig reference genome (Sscrofa10.2) using Tophat2. We identified 169 and 39 DEGs in the liver and muscle of JNP respectively, by comparison with Berkshire breed. Out of all identified genes, 41 genes in the liver and 9 genes in the muscle have given significant expression. Gene ontology (GO) terms of developmental process and KEGG pathway analysis showed that metabolic, immune response and protein binding were commonly enriched pathways in the two tissues. Further the heat map analysis by ArrayStar has shown the different levels of expression in JNP with respect to the Berkshire breed. The validation through real time PCR and western blotting also confirmed the differential expression of genes in both breeds. Genes pertaining to metabolic process and inflammatory and immune system are more enriched in Berkshire breed. This comparative transcriptome analysis of two tissues suggests a subset of novel marker genes which expressed differently between the JNP and Berkshire.
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Affiliation(s)
- Simrinder Singh Sodhi
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea
| | - Ki-Duk Song
- The Animal Genomics and Breeding Center, Hankyong National University, Anseong-si, Gyeonggi-do 456-749, South Korea
| | - Mrinmoy Ghosh
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea
| | - Neelesh Sharma
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea
| | - Sung Jin Lee
- Department of Animal Biotechnology, College of Animal Bioscience and Technology, Kangwon National University, Chuncheon 200-701, South Korea
| | - Jeong Hyun Kim
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea
| | - Nameun Kim
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea
| | - Raj Kumar Mongre
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea
| | - Pradeep Adhikari
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea
| | - Jin Young Kim
- Institute for Livestock Promotion, Jeju-do, Jeju 690-802, South Korea
| | - Sang Pyo Hong
- Institute for Livestock Promotion, Jeju-do, Jeju 690-802, South Korea
| | - Sung Jong Oh
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea
| | - Dong Kee Jeong
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea; Sustainable Agriculture Research Institute (SARI), Jeju National University, Jeju 690-756, South Korea.
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Jung EJ, Park HB, Lee JB, Yoo CK, Kim BM, Kim HI, Cho IC, Lim HT. Genome-wide association study identifies quantitative trait loci affecting hematological traits in an F2 intercross between Landrace and Korean native pigs. Anim Genet 2014; 45:534-41. [PMID: 24797309 DOI: 10.1111/age.12175] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2014] [Indexed: 11/30/2022]
Abstract
Changes affecting the status of health and robustness can bring about physiological alterations including hematological parameters in swine. To identify quantitative trait loci (QTL) associated with eight hematological traits (one leukocyte trait, six erythrocyte traits and one platelet trait), we conducted a genome-wide association study using the PorcineSNP60K BeadChip in a resource population derived from an intercross between Landrace and Korean native pigs. A total of 36 740 SNPs from 816 F2 progeny were analyzed for each blood-related trait after filtering for quality control. Data were analyzed by the genome-wide rapid association using mixed model and regression (GRAMMAR) approach. A total of 257 significant SNPs (P < 1.36 × 10(-6) ) on SSC3, 6, 8, 13 and 17 were identified for blood-related traits in this study. Interestingly, the genomic region between 17.9 and 130 Mb on SSC8 was found to be significantly associated with red blood cell, mean corpuscular volume and mean corpuscular hemoglobin. Our results include the identification of five significant SNPs within five candidate genes (KIT, IL15, TXK, ARAP2 and ERG) for hematopoiesis. Further validation of these identified SNPs could give valuable information for understanding the variation of hematological traits in pigs.
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Affiliation(s)
- E J Jung
- Department of Animal Science, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 660-701, Korea; Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 660-701, Korea
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Yoo CK, Park HB, Lee JB, Jung EJ, Kim BM, Kim HI, Ahn SJ, Ko MS, Cho IC, Lim HT. QTL analysis of body weight and carcass body length traits in an F2intercross between Landrace and Korean native pigs. Anim Genet 2014; 45:589-92. [DOI: 10.1111/age.12166] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2014] [Indexed: 11/30/2022]
Affiliation(s)
- C. K. Yoo
- Division of Applied Life Science (Brain Korea 21 Program); Graduate School of Gyeongsang National University; Jinju 660-701 Korea
| | - H. B. Park
- Institute of Agriculture and Life Sciences; Gyeongsang National University; Jinju 660-701 Korea
| | - J. B. Lee
- Division of Applied Life Science (Brain Korea 21 Program); Graduate School of Gyeongsang National University; Jinju 660-701 Korea
- Institute of Agriculture and Life Sciences; Gyeongsang National University; Jinju 660-701 Korea
| | - E. J. Jung
- Division of Applied Life Science (Brain Korea 21 Program); Graduate School of Gyeongsang National University; Jinju 660-701 Korea
- Institute of Agriculture and Life Sciences; Gyeongsang National University; Jinju 660-701 Korea
| | - B. M. Kim
- Division of Applied Life Science (Brain Korea 21 Program); Graduate School of Gyeongsang National University; Jinju 660-701 Korea
| | - H. I. Kim
- Division of Applied Life Science (Brain Korea 21 Program); Graduate School of Gyeongsang National University; Jinju 660-701 Korea
| | - S. J. Ahn
- Department of Information Statistics; RINS; Gyeongsang National University; Jinju 660-701 Korea
| | - M. S. Ko
- Subtropical Animal Experiment Station; National Institute of Animal Science; Rural Development Administration; Jeju 690-150 Korea
| | - I. C. Cho
- Subtropical Animal Experiment Station; National Institute of Animal Science; Rural Development Administration; Jeju 690-150 Korea
| | - H. T. Lim
- Institute of Agriculture and Life Sciences; Gyeongsang National University; Jinju 660-701 Korea
- Department of Animal Science; College of Agriculture and Life Sciences; Gyeongsang National University; Jinju 660-701 Korea
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Genome-wide copy number variations inferred from SNP genotyping arrays using a Large White and Minzhu intercross population. PLoS One 2013; 8:e74879. [PMID: 24098353 PMCID: PMC3787955 DOI: 10.1371/journal.pone.0074879] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 08/08/2013] [Indexed: 01/20/2023] Open
Abstract
Copy number variations (CNVs) are one of the main contributors to genetic diversity in animals and are broadly distributed in the genomes of swine. Investigating the performance and evolutionary impacts of pig CNVs requires comprehensive knowledge of their structure and function within and between breeds. In the current study, 4 different programs (i.e., GADA, PennCNV, QuantiSNP, and cnvPartition) were used to analyze Porcine SNP60 genotyping data of 585 pigs from one Large White × Minzhu intercross population to detect copy number variant regions (CNVRs). Overlapping CNVRs recalled by at least 2 programs were used to construct a powerful and comprehensive CNVR map, which contained 249 CNVRs (i.e., 70 gains, 43 losses, and 136 gains/losses) and covered 26.22% of the regions in the swine genome. Ten CNVRs, representing different predicted statuses, were selected for validation via quantitative real-time PCR (QPCR); 9/10 CNVRs (i.e., 90%) were validated. When being traced back to the F0 generation, 58 events were identified in only Minzhu F0 parents and 2 events were identified in only Large White F0 parents. A series of CNVR function analyses were performed. Some of the CNVRs functions were predicted, and several interesting CNVRs for meat quality traits and hematological parameters were obtained. A comprehensive and lower false rate genome-wide CNV map was constructed for Large White and Minzhu pig genomes in this study. Our results may provide an important basis for determining the relationship between CNVRs and important qualitative and quantitative traits. In addition, it can help to further understand genetic processes in pigs.
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Kang K, Seo DW, Lee JB, Jung EJ, Park HB, Cho IC, Lim HT, Lee JH. Identification of SNPs Affecting Porcine Carcass Weight with the 60K SNP Chip. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2013. [DOI: 10.5187/jast.2013.55.4.231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Zhang Z, Hong Y, Gao J, Xiao S, Ma J, Zhang W, Ren J, Huang L. Genome-wide association study reveals constant and specific loci for hematological traits at three time stages in a White Duroc × Erhualian F2 resource population. PLoS One 2013; 8:e63665. [PMID: 23691082 PMCID: PMC3656948 DOI: 10.1371/journal.pone.0063665] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 04/05/2013] [Indexed: 11/18/2022] Open
Abstract
Hematological traits are important indicators of immune function and have been commonly examined as biomarkers of disease and disease severity in humans. Pig is an ideal biomedical model for human diseases due to its high degree of similarity with human physiological characteristics. Here, we conducted genome-wide association studies (GWAS) for 18 hematological traits at three growth stages (days 18, 46 and 240) in a White Duroc × Erhualian F2 intercross. In total, we identified 38 genome-wide significant regions containing 185 genome-wide significant SNPs by single-marker GWAS or LONG-GWAS. The significant regions are distributed on pig chromosomes (SSC) 1, 4, 5, 7, 8, 10, 11, 12, 13, 17 and 18, and most of significant SNPs reside on SSC7 and SSC8. Of the 38 significant regions, 7 show constant effects on hematological traits across the whole life stages, and 6 regions have time-specific effects on the measured traits at early or late stages. The most prominent locus is the genomic region between 32.36 and 84.49 Mb on SSC8 that is associated with multiple erythroid traits. The KIT gene in this region appears to be a promising candidate gene. The findings improve our understanding of the genetic architecture of hematological traits in pigs. Further investigations are warranted to characterize the responsible gene(s) and causal variant(s) especially for the major loci on SSC7 and SSC8.
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Affiliation(s)
- Zhiyan Zhang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, China
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Molecular advances in QTL discovery and application in pig breeding. Trends Genet 2013; 29:215-24. [DOI: 10.1016/j.tig.2013.02.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 02/12/2013] [Accepted: 02/13/2013] [Indexed: 11/21/2022]
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Association of the gene encoding stearoyl-CoA desaturase (SCD) with fatty acid composition in an intercross population between Landrace and Korean native pigs. Mol Biol Rep 2012; 40:73-80. [PMID: 23124221 DOI: 10.1007/s11033-012-2014-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Accepted: 10/01/2012] [Indexed: 10/27/2022]
Abstract
Fatty acid (FA) composition is one of the most important parameters for the evaluation of meat quality. The stearoyl-CoA desaturase (SCD) gene is considered a positional candidate gene affecting FA composition in SSC14, based on previous quantitative trait loci studies. To evaluate the association of the SCD gene with FA composition in a Korean native pig × Landrace F(2) intercross population, we genotyped six single nucleotide polymorphisms (SNPs) of the SCD gene located in promoter region [2 SNPs (g.-353T>C, g.-233T>C)], exonic region [1 SNP (g.817C>T) in exon 2] and 3' UTR [3 SNPs (g.13311C>G, g.14384G>A, and g.14424C>T)] identified by massively parallel sequencing technology. Eighteen FA composition traits were measured in more than the 950 F(2) animals. A mixed-effect model was used to evaluate associations between these SNPs and FA composition traits in the F(2) intercross population. A detailed investigation detected that the five FA composition traits [palmitoleic acid (C16:1), stearic acid (C18:0), arachidic acid (C20:0), saturated FA, and unsaturated FA] were highly significant (P < 4.7 × 10(-5); C20:0) in association with the SNP g.-233T>C, SNP g.817C>T, SNP g.13311C>G and SNP g.14384G>A in the SCD gene, whereas SNP g.14424C>T was only significantly associated with palmitoleic acid (C16:1, P = 1.4 × 10(-3)). No significant association of FA composition traits with SNP g.-353T>C was detected. In particular, the SNP g.14384G>A accounted for 30.6 % of the additive genetic variance of palmitoleic acid (P = 1.9 × 10(-10)). These results suggest the SCD gene has a strong effect on FA composition in the crossbred pig population.
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A missense mutation (c.1963A<G) of the complementary component 2 (C2) gene is associated with serum Ca⁺⁺ concentrations in pigs. Mol Biol Rep 2012; 39:9291-7. [PMID: 22763733 DOI: 10.1007/s11033-012-1679-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Accepted: 06/05/2012] [Indexed: 10/28/2022]
Abstract
Serum Ca(++) levels play important roles in the humoral immunity. The aim of this study was to detect quantitative trait loci and the associated positional candidate genes affecting baseline serum Ca(++) concentrations. A genome-wide association study was conducted in an F(2) intercross population between Landrace and Korean native pigs using the porcine single nucleotide polymorphism (SNP) 60 K beadchip and the PLINK program based on linear regression. Data used in the study included 410 F(2) pigs. All experimental animals were genotyped with 36,613 SNP markers located throughout the pig autosomes. We identified a strong association between a SNP marker on chromosome 7 and serum Ca(++) levels (DIAS0002191, genomic control-corrected P = 7.7 × 10(-5)). The position of DIAS0002191 was closely located to SLA class III region containing the C2 gene encoding the complementary component 2 protein, a protein which is important in the humoral immune responses. De novo sequencing of the porcine C2 gene revealed a missense mutation [c.1963A<G (N655D)] and this missense mutation was also strongly associated with serum Ca(++) concentrations (genomic control-corrected P = 5.9 × 10(-5)). Further studies are necessary to investigate the effect of this missense mutation at a functional-molecular level. In conclusion, the missense mutation of the C2 gene identified in this study may help in elucidating the genetic factors underlying humoral immune reactions.
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QTL analysis of back fat thickness and carcass pH in an F2 intercross between Landrace and Korean native pigs. Mol Biol Rep 2012; 39:8327-33. [DOI: 10.1007/s11033-012-1682-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 06/05/2012] [Indexed: 10/28/2022]
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Luo W, Chen S, Cheng D, Wang L, Li Y, Ma X, Song X, Liu X, Li W, Liang J, Yan H, Zhao K, Wang C, Wang L, Zhang L. Genome-wide association study of porcine hematological parameters in a Large White × Minzhu F2 resource population. Int J Biol Sci 2012; 8:870-81. [PMID: 22745577 PMCID: PMC3385009 DOI: 10.7150/ijbs.4027] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 05/15/2012] [Indexed: 01/09/2023] Open
Abstract
Hematological traits, which are important indicators of immune function in animals, have been commonly examined as biomarkers of disease and disease severity in humans and animals. Genome-wide significant quantitative trait loci (QTLs) provide important information for use in breeding programs of animals such as pigs. QTLs for hematological parameters (hematological traits) have been detected in pig chromosomes, although these are often mapped by linkage analysis to large intervals making identification of the underlying mutation problematic. Single nucleotide polymorphisms (SNPs) are the common form of genetic variation among individuals and are thought to account for the majority of inherited traits. In this study, a genome-wide association study (GWAS) was performed to detect regions of association with hematological traits in a three-generation resource population produced by intercrossing Large White boars and Minzhu sows during the period from 2007 to 2011. Illumina PorcineSNP60 BeadChip technology was used to genotype each animal and seven hematological parameters were measured (hematocrit (HCT), hemoglobin (HGB), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), mean corpuscular volume (MCV), red blood cell count (RBC) and red blood cell volume distribution width (RDW)). Data were analyzed in a three step Genome-wide Rapid Association using the Mixed Model and Regression-Genomic Control (GRAMMAR-GC) method. A total of 62 genome-wide significant and three chromosome-wide significant SNPs associated with hematological parameters were detected in this GWAS. Seven and five SNPs were associated with HCT and HGB, respectively. These SNPs were all located within the region of 34.6-36.5 Mb on SSC7. Four SNPs within the region of 43.7-47.0 Mb and fifty-five SNPs within the region of 42.2-73.8 Mb on SSC8 showed significant association with MCH and MCV, respectively. At chromosome-wide significant level, one SNP at 29.2 Mb on SSC1 and two SNPs within the region of 26.0-26.2 Mb were found to be significantly associated with RBC and RDW, respectively. Many of the SNPs were located within previously reported QTL regions and appeared to narrow down the regions compared with previously described QTL intervals. In current research, a total of seven significant SNPs were found within six candidate genes SCUBE3, KDR, TDO, IGFBP7, ADAMTS3 and AFP. In addition, the KIT gene, which has been previously reported to relate to hematological parameters, was located within the region significantly associated with MCH and MCV and could be a candidate gene. These results of this study may lead to a better understanding of the molecular mechanisms of hematological parameters in pigs.
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Affiliation(s)
- Weizhen Luo
- Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Yoo CK, Cho IC, Lee JB, Jung EJ, Lim HT, Han SH, Lee SS, Ko MS, Kang T, Hwang JH, Park YS, Park HB. QTL analysis of clinical-chemical traits in an F₂ intercross between Landrace and Korean native pigs. Physiol Genomics 2012; 44:657-68. [PMID: 22496488 DOI: 10.1152/physiolgenomics.00172.2011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Clinical-chemical traits are essential when examining the health status of individuals. The aim of this study was to identify quantitative trait loci (QTL) and the associated positional candidate genes affecting clinical-chemical traits in a reciprocal F(2) intercross between Landrace and Korean native pigs. Following an overnight fast, 25 serum phenotypes related to clinical-chemical traits (e.g., hepatic function parameters, renal function parameters, electrolyte, lipids) were measured in >970 F(2) progeny. All experimental samples were subjected to genotyping analysis using 165 microsatellite markers located across the genome. We identified eleven genome-wide significant QTL in six chromosomal regions (SSC 2, 7, 8, 13, 14, and 15) and 59 suggestive QTL in 17 chromosomal regions (SSC 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, and 18). We also observed significant effects of reciprocal crosses on some of the traits, which would seem to result from maternal effect, QTL on sex chromosomes, imprinted genes, or genetic difference in mitochondrial DNA. The role of genomic imprinting in clinical-chemical traits also was investigated. Genome-wide analysis revealed a significant evidence for an imprinted QTL in SSC4 affecting serum amylase levels. Additionally, a series of bivariate linkage analysis provided strong evidence that QTL in SSC 2, 13, 15, and 18 have a pleiotropic effect on clinical-chemical traits. In conclusion, our study detected both novel and previously reported QTL influencing clinical-chemical traits in pigs. The identified QTL together with the positional candidate genes identified here could play an important role in elucidating the genetic structure of clinical-chemical phenotype variation in humans and swine.
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Affiliation(s)
- Chae-Kyoung Yoo
- Animal Science Major, Division of Applied Life Science (Brain Korea 21 Program) Gyeongsang National University, Jinju, Korea
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