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Suzuki M, Funasaka N, Yoshimura K, Inamori D, Watanabe Y, Ozaki M, Hosono M, Shindo H, Kawamura K, Tatsukawa T, Yoshioka M. Comprehensive expression analysis of hormone-like substances in the subcutaneous adipose tissue of the common bottlenose dolphin Tursiops truncatus. Sci Rep 2024; 14:12515. [PMID: 38822022 PMCID: PMC11143283 DOI: 10.1038/s41598-024-63018-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 05/23/2024] [Indexed: 06/02/2024] Open
Abstract
Marine mammals possess a specific subcutaneous fat layer called blubber that not only insulates and stores energy but also secretes bioactive substances. However, our understanding of its role as a secretory organ in cetaceans is incomplete. To exhaustively explore the hormone-like substances produced in dolphin subcutaneous adipose tissue, we performed seasonal blubber biopsies from captive female common bottlenose dolphins (Tursiops truncatus; N = 8, n = 32) and analyzed gene expression via transcriptomics. Analysis of 186 hormone-like substances revealed the expression of 58 substances involved in regulating energy metabolism, tissue growth/differentiation, vascular regulation, immunity, and ion/mineral homeostasis. Adiponectin was the most abundantly expressed gene, followed by angiopoietin protein like 4 and insulin-like growth factor 2. To investigate the endocrine/secretory responses of subcutaneous adipose tissue to the surrounding temperature, we subsequently compared the mean expression levels of the genes during the colder and warmer seasons. In the colder season, molecules associated with appetite suppression, vasodilation, and tissue proliferation were relatively highly expressed. In contrast, warmer seasons enhanced the expression of substances involved in tissue remodeling, immunity, metabolism, and vasoconstriction. These findings suggest that dolphin blubber may function as an active secretory organ involved in the regulation of metabolism, appetite, and tissue reorganization in response to changes in the surrounding environment, providing a basis for elucidating the function of hormone-like substances in group-specific evolved subcutaneous adipose tissue.
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Affiliation(s)
- Miwa Suzuki
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, 252-0880, Japan.
| | - Noriko Funasaka
- Cetacean Research Center, Graduate School of Bioresources, Mie University, Tsu, Mie, 514-8507, Japan
| | - Kazuma Yoshimura
- College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, 252-0880, Japan
| | - Daiki Inamori
- Taiji Whale Museum, Higashimuro, Wakayama, 649-5171, Japan
| | - Yurie Watanabe
- Taiji Whale Museum, Higashimuro, Wakayama, 649-5171, Japan
| | - Miki Ozaki
- Adventure World, Nishimuro, Wakayama, 649-2201, Japan
| | | | - Hideaki Shindo
- Shimonoseki Marine Science Museum, Shimonoseki, Yamaguchi, 750-0036, Japan
| | - Keiko Kawamura
- Shimonoseki Marine Science Museum, Shimonoseki, Yamaguchi, 750-0036, Japan
| | | | - Motoi Yoshioka
- Cetacean Research Center, Graduate School of Bioresources, Mie University, Tsu, Mie, 514-8507, Japan.
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Zeng Q, Gao H, Yin S, Peng Y, Yang F, Fu Y, Deng X, Chen Y, Hou X, Wang Q, Jin Z, Song G, He J, Yin Y, Xu K. Genome-Wide Association Study and Identification of Candidate Genes for Intramuscular Fat Fatty Acid Composition in Ningxiang Pigs. Animals (Basel) 2023; 13:3192. [PMID: 37893916 PMCID: PMC10603709 DOI: 10.3390/ani13203192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/03/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Ningxiang pigs exhibit a diverse array of fatty acids, making them an intriguing model for exploring the genetic underpinnings of fatty acid metabolism. We conducted a genome-wide association study using a dataset comprising 50,697 single-nucleotide polymorphisms (SNPs) and samples from over 600 Ningxiang pigs. Our investigation yielded novel candidate genes linked to five saturated fatty acids (SFAs), four monounsaturated fatty acids (MUFAs), and five polyunsaturated fatty acids (PUFAs). Significant associations with SFAs, MUFAs, and PUFAs were found for 37, 21, and 16 SNPs, respectively. Notably, some SNPs have significant PVE, such as ALGA0047587, which can explain 89.85% variation in Arachidic acid (C20:0); H3GA0046208 and DRGA0016063 can explain a total of 76.76% variation in Elaidic Acid (C18:1n-9(t)), and the significant SNP ALGA0031262 of Arachidonic acid (C20:4n-6) can explain 31.76% of the variation. Several significant SNPs were positioned proximally to previously reported genes. In total, we identified 11 candidate genes (hnRNPU, CEPT1, ATP1B1, DPT, DKK1, PRKG1, EXT2, MEF2C, IL17RA, ITGA1 and ALOX5), six candidate genes (ALOX5AP, MEDAG, ISL1, RXRB, CRY1, and CDKAL1), and five candidate genes (NDUFA4L2, SLC16A7, OTUB1, EIF4E and ROBO2) associated with SFAs, MUFAs, and PUFAs, respectively. These findings hold great promise for advancing breeding strategies aimed at optimizing meat quality and enhancing lipid metabolism within the intramuscular fat (IMF) of Ningxiang pigs.
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Affiliation(s)
- Qinghua Zeng
- Animal Nutrition Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Hu Gao
- Animal Nutrition Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Shishu Yin
- Animal Nutrition Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Yinglin Peng
- Hunan Institute of Animal & Veterinary Science, Changsha 410131, China
| | - Fang Yang
- Animal Nutrition Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Yawei Fu
- Animal Nutrition Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Xiaoxiao Deng
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Yue Chen
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Xiaohong Hou
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Qian Wang
- Animal Nutrition Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Zhao Jin
- Animal Nutrition Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Gang Song
- Animal Nutrition Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Jun He
- Animal Nutrition Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Yulong Yin
- Animal Nutrition Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Kang Xu
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
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Walendzik K, Kopcewicz M, Wiśniewska J, Opyd P, Machcińska-Zielińska S, Gawrońska-Kozak B. Dermal white adipose tissue development and metabolism: The role of transcription factor Foxn1. FASEB J 2023; 37:e23171. [PMID: 37682531 DOI: 10.1096/fj.202300873rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 08/10/2023] [Accepted: 08/18/2023] [Indexed: 09/09/2023]
Abstract
Intradermal adipocytes form dermal white adipose tissue (dWAT), a unique fat depot localized in the lower layer of the dermis. However, recognition of molecular factors regulating dWAT development, homeostasis, and bioactivity is limited. Using Foxn1-/- and Foxn1+/+ mice, we demonstrated that epidermally expressed Foxn1 regulates dWAT development and defines the adipogenic capacity of dermal fibroblasts. In intact and post-wounded skin, Foxn1 contributes to the initial stimulation of dWAT adipogenesis and participates in the modulation of lipid metabolism processes. Furthermore, Foxn1 activity strengthens adipogenic processes through Bmp2 and Igf2 signaling and regulates lipid metabolism in differentiated dermal fibroblasts. The results reveal the contribution of Foxn1 to dWAT metabolism, thus identifying possible targets for modulation and regulation of dWAT in physiological and pathological processes in the skin.
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Affiliation(s)
- Katarzyna Walendzik
- Biological Function of Food, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Marta Kopcewicz
- Biological Function of Food, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Joanna Wiśniewska
- Biological Function of Food, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Paulina Opyd
- Department of Animal Nutrition and Feed Science, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Sylwia Machcińska-Zielińska
- Biological Function of Food, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Barbara Gawrońska-Kozak
- Biological Function of Food, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
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Ampaporn K, Suwannasing R, Phongphanich P, Tunim S, Duangjinda M. The variation of insulin like growth factor 2 maker is associated with growth traits in Thai native (Kradon) pigs. Anim Biosci 2023; 36:1350-1356. [PMID: 37170502 PMCID: PMC10472148 DOI: 10.5713/ab.22.0431] [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: 11/11/2022] [Revised: 02/14/2023] [Accepted: 05/01/2023] [Indexed: 05/13/2023] Open
Abstract
OBJECTIVE This study was conducted to investigate polymorphisms of the melanocortin-4 receptor (MC4R) and insulin like growth factor 2 (IGF2) genes and to evaluate the growth traits affected by such polymorphisms in Thai native (Kradon) pigs. METHODS Blood samples and productive data from 91 Kradon pigs were collected. DNA was extracted and quantified, the IGF2 and MC4R genes were amplified, and the polymerase chain reaction (PCR) produces were digested using the PCR-restriction fragment length polymorphism (PCR-RFLP) technique. Genotyping was performed, and the association between genotypes and growth traits on the birth and weaning weights were evaluated. RESULTS The IGF2 intron7 g.162G>C variations in Kradon pigs were found in three genotypes: i) GG, ii) GC, and iii) CC. The GG genotype frequency was the highest followed by the GC and CC genotypes. The frequencies of the G and C alleles were 0.703 and 0.297, respectively. The MC4R genotype was found in only one genotype (GG). The IGF2 gene pattern was not associated with birth weight traits, whereas the IGF2 gene pattern was related to the weaning weight trait in Kradon pigs. Pigs with the CC and GC genotypes had higher weaning weights than ones with the GG genotype (p<0.001). CONCLUSION Thai native Kradon pigs with the CC and GC genotypes of the IGF2 gene have higher weaning weights than pigs with the GG genotype.
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Affiliation(s)
- Kessara Ampaporn
- Department of Animal Science, Faculty of Natural Resources, Rajamangala University of Technology Isan Sakon Nakon Campus, Sakon Nakon 47160,
Thailand
| | - Rattikan Suwannasing
- Department of Animal Science, Faculty of Natural Resources, Rajamangala University of Technology Isan Sakon Nakon Campus, Sakon Nakon 47160,
Thailand
| | - Pitchayanipa Phongphanich
- Animal Production and Management Division, Faculty of Natural Resources, Prince of Songkla University, Songkla 90112,
Thailand
| | - Supanon Tunim
- Animal Production and Management Division, Faculty of Natural Resources, Prince of Songkla University, Songkla 90112,
Thailand
| | - Monchai Duangjinda
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002,
Thailand
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Munyaneza JP, Kim M, Cho E, Jang A, Choo HJ, Lee JH. Association of single-nucleotide polymorphisms in dual specificity phosphatase 8 and insulin-like growth factor 2 genes with inosine-5'-monophosphate, inosine, and hypoxanthine contents in chickens. Anim Biosci 2023; 36:1357-1366. [PMID: 37402464 PMCID: PMC10472161 DOI: 10.5713/ab.23.0080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/21/2023] [Accepted: 05/22/2023] [Indexed: 07/06/2023] Open
Abstract
OBJECTIVE This study aimed to identify the single-nucleotide polymorphisms (SNPs) in the dual-specificity phosphatase 8 (DUSP8) and insulin-like growth factor 2 (IGF2) genes and to explore their effects on inosine-5'-monophosphate (IMP), inosine, and hypoxanthine contents in Korean native chicken -red-brown line (KNC-R Line). METHODS A total sample of 284 (males, n = 127; females n = 157) and 230 (males, n = 106; females, n = 124) aged of 10 weeks old KNC-R line was used for genotyping of DUSP8 and IGF2 genes, respectively. One SNP (rs313443014 C>T) in DUSP8 gene and two SNPs (rs315806609A/G and rs313810945T/C) in IGF2 gene were used for genotyping by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and KASP methods, respectively. The Two-way analysis of variance of the R program was used to associate DUSP8 and IGF2 genotypes with nucleotide contents in KNC-R chickens. RESULTS The DUSP8 (rs313443014 C>T) was polymorphic in KNC-R line and showed three genotypes: CC, CT, and TT. The IGF2 gene (rs315806609A/G and rs313810945T/C) was also polymorphic and had three genotypes per SNP, including GG, AG, and AA for the SNP rs315806609A/G and genotypes: CC, CT, and TT for the SNP rs313810945T/C. Association resulted into a strong significant association (p<0.01) with IMP, inosine, and hypoxanthine. Moreover, the significant effect of sex (p<0.05) on nucleotide content was also observed. CONCLUSION The SNPs in the DUSP8 and IGF2 genes might be used as genetic markers in the selection and production of chickens with highly flavored meat.
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Affiliation(s)
- Jean Pierre Munyaneza
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134,
Korea
| | - Minjun Kim
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134,
Korea
| | - Eunjin Cho
- Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134,
Korea
| | - Aera Jang
- Department of Applied Animal Science, College of Animal Life Science, Kangwon National University, Chuncheon 24341,
Korea
| | - Hyo Jun Choo
- Poultry Research Institute, National Institute of Animal Science, Pyeongchang 25342,
Korea
| | - Jun Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134,
Korea
- Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134,
Korea
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Kong Y, Liu C, Zhang X, Liu X, Li W, Li F, Wang X, Yue X. Characterization of fatty acid compositions in longissimus thoracis muscle and identification of candidate gene and SNPs related to polyunsaturated fatty acid in Hu sheep. J Anim Sci 2023; 101:skac382. [PMID: 36394948 PMCID: PMC9833039 DOI: 10.1093/jas/skac382] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022] Open
Abstract
Fatty acid (FA) composition contributes greatly to the quality and nutritional value of lamb meat. In the present study, FA was measured in longissimus thoracis (LT) muscles of 1,085 Hu sheep using gas chromatography. Comparative transcriptomic analysis was conducted in LT muscles to identify differentially expressed genes (DEGs) between six individuals with high polyunsaturated fatty acids (H-PUFA, 15.27% ± 0.42%) and six with low PUFA (L-PUFA, 5.22% ± 0.25%). Subsequently, the single nucleotide polymorphisms (SNPs) in a candidate gene PLIN2 were correlated with FA traits. The results showed a total of 29 FA compositions and 8 FA groups were identified, with the highest content of monounsaturated fatty acids (MUFA, 46.54%, mainly C18:1n9c), followed by saturated fatty acids (SFA, 44.32%, mainly C16:0), and PUFA (8.72%, mainly C18:2n6c), and significant correlations were observed among the most of FA traits. Transcriptomic analyses identified 110 upregulated and 302 downregulated DEGs between H-PUFA and L-PUFA groups. The functional enrichment analysis revealed three significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and 17 gene ontology (GO) terms, in which regulation of lipolysis in adipocytes, the AMPK signaling pathway, and the PPAR signaling pathway may play important roles in FA metabolism and biosynthesis. In addition, weighted gene co-expression network analysis (WGCNA) identified 37 module genes associated with PUFA-related traits. In general, PLIN1, LIPE, FABP4, LEP, ACACA, ADIPOQ, SCD, PCK2, FASN, PLIN2, LPL, FABP3, THRSP, and ACADVL may have a great impact on PUFA metabolism and lipid deposition. Four SNPs within PLIN2 were significantly associated with FA. Of those, SNP1 (g.287 G>A) was significantly associated with C18:1n9c and MUFA, and SNP4 (g.7807 T>C) was significantly correlated with PUFA (C18:3n3). In addition, the combined genotype of SNP1 (g.287 G>A), SNP3 (g.7664 T>C), and SNP4 (g.7807 T>C) were significantly correlated with C16:1, C17:0, C18:1C6, PUFA (C18:3n3, C22:6n3), and n-6/n-3 PUFA. These results contribute to the knowledge of the biological mechanisms and genetic markers involved in the composition of FA in Hu sheep.
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Affiliation(s)
- Yuanyuan Kong
- State Key Laboratory of Herbage Improvement and 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; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Chongyang Liu
- State Key Laboratory of Herbage Improvement and 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; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Xueying Zhang
- State Key Laboratory of Herbage Improvement and 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; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Xing Liu
- State Key Laboratory of Herbage Improvement and 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; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Wenqiao Li
- State Key Laboratory of Herbage Improvement and 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; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Fadi Li
- State Key Laboratory of Herbage Improvement and 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; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Xinji Wang
- Extension Station of Animal Husbandry and Veterinary Medicine in Minqin, Minqin County 733300, China
| | - Xiangpeng Yue
- State Key Laboratory of Herbage Improvement and 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; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
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Ahn J, Lee J, Kim DH, Hwang IS, Park MR, Cho IC, Hwang S, Lee K. Loss of Monoallelic Expression of IGF2 in the Adult Liver Via Alternative Promoter Usage and Chromatin Reorganization. Front Genet 2022; 13:920641. [PMID: 35938007 PMCID: PMC9355166 DOI: 10.3389/fgene.2022.920641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
In mammals, genomic imprinting operates via gene silencing mechanisms. Although conservation of the imprinting mechanism at the H19/IGF2 locus has been generally described in pigs, tissue-specific imprinting at the transcript level, monoallelic-to-biallelic conversion, and spatio-temporal chromatin reorganization remain largely uninvestigated. Here, we delineate spatially regulated imprinting of IGF2 transcripts, age-dependent hepatic mono- to biallelic conversion, and reorganization of topologically associating domains at the porcine H19/IGF2 locus for better translation to human and animal research. Whole-genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) of normal and parthenogenetic porcine embryos revealed the paternally hypermethylated H19 differentially methylated region and paternal expression of IGF2. Using a polymorphism-based approach and omics datasets from chromatin immunoprecipitation sequencing (ChIP–seq), whole-genome sequencing (WGS), RNA-seq, and Hi-C, regulation of IGF2 during development was analyzed. Regulatory elements in the liver were distinguished from those in the muscle where the porcine IGF2 transcript was monoallelically expressed. The IGF2 transcript from the liver was biallelically expressed at later developmental stages in both pigs and humans. Chromatin interaction was less frequent in the adult liver compared to the fetal liver and skeletal muscle. The duration of genomic imprinting effects within the H19/IGF2 locus might be reduced in the liver with biallelic conversion through alternative promoter usage and chromatin remodeling. Our integrative omics analyses of genome, epigenome, and transcriptome provided a comprehensive view of imprinting status at the H19/IGF2 cluster.
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Affiliation(s)
- Jinsoo Ahn
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH, United States
| | - Joonbum Lee
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH, United States
- The Ohio State University Interdisciplinary Human Nutrition Program, The Ohio State University, Columbus, OH, United States
| | - Dong-Hwan Kim
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH, United States
| | - In-Sul Hwang
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Jeonbuk, South Korea
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, Columbia University, New York, NY, United States
| | - Mi-Ryung Park
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Jeonbuk, South Korea
| | - In-Cheol Cho
- National Institute of Animal Science, Rural Development Administration, Jeju, South Korea
| | - Seongsoo Hwang
- Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Jeonbuk, South Korea
| | - Kichoon Lee
- Functional Genomics Laboratory, Department of Animal Sciences, The Ohio State University, Columbus, OH, United States
- The Ohio State University Interdisciplinary Human Nutrition Program, The Ohio State University, Columbus, OH, United States
- *Correspondence: Kichoon Lee,
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Ren Q, Li H, Xu F, Zhu Y, Zhang X, Fan T, Wei Z, Yuan F, Han F, Cong R. Effect of high-concentrate diets on mRNA expression of genes related to muscle fiber type and metabolism of psoas major muscle in goats. Anim Sci J 2022; 93:e13725. [PMID: 35508764 DOI: 10.1111/asj.13725] [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: 06/10/2021] [Revised: 03/14/2022] [Accepted: 04/01/2022] [Indexed: 11/27/2022]
Abstract
In the process of modern breeding, high-concentrate diets are widely used to meet the high energy nutritional requirements of animals but change the form of access to energy and nutrients and the way the organism metabolizes them. Goat psoas major (PM) muscle is a hybrid skeletal muscle whose characteristics are important for the motility and meat quality of goats. However, there are few studies on the effects of high-concentrate diets on the muscle type and metabolic characteristics of PM in goats. In this study, two treatment groups were set up: high concentrate group (HC) and control group (C). The expression of genes related to muscle type and metabolism of the PM was examined by quantitative PCR. The results showed that high concentrate promoted the conversion of PM fibers from intermediate to slow type at the mRNA level, improved the absorption, transport, and oxidation of fat by PM, and upregulated the expression of calpain system. These changes may be regulated by the involvement of differential expression of MSTN, Myf-5, and IGF-2. These results suggest that high concentrate may exert a positive effect on skeletal muscle function, metabolism, and meat quality in goats by affecting the expression of muscle type and metabolism-related genes.
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Affiliation(s)
- Qijun Ren
- Northwest A&F University, Xianyang, China
| | - Hanmei Li
- Northwest A&F University, Xianyang, China
| | | | - Yihan Zhu
- Northwest A&F University, Xianyang, China
| | | | | | | | | | - Fei Han
- Yangling Vocational & Technical College, Xianyang, China
| | - Rihua Cong
- Northwest A&F University, Xianyang, China
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Gozalo-Marcilla M, Buntjer J, Johnsson M, Batista L, Diez F, Werner CR, Chen CY, Gorjanc G, Mellanby RJ, Hickey JM, Ros-Freixedes R. Genetic architecture and major genes for backfat thickness in pig lines of diverse genetic backgrounds. Genet Sel Evol 2021; 53:76. [PMID: 34551713 PMCID: PMC8459476 DOI: 10.1186/s12711-021-00671-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 09/07/2021] [Indexed: 01/23/2023] Open
Abstract
Background Backfat thickness is an important carcass composition trait for pork production and is commonly included in swine breeding programmes. In this paper, we report the results of a large genome-wide association study for backfat thickness using data from eight lines of diverse genetic backgrounds. Methods Data comprised 275,590 pigs from eight lines with diverse genetic backgrounds (breeds included Large White, Landrace, Pietrain, Hampshire, Duroc, and synthetic lines) genotyped and imputed for 71,324 single-nucleotide polymorphisms (SNPs). For each line, we estimated SNP associations using a univariate linear mixed model that accounted for genomic relationships. SNPs with significant associations were identified using a threshold of p < 10–6 and used to define genomic regions of interest. The proportion of genetic variance explained by a genomic region was estimated using a ridge regression model. Results We found significant associations with backfat thickness for 264 SNPs across 27 genomic regions. Six genomic regions were detected in three or more lines. The average estimate of the SNP-based heritability was 0.48, with estimates by line ranging from 0.30 to 0.58. The genomic regions jointly explained from 3.2 to 19.5% of the additive genetic variance of backfat thickness within a line. Individual genomic regions explained up to 8.0% of the additive genetic variance of backfat thickness within a line. Some of these 27 genomic regions also explained up to 1.6% of the additive genetic variance in lines for which the genomic region was not statistically significant. We identified 64 candidate genes with annotated functions that can be related to fat metabolism, including well-studied genes such as MC4R, IGF2, and LEPR, and more novel candidate genes such as DHCR7, FGF23, MEDAG, DGKI, and PTN. Conclusions Our results confirm the polygenic architecture of backfat thickness and the role of genes involved in energy homeostasis, adipogenesis, fatty acid metabolism, and insulin signalling pathways for fat deposition in pigs. The results also suggest that several less well-understood metabolic pathways contribute to backfat development, such as those of phosphate, calcium, and vitamin D homeostasis. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00671-w.
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Affiliation(s)
- Miguel Gozalo-Marcilla
- The Roslin Institute, The University of Edinburgh, Midlothian, UK.,The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Jaap Buntjer
- The Roslin Institute, The University of Edinburgh, Midlothian, UK
| | - Martin Johnsson
- The Roslin Institute, The University of Edinburgh, Midlothian, UK.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Lorena Batista
- The Roslin Institute, The University of Edinburgh, Midlothian, UK
| | - Federico Diez
- The Roslin Institute, The University of Edinburgh, Midlothian, UK.,The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | | | - Ching-Yi Chen
- The Pig Improvement Company, Genus plc, Hendersonville, TN, USA
| | - Gregor Gorjanc
- The Roslin Institute, The University of Edinburgh, Midlothian, UK
| | - Richard J Mellanby
- The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - John M Hickey
- The Roslin Institute, The University of Edinburgh, Midlothian, UK
| | - Roger Ros-Freixedes
- The Roslin Institute, The University of Edinburgh, Midlothian, UK. .,Departament de Ciència Animal, Universitat de Lleida - Agrotecnio-CERCA Center, Lleida, Spain.
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10
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Criado-Mesas L, Ballester M, Crespo-Piazuelo D, Castelló A, Fernández AI, Folch JM. Identification of eQTLs associated with lipid metabolism in Longissimus dorsi muscle of pigs with different genetic backgrounds. Sci Rep 2020; 10:9845. [PMID: 32555447 PMCID: PMC7300017 DOI: 10.1038/s41598-020-67015-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 05/29/2020] [Indexed: 12/14/2022] Open
Abstract
Intramuscular fat content and its fatty acid composition affect porcine meat quality and its nutritional value. The present work aimed to identify genomic variants regulating the expression in the porcine muscle (Longissimus dorsi) of 45 candidate genes for lipid metabolism and fatty acid composition in three experimental backcrosses based on the Iberian breed. Expression genome-wide association studies (eGWAS) were performed between the muscle gene expression values, measured by real-time quantitative PCR, and the genotypes of 38,426 SNPs distributed along all chromosomes. The eGWAS identified 186 eSNPs located in ten Sus scrofa regions and associated with the expression of ACSM5, ACSS2, ATF3, DGAT2, FOS and IGF2 (FDR < 0.05) genes. Two expression quantitative trait loci (eQTLs) for IGF2 and ACSM5 were classified as cis-acting eQTLs, suggesting a mutation in the same gene affecting its expression. Conversely, ten eQTLs showed trans-regulatory effects on gene expression. When the eGWAS was performed for each backcross independently, only three common trans-eQTL regions were observed, indicating different regulatory mechanisms or allelic frequencies among the breeds. In addition, hotspot regions regulating the expression of several genes were detected. Our results provide new data to better understand the functional regulatory mechanisms of lipid metabolism genes in muscle.
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Affiliation(s)
- Lourdes Criado-Mesas
- Departament de Genòmica Animal, Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain.
| | - Maria Ballester
- Departament de Genètica i Millora Animal, Institut de Recerca y Tecnologia Agraroalimentàries (IRTA), Caldes de Montbui, Spain
| | - Daniel Crespo-Piazuelo
- Departament de Genòmica Animal, Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, UAB, Bellaterra, Spain
| | - Anna Castelló
- Departament de Genòmica Animal, Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, UAB, Bellaterra, Spain
| | - Ana I Fernández
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Josep M Folch
- Departament de Genòmica Animal, Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, UAB, Bellaterra, Spain
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11
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Albuquerque A, Óvilo C, Núñez Y, Benítez R, López-Garcia A, García F, Félix MDR, Laranjo M, Charneca R, Martins JM. Comparative Transcriptomic Analysis of Subcutaneous Adipose Tissue from Local Pig Breeds. Genes (Basel) 2020; 11:E422. [PMID: 32326415 PMCID: PMC7231169 DOI: 10.3390/genes11040422] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/07/2020] [Accepted: 04/11/2020] [Indexed: 12/12/2022] Open
Abstract
When compared to modern lean-type breeds, Portuguese local Alentejano (AL) and Bísaro (BI) pig breeds present a high potential for subcutaneous and intramuscular fat (IMF) deposition which contributes for better meat quality. The aim of this work was to explore the genome function to better understand the underlying physiological mechanisms associated with body fat accretion. Dorsal subcutaneous fat samples were collected at slaughter from adult animals (n = 4 for each breed) with ~150 kg body weight. Total RNA was obtained and sequenced for transcriptome analysis using DESeq2. A total of 458 differentially expressed (DE) genes (q-value < 0.05) were identified, with 263 overexpressed in AL and 195 in BI. Key genes involved in de novo fatty acid biosynthesis, elongation and desaturation were upregulated in AL such as ACLY, FASN, ME1, ELOVL6 and SCD. A functional enrichment analysis of the DE genes was performed using Ingenuity Pathway Analysis. Cholesterol synthesis is suggested to be higher in AL via SREBF2, SCAP and PPARG, while lipolytic activity may be more active in BI through GH and AMPK signalling. Increased signalling of CD40 together with the predicted activation of INSIG1 and INSIG2 in BI suggests that this breed is more sensitive to insulin whereas the AL is less sensitive like the Iberian breed.
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Affiliation(s)
- André Albuquerque
- MED-Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada & Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal;
| | - Cristina Óvilo
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain; (C.Ó.); (Y.N.); (R.B.); (A.L.-G.); (F.G.)
| | - Yolanda Núñez
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain; (C.Ó.); (Y.N.); (R.B.); (A.L.-G.); (F.G.)
| | - Rita Benítez
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain; (C.Ó.); (Y.N.); (R.B.); (A.L.-G.); (F.G.)
| | - Adrián López-Garcia
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain; (C.Ó.); (Y.N.); (R.B.); (A.L.-G.); (F.G.)
| | - Fabián García
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain; (C.Ó.); (Y.N.); (R.B.); (A.L.-G.); (F.G.)
| | - Maria do Rosário Félix
- MED & Departamento de Fitotecnia, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal;
| | - Marta Laranjo
- MED-Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada & Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal;
| | - Rui Charneca
- MED & Departamento de Medicina Veterinária, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal;
| | - José Manuel Martins
- MED & Departamento de Zootecnia, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
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