1
|
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.
Collapse
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
| |
Collapse
|
2
|
Zhao P, Gu L, Gao Y, Pan Z, Liu L, Li X, Zhou H, Yu D, Han X, Qian L, Liu GE, Fang L, Wang Z. Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits. Commun Biol 2023; 6:894. [PMID: 37652983 PMCID: PMC10471783 DOI: 10.1038/s42003-023-05234-x] [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: 03/02/2022] [Accepted: 08/09/2023] [Indexed: 09/02/2023] Open
Abstract
Transposable elements (TEs) are a major source of genetic polymorphisms and play a role in chromatin architecture, gene regulatory networks, and genomic evolution. However, their functional role in pigs and contributions to complex traits are largely unknown. We created a catalog of TEs (n = 3,087,929) in pigs and found that young SINEs were predominantly silenced by histone modifications, DNA methylation, and decreased accessibility. However, some transcripts from active young SINEs showed high tissue-specificity, as confirmed by analyzing 3570 RNA-seq samples. We also detected 211,067 dimorphic SINEs in 374 individuals, including 340 population-specific ones associated with local adaptation. Mapping these dimorphic SINEs to genome-wide associations of 97 complex traits in pigs, we found 54 candidate genes (e.g., ANK2 and VRTN) that might be mediated by TEs. Our findings highlight the important roles of young SINEs and provide a supplement for genotype-to-phenotype associations and modern breeding in pigs.
Collapse
Affiliation(s)
- Pengju Zhao
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lihong Gu
- Institute of Animal Science & Veterinary Medicine, Hainan Academy of Agricultural Sciences, No. 14 Xingdan Road, Haikou, 571100, China
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Zhangyuan Pan
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Lei Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Xingzheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Dongyou Yu
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xinyan Han
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lichun Qian
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, Denmark.
| | - Zhengguang Wang
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China.
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| |
Collapse
|
3
|
Lipo-nutritional quality of pork: the lipid composition, regulation, and molecular mechanisms of fatty acid deposition. ANIMAL NUTRITION 2023; 13:373-385. [DOI: 10.1016/j.aninu.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 12/13/2022] [Accepted: 03/01/2023] [Indexed: 03/09/2023]
|
4
|
Zhang XY, Yuan ZH, Li FD, Yue XP. Integrating transcriptome and metabolome to identify key genes regulating important muscular flavour precursors in sheep. Animal 2022; 16:100679. [PMID: 36481351 DOI: 10.1016/j.animal.2022.100679] [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: 02/23/2022] [Revised: 10/28/2022] [Accepted: 11/04/2022] [Indexed: 11/13/2022] Open
Abstract
Flavour precursors are the basis of meat flavour, and their metabolism is regulated by a variety of enzymes. Thus, it is of great significance to identify the key genes related to meat flavour precursors. In this study, the difference in flavour precursors and transcriptome between Hu sheep and Dorper with different intramuscular fat (IMF) content were investigated using widely targeted metabolomics and RNA-sequencing technologies. Then, the key genes regulating the metabolism of vital precursors were explored by integrating transcriptome and metabolome. Consequently, 594 metabolites were detected in sheep longissimus dorsi, and 76 differentially abundant metabolites (DAMs) were identified between Hu sheep and Dorper. No DAMs were observed between distinct IMF content groups within each breed. A total of 10 lysophospholipids (LPs), including four lysophospholipid ethanolamines and six lysophospholipid cholines, were identified as the main differential precursors between Hu sheep and Dorper. Furthermore, the weighted gene coexpression network analysis uncovered three differentially coexpression modules that were significantly associated with the content of differential LPs in Dorper. From the three modules, GLB1, PLD3, LPCAT2, DGKE, ACOT7, and CH25H genes were identified as key genes regulating the metabolism of LPs. This work provides an insight into understanding the difference in flavour between different sheep breeds, as well as a basis for further exploring the regulatory mechanism of key genes on LPs.
Collapse
Affiliation(s)
- X Y 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, PR China
| | - Z H Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou 225000, PR China
| | - F D 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, PR China
| | - X P 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, PR China.
| |
Collapse
|
5
|
Chemical Characteristics of Croatian Traditional Istarski pršut (PDO) Produced from Two Different Pig Genotypes. Molecules 2021; 26:molecules26144140. [PMID: 34299415 PMCID: PMC8303308 DOI: 10.3390/molecules26144140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 11/26/2022] Open
Abstract
Chemical characteristics of raw and processed Istarski pršut (PDO) produced from two different pig genotypes were studied with special emphasis on amino and fatty acid composition and factors of lipid stability. Raw hams of Large White (LW)xLandrace (L), and (LWxL)xDuroc (D) pig genotypes were used in the study (20 hams of each genotype). All left raw hams from each carcass were processed in accordance with the PDO specification of Istarski pršut, and other half (the right ones) of LWxL)xD genotype were used for analyses of raw hams (fresh muscles). Istarski pršut was evaluated on the basis of the chemical parameters of the raw and matured lean ham. The process of dry curing significantly influenced the chemical properties of Istarski pršut. Despite the higher content of intramuscular fat and polyunsaturated fatty acids, the fat of (LWxL)xD ham was much more resistant to hydrolysis and oxidation, suggesting that fatty acid profile and other factors, also play a significant role. Significant differences between pig genotypes in the amino acid and fatty acid profiles were found. The analyzed Istarski pršut may be distinguished by prints of multivariate chemometric statistical analysis, based on their amino acid and fatty acid compositions.
Collapse
|
6
|
Enhancing the Nutritional Value of Red Meat through Genetic and Feeding Strategies. Foods 2021; 10:foods10040872. [PMID: 33923499 PMCID: PMC8073878 DOI: 10.3390/foods10040872] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 12/20/2022] Open
Abstract
Consumption of red meat contributes to the intake of many essential nutrients in the human diet including protein, essential fatty acids, and several vitamins and trace minerals, with high iron content, particularly in meats with high myoglobin content. Demand for red meat continues to increase worldwide, particularly in developing countries where food nutrient density is a concern. Dietary and genetic manipulation of livestock can influence the nutritional value of meat products, providing opportunities to enhance the nutritional value of meat. Studies have demonstrated that changes in livestock nutrition and breeding strategies can alter the nutritional value of red meat. Traditional breeding strategies, such as genetic selection, have influenced multiple carcass and meat quality attributes relevant to the nutritional value of meat including muscle and fat deposition. However, limited studies have combined both genetic and nutritional approaches. Future studies aiming to manipulate the composition of fresh meat should aim to balance potential impacts on product quality and consumer perception. Furthermore, the rapidly emerging fields of phenomics, nutrigenomics, and integrative approaches, such as livestock precision farming and systems biology, may help better understand the opportunities to improve the nutritional value of meat under both experimental and commercial conditions.
Collapse
|
7
|
Zhang Z, Zhang Z, Oyelami FO, Sun H, Xu Z, Ma P, Wang Q, Pan Y. Identification of genes related to intramuscular fat independent of backfat thickness in Duroc pigs using single-step genome-wide association. Anim Genet 2020; 52:108-113. [PMID: 33073401 DOI: 10.1111/age.13012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/29/2020] [Accepted: 09/19/2020] [Indexed: 12/11/2022]
Abstract
Intramuscular fat (IMF) is an important meat-quality trait of pigs, which influences pork's shearing force, hydraulics, tenderness and juicy flavor. However, to achieve a higher percentage of lean meat, pigs with lower backfat thickness (BF) are intensively selected for, which may lead to a reduction in pork quality. Therefore, the objective of this study was to locate loci that affect IMF without changing BF. A single-step GWAS was performed on 950 Duroc pigs genotyped by a 50K SNP chip in order to detect genomic variants relevant to IMF and BF. The significant SNPs detected were afterwards divided into a BF subset (seven SNPs), an IMF subset (11 SNPs) and a subset of both traits (12 SNPs), according to their P-value and LD. After SNP and QTL annotation, our results indicated that SSC1: 167938652, 166363826, 164829874 and 167171587 might be associated with IMF without changing BF. In the subset of both traits, we found that the combined effect of ALGA0006602 (SSC1: 159538854) and 12784636 (SSC1: 160773437) might improve the IMF without changing BF. Our gene annotation result showed that TLE3, ITGA11, SMAD6, PAQR5 and [RNF152A/G × MC4RA/A ] genes might affect IMF independently of BF. We believe that the SNPs and genes identified in this study will be valuable for the future molecular breeding of IMF in Duroc pigs.
Collapse
Affiliation(s)
- Z Zhang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800# Dongchuan Road, Shanghai, East, 200240, China
| | - Z Zhang
- Department of Animal Science, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou, East, 310058, China
| | - F O Oyelami
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800# Dongchuan Road, Shanghai, East, 200240, China
| | - H Sun
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800# Dongchuan Road, Shanghai, East, 200240, China
| | - Z Xu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800# Dongchuan Road, Shanghai, East, 200240, China
| | - P Ma
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800# Dongchuan Road, Shanghai, East, 200240, China
| | - Q Wang
- Department of Animal Science, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou, East, 310058, China
| | - Y Pan
- Department of Animal Science, College of Animal Science, Zhejiang University, 866# Yuhangtang Road, Hangzhou, East, 310058, China
| |
Collapse
|
8
|
Identification of strong candidate genes for backfat and intramuscular fatty acid composition in three crosses based on the Iberian pig. Sci Rep 2020; 10:13962. [PMID: 32811870 PMCID: PMC7435270 DOI: 10.1038/s41598-020-70894-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 08/02/2020] [Indexed: 12/11/2022] Open
Abstract
Meat quality has an important genetic component and can be modified by the fatty acid (FA) composition and the amount of fat contained in adipose tissue and muscle. The present study aimed to find genomic regions associated with the FA composition in backfat and muscle (longissimus dorsi) in 439 pigs with three different genetic backgrounds but having the Iberian breed in common. Genome-wide association studies (GWAS) were performed between 38,424 single-nucleotide polymorphisms (SNPs) covering the pig genome and 60 phenotypic traits related to backfat and muscle FA composition. Nine significant associated regions were found in backfat on the Sus scrofa chromosomes (SSC): SSC1, SSC2, SSC4, SSC6, SSC8, SSC10, SSC12, and SSC16. For the intramuscular fat, six significant associated regions were identified on SSC4, SSC13, SSC14, and SSC17. A total of 52 candidate genes were proposed to explain the variation in backfat and muscle FA composition traits. GWAS were also reanalysed including SNPs on five candidate genes (ELOVL6, ELOVL7, FADS2, FASN, and SCD). Regions and molecular markers described in our study may be useful for meat quality selection of commercial pig breeds, although several polymorphisms were breed-specific, and further analysis would be needed to evaluate possible causal mutations.
Collapse
|