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Lai X, Zhang Z, Zhang Z, Liu S, Bai C, Chen Z, Qadri QR, Fang Y, Wang Z, Pan Y, Wang Q. Integrated microbiome-metabolome-genome axis data of Laiwu and Lulai pigs. Sci Data 2023; 10:280. [PMID: 37179393 PMCID: PMC10183000 DOI: 10.1038/s41597-023-02191-2] [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: 09/13/2022] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Excessive fat deposition can trigger metabolic diseases, and it is crucial to identify factors that can break the link between fat deposition and metabolic diseases. Healthy obese Laiwu pigs (LW) are high in fat content but resistant to metabolic diseases. In this study, we compared the fecal microbiome, fecal and blood metabolome, and genome of LW and Lulai pigs (LU) to identify factors that can block the link between fat deposition and metabolic diseases. Our results show significant differences in Spirochetes and Treponema, which are involved in carbohydrate metabolism, between LW and LU. The fecal and blood metabolome composition was similar, and some anti-metabolic disease components of blood metabolites were different between the two breeds of pigs. The predicted differential RNA is mainly enriched in lipid metabolism and glucose metabolism, which is consistent with the functions of differential microbiota and metabolites. The down-regulated gene RGP1 is strongly negatively correlated with Treponema. Our omics data would provide valuable resources for further scientific research on healthy obesity in both human and porcine.
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Affiliation(s)
- Xueshuang Lai
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310030, PR China
| | - Zhenyang Zhang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310030, PR China
| | - Zhe Zhang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310030, PR China
| | - Shengqiang Liu
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310030, PR China
- Hainan institute, Zhejiang University, Sanya, 310014, PR China
| | - Chunyan Bai
- Department of Animal Science, College of Animal Sciences, Jilin University, Changchui, 130015, PR China
| | - Zitao Chen
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310030, PR China
| | - Qamar Raza Qadri
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Yifei Fang
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310030, PR China
| | - Zhen Wang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310030, PR China
| | - Yuchun Pan
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310030, PR China.
- Hainan institute, Zhejiang University, Sanya, 310014, PR China.
| | - Qishan Wang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310030, PR China.
- Hainan institute, Zhejiang University, Sanya, 310014, PR China.
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Chen J, You R, Lv Y, Liu H, Yang G. Conjugated linoleic acid regulates adipocyte fatty acid binding protein expression via peroxisome proliferator-activated receptor α signaling pathway and increases intramuscular fat content. Front Nutr 2022; 9:1029864. [PMID: 36523338 PMCID: PMC9745092 DOI: 10.3389/fnut.2022.1029864] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/19/2022] [Indexed: 06/22/2024] Open
Abstract
Intramuscular fat (IMF) is correlated positively with meat tenderness, juiciness and taste that affected sensory meat quality. Conjugated linoleic acid (CLA) has been extensively researched to increase IMF content in animals, however, the regulatory mechanism remains unclear. Adipocyte fatty acid binding protein (A-FABP) gene has been proposed as candidates for IMF accretion. The purpose of this study is to explore the molecular regulatory pathways of CLA on intramuscular fat deposition. Here, our results by cell lines indicated that CLA treatment promoted the expression of A-FABP through activated the transcription factor of peroxisome proliferator-activated receptor α (PPARα). Moreover, in an animal model, we discovered that dietary supplemental with CLA significantly enhanced IMF deposition by up-regulating the mRNA and protein expression of PPARα and A-FABP in the muscle tissues of mice. In addition, our current study also demonstrated that dietary CLA increased mRNA expression of genes and enzymes involved in fatty acid synthesis and lipid metabolism the muscle tissues of mice. These findings suggest that CLA mainly increases the expression of A-FABP through PPARα signaling pathway and regulates the expression of genes and enzymes related to IMF deposition, thus increasing IMF content. These results contribute to better understanding the molecular mechanism of IMF accretion in animals for the improvement of meat quality.
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Affiliation(s)
| | | | | | | | - Guoqing Yang
- Laboratory of Animal Gene Engineering, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
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Malgwi IH, Halas V, Grünvald P, Schiavon S, Jócsák I. Genes Related to Fat Metabolism in Pigs and Intramuscular Fat Content of Pork: A Focus on Nutrigenetics and Nutrigenomics. Animals (Basel) 2022; 12:ani12020150. [PMID: 35049772 PMCID: PMC8772548 DOI: 10.3390/ani12020150] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/29/2021] [Accepted: 01/05/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary The intramuscular fat (IMF) or marbling is an essential pork sensory quality that influences the preference of the consumers and premiums for pork. IMF is the streak of visible fat intermixed with the lean within a muscle fibre and determines sensorial qualities of pork such as flavour, tenderness and juiciness. Fat metabolism and IMF development are controlled by dietary nutrients, genes, and their metabolic pathways in the pig. Nutrigenetics explains how the genetic make-up of an individual pig influences the pig’s response to dietary nutrient intake. Differently, nutrigenomics is the analysis of how the entire genome of an individual pig is affected by dietary nutrient intake. The knowledge of nutrigenetics and nutrigenomics, when harmonized, is a powerful tool in estimating nutrient requirements for swine and programming dietary nutrient supply according to an individual pig’s genetic make-up. The current paper aimed to highlight the roles of nutrigenetics and nutrigenomics in elucidating the underlying mechanisms of fat metabolism and IMF deposition in pigs. This knowledge is essential in redefining nutritional intervention for swine production and the improvement of some economically important traits such as growth performance, backfat thickness, IMF accretion, disease resistance etc., in animals. Abstract Fat metabolism and intramuscular fat (IMF) are qualitative traits in pigs whose development are influenced by several genes and metabolic pathways. Nutrigenetics and nutrigenomics offer prospects in estimating nutrients required by a pig. Application of these emerging fields in nutritional science provides an opportunity for matching nutrients based on the genetic make-up of the pig for trait improvements. Today, integration of high throughput “omics” technologies into nutritional genomic research has revealed many quantitative trait loci (QTLs) and single nucleotide polymorphisms (SNPs) for the mutation(s) of key genes directly or indirectly involved in fat metabolism and IMF deposition in pigs. Nutrient–gene interaction and the underlying molecular mechanisms involved in fatty acid synthesis and marbling in pigs is difficult to unravel. While existing knowledge on QTLs and SNPs of genes related to fat metabolism and IMF development is yet to be harmonized, the scientific explanations behind the nature of the existing correlation between the nutrients, the genes and the environment remain unclear, being inconclusive or lacking precision. This paper aimed to: (1) discuss nutrigenetics, nutrigenomics and epigenetic mechanisms controlling fat metabolism and IMF accretion in pigs; (2) highlight the potentials of these concepts in pig nutritional programming and research.
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Affiliation(s)
- Isaac Hyeladi Malgwi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell’ Università 16, 35020 Padova, Italy;
- Correspondence: ; Tel.: +39-33-17566768
| | - Veronika Halas
- Department of Farm Animal Nutrition, Kaposvár Campus, Hungarian University of Agriculture and Life Sciences, Guba Sándor Utca 40, 7400 Kaposvár, Hungary; (V.H.); (P.G.)
| | - Petra Grünvald
- Department of Farm Animal Nutrition, Kaposvár Campus, Hungarian University of Agriculture and Life Sciences, Guba Sándor Utca 40, 7400 Kaposvár, Hungary; (V.H.); (P.G.)
| | - Stefano Schiavon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell’ Università 16, 35020 Padova, Italy;
| | - Ildikó Jócsák
- Institute of Agronomy, Kaposvár Campus, Hungarian University of Agriculture and Life Sciences, Guba Sándor Utca 40, 7400 Kaposvár, Hungary;
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Zhang P, Fu Y, Zhang R, Shang P, Zhang H, Zhang B. Association of KCTD15 gene with fat deposition in pigs. J Anim Physiol Anim Nutr (Berl) 2021; 106:537-544. [PMID: 34106484 DOI: 10.1111/jpn.13587] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 04/12/2021] [Accepted: 05/11/2021] [Indexed: 12/27/2022]
Abstract
KCTD15 is associated with body mass index and fat deposition in humans, mice and chickens. However, the function of KCTD15 in pig fat deposition remains unclear. In this study, we cloned and analysed the cDNA sequence of porcine KCTD15. The full length of the mRNA sequence of KCTD15 is 4,091 bp, encoding 283 amino acids. The protein is hydrophilic, it has a relative molecular mass of about 31.9 kDa and an isoelectric point of 7.09 with no signal peptide sequence or transmembrane structure. Expression analysis showed that KCTD15 expression level was significantly higher in the tissues of Large White pigs (LW) than in those of Tibetan pigs (TP) and Diannan Small-ear pigs (DN) at 6 months of age, whereas its expression level in embryonic tissues of LW at 60 days was lower than that in tissues of TP and Wujin pigs (WJ). In pig primary adipocytes, the expression level of KCTD15 is high in the early stage of differentiation and gradually decreases in later stages. Additionally, the single-nucleotide polymorphism (SNP) site T-2030C (T/C mutation, located 2,030 bp upstream of the start codon) showed a dominant allele T with high promoter activity in the LW population and a dominant allele C in the TP and WJ populations. Our results indicate that KCTD15 is involved in pig fat deposition and that T-2030C is an important regulatory site for transcriptional activity, affecting fat deposition.
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Affiliation(s)
- Pan Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Yu Fu
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Ran Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Peng Shang
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi, China
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
| | - Bo Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, China
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Tunim S, Phasuk Y, Aggrey SE, Duangjinda M. Gene expression of fatty acid binding protein genes and its relationship with fat deposition of Thai native crossbreed chickens. Anim Biosci 2020; 34:751-758. [PMID: 32299161 PMCID: PMC7961282 DOI: 10.5713/ajas.20.0020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 04/06/2020] [Indexed: 01/16/2023] Open
Abstract
Objective The objectives of this study were to investigate the relationship between the mRNA expression of adipocyte type fatty acid binding protein (A-FABP) and heart type FABP (H-FABP) in Thai native chicken crossbreeds and evaluate the level of exotic inclusion in native chicken that will improve growth while maintaining its relatively low carcass fat. Methods The fat deposition traits and mRNA expression of A-FABP and H-FABP were evaluated at 6, 8, 10, and 12 weeks of age in 4 chicken breeds (n = 8/breed/wk) (100% Chee breed [CH] [100% Thai native chicken background], CH male and broiler female [Kaimook e-san1; KM1] [50% CH background], broiler male and KM1 female [Kaimook e-san2; KM2] [25% CH background], and broiler [BR]) using abdominal fat (ABF) and muscular tissues. Results The BR breed was only evaluated at 6 weeks of age. At week 6, the CH breed had a significantly lower A-FABP expression in ABF and intramuscular fat (IF) compared with the other breeds. At 8 to 12 weeks, the KM2 groups showed significant upregulation (p<0.05) of A-FABP in both ABF and IF compared to the CH and KM1 groups. The expression of H-FABP did not follow any consistent pattern in both ABF and IF across the different ages. Conclusion Some level of crossbreeding CH chickens can be done to improve growth rate while maintaining their low ABF and IF. The expression level of A-FABP correlate with most fat traits. There was no consistency of H-FABP expression across breed. A-FABPs is involved in fat deposition, genetic markers in these genes could be used in marker assisted studies to select against excessive fat accumulation.
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Affiliation(s)
- Supanon Tunim
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Yupin Phasuk
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand.,Research and Development Network Center for Animal Breeding (NCAB), Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Samuel E Aggrey
- NutriGenomics Laboratory, Department of Poultry Science, University of Georgia, Athens, GA 30602, USA
| | - Monchai Duangjinda
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand.,Research and Development Network Center for Animal Breeding (NCAB), Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
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High Altitude Adaptability and Meat Quality in Tibetan Pigs: A Reference for Local Pork Processing and Genetic Improvement. Animals (Basel) 2019; 9:ani9121080. [PMID: 31817035 PMCID: PMC6940921 DOI: 10.3390/ani9121080] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/20/2019] [Accepted: 11/20/2019] [Indexed: 12/11/2022] Open
Abstract
Simple Summary The increase in altitude will bring about a complex change in a series of elements of nature, which will have a profound impact on human production and life. Studying domestic animals in the native environment is an effective way to explore the impact of high altitude on human life, and at the same time is conducive to the development of local animal husbandry. Here, we found that the hypoxic adaptation of Tibetan pigs may be related to higher levels of VEGFA, HIF1 and myoglobin expression. The higher aerobic oxidative capacity of Tibetan pigs is beneficial to improve energy utilization, and the higher UFA content of Tibetan pigs is beneficial to cold resistance. In addition, Tibetan pigs have higher levels of BCAA and Myh2 expression, which serve to relieve muscle fatigue and improve endurance. In addition, it was observed that there are obvious differences in carcass and meat quality traits of different altitudes pigs. Taken together, our findings illustrate the adaptability of Tibetan pigs to high altitude from various perspectives and compare carcass and meat quality traits of three pig breeds. Abstract The carcass and meat quality traits of pig breeds living at three different altitudes (Yorkshire pigs, YP: 500m; Qingyu Pigs, QYP: 1500m; Tibetan pigs, TP: 2500m) were compared. It was observed that there are obvious differences in pig breeds with respect to performance parameters. Specifically, YP had the best carcass traits, showing high slaughter rates and leanest meat. Conversely, QYP had the highest back fat thickness and intramuscular fat (IMF) content. For the high-altitude breed TP, the animals exhibited low L* and high a* values. The genotypes contributing to the observed phenotypes were supported by a PCR analysis. The glycolytic genes expression (HK, PFK, PK) were highest in YP, whereas expression of genes related to adipogenesis (C/EBPα, FABP4, SCD1) were highest in QYP. As expected, genes associated with angiogenesis and hypoxia (HIF1a, VEGFA) were expressed at the highest levels in TP. The composition and proportion of amino and fatty acids in pig muscles at the three altitudes examined also varied substantially. Among the breeds, TP had the highest proportion of umami amino acids, whereas QYP had the highest proportion of sweet amino acids. However, TP also exhibited the highest proportion of essential fatty acids and the lowest proportion of n6:n3. This study explains the high-altitude adaptive evolution and the formation of meat quality differences in different altitude pigs from various angles and provides a reference for local pork food processing and genetic improvement of local pigs.
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Raza SHA, Khan R, Abdelnour SA, Abd El-Hack ME, Khafaga AF, Taha A, Ohran H, Mei C, Schreurs NM, Zan L. Advances of Molecular Markers and Their Application for Body Variables and Carcass Traits in Qinchuan Cattle. Genes (Basel) 2019; 10:E717. [PMID: 31533236 PMCID: PMC6771018 DOI: 10.3390/genes10090717] [Citation(s) in RCA: 25] [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: 08/07/2019] [Revised: 09/05/2019] [Accepted: 09/10/2019] [Indexed: 12/27/2022] Open
Abstract
This review considers the unique characteristics of Chinese cattle and intramuscular fat content (IMF) as factors influencing meat quality, including tenderness, flavor, and juiciness of meat. Due to its nutritional qualities, meat contributes to a healthy and balanced diet. The intramuscular fat content and eating quality of beef are influenced by many factors, which can generally be divided into on-farm and pre-slaughter factors (breed, sex of cattle, age at slaughter, housing system, diet, and pre-slaughter handling) and postmortem factors (post-slaughter processing, chilling temperature, and packaging). Meat quality traits can also be influenced by the individual genetic background of the animal. Worldwide, the function of genes and genetic polymorphisms that have potential effects on fattening of cattle and beef quality have been investigated. The use of DNA markers is recognized as a powerful and efficient approach to achieve genetic gain for desirable phenotypic characteristics, which is helpful for economic growth. The polymorphisms of the SIRT4, SIRT6, SIRT7, CRTC3, ABHD5, KLF6, H-FABP, and ELOVL6 genes for body and growth characteristics of cattle, and also for beef quality, are considered with the aim of highlighting the significance of beef intramuscular fat content, and that growth, body, and meat quality characteristics are polygenically regulated.
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Affiliation(s)
| | - Rajwali Khan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Sameh A Abdelnour
- Department of Animal Production, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt.
| | - Mohamed E Abd El-Hack
- Department of Poultry, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt.
| | - Asmaa F Khafaga
- Department of Pathology, Faculty of Veterinary Medicine, Alexandria University, Edfina 22758, Egypt.
| | - Ayman Taha
- Department of Animal Husbandry and Animal Wealth Development, Faculty of Veterinary Medicine, Alexandria University, Edfina 22578, Egypt.
| | - Husein Ohran
- Department of Physiology, University of Sarajevo, Veterinary Faculty, Zmaja od Bosne Sarajevo 9071000, Bosnia and Herzegovina.
| | - Chugang Mei
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Nicola M Schreurs
- Animal Science, School of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand.
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
- National Beef Cattle Improvement Center, Northwest A&F University, Yangling 712100, China.
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Wang H, Wang J, Yang DD, Liu ZL, Zeng YQ, Chen W. Expression of lipid metabolism genes provides new insights into intramuscular fat deposition in Laiwu pigs. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 33:390-397. [PMID: 31480195 PMCID: PMC7054625 DOI: 10.5713/ajas.18.0225] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/11/2019] [Indexed: 11/27/2022]
Abstract
Objective The objective of this study was to measure the special expression pattern of lipid metabolism genes and investigate the molecular mechanisms underlying intramuscular fat (IMF) deposition in Longissimus dorsi muscle of Laiwu pigs. Methods Thirty-six pigs (Laiwu n = 18; Duroc×Landrace×Yorkshire n = 18) were used for the measurement of the backfat thickness, marbling score, IMF content, and expression of lipid metabolism genes. Results Significant correlations were found between IMF content and the mRNA expression of lipid metabolism genes. Of the 14 fat deposition genes measured, fatty acid synthase (FASN) showed the strongest correlation (r = 0.75, p = 0.001) with IMF content, and of the 6 fat removal genes, carnitine palmitoyl transferase 1B (CPT1B) exhibited the greatest negative correlation (r = −0.66, p = 0.003) with IMF content in Laiwu pig. Multiple regression analysis showed that CPT1B, FASN, solute carrier family 27 member 1 (SLC27A1), and fatty acid binding protein 3 (FABP3) contributed 38% of the prediction value for IMF content in Laiwu pigs. Of these four variables, CPT1B had the greatest contribution to IMF content (14%) followed by FASN (11%), SLC27A1 (9%), and FABP3 (4%). Conclusion Our results indicate that the combined effects of an upregulation in fat deposition genes and downregulation in fat removal genes promotes IMF deposition in Laiwu pigs.
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Affiliation(s)
- Hui Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong 271000, China
| | - Jin Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong 271000, China
| | - Dan-Dan Yang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong 271000, China
| | - Zong-Li Liu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong 271000, China
| | - Yong-Qing Zeng
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong 271000, China
| | - Wei Chen
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong 271000, China
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Expression and single-nucleotide polymorphisms of the H-FABP gene in pigs. Gene 2019; 710:156-160. [PMID: 31173805 DOI: 10.1016/j.gene.2019.05.061] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 05/21/2019] [Accepted: 05/31/2019] [Indexed: 12/20/2022]
Abstract
Heart fatty acid-binding protein (H-FABP) belongs to a family of intracellular fatty acid-binding proteins that are involved in the transport of long-chain fatty acids. Previous studies have indicated that H-FABP is significantly associated with intramuscular fat (IMF) content in pig. In this study, we compared the mRNA and protein expression of H-FABP between Tibetan pig (with high IMF) and Large White pig (with low IMF). The expression of H-FABP at both mRNA and protein levels in the tissues of backfat, longissimus dorsi muscle and liver was found to be significantly higher in TP than in LW. Single-nucleotide polymorphisms (SNPs) in a 2 kb region upstream of the start codon of the gene were screened using Sanger sequencing. We accordingly identified three SNPs (C-1375G, C-314T and T-158G) between the TP and LW populations and genotyped these based on PCR-restriction fragment length polymorphisms (PCF-RFLPs) analysis. The results showed that the C-1375G site might regulate H-FABP gene expression and thus be associated with fat deposition in pigs. Our study provides important data for further investigating the regulatory mechanism of H-FABP for fat deposition in pigs.
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Wang Y, Ning C, Wang C, Guo J, Wang J, Wu Y. Genome-wide association study for intramuscular fat content in Chinese Lulai black pigs. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018; 32:607-613. [PMID: 30381738 PMCID: PMC6502724 DOI: 10.5713/ajas.18.0483] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/16/2018] [Indexed: 12/31/2022]
Abstract
Objective Intramuscular fat (IMF) content plays an important role in meat quality. Identification of single nucleotide polymorphisms (SNPs) and genes related to pig IMF, especially using pig populations with high IMF content variation, can help to establish novel molecular breeding tools for optimizing IMF in pork and unveil the mechanisms that underlie fat metabolism. Methods We collected muscle samples of 453 Chinese Lulai black pigs, measured IMF content by Soxhlet petroleum-ether extraction method, and genotyped genome-wide SNPs using GeneSeek Genomic Profiler Porcine HD BeadChip. Then a genome-wide association study was performed using a linear mixed model implemented in the GEMMA software. Results A total of 43 SNPs were identified to be significantly associated with IMF content by the cutoff p<0.001. Among these significant SNPs, the greatest number of SNPs (n = 19) were detected on Chr.9, and two linkage disequilibrium blocks were formed among them. Additionally, 17 significant SNPs are mapped to previously reported quantitative trait loci (QTLs) of IMF and confirmed previous QTLs studies. Forty-two annotated genes centering these significant SNPs were obtained from Ensembl database. Overrepresentation test of pathways and gene ontology (GO) terms revealed some enriched reactome pathways and GO terms, which mainly involved regulation of basic material transport, energy metabolic process and signaling pathway. Conclusion These findings improve our understanding of the genetic architecture of IMF content in pork and facilitate the follow-up study of fine-mapping genes that influence fat deposition in muscle.
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Affiliation(s)
- Yanping Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Chao Ning
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Cheng Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Jianfeng Guo
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Jiying Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Ying Wu
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China
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Jin S, Park HB, Seo D, Choi NR, Manjula P, Cahyadi M, Jung S, Jo C, Lee JH. Identification of quantitative trait loci for the fatty acid composition in Korean native chicken. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018; 31:1134-1140. [PMID: 29381899 PMCID: PMC6043436 DOI: 10.5713/ajas.17.0781] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/08/2017] [Accepted: 01/20/2018] [Indexed: 01/20/2023]
Abstract
OBJECTIVE Fatty acid composition is one of the most important meat quality traits because it can contribute to functional, sensorial, and nutritional factors. In this study, quantitative trait locus (QTL) analyses for fatty acid composition traits were investigated in thigh and breast meat of Korean native chicken (KNC). METHODS In total, 18 fatty acid composition traits were investigated from each meat sample using 83 parents, and 595 F1 chicks of 20 week old. Genotype assessment was performed using 171 informative DNA markers on 26 autosomes. The KNC linkage map was constructed by CRI-MAP software, which calculated genetic distances, with map orders between markers. The half-sib and full-sib QTL analyses were performed using GridQTL and SOLAR programs, respectively. RESULTS In total, 30 QTLs (12 in the thigh and 18 in the breast meat) were detected by the half-sib analysis and 7 QTLs (3 in the thigh and 4 in the breast meat) were identified by the full-sib analysis. CONCLUSION With further verification of the QTL regions using additional markers and positional candidate gene studies, these results can provide valuable information for determining causative mutations affecting the fatty acid composition of KNC meat. Moreover, these findings may aid in the selection of birds with favorable fatty acid composition traits.
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Affiliation(s)
- Shil Jin
- Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134,
Korea
| | - Hee Bok Park
- Subtropical Livestock Research Institute, National Institute of Animal Science, Jeju 63242,
Korea
| | - Dongwon Seo
- Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134,
Korea
| | - Nu Ri Choi
- Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134,
Korea
| | - Prabuddha Manjula
- Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134,
Korea
| | - Muhammad Cahyadi
- Department of Animal Science, Faculty of Agriculture, Sebelas Maret University, Surakarta 57126,
Indonesia
| | - Samooel Jung
- Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134,
Korea
| | - Cheorun Jo
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826,
Korea
| | - Jun Heon Lee
- Division of Animal & Dairy Science, Chungnam National University, Daejeon 34134,
Korea
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12
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Chen M, Wang J, Wang Y, Wu Y, Fu J, Liu JF. Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle. BMC Genet 2018; 19:31. [PMID: 29776331 PMCID: PMC5960162 DOI: 10.1186/s12863-018-0622-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 04/30/2018] [Indexed: 12/31/2022] Open
Abstract
Background Currently, genome-wide scans for positive selection signatures in commercial breed have been investigated. However, few studies have focused on selection footprints of indigenous breeds. Laiwu pig is an invaluable Chinese indigenous pig breed with extremely high proportion of intramuscular fat (IMF), and an excellent model to detect footprint as the result of natural and artificial selection for fat deposition in muscle. Result In this study, based on GeneSeek Genomic profiler Porcine HD data, three complementary methods, FST, iHS (integrated haplotype homozygosity score) and CLR (composite likelihood ratio), were implemented to detect selection signatures in the whole genome of Laiwu pigs. Totally, 175 candidate selected regions were obtained by at least two of the three methods, which covered 43.75 Mb genomic regions and corresponded to 1.79% of the genome sequence. Gene annotation of the selected regions revealed a list of functionally important genes for feed intake and fat deposition, reproduction, and immune response. Especially, in accordance to the phenotypic features of Laiwu pigs, among the candidate genes, we identified several genes, NPY1R, NPY5R, PIK3R1 and JAKMIP1, involved in the actions of two sets of neurons, which are central regulators in maintaining the balance between food intake and energy expenditure. Conclusions Our results identified a number of regions showing signatures of selection, as well as a list of functionally candidate genes with potential effect on phenotypic traits, especially fat deposition in muscle. Our findings provide insights into the mechanisms of artificial selection of fat deposition and further facilitate follow-up functional studies. Electronic supplementary material The online version of this article (10.1186/s12863-018-0622-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Minhui Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jiying Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Yanping Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Ying Wu
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Jinluan Fu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Jian-Feng Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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13
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Longissimus lumborum muscle transcriptome analysis of Laiwu and Yorkshire pigs differing in intramuscular fat content. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0540-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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Zhang T, Zhang X, Han K, Zhang G, Wang J, Xie K, Xue Q, Fan X. Analysis of long noncoding RNA and mRNA using RNA sequencing during the differentiation of intramuscular preadipocytes in chicken. PLoS One 2017; 12:e0172389. [PMID: 28199418 PMCID: PMC5310915 DOI: 10.1371/journal.pone.0172389] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 02/03/2017] [Indexed: 02/04/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) regulate metabolic tissue development and function, including adipogenesis. However, little is known about the function and profile of lncRNAs in intramuscular preadipocyte differentiation in chicken. Here, we identified lncRNAs in chicken intramuscular preadipocytes at different differentiation stages using RNA sequencing. A total of 1,311,382,604 clean reads and 25,435 lncRNAs were obtained from 12 samples. In total, 7,433 differentially expressed genes (4,698 lncRNAs and 2,735 mRNAs) were identified by pairwise comparison. These 7,433 differentially expressed genes were grouped into 11 clusters based on their expression patterns by K-means clustering. Using Weighted Gene Coexpression Network Analysis, we identified four stage-specific modules positively related to I0, I2, I4, and I6 stages and two stage-specific modules negatively related to I0 and I2 stages, respectively. Many well-known and novel pathways associated with intramuscular preadipocyte differentiation were identified. We also identified hub genes in each stage-specific module and visualized them in Cytoscape. Our analysis revealed many highly-connected genes, including XLOC_058593, BMP3, MYOD1, and LAMP3. This study provides a valuable resource for chicken lncRNA study and improves our understanding of the biology of preadipocyte differentiation in chicken.
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Affiliation(s)
- Tao Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China
| | - Xiangqian Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China
| | - Kunpeng Han
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China
| | - Genxi Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China
| | - Jinyu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China
- * E-mail:
| | - Kaizhou Xie
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China
| | - Qian Xue
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China
| | - Xiaomei Fan
- Vazyme Biotech Co.,Ltd., Economic and Technological Development Zone, Nanjing, Jiangsu, China
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15
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Tempfli K, Kiss B, Szalai K, Simon Z, Pongrácz L, Bali Papp Á. Differential expression of six genes in fat-type Hungarian Mangalica and other pigs. Arch Anim Breed 2016. [DOI: 10.5194/aab-59-259-2016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. In order to identify potential variances in gene expression of phenotypically different pig breeds, six fat-metabolism-related genes were analyzed in backfat and muscle tissues of fat-type Mangalica (MAN), Mangalica × Duroc (MD), and lean-type Hungarian Large White (HLW) and Pietrain × Duroc (PD) pigs by means of quantitative reverse transcription PCR (qRT-PCR). Higher (P < 0.05) adipocyte fatty-acid-binding protein (A-FABP) expression was observed in backfat and muscle tissues of purebred and crossbred MAN than in those of HLW and PD. In all breeds and crosses, adiponectin (ADIPOQ) was predominantly expressed in backfat at a similar level (P > 0.05), whereas muscle ADIPOQ expression was highest (P < 0.05) in MAN and MD. Levels of fatty acid synthase (FASN) mRNA were greatest in MAN, moderate in MD, and lowest in HLW and PD backfat and muscle. The fat mass and obesity-associated gene (FTO) was more abundant in MAN and MD backfat, whereas muscle expressions did not differ (P > 0.05) between breeds. Regarding leptin (LEP) expression, MAN produced the greatest levels in backfat, while HLW produced the lowest. In muscle, highest LEP was detected in MAN and MD. Between groups, perilipin 2 (PLIN2) was expressed similarly in backfat; however, PLIN2 was more abundant in muscle of MAN and MD than in that of HLW and PD. Differences in gene expression can contribute to the development of the characteristic fatty phenotype in MAN pigs. The identification of differentially expressed genes facilitates targeted sequencing and genotyping efforts for further studies.
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16
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Zhang B, Shang P, Qiangba Y, Xu A, Wang Z, Zhang H. The association of NR1H3 gene with lipid deposition in the pig. Lipids Health Dis 2016; 15:99. [PMID: 27229308 PMCID: PMC4880824 DOI: 10.1186/s12944-016-0269-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 05/20/2016] [Indexed: 01/14/2023] Open
Abstract
Background Nuclear receptor subfamily 1, group H, member 3 (NR1H3, an alias for Liver X receptor α, LXRα) is a member of the LXR nuclear receptor super family and is an important regulator of lipid and fatty acid accumulation in the liver, adipose and skeletal muscle. Methods In this study, single-nucleotide polymorphisms (SNPs) from six populations of pig (Sus scrofa) were screened by PCR-sequencing and genotyped, and its association with backfat thickness was analyzed in a population of New Huai line (NHP, n = 117). In addition, quantitative real-time PCR and western blot were used to measure expression of NR1H3 in the liver tissue, backfat and longissimus dorsi muscle of DSP (n = 10), TP (n = 10) and YY (n = 10) pigs. Results Three SNPs (exon2-C105T, exon2-G106C, and exon5-A201C) were screened and exon5-A201C was identified; the genotype frequencies were significantly different between indigenous and introduced breeds. The CC genotype was associated with higher backfat thickness than the AA and AC genotypes in the NYP. NR1H3 mRNA and protein expression were higher in the liver and longissimus dorsi of DSP and TP than in those of YY. This increased NR1H3 expression might be associated with higher lipid deposition. NR1H3 expression in the backfat of YY was not lower than that in DSP or TP, which might because NR1H3 has an alternative regulatory function for lipid metabolism in the subcutaneous fat of pigs. Conclusions Our results suggest that allele A of the exon5-A201C in NR1H3 may promote a reduction in backfat thickness, and differences in NR1H3 expression may be associated with differences in lipid deposition capacity among pigs.
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Affiliation(s)
- Bo Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, People's Republic of China
| | - Peng Shang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, People's Republic of China
| | - Yangzong Qiangba
- College of Agriculture and Animal Husbandry, Tibet University, Linzhi, 860000, People's Republic of China
| | - Aishi Xu
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, People's Republic of China
| | - Zhixiu Wang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, People's Republic of China
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd., Beijing, 100193, People's Republic of China.
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17
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Sweeney T, O'Halloran AM, Hamill RM, Davey GC, Gil M, Southwood OI, Ryan MT. Novel variation in the FABP3 promoter and its association with fatness traits in pigs. Meat Sci 2014; 100:32-40. [PMID: 25306509 DOI: 10.1016/j.meatsci.2014.09.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 09/08/2014] [Accepted: 09/17/2014] [Indexed: 01/28/2023]
Abstract
This study examines associations between SNPs in the promoter region of the fatty acid binding protein 3 (FABP3) gene and fatness traits in pure bred Large White (n=98), Duroc (n=99) and Pietrain (n=98) populations. In the Large White breed, SNP g.-634 C>A was associated a 27% increase in IMF (%) in the heterozygote (CA) and a 38% increase in the homozygote (CC) relative to the (AA) genotype in the M. semimembranosus (SM) muscle (P=0.02). While the associations observed in this breed were suggestive of significance in both the SM and in the M. longissimus thoracis et lumborum (LTL) (P=0.08), these associations no longer attained significance at thresholds adjusted for multiple testing. In conclusion, SNPs in the FABP3 promoter may contribute to IMF without influencing carcass fatness traits in pigs, however further confirmation of these associations in larger independent populations would be essential before their incorporation into breeding programmes.
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Affiliation(s)
- T Sweeney
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - A M O'Halloran
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - R M Hamill
- Teagasc, Ashtown Food Research Centre, Ashtown, Dublin 15, Ireland
| | - G C Davey
- Functional Genomics & Glycomics Group, Martin Ryan Institute, National University of Ireland Galway, Galway, Ireland
| | - M Gil
- IRTA, 17121, Monells, Girona, Spain
| | - O I Southwood
- Genus PLC/PIC, Alpha Building, London Road, Nantwich CW5 7JW, UK
| | - M T Ryan
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
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