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Zhang M, Sun L, Su R, Corazzin M, Yang Z, Dou L, Hu G, Zhang Y, Liu T, Guo Y, Zhao L, Su L, Tian J, Jin Y. Widely targeted metabolomic analysis reveals the dynamic changes of metabolites during postmortem chilled aging in Mongolian sheep. Food Chem 2024; 431:137035. [PMID: 37567080 DOI: 10.1016/j.foodchem.2023.137035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/18/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023]
Abstract
Postmortem aging is a value-added process for meat. The objective of this study was to evaluate the dynamic changes and metabolic pathways of metabolites in Mongolian sheep during early postmortem chilled aging. Widely targeted metabolomic was used to analyze the metabolites of mutton within five days of chilled aging. A total of 1093 metabolites were identified in Mongolian sheep, covering 16 subclasses. Multivariate statistical analysis showed that 467 metabolites had significant changes during aging, including amino acid and its metabolites, fatty acyl, and glycerophospholipid. In particular, 60 metabolites decreased, while other 407 metabolites increased with aging time. The Kyoto encyclopedia of genes and genomes pathway analysis revealed that protein digestion and absorption, amino acyl-trNA biosynthesis, unsaturated fatty acid biosynthesis, nucleotide metabolism and carbon metabolism were the main enrichment pathways in aging. These findings provide a more comprehensive insight into metabolic profiling and metabolic pathways during chilled aging in mutton.
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Affiliation(s)
- Min Zhang
- College of Food Science and Engineering, Integrative Research Base of Beef and Lamb Processing Technology, Inner Mongolia Agriculture University, China
| | - Lina Sun
- College of Food Science and Engineering, Integrative Research Base of Beef and Lamb Processing Technology, Inner Mongolia Agriculture University, China
| | - Rina Su
- Inner Mongolia Vocational College of Chemical Engineering, China
| | - Mirco Corazzin
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Italy
| | - Zhihao Yang
- College of Food Science and Engineering, Integrative Research Base of Beef and Lamb Processing Technology, Inner Mongolia Agriculture University, China
| | - Lu Dou
- College of Food Science and Engineering, Integrative Research Base of Beef and Lamb Processing Technology, Inner Mongolia Agriculture University, China
| | - Guanhua Hu
- College of Food Science and Engineering, Integrative Research Base of Beef and Lamb Processing Technology, Inner Mongolia Agriculture University, China
| | - Yue Zhang
- College of Food Science and Engineering, Integrative Research Base of Beef and Lamb Processing Technology, Inner Mongolia Agriculture University, China
| | - Ting Liu
- College of Food Science and Engineering, Integrative Research Base of Beef and Lamb Processing Technology, Inner Mongolia Agriculture University, China
| | - Yueying Guo
- College of Food Science and Engineering, Integrative Research Base of Beef and Lamb Processing Technology, Inner Mongolia Agriculture University, China
| | - Lihua Zhao
- College of Food Science and Engineering, Integrative Research Base of Beef and Lamb Processing Technology, Inner Mongolia Agriculture University, China
| | - Lin Su
- College of Food Science and Engineering, Integrative Research Base of Beef and Lamb Processing Technology, Inner Mongolia Agriculture University, China
| | - Jianjun Tian
- College of Food Science and Engineering, Integrative Research Base of Beef and Lamb Processing Technology, Inner Mongolia Agriculture University, China
| | - Ye Jin
- College of Food Science and Engineering, Integrative Research Base of Beef and Lamb Processing Technology, Inner Mongolia Agriculture University, China.
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Profiles of muscular amino acids, fatty acids, and metabolites in Shaziling pigs of different ages and relation to meat quality. SCIENCE CHINA. LIFE SCIENCES 2022:10.1007/s11427-022-2227-6. [PMID: 36564558 DOI: 10.1007/s11427-022-2227-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 09/21/2022] [Indexed: 12/25/2022]
Abstract
Pork meat is closely related to physicochemical alterations during growth and development, resulting in differences in nutritional value and meat flavor. This study aimed to evaluate the composition of amino acids, fatty acids, and metabolic profiles in the longissimus thoracis muscle (LM) of Shaziling pigs aged 30, 90, 150, 210, and 300 days. The results showed that the predominant fatty acids identified in the LM of Shaziling pigs were C16:0, C16:1, C18:0, C18:1n9c, and C18:2n6c. An opposite correlation was observed for C18:2n6c and n6/n3 polyunsaturated fatty acids (P<0.05). Alanine, aspartate, glutamate, D-glutamine, and D-glutamate metabolism were the main metabolic pathways for the Shaziling pig meat flavor (P<0.05). Moreover, the correlation coefficients revealed that the contents of anserine, C16:0, C16:1, and C18:1n9c were positively correlated with intramuscular fat and/or pH24h and were negatively correlated with the values of L* (lightness) and b* (yellowness) (P<0.05). In conclusion, age greatly affected the meat quality of Shaziling pigs, and the contents of muscular anserine, C16:0, C16:1, and C18:1n9c might be promising indicators for better meat quality.
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Differential Expression Analysis of tRNA-Derived Small RNAs from Subcutaneous Adipose Tissue of Obese and Lean Pigs. Animals (Basel) 2022; 12:ani12243561. [PMID: 36552481 PMCID: PMC9774726 DOI: 10.3390/ani12243561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Epigenetic factors, including non-coding RNA regulation, play a vital role in the development of obesity and have been well researched. Transfer RNA-derived small RNA (tsRNA) is a class of non-coding RNA proven to be involved in various aspects of mammalian biology. Here we take pigs as a model for obesity research and use tsRNA-seq to investigate the difference in tsRNA expression in the subcutaneous adipose tissue of obese and lean pigs to elucidate the role of tsRNA in obesity development. A total of 482 tsRNAs were identified in pig adipose tissue, of which 123 were significantly differentially accumulated tsRNAs compared with the control group. The tRF-5c was the main type of these tsRNAs. The largest number of tsRNAs produced was the Gly-carrying tRNA, which produced 81 tsRNAs. Functional enrichment analysis revealed that differential tsRNAs indirectly participated in MAPK, AMPK, insulin resistance, the TNF signaling pathway, adipocytokine signaling pathway, and other signaling pathways by interacting with target genes. These are involved in bioenergetic metabolic regulatory processes, suggesting that tsRNAs may influence these pathways to mediate the regulation of energy metabolism in porcine adipocytes to promote lipid deposition, thus contributing to obesity. Our findings suggest a potential function of tsRNA in regulating obesity development.
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Sun Y, Xiao Y, Li C, Yang J, Yang S, Yang B, Huang L. A parallel survey on the fatty acid composition in backfat and longissimus lumborum and comparison of their associations with growth and carcass traits in pigs. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.104984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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5
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Ogawa S, Kimata M, Tomiyama M, Satoh M. Heritability and genetic correlation estimates of semen production traits with litter traits and pork production traits in purebred Duroc pigs. J Anim Sci 2022; 100:6535633. [PMID: 35201314 PMCID: PMC9030147 DOI: 10.1093/jas/skac055] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/23/2022] [Indexed: 11/30/2022] Open
Abstract
We estimated heritabilities of semen production traits and their genetic correlations with litter traits and pork production traits in purebred Duroc pigs. Semen production traits were semen volume, sperm concentration, proportion of morphologically normal sperms, total number of sperm, and total number of morphologically normal sperm. Litter traits at farrowing were total number born, number born alive, number stillborn, total litter weight at birth, mean litter weight at birth, and piglet survival rate at birth. Litter traits at weaning were litter size at weaning, total litter weight at weaning, mean litter weight at weaning, and piglet survival rate from birth to weaning. Pork production traits were average daily gain, backfat thickness, and loin muscle area. We analyzed 45,913 semen collection records of 896 boars, 6,950 farrowing performance records of 1,400 sows, 2,237 weaning performance records of 586 sows, and individual growth performance records of 9,550 animals measured at approximately 5 mo of age. Heritabilities were estimated using a single-trait animal model. Genetic correlations were estimated using a 2-trait animal model. Estimated heritabilities of semen production traits ranged from 0.20 for sperm concentration to 0.29 for semen volume and were equal to or higher than those of litter traits, ranging from 0.06 for number stillborn and piglet survival rate at birth to 0.25 for mean litter weight at birth, but lower than those of pork production traits, ranging from 0.50 for average daily gain to 0.63 for backfat thickness. In many cases, the absolute values of estimated genetic correlations between semen production traits and other traits were smaller than 0.3. These estimated genetic parameters provide useful information for establishing a comprehensive pig breeding scheme. Genetic parameters of 5 semen production traits, 10 litter traits, and 3 pork production traits in purebred Duroc pigs was estimated. Heritabilities of semen production traits ranged from 0.20 for sperm concentration to 0.29 for semen volume and were equal to or higher than those of litter traits, ranging from 0.06 for number stillborn and piglet survival rate at birth to 0.25 for mean litter weight at birth, but lower than those of pork production traits, ranging from 0.50 for average daily gain to 0.63 for backfat thickness. In many cases, the absolute values of genetic correlations between semen production traits and other traits were smaller than 0.3. These estimated genetic parameters provide useful information for establishing a comprehensive pig breeding scheme.
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Affiliation(s)
- S Ogawa
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 980-8572, Japan
| | - M Kimata
- CIMCO Corporation, Koto-ku, Tokyo 136-0071, Japan
| | - M Tomiyama
- CIMCO Corporation, Koto-ku, Tokyo 136-0071, Japan
| | - M Satoh
- Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi 980-8572, Japan
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6
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Han Y, Liang C, Manthari RK, Yu Y, Zhang J, Wang J, Cao J. Distribution characteristics and regulation of amino acids and fatty acids in muscle and adipose tissues of sheep grown in natural grazing environment. Anim Sci J 2022; 93:e13769. [PMID: 36127314 DOI: 10.1111/asj.13769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 07/26/2022] [Accepted: 08/18/2022] [Indexed: 12/01/2022]
Abstract
The composition of amino acid and fatty acid has a vital function on meat quality and animal health. However, the underlying mechanism of amino acid and fatty acid metabolism in sheep during different grazing periods is still unclear. In this study, a total of 12 sheep were employed in different grazing periods. Our results showed that the composition of amino acids and fatty acids in muscle and adipose tissues was significantly altered between dry grass (DG) period and green grass (GG) period. Changes in the activities of the metabolism-related enzymes including BCKD, BCAT2, ACC, SCD, HSL, GSK3β, p-GSK3β, and FABP4 were observed in muscle and adipose during different grazing periods. In addition, the mRNA expression levels of ACC, FAS, SCD, HSL, LPL, and DGAT1 in muscle and adipose tissue were changed markedly in different grazing periods. Furthermore, the expression levels of mTOR and β-catenin/PPARγ/C/EBPα pathway-related proteins were predominantly altered in muscle and adipose among DG and GG. Taken together, all investigations simplified the process of amino acid and fatty acid metabolism disorders caused by different grazing periods, and the mTOR and β-catenin/PPARγ/C/EBPα play the essential role in this process, which provided an underlying mechanism of metabolism and meat quality.
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Affiliation(s)
- Yongli Han
- Shanxi Key Laboratory of Ecological Animal Science and Environmental Veterinary Medicine, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - Chen Liang
- College of Animal Science, Shanxi Agricultural University, Taigu, China
| | - Ram Kumar Manthari
- Department of Biotechnology, GITAM Institute of Science, Gandhi Institute of Technology and Management, Visakhapatnam, India
| | - Yuxiang Yu
- Shanxi Key Laboratory of Ecological Animal Science and Environmental Veterinary Medicine, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - Jianhai Zhang
- Shanxi Key Laboratory of Ecological Animal Science and Environmental Veterinary Medicine, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - Jundong Wang
- Shanxi Key Laboratory of Ecological Animal Science and Environmental Veterinary Medicine, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - Jinling Cao
- Shanxi Key Laboratory of Ecological Animal Science and Environmental Veterinary Medicine, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, China.,College of Food Science and Engineering, Shanxi Agricultural University, Taigu, China
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7
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Zappaterra M, Catillo G, Lo Fiego DP, Belmonte AM, Padalino B, Davoli R. Describing backfat and Semimembranosus muscle fatty acid variability in heavy pigs: Analysis of non-genetic factors. Meat Sci 2021; 183:108645. [PMID: 34399151 DOI: 10.1016/j.meatsci.2021.108645] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/27/2022]
Abstract
This study aimed to describe the multivariate structure of Semimembranosus muscle and backfat fatty acid (FA) composition in 798 Italian Large White heavy pigs and to investigate the effects of environmental factors and carcass characteristics on FA variations. The total FA variability in muscle and backfat was characterized by a negative correlation between saturated and polyunsaturated FAs, which strongly depended on the carcass adiposity. Slaughtering season was also relevant, with pigs slaughtered in autumn having more n-6 FAs and eicosadienoic acid in backfat, while pigs slaughtered in winter displayed more saturated FAs. Regarding Semimembranosus muscle, pigs with heavier belly cuts and slaughtered in autumn had higher proportions of cis-vaccenic and palmitoleic acids, while those slaughtered in summer had more saturated FAs. Slaughtering season emerged as a relevant factor shaping both backfat and muscle FA composition, indicating that more studies and attention should be paid to environmental factors, which may have effects on FA metabolism and deposition in finishing pigs.
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Affiliation(s)
- Martina Zappaterra
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Viale G. Fanin 46, I-40127 Bologna, Italy.
| | - Gennaro Catillo
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Centro di ricerca Zootecnia e Acquacoltura (Research Centre for Animal Production and Aquaculture), Via Salaria 31, I-00015 Monterotondo, Italy
| | - Domenico Pietro Lo Fiego
- Department of Life Sciences (DSV), University of Modena and Reggio Emilia, Via G. Amendola 2, I-42122 Reggio Emilia, Italy; Interdepartmental Research Centre for Agri-Food Biological Resources Improvement and Valorization (BIOGEST-SITEIA), University of Modena and Reggio Emilia, P. le Europa 1, I-42124 Reggio Emilia, Italy
| | - Anna Maria Belmonte
- Department of Life Sciences (DSV), University of Modena and Reggio Emilia, Via G. Amendola 2, I-42122 Reggio Emilia, Italy
| | - Barbara Padalino
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Viale G. Fanin 46, I-40127 Bologna, Italy
| | - Roberta Davoli
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Viale G. Fanin 46, I-40127 Bologna, Italy.
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8
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Hong JK, Cho KH, Kim YS, Chung HJ, Baek SY, Cho ES, Sa SJ. Genetic relationship between purebred and synthetic pigs for growth performance using single step method. Anim Biosci 2021; 34:967-974. [PMID: 32898957 PMCID: PMC8100493 DOI: 10.5713/ajas.20.0261] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/21/2020] [Indexed: 11/30/2022] Open
Abstract
Objective The objective of this study was to estimate the genetic correlation (rpc) of growth performance between purebred (Duroc and Korean native) and synthetic (WooriHeukDon) pigs using a single-step method. Methods Phenotypes of 15,902 pigs with genotyped data from 1,792 pigs from a nucleus farm were used for this study. We estimated the rpc of several performance traits between WooriHeukDon and purebred pigs: day of target weight (DAY), backfat thickness (BF), feed conversion rate (FCR), and residual feed intake (RFI). The variances and covariances of the studied traits were estimated by an animal multi-trait model that applied the Bayesian inference. Results rpc within traits was lower than 0.1 for DAY and BF, but high for FCR and RFI; in particular, rpc for RFI between Duroc and WooriHeukDon pigs was nearly 1. Comparison between different traits revealed that RFI in Duroc pigs was associated with different traits in WooriHeukDon pigs. However, the most of rpc between different traits were estimated with low or with high standard deviation. Conclusion The results indicated that there were substantial differences in rpc of traits in the synthetic WooriHeukDon pigs, which could be caused by these pigs having a more complex origin than other crossbred pigs. RFI was strongly correlated between Duroc and WooriHeukDon pigs, and these breeds might have similar single nucleotide polymorphism effects that control RFI. RFI is more essential for metabolism than other growth traits and these metabolic characteristics in purebred pigs, such as nutrient utilization, could significantly affect those in synthetic pigs. The findings of this study can be used to elucidate the genetic architecture of crossbred pigs and help develop new breeds with target traits.
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Huang Y, Zhou L, Zhang J, Liu X, Zhang Y, Cai L, Zhang W, Cui L, Yang J, Ji J, Xiao S, Ai H, Chen C, Ma J, Yang B, Huang L. A large-scale comparison of meat quality and intramuscular fatty acid composition among three Chinese indigenous pig breeds. Meat Sci 2020; 168:108182. [DOI: 10.1016/j.meatsci.2020.108182] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 05/07/2020] [Accepted: 05/07/2020] [Indexed: 01/26/2023]
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Wang H, Zhong J, Zhang C, Chai Z, Cao H, Wang J, Zhu J, Wang J, Ji Q. The whole-transcriptome landscape of muscle and adipose tissues reveals the ceRNA regulation network related to intramuscular fat deposition in yak. BMC Genomics 2020; 21:347. [PMID: 32381004 PMCID: PMC7203869 DOI: 10.1186/s12864-020-6757-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 04/27/2020] [Indexed: 02/07/2023] Open
Abstract
Background The Intramuscular fat (IMF) content in meat products, which is positively correlated with meat quality, is an important trait considered by consumers. The regulation of IMF deposition is species specific. However, the IMF-deposition-related mRNA and non-coding RNA and their regulatory network in yak (Bos grunniens) remain unknown. High-throughput sequencing technology provides a powerful approach for analyzing the association between transcriptome-related differences and specific traits in animals. Thus, the whole transcriptomes of yak muscle and adipose tissues were screened and analyzed to elucidate the IMF deposition-related genes. The muscle tissues were used for IMF content measurements. Results Significant differences were observed between the 0.5- and 2.5-year-old yaks. Several mRNAs, miRNAs, lncRNAs and circRNAs were generally expressed in both muscle and adipose tissues. Between the 0.5- and 2.5-year-old yaks, 149 mRNAs, 62 miRNAs, 4 lncRNAs, and 223 circRNAs were differentially expressed in muscle tissue, and 72 mRNAs, 15 miRNAs, 9 lncRNAs, and 211 circRNAs were differentially expressed in adipose tissue. KEGG annotation revelved that these differentially expressed genes were related to pathways that maintain normal biological functions of muscle and adipose tissues. Moreover, 16 mRNAs, 5 miRNAs, 3 lncRNAs, and 5 circRNAs were co-differentially expressed in both types of tissue. We suspected that these co-differentially expressed genes were involved in IMF-deposition in the yak. Additionally, LPL, ACADL, SCD, and FASN, which were previously shown to be associated with the IMF content, were identified in the competing endogenous RNA (ceRNA) regulatory network that was constructed on the basis of the IMF deposition-related genes. Three ceRNA subnetworks also revealed that TCONS-00016416 and its target SIRT1 “talk” to each other through the same miR-381-y and miR-208 response elements, whereas TCONS-00061798 and its target PRKCA, and TCONS-00084092 and its target LPL “talk” to each other through miR-122-x and miR-499-y response elements, respectively. Conclusion Taken together, our results reveal the potential mRNA and noncoding RNAs involved in IMF deposition in the yak, providing a useful resource for further research on IMF deposition in this animal species.
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Affiliation(s)
- Hui Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China.,Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Jincheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China. .,Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China.
| | - Chengfu Zhang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, the Tibet Academy of Agricultural and Animal Husbandry Science , Lhasa, Tibet, 850000, People's Republic of China
| | - Zhixin Chai
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China.,Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Hanwen Cao
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, the Tibet Academy of Agricultural and Animal Husbandry Science , Lhasa, Tibet, 850000, People's Republic of China
| | - Jikun Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China.,Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Jiangjiang Zhu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China.,Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Jiabo Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China.,Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Key Laboratory of Sichuan Province, Southwest Minzu University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Qiumei Ji
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, the Tibet Academy of Agricultural and Animal Husbandry Science , Lhasa, Tibet, 850000, People's Republic of China.
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Zappaterra M, Luise D, Zambonelli P, Mele M, Serra A, Costa LN, Davoli R. Association study between backfat fatty acid composition and SNPs in candidate genes highlights the effect of FASN polymorphism in large white pigs. Meat Sci 2019; 156:75-84. [DOI: 10.1016/j.meatsci.2019.05.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/08/2019] [Accepted: 05/13/2019] [Indexed: 12/30/2022]
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12
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Gol S, González-Prendes R, Bosch L, Tor M, Reixach J, Pena RN, Estany J. Linoleic acid metabolic pathway allows for an efficient increase of intramuscular fat content in pigs. J Anim Sci Biotechnol 2019; 10:33. [PMID: 31080594 PMCID: PMC6503358 DOI: 10.1186/s40104-019-0343-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/11/2019] [Indexed: 12/18/2022] Open
Abstract
Background Intramuscular fat (IMF) content is a relevant trait for high-quality meat products such as dry-cured ham, but increasing IMF has the undesirable correlated effect of decreasing lean growth. Thus, there is a need to find selection criteria for IMF independent from lean growth. In pigs, the proportion of linoleic (C18:2) and arachidonic (C20:4) acids decline with fat deposition and therefore they can be considered as indicators of fatness. The aim of this research was to estimate the genetic variation for C18:2 and C20:4 in IMF and their genetic correlations with IMF and lean growth traits, with the objective to assess their potential as specific biomarkers of IMF. The analysis was conducted using a full-pedigreed Duroc resource line with 91,448 records of body weight and backfat thickness (BT) at 180 days of age and 1371 records of fatty acid composition in the muscle gluteus medius. Results The heritability estimates for C18:2 and C20:4 in IMF, whether expressed in absolute (mg/g of muscle) or in relative (mg/g of fatty acid) terms, as well as for their ratio (C20:4/C18:2), were high (> 0.40), revealing that the C18:2 to C20:4 pathway is subjected to substantial genetic influence. Litter effects were not negligible, with values ranging from 8% to 15% of the phenotypic variance. The genetic correlations of C18:2 and C20:4 with IMF and BT were negative (- 0.75 to - 0.66, for IMF, and - 0.64 to - 0.36, for BT), if expressed in relative values, but almost null (- 0.04 to 0.07), if expressed in absolute values, except for C18:2 with IMF, which was highly positive (0.88). The ratio of C20:4 to C18:2 also displayed a stronger genetic correlation with IMF (- 0.59) than with BT (- 0.10). Conclusions The amount of C18:2 in muscle can be used as an IMF-specific biomarker. Selection for the absolute amount of C18:2 is expected to deliver a similar response outcome as selection for IMF at restrained BT. Further genetic analysis of the C18:2 metabolic pathway may provide new insights into differential fat deposition among adipose tissues and on candidate genes for molecular markers targeting specifically for one of them.
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Affiliation(s)
- Sofia Gol
- 1Department of Animal Science, Universitat de Lleida - Agrotecnio Center, 191 Rovira Roure, 25198 Lleida, Catalonia Spain
| | - Rayner González-Prendes
- 1Department of Animal Science, Universitat de Lleida - Agrotecnio Center, 191 Rovira Roure, 25198 Lleida, Catalonia Spain
| | - Lluís Bosch
- 2Department of Chemical, Agricultural and Food Technology Engineering, Universitat de Girona, Campus de Montilivi, 17071 Girona, Catalonia Spain
| | - Marc Tor
- 1Department of Animal Science, Universitat de Lleida - Agrotecnio Center, 191 Rovira Roure, 25198 Lleida, Catalonia Spain
| | - Josep Reixach
- Selección Batallé S.A., Av. Segadors s/n, 17421 Riudarenes, Catalonia Spain
| | - Ramona N Pena
- 1Department of Animal Science, Universitat de Lleida - Agrotecnio Center, 191 Rovira Roure, 25198 Lleida, Catalonia Spain
| | - Joan Estany
- 1Department of Animal Science, Universitat de Lleida - Agrotecnio Center, 191 Rovira Roure, 25198 Lleida, Catalonia Spain
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Zhang Y, Zhang J, Gong H, Cui L, Zhang W, Ma J, Chen C, Ai H, Xiao S, Huang L, Yang B. Genetic correlation of fatty acid composition with growth, carcass, fat deposition and meat quality traits based on GWAS data in six pig populations. Meat Sci 2019; 150:47-55. [DOI: 10.1016/j.meatsci.2018.12.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 12/08/2018] [Accepted: 12/16/2018] [Indexed: 10/27/2022]
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Ma H, Zhang S, Zhang K, Zhan H, Peng X, Xie S, Li X, Zhao S, Ma Y. Identifying Selection Signatures for Backfat Thickness in Yorkshire Pigs Highlights New Regions Affecting Fat Metabolism. Genes (Basel) 2019; 10:genes10040254. [PMID: 30925743 PMCID: PMC6523431 DOI: 10.3390/genes10040254] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/23/2019] [Accepted: 03/26/2019] [Indexed: 02/07/2023] Open
Abstract
Identifying the genetic basis of improvement in pigs contributes to our understanding of the role of artificial selection in shaping the genome. Here we employed the Cross Population Extended Haplotype Homozogysity (XPEHH) and the Wright's fixation index (FST) methods to detect trait-specific selection signatures by making phenotypic gradient differential population pairs, and then attempted to map functional genes of six backfat thickness traits in Yorkshire pigs. The results indicate that a total of 283 and 466 single nucleotide polymorphisms (SNPs) were identified as trait-specific selection signatures using FST and XPEHH, respectively. Functional annotation suggested that the genes overlapping with the trait-specific selection signatures such as OSBPL8, ASAH2, SMCO2, GBE1, and ABL1 are responsible for the phenotypes including fat metabolism, lean body mass and fat deposition, and transport in mouse. Overall, the study developed the methods of gene mapping on the basis of identification of selection signatures. The candidate genes putatively associated with backfat thickness traits can provide important references and fundamental information for future pig-breeding programs.
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Affiliation(s)
- Haoran Ma
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Saixian Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Kaili Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Huiwen Zhan
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xia Peng
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Shengsong Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yunlong Ma
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
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Lin R, Lin W, Chen Q, Huo J, Hu Y, Ye J, Xu J, Xiao T. Gene expression and promoter methylation of porcine uncoupling protein 3 gene. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018; 32:170-175. [PMID: 30056670 PMCID: PMC6325394 DOI: 10.5713/ajas.18.0116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 06/27/2018] [Indexed: 12/02/2022]
Abstract
Objective Uncoupling protein 3 gene (UCP3) is a candidate gene associated with the meat quality of pigs. The aim of this study was to explore the regulation mechanism of UCP3 expression and provide a theoretical basis for the research of the function of porcine UCP3 gene in meat quality. Methods Bisulfite sequencing polymerase chain reaction (PCR) and quantitative real-time PCR (Q-PCR) were used to analyze the methylation of UCP3 5′-flanking region and UCP3 mRNA expression in the adipose tissue or skeletal muscle of three pig breeds at different ages (1, 90, 210-day-old Putian Black pig; 90-day-old Duroc; and 90-day-old Dupu). Results Results showed that two cytosine-guanine dinucleotide (CpG) islands are present in the promoter region of porcine UCP3 gene. The second CpG island located in the core promoter region contained 9 CpG sites. The methylation level of CpG island 2 was lower in the adipose tissue and skeletal muscle of 90-day-old Putian Black pigs compared with 1-day-old and 210-day-old Putian Black pigs, and the difference also existed in the skeletal muscle among the three 90-day-old pig breeds. Furthermore, the obvious changing difference of UCP3 mRNA expression was observed in the skeletal muscle of different groups. However, the difference of methylation status and expression level of UCP3 gene was not significant in the adipose tissue. Conclusion Our data indicate that UCP3 mRNA expression level was associated with the methylation status of UCP3 promoter in the skeletal muscle of pigs.
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Affiliation(s)
- Ruiyi Lin
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Weimin Lin
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Qiaohui Chen
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Jianchao Huo
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yuping Hu
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Junxiao Ye
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Jingya Xu
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Tianfang Xiao
- College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
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17
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Effect of selection for intramuscular fat on the fatty acid composition of rabbit meat. Animal 2018; 12:2002-2008. [DOI: 10.1017/s1751731117003494] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Analysis of Differentially Expressed Genes in Gastrocnemius Muscle between DGAT1 Transgenic Mice and Wild-Type Mice. BIOMED RESEARCH INTERNATIONAL 2017; 2017:5404682. [PMID: 28386555 PMCID: PMC5366756 DOI: 10.1155/2017/5404682] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/22/2017] [Indexed: 11/17/2022]
Abstract
Adipose tissue was the major energy deposition site of the mammals and provided the energy for the body and released the external pressure to the internal organs. In animal production, fat deposition in muscle can affect the meat quality, especially the intramuscular fat (IMF) content. Diacylglycerol acyltransferase-1 (DGAT1) was the key enzyme to control the synthesis of the triacylglycerol in adipose tissue. In order to better understand the regulation mechanism of the DGAT1 in the intramuscular fat deposition, the global gene expression profiling was performed in gastrocnemius muscle between DGAT1 transgenic mice and wild-type mice by microarray. 281 differentially expressed transcripts were identified with at least 1.5-fold change and the p value < 0.05. 169 transcripts were upregulated and 112 transcripts were downregulated. Ten genes (SREBF1, DUSP1, PLAGL1, FKBP5, ZBTB16, PPP1R3C, CDC14A, GLUL, PDK4, and UCP3) were selected to validate the reliability of the chip's results by the real-time PCR. The finding of RT-PCR was consistent with the gene chip. Seventeen signal pathways were analyzed using KEGG pathway database and the pathways concentrated mainly on the G-protein coupled receptor protein signaling pathway, signal transduction, oxidation-reduction reaction, olfactory receptor activity, protein binding, and zinc ion binding. This study implied a function role of DGAT1 in the synthesis of TAG, insulin resistance, and IMF deposition.
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Chang HL, Lai YY, Wu MC, Sasaki O. Genetic correlations between male reproductive traits and growth traits in growth performance tested Duroc, Landrace and Yorkshire breed boars. Anim Sci J 2017; 88:1258-1268. [PMID: 28183152 DOI: 10.1111/asj.12776] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 11/13/2016] [Accepted: 12/12/2016] [Indexed: 11/30/2022]
Abstract
Male-related traits at 180-225 days of age for 6464 grow-finish performance tested boars were measured from 2000 to 2016. Heritability estimates and genetic correlations among average daily gain, feed efficiency, back fat thickness, teat counts, mounting libido, leg locomotion, penile length, sperm motility, sperm concentration and total sperm counts were estimated by VCE software using a multiple traits animal model in each breed. Growth-tested boars had heritability estimates of male reproductive traits in 0.34-0.56 of teat counts, 0.12-0.20 of libido, 0.08-0.12 of locomotion, 0.17-0.58 of penile length, 0.04-0.21 of sperm motility and concentration, 0.17-0.30 of total sperm counts. Total sperm counts were genetically positively correlated with penile length in all breeds. Boars with higher total sperm counts had genetically better libido and locomotion. Genetic correlation between feed efficiency and sperm motility and feed efficiency and sperm concentration were positive in Duroc and negative in Landrace and Yorkshire. Sperm motility and concentration were genetically negatively correlated with average daily gain in Yorkshire. Male reproductive traits of imported breeds could be improved with care in the change of growth traits, especially in Yorkshire.
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Affiliation(s)
- Hsiu-Luan Chang
- Department of Animal Science, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Yung-Yu Lai
- Livestock Research Institute, Tainan, Taiwan
| | - Ming-Che Wu
- Livestock Research Institute, Tainan, Taiwan
| | - Osamu Sasaki
- Division of Animal Breeding and Reproduction, Institute of Livestock and Grassland Science, NARO, Japan
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Genetic Marker Discovery in Complex Traits: A Field Example on Fat Content and Composition in Pigs. Int J Mol Sci 2016; 17:ijms17122100. [PMID: 27983643 PMCID: PMC5187900 DOI: 10.3390/ijms17122100] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/06/2016] [Accepted: 12/07/2016] [Indexed: 12/11/2022] Open
Abstract
Among the large number of attributes that define pork quality, fat content and composition have attracted the attention of breeders in the recent years due to their interaction with human health and technological and sensorial properties of meat. In livestock species, fat accumulates in different depots following a temporal pattern that is also recognized in humans. Intramuscular fat deposition rate and fatty acid composition change with life. Despite indication that it might be possible to select for intramuscular fat without affecting other fat depots, to date only one depot-specific genetic marker (PCK1 c.2456C>A) has been reported. In contrast, identification of polymorphisms related to fat composition has been more successful. For instance, our group has described a variant in the stearoyl-coA desaturase (SCD) gene that improves the desaturation index of fat without affecting overall fatness or growth. Identification of mutations in candidate genes can be a tedious and costly process. Genome-wide association studies can help in narrowing down the number of candidate genes by highlighting those which contribute most to the genetic variation of the trait. Results from our group and others indicate that fat content and composition are highly polygenic and that very few genes explain more than 5% of the variance of the trait. Moreover, as the complexity of the genome emerges, the role of non-coding genes and regulatory elements cannot be disregarded. Prediction of breeding values from genomic data is discussed in comparison with conventional best linear predictors of breeding values. An example based on real data is given, and the implications in phenotype prediction are discussed in detail. The benefits and limitations of using large SNP sets versus a few very informative markers as predictors of genetic merit of breeding candidates are evaluated using field data as an example.
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21
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Lim KS, Lee KT, Park JE, Chung WH, Jang GW, Choi BH, Hong KC, Kim TH. Identification of differentially expressed genes in longissimus muscle of pigs with high and low intramuscular fat content using RNA sequencing. Anim Genet 2016; 48:166-174. [DOI: 10.1111/age.12518] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/01/2016] [Indexed: 01/07/2023]
Affiliation(s)
- K. S. Lim
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science; Rural Development Administration; Wanju 565-851 Korea
- College of Life Science and Biotechnology; Korea University; Seoul 136-713 Korea
| | - K. T. Lee
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science; Rural Development Administration; Wanju 565-851 Korea
| | - J. E. Park
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science; Rural Development Administration; Wanju 565-851 Korea
| | - W. H. Chung
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science; Rural Development Administration; Wanju 565-851 Korea
| | - G. W. Jang
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science; Rural Development Administration; Wanju 565-851 Korea
| | - B. H. Choi
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science; Rural Development Administration; Wanju 565-851 Korea
| | - K. C. Hong
- College of Life Science and Biotechnology; Korea University; Seoul 136-713 Korea
| | - T. H. Kim
- Animal Genomics and Bioinformatics Division; National Institute of Animal Science; Rural Development Administration; Wanju 565-851 Korea
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Ibáñez-Escriche N, Magallón E, Gonzalez E, Tejeda JF, Noguera JL. Genetic parameters and crossbreeding effects of fat deposition and fatty acid profiles in Iberian pig lines. J Anim Sci 2016; 94:28-37. [PMID: 26812309 DOI: 10.2527/jas.2015-9433] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The aim of this study was to estimate the genetic and environmental parameters and crossbreeding effects on fatty acid and fat traits in the Iberian pig. Our final goal is to explore target selection traits and define crossbreeding strategies. The phenotypes were obtained under intensive management from 470 animals in a diallelic experiment involving Retinto, Torbiscal, and Entrepelado lines. The data set was composed of backfat thickness at the fourth rib (BFT), intramuscular fat (IMF) in the longissimus thoracis (LT), and the fatty acid profile for IMF and subcutaneous fat (SCF) traits. Data were analyzed through a Bayesian bivariate animal model by using a reparameterization of Dickerson's model. The results obtained showed an important genetic determinism for all traits analyzed with heritability ranging from 0.09 to 0.67. The common environment litter effect also had an important effect on IMF (0.34) and its fatty acid composition (0.06-0.53) at slaughter. The additive genetic correlation between BFT and IMF (additive genetic correlation [] = 0.31) suggested that it would be possible to improve lean growth independent of the IMF with an appropriate selection index. Furthermore, the high additive genetic correlation ( = 0.68) found between MUFA tissues would seem to indicate that either the LT or SCF could be used as the reference tissue for MUFA selection. The relevance of the crossbreeding parameters varied according to the traits analyzed. Backfat thickness at the fourth rib and the fatty acid profile of the IMF showed relevant differences between crosses, mostly due to line additive genetic effects associated with the Retinto line. On the contrary, those for IMF crosses were probably mainly attributable to heterosis effects. Particularly, heterosis effects were relevant for the Retinto and Entrepelado crosses (approximately 16% of the trait), which could be valuable for a crossbreeding system involving these lines.
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Zhang W, Bin Yang, Zhang J, Cui L, Ma J, Chen C, Ai H, Xiao S, Ren J, Huang L. Genome-wide association studies for fatty acid metabolic traits in five divergent pig populations. Sci Rep 2016; 6:24718. [PMID: 27097669 PMCID: PMC4838829 DOI: 10.1038/srep24718] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 04/05/2016] [Indexed: 01/09/2023] Open
Abstract
Fatty acid composition profiles are important indicators of meat quality and tasting flavor. Metabolic indices of fatty acids are more authentic to reflect meat nutrition and public acceptance. To investigate the genetic mechanism of fatty acid metabolic indices in pork, we conducted genome-wide association studies (GWAS) for 33 fatty acid metabolic traits in five pig populations. We identified a total of 865 single nucleotide polymorphisms (SNPs), corresponding to 11 genome-wide significant loci on nine chromosomes and 12 suggestive loci on nine chromosomes. Our findings not only confirmed seven previously reported QTL with stronger association strength, but also revealed four novel population-specific loci, showing that investigations on intermediate phenotypes like the metabolic traits of fatty acids can increase the statistical power of GWAS for end-point phenotypes. We proposed a list of candidate genes at the identified loci, including three novel genes (FADS2, SREBF1 and PLA2G7). Further, we constructed the functional networks involving these candidate genes and deduced the potential fatty acid metabolic pathway. These findings advance our understanding of the genetic basis of fatty acid composition in pigs. The results from European hybrid commercial pigs can be immediately transited into breeding practice for beneficial fatty acid composition.
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Affiliation(s)
- Wanchang Zhang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, P.R. China
| | - Bin Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, P.R. China
| | - Junjie Zhang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, P.R. China
| | - Leilei Cui
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, P.R. China
| | - Junwu Ma
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, P.R. China
| | - Congying Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, P.R. China
| | - Huashui Ai
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, P.R. China
| | - Shijun Xiao
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, P.R. China
| | - Jun Ren
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, P.R. China
| | - Lusheng Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, P.R. China
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Pig fatness in relation to FASN and INSIG2 genes polymorphism and their transcript level. Mol Biol Rep 2016; 43:381-9. [PMID: 26965892 PMCID: PMC4831998 DOI: 10.1007/s11033-016-3969-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 03/03/2016] [Indexed: 02/02/2023]
Abstract
Fat content and fatty acid (FA) profile influence meat quality in pigs. These parameters are important for consumers due to their preferences for healthy, high quality meat. The aim of this study was searching for polymorphisms and transcript levels of two positional and functional candidate genes, FASN and INSIG2, encoding proteins which take part in lipid metabolism. The molecular findings were analyzed in relation to fatness traits. Pigs of four commercial breeds were included: Polish Landrace (PL), Polish Large White (PLW), Duroc and Pietrain. DNA sequencing, 5′RACE technique and real time PCR and association analysis were applied. In total, 20 polymorphisms in 5′-flanking, 5′UTR and 3′UTR regions of FASN (12 novel polymorphisms) and INSIG2 (seven novel ones and one known) genes were found. Association study with fatness traits (PL n = 225, PLW n = 179) revealed that four polymorphisms (c.-2908G>A, c.-2335C>T, c.*42_43insCCCCA and c.*264A>G) of the FASN gene were associated with back fat thickness in PL and PLW. Since the polymorphisms were identified in regulatory sequences of the both genes also their transcript levels were studied in PLW (n = 23), PL (n = 22), Pietrain (n = 17) and Duroc (n = 23). The INSIG2 transcript level was positively correlated with monounsaturated FA contents in the longissimus thoracis et lumborum muscle. Several correlations were also found between three polymorphisms (c.*264A>G and c.-2335C>T in FASN, and c.-5527C>G in INSIG2) and the FA content. Our study showed that the FASN gene is a promising marker for subcutaneous fat tissue accumulation, while INSIG2 is a promising marker for FA composition.
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25
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Choy YH, Mahboob A, Cho CI, Choi JG, Choi IS, Choi TJ, Cho KH, Park BH. Genetic Parameters of Pre-adjusted Body Weight Growth and Ultrasound Measures of Body Tissue Development in Three Seedstock Pig Breed Populations in Korea. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:1696-702. [PMID: 26580436 PMCID: PMC4647077 DOI: 10.5713/ajas.14.0971] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 03/24/2015] [Accepted: 05/19/2015] [Indexed: 11/27/2022]
Abstract
The objective of this study was to compare the effects of body weight growth adjustment methods on genetic parameters of body growth and tissue among three pig breeds. Data collected on 101,820 Landrace, 281,411 Yorkshire, and 78,068 Duroc pigs, born in Korean swine breeder farms since 2000, were analyzed. Records included body weights on test day and amplitude (A)-mode ultrasound carcass measures of backfat thickness (BF), eye muscle area (EMA), and retail cut percentage (RCP). Days to 90 kg body weight (DAYS90), through an adjustment of the age based on the body weight at the test day, were obtained. Ultrasound measures were also pre-adjusted (ABF, EMA, AEMA, ARCP) based on their test day measures. The (co)variance components were obtained with 3 multi-trait animal models using the REMLF90 software package. Model I included DAYS90 and ultrasound traits, whereas model II and III accounted DAYS90 and pre-adjusted ultrasound traits. Fixed factors were sex (sex) and contemporary groups (herd-year-month of birth) for all traits among the models. Additionally, model I and II considered a linear covariate of final weight on the ultrasound measure traits. Heritability (h2) estimates for DAYS90, BF, EMA, and RCP ranged from 0.36 to 0.42, 0.34 to 0.43, 0.20 to 0.22, and 0.39 to 0.45, respectively, among the models. The h2 estimates of DAYS90 from model II and III were also somewhat similar. The h2 for ABF, AEMA, and ARCP were 0.35 to 0.44, 0.20 to 0.25, and 0.41 to 0.46, respectively. Our heritability estimates varied mostly among the breeds. The genetic correlations (rG) were moderately negative between DAYS90 and BF (−0.29 to −0.38), and between DAYS90 and EMA (−0.16 to −0.26). BF had strong rG with RCP (−0.87 to −0.93). Moderately positive rG existed between DAYS90 and RCP (0.20 to 0.28) and between EMA and RCP (0.35 to 0.44) among the breeds. For DAYS90, model II and III, its correlations with ABF, AEMA, and ARCP were mostly low or negligible except the rG between DAYS90 and AEMA from model III (0.27 to 0.30). The rG between AEMA and ABF and between AEMA and ARCP were moderate but with negative and positive signs, respectively; also reflected influence of pre-adjustments. However, the rG between BF and RCP remained non-influential to trait pre-adjustments or covariable fits. Therefore, we conclude that ultrasound measures taken at a body weight of about 90 kg as the test final should be adjusted for body weight growth. Our adjustment formulas, particularly those for BF and EMA, should be revised further to accommodate the added variation due to different performance testing endpoints with regard to differential growth in body composition.
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Affiliation(s)
- Yun Ho Choy
- Korea Animal Improvement Association, Seoul 137-811, Korea
| | - Alam Mahboob
- Korea Animal Improvement Association, Seoul 137-811, Korea
| | - Chung Il Cho
- Korea Animal Improvement Association, Seoul 137-811, Korea
| | - Jae Gwan Choi
- Korea Animal Improvement Association, Seoul 137-811, Korea
| | - Im Soo Choi
- Korea Animal Improvement Association, Seoul 137-811, Korea
| | - Tae Jeong Choi
- Korea Animal Improvement Association, Seoul 137-811, Korea
| | - Kwang Hyun Cho
- Korea Animal Improvement Association, Seoul 137-811, Korea
| | - Byoung Ho Park
- Korea Animal Improvement Association, Seoul 137-811, Korea
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Hong J, Kim D, Cho K, Sa S, Choi S, Kim Y, Park J, Schmidt GS, Davis ME, Chung H. Effects of genetic variants for the swine FABP3, HMGA1, MC4R, IGF2, and FABP4 genes on fatty acid composition. Meat Sci 2015; 110:46-51. [PMID: 26172243 DOI: 10.1016/j.meatsci.2015.06.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 04/28/2015] [Accepted: 06/24/2015] [Indexed: 12/13/2022]
Abstract
This study aimed to verify genetic relationships between fatty acid composition (FAC) and genotypes of several genes (FABP3, HMGA1, MC4R, IGF2, and FABP4) using pig breeds. The effects of genetic variations on FAC of the longissimus muscle were statistically significant with additive and dominance effects. The polymorphisms of FABP3 and IGF2 had the largest effects on stearic (C18:0, P=0.009) and γ-linoleic (C18:3n6, P=0.039) acids, respectively, whereas HMGA1 and FABP4 did not show significances. The analysis revealed that MC4R was significantly associated with palmitoleic acid (C16:ln7) and MUFA. Allele frequencies of the genes examined in this analysis were significantly skewed or fixed in the Korean native pig (KNP), whereas the allele frequencies of the crossbreds tended to fall between those of the purebreds except that HMGA1 and FABP4 had approximately the same allele frequencies with Duroc and KNP, respectively. The polymorphisms found in this study could be used as genetic markers in breeding programs to simultaneously change proportions of fatty acids in muscle tissues.
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Affiliation(s)
- Joonki Hong
- Swine Science Division, National Institute of Animal Science, Cheonan 330-801, Republic of Korea
| | - Duwan Kim
- Swine Science Division, National Institute of Animal Science, Cheonan 330-801, Republic of Korea
| | - Kyuho Cho
- Swine Science Division, National Institute of Animal Science, Cheonan 330-801, Republic of Korea
| | - Soojin Sa
- Swine Science Division, National Institute of Animal Science, Cheonan 330-801, Republic of Korea
| | - Sunho Choi
- Swine Science Division, National Institute of Animal Science, Cheonan 330-801, Republic of Korea
| | - Younghwa Kim
- Swine Science Division, National Institute of Animal Science, Cheonan 330-801, Republic of Korea
| | - Juncheol Park
- Swine Science Division, National Institute of Animal Science, Cheonan 330-801, Republic of Korea
| | - Gilberto Silber Schmidt
- International Technical Cooperation Center, Rural Development Administration, Suwon 441-707, Republic of Korea
| | - Michael E Davis
- The Ohio State University, Department of Animal Sciences, Columbus, OH 43210, USA
| | - Hoyoung Chung
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Suwon 441-701, Republic of Korea.
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Cabling MM, Kang HS, Lopez BM, Jang M, Kim HS, Nam KC, Choi JG, Seo KS. Estimation of Genetic Associations between Production and Meat Quality Traits in Duroc Pigs. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:1061-5. [PMID: 26104512 PMCID: PMC4478472 DOI: 10.5713/ajas.14.0783] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 11/26/2014] [Accepted: 02/13/2015] [Indexed: 11/27/2022]
Abstract
Data collected from 690 purebred Duroc pigs from 2009 to 2012 were used to estimate the heritability, and genetic and phenotypic correlations between production and meat quality traits. Variance components were obtained through the restricted maximum likelihood procedure using Wombat and SAS version 9.0. Animals were raised under the same management in five different breeding farms. The average daily gain, loin muscle area (LMA), backfat thickness (BF), and lean percent (LP) were measured as production traits. Meat quality traits included pH, cooking loss, lightness (L*), redness (a*), yellowness (b*), marbling score (MS), moisture content (MC), water holding capacity (WHC), and shear force. The results showed that the heritability estimates for meat quality traits varied largely from 0.19 to 0.79. Production traits were moderate to highly heritable from 0.41 to 0.73. Genotypically, the BF was positively correlated (p<0.05) with MC (0.786), WHC (0.904), and pH (0.328) but negatively correlated with shear force (−0.533). The results of genetic correlations indicated that selection for less BF could decrease pH, moisture content, and WHC and increase the shear force of meat. Additionally, a significant positive correlation was recorded between average daily gain and WHC, which indicates pork from faster-growing animals has higher WHC. Furthermore, selection for larger LMA and LP could increase MS and lightness color of meat. The meat quality and production traits could be improved simultaneously if desired. Hence, to avoid further deterioration of pork characteristics, appropriate selection of traits should be considered.
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Affiliation(s)
- M M Cabling
- Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Suncheon 540-950, Korea
| | - H S Kang
- Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Suncheon 540-950, Korea
| | - B M Lopez
- Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Suncheon 540-950, Korea
| | - M Jang
- Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Suncheon 540-950, Korea
| | - H S Kim
- Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Suncheon 540-950, Korea
| | - K C Nam
- Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Suncheon 540-950, Korea
| | - J G Choi
- Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Suncheon 540-950, Korea
| | - K S Seo
- Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Suncheon 540-950, Korea
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Ros-Freixedes R, Reixach J, Bosch L, Tor M, Estany J. Genetic correlations of intramuscular fat content and fatty acid composition among muscles and with subcutaneous fat in Duroc pigs1. J Anim Sci 2014; 92:5417-25. [DOI: 10.2527/jas.2014-8202] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- R. Ros-Freixedes
- Departament de Producció Animal – Agrotecnio Center, Universitat de Lleida, 191 Rovira Roure, 25198 Lleida, Catalonia, Spain
| | - J. Reixach
- Selección Batallé S.A., Av. Segadors s/n, 17421 Riudarenes, Spain
| | - L. Bosch
- Departament d'Enginyeria Química, Agrària i Tecnologia Agroalimentària, Universitat de Girona, Campus de Montilivi, 17071 Girona, Spain
| | - M. Tor
- Departament de Producció Animal – Agrotecnio Center, Universitat de Lleida, 191 Rovira Roure, 25198 Lleida, Catalonia, Spain
| | - J. Estany
- Departament de Producció Animal – Agrotecnio Center, Universitat de Lleida, 191 Rovira Roure, 25198 Lleida, Catalonia, Spain
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29
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Choi JG, Cho CI, Choi IS, Lee SS, Choi TJ, Cho KH, Park BH, Choy YH. Genetic parameter estimation in seedstock Swine population for growth performances. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 26:470-5. [PMID: 25049811 PMCID: PMC4093385 DOI: 10.5713/ajas.2012.12454] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 12/20/2012] [Accepted: 10/22/2012] [Indexed: 11/27/2022]
Abstract
The objective of this study was to estimate genetic parameters that are to be used for across-herd genetic evaluations of seed stock pigs at GGP level. Performance data with pedigree information collected from swine breeder farms in Korea were provided by Korea Animal Improvement Association (AIAK). Performance data were composed of final body weights at test days and ultrasound measures of back fat thickness (BF), rib eye area (EMA) and retail cut percentage (RCP). Breeds of swine tested were Landrace, Yorkshire and Duroc. Days to 90 kg body weight (DAYS90) were estimated with linear function of age and ADG calculated from body weights at test days. Ultrasound measures were taken with A-mode ultrasound scanners by trained technicians. Number of performance records after censoring outliers and keeping records pigs only born from year 2000 were of 78,068 Duroc pigs, 101,821 Landrace pigs and 281,421 Yorkshire pigs. Models included contemporary groups defined by the same herd and the same seasons of births of the same year, which was regarded as fixed along with the effect of sex for all traits and body weight at test day as a linear covariate for ultrasound measures. REML estimation was processed with REMLF90 program. Heritability estimates were 0.40, 0.32, 0.21 0.39 for DAYS90, ADG, BF, EMA, RCP, respectively for Duroc population. Respective heritability estimates for Landrace population were 0.43, 0.41, 0.22, and 0.43 and for Yorkshire population were 0.36, 0.38, 0.22, and 0.42. Genetic correlation coefficients of DAYS90 with BF, EMA, or RCP were estimated to be 0.00 to 0.09, −0.15 to −0.25, 0.22 to 0.28, respectively for three breeds populations. Genetic correlation coefficients estimated between BF and EMA was −0.33 to −0.39. Genetic correlation coefficient estimated between BF and RCP was high and negative (−0.78 to −0.85) but the environmental correlation coefficients between these two traits was medium and negative (near −0.35), which describes a highly correlated genetic response to selection on one or the other of these traits. Genetic Trends of all three breeds tend to be towards bigger EMA or greater RCP and shorter DAYS90 especially from generations born after year 2000.
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Affiliation(s)
- Jae Gwan Choi
- Animal Breeding and Genetics Division, National Institute of Animal Science, Songhwan-eup Shinbang-1-gill 114, Chonan, Korea
| | - Chung Il Cho
- Animal Breeding and Genetics Division, National Institute of Animal Science, Songhwan-eup Shinbang-1-gill 114, Chonan, Korea
| | - Im Soo Choi
- Animal Breeding and Genetics Division, National Institute of Animal Science, Songhwan-eup Shinbang-1-gill 114, Chonan, Korea
| | - Seung Soo Lee
- Animal Breeding and Genetics Division, National Institute of Animal Science, Songhwan-eup Shinbang-1-gill 114, Chonan, Korea
| | - Tae Jeong Choi
- Animal Breeding and Genetics Division, National Institute of Animal Science, Songhwan-eup Shinbang-1-gill 114, Chonan, Korea
| | - Kwang Hyun Cho
- Animal Breeding and Genetics Division, National Institute of Animal Science, Songhwan-eup Shinbang-1-gill 114, Chonan, Korea
| | - Byoung Ho Park
- Animal Breeding and Genetics Division, National Institute of Animal Science, Songhwan-eup Shinbang-1-gill 114, Chonan, Korea
| | - Yun Ho Choy
- Animal Breeding and Genetics Division, National Institute of Animal Science, Songhwan-eup Shinbang-1-gill 114, Chonan, Korea
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Muñoz M, Rodríguez MC, Alves E, Folch JM, Ibañez-Escriche N, Silió L, Fernández AI. Genome-wide analysis of porcine backfat and intramuscular fat fatty acid composition using high-density genotyping and expression data. BMC Genomics 2013; 14:845. [PMID: 24295214 PMCID: PMC4046688 DOI: 10.1186/1471-2164-14-845] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 11/25/2013] [Indexed: 01/15/2023] Open
Abstract
Background Porcine fatty acid composition is a key factor for quality and nutritive value of pork. Several QTLs for fatty acid composition have been reported in diverse fat tissues. The results obtained so far seem to point out different genetic control of fatty acid composition conditional on the fat deposits. Those studies have been conducted using simple approaches and most of them focused on one single tissue. The first objective of the present study was to identify tissue-specific and tissue-consistent QTLs for fatty acid composition in backfat and intramuscular fat, combining linkage mapping and GWAS approaches and conducted under single and multitrait models. A second aim was to identify powerful candidate genes for these tissue-consistent QTLs, using microarray gene expression data and following a targeted genetical genomics approach. Results The single model analyses, linkage and GWAS, revealed over 30 and 20 chromosomal regions, 24 of them identified here for the first time, specifically associated to the content of diverse fatty acids in BF and IMF, respectively. The analyses with multitrait models allowed identifying for the first time with a formal statistical approach seven different regions with pleiotropic effects on particular fatty acids in both fat deposits. The most relevant were found on SSC8 for C16:0 and C16:1(n-7) fatty acids, detected by both linkage and GWAS approaches. Other detected pleiotropic regions included one on SSC1 for C16:0, two on SSC4 for C16:0 and C18:2, one on SSC11 for C20:3 and the last one on SSC17 for C16:0. Finally, a targeted eQTL scan focused on regions showing tissue-consistent effects was conducted with Longissimus and fat gene expression data. Some powerful candidate genes and regions were identified such as the PBX1, RGS4, TRIB3 and a transcription regulatory element close to ELOVL6 gene to be further studied. Conclusions Complementary genome scans have confirmed several chromosome regions previously associated to fatty acid composition in backfat and intramuscular fat, but even more, to identify new ones. Although most of the detected regions were tissue-specific, supporting the hypothesis that the major part of genes affecting fatty acid composition differs among tissues, seven chromosomal regions showed tissue-consistent effects. Additional gene expression analyses have revealed powerful target regions to carry the mutation responsible for the pleiotropic effects. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-14-845) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- María Muñoz
- INIA, Mejora Genética Animal, 28040 Madrid, Spain.
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31
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Zomeño C, Blasco A, Hernández P. Divergent selection for intramuscular fat content in rabbits. II. Correlated responses on carcass and meat quality traits1. J Anim Sci 2013; 91:4532-9. [DOI: 10.2527/jas.2013-6417] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- C. Zomeño
- Institute for Animal Science and Technology, Universitat Politècnica de València, PO Box 22012, 46022 Valencia, Spain
| | - A. Blasco
- Institute for Animal Science and Technology, Universitat Politècnica de València, PO Box 22012, 46022 Valencia, Spain
| | - P. Hernández
- Institute for Animal Science and Technology, Universitat Politècnica de València, PO Box 22012, 46022 Valencia, Spain
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Pena RN, Noguera JL, Casellas J, Díaz I, Fernández AI, Folch JM, Ibáñez-Escriche N. Transcriptional analysis of intramuscular fatty acid composition in the longissimus thoracis muscle of Iberian × Landrace back-crossed pigs. Anim Genet 2013; 44:648-60. [PMID: 23826865 DOI: 10.1111/age.12066] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2013] [Indexed: 11/29/2022]
Abstract
This study aimed at identifying differential gene expression conditional on the fatty acid profile of the longissimus thoracis (Lt) muscle, a prime cut of economic relevance for fresh and cured pork production. A population of 110 Iberian (25%) × Landrace (75%) back-crossed pigs was used, because these two breeds exhibit extreme profiles of intramuscular saturated fatty acid, monounsaturated fatty acid (MUFA) and polyunsaturated fatty acid (PUFA) contents. Total RNA from Lt muscle was individually hybridized to GeneChip Porcine Genome arrays (Affymetrix). A principal component analysis was performed with data from the 110 animals to select 40 extreme animals based on the total fatty acid profile and the MUFA composition (MAP). Comparison of global transcription levels between extreme fatty acid profile pigs (n = 40) resulted in 219 differentially expressed probes (false discovery rate <0.10). Gene ontology, pathway and network analysis indicated that animals with higher percentages of PUFA exhibit a shift toward a more oxidative muscular metabolism state, with a raise in mitochondria function (PPARGC1A, ATF2), fatty acid uptake and oxidation (FABP5, MGLL). On the other hand, 87 probes were differentially expressed between MUFA composition groups (n = 40; false discovery rate <0.10). In particular, muscles rich in n-7 MUFA expressed higher levels of genes involved in lipid metabolism (GLUL, CRAT, PLA2G15) and lower levels of fatty acid elongation genes (ELOVL5). Moreover, the chromosomal position of FABP5, PAQR3, MGLL, PPARGC1A, GLUL and ELOVL5 co-localized with very relevant QTL for fat deposition and composition described in the same resource population. This study represents a complementary approach to identifying genes underlying these QTL effects.
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Affiliation(s)
- R N Pena
- Genètica i Millora Animal, IRTA, 191 Av. Rovira Roure, 25198, Lleida, Spain; Departament de Producció Animal, ETSEA, Universitat de Lleida, 191 Av. Rovira Roure, 25198, Lleida, Spain
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Casellas J, Vidal O, Pena RN, Gallardo D, Manunza A, Quintanilla R, Amills M. Genetics of serum and muscle lipids in pigs. Anim Genet 2013; 44:609-19. [DOI: 10.1111/age.12049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2013] [Indexed: 01/31/2023]
Affiliation(s)
- J. Casellas
- Departament de Ciència Animal i dels Aliments; Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
| | - O. Vidal
- Departament de Biologia; Universitat de Girona; Girona 17071 Spain
| | - R. N. Pena
- Departament de Producció Animal; Universitat de Lleida; Lleida 25198 Spain
| | - D. Gallardo
- Departament de Ciència Animal i dels Aliments; Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
| | - A. Manunza
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
| | | | - M. Amills
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
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Yeon SH, Lee SH, Choi BH, Lee HJ, Jang GW, Lee KT, Kim KH, Lee JH, Chung HY. Genetic variation of FASN is associated with fatty acid composition of Hanwoo. Meat Sci 2013; 94:133-8. [PMID: 23403305 DOI: 10.1016/j.meatsci.2013.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 12/31/2012] [Accepted: 01/02/2013] [Indexed: 10/27/2022]
Abstract
The objective of this study was to identify genetic variants in the bovine fatty acid synthase (FASN) gene and to evaluate associations with fatty acid composition from longissimus lumborum muscle using 90 purebred Hanwoo steers. Sequence alignments observed 6 genetic variants located in exons 20, 24, 32, 34, and 39, and PCR-RFLP analysis confirmed these variations. Genotypes of the g.15532A>C locus were significantly associated with Linolenic acid (C18:3), and genotypes of the g.17924G>A locus were significantly associated with Palmitic (C16:0), Palmitoleic (C16:1), Oleic (C18:1), saturated fatty acids, and unsaturated fatty acids. The analysis revealed that SFA and UFA showed significant correlations with fatty acid composition (Myristic (C14:0), Palmitic (C16:0), Stearic (C18:0), Oleic (C18:1), and Eicosenoic (C20:1) acids). Oleic acid (C18:1) was negatively correlated with Myristic (C14:0), Palmitic (C16:0), and Palmitoleic (C16:1) acids (P<0.001).
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Affiliation(s)
- S H Yeon
- National Institute of Animal Science, Pyeongchang, Republic of Korea
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35
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Hernández-Sánchez J, Amills M, Pena RN, Mercadé A, Manunza A, Quintanilla R. Genomic architecture of heritability and genetic correlations for intramuscular and back fat contents in Duroc pigs. J Anim Sci 2012; 91:623-32. [PMID: 23230112 DOI: 10.2527/jas.2012-5270] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genetic parameters such as heritability and correlations of fat traits in a Duroc population were dissected using molecular markers. The heritabilities of intramuscular fat in 2 muscles, the gluteus medius and LM, and back fat were 0.54, 0.48, and 0.23, respectively. The genetic correlations were well estimated with standardized SNP effects, being 0.65 between intramuscular fat traits and ∼0.37 between any intramuscular fat trait and back fat. Genetic correlations were overestimated when ignoring molecular information. Twelve chromosomes showed additive genetic variance for intramuscular fat compared with 8 for back fat. Population structure was accommodated using 4 different models. The number of significant, P < 5 × 10(-5) (suggestive, P < 2 × 10(-3)), SNP varied across models and ranged from 0 to 4 (2 to 261) for intramuscular fat in the gluteus medius, from 0 to 57 (9 to 564) for intramuscular fat in the LM, and from 3 to 4 (22 to 168) for back fat. Several SNP showed significant deviations from an additive mode of action. Only 2 SNP significantly affected 2 traits simultaneously.
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Affiliation(s)
- J Hernández-Sánchez
- IRTA, Genètica i Millora Animal, 191 Av. Alcalde Rovira Roure, 25198 Lleida, Spain.
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36
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Ros-Freixedes R, Reixach J, Tor M, Estany J. Expected genetic response for oleic acid content in pork1. J Anim Sci 2012; 90:4230-8. [DOI: 10.2527/jas.2011-5063] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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37
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Association of the gene encoding stearoyl-CoA desaturase (SCD) with fatty acid composition in an intercross population between Landrace and Korean native pigs. Mol Biol Rep 2012; 40:73-80. [PMID: 23124221 DOI: 10.1007/s11033-012-2014-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Accepted: 10/01/2012] [Indexed: 10/27/2022]
Abstract
Fatty acid (FA) composition is one of the most important parameters for the evaluation of meat quality. The stearoyl-CoA desaturase (SCD) gene is considered a positional candidate gene affecting FA composition in SSC14, based on previous quantitative trait loci studies. To evaluate the association of the SCD gene with FA composition in a Korean native pig × Landrace F(2) intercross population, we genotyped six single nucleotide polymorphisms (SNPs) of the SCD gene located in promoter region [2 SNPs (g.-353T>C, g.-233T>C)], exonic region [1 SNP (g.817C>T) in exon 2] and 3' UTR [3 SNPs (g.13311C>G, g.14384G>A, and g.14424C>T)] identified by massively parallel sequencing technology. Eighteen FA composition traits were measured in more than the 950 F(2) animals. A mixed-effect model was used to evaluate associations between these SNPs and FA composition traits in the F(2) intercross population. A detailed investigation detected that the five FA composition traits [palmitoleic acid (C16:1), stearic acid (C18:0), arachidic acid (C20:0), saturated FA, and unsaturated FA] were highly significant (P < 4.7 × 10(-5); C20:0) in association with the SNP g.-233T>C, SNP g.817C>T, SNP g.13311C>G and SNP g.14384G>A in the SCD gene, whereas SNP g.14424C>T was only significantly associated with palmitoleic acid (C16:1, P = 1.4 × 10(-3)). No significant association of FA composition traits with SNP g.-353T>C was detected. In particular, the SNP g.14384G>A accounted for 30.6 % of the additive genetic variance of palmitoleic acid (P = 1.9 × 10(-10)). These results suggest the SCD gene has a strong effect on FA composition in the crossbred pig population.
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Maharani D, Jung YK, Jo C, Jung WY, Nam KC, Seo KS, Lee SH, Lee JH. Evaluation of Three Candidate Genes Affecting Fatty Acid Composition in Pigs. Korean J Food Sci Anim Resour 2012. [DOI: 10.5851/kosfa.2012.32.1.6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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Rauw W, Diaz I, Francés F, Corella D, Soler J, Tibau J, Gomez-Raya L. The relationship between feed intake behaviour with intramuscular fat, cholesterol and fatty acid composition in pork. J Anim Breed Genet 2011; 129:289-97. [DOI: 10.1111/j.1439-0388.2011.00978.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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40
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Uemoto Y, Nakano H, Kikuchi T, Sato S, Ishida M, Shibata T, Kadowaki H, Kobayashi E, Suzuki K. Fine mapping of porcine SSC14 QTL and SCD gene effects on fatty acid composition and melting point of fat in a Duroc purebred population. Anim Genet 2011; 43:225-8. [PMID: 22404360 DOI: 10.1111/j.1365-2052.2011.02236.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The stearoyl-CoA desaturase (delta-9-desaturase; SCD) gene is a candidate gene for fatty acid composition. It is located on pig SSC14 in a region where quantitative trait loci (QTL) for fatty acid composition were previously detected in a Duroc purebred population. The objective of the present study was to fine map the QTL, to identify polymorphisms of the pig SCD gene and to examine the effects of SCD polymorphisms on fatty acid composition and melting point of fat in the population. The pigs were examined for fatty acid composition and melting point of inner and outer subcutaneous fat and inter- and intramuscular fat; the number of pigs examined was 479-521. Two SNPs (g.-353C>T and g.-233T>C) were identified in the promoter region of the SCD gene and were completely linked in the pigs from the base generation. In all pigs, 19 microsatellite markers and SCD haplotypes were then genotyped. Different statistical models were applied to evaluate the effects of QTL and the possible causality of the SCD gene variants with respect to the QTL. The results show that all significant QTL for C14:0, C18:0, C18:1 and melting point of fat were detected in the same region, located near the SCD gene. The results also show a significant association between SCD haplotypes and fatty acid composition and fat melting point in this population. These results indicate that the haplotype of the SCD gene has a strong effect on fatty acid composition and melting point of fat.
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Affiliation(s)
- Y Uemoto
- National Livestock Breeding Center, Nishigo, Fukushima, Japan.
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41
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Bonfatti V, Cecchinato A, Sturaro E, Gallo L, Carnier P. Computer image analysis traits of cross-sectioned dry-cured hams: A genetic analysis1. J Anim Sci 2011; 89:2326-35. [DOI: 10.2527/jas.2010-3675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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42
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Uemoto Y, Soma Y, Sato S, Ishida M, Shibata T, Kadowaki H, Kobayashi E, Suzuki K. Genome-wide mapping for fatty acid composition and melting point of fat in a purebred Duroc pig population. Anim Genet 2011; 43:27-34. [DOI: 10.1111/j.1365-2052.2011.02218.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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43
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Yang B, Navarro N, Noguera J, Muñoz M, Guo T, Yang K, Ma J, Folch J, Huang L, Pérez-Enciso M. Building phenotype networks to improve QTL detection: a comparative analysis of fatty acid and fat traits in pigs. J Anim Breed Genet 2011; 128:329-43. [DOI: 10.1111/j.1439-0388.2011.00928.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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44
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A review of the factors influencing the development of intermuscular adipose tissue in the growing pig. Meat Sci 2011; 88:213-20. [PMID: 21303725 DOI: 10.1016/j.meatsci.2011.01.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 01/10/2011] [Accepted: 01/10/2011] [Indexed: 11/21/2022]
Abstract
Compared with subcutaneous or abdominal fat depots of pig carcasses, intermuscular fat displays a number of original properties. It cannot be easily removed from fresh or processed meat delivered to consumers and has therefore an influence on consumer acceptability of pork. Particular compositional characteristics of intermuscular fat include low lipid content and small size of adipocytes. How age (or body weight), gender, castration, environmental temperature, feeding restriction, diet composition, as well as genetic factors affect intermuscular fat development and composition are surveyed in this review paper. Up to now, few studies have specifically dealt with the intermuscular compartment of body fat while very abundant information is available on the subcutaneous one. As a general rule, any factor, either genetic or non-genetic, which causes a decrease of whole carcass fat deposition generates a higher relative importance of the intermuscular fraction of total fat as well as an increased degree of unsaturation of constituent fatty acids.
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Yang KX, Ma JW, Guo YM, Guo TF, Zhao YG, Ding NS, Betti M, Plastow GS, Huang LS. Correlations between fat depot traits and fatty acid composition in abdominal subcutaneous adipose tissue and longissimus muscle: Results from a White Duroc × Erhualian intercross F2 population1. J Anim Sci 2010; 88:3538-45. [DOI: 10.2527/jas.2009-2602] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Association of genetic variants for FABP3 gene with back fat thickness and intramuscular fat content in pig. Mol Biol Rep 2010; 38:2161-6. [DOI: 10.1007/s11033-010-0344-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Accepted: 09/04/2010] [Indexed: 12/15/2022]
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Casellas J, Noguera JL, Reixach J, Díaz I, Amills M, Quintanilla R. Bayes factor analyses of heritability for serum and muscle lipid traits in Duroc pigs1. J Anim Sci 2010; 88:2246-54. [DOI: 10.2527/jas.2009-2205] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Genetic parameters for tissue and fatty acid composition of backfat, perirenal fat and longissimus muscle in Large White and Landrace pigs. Animal 2010; 4:497-504. [DOI: 10.1017/s1751731109991261] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Ntawubizi M, Colman E, Janssens S, Raes K, Buys N, De Smet S. Genetic parameters for intramuscular fatty acid composition and metabolism in pigs. J Anim Sci 2009; 88:1286-94. [PMID: 20042548 DOI: 10.2527/jas.2009-2355] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The aim of this study was to estimate genetic parameters for pork intramuscular fatty acid (FA) composition and indices for desaturase and elongase activities involved in n-3 and n-6 PUFA metabolism. The LM of 437 slaughter pigs was analyzed for FA composition (expressed as g/100 g of FA). Indices for enzyme activities were calculated from product to precursor FA ratios. Genetic parameters were estimated with single- and multi-trait animal models. The total FA content, reflecting the intramuscular fat content, was either included or not in the model. Results from the models without total FA content showed relatively high heritability estimates, generally above 0.50, for the proportion of the most important MUFA and PUFA, compared with much smaller values for the SFA. When total FA content was included in the models, heritability values decreased (P < 0.001) for most individual FA and for all sums of FA groups, except for C18:0, C18:3n-6, and C18:3n-3. Heritability estimates for the ratios C20:4n-6/C18:2n-6 and C22:6n-3/C18:3n-3, reflecting the overall conversion in the n-6 and n-3 PUFA pathway, respectively, were 0.29 and 0.35, respectively, with total FA content in the model and increased to 0.38 and 0.49, respectively, if total FA content was not in the model. Heritabilities for other more specific indices were of the same order. Genetic correlations between PUFA proportions and indices for enzyme activities with ADG were mostly negative, whereas the correlations with carcass lean meat percentage were mostly positive. It was concluded that there is meaningful genetic variation for long-chain PUFA metabolism that is only partly dependent on the carcass and muscle fat content. This may allow selection for improved FA composition of pork.
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Affiliation(s)
- M Ntawubizi
- Laboratory for Animal Nutrition and Animal Product Quality, Department of Animal Production, Ghent University, Proefhoevestraat 10, 9090 Melle, Belgium
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