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Li Z, Hu T, Li R, Li J, Wang Y, Li Y, Lin Y, Wang Y, Jiani X. Effect of DHCR7 on adipocyte differentiation in goats. Anim Biotechnol 2024; 35:2298399. [PMID: 38157229 DOI: 10.1080/10495398.2023.2298399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Cholesterol is regarded as a signaling molecule in regulating the metabolism and function of fat cells, in which 7-Dehydrocholesterol reductase (DHCR7) is a key enzyme that catalyzes the conversion of 7-dehydrocholesterol to cholesterol, however, the exact function of DHCR7 in goat adipocytes remains unknown. Here, the effect of DHCR7 on the formation of subcutaneous and intramuscular fat in goats was investigated in vitro, and the result indicated that the mRNA level of DHCR7 showed a gradual downward trend in subcutaneous adipogenesis, but an opposite trend in intramuscular adipogenesis. In the process of subcutaneous preadipocytes differentiation, overexpression of DHCR7 inhibited the expression of adipocytes differentiation marker genes (CEBP/α, CEBP/β, SREBP1 and AP2), lipid metabolism-related genes (AGPAT6, FASN, SCD1 and LPL), and the lipid accumulation. However, in intramuscular preadipocyte differentiation, DHCR7 overexpression showed a promoting effect on adipocyte differentiation marker genes (CEBP/α, CEBP/β, PPARγ and SREBP1) and lipid metabolism-related genes (GPAM, AGPAT6, DGAT1 and SCD1) expression, and on lipid accumulation. In summary, our work demonstrated that DHCR7 played an important role in regulating adipogenic differentiation and lipid metabolism in preadipocytes in goats, which is of great significance for uncovering the underlying molecular mechanism of adipocyte differentiation and improving goat meat quality.
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Affiliation(s)
- Zhibin Li
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Protection and Utilization of Ministry of Education/Sichuan Province, Southwest Minzu University, Chengdu, China
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Tingting Hu
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Protection and Utilization of Ministry of Education/Sichuan Province, Southwest Minzu University, Chengdu, China
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Ruiwen Li
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Jinlan Li
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Protection and Utilization of Ministry of Education/Sichuan Province, Southwest Minzu University, Chengdu, China
| | - Youli Wang
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Protection and Utilization of Ministry of Education/Sichuan Province, Southwest Minzu University, Chengdu, China
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yanyan Li
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Protection and Utilization of Ministry of Education/Sichuan Province, Southwest Minzu University, Chengdu, China
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yaqiu Lin
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Protection and Utilization of Ministry of Education/Sichuan Province, Southwest Minzu University, Chengdu, China
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yong Wang
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Protection and Utilization of Ministry of Education/Sichuan Province, Southwest Minzu University, Chengdu, China
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xing Jiani
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Protection and Utilization of Ministry of Education/Sichuan Province, Southwest Minzu University, Chengdu, China
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
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Yuan PQ, Lin S, Peng JY, Li YX, Liu YH, Wang P, Zhong HJ, Yang XM, Che LQ, Feng B, Batonon-Alavo DI, Mercier Y, Zhang XL, Lin Y, Xu SY, Li J, Zhuo Y, Wu D, Fang ZF. Effects of dietary methionine supplementation from different sources on growth performance and meat quality of barrows and gilts. Animal 2023; 17:100986. [PMID: 37820406 DOI: 10.1016/j.animal.2023.100986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 08/29/2023] [Accepted: 09/07/2023] [Indexed: 10/13/2023] Open
Abstract
Methionine is indispensable for growth and meat formation in pigs. However, it is still unclear that increasing dietary sulphur-containing amino acid (SAA) levels using different methionine sources affects the growth performance and meat quality of barrows and gilts. To investigate this, 144 pigs (half barrows and half gilts) were fed the control (100% SAA, CON), DL-Methionine (125% SAA, DL-Met)-supplemented, or OH-Methionine (125% SAA, OH-Met)-supplemented diets during the 11-110 kg period. The results showed that plasma methionine levels varied among treatments during the experimental phase, with increased plasma methionine levels observed following increased SAA consumption during the 25-45 kg period. In contrast, pigs fed the DL-Met diet had lower plasma methionine levels than those fed the CON diet (95-110 kg). Additionally, gilts fed the DL-Met or OH-Met diets showed decreased drip loss in longissimus lumborum muscle (LM) compared to CON-fed gilts. OH-Met-fed gilts had higher pH45min values than those fed the CON or DL-Met diets, whereas OH-Met-fed barrows had higher L45min values than those fed the CON or DL-Met diets. Moreover, increased consumption of SAA, regardless of the methionine source, tended to decrease the shear force of the LM in pigs. In conclusion, this study indicates that increasing dietary levels of SAA (+25%) appeared to improve the meat quality of gilts by decreasing drip loss and increasing meat tenderness.
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Affiliation(s)
- P Q Yuan
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, People's Republic of China; Key Laboratory of Agricultural Product Processing and Nutrition Health (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairsand, College of Food Science, Sichuan Agricultural University, Ya'an 625014, People's Republic of China
| | - S Lin
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, People's Republic of China; Key Laboratory of Urban Agriculture in South China, Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, People's Republic of China
| | - J Y Peng
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Y X Li
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Y H Liu
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - P Wang
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - H J Zhong
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - X M Yang
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - L Q Che
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - B Feng
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | | | - Y Mercier
- Adisseo France S.A.S, CERN, Commentry, France
| | - X L Zhang
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Y Lin
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - S Y Xu
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - J Li
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Y Zhuo
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - D Wu
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, People's Republic of China
| | - Z F Fang
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu 611130, People's Republic of China; Key Laboratory of Agricultural Product Processing and Nutrition Health (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairsand, College of Food Science, Sichuan Agricultural University, Ya'an 625014, People's Republic of China.
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Yuan S, Tian S, Meng C, Ji F, Zhou B, Rushdi HE, Ye M. The Identification of Functional Genes Affecting Fat-Related Meat Traits in Meat-Type Pigeons Using Double-Digest Restriction-Associated DNA Sequencing and Molecular Docking Analysis. Animals (Basel) 2023; 13:3256. [PMID: 37893980 PMCID: PMC10603692 DOI: 10.3390/ani13203256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/26/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
The Chinese indigenous Shiqi (SQ) pigeon and the imported White King (WK) pigeon are two meat-type pigeon breeds of economical and nutritional importance in China. They displayed significant differences in such meat quality traits as intramuscular fat (IMF) content and fatty acid (FA) compositions in the breast muscles. In this study, we aimed to screen candidate genes that could affect fat-related meat quality traits in meat-type pigeons. We investigated the polymorphic variations at the genomic level using double-digest restriction-associated DNA (ddRAD) sequencing in 12 squabs of SQ and WK pigeons that exhibited significant inter-breed differences in IMF content as well as FA and amino acid compositions in the breast muscles, and screened candidate genes influencing fat-related traits in squabs through gene ontology analysis and pathway analysis. By focusing on 6019 SNPs, which were located in genes with correct annotations and had the potential to induce changes in the encoded proteins, we identified 19 genes (ACAA1, ACAA2, ACACB, ACADS, ACAT1, ACOX3, ACSBG1, ACSBG2, ACSL1, ACSL4, ELOVL6, FADS1, FADS2, HACD4, HADH, HADHA, HADHB, MECR, OXSM) as candidate genes that could affect fat-related traits in squabs. They were significantly enriched in the pathways of FA metabolism, degradation, and biosynthesis (p < 0.05). Results from molecular docking analysis further revealed that three non-synonymous amino acid alterations, ACAA1(S357N), ACAA2(T234I), and ACACB(H1418N), could alter the non-bonding interactions between the enzymatic proteins and their substrates. Since ACAA1, ACAA2, and ACACB encode rate-limiting enzymes in FA synthesis and degradation, alterations in the enzyme-substrate binding affinity may subsequently affect the catalytic efficiency of enzymes. We suggested that SNPs in these three genes were worthy of further investigation into their roles in explaining the disparities in fat-related traits in squabs.
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Affiliation(s)
- Siyu Yuan
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (S.Y.); (S.T.); (C.M.)
| | - Shaoqi Tian
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (S.Y.); (S.T.); (C.M.)
| | - Chuang Meng
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (S.Y.); (S.T.); (C.M.)
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
| | - Feng Ji
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100089, China;
| | - Bin Zhou
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China;
| | - Hossam E. Rushdi
- Joint International Research Laboratory of Agricultural & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
| | - Manhong Ye
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China; (S.Y.); (S.T.); (C.M.)
- Joint International Research Laboratory of Agricultural & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
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4
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Hnokaew P, Moonmanee T, Phatsara C, Chongkasikit N, Trirawong P, Oluodo LA, Yammuen-Art S. Effect of UV-B irradiated vitamin D enriched yeast supplementation on milk performance and blood chemical profiles in dairy cows. Anim Biosci 2023; 36:1536-1545. [PMID: 37170501 PMCID: PMC10475374 DOI: 10.5713/ab.23.0013] [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: 01/13/2023] [Revised: 03/29/2023] [Accepted: 05/01/2023] [Indexed: 05/13/2023] Open
Abstract
OBJECTIVE The objective was to evaluate the effects of UV-B irradiated vitamin D-enriched yeast supplementation on milk yield, milk composition, vitamin D in milk, milk fatty acids, blood chemistry, and 25(OH)D status in dairy cows. METHODS Six Thai Friesian cows (milk production, 11.2±2.0 kg/d; body weight, 415.0±20.0 kg; and days in milk, 90.0±6.0) were allocated to each treatment in a 3×3 Latin square design, with three treatments and three periods. Each period of the Latin square lasted 49 days consisting of 14 days for diet adaptation and 35 days for sample collection. Dairy cows were randomly assigned to one of three treatments: i) feeding a basal diet without yeast (CON); ii) basal diet + 5 g of live yeast (75 IU/head/d of vitamin D2; LY); and iii) basal diet + 5 g of UV-B irradiated vitamin D enriched yeast (150,000 IU/head/d of vitamin D2; VDY). Feed intake and milk production were recorded daily, milk sample collection occurred on days 14 and 35 of each collection period, and blood plasma was collected on days 0, 7, 14, 21, 28, and 35 of each collection period. RESULTS The results show that after a trial period of 14 and 35 days, the VDY group had significantly higher vitamin D content in milk than the LY and CON groups (376.41 vs 305.15, 302.14 ng/L and 413.46 vs 306.76, 301.12 ng/L, respectively). At days 7, 14, 21, 28, and 35 of the experiment, cows fed the VDY group had significantly higher 25(OH)D2 status in blood than the CON and LY groups (51.07 vs 47.16, 48.05 ng/mL; 54.96 vs 45.43, 46.91 ng/mL; 56.16 vs 46.87, 47.16 ng/mL; 60.67 vs 44.39, 46.17 ng/mL and 63.91 vs 45.88, 46.88 ng/mL), respectively. CONCLUSION In conclusion, UV-B irradiated vitamin D-enriched yeast supplementation could improve vitamin D content in the milk and 25(OH)D status in dairy cows during the lactation period.
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Affiliation(s)
- Patipan Hnokaew
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200,
Thailand
| | - Tossapol Moonmanee
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200,
Thailand
- Innovative Agriculture Research Center, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200,
Thailand
| | - Chirawath Phatsara
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200,
Thailand
| | - Nattaphon Chongkasikit
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200,
Thailand
| | - Prayad Trirawong
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200,
Thailand
- Department of Animal Science, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom 73140,
Thailand
| | - Lukman Abiola Oluodo
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200,
Thailand
- Outreach Department, Rubber Research Institute of Nigeria, Benin City, 1069,
Nigeria
| | - Saowaluck Yammuen-Art
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200,
Thailand
- Innovative Agriculture Research Center, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200,
Thailand
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Yang M, Zhang R, Liu X, Shi G, Liu H, Wang L, Hou X, Shi L, Wang L, Zhang L. Integrating genome-wide association study with RNA-seq revealed DBI as a good candidate gene for intramuscular fat content in Beijing black pigs. Anim Genet 2023; 54:24-34. [PMID: 36305366 DOI: 10.1111/age.13270] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 10/04/2022] [Accepted: 10/08/2022] [Indexed: 01/07/2023]
Abstract
Increasing intramuscular fat (IMF) content can enhance the sensory quality of meat, including tenderness, juiciness, flavor, and color. Genome-wide association study and RNA-sequencing (RNA-seq) analysis were used to identify candidate IMF genes in Beijing Black pigs, a popular species among consumers in northern China. Two and three single nucleotide polymorphisms were significantly associated with IMF in SSC13 and SSC15 respectively. Solute carrier family 4 member 7 (SLC4A7) on SSC13 and insulin induced gene 2 (INSIG2), coiled-coil domain containing 93 (CCDC93), and diazepam binding inhibitor acyl-CoA binding protein (DBI) on SSC15 are good candidate genes in this population. Furthermore, RNA-seq analysis was performed between high and low IMF groups, and 534 differentially expressed genes were identified. In addition, based on differentially expressed genes, Kyoto Encyclopedia of Genes and Genomes analysis revealed that peroxisome proliferator-activated receptors and FoxO signaling pathway pathways might contribute to IMF. Moreover, the DBI gene was identified as a candidate for IMF both by genome-wide association study and RNA-seq analysis, suggesting that it might be a crucial candidate gene for influencing IMF in Beijing Black pigs.
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Affiliation(s)
- Man Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Run Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiance Liu
- Beijing Heiliu Animal Husbandry Technology Co, Ltd, Beijing, China
| | - Guohua Shi
- Beijing Heiliu Animal Husbandry Technology Co, Ltd, Beijing, China
| | - Hai Liu
- Beijing Heiliu Animal Husbandry Technology Co, Ltd, Beijing, China
| | - Ligang Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinhua Hou
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijun Shi
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lixian Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Longchao Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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6
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Kong Y, Liu C, Zhang X, Liu X, Li W, Li F, Wang X, Yue X. Characterization of fatty acid compositions in longissimus thoracis muscle and identification of candidate gene and SNPs related to polyunsaturated fatty acid in Hu sheep. J Anim Sci 2023; 101:skac382. [PMID: 36394948 PMCID: PMC9833039 DOI: 10.1093/jas/skac382] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022] Open
Abstract
Fatty acid (FA) composition contributes greatly to the quality and nutritional value of lamb meat. In the present study, FA was measured in longissimus thoracis (LT) muscles of 1,085 Hu sheep using gas chromatography. Comparative transcriptomic analysis was conducted in LT muscles to identify differentially expressed genes (DEGs) between six individuals with high polyunsaturated fatty acids (H-PUFA, 15.27% ± 0.42%) and six with low PUFA (L-PUFA, 5.22% ± 0.25%). Subsequently, the single nucleotide polymorphisms (SNPs) in a candidate gene PLIN2 were correlated with FA traits. The results showed a total of 29 FA compositions and 8 FA groups were identified, with the highest content of monounsaturated fatty acids (MUFA, 46.54%, mainly C18:1n9c), followed by saturated fatty acids (SFA, 44.32%, mainly C16:0), and PUFA (8.72%, mainly C18:2n6c), and significant correlations were observed among the most of FA traits. Transcriptomic analyses identified 110 upregulated and 302 downregulated DEGs between H-PUFA and L-PUFA groups. The functional enrichment analysis revealed three significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and 17 gene ontology (GO) terms, in which regulation of lipolysis in adipocytes, the AMPK signaling pathway, and the PPAR signaling pathway may play important roles in FA metabolism and biosynthesis. In addition, weighted gene co-expression network analysis (WGCNA) identified 37 module genes associated with PUFA-related traits. In general, PLIN1, LIPE, FABP4, LEP, ACACA, ADIPOQ, SCD, PCK2, FASN, PLIN2, LPL, FABP3, THRSP, and ACADVL may have a great impact on PUFA metabolism and lipid deposition. Four SNPs within PLIN2 were significantly associated with FA. Of those, SNP1 (g.287 G>A) was significantly associated with C18:1n9c and MUFA, and SNP4 (g.7807 T>C) was significantly correlated with PUFA (C18:3n3). In addition, the combined genotype of SNP1 (g.287 G>A), SNP3 (g.7664 T>C), and SNP4 (g.7807 T>C) were significantly correlated with C16:1, C17:0, C18:1C6, PUFA (C18:3n3, C22:6n3), and n-6/n-3 PUFA. These results contribute to the knowledge of the biological mechanisms and genetic markers involved in the composition of FA in Hu sheep.
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Affiliation(s)
- Yuanyuan Kong
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Chongyang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Xueying Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Xing Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Wenqiao Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Fadi Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Xinji Wang
- Extension Station of Animal Husbandry and Veterinary Medicine in Minqin, Minqin County 733300, China
| | - Xiangpeng Yue
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
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7
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Óvilo C, Trakooljul N, Núñez Y, Hadlich F, Murani E, Ayuso M, García-Contreras C, Vázquez-Gómez M, Rey AI, Garcia F, García-Casco JM, López-Bote C, Isabel B, González-Bulnes A, Wimmers K, Muñoz M. SNP discovery and association study for growth, fatness and meat quality traits in Iberian crossbred pigs. Sci Rep 2022; 12:16361. [PMID: 36180572 PMCID: PMC9525691 DOI: 10.1038/s41598-022-20817-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/19/2022] [Indexed: 11/22/2022] Open
Abstract
Iberian pigs and its crosses are produced to obtain high-quality meat products. The objective of this work was to evaluate a wide panel of DNA markers, selected by biological and functional criteria, for association with traits related to muscle growth, fatness, meat quality and metabolism. We used 18 crossbred Iberian pigs with divergent postnatal growth patterns for whole genome sequencing and SNP discovery, with over 13 million variants being detected. We selected 1023 missense SNPs located on annotated genes and showing different allele frequencies between pigs with makerdly different growth patterns. We complemented this panel with 192 candidate SNPs obtained from literature mining and from muscle RNAseq data. The selected markers were genotyped in 480 Iberian × Duroc pigs from a commercial population, in which phenotypes were obtained, and an association study was performed for the 1005 successfully genotyped SNPs showing segregation. The results confirmed the effects of several known SNPs in candidate genes (such as LEPR, ACACA, FTO, LIPE or SCD on fatness, growth and fatty acid composition) and also disclosed interesting effects of new SNPs in less known genes such as LRIG3, DENND1B, SOWAHB, EPHX1 or NFE2L2 affecting body weight, average daily gain and adiposity at different ages, or KRT10, NLE1, KCNH2 or AHNAK affecting fatness and FA composition. The results provide a valuable basis for future implementation of marker-assisted selection strategies in swine and contribute to a better understanding of the genetic architecture of relevant traits.
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Affiliation(s)
- C Óvilo
- Departamento Mejora Genética Animal, INIA-CSIC, Madrid, Spain.
| | - N Trakooljul
- Research Institute for Farm Animal Biology, FBN, Dummerstorf, Germany
| | - Y Núñez
- Departamento Mejora Genética Animal, INIA-CSIC, Madrid, Spain
| | - F Hadlich
- Research Institute for Farm Animal Biology, FBN, Dummerstorf, Germany
| | - E Murani
- Research Institute for Farm Animal Biology, FBN, Dummerstorf, Germany
| | - M Ayuso
- CoPeD, Department of Veterinary Sciences, University of Antwerp, Wilrijk, Belgium
| | - C García-Contreras
- Department of Nutrition and Sustainable Animal Production, CSIC, Granada, Spain
| | | | - A I Rey
- Departamento de Producción Animal, Facultad de Veterinaria, UCM, Madrid, Spain
| | - F Garcia
- Departamento Mejora Genética Animal, INIA-CSIC, Madrid, Spain
| | | | - C López-Bote
- Departamento de Producción Animal, Facultad de Veterinaria, UCM, Madrid, Spain
| | - B Isabel
- Departamento de Producción Animal, Facultad de Veterinaria, UCM, Madrid, Spain
| | - A González-Bulnes
- Facultad de Medicina Veterinaria, Universidad Cardenal Herrera-CEU, Valencia, Spain
| | - K Wimmers
- Research Institute for Farm Animal Biology, FBN, Dummerstorf, Germany
| | - M Muñoz
- Departamento Mejora Genética Animal, INIA-CSIC, Madrid, Spain
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Improvement of Intramuscular Fat in longissimus Muscle of Finishing Thai Crossbred Black Pigs by Perilla Cake Supplementation in a Low-Lysine Diet. Foods 2022; 11:foods11070907. [PMID: 35406994 PMCID: PMC8997464 DOI: 10.3390/foods11070907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/17/2022] [Accepted: 03/20/2022] [Indexed: 11/16/2022] Open
Abstract
This study was conducted to find out the effects of perilla cake (PC) supplementation in a low-lysine diet on Thai crossbred finishing pigs’ productivity, carcass and meat quality, and fatty acid composition. For six weeks, a total of 21 barrows of finishing pigs were fed with three dietary treatments (T1: basal diet, T2: 2.5 percent PC supplementation in a low-lysine diet, and T3: 4.5 percent PC supplementation in a low-lysine diet). The results show that the intramuscular fat and marbling score was significantly increased by T2 and T3. On the other hand, it was found that the boiling loss and shear force value were significantly decreased by T2 and T3 (p < 0.05). In a low-lysine diet, dietary PC supplementation caused a significant increase in malondialdehyde levels in meat (p < 0.05) compared with the basal diet. It was also shown that alpha-linolenic acid level in backfat and the longissimus thoracis et lumborum muscle was increased considerably by T2 and T3. Therefore, supplementing PC in a low-lysine diet may be an alternative strategy for improving the meat quality of late-phase pigs.
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Mekchay S, Pothakam N, Norseeda W, Supakankul P, Teltathum T, Liu G, Naraballobh W, Khamlor T, Sringarm K, Krutmuang P. Association of IFNA16 and TNFRSF19 Polymorphisms with Intramuscular Fat Content and Fatty Acid Composition in Pigs. BIOLOGY 2022; 11:109. [PMID: 35053107 PMCID: PMC8773020 DOI: 10.3390/biology11010109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/18/2021] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
Interferon-alpha-16 (IFNA16) and tumor necrosis factor receptor superfamily member 19 (TNFRSF19) are cytokines that may play a role in adipogenesis and fatness. Single nucleotide polymorphisms (SNPs) of the porcine IFNA16 and TNFRSF19 genes were verified and their association with intramuscular fat (IMF) content and fatty acid (FA) composition were evaluated in commercial crossbred pigs. Two non-synonymous SNPs of the porcine IFNA16 c.413G > A and TNFRSF19 c.860G > C loci were detected in commercial crossbred pigs. The porcine IFNA16 c.413G >A polymorphism was significantly associated with stearic acid, total saturated FAs (SFAs), and the ratio of monounsaturated FAs (MUFAs) to SFAs (p < 0.05). Furthermore, the porcine TNFRSF19 c.860G > C polymorphism was found to be significantly associated with IMF content and arachidic acid levels (p < 0.05). The results revealed that porcine IFNA16 and TNFRSF19 polymorphisms are related to IMF content and/or FA composition and affirmed the importance of these cytokine genes as potential candidate genes for lipid deposition and FA composition in the muscle tissue of pigs.
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Affiliation(s)
- Supamit Mekchay
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; (N.P.); (W.N.); (T.K.); (K.S.)
- Center of Excellence on Agricultural Biotechnology: (AG-BIO/MHESI), Bangkok 10900, Thailand
- Cluster of Research and Development of Pharmaceutical and Natural Products Innovation for Human or Animal, Chiang Mai University, Chiang Mai 50200, Thailand
- Innovative Agriculture Research Center, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Nanthana Pothakam
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; (N.P.); (W.N.); (T.K.); (K.S.)
- Center of Excellence on Agricultural Biotechnology: (AG-BIO/MHESI), Bangkok 10900, Thailand
- Veterinary, Conservation and Research Section, Animal Management Division, Chiang Mai Night Safari, Chiang Mai 50230, Thailand
| | - Worrarak Norseeda
- Department of Agriculture, Faculty of Agricultural Technology, Lampang Rajabhat University, Lampang 52100, Thailand;
| | - Pantaporn Supakankul
- Division of Animal Science, School of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand;
| | - Tawatchai Teltathum
- Mae Hong Son Livestock Research and Breeding Center, Mae Hong Son 58000, Thailand;
| | - Guisheng Liu
- Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China;
- Hubei Key Lab for Animal Embryo Engineering and Molecular Breeding, Wuhan 430064, China
| | - Watcharapong Naraballobh
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; (N.P.); (W.N.); (T.K.); (K.S.)
- Innovative Agriculture Research Center, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Trisadee Khamlor
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; (N.P.); (W.N.); (T.K.); (K.S.)
| | - Korawan Sringarm
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; (N.P.); (W.N.); (T.K.); (K.S.)
- Cluster of Research and Development of Pharmaceutical and Natural Products Innovation for Human or Animal, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Patcharin Krutmuang
- Innovative Agriculture Research Center, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand;
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
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Pewan SB, Otto JR, Huerlimann R, Budd AM, Mwangi FW, Edmunds RC, Holman BWB, Henry MLE, Kinobe RT, Adegboye OA, Malau-Aduli AEO. Next Generation Sequencing of Single Nucleotide Polymorphic DNA-Markers in Selecting for Intramuscular Fat, Fat Melting Point, Omega-3 Long-Chain Polyunsaturated Fatty Acids and Meat Eating Quality in Tattykeel Australian White MARGRA Lamb. Foods 2021; 10:foods10102288. [PMID: 34681337 PMCID: PMC8535056 DOI: 10.3390/foods10102288] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/13/2021] [Accepted: 09/17/2021] [Indexed: 01/14/2023] Open
Abstract
Meat quality data can only be obtained after slaughter when selection decisions about the live animal are already too late. Carcass estimated breeding values present major precision problems due to low accuracy, and by the time an informed decision on the genetic merit for meat quality is made, the animal is already dead. We report for the first time, a targeted next-generation sequencing (NGS) of single nucleotide polymorphisms (SNP) of lipid metabolism genes in Tattykeel Australian White (TAW) sheep of the MARGRA lamb brand, utilizing an innovative and minimally invasive muscle biopsy sampling technique for directly quantifying the genetic worth of live lambs for health-beneficial omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA), intramuscular fat (IMF), and fat melting point (FMP). NGS of stearoyl-CoA desaturase (SCD), fatty acid binding protein-4 (FABP4), and fatty acid synthase (FASN) genes identified functional SNP with unique DNA marker signatures for TAW genetics. The SCD g.23881050T>C locus was significantly associated with IMF, C22:6n-3, and C22:5n-3; FASN g.12323864A>G locus with FMP, C18:3n-3, C18:1n-9, C18:0, C16:0, MUFA, and FABP4 g.62829478A>T locus with IMF. These add new knowledge, precision, and reliability in directly making early and informed decisions on live sheep selection and breeding for health-beneficial n-3 LC-PUFA, FMP, IMF and superior meat-eating quality at the farmgate level. The findings provide evidence that significant associations exist between SNP of lipid metabolism genes and n-3 LC-PUFA, IMF, and FMP, thus underpinning potential marker-assisted selection for meat-eating quality traits in TAW lambs.
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Affiliation(s)
- Shedrach Benjamin Pewan
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
- National Veterinary Research Institute, Private Mail Bag 01 Vom, Plateau State, Nigeria
| | - John Roger Otto
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
| | - Roger Huerlimann
- Marine Climate Change Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan;
- Centre for Sustainable Tropical Fisheries and Aquaculture and Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia;
| | - Alyssa Maree Budd
- Centre for Sustainable Tropical Fisheries and Aquaculture and Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia;
| | - Felista Waithira Mwangi
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
| | - Richard Crawford Edmunds
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
| | | | - Michelle Lauren Elizabeth Henry
- Gundagai Meat Processors, 2916 Gocup Road, South Gundagai, NSW 2722, Australia;
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Robert Tumwesigye Kinobe
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
| | - Oyelola Abdulwasiu Adegboye
- Public Health and Tropical Medicine Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia;
| | - Aduli Enoch Othniel Malau-Aduli
- Animal Genetics and Nutrition, Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia; (S.B.P.); (J.R.O.); (F.W.M.); (R.C.E.); (R.T.K.)
- Correspondence: ; Tel.: +61-747-815-339
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11
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Pothakam N, Supakankul P, Norseeda W, Liu G, Teltathum T, Naraballobh W, Khamlor T, Sringarm K, Mekchay S. Association of adipocytokine IL-1A and IL-6 genes with intramuscular fat content and fatty acid composition in pigs. Meat Sci 2021; 179:108554. [PMID: 34000609 DOI: 10.1016/j.meatsci.2021.108554] [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: 10/20/2020] [Revised: 03/22/2021] [Accepted: 05/07/2021] [Indexed: 12/18/2022]
Abstract
Several adipocytokines are involved in inflammatory and immune responses as well as regulated fat deposition and lipid metabolism in mammals. This study aimed to verify the polymorphisms of the porcine interleukin 1A (IL-1A) and interleukin 6 (IL-6) genes and to assess their association with intramuscular fat (IMF) content and fatty acid (FA) composition in commercial crossbred pigs. Two single nucleotide polymorphisms (SNPs) of the porcine IL-1A g.43722547A>G and IL-6 g.91508173C>T loci were found to be segregating in these crossbred pigs. Furthermore, the porcine IL-1A g.43722547A>G polymorphism was found to be significantly associated with myristic, palmitic, palmitoleic, and eicosadienoic acid levels. Moreover, the porcine IL-6 g.91508173C>T polymorphism was significantly associated with IMF content and homolinolenic acid levels. These results suggest that the polymorphisms of the porcine IL-1A and IL-6 genes correlated with lipid content and FA composition and confirmed the importance of the adipocytokine IL-1A and IL-6 genes as candidate genes for fatty acid composition in the muscles of pigs.
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Affiliation(s)
- Nanthana Pothakam
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand; Graduate School, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Pantaporn Supakankul
- Division of Animal Science, School of Agriculture and Natural Resources, University of Phayao, Phayao 56000, Thailand
| | - Worrarak Norseeda
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand; Graduate School, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Guisheng Liu
- Institute of Animal Science and Veterinary Medicine, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; Hubei Key Lab for Animal Embryo Engineering and Molecular Breeding, Wuhan 430064, China
| | - Tawatchai Teltathum
- Mae Hong Son Livestock Research and Breeding Center, Mae Hong Son 58000, Thailand
| | - Watcharapong Naraballobh
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Trisadee Khamlor
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Korawan Sringarm
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand; Cluster of Research and Development of Pharmaceutical and Natural Products Innovation for Human or Animal, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Supamit Mekchay
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand; Cluster of Research and Development of Pharmaceutical and Natural Products Innovation for Human or Animal, Chiang Mai University, Chiang Mai 50200, Thailand; Innovative Agriculture Research Center, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand.
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12
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Identification of strong candidate genes for backfat and intramuscular fatty acid composition in three crosses based on the Iberian pig. Sci Rep 2020; 10:13962. [PMID: 32811870 PMCID: PMC7435270 DOI: 10.1038/s41598-020-70894-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 08/02/2020] [Indexed: 12/11/2022] Open
Abstract
Meat quality has an important genetic component and can be modified by the fatty acid (FA) composition and the amount of fat contained in adipose tissue and muscle. The present study aimed to find genomic regions associated with the FA composition in backfat and muscle (longissimus dorsi) in 439 pigs with three different genetic backgrounds but having the Iberian breed in common. Genome-wide association studies (GWAS) were performed between 38,424 single-nucleotide polymorphisms (SNPs) covering the pig genome and 60 phenotypic traits related to backfat and muscle FA composition. Nine significant associated regions were found in backfat on the Sus scrofa chromosomes (SSC): SSC1, SSC2, SSC4, SSC6, SSC8, SSC10, SSC12, and SSC16. For the intramuscular fat, six significant associated regions were identified on SSC4, SSC13, SSC14, and SSC17. A total of 52 candidate genes were proposed to explain the variation in backfat and muscle FA composition traits. GWAS were also reanalysed including SNPs on five candidate genes (ELOVL6, ELOVL7, FADS2, FASN, and SCD). Regions and molecular markers described in our study may be useful for meat quality selection of commercial pig breeds, although several polymorphisms were breed-specific, and further analysis would be needed to evaluate possible causal mutations.
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13
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Tiezzi F, Brito LF, Howard J, Huang YJ, Gray K, Schwab C, Fix J, Maltecca C. Genomics of Heat Tolerance in Reproductive Performance Investigated in Four Independent Maternal Lines of Pigs. Front Genet 2020; 11:629. [PMID: 32695139 PMCID: PMC7338773 DOI: 10.3389/fgene.2020.00629] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/26/2020] [Indexed: 12/12/2022] Open
Abstract
Improving swine climatic resilience through genomic selection has the potential to minimize welfare issues and increase the industry profitability. The main objective of this study was to investigate the genetic and genomic determinism of tolerance to heat stress in four independent purebred populations of swine. Three female reproductive traits were investigated: total number of piglets born (TNB), number of piglets born alive (NBA) and average birth weight (ABW). More than 80,000 phenotypic and 12,000 genotyped individuals were included in this study. Genomic random-regression models were fitted regressing the phenotypes of interest on a set of 95 environmental covariates extracted from public weather station records. The models yielded estimates of (genomic) reactions norms for individual pigs, as indicator of heat tolerance. Heat tolerance is a heritable trait, although the heritabilities are larger under comfortable than heat-stress conditions (larger than 0.05 vs. 0.02 for TNB; 0.10 vs. 0.05 for NBA; larger than 0.20 vs. 0.10 for ABW). TNB showed the lowest genetic correlation (-38%) between divergent climatic conditions, being the trait with the strongest impact of genotype by environment interaction, while NBA and ABW showed values slightly negative or equal to zero reporting a milder impact of the genotype by environment interaction. After estimating genetic parameters, a genome-wide association study was performed based on the single-step GBLUP method. Heat tolerance was observed to be a highly polygenic trait. Multiple and non-overlapping genomic regions were identified for each trait based on the genomic breeding values for reproductive performance under comfortable or heat stress conditions. Relevant regions were found on chromosomes (SSC) 1, 3, 5, 6, 9, 11, and 12, although there were important regions across all autosomal chromosomes. The genomic region located on SSC9 appears to be of particular interest since it was identified for two traits (TNB and NBA) and in two independent populations. Heat tolerance based on reproductive performance indicators is a heritable trait and genetic progress for heat tolerance can be achieved through genetic or genomic selection. Various genomic regions and candidate genes with important biological functions were identified, which will be of great value for future functional genomic studies.
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Affiliation(s)
- Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, NC, United States
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Jeremy Howard
- Smithfield Premium Genetics, Rose Hill, NC, United States
| | - Yi Jian Huang
- Smithfield Premium Genetics, Rose Hill, NC, United States
| | - Kent Gray
- Smithfield Premium Genetics, Rose Hill, NC, United States
| | | | - Justin Fix
- The Maschhoffs LLC, Carlyle, IL, United States
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, United States
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Evaluation of SCD, ACACA and FASN Mutations: Effects on Pork Quality and Other Production Traits in Pigs Selected Based on RNA-Seq Results. Animals (Basel) 2020; 10:ani10010123. [PMID: 31940936 PMCID: PMC7023423 DOI: 10.3390/ani10010123] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/07/2020] [Accepted: 01/10/2020] [Indexed: 12/20/2022] Open
Abstract
Simple Summary This study aimed to evaluate mutations within three candidate genes (SCD, ACACA, FASN) for their effects on fattening and slaughter characteristics, as well as meat quality traits, including intramuscular fat (IMF) level in pork. They were selected within differentially expressed genes activated in response to variable backfat content obtained using the RNA sequencing method. The RNA-seq analysis identifies mutations/SNPs located in the mRNA and could be a useful tool for prediction of genetic markers in farm animals. The results showed that selection for FASN A allele in Polish Large White pigs could lead to improved meat quality traits such as water exudation and meat colour. However, analysed polymorphisms showed only slight effects on fat metabolism and IMF content. Abstract In recent years, pig producers have struggled with the problem of low intramuscular fat levels in pork, which impacts palatability and ultimately meat quality. Reduced levels of intramuscular fat are likely the result of breeding objectives aimed at increasing lean meat content. In this study, three mutations within candidate genes for fat content (SCD, ACACA, and FASN) were selected, based on RNA-seq results and the relationship between polymorphisms in genes related to lipid metabolism, fattening and slaughter characteristics, as well as pork quality, including IMF level, were evaluated to identify selection markers. Moreover, their impact on gene expression was also examined. The PCR–RFLP (polymerase cha- in reaction – restriction fragments length) method was used to establish genotypes and effect sizes of potential genetic markers were estimated using a GLM model. It was identified that a FASN missense variant was positively associated with the expression level of this gene, which suggested its linkage with a mutation having a regulatory function. The association study indicated that the FASN missense variant may play a role in the determination of feed conversion and meat colour. In turn, a mutation in the ACACA gene showed a relationship with IMF content in the Puławska breed where the differences reached as much as 20%. We suggest considering all three mutations in further studies based on different pig populations due to the crucial role of SCD, ACACA, and FASN genes in lipid metabolism.
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