1
|
Yan E, Tan M, Jiao N, He L, Wan B, Zhang X, Yin J. Lysine 2-hydroxyisobutyrylation levels determined adipogenesis and fat accumulation in adipose tissue in pigs. J Anim Sci Biotechnol 2024; 15:99. [PMID: 38992763 PMCID: PMC11242017 DOI: 10.1186/s40104-024-01058-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 06/03/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Excessive backfat deposition lowering carcass grade is a major concern in the pig industry, especially in most breeds of obese type pigs. The mechanisms involved in adipogenesis and fat accumulation in pigs remain unclear. Lysine 2-hydroxyisobutyrylation (Khib), is a novel protein post-translational modification (PTM), which play an important role in transcription, energy metabolism and metastasis of cancer cells, but its role in adipogenesis and fat accumulation has not been shown. RESULTS In this study, we first analyzed the modification levels of acetylation (Kac), Khib, crotonylation (Kcr) and succinylation (Ksu) of fibro-adipogenic progenitors (FAPs), myogenic precursors (Myo) and mesenchymal stem cells (MSCs) with varied differentiation potential, and found that only Khib modification in FAPs was significantly higher than that in MSCs. Consistently, in parallel with its regulatory enzymes lysine acetyltransferase 5 (KAT5) and histone deacetylase 2 (HDAC2) protein levels, the Khib levels increased quadratically (P < 0.01) during adipogenic differentiation of FAPs. KAT5 knockdown in FAPs inhibited adipogenic differentiation, while HDAC2 knockdown enhanced adipogenic differentiation. We also demonstrated that Khib modification favored to adipogenic differentiation and fat accumulation by comparing Khib levels in FAPs and backfat tissues both derived from obese-type pigs (Laiwu pigs) and lean-type pigs (Duroc pigs), respectively. Accordingly, the expression patterns of KAT5 and HDAC2 matched well to the degree of backfat accumulation in obese- and lean-type pigs. CONCLUSIONS From the perspective of protein translational modification, we are the first to reveal the role of Khib in adipogenesis and fat deposition in pigs, and provided new clues for the improvement of fat accumulation and distribution as expected via genetic selection and nutritional strategy in obese-type pigs.
Collapse
Affiliation(s)
- Enfa Yan
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Mingyang Tan
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ning Jiao
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, 271018, Shandong Province, China
| | - Linjuan He
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Boyang Wan
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xin Zhang
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
- Molecular Design Breeding Frontier Science Center of the Ministry of Education (MOE), Beijing, 100193, China.
| | - Jingdong Yin
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
- Molecular Design Breeding Frontier Science Center of the Ministry of Education (MOE), Beijing, 100193, China.
| |
Collapse
|
2
|
Zeng Q, Gao H, Yin S, Peng Y, Yang F, Fu Y, Deng X, Chen Y, Hou X, Wang Q, Jin Z, Song G, He J, Yin Y, Xu K. Genome-Wide Association Study and Identification of Candidate Genes for Intramuscular Fat Fatty Acid Composition in Ningxiang Pigs. Animals (Basel) 2023; 13:3192. [PMID: 37893916 PMCID: PMC10603709 DOI: 10.3390/ani13203192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/03/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Ningxiang pigs exhibit a diverse array of fatty acids, making them an intriguing model for exploring the genetic underpinnings of fatty acid metabolism. We conducted a genome-wide association study using a dataset comprising 50,697 single-nucleotide polymorphisms (SNPs) and samples from over 600 Ningxiang pigs. Our investigation yielded novel candidate genes linked to five saturated fatty acids (SFAs), four monounsaturated fatty acids (MUFAs), and five polyunsaturated fatty acids (PUFAs). Significant associations with SFAs, MUFAs, and PUFAs were found for 37, 21, and 16 SNPs, respectively. Notably, some SNPs have significant PVE, such as ALGA0047587, which can explain 89.85% variation in Arachidic acid (C20:0); H3GA0046208 and DRGA0016063 can explain a total of 76.76% variation in Elaidic Acid (C18:1n-9(t)), and the significant SNP ALGA0031262 of Arachidonic acid (C20:4n-6) can explain 31.76% of the variation. Several significant SNPs were positioned proximally to previously reported genes. In total, we identified 11 candidate genes (hnRNPU, CEPT1, ATP1B1, DPT, DKK1, PRKG1, EXT2, MEF2C, IL17RA, ITGA1 and ALOX5), six candidate genes (ALOX5AP, MEDAG, ISL1, RXRB, CRY1, and CDKAL1), and five candidate genes (NDUFA4L2, SLC16A7, OTUB1, EIF4E and ROBO2) associated with SFAs, MUFAs, and PUFAs, respectively. These findings hold great promise for advancing breeding strategies aimed at optimizing meat quality and enhancing lipid metabolism within the intramuscular fat (IMF) of Ningxiang pigs.
Collapse
Affiliation(s)
- Qinghua Zeng
- Animal Nutrition Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Hu Gao
- Animal Nutrition Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Shishu Yin
- Animal Nutrition Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Yinglin Peng
- Hunan Institute of Animal & Veterinary Science, Changsha 410131, China
| | - Fang Yang
- Animal Nutrition Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Yawei Fu
- Animal Nutrition Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Xiaoxiao Deng
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Yue Chen
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Xiaohong Hou
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Qian Wang
- Animal Nutrition Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Zhao Jin
- Animal Nutrition Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Gang Song
- Animal Nutrition Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
| | - Jun He
- Animal Nutrition Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Yulong Yin
- Animal Nutrition Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Kang Xu
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha 410125, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| |
Collapse
|
3
|
EL Nagar AG, Heddi I, Sosa-Madrid BS, Blasco A, Hernández P, Ibáñez-Escriche N. Genome-Wide Association Study of Maternal Genetic Effects on Intramuscular Fat and Fatty Acid Composition in Rabbits. Animals (Basel) 2023; 13:3071. [PMID: 37835677 PMCID: PMC10571580 DOI: 10.3390/ani13193071] [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: 08/31/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Maternal genetic effects (MGE) could affect meat quality traits such as intramuscular fat (IMF) and its fatty acid composition. However, it has been scarcely studied, especially in rabbits. The objectives of the present study were, first, to assess the importance of MGE on intramuscular fat and fatty acid composition by applying a Bayesian maternal animal model in two rabbit lines divergently selected for IMF. The second objective was to identify genomic regions and candidate genes of MGE that are associated with the traits of these offspring, using Bayesian methods in a Genome Wide Association Study (GWAS). Quantitative analyses were performed using data from 1982 rabbits, and 349 animals from the 9th generation and 76 dams of the 8th generation with 88,512 SNPs were used for the GWAS. The studied traits were IMF, saturated fatty acids (total SFA, C14:0; myristic acid, C16:0; palmitic acid and C18:0; stearic acid), monounsaturated fatty acids (total MUFA, C16:1n-7; palmitoleic acid and C18:1n-9; oleic acid), polyunsaturated fatty acids (total PUFA, C18:2n-6; linoleic acid, C18:3n-3; α-linolenic acid and C20:4n-6; arachidonic acid), MUFA/SFA and PUFA/SFA. The proportion of phenotypic variance explained by the maternal genetic effect ranged from 8 to 22% for IMF, depending on the model. For fatty acid composition, the proportion of phenotypic variance explained by maternal genetic effects varied from 10% (C18:0) to 46% (MUFA) in a model including both direct and additive maternal genetic effects, together with the common litter effect as a random variable. In particular, there were significant direct maternal genetic correlations for C16:0, C18:1n9, C18:2n6, SFA, MUFA, and PUFA with values ranging from -0.53 to -0.89. Relevant associated genomic regions were located on the rabbit chromosomes (OCU) OCU1, OCU5 and OCU19 containing some relevant candidates (TANC2, ACE, MAP3K3, TEX2, PRKCA, SH3GL2, CNTLN, RPGRIP1L and FTO) related to lipid metabolism, binding, and obesity. These regions explained about 1.2 to 13.9% of the total genomic variance of the traits studied. Our results showed an important maternal genetic effect on IMF and its fatty acid composition in rabbits and identified promising candidate genes associated with these traits.
Collapse
Affiliation(s)
- Ayman G. EL Nagar
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain; (A.G.E.N.)
- Department of Animal Production, Faculty of Agriculture at Moshtohor, Benha University, Benha 13736, Egypt
| | - Imen Heddi
- Centro Regional de Selección y Reproducción Animal (CERSYRA), Av. del Vino, 10, 13300 Valdepeñas, Spain
| | - Bolívar Samuel Sosa-Madrid
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain; (A.G.E.N.)
| | - Agustín Blasco
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain; (A.G.E.N.)
| | - Pilar Hernández
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain; (A.G.E.N.)
| | - Noelia Ibáñez-Escriche
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain; (A.G.E.N.)
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Luo X, Li J, Xiao C, Sun L, Xiang W, Chen N, Lei C, Lei H, Long Y, Long T, Suolang Q, Yi K. Whole-Genome Resequencing of Xiangxi Cattle Identifies Genomic Diversity and Selection Signatures. Front Genet 2022; 13:816379. [PMID: 35711927 PMCID: PMC9196905 DOI: 10.3389/fgene.2022.816379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 04/13/2022] [Indexed: 01/11/2023] Open
Abstract
Understanding the genetic diversity in Xiangxi cattle may facilitate our efforts toward further breeding programs. Here we compared 23 Xiangxi cattle with 78 published genomes of 6 worldwide representative breeds to characterize the genomic variations of Xiangxi cattle. Based on clustering models in population structure analysis, we displayed that Xiangxi cattle had a mutual genome ancestor with Chinese indicine, Indian indicine, and East Asian taurine. Population genetic diversity was analyzed by four methods (nucleotide diversity, inbreeding coefficient, linkage disequilibrium decay and runs of homozygosity), and we found that Xiangxi cattle had higher genomic diversity and weaker artificial selection than commercial breed cattle. Using four testing methods (θπ, CLR, FST, and XP-EHH), we explored positive selection regions harboring genes in Xiangxi cattle, which were related to reproduction, growth, meat quality, heat tolerance, and immune response. Our findings revealed the extent of sequence variation in Xiangxi cattle at the genome-wide level. All of our fruitful results can bring about a valuable genomic resource for genetic studies and breed protection in the future.
Collapse
Affiliation(s)
- Xiaoyu Luo
- Hunan Institute of Animal and Veterinary Science, Changsha, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Jianbo Li
- Hunan Institute of Animal and Veterinary Science, Changsha, China.,Xiangxi Cattle Engineering Technology Center of Hunan Province, Huayuan, China
| | - Chentong Xiao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Luyang Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Weixuan Xiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China.,School of Life Science, University of Bristol, Bristol, United Kingdom
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Hong Lei
- Hunan Institute of Animal and Veterinary Science, Changsha, China.,Xiangxi Cattle Engineering Technology Center of Hunan Province, Huayuan, China
| | - Yun Long
- Xiangxi Cattle Engineering Technology Center of Hunan Province, Huayuan, China.,Hunan De Nong Animal Husbandry Group Co. Ltd., Huayuan, China
| | - Ting Long
- Xiangxi Cattle Engineering Technology Center of Hunan Province, Huayuan, China.,Hunan De Nong Animal Husbandry Group Co. Ltd., Huayuan, China
| | - Quji Suolang
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa, China
| | - Kangle Yi
- Hunan Institute of Animal and Veterinary Science, Changsha, China.,Xiangxi Cattle Engineering Technology Center of Hunan Province, Huayuan, China
| |
Collapse
|
6
|
Schumacher M, DelCurto-Wyffels H, Thomson J, Boles J. Fat Deposition and Fat Effects on Meat Quality—A Review. Animals (Basel) 2022; 12:ani12121550. [PMID: 35739885 PMCID: PMC9219498 DOI: 10.3390/ani12121550] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/01/2022] [Accepted: 06/13/2022] [Indexed: 01/12/2023] Open
Abstract
Simple Summary Animal fat deposition has a major impact on the meat yield from individual carcasses as well the perceived eating quality for consumers. Understanding the impact of livestock production practices on fat deposition and the molecular mechanisms activated will lead to a better understanding of finishing livestock. This enhanced understanding will also lead to the increased efficiency and improved sustainability of practices for livestock production. The impact of fat storage on physiological functions and health are also important. This review brings together both the production practices and the current understanding of molecular processes associated with fat deposition. Abstract Growth is frequently described as weight gain over time. Researchers have used this information in equations to predict carcass composition and estimate fat deposition. Diet, species, breed, and gender all influence fat deposition. Alterations in diets result in changes in fat deposition as well as the fatty acid profile of meat. Additionally, the amount and composition of the fat can affect lipid stability and flavor development upon cooking. Fat functions not only as a storage of energy and contributor of flavor compounds, but also participates in signaling that affects many aspects of the physiological functions of the animal. Transcription factors that are upregulated in response to excess energy to be stored are an important avenue of research to improve the understanding of fat deposition and thus, the efficiency of production. Additionally, further study of the inflammation associated with increased fat depots may lead to a better understanding of finishing animals, production efficiency, and overall health.
Collapse
|
7
|
He X, Wu R, Yun Y, Qin X, Chen L, Han Y, Wu J, Sha L, Borjigin G. Transcriptome analysis of messenger RNA and long noncoding RNA related to different developmental stages of tail adipose tissues of sunite sheep. Food Sci Nutr 2021; 9:5722-5734. [PMID: 34646540 PMCID: PMC8498062 DOI: 10.1002/fsn3.2537] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 08/03/2021] [Accepted: 08/09/2021] [Indexed: 12/18/2022] Open
Abstract
The tail fat of sheep is the most typical deposited fat, and it can be widely used in human daily life, such as diet, cosmetics, and industrial raw materials. To understand the potential regulatory mechanism of different growth stages of tail fat in Sunite sheep, we performed high-throughput RNA sequencing to characterize the long noncoding RNA (lncRNA) and messenger RNA (mRNA) expression profiles of the sheep tail fat at the age of 6, 18, and 30 months. A total of 223 differentially expressed genes (DEGs) and 148 differentially expressed lncRNAs were found in the tail fat of 6-, 18-, and 30-month-old sheep. Based on functional analysis, we found that fat-related DEGs were mainly expressed at 6 months of age and gradually decreased at 18 and 30 months of age. The target gene prediction analysis shows that most of the lncRNAs target more than 20 mRNAs as their transregulators. Further, we obtained several fat-related differentially expressed target genes; these target genes interact with different differentially expressed lncRNAs at various ages and play an important role in the development of tail fat. Based on the DEGs and differentially expressed lncRNAs, we established three co-expression networks for each comparison group. Finally, we concluded that the development of the sheep tail fat is more active during the early stage of growth and gradually decreases with the increase in age. The mutual regulation of lncRNAs and mRNAs may play a key role in this complex biological process.
Collapse
Affiliation(s)
- Xige He
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Rihan Wu
- College of Biochemistry and EngineeringHohhot Vocational CollegeHohhotChina
| | - Yueying Yun
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
- School of Life Science and TechnologyInner Mongolia University of Science and TechnologyBaotouChina
| | - Xia Qin
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Lu Chen
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Yunfei Han
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Jindi Wu
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Lina Sha
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Gerelt Borjigin
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| |
Collapse
|
8
|
Babigumira BM, Sölkner J, Mészáros G, Pfeiffer C, Lewis CRG, Ouma E, Wurzinger M, Marshall K. A Mix of Old British and Modern European Breeds: Genomic Prediction of Breed Composition of Smallholder Pigs in Uganda. Front Genet 2021; 12:676047. [PMID: 34249095 PMCID: PMC8261304 DOI: 10.3389/fgene.2021.676047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Pig herds in Africa comprise genotypes ranging from local ecotypes to commercial breeds. Many animals are composites of these two types and the best levels of crossbreeding for particular production systems are largely unknown. These pigs are managed without structured breeding programs and inbreeding is potentially limiting. The objective of this study was to quantify ancestry contributions and inbreeding levels in a population of smallholder pigs in Uganda. The study was set in the districts of Hoima and Kamuli in Uganda and involved 422 pigs. Pig hair samples were taken from adult and growing pigs in the framework of a longitudinal study investigating productivity and profitability of smallholder pig production. The samples were genotyped using the porcine GeneSeek Genomic Profiler (GGP) 50K SNP Chip. The SNP data was analyzed to infer breed ancestry and autozygosity of the Uganda pigs. The results showed that exotic breeds (modern European and old British) contributed an average of 22.8% with a range of 2-50% while "local" blood contributed 69.2% (36.9-95.2%) to the ancestry of the pigs. Runs of homozygosity (ROH) greater than 2 megabase (Mb) quantified the average genomic inbreeding coefficient of the pigs as 0.043. The scarcity of long ROH indicated low recent inbreeding. We conclude that the genomic background of the pig population in the study is a mix of old British and modern pig ancestries. Best levels of admixture for smallholder pigs are yet to be determined, by linking genotypes and phenotypic records.
Collapse
Affiliation(s)
- Brian Martin Babigumira
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
- International Livestock Research Institute, Kampala, Uganda
| | - Johann Sölkner
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Gábor Mészáros
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Christina Pfeiffer
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
- PIG Austria GmbH, Steinhaus, Wels, Austria
| | | | - Emily Ouma
- International Livestock Research Institute, Kampala, Uganda
| | - Maria Wurzinger
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Karen Marshall
- International Livestock Research Institute, Nairobi, Kenya
| |
Collapse
|
9
|
Effect of season, feeding, and anatomical region on the triacylglycerol profile of Iberian pig fat. Food Chem 2021; 361:130070. [PMID: 34023684 DOI: 10.1016/j.foodchem.2021.130070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 04/11/2021] [Accepted: 05/08/2021] [Indexed: 11/21/2022]
Abstract
The work studies the effects of season, feeding type, and anatomical region on the Iberian pig fat triacylglycerol (TAG) profiles, considered as compositional data (CoDa). The analysis consisted of applying exploratory tools in the simplex and standard multivariate techniques to data transformed into the Euclidean space (ilr coordinates). Compositional biplot showed differences in TAG containing palmitic (P) and oleic (O) acids between the 2005 and 2003/2004 seasons but not within these. PPP (clr variance, 0.139), OLL (0.095), PPS (0.075), POPo + PLP (0.074), and PSS (0.629) showed high CoDa variability among treatments. The ANOVA analysis found significant (p ≤ 0.05) effects of season, feeding type, and anatomical region on pig fat TAG profile, but only that for 2005 season was well predicted (97.5%) by discriminant analysis (DA). Overall, season was more influential on the Iberian pig fat TAG profile than montanera length and sampling region, which effects were not significant for some statistical techniques.
Collapse
|
10
|
Quality and Shelf Life of Fresh Meat from Iberian Pigs as Affected by a New Form of Presentation of Oleic Acid and an Organic-Acid Mix in the Diet. Foods 2021; 10:foods10050985. [PMID: 33946329 PMCID: PMC8144970 DOI: 10.3390/foods10050985] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/24/2021] [Accepted: 04/27/2021] [Indexed: 11/17/2022] Open
Abstract
The objective of the study was to evaluate the inclusion of a novel form of oleic acid and an organic-acid mix in the diet of Iberian pigs, and their effect on the quality and shelf-life of the pig meat. 200 castrated male Iberian pigs were randomly assigned to four groups. Diets included different fat sources: pig fat (G1), solid oleic acid (G2), oleic-high sunflower oil with solid oleic (G3); a diet of G3 supplemented with organic-acid mix (G4). Pigs were slaughtered at 182 days. Back fat and the longissimus thoracis et lumborum muscles were removed, and nutritive and sensory quality were analyzed. The shelf-life of meat packaged (70%O2/30CO2) during retail storage up to 21 days were studied. A higher percentage of oleic acid and MUFA, and lower SFA were observed in subcutaneous fat on a G2 diet. G2 resulted in the highest muscle fat content, and G4, the highest cooking losses. In sensory analysis, marbling, tenderness and chewiness were higher in the G2 samples. No differences were found in the bacterial count and sensorial analysis depending on storage time at the end of the experiment, but a lower total viable count was showed at the start of the study in the G4 samples. These results suggest a better assimilation of solid oleic acid. However, the organic-acid mix requires further studies.
Collapse
|
11
|
Villaplana-Velasco A, Noguera JL, Pena RN, Ballester M, Muñoz L, González E, Tejeda JF, Ibáñez-Escriche N. Comparative Transcriptome Profile between Iberian Pig Varieties Provides New Insights into Their Distinct Fat Deposition and Fatty Acids Content. Animals (Basel) 2021; 11:ani11030627. [PMID: 33673436 PMCID: PMC7997154 DOI: 10.3390/ani11030627] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 11/16/2022] Open
Abstract
The high deposition of intramuscular fat and the content of oleic fatty acid are characteristic of the Iberian pig. These two parameters present great variability and are differentiated amongst the varieties that make up the Iberian pig population. Although previous studies generated evidence for causal genes and polymorphisms associated to the adipogenic potential of the Iberian pig, there is little information about how genetic expression influences this trait's variability. The aim of this study was to analyses the expression profile between two varieties of Iberian pig (Torbiscal and Retinto) and their reciprocal crosses differentiated in their intramuscular fat (IMF) content and fatty acid (FA) composition in the Longissimus thoracis muscle using an RNA-seq approach. Our results corroborate that the Retinto variety is the fattiest amongst all studied varieties as its upregulated genes, such as FABP3 and FABP5, SLC27A1 and VEGFA among others, contribute to increasing adiposity. In its turn, Torbiscal pigs showed an upregulation of genes associated with the inhibition of fat deposition such as ADIPOQ and CPT1A. Further genetic variation analysis in these Iberian varieties showed relevant associations for SNP located within the differentially expressed genes with IMF and FA content. Thus, the differences found in the genetic architecture and the muscle transcriptome of these Iberian varieties might explain the variability in their fat content and composition and hence, their meat quality.
Collapse
Affiliation(s)
- Ana Villaplana-Velasco
- Genetics and Genomics, The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, Edinburgh EH25 9RG, UK;
- Centre for Medical Informatics, Usher Institute, The University of Edinburgh, 9 Little France Road, Edinburgh EH16 4UX, UK
| | | | - Ramona Natacha Pena
- Departament de Ciència Animal, Universitat de Lleida-Agrotecnio Center, 25198 Lleida, Spain;
| | - Maria Ballester
- Animal Breeding and Genetics Program, IRTA, Torre Marimon, 08140 Caldes de Montbui, Spain;
| | | | - Elena González
- Department of Animal Production and Food Science, Research University Institute of Agricultural Resources (INURA), Escuela de Ingenierías Agrarias, Universidad de Extremadura, 06007 Badajoz, Spain; (E.G.); (J.F.T.)
| | - Juan Florencio Tejeda
- Department of Animal Production and Food Science, Research University Institute of Agricultural Resources (INURA), Escuela de Ingenierías Agrarias, Universidad de Extremadura, 06007 Badajoz, Spain; (E.G.); (J.F.T.)
| | - Noelia Ibáñez-Escriche
- Department for Animal Science and Tecnology, Universistat Politécnica de València, 46022 Valencia, Spain
- Correspondence: ; Tel.: +34-963-877-438
| |
Collapse
|
12
|
Laghouaouta H, Sosa-Madrid BS, Zubiri-Gaitán A, Hernández P, Blasco A. Novel Genomic Regions Associated with Intramuscular Fatty Acid Composition in Rabbits. Animals (Basel) 2020; 10:ani10112090. [PMID: 33187110 PMCID: PMC7697864 DOI: 10.3390/ani10112090] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/08/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022] Open
Abstract
Intramuscular fat (IMF) content and its composition affect the quality of meat. Selection for IMF generated a correlated response on its fatty acid composition. The increase of IMF content is associated with an increase of its saturated (SFA) and monounsaturated (MUFA) fatty acids, and consequently a decrease of polyunsaturated fatty acids (PUFA). We carried out a genome wide association study (GWAS) for IMF composition on two rabbit lines divergently selected for IMF content, using a Bayes B procedure. Association analyses were performed using 475 individuals and 90,235 Single Nucleotide Polymorphisms (SNPs). The main objectives were to identify genomic regions associated with the IMF composition and to generate a list of candidate genes. Genomic regions associated with the intramuscular fatty acid composition were spread across different rabbit chromosomes (OCU). An important region at 34.0-37.9 Mb on OCU1 was associated with C14:0, C16:0, SFA, and C18:2n6, explaining 3.5%, 11.2%, 11.3%, and 3.2% of the genomic variance, respectively. Another relevant genomic region was found to be associated at 46.0-48.9 Mb on OCU18, explaining up to 8% of the genomic variance of MUFA/SFA. The associated regions harbor several genes related to lipid metabolism, such as SCD, PLIN2, and ERLIN1. The main genomic regions associated with the fatty acids were not previously associated with IMF content in rabbits. Nonetheless, MTMR2 is the only gene that was associated with both the IMF content and composition in rabbits. Our study highlighted the polygenic nature of the fatty acids in rabbits and elucidated its genetic background.
Collapse
|
13
|
Gomez-Samblas M, Vilchez S, Ortega-Velázquez R, Fuentes MV, Osuna A. Absence of Toxoplasma gondii in 100% Iberian products from experimentally infected pigs cured following a specific traditional process. Food Microbiol 2020; 95:103665. [PMID: 33397604 DOI: 10.1016/j.fm.2020.103665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 10/21/2020] [Accepted: 10/21/2020] [Indexed: 11/29/2022]
Abstract
Infection with Toxoplasma gondii in humans has usually been related to the consumption of raw, undercooked or cured meat. Our study is based on the detection of T. gondii in cured legs and shoulders made from 100% Iberian sows fed mainly with acorn and raised as outdoor livestock in Aracena (Spain), which having been elaborated following a specific curing process (time period and location). An outdoor farm with a total of 636 animals was studied, showing a seroprevalence of 10% for the parasite T. gondii. Twenty individuals were chosen to be experimentally infected and slaughtered 60 days post-infection. Their legs and shoulders were processed to make 100% Iberian ham legs and shoulders. The meat ready to be eaten was analyzed by quantification and viability assays using magnetic capture real-time qPCR and bioassay techniques proving that this specific traditional "Cinco Jotas" curing process 100% Iberian ham is strong enough to eliminate the parasite T. gondii, resulting in a safe product for consumers.
Collapse
Affiliation(s)
- Mercedes Gomez-Samblas
- Instituto de Biotecnología, Universidad de Granada, Campus Universitario Fuentenueva, 18071, Granada, Spain; Grupo de Bioquímica y Parasitología Molecular. Departamento de Parasitología, Universidad de Granada, Campus Universitario Fuentenueva, 18071, Granada, Spain.
| | - Susana Vilchez
- Instituto de Biotecnología, Universidad de Granada, Campus Universitario Fuentenueva, 18071, Granada, Spain; Departamento de Bioquímica y Biología Molecular I, Universidad de Granada, Campus Universitario Fuentenueva, 18071, Granada, Spain
| | - Rocío Ortega-Velázquez
- Sanchez Romero Carvajal Jabugo SA, ctra. San Juan del Puerto s/n, 21290, Jabugo, Huelva, Spain
| | - Màrius V Fuentes
- Parasites & Health Research Group, Departament de Farmàcia i Tecnologia Farmacèutica i Parasitologia, Facultat de Farmàcia, Universitat de València, Av. Vicent, Andrés Estellés s/n, 46100, Burjassot, València, Spain
| | - Antonio Osuna
- Instituto de Biotecnología, Universidad de Granada, Campus Universitario Fuentenueva, 18071, Granada, Spain; Grupo de Bioquímica y Parasitología Molecular. Departamento de Parasitología, Universidad de Granada, Campus Universitario Fuentenueva, 18071, Granada, Spain.
| |
Collapse
|
14
|
Fernández-Barroso MÁ, Caraballo C, Silió L, Rodríguez C, Nuñez Y, Sánchez-Esquiliche F, Matos G, García-Casco JM, Muñoz M. Differences in the Loin Tenderness of Iberian Pigs Explained through Dissimilarities in Their Transcriptome Expression Profile. Animals (Basel) 2020; 10:ani10091715. [PMID: 32971875 PMCID: PMC7552750 DOI: 10.3390/ani10091715] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/10/2020] [Accepted: 09/18/2020] [Indexed: 02/06/2023] Open
Abstract
Simple Summary The Iberian pig is the most representative autochthonous breed of the Mediterranean region with unique genetic and phenotypic characteristics. The breed has been successfully preserved by its high-quality meat and high-priced products. Tenderness is one of the most relevant meat quality traits, and meat tenderization is influenced by genetic and environmental effects such as pre-slaughter handling and post-mortem conditions. Tenderness could be included in Iberian pig breeding programs, mainly focused on the improvement of premium-cuts percentage, in order to avoid the meat quality decline. A better biological understanding of this trait is needed. In the current study, we analyze the transcriptome of pigs divergent for Warner–Bratzler shear force through RNA-seq technique for the identification, characterization and quantification of candidate genes involved in biological pathways, networks and functions affecting meat tenderness. Abstract Tenderness is one of the most important meat quality traits and it can be measured through shear force with the Warner–Bratzler test. In the current study, we use the RNA-seq technique to analyze the transcriptome of Longissimus dorsi (LD) muscle in two groups of Iberian pigs (Tough and Tender) divergent for shear force breeding values. We identified 200 annotated differentially expressed genes (DEGs) and 245 newly predicted isoforms. The RNAseq expression results of 10 genes were validated with quantitative PCR (qPCR). Functional analyses showed an enrichment of DE genes in biological processes related to proteolysis (CTSC, RHOD, MYH8, ACTC1, GADD45B, CASQ2, CHRNA9 and ANKRD1), skeletal muscle tissue development (ANKRD1, DMD, FOS and MSTN), lipid metabolism (FABP3 and PPARGC1A) and collagen metabolism (COL14A1). The upstream analysis revealed a total of 11 transcription regulatory factors that could regulate the expression of some DEGs. Among them, IGF1, VGLL3 and PPARG can be highlighted since they regulate the expression of genes involved in biological pathways that could affect tenderness. The experiment revealed a set of candidate genes and regulatory factors suggestive to search polymorphisms that could be incorporated in a breeding program for improving meat tenderness.
Collapse
Affiliation(s)
- Miguel Ángel Fernández-Barroso
- Centro Nacional de I+D del Cerdo Ibérico (CENIDCI), INIA, 06300 Zafra, Spain; (C.C.); (J.M.G.-C.)
- Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain; (L.S.); (C.R.); (Y.N.); (M.M.)
- Correspondence:
| | - Carmen Caraballo
- Centro Nacional de I+D del Cerdo Ibérico (CENIDCI), INIA, 06300 Zafra, Spain; (C.C.); (J.M.G.-C.)
- Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain; (L.S.); (C.R.); (Y.N.); (M.M.)
| | - Luis Silió
- Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain; (L.S.); (C.R.); (Y.N.); (M.M.)
| | - Carmen Rodríguez
- Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain; (L.S.); (C.R.); (Y.N.); (M.M.)
| | - Yolanda Nuñez
- Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain; (L.S.); (C.R.); (Y.N.); (M.M.)
| | | | - Gema Matos
- Sánchez Romero Carvajal—Jabugo, SRC, 21290 Huelva, Spain; (F.S.-E.); (G.M.)
| | - Juan María García-Casco
- Centro Nacional de I+D del Cerdo Ibérico (CENIDCI), INIA, 06300 Zafra, Spain; (C.C.); (J.M.G.-C.)
- Departamento de Mejora Genética Animal, INIA, 28040 Madrid, Spain; (L.S.); (C.R.); (Y.N.); (M.M.)
| | - María Muñoz
- Centro Nacional de I+D del Cerdo Ibérico (CENIDCI), INIA, 06300 Zafra, Spain; (C.C.); (J.M.G.-C.)
| |
Collapse
|
15
|
Maternal Transmission Ratio Distortion in Two Iberian Pig Varieties. Genes (Basel) 2020; 11:genes11091050. [PMID: 32899475 PMCID: PMC7563664 DOI: 10.3390/genes11091050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 12/30/2022] Open
Abstract
Transmission ratio distortion (TRD) is defined as the allele transmission deviation from the heterozygous parent to the offspring from the expected Mendelian genotypic frequencies. Although TRD can be a confounding factor in genetic mapping studies, this phenomenon remains mostly unknown in pigs, particularly in traditional breeds (i.e., the Iberian pig). We aimed to describe the maternal TRD prevalence and its genomic distribution in two Iberian varieties. Genotypes from a total of 247 families (dam and offspring) of Entrepelado (n = 129) and Retinto (n = 118) Iberian varieties were analyzed. The offspring were sired by both ungenotyped purebred Retinto and Entrepelado Iberian boars, regardless of the dam variety used. After quality control, 16,246 single-nucleotide polymorphisms (SNPs) in the Entrepelado variety and 9744 SNPs in the Retinto variety were analyzed. Maternal TRD was evaluated by a likelihood ratio test under SNP-by-SNP, adapting a previous model solved by Bayesian inference. Results provided 68 maternal TRD loci (TRDLs) in the Entrepelado variety and 24 in the Retinto variety (q < 0.05), with mostly negative TRD values, increasing the transmission of the minor allele. In addition, both varieties shared ten common TRDLs. No strong evidence of biological effects was found in genes with TRDLs. However, some biological processes could be affected by TRDLs, such as embryogenesis at different levels and lipid metabolism. These findings could provide useful insight into the genetic mechanisms to improve the swine industry, particularly in traditional breeds.
Collapse
|
16
|
Ropka-Molik K, Pawlina-Tyszko K, Żukowski K, Tyra M, Derebecka N, Wesoły J, Szmatoła T, Piórkowska K. Identification of Molecular Mechanisms Related to Pig Fatness at the Transcriptome and miRNAome Levels. Genes (Basel) 2020; 11:E600. [PMID: 32485856 PMCID: PMC7348756 DOI: 10.3390/genes11060600] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/13/2020] [Accepted: 05/27/2020] [Indexed: 12/29/2022] Open
Abstract
Fat deposition and growth rate are closely related to pork quality and fattening efficiency. The next-generation sequencing (NGS) approach for transcriptome and miRNAome massive parallel sequencing of adipocyte tissue was applied to search for a molecular network related to fat deposition in pigs. Pigs were represented by three breeds (Large White, Pietrain, and Hampshire) that varied in fat content within each breed. The obtained results allowed for the detection of significant enrichment of Gene Ontology (GO) terms and pathways associated directly and indirectly with fat deposition via regulation of fatty acid metabolism, fat cell differentiation, inflammatory response, and extracellular matrix (ECM) organization and disassembly. Moreover, the results showed that adipocyte tissue content strongly affected the expression of leptin and other genes related to a response to excessive feed intake. The findings indicated that modification of genes and miRNAs involved in ECM rearrangements can be essential during fat tissue growth and development in pigs. The identified molecular network within genes and miRNAs that were deregulated depending on the subcutaneous fat level are proposed as candidate factors determining adipogenesis, fatness, and selected fattening characteristics in pigs.
Collapse
Affiliation(s)
- Katarzyna Ropka-Molik
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland; (K.P.-T.); (T.S.); (K.P.)
| | - Klaudia Pawlina-Tyszko
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland; (K.P.-T.); (T.S.); (K.P.)
| | - Kacper Żukowski
- Department of Cattle Breeding, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland;
| | - Mirosław Tyra
- Department of Pig Breeding, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland;
| | - Natalia Derebecka
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Uniwersytetu Poznanskiego street 6, 61-614 Poznań, Poland; (N.D.); (J.W.)
| | - Joanna Wesoły
- Laboratory of High Throughput Technologies, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Uniwersytetu Poznanskiego street 6, 61-614 Poznań, Poland; (N.D.); (J.W.)
| | - Tomasz Szmatoła
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland; (K.P.-T.); (T.S.); (K.P.)
- University Centre of Veterinary Medicine, University of Agriculture in Kraków, Al. Mickiewicza 24/28, 30-059 Kraków, Poland
| | - Katarzyna Piórkowska
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland; (K.P.-T.); (T.S.); (K.P.)
| |
Collapse
|
17
|
Genome-wide association study identifies quantitative trait loci regions involved in muscle acidic profile in Large White heavy pigs. Animal 2020; 14:1342-1350. [PMID: 32037995 DOI: 10.1017/s1751731120000099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The widespread use of genome-wide association studies resulted in the discovery of genomic regions associated with fatty acid (FA) composition in different porcine tissues, but little information exists about the genes involved in FA composition of meat obtained from heavy pigs selected for the production of Italian dry-cured hams. To this objective, we genotyped with a single nucleotide polymorphism (SNP) panel 795 Italian Large White heavy pigs to identify the markers and genomic regions associated with Semimembranosus muscle FA profile. Heritability estimates for intramuscular fat FA profile were of low-to-moderate magnitude, suggesting that these traits may be improved with genomic selection. On the whole, 45 SNPs were significantly associated with 14 FAs, and 4 of them (ALGA008109, ALGA0081097, CASI0010164 and SIRI0000267) were associated with more than 1 FA. The palmitoleic : palmitic and oleic : stearic ratios displayed the highest number of significant markers and the most significant associations (Bonferroni adjusted P < 5.00E-07). Of particular interest, the palmitoleic : palmitic ratio was strongly associated with markers located at 111 to 114 Mb on chromosome 14, in the same chromosomal region where Stearoyl-CoA desaturase Δ9 (SCD) gene is located. Several significant chromosomal regions were found; some of them harbour key genes playing pivotal roles in FA desaturation and elongation, such as SCD and some members of the Elongation of Very Long-Chain FA (ELOVL) gene family. The results suggest that the identification of causal mutations in these regions may provide a set of markers useful for selection schemes aimed at improving FA composition in pork products.
Collapse
|
18
|
de Araujo Neto FR, Santos DJDA, Fernandes Júnior GA, Aspilcueta-Borquis RR, Nascimento AVD, de Oliveira Seno L, Tonhati H, de Oliveira HN. Genome-wide association studies for growth traits in buffaloes using the single step genomic BLUP. J Appl Genet 2019; 61:113-115. [PMID: 31673966 DOI: 10.1007/s13353-019-00528-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/11/2019] [Accepted: 10/16/2019] [Indexed: 01/12/2023]
Abstract
Growth traits are important for the profitability of buffalo breeding systems, since in general, these animals are raised both for meat and milk. In this study, the single-step genomic BLUP method was employed to prospect the genomic regions' associated with weight at standard ages of 100, 210, 365, and 550 days in a buffalo population, aiming to identify genes with stronger expression for those characteristics. We found 6, 1, 2, and 5 SNPs significantly associated (p value < 10-5) with weight at 100, 210, 365, and 550 days of age, respectively, where those SNPs respectively explained 0.164, 0.040, 0.044, and 0.213% of the additive variance of each trait. SNP AX-85099682 (BBU24) was significant for weight at 100, 210, and 365 days, indicating the existence of a possible QTL affecting the initial growth rate of buffaloes. All told, eight genes (CBLB, TRNAG-UCC, GADD45B, LOC112583811, MGAT4C, KCNMA1, SLC5A2, and TGFB1I1) were identified as candidates for the growth traits of buffaloes. However, molecular and gene expression studies are necessary to validate these genes for subsequent use in programs for genetic improvement of the species.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Humberto Tonhati
- Universidade Estadual Paulista Júlio de Mesquita Filho, Câmpus de Jaboticabal, São Paulo, Brazil
| | | |
Collapse
|
19
|
Comprehensive Evaluation of Parameters Affecting One-Step Method for Quantitative Analysis of Fatty Acids in Meat. Metabolites 2019; 9:metabo9090189. [PMID: 31540389 PMCID: PMC6780067 DOI: 10.3390/metabo9090189] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 09/03/2019] [Accepted: 09/10/2019] [Indexed: 01/04/2023] Open
Abstract
Despite various direct transmethylation methods having been published and applied to analysis of meat fatty acid (FA) composition, there are still conflicting ideas about the best method for overcoming all the difficulties posed by analysis of complex mixtures of FA in meat. This study performed a systematic investigation of factors affecting a one-step method for quantitative analysis of fatty acids in freeze-dried animal tissue. Approximately 280 reactions, selected using factorial design, were performed to investigate the effect of temperature, reaction time, acid concentration, solvent volume, sample weight and sample moisture. The reaction yield for different types of fatty acids, including saturated, unsaturated (cis, trans and conjugated) and long-chain polyunsaturated fatty acids was determined. The optimised condition for one-step transmethylation was attained with four millilitres 5% sulfuric acid in methanol (as acid catalyst), four millilitres toluene (as co-solvent), 300 mg of freeze-dried meat and incubation at 70 °C for 2 h, with interim mixing by inversion at 30, 60 and 90 min for 15 s. The optimised condition was applied to meat samples from different species, covering a broad range of fat content and offers a simplified and reliable method for analysis of fatty acids from meat samples.
Collapse
|
20
|
Carrapiso AI, Tejeda JF, Noguera JL, Ibáñez-Escriche N, González E. Effect of the genetic line and oleic acid-enriched mixed diets on the subcutaneous fatty acid composition and sensory characteristics of dry-cured shoulders from Iberian pig. Meat Sci 2019; 159:107933. [PMID: 31487571 DOI: 10.1016/j.meatsci.2019.107933] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 08/05/2019] [Accepted: 08/27/2019] [Indexed: 10/26/2022]
Abstract
The aim of this study was to research the effect of the genetic background (Retinto, Torbiscal, and their reciprocal crosses) on the subcutaneous fatty acids and the sensory characteristics of dry-cured shoulders from Iberian pig, and also to investigate whether there is some interaction between genotype and diet composition when pigs are reared indoors, to obtain information to improve the selection strategies for purebred Iberian pig. The genetic background affected both the fatty acid composition (C17:0, C17:1 n-7, C18:3 n-3 and C20:0 were significantly different) and the sensory characteristics (marbling, lean fibrousness, and flavour intensity and persistence were significantly influenced), which indicates that they should be taken into account in the selection strategies for purebred Iberian pig. In a similar way, the genotype × diet composition interaction also should be taken into account when selecting a genetic line or cross to be fed indoors on a particular diet because of its repercussion on the sensory characteristics.
Collapse
Affiliation(s)
- Ana Isabel Carrapiso
- Research Group TALICA, Escuela de Ingenierías Agrarias, Universidad de Extremadura, 06007 Badajoz, Spain; University Institute of Agricultural Resources (INURA), Universidad de Extremadura, 06006 Badajoz, Spain.
| | - Juan Florencio Tejeda
- Research Group TALICA, Escuela de Ingenierías Agrarias, Universidad de Extremadura, 06007 Badajoz, Spain; University Institute of Agricultural Resources (INURA), Universidad de Extremadura, 06006 Badajoz, Spain
| | | | - Noelia Ibáñez-Escriche
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Elena González
- Research Group TALICA, Escuela de Ingenierías Agrarias, Universidad de Extremadura, 06007 Badajoz, Spain; University Institute of Agricultural Resources (INURA), Universidad de Extremadura, 06006 Badajoz, Spain
| |
Collapse
|