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Yang Y, Wang X, Li M, Wang S, Wang H, Chen Q, Lu S. Identification of potential obese-specific biomarkers and pathways associated with abdominal subcutaneous fat deposition in pig using a comprehensive bioinformatics strategy. PeerJ 2024; 12:e17486. [PMID: 38832038 PMCID: PMC11146330 DOI: 10.7717/peerj.17486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/08/2024] [Indexed: 06/05/2024] Open
Abstract
Abdominal subcutaneous fat deposition (ASFD) is not only related to meat quality in the pig industry but also to human health in medicine. It is of great value to elucidate the potential molecular mechanisms of ASFD. The present study aims to identify obese-specific biomarkers and key pathways correlated with ASFD in pigs. The ASF-related mRNA expression dataset GSE136754 was retrieved from the Gene Expression Omnibus (GEO) database and systematically analyzed using a comprehensive bioinformatics method. A total of 565 differentially expressed genes (DEGs) were identified between three obese and three lean pigs, and these DEGs were mainly involved in the p53 signaling pathway, MAPK signaling pathway and fatty acid metabolism. A protein-protein interaction (PPI) network, consisting of 540 nodes and 1,065 edges, was constructed, and the top ten genes with the highest degree scores-ABL1, HDAC1, CDC42, HDAC2, MRPS5, MRPS10, MDM2, JUP, RPL7L1 and UQCRFS1-were identified as hub genes in the whole PPI network. Especially HDAC1, MDM2, MRPS10 and RPL7L1 were identified as potential robust obese-specific biomarkers due to their significant differences in single gene expression levels and high ROC area; this was further verified by quantitative real-time PCR (qRT-PCR) on abdominal subcutaneous fat samples from obese-type (Saba) and lean-type (Large White) pigs. Additionally, a mRNA-miRNA-lncRNA ceRNA network consisting of four potential biomarkers, 15 miRNAs and 51 lncRNAs was established, and two targeted lncRNAs with more connections, XIST and NEAT1, were identified as potentially important regulatory factors. The findings of this study may provide novel insights into the molecular mechanism involved in ASFD.
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Affiliation(s)
- Yongli Yang
- Faculty of Animal Science and Technology, Yunnan Agricuture University, Kunming, China
| | - Xiaoyi Wang
- Faculty of Animal Science and Technology, Yunnan Agricuture University, Kunming, China
| | - Mingli Li
- Faculty of Animal Science and Technology, Yunnan Agricuture University, Kunming, China
| | - Shuyan Wang
- Faculty of Animal Science and Technology, Yunnan Agricuture University, Kunming, China
| | - Huiyu Wang
- Faculty of Animal Science and Technology, Yunnan Agricuture University, Kunming, China
- Faculty of Animal Science, Xichang University, Xichang, China
| | - Qiang Chen
- Faculty of Animal Science and Technology, Yunnan Agricuture University, Kunming, China
| | - Shaoxiong Lu
- Faculty of Animal Science and Technology, Yunnan Agricuture University, Kunming, China
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Lee YS, Son S, Lee HK, Lee RH, Shin D. Elucidating breed-specific variants of native pigs in Korea: insights into pig breeds' genomic characteristics. Anim Cells Syst (Seoul) 2022; 26:338-347. [PMID: 36605594 PMCID: PMC9809348 DOI: 10.1080/19768354.2022.2141316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Although conserving native pig breeds is important in Korea, research on the genomic aspects to identify breed-specific variations in native pig breeds is uncommon. Single nucleotide polymorphisms (SNPs) can be a powerful source for identifying breed-specific variants. We used whole genome sequencing data, including Jeju Native Pig (JNP), Korean Native Pig (KNP), Korean Wild Boar (KWB), and other western commercial pig breeds to determine native pig breed-specific SNPs. Furthermore, the goal was not only to determine the genomic specificity of native pig breeds but also to identify SNPs that carry breed-specific information (breed-informative SNPs) that can be related to breed characteristics. The representative characteristics of native pigs are their unique meat quality and disease resistance. We surveyed the gene ontology (GO) of native pigs with breed-specific SNPs. Examining the genes associated with GO may contribute to revealing the reasons for the unique characteristics of native pig breeds. The enriched GOs terms were neuron projection development, cell surface receptor signaling pathway, ion homeostasis in JNP, cell adhesion and wound healing in KNP, and DNA repair and reproduction in KWB. We expect that this study of breed-specific SNPs will enable us to gain a deeper understanding of native pigs in Korea.
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Affiliation(s)
- Young-Sup Lee
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Seungwoo Son
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Hak-Kyo Lee
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea,Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Ra Ham Lee
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea, Ra Ham Lee Department of Animal Biotechnology, Jeonbuk National University, Jeonju54896, Republic of Korea; Donghyun Shin Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju54896, Republic of Korea
| | - Donghyun Shin
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, Republic of Korea, Ra Ham Lee Department of Animal Biotechnology, Jeonbuk National University, Jeonju54896, Republic of Korea; Donghyun Shin Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju54896, Republic of Korea
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Genome-Wide Association Study of Growth Traits in a Four-Way Crossbred Pig Population. Genes (Basel) 2022; 13:genes13111990. [DOI: 10.3390/genes13111990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 11/04/2022] Open
Abstract
Growth traits are crucial economic traits in the commercial pig industry and have a substantial impact on pig production. However, the genetic mechanism of growth traits is not very clear. In this study, we performed a genome-wide association study (GWAS) based on the specific-locus amplified fragment sequencing (SLAF-seq) to analyze ten growth traits on 223 four-way intercross pigs. A total of 227,921 highly consistent single nucleotide polymorphisms (SNPs) uniformly dispersed throughout the entire genome were used to conduct GWAS. A total of 53 SNPs were identified for ten growth traits using the mixed linear model (MLM), of which 18 SNPs were located in previously reported quantitative trait loci (QTL) regions. Two novel QTLs on SSC4 and SSC7 were related to average daily gain from 30 to 60 kg (ADG30–60) and body length (BL), respectively. Furthermore, 13 candidate genes (ATP5O, GHRHR, TRIM55, EIF2AK1, PLEKHA1, BRAP, COL11A2, HMGA1, NHLRC1, SGSM1, NFATC2, MAML1, and PSD3) were found to be associated with growth traits in pigs. The GWAS findings will enhance our comprehension of the genetic architecture of growth traits. We suggested that these detected SNPs and corresponding candidate genes might provide a biological foundation for improving the growth and production performance of pigs in swine breeding.
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Salgado Pardo JI, Delgado Bermejo JV, González Ariza A, León Jurado JM, Marín Navas C, Iglesias Pastrana C, Martínez Martínez MDA, Navas González FJ. Candidate Genes and Their Expressions Involved in the Regulation of Milk and Meat Production and Quality in Goats ( Capra hircus). Animals (Basel) 2022; 12:ani12080988. [PMID: 35454235 PMCID: PMC9026325 DOI: 10.3390/ani12080988] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/21/2022] [Accepted: 04/07/2022] [Indexed: 12/13/2022] Open
Abstract
Simple Summary During the present decade, highly selected caprine farming has increased in popularity due to the hardiness and adaptability inherent to goats. Recent advances in genetics have enabled the improvement in goat selection efficiency. The present review explores how genetic technologies have been applied to the goat-farming sector in the last century. The main candidate genes related to economically relevant traits are reported. The major source of income in goat farming derives from the sale of milk and meat. Consequently, yield and quality must be specially considered. Meat-related traits were evaluated considering three functional groups (weight gain, carcass quality and fat profile). Milk traits were assessed in three additional functional groups (milk production, protein and fat content). Abstract Despite their pivotal position as relevant sources for high-quality proteins in particularly hard environmental contexts, the domestic goat has not benefited from the advances made in genomics compared to other livestock species. Genetic analysis based on the study of candidate genes is considered an appropriate approach to elucidate the physiological mechanisms involved in the regulation of the expression of functional traits. This is especially relevant when such functional traits are linked to economic interest. The knowledge of candidate genes, their location on the goat genetic map and the specific phenotypic outcomes that may arise due to the regulation of their expression act as a catalyzer for the efficiency and accuracy of goat-breeding policies, which in turn translates into a greater competitiveness and sustainable profit for goats worldwide. To this aim, this review presents a chronological comprehensive analysis of caprine genetics and genomics through the evaluation of the available literature regarding the main candidate genes involved in meat and milk production and quality in the domestic goat. Additionally, this review aims to serve as a guide for future research, given that the assessment, determination and characterization of the genes associated with desirable phenotypes may provide information that may, in turn, enhance the implementation of goat-breeding programs in future and ensure their sustainability.
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Affiliation(s)
- Jose Ignacio Salgado Pardo
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
| | - Juan Vicente Delgado Bermejo
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
| | - Antonio González Ariza
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
| | - José Manuel León Jurado
- Agropecuary Provincial Center of Córdoba, Provincial Council of Córdoba, 14014 Córdoba, Spain;
| | - Carmen Marín Navas
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
| | - Carlos Iglesias Pastrana
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
| | - María del Amparo Martínez Martínez
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
| | - Francisco Javier Navas González
- Department of Genetics, Faculty of Veterinary Sciences, University of Córdoba, 14014 Córdoba, Spain; (J.I.S.P.); (J.V.D.B.); (A.G.A.); (C.M.N.); (C.I.P.); (M.d.A.M.M.)
- Institute of Agricultural Research and Training (IFAPA), Alameda del Obispo, 14004 Córdoba, Spain
- Correspondence: ; Tel.: +34-63-853-5046 (ext. 621262)
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Hepatic transcriptome analysis identifies genes, polymorphisms and pathways involved in the fatty acids metabolism in sheep. PLoS One 2021; 16:e0260514. [PMID: 34941886 PMCID: PMC8699643 DOI: 10.1371/journal.pone.0260514] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 11/12/2021] [Indexed: 12/02/2022] Open
Abstract
Fatty acids (FA) in ruminants, especially unsaturated FA (USFA) have important impact in meat quality, nutritional value, and flavour quality of meat, and on consumer’s health. Identification of the genetic factors controlling the FA composition and metabolism is pivotal to select sheep that produce higher USFA and lower saturated (SFA) for the benefit of sheep industry and consumers. Therefore, this study was aimed to investigate the transcriptome profiling in the liver tissues collected from sheep with divergent USFA content in longissimus muscle using RNA deep-sequencing. From sheep (n = 100) population, liver tissues with higher (n = 3) and lower (n = 3) USFA content were analysed using Illumina HiSeq 2500. The total number of reads produced for each liver sample were ranged from 21.28 to 28.51 million with a median of 23.90 million. Approximately, 198 genes were differentially regulated with significance level of p-adjusted value <0.05. Among them, 100 genes were up-regulated, and 98 were down-regulated (p<0.01, FC>1.5) in the higher USFA group. A large proportion of key genes involved in FA biosynthesis, adipogenesis, fat deposition, and lipid metabolism were identified, such as APOA5, SLC25A30, GFPT1, LEPR, TGFBR2, FABP7, GSTCD, and CYP17A. Pathway analysis revealed that glycosaminoglycan biosynthesis- keratan sulfate, adipokine signaling, galactose metabolism, endocrine and other factors-regulating calcium metabolism, mineral metabolism, and PPAR signaling pathway were playing important regulatory roles in FA metabolism. Importantly, polymorphism and association analyses showed that mutation in APOA5, CFHR5, TGFBR2 and LEPR genes could be potential markers for the FA composition in sheep. These polymorphisms and transcriptome networks controlling the FA variation could be used as genetic markers for FA composition-related traits improvement. However, functional validation is required to confirm the effect of these SNPs in other sheep population in order to incorporate them in the sheep breeding program.
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Xing K, Liu H, Zhang F, Liu Y, Shi Y, Ding X, Wang C. Identification of key genes affecting porcine fat deposition based on co-expression network analysis of weighted genes. J Anim Sci Biotechnol 2021; 12:100. [PMID: 34419151 PMCID: PMC8379819 DOI: 10.1186/s40104-021-00616-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 07/01/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fat deposition is an important economic consideration in pig production. The amount of fat deposition in pigs seriously affects production efficiency, quality, and reproductive performance, while also affecting consumers' choice of pork. Weighted gene co-expression network analysis (WGCNA) is effective in pig genetic studies. Therefore, this study aimed to identify modules that co-express genes associated with fat deposition in pigs (Songliao black and Landrace breeds) with extreme levels of backfat (high and low) and to identify the core genes in each of these modules. RESULTS We used RNA sequences generated in different pig tissues to construct a gene expression matrix consisting of 12,862 genes from 36 samples. Eleven co-expression modules were identified using WGCNA and the number of genes in these modules ranged from 39 to 3,363. Four co-expression modules were significantly correlated with backfat thickness. A total of 16 genes (RAD9A, IGF2R, SCAP, TCAP, SMYD1, PFKM, DGAT1, GPS2, IGF1, MAPK8, FABP, FABP5, LEPR, UCP3, APOF, and FASN) were associated with fat deposition. CONCLUSIONS RAD9A, TCAP, SMYD1, PFKM, GPS2, and APOF were the key genes in the four modules based on the degree of gene connectivity. Combining these results with those from differential gene analysis, SMYD1 and PFKM were proposed as strong candidate genes for body size traits. This study explored the key genes that regulate porcine fat deposition and lays the foundation for further research into the molecular regulatory mechanisms underlying porcine fat deposition.
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Affiliation(s)
- Kai Xing
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Huatao Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Fengxia Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yibing Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yong Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiangdong Ding
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
| | - Chuduan Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
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Goat Genomic Resources: The Search for Genes Associated with Its Economic Traits. Int J Genomics 2020; 2020:5940205. [PMID: 32904540 PMCID: PMC7456479 DOI: 10.1155/2020/5940205] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/30/2020] [Accepted: 07/24/2020] [Indexed: 11/25/2022] Open
Abstract
Goat plays a crucial role in human livelihoods, being a major source of meat, milk, fiber, and hides, particularly under adverse climatic conditions. The goat genomics related to the candidate gene approach is now being used to recognize molecular mechanisms that have different expressions of growth, reproductive, milk, wool, and disease resistance. The appropriate literature on this topic has been reviewed in this article. Several genetic characterization attempts of different goats have reported the existence of genotypic and morphological variations between different goat populations. As a result, different whole-genome sequences along with annotated gene sequences, gene function, and other genomic information of different goats are available in different databases. The main objective of this review is to search the genes associated with economic traits in goats. More than 271 candidate genes have been discovered in goats. Candidate genes influence the physiological pathway, metabolism, and expression of phenotypes. These genes have different functions on economically important traits. Some genes have pleiotropic effect for expression of phenotypic traits. Hence, recognizing candidate genes and their mutations that cause variations in gene expression and phenotype of an economic trait can help breeders look for genetic markers for specific economic traits. The availability of reference whole-genome assembly of goats, annotated genes, and transcriptomics makes comparative genomics a useful tool for systemic genetic upgradation. Identification and characterization of trait-associated sequence variations and gene will provide powerful means to give positive influences for future goat breeding program.
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Pu Y, Zhang Y, Zhang T, Han J, Ma Y, Liu X. Identification of Novel lncRNAs Differentially Expressed in Placentas of Chinese Ningqiang Pony and Yili Horse Breeds. Animals (Basel) 2020; 10:E119. [PMID: 31940795 PMCID: PMC7022612 DOI: 10.3390/ani10010119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/30/2019] [Accepted: 01/09/2020] [Indexed: 12/24/2022] Open
Abstract
As a nutrient sensor, the placenta plays a key role in regulating fetus growth and development. Long non-coding RNAs (lncRNAs) have been shown to regulate growth-related traits. However, the biological function of lncRNAs in horse placentas remains unclear. To compare the expression patterns of lncRNAs in the placentas of the Chinese Ningqiang (NQ) and Yili (YL) breeds, we performed a transcriptome analysis using RNA sequencing (RNA-seq) technology. NQ is a pony breed with an average adult height at the withers of less than 106 cm, whereas that of YL is around 148 cm. Based on 813 million high-quality reads and stringent quality control procedures, 3011 transcripts coding for 1464 placental lncRNAs were identified and mapped to the horse reference genome. We found 107 differentially expressed lncRNAs (DELs) between NQ and YL, including 68 up-regulated and 39 down-regulated DELs in YL. Six (TBX3, CACNA1F, EDN3, KAT5, ZNF281, TMED2, and TGFB1) out of the 233 genes targeted by DELs were identified as being involved in limb development, skeletal myoblast differentiation, and embryo development. Two DELs were predicted to target the TBX3 gene, which was found to be under strong selection and associated with small body size in the Chinese Debao pony breed. This finding suggests the potential functional significance of placental lncRNAs in regulating horse body size.
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Affiliation(s)
- Yabin Pu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Y.P.); (Y.Z.)
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China;
| | - Yanli Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Y.P.); (Y.Z.)
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China;
| | - Tian Zhang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China;
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China;
- International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | - Yuehui Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Y.P.); (Y.Z.)
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China;
| | - Xuexue Liu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Y.P.); (Y.Z.)
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China;
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Xing K, Wang K, Ao H, Chen S, Tan Z, Wang Y, Xitong Z, Yang T, Zhang F, Liu Y, Ni H, Sheng X, Qi X, Wang X, Guo Y, Wang C. Comparative adipose transcriptome analysis digs out genes related to fat deposition in two pig breeds. Sci Rep 2019; 9:12925. [PMID: 31501489 PMCID: PMC6733950 DOI: 10.1038/s41598-019-49548-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 08/22/2019] [Indexed: 12/13/2022] Open
Abstract
Fatness traits are important in pigs because of their implications for fattening efficiency, meat quality, reproductive performance and immunity. Songliao black pigs and Landrace pigs show important differences in production and meat quality traits, including fatness and muscle growth. Therefore, we used a high-throughput massively parallel RNA-seq approach to identify genes differentially expressed in backfat tissue between these two breeds (six pigs in each). An average of 37.87 million reads were obtained from the 12 samples. After statistical analysis of gene expression data by edgeR, a total of 877 differentially expressed genes were detected between the two pig breeds, 205 with higher expression and 672 with lower expression in Songliao pigs. Candidate genes (LCN2, CES3, DGKB, OLR1, LEP, PGM1, PCK1, ACACB, FADS1, FADS2, MOGAT2, SREBF1, PPARGC1B) with known effects on fatness traits were included among the DEGs. A total of 1071 lncRNAs were identified, and 85 of these lncRNAs were differentially expressed, including 53 up-regulated and 32 down-regulated lncRNAs, respectively. The differentially expressed genes and lncRNAs involved in glucagon signaling pathway, glycolysis/gluconeogenesis, insulin signaling pathway, MAPK signaling pathway and so on. Integrated analysis potential trans-regulating or cis-regulating relation between DEGs and DE lncRNAs, suggested lncRNA MSTRG.2479.1 might regulate the expressed level of VLDLR affecting porcine fat metabolism. These results provide a number of candidate genes and lncRNAs potentially involved in porcine fat deposition and provide a basis for future research on the molecular mechanisms underlying in fat deposition.
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Affiliation(s)
- Kai Xing
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Kejun Wang
- College of animal science and veterinary medicine, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Hong Ao
- State Key Laboratory for Animal Nutrition, Key Laboratory for Domestic Animal Genetic Resources and Breeding of the Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Shaokang Chen
- Beijing General Station of Animal Husbandry, Beijing, 100125, China
| | - Zhen Tan
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yuan Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Zhao Xitong
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ting Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Fengxia Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yibing Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Hemin Ni
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Xihui Sheng
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Xiaolong Qi
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Xiangguo Wang
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Yong Guo
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China.
| | - Chuduan Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Fan H, Hou Y, Sahana G, Gao H, Zhu C, Du L, Zhao F, Wang L. A Transcriptomic Study of the Tail Fat Deposition in Two Types of Hulun Buir Sheep According to Tail Size and Sex. Animals (Basel) 2019; 9:ani9090655. [PMID: 31491862 PMCID: PMC6770480 DOI: 10.3390/ani9090655] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/28/2019] [Accepted: 08/30/2019] [Indexed: 01/19/2023] Open
Abstract
Simple Summary Based on tail types, Hulun Buir sheep were divided into two lines including small and big fat-tailed, but these two lines have similar genetic background. In this study, we investigated the morphology and transcription level differences of tail fat between these two lines. The RNA-seq analyses indicated several differentially expressed genes when compared between sexes or two tail sizes. Interestingly, we also found an obvious sex difference in the fat metabolism in Hulun Buir sheep. Two different co-expression networks were only shown either in male or in female sheep. Our findings will provide theoretical background in understanding the genetic mechanism of fat deposition in sheep. Abstract Hulun Buir sheep of similar genetic background were divided into two lines based on tail types: Small- and big fat-tailed. To explore the molecular mechanism of fat deposition in sheep tails, we firstly evaluated the morphology and transcription level differences of tail fat between these two lines. RNA-Seq technology was used to identify differentially expressed genes (DEGs) in phenotypic extremes of tail sizes. Five comparisons were performed taking into account two factors, sex and tail type. We screened out 373 DEGs between big-tailed and small-tailed Hulun Buir sheep, and 775 and 578 DEGs between two types of tails in male and female sheep, respectively. The results showed an obvious sex difference in the fat metabolism in sheep based on gene ontology (GO), pathway, and network analyses. Intriguingly, there were two different co-expression networks only respectively shown in male and female sheep, which were insulin-related network acting on upstream pathways and PPARG-related network effect in downstream pathways. Furthermore, these two networks were linked by a classic pathway of regulating adipogenesis. This is the first study to investigate the sex differences of fat metabolism in domestic animals, and it demonstrates a new experimental way to study fat metabolism. Our findings will provide theoretical background in understanding the tail-size phenotype in sheep and can be exploited in breeding small-tailed sheep.
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Affiliation(s)
- Hongying Fan
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Key Laboratory of Mariculture, Ocean University of China, Qingdao 266000, China
| | - Yali Hou
- Beijing Institute of Genomics, Chinese Academy of Sciences and University of Chinese Academy of Sciences, Beijing 100101, China
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Hongding Gao
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Caiye Zhu
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lixin Du
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fuping Zhao
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Lixian Wang
- Key Laborary of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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11
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Identification of lncRNAs and Genes Responsible for Fatness and Fatty Acid Composition Traits between the Tibetan and Yorkshire Pigs. Int J Genomics 2019; 2019:5070975. [PMID: 31281828 PMCID: PMC6589220 DOI: 10.1155/2019/5070975] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 02/10/2019] [Accepted: 03/03/2019] [Indexed: 12/15/2022] Open
Abstract
Tibetan pigs from the Tibetan Plateau are characterized with a significant phenotypic difference relative to lowland pigs. In this study, a significant difference of the fatness and fatty acid composition traits was observed between the Tibetan and Yorkshire pigs. To uncover the involved mechanism, the expression profile of long noncoding RNAs (lncRNAs) and genes was compared between them. After serial filtered steps, 1,964 lncRNAs were obtained through our computational pipeline. In total, 63 and 715 lncRNAs and genes were identified to be differentially expressed. Evidence from cis- and trans-targeting analysis of lncRNAs demonstrated that some lncRNAs, such as MSTRG.14097 and MSTRG.8034, played important roles in the fatness and fatty acid composition traits. Bioinformatics analysis revealed that many candidate genes were responsible for the two traits. Of these, FASN, ACACA, SCD, ME3, PDHB, ACSS1, ACSS2, and ACLY were identified, which functioned in regulating the level of hexadecanoic acid, hexadecenoic acid, octadecenoic acid, and monounsaturated fatty acid. And LPGAT1, PDK4, ACAA1, and ADIPOQ were associated with the content of stearic acid, octadecadienoic acid, and polyunsaturated fatty acid. Candidate genes, which were responsible for fatness trait, consisted of FGF2, PLAG1, ADIPOQ, IRX3, MIF, IL-34, ADAM8, HMOX1, Vav1, and TLR8. In addition, association analysis also revealed that 34 and 57 genes significantly correlated to the fatness and fatty acid composition trait, respectively. Working out the mechanism caused by these lncRNAs and candidate genes is proven to be complicated but is invaluable to our understanding of fatness and fatty acid composition traits.
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12
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The first comprehensive description of the expression profile of genes involved in differential body growth and the immune system of the Jeju Native Pig and miniature pig. Amino Acids 2018; 51:495-511. [PMID: 30519757 DOI: 10.1007/s00726-018-2685-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 11/29/2018] [Indexed: 12/12/2022]
Abstract
Sus scrofa provides a major source of animal protein for humans as well as being an excellent biomedical model. This study was carried out to understand, in detail, the genetic and functional variants of Jeju Native Pigs and miniature pigs through differential expression profiling of the genes controlling their immune response, growth performance, and meat quality. The Illumina HiSeq 2000 platform was used for generating 1.3 billion 90 bp paired-end reads, which were mapped to the S. scrofa genome using TopHat2. A total of 2481 and 2768 genes were differentially expressed with 8-log changes in muscle and liver samples, respectively. Five hundred forty-eight genes in muscle and 642 genes in liver samples had BLAST matches within the non-redundant database. GO process and pathway analyses showed enhanced biological processes related to the extracellular structural organization and skeletal muscle cell differentiation in muscle tissue, whereas the liver tissue shares functions related to the inflammatory response. Herein, we identify inflammatory regulatory genes in miniature pigs and growth response genes in Jeju Native Pigs, information which can provide a stronger base for the selection of breeding stock and facilitate further in vitro and in vivo studies for therapeutic purposes.
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13
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Song B, Di S, Cui S, Chen N, Wang H, Wang X, Gao Q, Tong G, Wang H, Huang X, Ding L, Gao Y, Liu J, Wang X. Distinct Patterns of PPARγ Promoter Usage, Lipid Degradation Activity, and Gene Expression in Subcutaneous Adipose Tissue of Lean and Obese Swine. Int J Mol Sci 2018; 19:ijms19123892. [PMID: 30563100 PMCID: PMC6321263 DOI: 10.3390/ijms19123892] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/03/2018] [Accepted: 12/03/2018] [Indexed: 12/11/2022] Open
Abstract
Subcutaneous adipose tissue is a loose connective tissue specializing in the regulation of energy storage and metabolization. In domesticated pigs (Sus scrofa), the temporal development of subcutaneous adipose tissue is critical for meat production. However, the regulation of adipose tissue development remains unclear. Here, the subcutaneous adipose tissue development was characterized and compared in lean (Danish-Landrace) and obese (Min) pigs at juvenile and the juvenile-to-adult growth stages. Using RNA sequencing, we profiled the transcriptome of subcutaneous adipose tissue isolated from 4- and 16-week-old pigs and identified 24,718 expressed transcription units. Of them, 6327 genes were differentially expressed between the breeds and/or developmental stages. Compared with obese pigs, upregulated genes in lean pigs showed significant function and pathway enrichment in fatty acid degradation and mitochondrial functions. Further analysis uncovered the distinct usage preferences of the three alternative peroxisomeproliferator-activatedreceptorγ (PPARγ) promoters associated with the development of subcutaneous adipose tissue in both breeds. Transcriptome analysis of subcutaneous adipose tissue in lean and obese pigs suggested that marker-assisted selection of fatty acid degradation and PPARγ signaling pathways could be important directions for future pork quality improvement and modern breeding.
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Affiliation(s)
- Bin Song
- The Northeast Agricultural University, 59 Mucai St, Xiangfang District, Harbin 150030, China.
- Animal Science Institute of Heilongjiang Province, 2 Heyi St, Longsha District, Qiqihaer 161005, China.
| | - Shengwei Di
- The Northeast Agricultural University, 59 Mucai St, Xiangfang District, Harbin 150030, China.
| | - Shiquan Cui
- The Northeast Agricultural University, 59 Mucai St, Xiangfang District, Harbin 150030, China.
| | - Na Chen
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xuan Wang
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
- Department of Biological Sciences, Xian Jiaotong-Liverpool University, Suzhou 215123, China.
| | - Qian Gao
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Guizhi Tong
- Animal Science Institute of Heilongjiang Province, 2 Heyi St, Longsha District, Qiqihaer 161005, China.
| | - Hongbao Wang
- Animal Science Institute of Heilongjiang Province, 2 Heyi St, Longsha District, Qiqihaer 161005, China.
| | - Xuankai Huang
- The Northeast Agricultural University, 59 Mucai St, Xiangfang District, Harbin 150030, China.
- Animal Science Institute of Heilongjiang Province, 2 Heyi St, Longsha District, Qiqihaer 161005, China.
| | - Liyan Ding
- Animal Science Institute of Heilongjiang Province, 2 Heyi St, Longsha District, Qiqihaer 161005, China.
| | - Ying Gao
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Jun Liu
- The Northeast Agricultural University, 59 Mucai St, Xiangfang District, Harbin 150030, China.
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Xibiao Wang
- The Northeast Agricultural University, 59 Mucai St, Xiangfang District, Harbin 150030, China.
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14
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Jiang Q, Sun B, Liu Q, Cai M, Wu R, Wang F, Yao Y, Wang Y, Wang X. MTCH2 promotes adipogenesis in intramuscular preadipocytes via an m 6A-YTHDF1-dependent mechanism. FASEB J 2018; 33:2971-2981. [PMID: 30339471 DOI: 10.1096/fj.201801393rrr] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Intramuscular fat is considered a potential factor that is associated with meat quality in animal production and insulin resistance in humans. N6-methyladenosine (m6A) modification of mRNA plays an important role in regulating adipogenesis. However, the effects of m6A on the adipogenesis of intramuscular preadipocytes and associated mechanisms remain unknown. Here, we performed m6A sequencing to compare m6A methylome of the longissimus dorsi muscles (LDMs) between Landrace pigs (lean-type breed) and Jinhua pigs (obese-type breed with higher levels of intramuscular fat). Transcriptome-wide m6A profiling of porcine LDMs was highly conserved with humans and mice. Furthermore, we identified a unique methylated gene in Jinhua pigs named mitochondrial carrier homology 2 ( MTCH2). The m6A levels of MTCH2 mRNA were reduced by introducing a synonymous mutation, and adipogenesis test results showed that the MTCH2 mutant was inferior with regard to adipogenesis compared with the MTCH2 wild-type. We then found that MTCH2 protein expression was positively associated with m6A levels, and an YTH domain family protein 1-RNA immunoprecipitation-quantitative PCR assay indicated that MTCH2 mRNA was a target of the YTH domain family protein 1. This study provides comprehensive m6A profiles of LDM transcriptomes in pigs and suggests an essential role for m6A modification of MTCH2 in intramuscular fat regulation.-Jiang, Q., Sun, B., Liu, Q., Cai, M., Wu, R., Wang, F., Yao, Y., Wang, Y., Wang, X. MTCH2 promotes adipogenesis in intramuscular preadipocytes via an m6A-YTHDF1-dependent mechanism.
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Affiliation(s)
- Qin Jiang
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Baofa Sun
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; and
| | - Qing Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Min Cai
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Ruifan Wu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Fengqin Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, China.,Key Laboratory of Animal Nutrition and Feed Science in Eastern China, Ministry of Agriculture, Hangzhou, China
| | - Yongxi Yao
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yizhen Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, China.,Key Laboratory of Animal Nutrition and Feed Science in Eastern China, Ministry of Agriculture, Hangzhou, China
| | - Xinxia Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, China.,Key Laboratory of Animal Nutrition and Feed Science in Eastern China, Ministry of Agriculture, Hangzhou, China
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15
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do Nascimento NC, Guimaraes AMS, Dos Santos AP, Chu Y, Marques LM, Messick JB. RNA-Seq based transcriptome of whole blood from immunocompetent pigs (Sus scrofa) experimentally infected with Mycoplasma suis strain Illinois. Vet Res 2018; 49:49. [PMID: 29914581 PMCID: PMC6006945 DOI: 10.1186/s13567-018-0546-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/12/2018] [Indexed: 12/25/2022] Open
Abstract
Pigs are popular animal models in biomedical research. RNA-Seq is becoming the predominant tool to investigate transcriptional changes of the pig’s response to infection. The high sensitivity of this tool requires a strict control of the study design beginning with the selection of healthy animals to provide accurate interpretation of research data. Pigs chronically infected with Mycoplasma suis often show no obvious clinical signs, however the infection may affect the validity of animal research. The goal of this study was to investigate whether or not this silent infection is also silent at the host transcriptional level. Therefore, immunocompetent pigs were experimentally infected with M. suis and transcriptional profiles of whole blood, generated by RNA-Seq, were analyzed and compared to non-infected animals. RNA-Seq showed 55 differentially expressed (DE) genes in the M. suis infected pigs. Down-regulation of genes related to innate immunity (tlr8, chemokines, chemokines receptors) and genes containing IFN gamma-activated sequence (gbp1, gbp2, il15, cxcl10, casp1, cd274) suggests a general suppression of the immune response in the infected animals. Sixteen (29.09%) of the DE genes were involved in two protein interaction networks: one involving chemokines, chemokine receptors and interleukin-15 and another involving the complement cascade. Genes related to vascular permeability, blood coagulation, and endothelium integrity were also DE in infected pigs. These findings suggest that M. suis subclinical infection causes significant alterations in blood mRNA levels, which could impact data interpretation of research using pigs. Screening of pigs for M. suis infection before initiating animal studies is strongly recommended.
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Affiliation(s)
- Naíla C do Nascimento
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA.
| | - Ana M S Guimaraes
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA.,Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil
| | - Andrea P Dos Santos
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA
| | - Yuefeng Chu
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA.,State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute of CAAS, Lanzhou, China
| | - Lucas M Marques
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, São Paulo, Brazil.,Multidisciplinary Institute of Health, Federal University of Bahia, Vitória da Conquista, Bahia, Brazil
| | - Joanne B Messick
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA.
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16
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Ghosh M, Sharma N, Singh AK, Gera M, Pulicherla KK, Jeong DK. Transformation of animal genomics by next-generation sequencing technologies: a decade of challenges and their impact on genetic architecture. Crit Rev Biotechnol 2018; 38:1157-1175. [PMID: 29631431 DOI: 10.1080/07388551.2018.1451819] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
For more than a quarter of a century, sequencing technologies from Sanger's method to next-generation high-throughput techniques have provided fascinating opportunities in the life sciences. The continuing upward trajectory of sequencing technologies will improve livestock research and expedite the development of various new genomic and technological studies with farm animals. The use of high-throughput technologies in livestock research has increased interest in metagenomics, epigenetics, genome-wide association studies, and identification of single nucleotide polymorphisms and copy number variations. Such studies are beginning to provide revolutionary insights into biological and evolutionary processes. Farm animals, such as cattle, swine, and horses, have played a dual role as economically and agriculturally important animals as well as biomedical research models. The first part of this study explores the current state of sequencing methods, many of which are already used in animal genomic studies, and the second part summarizes the state of cattle, swine, horse, and chicken genome sequencing and illustrates its achievements during the last few years. Finally, we describe several high-throughput sequencing approaches for the improved detection of known, unknown, and emerging infectious agents, leading to better diagnosis of infectious diseases. The insights from viral metagenomics and the advancement of next-generation sequencing will strongly support specific and efficient vaccine development and provide strategies for controlling infectious disease transmission among animal populations and/or between animals and humans. However, prospective sequencing technologies will require further research and in-field testing before reaching the marketplace.
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Affiliation(s)
- Mrinmoy Ghosh
- a Department of Animal Biotechnology , Jeju National University , Jeju-Do , Republic of Korea
| | - Neelesh Sharma
- b Department of Veterinary Science and Animal Husbandry , Sher-e-Kashmir University of Agricultural Sciences and Technology , R.S. Pura , India
| | - Amit Kumar Singh
- a Department of Animal Biotechnology , Jeju National University , Jeju-Do , Republic of Korea
| | - Meeta Gera
- a Department of Animal Biotechnology , Jeju National University , Jeju-Do , Republic of Korea
| | | | - Dong Kee Jeong
- a Department of Animal Biotechnology , Jeju National University , Jeju-Do , Republic of Korea
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17
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Foley NM, Hughes GM, Huang Z, Clarke M, Jebb D, Whelan CV, Petit EJ, Touzalin F, Farcy O, Jones G, Ransome RD, Kacprzyk J, O’Connell MJ, Kerth G, Rebelo H, Rodrigues L, Puechmaille SJ, Teeling EC. Growing old, yet staying young: The role of telomeres in bats' exceptional longevity. SCIENCE ADVANCES 2018; 4:eaao0926. [PMID: 29441358 PMCID: PMC5810611 DOI: 10.1126/sciadv.aao0926] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 01/10/2018] [Indexed: 05/02/2023]
Abstract
Understanding aging is a grand challenge in biology. Exceptionally long-lived animals have mechanisms that underpin extreme longevity. Telomeres are protective nucleotide repeats on chromosome tips that shorten with cell division, potentially limiting life span. Bats are the longest-lived mammals for their size, but it is unknown whether their telomeres shorten. Using >60 years of cumulative mark-recapture field data, we show that telomeres shorten with age in Rhinolophus ferrumequinum and Miniopterus schreibersii, but not in the bat genus with greatest longevity, Myotis. As in humans, telomerase is not expressed in Myotis myotis blood or fibroblasts. Selection tests on telomere maintenance genes show that ATM and SETX, which repair and prevent DNA damage, potentially mediate telomere dynamics in Myotis bats. Twenty-one telomere maintenance genes are differentially expressed in Myotis, of which 14 are enriched for DNA repair, and 5 for alternative telomere-lengthening mechanisms. We demonstrate how telomeres, telomerase, and DNA repair genes have contributed to the evolution of exceptional longevity in Myotis bats, advancing our understanding of healthy aging.
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Affiliation(s)
- Nicole M. Foley
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
| | - Graham M. Hughes
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
| | - Zixia Huang
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
| | - Michael Clarke
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
| | - David Jebb
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
| | - Conor V. Whelan
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
| | - Eric J. Petit
- Ecologie et Santé des Ecosystèmes (ESE), Ecology and Ecosystem Health, Agrocampus Ouest, INRA, 35042 Rennes, France
| | - Frédéric Touzalin
- Laboratoire Évolution et Diversité Biologique, UMR 5174: Université Toulouse III, CNRS, ENFA, 118 Route de Narbonne, 31062 Toulouse cedex 9, France
| | - Olivier Farcy
- Le Groupe Chiroptères de Bretagne Vivante/SEPNB, 19 rue Gouesnou BP 62132, 29221 Brest cedex 2, France
| | - Gareth Jones
- School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TH, UK
| | - Roger D. Ransome
- School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TH, UK
| | - Joanna Kacprzyk
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
| | - Mary J. O’Connell
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Gerald Kerth
- University of Greifswald, Loitzer Strasse 26, 17489 Greifswald, Germany
| | - Hugo Rebelo
- School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TH, UK
- CIBIO-InBIO, Universidade do Porto, Campus de Agrário Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal
- CEABN-InBIO, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-015 Lisboa, Portugal
| | - Luísa Rodrigues
- Instituto da Conservação da Natureza e das Florestas, Avenida da República 16-16B, 1050-191 Lisboa, Portugal
| | - Sébastien J. Puechmaille
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
- University of Greifswald, Loitzer Strasse 26, 17489 Greifswald, Germany
| | - Emma C. Teeling
- School of Biology and Environmental Science, Science Centre West, University College Dublin, Belfield, Dublin 4, Ireland
- Corresponding author.
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18
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Tao X, Liang Y, Yang X, Pang J, Zhong Z, Chen X, Yang Y, Zeng K, Kang R, Lei Y, Ying S, Gong J, Gu Y, Lv X. Transcriptomic profiling in muscle and adipose tissue identifies genes related to growth and lipid deposition. PLoS One 2017; 12:e0184120. [PMID: 28877211 PMCID: PMC5587268 DOI: 10.1371/journal.pone.0184120] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 08/18/2017] [Indexed: 11/23/2022] Open
Abstract
Growth performance and meat quality are important traits for the pig industry and consumers. Adipose tissue is the main site at which fat storage and fatty acid synthesis occur. Therefore, we combined high-throughput transcriptomic sequencing in adipose and muscle tissues with the quantification of corresponding phenotypic features using seven Chinese indigenous pig breeds and one Western commercial breed (Yorkshire). We obtained data on 101 phenotypic traits, from which principal component analysis distinguished two groups: one associated with the Chinese breeds and one with Yorkshire. The numbers of differentially expressed genes between all Chinese breeds and Yorkshire were shown to be 673 and 1056 in adipose and muscle tissues, respectively. Functional enrichment analysis revealed that these genes are associated with biological functions and canonical pathways related to oxidoreductase activity, immune response, and metabolic process. Weighted gene coexpression network analysis found more coexpression modules significantly correlated with the measured phenotypic traits in adipose than in muscle, indicating that adipose regulates meat and carcass quality. Using the combination of differential expression, QTL information, gene significance, and module hub genes, we identified a large number of candidate genes potentially related to economically important traits in pig, which should help us improve meat production and quality.
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Affiliation(s)
- Xuan Tao
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Yan Liang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Xuemei Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Jianhui Pang
- Chengdu Biotechservice Institute, Chengdu, Sichuan, China
| | - Zhijun Zhong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Xiaohui Chen
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Yuekui Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Kai Zeng
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Runming Kang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Yunfeng Lei
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Sancheng Ying
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Jianjun Gong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Yiren Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
- * E-mail: (YRG); (XBL)
| | - Xuebin Lv
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
- * E-mail: (YRG); (XBL)
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19
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Global transcriptome analysis identifies differentially expressed genes related to lipid metabolism in Wagyu and Holstein cattle. Sci Rep 2017; 7:5278. [PMID: 28706200 PMCID: PMC5509646 DOI: 10.1038/s41598-017-05702-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 06/01/2017] [Indexed: 11/22/2022] Open
Abstract
Fat deposition of beef cattle varies between breeds. However, the regulation mechanism is still not elucidated completely at molecular level. In the present study, we comparatively analyzed transcriptome of subcutaneous adipose tissue between Wagyu and Holstein cattle with a significant difference in fat deposition to identify key genes associated with fat metabolism and adipogenesis by high-throughput RNA-seq technology. A total of 59,149,852 and 69,947,982 high quality reads were generated, respectively. With further analysis, 662 differentially expressed genes were identified. Gene Ontology and KEGG pathway analysis revealed that many differentially expressed genes were enriched in several biological processes and pathways relevant to adipogenesis and lipid metabolism, in which PPAR and fatty acid metabolism signaling pathways with related genes such as PPARγ, PLIN2 and ELOVL6 et al. play a critical role. Protein-protein interaction network analysis showed EGR1, FOS, SERPINE1, AGT, MMP2 may have great impact on adipocyte differentiation and adipogenesis. Moreover, potential alternative splicing events and single nucleotide polymorphisms (SNPs) were also identified. In summary, we comprehensively analyzed and discussed the transcriptome of subcutaneous adipose tissue of Wagyu and Holstein cattle, which might provide a theoretical basis for better understanding molecular mechanism of fat metabolism and deposition in beef cattle.
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Whole Blood Transcriptome Sequencing Reveals Gene Expression Differences between Dapulian and Landrace Piglets. BIOMED RESEARCH INTERNATIONAL 2017; 2016:7907980. [PMID: 28105431 PMCID: PMC5220446 DOI: 10.1155/2016/7907980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 11/04/2016] [Accepted: 11/27/2016] [Indexed: 11/18/2022]
Abstract
There is little genomic information regarding gene expression differences at the whole blood transcriptome level of different pig breeds at the neonatal stage. To solve this, we characterized differentially expressed genes (DEGs) in the whole blood of Dapulian (DPL) and Landrace piglets using RNA-seq (RNA-sequencing) technology. In this study, 83 DEGs were identified between the two breeds. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses identified immune response and metabolism as the most commonly enriched terms and pathways in the DEGs. Genes related to immunity and lipid metabolism were more highly expressed in the DPL piglets, while genes related to body growth were more highly expressed in the Landrace piglets. Additionally, the DPL piglets had twofold more single nucleotide polymorphisms (SNPs) and alternative splicing (AS) than the Landrace piglets. These results expand our knowledge of the genes transcribed in the piglet whole blood of two breeds and provide a basis for future research of the molecular mechanisms underlying the piglet differences.
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Hu J, Yang D, Wang H, Li C, Zeng Y, Chen W. CpG Oligodeoxynucleotides Induce Differential Cytokine and Chemokine Gene Expression Profiles in Dapulian and Landrace Pigs. Front Microbiol 2016; 7:1992. [PMID: 28018321 PMCID: PMC5156958 DOI: 10.3389/fmicb.2016.01992] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 11/28/2016] [Indexed: 12/16/2022] Open
Abstract
Oligodeoxynucleotides containing unmethylated CpG motifs (CpG ODN) mimic the immunostimulatory activity of microbial DNA by interacting with Toll-like receptor 9 (TLR9) to activate both the innate and adaptive immune responses in different species. However, few studies have been published to compare the effects of CpG ODN on different pig breeds. Therefore, in this study, whole blood gene expression profiles of DPL and Landrace pigs treated with CpG ODN were studied using RNA-seq technology. Five Hundred differentially expressed genes (DEGs) were identified between the two breeds. DPL pigs had significantly higher number of immune-relevant DEGs than the Landrace pigs after CpG ODN treatment. Pathway analysis showed that cytokine-cytokine receptor interaction and chemokine signaling pathway were the major enriched pathways of the immune-relevant DEGs. Further in vitro experiments showed that PBMCs of the DPL pigs had significantly higher levels of TLR9 mRNA than those of the Landrace pigs, both before and after CpG ODN stimulation. Cytokine and chemokine induction in the PBMCs of both breeds were also measured after CpG ODN stimulation. Our data showed that mRNA levels of cytokines (IFNα, IL8, IL12 p40) and chemokines (CXCL9, CXCL13) were significantly higher in the PBMCs of the DPL pigs than those of the Landrace pigs. Taken together, our data provide new information regarding the pig breed difference in response to CpG ODN stimulation and that higher levels of TLR9 mRNA in DPL pigs may be a major contributor for disease resistance.
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Affiliation(s)
| | | | | | | | - Yongqing Zeng
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Shandong Agricultural UniversityTai'an, China
| | - Wei Chen
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, Shandong Agricultural UniversityTai'an, China
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22
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Wang X, Liu J, Zhou G, Guo J, Yan H, Niu Y, Li Y, Yuan C, Geng R, Lan X, An X, Tian X, Zhou H, Song J, Jiang Y, Chen Y. Whole-genome sequencing of eight goat populations for the detection of selection signatures underlying production and adaptive traits. Sci Rep 2016; 6:38932. [PMID: 27941843 PMCID: PMC5150979 DOI: 10.1038/srep38932] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 11/16/2016] [Indexed: 12/25/2022] Open
Abstract
The goat (Capra hircus) is one of the first farm animals that have undergone domestication and extensive natural and artificial selection by adapting to various environments, which in turn has resulted in its high level of phenotypic diversity. Here, we generated medium-coverage (9–13×) sequences from eight domesticated goat breeds, representing morphologically or geographically specific populations, to identify genomic regions representing selection signatures. We discovered ~10 million single nucleotide polymorphisms (SNPs) for each breed. By combining two approaches, ZHp and di values, we identified 22 genomic regions that may have contributed to the phenotypes in coat color patterns, body size, cashmere traits, as well as high altitude adaptation in goat populations. Candidate genes underlying strong selection signatures including coloration (ASIP, KITLG, HTT, GNA11, and OSTM1), body size (TBX15, DGCR8, CDC25A, and RDH16), cashmere traits (LHX2, FGF9, and WNT2), and hypoxia adaptation (CDK2, SOCS2, NOXA1, and ENPEP) were identified. We also identified candidate functional SNPs within selected genes that may be important for each trait. Our results demonstrated the potential of using sequence data in identifying genomic regions that are responsible for agriculturally significant phenotypes in goats, which in turn can be used in the selection of goat breeds for environmental adaptation and domestication.
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Affiliation(s)
- Xiaolong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Jing Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Guangxian Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Jiazhong Guo
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, 625000, China
| | - Hailong Yan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.,College of Life Science, Yulin University, Yulin, 719000, China
| | - Yiyuan Niu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yan Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of CAAS, Lanzhou 730050, China
| | - Rongqing Geng
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.,College of Pharmacy, Yancheng Teachers University, Yancheng, 224051, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiaopeng An
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | | | - Huangkai Zhou
- Guangzhou Gene de-novo Biotechnology Co. Ltd. Guangzhou, 510000, China
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742,USA
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
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Comparative Transcriptomic Analyses by RNA-seq to Elucidate Differentially Expressed Genes in the Muscle of Korean Thoroughbred Horses. Appl Biochem Biotechnol 2016; 180:588-608. [DOI: 10.1007/s12010-016-2118-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/05/2016] [Indexed: 12/27/2022]
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Transcriptomic Analysis Identifies Candidate Genes and Gene Sets Controlling the Response of Porcine Peripheral Blood Mononuclear Cells to Poly I:C Stimulation. G3-GENES GENOMES GENETICS 2016; 6:1267-75. [PMID: 26935416 PMCID: PMC4856078 DOI: 10.1534/g3.116.028290] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Polyinosinic-polycytidylic acid (poly I:C), a synthetic dsRNA analog, has been demonstrated to have stimulatory effects similar to viral dsRNA. To gain deep knowledge of the host transcriptional response of pigs to poly I:C stimulation, in the present study, we cultured and stimulated peripheral blood mononuclear cells (PBMC) of piglets of one Chinese indigenous breed (Dapulian) and one modern commercial breed (Landrace) with poly I:C, and compared their transcriptional profiling using RNA-sequencing (RNA-seq). Our results indicated that poly I:C stimulation can elicit significantly differentially expressed (DE) genes in Dapulian (g = 290) as well as Landrace (g = 85). We also performed gene set analysis using the Gene Set Enrichment Analysis (GSEA) package, and identified some significantly enriched gene sets in Dapulian (g = 18) and Landrace (g = 21). Most of the shared DE genes and gene sets were immune-related, and may play crucial rules in the immune response of poly I:C stimulation. In addition, we detected large sets of significantly DE genes and enriched gene sets when comparing the gene expression profile between the two breeds, including control and poly I:C stimulation groups. Besides immune-related functions, some of the DE genes and gene sets between the two breeds were involved in development and growth of various tissues, which may be correlated with the different characteristics of the two breeds. The DE genes and gene sets detected herein provide crucial information towards understanding the immune regulation of antiviral responses, and the molecular mechanisms of different genetic resistance to viral infection, in modern and indigenous pigs.
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Xing K, Zhu F, Zhai L, Chen S, Tan Z, Sun Y, Hou Z, Wang C. Identification of genes for controlling swine adipose deposition by integrating transcriptome, whole-genome resequencing, and quantitative trait loci data. Sci Rep 2016; 6:23219. [PMID: 26996612 PMCID: PMC4800386 DOI: 10.1038/srep23219] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 03/02/2016] [Indexed: 12/29/2022] Open
Abstract
Backfat thickness is strongly associated with meat quality, fattening efficiency, reproductive performance, and immunity in pigs. Fat storage and fatty acid synthesis mainly occur in adipose tissue. Therefore, we used a high-throughput massively parallel sequencing approach to identify transcriptomes in adipose tissue, and whole-genome differences from three full-sibling pairs of pigs with opposite (high and low) backfat thickness phenotypes. We obtained an average of 38.69 million reads for six samples, 78.68% of which were annotated in the reference genome. Eighty-nine overlapping differentially expressed genes were identified among the three pair comparisons. Whole-genome resequencing also detected multiple genetic variations between the pools of DNA from the two groups. Compared with the animal quantitative trait loci (QTL) database, 20 differentially expressed genes were matched to the QTLs associated with fatness in pigs. Our technique of integrating transcriptome, whole-genome resequencing, and QTL database information provided a rich source of important differentially expressed genes and variations. Associate analysis between selected SNPs and backfat thickness revealed that two SNPs and one haplotype of ME1 significantly affected fat deposition in pigs. Moreover, genetic analysis confirmed that variations in the differentially expressed genes may affect fat deposition.
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Affiliation(s)
- Kai Xing
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Feng Zhu
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - LiWei Zhai
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - ShaoKang Chen
- Beijing General Station of Animal Husbandry, Beijing 100125, China
| | - Zhen Tan
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - YangYang Sun
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - ZhuoCheng Hou
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - ChuDuan Wang
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China
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26
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Zhang X, Huang L, Wu T, Feng Y, Ding Y, Ye P, Yin Z. Transcriptomic Analysis of Ovaries from Pigs with High And Low Litter Size. PLoS One 2015; 10:e0139514. [PMID: 26426260 PMCID: PMC4591126 DOI: 10.1371/journal.pone.0139514] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 09/13/2015] [Indexed: 01/03/2023] Open
Abstract
Litter size is one of the most important economic traits for pig production as it is directly related to the production efficiency. Litter size is affected by interactions between multiple genes and the environment. While recent studies have identified some genes associated with prolificacy in pigs, transcriptomic studies of specific genes affecting litter size in porcine ovaries are rare. In order to identify candidate genes associated with litter size in swine, we assessed gene expression differences between the ovaries of Yorkshire pigs with extremely high and low litter sizes using the RNA-Seq method. A total of 1 243 differentially expressed genes were identified: 897 genes were upregulated and 346 genes were downregulated in high litter size ovary samples compared with low litter size ovary samples. A large number of these genes related to steroid hormone regulation in animal ovaries, including 59 Gene Ontology terms and 27 Kyoto Encyclopedia of Genes and Genomes pathways involved in steroid biosynthesis and ovarian steroidogenesis. From these differentially expressed genes, we identified a total of 11 genes using a bioinformatics screen that may be associated with high litter size in Yorkshire pigs. These results provide a list of new candidate genes for porcine litter size and prolificacy to be further investigated.
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Affiliation(s)
- Xiaodong Zhang
- Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding of Anhui province, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui Province, People’s Republic of China
| | - Long Huang
- Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding of Anhui province, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui Province, People’s Republic of China
| | - Tao Wu
- Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding of Anhui province, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui Province, People’s Republic of China
| | - Yifang Feng
- Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding of Anhui province, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui Province, People’s Republic of China
| | - Yueyun Ding
- Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding of Anhui province, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui Province, People’s Republic of China
| | - Pengfei Ye
- Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding of Anhui province, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui Province, People’s Republic of China
| | - Zongjun Yin
- Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding of Anhui province, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui Province, People’s Republic of China
- * E-mail:
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27
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Xing K, Zhu F, Zhai L, Liu H, Wang Y, Wang Z, Chen S, Hou Z, Wang C. Integration of transcriptome and whole genomic resequencing data to identify key genes affecting swine fat deposition. PLoS One 2015; 10:e0122396. [PMID: 25849573 PMCID: PMC4388518 DOI: 10.1371/journal.pone.0122396] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 02/21/2015] [Indexed: 12/17/2022] Open
Abstract
Fat deposition is highly correlated with the growth, meat quality, reproductive performance and immunity of pigs. Fatty acid synthesis takes place mainly in the adipose tissue of pigs; therefore, in this study, a high-throughput massively parallel sequencing approach was used to generate adipose tissue transcriptomes from two groups of Songliao black pigs that had opposite backfat thickness phenotypes. The total number of paired-end reads produced for each sample was in the range of 39.29-49.36 millions. Approximately 188 genes were differentially expressed in adipose tissue and were enriched for metabolic processes, such as fatty acid biosynthesis, lipid synthesis, metabolism of fatty acids, etinol, caffeine and arachidonic acid and immunity. Additionally, many genetic variations were detected between the two groups through pooled whole-genome resequencing. Integration of transcriptome and whole-genome resequencing data revealed important genomic variations among the differentially expressed genes for fat deposition, for example, the lipogenic genes. Further studies are required to investigate the roles of candidate genes in fat deposition to improve pig breeding programs.
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Affiliation(s)
- Kai Xing
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Feng Zhu
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Liwei Zhai
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Huijie Liu
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yuan Wang
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhijun Wang
- Tianjin Ninghe primary pig breeding farm, Ninghe, 301500, Tianjin, China
| | - Shaokang Chen
- Animal husbandry and veterinary station of Beijing, Beijing, 100125, Beijing, China
| | - Zhuocheng Hou
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Chuduan Wang
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
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