1
|
Cendron F, Rosani U, Franzoi M, Boselli C, Maggi F, De Marchi M, Penasa M. Analysis of miRNAs in milk of four livestock species. BMC Genomics 2024; 25:859. [PMID: 39277740 PMCID: PMC11401297 DOI: 10.1186/s12864-024-10783-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 09/09/2024] [Indexed: 09/17/2024] Open
Abstract
BACKGROUND Milk is essential for mammalian nutrition because it provides vital nutrients for growth and development. Milk composition, which is influenced by genetic and environmental factors, supports lactation, a complex process crucial for milk production and quality. Recent research has focused on noncoding RNAs, particularly microRNAs (miRNAs), which are present in body fluids and regulate gene expression post-transcriptionally. This study comprehensively characterizes miRNAs in milk of four livestock species, namely Bubalus bubalis, Capra hircus, Equus asinus, and Ovis aries and identifies potential target genes. RESULTS High-throughput sequencing of milk RNA resulted in distinct read counts across species: B. bubalis (8,790,441 reads), C. hircus (12,976,275 reads), E. asinus (9,385,067 reads), and O. aries (7,295,297 reads). E. asinus had the highest RNA mapping rate (94.6%) and O. aries the lowest (84.8%). A substantially greater proportion of miRNAs over other small RNAs was observed for the donkey milk sample (7.74%) compared to buffalo (0.87%), goat (1.57%), and sheep (1.12%). Shared miRNAs, which included miR-200a, miR-200b, miR-200c, and miR-23a among others, showed varying expression levels across species, confirmed by qPCR analysis. Functional annotation of predicted miRNA target genes highlighted diverse roles, with an enrichment in functions linked to metabolism and immunity. Pathway analysis identified immune response pathways as significant, with several miRNAs targeting specific genes across species, suggesting their regulatory function in milk. CONCLUSIONS Both conserved and species-specific miRNAs were detected in milk of the investigated species. The identified target genes of these miRNAs have important roles in neonatal development, adaptation, growth, and immune response. Furthermore, they influence milk and meat production traits in livestock.
Collapse
Affiliation(s)
- Filippo Cendron
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale Dell'Università 16, Legnaro (PD), 35020, Italy.
| | - Umberto Rosani
- Department of Biology (DiBio), University of Padova, Viale Giuseppe Colombo 3, Padua, 35131, Italy
| | - Marco Franzoi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale Dell'Università 16, Legnaro (PD), 35020, Italy
| | - Carlo Boselli
- Istituto Zooprofilattico Sperimentale del Lazio E Della Toscana "M. Aleandri" - National Reference Centre for Ovine and Caprine Milk and Dairy Products Quality (C.Re.L.D.O.C.), Rome, 00178, Italy
| | - Flavio Maggi
- Azienda Sanitaria Locale, Roma 4, Distretto 4, Via G. Verdi 1, Rignano Flaminio, Rome, 00068, Italy
| | - Massimo De Marchi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale Dell'Università 16, Legnaro (PD), 35020, Italy
| | - Mauro Penasa
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale Dell'Università 16, Legnaro (PD), 35020, Italy
| |
Collapse
|
2
|
Li J, Chen Z, Bai Y, Wei Y, Guo D, Liu Z, Niu Y, Shi B, Zhang X, Cai Y, Zhao Z, Hu J, Wang J, Liu X, Li S, Zhao F. Integration of ATAC-Seq and RNA-Seq Analysis to Identify Key Genes in the Longissimus Dorsi Muscle Development of the Tianzhu White Yak. Int J Mol Sci 2023; 25:158. [PMID: 38203329 PMCID: PMC10779322 DOI: 10.3390/ijms25010158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
During the postnatal stages, skeletal muscle development undergoes a series of meticulously regulated alterations in gene expression. However, limited studies have employed chromatin accessibility to unravel the underlying molecular mechanisms governing muscle development in yak species. Therefore, we conducted an analysis of both gene expression levels and chromatin accessibility to comprehensively characterize the dynamic genome-wide chromatin accessibility during muscle growth and development in the Tianzhu white yak, thereby elucidating the features of accessible chromatin regions throughout this process. Initially, we compared the differences in chromatin accessibility between two groups and observed that calves exhibited higher levels of chromatin accessibility compared to adult cattle, particularly within ±2 kb of the transcription start site (TSS). In order to investigate the correlation between alterations in chromatin accessible regions and variations in gene expression levels, we employed a combination of ATAC-seq and RNA-seq techniques, leading to the identification of 18 central transcriptional factors (TFs) and 110 key genes with significant effects. Through further analysis, we successfully identified several TFs, including Sp1, YY1, MyoG, MEF2A and MEF2C, as well as a number of candidate genes (ANKRD2, ANKRD1, BTG2 and LMOD3) which may be closely associated with muscle growth and development. Moreover, we constructed an interactive network program encompassing hub TFs and key genes related to muscle growth and development. This innovative approach provided valuable insights into the molecular mechanism underlying skeletal muscle development in the postnatal stages of Tianzhu white yaks while also establishing a solid theoretical foundation for future research on yak muscle development.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Zhidong Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | | | | | | | | |
Collapse
|
3
|
Almiñana C, Dubuisson F, Bauersachs S, Royer E, Mermillod P, Blesbois E, Guignot F. Unveiling how vitrification affects the porcine blastocyst: clues from a transcriptomic study. J Anim Sci Biotechnol 2022; 13:46. [PMID: 35303969 PMCID: PMC8932223 DOI: 10.1186/s40104-021-00672-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/24/2021] [Indexed: 12/13/2022] Open
Abstract
Background Currently, there is a high demand for efficient pig embryo cryopreservation procedures in the porcine industry as well as for genetic diversity preservation and research purposes. To date, vitrification (VIT) is the most efficient method for pig embryo cryopreservation. Despite a high number of embryos survives in vitro after vitrification/warming procedures, the in vivo embryo survival rates after embryo transfer are variable among laboratories. So far, most studies have focused on cryoprotective agents and devices, while the VIT effects on porcine embryonic gene expression remained unclear. The few studies performed were based on vitrified/warmed embryos that were cultured in vitro (IVC) to allow them to re–expand. Thus, the specific alterations of VIT, IVC, and the cumulative effect of both remained unknown. To unveil the VIT-specific embryonic alterations, gene expression in VIT versus (vs.) IVC embryos was analyzed. Additionally, changes derived from both VIT and IVC vs. control embryos (CO) were analyzed to confirm the VIT embryonic alterations. Three groups of in vivo embryos at the blastocyst stage were analyzed by RNA–sequencing: (1) VIT embryos (vitrified/warmed and cultured in vitro), (2) IVC embryos and (3) CO embryos. Results RNA–sequencing revealed three clearly different mRNA profiles for VIT, IVC and CO embryos. Comparative analysis of mRNA profiles between VIT and IVC identified 321, differentially expressed genes (DEG) (FDR < 0.006). In VIT vs. CO and IVC vs. CO, 1901 and 1519 DEG were found, respectively, with an overlap of 1045 genes. VIT-specific functional alterations were associated to response to osmotic stress, response to hormones, and developmental growth. While alterations in response to hypoxia and mitophagy were related to the sum of VIT and IVC effects. Conclusions Our findings revealed new insights into the VIT procedure-specific alterations of embryonic gene expression by first comparing differences in VIT vs. IVC embryos and second by an integrative transcriptome analysis including in vivo control embryos. The identified VIT alterations might reflect the transcriptional signature of the embryo cryodamage but also the embryo healing process overcoming the VIT impacts. Selected validated genes were pointed as potential biomarkers that may help to improve vitrification. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-021-00672-1.
Collapse
Affiliation(s)
- C Almiñana
- UMR PRC, INRAE 0085, CNRS 7247, Université de Tours, IFCE, F, -37380, Nouzilly, France. .,Functional Genomics Group, Institute of Veterinary Anatomy, VetSuisse Faculty Zurich, University of Zurich, Zürich, Switzerland.
| | - F Dubuisson
- UMR PRC, INRAE 0085, CNRS 7247, Université de Tours, IFCE, F, -37380, Nouzilly, France
| | - S Bauersachs
- Functional Genomics Group, Institute of Veterinary Anatomy, VetSuisse Faculty Zurich, University of Zurich, Zürich, Switzerland
| | - E Royer
- UEPAO, INRAE, F, -37380, Nouzilly, France
| | - P Mermillod
- UMR PRC, INRAE 0085, CNRS 7247, Université de Tours, IFCE, F, -37380, Nouzilly, France
| | - E Blesbois
- UMR PRC, INRAE 0085, CNRS 7247, Université de Tours, IFCE, F, -37380, Nouzilly, France
| | - F Guignot
- UMR PRC, INRAE 0085, CNRS 7247, Université de Tours, IFCE, F, -37380, Nouzilly, France
| |
Collapse
|
4
|
Liu X, Zhang J, Xiong X, Chen C, Xing Y, Duan Y, Xiao S, Yang B, Ma J. An Integrative Analysis of Transcriptome and GWAS Data to Identify Potential Candidate Genes Influencing Meat Quality Traits in Pigs. Front Genet 2021; 12:748070. [PMID: 34745221 PMCID: PMC8567094 DOI: 10.3389/fgene.2021.748070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
Understanding the genetic factors behind meat quality traits is of great significance to animal breeding and production. We previously conducted a genome-wide association study (GWAS) for meat quality traits in a White Duroc × Erhualian F2 pig population using Illumina porcine 60K SNP data. Here, we further investigate the functional candidate genes and their network modules associated with meat quality traits by integrating transcriptomics and GWAS information. Quantitative trait transcript (QTT) analysis, gene expression QTL (eQTL) mapping, and weighted gene co-expression network analysis (WGCNA) were performed using the digital gene expression (DGE) data from 493 F2 pig's muscle and liver samples. Among the quantified 20,108 liver and 23,728 muscle transcripts, 535 liver and 1,014 muscle QTTs corresponding to 416 and 721 genes, respectively, were found to be significantly (p < 5 × 10-4) correlated with 22 meat quality traits measured on longissiums dorsi muscle (LM) or semimembranosus muscle (SM). Transcripts associated with muscle glycolytic potential (GP) and pH values were enriched for genes involved in metabolic process. There were 42 QTTs (for 32 genes) shared by liver and muscle tissues, of which 10 QTTs represent GP- and/or pH-related genes, such as JUNB, ATF3, and PPP1R3B. Furthermore, a genome-wide eQTL mapping revealed a total of 3,054 eQTLs for all annotated transcripts in muscle (p < 2.08 × 10-5), including 1,283 cis-eQTLs and 1771 trans-eQTLs. In addition, WGCNA identified five modules relevant to glycogen metabolism pathway and highlighted the connections between variations in meat quality traits and genes involved in energy process. Integrative analysis of GWAS loci, eQTL, and QTT demonstrated GALNT15/GALNTL2 and HTATIP2 as strong candidate genes for drip loss and pH drop from postmortem 45 min to 24 h, respectively. Our findings provide valuable insights into the genetic basis of meat quality traits and greatly expand the number of candidate genes that may be valuable for future functional analysis and genetic improvement of meat quality.
Collapse
Affiliation(s)
- Xianxian Liu
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Junjie Zhang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Xinwei Xiong
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Congying Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yuyun Xing
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yanyu Duan
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Shijun Xiao
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Bin Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Junwu Ma
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| |
Collapse
|
5
|
Vitali M, Sirri R, Zappaterra M, Zambonelli P, Giannini G, Lo Fiego DP, Davoli R. Functional analysis finds differences on the muscle transcriptome of pigs fed an n-3 PUFA-enriched diet with or without antioxidant supplementations. PLoS One 2019; 14:e0212449. [PMID: 30785965 PMCID: PMC6382273 DOI: 10.1371/journal.pone.0212449] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/01/2019] [Indexed: 12/11/2022] Open
Abstract
Supplementing pig diets with n-3 polyunsaturated fatty acids (n-3 PUFA) may produce meat products with an increased n-3 fatty acid content, and the combined antioxidants addition could prevent lipid oxidation in the feed. However, to date, the effects of these bioactive compounds at the molecular level in porcine skeletal muscle are mostly unknown. This study aimed to analyse changes in the Longissimus thoracis transcriptome of 35 pigs fed three diets supplemented with: linseed (L); linseed, vitamin E and Selenium (LES) or linseed and plant-derived polyphenols (LPE). Pigs were reared from 80.8 ± 5.6 kg to 151.8 ± 9.9 kg. After slaughter, RNA-Seq was performed and 1182 differentially expressed genes (DEGs) were submitted to functional analysis. The L vs LES comparison did not show differences, while L vs LPE showed 1102 DEGs and LES vs LPE 80 DEGs. LPE compared to the other groups showed the highest number of up-regulated genes involved in preserving muscle metabolism and structure. Results enlighten that the combined supplementation of bioactive lipids (n-3 PUFA from linseed) with plant extracts as a source of polyphenols increases, compared to the only addition of linseed, the expression of genes involved in mRNA metabolic processes and transcriptional regulation, glucose uptake and, finally, in supporting muscle development and physiology. These results improve the knowledge of the biological effect of bioactive compounds in Longissimus thoracis muscle, and sustain the growing interest over their use in pig production.
Collapse
Affiliation(s)
- Marika Vitali
- Interdepartmental Centre for Industrial Agrifood Research (CIRI- AGRO), University of Bologna, Cesena, Italy
| | - Rubina Sirri
- Interdepartmental Centre for Industrial Agrifood Research (CIRI- AGRO), University of Bologna, Cesena, Italy
| | - Martina Zappaterra
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Paolo Zambonelli
- Interdepartmental Centre for Industrial Agrifood Research (CIRI- AGRO), University of Bologna, Cesena, Italy
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Giulia Giannini
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Domenico Pietro Lo Fiego
- Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
- Interdepartmental Research Centre for Agri-Food Biological Resources Improvement and Valorisation (BIOGEST-SITEIA), University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Roberta Davoli
- Interdepartmental Centre for Industrial Agrifood Research (CIRI- AGRO), University of Bologna, Cesena, Italy
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| |
Collapse
|
6
|
Malau-Aduli AEO, Kashani A. Molecular genetics-nutrition interactions in the expression of AANAT, ADRB3, BTG2 and FASN genes in the heart, kidney and liver of Australian lambs supplemented with Spirulina (Arthrospira platensis). Genes Genomics 2015. [DOI: 10.1007/s13258-015-0294-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
7
|
Ponsuksili S, Siengdee P, Du Y, Trakooljul N, Murani E, Schwerin M, Wimmers K. Identification of common regulators of genes in co-expression networks affecting muscle and meat properties. PLoS One 2015; 10:e0123678. [PMID: 25875247 PMCID: PMC4397042 DOI: 10.1371/journal.pone.0123678] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 02/21/2015] [Indexed: 12/21/2022] Open
Abstract
Understanding the genetic contributions behind skeletal muscle composition and metabolism is of great interest in medicine and agriculture. Attempts to dissect these complex traits combine genome-wide genotyping, expression data analyses and network analyses. Weighted gene co-expression network analysis (WGCNA) groups genes into modules based on patterns of co-expression, which can be linked to phenotypes by correlation analysis of trait values and the module eigengenes, i.e. the first principal component of a given module. Network hub genes and regulators of the genes in the modules are likely to play an important role in the emergence of respective traits. In order to detect common regulators of genes in modules showing association with meat quality traits, we identified eQTL for each of these genes, including the highly connected hub genes. Additionally, the module eigengene values were used for association analyses in order to derive a joint eQTL for the respective module. Thereby major sites of orchestrated regulation of genes within trait-associated modules were detected as hotspots of eQTL of many genes of a module and of its eigengene. These sites harbor likely common regulators of genes in the modules. We exemplarily showed the consistent impact of candidate common regulators on the expression of members of respective modules by RNAi knockdown experiments. In fact, Cxcr7 was identified and validated as a regulator of genes in a module, which is involved in the function of defense response in muscle cells. Zfp36l2 was confirmed as a regulator of genes of a module related to cell death or apoptosis pathways. The integration of eQTL in module networks enabled to interpret the differentially-regulated genes from a systems perspective. By integrating genome-wide genomic and transcriptomic data, employing co-expression and eQTL analyses, the study revealed likely regulators that are involved in the fine-tuning and synchronization of genes with trait-associated expression.
Collapse
Affiliation(s)
- Siriluck Ponsuksili
- Institute for ‘Genome Biology’, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Puntita Siengdee
- Institute for ‘Genome Biology’, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Yang Du
- Institute for ‘Genome Biology’, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Nares Trakooljul
- Institute for ‘Genome Biology’, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Eduard Murani
- Institute for ‘Genome Biology’, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Manfred Schwerin
- Institute for ‘Genome Biology’, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
| | - Klaus Wimmers
- Institute for ‘Genome Biology’, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196 Dummerstorf, Germany
- * E-mail:
| |
Collapse
|
8
|
Kashani A, Holman BWB, Nichols PD, Malau-Aduli AEO. Effect of dietary supplementation with Spirulina on the expressions of AANAT, ADRB3, BTG2 and FASN genes in the subcutaneous adipose and Longissimus dorsi muscle tissues of purebred and crossbred Australian sheep. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2015; 57:8. [PMID: 26290728 PMCID: PMC4540301 DOI: 10.1186/s40781-015-0047-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 02/12/2015] [Indexed: 01/27/2023]
Abstract
BACKGROUND The demand for healthy, lean and consistent meat products containing low saturated fatty acid content and high quality polyunsaturated fatty acids (PUFA), especially long-chain (≥C20) omega-3 PUFA, has increased in recent times. Fat deposition is altered by both the genetic background and dietary supplements, and this study aimed to assess the effect of dietary Spirulina supplementation levels on the mRNA expression patterns of genes controlling lipid metabolism in the subcutaneous adipose tissue (SAT) and Longissimus dorsi (ld) muscle of Australian crossbred sheep. METHODS Twenty-four weaned lambs belonging to four breeds under the same management conditions were maintained on ryegrass pasture and fed three levels of Spirulina supplement (control, low and high). In terms of nutrient composition, Spirulina is a nutrient-rich supplement that contains all essential amino acids, vitamins and minerals. It also is a rich source of carotenoids and fatty acids, especially gamma-linolenic acid (GLA) that infer health benefits. After slaughter, subcutaneous adipose tissue (SAT) and ld samples were subjected to mRNA extraction and reverse transcription using quantitative polymerase chain reaction (RT-qPCR) to assess the mRNA expression levels of the Aralkylamine N-acetyltransferase (AANAT), Adrenergic beta-3 receptor (ADRB3), B-cell translocation gene 2 (BTG2) and Fatty acid synthase (FASN) genes, which are associated with lipid metabolism. RESULTS Both low and high Spirulina supplementation levels strongly up-regulated the transcription of all the selected genes in both SAT and ld tissues (mostly in the subcutaneous adipose), but sheep breed and sex did not influence the gene expression patterns in these tissues. CONCLUSIONS The evidence indicates that high Spirulina supplementation level resulted in a decrease in intramuscular fat content in Australian purebred and crossbred sheep due to the enhanced production of melatonin in sheep muscle tissues and strong up-regulation of mRNA expression of BTG2 in SAT which negatively affected fat deposition. In contrast, low Spirulina supplementation level strongly up-regulated the ADRB3 and FASN genes responsible for fat production. These findings are consistent with the observed phenotypic data suggesting that low Spirulina supplementation level can increase lamb production, with higher long-chain PUFA content.
Collapse
Affiliation(s)
- Arash Kashani
- />Animal Science and Genetics, Tasmanian Institute of Agriculture, School of Land and Food, Faculty of Science, Engineering and Technology, University of Tasmania, Private Bag 54 Sandy Bay, Hobart, Tasmania 7001 Australia
| | - Benjamin William Behrens Holman
- />New South Wales Department of Primary Industries, Centre for Red Meat and Sheep Development, Cowra, 2794 New South Wales Australia
| | - Peter David Nichols
- />CSIRO Food and Nutrition, Oceans and Atmosphere Flagships, Hobart, TAS 7001, Australia
| | - Aduli Enoch Othniel Malau-Aduli
- />Animal Science and Genetics, Tasmanian Institute of Agriculture, School of Land and Food, Faculty of Science, Engineering and Technology, University of Tasmania, Private Bag 54 Sandy Bay, Hobart, Tasmania 7001 Australia
- />Veterinary and Biomedical Sciences, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, Queensland 4811 Australia
| |
Collapse
|
9
|
Pérez-Montarelo D, Madsen O, Alves E, Rodríguez MC, Folch JM, Noguera JL, Groenen MAM, Fernández AI. Identification of genes regulating growth and fatness traits in pig through hypothalamic transcriptome analysis. Physiol Genomics 2013; 46:195-206. [PMID: 24280257 DOI: 10.1152/physiolgenomics.00151.2013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Previous studies on Iberian × Landrace (IBMAP) pig intercrosses have enabled the identification of several quantitative trait locus (QTL) regions related to growth and fatness traits; however, the genetic variation underlying those QTLs are still unknown. These traits are not only relevant because of their impact on economically important production traits, but also because pig constitutes a widely studied animal model for human obesity and obesity-related diseases. The hypothalamus is the main gland regulating growth, food intake, and fat accumulation. Therefore, the aim of this work was to identify genes and/or gene transcripts involved in the determination of growth and fatness in pig by a comparison of the whole hypothalamic transcriptome (RNA-Seq) in two groups of phenotypically divergent IBMAP pigs. Around 16,000 of the ∼25.010 annotated genes were expressed in these hypothalamic samples, with most of them showing intermediate expression levels. Functional analyses supported the key role of the hypothalamus in the regulation of growth, fat accumulation, and energy expenditure. Moreover, 58,927 potentially new isoforms were detected. More than 250 differentially expressed genes and novel transcript isoforms were identified between the two groups of pigs. Twenty-one DE genes/transcripts that colocalized in previously identified QTL regions and/or whose biological functions are related to the traits of interest were explored in more detail. Additionally, the transcription factors potentially regulating these genes and the subjacent networks and pathways were also analyzed. This study allows us to propose strong candidate genes for growth and fatness based on expression patterns, genomic location, and network interactions.
Collapse
Affiliation(s)
- Dafne Pérez-Montarelo
- Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | | | | | | | | | | | | | | |
Collapse
|
10
|
Gene expression profile associated with the reversine-mediated transdifferentiation of NIH-3T3 fibroblast cells into osteoblasts. BIOCHIP JOURNAL 2013. [DOI: 10.1007/s13206-013-7311-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|