Hepatic transcriptome analysis identifies genes, polymorphisms and pathways involved in the fatty acids metabolism in sheep
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 pr...
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| Veröffentlicht in: | PloS one 2021-12, Vol.16 (12), p.e0260514-e0260514 |
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| creator | Gunawan, Asep Listyarini, Kasita Harahap, Ratna Sholatia Jakaria Roosita, Katrin Sumantri, Cece Inounu, Ismeth Akter, Syeda Hasina Islam, Md Aminul Uddin, Muhammad Jasim |
| description | 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 |
| doi_str_mv | 10.1371/journal.pone.0260514 |
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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.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0260514</identifier><identifier>PMID: 34941886</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Adipogenesis ; Analysis ; Animal husbandry ; Animal populations ; Animal sciences ; Animals ; Biology and Life Sciences ; Biomarkers ; Biomarkers - metabolism ; Biosynthesis ; Calcium metabolism ; Composition ; Computer and Information Sciences ; Consumers ; Divergence ; Fat metabolism ; Fatty acids ; Fatty Acids - genetics ; Fatty Acids - metabolism ; Flavor ; Flavors ; Galactose ; Gene expression ; Gene Expression Profiling ; Gene Regulatory Networks ; Gene sequencing ; Genes ; Genetic factors ; Genetic markers ; Genomics ; Glycosaminoglycans ; High-Throughput Nucleotide Sequencing ; Identification and classification ; Keratan sulfate ; Lipid metabolism ; Lipid Metabolism - genetics ; Lipids ; Liver ; Liver - metabolism ; Measurement ; Meat ; Medicine and Health Sciences ; Metabolism ; Methods ; Mineral metabolism ; Muscles ; Mutation ; Nutritive value ; Peroxisome proliferator-activated receptors ; Polymorphism ; Polymorphism, Genetic ; Quality control ; Research and analysis methods ; RNA sequencing ; Sheep ; Sheep - genetics ; Sheep - metabolism ; Sheep breeding ; Signal Transduction ; Signaling ; Single-nucleotide polymorphism ; Sulfates ; Transcriptome ; Transcriptomes ; Veterinary medicine ; Zoology</subject><ispartof>PloS one, 2021-12, Vol.16 (12), p.e0260514-e0260514</ispartof><rights>COPYRIGHT 2021 Public Library of Science</rights><rights>2021 Gunawan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2021 Gunawan et al 2021 Gunawan et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-359a4a8e51ff6cd73c6de0a1f4f6e87b55738794c1e69b8b2db741fb07ab775e3</citedby><cites>FETCH-LOGICAL-c692t-359a4a8e51ff6cd73c6de0a1f4f6e87b55738794c1e69b8b2db741fb07ab775e3</cites><orcidid>0000-0003-0468-2443</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8699643/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8699643/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34941886$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Zappaterra, Martina</contributor><creatorcontrib>Gunawan, Asep</creatorcontrib><creatorcontrib>Listyarini, Kasita</creatorcontrib><creatorcontrib>Harahap, Ratna Sholatia</creatorcontrib><creatorcontrib>Jakaria</creatorcontrib><creatorcontrib>Roosita, Katrin</creatorcontrib><creatorcontrib>Sumantri, Cece</creatorcontrib><creatorcontrib>Inounu, Ismeth</creatorcontrib><creatorcontrib>Akter, Syeda Hasina</creatorcontrib><creatorcontrib>Islam, Md Aminul</creatorcontrib><creatorcontrib>Uddin, Muhammad Jasim</creatorcontrib><title>Hepatic transcriptome analysis identifies genes, polymorphisms and pathways involved in the fatty acids metabolism in sheep</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>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.</description><subject>Adipogenesis</subject><subject>Analysis</subject><subject>Animal husbandry</subject><subject>Animal populations</subject><subject>Animal sciences</subject><subject>Animals</subject><subject>Biology and Life Sciences</subject><subject>Biomarkers</subject><subject>Biomarkers - metabolism</subject><subject>Biosynthesis</subject><subject>Calcium metabolism</subject><subject>Composition</subject><subject>Computer and Information Sciences</subject><subject>Consumers</subject><subject>Divergence</subject><subject>Fat metabolism</subject><subject>Fatty acids</subject><subject>Fatty Acids - genetics</subject><subject>Fatty Acids - metabolism</subject><subject>Flavor</subject><subject>Flavors</subject><subject>Galactose</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Regulatory Networks</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetic factors</subject><subject>Genetic markers</subject><subject>Genomics</subject><subject>Glycosaminoglycans</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Identification and classification</subject><subject>Keratan sulfate</subject><subject>Lipid metabolism</subject><subject>Lipid Metabolism - genetics</subject><subject>Lipids</subject><subject>Liver</subject><subject>Liver - metabolism</subject><subject>Measurement</subject><subject>Meat</subject><subject>Medicine and Health Sciences</subject><subject>Metabolism</subject><subject>Methods</subject><subject>Mineral metabolism</subject><subject>Muscles</subject><subject>Mutation</subject><subject>Nutritive value</subject><subject>Peroxisome proliferator-activated receptors</subject><subject>Polymorphism</subject><subject>Polymorphism, Genetic</subject><subject>Quality control</subject><subject>Research and analysis methods</subject><subject>RNA sequencing</subject><subject>Sheep</subject><subject>Sheep - genetics</subject><subject>Sheep - metabolism</subject><subject>Sheep breeding</subject><subject>Signal Transduction</subject><subject>Signaling</subject><subject>Single-nucleotide polymorphism</subject><subject>Sulfates</subject><subject>Transcriptome</subject><subject>Transcriptomes</subject><subject>Veterinary 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transcriptome analysis identifies genes, polymorphisms and pathways involved in the fatty acids metabolism in sheep</title><author>Gunawan, Asep ; Listyarini, Kasita ; Harahap, Ratna Sholatia ; Jakaria ; Roosita, Katrin ; Sumantri, Cece ; Inounu, Ismeth ; Akter, Syeda Hasina ; Islam, Md Aminul ; Uddin, Muhammad Jasim</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-359a4a8e51ff6cd73c6de0a1f4f6e87b55738794c1e69b8b2db741fb07ab775e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Adipogenesis</topic><topic>Analysis</topic><topic>Animal husbandry</topic><topic>Animal populations</topic><topic>Animal sciences</topic><topic>Animals</topic><topic>Biology and Life Sciences</topic><topic>Biomarkers</topic><topic>Biomarkers - metabolism</topic><topic>Biosynthesis</topic><topic>Calcium metabolism</topic><topic>Composition</topic><topic>Computer and Information 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Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Gunawan, Asep</au><au>Listyarini, Kasita</au><au>Harahap, Ratna Sholatia</au><au>Jakaria</au><au>Roosita, Katrin</au><au>Sumantri, Cece</au><au>Inounu, Ismeth</au><au>Akter, Syeda Hasina</au><au>Islam, Md Aminul</au><au>Uddin, Muhammad Jasim</au><au>Zappaterra, Martina</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Hepatic transcriptome analysis identifies genes, polymorphisms and pathways involved in the fatty acids metabolism in sheep</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2021-12-23</date><risdate>2021</risdate><volume>16</volume><issue>12</issue><spage>e0260514</spage><epage>e0260514</epage><pages>e0260514-e0260514</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><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.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>34941886</pmid><doi>10.1371/journal.pone.0260514</doi><tpages>e0260514</tpages><orcidid>https://orcid.org/0000-0003-0468-2443</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2021-12, Vol.16 (12), p.e0260514-e0260514 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_2613260482 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Adipogenesis Analysis Animal husbandry Animal populations Animal sciences Animals Biology and Life Sciences Biomarkers Biomarkers - metabolism Biosynthesis Calcium metabolism Composition Computer and Information Sciences Consumers Divergence Fat metabolism Fatty acids Fatty Acids - genetics Fatty Acids - metabolism Flavor Flavors Galactose Gene expression Gene Expression Profiling Gene Regulatory Networks Gene sequencing Genes Genetic factors Genetic markers Genomics Glycosaminoglycans High-Throughput Nucleotide Sequencing Identification and classification Keratan sulfate Lipid metabolism Lipid Metabolism - genetics Lipids Liver Liver - metabolism Measurement Meat Medicine and Health Sciences Metabolism Methods Mineral metabolism Muscles Mutation Nutritive value Peroxisome proliferator-activated receptors Polymorphism Polymorphism, Genetic Quality control Research and analysis methods RNA sequencing Sheep Sheep - genetics Sheep - metabolism Sheep breeding Signal Transduction Signaling Single-nucleotide polymorphism Sulfates Transcriptome Transcriptomes Veterinary medicine Zoology |
| title | Hepatic transcriptome analysis identifies genes, polymorphisms and pathways involved in the fatty acids metabolism in sheep |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-02T07%3A40%3A37IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Hepatic%20transcriptome%20analysis%20identifies%20genes,%20polymorphisms%20and%20pathways%20involved%20in%20the%20fatty%20acids%20metabolism%20in%20sheep&rft.jtitle=PloS%20one&rft.au=Gunawan,%20Asep&rft.date=2021-12-23&rft.volume=16&rft.issue=12&rft.spage=e0260514&rft.epage=e0260514&rft.pages=e0260514-e0260514&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0260514&rft_dat=%3Cgale_plos_%3EA687760041%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2613260482&rft_id=info:pmid/34941886&rft_galeid=A687760041&rft_doaj_id=oai_doaj_org_article_94420173223348cabf9a42292fbdb9f8&rfr_iscdi=true |