A Genome-Wide mRNA Screen and Functional Analysis Reveal FOXO3 as a Candidate Gene for Chicken Growth
Chicken growth performance provides direct economic benefits to the poultry industry. However, the underlying genetic mechanisms are unclear. The objective of this study was to identify candidate genes associated with chicken growth and investigate their potential mechanisms. We used RNA-Seq to stud...
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| description | Chicken growth performance provides direct economic benefits to the poultry industry. However, the underlying genetic mechanisms are unclear. The objective of this study was to identify candidate genes associated with chicken growth and investigate their potential mechanisms. We used RNA-Seq to study the breast muscle transcriptome in high and low tails of Recessive White Rock (WRRh, WRRl) and Xinghua chickens (XHh, XHl). A total of 60, 23, 153 and 359 differentially expressed genes were detected in WRRh vs. WRRl, XHh vs. XHl, WRRh vs. XHh and WRRl vs. XHl, respectively. GO, KEGG pathway and gene network analyses showed that CEBPB, FBXO32, FOXO3 and MYOD1 played key roles in growth. The functions of FBXO32 and FOXO3 were validated. FBXO32 was predominantly expressed in leg muscle, heart and breast muscle. After decreased FBXO32 expression, growth-related genes such as PDK4, IGF2R and IGF2BP3 were significantly down-regulated (P < 0.05). FBXO32 was significantly (P < 0.05) associated with carcass and meat quality traits, but not growth traits. FOXO3 was predominantly expressed in breast and leg muscle. In both of these tissues, the FOXO3 mRNA level in XH was significantly higher than that in WRR chickens with normal body weight (P < 0.05). In DF-1 cells, siRNA knockdown of FOXO3 significantly (P < 0.01) inhibited the MYOD expression and significantly up-regulated (P < 0.01 or P < 0.05) the expression of growth-related genes including CEBPB, FBXO32, GH, GHR, IGF1R, IGF2R, IGF2BP1, IGF2BP3, INSR, PDK1 and PDK4. Moreover, 18 SNPs were identified in FOXO3. G66716193A was significantly (P < 0.05) associated with growth traits. The sites C66716002T, C66716195T and A66716179G were significantly (P < 0.05) associated with growth or carcass traits. These results demonstrated that FOXO3 is a candidate gene influencing chicken growth. Our observations provide new clues to understand the molecular basis of chicken growth. |
| doi_str_mv | 10.1371/journal.pone.0137087 |
| format | Article |
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However, the underlying genetic mechanisms are unclear. The objective of this study was to identify candidate genes associated with chicken growth and investigate their potential mechanisms. We used RNA-Seq to study the breast muscle transcriptome in high and low tails of Recessive White Rock (WRRh, WRRl) and Xinghua chickens (XHh, XHl). A total of 60, 23, 153 and 359 differentially expressed genes were detected in WRRh vs. WRRl, XHh vs. XHl, WRRh vs. XHh and WRRl vs. XHl, respectively. GO, KEGG pathway and gene network analyses showed that CEBPB, FBXO32, FOXO3 and MYOD1 played key roles in growth. The functions of FBXO32 and FOXO3 were validated. FBXO32 was predominantly expressed in leg muscle, heart and breast muscle. After decreased FBXO32 expression, growth-related genes such as PDK4, IGF2R and IGF2BP3 were significantly down-regulated (P < 0.05). FBXO32 was significantly (P < 0.05) associated with carcass and meat quality traits, but not growth traits. FOXO3 was predominantly expressed in breast and leg muscle. In both of these tissues, the FOXO3 mRNA level in XH was significantly higher than that in WRR chickens with normal body weight (P < 0.05). In DF-1 cells, siRNA knockdown of FOXO3 significantly (P < 0.01) inhibited the MYOD expression and significantly up-regulated (P < 0.01 or P < 0.05) the expression of growth-related genes including CEBPB, FBXO32, GH, GHR, IGF1R, IGF2R, IGF2BP1, IGF2BP3, INSR, PDK1 and PDK4. Moreover, 18 SNPs were identified in FOXO3. G66716193A was significantly (P < 0.05) associated with growth traits. The sites C66716002T, C66716195T and A66716179G were significantly (P < 0.05) associated with growth or carcass traits. These results demonstrated that FOXO3 is a candidate gene influencing chicken growth. Our observations provide new clues to understand the molecular basis of chicken growth.]]></description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0137087</identifier><identifier>PMID: 26366565</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Agriculture ; Animal sciences ; Animals ; Avian Proteins - genetics ; Avian Proteins - metabolism ; Body weight ; Breast muscle ; Cell Line ; Chickens ; Chickens - genetics ; Chickens - growth & development ; Chickens - metabolism ; DNA methylation ; Female ; Forkhead Transcription Factors - genetics ; Forkhead Transcription Factors - metabolism ; FOXO3 protein ; Functional analysis ; Gene expression ; Gene Expression Regulation, Developmental ; Genes ; Genetics ; Genome-Wide Association Study ; Genomes ; Genomics ; Growth hormone ; Insulin-like growth factor II receptors ; Leg ; Meat ; Muscle Proteins - genetics ; Muscle Proteins - metabolism ; Muscles ; Musculoskeletal system ; MyoD protein ; Oncorhynchus mykiss ; Polymorphism, Single Nucleotide ; Poultry ; Proteins ; Quantitative Trait Loci ; Ribonucleic acid ; RNA ; RNA, Messenger - analysis ; Sequence Analysis, RNA - methods ; Single-nucleotide polymorphism ; siRNA ; Studies ; Transcription factors ; Zoology</subject><ispartof>PloS one, 2015-09, Vol.10 (9), p.e0137087-e0137087</ispartof><rights>2015 Chen 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>2015 Chen et al 2015 Chen et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c526t-bed37cd1b229947754ed2b1ad23d0fb1dd3c2e793d8b906255e23bbaefcd45ad3</citedby><cites>FETCH-LOGICAL-c526t-bed37cd1b229947754ed2b1ad23d0fb1dd3c2e793d8b906255e23bbaefcd45ad3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4569328/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4569328/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79343,79344</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26366565$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Chen, Biao</creatorcontrib><creatorcontrib>Xu, Jiguo</creatorcontrib><creatorcontrib>He, Xiaomei</creatorcontrib><creatorcontrib>Xu, Haiping</creatorcontrib><creatorcontrib>Li, Guihuan</creatorcontrib><creatorcontrib>Du, Hongli</creatorcontrib><creatorcontrib>Nie, Qinghua</creatorcontrib><creatorcontrib>Zhang, Xiquan</creatorcontrib><title>A Genome-Wide mRNA Screen and Functional Analysis Reveal FOXO3 as a Candidate Gene for Chicken Growth</title><title>PloS one</title><addtitle>PLoS One</addtitle><description><![CDATA[Chicken growth performance provides direct economic benefits to the poultry industry. However, the underlying genetic mechanisms are unclear. The objective of this study was to identify candidate genes associated with chicken growth and investigate their potential mechanisms. We used RNA-Seq to study the breast muscle transcriptome in high and low tails of Recessive White Rock (WRRh, WRRl) and Xinghua chickens (XHh, XHl). A total of 60, 23, 153 and 359 differentially expressed genes were detected in WRRh vs. WRRl, XHh vs. XHl, WRRh vs. XHh and WRRl vs. XHl, respectively. GO, KEGG pathway and gene network analyses showed that CEBPB, FBXO32, FOXO3 and MYOD1 played key roles in growth. The functions of FBXO32 and FOXO3 were validated. FBXO32 was predominantly expressed in leg muscle, heart and breast muscle. After decreased FBXO32 expression, growth-related genes such as PDK4, IGF2R and IGF2BP3 were significantly down-regulated (P < 0.05). FBXO32 was significantly (P < 0.05) associated with carcass and meat quality traits, but not growth traits. FOXO3 was predominantly expressed in breast and leg muscle. In both of these tissues, the FOXO3 mRNA level in XH was significantly higher than that in WRR chickens with normal body weight (P < 0.05). In DF-1 cells, siRNA knockdown of FOXO3 significantly (P < 0.01) inhibited the MYOD expression and significantly up-regulated (P < 0.01 or P < 0.05) the expression of growth-related genes including CEBPB, FBXO32, GH, GHR, IGF1R, IGF2R, IGF2BP1, IGF2BP3, INSR, PDK1 and PDK4. Moreover, 18 SNPs were identified in FOXO3. G66716193A was significantly (P < 0.05) associated with growth traits. The sites C66716002T, C66716195T and A66716179G were significantly (P < 0.05) associated with growth or carcass traits. These results demonstrated that FOXO3 is a candidate gene influencing chicken growth. Our observations provide new clues to understand the molecular basis of chicken growth.]]></description><subject>Agriculture</subject><subject>Animal sciences</subject><subject>Animals</subject><subject>Avian Proteins - genetics</subject><subject>Avian Proteins - metabolism</subject><subject>Body weight</subject><subject>Breast muscle</subject><subject>Cell Line</subject><subject>Chickens</subject><subject>Chickens - genetics</subject><subject>Chickens - growth & development</subject><subject>Chickens - metabolism</subject><subject>DNA methylation</subject><subject>Female</subject><subject>Forkhead Transcription Factors - genetics</subject><subject>Forkhead Transcription Factors - metabolism</subject><subject>FOXO3 protein</subject><subject>Functional analysis</subject><subject>Gene expression</subject><subject>Gene Expression Regulation, Developmental</subject><subject>Genes</subject><subject>Genetics</subject><subject>Genome-Wide Association Study</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Growth hormone</subject><subject>Insulin-like growth factor II receptors</subject><subject>Leg</subject><subject>Meat</subject><subject>Muscle Proteins - genetics</subject><subject>Muscle Proteins - metabolism</subject><subject>Muscles</subject><subject>Musculoskeletal system</subject><subject>MyoD protein</subject><subject>Oncorhynchus mykiss</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Poultry</subject><subject>Proteins</subject><subject>Quantitative Trait Loci</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA, Messenger - analysis</subject><subject>Sequence Analysis, RNA - methods</subject><subject>Single-nucleotide polymorphism</subject><subject>siRNA</subject><subject>Studies</subject><subject>Transcription factors</subject><subject>Zoology</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNptkl1v0zAUhiMEYmPwDxBY4oabFH87uUGqKlomTVQaILizHPtkdUnjYidD-_e4azZtiBt_HL_nOcf2WxSvCZ4RpsiHbRhjb7rZPvQwwzmEK_WkOCU1o6WkmD19sD4pXqS0xViwSsrnxQmVTEohxWkBc7SCPuyg_OEdoN3llzn6aiNAj0zv0HLs7eBDroPmebhJPqFLuIa8X65_rhkyCRm0yFLvzAAHFqA2RLTYePsrQ1Yx_Bk2L4tnrekSvJrms-L78tO3xefyYr06X8wvSiuoHMoGHFPWkYbSuuZKCQ6ONsQ4yhxuG-IcsxRUzVzV1FhSIYCypjHQWseFceyseHvk7ruQ9PRCSRNFaloJxllWnB8VLpit3ke_M_FGB-P1bSDEK23i4G0HuiUtF7bG0LaCu1oaJa2BhlsgnIM6sD5O1cZmB85CP0TTPYI-Pun9Rl-Fa82FzD9TZcD7CRDD7xHSoHc-Weg600MYb_umqiJY8Sx994_0_7fjR5WNIaUI7X0zBOuDa-6y9ME1enJNTnvz8CL3SXc2YX8B6fLAIA</recordid><startdate>20150914</startdate><enddate>20150914</enddate><creator>Chen, Biao</creator><creator>Xu, Jiguo</creator><creator>He, Xiaomei</creator><creator>Xu, Haiping</creator><creator>Li, Guihuan</creator><creator>Du, Hongli</creator><creator>Nie, Qinghua</creator><creator>Zhang, Xiquan</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20150914</creationdate><title>A Genome-Wide mRNA Screen and Functional Analysis Reveal FOXO3 as a Candidate Gene for Chicken Growth</title><author>Chen, Biao ; Xu, Jiguo ; He, Xiaomei ; Xu, Haiping ; Li, Guihuan ; Du, Hongli ; Nie, Qinghua ; Zhang, Xiquan</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c526t-bed37cd1b229947754ed2b1ad23d0fb1dd3c2e793d8b906255e23bbaefcd45ad3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Agriculture</topic><topic>Animal sciences</topic><topic>Animals</topic><topic>Avian Proteins - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Chen, Biao</au><au>Xu, Jiguo</au><au>He, Xiaomei</au><au>Xu, Haiping</au><au>Li, Guihuan</au><au>Du, Hongli</au><au>Nie, Qinghua</au><au>Zhang, Xiquan</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A Genome-Wide mRNA Screen and Functional Analysis Reveal FOXO3 as a Candidate Gene for Chicken Growth</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2015-09-14</date><risdate>2015</risdate><volume>10</volume><issue>9</issue><spage>e0137087</spage><epage>e0137087</epage><pages>e0137087-e0137087</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract><![CDATA[Chicken growth performance provides direct economic benefits to the poultry industry. However, the underlying genetic mechanisms are unclear. The objective of this study was to identify candidate genes associated with chicken growth and investigate their potential mechanisms. We used RNA-Seq to study the breast muscle transcriptome in high and low tails of Recessive White Rock (WRRh, WRRl) and Xinghua chickens (XHh, XHl). A total of 60, 23, 153 and 359 differentially expressed genes were detected in WRRh vs. WRRl, XHh vs. XHl, WRRh vs. XHh and WRRl vs. XHl, respectively. GO, KEGG pathway and gene network analyses showed that CEBPB, FBXO32, FOXO3 and MYOD1 played key roles in growth. The functions of FBXO32 and FOXO3 were validated. FBXO32 was predominantly expressed in leg muscle, heart and breast muscle. After decreased FBXO32 expression, growth-related genes such as PDK4, IGF2R and IGF2BP3 were significantly down-regulated (P < 0.05). FBXO32 was significantly (P < 0.05) associated with carcass and meat quality traits, but not growth traits. FOXO3 was predominantly expressed in breast and leg muscle. In both of these tissues, the FOXO3 mRNA level in XH was significantly higher than that in WRR chickens with normal body weight (P < 0.05). In DF-1 cells, siRNA knockdown of FOXO3 significantly (P < 0.01) inhibited the MYOD expression and significantly up-regulated (P < 0.01 or P < 0.05) the expression of growth-related genes including CEBPB, FBXO32, GH, GHR, IGF1R, IGF2R, IGF2BP1, IGF2BP3, INSR, PDK1 and PDK4. Moreover, 18 SNPs were identified in FOXO3. G66716193A was significantly (P < 0.05) associated with growth traits. The sites C66716002T, C66716195T and A66716179G were significantly (P < 0.05) associated with growth or carcass traits. These results demonstrated that FOXO3 is a candidate gene influencing chicken growth. Our observations provide new clues to understand the molecular basis of chicken growth.]]></abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>26366565</pmid><doi>10.1371/journal.pone.0137087</doi><oa>free_for_read</oa></addata></record> |
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| recordid | cdi_plos_journals_1719285343 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Free Full-Text Journals in Chemistry; Public Library of Science (PLoS) |
| subjects | Agriculture Animal sciences Animals Avian Proteins - genetics Avian Proteins - metabolism Body weight Breast muscle Cell Line Chickens Chickens - genetics Chickens - growth & development Chickens - metabolism DNA methylation Female Forkhead Transcription Factors - genetics Forkhead Transcription Factors - metabolism FOXO3 protein Functional analysis Gene expression Gene Expression Regulation, Developmental Genes Genetics Genome-Wide Association Study Genomes Genomics Growth hormone Insulin-like growth factor II receptors Leg Meat Muscle Proteins - genetics Muscle Proteins - metabolism Muscles Musculoskeletal system MyoD protein Oncorhynchus mykiss Polymorphism, Single Nucleotide Poultry Proteins Quantitative Trait Loci Ribonucleic acid RNA RNA, Messenger - analysis Sequence Analysis, RNA - methods Single-nucleotide polymorphism siRNA Studies Transcription factors Zoology |
| title | A Genome-Wide mRNA Screen and Functional Analysis Reveal FOXO3 as a Candidate Gene for Chicken Growth |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-03T08%3A32%3A27IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=A%20Genome-Wide%20mRNA%20Screen%20and%20Functional%20Analysis%20Reveal%20FOXO3%20as%20a%20Candidate%20Gene%20for%20Chicken%20Growth&rft.jtitle=PloS%20one&rft.au=Chen,%20Biao&rft.date=2015-09-14&rft.volume=10&rft.issue=9&rft.spage=e0137087&rft.epage=e0137087&rft.pages=e0137087-e0137087&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0137087&rft_dat=%3Cproquest_plos_%3E1712781074%3C/proquest_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1719285343&rft_id=info:pmid/26366565&rft_doaj_id=oai_doaj_org_article_f1f45c90eff54d96a76caeb4ce144e73&rfr_iscdi=true |