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Identification of eQTLs and differential gene expression associated with fetal programming in beef cattle
This study assessed differential gene expression and identified expression quantitative trait loci (eQTLs) from samples of Longissimus lumborum muscle from bulls at 15 months of age submitted to different prenatal nutrition. Upon confirmation of pregnancy, 126 dams were separated into three diet tre...
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| Published in: | Journal of applied genetics 2022-12, Vol.63 (4), p.717-728 |
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| Main Authors: | , , , , , , , , , |
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| cited_by | cdi_FETCH-LOGICAL-c452t-5091c34bbff09695eac1ab090010d088206f1a605fa8b0194fc69c1e815106fe3 |
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| cites | cdi_FETCH-LOGICAL-c452t-5091c34bbff09695eac1ab090010d088206f1a605fa8b0194fc69c1e815106fe3 |
| container_end_page | 728 |
| container_issue | 4 |
| container_start_page | 717 |
| container_title | Journal of applied genetics |
| container_volume | 63 |
| creator | Polizel, Guilherme Henrique Gebim Cesar, Aline Silva Mello Cracco, Roberta Cavalcante Fernandes, Arícia Christofaro Reginato, Gustavo Morandini Xavier, Pedro Luiz Porfirio Mortari, Isabela Furlan, Édison Fukumasu, Heidge Santana, Miguel Henrique de Almeida |
| description | This study assessed differential gene expression and identified expression quantitative trait loci (eQTLs) from samples of
Longissimus lumborum
muscle from bulls at 15 months of age submitted to different prenatal nutrition. Upon confirmation of pregnancy, 126 dams were separated into three diet treatments varying the period of inclusion of energy protein supplementation (NP, PP, and FP). At calving, 63 males were genotyped with GGP LD BeadChip. The skeletal muscle of 15 bulls was sequenced (RNA-seq) at 15 months of age. The EdgeR package was used for differential gene expression and principal component analysis (PCA), and the Matrix eQTL package was used for the eQTLs analysis (R statistical). The functional enrichment analysis was performed using the MetaCore® software. No genes differentially expressed were found between treatments (FDR > 0.05); nevertheless, we found 179 cis-tag-eQTLs and 20,762 trans-tag-eQTLs (FDR |
| doi_str_mv | 10.1007/s13353-022-00711-1 |
| format | article |
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Longissimus lumborum
muscle from bulls at 15 months of age submitted to different prenatal nutrition. Upon confirmation of pregnancy, 126 dams were separated into three diet treatments varying the period of inclusion of energy protein supplementation (NP, PP, and FP). At calving, 63 males were genotyped with GGP LD BeadChip. The skeletal muscle of 15 bulls was sequenced (RNA-seq) at 15 months of age. The EdgeR package was used for differential gene expression and principal component analysis (PCA), and the Matrix eQTL package was used for the eQTLs analysis (R statistical). The functional enrichment analysis was performed using the MetaCore® software. No genes differentially expressed were found between treatments (FDR > 0.05); nevertheless, we found 179 cis-tag-eQTLs and 20,762 trans-tag-eQTLs (FDR < 0.05) after linkage disequilibrium analysis. The functional enrichment analysis identified terms from gene ontology related to genes associated to trans-eQTLs (FDR < 0.05) as well as metabolic pathways (> gScore). Most biological pathways and genes found had been previously associated to fetal programming. The different prenatal supplementation strategies did not impact on muscle transcriptome of bulls. Additionally, there is a link between genotype and gene expression levels related to developmental traits in Nellore cattle.</description><identifier>ISSN: 1234-1983</identifier><identifier>EISSN: 2190-3883</identifier><identifier>DOI: 10.1007/s13353-022-00711-1</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Animal Genetics and Genomics ; Animal Genetics • Original Paper ; Beef cattle ; Biomedical and Life Sciences ; Cattle ; computer software ; energy ; Fetuses ; Gene expression ; gene expression regulation ; Gene mapping ; gene ontology ; Gene set enrichment analysis ; Genes ; Genetic aspects ; genotype ; Genotypes ; genotyping ; Human Genetics ; Life Sciences ; Linkage analysis ; Linkage disequilibrium ; longissimus muscle ; Metabolic pathways ; Microbial Genetics and Genomics ; Muscles ; Nellore ; Nutrition ; Plant Genetics and Genomics ; Pregnancy ; Prenatal experience ; principal component analysis ; Principal components analysis ; protein supplements ; Quantitative trait loci ; quantitative traits ; sequence analysis ; Skeletal muscle ; transcriptome ; Transcriptomes</subject><ispartof>Journal of applied genetics, 2022-12, Vol.63 (4), p.717-728</ispartof><rights>The Author(s), under exclusive licence to Institute of Plant Genetics Polish Academy of Sciences 2022</rights><rights>COPYRIGHT 2022 Springer</rights><rights>The Author(s), under exclusive licence to Institute of Plant Genetics Polish Academy of Sciences 2022.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c452t-5091c34bbff09695eac1ab090010d088206f1a605fa8b0194fc69c1e815106fe3</citedby><cites>FETCH-LOGICAL-c452t-5091c34bbff09695eac1ab090010d088206f1a605fa8b0194fc69c1e815106fe3</cites><orcidid>0000-0002-8497-9898</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,777,781,27905,27906</link.rule.ids></links><search><creatorcontrib>Polizel, Guilherme Henrique Gebim</creatorcontrib><creatorcontrib>Cesar, Aline Silva Mello</creatorcontrib><creatorcontrib>Cracco, Roberta Cavalcante</creatorcontrib><creatorcontrib>Fernandes, Arícia Christofaro</creatorcontrib><creatorcontrib>Reginato, Gustavo Morandini</creatorcontrib><creatorcontrib>Xavier, Pedro Luiz Porfirio</creatorcontrib><creatorcontrib>Mortari, Isabela</creatorcontrib><creatorcontrib>Furlan, Édison</creatorcontrib><creatorcontrib>Fukumasu, Heidge</creatorcontrib><creatorcontrib>Santana, Miguel Henrique de Almeida</creatorcontrib><title>Identification of eQTLs and differential gene expression associated with fetal programming in beef cattle</title><title>Journal of applied genetics</title><addtitle>J Appl Genetics</addtitle><description>This study assessed differential gene expression and identified expression quantitative trait loci (eQTLs) from samples of
Longissimus lumborum
muscle from bulls at 15 months of age submitted to different prenatal nutrition. Upon confirmation of pregnancy, 126 dams were separated into three diet treatments varying the period of inclusion of energy protein supplementation (NP, PP, and FP). At calving, 63 males were genotyped with GGP LD BeadChip. The skeletal muscle of 15 bulls was sequenced (RNA-seq) at 15 months of age. The EdgeR package was used for differential gene expression and principal component analysis (PCA), and the Matrix eQTL package was used for the eQTLs analysis (R statistical). The functional enrichment analysis was performed using the MetaCore® software. No genes differentially expressed were found between treatments (FDR > 0.05); nevertheless, we found 179 cis-tag-eQTLs and 20,762 trans-tag-eQTLs (FDR < 0.05) after linkage disequilibrium analysis. The functional enrichment analysis identified terms from gene ontology related to genes associated to trans-eQTLs (FDR < 0.05) as well as metabolic pathways (> gScore). Most biological pathways and genes found had been previously associated to fetal programming. The different prenatal supplementation strategies did not impact on muscle transcriptome of bulls. Additionally, there is a link between genotype and gene expression levels related to developmental traits in Nellore cattle.</description><subject>Animal Genetics and Genomics</subject><subject>Animal Genetics • Original Paper</subject><subject>Beef cattle</subject><subject>Biomedical and Life Sciences</subject><subject>Cattle</subject><subject>computer software</subject><subject>energy</subject><subject>Fetuses</subject><subject>Gene expression</subject><subject>gene expression regulation</subject><subject>Gene mapping</subject><subject>gene ontology</subject><subject>Gene set enrichment analysis</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>genotype</subject><subject>Genotypes</subject><subject>genotyping</subject><subject>Human Genetics</subject><subject>Life Sciences</subject><subject>Linkage analysis</subject><subject>Linkage disequilibrium</subject><subject>longissimus muscle</subject><subject>Metabolic pathways</subject><subject>Microbial Genetics and Genomics</subject><subject>Muscles</subject><subject>Nellore</subject><subject>Nutrition</subject><subject>Plant Genetics and Genomics</subject><subject>Pregnancy</subject><subject>Prenatal experience</subject><subject>principal component analysis</subject><subject>Principal components analysis</subject><subject>protein supplements</subject><subject>Quantitative trait loci</subject><subject>quantitative traits</subject><subject>sequence analysis</subject><subject>Skeletal muscle</subject><subject>transcriptome</subject><subject>Transcriptomes</subject><issn>1234-1983</issn><issn>2190-3883</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><recordid>eNp9kU-LFDEQxYMoOK5-AU8BL156tyrpTHeOy-KfhYFFWM8hna60WbrTY5JB_famHVEUkRxCUr_3eNRj7CXCJQJ0VxmlVLIBIZr6RGzwEdsJ1NDIvpeP2Q6FbBvUvXzKnuX8ACD7thM7Fm5HiiX44GwJa-Sr5_Th_pC5jSMfg_eUtrmd-USROH09Jsp5I23Oqwu20Mi_hPKJeyqVOqZ1SnZZQpx4iHwg8rxal5mesyfezple_Lwv2Me3b-5v3jeHu3e3N9eHxrVKlEaBRifbYfAe9F4rsg7tABoAYYS-F7D3aPegvO0HQN16t9cOqUeFdUTygr0--9Yon0-Ui1lCdjTPNtJ6ykaikh0K0euKvvoLfVhPKdZ0RnSyIgh1r7-oyc5kQvRrSdZtpua6E6ouVims1OU_qHpGWoJbI_lQ__8QiLPApTXnRN4cU1hs-mYQzFaqOZdqaqnmR6lmE8mzKFc4TpR-J_6P6jsqv6Kq</recordid><startdate>20221201</startdate><enddate>20221201</enddate><creator>Polizel, Guilherme Henrique Gebim</creator><creator>Cesar, Aline Silva Mello</creator><creator>Cracco, Roberta Cavalcante</creator><creator>Fernandes, Arícia Christofaro</creator><creator>Reginato, Gustavo Morandini</creator><creator>Xavier, Pedro Luiz Porfirio</creator><creator>Mortari, Isabela</creator><creator>Furlan, Édison</creator><creator>Fukumasu, Heidge</creator><creator>Santana, Miguel Henrique de Almeida</creator><general>Springer Berlin Heidelberg</general><general>Springer</general><general>Springer Nature B.V</general><scope>AAYXX</scope><scope>CITATION</scope><scope>7S9</scope><scope>L.6</scope><orcidid>https://orcid.org/0000-0002-8497-9898</orcidid></search><sort><creationdate>20221201</creationdate><title>Identification of eQTLs and differential gene expression associated with fetal programming in beef cattle</title><author>Polizel, Guilherme Henrique Gebim ; Cesar, Aline Silva Mello ; Cracco, Roberta Cavalcante ; Fernandes, Arícia Christofaro ; Reginato, Gustavo Morandini ; Xavier, Pedro Luiz Porfirio ; Mortari, Isabela ; Furlan, Édison ; Fukumasu, Heidge ; Santana, Miguel Henrique de Almeida</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c452t-5091c34bbff09695eac1ab090010d088206f1a605fa8b0194fc69c1e815106fe3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Animal Genetics and Genomics</topic><topic>Animal Genetics • Original Paper</topic><topic>Beef cattle</topic><topic>Biomedical and Life Sciences</topic><topic>Cattle</topic><topic>computer software</topic><topic>energy</topic><topic>Fetuses</topic><topic>Gene expression</topic><topic>gene expression regulation</topic><topic>Gene mapping</topic><topic>gene ontology</topic><topic>Gene set enrichment analysis</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>genotype</topic><topic>Genotypes</topic><topic>genotyping</topic><topic>Human Genetics</topic><topic>Life Sciences</topic><topic>Linkage analysis</topic><topic>Linkage disequilibrium</topic><topic>longissimus muscle</topic><topic>Metabolic pathways</topic><topic>Microbial Genetics and Genomics</topic><topic>Muscles</topic><topic>Nellore</topic><topic>Nutrition</topic><topic>Plant Genetics and Genomics</topic><topic>Pregnancy</topic><topic>Prenatal experience</topic><topic>principal component analysis</topic><topic>Principal components analysis</topic><topic>protein supplements</topic><topic>Quantitative trait loci</topic><topic>quantitative traits</topic><topic>sequence analysis</topic><topic>Skeletal muscle</topic><topic>transcriptome</topic><topic>Transcriptomes</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Polizel, Guilherme Henrique Gebim</creatorcontrib><creatorcontrib>Cesar, Aline Silva Mello</creatorcontrib><creatorcontrib>Cracco, Roberta Cavalcante</creatorcontrib><creatorcontrib>Fernandes, Arícia Christofaro</creatorcontrib><creatorcontrib>Reginato, Gustavo Morandini</creatorcontrib><creatorcontrib>Xavier, Pedro Luiz Porfirio</creatorcontrib><creatorcontrib>Mortari, Isabela</creatorcontrib><creatorcontrib>Furlan, Édison</creatorcontrib><creatorcontrib>Fukumasu, Heidge</creatorcontrib><creatorcontrib>Santana, Miguel Henrique de Almeida</creatorcontrib><collection>CrossRef</collection><collection>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><jtitle>Journal of applied genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Polizel, Guilherme Henrique Gebim</au><au>Cesar, Aline Silva Mello</au><au>Cracco, Roberta Cavalcante</au><au>Fernandes, Arícia Christofaro</au><au>Reginato, Gustavo Morandini</au><au>Xavier, Pedro Luiz Porfirio</au><au>Mortari, Isabela</au><au>Furlan, Édison</au><au>Fukumasu, Heidge</au><au>Santana, Miguel Henrique de Almeida</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of eQTLs and differential gene expression associated with fetal programming in beef cattle</atitle><jtitle>Journal of applied genetics</jtitle><stitle>J Appl Genetics</stitle><date>2022-12-01</date><risdate>2022</risdate><volume>63</volume><issue>4</issue><spage>717</spage><epage>728</epage><pages>717-728</pages><issn>1234-1983</issn><eissn>2190-3883</eissn><abstract>This study assessed differential gene expression and identified expression quantitative trait loci (eQTLs) from samples of
Longissimus lumborum
muscle from bulls at 15 months of age submitted to different prenatal nutrition. Upon confirmation of pregnancy, 126 dams were separated into three diet treatments varying the period of inclusion of energy protein supplementation (NP, PP, and FP). At calving, 63 males were genotyped with GGP LD BeadChip. The skeletal muscle of 15 bulls was sequenced (RNA-seq) at 15 months of age. The EdgeR package was used for differential gene expression and principal component analysis (PCA), and the Matrix eQTL package was used for the eQTLs analysis (R statistical). The functional enrichment analysis was performed using the MetaCore® software. No genes differentially expressed were found between treatments (FDR > 0.05); nevertheless, we found 179 cis-tag-eQTLs and 20,762 trans-tag-eQTLs (FDR < 0.05) after linkage disequilibrium analysis. The functional enrichment analysis identified terms from gene ontology related to genes associated to trans-eQTLs (FDR < 0.05) as well as metabolic pathways (> gScore). Most biological pathways and genes found had been previously associated to fetal programming. The different prenatal supplementation strategies did not impact on muscle transcriptome of bulls. Additionally, there is a link between genotype and gene expression levels related to developmental traits in Nellore cattle.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><doi>10.1007/s13353-022-00711-1</doi><tpages>12</tpages><orcidid>https://orcid.org/0000-0002-8497-9898</orcidid></addata></record> |
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| subjects | Animal Genetics and Genomics Animal Genetics • Original Paper Beef cattle Biomedical and Life Sciences Cattle computer software energy Fetuses Gene expression gene expression regulation Gene mapping gene ontology Gene set enrichment analysis Genes Genetic aspects genotype Genotypes genotyping Human Genetics Life Sciences Linkage analysis Linkage disequilibrium longissimus muscle Metabolic pathways Microbial Genetics and Genomics Muscles Nellore Nutrition Plant Genetics and Genomics Pregnancy Prenatal experience principal component analysis Principal components analysis protein supplements Quantitative trait loci quantitative traits sequence analysis Skeletal muscle transcriptome Transcriptomes |
| title | Identification of eQTLs and differential gene expression associated with fetal programming in beef cattle |
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