Gene co-expression network analysis reveals positive effects of concentrate supplementation on energy metabolism in early-weaned Nellore calves
IntroductionTo determine the impact of early weaning combined with concentrate supplementation on skeletal muscle energy metabolism, we profiled gene co-expression networks in Bos indicus (Nellore) calves.Material and methodsLongissimus thoracis biopsies were collected from eight calves per treatmen...
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Frontiers Media S.A.
2025-04-01
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| Series: | Frontiers in Animal Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fanim.2025.1533043/full |
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| author | Gustavo Henrique Russo Gustavo Lucas Bezerra Tinoco Marcelo Ricardo Vicari Rebeca Soares Nogueira Paloma Leandra Garcia Melo Juliana Akamine Torrecilhas Rogério Curi Philipe Moriel Welder Angelo Baldassini Welder Angelo Baldassini Luis Artur Loyola Chardulo Luis Artur Loyola Chardulo Guilherme Luis Pereira Guilherme Luis Pereira |
| author_facet | Gustavo Henrique Russo Gustavo Lucas Bezerra Tinoco Marcelo Ricardo Vicari Rebeca Soares Nogueira Paloma Leandra Garcia Melo Juliana Akamine Torrecilhas Rogério Curi Philipe Moriel Welder Angelo Baldassini Welder Angelo Baldassini Luis Artur Loyola Chardulo Luis Artur Loyola Chardulo Guilherme Luis Pereira Guilherme Luis Pereira |
| author_sort | Gustavo Henrique Russo |
| collection | DOAJ |
| description | IntroductionTo determine the impact of early weaning combined with concentrate supplementation on skeletal muscle energy metabolism, we profiled gene co-expression networks in Bos indicus (Nellore) calves.Material and methodsLongissimus thoracis biopsies were collected from eight calves per treatment (conventional and early weaning) at 120 and 205 days of age (longitudinal sampling). All calves grazed Brachiaria decumbens pasture until 120 days. Subsequently, early weaned calves received a 1% body weight concentrate supplement (20% CP, 75% TDN) post-weaning. Total RNA was extracted, and 32 mRNA libraries were generated for RNA sequencing. Using normalized count matrix, we constructed gene co-expression modules using webCEMiTool and performed over-representation analysis (ORA) for pathway enrichment (KEGG). Additionally, we used Gene Set Enrichment Analysis (GSEA) to evaluate the regulatory activity (up- or downregulation) of identified gene modules.ResultsResults: Modules associated with pathways such as insulin signaling, unsaturated fatty acid biosynthesis, and PPAR signaling showed a significantly higher proportion of upregulated genes. Key hub genes within these early weaning-related modules were linked to lipid synthesis and adipocyte differentiation. Thus, early weaning followed by concentrate supplementation modified the gene expression profile, enhancing pathways involved in energy metabolism, adipogenesis, lipogenesis, and lipolysis inhibition.DiscussionThese findings suggest that early nutritional intervention can positively influence metabolic pathways associated with growth and body composition in Nellore calves. Despite the multifactorial nature of these traits and their susceptibility to modification during post-weaning phases, the current results demonstrate potential for long-term positive effects on carcass composition and final product quality. |
| format | Article |
| id | doaj-art-cf967fa0ea9d409b89b6ed50f1d1fd87 |
| institution | OA Journals |
| issn | 2673-6225 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Animal Science |
| spelling | doaj-art-cf967fa0ea9d409b89b6ed50f1d1fd872025-08-20T02:29:50ZengFrontiers Media S.A.Frontiers in Animal Science2673-62252025-04-01610.3389/fanim.2025.15330431533043Gene co-expression network analysis reveals positive effects of concentrate supplementation on energy metabolism in early-weaned Nellore calvesGustavo Henrique Russo0Gustavo Lucas Bezerra Tinoco1Marcelo Ricardo Vicari2Rebeca Soares Nogueira3Paloma Leandra Garcia Melo4Juliana Akamine Torrecilhas5Rogério Curi6Philipe Moriel7Welder Angelo Baldassini8Welder Angelo Baldassini9Luis Artur Loyola Chardulo10Luis Artur Loyola Chardulo11Guilherme Luis Pereira12Guilherme Luis Pereira13School of Agriculture and Veterinary Sciences (FCAV), São Paulo State University (UNESP), Jaboticabal, SP, BrazilSchool of Agriculture and Veterinary Sciences (FCAV), São Paulo State University (UNESP), Jaboticabal, SP, BrazilDepartment of Structural, Molecular Biology and Genetics, Ponta Grossa State University (UEPG), Ponta Grossa, PR, BrazilSchool of Veterinary and Animal Science (FMVZ), São Paulo State University (UNESP), Botucatu, SP, BrazilSchool of Agriculture and Veterinary Sciences (FCAV), São Paulo State University (UNESP), Jaboticabal, SP, BrazilSchool of Veterinary and Animal Science (FMVZ), São Paulo State University (UNESP), Botucatu, SP, BrazilSchool of Veterinary and Animal Science (FMVZ), São Paulo State University (UNESP), Botucatu, SP, BrazilRange Cattle Research & Education Center, University of Florida, Ona, FL, United StatesSchool of Agriculture and Veterinary Sciences (FCAV), São Paulo State University (UNESP), Jaboticabal, SP, BrazilSchool of Veterinary and Animal Science (FMVZ), São Paulo State University (UNESP), Botucatu, SP, BrazilSchool of Agriculture and Veterinary Sciences (FCAV), São Paulo State University (UNESP), Jaboticabal, SP, BrazilSchool of Veterinary and Animal Science (FMVZ), São Paulo State University (UNESP), Botucatu, SP, BrazilSchool of Agriculture and Veterinary Sciences (FCAV), São Paulo State University (UNESP), Jaboticabal, SP, BrazilSchool of Veterinary and Animal Science (FMVZ), São Paulo State University (UNESP), Botucatu, SP, BrazilIntroductionTo determine the impact of early weaning combined with concentrate supplementation on skeletal muscle energy metabolism, we profiled gene co-expression networks in Bos indicus (Nellore) calves.Material and methodsLongissimus thoracis biopsies were collected from eight calves per treatment (conventional and early weaning) at 120 and 205 days of age (longitudinal sampling). All calves grazed Brachiaria decumbens pasture until 120 days. Subsequently, early weaned calves received a 1% body weight concentrate supplement (20% CP, 75% TDN) post-weaning. Total RNA was extracted, and 32 mRNA libraries were generated for RNA sequencing. Using normalized count matrix, we constructed gene co-expression modules using webCEMiTool and performed over-representation analysis (ORA) for pathway enrichment (KEGG). Additionally, we used Gene Set Enrichment Analysis (GSEA) to evaluate the regulatory activity (up- or downregulation) of identified gene modules.ResultsResults: Modules associated with pathways such as insulin signaling, unsaturated fatty acid biosynthesis, and PPAR signaling showed a significantly higher proportion of upregulated genes. Key hub genes within these early weaning-related modules were linked to lipid synthesis and adipocyte differentiation. Thus, early weaning followed by concentrate supplementation modified the gene expression profile, enhancing pathways involved in energy metabolism, adipogenesis, lipogenesis, and lipolysis inhibition.DiscussionThese findings suggest that early nutritional intervention can positively influence metabolic pathways associated with growth and body composition in Nellore calves. Despite the multifactorial nature of these traits and their susceptibility to modification during post-weaning phases, the current results demonstrate potential for long-term positive effects on carcass composition and final product quality.https://www.frontiersin.org/articles/10.3389/fanim.2025.1533043/fulladipose tissuebeef cattlegene co-expression moduleshub genesperoxisome proliferator-activated receptor gamma |
| spellingShingle | Gustavo Henrique Russo Gustavo Lucas Bezerra Tinoco Marcelo Ricardo Vicari Rebeca Soares Nogueira Paloma Leandra Garcia Melo Juliana Akamine Torrecilhas Rogério Curi Philipe Moriel Welder Angelo Baldassini Welder Angelo Baldassini Luis Artur Loyola Chardulo Luis Artur Loyola Chardulo Guilherme Luis Pereira Guilherme Luis Pereira Gene co-expression network analysis reveals positive effects of concentrate supplementation on energy metabolism in early-weaned Nellore calves Frontiers in Animal Science adipose tissue beef cattle gene co-expression modules hub genes peroxisome proliferator-activated receptor gamma |
| title | Gene co-expression network analysis reveals positive effects of concentrate supplementation on energy metabolism in early-weaned Nellore calves |
| title_full | Gene co-expression network analysis reveals positive effects of concentrate supplementation on energy metabolism in early-weaned Nellore calves |
| title_fullStr | Gene co-expression network analysis reveals positive effects of concentrate supplementation on energy metabolism in early-weaned Nellore calves |
| title_full_unstemmed | Gene co-expression network analysis reveals positive effects of concentrate supplementation on energy metabolism in early-weaned Nellore calves |
| title_short | Gene co-expression network analysis reveals positive effects of concentrate supplementation on energy metabolism in early-weaned Nellore calves |
| title_sort | gene co expression network analysis reveals positive effects of concentrate supplementation on energy metabolism in early weaned nellore calves |
| topic | adipose tissue beef cattle gene co-expression modules hub genes peroxisome proliferator-activated receptor gamma |
| url | https://www.frontiersin.org/articles/10.3389/fanim.2025.1533043/full |
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