Meta-analysis across Nellore cattle populations identifies common metabolic mechanisms that regulate feed efficiency-related traits
Abstract Background Feed efficiency (FE) related traits play a key role in the economy and sustainability of beef cattle production systems. The accurate knowledge of the physiologic background for FE-related traits can help the development of more efficient selection strategies for them. Hence, mul...
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| Format: | Article |
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BMC
2022-06-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-022-08671-w |
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| author | Lucio F. M. Mota Samuel W. B. Santos Gerardo A. Fernandes Júnior Tiago Bresolin Maria E. Z. Mercadante Josineudson A. V. Silva Joslaine N. S. G. Cyrillo Fábio M. Monteiro Roberto Carvalheiro Lucia G. Albuquerque |
| author_facet | Lucio F. M. Mota Samuel W. B. Santos Gerardo A. Fernandes Júnior Tiago Bresolin Maria E. Z. Mercadante Josineudson A. V. Silva Joslaine N. S. G. Cyrillo Fábio M. Monteiro Roberto Carvalheiro Lucia G. Albuquerque |
| author_sort | Lucio F. M. Mota |
| collection | DOAJ |
| description | Abstract Background Feed efficiency (FE) related traits play a key role in the economy and sustainability of beef cattle production systems. The accurate knowledge of the physiologic background for FE-related traits can help the development of more efficient selection strategies for them. Hence, multi-trait weighted GWAS (MTwGWAS) and meta-analyze were used to find genomic regions associated with average daily gain (ADG), dry matter intake (DMI), feed conversion ratio (FCR), feed efficiency (FE), and residual feed intake (RFI). The FE-related traits and genomic information belong to two breeding programs that perform the FE test at different ages: post-weaning (1,024 animals IZ population) and post-yearling (918 animals for the QLT population). Results The meta-analyze MTwGWAS identified 14 genomic regions (-log10(p -value) > 5) regions mapped on BTA 1, 2, 3, 4, 7, 8, 11, 14, 15, 18, 21, and 29. These regions explained a large proportion of the total genetic variance for FE-related traits across-population ranging from 20% (FCR) to 36% (DMI) in the IZ population and from 22% (RFI) to 28% (ADG) in the QLT population. Relevant candidate genes within these regions (LIPE, LPL, IGF1R, IGF1, IGFBP5, IGF2, INS, INSR, LEPR, LEPROT, POMC, NPY, AGRP, TGFB1, GHSR, JAK1, LYN, MOS, PLAG1, CHCD7, LCAT, and PLA2G15) highlighted that the physiological mechanisms related to neuropeptides and the metabolic signals controlling the body's energy balance are responsible for leading to greater feed efficiency. Integrated meta-analysis results and functional pathway enrichment analysis highlighted the major effect of biological functions linked to energy, lipid metabolism, and hormone signaling that mediates the effects of peptide signals in the hypothalamus and whole-body energy homeostasis affecting the genetic control of FE-related traits in Nellore cattle. Conclusions Genes and pathways associated with common signals for feed efficiency-related traits provide better knowledge about regions with biological relevance in physiological mechanisms associated with differences in energy metabolism and hypothalamus signaling. These pleiotropic regions would support the selection for feed efficiency-related traits, incorporating and pondering causal variations assigning prior weights in genomic selection approaches. |
| first_indexed | 2024-12-12T16:34:58Z |
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| id | doaj.art-ab337a5ca8d74b8884ed1582f430ebe4 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-12T16:34:58Z |
| publishDate | 2022-06-01 |
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| spelling | doaj.art-ab337a5ca8d74b8884ed1582f430ebe42022-12-22T00:18:41ZengBMCBMC Genomics1471-21642022-06-0123111210.1186/s12864-022-08671-wMeta-analysis across Nellore cattle populations identifies common metabolic mechanisms that regulate feed efficiency-related traitsLucio F. M. Mota0Samuel W. B. Santos1Gerardo A. Fernandes Júnior2Tiago Bresolin3Maria E. Z. Mercadante4Josineudson A. V. Silva5Joslaine N. S. G. Cyrillo6Fábio M. Monteiro7Roberto Carvalheiro8Lucia G. Albuquerque9School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SPSchool of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SPSchool of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SPSchool of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SPInstitute of Animal Science, Beef Cattle Research CenterNational Council for Science and Technological DevelopmentInstitute of Animal Science, Beef Cattle Research CenterInstitute of Animal Science, Beef Cattle Research CenterSchool of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SPSchool of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SPAbstract Background Feed efficiency (FE) related traits play a key role in the economy and sustainability of beef cattle production systems. The accurate knowledge of the physiologic background for FE-related traits can help the development of more efficient selection strategies for them. Hence, multi-trait weighted GWAS (MTwGWAS) and meta-analyze were used to find genomic regions associated with average daily gain (ADG), dry matter intake (DMI), feed conversion ratio (FCR), feed efficiency (FE), and residual feed intake (RFI). The FE-related traits and genomic information belong to two breeding programs that perform the FE test at different ages: post-weaning (1,024 animals IZ population) and post-yearling (918 animals for the QLT population). Results The meta-analyze MTwGWAS identified 14 genomic regions (-log10(p -value) > 5) regions mapped on BTA 1, 2, 3, 4, 7, 8, 11, 14, 15, 18, 21, and 29. These regions explained a large proportion of the total genetic variance for FE-related traits across-population ranging from 20% (FCR) to 36% (DMI) in the IZ population and from 22% (RFI) to 28% (ADG) in the QLT population. Relevant candidate genes within these regions (LIPE, LPL, IGF1R, IGF1, IGFBP5, IGF2, INS, INSR, LEPR, LEPROT, POMC, NPY, AGRP, TGFB1, GHSR, JAK1, LYN, MOS, PLAG1, CHCD7, LCAT, and PLA2G15) highlighted that the physiological mechanisms related to neuropeptides and the metabolic signals controlling the body's energy balance are responsible for leading to greater feed efficiency. Integrated meta-analysis results and functional pathway enrichment analysis highlighted the major effect of biological functions linked to energy, lipid metabolism, and hormone signaling that mediates the effects of peptide signals in the hypothalamus and whole-body energy homeostasis affecting the genetic control of FE-related traits in Nellore cattle. Conclusions Genes and pathways associated with common signals for feed efficiency-related traits provide better knowledge about regions with biological relevance in physiological mechanisms associated with differences in energy metabolism and hypothalamus signaling. These pleiotropic regions would support the selection for feed efficiency-related traits, incorporating and pondering causal variations assigning prior weights in genomic selection approaches.https://doi.org/10.1186/s12864-022-08671-wBeef cattleEnergy homeostasisFeed efficiency traitsGWASRegulatory pathways |
| spellingShingle | Lucio F. M. Mota Samuel W. B. Santos Gerardo A. Fernandes Júnior Tiago Bresolin Maria E. Z. Mercadante Josineudson A. V. Silva Joslaine N. S. G. Cyrillo Fábio M. Monteiro Roberto Carvalheiro Lucia G. Albuquerque Meta-analysis across Nellore cattle populations identifies common metabolic mechanisms that regulate feed efficiency-related traits BMC Genomics Beef cattle Energy homeostasis Feed efficiency traits GWAS Regulatory pathways |
| title | Meta-analysis across Nellore cattle populations identifies common metabolic mechanisms that regulate feed efficiency-related traits |
| title_full | Meta-analysis across Nellore cattle populations identifies common metabolic mechanisms that regulate feed efficiency-related traits |
| title_fullStr | Meta-analysis across Nellore cattle populations identifies common metabolic mechanisms that regulate feed efficiency-related traits |
| title_full_unstemmed | Meta-analysis across Nellore cattle populations identifies common metabolic mechanisms that regulate feed efficiency-related traits |
| title_short | Meta-analysis across Nellore cattle populations identifies common metabolic mechanisms that regulate feed efficiency-related traits |
| title_sort | meta analysis across nellore cattle populations identifies common metabolic mechanisms that regulate feed efficiency related traits |
| topic | Beef cattle Energy homeostasis Feed efficiency traits GWAS Regulatory pathways |
| url | https://doi.org/10.1186/s12864-022-08671-w |
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