Genome-wide association study for feed efficiency indicator traits in Nellore cattle considering genotype-by-environment interactions
IntroductionFeed efficiency is a key factor in animal production sustainability, directly affecting production costs, environmental efficiency, and farmer profitability. The inclusion of feeding efficiency traits in cattle breeding programs has occurred later than other species due to longer life cy...
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Frontiers Media S.A.
2025-06-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2025.1539056/full |
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| author | João B. Silva Neto João B. Silva Neto Luiz F. Brito Lucio Flavio M. Mota Claudio U. Magnabosco Fernando Baldi |
| author_facet | João B. Silva Neto João B. Silva Neto Luiz F. Brito Lucio Flavio M. Mota Claudio U. Magnabosco Fernando Baldi |
| author_sort | João B. Silva Neto |
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| description | IntroductionFeed efficiency is a key factor in animal production sustainability, directly affecting production costs, environmental efficiency, and farmer profitability. The inclusion of feeding efficiency traits in cattle breeding programs has occurred later than other species due to longer life cycles and the high costs associated with measuring feed intake. However, genomic selection has facilitated the inclusion of difficult-to-measure traits in selection schemes. Thus, understanding the genetic basis of feed efficiency, particularly under varying environmental conditions, is essential.MethodsThis study aimed to identify genomic regions associated with dry matter intake (DMI) and residual feed intake (RFI) in Nellore cattle by performing a genome-wide association study (GWAS) based on single-step genomic reaction norm models that account for genotype-by-environment interactions (G×E). Phenotypic data from 23,170 young bulls and heifers were collected across 301 feed efficiency trials. Genomic windows explaining more than 1% of the total direct additive genetic variance were identified for both the intercept and slope components of the reaction norm for each trait.ResultsFor RFI, ten and eleven genomic windows explained more than 1% of the genetic variance for the intercept and slope, respectively. For DMI, 12 windows were identified for the intercept and 17 for the slope. Within these regions, Multiple protein-coding genes were annotated (RFI: 66 for intercept and 47 for slope; DMI: 107 for intercept and 109 for slope), which are involved in key biological processes such as insulin, leptin, glucose, protein, and lipid metabolism; energy balance; heat stress response; feeding behavior; digestion; and nutrient absorption.DiscussionThe results highlight the functional diversity of genes involved in feed efficiency and their dynamic response to environmental variation. While certain genes remained central across environments, others were specifically important under more challenging conditions, emphasizing the role of G×E in regulating these traits. Furthermore, the magnitude and direction of SNP effects varied across environmental gradients, reinforcing the relevance of G×E. Consequently, genomic estimated breeding values for DMI and RFI also differed between environmental extremes. These findings underscore the adaptability of genetic networks to environmental changes and are essential for refining strategies to improve feed efficiency in Nellore cattle. |
| format | Article |
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| institution | DOAJ |
| issn | 1664-8021 |
| language | English |
| publishDate | 2025-06-01 |
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| spelling | doaj-art-cd6450abdae84a018e08d22c5d9f0d5e2025-08-20T03:20:27ZengFrontiers Media S.A.Frontiers in Genetics1664-80212025-06-011610.3389/fgene.2025.15390561539056Genome-wide association study for feed efficiency indicator traits in Nellore cattle considering genotype-by-environment interactionsJoão B. Silva Neto0João B. Silva Neto1Luiz F. Brito2Lucio Flavio M. Mota3Claudio U. Magnabosco4Fernando Baldi5Department of Animal Science, School of Agricultural and Veterinarian Sciences (FCAV), São Paulo State University (UNESP), Jaboticabal, BrazilDepartment of Animal Sciences, Purdue University, West Lafayette, IN, United StatesDepartment of Animal Sciences, Purdue University, West Lafayette, IN, United StatesDepartment of Animal Science, School of Agricultural and Veterinarian Sciences (FCAV), São Paulo State University (UNESP), Jaboticabal, BrazilCerrados Agricultural Research Center, Embrapa Rice and Beans, Santo Antônio de Goiás, BrazilDepartment of Animal Science, School of Agricultural and Veterinarian Sciences (FCAV), São Paulo State University (UNESP), Jaboticabal, BrazilIntroductionFeed efficiency is a key factor in animal production sustainability, directly affecting production costs, environmental efficiency, and farmer profitability. The inclusion of feeding efficiency traits in cattle breeding programs has occurred later than other species due to longer life cycles and the high costs associated with measuring feed intake. However, genomic selection has facilitated the inclusion of difficult-to-measure traits in selection schemes. Thus, understanding the genetic basis of feed efficiency, particularly under varying environmental conditions, is essential.MethodsThis study aimed to identify genomic regions associated with dry matter intake (DMI) and residual feed intake (RFI) in Nellore cattle by performing a genome-wide association study (GWAS) based on single-step genomic reaction norm models that account for genotype-by-environment interactions (G×E). Phenotypic data from 23,170 young bulls and heifers were collected across 301 feed efficiency trials. Genomic windows explaining more than 1% of the total direct additive genetic variance were identified for both the intercept and slope components of the reaction norm for each trait.ResultsFor RFI, ten and eleven genomic windows explained more than 1% of the genetic variance for the intercept and slope, respectively. For DMI, 12 windows were identified for the intercept and 17 for the slope. Within these regions, Multiple protein-coding genes were annotated (RFI: 66 for intercept and 47 for slope; DMI: 107 for intercept and 109 for slope), which are involved in key biological processes such as insulin, leptin, glucose, protein, and lipid metabolism; energy balance; heat stress response; feeding behavior; digestion; and nutrient absorption.DiscussionThe results highlight the functional diversity of genes involved in feed efficiency and their dynamic response to environmental variation. While certain genes remained central across environments, others were specifically important under more challenging conditions, emphasizing the role of G×E in regulating these traits. Furthermore, the magnitude and direction of SNP effects varied across environmental gradients, reinforcing the relevance of G×E. Consequently, genomic estimated breeding values for DMI and RFI also differed between environmental extremes. These findings underscore the adaptability of genetic networks to environmental changes and are essential for refining strategies to improve feed efficiency in Nellore cattle.https://www.frontiersin.org/articles/10.3389/fgene.2025.1539056/fullBos indicusbeef cattledry matter intakeGWASresidual feed intakeregulatory pathways |
| spellingShingle | João B. Silva Neto João B. Silva Neto Luiz F. Brito Lucio Flavio M. Mota Claudio U. Magnabosco Fernando Baldi Genome-wide association study for feed efficiency indicator traits in Nellore cattle considering genotype-by-environment interactions Frontiers in Genetics Bos indicus beef cattle dry matter intake GWAS residual feed intake regulatory pathways |
| title | Genome-wide association study for feed efficiency indicator traits in Nellore cattle considering genotype-by-environment interactions |
| title_full | Genome-wide association study for feed efficiency indicator traits in Nellore cattle considering genotype-by-environment interactions |
| title_fullStr | Genome-wide association study for feed efficiency indicator traits in Nellore cattle considering genotype-by-environment interactions |
| title_full_unstemmed | Genome-wide association study for feed efficiency indicator traits in Nellore cattle considering genotype-by-environment interactions |
| title_short | Genome-wide association study for feed efficiency indicator traits in Nellore cattle considering genotype-by-environment interactions |
| title_sort | genome wide association study for feed efficiency indicator traits in nellore cattle considering genotype by environment interactions |
| topic | Bos indicus beef cattle dry matter intake GWAS residual feed intake regulatory pathways |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2025.1539056/full |
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