Genome-wide association and functional genomic analyses for udder conformation traits derived from data recorded by robotic milking systems in American Holstein cattle
[EN] The implementation of automatic milking systems (AMS) in modern dairy farming has significantly facilitated genetic evaluation of udder conformation traits in dairy cattle. As AMS-based udder conformation traits are highly heritable in Holstein cattle, this study aimed to identify genomic regio...
| Autores: | , , , , , , , |
|---|---|
| Tipo de recurso: | artículo |
| Estado: | Versión publicada |
| Fecha de publicación: | 2025 |
| País: | España |
| Institución: | Universidad de León |
| Repositorio: | BULERIA. Repositorio Institucional de la Universidad de León |
| OAI Identifier: | oai:dnet:buleria_____::63d6546f0eaf7532d80c8fe62377fedb |
| Acceso en línea: | https://www.sciencedirect.com/science/article/pii/S0022030225008124?via%3Dihub https://hdl.handle.net/10612/28187 |
| Access Level: | acceso abierto |
| Palabra clave: | Genética Producción animal Dairy cattle Functional enrichment GWAS Quantitative trait loci Milking robots 3104 Producción Animal 3109.02 Genética |
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| dc.title.none.fl_str_mv |
Genome-wide association and functional genomic analyses for udder conformation traits derived from data recorded by robotic milking systems in American Holstein cattle |
| title |
Genome-wide association and functional genomic analyses for udder conformation traits derived from data recorded by robotic milking systems in American Holstein cattle |
| spellingShingle |
Genome-wide association and functional genomic analyses for udder conformation traits derived from data recorded by robotic milking systems in American Holstein cattle Medeiros, Gabriel C. Genética Producción animal Dairy cattle Functional enrichment GWAS Quantitative trait loci Milking robots 3104 Producción Animal 3109.02 Genética |
| title_short |
Genome-wide association and functional genomic analyses for udder conformation traits derived from data recorded by robotic milking systems in American Holstein cattle |
| title_full |
Genome-wide association and functional genomic analyses for udder conformation traits derived from data recorded by robotic milking systems in American Holstein cattle |
| title_fullStr |
Genome-wide association and functional genomic analyses for udder conformation traits derived from data recorded by robotic milking systems in American Holstein cattle |
| title_full_unstemmed |
Genome-wide association and functional genomic analyses for udder conformation traits derived from data recorded by robotic milking systems in American Holstein cattle |
| title_sort |
Genome-wide association and functional genomic analyses for udder conformation traits derived from data recorded by robotic milking systems in American Holstein cattle |
| dc.creator.none.fl_str_mv |
Medeiros, Gabriel C. Ferraz, Jose Bento S. Sousa, Luis Paulo B. Chen, Shi-Yi Suárez Vega, Aroa Pedrosa, Victor B. Rojas de Oliveira, Hinayah Brito, Luiz |
| author |
Medeiros, Gabriel C. |
| author_facet |
Medeiros, Gabriel C. Ferraz, Jose Bento S. Sousa, Luis Paulo B. Chen, Shi-Yi Suárez Vega, Aroa Pedrosa, Victor B. Rojas de Oliveira, Hinayah Brito, Luiz |
| author_role |
author |
| author2 |
Ferraz, Jose Bento S. Sousa, Luis Paulo B. Chen, Shi-Yi Suárez Vega, Aroa Pedrosa, Victor B. Rojas de Oliveira, Hinayah Brito, Luiz |
| author2_role |
author author author author author author author |
| dc.contributor.none.fl_str_mv |
Producción Animal Facultad de Veterinaria |
| dc.subject.none.fl_str_mv |
Genética Producción animal Dairy cattle Functional enrichment GWAS Quantitative trait loci Milking robots 3104 Producción Animal 3109.02 Genética |
| topic |
Genética Producción animal Dairy cattle Functional enrichment GWAS Quantitative trait loci Milking robots 3104 Producción Animal 3109.02 Genética |
| description |
[EN] The implementation of automatic milking systems (AMS) in modern dairy farming has significantly facilitated genetic evaluation of udder conformation traits in dairy cattle. As AMS-based udder conformation traits are highly heritable in Holstein cattle, this study aimed to identify genomic regions, QTL, and genes significantly associated with 3 udder conformation traits derived from Cartesian coordinates recorded by AMS in American Holstein cows. The traits evaluated included udder depth (UD), udder balance (UB), and distance front-rear (DFR). Phenotypic data consisted of 4,232,026 visit records to 36 Lely Astronaut A5 AMS robots for 4,280 American Holstein cows. A total of 4,118 cows also had genomic information for 57,598 SNPs. The SNP effects, together with their approximate P-values and proportion of the total additive genetic variance explained by them, were back solved from the GEBV using the POSTGSF90 software (version 2024-12-26, BLUPF90 Family of Programs, University of Georgia, Athens, GA). Multiple testing correction was applied using a modified Bonferroni method based on the number of independent chromosomal segments, and functional enrichment analyses were performed for the candidate positional genes and QTL. We identified 5 (BTA4, BTA22, and BTA29), 15 (BTA2, BTA8, BTA9, BTA15, BTA18, BTA23, and BTA26), and 19 (BTA1, BTA4, BTA6, BTA9, BTA10, BTA14, BTA17, BTA18, BTA23, and BTA25) genome-wide SNPs significantly associated with UB, DFR, and UD, respectively. There were no significant SNPs capturing more than 0.5% of the total additive genetic variance, highlighting the highly polygenic nature of these traits. The candidate genes overlapping with these genomic regions were previously reported to have biological functions that included but were not limited to transcription regulation, DNA repair mechanisms, inflammatory responses, epithelial differentiation processes, nutrient transport, extracellular matrix stabilization, cell division, and immune regulation. The strongest candidate genes associated with udder conformation traits are AFM, AFP, CREBBP, NLRP12, SP3, EBF2, B4GALT1, HDAC9, CDK13, and KDM2A. Furthermore, many QTL known to be associated with various milk production, reproduction, and health traits overlapped with the significant SNPs identified in this study. In summary, we identified significant genetic markers, candidate genes, and genomic regions associated with these traits, offering insights into the genetic architecture underlying udder conformation in Holstein cattle and its implications for dairy production |
| publishDate |
2025 |
| dc.date.none.fl_str_mv |
2025 |
| dc.type.none.fl_str_mv |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion |
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article |
| status_str |
publishedVersion |
| dc.identifier.none.fl_str_mv |
https://www.sciencedirect.com/science/article/pii/S0022030225008124?via%3Dihub https://hdl.handle.net/10612/28187 |
| url |
https://www.sciencedirect.com/science/article/pii/S0022030225008124?via%3Dihub https://hdl.handle.net/10612/28187 |
| dc.language.none.fl_str_mv |
Inglés |
| language_invalid_str_mv |
Inglés |
| dc.rights.none.fl_str_mv |
http://creativecommons.org/licenses/by-nc-nd/4.0/ info:eu-repo/semantics/openAccess |
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http://creativecommons.org/licenses/by-nc-nd/4.0/ |
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openAccess |
| dc.publisher.none.fl_str_mv |
Elsevier |
| publisher.none.fl_str_mv |
Elsevier |
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reponame:BULERIA. Repositorio Institucional de la Universidad de León instname:Universidad de León |
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Universidad de León |
| reponame_str |
BULERIA. Repositorio Institucional de la Universidad de León |
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BULERIA. Repositorio Institucional de la Universidad de León |
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1869402714152108032 |
| spelling |
Genome-wide association and functional genomic analyses for udder conformation traits derived from data recorded by robotic milking systems in American Holstein cattleMedeiros, Gabriel C.Ferraz, Jose Bento S.Sousa, Luis Paulo B.Chen, Shi-YiSuárez Vega, AroaPedrosa, Victor B.Rojas de Oliveira, HinayahBrito, LuizGenéticaProducción animalDairy cattleFunctional enrichmentGWASQuantitative trait lociMilking robots3104 Producción Animal3109.02 Genética[EN] The implementation of automatic milking systems (AMS) in modern dairy farming has significantly facilitated genetic evaluation of udder conformation traits in dairy cattle. As AMS-based udder conformation traits are highly heritable in Holstein cattle, this study aimed to identify genomic regions, QTL, and genes significantly associated with 3 udder conformation traits derived from Cartesian coordinates recorded by AMS in American Holstein cows. The traits evaluated included udder depth (UD), udder balance (UB), and distance front-rear (DFR). Phenotypic data consisted of 4,232,026 visit records to 36 Lely Astronaut A5 AMS robots for 4,280 American Holstein cows. A total of 4,118 cows also had genomic information for 57,598 SNPs. The SNP effects, together with their approximate P-values and proportion of the total additive genetic variance explained by them, were back solved from the GEBV using the POSTGSF90 software (version 2024-12-26, BLUPF90 Family of Programs, University of Georgia, Athens, GA). Multiple testing correction was applied using a modified Bonferroni method based on the number of independent chromosomal segments, and functional enrichment analyses were performed for the candidate positional genes and QTL. We identified 5 (BTA4, BTA22, and BTA29), 15 (BTA2, BTA8, BTA9, BTA15, BTA18, BTA23, and BTA26), and 19 (BTA1, BTA4, BTA6, BTA9, BTA10, BTA14, BTA17, BTA18, BTA23, and BTA25) genome-wide SNPs significantly associated with UB, DFR, and UD, respectively. There were no significant SNPs capturing more than 0.5% of the total additive genetic variance, highlighting the highly polygenic nature of these traits. The candidate genes overlapping with these genomic regions were previously reported to have biological functions that included but were not limited to transcription regulation, DNA repair mechanisms, inflammatory responses, epithelial differentiation processes, nutrient transport, extracellular matrix stabilization, cell division, and immune regulation. The strongest candidate genes associated with udder conformation traits are AFM, AFP, CREBBP, NLRP12, SP3, EBF2, B4GALT1, HDAC9, CDK13, and KDM2A. Furthermore, many QTL known to be associated with various milk production, reproduction, and health traits overlapped with the significant SNPs identified in this study. In summary, we identified significant genetic markers, candidate genes, and genomic regions associated with these traits, offering insights into the genetic architecture underlying udder conformation in Holstein cattle and its implications for dairy productionSIThis research was funded by the Agriculture and Food Research Initiative Competitive Grant number 202267021-37022 from the USDA National Institute of Food and Agriculture. The first author was financially supported by the São Paulo Research Foundation (Fundação de Amparo à Pesquisa do Estado de São Paulo—FAPESP) through the grant: 2024/20474-1. We are very grateful for the support received from the Purdue College of Agriculture and Purdue Ag Data Services for supporting the development of the Purdue Animal Sciences Data Ecosystem (PASDE; Boerman et al., 2025), which is a platform for automatically gathering, integrating, and storing large-scale datasets from precision dairy farms to be used for this type of research. The authors thank Homestead Dairy, LLC (Plymouth, IN) and especially Brian and Jill Houin for inviting us on their farm and for allowing our research group to use their farm records. We also thank Lely (Maassluis, the Netherlands) for giving us access to their system for extracting the datasets. Supplemental material for this article is available at https: / / doi .org/ 10 .6084/ m9 .figshare .28967747. No human or animal subjects were used, so this analysis did not require approval by an Institutional Animal Care and Use Committee or Institutional Review Board. The authors have not stated any conflicts of interestElsevierProducción AnimalFacultad de Veterinaria2025info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttps://www.sciencedirect.com/science/article/pii/S0022030225008124?via%3Dihubhttps://hdl.handle.net/10612/28187reponame:BULERIA. Repositorio Institucional de la Universidad de Leóninstname:Universidad de LeónIngléshttp://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccessoai:dnet:buleria_____::63d6546f0eaf7532d80c8fe62377fedb2026-06-24T12:43:27Z |
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15,198674 |