Abstract
Composite breeds, including Brangus, are widely utilized in subtropical and tropical regions to harness the advantages of both Bos t. taurus and Bos t. indicus breeds. The formation and subsequent selection of composite breeds may result in discernible signatures of selection and shifts in genomic population structure. The objectives of this study were to 1) assess genomic inbreeding, 2) identify signatures of selection, 3) assign functional roles to these signatures in a commercial Brangus herd, and 4) contrast signatures of selection between selected and non-selected cattle from the same year. A total of 4035 commercial Brangus cattle were genotyped using the GGP-F250K array. Runs of Homozygosity (ROH) were used to identify signatures of selection and calculate genomic inbreeding. Quantitative trait loci (QTL) enrichment analysis and literature search identified phenotypic traits linked to ROH islands. Genomic inbreeding averaged 5%, primarily stemming from ancestors five or more generations back. A total of nine ROH islands were identified, QTL enrichment analysis revealed traits related to growth, milk composition, carcass, reproductive, and meat quality traits. Notably, the ROH island on BTA14 encompasses the pleiomorphic adenoma (PLAG1) gene, which has been linked to growth, carcass, and reproductive traits. Moreover, ROH islands associated with milk yield and composition were more pronounced in selected replacement heifers of the population, underscoring the importance of milk traits in cow-calf production. In summary, our research sheds light on the changing genetic landscape of the Brangus breed due to selection pressures and reveals key genomic regions impacting production traits.
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Data availability
Genomic data are available through the European Variation Archive (EVA), accession number PRJEB60100.
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Acknowledgements
The authors thank the Seminole Tribe for access to records.
Funding
This research was supported by USDA-NIFA Grant #2017–67007-26143, USDA-NIFA Grant # 2020–67015-30820, and Florida Agricultural Experiment Station Hatch FLA-ANS-005548.
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All authors contributed to the design of the study. Material preparation, data collection and analysis were performed by Gabriel A. Zayas, Eduardo E. Rodriguez and Aakilah S. Hernandez under the guidance of Fernanda M. Rezende, and Raluca G. Mateescu. The first manuscript was written by Gabriel A. Zayas, and all authors read and approved the final manuscript.
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Zayas, G.A., Rodriguez, E.E., Hernandez, A.S. et al. Exploring genomic inbreeding and selection signatures in a commercial Brangus herd through functional annotation. J Appl Genetics 65, 383–394 (2024). https://doi.org/10.1007/s13353-024-00859-y
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DOI: https://doi.org/10.1007/s13353-024-00859-y