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ORIGINAL RESEARCH article

Front. Genet.
Sec. Livestock Genomics
Volume 15 - 2024 | doi: 10.3389/fgene.2024.1478788

Genome-wide association and functional genomic analyses for body conformation traits in North American Holstein cattle

Provisionally accepted
Luis Paulo B. Sousa Junior Luis Paulo B. Sousa Junior 1,2Luis Fernando B. Pinto Luis Fernando B. Pinto 1,2Valdecy A. Cruz Valdecy A. Cruz 2Gerson de Oliveira Jr Gerson de Oliveira Jr 3Hinayah Rojas De Oliveira Hinayah Rojas De Oliveira 1Tatiane S. Chud Tatiane S. Chud 3Victor B. Pedrosa Victor B. Pedrosa 1Filippo Miglior Filippo Miglior 3Flavio Schenkel Flavio Schenkel 3Luiz F. Brito Luiz F. Brito 1*
  • 1 Purdue University, West Lafayette, United States
  • 2 Federal University of Bahia (UFBA), Salvador, Bahia, Brazil
  • 3 University of Guelph, Guelph, Ontario, Canada

The final, formatted version of the article will be published soon.

    Body conformation traits are directly associated with longevity, fertility, health, and workability in dairy cows and have been under direct genetic selection for many decades in various countries worldwide. The main objectives of this study were to perform genome-wide association studies and functional enrichment analyses for fourteen body conformation traits using imputed high-density single nucleotide polymorphism (SNP) genotypes. The traits analyzed include body condition score (BCS), body depth (BD), bone quality (BQ), chest width (CW), dairy capacity (DC), foot angle (FAN), front legs view (FLV), heel depth (HDe), height at front end (HFE), locomotion (LOC), rear legs rear view (RLRV), rear legs side view (RLSV), stature (ST), and a composite feet and legs score index (FL) of Holstein cows scored in Canada. De-regressed estimated breeding values from a dataset of 39,135 North American Holstein animals were used as pseudo-phenotypes in the genome-wide association analyses. A mixed linear model was used to estimate the SNP effects, which ranged from 239,533 to 242,747 markers depending on the trait analyzed. Genes and quantitative trait loci (QTL) located up to 100 Kb upstream or downstream of the significant SNPs previously cited in the Animal QTLdb were detected, and functional enrichment analyses were performed for the candidate genes identified for each trait.

    Keywords: dairy cattle, high density genotypes, GWAS, Type traits, Imputation

    Received: 10 Aug 2024; Accepted: 10 Oct 2024.

    Copyright: © 2024 Sousa Junior, Pinto, Cruz, de Oliveira Jr, Rojas De Oliveira, Chud, Pedrosa, Miglior, Schenkel and Brito. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Luiz F. Brito, Purdue University, West Lafayette, United States

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