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Chen SY, Schenkel FS, Melo ALP, Oliveira HR, Pedrosa VB, Araujo AC, Melka MG, Brito LF. Identifying pleiotropic variants and candidate genes for fertility and reproduction traits in Holstein cattle via association studies based on imputed whole-genome sequence genotypes. BMC Genomics 2022; 23:331. [PMID: 35484513 PMCID: PMC9052698 DOI: 10.1186/s12864-022-08555-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 04/12/2022] [Indexed: 02/06/2023] Open
Abstract
Background Genetic progress for fertility and reproduction traits in dairy cattle has been limited due to the low heritability of most indicator traits. Moreover, most of the quantitative trait loci (QTL) and candidate genes associated with these traits remain unknown. In this study, we used 5.6 million imputed DNA sequence variants (single nucleotide polymorphisms, SNPs) for genome-wide association studies (GWAS) of 18 fertility and reproduction traits in Holstein cattle. Aiming to identify pleiotropic variants and increase detection power, multiple-trait analyses were performed using a method to efficiently combine the estimated SNP effects of single-trait GWAS based on a chi-square statistic. Results There were 87, 72, and 84 significant SNPs identified for heifer, cow, and sire traits, respectively, which showed a wide and distinct distribution across the genome, suggesting that they have relatively distinct polygenic nature. The biological functions of immune response and fatty acid metabolism were significantly enriched for the 184 and 124 positional candidate genes identified for heifer and cow traits, respectively. No known biological function was significantly enriched for the 147 positional candidate genes found for sire traits. The most important chromosomes that had three or more significant QTL identified are BTA22 and BTA23 for heifer traits, BTA8 and BTA17 for cow traits, and BTA4, BTA7, BTA17, BTA22, BTA25, and BTA28 for sire traits. Several novel and biologically important positional candidate genes were strongly suggested for heifer (SOD2, WTAP, DLEC1, PFKFB4, TRIM27, HECW1, DNAH17, and ADAM3A), cow (ANXA1, PCSK5, SPESP1, and JMJD1C), and sire (ELMO1, CFAP70, SOX30, DGCR8, SEPTIN14, PAPOLB, JMJD1C, and NELL2) traits. Conclusions These findings contribute to better understand the underlying biological mechanisms of fertility and reproduction traits measured in heifers, cows, and sires, which may contribute to improve genomic evaluation for these traits in dairy cattle. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08555-z.
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Affiliation(s)
- Shi-Yi Chen
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907-2041, USA.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Ana L P Melo
- Department of Reproduction and Animal Evaluation, Rural Federal University of Rio de Janeiro, Seropédica, RJ, 23897-000, Brazil
| | - Hinayah R Oliveira
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907-2041, USA.,Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Victor B Pedrosa
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907-2041, USA.,Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil
| | - Andre C Araujo
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907-2041, USA
| | - Melkaye G Melka
- Department of Animal and Food Science, University of Wisconsin River Falls, River Falls, WI, 54022, USA
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907-2041, USA. .,Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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