Bayesian-genome-wide association study and post-GWAS on reproductive traits of Holstein dairy cattle

Bayesian multiple regression models are often used for genomic selection, where all markers are adjusted simultaneously as random effects to reduce the false-discovery rate. The purpose of this research was to identify individual candidate genes for some reproductive traits in Holstein cattle throug...

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Bibliographic Details
Published in:Journal of dairy research 2024-05, Vol.91 (2), p.146-155
Main Authors: Jabbari Tourchi, Jeyran, Alijani, Sadegh, Rafat, Seyed Abbas, Abbasi, Mokhtar Ali
Format: Article
Language:English
Subjects:
AKT1 protein
Animals
Bayesian analysis
Breeding of animals
Cattle
Cluster analysis
Dairy cattle
Estimates
Gene set enrichment analysis
Genes
Genetic analysis
Genetic diversity
Genetic variance
Genome-wide association studies
Genomes
Genomic analysis
Mathematical models
Methods
Multiple regression models
Nucleotides
Parameter estimation
Polymorphism
Quality control
Regression analysis
Single-nucleotide polymorphism
Software
Somatic chromosomes
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Summary:Bayesian multiple regression models are often used for genomic selection, where all markers are adjusted simultaneously as random effects to reduce the false-discovery rate. The purpose of this research was to identify individual candidate genes for some reproductive traits in Holstein cattle through genome wide association studies (GWAS) using a Bayesian method in combination with post-GWAS analysis. Reproductive traits included: days open (DO), pregnancy rate (PR), calving interval (CI) and age at first calving (AFC). The animals were genotyped using single-nucleotide polymorphism (SNP) panels of different densities imputed to a 50 K SNP density. After quality control, we included 2400 genotyped animals. According to the Bayesian analysis, there were 19 windows with an explained additive genetic variance of >0.1 percent for CI, DO, AFC and PR in Holstein cattle, which were 3, 3, 6 and 7, respectively. Using Bayesian analysis, 79 genes were located within or nearby (250-kb) 19 significant SNPs/windows in the Bos taurus autosomes. Among these genes, we identified 25 candidate genes for reproductive traits, namely CHD7, CLVS1, EVX2, MAT2B, NUDCD2, GPR39, NCKAP5, LYPD1, HOXD13, SEMA5B, CCNG1, SEMA5A, BRF1, PSEN2, CACHD1, SUGTA, ELF1, SNORA70, AKT1, TM2D1, SLF1, MCTPA, PAB2A, MTRF1 and ADCY2. Additionally, another nine candidate genes (CLVS1, GPR39, CENPF, AMOT, ARF1, CCDC186, ADCY2, BDP1 and AMOTL1) were identified in the network cluster analysis as hub genes for reproductive traits. The results of gene set enrichment analysis (GSEA) and pathway analysis, suggest that the most important gene ontology term involving cellular metabolic process was related to the AFC trait. To summarize, Bayesian methods were used to identify SNPs and candidate genes that could be useful in genomic selection to improve reproductive traits of Holstein dairy cattle.
ISSN:0022-0299
1469-7629
DOI:10.1017/S0022029924000414