Characterization of intronic SNP located in candidate genes influencing cattle temperament

Authors: RUIZ-DE LA CRUZ, GILBERTO - Instituto Politécnico Nacional, Centro De Desarrollo De Productos Bioticos (CEPROBI); SIFUENTES-RINCON, ANA - Instituto Politécnico Nacional, Centro De Desarrollo De Productos Bioticos (CEPROBI); PAREDES-SANCHEZ, FRANCISCO - Instituto Politécnico Nacional, Centro De Desarrollo De Productos Bioticos (CEPROBI); PARRA-BRACAMONTES, GASPAR - Instituto Politécnico Nacional, Centro De Desarrollo De Productos Bioticos (CEPROBI); Casas, Eduardo; WELSH JR, THOMAS - Texas A&M University; RILEY, DAVID - Texas A&M University; PERRY, GEORGE - Texas A&M University; RANDEL, RONALD - Texas A&M University

Submitted to: Brazilian Journal of Animal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/19/2023
Publication Date: 6/16/2023
Citation: Ruiz-De La Cruz, G., Sifuentes-Rincon, A.M., Paredes-Sanchez, F.A., Parra-Bracamontes, G., Casas, E., Welsh Jr, T.H., Riley, D., Perry, G., Randel, R.D. 2023. Characterization of intronic SNP located in candidate genes influencing cattle temperament. Brazilian Journal of Animal Science. 52. Article e20220057. https://doi.org/10.37496/rbz5220220057.
DOI: https://doi.org/10.37496/rbz5220220057

Interpretive Summary: Cattle temperament is an economically relevant trait in cattle. Brahman is known to be temperamental when compared to European breeds. The objective of this study was to confirm the effect of five variants in the DNA, known as single nucleotide polymorphisms (SNPs), previously associated with temperament in Brahman cattle. In a previous study, 5 SNPs in four genes (CACNG4, EXOC4, NRXN3, and SLC9A4) were associated with temperament. In the present study, one of the five SNPs was confirmed as associated with temperament. The SNP was located in the CACNG4 gene. The study replicates the association of one SNP in an independent cattle population.

Technical Abstract: The objective of this study was to evaluate the effect of intronic single nucleotide polymorphisms (SNP) on temperament traits in a Brahman cattle population. The SNP located in CACNG4, EXOC4, NRXN3, and SLC9A4 candidate genes were genotyped in 250 animals with temperament records of exit velocity, pen score, and temperament score. Rs3423464051:G>A in the CACNG4 gene was associated with exit velocity and temperament score. An in silico analysis of the five intronic SNP showed that alternative alleles of CACNG4-rs3423464051, EXOC4-rs109393235, and SLC9A4-rs109722627 SNP could alter branch point sites during splicing, while a protein–protein interaction network analysis demonstrated a GRIA2 gene-mediated interaction between CACNG4 and NRXN3. The present results support previously reported evidence regarding bovine temperament-related candidate genes, particularly CACNG4, which is a confirmed candidate gene in need of more detailed analyses to reveal its role in temperament-related traits.