Identification of candidate genes and SNPs related to cattle temperament using a GWAS analysis coupled with an interacting network analysis

Authors: PAREDES-SANCHEZ, FRANCISCO - Instituto Politécnico Nacional, Centro De Desarrollo De Productos Bioticos (CEPROBI); SIFUENTES-RINCON, ANA - Instituto Politécnico Nacional, Centro De Desarrollo De Productos Bioticos (CEPROBI); LARA-RAMIREZ, E - Instituto Tecnológico De Zacatepec; Casas, Eduardo; RODRIGUEZ-ALMEIDA, FELIPE - Universidad Autonoma De Chihuahua; HERRERA-MAYORGA, ELSA - Universidad Autonoma De Chihuahua; RANDAL, RONALD - Texas A&M Agrilife

Submitted to: La Revista Mexicana de Ciencias Pecuarias
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/16/2022
Publication Date: 1/3/2023
Citation: Paredes-Sanchez, F.A., Sifuentes-Rincon, A.M., Lara-Ramirez, E.E., Casas, E., Rodriguez-Almeida, F.A., Herrera-Mayorga, E.V., Randal, R.D. 2023. Identification of candidate genes and SNPs related to cattle temperament using a GWAS analysis coupled with an interacting network analysis. La Revista Mexicana de Ciencias Pecuarias. 14(1):1-22. https://doi.org/10.22319/rmcp.v14i1.6077.
DOI: https://doi.org/10.22319/rmcp.v14i1.6077

Interpretive Summary: Temperament is an economically relevant trait that impacts animal welfare and productive traits. Temperament comprises a range of behaviors including nervousness, docility, aggressiveness, etc. The objective of this study was to establish if temperament in Angus and Brangus cattle had a genetic component, and to establish where in the genetic material (genome) were the genes influencing temperament. A region of chromosome 6 was identified as harboring genes associated with temperament. Within this region of chromosome 6, the GPRIN3, MMRN1, and SNCA genes, could potentially be considered as candidates for temperament; however, because its reported functional implications in human, SNCA was proposed as the primary candidate gene for predicting cattle temperament. After studying the structure of this gene, it was postulated that variations in the DNA make it the likely candidate to explain temperament in Angus and Brangus cattle.

Technical Abstract: Background: Cattle temperament, defined as the animal’s response to handling, has been studied in different breeds and has been shown to affect growth, health, and carcass quality. The objective of this study was to identify genomic regions and genes associated with beef cattle temperament. Results: A total of 139,376 SNPs were used to determine genomic regions associated with beef cattle temperament. Markers rs133956611 (p-value 2.65 E-06) and rs81144933 (p-value 9.58 E-06) were associated with the trait of interest; rs133956611 maps to over 222 kb downstream to the alpha-synuclein (SNCA) and multimerin 1 (MMRN1) genes on BTA6, and rs81144933 maps to over 344 kb upstream to GPRIN family member 3 (GPRIN3) on the same chromosome. Because of its reported functional implications in humans, SNCA is proposed as a strong candidate for predicting cattle temperament. An in silico analysis of the functional and structural impact of four nsSNP (A30P, R32K, H99Q, M100L) located at bovine SNCA gene, showed that the AR3032PK haplotype causes a complete change in the interaction pattern, changing the interaction of its protein partner synphilin-1 (SNCAIP), from an N-terminal A2 lipid-binding alpha helix domain to a non-amyloid ß component (NAC) domain; therefore, A30P and R32K might be strong candidates for an association with temperament. Conclusions: A region on BTA6 (36655249-36676986 bp) was associated with exit velocity in beef cattle, this region harbours the GPRIN3, MMRN1 and SNCA genes. According to their reported biological activities, which includes dopamine release and transport regulation, we focus on the bovine SNCA gene. On the basis of an in silico analysis of its nsSNPs, the bovine SNCA gene is proposed as a new candidate associated with temperament in Angus and Brangus cattle.