Selection signatures in a Rarámuri Criollo cattle population introduced to the Southwestern United States

Authors: SPETTER, M - New Mexico State University; UTSUMI, S - New Mexico State University; ARMSTRONG, E - Universidad De La República; RODRIGUEZ-ALMEIDA, F - Universidad Autonoma De Chihuahua; ROSS, P - St Genetics; Macon, Lara; JARA, E - University Of Montevideo; COX, ANDREW - New Mexico State University; PEREA, A - New Mexico State University; FUNK, MICHA - New Mexico State University; REDD, M - The Nature Conservancy; Cibils, Andres; Spiegal, Sheri; Estell, Richard

Submitted to: Journal of Animal Science Supplement
Publication Type: Proceedings
Publication Acceptance Date: 9/1/2025
Publication Date: 10/1/2025
Citation: Spetter, M.J., Utsumi, S.A., Armstrong, E.M., Rodriguez-Almeida, F.A., Ross, P.J., Macon, L.K., Jara, E., Cox, A., Perea, A.R., Funk, M., Redd, M., Cibils, A.F., Spiegal, S.A., Estell, R.E. 2025. Selection signatures in a Rarámuri Criollo cattle population introduced to the Southwestern United States. Journal of Animal Science Supplement. 103 (Supplement_3):342-343. https://doi.org/10.1093/jas/skaf300.396.
DOI: https://doi.org/10.1093/jas/skaf300.396

Interpretive Summary:

Technical Abstract: Rarámuri Criollo (RC) is a heritage cattle biotype introduced to the U.S. Southwest from the Sierra Madre region of the Copper Canyon of Chihuahua, Mexico. These cattle have been raised by the Tarahumara communities for approximately five centuries with minimal artificial selection or crossbreeding. Research conducted at the USDA-ARS Jornada Experimental Range (JER) in the Chihuahuan Desert has demonstrated the phenotypic plasticity and adaptation of RC cattle to the harsh ecological and climatic conditions of southwestern rangelands. Additionally, genomic studies have shown that the RC cattle constitute a distinct genetic pool within the Criollo cattle biotypes. The objective of this study was to further characterize the genetic diversity of the RC biotype by identifying selection signatures potentially associated with valuable adaptation and performance traits. Ear tissue samples were collected from 152 animals and genotyped using a ~64K SNP Chip (Genetic Visions-STTM). Genotype quality control and relatedness test were conducted using PLINK v2.0, resulting in the retention of 53,752 SNPs and 90 animals. Selection signatures were identified using three methods: Tajima’s D statistics, Runs of Homozygosity, and integrated Haplotype Score. Only SNPs identified by at least two methods were considered under positive selection. Candidate regions were defined as those located within ± 250 kb of each candidate SNP. Genes were annotated using the BovineMine Database v1.6, with coordinates based on the ARS-UCD1.2 genome assembly. Quantitative Trait Loci (QTL) annotation and enrichment analysis were performed using the R package GALLO v1.1, with annotations derived from the Animal Genome cattle QTL database. In total, 42 SNPs spanning 7 chromosomes (1, 2, 6, 7, 13, 18, and 22) were detected. Gene annotation identified 89 candidate genes associated with a wide range of traits, including milk yield and composition, growth, meat and carcass, reproduction, metabolic homeostasis, health, and coat color. A total of 517 QTL were annotated within the candidate regions. The two most frequent QTL types were associated with ‘milk’ and ‘meat and carcass’, while ‘reproduction’, ‘production’, ‘exterior (morphology)’ and ‘health’ were less frequently identified. Enrichment analysis revealed that the most significantly enriched traits included tenderness score, shear force, milk casein content, milk mineral content, and birth index, among others. These findings should be further supported by additional genome-wide association studies, transcriptome profiling, fine mapping, and other analyses. The identification of selection signatures in RC cattle support the adaptation of these cattle to the harsh climatic and nutritional conditions of the southwestern US while retaining desirable levels of production, reproductive and maternal attributes.