Genetic Diversity, Admixture, and Selection Signatures in a Rarámuri Criollo Cattle Population Introduced to the Southwestern United States

Spetter, Maximiliano J.; Utsumi, Santiago A.; Armstrong, Eileen M.; Rodríguez Almeida, Felipe A.; Ross, Pablo J.; Macon, Lara; Jara, Eugenio; Cox, Andrew; Perea, Andrés R.; Funk, Micah; Redd, Matthew; Cibils, Andrés F.; Spiegal, Sheri A.; Estell, Richard E.

doi:10.3390/ijms26104649

Open AccessArticle

Genetic Diversity, Admixture, and Selection Signatures in a Rarámuri Criollo Cattle Population Introduced to the Southwestern United States

by

Maximiliano J. Spetter

^1,*

,

Santiago A. Utsumi

¹

,

Eileen M. Armstrong

²

,

Felipe A. Rodríguez Almeida

³

,

Pablo J. Ross

⁴,

Lara Macon

⁵

,

Eugenio Jara

²,

Andrew Cox

¹,

Andrés R. Perea

¹

,

Micah Funk

¹,

Matthew Redd

⁶,

Andrés F. Cibils

⁷

,

Sheri A. Spiegal

⁵ and

Richard E. Estell

^5,*

¹

Department of Animal and Range Sciences, New Mexico State University, Las Cruces, NM 88003, USA

²

Unidad de Genética y Mejora Animal, Departamento de Producción Animal, Facultad de Veterinaria, Universidad de la República, Montevideo 10129, Uruguay

³

Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Chihuahua 31453, Mexico

⁴

Inguran LLC Dba STgenetics, Navasota, TX 77868, USA

⁵

USDA Agricultural Research Service Jornada Experimental Range, Las Cruces, NM 88003, USA

⁶

Dugout Ranch/Canyonlands Research Center, The Nature Conservancy, Monticello, UT 84535, USA

⁷

USDA Southern Plains Climate Hub, Oklahoma and Central Plains Agricultural Research Center, El Reno, OK 73036, USA

^*

Authors to whom correspondence should be addressed.

Int. J. Mol. Sci. 2025, 26(10), 4649; https://doi.org/10.3390/ijms26104649

Submission received: 28 March 2025 / Revised: 3 May 2025 / Accepted: 10 May 2025 / Published: 13 May 2025

(This article belongs to the Special Issue Molecular Genetics and Genomics of Ruminants)

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Abstract

Rarámuri Criollo (RC) cattle have been raised by the isolated Tarahumara communities of Chihuahua, Mexico, for nearly 500 years, mostly under natural selection and minimal management. RC cattle were introduced to the United States Department of Agriculture-Agricultural Research Service Jornada Experimental Range (RCJER) in 2005 to begin evaluations of beef production performance and their adaptation to the harsh ecological and climatic conditions of the Northern Chihuahuan Desert. While this research unveiled crucial information on their phenotypic plasticity and adaptation, the genetic diversity and structure of the RCJER population remains poorly understood. This study analyzed the genetic diversity, population structure, ancestral composition, and selection signatures of the RCJER herd using a ~64 K SNP array. The RCJER herd exhibits moderate genetic diversity and low population stratification with no evident clustering, suggesting a shared genetic background among different subfamilies. Admixture analysis revealed the RCJER herd represents a distinctive genetic pool within the Criollo cattle breeds, with significant Iberian ancestry. Selection signatures identified candidate genes and quantitative trait loci (QTL) for traits associated with milk composition, growth, meat and carcass, reproduction, metabolic homeostasis, health, and coat color. The RCJER population represents a distinctive genetic resource adapted to harsh environmental conditions while maintaining productive and reproductive attributes. These findings are crucial to ensuring the long-term genetic conservation of the RCJER and their strategic expansion into locally adapted beef production systems in the USA.

Keywords: Creole cattle; heritage genetics; single nucleotide polymorphisms; population structure; positive selection

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MDPI and ACS Style

Spetter, M.J.; Utsumi, S.A.; Armstrong, E.M.; Rodríguez Almeida, F.A.; Ross, P.J.; Macon, L.; Jara, E.; Cox, A.; Perea, A.R.; Funk, M.; et al. Genetic Diversity, Admixture, and Selection Signatures in a Rarámuri Criollo Cattle Population Introduced to the Southwestern United States. Int. J. Mol. Sci. 2025, 26, 4649. https://doi.org/10.3390/ijms26104649

AMA Style

Spetter MJ, Utsumi SA, Armstrong EM, Rodríguez Almeida FA, Ross PJ, Macon L, Jara E, Cox A, Perea AR, Funk M, et al. Genetic Diversity, Admixture, and Selection Signatures in a Rarámuri Criollo Cattle Population Introduced to the Southwestern United States. International Journal of Molecular Sciences. 2025; 26(10):4649. https://doi.org/10.3390/ijms26104649

Chicago/Turabian Style

Spetter, Maximiliano J., Santiago A. Utsumi, Eileen M. Armstrong, Felipe A. Rodríguez Almeida, Pablo J. Ross, Lara Macon, Eugenio Jara, Andrew Cox, Andrés R. Perea, Micah Funk, and et al. 2025. "Genetic Diversity, Admixture, and Selection Signatures in a Rarámuri Criollo Cattle Population Introduced to the Southwestern United States" International Journal of Molecular Sciences 26, no. 10: 4649. https://doi.org/10.3390/ijms26104649

APA Style

Spetter, M. J., Utsumi, S. A., Armstrong, E. M., Rodríguez Almeida, F. A., Ross, P. J., Macon, L., Jara, E., Cox, A., Perea, A. R., Funk, M., Redd, M., Cibils, A. F., Spiegal, S. A., & Estell, R. E. (2025). Genetic Diversity, Admixture, and Selection Signatures in a Rarámuri Criollo Cattle Population Introduced to the Southwestern United States. International Journal of Molecular Sciences, 26(10), 4649. https://doi.org/10.3390/ijms26104649

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Genetic Diversity, Admixture, and Selection Signatures in a Rarámuri Criollo Cattle Population Introduced to the Southwestern United States

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