Characterization of experimental cattle populations from Argentina with a low‐density SNP genotyping panel

Abstract

Resources project (IMAGE; https://www.image h2020. eu/) was funded by the European Union to develop tools for the characterization of animal genetic resources. One of the objectives of the project was the development of a multi-species 60 K SNP array that would be accessible at low cost to capture biodiversity and particularly for the molecular characterisation of gene banks. The developed IMAGE001 array has 10 K SNP for cattle (see more information in Additional File 1

Genomic analysis of inbreeding level, kinship and breed relationships in Creole cattle from South America

“…Furthermore, the loss of population purity by gene introgression could affect the local fitness (outbreeding depression) of these valuable genetic resources. However, the present analysis shows that the studied populations still exhibit levels of genetic diversity (H E and H O ranging between 0.352 and 0.462), comparable with those reported for other cattle breeds (e.g., Cañas-Álvarez et al, 2015;Kawaguchi et al, 2022;McTavish et al, 2013;Michiels et al, 2023;Saravanan et al, 2022). In agreement with these relatively high values of genetic diversity, the Creole cattle populations showed low average inbreeding levels measured through two methods.…”

“…High genetic similarity to notat-risk breeds indicates low distinctiveness and thus diminishes the conservation of a conthat economic resources are usually limited. In this work, we addressed this issue through PCA and analyses, showing that the extreme position of CrAr in PC2 agrees with data reported by Michiels et al (2023) using low density microarrays. However, this contrasts with previous results based on microsatellite data showing that the Argentine and Bolivian Creole populations are located at an intermediate position (Lirón, Bravi, et al, 2006;.…”

“…On the contrary, Bolivia Creole cattle from the highland plain evidenced introgression with Ho, which could be explained by the introduction of this breed to improve dairy production during the last decade. Also, in agreement with Michiels et al (2023), CrAr appeared as a highly differentiated genetic pool when the K-value increased (K3), probably because of the routes of colonization of South America (Martínez et al, 2012).…”

“…In recent years, Creole cattle studies have migrated to genomic analysis, mainly using low-and medium-density single nucleotide polymorphism (SNP) microarrays (Campos et al, 2017;Corredor et al, 2023). In this sense, Falomir-Lockhart et al (2019) studied the origin of the polled mutation in Argentine Creole cattle, and other works described the genetic diversity and genetic structure of Argentine Creole cattle and explored their relationship with Creole cattle from other Latin American countries (McTavish et al, 2013;Michiels et al, 2023;Raschia & Poli, 2021). This genomic approach has improved the precision of studies conducted with microsatellites and uniparental markers by carrying out analysis of breed composition and gene introgression as well as breed and individual relationships.…”

“…The conservation of animal genetic resources refers to measures taken to prevent the loss of genetic diversity in livestock populations, including the protection of breeds from extinction (FAO, 2007). Several countries, such as Argentina, Bolivia and Brazil, have established conservation plans to preserve Creole populations (da Silva Mariante, 1990a, 1990bMichiels et al, 2023). These plans are fundamental because endangered native populations are naturally adapted to the local environment and contribute a high proportion of the species genetic diversity.…”