Genomic variability and population structure of six Colombian cattle breeds

Tropical Animal Health and Production (2023) 55:185 https://doi.org/10.1007/s11250-023-03574-8 REGULAR ARTICLES Genomic variability and population structure of six Colombian cattle breeds Rodrigo Martinez1 · Diego Bejarano1 · Julián Ramírez1 · Ricardo Ocampo1 Juan Esteban Perez1 · Héctor Guillermo Onofre1 · Juan Felipe Rocha1 · Nelson Polanco1 · Received: 3 September 2022 / Accepted: 29 March 2023 © The Author(s) 2023 Abstract Analyses of the genetic diversity of indigenous cattle are essential for implementing conservation programs, promoting their sustainable use and maintaining productive advantages offered by these breeds in local conditions. The aim of this study was to investigate the genetic diversity and population structure of six Colombian cattle breeds: Blanco Orejinegro (BON), Costeño con Cuernos (CCC), Romosinuano (ROM), Sanmartinero (SAM), Casanareño (CAS), and Hartón del Valle (HDV). Two additional breed groups were included for comparison: Zebu (CEB) and a crossbreed of Colombian cattle breeds × Zebu. Genetic diversity within breeds was analyzed using expected heterozygosity (He), inbreeding coefficient (f), and runs of homozygosity (ROH). Population structure was assessed using model-based clustering (ADMIXTURE) and principal components analysis (PCA). Zebu cattle showed the lowest genetic diversity (He = 0.240). Breeds with the highest genetic diversity level were HDV and BON (He = 0.350 and 0.340, respectively). Inbreeding was lower for Colombian cattle breeds ranging between 0.005 and 0.045. Overall, the largest average genetic distance was found among the group of Colombian cattle breeds and Zebu, while the smallest was found between ROM and CCC. Model-based clustering revealed some level of admixture among HDV and CAS cattle which is consistent with their recent history. The results of the present study provide a useful insight on the genetic structure of Colombian cattle breeds. Keywords Admixture · Beadchip · Bovine · Genetic variability · SNP Introduction Modern cattle descend from independently domesticated lineages of Taurine and Indicine cattle, which diverged more than 200,000 years ago, with numerous breeds having hybrid ancestry between these different lineages (Murray et al. 2010). Regarding Indicine cattle, Colombia has one of the biggest Zebu populations in the world. These animals have been used in crossbreeding mating systems with Colombian creole cattle, which were originally brought to America by the Spaniards five centuries ago (Martinez et al. 2012). Population structure analysis and breed diversity have provided insight into the origin and evolution of these cattle (Ocampo et al. 2021a, b), and the genetic structure in Colombian breeds such as Blanco Orejinegro (BON) (Martinez et al. 2013) by using * Ricardo Ocampo 1 Corporación Colombiana de Investigación Agropecuaria – Agrosavia, Mosquera, Cundinamarca, Colombia low-density panels of microsatellite markers. However, thousands of single nucleotide polymorphisms (SNP) evenly distributed along the genome are currently available to perform genome-wide population analyses in livestock populations (Decker et al. 2014). SNP genotyping has become an important tool for animal breeding, with different methods available to identify population stratification. These new genotyping techniques offer the possibility to perform thorough assessments of the genetic structure and the relationships between cattle populations. This improves previous population genetic parameter reports like the fixation index (FST) or inbreeding coefficients, usually estimated from just few genetic markers (Corbin et al. 2012). FST is a fixation index that evaluates genetic diversity of animal populations and allows determining the relative genetic distance between these populations (Brito et al. 2017). It is estimated from allele frequencies and their variance, and it has also been used to identify loci under selection (Flori et al. 2009). Inbreeding coefficients on the other hand, which have been calculated from 13 Vol.:(0123456789) 185 Page 2 of 8 pedigree records, are now estimated along with coancestry coefficients by using high-density SNP arrays. Genome-wide estimates of these parameters have higher accuracy as they represent the actual genome percentage that is homozygous (inbreeding) or the actual genome percentage shared by two individuals (coancestry), while pedigree-based estimates are only expectations of such percentages. Moreover, genomewide estimates can include relationships due to very distant common ancestors, which are not captured by pedigreebased estimates (Cortes et al. 2019). These population parameters are useful to implement different genome wide evaluation studies (Cortes et al. 2019). Genomic selection causes a larger reduction in inbreeding rates per generation than traditional pedigree best linear unbiased prediction (BLUP) selection; however, it is not inbreeding free. Therefore, measuring and controlling inbreeding is necessary (Ocampo et al. 2019). Consequently, the understanding of the genetic structure across populations is important to achieve genetic progress by using genomewide association studies and genomic selection strategies (Kijas et al. 2009). Furthermore, genetic diversity and population structure studies among cattle breeds are essential for genetic improvement and for the understanding of their adaptation and the use and conservation of these animal resources (Ocampo et al. 2021a, b). Considering this, the aim of this study was to investigate the genetic diversity and population structure within and among seven Colombian cattle breeds using the BovineSNP50 BeadChip to explore the inclusion of these cattle populations in future genomic selection programs. Materials and methods Population This study included a total of 2182 individuals of Blanco Orejinegro (BON, n = 658), Romosinuano (ROM, n = 569), Costeño con Cuernos (CCC, n = 464), San Martinero (SAM, n = 293), Casanareño (CAS, n = 50), and Hartón del Valle (HDV, n = 34). These animals belong to the Sistema de Bancos de Germoplasma de la Nación para la Alimentación y la Agricultura (SBGNAA; System of National Germplasm Banks for Food and Agriculture of Colombia), which the Colombian Corporation for Agricultural Research (AGROSAVIA) guard and manage. A mating strategy (Nomura and Yonezawa 1996) has been implemented to control inbreeding in these creole cattle populations kept in situ. It involves the splitting of breed groups into several families, with mating males being moved periodically to neighboring families in a circular pattern. Data from the purebred Zebu (CEB, n = 34) and the crossbred populations BON × Zebu 13 Tropical Animal Health and Production (2023) 55:185 (n = 61) and ROM × Zebu (n = 19) were obtained from commercial herds. Creole cattle populations were located in research centers of AGROSAVIA across the country. There was no need to apply for approval from the Animal Care and Us (...truncated)