ABSTRACT. Knowledge of population structure, genetic variability and introgression of foreign breeds is crucial to focus efforts for the conservation of indigenous genetic resources. This study aimed to analyze the genetic diversity of six Casanareño populations cattle using 11 microsatellite markers. Blood samples were obtained from 212 unrelated individuals which were amplified by PCR and analyzed. We observed a total of 156 alleles with a polymorphic information content average of 0.742, which shows that the panel used was very informative. The observed heterozygosity estimates varied from 0.788 in MF to 0.690 in CY. There was a deficit of heterozygous individuals in the general population (F IS = 0.059) caused by high consanguinity and the proportion of the genetic variance due to the differences between the different subpopulations was 4%. Both the Bayesian grouping analysis and the phylogenetic tree showed a reliable clustering pattern, which revealed two main clusters in Casanareño cattle which can be the result of geographical isolation, reproductive practices and absorption to zebu breeds. Four out of six subpopulations presented effective population sizes below the critical level defined by the FAO of 50 individuals, so it is recommended to form a conservation nucleus of the Casanareño breed with a well-defined mating scheme to minimize consanguinity and the intensive use of few males to maintain genetic diversity and prevent the breed from becoming extinct.

RESUMEN. El conocimiento de la estructura poblacional, la variabilidad genética y la introgresión de razas foráneas es crucial para enfocar esfuerzos para la conservación de los recursos genéticos autóctonos. Este estudio tuvo por objetivo analizar la diversidad genética de una población de bovinos Casanareño de seis sitios en Colombia usando 11 marcadores microsatélites. Se obtuvieron muestras de sangre de 212 individuos no emparentados las cuales fueron amplificadas por PCR y analizadas. Se observaron 156 alelos con contenido de información polimórfica promedio de 0.742, lo que demuestra que el panel utilizado fue informativo. Las estimaciones de la heterocigosidad observada variaron de 0.788 en MF a 0.690 en CY. Se presentó un déficit de individuos heterocigotos en la población general (F IS = 0.059) causado por la alta consanguinidad y la proporción de la varianza genética debida a diferencias entre las distintas subpoblaciones fue del 4%. Tanto el análisis de agrupamiento bayesiano como el árbol filogenético mostraron un patrón de agrupamiento similar, que reveló dos clústeres principales en los bovinos Casanareño el cual puede ser resultado del aislamiento geográfico, prácticas reproductivas y la absorción hacia razas cebuinas. Cuatro de seis subpoblaciones presentaron tamaños efectivos poblacionales inferiores al nivel crítico definido por la FAO de 50 individuos por lo que se recomienda conformar un núcleo de conservación de la raza Casanareño con un esquema de apareamiento bien definido para minimizar la consanguinidad y el uso intensivo de pocos machos para mantener la diversidad genética y evitar que la raza se extinga.

Abstract The linkage disequilibrium (LD) between molecular markers affects the accuracy of genome-wide association studies and genomic selection application. High-density genotyping platforms allow identifying the genotype of thousands of single nucleotide polymorphisms (SNPs) distributed throughout the animal genomes, which increases the resolution of LD evaluations. This study evaluated the distribution of minor allele frequencies (MAF) and the level of LD in the Colombian Creole cattle breeds Blanco Orejinegro (BON) and Romosinuano (ROMO) using a medium density SNP panel (BovineSNP50K_v2). The LD decay in these breeds was lower than those reported for other taurine breeds, achieving optimal LD values (r2 ≥ 0.3) up to a distance of 70 kb in BON and 100 kb in ROMO, which is possibly associated with the conservation status of these cattle populations and their effective population size. The average MAF for both breeds was 0.27 ± 0.14 with a higher SNP proportion having high MAF values (≥ 0.3). The LD levels and distribution of allele frequencies found in this study suggest that it is possible to have adequate coverage throughout the genome of these breeds using the BovineSNP50K_v2, capturing the effect of most QTL related with productive traits, and ensuring an adequate prediction capacity in genomic analysis.