A comparative analysis of SLA-DRB1 genetic diversity in Colombian (creoles and commercial line) and worldwide swine populations

Analysing pig class II mayor histocompatibility complex (MHC) molecules is mainly related to antigen presentation. Identifying frequently-occurring alleles in pig populations is an important aspect to be considered when developing peptide-based vaccines. Colombian creole pig populations have had to adapt to local conditions since entering Colombia; a recent census has shown low amounts of pigs which is why they are considered protected by the Colombian government. Commercial hybrids are more attractive regarding production. This research has been aimed at describing the allele distribution of Colombian pigs from diverse genetic backgrounds and comparing Colombian SLA-DRB1 locus diversity to that of internationally reported populations. Twenty SLA-DRB1 alleles were identified in the six populations analysed here using sequence-based typing. The amount of alleles ranged from six (Manta and Casco Mula) to nine (San Pedreño). Only one allele (01:02) having > 5% frequency was shared by all three commercial line populations. Allele 02:01:01 was shared by five populations (around > 5% frequency). Global FST indicated that pig populations were clearly structured, as 20.6% of total allele frequency variation was explained by differences between populations (FST = 0.206). This study’s results confirmed that the greatest diversity occurred in wild boars, thereby contrasting with low diversity in domestic pig populations.This work was supported by the Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A)

Análisis de diversidad genética en cerdo criollo san pedreño utilizando datos de pedigrí

Colombia has three indigenous swine breeds (San Pedreño, Zungo and Casco de Mula), which are in the country approximately 500 years ago and are at risk of disappearing due to their reduced populations and the preferential use of improved foreign breeds in the production systems. In order to preserve the indigenous breeds, germplasm banks were created, whose populations have been maintained as closed nucleus. The objective of this study was to perform a pedigree analysis to characterize the genetic structure of the San Pedreño pig population of the germplasm bank. Genealogical information collected between 2008-2017 was analyzed to estimate the generational interval, pedigree completeness level, consanguinity and its evolution over time. The animals born between the years 2015 and 2017 were selected as the reference population to estimate the effective population size and parameters derived from the probability of gene origin. The average generational interval for the period studied was 2.13 years and the general consanguinity was 4.66%. For the reference population, the consanguinity was 6.73% and the effective population size was 25.31, while the effective number of founders and ancestors was 13 and 7 individuals, respectively, which has led to bottlenecks in the population. The results indicate that in order to maintain genetic variability and reduce inbreeding levels it is necessary to include unrelated individuals from other populations.Colombia cuenta con tres razas de cerdos criollos (San Pedreño, Zungo y Casco de Mula), los cuales se encuentran en el país hace 500 años aproximadamente y están en riesgo de desaparecer debido a sus reducidas poblaciones y al uso preferente de razas foráneas mejoradas en los sistemas de producción. Para conservar las razas criollas se crearon los bancos de germoplasma, cuyas poblaciones se han mantenido como núcleos cerrados. El objetivo del estudio fue realizar un análisis de pedigrí para caracterizar la estructura genética de la población de cerdos San Pedreño del banco de germoplasma. Información genealógica colectada entre 2008-2017 se analizó para estimar el intervalo generacional, nivel de integridad del pedigrí, consanguinidad y evolución a través del tiempo. Los animales nacidos entre 2015 y 2017 se seleccionaron como población de referencia para estimar el tamaño efectivo poblacional y parámetros derivados de la probabilidad del origen genético. El intervalo generacional promedio para el periodo estudiado fue de 2.13 años y la consanguinidad general de 4.66%. Para la población de referencia, la consanguinidad fue del 6.73% y el tamaño efectivo poblacional de 25.31, en tanto que el número efectivo de fundadores y ancestros fue de 13 y 7 individuos, respectivamente; lo que ha conllevado a cuellos de botella en la población. Los resultados indican que para mantener la variabilidad genética y reducir los niveles de consanguinidad es necesario incluir individuos no emparentados de otras poblaciones