Browsing by Author "Hämäläinen, Aurora"

The traditional method of estimating inbreeding is based on pedigree information, which only considers the known common ancestors of the animals. In recent years, the animal breeding sector has introduced new genomic tools in breeding schemes. The aim of this study was to estimate and compare the level of inbreeding in Finnish Yorkshire and Finnish Landrace pigs using pedigree and genomic methods. Data consisted of pedigree and genotype information from both breeds. In pedigree data there were 503 315 Landrace and 549 296 Yorkshire animals after pruning for pedigree completeness and errors in the data. In the genotype data, there were 522 individuals of Landrace and 934 individuals of Yorkshire animals after pruning. Inbreeding coefficients (FPED) were estimated from pedigree data using RelaX2 program and for genomic data using PLINK by detecting runs of homozygosity (FROH). Percentage of homozygosity (FPH) was also studied from genomic data. Yearly rate of inbreeding based on pedigree raised steadily. Average inbreeding coefficients from year 2014 were 0.10 for Landrace and 0.15 for Yorkshire. The average inbreeding coefficient based on ROHs for animals born in year 2014 were 0.21 for Landrace and 0.25 for Yorkshire animals. Correlation between pedigree-based estimate and genomic-based FROH was found to be quite low for both breeds; 0.51 for Landrace and 0.58 for Yorkshire. The correlation between the two genomic based methods FROH and FPH was high, 0.86 for Landrace and 0.89 for Yorkshire. The level of inbreeding was found to be quite high in both breeds. The genomic-based estimates were higher overall than pedigree-based estimates, which indicates that pedigree data are missing some common ancestors. Based on the results, the level of inbreeding in Finnish pig breeds should be monitored to maintain sufficient genetic diversity in the populations.