Evaluation of pedigree structure, inbreeding levels, and inbreeding depression in reproduction traits in two Polish Złotnicka native pig breeds

This study aimed to assess the pedigree structure, estimate the level of inbreeding, and determine its impact on reproductive traits in two native Polish pig breeds covered by genetic resource conservation programs: Złotnicka White (ZW) and Złotnicka Spotted (ZS). The inbreeding coefficient was estimated using the classical Wright’s method and, for the first time, in those breeds, the modified VanRaden’s method, which accounts for incomplete pedigree information. The analysis included pedigree data collected between 1953 and 2021 for 6,126 ZW and 5,934 ZS individuals. The average inbreeding coefficients for the ZW breed were 9.97% (Wright) and 26.34% (VanRaden), whereas those for the ZS breed were 9.38% and 21.3%, respectively. In the ZS population, a substantial increase in inbreeding per generation was observed, exceeding the recommended threshold of 1%; i.e. 1.47% using Wright’s method and 1.25% using VanRaden’s method. Effective population size estimates indicated a risk of reduced genetic diversity, particularly according to VanRaden’s method. Further analysis of reproductive traits did not confirm clear or consistent effects of inbreeding depression. In ZW sows, statistically significant but irregular differences were found between inbreeding classes, whereas in ZS pigs, no significant effects were found. Those results should be interpreted with caution, given the incomplete pedigree information available for part of the population. Overall, the effect of inbreeding on the number of piglets born alive and surviving to 21 days was weak and of limited biological relevance. The results emphasise the need for intensified measures to control the increase in inbreeding and to maintain genetic diversity in these native pig populations.