Analysis of genetic variability and population structure of the Mangalica pig breed using pedigree data

Abstract

The maintenance of genetic diversity (GD) and low rate of inbreeding are two main goals for any conservation programs, especially in a small, closed population which is likely to violate these conservation targets in a long run. Among the conservation programs in Hungary probably the most characterizing is that of the Mangalica pigs, which is an autochthonous Hungarian pig breed group that has been preserved for biological diversity since 1973. The current study aimed to expose the evolution of population structure, GD and inbreeding coefficient with different approaches by analysing the pedigree of these breeds in the context of the conservation program. Genealogy analysis used the data of 12,808, 2393 and 3963 Blonde, Swallow-Belly and Red breeding animals born between 1980 and 2021, respectively. The reference populations (REF2021) were defined as breeding animals born between 2016 and 2021. Pedigree completeness was more than 90% in the fifth generation and the complete generation equivalent ranged from 4.29 to 7.08 and from 6.87 to 9.73 for the whole and the reference populations (REF2021), respectively. Generation interval on average was vary from 3.06 to 3.45 years with the longer pathways to the son. Most of different estimated inbreeding coefficient showed increased trends through pedigrees except for the Kalinowski new inbreeding coefficient (FNew) which decreased in all breeds in the last decade. The mean Wright inbreeding coefficient (Fw) was low, being 5.50%, 4.30% and 7.54% for the Blonde, Swallow-Belly, and Red reference populations (REF2021), respectively. Fw showed strong correlation with FNew but low correlation with FBal while the two types of ancestral inbreeding coefficients (FBal and FKal) were ranging from moderate strong to strong correlation in every breed. Effective population size of the reference populations (REF2021) was 85.57, 76.91, and 57.56, respectively. Based on the predicted future inbreeding for the next 25 years only the Red Mangalica breed was predicted to be “Transitional” in the endangerment categories. The GD loss in these three breeds was 5.6%, 5.7% and 8.7%, respectively, in which the loss due to genetic drift was decisive compared to the unequal founder contributions. In conclusion, the three populations at the present and in the next few generations are having optimistic perspective in terms of GD. These populations should be focused on reducing new inbreeding in mating plans and the Red population need to be monitored more carefully because of its current highest GD loss, smallest effective population size and highest inbreeding coefficient.