Comparison of ancestral, partial, and genomic inbreeding in a local pig breed to achieve genetic diversity

Abstract

Inbreeding is omnipresent and unavoidable in population genetics. High levels of inbreeding result in a reduction of genetic diversity and inbreeding depression. The avoidance of inbreeding is a primary goal for the management of small populations and very important for the design of breeding programmes in order to create productive progeny. The objective of this study was investigate how to maintain genetic diversity in the progeny of 76 selection candidates of a local pig breed by identifying individual relatedness and different inbreeding coefficients. In addition, valuable comparisons of ancestral, partial, and genomic inbreeding were examined. The data-set included the pedigree of 1273 individuals born between 1980 and 2015 and genotypes of selection candidates born between 2004 and 2014. Classical, ancestral, and partial inbreeding coefficients were calculated based on pedigree information. Genomic coefficients were calculated by using four approaches: (I) variance of additive genetic values, (II) SNP homozygosity, (III) uniting gametes, and (IV) runs of homozygosity. Inbreeding levels of selection candidates were not high and just a few animals showed increased inbreeding coefficients. This result was in accordance with estimated relatedness among individuals. The lowest and highest pedigree inbreeding were estimated within partial (0.004–0.006) and ancestral concepts (0.024–0.090). Genomic inbreeding was low and showed an obvious difference between different genomic coefficients (0.000–0.012). Correlations between pedigree and genomic inbreeding coefficients ranged from − 0.44 to 0.57. Ballou’s concept of ancestral inbreeding was moderately correlated with genomic estimators of homozygosity (0.39), uniting gametes (0.24), and runs of homozygosity (0.49). Kalinowski’s concept of ancestral inbreeding was negatively correlated with genomic inbreeding measurements regarding the variance of additive genetic values (− 0.44) and uniting gametes (− 0.29). Correlations of partial inbreeding varied between 0.22 and 0.48, where Kalinowski’s concept of ‘new’ inbreeding was positively correlated with all genomic inbreeding coefficients (0.25–0.48). However, Lacy’s concept of partial inbreeding correlated positively with genomic inbreeding regarding homozygosity (0.26) and runs of homozygosity (0.22). Ancestral and partial inbreeding can have great importance concerning purging of deleterious alleles through individual mating to obtain genetic diversity especially for small populations. Inbreeding estimators based on ROH may represent ancestral and partial inbreeding concepts better than genomic coefficients of additive genetic values, SNP homozygosity, or uniting gametes.