Using Pedigree and Genomic Data toward Better Management of Inbreeding in Italian Dairy Sheep and Goat Breeds

SIMPLE SUMMARY: The inbreeding coefficient is relevant for managing livestock and safeguarding biodiversity, especially in small populations. Small ruminant breeders mainly rely on pedigree information, but genomics is increasingly gaining ground as a tool to face possible pedigree inaccuracies. This study investigates pedigree-based (F(PED)) and genomic (F(ROH) and F(GRM)) inbreeding in a representative number of Italian sheep and goat populations. Indeed, even though it has been widely studied in cattle, there is still little knowledge about the relationship between these coefficients in small ruminants, which are characterized by a different population structure, often with unconnected farms. Mean inbreeding values were low, F(ROH) being the highest, with breed differences due to different managements; the correlation between F(PED) and F(ROH) was the strongest and directly related to pedigree depth. Moreover, we estimated F(PED) from F(ROH) using a linear regression model. Since massive genotyping is not affordable to small ruminant breeders, it is important to understand the distinction and relationship between differently calculated inbreeding coefficients, also in view of the introduction of genomic enhanced breeding values. Our study highlights the importance of accurate pedigree information and, especially if not obtainable, of genotyping animals. Correct data contribute to mitigate inbreeding depression and loss of genetic variability. ABSTRACT: The inbreeding coefficient is an important parameter for livestock management. Small ruminant breeders and associations mainly rely on pedigree information, but genomic tools are gaining relevance, overcoming possible pedigree inconsistencies. This study investigates the relationship between pedigree-based and genomic inbreeding in two goat and four sheep dairy breeds. Pedigree and genomic data (medium-density SNPchip) were obtained for 3107 goats and 2511 sheep. We estimated pedigree depth (number of fully traced generations, FullGen) and inbreeding (F(PED)), as well as two genomic inbreeding indexes, using runs of the homozygosity (F(ROH)) and genomic relationship matrix (F(GRM)). The correlation between the inbreeding coefficients was assessed. A linear regression model (LRM) was fitted for estimating F(PED) from F(ROH). After quality control on genomic data, we retained 5085 animals. Mean inbreeding values were low, with higher F(ROH) than F(PED) and F(GRM). Breed differences can partially depend on different managements. The correlation between F(PED) and F(ROH) was the highest and directly related to pedigree depth. The best LRM was chosen for FullGen ≥4 and ≥6 for goats and sheep, respectively; after excluding animals with extreme residuals, a new refined regression equation was calculated. Since massive genotyping is not affordable to small ruminant breeders, it is important to understand the distinction and relationship between differently calculated inbreeding coefficients, also in view of the introduction of genomic enhanced breeding values. Our study highlights the importance of accurate pedigree information and, especially if not obtainable, of calculating genomic-based inbreeding coefficients. A better estimation of animals’ relatedness contributes to improve animal breeding and conservation.