Genomic Tools for the Characterization of Local Animal Genetic Resources: Application in Mascaruna Goat

Abstract

Italy contains a large number of local goat populations, some of which do not have a recognized genetic structure. The "Mascaruna" is a goat population reared for milk production in Sicily. In this study, a total of 72 individuals were genotyped with the Illumina Goat_IGGC_65K_v2 BeadChip with the aim to characterize the genetic diversity, population structure and relatedness with another 31 Italian goat populations. The results displayed a moderate level of genetic variability for Mascaruna, in concordance with the estimated values for Italian goats. Runs of homozygosity islands are linked to genes involved in milk production, immune response and local adaptation. Population structure analyses separated Mascaruna from the other goat populations, indicating a clear genetic differentiation. Although they are not conclusive, our current results represent a starting point for the creation of monitoring and conservation plans. Additional analyses and a wider sampling would contribute to refine and validate these results. Finally, our study describing the diversity and structure of Mascaruna confirms the usefulness of applied genomic analyses as valid tools for the study of the local uncharacterized genetic resources.

Keywords: genetic structure; local goat; single nucleotide polymorphisms.

Figure 1

Mascaruna goats.

Figure 2

Manhattan plot of the incidence of each SNP in the runs of homozygosity in Mascaruna goat. A threshold of 0.25 was chosen to detect the islands.

Figure 3

Multidimensional scaling analysis among 32 goat populations using the average coordinates of eigenvalues of C1 and C2. For the full definition of populations, see Table 1 (Mascaruna = MAS).

Figure 4

Multidimensional scaling analysis between Mascaruna and the southern goat populations. For full definition of the populations, see Table 1.

Figure 5

Neighbor-net graph based on Reynolds genetic distances among 32 goat populations. For the full definition of populations, see Table 1 (Mascaruna = MAS).

Figure 6

Population structure for 32 goat populations inferred from the ADMIXTURE analysis with K values from 2 through 8. For the full definition of populations, see Table 1 (Mascaruna = MAS).

Figure 7

TREEMIX analysis with the most supported number of migration events (m = 1). For the full definition of populations, see Table 1 (Mascaruna = MAS).