Characterization of heterozygosity-rich regions in Italian and worldwide goat breeds

Abstract

Heterozygosity-rich regions (HRR) are genomic regions of high heterozygosity, which may harbor loci related to key functional traits such as immune response, survival rate, fertility, and other fitness traits. This study considered 30 Italian and 19 worldwide goat breeds genotyped with the Illumina GoatSNP50k BeadChip. The aim of the work was to study inter-breed relationships and HRR patterns using Sliding Window (SW) and Consecutive Runs (CR) detection methods. Genetic relationships highlighted a clear separation between non-European and European breeds, as well as the north-south geographic cline within the latter. The Pearson correlation coefficients between the descriptive HRR parameters obtained with the SW and CR methods were higher than 0.9. A total of 166 HRR islands were detected. CHI1, CHI11, CHI12 and CHI18 were the chromosomes harboring the highest number of HRR islands. The genes annotated in the islands were linked to various factors such as productive, reproductive, immune, and environmental adaptation mechanisms. Notably, the Montecristo feral goat showed the highest number of HRR islands despite the high level of inbreeding, underlining potential balancing selection events characterizing its evolutionary history. Identifying a species-specific HRR pattern could provide a clearer view of the mechanisms regulating the genome modelling following anthropogenic selection combined with environmental interaction.

Figure 1

Multidimensional scaling (MDS) plot according to C1 (29.88%) and C2 (11.25%) components. The geographical clusters are represented by different shades of a color. See Table 1 for a full definition of the dataset.

Figure 2

Boxplots of the Heterozigosity-rich regions (HRR) indices aggregated by geographic area. (a) N_HRR = average number of HRR per breed, (b) L_HRR = average length of HRR per breed (in Mbp), (c) S_HRR = mean genome length covered by HRR segments (in Mbp), (d) D_HRR = average coefficient of diversity. The different colors indicate the two approaches, CR (blue) and SW (light blue). Each boxplot extends from the 25th to the 75th percentile and shows the average (red dashed line) and the median (black horizontal line) group value. The black dots represent the single-breed results.

Figure 3

Graphical distribution of Heterozigosity-Rich Regions (HRR) islands per chromosome. Detected HRR in the meta-population (a) and per breed (b). The gap between consecutive islands within a chromosome and between consecutive chromosomes do not correspond to the real distance in bps.