Genomic Analysis Revealed Hotspots of Genetic Adaptation and Risk of Disappearance in Brazilian Goat Populations

The conservation of genetic resources is crucial for maintaining biological diversity and ensuring the sustainability of animal production. Characterizing regions of homozygosity (ROHs), heterozygosity-rich regions (HRRs), and levels of inbreeding is crucial for the management and conservation of livestock populations. In Brazil, little is known about these genomic parameters in Marota goats. Thus, this study aimed to evaluate these characteristics to support conservation strategies for these breeds.

Genomic analyses were conducted using the Illumina Goat SNP50 BeadChip to investigate ROH, HRR, and to estimate the inbreeding coefficient derived from ROHs (F_ROH) in Marota and Anglo-Nubian goats. This study evaluated 192 individuals from three distinct herds. ROHs were classified according to their length; genes located within both ROH and HRR regions were identified and functionally annotated to explore their potential biological significance.

Genomic analysis identified a total of 22,872 ROHs in the studied goats. The average number of ROHs per individual varied between breeds, with Anglo-Nubian goats exhibiting an average of 74.73 ROHs, while Marota goats had an average of 173.85 ROHs. Inbreeding coefficients based on ROHs in Marota goats varied widely (0.040-0.283), reflecting recent reductions in effective population size. Functional annotation revealed that several genes with overlapping ROH and HRR islands, such as ZBTB11, IL18, and LPO, were significantly enriched in immune-related pathways. Additionally, candidate genes associated with adaptive traits, such as TEX12, YPEL5, CAPN14, and GALNT14, were identified and were linked to embryonic development, body growth, lipid metabolism, and brain function.

The ROHs and HRRs analyses in Marota and Anglo-Nubian goats revealed distinct patterns of genomic inbreeding and potential adaptive genetic regions. These findings emphasize the genetic distinctiveness of the Marota breed and underscore the importance of incorporating genomic data into conservation planning. The identification of candidate genes in islands with ROHs and HRRs provides valuable insights for guiding conservation priorities and managing genetic diversity in Brazilian goat populations.