International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.3, 134-143 http://ecoevopublisher.com/index.php/ijmec 139 were absent in farm goats but still visible in wild relatives (Li et al., 2023b). Such deletions mostly involve genes related to behavior or reproduction, suggesting the "pruning" of genes during the domestication process. Regional differences are equally distinct: African goats are more likely to carry antiparasitic and heat-tolerant alleles, while East Asian goats are rich in variations that determine coat color and body size (Britol et al., 2017; Bao et al., 2019; Nanaei et al., 2023). Many loci related to domestication are common in farmed populations but rare in wild populations, and this pattern conforms to the characteristics of rapid selection (Dai et al., 2023). More notably, similar changes have occurred in the growth and reproductive pathways of goats and sheep, reflecting parallel evolution under livestock pressure (Yang et al., 2024). Figure 2 Adaptive immune mechanisms in goats (Adopted from Lu et al., 2025) Image caption: Abbreviations in the figure: TLRs-toll-like receptors, NLR-NOD-like receptors, ROS-reactive oxygen species, iNOS-inducible nitric oxide synthase, IL-interleukin, TNF-α-tumor necrosis factor-α, MyD88-myeloid differentiation primary response protein 88 (Adopted fromLu et al., 2025) 6 The Application of the Pan-genome in the Research of Goat Evolution and Domestication 6.1 The contribution of genomic structural changes during domestication events Goat domestication was accompanied by significant genomic structural remodeling, and the pan-genome revealed its important role in domesticated traits (Li et al., 2023b). Domestic groups lost some genes related to sensation, stress and social interaction, reduced alertness and aggression, and showed a negative selection of wildness and reproductive cycle. Some structural variations directly shape the phenotype. For instance, a deletion of approximately 12 kb leads to a hornless trait, which, although accompanied by recessive defects, is fixed due to its advantage in breeding. Gene infiltration also provides an additional source of variation for domestication. Some body type and coat color genes may originate from hybridization with wild ibex (Dai et al., 2023). For example, the genes of the Caucasian ibex enhance cold resistance, and the genes of the Markhor sheep enhance the ability to tolerate poor soil feed (Bao et al., 2019). The pan-genome thus becomes an important tool for analyzing the genetic mechanism of the domestication process. 6.2 Reassessment of genetic diversity and breeding potential With only a few genetic markers, the diversity of goats is often not fully observed. The introduction of the pan-genome can incorporate multiple types of DNA variations into the analysis together. Minor changes like SNPS are easier to detect, and larger structural differences are also clearer. The available marker set was expanded, and the success rate of genome selection increased accordingly (Li et al., 2023b). It is also possible to locate population-specific genes missing in the reference genome, such as genes related to disease resistance or heat tolerance in African and South Asian goats (Sasazaki et al., 2021), bringing new materials for breeding.
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