International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.3, 134-143 http://ecoevopublisher.com/index.php/ijmec 135 and domesticated species can be comprehensively analyzed to reveal the phylogenetic sources and effects of genomic variations during domestication (Bao et al., 2019; Sasazaki et al., 2023; Liu et al., 2024). On the other hand, the genes and sequences specific to goat breeds in different ecological environments can be captured, which is helpful for analyzing the broad adaptability basis of goats (Li et al., 2020; Nanaei et al., 2023). This study aims to construct and analyze the pan-genome of the genus Goats, systematically explain the roles of the core and variable genomes in the evolution, domestication and environmental adaptation of goats, review the species classification, domestication history and existing genomic research background of the genus goats, then introduce the methodological route of pan-genome construction, and further analyze the conserved function of the core genome and the adaptive characteristics of the variable genome At the same time, the application prospects and challenges faced by the pan-genome in the research of goat evolution and breeding were also discussed. This research not only provides new evidence for analyzing the past evolutionary path of goats, but also offers valuable support for future-oriented goat breeding and the conservation of endangered wild goats. 2 The Background of Classification, Domestication and Genomic Research of the Genus Goats 2.1 Diversity of wild goat species The Capra genus encompasses a variety of wild goats and wild goats, mainly distributed in the high mountains and rugged regions of Eurasia and northeastern Africa. Many groups have long lived in isolated areas and evolved independently, thus showing obvious genetic differentiation (Nair et al., 2021). They are related to domestic goats, but there are significant differences in chromosome composition and genomic sequence (Bao et al., 2019). In recent years, large-scale sequencing has begun to incorporate the genomes of wild goats. Take the vargoat project as an example. The whole genome data of 1 159 goats worldwide were collected, among which 35 represented 8 wild species (Denoyelle et al., 2021). These results further highlight the genetic gap between wild and domestic goats and provide key information for analyzing the infiltration of wild genes into domestic goat breeds (Bao et al., 2019). 2.2 Domestication centers and events of domestic goats Domestic goats (Capra hircus) first came from Southwest Asia, where they were domesticated from wild Persian goats (C. aegagrus) about 8 000~10 000 BC (Zheng et al., 2020; Wang et al., 2021). Archaeology and paleogenomics suggest that goat domestication was not a single event but a “mosaic” process with several sources and stages (Daly et al., 2018). Studies of ancient genomes show that in different areas of the Fertile Crescent, such as the Zagros Mountains and Anatolian Plateau, goats were domesticated separately, and later gene flow took place between groups. At the Ganj Dareh site in Iran, mud bricks with goat hoof marks were found, showing their early presence in human settlements (Figure 1). In addition, genome sequencing of goat remains from about 10,000 years ago in the Zagros Mountains showed that these early herds were closely linked to nearby wild goats but also showed genetic gaps from goats in other regions, supporting a multi-center domestication pattern (Daly et al., 2021). Figure 1 Archaeozoological evidence for goat management at Ganj Dareh (Adopted from Daly et al., 2021) Image caption: Hoofprints in mud-brick at GanjDareh (sample 270, context 2033, lowest level of collapse from Smith exca-vation); Inset displays likely individual hoof impressions (Adopted from Daly et al., 2021)
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