International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.3, 134-143 http://ecoevopublisher.com/index.php/ijmec 136 After humans began raising goats, flocks of sheep were frequently transported to brand-new territories far from their native habitats. Migration then began, with groups spreading outward and their footprints spread across many landscapes. In unfamiliar environments, domestic goats frequently encounter and crossbreed with local wild goats. Genomic evidence suggests that early hybridization events with Caucasian wild goats and falconeri (C. falconeri) did occur, thereby introducing new genetic variations into domesticated populations (Bao et al., 2019; Sasazaki et al., 2021). These ancient gene exchanges still leave traces in DNA to this day. At present, domestic goats around the world have largely merged into several major lineages. Each lineage corresponds one-to-one with specific geographical regions and also reflects the initial domestication centers (Colli et al., 2018; Bian et al., 2024). 2.3 Broad phenotypic adaptability of goats Goats are well known for adapting to many different habitats. Over time, they were taken to all parts of the world, from cold mountains to hot deserts and even wet tropical zones, and could still live and reproduce (Nanaei et al., 2023). Local breeds developed traits suited to their environments through natural selection and human breeding. For example, goats in the Qinghai–Tibet Plateau and Himalayas show high-altitude adaptations to survive low oxygen. Studies have shown that certain alleles of EPAS1 are positively selected in plateau goats, enhancing their blood oxygen-carrying capacity and helping goats overcome the hypoxic environment at high altitudes (Lu et al., 2025). For instance, in the arid and hot regions of the Middle East and North Africa, goat breeds have demonstrated tolerance to high-temperature and water-scarce environments. Some tropical native goats have special physiological mechanisms in body temperature regulation, metabolism and skin heat dissipation, and genes such as heat shock proteins (such as HSP70) in their genomes show selection signals (Li et al., 2020). Recent studies have also found that goats living in desert environments such as the Arabian Peninsula have specific variations in their genomes that originated from ancient wild species, which may have been introduced through ancient hybridization and are associated with drought tolerance traits (Sasazaki et al., 2021). In alpine and cold environments, goats in regions such as Siberia and Mongolia have thick and dense coats and stronger heat production capacity, and adaptive changes have also occurred in heat-related genes such as UCP1 (Li et al., 2020). 3 The Current Status of Genomic Research on the Genus Goats 3.1 Classification and distribution of the genus goats The genus Gobius includes domestic goats and several wild relatives. Together they form a distinct group in the subfamily Gobiinae. Genetic and evolutionary data show that the domestic goat (C. hircus) is closest to the Persian wild goat (C. aegagrus). Other wild forms-Siberian wild goat, alpine wild goat (C. ibex), Caucasian wild goat, and the Markhor (C. falconeri)-sit on separate side lineages (Bao et al., 2019). These species live mainly in the Old World’s mountain regions. Long geographic isolation has shaped clear patterns of spread and split (Nair et al., 2021). Scientists have studied goat genes from around the world. They found that today's farm goats still carry some genes from their wild relatives. For example, some goat breeds in Europe and the Middle East have special mitochondrial types that came from Alpine or Caucasian wild goats (Bao et al., 2019). This shows that wild and domestic goats mixed long ago. Other studies looked at DNA markers from goats in Asia, Africa, and Europe. They found that goat groups are very different between regions. These studies also found signs that goats moved with ancient people when they migrated (Colli et al., 2018). 3.2 Existing reference genome resources and limitations Research on the goat genome began with the construction of reference genomes for individual breeds. The first goat reference genome was from the Yunnan Black goat, and a genome sequence of approximately 2.6 billion bases was published in 2013 (Dong et al., 2013). Subsequently, the United States Department of Agriculture team constructed a higher-quality goat reference genome ARS1 in 2017 using advanced single-molecule sequencing and chromosome conformation capture techniques (Bickhart et al., 2017). These reference genomes provide an
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