International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.1, 19-29 http://ecoevopublisher.com/index.php/ijmec 19 Research Report Open Access The Role of Horizontal Gene Transfer and Structural Variation in the Adaptation of Goats to Diverse Environments Wei Liu, Jia Xuan Institute of Life Science, Jiyang College of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China Corresponding author: jia.xuan@jicat.org International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.1 doi: 10.5376/ijmec.2025.15.0003 Received: 21 Dec., 2024 Accepted: 27 Jan., 2025 Published: 10 Feb., 2025 Copyright © 2025 Liu and Xuan, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Liu W., and Xuan J., 2025, The role of horizontal gene transfer and structural variation in the adaptation of goats to diverse environments, International Journal of Molecular Ecology and Conservation, 15(1): 19-29 (doi: 10.5376/ijmec.2025.15.0003) Abstract This study analyzed the adaptive traits and genetic basis of goats, focusing on the research progress on HGT and SV in goat environmental adaptation in recent years, analyzing the mechanism of their role in goat adaptation to high-altitude hypoxia, drought, heat and severe cold, as well as the synergistic effect of HGT and SV and their evolutionary significance. The study found that horizontal gene transfer (HGT) and genome structural variation (SV) are two important factors driving the adaptive evolution of goats. New functional genes have been introduced into goats, such as endogenous retrovirus integration to promote placental function, which may improve their ability to adapt to the environment. SV includes large fragment insertion, deletion, duplication, translocation and other variations in the genome, which can significantly change gene dosage and regulatory network, and is a key factor affecting goat phenotypic diversity and environmental adaptability. In addition, this study also looks forward to the use of omics technology and functional experiments to further study HGT and SV, and explores the application prospects of these new knowledge in goat genetic improvement and protection. A deeper understanding of horizontal gene transfer and structural variation will help reveal the genetic mechanisms of goat environmental adaptation, enrich evolutionary biology theory, and provide new ideas for livestock breeding and biodiversity conservation. Keywords Goat; Horizontal gene transfer; Structural variation; Environmental adaptation; Genome evolution 1 Introduction Goats are one of the earliest domesticated livestock. They are raised in diverse environments on almost all continents around the world, from alpine tundra to tropical deserts, and show strong environmental adaptability. This wide adaptability makes goats an important model for studying the adaptive evolution of mammals. Under long-term natural selection and artificial breeding, different breeds of goats have formed unique adaptation characteristics to climatic conditions (such as high-altitude hypoxia, drought and heat, severe cold, etc.), and their genomes have left genetic imprints of adaptive evolution (Peng et al., 2024a). Traditionally, genetic studies on the environmental adaptability of goats have focused on single nucleotide polymorphisms (SNPs) and the screening of candidate genes. However, recent advances in genomics have revealed that horizontal gene transfer and structural variation play an important role in the adaptive evolution of species (Dai et al., 2021). Horizontal gene transfer refers to the "horizontal" transmission process of genetic material from parents to offspring. It has long been believed to occur mainly in the microbial field, but there is increasing evidence that HGT events also occur in eukaryotes (including vertebrates), which have an impact on host evolution (Sun et al., 2015; Huang et al., 2017). On the other hand, structural variation is a large fragment variation of ≥50 bp in length in the genome, including copy number variation (such as gene duplication or deletion), inversion, translocation and large insertion/deletion, which can cause gene dosage changes or regulatory element rearrangements, thereby having a greater impact on phenotype and adaptability (Bian et al., 2024; Zhang et al., 2024). Because the magnitude of genomic changes caused by structural variation is much greater than that of point mutations, they often play a key role in the evolution of adaptive traits and complex traits (Bian et al., 2024). With the development of computational biology, more and more dedicated software and pipelines are used to detect HGT events. HGT provides a new perspective for understanding goat genome evolution that is different from the traditional concept, that is, the gene pool is not a closed system, and species can quickly expand their
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