Bioscience Evidence 2025, Vol.15, No.5, 209-218 http://bioscipublisher.com/index.php/be 216 7.3 Role of CRISPR and functional genomics in validating phylogenetic inferences Gene editing technologies such as CRISPR have provided new tools for verifying candidate genes in phylogenetic research. Genomics has identified many genes related to domestication and traits, but the specific functions of these genes still need to be experimentally confirmed (Rubin et al., 2010; Qanbari et al., 2019; Wang et al., 2021; Wen et al., 2025). By using CRISPR knockout or knock-in technology, the impact of a certain gene variation on phenotypes can be directly tested, and the relationship between genes and traits can be verified. At the same time, by integrating functional genomics methods, such as single-cell transcriptomics and epigenetic editing, a deeper understanding of the roles of key genes in different tissues and developmental stages can be achieved. This will make phylogenetic inference more accurate and more biologically significant (Hou et al., 2020). 8 Concluding Remarks Domestic chickens (Gallus gallus domesticus) have undergone significant genetic and appearance changes during the domestication process. Compared with wild free-range chickens (such as red free-range chickens), domestic chickens differ greatly in growth rate, body size, egg production, skin color, behavior and reproductive cycle. These changes are mainly driven by artificial selection, environmental adaptation and gene exchange. For instance, the BCO2 gene and the TSHR gene are strongly selected in domestic chickens. The former is related to skin pigmentation, while the latter is associated with the breeding season. In addition, different domestic chicken breeds also show significant differences in body size, egg production and usage. Some mainly lay eggs, some produce meat, and some are ornamental breeds. Phylogenetic markers (such as whole-genome SNPS, mitochondrial DNA and microsatellites, etc.) are important tools for studying the evolution of domestic chickens and pheasants. Through these molecular markers, researchers can track whether domestic chickens have multiple origins, identify selected gene regions, recognize genes related to traits, and also reconstruct the lineage relationship between domestic chickens and pheasants. For instance, mitochondrial DNA and whole-genome data reveal that domestic chickens come from the distribution areas of multiple red pheasant subspecies and have also engaged in gene exchange with other pheasants during their spread. Phylogenetic markers have also helped to identify functional regions in the domestic chicken genome that have been retained due to domestication and artificial selection. A lot of evidence indicates that hybridization and gene infiltration have played an important role in the evolution of domestic chickens. Domestic chickens not only have a close genetic relationship with red purebred chickens, but also have undergone multiple gene exchanges with gray purebred chickens, Ceylon purebred chickens, green purebred chickens, etc. These gene flows increase the genetic diversity of domestic chickens and also affect important traits such as skin color, growth rate and immunity. For instance, the genetic infiltration of the grey pheasant has brought about the yellow skin of domestic chickens, while other fragments are related to growth and environmental adaptation. Meanwhile, the gene exchange between modern domestic chickens and wild purebred chickens has also led to the loss of some wild genotypes. Therefore, it is very important to protect the genetic diversity of wild purebred chickens. Acknowledgments We would like to express our gratitude to the two anonymous peer researchers for their constructive suggestions on our manuscript. Conflict of Interest Disclosure The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. References Bélteky J., Agnvall B., Bektic L., Höglund A., Jensen P., and Guerrero-Bosagna C., 2018, Epigenetics and early domestication: differences in hypothalamic DNA methylation between red junglefowl divergently selected for high or low fear of humans, Genetics, Selection, Evolution: GSE, 50: 13. https://doi.org/10.1186/s12711-018-0384-z Bondoc O., and Santiago R., 2013, The use of DNA barcodes in the evolutionary analysis of domestic breeds and strains of chicken (Gallus gallus domesticus) in the Philippines, Philippine Agricultural Scientist, 95(4): 358-369.
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