Bioscience Evidence 2025, Vol.15, No.5, 209-218 http://bioscipublisher.com/index.php/be 215 grouse, the Ceylon grouse and the green grouse, etc. also participated in gene exchange, forming a history of multiple origins and multiple hybridization (Liu et al., 2006; Yw et al., 2012; Lawal et al., 2019; Wang et al., 2020; Zhao et al., 2024). These results indicate that animal domestication is not a process of a single ancestor, but involves multiple gene flows and independent domestication in different regions (Hata et al., 2021). Meanwhile, selective sweeping and rapid differentiation of trait related genes emerged in domestic chickens during domestication, demonstrating the combined effect of artificial selection and natural selection (Rubin et al., 2010; Qanbari et al., 2019; Wang et al., 2021). 6.2 Conservation strategies for wild junglefowls Wild free-range chickens are the ancestors of domestic chickens and retain rich genetic diversity, making them an important resource. However, the genetic exchange between modern domestic chickens and wild purebred chickens has caused some wild groups to lose their original genotypes. Studies have found that in some wild populations, the proportion of gene infiltration in domestic chickens is as high as 20%-50%, posing a threat to their genetic integrity (Lawal et al., 2019; Wu et al., 2023; Zhao et al., 2024). Conservation strategies include: strengthening genetic surveillance, giving priority to protecting populations with less gene infiltration, using molecular markers (such as mtDNA, SNPs) to track wild-type genes, and reducing genetic pollution (Bondoc and Santiago, 2013; Hata et al., 2021; Wu et al., 2023). The genetic diversity of wild free-range chickens is also of great significance for future poultry breeding and adaptation improvement (Lawal et al., 2019; Wu et al., 2023). 6.3 Application of phylogenetic markers in breeding programs (disease resistance, climate adaptation) Phylogenetic markers (such as SNPS, mtDNA and functional genes) have been widely applied in chicken breeding at home. Through genome-wide screening and molecular marker-assisted selection (MAS), researchers can identify gene regions related to production traits, disease resistance, and climate adaptation, such as BCO2, TSHR, IGF1, and LEPR (Rubin et al., 2010; Qanbari et al., 2019; Larkina et al., 2021). These markers can not only increase yield but also play a role in disease resistance and environmental tolerance improvement. For example, the heat shock protein gene helps domestic chickens adapt to high temperatures (Zhao et al., 2024). Meanwhile, by combining linkage disequilibrium (LD) and population structure analysis, tag selection can also be optimized to reduce costs and improve efficiency. 7 Future Directions 7.1 Integration of multi-omics (genomics, transcriptomics, epigenomics) Future research will need to combine different types of data, such as genomes, transcriptomes and epigenomes. Only in this way can we have a more comprehensive understanding of the genetic regulation methods of domestic chickens and pheasants during evolution. Nowadays, genomic sequencing has identified many selection signals related to domestication and trait differences (Rubin et al., 2010; Qanbari et al., 2019; Wang et al., 2021; Wen et al., 2025). However, if one only looks at one type of data, it is difficult to explain how complex traits are formed. Combining multiple omics can simultaneously study the effects of gene variation, gene expression and epigenetic modifications. For instance, studies have revealed similar evolution of behavioral traits by comparing brain transcriptome and genomic signals (Hou et al., 2020). In the future, this multi-omics analysis should continue to be promoted to identify key regulatory networks and important genes, providing more theoretical support for poultry breeding and adaptability research. 7.2 Advances in ancient DNA for tracing early domestication events The development of ancient DNA technology has brought new ideas to the study of the early domestication and gene flow of domestic chickens. By analyzing the DNA of ancient chicken bones at archaeological sites, it was found that some trait genes of modern domestic chickens (such as TSHR and BCO2) were not fixed very early, but were strongly selected in modern times (Flink et al., 2014). In addition, by combining ancient DNA with the whole genome, the processes of multiple origins, interspecific hybridization and gene infiltration in domestic chickens can be observed more clearly (Flink et al., 2014; Lawal et al., 2019; Wang et al., 2020; Zhao et al., 2024). In the future, with the advancement of sequencing and DNA extraction methods, ancient DNA research can more accurately reconstruct the history of domestication, diffusion and trait evolution of domestic chickens.
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