Bioscience Evidence 2025, Vol.15, No.5, 209-218 http://bioscipublisher.com/index.php/be 213 chickens and wild free-range chickens have significant differences in many gene loci, such as BCO2, TSHR, IGF1 and CORIN. These genes are related to morphology, pigment, metabolism, reproduction and behavior (Rubin et al., 2010; Qanbari et al., 2019; Wang et al., 2021; Zhao et al., 2024). Meanwhile, there are more harmful mutations in the genome of domestic chickens, which is in line with the "domestication cost" hypothesis, that is, when favorable traits are obtained through artificial selection, unfavorable variations will also accumulate (Mehlhorn and Caspers, 2021; Wang et al., 2021). Furthermore, changes in gene structure (such as deletions and duplications) and the introduction of exogenous genes (such as the BCO2 gene of the gray pheasant) have also increased the genetic diversity of domestic chickens (Lawal et al., 2019; Piegu et al., 2020; Zhao et al., 2024). 5 Case Study: Using Phylogenetic Markers to Trace Domestic and Wild Lineages 5.1 Example: analysis of mtDNA haplotypes showing multiple domestication centers in Southeast Asia and South China Mitochondrial DNA (mtDNA) is often used as a maternal genetic marker to study the origin of domestic chickens. Many large-scale studies have found that domestic chickens and red pheasants (Gallus gallus) have multiple haplotype clusters (A-I) that are quite different. These haplotypes exist independently in Southeast Asia, South China and the Indian subcontinent, etc., suggesting that domestic chickens may have domestication centers in these places. For instance, domestic chickens and red pheasants in Thailand, Yunnan and Vietnam exhibit rich haplotype differences, some of which exist only in specific regions, indicating multiple domestication and complex diffusion processes (Liu et al., 2006; Yw et al., 2012; Hata et al., 2021; Kanakachari et al., 2023) (Figure 2). 5.2 Highlight how SNPs revealed introgression from wild Gallus sonneratii into South Asian domestic chickens Genome-wide SNP analysis revealed that domestic chickens in South Asia carry a considerable number of gene fragments from the grey grouse (Gallus sonneratii). These fragments indicate the presence of bidirectional gene infiltration (Lawal et al., 2019; Zhao et al., 2024). The infiltrated regions not only include the known BCO2 genes, but also genes related to growth and immunity, such as IGFBP2, TKT, TIMP3, HSPB2 and CRYAB. This indicates that the grey pheasant has a significant impact on the genetic diversity and adaptability of domestic chickens. 5.3 Demonstrate functional impact: e.g., yellow skin allele traced back to G. sonneratii via phylogenetic analysis Phylogenetic analysis shows that the yellow skin of domestic chickens can be traced back to the gray grouse. Research has found that the BCO2 gene alleles of domestic chickens and gray pheasants are very similar, and BCO2 fragments from gray pheasants can be detected in many domestic chicken breeds. This indicates that yellow skin was introduced into domestic chickens through gene infiltration and was subsequently strongly selected (Zhao et al., 2024; Wu et al., 2023). This result reveals the genetic basis of the phenotypic diversity of domestic chickens and also indicates that functional gene flow is of great significance in domestication. 5.4 Comparative insight: how gene flow shaped adaptive traits like feather pattern and skin pigmentation Gene flow and hybridization have played a key role in the domestication and evolution of domestic chickens. In addition to yellow skin, traits such as feather patterns and skin pigmentation are also influenced by the infiltration of wild species genes. Genome-wide comparisons and selective scans have revealed significant differences between domestic chickens and wild purebred chickens in many genes related to development, immunity, reproduction and vision. These variations are directly related to the appearance diversity and environmental adaptation of domestic chickens (Rubin et al., 2010; Lawal et al., 2019; Wu et al., 2023). Therefore, gene flow not only increases the genetic resources of domestic chickens but also helps them adapt to different ecological environments.
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