International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 10-28 http://ecoevopublisher.com/index.php/ijmeb 16 and also left traces of linkage disequilibrium and selection sweeps in the genome. Through genome scanning, researchers have identified a series of candidate genes related to important economic traits of domestic chickens, which show high-frequency variation or specific haplotypes in domestic chicken breeds, but rarely appear in wild red jungle fowl, reflecting the cumulative effect of artificial selection. Domestication first changed the comprehensive traits of domestic chickens, such as behavior and physiological rhythm, making them easier to raise and breed. The most typical case is the aforementioned TSHR gene mutation, which weakens the restriction of photoperiod on reproduction and enables domestic chickens to lay eggs all year round. This mutation meets the human need for continuous egg sources, so it is almost fixed in domestic chickens and becomes one of the genetic markers of domestic chicken domestication. At the same time, the THSR mutation also affects metabolism and behavior, making domestic chickens more docile and easy to manage. Another important physiological trait is that domestic chickens grow faster and are larger than wild jungle fowl, which is related to human selection for broiler production. Whole-genome association studies have found that genes related to the growth hormone pathway in domestic chickens, such as IGF1 and GHR, have specific allele combinations that can increase growth rate (Ouyang et al., 2022). Pan-genome analysis further reveals hidden variations that control growth traits: for example, in small chicken breeds, there is a specific deletion in the promoter of the IGF2BP1 gene, which leads to decreased expression, thereby limiting body growth. This deletion does not exist in large breeds, showing that people use this gene variation when breeding chickens for different purposes. Other studies have shown that genes related to hunger and feeding regulation in the chicken genome, such as NPY, may also have undergone selective changes, making domestic chickens more willing to eat and easier to grow fat to adapt to the rich feed in the domestic environment. Driven by both human aesthetics and practicality, the morphological diversity of domestic chickens far exceeds that of wild jungle fowl, and many traits are the product of artificial selection. For example, coat color and skin color are important appearance characteristics of domestic chickens: wild jungle fowl males have gorgeous feathers while hens have gray-brown feathers, but the feather colors of domestic chicken breeds can be white, black, red, mottled, etc. Genomic studies have found that a variety of pigmentation-related genes are subject to selection. Different alleles of the MC1R gene cause the coat color to change from red to black, which is the dominant genetic pattern. The allele of this gene is fixed in black-feathered breeds (Dharmayanthi et al., 2022). The color of the skin and tibia is determined by genes such as BCO2 and EDNRB2: yellow-skinned chickens carry an inactivating mutation in the BCO2 gene, which causes the carotenoids in corn feed to be deposited under the skin; some white-feathered black-bone chickens have excessive melanin deposition in the dermis of the skin due to large fragment duplications in the adjacent region of the EDN3 gene, presenting a black skin phenotype. In terms of ornamental traits such as crown type and feather type, humans have also carried out targeted breeding. The wild type of domestic chicken has a single comb, but a variety of variant comb types such as pea comb and rose comb have appeared in the breed. The pea comb trait is caused by an insertion in the first intron of the SOX5 gene, which causes the gene to be abnormally expressed and changes the comb development. The rose comb comes from an inversion on chromosome 7 containing the HMGA2 gene, which affects the structure of the comb and is related to egg production (Dorshorst et al., 2011). Feather traits such as silk feathers (downy feathers) originate from a missense mutation in the KRT75 keratin gene, which leads to abnormal rachis structure; tailless feathers and curly feathers are also caused by TBXT gene deletion and KRT75 mutation, respectively. These mutations usually reduce fitness in the wild, but they are preserved and fixed in specific strains under human selection, forming a rich variety resource of domestic chickens. 4.2 Domestication bottleneck and genetic diversity loss The domestication process is often accompanied by population bottlenecks and inbreeding, which will leave traces of reduced genetic diversity in the chicken genome. Wild jungle fowl populations usually live in diverse environments and have large population sizes, with high levels of genetic diversity; however, domestic chickens, due to their origin from limited domesticated individuals and long-term artificial selection and directional breeding, have significantly reduced their effective population size and relatively narrowed their genomic
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