International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 10-28 http://ecoevopublisher.com/index.php/ijmeb 18 This inversion changes the regulatory region, resulting in changes in the coronoid morphology, and also affects the egg-laying performance of hens (because the HMGA2 gene carried by the inversion affects the secretion of reproductive hormones). For example, in bantam breeds, a duplication and inversion near the GH growth hormone receptor gene led to growth plate development disorders, shortening their limbs. By scanning the genomes of different chicken breeds for copy number variation, researchers have found multiple CNV regions associated with traits. A study on chicken beak deformity traits showed that in chickens with long upper beaks, the LRIG2 gene had an increased copy number. GWAS analysis locked the CNV in this region as a candidate causal variant. Another study on egg production and reproductive traits found that the PRLR prolactin receptor gene had partial gene duplication in high-producing laying hens, which enhanced the prolactin signal and prolonged the peak egg-laying period (Bai et al., 2018). These examples show that changing gene dosage or structure through CNV can significantly affect the phenotype and become a target for artificial selection. Compared with point mutations, CNVs often affect large genomic regions and may change the expression of multiple genes at once, which is one of the mechanisms for rapid trait variation. Another famous structural variation case in domesticated chickens is the FM (Fibromelanosis) locus of black-bone chickens. Black-bone chickens have black connective tissue and internal organs all over their bodies. This trait originates from a repeated insertion of about 100 kb on chromosome 20, which activates the abnormal expression of the EDN3 gene, resulting in the deposition of melanin all over the body. This structural mutation was originally extremely rare, but it was consciously selected and fixed in ancient China to form the black-bone chicken breed. Another example is the soft silky feathers of the "silk feather" chicken, which are caused by an allele of the KRT75 gene containing an 18 bp deletion. This deletion is located in the coding region and affects the keratin structure. The silky chicken also carries a dominant mutation that causes the skin on the tibia to be blue. This trait is similar to black skin, both of which originate from increased melanin deposition and are caused by structural variations of different genes. In terms of muscle development traits, the study found that in breeds with high leg muscle fat deposition, there was an increase in the number of copies of the AMPD1 gene, which changed the muscle metabolism pattern and made it easier to deposit fat (this was used to breed flavored broilers). It can be seen that people may have inadvertently selected various CNVs and structural rearrangements in different breeding directions, and these variations have left a significant mark in the genome. 5 Evolution of Functional Genes Associated with Chicken Traits 5.1 Accelerated evolution in growth and development genes In the process of domestic chickens from wild to domestic, the growth rate and body size have changed significantly. Compared with the small size and seasonal growth pattern of wild jungle fowl, domestic chickens show faster juvenile growth and larger adult weight under artificial breeding. Behind this phenotypic change is the accelerated evolution and functional variation of a series of growth and development regulatory genes. Comparative genomic analysis showed that several growth-related genes in the domestic chicken genome showed a higher non-synonymous mutation rate or selection pressure than wild jungle fowl. For example, the IGF1 (insulin-like growth factor 1) gene has specific haplotypes in different strains of domestic chickens, which is speculated to be the result of early domestication selection, which accelerates the bone and muscle growth of domestic chickens in the juvenile stage (Ouyang et al., 2022). In addition, multiple genes in the TH (thyroid hormone) signaling pathway have also mutated in domestic chickens, including a regulatory mutation in the THRA gene of the thyroid hormone receptor, which reduces the sensitivity of domestic chickens to thyroid hormones, thereby breaking the seasonal growth rhythm of wild-type chickens (Cai et al., 2022). Together, these changes have contributed to the high growth rate and reproductive capacity of domestic chickens throughout most of the year. Pan-genome studies provide a new way to discover hidden mutations in growth and development genes. Wang et al. (2021) constructed a graphical pan-genome of chickens and found that in some breeds, there was a promoter deletion in the LEPR (leptin receptor) gene, which led to a weakened leptin signal, thereby increasing feed intake
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