International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 10-28 http://ecoevopublisher.com/index.php/ijmeb 22 6 Case Study: Comparative Genomics of East Asian Chicken Lineages 6.1 Genome comparisons between Chinese indigenous chickens and red junglefowl China has rich local breed resources of domestic chickens. So far, there are more than 110 local chicken breeds listed in the National Catalogue of Livestock and Poultry Genetic Resources in my country, covering a variety of types such as yellow-feathered broilers, fast-growing white chickens, fighting chickens, and ornamental chickens. These native chicken breeds are similar to their wild ancestor, the Red Junglefowl, in the genome, and each has unique variations. The genomes of most Chinese native chickens are highly similar to those of the Red Junglefowl, and the shared allele frequencies account for the vast majority (>90%). This shows that the gene pool of domestic chickens is mainly derived from the genetic basis of the Red Junglefowl, and the domestication time is relatively short relative to the evolutionary scale, and a large number of random mutations have not accumulated. Especially in the conserved gene regions of the autosomes, such as basic metabolic and developmental genes, the sequences of native chickens and Red Junglefowl are almost the same. But at the same time, there are significant differences between native chickens and Red Junglefowl in some gene regions related to the adaptation of domestic chickens to the human environment and production performance. For example, a study of mitochondrial D-loop variation in 12 local chicken breeds in Guangdong Province found that they contained all the main maternal haplotypes of red junglefowl, but the frequency distribution was different. Most local chicken breeds are dominated by the B-lineage haplotype of red junglefowl, and a few, such as Huiyang bearded chicken, are also rich in the E-lineage haplotype of Southeast Asian junglefowl. This shows that Chinese native chickens share multiple points with red junglefowl in terms of maternal ancestry, but have also mixed in some genetic components of junglefowl from other regions, making their haplotype composition more diverse (Huang et al., 2018). In terms of nuclear genome, the differences between Chinese native chickens and red junglefowl are mainly reflected in the trait gene regions that are subject to artificial selection. The researchers conducted whole-genome resequencing on multiple Chinese local breeds and found that each breed has some specific selection signal peaks. For example, Wuling Mountain Chicken has a high-frequency non-synonymous mutation in the EPAS1 gene, which may be related to the high-altitude environment in which it lives; the haplotype of Xianju Chicken near the TSHR gene is significantly different from that of Red Junglefowl, suggesting that special selection was made for its reproductive rhythm during domestication (Guo et al., 2022). Some local breeds have accumulated alleles that red junglefowl do not have due to their unique breeding history. For example, the colored shell egg-laying chicken breed carries a unique mutation in the SLCO1B3 transporter gene, resulting in a powder-blue eggshell, a trait that red junglefowl do not have (introgression of green shell egg-laying chicken genes from southern Tibet). Another example is that Sichuan fighting chickens retain a rare allele of the CACNA1C gene in red junglefowl, making it more excitable. These examples show that Chinese native chickens have inherited the common genome of red junglefowl and, through artificial or natural selection, have acquired some unique variations that distinguish them in phenotype and adaptability. It is worth mentioning that the protection of local chicken breed diversity is very important because they may contain precious alleles that red junglefowl do not have. Studies have found that the average heterozygosity of some local breeds is even higher than that of wild red junglefowl, which may be attributed to historical hybridization and large population size. For example, the microsatellite polymorphism and nucleotide diversity of well-preserved breeds such as Wenchang chicken and Xianju chicken are not lower than those of wild junglefowl. On the contrary, the genetic diversity of some over-cultivated commercial matching lines has significantly decreased, and it is necessary to broaden the genetic base by introducing local germplasm. Therefore, comparing the genomes of local chickens and red junglefowl is not only a scientific issue in studying domestication, but also can guide the utilization of genetic resources and breed improvement strategies. Through genome analysis, we can establish a "genomic profile" for each local breed, clarify its similar and different gene regions with red junglefowl, and use them in breeding in a targeted manner or maintain its characteristic traits. 6.2 Genetic structure and breeding history of local breeds Due to geographical isolation and artificial breeding, Chinese local chicken breeds have formed their own relatively independent genetic structures. At the molecular level, different breeds have systematic differences in
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