International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 10-28 http://ecoevopublisher.com/index.php/ijmeb 23 allele frequency and haplotype composition, which can be revealed through population structure analysis. Population genetic analysis of native chickens in various parts of China shows that they can be roughly divided into two main genetic clusters, northern type and southern type, as well as several transitional types. For example, Xinjiang Kazakh chickens, Shanxi Sanhuang chickens and other northern native chickens are closer to the red junglefowl in Tibet and Xinjiang, while Hainan Wenchang chickens, Yunnan Camellia chickens and other southern native chickens have more common ancestors with the Yunnan red junglefowl lineage (Guo et al., 2022). This pattern is consistent with the history of the spread of domestic chickens to the north and west: northern breeds may have originated from early domestic chickens spread through India and Xinjiang, and southern breeds are mostly derived from local domesticated chickens in South China. Each local breed often has its own specific breeding history. For example, the Pudong chicken in the suburbs of Shanghai is known for its large body and early maturity. From the genome, it carries some alleles derived from Western broiler chickens, suggesting that it has been hybridized and improved with introduced foreign breeds in modern times. For another example, Anhui Xuanzhou chicken was famous for its high egg production in the 20th century. An obvious selection signal was found in the genome near NR5A2 (steroid hormone synthesis regulatory gene), corresponding to its domestication of high reproductive performance (Ouyang et al., 2022). For example, Shandong Longkou Sanhuang Chicken is famous for its yellow hair, yellow legs, and yellow beak. Its MC1R and BCO2 genotypes are significantly different from those of ordinary native chickens. They respectively fix the alleles that control less melanin and non-decomposition of carotenoids, thus showing a yellow body. These examples show that local breeds have formed a stable genetic structure under long-term artificial selection, that is, a specific combination of alleles, which makes them meet people's needs in terms of morphology and production performance. Using whole genome data can also trace gene exchange events during the breeding process. Many local chicken breeds do not have a single origin, but are the product of multiple hybridizations in history. For example, a study of Chinese fighting cock breeds found that fighting cock breeds in different regions have considerable gene exchanges with each other (due to cross-regional competitions and trade), forming two major branches in the north and south in terms of genetic structure and mixed with local breed components. For example, although the Zhuang chicken in Guangxi and the Wuzhi fighting cock in Henan are located far away, they have common ancestral contributions genetically, indicating that there may have been fighting cock exchanges in the past (Figure 2) (Ren et al., 2023). For example, some yellow-feathered broiler breeds (such as Qingyuan Ma chicken and Hetian chicken) introduced the blood of foreign breeds such as White Rock to improve meat production performance after the reform and opening up. The genome structure analysis clearly detected that there were 15%-20% “exogenous blocks” on the chromosomes of these breeds, corresponding to the genetic fragments of foreign breed chickens. This introduction and hybridization history may lack detailed records in traditional pedigrees, but the genome can reveal it, thereby restoring the breeding process. Figure 2 Geographical location of chickens (Adopted from Ren et al., 2023)
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