Genetic diversity and breed identification of Chinese and Vietnamese local chicken breeds based on microsatellite analysis

South Asia and Southeast Asia are the origins of domestic chickens and are rich in poultry genetic resources, resulting in many unique local chicken breeds. However, with the rapid intensification of poultry farming worldwide, many local chicken breeds are threatened with extinction. In response to China's "One Belt, One Road" policy, it is imperative to strengthen the conservation and breeding of local chicken breeds in China and Vietnam. This study characterized 18 microsatellite molecular genetic markers to analyze the genetic diversity of 21 local chicken populations in southern China (Yunnan and Guangxi Provinces) and Vietnam, breed identification tags for microsatellite loci were constructed. The results showed that a total of 377 alleles were detected in all breeds, and the most alleles (44) and the highest polymorphic information content (0.7820) were detected at the LEI0094 locus. The average polymorphic information content (PIC) content of the whole population was 0.65, indicating moderate polymorphism. The genetic diversity of the whole population was rich, except for two loci MCW0111 and MCW0016, that showed heterozygote excess at microsatellite loci, and the population had high genetic differentiation. The Vietnamese breeds showed low pairwise fixation coefficient (FST) and Nei's standard genetic distance (DS) between them. According to the neighbor-joining dendrogram constructed by DS and the analysis of population genetic structure using the structure program, Longshengfeng chicken, Yunlong dwarf chicken, Tengchong white chicken, Xiayan chicken, and Daweishan mini chicken are similar, and Xishuangbanna game fowl, Wuding chicken, and Lanping silky chicken are similar to Yanjin black-bone chicken. In addition, excluding Dongtao chicken, other Vietnamese breeds are clustered together, indicating that the southern chicken breeds are closely related and have experienced better breeding. Overall, the whole population is rich in genetic resources, and the chicken breeds in the three regions are genetically close because of geographical factors and human activities. Dongtao chicken in Vietnamese, Chinese Yunnan local chicken breeds (Gallus gallus spadiceus), and red jungle fowl chickens (Gallus gallus) may have the same origin. We also constructed unique microsatellite molecular markers for 20 cultivars using 15 microsatellite loci. This study provides valuable insights to facilitate breed identification, improve cultivar protection, and new germplasm construction. We analyzed the genetic diversity of local chicken breeds in southern China and Vietnam using microsatellite technology and described the affinities of these chicken breeds. Moreover, unique molecular tags were constructed for these breeds through unique allelic loci. Lay Summary China's Yunnan, Guangxi, and Vietnam are rich in biodiversity, and a wide variety of local chicken breeds exist. Due to the rapid development of intensive farming, the biodiversity of chicken breeds in these two regions has gradually decreased. To protect the diversity of local breeds, and to promote the exchange of germplasm resources and the creation of new germplasm between China and Vietnam, this study analyzed the genetic diversity of some chicken breeds in Yunnan, Guangxi, and Vietnam by using microsatellite molecular markers. Studies have shown that the entire population has rich genetic resources, and Vietnamese chickens have a strong kinship with some local chicken breeds in Yunnan Province, China, and there is also a high degree of hybridization between Vietnamese local chickens. In addition, since some chicken breeds have more similarities in appearance, this study constructed unique molecular tags for different breed-specific alleles as one of the methods to accurately distinguish different breeds for breed protection and subsequent breeding.