Whole-genome sequencing revealed the population structure of Fujian chicken breeds

Indigenous chicken breeds from Fujian Province, China, exhibit unique and distinctive phenotypic characteristics, including morphology, behaviour, integumentary pigmentation, feather colouration, and production performance. However, the underlying genetic basis governing these specific traits remains unclear. This study aimed to elucidate the population structure of six Fujian local chicken breeds [Bairong chickens (BRCs), Jinhu chickens (JHCs), Minqing chickens (MQCs), Dehua chickens (DHCs), Xiangdong chickens (XDCs), and Hetian chickens (HTCs)] in terms of their genetic resources within the province. The whole-genome resequencing revealed 8 678 612 single nucleotide polymorphisms (SNPs) in a cohort of 36 chickens. The results revealed a partial mismatch between the clustering patterns and geographic distributions of the six populations, with BRC displaying a noticeable genetic divergence from other chickens. Moreover, the genetic distance between XDC and HTC in Longyan County was relatively close and converged with JHC, MQC, and DHC into a subgroup. These findings provide a comprehensive understanding of the intrinsic characteristics and utilisation prospects of chicken germplasm resources in Fujian Province.