Phuphan chicken breeds: classification as varieties or distinct breeds with three derivative groups using microsatellite genotyping.

Objective: Indigenous and local breeds, such as Phuphan chickens, are vital due to their adaptability and nutritional value. However, the precise origin, historical records, and genetic diversity of Phuphan chickens remain unclear. This study aimed to evaluate origin and genetic diversity of four Phuphan chicken groups from the Phuphan Royal Development Study Centre.

Methods: This study assesses four groups of Phuphan chicken: Phuphan black 1 (SK-B1), Phuphan black 2 (KU-BM/F), Phuphan white (KU-WM/F), and Phuphan color (KU-VM/F) using 28 microsatellite markers and comparing them with those of other Thai chicken breeds within "The Siam Chicken Bioresource Project" database.

Results: The results highlighted significant genetic diversity among these groups (mean expected heterozygosity [He] = 0.623±0.014; Allelic richness [AR] = 4.594±0.124), indicating effective management through the breeding program of the Phuphan Royal Development Study Centre. Population structure analyses revealed distinct gene pools, emphasizing the genetic uniqueness of SK-B1 relative to the other three groups. Bayesian inference validated historical genetic exchanges, primarily among KU-BM/F, KU-WM/F, and KU-VM/F, with limited exchanges involving SK-B1. This suggests that the Phuphan chicken groups share a common lineage, primarily distinguished by variations in plumage color, resulting from residual selection processes. Microsatellite markers pinpointed the loci LEI0234, MCW206, MCW0016, MCW0222, MCW0098, MCW0165, and ADL0278 as potentially subject to directional selection and associated with plumage color variation among the Phuphan chicken groups. Comparative evaluations with other Thai indigenous local chickens and red junglefowl revealed a closer affinity of SK-B1 to existing Thai chicken breeds, suggesting it may represent a variant of these breeds. Alternatively, KU-BM/F, KU-WM/F, and KU-VM/F, which exhibited comparable external characteristics, may constitute a novel breed of Phuphan chicken.

Conclusion: The findings may enhance understanding on genetic architecture of Phuphan chicken groups and contribute to Thailand's economic growth while preserving the genetic diversity of the indigenous chickens.