Adaptive signatures in Vietnamese chickens reveal a Southeast Asian reservoir for climate resilience and meat quality.

Vietnamese indigenous chickens and their wild progenitors represent a critical but under-characterized reservoir of avian genetic diversity. This study used a multi-locus approach, incorporating 28 neutral microsatellite markers and candidate functional genes (HSP70, HSP90, and ADSL). We successfully delineated the genetic structure and adaptive potential of 12 native Vietnamese indigenous chicken populations and red junglefowl (Gallus gallus). Microsatellite analysis revealed high genetic diversity (411 alleles) and significant regional structuring into three primary groups, suggesting extensive historical gene flow and shared ancestral heritage with Thai indigenous breeds. High-throughput sequencing of functional loci identified five novel HSP70, 10 novel HSP90, and five novel ADSL alleles, underscoring the unique genetic heritage of Vietnamese avian resources. Selective signature analyses confirmed that, while purifying selection maintains core protein stability, specific codons, notably in HSP70 (18, 33, 41, and 42) and HSP90 (7), exhibit putative signals of positive selection. These loci emerge as compelling candidates for functional studies underlying thermal adaptation. Moreover, the meat quality gene ADSL exhibited diversifying selection at codon 58, highlighting a candidate molecular marker for the potential enhancement of savoriness and inosine monophosphate content. These findings, which reconcile neutral population structure with candidate signals of localized adaptive divergence, address a critical regional knowledge gap and provide a scientific foundation for future marker-assisted selection programs. By integrating these results into the Siam Chicken Bioresource Project, this study promotes transboundary conservation and the sustainable development of climate-resilient poultry systems in a warming world.