Abstract
Background
In Tibet, two most important breeds are Tibetan chicken and Lhasa white chicken, and the duo exhibit specific adaptations to high altitude and produce indispensable protein for humans living in the plateau. These breeds were partly included in conservation plans as their biodiversity is important as a genetic resource. However, population genetic analysis of the chickens is rarely investigated. Based on whole-genome sequencing data of 113 chickens from 4 Tibetan chicken population including Shigatse (SH), Nyemo (NM), Dagze (DZ) and Nyingchi (LZ), as well as Lhasa white (LW) chicken population, we performed genetic diversity and differentiation, run of homozygosity (ROH), genomic inbreeding and selection signature analyses.
Results
Our results showed high genetic diversity across the five chicken populations. The linkage disequilibrium decay was highest in LZ, and moderate level of genetic differentiation was found between LZ and other populations (Fst ranging from 0.05 to 0.10). Furthermore, the highest ROH-based inbreeding estimate (FROH) was 0.11 in LZ, whereas it ranges from 0.04 to 0.06 in the other four chicken populations. In total, 74, 111, 62, 42 and 54 ROHs containing SNPs with concurrency ranked top 1% were identified for SH, NM, DZ, LZ and LW, respectively. BDNF, CCDC34, LGR4, LIN7C, GLS, LOC101747789, MYO1B, STAT1 and STAT4 were shared genes harbored by these ROHs in the five populations, suggesting their important roles in adaptation of the chickens. Combined with selection signature analysis, we also identified a common candidate genomic region harboring AMY2A, NTNG1 and VAV3 genes. These genes have been reported to contribute to digestion, neurite growth and high-altitude adaptation, which could be involved in selection during evolution process.
Conclusions
High genetic diversity was observed in Tibetan native chickens. Nyingchi population, possessing highest FROH, is genetically distant from other chicken population. Candidate genes in ROH islands could aid the genetic characterization of the five Tibetan native chicken populations. Our findings contribute to the understanding of genetic diversity and offer valuable insights for the genetic mechanism of adaptation, as well as provide veritable tools that can help in the design and implementation of breeding and conservation strategies for Tibetan native chickens.