Identification of candidate genes related to highland adaptation from multiple Chinese local chicken breeds by whole genome sequencing analysis

Abstract

Understanding the genetic mechanism of highland adaptation is of great importance for breeding improvement of Tibetan chickens (TBC). Some studies of TBC have identified some candidate genes and pathways from multiple subgroups, but the related genetic mechanisms remain largely unknown. Different genetic backgrounds and the independent genetic basis of highland adaptation make it difficult to identity the selective region of highland adaptation with all TBC samples. In this study, we conducted preanalysis in a large-scale population to select a TBC subgroup with the purest and highest level of highland-specific lineage for the further analysis. Finally, the 37 samples from a TBC subgroup and 19 Lahsa White chickens were used to represent the highland group for further analysis with 80 samples from five Chinese local lowland breeds as controls. Population structure analysis revealed that highland adaptation significantly affected population stratification in Chinese local chicken breeds. Genome-wide selection signal analysis identified 201 candidate genes associated with highland adaptation of TBC, and these genes were significantly enriched in calcium signaling, vascular smooth muscle contraction and the cellular response to oxidative stress pathways.Additionally, we identified a narrow 1.76 kb region containing an overlapping region between HBZ and an active enhancer, and our identified region showed a highly significant signal. The highland group selected the haplotype with high activity to improve the oxygen-carrying capacity, thus being adapted to

Genetic structure and characteristics of Tibetan chickens

“…This finding is in line with the recent discovery by The Functional Annotation of Animal Genomes consortium that core set of regulatory elements are functionally conserved, whereas its specific sequence and genomic position are not ( Kern et al, 2021 ). We have a parallel project aimed at further investigating the underlying genetic basis of highland adaptation in TBC ( Nan et al, 2023 ). Integrative multiomic analyses would shed lights in further investigating the underlying genetic basis of highland adaptation in TBC.…”

Genomic insights into local adaptation and phenotypic diversity of Wenchang chickens

“…Understanding the genetic foundation of local adaptation in chickens is pivotal for sustainable poultry breeding and conservation, especially in preserving unique breeds like the Wenchang chickens. These endeavors not only help in preserving genetic diversity but also provide valuable insights for targeted breeding programs, ensuring the breed's resilience and productivity in diverse environments ( Restoux et al., 2022 ; Nan et al., 2023 ).…”