Abstract
BackgroundIn Tibet, the two most important breeds are Tibetan chicken and Lhasa white chicken, and the duo exhibit specific adaptations to the high altitude thereby supplying proteins for humans living in the plateau. These breeds are partly included in the conservation plans because they represent important chicken genetic resources. However, the genetic diversity of these chickens is rarely investigated. Based on whole-genome sequencing data of 113 chickens from 4 populations of Tibetan chicken including Shigatse (SH), Nyemo (NM), Dagze (DZ) and Nyingchi (LZ), as well as Lhasa white (LW) chicken breed, we investigated the genetic diversity of these chicken breeds by genetic differentiation, run of homozygosity (ROH), genomic inbreeding and selection signature analyses.ResultsOur results revealed high genetic diversity across the five chicken populations. The linkage disequilibrium decay was highest in LZ, while subtle 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) of 0.11 was observed in LZ. In other populations, the FROH ranged from 0.04 to 0.06. In total, 74, 111, 62, 42 and 54 ROH islands containing SNPs ranked top 1% for concurrency were identified in SH, NM, DZ, LZ and LW, respectively. Genes common to the ROH islands in the five populations included BDNF, CCDC34, LGR4, LIN7C, GLS, LOC101747789, MYO1B, STAT1 and STAT4. This suggested their essential roles in adaptation of the chickens. We also identified a common candidate genomic region harboring AMY2A, NTNG1 and VAV3 genes in all populations. These genes had been implicated in digestion, neurite growth and high-altitude adaptation.ConclusionsHigh genetic diversity is observed in Tibetan native chickens. Inbreeding is more intense in the Nyingchi population which is also genetically distant from other chicken populations. Candidate genes in ROH islands are likely to be the drivers of adaptation to high altitude exhibited by the five Tibetan native chicken populations. Our findings contribute to the understanding of genetic diversity offer valuable insights for the genetic mechanism of adaptation, and provide veritable tools that can help in the design and implementation of breeding and conservation strategies for Tibetan native chickens.
Highlights
In Tibet, the two most important breeds are Tibetan chicken and Lhasa white chicken, and the duo exhibit specific adaptations to the high altitude thereby supplying proteins for humans living in the plateau
The objectives of the present study were to (i) evaluate the genetic diversity of Tibetan chickens reared in different areas of the Tibetan plateau using whole-genome sequencing data, (ii) detect run of homozygosity (ROH) within each chicken population and evaluate the genomic inbreeding and (iii) reveal the genomic regions of ROH islands that may influence the adaptation of Tibetan native chicken to high altitude
Summary of the genetic diversity parameters The genetic diversity for Shigatse (SH), Neymo (NM), Dagze (DZ), Nyingchi (LZ) and Lhasa white (LW) chicken populations was evaluated by observed heterozygosity (Ho), expected heterozygosity (He) and multiplelocus heterozygosity (MLH) using eligible SNPs under Hardy–Weinberg equilibrium
Summary
In Tibet, the two most important breeds are Tibetan chicken and Lhasa white chicken, and the duo exhibit specific adaptations to the high altitude thereby supplying proteins for humans living in the plateau. These breeds are partly included in the conservation plans because they represent important chicken genetic resources. The Tibetan plateau is the largest high-altitude area on earth with an average altitude exceeding 4000 m, representing 25% of the landmass of China. This high-altitude environment becomes a habitat for many unique animal genetic resources. Population genomic analysis was rarely conducted to explore the diversity of the chicken populations reared in Tibet and to guide genetic resource conservation and utilization efforts
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