Genomic analysis of Nigerian indigenous chickens reveals their genetic diversity and adaptation to heat-stress

Mifta P. Rachman, Oladeji Bamidele, Tadelle Dessie, Jacqueline Smith, Olivier Hanotte, Almas Gheyas

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

Indigenous poultry breeds from Africa can survive in harsh tropical environments (such as long arid seasons, excessive rain and humidity, and extreme heat) and are resilient to disease challenges, but they are not productive compared to their commercial counterparts. Their adaptive characteristics are in response to natural selection or to artificial selection for production traits that have left selection signatures in the genome. Identifying these signatures of positive selection can provide insight into the genetic bases of tropical adaptations observed in indigenous poultry and thereby help to develop robust and high-performing breeds for extreme tropical climates. Here, we present the first large-scale whole-genome sequencing analysis of Nigerian indigenous chickens from different agro-climatic conditions, investigating their genetic diversity and adaptation to tropical hot climates (extreme arid and extreme humid conditions). The study shows a large extant genetic diversity but low level of population differentiation. Using different selection signature analyses, several candidate genes for adaptation were detected, especially in relation to thermotolerance and immune response (e.g., cytochrome P450 2B4-like, TSHR, HSF1, CDC37, SFTPB, HIF3A, SLC44A2, and ILF3 genes). These results have important implications for conserving valuable genetic resources and breeding improvement of chickens for thermotolerance.
Original languageEnglish
Article number2209
Pages (from-to)1-13
Number of pages13
JournalScientific Reports
Volume14
Issue number1
Early online date26 Jan 2024
DOIs
Publication statusPublished - 26 Jan 2024

Keywords / Materials (for Non-textual outputs)

  • Animals
  • Chickens/genetics
  • Genetic Variation
  • Genome
  • Genomics/methods
  • Hot Temperature
  • Polymorphism, Single Nucleotide
  • Selection, Genetic

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