Genomic Analyses for Selective Signatures and Genes Involved in Hot Adaptation Among Indigenous Chickens From Different Tropical Climate Regions

Abstract

Climate change, especially weather extremes like extreme cold or extreme hot, is a major challenge for global livestock. One of the animal breeding goals for sustainable livestock production should be to breed animals with excellent climate adaptability. Indigenous livestock and poultry are well adapted to the local climate, and they are good resources to study the genetic footprints and mechanism of the resilience to weather extremes. In order to identify selection signatures and genes that might be involved in hot adaptation in indigenous chickens from different tropical climates, we conducted a genomic analysis of 65 indigenous chickens that inhabit different climates. Several important unique positively selected genes (PSGs) were identified for each local chicken group by the cross-population extended haplotype homozygosity (XP-EHH). These PSGs, verified by composite likelihood ratio, genetic differentiation index, nucleotide diversity, Tajima’s D, and decorrelated composite of multiple signals, are related to nerve regulation, vascular function, immune function, lipid metabolism, kidney development, and function, which are involved in thermoregulation and hot adaptation. However, one common PSG was detected for all three tropical groups of chickens via XP-EHH but was not confirmed by other five types of selective sweep analyses. These results suggest that the hot adaptability of indigenous chickens from different tropical climate regions has evolved in parallel by taking different pathways with different sets of genes. The results from our study have provided reasonable explanations and insights for the rapid adaptation of chickens to diverse tropical climates and provide practical values for poultry breeding.

Fourth Report on Chicken Genes and Chromosomes 2022

“…Considering the constraints of SNP arrays and the reduction of DNA sequencing costs, NGS-based WGS approach is now the most popular tool to infer the evolutionary history of chicken genomes, to assess the genetic diversity and population genetic structure at regional, continental, and global scales, to identify the genetic controls of specific traits of interest, and to screen for the signatures of selection for productive traits and environmental adaptation [Rubin et al, 2010;Mugal et al, 2013;Wang MS et al, 2015, 2016a, 2016bGuo X, , 2022Guo Y et al, , 2021Zhang et al, 2016Zhang et al, , 2022Li D et al, , 2019Boschiero et al, 2018;Derks et al, 2018;Lawal et al, 2018Lawal et al, , 2020Sohrabi et al, 2018;Almeida et al, 2019;Talebi et al, 2020;Tiley et al, 2020;Wang Q et al, 2020;Gheyas et al, 2021Gheyas et al, , 2022Li YD et al, 2021;Mariadassou et al, 2021;Rostamzadeh Mahdabi et al, 2021;Tan et al, 2021;Yang Z et al, 2021;Asadollahpour Nanaei et al, 2022;Chen X et al, 2022;Gao et al, 2022;Geibel et al, 2022;Li Y et al, 2022;Sun et al, 2022;Wang S et al, 2022;Xu et al, 2022;Yuan J et al, 2022;Zeng et al, 2022].…”

Whole genome resequencing reveals the adaptability of native chickens to drought, tropical and frigid environments in Xinjiang

“…Mutations in the AGMO gene, an enzyme dependent on tetrahydrobiopterin and iron, have been linked to reduced glucose-stimulated insulin response, type 2 diabetes, and susceptibility to intracranial aneurysms. This gene may have enabled Indonesian chickens to challenge hot and humid climates ( Xu et al, 2022 ). Additionally, the glutamate receptor ionophil delta 2 gene ( GRID2 ) is a multichannel membrane protein, that plays a significant role in regulating mitochondrial morphogenesis, dendritic development, and synaptic formation in Purkinje cells ( Huang et al, 2022 ).…”

Genomic insights into local adaptation and phenotypic diversity of Wenchang chickens

“…After early domestication in southwestern China and Southeast Asia ( Wang et al., 2020 ; Peng et al., 2022 ; Peters et al., 2022 ), chickens spread worldwide through multiple human migrations ( Lawal and Hanotte, 2021 ). Consequently, various local breeds of chickens have been developed, adapted to diverse environmental conditions such as tropical climates ( Tian et al., 2020 ; Xu et al, 2022 ; Shi et al., 2023 ), high altitudes ( Wang et al., 2015 ), and cold tolerance ( Xu et al., 2021 ; Zhao et al., 2022 ; Shi et al., 2023 ). These locally adapted characteristics make these breeds not only an economic foundation for smallholder farmers but also valuable genetic resources for poultry breeding and improvement ( Jia et al., 2016 ; Bettridge et al., 2018 ).…”