Comparative Genomics and Transcriptomics of Heat Stress in Chicken and Guineafowl Populations from Selected Countries in Africa, Asia, and Europe

Abstract

Poultry farming is a crucial component of the global agriculture industry, providing a significant source of protein and economic livelihoods to millions of people worldwide. However, climate change has led to an increase in extreme weather conditions, including rising temperatures, which can negatively impact poultry production. Heat stress, a physiological response to high temperatures, has been identified as a major challenge affecting poultry health and performance, leading to reduced growth rates, decreased egg production, and increased mortality rates. Understanding the genetic and molecular mechanisms underlying heat stress response in different poultry breeds is essential for developing effective strategies to mitigate its impact on poultry farming. This study aimed to investigate the comparative genomics and transcriptomics of heat stress in chicken and guineafowls from selected countries in Africa, Asia, and Europe. Chicken (Gallus gallus domesticus) and guineafowls (Numida meleagris) are two important poultry breeds widely raised for their meat and egg production, as well as for their cultural significance in various regions of the world. By comparing the genetic and molecular responses to heat stress in these two poultry species from different geographic locations, this study sought to identify candidate genes, and molecular pathways that are associated with heat stress tolerance. This study utilized the “omics” techniques (genomics and transcriptomics), to investigate the signatures of selection for heat stress in chicken, and guineafowls. Three methods: Fixation index (FST), Integrate Haplotype Score (iHS), and Cross-population Extended Haplotype Homozygosity (XP-EHH) were used for the detection of signatures of selection for heat stress. Blood samples from 20 chicken were obtained for whole genome sequencing from Lamu, Kilifi, Mombasa, and Kwale. An additional 14 chicken whole genome sequences were downloaded from the NCBI SRA archive for comparative genomics. For the guineafowls, 16 blood samples from Laikipia, Lamu, Kilifi, and Taita Taveta were obtained for whole genome sequence analysis. An additional 56 guineafowl whole genome sequences were downloaded from the NCBI SRA archive. Through the signatures of selection methods, several candidate genes such as CNBP, COL1A1, YWHAE, PPARG, SREBF1, ATP6V0 and LRRC8A ATP2A2, TBXAS1, PER2, BOK, and RAF1 were selected in the chicken genomes. These candidate genes were subjected to annotation and several pathways including response to oxidative stress, localization, metabolic process, cellular process, developmental process, response to stimuli, signaling, and homeostatic process, that play a role in heat stress were identified. In the guineafowl genomes, some of the significant candidate genes that were selected included the MAPK1, SLC27A4, ATP5MF, PPARG, SREBF1, ATP6V0 and LRRC8A BRAF, CRYGN, and ANGPT2. These genes were annotated and found to play a role in several significant pathways like localization, metabolic process, positive regulation of the biological process, cellular process, signaling, and response to stimuli. Some pathways that were significant for both the chicken and guineafowl genomes included the metabolic process, localization, signaling, cellular process, and response to stimuli. Some of the candidate genes that were selected for both chicken and guineafowls include the PPARG, SREBF1, ATP6V0 and LRRC8A. RNA sequencing was used to profile the kidney tissue of 13 chicken and 13 guineafowls from Lamu and Mombasa Counties. At a false discovery rate (FDR) < 0.05, 278 DEGs were identified in chicken kidney tissue samples from these regions. Among these, 129 were upregulated (e.g., CD36, ANGPTL4, PLIN1, GLRA3, GABRA4) and 149 were downregulated (e.g., GABRA2, C3, GHRHR, GHSR, GRIA3, ACSL6, VTN). In guineafowl kidney tissue samples, a total of 349 DEGs were identified, among these, 190 were upregulated (e.g., SDR16C5, RETSAT, ALDH1A1, BCO1, ACSM3, AKR1D1, MDH2, CYP24A1) and 159 were downregulated (e.g., PAH, MAPK12, GRM1, RAG1, CARNS1, CNDP1, FTCD, HTR2A, MYLK2, AOX1). Gene Ontology (GO) enrichment analysis revealed that in the chicken samples, these genes were significantly enriched for metabolic and developmental processes, whereas in guineafowls, they were prominently enriched for metabolic biological processes. Similarly, when conducting KEGG pathway analysis on the DEGs from chicken kidney tissue samples, it was observed that pathways related to neuroactive ligand-receptor interaction, the PPAR signaling pathway, the Adipocytokine signaling pathway, and ECM-receptor interaction were differentially enriched. In guineafowls, the KEGG pathway analysis of DEGs indicated differential enrichment in metabolic pathways, neuroactive ligand-receptor interaction, the calcium signaling pathway, and the FoxO signaling pathway. The study's discoveries have offered fresh perspectives on the intricate relationship between genetic and environmental elements in poultry's response to heat stress. The identification and selection of genes associated with heat tolerance enhances our comprehension of the molecular mechanisms implicated in heat stress among poultry. Consequently, this provides a promising and sustainable approach for breeding heat-tolerant poultry. This approach effectively addresses the challenges posed by heat stress, particularly in the context of climate change, and ultimately contributes to ensuring food security.