Avian

Genomic characteristics of heat tolerance-related variations among native and commercial chicken populations

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Abstract

Global warming-induced heat stress reduces productivity and compromises poultry survivability, resulting in substantial economic losses in poultry production. Chickens are particularly vulnerable to heat stress because of their limited thermoregulatory capacity. Korean native chickens (KNCs) represent valuable indigenous genetic resources that have undergone long-term adaptation to the native environment. However, the genetic basis of heat tolerance in KNCs remains insufficiently explored. In this study, we investigated genetic diversity and population differentiation by analyzing single nucleotide polymorphism (SNP) variation across 19 reported heat tolerance candidate genes (SOCS2, HSPH1, ARPP21, RB1CC1, HSF1, PLCB4, CITED2, HSF3, TSHR, HSP90AA1, HSP70, SIRT1, NFKB2, BAG3, HSP60, PRKCA, HSP25, CDC3, and LPAR2). A total of 129 chickens were analyzed, comprising six KNC lines (gray-brown, black, red-brown, yellow-brown, white, and Yeonsan Ogye), tropical native chickens from five countries (Indonesia, Bangladesh, Sri Lanka, Thailand, and Vietnam), and commercial breeds (Italian White Leghorn, Iranian commercial broiler, U.S. Rhode Island Red, and U.S. White Plymouth Rock). Next-generation sequencing (NGS) data were derived from open data repositories (Galbase and NABIC), and after quality control, 8,197 SNPs were retained for analysis. FST and genetic distance analyses revealed strong genetic differentiation of KNCs from other populations. Principal component analysis (PCA) revealed separation between KNCs and all other populations along the first principal component (PC1). SNP loading analysis identified major contributions from several candidate genes, including PLCB4, PRKCA, and ARPP21. SNPs within PLCB4 accounted for 23.3% of the total PC1 loading, increasing to 42.1% when only the top 1% of SNPs by absolute loading were considered. Given its known involvement in immune regulation and oxidative stress responses, PLCB4 may play a role in genetic differentiation related to heat stress adaptation. PRKCA, HSP60, and TSHR genes also showed increased proportional contributions under stricter percentile thresholds, further supporting their relevance as candidate genes. To evaluate the contribution of high-impact variants to population structure, SNPs within the top 1% and 5% of absolute PC1 loadings were extracted and used for PCA. These analyses further clarified the separation between KNCs and other populations, while tropical native and commercial populations formed more compact clusters. These patterns reinforce the pronounced genetic separation of KNCs from other populations, indicating that KNCs harbor substantial genetic diversity. Furthermore, the genetic structures of tropical native chickens appear to reflect long-term thermal selection associated with heat tolerance, whereas commercial populations are predominantly shaped by artificial selection. Overall, this study suggests that variations in major heat tolerance-related genes may contribute to genetic differentiation between KNCs and all other populations. Although phenotypic data were not available to directly assess heat stress responses, these findings provide genomic insights into heat tolerance-related gene diversity in KNCs and provide a foundation for future phenotype-integrated analyses and heat-tolerance breeding strategies.

Keywords: 2026

How to Cite:

Cho, E., Kim, J., Fernando, R. & Lee, E., (2026) “Genomic characteristics of heat tolerance-related variations among native and commercial chicken populations”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2286705. doi: https://doi.org/10.31274/wcgalp.24098

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