Abstract
The acute thermal response has been extensively studied in commercial chickens because of the adverse effects of heat stress on poultry production worldwide. Here, we performed whole-genome resequencing of autochthonous Niya chicken breed native to the Taklimakan Desert region as well as of 11 native chicken breeds that are widely distributed and reared under native humid and temperate areas. We used combined statistical analysis to search for putative genes that might be related to the adaptation of hot arid and harsh environment in Niya chickens. We obtained a list of intersected candidate genes with log2 θπ ratio, FST and XP-CLR (including 123 regions of 21 chromosomes with the average length of 54.4 kb) involved in different molecular processes and pathways implied complex genetic mechanisms of adaptation of native chickens to hot arid and harsh environments. We identified several selective regions containing genes that were associated with the circulatory system and blood vessel development (BVES, SMYD1, IL18, PDGFRA, NRP1, and CORIN), related to central nervous system development (SIM2 and NALCN), related to apoptosis (CLPTM1L, APP, CRADD, and PARK2) responded to stimuli (AHR, ESRRG FAS, and UBE4B) and involved in fatty acid metabolism (FABP1). Our findings provided the genomic evidence of the complex genetic mechanisms of adaptation to hot arid and harsh environments in chickens. These results may improve our understanding of thermal, drought, and harsh environment acclimation in chickens and may serve as a valuable resource for developing new biotechnological tools to breed stress-tolerant chicken lines and or breeds in the future.
Highlights
Domestic chickens (Gallus gallus domesticus) were most likely domesticated from wild Red Jungle Fowls (Miao et al, 2013; Wang M.-S. et al, 2020) and became the most abundant domestic animals all over the world (Lawler, 2014)
The acute heat response has been extensively studied in commercial chickens because of the adverse effects of heat stress on poultry production worldwide (Nawab et al, 2018) and some studies have been done to exam the environmental adaptability of native chickens (Elbeltagy et al, 2019; Walugembe et al, 2019; Wang Q. et al, 2020), there are short of reports on the genetic mechanisms of domestic chickens adapting to naturally occurring hot arid and harsh environments with multiple stressors in China
5.50 M SNPs were detected in each native chicken individual, and an average of 93.27% of the SNPs were validated in the chicken dbSNP (Build 151) database (Supplementary Table 4), indicating the high reliability of the called SNP variations in this study
Summary
Domestic chickens (Gallus gallus domesticus) were most likely domesticated from wild Red Jungle Fowls (Miao et al, 2013; Wang M.-S. et al, 2020) and became the most abundant domestic animals all over the world (Lawler, 2014). Considering the characteristics of short reproductive and growth periods and large clutch sizes, chickens can be used as ideal models to study genetic adaptations to environments. The acute heat response has been extensively studied in commercial chickens because of the adverse effects of heat stress on poultry production worldwide (Nawab et al, 2018) and some studies have been done to exam the environmental adaptability of native chickens (Elbeltagy et al, 2019; Walugembe et al, 2019; Wang Q. et al, 2020), there are short of reports on the genetic mechanisms of domestic chickens adapting to naturally occurring hot arid and harsh environments with multiple stressors (e.g., heat stress, drought, and other adverse stimuli) in China
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