PRJNA576318
Gallus gallus gallus Transcriptome or Gene expression
The aim of this study was to identify the genes involved in the comb development and to provide insights into molecular mechanism of comb formation in chickens. Fixation index (Fst) and average number of base differences (?p) of two groups of males with large and small combs were calculated based on whole-genome resequencing data. The chromosome regions with larger Fst value and smaller ?p were considered as candidate regions of selection. Through further annotation of gene functions and pathways, we sought to screen possible selected genes associated with comb development. By screening whole genome resequencing data, the Fst and ?p were calculated using a 40Kb sliding window strategy. Eight regions were identified. QTLs (FOX1 gene) related to comb length were found on chromosome 1. QTLs (GLP1R, BTBD9, MIR6633, MDGA1 genes) related to comb weight were found on chromosome 3. QTLs (ALDH1A1, TMC1, ANXA1 genes) associated with comb area were found on the Z chromosome. Twenty genes, Wnt signaling pathway and neuroactive ligand-receptor interaction signaling pathway directly or indirectly related to comb growth and development were found through functional annotation and Go analysis using PANTHER. Among the selected genes LYN, GLP1R, FOX1, TBK1, STRAP, ST6GALNAC) and Wnt signaling pathways were related to immunity. MDGAl, BTBD9, MTSS1, SrGAPs and neuroactive ligand receptor interaction signaling pathways related to neural function were screened. ALDH1A1, ANXAl, THBS, HIF-1a, ACTN1 genes were related to heat dissipation. Among the selected genes FOX1, MDGAl and ANXAl associated with immunity, neurological function, and heat dissipation function coincided with genes affecting the length, weight, and area of the comb. Comprehensive analysis suggested that comb development was due to multiple genes and signaling pathways.