荣昌猪芯片数据选择信号检测OA

Selection Signatures based on SNP chip data was used to identify candidate genes associated with important economic traits in Rongchang pigs,providing a reference for the genetic analysis of local pig breeds.A total of 377 Rongchang pigs were genotyped using a 50 K SNP chip,detecting 48022 SNPs.After quality control,32281 valid SNPs were retained for selection signatures.Two methods,iHS and CLR,were employed to detect selective regions across the whole genome,and next significant SNPs identified by both methods were annotated and subjected to functional screening.The results showed that iHS detected 223 significant SNPs distributed across all chromosomes,while the CLR method identified 178 significant selective windows containing a total of 3505 SNPs.Eleven significant SNPs were overlaped by two methods.Annotation of these 11 SNPs revealed 25 genes,among which candidate genes related to important economic traits were further screened,including the body size-related gene HMGA1,and fat deposition and muscle development-related genes COL14A1,SPDEF,PACSIN1,and NUDT3.In summary,Selection signatures of SNP chip data from Rongchang pigs identified 11 significant selective SNPs annotated to 25 genes,which may serve as candidate genes related to body size(HMGA1),fat deposition,and muscle development(COL14A1,SPDEF,PACSIN1,NUDT3)in Rongchang pigs.