CONCLUSION
A total of 1,122,858 InDels were detected based on the whole genome resequencing data of 46 Australian Boer goats and 81 local goats. Among which, 11,229 candidate InDels with top 1% high signal were screened, and 1,239 candidate genes were annotated. Gene enrichment experiment identified important genes from muscle development, reproduction, immunity, and metabolism. The results provide a theoretical basis for the study of related genetic mechanisms in goats and valuable foundation for molecular breeding in goats.