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The present broad range of sheep phenotypic variation is the consequence of selection for various production characteristics such as wool, milk, meat, and natural adaptability to diverse situations. In the current study, the genomic data of 79 animals from three Indian sheep breeds (Changthangi, Deccani, and Garole) were explored to decipher regions under positive selection for various productive traits using various statistical tools. We found 61, 102 regions using Tajima’s D, CLR and 58, 38, and 71 regions using F ST , FLK, and hapFLK, respectively, under selective sweep. Significant candidate genes related to various important traits, such as  KLHL  for fibre diameter and the  OMA1  gene for feed-induced thermogenesis in Changthangi, were identified. In addition, the  SYCP2  and  NAPAS3  genes were found to be associated with seasonal reproductivity, and  BMPR1B  for fertilization capacity in Garole. In a previous study, the  HSPA6  gene (Garole) was found to be associated with thermo-tolerance in the Angus sheep breed. The outcomes discussed here provide a basis for detecting selective sweeps that underlie genetic variations of traits that have functional importance.

Revealing Genomic Footprints of Selection for Fiber and Production Traits in Three Indian Sheep Breeds