Gene annotation revealed functionally relevant candidates associated with skeletal growth and development (MTX2, FGF12, IGF, PPARGC1A, LIPC, LY86, and IL33).<h4>Discussion</h4>These findings provide new insights into the genetic basis of brachycephaly in Duolang sheep and offer strategies for genetic improvement, contributing to broader research on skeletal development and growth regulation in livestock. Here, FGF12 is linked to Brachycephaly.