The association analysis identified 26 genome windows containing several putative candidate genes, such as TMEM241, AP4S1, FTO, HYAL2, BBS2, CD52, CRYBG2, PIGV, WDTC1, EEF1A2, GBA2, FNIP1, ACSL6, STARD10, VPS26B, ACAD8, GLB1L3, NRN1L, LCAT, and SLC7A6. These genes contributed to FE traits in Egyptian goats, as they are involved in obesity, metabolism, and the transport of energy, vitamins, fatty acids, proteins, and lipids through diverse biological pathways. Here, BBS2 is linked to obesity due to melanocortin 4 receptor deficiency.