Genetic variation landscape of sheep GDF9 gene from global ewes breeds and their association with gestation days

Growth differentiation Factor 9 (GDF9) has been confirmed to be closely related to the reproductive capacity of sheep. This study systematically investigated the genetic variation of the GDF9 gene across 75 global sheep breeds (n = 2,409) and explored its association with gestation days in Australian White sheep (AUW, n = 120). Through whole-genome sequencing and SNP analysis, 49 SNPs (26 located in introns, 22 in exons, and 1 in the 3' UTR region) and 20 InDel loci were identified within GDF9 gene. Haplotype analysis revealed six major haplotypes strongly correlated with geographical population distribution. Association studies in Australian White sheep demonstrated a significant difference between three SNPs loci (g.42115010T > C, g.42115254T > C, and g.42114509T > C) and gestation days: primiparous ewes with the CC genotype at g.42,115,010 exhibited the shortest gestation days (146.42 ± 2.57 days, P = 0.030), while fourth-parity ewes with the AG genotype at g.42,114,509 showed an abnormally prolonged gestation (155.00 ± 12.81 days, P = 0.030). Key missense mutations (e.g., E241K, R87H) were predicted to alter protein 3D structure, suggesting functional impacts on reproductive regulation. Despite limited sample sizes in certain parity groups, suggests that GDF9 may serve a potential genetic marker for optimizing reproductive efficiency, offering molecular strategies to shorten primiparous gestation and uncovering its evolutionary role in sheep domestication.