The significant deposition of tail fat in sheep has a profound impact on the economic benefits of animal husbandry. Furthermore, increasing the litter size is a crucial means of enhancing economic benefits. The BMPR1B and T/Brachyury genes are considered major functional genes that could affect sheep litter size and tail bone number, respectively. In this study, we employed direct sequencing to identify specific mutations of the BMPR1B gene in Gobi short tail sheep and carried out genotyping using MassARRAY technology for each variant of both the BMPR1B and T genes. Significant associations were demonstrated between the c.687G>A mutation of BMPR1B and the litter size in both the Gobi short tail sheep and Ujimqin sheep breeds. Meanwhile, the g.30058882_30058873GCAGATTAAAIndel mutation was significantly associated with the litter size in Gobi short tail sheep. These findings may provide valuable genetic markers for expanding sheep litter size. In addition, we also confirmed that the frequency of tail-bone-number-related T alleles was significantly higher in Gobi short tail sheep than in longer-tailed Ujimqin sheep.

Reproductive performance in sheep plays a crucial role in determining the economic efficiency of the industry, with increasing litter size being a key focus for genetic improvement. The BMP15 gene is widely recognized as a major gene influencing sheep fertility. In this study, specific mutations in the BMP15 gene of Gobi short tail sheep were identified through direct sequencing, and these mutations were genotyped using the MassARRAY system. The g.54285159_54285161TTA indel was significantly associated with litter size in Gobi short tail sheep (p < 0.05). Three mutations, including g.54291460G>A, g.54288671C>T, and the g.54285159_54285161TTA indel, were significantly associated with litter size in Ujimqin sheep (p < 0.05). Furthermore, the promoter activity analysis demonstrated that the A allele exhibited significantly higher promoter activity compared to the G allele of the g.54291460G>A mutation. These findings highlight valuable genetic markers for improving sheep litter size and provide a robust theoretical foundation for further research on the BMP15 gene’s role in reproduction.