Genome wide association studies of growth differentiation factor 9 (GDF9) gene in indigenous sheep in Khyber Pakhtunkhwa, Pakistan

Polymorphism contributes to variations in phenotypic traits among sheep breeds. Growth differentiation factor 9 is a key regulator of growth and reproductive performance in sheep. This study aimed to identify single nucleotide polymorphisms in six local sheep breeds from Khyber Pakhtunkhwa and to assess the association of these SNPs with reproductive traits. Blood samples were collected and genotyped using Next Generation Sequencing, which revealed 89 SNPs across the six breeds. The majority (94.3%) of these SNPs were located in upstream regions, suggesting a modifier role, while 5.7% were synonymous variants with minimal impact on amino acid sequence. A T-C synonymous variant (p. Leu159Leu) was found in Balkhi, Damani, Kaghani, and Kari breeds, indicating a low impact on protein structure. An additional T-C SNP (p. Glu326Glu) with a similarly low impact was observed specifically in the Hashtnagri breed. Twelve SNPs showed a positive correlation with litter size, with the Kari and Hashtnagri breeds exhibiting higher litter sizes. In conclusion, the majority of identified SNPs appear to act as modifiers, and 12 SNPs are specifically associated with litter size.