Investigation of SNPs in GDF9 gene and their relationship with some reproductive traits of Ossimi and Rahmani sheep in different lambing seasons

Abstract Background Fertility is an important economic trait for sheep breeding. The growth differentiation factor 9 (GDF9) is a key gene influencing the reproductive traits in sheep. We focused on investigating SNPs in the GDF9 gene and their relationship with some reproductive traits like pre-mating weight, lambing weight, litter size (LS), DRIL (days from rams’ introduction to lambing), lamb birth weight, lamb gender and survival rate in Ossimi and Rahmani sheep. PCR, Single‑strand conformational polymorphism and sequencing were performed on the genomic DNA of 231 ewes (144 Ossimi and 87 Rahmani) to demonstrate polymorphisms in a fragment of 274 bp within exon 2 of the GDF9 gene. Results Two linked SNPs (A/G and G/A) were observed in GDF9 gene in Ossimi and Rahmani sheep, revealed by two haplotypes (AAGG and AGGA). For Rahmani sheep, the haplotype AGGA was significantly (P value < 0.001) higher than AAGG in lambing weight and LS (1.40 ± 0.02) but AAGG was markedly higher in pre-mating weight and lamb birth weight. In Ossimi sheep, the AGGA haplotype was significantly (P value < 0.0001) greater in pre-mating weight, lambing weight and lamb birth weight than AAGG. The effect of the interaction of GDF9 gene polymorphism and the lambing season showed that in Rahmani sheep AGGA haplotype in winter was significantly (P value is < 0.0001) increased in pre-mating weight and LS (1.80 ± 0.03) than other interactions but it was significantly (P value < 0.0001) higher for lambing weight and lower in DRIL (159.0 ± 1.0) in spring than other seasons. In Ossimi sheep AGGA haplotype in spring was significantly higher in pre-mating weight, lambing weight, LS (1.50 ± 0.07) and lamb birth weight but lower in DRIL (163.17 ± 2.71 days) than in other seasons. The ewes with the AAGG haplotype gave birth to more males (56.3%) than the heterozygous ones (33.3%) in Ossimi sheep, unlike Rahmani. Conclusion SNPs in the GDF9 gene can be used as potential genetic markers for reproductive traits in Ossimi and Rahmani sheep where AGGA can be the desirable haplotype for litter size, DRIL, lamb birth weight, ewe pre-mating weight and ewe lambing weight.