This study aimed to identify and evaluate the effects of single nucleotide polymorphisms (SNPs) within miR-9 and miR-27a genes and their promoters, as well as 30UTR regions of KITLG and IGF1 genes on itter size in Markhoz goats. PCR-SSCP analysis revealed different band patterns and sequencing results confirmed four SNPs including a C/A, a A/G, a C/T and a A/G substitution located in the promoter region of miR-9 gene, 48 bp upstream of miR-9 seed region within the 30UTR of KITLG gene, 37 bp downstream of miR-27a gene and 39 bp upstream of miR-9 seed region within the 30UTR of IGF1 gene, respectively. The results of the least-square analyses indicated that AA genotype of miR-9 gene strongly and positively affects litter size in Markhoz goats (P < 0.01). Furthermore, the results of the logistic regression analyses confirmed that the A allele of miR-9 gene has a tremendous impact on litter size in Markhoz goats (P < 0.01). Scanning the promoter region of miR-9 gene showed that changing C allele to A may prevent HES1, HES2, NRF1 and TCFL5 transcription factors (TFs) from binding to the promoter, which can reduce the expression of miR-9 gene. Principle component analysis (PCA) showed that approximately 60% of the variation of the data set was explained by two of four SNPs. Also, the biplot from the PCA showed a strong association between litter size and C/A polymorphism of miR-9 promoter. Linkage disequilibrium analysis revealed a very slight linkage among investigated loci.
