Litter size is an important economical trait in sheep and goat breeding. Applying traditional animal breeding systems such as selection and mating based on phenotypic evaluations are time-consuming and usually costly. In this case, molecular genetics can be an alternative solution. Some genetics studies have proven that litter size is genetically determined by the action of single genes with a major effect, named fecundity genes. This study was carried out to detect polymorphism in GDF9 gene. Ninety one Najdi goats of 3 locations in northwest, southeast and center of Khouzestan and 27 Lori-Bakhtiari goats, in 2 locations, north-eastern and south-eastern of province were selected randomly. After extracting of DNA, amplification of a 295 bp fragment of exon 2 of GDF9 gene was performed using specific primers. In this research three SSCP patterns for exon 2 of GDF9 gene in two breeds of goats were found in Khuzestan Province. However, no significant correlation between the observed patterns and the multiple pregnancy rate was observed in the two goat breeds. Allele A in Najdi goat populations of the northwest and southeast, and in Lori-Bakhtiari goats of northeast and southeast have the highest frequency. AB genotype had the highest frequency in Najdi goats of southeast and middle populations while, in the northwest population, the AA genotype was more frequent. The populations of Lori-Bakhtiari goats in all studied locations (northeast and southeast) exhibit the AA genotype as the most frequent genotype.
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