Detection of GDF9 Exon2 SNPs and Investigation of their Association with Prolificacy in Two Egyptian Goat Breeds

Abstract

The high prolific Zaraibi and low prolific Barki are among Egypt's most common indigenous goat breeds. The prolificacy of goat herds can be increased by selecting animals having single-nucleotide polymorphisms (SNPs) in fecundity-related genes. Herein, we detailed the use of DNA sequences followed by quantitative polymerase chain reaction (qPCR) and high-resolution melting curve (HRM) analysis to detect SNPs in exon 2 of the prolificacy-linked gene GDF9 and investigate their association with prolificacy in Zaraibi (n = 100) and Barki (n = 100) goats. The results of DNA sequencing (n = 20/breed) were used as a reference for genotyping the remaining DNA samples using qPCR-HRM. A non-synonymous SNP p.V371M/c.1111G>A in was detected in GDF9 of Zaraibi goats, however, Barki goats were monomorphic for this locus. The three genotypes of the c.1111G>A SNPs were significantly associated with litter size in Zaraibi goats. Homozygous mutant genotypes (c.1111AA) had significantly higher litter sizes than other genotypes (P < 0.05). Based on these findings, we recommend selecting Zaraibi goats with c.1111AA genotypes to increase the prolificacy of this breed.