Fecundity gene SNPs as informative markers for assessment of Indian goat genetic architecture

Single nucleotide polymorphisms (SNPs) are the most abundant form of DNA polymorphism which can be used as simple genetic markers for many breeding applications as well as for population studies. SNPs in fecundity (Fec) genes viz. BMPR1B, GDF9 and BMP15 were genotyped in Indian goat breeds to assess their basic population parameters and genetic structuring, using simple and economical methods of PCR-RFLP and Tetra-primer ARMS PCR. Three hundred and ninety one animals of seven different goat breeds differing in prolificacy, utility and geographic distribution were employed for diversity assessment at six loci in these Fec genes. Four loci were polymorphic in all the breeds with varied allelic frequencies. Statistical analysis revealed that breeds differed with respect to genetic variability as observed heterozygosity varied from 0.163 (Ganjam) to 0.359 (Jakhrana). Sangamneri and Osmanabadi were least differentiated (0.003) whereas Jakhrana and Black Bengal were most differentiated (0.048) on the basis of genetic distance. The genetic distance as well as PCA analysis indicated that breeds are grouped according to their geographical distribution. The genetic diversity based on fecundity genes presented here is an essential step towards the future exploitation of the available goat genetic resources in research and breeding programs.