Haplotype Block Analysis of FSHR Gene in Sragen and Jabres Cattle

The Follicle Stimulating Hormone (FSHR) is an anterior pituitary gonadotropin belonging to the family of glycoprotein hormones. The gene controls growth and fecundity in cattle.   Blood samples of Sragen cattle (10 samples) and Jabres cattle (19 samples) were used for DNA extraction to define the single nucleotide polymorphism (SNP). Three SNPs have been detected, namely SNP g.175A/G (SNP1), SNP g.227T/C (SNP2) and SNP g.275A/C (SNP3). Three blocks (SNPs combination) have been analyzed for haplotype block using haploview. As a result, all the blocks have high D' (D prime: 1.0). The highest LOD and r-squared were detected in block 1 (SNP1&2 combination), 9.23 and 1.0, respectively. Two of the blocks having similar LOD (1.23) and r-squared (0.28). Two haplotypes frequencies are defined in SNP1&2 combinations/block 1 (GT/79.3% ; CC/20.7%). Three haplotypes have been detected in SNP2&3 combinations (block 2), namely TC, TA and CA, with genotype frequency are 51.7%, 27.6% and 20.7%, respectively. Similarly, SNP1&3 combinations (block 3) indicate three haplotypes with the same frequency but different genotypes; GC, GA and CA, respectively. In conclusion, the haplotype from block 1 (SNP1&2 combination) could be used for further association analysis with reproduction traits in Sragen and Jabres cattle.