Combined effects of three novel SNPs within goat LHX3 gene on milk performance

In this study, single nucleotide polymorphisms (SNPs) of LHX3 gene were detected by DNA sequencing based on DNA pools and PCR-RFLP method in 792 goats belonging to three Chinese indigenous breeds (Guanzhong dairy, Xinong Sannen dairy, Inner Mongolia white cashmere). The results revealed three novel mutations (AY923832:g.7778A>T; g.8035T>C; g.10592C>T), which were named as P2-DraI, P3-HinfI and P4-MspI loci, respectively. The linkage disequilibrium analysis demonstrated P3-HinfI and P4-MspI loci were strongly linked (r ²>0.33) in all the analyzed populations. Each SNP produced no significant (p>0.05) effects on milk performance. However, the two-loci and three-loci combined genotypes had more profound impacts on milk yield than in separation. The individuals with diplotype AATT (P2-DraI/P3-HinfI) showed significantly (p<0.05) higher milk yield than those with diplotypes ATTT, TTTT, ATTC, and AACC. Diplotype TTCCTT (P2-DraI/P3-HinfI/P4-MspI) carriers had significantly (p< 0.05) higher milk yield than those with diplotypes ATTTCC and AACCTC. These combined effects of LHX3 gene polymorphisms indicated that this gene had significant effect on milk performance and its corresponding combined diplotypes could be regarded as potential genetic markers of milk performance.