SNP Analysis Of GHRHR And BTN1A1 Genes Their Associations With Economic Traits In Dairy Goats

The PCR-SSCP, PCR-RFLP, CRS-PCR-RFLP and DNA pool sequencing techniques were applied to detect the genetic diversity of the GHRHR (P1-P7) and BTN1A1 (M1-M6) genes in XNSN and GZ dairy goats and association analysis were carried out to evaluate the effects of genotypes of candidate genes on economic traits of the two dairy breeds. The objects were to discover the dominant genetypes and to provide scientific grounds for foundation of molecular marker database for genetic breeding. The results were as follows:1. Association between genetic variation of GHRHR gene and growth traits in XNSN and GZ dairy goatThe varations of seven loci (P1-P7) include GHRHR gene nine exons were studied in 708 dairy goats. In XNSN and GZ dairy goat, the polymorphisms were found in P3, P4 and P7 loci, while P1, P2, P5 and P6 loci were not. The results showed four novel single nucleotide polymorphisms (SNPs): NC₀07302:g.5203C>T, 7307C>G, 9583G>A and 9668A>C. In detail, the novel SNP C>T in the 5203rd nucleotide identified a missense mutation: CCC (Pro)>TCC (Phe) at position 116aa of the goat GHRHR (423aa). There were two genotypes in the P3 locus of GHRHR gene: A3A3 and A3B3. Genotype A3A3 was the dominant genotype and allele A3 was the dominant allele. In P4 and P7 loci of GHRHR gene was discovered three genetypes. A4A4 and A7A7 was the dominant genotype in the body height and body length and allele A4 and A7 was the dominant allele. Besides, 9583G>A and 9668A>C polymorphism were in complete linkage disequilibrium. The genetic diversity analysis revealed that the Guanzhong dairy goat possessed intermediate genetic diversity in P3 and P7 loci, and the Xinong Sannen dairy goat belonged to poor genetic diversity in P4 locus. Theχ2 test of the genotype distributions showed that there was no significant difference between three SNPs loci of the two populations (P>0.05). The two dairy goat breeds were all in Hardy-Weinberg disequilibrium. Association analysis result between every polymophic locus and growth traits showed that different genotypes of P3 locus significantly affect on body length, body height and chest circumference in GZ dairy goat(P<0.05). However, in XNSN population, significant statistical difference was only found in body height and body length (P<0.05). In P4 and P7 loci, no significant associations were detected between any variant sites and body length, body height and chest circumference, as well as for the milk traits (P>0.05).2. Association between genetic variation of BTN1A1 gene and milk traits in two dairy goat breedsWe investigated genetic varations of BTN1A1 gene (M1-M6 loci) including the all exons and the 5'and 3'untranslated region in the two dairy goat breeds. The results revealed a novel mutation: XM₀01494179:g.8659 C>T, which identified a missense mutation at BTN1A1 locus: CTT (Leu)> TTT (Phe) at position 377 aa of the BTN1A1 (526 aa). We detected this SNP by creating restriction enzyme cutting site method and found three genotypes: CC, TC and TT. Genotype CC was the dominant genotype and C allele was the dominant allele in milk yield and milk protein aspects. The frequencies of genotype CC in Xinong Sannen dairy and Guanzhong dairy populations were 0.726 and 0.415. According to the classification of polymorphism information content (PIC), Guanzhong dairy goat was intermediate polymorphic at this locus and the Xinong Sannen dairy goat belonged to poor genetic diversity. The two dairy goat breeds were all in Hardy-Weinberg disequilibrium. Association analysis demonstrated: CC genotype significant differences between TT genotypes in first milk yield,milk protein and milk fat (P<0.05).