Clone, Polymorphism Detection And Association Analysis With Economic Traits Of SCD Gene In Dairy Goat

Stearoyl-CoA desaturase (SCD) is an iron-containing enzyme involving in the biosynthesis of monounsaturated fatty acids (MUFA) in mammary gland and adipose tissue. In ruminants, several studies have reported that variations in SCD gene are significantly associated with beef and milk fatty acid composition. In this study, we detected the polymorphisms of goat SCD gene by DNA Pooling, PCR-SSCP, PCR-RFLP and Sequencing methods in 708 dairy goats including Xinong Saanen and Guanzhong breed. These variations were associated with a series of economic traits (Wither height, Body Length, Heart girth, milk composition and milk yield of the first three lactation) in order to assist the construction of molecular markers database and the breeding of Chinese excellent dairy goat breeds. The whole CDS region of SCD gene was also obtained by RT-PCR. The results are as follows:1. Polymorphisms of SCD gene in two Chinese dairy goat breedsThis research identified 5 bases variations of SCD gene in Exon 3 (AF 325499:EX3₁5G>A,EX3₆8A>G), Intron 3 (IVS3+55A>G), Exon 5 (EX5₁12G>T) and 3'UTR (r.3178-3180 Del TGT). Among them, we identified a missense mutation (EX3₁5G>A), which caused the 109th amino acid of SCD protein from Val to Met. EX3₆8A>G and EX5₁12G>T were synonymous mutation.The missense mutation (EX3₁5G>A) in E-3.1 locus of SCD gene was identified by the restrict enzyme NdeI. Both of the two dairy goat breeds possessed low genetic diversity. This locus was in Hardy-Weinberg equilibrium in Xinong Saanen dairy goat breed, whereas not in Guanzhong dairy goat breeds. Two mutations (EX3₁5G>A and IVS3+55A>G), which created two restrict enzyme MspI recognition site, were identified in E-3.2 locus of SCD gene by the restrict enzyme MspI. In the EX3₆8A>G locus, both of the two dairy goat breeds possessed moderate genetic diversity and were in Hardy-Weinberg disequilibrium. In the IVS3+55A>G locus, both of the two dairy goat breeds possessed low genetic diversity because the PIC in two breeds were below 0.25. This locus was in Hardy-Weinberg equilibrium in Xinong Saanen dairy goat breed, whereas not in Guanzhong dairy goat breed. This research identified the genetic variants in E-5 and 3'UTR locus using PCR-SSCP and sequencing methods. In E-5 locus, EX5₁12G>T was a synonymous mutation. Both of the two dairy goat breeds possessed low genetic diversity in this locus because the PIC in two breeds was below 0.1. Both of the two breeds were in Hardy-Weinberg disequilibrium in EX5₁12G>T locus. This research identified the 3-bp deletion in 3'UTR locus, both of the two dairy goat breeds possessed low genetic diversity in this locus because the PIC of the two breeds were below 0.2. This locus was in Hardy-Weinberg equilibrium in Xinong Saanen dairy goat breed, whereas not in Guanzhong dairy goat breed.2. Relationsships between genetic variations of SCD gene and economic traitsIn E-3.1 locus, individuals with genotype VV possesses significantly larger body length than individuals with genotype VM in Guanzhong dairy goat breed (P<0.05). No significant differences were found in Xinong Sannen dairy goat breed. This research identified 2 bases variations in E-3.2 locus. In EX3₆8A>G locus, individuals with genotype G1G1 possesses significantly larger withers height and body length than individuals with genotype A1G1 in Guanzhong dairy goat breed (P<0.05), individuals with genotype G1G1 possesses significantly larger body length and higher milk yield in first lactation than individuals with genotype A1A1 (P<0.05). In IVS3+55A>G locus, individuals with genotype A2A2 possesses significantly larger body length than individuals with genotype A2G2 in Guanzhong dairy goat breed (P<0.05); no significant differences were found in grow traits between individuals with different genotypes in Xinong Sannen dairy goat breed. In E-5 locus, No significant differences were found in various index between individuals with different genotypes in both Guanzhong and Xinong Sannen dairy goat breed. In 3'UTR locus, individuals with genotype DD possesses significantly higher withers height than individuals with genotype WW in Guanzhong dairy goat breed (P<0.05), individuals with genotype WD possesses significantly higher milk fat and total solid than individuals with genotype WW in Xinong Sannen dairy goat breed(P<0.05). The association analysis between combined genotypes and economic traits in Xinong Saanen dairy goat breed revealed: individuals with XN6 had significant lager withers height than XN2 and XN5; XN6 has significant lager milk yield in first lactation than XN1å’ŒXN2 individuals.3. Clone the CDS of SCD geneThe full length of the SCD gene CDS was 1080 bp, which encoded a polypeptide of 359 amino acids. The homologies of cDNA nucleotide sequence of SCD gene with the counterparts of ovis (NM₀01009254), bovine (NM₁73959), swine (NM₂13781), homo(AF097514)and mouse (NM₀09127) were 98%, 95%, 90%, 86% and 82% respectively; and the homologies of peptide sequence were 98%,94%,88%,86% and 83% respectively. The molecular weight and IP of SCD is 41.58 KDa and 9.19 respectively. SCD protein has 7 hydrophobic regions and 4 transmembrane domains.