Genetic effects of SCD1 gene promoter polymorphism on serum biochemical indexes in ducks

ObjectiveThe genetic effects of duck SCD1 gene promoter polymorphism and serum biochemical indexes were analyzed to reveal the physiological regulation mechanism of duck SCD1 gene promoter and provide reference for future research on gene SCD1 and breeding of genetic markers.MethodGenetic variation of duck SCD1 gene promoter region was detected through a combination use of polymerase chain reaction restriction and fragment length polymorphism (PCR-RFLP)and DNA direct sequencing technology on the basis of constructing a DNA pool. Single nucleotide polymor-phisms(SNP)loci were aligned by online promoter analysis software to predict the effects of SNP loci on transcription factors in duck SCD1 gene promoter region(g.952260-g.954527). Genetic effects of promoter restriction site variation on serum biochemical indexes in parental generation Cherry Valley ducks were analyzed by SPSS 19.0 software.ResultEleven SNPs loci were detected in g.952260-g.954527 region in Cherry Valley duck SCD1 gene promoter. Among them, g. 952323C>A and g. 952661A>G site mutations led to disappearance of the original transcription factors D1 and Sp1 re-spectively;g. 952702 A>G site mutation produced a new transcription factor TEC1;no transcription factor binding sites or new transcription factor binding sites were found in g. 952591T>C,g. 952868A>T,g. 952869T>G,g. 952971G>C and g. 953301T>C mutation regions;g. 952873T>G and g. 954401T>C mutations led no change to transcription factors;g.954239C>T site mutation changed original transcription factors from Sp1,Sp1,Tra-1,and AP-2αto Sp1,Tra-1,ETF, and Sp1. Comparative analysis by PCR-Bgl II-RFLP method and direct sequencing showed that g. 952868A>T and g. 952869T>G double base mutation led to the change of original sequence from AGA952868T952869CT to AGT952868G952869CT, which produced new Bgl II enzyme cutting site. Three genotypes namely CC(2268 bp),CD(2268+1659+2268 bp)and DD(1659+609 bp),and two alleles(C and D)were produced. CC genotype and C allele were dominant genotype and dominant allele respectively,whose frequencies were 0.710 and 0.805. Effective alleles(Ne)and polymorphism informa-tion content(PIC) were 1.458 and 0.265 respectively,belonging to moderate polymorphism. Chi-square(χ2) results showed that genotypes distribution caused by Bgl II enzyme cutting site mutation greatly deviated from the Hardy-Wein-berg equilibrium(χ2>χ20.01,P<0.01). The correlation analysis between Bgl II enzyme cutting site mutation and serum bio-chemical indexes in parental Cherry Valley ducks showed that the serum biochemical markers of DD genotype in Cherry Valley duck were slightly better than those of the other two genotypes.ConclusionEleven SNPs loci are detected in SCD1 gene promoter region g. 952260-g. 954527 of Cherry Valley duck. Among them,g. 952868A>T and g. 952869T>G site variations produce a new Bgl II enzyme cutting site,and this enzyme cutting site may have regulatory effects on duck serum biochemical indexes.