The MRNA Expression And SNPs Analysis Of Candidate Genes Associated With Beak Deformity Trait In Beijing-You Chickens

A certain frequencies (about0.5-2.5%) of beak deformity (crossed beaks) in various indigenous chickens has been reported, which severely impacts on the growth and production performance of chickens by the decreasing of feed and water intake which results some economic losses. Based on the former results (DGE test), this paper selected six genes including BMP4, CK19, Claw keratin-like, LPL, ALDH7A1and GLA for analyzing mRNA expression and SNPs. The polymorphisms of candidate genes were studied, and their associations with the beak deformity trait in Beijing-You chickens and the differential expression of those genes between deformed and normal beak tissues were analyzed in this research, aiming to provide theoretical and scientific foundation for screening such candidate genes, find out the mechanism of beak deformity trait in the field of molecular genetics, and also to provide some references for molecular marker-assisted breeding.Chickens with deformed beaks and their sibs (n=9each group) were chosen at56-days of age for sample selection of beaks. Real-time quantitative PCR was used to analyze the differences of mRNA expression of those genes between deformed and normal beak tissues. Meanwhile, the same chickens (n=18each group) were chosen at56-days of age. Single nucleotide polymorphisms (SNPs) were detected on promoter,5’UTR,3’UTR, all the exons and introns of candidate genes by direct sequencing. The genotype frequencies were analyzed and compared between beak deformity and normal birds. The results were as follows:Trial1:The relative expression levels of candidate genes in deformed and normal beak tissues were detected by real-time quantitative PCR. The results showed that the expression levels of BMP4, Claw keratin-like and LPL genes’mRNA in deformed beaks were significantly higher than normal ones (P<0.05); while the expression levels of CK19, ALDH7A1and GLA genes were significant higher than deformed ones (P<0.05). This research got the same results with the DGE test (the results with high reliability and accuracy) and made a further step to reveal that the expression of candidate genes probably had some regulatory effects on the beak deformity trait.Trial2:SNPs of candidate genes were detected by direct sequencing and45SNPs were screened out. The genotype frequencies of every locus were analyzed and compared between beak deformity and normal birds. The results showed that no mutations were detected in beak deformity birds at G-272A locus of promoter region of gene CK19, whereas individuals with different genotypes had significant differences with normal birds (P<0.05). No mutations were detected in normal birds at A7816T locus of intron7of gene ALDH7A1, but individuals with different genotypes had significant differences with beak deformity birds (P<0.05). And no mutations were detected in beak deformity birds at C4815T locus of exon7of gene GLA, but individuals with different genotypes had significant differences with normal birds (P<0.05); while mutations were detected in both beak deformity and normal birds at A4552C locus of intron6of this gene with highly significant differences (P<0.01). Other loci had no significant differences (P>0.05).Combined with the results of trial one and trial two, gene CK19, ALDH7A1and GLA had significant differences loci of genotype frequencies and also expression levels between beak deformity and normal birds. Therefore, we draw a conclusion that these three genes may be acted as key candidate genes in the formation of beak deformity for further research.