Genotyping of flavin-containing mono-oxygenase 3 (FMO3) gene by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and mismatch amplification mutation assay (MAMA-PCR) in chickens

Abstract

Fishy smelling off-flavour of chicken meat is caused by a mutation (FMO3 c.985A>T) in exon 7 of flavincontaining mono-oxygenase 3 (FMO3) gene. Comparative analysis of the causative mutation in FMO3 gene in different chickens using two different methods was reported. Polymerase chain reactionrestriction fragment length polymorphism (PCR-RFLP) method was based on general primers, whereas another employed method was the mismatch amplification mutation assay (MAMA) primers. Seventy (22.88%) of the 306 samples were genotyped using PCR-RFLP, 194 (63.40%) of the 306 samples were genotyped using MAMA-PCR and 42 (13.72%) of the 306 samples were genotyped by both of PCR-RFLP and MAMA-PCR and genotyping data were validated by DNA sequencing. The results show that the genotyping accuracy for PCR-RFLP was 90.48% in AA, 85.42% in AT and 95.35% in TT and 100% in AA, 98% in AT and 96% in TT for MAMA-PCR. This study suggests that the MAMA-PCR is more effective, accurate, easy, fast, efficient and reliable than PCR-RFLP.

Key words: FMO3 gene, chicken, mutation, PCR-RFLP, MAMA-PCR.