Identification and characterization of a polymorphic mono-nucleotide microsatellite within 16S rRNA gene in chicken mitochondrial genome
2009
Zhao, S., Gansu Agricultural Univ., Lanhou 730070, Gansu (China). Coll. of Animal Science and Technology | Hanotte, O., University of Nottingham, University Park, NG 2RD Nottingham (United Kingdom). School of Biology | Han, J., International Livestock Research Inst.., P.O. Box 30709, Nairobi 00100 (Kenya)
An alignment of 17 complete mitochondrial DNA(mtDNA) sequences of chickens and jungle fowls revealed a perfect mono-nucleotide microsatellite repeat unit consisting of between 8 and 13 Cs within the 16S rRNA gene in nine samples. However, the remaining eight sequences had three kinds of interrupted non-polymorphic fragments-(C)sub 4 T(C)sub 5, (C)sub 4 T(C)sub 6 and (C) sub 4 T(C) sub 3 (TC)-within the same region. To characterize this microsatellite, 344 samples of indigenous and commercial chicken populations as well as wild red jungle fowls were genotyped. Thirty-five were for the sequenced for the same region. Both genotyping and sequencing results confirmed the presence of these two types of structures in chicken mtDNA genome while the wild red jungle fowl samples only possessed one of the interrupted fragments, (C)sub 4 T(C) sub 5. Among the chickens analyzed, the two structures showed a clear pattern of geographic distribution. The perfect repeats were mainly detected in indigenous chickens from West Asia including Bangladesh, Myanmar and Pakistan and in the majority of commercial chickens. The interrupted fragment, also (C)sub 4 T(C)sub 5, occurred predominantly among indigenous chickens from south and Southeast Asia including China, Korea and Papua New Guinea. This polymorphic mono-nucleotide microsatellite, the first of its kind being validated in the avian mitochondrial genome, could be useful in providing insights into the evolutionary mechanism of polymorphic and/or instability of mtDNA microsatellite and also into a better estimation of the mutation rate of such microsatellite in birds.
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