Development of multilocus putatively neutral DNA markers in the X-chromosome for population genetic studies in humans.

Naazneen Khan, Anita Chittoria, Veena Pande, Yogesh Kumar Jaiswal, Aparup Das

Index: Ann. Hum. Biol. 39(4) , 281-9, (2012)

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Abstract

It has now been well documented that the type (coding, non-coding) and location (nuclear, mitochondrial etc.) of genetic markers heavily influence evolutionary inferences; realistic assumptions can be drawn if multiple putatively neutral DNA fragments spread across the genome are used.To infer human population history, Single Nucleotide Polymorphisms (SNPs), located in the non-coding regions of different genes in the X-chromosome have been developed as 'putatively neutral markers'.A population sample consisting of 16 male individuals from the western part of India was utilized for sequencing eight DNA fragments located in introns of three genes (Duchenne muscular dystrophy, Factor IX and Pyruvate dehydrogenase E1 sub-unit) on the human X-chromosome. PCR amplification and DNA sequencing confirmed the polymorphic status of all the fragments.Twenty nine SNPs were found to be segregating in the Western Indian population samples. Using these SNPs the nucleotide diversity and demographic parameters of the Western Indian population were estimated. Several tests of neutrality ascertained that all eight fragments evolve putatively neutrally. Further, linkage disequilibrium analyses confirmed this fact.All eight DNA fragments seem to bear the characteristics to be considered as 'putatively neutral genetic markers' and thus, could be utilized for inference of human population and demographic histories.