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Genetic polymorphism study at 15 autosomal locus in central Indian population.

Shrivastava P, Jain T, Trivedi VB - Springerplus (2015)

Bottom Line: Locus wise allele frequencies of the studied population were compared with the other published populations.Also the Clustering pattern and genetic distance of studied populations is compared and presented with various populations.The studied population showed the genetic proximity with geographically close populations of India and significant genetic variation with distant populations which is also evident by clustering pattern of the NJ tree and the PCA plot.

View Article: PubMed Central - PubMed

Affiliation: DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Govt. of MP, Sagar, 470001 India.

ABSTRACT
The analysis of 15 autosomal STR locus (TH01, D3S1358, vWA, D21S11, TPOX, D7S820, D19S433, D5S818, D2S1338, D16S539, CSF1PO, D13S317, FGA, D18S51, D8S1179) was done in 582 healthy unrelated individuals (Male-366, Female-216) originating from the various geographical regions of Madhya Pradesh, India. All locus fall under Hardy-Weinberg equilibrium except TPOX. These STR loci were highly informative and discriminating with combined power of discrimination (CPD) >0.99999. Locus wise allele frequencies of the studied population were compared with the other published populations. Also the Clustering pattern and genetic distance of studied populations is compared and presented with various populations. The studied population showed the genetic proximity with geographically close populations of India and significant genetic variation with distant populations which is also evident by clustering pattern of the NJ tree and the PCA plot.

No MeSH data available.


NJ tree for the studied population with other reported populations from different countries based on Nei’s genetic distances
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Fig2: NJ tree for the studied population with other reported populations from different countries based on Nei’s genetic distances

Mentions: The expected heterozygosity and the power of discrimination calculated from allele frequencies obtained from central Indian population revealed that in combination, the 15 autosomal STRs have a high forensic efficacy. Locus wise allele frequencies of studied population were compared at all 15 loci with the other published Indian populations including geographically close populations viz. Chenchu (Andhra Pradesh), Lambadi (Andhra Pradesh), Yerucula (Andhra Pradesh) and Naikpood (Andhra Pradesh) (Bindu et al. 2005), Adimiong (Arunachal Pradesh) and Adipasi (Arunachal Pradesh) (Krithika et al. 2007), Munda (Chotanagpur), Santal (Chotanagpur) and Oraon (Chotanagpur) (Banerjee et al. 2005), Kora (Bengal), Lodha (Bengal) and Maheli (Bengal) (Singh et al. 2006), Bhil (Gujrat) (Chaudhari and Dahiya 2014), Balmiki (Punjab), Sakaldwipi Brahmin (Jharkhand), Munda (Jharkhand), Konkanastha Brahmin (Maharashtra), Mahadev Koli (Maharashtra), Iyengar (Tamilnadu), Kurumans (Tamilnadu), Tripuri (Tripura) and Riang (Tripura) (Ghosh et al. 2011), Bhil (Madhya Pradesh) (Shrivastava et al. 2015b) populations using Pairwise Fst distance ranging from −0.003 to 0.247 (Tables 5, 6, 7, 8). Central Indian population showed a considerable genetic distance with other published indian population which were used for comparison (Table 1). Central Indian population showed significant variation at 14 loci with Lodha (Bengal), at 11 loci with Adi pasi population (Arunachal Pradesh) and Kora population (Bengal), at 10 loci with Yerukula population (Andhra Pradesh) and Maheli population (Bengal), at 9 loci with Adiminyong population (Arunachal Pradesh), at 8 loci with Naikpod Gond population (Andhra Pradesh) and Oraon population (Chotanagpur), at 7 loci with Riang population (Tripura) and Munda population (Chotanagpur), at 6 loci with Chencheu population (Andhra Pradesh), Santal population (Chotanagpur) and Mahadev koli population (Maharashtra), at 5 loci with Bhil (Gujrat), at 4 loci with Tripuri population (Tripura), at 3 locus with Munda population (Jharkhand) and Sakaldwipi brahmin population (Jharkhand), at 2 loci with Konkanastha Brahmin population (Maharashtra), Kurumans population (Tamilnadu), Balmiki population (Punjab) and Bhil population (Madhya Pradesh) and at 1 locus with Iyengar (Tamilnadu). Central Indian population showed no significant variation from Lambadi population (Andhra Pradesh). Neighbour Joining dendrogram (Figs. 1, 2) based on Nei’s genetic distance (Nei 1972) showed genetic relationships of the studied population with other Indian published populations. The grouping of populations in PCA plot (Fig. 3) is also found consistent with the clustering pattern observed in the NJ tree.Table 5


Genetic polymorphism study at 15 autosomal locus in central Indian population.

Shrivastava P, Jain T, Trivedi VB - Springerplus (2015)

NJ tree for the studied population with other reported populations from different countries based on Nei’s genetic distances
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4627979&req=5

Fig2: NJ tree for the studied population with other reported populations from different countries based on Nei’s genetic distances
Mentions: The expected heterozygosity and the power of discrimination calculated from allele frequencies obtained from central Indian population revealed that in combination, the 15 autosomal STRs have a high forensic efficacy. Locus wise allele frequencies of studied population were compared at all 15 loci with the other published Indian populations including geographically close populations viz. Chenchu (Andhra Pradesh), Lambadi (Andhra Pradesh), Yerucula (Andhra Pradesh) and Naikpood (Andhra Pradesh) (Bindu et al. 2005), Adimiong (Arunachal Pradesh) and Adipasi (Arunachal Pradesh) (Krithika et al. 2007), Munda (Chotanagpur), Santal (Chotanagpur) and Oraon (Chotanagpur) (Banerjee et al. 2005), Kora (Bengal), Lodha (Bengal) and Maheli (Bengal) (Singh et al. 2006), Bhil (Gujrat) (Chaudhari and Dahiya 2014), Balmiki (Punjab), Sakaldwipi Brahmin (Jharkhand), Munda (Jharkhand), Konkanastha Brahmin (Maharashtra), Mahadev Koli (Maharashtra), Iyengar (Tamilnadu), Kurumans (Tamilnadu), Tripuri (Tripura) and Riang (Tripura) (Ghosh et al. 2011), Bhil (Madhya Pradesh) (Shrivastava et al. 2015b) populations using Pairwise Fst distance ranging from −0.003 to 0.247 (Tables 5, 6, 7, 8). Central Indian population showed a considerable genetic distance with other published indian population which were used for comparison (Table 1). Central Indian population showed significant variation at 14 loci with Lodha (Bengal), at 11 loci with Adi pasi population (Arunachal Pradesh) and Kora population (Bengal), at 10 loci with Yerukula population (Andhra Pradesh) and Maheli population (Bengal), at 9 loci with Adiminyong population (Arunachal Pradesh), at 8 loci with Naikpod Gond population (Andhra Pradesh) and Oraon population (Chotanagpur), at 7 loci with Riang population (Tripura) and Munda population (Chotanagpur), at 6 loci with Chencheu population (Andhra Pradesh), Santal population (Chotanagpur) and Mahadev koli population (Maharashtra), at 5 loci with Bhil (Gujrat), at 4 loci with Tripuri population (Tripura), at 3 locus with Munda population (Jharkhand) and Sakaldwipi brahmin population (Jharkhand), at 2 loci with Konkanastha Brahmin population (Maharashtra), Kurumans population (Tamilnadu), Balmiki population (Punjab) and Bhil population (Madhya Pradesh) and at 1 locus with Iyengar (Tamilnadu). Central Indian population showed no significant variation from Lambadi population (Andhra Pradesh). Neighbour Joining dendrogram (Figs. 1, 2) based on Nei’s genetic distance (Nei 1972) showed genetic relationships of the studied population with other Indian published populations. The grouping of populations in PCA plot (Fig. 3) is also found consistent with the clustering pattern observed in the NJ tree.Table 5

Bottom Line: Locus wise allele frequencies of the studied population were compared with the other published populations.Also the Clustering pattern and genetic distance of studied populations is compared and presented with various populations.The studied population showed the genetic proximity with geographically close populations of India and significant genetic variation with distant populations which is also evident by clustering pattern of the NJ tree and the PCA plot.

View Article: PubMed Central - PubMed

Affiliation: DNA Fingerprinting Unit, State Forensic Science Laboratory, Department of Home (Police), Govt. of MP, Sagar, 470001 India.

ABSTRACT
The analysis of 15 autosomal STR locus (TH01, D3S1358, vWA, D21S11, TPOX, D7S820, D19S433, D5S818, D2S1338, D16S539, CSF1PO, D13S317, FGA, D18S51, D8S1179) was done in 582 healthy unrelated individuals (Male-366, Female-216) originating from the various geographical regions of Madhya Pradesh, India. All locus fall under Hardy-Weinberg equilibrium except TPOX. These STR loci were highly informative and discriminating with combined power of discrimination (CPD) >0.99999. Locus wise allele frequencies of the studied population were compared with the other published populations. Also the Clustering pattern and genetic distance of studied populations is compared and presented with various populations. The studied population showed the genetic proximity with geographically close populations of India and significant genetic variation with distant populations which is also evident by clustering pattern of the NJ tree and the PCA plot.

No MeSH data available.