Papers published

Genetic affinities among the lower castes and tribal groups of India: inference from Y chromosome and mitochondrial DNA

Ismail Thanseem; Kumarasamy Thangaraj; Gyaneshwer Chaubey; Vijay Kumar Singh; Lakkakula VKS Bhaskar; B Mohan Reddy; Alla G Reddy and Lalji Singh

Abstract

Background

India is a country with enormous social and cultural diversity due to its positioning on the crossroads of many historic and pre-historic human migrations. The hierarchical caste system in the Hindu society dominates the social structure of the Indian populations. The origin of the caste system in India is a matter of debate with many linguists and anthropologists suggesting that it began with the arrival of Indo-European speakers from Central Asia about 3500 years ago. Previous genetic studies based on Indian populations failed to achieve a consensus in this regard. We analysed the Y-chromosome and mitochondrial DNA of three tribal populations of southern India, compared the results with available data from the Indian subcontinent and tried to reconstruct the evolutionary history of Indian caste and tribal populations.

Results

No significant difference was observed in the mitochondrial DNA between Indian tribal and caste populations, except for the presence of a higher frequency of west Eurasian-specific haplogroups in the higher castes, mostly in the north western part of India. On the other hand, the study of the Indian Y lineages revealed distinct distribution patterns among caste and tribal populations. The paternal lineages of Indian lower castes showed significantly closer affinity to the tribal populations than to the upper castes. The frequencies of deep-rooted Y haplogroups such as M89, M52, and M95 were higher in the lower castes and tribes, compared to the upper castes.

Conclusion

The present study suggests that the vast majority (>98%) of the Indian maternal gene pool, consisting of Indio-European and Dravidian speakers, is genetically more or less uniform. Invasions after the late Pleistocene settlement might have been mostly male-mediated. However, Y-SNP data provides compelling genetic evidence for a tribal origin of the lower caste populations in the subcontinent. Lower caste groups might have originated with the hierarchical divisions that arose within the tribal groups with the spread of Neolithic agriculturalists, much earlier than the arrival of Aryan speakers. The Indo-Europeans established themselves as upper castes among this already developed caste-like class structure within the tribes.

Single Nucleotide Polymorphisms of the Alcohol Dehydrogenase Genes among the 28 Caste and Tribal Populations of India

B. M. Reddy, A. N. S. Reddy, T. Nagaraja, L.V. K. S. Bhaskar, K. Thangaraj, A. G. Reddy and L. Singh

Int J Hum Genet, 6(4): 309-316 (2006)

ABSTRACT We report single nucleotide polymorphisms (SNPs) at the four sites in ADH2 and ADH3 genes among the 28 populations from southern parts of Andhra Pradesh, India. A total of 1048 individuals belonging to 28 endogamous populations distributed in the contiguous areas of the 6 southernmost districts of Andhra Pradesh were enrolled for the present study. Genotyping involved PCR and sequencing. We sequenced exon 3 and 9 of ADH2 and exon 8 of ADH3, besides the ADH2 3’UTR- rs17033 (72 bases down stream of ADH2 Arg369Cys). The two sites of ADH2 (Arg47His and Arg369Cys) are found to be completely monomorphic showing only Arg47 and 369Arg (ADH2*1 allele), the remaining two sites were polymorphic. None of the 28 populations of this study deviated significantly from Hardy Weinberg Equilibrium proportions. The allele frequencies do not show any clear trend across socioeconomic groups. The degree of heterogeneity in the genotype frequencies among the hierarchical groups is significant for Ile349Val (df = 12; χ2 = 22.050) and not for the 3’UTR rs17033 (df = 6; χ2 = 9.765). The haplotype distribution among the hierarchical groups is found to be highly homogeneous and statistically nonsignificant (χ2 = 0.248, df = 18). Linkage disequilibrium does not exist between the two-polymorhic loci. The results were interpreted in the light of cultural patterns of the Indian hierarchical society.

Single nucleotide polymorphisms in alcohol dehydrogenase genes among some Indian populations

V. R. Rao ^, L. V. K. S. Bhaskar , C. Annapurna , A. G. Reddy , K. Thangaraj , A. Papa Rao , Lalji Singh

Abstract: Seven ADH genes, identified until now, located in the long arm of human chromosome 4, produce seven different isozymes involved in the metabolism of ethanol to acetaldehyde. Of the more than 500 SNPs reported in the coding and non-coding regions of these genes in the world databases, 11 are more extensively studied. Three SNPs, ADH1B Arg47His (Exon3), ADH1B Arg369Cys (Exon9) and ADH1C Val349Ile (Exon8), are functionally validated in terms of phenotype-genotype correlations and are in specific linkage disequilibrium (LD) with non-coding SNPs. However, the frequency of each SNP and configuration of LD varies among populations. The Indian populations studied were conspicuous by the complete absence of African specific allele ADH1B*369Cys, the negligible frequency of East Asian specific ADH1B*47His allele and the presence of a novel SNP ADH1B A3529G (Intron3). The ADH1C*349Ile was the only functional allele polymorphic with a strong LD block in all the populations studied and the high F_st value observed for the non-coding ADH1B Rsa1 variant was in conformity with world populations.

Allelic variation at the NPY gene in 14 Indian populations

L. V. K. S. Bhaskar, K. Thangaraj, A. M. Shah, G. Pardhasaradhi, K. Praveen Kumar, A.G. Reddy, A. Papa Rao, C. J. Mulligan, Lalji Singh and V. R. Rao

Abstract: NPY is a 36-aminoacid peptide expressed in several areas of the nervous system. Neuropeptide Y (NPY) receptors represent a widely diffused system that is involved in the regulation of multiple biological functions. The human NPY gene is located in chromosome 7. The functional significance of coding Leu7Pro polymorphism in the signal peptide of preproNPY is known. Six hundred and fifty four individuals of 14 ethnic Indian populations were screened for three mutations in the NPY gene, including Leu7Pro. We found the Pro7 frequencies among the studied populations were much higher than in previous studies from other parts of the world. The highest allele frequency of Pro7 was detected in the Kota population in the Nilgiri Hill region of south India and may reflect a past founder event or genetic drift. All populations followed Hardy Weinberg equilibrium for the assayed markers. A total of five haplotypes were observed out of which only two were found to be in high frequency in all populations. No linkage disequilibrium (LD) was observed across the tested alleles in any population with the exception of Leu7Pro and Ser50Ser in the Badaga population (χ2=13.969; p=0.0001).

Anthropological Perspective of the Single Nucleotide Polymorphisms in the NPY and DRD2 Genes among the Socio-Economically Stratified Populations of Andhra Pradesh, India

B. Mohan Reddy, A.N. Srikar Reddy, T. Nagaraju, L.V. K. S. Bhaskar, H.P. Singh, V. M. Naidu, K. Thangaraj, A.Govardhan Reddy, A. Nirmala, Lalji Singh

International Journal of Human Genetics, 07(4): 277-284; 2007

ABSTRACT: We report single nucleotide polymorphisms (SNP) at the two sites each of NPY and DRD2-Taq1 loci among the 28 populations from southern parts of Andhra Pradesh, India. The average allele frequency at these sites in these populations categorized into upper, middle and lower ranking castes, Muslims and tribes were also carried out in order to test if there is any trend in the allele frequency of some of these SNPs that are implicated in alcoholism. This was felt important as some of these hierarchical low ranking groups and tribes traditionally are known for addictive behavior, especially to alcohol, as against the prohibitive norms among most of the higher ranking castes. The trend in average allele frequency although suggests some association with these traditional behavioral patterns, the case control studies are required before inferring exact nature of this association. The bivariate plot between the NPY-C and Taq1A1 mean allele frequencies in the 28 populations and the lack of significant association between the genotypes of these two SNPs at the individual level rules out any possibility of co-adaptation between these two alleles, despite both being somewhat implicated in alcoholism.

Single Nucleotide Polymorphisms of ALDH2 gene in six Indian populations

L. V. K. S. Bhaskar, K. Thangaraj, Michael Osier, A.G. Reddy, A. Papa Rao, Lalji Singh and V. R. Rao

^{Annals of Human Biology, 34(6): 607-619; 2007}

Abstract:

Background: Aldehyde dehydrogenase-2 (ALDH2) degrades acetaldehyde metabolized from ethanol. Its encoding gene ALDH2 has a functional polymorphism, ALDH2 Glu487Lys associated with low enzyme activity.

Aim: Since Glu487Lys of this locus is fixed for the functional subunit in all non-East Asian populations; we examined this polymorphism along with G–357A promoter (SacI) and other four intronic loci to identify informative markers to study the role of this gene in Indian populations.

Subjects and methods: A total of 397 males belonging to six ethnic populations, from four linguistic groups of India were included in the present study. No test was performed to detect the phenotype of alcoholism. Genotype of ALDH2*E487K, and G–357A promoter site along with four non–coding Single Nucleotide Polymorphisms (SNPs) in the upstream of this polymorphism were determined by PCR and sequencing.

Results: All of the subjects were found to have the common homozygous genotype (ALDH2*1/ALDH2*1) for the E487K site. Allele frequencies of non–coding SNPs varied among populations but genetic variance (Fst) indicated little variation among populations. Only four major SNP-defined haplotypes accounted for almost all chromosomes in all populations. The ancestral haplotype was found in high frequency in all populations and linkage disequilibrium (LD) was strong and highly significant between all sites (P<0.05).

Conclusion: The small number of haplotypes in this region is suggestive of strong LD across the region confirms the global long range LD at around the ALDH2 locus. This study provides a baseline for future research into the role of the ALDH2 locus in alcoholism in Indian populations.

Maternal Footprints of Southeast Asians in North India

Kumarasamy Thangaraj, Gyaneshwer Chaubey, Toomas Kivisild, Vijay Kumar Singh, Selvi-Rani Deepa, Thanseem Ismail, Denise Carvalho-Silva, Mait Metspalu, LVKS Bhaskar, Sharat Chandra, Niharika Adarsh, Abhilasha Verma, Inaganti Amara Jyothi, Chandana Basu Mallick, Nidhi Shrivastava, Ragala Devasena, Babita Kumari, Amit Kumar Singh, Shailendra Kumar Dhar Diwedi, Shefali Singh, Geeta Rao, Pranav Gupta, Kavita Kumari, Afsar Basha, K. R Bhargavi, Albert Lalremruata, Aravind Kumar Gupta, K. K. Reddy. A. Papa Rao, Alla G. Reddy, Richard Villems, Chris Tyler-Smith, Lalji Singh. Hum Hered 2008;66:1-9 (DOI: 10.1159/000114160)

Abstract:

We have analyzed 7,137 samples from 125 different caste, tribal and religious groups of India and 99 samples from three populations of Nepal for the length variation in the COII/tRNALys region of mtDNA. Samples showing length variation were subjected to detailed phylogenetic analysis based on HVS-I and informative coding region sequence variation. The overall frequencies of the 9-bp deletion and insertion variants in South Asia were 1.9 and 0.6%, respectively. We have also defined a novel deep-rooting haplogroup M43 and identified the rare haplogroup H14 in Indian populations carrying the 9-bp deletion by complete mtDNA sequencing. Moreover, we redefined haplogroup M6 and dissected it into two well-defined subclades. The presence of haplogroups F1 and B5a in Uttar Pradesh suggests minor maternal contribution from Southeast Asia to Northern India. The occurrence of haplogroup F1 in the Nepalese sample implies that Nepal might have served as a bridge for the flow of eastern lineages to India. The presence of R6 in the Nepalese, on the other hand, suggests that the gene flow between India and Nepal has been reciprocal.

Genetic heterogeneity in the Indian stocks of seahorse (Hippocampus kuda and Hippocampus trimaculatus) inferred from mtDNA

Mukunda Goswami, Kumaraswamy Thangaaraj, Binod Chaudhary, LVKS. Bhaskar, Achamveettil Gopalakrishnan, M Joshi, Lalji Singh, Wazir Lakra. cytochrome b gene. Hydrobiologia (2009) 621:213–221.

Genetic stock structure analysis of two seahorse species from the south east and south west coasts of India (37 samples of Hippocampus kuda and 39 samples of Hippocampus trimaculatus from Kollam (Kerala) and Mandapam (Tamil Nadu)) was carried out through sequence variation analysis of a 350 bp cytochrome b fragment of mitochondrial DNA. This was taken up to support the breeding and restocking programme of these species in natural habitats for conservation purpose. The occurrence of strong genetic subdivision among the samples, detected by the analysis of molecular variance (AMOVA), and significant ΦST values indicated that stocks of both the species in the two Indian coasts are distinct. The findings of the present study have important implications for conservation and management of these two species and we recommend stock-specific, breeding assisted sea-ranching programme for H. kuda and H. trimaculatus along the Indian coasts.

Molecular genetic analysis of Neuropeptide Y (NPY) gene in patients with cardiac arrhythmia
L.V.K.S. Bhaskar, K. Thangaraj, Pallavi Subramanian, P.S Dandapani, Solomon F. D. Paul. . Sri Ramachandra Journal of medicine, August 2008, 8-13.

Background: The heart is powered by an electrical impulse that signals the heart to contract, each at a proper time. Cardiac arrhythmia is any group of conditions in which the electrical activity of the heart is irregular or is faster or slower than normal. In arrhythmia, the heart rate either goes beyond 100 or below 60 beats per minute and this is called tachycardia and bradycardia respectively. NPY is co release with norepinephrine during sympathetic nerve stimulation, and is extensively involved in cardiovascular regulation because it modulates heart rate, cardiac excitability, and ventricular function as well as coronary blood flow.
Materials and Methods: In this study, we included 40 arrhythmia and 46 healthy unrelated individuals to examine the NPY gene polymorphisms. All four exons were screened using PCR and sequencing method.
Results: Three polymorphisms (Leu7Pro, Ser50Ser and A7735G) and one novel mutation (G172T) were obtained. Association was found only between one marker (Ser50Ser) and the arrhythmia. Weak linkage disequilibrium (LD) was seen between all the pairs of SNPs. The LD between Ser50Ser and A7735G was found to be significant. The distribution of haplotypes in arrhythmia and normal was not statistically significant.
Conclusion: NPY gene Leu7Pro polymorphism, which has been reported earlier as a potential cause for many of the cardiac problems, is not associated with arrhythmia in Indian population.

Current concepts in genetics of nonsyndromic clefts.
Jyotsna Murthy, L. V. K. S. Bhaskar. Indian J Plast Surg Jan-June 2009 Vol 42 Issue 1

Nonsyndromic cleft lip and palate is a complex genetic disorder with variable phenotype, largely attributed to the interactions of the environment and multiple genes, each potentially having small effects. Numerous genes have been reported in studies demonstrating associations and/or linkage of the cleft lip and palate phenotypes to alleles of microsatellite markers and single nucleotide polymorphisms within specific genes that regulate transcription factors, growth factors, cell signalling and detoxification metabolisms. Although the studies reporting these observations are compelling, most of them lack statistical power. This review compiles the evidence that supports linkage and associations to the various genetic loci and candidate genes. Whereas significant progress has been made in the field of cleft lip and palate genetics in the past decade, the roles of the genes and genetic variations within the numerous candidate genes that have been found to associate with the expression of the orofacial cleft phenotype remain to be determined.

Dopamine transporter (DAT1) VNTR polymorphism in 12 Indian populations

LVKS Bhaskar, Kumarasamy Thangaraj, Connie J. Mulligan, Samiksha Wasnik, Amrita Nandan, Varun Kumar Sharma, Vishwas Sharma, Alla Govardhana Reddy, Lalji Singh and Vadlamudi Raghavendra Rao., Neurological Sciences 2009, 10.1007/s10072-009-0139-2.

The dopamine transporter (DAT1) is a membrane spanning protein that binds the neurotransmitter dopamine and performs re-uptake of dopamine from the synapse into a neuron. The gene encoding DAT1 consists of 15 exons spanning 60 kb on chromosome 5p15.32. Several studies have investigated the possible associations between variants in DAT1 gene and psychiatric disorders. The present study aimed to determine the distribution of the variable number of tandem repeat (VNTR) polymorphism in the 3′ untranslated region of DAT1 in 12 Indian populations. A total of 471 healthy unrelated individuals in 12 Indian populations from 3 linguistic groups were included in the present study. The analysis was carried out using PCR and electrophoresis. Overall, 4 alleles of the DAT1 40-bp VNTR, ranging from 7 to 11 repeats were detected. Heterozygosity indices were low and varied from 0.114 to 0.406. The results demonstrate the variability of the DAT1 40-bp VNTR polymorphism in Indian populations and revealed a high similarity with East Asian populations.

Neuropeptide Y gene functional polymorphism influences susceptibility to hypertension in Indian population

LVKS Bhaskar , K Thangaraj , A L Non , K Praveen Kumar , G Pardhasaradhi , L Singh & V R Rao Journal of Human Hypertension advance online publication, 24 December 2009; doi:10.1038/jhh.2009.104

Hypertension is an independent determinant of cardiovascular risk, a phenotype that usually has a strong genetic component. Neuropeptide Y (NPY) plays an important role in BP homeostasis. The aim of this study was to investigate the possible influence of NPY polymorphisms on hypertension in a South Indian population. A total of 252 subjects (132 controls and 120 hypertensives) were analysed for T1128C, G1258A and A7735G polymorphisms in the NPY gene. Body mass index (BMI), pulse, SBP and DBP were assessed. Direct sequencing of PCR products was adopted for genotyping. All three polymorphisms were found to be in Hardy–Weinberg equilibrium. Additive, dominant and recessive models were tested using multivariate regression analysis. The results of our study reveal a significant association between T1128C and hypertension even after adjusting for age, sex and BMI. The adjusted OR (95|[percnt]| confidence interval) for the recessive model was 0.56 (0.33–0.95). The other two polymorphic sites (G1258A and A7735G) are not associated with hypertension. The Pro7 allele of the T1128C polymorphic site-containing haplotype (CGA) is associated with hypertension (P|[equals]|0.049), but the combined haplotypes did not show any evidence of haplotype–phenotype association (global P|[equals]|0.129). These data support the hypothesis that hypertension is influenced by the NPY T1128C polymorphism.

Neuropeptide Y Gene Polymorphisms are Not Associated With Obesity in a South Indian Population

LVKS Bhaskar, K. Thangaraj, G. Pardhasaradhi, K. Praveen Kumar, Lalji Singh, V.R.Rao. European journal of clinical nutrition, 2010

Background: Neuropeptide Y (NPY) gene has been shown to play a critical role in the regulation of satiety, reproduction, central endocrine and cardiovascular systems. Among the primary functions associated with NPY are its acute effects on feeding behavior and energy expenditure.

Objective: To evaluate the relationship between obesity and neuropeptide Y gene polymorphisms in a South Indian Population.

Design: Three polymorphisms in NPY (Leu7Pro, Ser50Ser and A7735G) were analysed in 263 individuals of an endogamous Kota population. Based on BMI, they were divided in to two groups. Associations were tested using Logistic regression and haplotype analyses and linkage disequilibrium.

Results: There was no evidence of deviation for Hardy-Weinberg equilibrium. Logistic regression analysis did not reveal significant association with obesity and NPY SNPs in the present study. All three SNPs were in weak LD with low r2 values. Haplotype analysis also did not yield significant association between NPY gene and obesity (Global p=0.756).

Conclusions: Our study did not validate the association between previously implicated SNPs in NPY gene and the Obesity in an Indian population. Population specific validation of putative associations has far reaching implications for the future personal genomics medicine applications.

Population-based case-control study of DRD2 gene polymorphisms and Alcoholism

LVKS Bhaskar , K Thangaraj , A L Non, L Singh & V R Rao. Journal of Addictive diseases. 2010.

There are several independent lines of evidence for genetic contributions to vulnerability to alcoholism. Dopamine is thought to play a major role in the mechanism of reward and reinforcement in response to alcohol. D2 dopamine receptor (DRD2) gene has been among the stronger candidate genes implicated in alcoholism. In this study, alcohol use was assessed in 196 randomly selected Kota individuals of Nilgiri Hills, South India. Six DRD2 SNPs were assessed in 81 alcoholics and 151 controls to evaluate the association between single nucleotide polymorphisms (SNPs) and alcoholism. Of the three models (dominant, recessive, and additive) tested for association between alcoholism and DRD2 SNPs, only the additive model shows association for three loci (rs1116313, TaqID and rs2734835). Out of six studied polymorphisms, five are in strong linkage disequilibrium (LD) forming onesingle haplotype block. Though the global haplotype analysis with these five SNPs was not significant, haplotype analysis using all six SNPs yielded a global P value of 0.033, even after adjusting for age. These findings support the importance of dopamine receptor gene polymorphisms in alcoholism. Further studies to replicate these findings in different populations are needed to confirm these results.