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1.  Genetic affinities among the lower castes and tribal groups of India: inference from Y chromosome and mitochondrial DNA 
BMC Genetics  2006;7:42.
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.
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.
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.
PMCID: PMC1569435  PMID: 16893451
2.  Genetic variation in South Indian castes: evidence from Y-chromosome, mitochondrial, and autosomal polymorphisms 
BMC Genetics  2008;9:86.
Major population movements, social structure, and caste endogamy have influenced the genetic structure of Indian populations. An understanding of these influences is increasingly important as gene mapping and case-control studies are initiated in South Indian populations.
We report new data on 155 individuals from four Tamil caste populations of South India and perform comparative analyses with caste populations from the neighboring state of Andhra Pradesh. Genetic differentiation among Tamil castes is low (RST = 0.96% for 45 autosomal short tandem repeat (STR) markers), reflecting a largely common origin. Nonetheless, caste- and continent-specific patterns are evident. For 32 lineage-defining Y-chromosome SNPs, Tamil castes show higher affinity to Europeans than to eastern Asians, and genetic distance estimates to the Europeans are ordered by caste rank. For 32 lineage-defining mitochondrial SNPs and hypervariable sequence (HVS) 1, Tamil castes have higher affinity to eastern Asians than to Europeans. For 45 autosomal STRs, upper and middle rank castes show higher affinity to Europeans than do lower rank castes from either Tamil Nadu or Andhra Pradesh. Local between-caste variation (Tamil Nadu RST = 0.96%, Andhra Pradesh RST = 0.77%) exceeds the estimate of variation between these geographically separated groups (RST = 0.12%). Low, but statistically significant, correlations between caste rank distance and genetic distance are demonstrated for Tamil castes using Y-chromosome, mtDNA, and autosomal data.
Genetic data from Y-chromosome, mtDNA, and autosomal STRs are in accord with historical accounts of northwest to southeast population movements in India. The influence of ancient and historical population movements and caste social structure can be detected and replicated in South Indian caste populations from two different geographic regions.
PMCID: PMC2621241  PMID: 19077280
3.  Population Differentiation of Southern Indian Male Lineages Correlates with Agricultural Expansions Predating the Caste System 
PLoS ONE  2012;7(11):e50269.
Previous studies that pooled Indian populations from a wide variety of geographical locations, have obtained contradictory conclusions about the processes of the establishment of the Varna caste system and its genetic impact on the origins and demographic histories of Indian populations. To further investigate these questions we took advantage that both Y chromosome and caste designation are paternally inherited, and genotyped 1,680 Y chromosomes representing 12 tribal and 19 non-tribal (caste) endogamous populations from the predominantly Dravidian-speaking Tamil Nadu state in the southernmost part of India. Tribes and castes were both characterized by an overwhelming proportion of putatively Indian autochthonous Y-chromosomal haplogroups (H-M69, F-M89, R1a1-M17, L1-M27, R2-M124, and C5-M356; 81% combined) with a shared genetic heritage dating back to the late Pleistocene (10–30 Kya), suggesting that more recent Holocene migrations from western Eurasia contributed <20% of the male lineages. We found strong evidence for genetic structure, associated primarily with the current mode of subsistence. Coalescence analysis suggested that the social stratification was established 4–6 Kya and there was little admixture during the last 3 Kya, implying a minimal genetic impact of the Varna (caste) system from the historically-documented Brahmin migrations into the area. In contrast, the overall Y-chromosomal patterns, the time depth of population diversifications and the period of differentiation were best explained by the emergence of agricultural technology in South Asia. These results highlight the utility of detailed local genetic studies within India, without prior assumptions about the importance of Varna rank status for population grouping, to obtain new insights into the relative influences of past demographic events for the population structure of the whole of modern India.
PMCID: PMC3508930  PMID: 23209694
4.  Presence of three different paternal lineages among North Indians: A study of 560 Y chromosomes 
Annals of human biology  2009;36(1):46-59.
The genetic structure, affinities, and diversity of the 1 billion Indians hold important keys to numerous unanswered questions regarding the evolution of human populations and the forces shaping contemporary patterns of genetic variation. Although there have been several recent studies of South Indian caste groups, North Indian caste groups, and South Indian Muslims using Y-chromosomal markers, overall, the Indian population has still not been well studied compared to other geographical populations. In particular, no genetic study has been conducted on Shias and Sunnis from North India.
This study aims to investigate genetic variation and the gene pool in North Indians.
Subjects and methods
A total of 32 Y-chromosomal markers in 560 North Indian males collected from three higher caste groups (Brahmins, Chaturvedis and Bhargavas) and two Muslims groups (Shia and Sunni) were genotyped.
Three distinct lineages were revealed based upon 13 haplogroups. The first was a Central Asian lineage harbouring haplogroups R1 and R2. The second lineage was of Middle-Eastern origin represented by haplogroups J2*, Shia-specific E1b1b1, and to some extent G* and L*. The third was the indigenous Indian Y-lineage represented by haplogroups H1*, F*, C* and O*. Haplogroup E1b1b1 was observed in Shias only.
The results revealed that a substantial part of today’s North Indian paternal gene pool was contributed by Central Asian lineages who are Indo-European speakers, suggesting that extant Indian caste groups are primarily the descendants of Indo-European migrants. The presence of haplogroup E in Shias, first reported in this study, suggests a genetic distinction between the two Indo Muslim sects. The findings of the present study provide insights into prehistoric and early historic patterns of migration into India and the evolution of Indian populations in recent history.
PMCID: PMC2755252  PMID: 19058044
Paternal lineages; Y-chromosomal markers; North Indians; migration
5.  Molecular insight into the genesis of ranked caste populations of western India based upon polymorphisms across non-recombinant and recombinant regions in genome 
Genome Biology  2005;6(8):P10.
To trace admixture and genesis of caste populations of western India, polymorphisms were examined across non-recombining 20 Y-SNPs, 20 Y-STRs, 18 mtDNA diagnostic sites, HVS-1 plus HVS-2 regions; and recombining 15 highly polymorphic autosomal STRs in four predominant caste populations- upper-ranking Desasth-brahmin and Chitpavan-brahmin; a middle-ranking Kshtriya Maratha; and a lower-rank peasant Dhangar.
Large-scale trade and cultural contacts between coastal populations of western India and Western-Eurasians paved for extensive immigration and genesis of wide spectrum of admixed gene pool. To trace admixture and genesis of caste populations of western India, we have examined polymorphisms across non-recombining 20 Y-SNPs, 20 Y-STRs, 18 mtDNA diagnostic sites, HVS-1 plus HVS-2 regions; and recombining 15 highly polymorphic autosomal STRs in four predominant caste populations- upper-ranking Desasth-brahmin and Chitpavan-brahmin; a middle-ranking Kshtriya Maratha; and a lower-rank peasant Dhangar.
The generated genomic data was compared with putative parental populations- Central Asians, West Asians and Europeans using AMOVA, PC plot, and admixture estimates. Overall, disparate uniparental ancestries, and l.1% GST value for biparental markers among four studied caste populations linked well with their exchequer demographic histories. Marathi-speaking ancient Desasth-brahmin shows substantial admixture from Central Asian males but Paleolithic maternal component support their Scytho-Dravidian origin. Chitpavanbrahmin demonstrates younger maternal component and substantial paternal gene flow from West Asia, thus giving credence to their recent Irano-Scythian ancestry from Mediterranean or Turkey, which correlated well with European-looking features of this caste. This also explains their untraceable ethno-history before 1000 years, brahminization event and later amalgamation by Maratha. The widespread Palaeolithic mtDNA haplogroups in Maratha and Dhangar highlight their shared Proto-Asian ancestries. Maratha males harboured Anatolianderived J2 lineage corroborating the blending of farming communities. Dhangar heterogeneity is ascribable to predominantly South-Asian males and West-Eurasian females.
The genomic data-sets of this study provide ample genomic evidences of diverse origins of four ranked castes and synchronization of caste stratification with asymmetrical gene flows from Indo-European migration during Upper Paleolithic, Neolithic, and later dates. However, subsequent gene flows among these castes living in geographical proximity, have diminished significant genetic differentiation as indicated by AMOVA and structure.
PMCID: PMC4071276
6.  The Grandest Genetic Experiment Ever Performed on Man? – A Y-Chromosomal Perspective on Genetic Variation in India 
We have analysed Y-chromosomal data from Indian caste, Indian tribal and East Asian populations in order to investigate the impact of the caste system on male genetic variation. We find that variation within populations is lower in India than in East Asia, while variation between populations is overall higher. This observation can be explained by greater subdivision within the Indian population, leading to more genetic drift. However, the effect is most marked in the tribal populations, and the level of variation between caste populations is similar to the level between Chinese populations. The caste system has therefore had a detectable impact on Y-chromosomal variation, but this has been less strong than the influence of the tribal system, perhaps because of larger population sizes in the castes, more gene flow or a shorter period of time.
PMCID: PMC2987567  PMID: 21103011
Y chromosome; genetic variation; Indian caste system; endogamy; population substructure
7.  Genetic affinities between endogamous and inbreeding populations of Uttar Pradesh 
BMC Genetics  2007;8:12.
India has experienced several waves of migration since the Middle Paleolithic. It is believed that the initial demic movement into India was from Africa along the southern coastal route, approximately 60,000–85,000 years before present (ybp). It has also been reported that there were two other major colonization which included eastward diffusion of Neolithic farmers (Elamo Dravidians) from Middle East sometime between 10,000 and 7,000 ybp and a southern dispersal of Indo Europeans from Central Asia 3,000 ybp. Mongol entry during the thirteenth century A.D. as well as some possible minor incursions from South China 50,000 to 60,000 ybp may have also contributed to cultural, linguistic and genetic diversity in India. Therefore, the genetic affinity and relationship of Indians with other world populations and also within India are often contested. In the present study, we have attempted to offer a fresh and immaculate interpretation on the genetic relationships of different North Indian populations with other Indian and world populations.
We have first genotyped 20 tetra-nucleotide STR markers among 1800 north Indian samples of nine endogamous populations belonging to three different socio-cultural strata. Genetic distances (Nei's DA and Reynold's Fst) were calculated among the nine studied populations, Caucasians and East Asians. This analysis was based upon the allelic profile of 20 STR markers to assess the genetic similarity and differences of the north Indian populations. North Indians showed a stronger genetic relationship with the Europeans (DA 0.0341 and Fst 0.0119) as compared to the Asians (DA 0.1694 and Fst – 0.0718). The upper caste Brahmins and Muslims were closest to Caucasians while middle caste populations were closer to Asians. Finally, three phylogenetic assessments based on two different NJ and ML phylogenetic methods and PC plot analysis were carried out using the same panel of 20 STR markers and 20 geo-ethnic populations. The three phylogenetic assessments revealed that north Indians are clustering with Caucasians.
The genetic affinities of Indians and that of different caste groups towards Caucasians or East Asians is distributed in a cline where geographically north Indians and both upper caste and Muslim populations are genetically closer to the Caucasians.
PMCID: PMC1855350  PMID: 17417972
8.  Influence of language and ancestry on genetic structure of contiguous populations: A microsatellite based study on populations of Orissa 
BMC Genetics  2005;6:4.
We have examined genetic diversity at fifteen autosomal microsatellite loci in seven predominant populations of Orissa to decipher whether populations inhabiting the same geographic region can be differentiated on the basis of language or ancestry. The studied populations have diverse historical accounts of their origin, belong to two major ethnic groups and different linguistic families. Caucasoid caste populations are speakers of Indo-European language and comprise Brahmins, Khandayat, Karan and Gope, while the three Australoid tribal populations include two Austric speakers: Juang and Saora and a Dravidian speaking population, Paroja. These divergent groups provide a varied substratum for understanding variation of genetic patterns in a geographical area resulting from differential admixture between migrants groups and aboriginals, and the influence of this admixture on population stratification.
The allele distribution pattern showed uniformity in the studied groups with approximately 81% genetic variability within populations. The coefficient of gene differentiation was found to be significantly higher in tribes (0.014) than caste groups (0.004). Genetic variance between the groups was 0.34% in both ethnic and linguistic clusters and statistically significant only in the ethnic apportionment. Although the populations were genetically close (FST = 0.010), the contemporary caste and tribal groups formed distinct clusters in both Principal-Component plot and Neighbor-Joining tree. In the phylogenetic tree, the Orissa Brahmins showed close affinity to populations of North India, while Khandayat and Gope clustered with the tribal groups, suggesting a possibility of their origin from indigenous people.
The extent of genetic differentiation in the contemporary caste and tribal groups of Orissa is highly significant and constitutes two distinct genetic clusters. Based on our observations, we suggest that since genetic distances and coefficient of gene differentiation were fairly small, the studied populations are indeed genetically similar and that the genetic structure of populations in a geographical region is primarily influenced by their ancestry and not by socio-cultural hierarchy or language. The scenario of genetic structure, however, might be different for other regions of the subcontinent where populations have more similar ethnic and linguistic backgrounds and there might be variations in the patterns of genomic and socio-cultural affinities in different geographical regions.
PMCID: PMC549189  PMID: 15694006
9.  Genetic structure of four socio-culturally diversified caste populations of southwest India and their affinity with related Indian and global groups 
BMC Genetics  2004;5:23.
A large number of microsatellites have been extensively used to comprehend the genetic diversity of different global groups. This paper entails polymorphism at 15 STR in four predominant and endogamous populations representing Karnataka, located on the southwest coast of India. The populations residing in this region are believed to have received gene flow from south Indian populations and world migrants, hence, we carried out a detailed study on populations inhabiting this region to understand their genetic structure, diversity related to geography and linguistic affiliation and relatedness to other Indian and global migrant populations.
Various statistical analyses were performed on the microsatellite data to accomplish the objectives of the paper. The heretozygosity was moderately high and similar across the loci, with low average GST value. Iyengar and Lyngayat were placed above the regression line in the R-matrix analysis as opposed to the Gowda and Muslim. AMOVA indicated that majority of variation was confined to individuals within a population, with geographic grouping demonstrating lesser genetic differentiation as compared to linguistic clustering. DA distances show the genetic affinity among the southern populations, with Iyengar, Lyngayat and Vanniyar displaying some affinity with northern Brahmins and global migrant groups from East Asia and Europe.
The microsatellite study divulges a common ancestry for the four diverse populations of Karnataka, with the overall genetic differentiation among them being largely confined to intra-population variation. The practice of consanguineous marriages might have attributed to the relatively lower gene flow displayed by Gowda and Muslim as compared to Iyengar and Lyngayat. The various statistical analyses strongly suggest that the studied populations could not be differentiated on the basis of caste or spatial location, although, linguistic affinity was reflected among the southern populations, distinguishing them from the northern groups. Our study also indicates a heterogeneous origin for Lyngayat and Iyengar owing to their genetic proximity with southern populations and northern Brahmins. The high-ranking communities, in particular, Iyengar, Lyngayat, Vanniyar and northern Brahmins might have experienced genetic admixture from East Asian and European ethnic groups.
PMCID: PMC515297  PMID: 15317657
10.  Genomic view on the peopling of India 
India is known for its vast human diversity, consisting of more than four and a half thousand anthropologically well-defined populations. Each population differs in terms of language, culture, physical features and, most importantly, genetic architecture. The size of populations varies from a few hundred to millions. Based on the social structure, Indians are classified into various caste, tribe and religious groups. These social classifications are very rigid and have remained undisturbed by emerging urbanisation and cultural changes. The variable social customs, strict endogamy marriage practices, long-term isolation and evolutionary forces have added immensely to the diversification of the Indian populations. These factors have also led to these populations acquiring a set of Indian-specific genetic variations responsible for various diseases in India. Interestingly, most of these variations are absent outside the Indian subcontinent. Thus, this review is focused on the peopling of India, the caste system, marriage practice and the resulting health and forensic implications.
PMCID: PMC3514343  PMID: 23020857
Admixture; caste; Indians; mtDNA; tribe; Y-chromosome
11.  Gender variation in morphological patterns of lip prints among some north Indian populations 
Personal identification is an integral part of forensic investigations. For the same, DNA profiling and fingerprints are the most commonly used tools. But these evidences are not ubiquitous and may not necessarily be obtained from the crime scene. In such a scenario, other physical and trace evidences play a pivotal role and subsequently the branches employed are forensic osteology, odontology, biometrics, etc. A relatively recent field in the branch of forensic odontology is cheiloscopy or the study of lip prints. A comparison of lip prints from the crime scene and those obtained from the suspects may be useful in the identification or narrowing down the investigation.
The purpose of the present study is to determine the gender and population variability in the morphological patterns of lip prints among brahmins, Jats, and scheduled castes of Delhi and Haryana, India.
Settings and Design:
Samples were collected from Jats, brahmins, and scheduled castes of Delhi and Haryana. The total sample size consisted of 1399 individuals including 781 males and 618 females in the age group of 8–60 years. Care was taken not to collect samples from genetically related individuals. The technique was standardized by recording lip prints of 20 persons and analyzing them.
Materials and Methods:
Lip prints were collected by using a corporate's invisible tape and analyzed using a hand lens. The patterns were studied along the entire length and breadth of both the upper and the lower lip. The data were analyzed by SPSS statistical package version 17 to determine the frequencies and percentages of occurrence of the pattern types in each population group and a comparison between males and females among the groups was carried out by using the z test.
Results and Conclusions:
The z-test comparison between patterns of males and females shows significant differences with respect to pattern types I’, II, III, and IV among brahmins; I’, II, III, IV, and Y among Jats; and I, I’, II, III, and V among scheduled castes. Thus, it can be concluded that the variability of the lip print pattern can help sex differentiation among groups and that more studies on the lip print pattern should be carried out to bring new dimensions to forensic anthropology and to aid the law enforcement agencies.
PMCID: PMC3470412  PMID: 23087577
Cheiloscopy; gender; population variability
12.  Women's health in a rural community in Kerala, India: do caste and socioeconomic position matter? 
To examine the social patterning of women's self‐reported health status in India and the validity of the two hypotheses: (1) low caste and lower socioeconomic position is associated with worse reported health status, and (2) associations between socioeconomic position and reported health status vary across castes.
Cross‐sectional household survey, age‐adjusted percentages and odds ratios, and multilevel multinomial logistic regression models were used for analysis.
A panchayat (territorial decentralised unit) in Kerala, India, in 2003.
4196 non‐elderly women.
Outcome measures
Self‐perceived health status and reported limitations in activities in daily living.
Women from lower castes (scheduled castes/scheduled tribes (SC/ST) and other backward castes (OBC) reported a higher prevalence of poor health than women from forward castes. Socioeconomic inequalities were observed in health regardless of the indicators, education, women's employment status or household landholdings. The multilevel multinomial models indicate that the associations between socioeconomic indicators and health vary across caste. Among SC/ST and OBC women, the influence of socioeconomic variables led to a “magnifying” effect, whereas among forward caste women, a “buffering” effect was found. Among lower caste women, the associations between socioeconomic factors and self‐assessed health are graded; the associations are strongest when comparing the lowest and highest ratings of health.
Even in a relatively egalitarian state in India, there are caste and socioeconomic inequalities in women's health. Implementing interventions that concomitantly deal with caste and socioeconomic disparities will likely produce more equitable results than targeting either type of inequality in isolation.
PMCID: PMC2465509  PMID: 17108296
13.  Phylogeography of mtDNA haplogroup R7 in the Indian peninsula 
Human genetic diversity observed in Indian subcontinent is second only to that of Africa. This implies an early settlement and demographic growth soon after the first 'Out-of-Africa' dispersal of anatomically modern humans in Late Pleistocene. In contrast to this perspective, linguistic diversity in India has been thought to derive from more recent population movements and episodes of contact. With the exception of Dravidian, which origin and relatedness to other language phyla is obscure, all the language families in India can be linked to language families spoken in different regions of Eurasia. Mitochondrial DNA and Y chromosome evidence has supported largely local evolution of the genetic lineages of the majority of Dravidian and Indo-European speaking populations, but there is no consensus yet on the question of whether the Munda (Austro-Asiatic) speaking populations originated in India or derive from a relatively recent migration from further East.
Here, we report the analysis of 35 novel complete mtDNA sequences from India which refine the structure of Indian-specific varieties of haplogroup R. Detailed analysis of haplogroup R7, coupled with a survey of ~12,000 mtDNAs from caste and tribal groups over the entire Indian subcontinent, reveals that one of its more recently derived branches (R7a1), is particularly frequent among Munda-speaking tribal groups. This branch is nested within diverse R7 lineages found among Dravidian and Indo-European speakers of India. We have inferred from this that a subset of Munda-speaking groups have acquired R7 relatively recently. Furthermore, we find that the distribution of R7a1 within the Munda-speakers is largely restricted to one of the sub-branches (Kherwari) of northern Munda languages. This evidence does not support the hypothesis that the Austro-Asiatic speakers are the primary source of the R7 variation. Statistical analyses suggest a significant correlation between genetic variation and geography, rather than between genes and languages.
Our high-resolution phylogeographic study, involving diverse linguistic groups in India, suggests that the high frequency of mtDNA haplogroup R7 among Munda speaking populations of India can be explained best by gene flow from linguistically different populations of Indian subcontinent. The conclusion is based on the observation that among Indo-Europeans, and particularly in Dravidians, the haplogroup is, despite its lower frequency, phylogenetically more divergent, while among the Munda speakers only one sub-clade of R7, i.e. R7a1, can be observed. It is noteworthy that though R7 is autochthonous to India, and arises from the root of hg R, its distribution and phylogeography in India is not uniform. This suggests the more ancient establishment of an autochthonous matrilineal genetic structure, and that isolation in the Pleistocene, lineage loss through drift, and endogamy of prehistoric and historic groups have greatly inhibited genetic homogenization and geographical uniformity.
PMCID: PMC2529308  PMID: 18680585
14.  Fine-mapping of a QTL influencing pork tenderness on porcine chromosome 2 
BMC Genetics  2007;8:69.
In a previous study, a quantitative trait locus (QTL) exhibiting large effects on both Instron shear force and taste panel tenderness was detected within the Illinois Meat Quality Pedigree (IMQP). This QTL mapped to the q arm of porcine chromosome 2 (SSC2q). Comparative analysis of SSC2q indicates that it is orthologous to a segment of human chromosome 5 (HSA5) containing a strong positional candidate gene, calpastatin (CAST). CAST polymorphisms have recently been shown to be associated with meat quality characteristics; however, the possible involvement of other genes and/or molecular variation in this region cannot be excluded, thus requiring fine-mapping of the QTL.
Recent advances in porcine genome resources, including high-resolution radiation hybrid and bacterial artificial chromosome (BAC) physical maps, were utilized for development of novel informative markers. Marker density in the ~30-Mb region surrounding the most likely QTL position was increased by addition of eighteen new microsatellite markers, including nine publicly-available and nine novel markers. Two newly-developed markers were derived from a porcine BAC clone containing the CAST gene. Refinement of the QTL position was achieved through linkage and haplotype analyses. Within-family linkage analyses revealed at least two families segregating for a highly-significant QTL in strong positional agreement with CAST markers. A combined analysis of these two families yielded QTL intervals of 36 cM and 7 cM for Instron shear force and taste panel tenderness, respectively, while haplotype analyses suggested further refinement to a 1.8 cM interval containing CAST markers. The presence of additional tenderness QTL on SSC2q was also suggested.
These results reinforce CAST as a strong positional candidate. Further analysis of CAST molecular variation within the IMQP F1 boars should enhance understanding of the molecular basis of pork tenderness, and thus allow for genetic improvement of pork products. Furthermore, additional resources have been generated for the targeted investigation of other putative QTL on SSC2q, which may lead to further advancements in pork quality.
PMCID: PMC2213680  PMID: 17935628
15.  Determinants of Prelacteal Feeding in Rural Northern India 
Prelacteal feeding is an underestimated problem in a developing country like India, where infant mortality rate is quite high. The present study tried to find out the factors determining prelacteal feeding in rural areas of north India.
A crosssectional study was conducted among recently delivered women of rural Uttar Pradesh, India. Multistage random sampling was used for selecting villages. From them, 352 recently delivered women were selected as the subjects, following systematic random sampling. Chi-square test and logistic regression were used to find out the predictors for prelacteal feeding.
Overall, 40.1% of mothers gave prelacteal feeding to their newborn. Factors significantly associated with such practice, after simple logistic regression, were age, caste, socioeconomic status, and place of delivery. At multivariate level, age (odds ratio (OR) = 1.76, 95% confidence interval (CI) = 1.13-2.74), caste and place of delivery (OR = 2.23, 95% CI = 1.21-4.10) were found to determine prelacteal feeding significantly, indicating that young age, high caste, and home deliveries could affect the practice positively.
The problem of prelacteal feeding is still prevalent in rural India. Age, caste, and place of delivery were associated with the problem. For ensuring neonatal health, the problem should be addressed with due gravity, with emphasis on exclusive breast feeding.
PMCID: PMC4050689  PMID: 24932400
Breast feeding; colostrum; infant feeding; prelacteal feeding; rural India
16.  A Shared Y-chromosomal Heritage between Muslims and Hindus in India 
Human genetics  2006;120(4):543-551.
Arab forces conquered the Indus Delta region in 711 A.D. and, although a Muslim state was established there, their influence was barely felt in the rest of South Asia at that time. By the end of the tenth century, Central Asian Muslims moved into India from the northwest and expanded throughout the subcontinent. Muslim communities are now the largest minority religion in India, comprising more than 138 million people in a predominantly Hindu population of over one billion. It is unclear whether the Muslim expansion in India was a purely cultural phenomenon or had a genetic impact on the local population. To address this question from a male perspective, we typed eight microsatellite loci and 16 binary markers from the Y chromosome in 246 Muslims from Andhra Pradesh, and compared them to published data on 4,204 males from China, Central Asia, other parts of India, Sri Lanka, Pakistan, Iran, the Middle East, Turkey, Egypt and Morocco. We find that the Muslim populations in general are genetically closer to their non-Muslim geographical neighbors than to other Muslims in India, and that there is a highly significant correlation between genetics and geography (but not religion). Our findings indicate that, despite the documented practice of marriage between Muslim men and Hindu women, Islamization in India did not involve large-scale replacement of Hindu Y chromosomes. The Muslim expansion in India was predominantly a cultural change and was not accompanied by significant gene flow, as seen in other places, such as China and Central Asia.
PMCID: PMC2590854  PMID: 16951948
Y-chromosomal polymorphism; India; Muslim; Hindu
17.  Haemoglobin S and βThal: Their Distribution in Maharashtra, India 
It has been more than six decades since the first report of sickle cell anaemia in Indian subcontinent. Since then the researchers have been reported various haemoglobin varients prevalent in India, they are HbS, HbβT, HbE and HbD. Earlier studies were confined to tribal and scheduled castes populations as if sickle haemoglobin was restricted to these two groups only. Since a decade or so, few studies on haemoglobinopathies from other Indian populations are available. Examination of premarital age group of 5172 Indian subjects (2762 males and 2410 females) from eastern Maharashtra of India showed high incidences of HbS (0-33 per cent) and HbβT (0-10 per cent) in different ethnic groups. In present study cumulative gene frequency for HbS and HbβT was found to be of 6.1 per cent and 2.3 per cent respectively. In present study sickle cell gene has been found in general categories of Indian populations besides scheduled castes and tribal populations. In Scheduled tribes HbS ranges from 0-24 per cent, in Scheduled castes and Nomadic tribal groups, HbS ranges from 0-13 per cent, in Other Backward caste categories it varies from 0-20 per cent while in higher caste populations it ranges from 0-5 per cent. The incidences of HbS are much higher among tribal groups than that found in other caste populations. The incidences of homozygous individuals are very few in HbS and HbβT. The hitherto regional and populations specific HbβT haemoglobin variant in Sindhi and Bengali communities is gradually spreading in other populations of Maharashtra as evident from the present study. Lesser value of MCV, MCH and MCHC in homozygous HbβT is due to impairments of synthesis β-globin chain. The subject with the presence of β-thalassaemia is accompanied by raised level of HbA2. Unusual higher values of RBC and WBC suggest the high concentration of hypochromic microcytosis in anemia. The means of MCV MCH and MCHC in HbβT are much lower than the normal ranges compared to HbS.
PMCID: PMC3708271  PMID: 23847457
haemoglobinopathies; sickle cell anemia; thalassaemia; eastern maharashtra; India
18.  Are marginalized women being left behind? A population-based study of institutional deliveries in Karnataka, India 
BMC Public Health  2012;12:30.
While India has made significant progress in reducing maternal mortality, attaining further declines will require increased skilled birth attendance and institutional delivery among marginalized and difficult to reach populations.
A population-based survey was carried out among 16 randomly selected rural villages in rural Mysore District in Karnataka, India between August and September 2008. All households in selected villages were enumerated and women with children 6 years of age or younger underwent an interviewer-administered questionnaire on antenatal care and institutional delivery.
Institutional deliveries in rural areas of Mysore District increased from 51% to 70% between 2002 and 2008. While increasing numbers of women were accessing antenatal care and delivering in hospitals, large disparities were found in uptake of these services among different castes. Mothers belonging to general castes were almost twice as likely to have an institutional birth as compared to scheduled castes and tribes. Mothers belonging to other backward caste or general castes had 1.8 times higher odds (95% CI: 1.21, 2.89) of having an institutional delivery as compared to scheduled castes and tribes. In multivariable analysis, which adjusted for inter- and intra-village variance, Below Poverty Line status, caste, and receiving antenatal care were all associated with institutional delivery.
The results of the study suggest that while the Indian Government has made significant progress in increasing antenatal care and institutional deliveries among rural populations, further success in lowering maternal mortality will likely hinge on the success of NRHM programs focused on serving marginalized groups. Health interventions which target SC/ST may also have to address both perceived and actual stigma and discrimination, in addition to providing needed services. Strategies for overcoming these barriers may include sensitization of healthcare workers, targeted health education and outreach, and culturally appropriate community-level interventions. Addressing the needs of these communities will be critical to achieving Millennium Development Goal Five by 2015.
PMCID: PMC3269389  PMID: 22240002
Reproductive health; Millennium Development Goals; Maternal mortality; India; Women's health
19.  Understanding patterns of temporary method use among urban women from Uttar Pradesh, India 
BMC Public Health  2014;14(1):1018.
Almost one in five contraceptive users in India uses a temporary method. It is important to understand user profiles and method use patterns for optimal program targeting.
This analysis examines differences in demographic characteristics, discontinuation and use patterns of temporary method users among a representative sample of urban women from four cities in Uttar Pradesh, India.
Individual data from a panel of women aged 15–49 were collected in 2010 in Agra, Aligarh, Allahabad, and Gorakhpur and follow-up data from the same women were collected in 2012. A contraceptive calendar was used to collect month-by-month data on contraceptive use, non-use, discontinuation, reason for discontinuation, and pregnancy and birth, covering the approximately two-year period between the baseline and midterm surveys. The analysis sample is 4,023 non-sterilized women in union at baseline. A descriptive comparison is made of socio-demographic characteristics, fertility desires, discontinuation, method switching, and pregnancy outcomes. Reasons for discontinuation are assessed by the order of discontinuation.
There were a number of socio-demographic differences between users of temporary methods during the calendar period; by education, wealth, and caste. Notably, women who used only condoms during this time had the most education, were the least likely to be poor, and the least likely to be from a scheduled caste or tribe as compared to users of other temporary methods. Compared to the full sample of women, users of temporary methods during this period were less likely to reside in slum areas. The group of multiple method users was small in comparison to the groups of women using a single method throughout the calendar period. This indicates that there was little method switching between condoms, traditional methods, and other forms of modern methods reported in the calendar.
The calendar may not be well-suited to measure coital-dependent contraceptive use (e.g., condoms and traditional methods), as "continuous" monthly use may be overstated. A coital episode-specific data collection tool may produce more accurate records of contraceptive use in such contexts. Research findings also lead to useful programmatic recommendations for addressing unmet need and unintended pregnancies in urban Uttar Pradesh and beyond.
PMCID: PMC4190301  PMID: 25266733
Contraceptives; Family planning; India; Contraceptive patterns; Reversible methods; Condoms; Traditional methods; Urban
20.  Genetic and functional evaluation of the role of DLL1 in susceptibility to visceral leishmaniasis in India 
Chromosome 6q26–27 is linked to susceptibility to visceral leishmaniasis (VL) in Brazil and Sudan. DLL1 encoding the Delta-like 1 ligand for Notch 3 was implicated as the etiological gene. DLL1 belongs to the family of Notch ligands known to selectively drive antigen-specific CD4 T helper 1 cell responses, which are important in protective immune response in leishmaniasis. Here we provide further genetic and functional evidence that supports a role for DLL1 in a well-powered population-based study centred in the largest global focus of VL in India. Twenty-one single nucleotide polymorphisms (SNPs) at PHF10/C6orf70/DLL1/FAM120B/PSMB1/TBP were genotyped in 941 cases and 992 controls. Logistic regression analysis under an additive model showed association between VL and variants at DLL1 and FAM120B, with top associations (rs9460106, OR=1.17, 95%CI 1.01–1.35, P=0.033; rs2103816, OR=1.16, 95%CI 1.01–1.34, P=0.039) robust to analysis using caste as a covariate to take account of population substructure. Haplotype analysis taking population substructure into account identified a common 2-SNP risk haplotype (frequency 0.43; P=0.028) at FAM120B, while the most significant protective haplotype (frequency 0.18; P=0.007) was a 5-SNP haplotype across the interval 5’ of both DLL1 (negative strand) and FAM120B (positive strand) and extending to intron 4 of DLL1. Quantitative RT/PCR was used to compare expression of 6q27 genes in paired pre- and post-treatment splenic aspirates from VL patients (N=19). DLL1 was the only gene to show differential expression that was higher (P<0.0001) in pre- compared to post-treatment samples, suggesting that regulation of gene expression was important in disease pathogenesis. This well-powered genetic and functional study in an Indian population provides evidence supporting DLL1 as the etiological gene contributing to susceptibility to VL at Chromosome 6q27, confirming the potential for polymorphism at DLL1 to act as a genetic risk factor across the epidemiological divides of geography and parasite species.
PMCID: PMC3651914  PMID: 22561395
visceral leishmaniasis; DLL1; genetic association; Notch signalling
21.  Genetic diversity in India and the inference of Eurasian population expansion 
Genome Biology  2010;11(11):R113.
Genetic studies of populations from the Indian subcontinent are of great interest because of India's large population size, complex demographic history, and unique social structure. Despite recent large-scale efforts in discovering human genetic variation, India's vast reservoir of genetic diversity remains largely unexplored.
To analyze an unbiased sample of genetic diversity in India and to investigate human migration history in Eurasia, we resequenced one 100-kb ENCODE region in 92 samples collected from three castes and one tribal group from the state of Andhra Pradesh in south India. Analyses of the four Indian populations, along with eight HapMap populations (692 samples), showed that 30% of all SNPs in the south Indian populations are not seen in HapMap populations. Several Indian populations, such as the Yadava, Mala/Madiga, and Irula, have nucleotide diversity levels as high as those of HapMap African populations. Using unbiased allele-frequency spectra, we investigated the expansion of human populations into Eurasia. The divergence time estimates among the major population groups suggest that Eurasian populations in this study diverged from Africans during the same time frame (approximately 90 to 110 thousand years ago). The divergence among different Eurasian populations occurred more than 40,000 years after their divergence with Africans.
Our results show that Indian populations harbor large amounts of genetic variation that have not been surveyed adequately by public SNP discovery efforts. Our data also support a delayed expansion hypothesis in which an ancestral Eurasian founding population remained isolated long after the out-of-Africa diaspora, before expanding throughout Eurasia.
PMCID: PMC3156952  PMID: 21106085
22.  Trans-Regulation of Mouse Meiotic Recombination Hotspots by Rcr1 
PLoS Biology  2009;7(2):e1000036.
Meiotic recombination is required for the orderly segregation of chromosomes during meiosis and for providing genetic diversity among offspring. Among mammals, as well as yeast and higher plants, recombination preferentially occurs at highly delimited chromosomal sites 1–2 kb long known as hotspots. Although considerable progress has been made in understanding the roles various proteins play in carrying out the molecular events of the recombination process, relatively little is understood about the factors controlling the location and relative activity of mammalian recombination hotspots. To search for trans-acting factors controlling the positioning of recombination events, we compared the locations of crossovers arising in an 8-Mb segment of a 100-Mb region of mouse Chromosome 1 (Chr 1) when the longer region was heterozygous C57BL/6J (B6) × CAST/EiJ (CAST) and the remainder of the genome was either similarly heterozygous or entirely homozygous B6. The lack of CAST alleles in the remainder of the genome resulted in profound changes in hotspot activity in both females and males. Recombination activity was lost at several hotspots; new, previously undetected hotspots appeared; and still other hotspots remained unaffected, indicating the presence of distant trans-acting gene(s) whose CAST allele(s) activate or suppress the activity of specific hotspots. Testing the activity of three activated hotspots in sperm samples from individual male progeny of two genetic crosses, we identified a single trans-acting regulator of hotspot activity, designated Rcr1, that is located in a 5.30-Mb interval (11.74–17.04 Mb) on Chr 17. Using an Escherichia coli cloning assay to characterize the molecular products of recombination at two of these hotspots, we found that Rcr1 controls the appearance of both crossover and noncrossover gene conversion events, indicating that it likely controls the sites of the double-strand DNA breaks that initiate the recombination process.
Author Summary
Recombination is an essential aspect of meiosis, ensuring proper contact and exchange of genetic material between homologous parental chromosomes, as well as their subsequent segregation to produce haploid gametes. In humans and mice, recombination events are located at preferential sites termed hotspots, whose placement and activity are tightly regulated. We have now identified a hotspot-regulating locus in mammals, Rcr1, that simultaneously controls the locations of multiple hotspots. The discovery of Rcr1 indicates the existence of a newly emerging class of genes important in the recombination processes. Gaining further insights into their function may contribute to a better understanding of genetic factors underlying human fertility and evolution.
Rcr1 is identified as atrans-regulator of meiotic recombination hotspots that appears to act at the initiation of recombination and that maps to a 5.3-megabase region on mouse Chromosome 17.
PMCID: PMC2642880  PMID: 19226189
23.  Clonal reproduction and genetic caste differences in a queen-polymorphic ant, Vollenhovia emeryi 
Biology Letters  2006;2(3):359-363.
Most social Hymenoptera are characterized by simple haploid sex determination and environment-based caste differentiation. This appears to be strikingly different in the queen-polymorphic ant Vollenhovia emeryi. Almost all long- and short-winged queens from a population in Central Japan were homozygous at three microsatellite loci, whereas workers were mostly heterozygous, suggesting either a complex system of genetic caste determination or, more likely, the production of female sexuals from unfertilized eggs by thelytokous parthenogenesis and of workers from fertilized eggs. Furthermore, male genotypes were not compatible with those of the queens and had exclusively the paternal allele found in the sterile, heterozygous workers, probably because males are produced from fertilized eggs after the exclusion of maternal nuclear DNA as recently reported for Wasmannia auropunctata. The genus Vollenhovia might provide an interesting model system to trace the evolution of unusual caste and sex determination systems.
PMCID: PMC1686177  PMID: 17148403
ant; caste; genetic; parthenogenesis; Vollenhovia
24.  Distribution of CC-chemokine receptor-5-∆32 allele among the tribal and caste population of Vidarbha region of Maharashtra state 
Genetic relationships among the ethnic groups are not uniform across the geographical region. Considering this assumption, we analyzed the frequency of the CC-chemokine receptor-5 (CCR5)-∆32 allele of the CCR5 chemokine receptor, which is considered a Caucasian marker, in Bhil tribal and Brahmin caste sample sets from the population.
108 blood samples were collected from 6 tribe's populations and a caste population from the district of Vidarbha region.
The presence of low frequencies of CCR5-Δ32 in an individual of Bhil tribe (0.034, χ2 value 0.017) in the present study implies that these communities may have a better resistance toward human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) than the other studied tribe sample, as non-show such mutation.
The marginal presence of the allele seen in the studied tribal population could be due to gene flow from the people of European descent. However, lack of the homozygous CCR5-Δ32 mutation and the low prevalence of heterozygous CCR5-Δ32 mutations suggest that the Indians are highly susceptible to HIV/AIDS, and this correlates with the highest number of HIV/AIDS infected individuals in India.
PMCID: PMC3722632  PMID: 23901195
Allele frequency; CC-chemokine receptor-5-∆32; India; genetic polymorphism; tribes; Vidarbha
25.  High-Resolution Mapping of a Genetic Locus Regulating Preferential Carbohydrate Intake, Total Kilocalories, and Food Volume on Mouse Chromosome 17 
PLoS ONE  2014;9(10):e110424.
The specific genes regulating the quantitative variation in macronutrient preference and food intake are virtually unknown. We fine mapped a previously identified mouse chromosome 17 region harboring quantitative trait loci (QTL) with large effects on preferential macronutrient intake-carbohydrate (Mnic1), total kilcalories (Kcal2), and total food volume (Tfv1) using interval-specific strains. These loci were isolated in the [C57BL/6J.CAST/EiJ-17.1-(D17Mit19-D17Mit50); B6.CAST-17.1] strain, possessing a ∼40.1 Mb region of CAST DNA on the B6 genome. In a macronutrient selection paradigm, the B6.CAST-17.1 subcongenic mice eat 30% more calories from the carbohydrate-rich diet, ∼10% more total calories, and ∼9% more total food volume per body weight. In the current study, a cross between carbohydrate-preferring B6.CAST-17.1 and fat-preferring, inbred B6 mice was used to generate a subcongenic-derived F2 mapping population; genotypes were determined using a high-density, custom SNP panel. Genetic linkage analysis substantially reduced the 95% confidence interval for Mnic1 (encompassing Kcal2 and Tfv1) from 40.1 to 29.5 Mb and more precisely established its boundaries. Notably, no genetic linkage for self-selected fat intake was detected, underscoring the carbohydrate-specific effect of this locus. A second key finding was the separation of two energy balance QTLs: Mnic1/Kcal2/Tfv1 for food intake and a newly discovered locus regulating short term body weight gain. The Mnic1/Kcal2/Tfv1 QTL was further de-limited to 19.0 Mb, based on the absence of nutrient intake phenotypes in subcongenic HQ17IIa mice. Analyses of available sequence data and gene ontologies, along with comprehensive expression profiling in the hypothalamus of non-recombinant, cast/cast and b6/b6 F2 controls, focused our attention on candidates within the QTL interval. Zfp811, Zfp870, and Btnl6 showed differential expression and also contain stop codons, but have no known biology related to food intake regulation. The genes Decr2, Ppard and Agapt1 are more appealing candidates because of their involvement in lipid metabolism and down-regulation in carbohydrate-preferring animals.
PMCID: PMC4203797  PMID: 25330228

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