Population genetic analysis among five Indian population groups using six microsatellite markers

Abstract Genetic variation at six tetranucleotide microsatellites (HUMTHO1, HUMVWA, F13A01, D3S1359, D12S66, and D12S67) has been determined in five endogamous ethnic population groups of India belonging to two major linguistic families. The populations analyzed were Konkanastha Brahmins and Marathas (Maharashtra state) from the Indo-Aryan linguistic family and Nairs, Ezhavas, and Muslims (Kerala state) from the Dravidian family. All six loci show high gene diversity, ranging from 0.63 + or - 0.04 to 0.84 + or - 0.02. The average G^sub ST^ value observed was 1.7%, indicating that the differences between the populations account for less than 2% of the diversity, while the genetic variation is high within the five population groups studied (>98%). The phylogenetic tree fails to show any clear cluster. The absence of any cluster along with low average G^sub ST^ is suggestive of substantial genetic similarity among the studied populations, in spite of clear geographical, linguistic, and cultural barriers. This similarity indicates either a greater gene flow between these groups or, alternatively, may reflect a recent evolution for them, considering that the Indian caste system evolved only about 3000 years ago.

KEY WORDS: MICROSATELLITES, INDIAN POPULATION, HUMTHO1, HUMVWA, F13A01, D3S1359, D12S66, D12S67

The Indian subcontinent holds a fascinating mosaic of people from rich social, cultural, genetic, and linguistic streams (Cavalli-Sforza et al. 1994) coexisting in close proximity. Languages spoken in India can be classified into four major families: Austric, Dravidian, Indo-European, and Sino-Tibetan (Gadgil et al. 1998). A large part of the Indian mainland population speaks Indo-European and Dravidian languages. The majority of the total population (82%) practices Hinduism. The Indian population is structured into 40,000 endogamous groups, of which 37,000 groups belong to the Hindu caste system (Malhotra 1984). Approximately 12% of the Indian population is Muslim, forming the largest religious minority group in India (1991 census of India).

In the present study we have characterized five Indian ethnic population groups using six polymorphic microsatellites. The populations used in this study include two Indo-European-speaking groups from the western Indian state of Maharashtra (Konkanastha Brahmins, also called Konkanasthas, and Marathas) and three Dravidian-speaking population groups from the state of Kerala, located on the southwestern coast of India (Nairs, Ezhavas, and Muslims). The two Maharastrian groups speak the local language "Marathi," while the three Kerala populations speak "Malayalam." In general, Konkanastha Brahmins are distributed all over coastal Maharashtra and are traditionally a priestly caste. Marathas are spread over all of Maharashtra and are primarily agriculturists (Sanghvi 1954). Nairs formed the military class in ancient times (Singh 1998a), while Ezhavas are fundamentally agriculturists (Singh 1998b). Both these groups follow a matrilineal system. Muslims, a religio-ethnic group, form a sizeable ~23% of the total population of Kerala and are traditionally traders (Singh 1998c).

Hypervariable microsatellites or short tandem repeats (STRs) of 2 to 6 base-pair (bp) repeat units are widespread throughout the human genome and display high variability among individuals in a population, making them useful markers for studies of evolutionary relationships among populations. Recently, a number of studies on DNA polymorphisms among selected Indian population groups using microsatellites have been conducted to unravel the abundant genetic variation existing in India (Deka et al. 1995, 1999; Watson et al. 1998; Mukherjee et al. 1999; Agrawal et al. 2001; Chattopadhyay et al. 2001; Dutta and Kashyap 2000, 2001a,b; Reddy et al. 2001a,b; Dutta et al. 2000, 2002; Das et al. 2002a; Ghosh and Seshadri 2002a,b). However, no data on microsatellites are available on these five population groups. Therefore, we have studied these populations using six tetranucleotide markers: HUMTHO1, F13A01, HUMVWA, D3S1359, D12S66, and D12S67 (Table 1). These loci were chosen on the basis of their heterozygosity and their feasibility for rapid analysis using polymerase chain reaction (PCR). The fundamental aim of the present study is to characterize the genetic relationships between the five diverse ethnic populations of India derived from two linguistic families and to ascertain, if possible, the gene flow among them, based on the extent of diversity and genetic differentiation between these groups.

Materials and Methods

Samples. Peripheral blood samples were collected in sterile EDTA vacutainers by trained paramedical staff. Around 300 random, unrelated healthy adult volunteers were chosen for this study. Blood samples for Konkanasthas and Marathas were collected from the city of Mumbai, state of Maharashtra, through the Medical Division of Bhabha Atomic Research Centre, Mumbai. Blood samples for Nairs, Ezhavas, and Muslims were collected from Karunagapally Hospital, district of Kollam, state of Kerala, through the Low Level Radiation Research Laboratory, Bhabha Atomic Research Centre, Kollam. All the groups were easily accessible at the respective units.