Genomic analysis of mitochondrial DNA in the Indigenous groups of Malaysia

¹Lih-Chun Hong, ²Mun-Yik Fong, ³Juli Edo, ¹Maude Elvira Phipps
¹University of Malaya, Department of Molecular Medicine, Faculty of Medicine, 50603 Kuala Lumpur, Malaysia, ²University of Malaya, Department of Parasitology, Faculty of Medicine, 50603 Kuala Lumpur, Malaysia, ³University of Malaya, Center for Malaysian Pribumi Studies, Institute of Research Management and Consultancy, 50603 Kuala Lumpur, Malaysia

Polymorphisms in the control and coding regions of mitochondrial DNA (mtDNA) were analyzed in four Indigenous groups (N=188). A total of 64 different mtDNA haplotypes were elucidated. Of the 64 sequences observed, 44% were unique and 56% were shared by more than one individual. We report seven novel polymorphisms, with three in the HVS-1 and four in HVS-2 segments that have hitherto not been reported. These polymorphisms have been submitted to MITOMAP database. Most mtDNA variants belonged to three major haplogroups M, N and R. The majority of the haplogroups were found to be exclusive to the Indigenous groups in Malaysia. The most frequent were haplogroups including M21a and R21, which both reflect very old lineages, deeply rooted in South East Asian populations. This was evident in about 80% of the Negritos (Jehai and Kensiu) that were genotyped. Haplogroups N21 (24%) and N22 (8%) were predominantly found in Temuan whilst haplogroup N9a6a was predominant in Bidayuh (40%). Haplogroups indicative of South and Central Asia distributions were observed in variable frequencies. The Temuan comprise the most diverse group followed by Jehai and Bidayuh. The least diverse were the Kensiu. In our study cohort, the lower levels of genetic diversity in these four groups in contrast to majority of the Asian population (0.798 - 0.872) are indicative of genetic drift and may reflect bottleneck effects due to relatively long periods of isolation. The 9bp deletion in the MT-CO2/MT-TK (tRNALys) intergenic region of mtDNA (n.p. 8271-8281) was detected in 10.1% of the participants investigated. This deletion was identified in a Kensiu individual, five Bidayuh and the majority of Temuan (28%), but not detected in Jehai. Our results support the current view that Malaysia is home to some of the oldest groups to have migrated out of Africa.