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Genetic Characterization of Mitochondrial Dna in Makrani and Kalashi Population from Pakistan

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Genetic Characterization of Mitochondrial Dna in Makrani and Kalashi Population from Pakistan GENETIC CHARACTERIZATION OF MITOCHONDRIAL DNA IN MAKRANI AND KALASHI POPULATION FROM PAKISTAN BY MUHAMMAD HASSAN SIDDIQI DEPARTMENT OF ZOOLOGY UNIVERSITY OF THE PUNJAB QUAID-I-AZAM CAMPUS LAHORE, PAKISTAN (2014) GENETIC CHARACTERIZATION OF MITOCHONDRIAL DNA IN MAKRANI AND KALASHI POPULATION FROM PAKISTAN A THESIS SUBMITTED TO UNIVERSITY OF THE PUNJAB IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN ZOOLOGY BY MUHAMMAD HASSAN SIDDIQI SUPERVISOR PROF. DR. TANVEER AKHTAR DEPARTMENT OF ZOOLOGY UNIVERSITY OF THE PUNJAB QUAID-I-AZAM CAMPUS LAHORE, PAKISTAN (2014) IN THE NAME OF ALLAH, THE MOST BENEFICENT, THE MOST MERCIFUL AL QURAN Translation: O ye, who believe, stand out firmly for justice, as witnesses to Allah, even as against yourselves, or your parents, or your kin, or whether it be (against) rich or poor: for Allah can best protect both. Follow not the lusts (of your hearts), lest ye swerve and if ye distort (justice) or decline to do justice, verily Allah is well acquainted with all that ye do (Quran 4:135). CERTIFICATE This is to certify that the research work described in this thesis is the original work of the author Mr. Muhammad Hassan Siddiqi and has been carried out under my direct supervision. I have personally gone through all the data/results/materials reported in the manuscript and certify their correctness/authenticity. I further certify that the material included in this thesis have not been used in part or full in a manuscript already submitted or in the process of submission in partial/complete fulfillment of the award of any other degree from any other institution. I also certify that the thesis has been prepared under my supervision according to the prescribed format and I endorse its evaluation for the award of Ph.D. degree through the official procedures of the University. Prof. Dr. Tanveer Akhtar Supervisor Department of Zoology, University of the Punjab, Lahore DEDICATION This work is dedicated to my Father, Mother (Late) and brother Muhammad Aslam (Late) who have been the source of inspiration since my childhood and who were always there to help me, gave me courage and strength to accomplish all the goals of my life including this prestigious research achievement. You are a part of every page, every thought and all the work. CONTENTS Title Page No. SUMMARY ..................................................................................................................i 1. INTRODUCTION...................................................................................................1 2. LITERATURE REVIEW ......................................................................................6 2.1 Hypervariable Sites .....................................................................................10 2.2 Haplogroups ................................................................................................10 2.2.1 African Haplogroups ..........................................................................11 2.2.2 West Eurasian Haplogroups ...............................................................11 2.2.3 Southeast Asian Haplogroup..............................................................13 2.3 The Role of the mtDNA in Ancestry Studies ...............................................14 3. MATERIALS AND METHODS ..........................................................................16 3.1 Sample Collection Areas.............................................................................16 3.2 Makrani Population .....................................................................................17 3.2.1. Sample Collection .............................................................................17 3.3. Kalash Population ......................................................................................20 3.3.1. Sample Collectio ...............................................................................20 3.4 DNA Extraction and Quantification ...........................................................25 3.5 PCR Amplification......................................................................................25 3.5.1. Preparation of Agarose Gel ...............................................................27 3.6. Sequencing .................................................................................................27 3.7. Statistical Analysis .....................................................................................28 4. RESULTS ...............................................................................................................29 4.1. Sampled populations ..................................................................................29 4.2. Genomic DNA quality and PCR amplification of mtDNA control region 29 4.3. Sequencing the control region of mitochondrial DNA ..............................29 4.4. Reconstruction and alignment with rCRS..................................................39 4.5. Identification of haplotypes and assignment of haplogroups ....................45 4.6. Frequency of mtDNA haplogroups ............................................................55 4.7 The Haplogroups Diversity within Sub-ethnic group of Kalash Population 56 4.8 Frequency of mtDNA Haplogroups ............................................................58 4.9. The Construction of Median Joining (MJ) Networks ................................59 4.10 The Occurrence and Distribution of Nucleotide Variations in mtDNA Control Region ..................................................................................................61 4.11. Heteroplasmy ...........................................................................................65 4.11.1. Point heteroplasmy..........................................................................65 4.11.2. Length heteroplasmy .......................................................................68 4.12. Comparison of haplogroup frequencies and continental origins in Sub- populations of Pakistan .....................................................................................70 4.13. Comparative statistical analyses of different Pakistani subpopulations ..74 5. DISCUSSION ..........................................................................................................75 REFRENCES ..............................................................................................................86 APPENDIX SUMMARY Mitochondrial DNA (mtDNA) analysis has gained importance in forensic investigations especially for cases where the genomic DNA found is highly degraded or very less in quantity. Due to the high copy number of mtDNA in a cell increases the possibility of some copies of mtDNA to be intact in such samples. The variations in mitochondrial genome have been proven to be the most powerful genetic marker for investigating gene pools and tracing maternal genetic relatedness of the suspect. The control region of mtDNA including hypervariable segments (HVSI, HVSII and HVSIII) has been considered the most important chunk of polymorphic DNA in the mitochondrial genome. This study reports the haplotype data of mtDNA control region (spanning positions 16,024–16,569 and 1–576) including hypervariable segments (HVSI, HVSII and HVSIII) for two-genetically distinct and isolated populations of Pakistan i.e. Makrani & Kalashi. The genetic and forensic parameters were studied by sequencing the entire mitochondrial DNA control region of 100 unrelated Makrani individuals (males, n = 96; females, n = 4) and 111 Kalashi individuals (males, n = 63; females, n = 48). A total of 149 polymorphic positions were detected in Makrani population. Based on the entire profile of mutations along the mtDNA control region comparative to revised Cambridge Reference Sequence (rCRS), seventy different haplotypes were observed in the Makrani with 54 unique and 16 haplotypes shared by more than one individual in the population. Point heteroplasmy was observed at 5 different positions in Makrani accounting for 13% of the individuals. Only one individual presented more than one point heteroplasmy in the Makranis. Median Joining Network analysis showed the substantial divergence among the haplotypes in Makrani population. In Kalashi population, a total of 47 polymorphic positions were detected. After comparing with rCRS, 14 different haplotypes were observed in the Kalashi population with 5 unique and 9 haplotypes shared by more than one individual. Point heteroplasmy was observed at 6 different positions accounting for 58.56% of the individuals. In this case, three individuals presented more than one point heteroplasmy. Limited divergence among the haplotypes has been observed in Kalashi population while plotting Median Joining Network. i Based on identified haplotypes, the Makranis showed admixed mtDNA pool consisting of African haplogroups (28%), West Eurasian haplogroups (26%), South Asian haplogroups (24%), and East Asian haplogroups (2%), however, the origin of the remaining individuals (20%) could not be confidently assigned in this population. Moreover, two haplotypes observed in the Makranis, both carrying a characteristic combination of two mutations in HVSII (154C and194T) could not be confidently assigned to a known (sub) haplogroups, although the presence of both 16223T and 489C indicate membership within macro-haplogroup M; this lineage was therefore tentatively assigned to haplogroup named ‘‘M-154-194’’. Future studies performing complete mitogenome sequencing, may elucidate the precise phylogenetic
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