DOI: 10.31038/JMG.2021411

Abstract

Haplotypes and allele frequencies for the 17 Y-chromosomal short tandem repeat (Y-STR) loci, DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635, DYS392, Y GATA H4, DYS437, DYS438 and DYS448 were determined in a sample of “On To’rt Urıw” tribes 100 unrelated Karakalpak males living in the regions of Xojeli (20), Taxiatosh (20), Shimbai (20), Konirat (20) and Moynaq (20) using the Y-filer PCR Amplification Kit (Thermo Fisher Scientific). The gene diversity was 0.9998 (standard error: 0.005). The haplotype diversity calculated from the 17 Y-STR loci was 0.9977 and the discrimination capacity was 0.8890. The DYS385 locus showed the highest gene diversity value (0.8765), while the DYS391 locus showed the lowest gene diversity value (0.5033).

Keywords

DNA analysis, Y chromosome, Population data

Introduction

There have been few reports regarding genetic polymorphisms at the Y-STR loci in Karakalpak population [1-4]. The Karakalpaks are a heterogenous people, their appearance ranging from European to Mongoloid. The Karakalpaks as a whole are divided into two divisions, known as arıs, the Qon’ırat and the On To’rt Urıw. The term On To’rt Urıw, which means fourteen tribes, is somewhat misleading since the On To’rt Urıw are actually composed of just four tribes: the Qıtay, Qıpshaq, Keneges, and the Man’g’ıt. Also, The four tribes of the On To’rt Urıw are also divided into clans: the Qıtay into 12, the Qıpshaq into 13, the Keneges into 8, and the Man’g’ıt into 4. The difference between a tribe and a clan is defined by matrimonial alliances. The Karakalpaks practice exogamy. It is not possible to marry within one’s own clan, but it is possible to marry into another clan within one’s own tribe.

The world population of Karakalpaks is probably less than 600,000, making them one of the smallest Turkic groups in Central Asia. About 80% live in the Autonomous Republic of Karakalpakstan, the remainder being mainly located in other parts of Uzbekistan and Kazakhstan. For comparison, the Qazaqs may number up to 14 million worldwide, of which only 8½ million (about 60%) live in Kazakhstan. Surprisingly the Karakalpaks are not the dominant population of Karakalpakstan – they make up less than one third of the population and are just outnumbered by Uzbeks, some of whom have moved into southern Karakalpakstan from other parts of Uzbekistan in recent years. This study aimed to investigate the haplotypes and allele frequencies for the 17 Y-STR loci in population and establish forensic DNA database.

Materials and Methods

Objects of the Research

The subjects of the study were blood samples and dried saliva on sterile gauze tampons, selected from 100 individuals.

DNA Extraction

Genomic DNA was extracted from peripheral blood and dried saliva samples using the phenol-chloroform-isoamyl alcohol method.

DNA Quantification

After isolation, the quantity of genomic DNA of each sample was determined by quantitative real-time polymerase chain reaction (PCR) using the Quantifiler™ Human Male DNA Quantification kit (Thermo Fisher Scientific), which includes internal positive control to test for the presence of PCR inhibitors in the DNA extracts. Quantitative real-time PCR was performed on 7500 Real-Time PCR System (Applied Biosystems).

PCR Amplification and Detection

To ensure successful amplification, 0.5 ng to 1 ng of DNA was used for each multiplex amplification reaction. All thermal cycling was conducted on Applied Biosystems® GeneAmp® PCR System 9700 thermal cyclers. PCR amplification using Y-filer PCR Amplification Kit (Thermo Fisher Scientific) was performed as recommended by the manufacturer, although half of the recommended reaction volume (12.5 μl) was used.

Separation and detection of the 17 Y-STR loci were performed using the 3130xl Genetic Analyser (Applied Biosystems) 16-capillary array system and filter set G5. Each sample was prepared by adding 1 mL PCR product to 14 mL of Hi-Di™ formamide and 0.4 mL GeneScanTM-500 LIZ™ internal size standard (Thermo Fisher Scientific).

The sample run data were analyzed, together with an allelic ladder and positive and negative controls, using GeneMapper ID-X v3.2 (Applied Biosystems) software.

Table 1: