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Saudi Arabian Y-Chromosome diversity and its relationship with nearby regions
Human origins and migration models proposing the Horn of Africa as a prehistoric exit route to Asia have stimulated molecular genetic studies in the region using uniparental loci. However, from a Y-chromosome perspective, Saudi Arabia, the largest country of the region, has not yet been surveyed. To address this gap, a sample of 157 Saudi males was analyzed at high resolution using 67 Y-chromosome binary markers. In addition, haplotypic diversity for its most prominent J-M267 lineage was estimated using a set of 17 Y-specific STR loci.
Saudi Arabia differentiates from other Arabian Peninsula countries by a higher presence of J2-M172 lineages. It is significantly different from Yemen mainly due to a comparative reduction of sub-Saharan Africa E1-M123 and Levantine J1-M267 male lineages. Around 14% of the Saudi Arabia Y-chromosome pool is typical of African biogeographic ancestry, 17% arrived to the area from the East across Iran, while the remainder 69% could be considered of direct or indirect Levantine ascription. Interestingly, basal E-M96* (n = 2) and J-M304* (n = 3) lineages have been detected, for the first time, in the Arabian Peninsula. Coalescence time for the most prominent J-M267 haplogroup in Saudi Arabia (11.6 ± 1.9 ky) is similar to that obtained previously for Yemen (11.3 ± 2) but significantly older that those estimated for Qatar (7.3 ± 1.8) and UAE (6.8 ± 1.5).
All sample collecting and genotyping tasks were performed by the Saudi Arabian collaborators of this study. Buccal swabs or peripheral blood were obtained from 157 paternally unrelated Saudi Arab males whose all known paternal lineages, at least for two generations, were of Saudi Arabia origin. Due to its moderate size we have not performed a regional subdivision of the sample. Informed consent was obtained from all the participants. This research followed the tenets of the Declaration of Helsinki. DNA was extracted using the Nucleon™ BACC Genomic DNA Extraction Kit (GE healthcare, Piscataway, NJ, USA). Sixty-seven Y-Chromosome binary genetic markers were genotyped hierarchically. Primers, polymorphic positions and haplogroup nomenclature were as recently actualized [16]. After amplification and purification, haplogroup typing was carried out in all cases by direct sequencing on the ABI 3130 xI Genetic Analyzer (Applied Biosystems, Foster city, CA, USA). The following 17 Y-STR loci: DYS19, DYS385 a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and Y-GATA H4 were amplified in a Gene Am PCR System 2700 (Applied Biosystems) using the AmpF/STR Yfiler Amplification Kit (Applied Biosystems) following the manufacturers instructions. DNA fragment separation was carried out in an ABI Prism 3100 Genetic Analyzer (Applied Biosystems). STR alleles were identified by comparison to a commercial allelic ladder using Genotyper 3.7 NT software.
Our Saudi Arabia sample was compared to other Arabian Peninsula populations and to surrounding areas using data from previous studies performed at a similar level of haplogroup resolution. These samples comprise, 72 Qatari, 164 United Arab Emirate and 62 Yemeni ; 121 Omani and 147 Egyptian ; 201 Somalis [ 916 Lebanese; 146 Jordanian ; 203 Iraqi (139 from Al-Zahery et al. [20] and 64 from Sanchez et al. )0
Only 27 of the 67 binary markers analyzed were informative in defining the haplogroup census of the Saudi Arabian sample (Table (Table1).1). The following 40 polymorphisms (M60, M130, M217, M174, P147, M33, M75, P177, P2, M215, M78, M81, M123, M329, M89, M282, M201, P20, P16, M286, M52, M197, M370, M170, M172, M410, M92, M241, M9, M20, M317, M231, M214, M119, M207, M173, M343, P25, M18 and M124)
All sample collecting and genotyping tasks were performed by the Saudi Arabian collaborators of this study. Buccal swabs or peripheral blood were obtained from 157 paternally unrelated Saudi Arab males whose all known paternal lineages, at least for two generations, were of Saudi Arabia origin. Due to its moderate size we have not performed a regional subdivision of the sample. Informed consent was obtained from all the participants. This research followed the tenets of the Declaration of Helsinki. DNA was extracted using the Nucleon™ BACC Genomic DNA Extraction Kit (GE healthcare, Piscataway, NJ, USA). Sixty-seven Y-Chromosome binary genetic markers were genotyped hierarchically. Primers, polymorphic positions and haplogroup nomenclature were as recently actualized [16]. After amplification and purification, haplogroup typing was carried out in all cases by direct sequencing on the ABI 3130 xI Genetic Analyzer (Applied Biosystems, Foster city, CA, USA). The following 17 Y-STR loci: DYS19, DYS385 a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and Y-GATA H4 were amplified in a Gene Am PCR System 2700 (Applied Biosystems) using the AmpF/STR Yfiler Amplification Kit (Applied Biosystems) following the manufacturers instructions. DNA fragment separation was carried out in an ABI Prism 3100 Genetic Analyzer (Applied Biosystems). STR alleles were identified by comparison to a commercial allelic ladder using Genotyper 3.7 NT software.
Our Saudi Arabia sample was compared to other Arabian Peninsula populations and to surrounding areas using data from previous studies performed at a similar level of haplogroup resolution. These samples comprise, 72 Qatari, 164 United Arab Emirate and 62 Yemeni ; 121 Omani and 147 Egyptian ; 201 Somalis [ 916 Lebanese; 146 Jordanian ; 203 Iraqi (139 from Al-Zahery et al. [20] and 64 from Sanchez et al. )0
Only 27 of the 67 binary markers analyzed were informative in defining the haplogroup census of the Saudi Arabian sample (Table (Table1).1). The following 40 polymorphisms (M60, M130, M217, M174, P147, M33, M75, P177, P2, M215, M78, M81, M123, M329, M89, M282, M201, P20, P16, M286, M52, M197, M370, M170, M172, M410, M92, M241, M9, M20, M317, M231, M214, M119, M207, M173, M343, P25, M18 and M124)