Effective resolution of the Y chromosome sublineages of the Iberian haplogroup R1b-DF27 with forensic purposes

Abstract

Single-nucleotide polymorphisms (SNPs) found within the non-recombining region of the Y chromosome (NRY) represent a powerful tool in forensic genetics for inferring the paternal ancestry of a vestige and complement the determination of biogeographical origin in combination with other markers like AIMs. In the present study, we introduce a panel of 15 Y-SNPs for a fine-resolution subtyping of the haplogroup R1b-DF27, in a single minisequencing reaction. This is the first minisequencing panel that allows a fine subtyping of R1b-DF27, which displays high frequencies in Iberian and Iberian-influenced populations. This panel includes subhaplogroups of DF27 that display moderate geographical differentiation, of interest to link a sample with a specific location of the Iberian Peninsula or with Iberian ancestry. Conversely, part of the intricacy of a new minisequencing panel is to have all the included variants available to test the effectiveness of the analysis method. We have overcome the absence of the least common variants through site-directed mutagenesis. Overall, the results show that our panel is a robust and effective method for subtyping R1b-DF27 lineages from a minimal amount of DNA, and its high resolution enables to improve male lineage discrimination in Iberian and Southwest European descent individuals. The small length of the amplicons and its reproducibility makes this assay suitable for forensic and population genetics purposes.

Genetic Reconstruction and Forensic Analysis of Chinese Shandong and Yunnan Han Populations by Co-Analyzing Y Chromosomal STRs and SNPs

“…In total, 55 null alleles were observed at 14 different loci (DYS448, DYS390, DYS391, DYS456, DYS481, DYS460, DYS458, DYS449, DYS570, DYS576, DYS627, DYS518, and DYF387S1a/b). Furthermore, 71 micro-variants were found in 69 samples, including 8 single-copy loci, i.e., DYS518 ( (19,21), and DYS456 (15,16) were reported for the first time. All samples with variants are co-listed with their Y haplogroup affiliations in Table S2.…”

“…For forensic applications, population investigations by Y-STRs also generate much knowledge on inter-relationships among distinct male populations. In order to dissect the genetic structure of male populations, co-analysis of Y-STR and Y-SNP was conducted for diverse populations [10][11][12][13][14][15][16][17] but not for the majority of Chinese Han populations. In this research, preliminary comparative studies were conducted by genotyping commonly used Y-STRs and low-resolution Y-SNPs in two Chinese populations-Shandong Han and Yunnan Han-to characterize the patrilineal patterns in population genetics.…”

Forensic DNA Analysis

“…A study of the Y-SNPs in the Flemish population identified the variant alleles in 270 male samples . Fifteen new SNPs were developed with the purpose of performing high resolution subtyping of the haplogroup R1b-DF27, which displays high frequencies in Iberian and Iberian-influenced populations …”

“…125 Fifteen new SNPs were developed with the purpose of performing high resolution subtyping of the haplogroup R1b-DF27, which displays high frequencies in Iberian and Iberian-influenced populations. 126 Similarly, research studies on X-SNPs have been performed. Two different research groups applied the MALDI-TOF MS techniques to their samples in order to analyze a variety of X-SNPs in different populations.…”

Y-chromosome target enrichment reveals rapid expansion of haplogroup R1b-DF27 in Iberia during the Bronze Age transition

“…This impact was even more pronounced in the Y chromosome, due to an almost complete genetic replacement of the diverse Copper Age lineages with R1b-M269 14 . One branch of this haplogroup, R1b-P312, is the most abundant in West Europe 13 and in turn, it splits into three main subbranches: U152, frequent in Northern Italy and the Alps regions 15 ; L21, more restricted to Ireland and the British Islands 16 ; and DF27, predominant in the Iberian Peninsula [17][18][19][20] . In this project, we focus on R1b-DF27, which has a high frequency in the Peninsula, reaching 40% of the Y-chromosome haplogroups both in Spain and Portugal, while it is much rarer elsewhere 21 .…”