Sequence diversity and forensic efficiency of Y-STRs in the Han population of Yunnan Province, Southwest China.

Y-chromosomal short tandem repeat (Y-STR) loci are highly valuable for forensic identification, paternal kinship testing, and population genetics. Traditional length-based genotyping methods are unable to capture sequence variations within the repeat regions. In contrast, massively parallel sequencing (MPS) can distinguish alleles of identical length but differing internal sequences, thereby enhancing both the resolution of polymorphism detection and the overall efficiency of forensic applications. To characterize the Y-STR diversity in the Yunnan Han population, we applied MPS to genotype 86 Y-STR loci in 302 unrelated male individuals. When flanking regions were included, we detected a total of 757 alleles at the sequence level, compared with only 491 alleles identified by length-based typing-a substantial increase. Among these loci, 37 showed an increase in allele counts and eight exhibited an increase exceeding 100%. Haplotype diversity (HD) increased from 0.9984 to 0.9986, and the discrimination capacity (DC) improved from 0.8510 to 0.8642. Sequence analysis revealed repeat pattern variations (RPVs) in the core repeat region. It also revealed single‑nucleotide substitutions (SNPs) and insertions/deletions (InDels) in the repeat and flanking regions. Collectively, these variant types contributed to the observed increase in polymorphism. Population genetic analysis indicated that the Yunnan Han population is most closely related to the Han populations from Sichuan and Chongqing, while all Han groups clustered separately from the ethnic minority populations examined. In summary, Y-STR typing based on sequences can reveal hidden genetic variation, improve forensic identification of individuals, and provide important information on the fine-scale paternal genetic structure of the Yunnan Han population.