Abstract
We have screened the nearly complete DNA sequence of the human Y chromosome for microsatellites (short tandem repeats) that meet the criteria of having a repeat-unit size of > or = 3 and a repeat count of > or = 8 and thus are likely to be easy to genotype accurately and to be polymorphic. Candidate loci were tested in silico for novelty and for probable Y specificity, and then they were tested experimentally to identify Y-specific loci and to assess their polymorphism. This yielded 166 useful new Y-chromosomal microsatellites, 139 of which were polymorphic, in a sample of eight diverse Y chromosomes representing eight Y-SNP haplogroups. This large sample of microsatellites, together with 28 previously known markers analyzed here--all sharing a common evolutionary history--allowed us to investigate the factors influencing their variation. For simple microsatellites, the average repeat count accounted for the highest proportion of repeat variance (approximately 34%). For complex microsatellites, the largest proportion of the variance (again, approximately 34%) was explained by the average repeat count of the longest homogeneous array, which normally is variable. In these complex microsatellites, the additional repeats outside the longest homogeneous array significantly increased the variance, but this was lower than the variance of a simple microsatellite with the same total repeat count. As a result of this work, a large number of new, highly polymorphic Y-chromosomal microsatellites are now available for population-genetic, evolutionary, genealogical, and forensic investigations.
Highlights
Microsatellites, or short tandem repeats (STRs), consist of repetitions of a 1–6-bp unit
Genomewide analysis of the published human DNA sequence has demonstrated that the density of microsatellites у12 bp in length is similar on all chromosomes, including the euchromatic portion of the Y chromosome (Subramanian et al 2003), so more Y-chromosomal loci should be present
Most of the loci investigated by Subramanian and colleagues were short and monomorphic, but longer, polymorphic microsatellites can readily be identified from sequence data by use of the program Tandem Repeats Finder (Benson 1999; Ayub et al 2000)
Summary
Microsatellites, or short tandem repeats (STRs), consist of repetitions of a 1–6-bp unit. The number of repetitions (repeat count) can vary between individuals, so microsatellites have proved to be useful markers in several areas of genetics, including gene mapping, forensic investigations, and evolutionary studies. Microsatellites from the nonrecombining portion of the human Y chromosome have an important role in forensic genetics, where they have become the markers of choice, in cases involving sexual assault or in paternity testing when the putative father is not available Received February 9, 2004; accepted for publication March 17, 2004; electronically published May 7, 2004. Manfred Kayser, Department of Forensic Molecular Biology, Erasmus MC–University Medical Centre Rotterdam, Medical-Genetic Cluster, P.O. Box 1738, 3000 DR Rotterdam, The Netherlands.
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