Identification and characterisation of novel human Y-chromosomal microsatellites from sequence database information

Abstract

1.33 Mb of sequence from the human Y chromosome was searched for tri- to hexanucleotide microsatellites. Twenty loci containing a stretch of eight or more repeat units with complete repeat sequence homo-geneity were found, 18 of which were novel. Six loci (one tri-, four tetra- and one pentanucleotide) were assembled into a single multiplex reaction and their degree of polymorphism was investigated in a sample of 278 males from Pakistan. Diversities of the individual loci ranged from 0.064 to 0.727 in Pakistan, while the haplotype diversity was 0.971. One population, the Hazara, showed particularly low diversity, with predominantly two haplotypes. As the sequence builds up in the databases, direct methods such as this will replace more biased and technically demanding indirect methods for the isolation of microsatellites.

Figure 1

Location of the novel microsatellites on the Y chromosome relative to the previously identified microsatellite loci. (a) Known loci mapped on a panel of deleted Y chromosomes by Carvalho-Silva et al. (16). The Y-specific portion of the short arm was divided into seven intervals, shown here as equal in size; the centromere (CEN) lies in interval 8 and the euchromatic portion of the long arm was divided into 13 intervals. (b) Known loci identified in the sequence information available from GenBank and positioned according to the RH mapping information given on http://www.ncbi.nlm.nih.gov/genome/seq/chr.cgi?CHR=Y . In (a) and (b), the location of the new microsatellites is shown by the black square. (c) Positions of known and novel loci in more detail in the NT_001402 contig.