title: Using blocks of linked single nucleotide polymorphisms as highly polymorphic genetic markers for parentage analysis.
abstract: Single nucleotide polymorphisms (SNPs) are plentiful in most genomes and amenable to high throughput genotyping, but they are not yet popular for parentage or paternity analysis. The markers are bi-allelic, so individually they contain little information about parentage, and in nonmodel organisms the process of identifying large numbers of unlinked SNPs can be daunting. We explore the possibility of using blocks of between three and 26 linked SNPs as highly polymorphic molecular markers for reconstructing male genotypes in polyandrous organisms with moderate (five offspring) to large (25 offspring) clutches of offspring. Haplotypes are inferred for each block of linked SNPs using the programs Haplore and Phase 2.1. Each multi-SNP haplotype is then treated as a separate allele, producing a highly polymorphic, 'microsatellite-like' marker. A simulation study is performed using haplotype frequencies derived from empirical data sets from Drosophila melanogaster and Mus musculus populations. We find that the markers produced are competitive with microsatellite loci in terms of single parent exclusion probabilities, particularly when using six or more linked SNPs to form a haplotype. These markers contain only modest rates of missing data and genotyping or phasing errors and thus should be seriously considered as molecular markers for parentage analysis, particularly when the study is interested in the functional significance of polymorphisms across the genome.
authors.affiliation: Centre for Mathematical Biology, Massey University, Private Bag 102-904, North Shore Mail Centre, Auckland 0745, New Zealand, Institute of Information and Mathematical Sciences, Massey University, Private Bag 102-904, North Shore Mail Centre, Auckland 0745, New Zealand, Dana Farber Cancer Research Center, Boston, MA 02115, USA, Department of Biological Sciences, Binghamton University, PO Box 6000, Binghamton, NY 13902, USA.
authors.forename: Beatrix
authors.initials: B
authors.lastname: Jones
authors.forename: Daniel
authors.initials: D
authors.lastname: Walsh
authors.forename: Lillian
authors.initials: L
authors.lastname: Werner
authors.forename: Anthony
authors.initials: A
authors.lastname: Fiumera