How many SNPs are enough?

Peter E. Smouse

Research output: Contribution to journalReview articlepeer-review

19 Scopus citations


Since the days of allozyme analysis, we have been enamored with the idea that if we just had enough polymorphic mendelian loci, we could gauge the inbreeding level of individuals by measuring heterozygosity and simultaneously measure the degree of genetic relatedness between pairs of individuals. Given Mendel's Laws, we have always known that we would need numerous independently segregating loci to achieve any reasonable degree of accuracy. Santure et al. (2010, this issue) use a 771 marker SNP panel to assess heterozygosity levels and to assess pairwise relatedness, and compare both with theoretical expectations obtained from a carefully recorded pedigree of a zebra finch breeding colony, as a function of increasing numbers of SNP markers. They also compare the SNP results with those from a 20-locus microsatellite panel, showing that adding SNPs to a fairly large microsatellite panel improves accuracy, but given an existing panel of 125 SNPs, little is to be gained by adding microsatellites. They show that the accuracy available for estimating individual levels of inbreeding is somewhat limited. They also show that the average pairwise relatedness measures bracket pedigree relationship very nicely, but the variances for individual pairs remain substantial, even with a very large panel.

Original languageEnglish (US)
Pages (from-to)1265-1266
Number of pages2
JournalMolecular Ecology
Issue number7
StatePublished - Apr 2010

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics


  • Heterozygosity
  • Microsatellites
  • Relatedness
  • SNPs


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