NEWS AND VIEWS†
How many SNPs are enough?
Article first published online: 19 MAR 2010
© 2010 Blackwell Publishing Ltd
Volume 19, Issue 7, pages 1265–1266, April 2010
How to Cite
SMOUSE, P. E. (2010), How many SNPs are enough?. Molecular Ecology, 19: 1265–1266. doi: 10.1111/j.1365-294X.2010.04555.x
- Issue published online: 19 MAR 2010
- Article first published online: 19 MAR 2010
- Received 21 December 2009; revision received 24 December 2009; accepted 29 December 2009
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.