A major zebrafish polymorphism resource for genetic mapping

Abstract

We have identified 645,088 candidate polymorphisms in zebrafish and observe a single nucleotide polymorphism (SNP) validation rate of 71% to 86%, improving with polymorphism confidence score. Variant sites are non-random, with an excess of specific novel T- and A-rich motifs. We positioned half of the polymorphisms on zebrafish genetic and physical maps as a resource for positional cloning. We further demonstrate bulked segregant analysis using the anchored SNPs as a method for high-throughput genetic mapping in zebrafish.

Figure 1

Distribution of SNPs within the Zv6 draft zebrafish genome assembly. SNP density is represented by color, where blank areas indicate absence of SNPs of finished clones. The number of candidate SNPs of confidence score ≥4 is indicated at the bottom of each chromosome. SNPs are distributed among 4,319 BACs (an additional 91 were not included in Zv6) representing 39% of the draft genome.

Figure 2

Comparison of positions of SNPs anchored on four genetic maps and on the draft sequence assembly of chromosome 7. Finished clones harboring newly discovered polymorphisms are anchored on a genetic map by content of previously mapped markers. Clone positions on meiotic maps (heat shock (HS) and Boston MGH), radiation hybrid maps (T51 and LN54), and the Zv6 draft physical sequence assembly are provided. Where a clone is common to two adjacent maps, a connecting line indicates corresponding positions. The asterisk indicates the position of BAC zC258D20, linked to the trilobite locus.

Figure 3

Bulked segregant analysis of the trilobite locus employing anchored SNPs. Scatter plots provide SNP genotype data for a linked SNP (upper panel) and an unlinked SNP (lower panel). Data of individual embryo DNA is presented to the left and data of DNA pools is presented to the right. Under each plot is a further schematic representation of DNA sample genotype: 10 wild-type embryos, 50 mutant embryos, 1 wild-type embryo DNA pool, or 5 mutant embryo DNA pools. Homozygotes are shown in yellow or blue, heterozygotes are in red, and negative controls are in black. The data point of the wild-type pool at the linked SNP (top right) is intermediate between the position of a G/T heterozygote and G/G homozygote. Plot axes are in milli-polarization units, indicating relative dye terminator incorporation with single nucleotide primer extension detected by fluorescence polarization.