Assessment of polymorphism in zebrafish mapping strains

Abstract

To assess the level of heterozygosity within two commonly used inbred mapping zebrafish strains, C32 and SJD, we genotyped polymorphic CA-repeat markers randomly dispersed throughout the zebrafish genome. (For clarity purposes we will primarily use the term polymorphic to define polymorphism between strains, and the term heterozygous to address heterogeneity within a strain.) Eight male individuals each from C32 and SJD stocks were typed for 235 and 183 markers, respectively. Over 90% of the markers typed were polymorphic between these two strains. We found a limited number of heterozygous markers persisting in clusters within each inbred line. In the SJD strain, these were mainly limited to a few telomeric regions or regions otherwise distant from centromeres. As expected, centromeric regions were homozygous in the SJD strain, consistent with its derivation from a single half-tetrad individual. In contrast, heterozygous clusters were distributed randomly throughout the genome in the C32 strain, and these clusters could be detected with linked polymorphic markers. Nevertheless, most regions of the C32 strain are homozygous for CA-repeat markers in current stocks. This identification of the heterozygous regions within C32 and SJD lines should permit rapid fixation of these remaining regions in future generations of inbreeding. In addition, we established levels of polymorphism between the inbred, C32 and SJD, strains and three other commonly used strains, the *AB, WIK, and Florida wild type (hereafter referred as EKK), with CA-repeat markers as well as SSCP polymorphisms. These data will maximize the use of these strains in mapping experiments.

Figure 1

Heterozygosity data for the C32 and SJD strains. Marker positions derived from Knapik et al. (1998) and Shimoda et al. (1999). Centromere positions are from those determined by Johnson et al. (1996), with markers genotyped on both panels. The relationship of markers on LG 4 to its centromere has not been determined. The left forward hatched rectangles indicate homozygous regions in the C32 strain and the right backward hatched regions indicate homozygous regions in the SJD strains. Centromeres are depicted as solid black rectangles. The heterozygous regions in both strains are shown in gray. The extent of these regions is given as a midpoint between a heterozygous marker and the next adjacent tested maker that was not polymorphic. Markers that did not amplify an SJD allele, but amplify in the C32 strain are designated by #. If a C32 allele was equal in size to the SJD allele, the marker is denoted by an asterisk (*). Sizes of bands were estimated from acrylamide and agarose gels (see Table 1).

Figure 2

Examples of polymorphisms scored in the C32, SJD, *AB, WIK, and EKK individuals. (A) acrylamide gel data for markers Z3424, Z10852, and Z11696 on LG 13 heterozygous in the C32 strains and reconstructed genotypes for these heterozygous markers; (B) acrylamide gel data for markers Z858, Z24, and Z5223 on LG 15 and reconstructed genotypes for these heterozygous markers; (C) acrylamide gel data for SSCP marker rara2a in the C32, SJD, WIK, *AB, and EKK strains with alleles scored underneath.