Genetic variation in the zebrafish

Abstract

Although zebrafish was introduced as a laboratory model organism several decades ago and now serves as a primary model for developmental biology, there is only limited data on its genetic variation. An establishment of a dense polymorphism map becomes a requirement for effective linkage analysis and cloning approaches in zebrafish. By comparing ESTs to whole-genome shotgun data, we predicted >50,000 high-quality candidate SNPs covering the zebrafish genome with average resolution of 41 kbp. We experimentally validated ∼65% of a randomly sampled subset by genotyping 16 samples from seven commonly used zebrafish strains. The analysis reveals very high nucleotide diversity between zebrafish isolates. Even with the limited number of samples that we genotyped, zebrafish isolates revealed considerable interstrain variation, ranging from 7% (inbred) to 37% (wild-derived) of polymorphic sites being heterozygous. The increased proportion of polymorphic over monomorphic sites results in five times more frequent observation of a three allelic variant compared with human or mouse. Phylogenetic analysis shows that comparisons between even the least divergent strains used in our analysis may provide one informative marker approximately every 500 nucleotides. Furthermore, the number of haplotypes per locus is relatively large, reflecting independent establishment of the different lines from wild isolates. Finally, our results suggest the presence of prominent C-to-U and A-to-I RNA editing events in zebrafish. Overall, the levels and organization of genetic variation between and within commonly used zebrafish strains are markedly different from other laboratory model organisms, which may affect experimental design and interpretation.[The polymorphism and genotype data from this study have been submitted to dbSNP under accession nos. ss49785942-ss49839678.]The zebrafish (Danio rerio) serves as a unique model for vertebrate development and pharmacological studies (Zon and Peterson 2005). With a draft genome assembly available and thousands of mutants described (Granato and Nusslein-Volhard 1996), a dense map with genetic markers is essential for linkage analysis and cloning approaches. Previous studies employed RAPD (Postlethwait et al. 1994), CA-repeat or simple sequence length polymorphism (SSLP) markers (Shimoda et al. 1999), or singlestrand conformational polymorphism (SSCP) markers (Woods et al. 2005) to place >7000 independent markers on various mapping panels. Despite these advances, there is an increasing demand for higher map density that is required for effective positional cloning (Beier 1998).There are several key advantages that distinguish another type of marker, single nucleotide polymorphism (SNP), as a marker of choice for many genetic studies. To mention a few, SNPs are the most common type of variation in genomes, allowing the generation of ultra-dense genetic maps, and there are efficient low-and high-throughput typing procedures for SNPs currently available (for review, see Vignal et al. 2002). Until now only...

Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis

“…Using these criteria, we interrogated the zebrafish genome for relative DNA gains and losses at an effective resolution of ∼4 kb. We attribute the observed log 2 ratio differences between individuals to actual CNVs, because SNPs in zebrafish are thought to occur approximately once every 0.5-3 kb (2,18), and at least three SNPs within a 60-mer are required to sufficiently alter probe binding efficiency on our array platform. These experiments identified a total of 31,749 CNVs across all 80 fish (Fig.…”

Evidence for a core gut microbiota in the zebrafish

“…All of the labreared domesticated zebrafish lines sampled in this study are derived from the same AB line established at the University of Oregon or one of its derivatives (Table 1) Supplementary Table S3), as well as the 21 OTUs shared between all three locations, which may comprise a 'core' zebrafish gut microbiota (see Supplementary Table S4). domesticated zebrafish are not inbred and retain significant genetic polymorphisms (Rawls et al, 2003;Guryev et al, 2006). Therefore bottleneck effects and genetic drift within different lab facilities could contribute to the observed interindividual variation in gut microbiota composition.…”

Characterization and expression pattern analysis of the facilitative glucose transporter 10 gene (slc2a10) in Danio rerio

“…The ClustalW multiple sequence alignment of all these sequences and those deposited in GenBank (accession nos: XM_679477 and NM_001111163) revealed a total of 25 SNPs in the slc2a10 coding region, nine of which are missense substitutions (Table 1). These nucleotide differences are likely due to high genetic variation existing in the different zebrafish strains (Guryev et al, 2006). Moreover, we did not find the p.K284E variant identified in clone no.…”