Dataset Information

Generation of highly homogeneous strains of zebrafish through full sib-pair mating.

ABSTRACT: Genetically homogeneous populations, such as inbred strains, are powerful experimental tools that are ideally suited for studying immunology, cancer, and genetics of complex traits. The zebrafish, Danio rerio, has been underutilized in these research areas because homogeneous strains of experimental fish have not been available in tractable condition. Here, we attempted to inbreed two zebrafish wild-type strains, Tübingen and India, through full sib-pair mating. Although the inbred Tübingen strain failed to thrive and was lost after 13 generations, an inbred India strain (IM) has been maintained successfully. The IM strain has endured 16 generations of inbreeding and has maintained a healthy condition. Two additional strains, IM12m and IM14m, were established as closed colonies from the branches of the IM strain. Genotype analyses using genetic markers revealed a dramatic decrease in polymorphisms (62% dropped to 5%) in both IM (generation 14) and the two closed colonies. This indicates a high level of homogeneity in these strains. Furthermore, scale transplantations between individuals within each strain were successful. These data suggest that extremely homogeneous zebrafish strains have been established, thereby creating a valuable resource for practical application.

SUBMITTER: Shinya M

PROVIDER: S-EPMC3276154 | biostudies-literature | 2011 Oct

REPOSITORIES: biostudies-literature

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Generation of highly homogeneous strains of zebrafish through full sib-pair mating.

Shinya Minori M Sakai Noriyoshi N

G3 (Bethesda, Md.) 20111001 5

Genetically homogeneous populations, such as inbred strains, are powerful experimental tools that are ideally suited for studying immunology, cancer, and genetics of complex traits. The zebrafish, Danio rerio, has been underutilized in these research areas because homogeneous strains of experimental fish have not been available in tractable condition. Here, we attempted to inbreed two zebrafish wild-type strains, Tübingen and India, through full sib-pair mating. Although the inbred Tübingen stra ...[more]

PMID: 22384348

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Project description:BACKGROUND: It is widely known that castration has a significant effect on the accumulation of adipose tissue. microRNAs (miRNAs) are known to be involved in fat deposition and to be regulated by the androgen-induced androgen receptor (AR). However, there is little understanding of the relationship between miRNAs and fat deposition after castration. In this study, the high-throughput SOLiD sequencing approach was used to identify and characterize miRNA expression in backfat from intact and castrated full-sib male 23-week-old pigs. The patterns of adipogenesis and fat deposition were compared between castrated and intact male pigs. RESULTS: A total of 366 unique miRNA genes were identified, comprising 174 known pre-miRNAs and 192 novel pre-miRNAs. One hundred and sixty-seven pre-miRNAs were common to both castrated (F3) and intact (F4) male pig small RNA libraries. The novel pre-miRNAs encoded 153 miRNAs/miRNA*s and 141 miRNAs/miRNA*s in the F3 and F4 libraries, respectively. One hundred and seventy-seven miRNAs, including 45 up- and 132 down-regulated, had more than 2-fold differential expression between the castrated and intact male pigs (p-value < 0.001). Thirty-five miRNAs were further selected, based on the expression abundance and differentiation between the two libraries, to predict their targets in KEGG pathways. KEGG pathway analyses suggested that miRNAs differentially expressed between the castrated and intact male pigs are involved in proliferation, apoptosis, differentiation, migration, adipose tissue development and other important biological processes. The expression patterns of eight arbitrarily selected miRNAs were validated by stem-loop reverse-transcription quantitative polymerase chain reaction. These data confirmed the expression tendency observed with SOLiD sequencing. miRNA isomiRs and mirtrons were also investigated in this study. Mirtrons are a recently described category of miRNA relying on splicing rather than processing by the microprocessor complex to generate the RNAi pathway. The functions of miRNAs important for regulating fat deposition were also investigated in this study. CONCLUSIONS: This study expands the number of fat-deposition-related miRNAs in pig. The results also indicate that castration can significantly affect the expression patterns of fat-related miRNAs. The differentially expressed miRNAs may play important roles in fat deposition after castration.

Project description:Spousal comparisons have been proposed as a design that can both reduce confounding and estimate effects of the shared adulthood environment. However, assortative mating, the process by which individuals select phenotypically (dis)similar mates, could distort associations when comparing spouses. We evaluated the use of spousal comparisons, as in the within-spouse pair (WSP) model, for aetiological research such as genetic association studies. We demonstrated that the WSP model can reduce confounding but may be susceptible to collider bias arising from conditioning on assorted spouse pairs. Analyses using UK Biobank spouse pairs found that WSP genetic association estimates were smaller than estimates from random pairs for height, educational attainment, and BMI variants. Within-sibling pair estimates, robust to demographic and parental effects, were also smaller than random pair estimates for height and educational attainment, but not for BMI. WSP models, like other within-family models, may reduce confounding from demographic factors in genetic association estimates, and so could be useful for triangulating evidence across study designs to assess the robustness of findings. However, WSP estimates should be interpreted with caution due to potential collider bias. Author summary There is growing evidence that genome-wide association studies capture associations relating to environmental factors, such as indirect effects from parental genotypes. Within-family models such as sibling comparisons can be used to disentangles these different sources of association but are limited by the paucity of sibling data in large biobanks. Within-spouse pair models are a potentially tractable model because spouses share environmental factors in adulthood and may also share early-life environmental factors. Here, we evaluated the application of within-spouse models in genetic association studies, specifically considering assortative mating, a phenomenon whereby individuals may select a phenotypically similar partner. We found that within-spouse pair models can detect genuine confounding in genetic association estimates but are potentially susceptible to collider bias induced by comparing assorted pairs. Within-spouse pair estimates could be useful when combining evidence from different study designs.

Dataset Information

Generation of highly homogeneous strains of zebrafish through full sib-pair mating.

Publications

Generation of highly homogeneous strains of zebrafish through full sib-pair mating.

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