Zebrafish chromosome banding

Pijnacker, L. P.; Ferwerda, M. A.

doi:10.1139/g95-140

Cited by 40 publications

(37 citation statements)

References 3 publications

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“…Despite the high quality of the zebrafish reference genome (Howe et al 2013), many scaffolds remain unassembled, especially in areas rich in repeats, such as the heterochromatic and late-replicating right arm of zebrafish cytogenetic chromosome 3 (genetic linkage group 4, Ensembl Chr4) (Pijnacker and Ferwerda 1995;Daga et al 1996;Amores and Postlethwait 1999;Traut and Winking 2001;Phillips et al 2006;Anderson et al 2012;Howe et al 2013). Some RAD-tags that were strongly associated with sex reside on scaffolds that are either unassembled or are on Chr14 in Zv9.…”

Section: Mapping Unassembled Scaffoldsmentioning

confidence: 99%

“…Cytogeneticists numbered zebrafish chromosomes based on physical length (Pijnacker and Ferwerda 1995;Daga et al 1996;Gornung et al 1997Gornung et al , 2000Amores and Postlethwait 1999;Sola and Gornung 2001), so zebrafish genetic linkage group number and cytogenetic chromosome number are generally not the same. We assigned genetic linkage groups to physical chromosomes by fluorescent in situ hybridization (Phillips et al 2006), which showed that, for example, cytogenetic chromosome 3 is linkage group 4, called chromosome 4 in the reference genome and Chr4 in this work.…”

Section: Rad-tag Genotypingmentioning

confidence: 99%

“…Zebrafish does not, however, have a typical environmental sex-determination (ESD) mechanism like some sauropsids for which temperature is a cue (Charnier 1966;Lang and Andrews 1994;Merchant-Larios and Diaz-Hernandez 2013;Mork et al 2014). It is more probable that zebrafish is like medaka (Oryzias latipes) in having a genetic sex-determination mechanism that is sensitive to environmental conditions (Hattori et al 2007; Sato et al 2005;Selim et al 2009;Hayashi et al 2010).Zebrafish not only lacks classic ESD, but most stocks investigated do not have cytogenetically detectable chromosomal sex determination (Schreeb et al 1993;Pijnacker and Ferwerda 1995;Daga et al 1996;Gornung et al 1997;Amores and Postlethwait 1999;Gornung et al 2000;Sola and Gornung 2001;Traut and Winking 2001;Phillips et al 2006). In contrast, the only investigation of zebrafish taken directly from nature in India concluded that zebrafish females are the heterogametic sex (Sharma et al 1998).…”

mentioning

confidence: 99%

“…Zebrafish linkage group numbers assigned based on genetic length (Postlethwait et al 1994;Johnson et al 1996) are given the name "chromosome" in the Zv9 version of the zebrafish reference genome; here we abbreviate "linkage group" as Chr according to zebrafish nomenclature conventions (https:// wiki.zfin.org/display/general/zfin+zebrafish+nomenclature+ guidelines). Cytogeneticists numbered zebrafish chromosomes based on physical length (Pijnacker and Ferwerda 1995;Daga et al 1996;Gornung et al 1997Gornung et al , 2000Amores and Postlethwait 1999;Sola and Gornung 2001), so zebrafish genetic linkage group number and cytogenetic chromosome number are generally not the same. We assigned genetic linkage groups to physical chromosomes by fluorescent in situ hybridization (Phillips et al 2006), which showed that, for example, cytogenetic chromosome 3 is linkage group 4, called chromosome 4 in the reference genome and Chr4 in this work.…”

mentioning

confidence: 99%

“…Zebrafish not only lacks classic ESD, but most stocks investigated do not have cytogenetically detectable chromosomal sex determination (Schreeb et al 1993;Pijnacker and Ferwerda 1995;Daga et al 1996;Gornung et al 1997;Amores and Postlethwait 1999;Gornung et al 2000;Sola and Gornung 2001;Traut and Winking 2001;Phillips et al 2006). In contrast, the only investigation of zebrafish taken directly from nature in India concluded that zebrafish females are the heterogametic sex (Sharma et al 1998).…”

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confidence: 99%

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Wild Sex in Zebrafish: Loss of the Natural Sex Determinant in Domesticated Strains

et al. 2014

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Sex determination can be robustly genetic, strongly environmental, or genetic subject to environmental perturbation. The genetic basis of sex determination is unknown for zebrafish (Danio rerio), a model for development and human health. We used RADtag population genomics to identify sex-linked polymorphisms. After verifying this "RAD-sex" method on medaka (Oryzias latipes), we studied two domesticated zebrafish strains (AB and TU), two natural laboratory strains (WIK and EKW), and two recent isolates from nature (NA and CB). All four natural strains had a single sex-linked region at the right tip of chromosome 4, enabling sex genotyping by PCR. Genotypes for the single nucleotide polymorphism (SNP) with the strongest statistical association to sex suggested that wild zebrafish have WZ/ZZ sex chromosomes. In natural strains, "male genotypes" became males and some "female genotypes" also became males, suggesting that the environment or genetic background can cause female-to-male sex reversal. Surprisingly, TU and AB lacked detectable sex-linked loci. Phylogenomics rooted on D. nigrofasciatus verified that all strains are monophyletic. Because AB and TU branched as a monophyletic clade, we could not rule out shared loss of the wild sex locus in a common ancestor despite their independent domestication. Mitochondrial DNA sequences showed that investigated strains represent only one of the three identified zebrafish haplogroups. Results suggest that zebrafish in nature possess a WZ/ZZ sex-determination mechanism with a major determinant lying near the right telomere of chromosome 4 that was modified during domestication. Strains providing the zebrafish reference genome lack key components of the natural sex-determination system but may have evolved variant sex-determining mechanisms during two decades in laboratory culture.. . .researchers using standard lines of zebrafish that have long been maintained in laboratories are often plagued by severe sex ratio distortions. . .. C. Lawrence, J. P. Ebersole, and R. V. Kesseli (2008) C ONSIDERING the fundamental importance of sex for species propagation, it is surprising that primary sexdetermining mechanisms are not strongly conserved among animal taxa (Bull 1983;Charlesworth 1996;Ming et al. 2011;Bachtrog et al. 2014). Closely related species or even populations of the same species can have different sexdetermining mechanisms (Takehana et al. 2007;Ross et al. 2009;Kobayashi et al. 2013;Heule et al. 2014;Larney et al. 2014). Zebrafish (Danio rerio) is a popular model for studies of vertebrate development, behavior, physiology, evolution, disease, and human health (Mills et al. 2007;Seth et al. 2013;Braasch et al. 2014;Ota and Kawahara 2014;Wilkinson et al. 2014), but researchers struggle with highly variable and distorted sex ratios, and investigations into the genetic nature of zebrafish sex determination are conflicting. To help understand these issues, we conducted a population genomic study of sex determination in multiple zebrafish strains. Zebrafish exhibit...

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Section: Mapping Unassembled Scaffoldsmentioning

confidence: 99%

Section: Rad-tag Genotypingmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Wild Sex in Zebrafish: Loss of the Natural Sex Determinant in Domesticated Strains

et al. 2014

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Comparative analysis of the testis and ovary transcriptomes in zebrafish by combining experimental and computational tools

Chia

Bártfai

et al. 2004

Comp Funct Genom

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Studies on the zebrafish model have contributed to our understanding of several important developmental processes, especially those that can be easily studied in the embryo. However, our knowledge on late events such as gonad differentiation in the zebrafish is still limited. Here we provide an analysis on the gene sets expressed in the adult zebrafish testis and ovary in an attempt to identify genes with potential role in (zebra)fish gonad development and function. We produced 10 533 expressed sequence tags (ESTs) from zebrafish testis or ovary and downloaded an additional 23 642 gonad-derived sequences from the zebrafish EST database. We clustered these sequences together with over 13 000 kidney-derived zebrafish ESTs to study partial transcriptomes for these three organs. We searched for genes with gonad-specific expression by screening macroarrays containing at least 2600 unique cDNA inserts with testis-, ovary- and kidney-derived cDNA probes. Clones hybridizing to only one of the two gonad probes were selected, and subsequently screened with computational tools to identify 72 genes with potentially testis-specific and 97 genes with potentially ovary-specific expression, respectively. PCR-amplification confirmed gonad-specificity for 21 of the 45 clones tested (all without known function). Our study, which involves over 47 000 EST sequences and specialized cDNA arrays, is the first analysis of adult organ transcriptomes of zebrafish at such a scale. The study of genes expressed in adult zebrafish testis and ovary will provide useful information on regulation of gene expression in teleost gonads and might also contribute to our understanding of the development and differentiation of reproductive organs in vertebrates.

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Evaluation of a 40 day Assay for Testing Endocrine Disrupters: Effects of an Anti-Estrogen and an Aromatase Inhibitor on Sex Ratio and Vitellogenin Concentrations in Juvenile Zebrafish (Danio rerio)

Andersen

Kinnberg

Holbech

et al. 2004

Fish Physiol Biochem

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In the present study, the effects of the anti-estrogen ZM 189,156 and the aromatase inhibitor fadrozole were evaluated in a 40-day juvenile assay developed for screening of endocrine disrupting chemicals. Juvenile zebrafish were exposed from 20 to 60 days post hatch (dph) to ZM 189, 154 (100 lg l )1 and 200 lg l )1 ) and fadrozole (10, 32, and 100 lg l )1 ). VTG concentrations were measured at 38 dph by the use of a direct noncompetitive sandwich ELISA and sex ratios were determined at 60 dph by histological examination of the gonads. A small but significant increase in VTG concentrations was observed in fish exposed to ZM 189, 156 (100 and 200 lg l )1 ) and fadrozole (10 and 100 lg l )1 ) compared to control groups. In fish exposed to ZM 189, 156 and fadrozole, the percentage of females declined and the number of undifferentiated fish increased. These findings show that exposure of juvenile zebrafish to an aromatase inhibitor or an antiestrogen during early development inhibits differentiation and development of female gonads. The data presented, furthermore, show that the 40-day juvenile assay may be suitable for screening endocrine disrupting chemicals acting as anti-estrogens and aromatase inhibitors.Abbreviations: Fad -fadrozole; ZM -ZM 189, 156

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Zebrafish chromosome banding

Cited by 40 publications

References 3 publications

Wild Sex in Zebrafish: Loss of the Natural Sex Determinant in Domesticated Strains

Wild Sex in Zebrafish: Loss of the Natural Sex Determinant in Domesticated Strains

Comparative analysis of the testis and ovary transcriptomes in zebrafish by combining experimental and computational tools

Evaluation of a 40 day Assay for Testing Endocrine Disrupters: Effects of an Anti-Estrogen and an Aromatase Inhibitor on Sex Ratio and Vitellogenin Concentrations in Juvenile Zebrafish (Danio rerio)

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