Zebrafish Genetic Map with 2000 Microsatellite Markers

Shimoda, Nobuyoshi; Knapik, Ela W.; Ziniti, John; Sim, Chäng; Yamada, Eri; Kaplan, Selçuk; Jackson, Donald; Sauvage, FJ de; Jacob, Howard J.; Fishman, Mark C.

doi:10.1006/geno.1999.5824

Cited by 328 publications

(280 citation statements)

References 20 publications

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“…Our linkage analysis successfully identified all 73 linkage groups. The linkage map provides high resolution, and the average recombination rate across all linkage groups in E. sinensis is 3.09 cM Mb − 1 , which is much higher than those reported in many other animals, such as mouse (0.5 cM Mb − 1 ), catfish (1.65 cM Mb − 1 ), zebrafish (1.35 cM Mb − 1 ), scallop (1.3 cM Mb − 1 ) and shrimp (1.9 cM Mb − 1 ) (Shimoda et al, 1999;Jensen-Seaman et al, 2004;Kucuktas et al, 2009;Huang et al, 2011;Baranski et al, 2014;Jiao et al, 2014). This suggests that QTLs, if identified, can be narrowed down to quite small genomic region in E. sinensis.…”

Section: Discussionmentioning

confidence: 60%

High-density linkage mapping aided by transcriptomics documents ZW sex determination system in the Chinese mitten crab Eriocheir sinensis

et al. 2015

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The sex determination system in crabs is believed to be XY-XX from karyotypy, but centromeres could not be identified in some chromosomes and their morphology is not completely clear. Using quantitative trait locus mapping of the gender phenotype, we revealed a ZW-ZZ sex determination system in Eriocheir sinensis and presented a high-density linkage map covering~98.5% of the genome, with 73 linkage groups corresponding to the haploid chromosome number. All sex-linked markers in the family we used were located on a single linkage group, LG60, and sex linkage was confirmed by genome-wide association studies (GWAS). Forty-six markers detected by GWAS were heterozygous and segregated only in the female parent. The female LG60 was thus the putative W chromosome, with the homologous male LG60 as the Z chromosome. The putative Z and W sex chromosomes were identical in size and carried many homologous loci. Sex ratio (5:1) skewing towards females in induced triploids using unrelated animals also supported a ZW-ZZ system. Transcriptome data were used to search for candidate sex-determining loci, but only one LG60 gene was identified as an ankyrin-2 gene. Double sex-and mab3-related transcription factor 1 (Dmrt1), a Z-linked gene in birds, was located on a putative autosome. With complete genome sequencing and transcriptomic data, more genes on putative sex chromosomes will be characterised, thus leading towards a comprehensive understanding of the sex determination and differentiation mechanisms of E. sinensis, and decapod crustaceans in general.

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Section: Discussionmentioning

confidence: 60%

High-density linkage mapping aided by transcriptomics documents ZW sex determination system in the Chinese mitten crab Eriocheir sinensis

et al. 2015

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“…The atp␣3A gene maps to LG 16 close to the Hoxab cluster, and atp␣3B maps to LG 19 near the Hoxaa cluster. Both atp␣1A2a and atp␣1A2b map to LG 1 in the same interval as atp␣1A1 and atp␣1B1, whereas atp␣1B2 maps to LG 9 between markers z9112 and z20031 (Shimoda et al 1999). …”

Section: Map Positions Of the Zebrafish Catalytic Subunitsmentioning

confidence: 94%

Partitioning of Tissue Expression Accompanies Multiple Duplications of the Na+/K+ ATPase α Subunit Gene

Serluca

Sidow²,

Mably³

et al. 2001

Genome Res.

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Vertebrate genomes contain multiple copies of related genes that arose through gene duplication. In the past it has been proposed that these duplicated genes were retained because of acquisition of novel beneficial functions. A more recent model, the duplication-degeneration-complementation hypothesis (DDC), posits that the functions of a single gene may become separately allocated among the duplicated genes, rendering both duplicates essential. Thus far, empirical evidence for this model has been limited to theengrailed and sox family of developmental regulators, and it has been unclear whether it may also apply to ubiquitously expressed genes with essential functions for cell survival. Here we describe the cloning of three zebrafish α subunits of the Na(+),K(+)-ATPase and a comprehensive evolutionary analysis of this gene family. The predicted amino acid sequences are extremely well conserved among vertebrates. The evolutionary relationships and the map positions of these genes and of other α-like sequences indicate that both tandem and ploidy duplications contributed to the expansion of this gene family in the teleost lineage. The duplications are accompanied by acquisition of clear functional specialization, consistent with the DDC model of genome evolution.[The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AY028628, AY028629, and AY028630]

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“…Linkage between tre and simple sequence-length polymorphism (SSLP) markers was analyzed as previously described in ref. 18. Total mRNA was extracted from pools of 50 homozygous mutant embryos or 50 of their wild-type siblings (RNAwiz, Ambion) for cDNA synthesis (Access RT-PCR system, Promega).…”

Section: Methodsmentioning

confidence: 99%

Mutation in sodium–calcium exchanger 1 (NCX1) causes cardiac fibrillation in zebrafish

Langenbacher

Dong

Shu

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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Cardiac fibrillation, a form of cardiac arrhythmia, is the most common cause of embolic stroke and death associated with heart failure. The molecular mechanisms underlying cardiac fibrillation are largely unknown. Here we report a zebrafish model for cardiac fibrillation. The hearts of zebrafish tremblor (tre) mutants exhibit chaotic movements and fail to develop synchronized contractions. Calcium imaging showed that normal calcium transients are absent in tre cardiomyocytes, and molecular cloning of the tre mutation revealed that the tre locus encodes the zebrafish cardiac-specific sodium-calcium exchanger (NCX) 1, NCX1h. Forced expression of NCX1h or other calcium-handling molecules restored synchronized heartbeats in tre mutant embryos in a dosage-dependent manner, demonstrating the critical role of calcium homeostasis in maintaining embryonic cardiac function. By creating mosaic zebrafish embryos, we showed that sporadic NCX1h-null cells were not sufficient to disrupt normal cardiac function, but clustered wild-type cardiomyocytes contract in unison in tre mutant hearts. These data signify the essential role of calcium homeostasis and NCX1h in establishing rhythmic contraction in the embryonic zebrafish heart. calcium homeostasis ͉ cardiac arrhythmia ͉ heart T he heart is a muscular pump that drives circulation throughout the body. It is of the utmost importance to establish rhythmic and synchronized cardiac contraction early in development to ensure proper growth and survival of the embryo.Calcium plays an essential role in regulating cardiac cycles. As a wave of depolarization passes through the heart, a small amount of calcium is permitted to enter the cardiomyocytes through voltage-dependent L-type calcium channels. This small calcium influx then triggers the release of a larger amount of calcium from the sarcoplasmic reticulum via ryanodine receptors, resulting in an abrupt increase in cytosolic calcium levels and cardiac contraction. Relaxation is accomplished by resequestering of calcium to the sarcoplasmic reticulum by sarcoendoplasmic reticular Ca 2ϩ -ATPase2 (SERCA2) and extrusion of calcium from the cell by NCX1 and plasma membrane Ca 2ϩ -ATPase (PMCA). Abnormal calcium handling caused by altered expression levels or protein activities of NCX1 and SERCA2, or by mutations in ryanodine receptors, have been associated with cardiac diseases, such as heart failure and arrhythmia, and with sudden death in humans and animal models (1-6). In addition, genetic studies in the zebrafish demonstrate that L-type calcium channels and the sodium pump (a modulator of NCX activity) are indispensable for embryonic cardiac function (7,8). These findings underscore the critical roles of calcium in embryonic and adult cardiac physiology.Three NCX genes have been identified in mammals. NCX2 and NCX3 are expressed predominantly in the brain and skeletal muscle, respectively, whereas NCX1 is virtually ubiquitous (9). NCX1 is highly expressed in the heart and is considered to be the primary mechanism for calcium extrusion...

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Zebrafish Genetic Map with 2000 Microsatellite Markers

Cited by 328 publications

References 20 publications

High-density linkage mapping aided by transcriptomics documents ZW sex determination system in the Chinese mitten crab Eriocheir sinensis

High-density linkage mapping aided by transcriptomics documents ZW sex determination system in the Chinese mitten crab Eriocheir sinensis

Partitioning of Tissue Expression Accompanies Multiple Duplications of the Na+/K+ ATPase α Subunit Gene

Mutation in sodium–calcium exchanger 1 (NCX1) causes cardiac fibrillation in zebrafish

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