A SNP Map of the Rat Genome Generated from cDNA Sequences

Zimdahl, Heike; Nyakatura, Gerald; Brandt, Petra; Schulz, Herbert; Hummel, Oliver; Fartmann, Berthold; Brett, David; Droege, Marcus; Monti, Jan; Lee, Youngae; Sun, Yinyan; Zhao, Shaying; Winter, Eitan; Ponting, Chris P.; Chen, Yuan; Kasprzyk, Arek; Birney, Ewan; Ganten, Detlev; Hübner, Norbert

doi:10.1126/science.1092427

Cited by 51 publications

(36 citation statements)

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“…More specific information could be uncovered if the sequences for these genes could be compared between the BN, SS, and SS-BN strains to identify polymorphisms that may indicate altered gene function and a propensity to proteinuria. To this end, efforts towards a unified rat single nucleotide polymorphism (SNP) map may be most informative [16].…”

Section: Discussionmentioning

confidence: 99%

“…At the time of this analysis, PhysGen has bred adult consomic strains subjected to the "Renal B" protocol for rat chromosomes 1, 2, 4, 6,7, 9, 11,13, 16,18, and 20, and for the rat Y chromosome. For chromosomes 2,4,6,7,9,11,13,16,18,20, and Y, consomic strains consisted of the specific Brown-Norway (BN) rat chromosome introgressed within a Dahl salt-sensitive (SS) rat background. The chromosome 1 consomic strain consisted of BN chromosome 1 within a fawn-hooded hypertensive (FHH) rat background.…”

Section: Consomic Rat Strains and Phenotyping Protocolsmentioning

confidence: 99%

“…We stratified protocol analyses by gender, allowing for analysis of X-chromosome effects as well. Therefore, our analysis included consomic or congenic strains covering 15 of the 22 rat chromosomes (1,2,4,6,7,8,9,11,12,13,16,18,20, X, and Y). Although the PhysGen database includes animals subjected to hypoxia, only those rats in the normoxic group were included in our analysis in order to avoid confounding molecular effects due to hypoxia.…”

Section: Consomic Rat Strains and Phenotyping Protocolsmentioning

confidence: 99%

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Chromosomes 18 and X are quantitative trait loci for nephrotic-range proteinuria in rats

2005

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Numerous cellular and molecular perturbations have been studied to elucidate the pathogenic mechanisms underlying nephrotic-range proteinuria, which may in turn shed light on disease-specific mechanisms. We have analyzed the publicly available data from the PhysGen partial panel of consomic rats to determine whether there are quantitative trait loci that associate with nephroticrange proteinuria. As of this writing, consomic rat strains subjected to the renal protocol have been bred by the Program for Genomic Applications for 15 of the 22 rat chromosomes for both genders, predominantly with the Brown-Norway (BN) and Dahl salt-sensitive (SS) strains as parents. We defined chromosomes of interest as consomic SS-xBN strains whose phenotype measurements differed significantly from SS but not BN strains, stratified by gender. We filtered and clustered differentially expressed genes by function in renal tissue from relevant strains. Proteinuria was significantly higher in male SS vs. male SS-18BN, and it was significantly higher in male SS vs. female SS. Functional clustering of differentially expressed genes yielded two specific functional clusters: apoptosis (p=0.022) and angiogenesis (p=0.046). Gene expression profiles demonstrated differential expression of apoptotic and angiogenic genes. However, TUNEL stains of renal tissue showed no significant difference in the number of apoptotic nuclei. We conclude that chromosomes 18 and X are quantitative trait loci for nephrotic-range proteinuria in rats.

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Section: Discussionmentioning

confidence: 99%

Section: Consomic Rat Strains and Phenotyping Protocolsmentioning

confidence: 99%

Section: Consomic Rat Strains and Phenotyping Protocolsmentioning

confidence: 99%

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Chromosomes 18 and X are quantitative trait loci for nephrotic-range proteinuria in rats

2005

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“…SHR and BN rats are founder strains for the BXH/HXB RI strains, one of the largest rodent RI panels for analysis of cardiovascular and metabolic phenotypes. 22 The investigation was facilitated by the availability of the reference BN genome sequence, 4 of tens of thousands of rat SNPs, 23,24 of a dense genetic map, 25,26 and of the previous mapping of more than 70 physiological and pathophysiological phenotypes in this RI panel. 27 The next step in the investigation was to use expression levels in the RI strains as "expression" phenotypes, the transcripts being expression traits.…”

Section: Integrating Genetic Linkage With Expression Profilingmentioning

confidence: 99%

Novel Integrative Approaches to the Identification of Candidate Genes in Hypertension

Hübner

Yagil

2006

Hypertension

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Abstract-Hypertension, diabetes, and obesity are common diseases that are genetically expressed as complex traits. The clinical expression of these diseases, which run in families but have no clear pattern of inheritance, has been attributed to the interaction between multiple genes and the environment. Identifying the underlying genes, a crucial step in understanding the molecular pathogenesis of complex diseases, has had limited success so far, stressing the need for novel strategies to move this process forward. Innovative integrative genetic-genomic approaches have been proposed recently for the identification of new high-priority candidate genes. These strategies, which combine expression profiling with genetic linkage in different ways, may represent a breakthrough in the search for the genes involved in complex diseases. (Hypertension. 2006;47:1-5.)

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“…A genome with highdensity SNP coverage serves as a powerful tool for whole genome association studies because it can be used to detect linkage disequilibrium (Liu et al, 2011). Research has shown that SNP markers are very powerful markers for linkage mapping, construction of large-number populations, and identification of complex traits in humans (Wang et al, 1998), along with other model species (Zimdahl et al, 2004;Guryev et al, 2006). SNP markers have also been widely used to construct aquaculture fish linkage maps Lien et al, 2011;Wang et al, 2011b).…”

Section: Introductionmentioning

confidence: 99%

Genetic analysis of QTL for eye cross and eye diameter in common carp (Cyprinus carpio L.) using microsatellites and SNPs

et al. 2015

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ABSTRACT.A group of 107 F 1 hybrid common carp was used to construct a linkage map using JoinMap 4.0. A total of 4877 microsatellite and single nucleotide polymorphism (SNP) markers isolated from a genomic library (978 microsatellite and 3899 SNP markers) were assigned to construct the genetic map, which comprised 50 linkage groups. The total length of the linkage map for the common carp was 4775.90 cM with an average distance between markers of 0.98 cM. Ten quantitative trait loci (QTL) were associated with eye diameter, corresponding to 10.5-57.2% of the total phenotypic variation. Twenty QTL were related to eye cross, contributing to 10.8-36.9% of the total phenotypic variation. Two QTL for eye diameter and four QTL for eye cross each accounted for more than 20% of the total phenotypic variation and were considered to be major QTL. One growth factor related to eye diameter was observed on LG10 of the common carp genome, and three growth factors related to eye cross were observed on LG10, S.B. Jin et al. 3558©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (2): 3557-3569 (2015) LG35, and LG44 of the common carp genome. The significant positive relationship of eye cross and eye diameter with other commercial traits suggests that eye diameter and eye cross can be used to assist in indirect selection for many commercial traits, particularly body weight. Thus, the growth factor for eye cross may also contribute to the growth of body weight, implying that aggregate breeding could have multiple effects. These findings provide information for future genetic studies and breeding of common carp.

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A SNP Map of the Rat Genome Generated from cDNA Sequences

Cited by 51 publications

References 4 publications

Chromosomes 18 and X are quantitative trait loci for nephrotic-range proteinuria in rats

Chromosomes 18 and X are quantitative trait loci for nephrotic-range proteinuria in rats

Novel Integrative Approaches to the Identification of Candidate Genes in Hypertension

Genetic analysis of QTL for eye cross and eye diameter in common carp (Cyprinus carpio L.) using microsatellites and SNPs

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