The proto-oncogene C-KIT maps to canid B-chromosomes

Graphodatsky, Alexander S.; Kukekova, Anna V.; Yudkin, Dmitry V.; Trifonov, Vladimir A.; Vorobieva, Nadezhda V.; Beklemisheva, Violetta R.; Perelman, Polina L.; Graphodatskaya, Daria; Trut, Lyudmila N.; Yang, Fengtang; Ferguson‐Smith, Malcolm A.; Acland, Gregory M.; Aguirre, Gustavo D.

doi:10.1007/s10577-005-7474-9

Cited by 72 publications

(93 citation statements)

References 28 publications

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“…Interestingly, allele frequencies of these markers, which were linked to genes potentially associated with tameness/habituation or aggression (Kukekova et al 2004), differed between the two California populations. Despite previously reported polymorphism (Graphodatsky et al 2005), the C-KIT SNPs were monomorphic in our sample.…”

Section: Single Nucleotide Polymorphisms á Snps á Vulpes Vulpescontrasting

confidence: 99%

“…1 C-KIT SNPs reported by Graphodatsky et al (2005) were monomorphic among all foxes used in this study 2 SNP marker failed to amplify in the assay 3 Three SNPs monomorphic in the two California populations (O-INU055D, O-INU055G, O-REN54P11A) had relatively high heterozygosity in eight red foxes from the United Kingdom; three other SNPs monomorphic in the California samples (SL-35b, SL49a, O-C04.140B) had the other allele present (but rare) in another North American population 4 The genotyping accuracy was assessed for sex loci (from both markers together) based on a subset of individuals for which phenotypic sex was known, for coat-color loci (all three markers together) based on seven fur-farm foxes representing all but two possible genotypes (Mc1R heterozygous with Agouti heterozygous and homozygous wild type) and 61 wild-caught red-phase individuals, and for Cytb (both markers together) and genomic loci relative to a subset of individuals that was sequenced directly…”

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confidence: 99%

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A medium-throughput SNP assay for detecting genetic variation in coding and non-coding portions of the red fox genome

Sacks

Våge

Statham

2009

Conservation Genet Resour

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SNPs are fast becoming the marker of choice in population genetics studies of model organisms. However, a lack of efficient means to assay sufficient numbers of SNPs in non-model organisms has prevented their widespread use for conservation-related applications. We established a SNP genotyping assay (including development of new SNP markers) for detection of genetic variation in coding and non-coding parts of the fox genome, using a 96-locus multiplex format. Coding SNPs were associated with Agouti and Mc1r coat-color alleles, phylogenetically basal mitochondrial mutations, sex markers, B-chromosome protooncogenes, and serotonin-receptor genes. Non-coding SNPs (n = 51) included 27 newly described microsatellite-linked SNPs. A panel of red foxes (n = 96) was used to characterize minor allele frequencies and Hardy-Weinberg equilibrium. Genotyping accuracy was 99% for 72 SNPs relative to sequenced and known-phenotype animals.Keywords Coat-color Á Red fox Á Single nucleotide polymorphisms Á SNPs Á Vulpes vulpes Single nucleotide polymorphisms (SNPs) occur in coding and non-coding regions of the genome and are, in principle, the ideal marker for population genetics studies (Morin et al. 2004). However, because SNPs are typically biallelic, large numbers of markers are required for most applications, which has thus far prevented their widespread application in studies of non-model species, including most threatened and endangered species. While various approaches have been successfully used to discover moderate numbers of SNPs in non-model organisms (e.g., Sacks and Louie 2008), published genotyping assays used in conservation-related applications rarely involve more than a dozen or so multiplexed markers. As part of a broader research project aimed at conservation of threatened red fox (Vulpes vulpes) populations, we developed several new SNP markers and a multiplex assay for genotyping 96 coding and non-coding SNPs in red foxes. Here, we describe these markers along with the assay and its validation.We used the Golden Gate platform and BeadXpress reader (Illumina, Inc., San Diego, California), which supported genotyping assays of up to 96 SNPs per well and a 96-well format (9,216 reactions;Fan et al. 2006). Sequences containing SNPs were submitted to Illumina's proprietary Assay Design Tool (http://www.illumina.com), and a subset of 96 loci was selected based on the manufacturer's design Electronic supplementary material The online version of this article

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Section: Single Nucleotide Polymorphisms á Snps á Vulpes Vulpescontrasting

confidence: 99%

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confidence: 99%

A medium-throughput SNP assay for detecting genetic variation in coding and non-coding portions of the red fox genome

Sacks

Våge

Statham

2009

Conservation Genet Resour

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“…The B chromosomes range in size and are characterized as Bi, Bii, and Biii types (Becker et al, 2011). The proto-oncogene KIT is present on all B chromosomes of the Chinese raccoon dog, in addition to chromosome 6 (Graphodatsky et al, 2005;Yudkin et al, 2007;Becker et al, 2011). The proto-oncogene KIT is also localized on all B chromosomes of red fox and the structure and sequence of the B-specific KIT were found to be highly conserved (Graphodatsky et al, 2005;Yudkin et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

“…KIT is the first protein-coding autosomal gene to be found on mammalian B chromosomes (Graphodatsky et al, 2005). To investigate whether KIT located on the B chromosomes exhibits transcriptional activity in the Chinese raccoon dog, we cloned, sequenced, and compared the partial sequence of KIT at both genomic DNA and mRNA levels.…”

Section: Introductionmentioning

confidence: 99%

Identification of polymorphisms and transcriptional activity of the proto-oncogene KIT located on both autosomal and B chromosomes of the Chinese raccoon dog

Zhang

Zhu

et al. 2016

Genet. Mol. Res.

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ABSTRACT. B chromosomes are dispensable and co-exist with autosomal and sex chromosomes. The karyotype of the Chinese raccoon dog (Nyctereutes procyonoides procyonoides) comprises 0-4 B chromosomes. The proto-oncogene KIT is found on all B chromosomes of the Chinese raccoon dog. In the present study, partial DNA and mRNA sequences of KIT were amplified and sequenced from four individuals containing B chromosomes. Sequence analyses revealed that polymorphisms including single nucleotide polymorphisms (SNPs) and inserts/deletions were rich in the KIT gene of Chinese raccoon dog at the genomic level. However, no polymorphism was detected at the mRNA level. A comparison of mRNA sequences from Chinese raccoon dogs with the corresponding sequences derived from arctic fox and dog, which do not contain B chromosomes, revealed the mRNA sequences of the 10 SNPs to be identical between these three species. Therefore, these findings suggest that KIT located on the B chromosomes in Chinese raccoon dog lacks transcriptional activity.

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“…B chromosomes were generally believed not to contain genes of major importance, and fluorescence in situ hybridization (FISH) experiments using fox probes against dog chromosome spreads (Yang et al 1999) support this belief. However, the recent discovery of a highly conserved and seemingly functional C-KIT proto-oncogene copy on a fox B-chromosome suggests that this hypothesis should probably be revisited (Graphodatsky et al 2005).…”

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confidence: 99%