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Table 1 Candidate genes for Cairn terrier ocular melanosis with markers, chromosomal positions, and PCR primers

From: Exclusion of eleven candidate genes for ocular melanosis in cairn terriers

Gene, Protein, Positiona

Markerb[Restriction enzyme]

Marker Positionc

Distance (kb)d

P valuese

LYST Lysosomal Trafficking Regulator chr4:7,128,220-7,294,031

Microsat 1 (TTTTC)18(TTTTC)11

1§

345

1.00 × 10-5

Microsat 2 (GAAA)5 (GAAA)13

2§

368

MC1R Melanocortin 1 receptor chr5:66,692,398-66,693,344

SNP 1 (BICF2P987741)

2∆

560

1.34 × 10-5

SNP 2 (BICF2S23213233) [SsiI]

1∆

24

SILV Silverchr10:3,273,996-3,279,352

Microsat 1 (GAAA)7(GAAA)17

2§

60

1.00 × 10-5

Microsat 2 (TTTC)15(TTCC)13

1§

226

TYRP1 Tyrosinase related protein 1 chr11:36,344,712-36,361,793

SNP 1 (BICF2S23051528) [BC1I]

1∆

224

2.15 × 10-5

In/Del

2∆

96

GPNMB Glycoprotein NMB chr14:39,877,810-39,905,589

SNP 1 (BICF2P753624) [HpyCH4V]

M1°

26

1.59 × 10-4

SNP 2 (BICF2P134952)

2∆

1200

MITF Microphthalmia transcription factor chr20:24,853,657-24,884,775

SNP 1 (BICF2G630233682) [BspHI]

2∆

73

3.80 × 10-5

SNP 2 (BICF2S23248988)

1∆

521

TYR Tyrosinasechr21:13,797,070-13,891,317

Microsat 1 (GAAA)17(GGAA)20(GAAA)10

2§

428

1.00 × 10-9

Microsat 2 (TTTC)10(TTTC)4(TTTC)13

1§

70

TYRP2 (DCT) Tyrosinase related protein 2 chr22:48,219,817-48,254,000

SNP 1 (BICF2S23137809) [sequenced]

M2°

33

8.47 × 10-4

SNP 2 (BICF2P452919) [RsaI]

M1°

8

ASIP Agouti signaling protein chr24:26,327,360-26,366,307

SNP 1 (BICF2P1186810) [MesI]

1∆

340

3.57 × 10-5

In/Del

2∆

105

COMT Catechol-O-Methyltransferase chr26:32,426,959-32,432,523

SNP 1 (BICF2S22923369) [ApaLI]

2∆

82

8.20 × 10-5

Microsat 1 (TTTA)15

1§

676

GSK3B Glycogen Synthase Kinase 3-Beta chr33:26,516,949-26,699,712

Microsat 1 (CTATT)14

M2*

146

1.00 × 10-5

Microsat 2 (TTTA)13

M2*

143

  1. Key:
  2. a. Genes are listed in chromosomal order as obtained from the May 2005 build of the canine reference genome (UCSC Genome Browser:http://genome.ucsc.edu/), with the encoded proteins provided under the gene names.
  3. b. Microsatellite-based markers are shown with the repeat type and number of perfect repeats present in the canine reference genome. Repeat blocks are separated by one to several nucleotides that do not match the perfect repeat. SNPs are listed with Broad Institute CanFam 2.0 SNP designation (http://www.broadinstitute.org/mammals/dog). One marker for ASIP is an in/del of an undefined but variable nature. The restriction enzyme used for PCR-restriction enzyme method of genotyping SNPs is shown in square brackets. Note some were genotyped by sequencing.
  4. c. The location of each marker is given with respect to coding region of each gene as seen in the 2005 canine reference genome on UCSC Genome Browser. Designations are upstream (1) or downstream (2) of the gene start site, or within the gene upstream of the exact midpoint (M1) or to the downstream of the midpoint (M2).
  5. d. Distances are given from each marker to furthest end of the gene from that marker.
  6. e. Each P value is the probability (combined probability of the two markers) of falsely excluding the true causative gene (see Additional file2: Supplementary Methods for an example of how this was calculated). The method used for each marker is indicated in the column showing marker position: § used microsatellite mutation rate, ∆ used rate of recombination between marker and coding region, o used rate of recombination from marker to nearest end of the coding region (probability of the recombination WITHIN the gene), * Clark’s method for haplotype analysis[10].
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Journal of Negative Results in BioMedicine

ISSN: 1477-5751

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