Inter-genic. UBTD2. HO. REN169D01. CFA14. Dinucleotide. 199-221. HEX. MF. [3]. Inter-genic. ABCB5. HO. AHTh260. CFA16. Dinucleotide. 230-254. HEX. MF.
S1 Table. Description of the genotyped autosomal (CFA) microsatellites (STR).
Locus AHTk211 CXX279 REN169O18 INU055 REN54P11 AHT137 REN169D01 AHTh260 AHTk253 INU005 INU030 FH2848 REN162C04 AHTh171 REN247M23 FH2004 FH2088 FH2096 FH2137 CPH2 CPH8 FH2079 CPH4
Chromosome
STR repeat size
CFA26 CFA22 CFA29 CFA10 CFA18 CFA11 CFA14 CFA16 CFA23 CFA33 CFA12 CFA2 CFA7 CFA6 CFA15 CFA11 CFA15 CFA11 CFA3 CFA32 CFA13 CFA24 CFA15
Dinucleotide Dinucleotide Dinucleotide Dinucleotide Dinucleotide Dinucleotide Dinucleotide Dinucleotide Dinucleotide Dinucleotide Dinucleotide Dinucleotide Dinucleotide Dinucleotide Dinucleotide Tetranucleotide Tetranucleotide Tetranucleotide Dinucleotide Dinucleotide Dinucleotide Tetranucleotide Dinucleotide
Allele sizes Dye label Multiplex Reference (bp) 79-101 109-133 150-170 190-216 222-244 126-156 199-221 230-254 277-297 102-136 139-157 222-244 192-212 215-239 258-282 104-202 91-139 86-110 140-192 88-106 191-219 246-282 130-155
FAM FAM FAM FAM FAM HEX HEX HEX HEX NED NED NED PET PET PET PET FAM HEX HEX NED FAM FAM NED
MF MF MF MF MF MF MF MF MF MF MF MF MF MF MF M1 M1 M1 M1 M1 M1 M2 M2
[1] [2] [3] Finnzymes [3] [4] [3] [5] [1] Finnzymes Finnzymes [5] [3] [5] [3] [6] [6] [6] [6] [7] [7] [6] [7]
Genomic contexta Inter-genic Inter-genic Inter-genic Inter-genic Intronic Inter-genic Inter-genic NA Inter-genic Intronic Intronic Inter-genic Intronic Intronic Inter-genic Intronic Inter-genic Inter-genic Inter-genic Intronic Inter-genic Inter-genic Intronic
Gene location / Sourcea Nearest genea LHX5 CLYBL CAP1 ETAA1 MAGI2 UBTD2 ABCB5 NA RPS2P32 PARP9 GRIK2 LINC00710 DNM3 SRM3 LIN7A PTPRD FHDC1 DDX43 CHD1 SCD5 LOC1720 PTNP1 ANKS1B
HO HO HO HO HO HO HO NA HO HO HO HO HO HO HO RS, HO HO HO HO RS, HO HO HO HO
CPH5 CPH12 C09.250 C20.253 AHT132 C27.442 FH2010 PEZ1 PEZ5 AHT103 AHT111 FH2001 C09.173 C13.758 CPH9 CPH14
a
CFA15 CFA8 CFA9 CFA20 CFA2 CFA27 CFA24 CFA7 CFA12 CFA4 CFA2 CFA23 CFA9 CFA13 CFA28 CFA5
Dinucleotide Dinucleotide Dinucleotide Dinucleotide Dinucleotide Dinucleotide Tetranucleotide Tetranucleotide Tetranucleotide Dinucleotide Dinucleotide Tetranucleotide Dinucleotide Dinucleotide Dinucleotide Dinucleotide
102-124 188-214 121-145 90-120 160-172 158-172 216-240 99-131 95-119 71-89 72-92 123-155 100-118 220-244 139-151 185-205
HEX FAM PET NED PET HEX NED HEX PET HEX NED PET FAM NED HEX PET
M2 M2 M2 M2 M3 M3 M3 M3 M3 M4 M4 M4 M4 M4 M4 M4
[7] Inter-genic [7] Intronic [2] Intronic [2] Intronic N. Holmes Inter-genic [2] Intronic [6] Intronic [8] NA [8] Inter-genic [4] Inter-genic [4] Intronic [6] Inter-genic [2] Intronic/Exonic [9] Inter-genic [7] Inter-genic [7] NA
ATAD2B NPAS3 NXN FHIT CALML3 SLC11A2 PLK1S1 NA FBXL4 RANBP3L IL22RA1 ARHGEF26 ABCA5 FER1L6 ZFHX4-AS1 NA
HO RG, HO HO RS, HO HO HO RG, HO NA HO HO HO HO RS, HO HO HO NA
Genomic context, gene location, source. Primer locations along the reference dog genome (CanFam3.1 assembly) have been identified either via the UniSTS
database at NCBI (http://www.ncbi.nlm.nih.gov/genome/sts/), or by in-silico PCR via the USCS genome browser (http://genome.ucsc.edu/). The UCSC genome browser was also used to identify the genomic context of each STR, which were classified as inter-genic, intronic or exonic, in relation to the annotated dog genes available from RefGene (RG), RefSeq (RS), or to the presence of human orthologous transcripts (HO). NA = locus not mapped in the reference dog chromosomes (CanFam3.1 assembly).
References 1. Thomas R, Holmes N, Fischer P, Dickens H, Breen M, et al. (1997) Eight canine microsatellites. Animal Genetics 28: 153-154. 2. Ostrander EA, Sprague GF, Rine J (1993) Identification and characterization of dinucleotide repeat (CA) markers for genetic mapping in dog. Genomics 16: 207213. 3. Guyon R, Lorentzen TD, Hitte C, Kim L, Cadieu E, et al. (2003) A 1-Mb resolution radiation hybrid map of the canine genome. Proceedings of the National Academy of Sciences 100: 5296-5301. 4. Holmes N, Humphreys S, Binns M, Holliman A, Curtis R, et al. (1993) Isolation and characterization of microsatellites from the canine genome. Animal Genetics 24: 289-292. 5. Breen M, Jouquand S, Renier C, Mellersh CS, Hitte C, et al. (2001) Chromosomespecific single-locus FISH probes allow anchorage of an 1800-marker integrated radiation-hybrid/linkage map of the domestic dog genome to all chromosomes. Genome Research 11: 1784-1795. 6. Francisco L, Langsten A, Mellersh C, Neal C, Ostrander E (1996) A class of highly polymorphic tetranucleotide repeats for canine genetic mapping. Mammalian Genome 7: 359-362. 7. Fredholm M, Winterø A (1995) Variation of short tandem repeats within and between species belonging to the Canidae family. Mammalian Genome 6: 11-18. 8. Neff MW, Broman KW, Mellersh CS, Ray K, Acland GM, et al. (1999) A secondgeneration genetic linkage map of the domestic dog, Canis familiaris. Genetics 151: 803-820. 9. Mellersh CS, Langston AA, Acland GM, Fleming MA, Ray K, et al. (1997) A linkage map of the canine genome. Genomics 46: 326-336.
