Cattle (Bovine) STRs
As with human DNA, genetic material obtained from cows contains short tandem repeat (STR) markers that are highly variable among individuals and thus useful in differentiating between animals. Below is a list of some of the cattle STR loci described in the literature and used by the International Society of Animal Genetics (ISAG).
STR Loci
Cattle STR information kindly provided by Leanne van de Goor (VHL): Locus name, chromosomal location, repeat structure and repeat sequence, original reference, primer sequences, and the true size ranges of the amplicons.
|
Locus |
Chromosomal location |
Repeat structure |
Repeat sequence |
Original reference |
Primer sequences (Forward and Reverse) |
Amplicon length (bp) |
|
BM1818 |
D23S21 |
simple |
(TG)n |
Bishop et al. (1994) |
F: AGCTGGGAATATAACCAAAGG R: AGTGCTTTCAAGGTCCATGC |
253-277 |
|
BM1824 |
D1S34 |
simple |
(GT)n |
Barendse et al. (1994) |
F: GAGCAAGGTGTTTTTCCAATC R: CATTCTCCAACTGCTTCCTTG |
176-188 |
|
BM2113 |
D2S26 |
simple |
(CA)n |
Sunden et al. (1993) |
F: GCTGCCTTCTACCAAATACCC R: CTTCCTGAGAGAAGCAACACC |
124-146 |
|
CSRM60 |
D10S5 |
simple |
(AC)n |
Baylor College of Medicine Human Genome Sequencing Center (2006) |
F: AAGATGTGATCCAAGAGAGAGGCA R: AGGACCAGATCGTGAAAGGCATAG |
91-117 |
|
CSSM66 |
D14S31 |
simple |
(AC)n |
Barendse et al. (1994) |
F: AATTTAATGCACTGAGGAGCTTGG R: ACACAAATCCTTTCTGCCAGCTGA |
177-203 |
|
ETH3 |
D19S2 |
compound |
(GT)nAC(GT)6 |
Solinas-Toldo et al. (1993) |
F: GAACCTGCCTCTCCTGCATTGG R: ACTCTGCCTGTGGCCAAGTAGG |
100-128 |
|
ETH10 |
D5S3 |
simple |
(AC)n |
Solinas-Toldo et al. (1993) |
F: GTTCAGGACTGGCCCTGCTAACA R: CCTCCAGCCCACTTTCTCTTCTC |
206-222 |
|
ETH225 |
D9S2 |
compound |
(TG)4CG(TG)(CA)n |
Steffen et al. (1993) |
F: GATCACCTTGCCACTATTTCCT R: ACATGACAGCCAGCTGCTACT |
139-157 |
|
HAUT27 |
D26S21 |
simple |
(AC)n |
Thieven et al. (1997) |
F: TTTTATGTTCATTTTTTGACTGG R: AACTGCTGAAATCTCCATCTTA |
137-155 |
|
ILSTS006 |
D7S8 |
simple |
(GT)n |
Brezinsky et al. (1993) |
F: TGTCTGTATTTCTGCTGTGG R: ACACGGAAGCGATCTAAACG |
279-297 |
|
INRA023 |
D3S10 |
simple |
(AC)n |
Vaiman et al. (1994) |
F: GAGTAGAGCTACAAGATAAACTTC R: TAACTACAGGGTGTTAGATGAACTC |
201-225 |
|
SPS115 |
D15 |
compound |
(CA)nTA(CA)6 |
Baylor College of Medicine Human Genome Sequencing Center (2006) |
F: AAAGTGACACAACAGCTTCACCAG R: AACCGAGTGTCCTAGTTTGGCTGTG |
247-261 |
|
TGLA53 |
D16S3 |
compound |
(TG)6CG(TG)4(TA)n |
Georges & Massey (1992) |
F: GCTTTCAGAAATAGTTTGCATTCA R: ATCTTCACATGATATTACAGCAGA |
151-187 |
|
TGLA122 |
D21S6 |
compound |
(AC)n(AT)n |
Georges & Massey (1992) |
F: AATCACATGGCAAATAAGTACATAC R: CCCTCCTCCAGGTAAATCAGC |
136-182 |
|
TGLA126 |
D20S1 |
simple |
(TG)n |
Georges & Massey (1992) |
F: CTAATTTAGAATGAGAGAGGCTTCT R: TTGGTCCTCTATTCTCTGAATATTCC |
111-127 |
|
TGLA227 |
D18S1 |
simple |
(TG)n |
Georges & Massey (1992) |
F: GGAATTCCAAATCTGTTAATTTGCT R: ACAGACAGAAACTCAATGAAAGCA |
76-104 |
STR Kits
ThermoFisher Scientific offers several bovine STR typing kits: https://www.thermofisher.com/nl/en/home/brands/thermo-scientific/molecular-biology/thermo-scientific-specialized-molecular-biology-applications/genotyping-thermo-scientific/bovine-genotyping-thermo-scientific.html
Example Cattle Electropherogram (kindly provided by Leanne van de Goor (VHL))
Allele Nomenclature (ISAG Size to Repeat Number Conversion)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Repeat number |
BM1818 |
BM1824 |
BM2113 |
CSRM60 |
CSSM66 |
ETH3 |
ETH10 |
ETH225 |
HAUT27 |
ILSTS006 |
INRA023 |
SPS115 |
TGLA53 |
TGLA122 |
TGLA126 |
TGLA227 |
|
11 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
75 |
|
12 |
|
178 |
121 |
|
|
|
|
|
|
|
|
|
|
|
|
77 |
|
13 |
256 |
180 |
123 |
|
|
|
|
|
|
198 |
|
|
|
|
79 |
|
|
14 |
258 |
182 |
125 |
88 |
|
|
209 |
140 |
|
200 |
|
|
137 |
109 |
81 |
|
|
15 |
260 |
184 |
127 |
90 |
179 |
103 |
|
142 |
|
202 |
|
|
139 |
111 |
83 |
|
|
16 |
262 |
|
129 |
92 |
181 |
|
213 |
144 |
284 |
204 |
|
|
141 |
113 |
85 |
|
|
17 |
264 |
188 |
131 |
94 |
183 |
|
215 |
146 |
286 |
206 |
|
|
143 |
115 |
87 |
|
|
18 |
266 |
190 |
133 |
96 |
185 |
109 |
217 |
148 |
288 |
208 |
|
|
145 |
117 |
89 |
|
|
19 |
268 |
|
135 |
98 |
187 |
|
219 |
140 |
150 |
290 |
210 |
|
154 |
147 |
119 |
91 |
|
20 |
270 |
|
137 |
100 |
189 |
113 |
221 |
142 |
152 |
292 |
212 |
|
156 |
149 |
121 |
93 |
|
21 |
272 |
|
139 |
102 |
191 |
115 |
223 |
144 |
154 |
294 |
214 |
248 |
158 |
151 |
123 |
95 |
|
22 |
|
|
141 |
104 |
193 |
117 |
225 |
146 |
156 |
296 |
216 |
250 |
160 |
153 |
125 |
97 |
|
23 |
|
|
143 |
106 |
195 |
119 |
|
148 |
158 |
298 |
218 |
252 |
162 |
155 |
|
99 |
|
24 |
|
|
|
108 |
197 |
121 |
|
150 |
|
300 |
220 |
254 |
164 |
157 |
|
101 |
|
25 |
280 |
|
|
|
199 |
123 |
|
152 |
|
302 |
222 |
256 |
166 |
159 |
|
103 |
|
26 |
|
|
|
|
201 |
125 |
|
|
|
|
|
258 |
168 |
161 |
|
|
|
27 |
|
|
|
114 |
|
127 |
|
|
|
|
|
260 |
170 |
163 |
|
|
|
27.1 |
|
|
|
|
|
|
|
|
|
|
|
261 |
|
|
|
|
|
28 |
|
|
|
|
205 |
129 |
|
158 |
|
|
|
262 |
172 |
165 |
|
|
|
29 |
|
|
|
|
|
131 |
|
|
|
|
|
|
174 |
167 |
|
|
|
30 |
|
|
|
|
|
|
|
|
|
|
|
|
176 |
169 |
|
|
|
31 |
|
|
|
|
|
|
|
|
|
|
|
|
178 |
171 |
|
|
|
32 |
|
|
|
|
|
|
|
|
|
|
|
|
180 |
173 |
|
|
|
33 |
|
|
|
|
|
|
|
|
|
|
|
|
182 |
175 |
|
|
|
34 |
|
|
|
|
|
|
|
|
|
|
|
|
184 |
177 |
|
|
|
35 |
|
|
|
|
|
|
|
|
|
|
|
|
186 |
179 |
|
|
|
36 |
|
|
|
|
|
|
|
|
|
|
|
|
188 |
181 |
|
|
|
37 |
|
|
|
|
|
|
|
|
|
|
|
|
190 |
183 |
|
|
[During the ISAG conference in Salt Lake City (July 23rd – 27th 2016) it was decided that 158 is the correct ISAG nomenclature for the ETH225 28 allele http://www.isag.us/Docs/Workshop_report_CMMPT_2016.pdf]
Population Data
Sequence information and allele frequencies from 16 bovine STR loci (kindly provided by Leanne van de Goor (VHL))
Publications:
Barendse, W., et al. (1994) A genetic linkage map of the bovine genome. Nature Genetics 6: 227.
Baylor College of Medicine Human Genome Sequencing Center. (2006) Bovine Whole Genome Assembly release Btau_3.1. Available at http://www.hgsc.bcm.tmc.edu/projects/bovine/.
Bishop, M.D., et al. (1994) A genetic linkage map for cattle. Genetics 136: 619-639.
Brezinsky, L., et al. (1993) ILSTS006: a polymorphic bovine microsatellite. Animal Genetics 24: 73.
Budowle, B., et al. (2005) Recommendations for animal DNA forensic and identity testing. Int. J. Legal Med. 119: 295-302.
Georges, M. and Massey, J. (1992) Polymorphic DNA markers in Bovidae. World Intellectual Property Organization. Geneva (Patent application WO PUBL NO 92/13102).
Solinas-Toldo, S., et al. (1993) Physically mapped, cosmid-derived microsatellite markers as anchor loci on bovine chromosomes. Mammalian Genome 4: 720-727.
Steffen, P., et al. (1993) Isolation and mapping of polymorphic microsatellites in cattle. Animal Genetics 24: 121.
Sunden, S.L.F., et al. (1993) A highly polymorphic bovine microsatellite locus: BM2113. Animal Genetics 24: 69.
Thieven, U., et al. (1997) Polymorphic CA-microsatellites for the integration of the bovine genetic and physical map. Mammalian Genome 8: 52.
Vaiman, D., et al. (1994) A set of 99 cattle microsatellites: characterization, synteny mapping, and polymorphism. Mammalian Genome 5: 288-297.
van de Goor, L.H.P. and van Haeringen, W.A. (2007) Identification of stolen cattle using 22 microsatellite markers. Nonhuman DNA Typing: Theory and Casework Applications (edited by Heather Miller Coyle). CRC Press: Boca Raton, FL, pp 122-123.
van de Goor, L.H.P., Panneman, H., van Haeringen, W.A. (2009) A proposal for standardization in forensic bovine DNA typing: allele nomenclature of 16 cattle-specific short tandem repeat loci. Animal Genetics 40: 630-636.
van de Goor, L.H.P., Koskinen, M.T., van Haeringen, W.A. (2011) Population studies of 16 bovine STR loci for forensic purposes. Int. J. Legal Med. 125: 111-119.
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Last Updated: 10/18/2016