Effectiveness of bovine microsatellites in resolving paternity cases in American bison, Bison bison L

Effectiveness of bovine microsatellites inresolving paternity cases in American bison,Bison bison L.G Mommens, A Van Zeveren, L J Peelman

Summary

A set of 33 cattle microsatellite primer pairs was

tested with the DNA of American bison from a

captive population in Belgium and evaluated

for usefulness in parentage testing. Two primer

sets did not amplify and three were mono-

morphic. Among the polymorphic markers, the

number of alleles ranged from two to nine.

Heterozygosity, polymorphism information

content (PIC) and probability of exclusion (PE)

values were low by comparison with those

obtained with the same markers in cattle. Two

methods of estimating PE were used, one which

assumed equal allele frequencies between par-

ental sexes and another which took into account

differences in allele frequencies between par-

ental sexes. An internationally accepted set of

nine microsatellites gives cumulative PE values

of 0z98 and 0z97, respectively, for the two

methods. The potential of this marker set to

identify bison ´ cattle hybrids is discussed.

Because bison and cattle have a common

ancestor, these microsatellites are a useful way

to establish genetic distances and can lead to

the construction of phylogenetic trees.

Keywords: cattle microsatellites, bison, prob-

ability of exclusion, parentage testing

Introduction

In 1992, about 200 American plains bison, Bison

bison L., were imported to Belgium by a breeder

association, Bison d'Ardenne. The animals

originated from three locations in the USA:

Durham Ranches in Wyoming, KenMar Buffalo

Ranch in North Dakota and Sand Lake Bison

Inc. in Wisconsin. Five wood bison cows, Bison

bison athabascae, from the Hellabrunn Zoo of

Munich, Germany, were added to the breeding

group. Pasture breeding schemes of large groups

of cows with several bulls among them led to

situations of unknown paternity among calves.

To avoid inbreeding, Belgian breeders have

requested parentage testing for pedigree control.

The use of blood group and protein polymorph-

isms is not appropriate for this purpose because

bison have low levels of genetic variation for

such markers (Schmid & Buschmann 1985;

Stormont 1987, 1993) which are insufficient to

determine paternity effectively.

In cattle, microsatellite DNA typing has

become a powerful tool to solve dubious

paternity cases where blood typing tests have

failed to determine paternity (Glowatzki-Mullis

et al. 1995). Microsatellites are short sequences

of 1±5 base pair (bp) motifs repeated in a head-

to-tail arrangement from two to 40 times, the so-

called short tandem repeats (Willard 1989).

Almost a thousand microsatellites are now

well-defined and mapped in cattle (Barendse

et al. 1994; Bishop et al. 1994). Cattle and bison

are members of the family Bovidae and belong

to the same subfamily Bovinae (Baker & Man-

well 1991). Conservation of position of repeti-

tive sequences in the genomes of the two

species is to be expected, and thus, primers for

cattle microsatellites could be used for assaying

microsatellite variation in bison. Findings with

regard to genetic variation of microsatellite DNA

markers in bison and the usefulness of such

markers for parentage testing are reported in the

present study.

Material and methods

Choice of animals and microsatellites

Sixty bison were chosen to build up a repre-

sentative sample of the imported population,

comprising all nine imported bulls and 51 cows.

A total of 33 bovine microsatellites, mapping to

19 chromosomes, were used for testing DNA

samples from these animals. Thirty-one of these

markers were selected from the second and

third cattle DNA comparison test of the Inter-

national Society for Animal Genetics (ISAG)

and include 11 markers commercially available

as a kit (StockMarksTM for Cattle Paternity,

Applied Biosystems Division, Perkin-Elmer,

Foster City, CA). Marker identification, multi-

plexing combinations and chromosome location

are listed in Table 1. Two markers were

Animal Genetics,

1998, 29, 12±18

G MommensCattle Blood Typing La-boratory, National Cattle

Breeders Association,

Malle, Belgium

A Van ZeverenL J PeelmanDepartment of Animal

Nutrition, Genetics,Breeding and Ethology,

University of Ghent, Fa-

culty of Veterinary Med-

i c i n e , M e r e l b e k e ,Belgium

ã 1998 International Society for Animal Genetics 12

Correspondence: Dr G Mommens.

Accepted 2 November 1997

described by Mommens et al. (1994). Blood

samples were collected in 10 ml VacutainerTM

tubes containing EDTA-K3 as anti-coagulant.

Amplification and detection

A quick DNA purification method, based on

Tris±EDTA buffer and proteinase K, but without

phenol/chloroform extraction, was carried out

on 50 ml of whole blood (Coppieters et al. 1992).

The 5 ml polymerase chain reaction (PCR) mix

comprised 50 ng template DNA, primers each

from 0z0165 mM to 0z2 mM, dNTPs each at

200 mM, 0z125 units of Taq Polymerase, 10 mM

Tris±HCl (pH 8z3), 50 mM KCl and MgCl2

concentration related to the multiplex. Forward

primers were 59 end-labelled with FluorePrime

or CY5 for detection on an A.L.F., respectively,

A.L.F. Express DNA sequencer (Pharmacia,

Uppsala, Sweden). The PCR parameters for

each multiplex followed recommendations

given for the ISAG cattle comparison test. PCR

products were separated on a 4% Liquigel gel

with 7 M urea. Sizes were determined by using a

composed known-size allele ladder as external

standard in the first and last lane. Designation

of the alleles was in accordance with the

accepted base pair size of the comparison test

reference animals of the ISAG.

Statistical calculations

Estimates of heterozygosity, polymorphism

information content (PIC) and probability of

exclusion (PE) were based on allele frequencies

obtained by direct counting. Heterozygosity was

estimated according to Nei (1973). The PIC

values were calculated by the formula of

Botstein et al. (1980).

The effectiveness of single markers for

parentage testing was evaluated by estimation

of PE based on two different methods. The

method of Jamieson (1979) is appropriate for

situations in which one of the parents is known,

a condition that is met only if dams are

confirmed at the birth of calves. On the other

hand, if the herd of bison in Belgium is

considered as a finite, closed population and

matings are random, calculation of PE according

to Chakraborty et al. (1988) is possible. This

latter method assumes unequal allele frequen-

cies between sexes. The combined PE for each

multiplex was calculated according to Jamieson

(1994).

Results

Allele frequencies for each sex, PIC and PE

estimates for 33 microsatellites are given in

Table 1. Two microsatellites (INRA063 and

HEL1) failed to amplify or produced only a

very weak signal. INRA023, CSSM036 and

TGLA227 were monomorphic. The remaining

28 microsatellites were polymorphic, with

number of alleles ranging from two to nine. A

comparison of allele size ranges between these

bison samples and various cattle breeds sug-

gests bison-specific alleles in 12 microsatellites.

Seventeen resolved parentage cases analysed

with these markers gave no evidence for the

presence of null alleles. Heterozygosities ranged

from 0z12 (AGLA293) to 0z83 (BM1824). Accord-

ingly, AGLA293 showed the lowest PIC value

(0z12), whereas BM1824 had the highest (0z80).

Table 1. Polymorphism and allele-frequency-based values for cattle microsatellites on bison (PE: probability of exclusion)

Allele frequencies

Microsatellite Bovine Males Females Total Hetero-

designation chr. Alleles (n = 9) (n = 51) (n = 60) zygositya PICb PEc PEd

ETH3 19 115 0z000 0z020 0z017

117 0z944 0z931 0z933

119 0z056 0z049 0z050 0z13 0z12 0z06 0z05

ETH225 9 156 0z778 0z676 0z692

158 0z222 0z059 0z083

168´* 0z000 0z265 0z225 0z46 0z41 0z23 0z16

ETH10 5 211 0z944 0z872 0z883

213 0z056 0z108 0z100

217 0z000 0z020 0z017 0z21 0z19 0z10 0z04

PEe for multiplex 1 0z35 0z24

INRA005 12 110´* 0z111 0z049 0z058

116 0z444 0z667 0z633

118 0z278 0z255 0z259

ã 1998 International Society for Animal Genetics, Animal Genetics 29, 12±18

13

Bovine

microsatellites and

paternity in

American bison

Table 1. Continued

Allele frequencies



120 0z167 0z029 0z050 0z53 0z47 0z28 0z43

INRA063 18 No amplification detected

INRA023 3 192´* 1z000 1z000 1z000 0z00 0z00 0z00 0z00


HEL1 15 No amplification detected

HEL5 21 137´* 0z444 0z441 0z442

145 0z056 0z030 0z033

147 0z000 0z186 0z158

151 0z500 0z343 0z367 0z64 0z57 0z36 0z27

HEL13 11 185 0z056 0z059 0z058

187 0z056 0z108 0z100

189 0z888 0z833 0z842 0z28 0z26 0z14 0z10


BM2113 2 125 0z056 0z059 0z059

127 0z056 0z256 0z225

131 0z056 0z108 0z100

133 0z056 0z039 0z042

141 0z608 0z382 0z417

143 0z056 0z088 0z083

145 0z056 0z000 0z008

147 0z000 0z039 0z033

151´* 0z056 0z029 0z033 0z75 0z72 0z55 0z42

BM1824 1 176 0z000 0z020 0z017

178 0z167 0z235 0z225

182 0z111 0z196 0z183

188 0z056 0z098 0z092

190 0z222 0z176 0z183

192 0z000 0z010 0z008

194 0z222 0z069 0z092

196 0z222 0z196 0z200 0z83 0z80 0z64 0z62

BM1818 23 250 0z056 0z029 0z034

258 0z000 0z010 0z008

260 0z888 0z931 0z925

272 0z000 0z010 0z008

274 0z056 0z020 0z025 0z14 0z14 0z07 0z10


CSSM014 4 137 0z722 0z814 0z800

139 0z056 0z068 0z067

141 0z222 0z118 0z133 0z34 0z31 0z17 0z21

CSSM016 11 171 1z000 0z804 0z833

173 0z000 0z147 0z125

175 0z000 0z049 0z042 0z29 0z26 0z14 0z00

CSSM022 5 219 0z611 0z460 0z483

221 0z167 0z225 0z217

223 0z000 0z010 0z008

225 0z222 0z245 0z242

227 0z000 0z020 0z017

233´* 0z000 0z010 0z008

235´* 0z000 0z010 0z008

239´* 0z000 0z020 0z017 0z66 0z61 0z40 0z29


SPS113 10 131´* 0z611 0z725 0z708

133´* 0z389 0z275 0z292 0z41 0z33 0z16 0z19

CSSM036 14 159´* 1z000 1z000 1z000 0z00 0z00 0z00 0z00


Table 1. Continued

Allele frequencies



SPS115 15 244 0z056 0z059 0z058

246 0z222 0z225 0z225

248 0z000 0z020 0z017

250 0z222 0z284 0z275

252 0z278 0z137 0z158

254 0z222 0z275 0z267 0z77 0z74 0z55 0z55


CSSM047 8 147 0z056 0z059 0z058

159 0z056 0z010 0z017

161 0z611 0z627 0z625

163 0z166 0z186 0z183

165 0z111 0z118 0z117 0z56 0z52 0z33 0z36

CSSM042 2 171´* 0z666 0z529 0z550

173´* 0z056 0z137 0z125

175´* 0z278 0z324 0z317

177 0z000 0z010 0z008 0z58 0z51 0z30 0z22


TGLA48 7 77 0z167 0z049 0z067

79 0z389 0z578 0z550

83 0z444 0z373 0z383 0z55 0z45 0z33

TGLA263 3 113 0z444 0z510 0z500

115 0z000 0z020 0z017

117 0z444 0z352 0z366

119 0z056 0z020 0z025

121 0z056 0z098 0z092 0z61 0z53 0z33 0z31

TGLA53 16 154 0z000 0z020 0z017

156 0z278 0z265 0z266

158 0z444 0z578 0z558

160 0z111 0z029 0z042

162 0z167 0z088 0z100

164 0z000 0z020 0z017 0z60 0z55 0z35 0z43

MGTG7 23 280 0z111 0z118 0z117

286 0z500 0z382 0z400

290 0z222 0z118 0z358

292 0z111 0z382 0z117

294 0z056 0z000 0z008 0z68 0z63 0z42 0z43


TGLA57 1 90 0z056 0z029 0z033

92 0z000 0z059 0z050

94 0z222 0z137 0z150

96 0z000 0z039 0z033

98 0z111 0z186 0z175

100 0z167 0z226 0z217

102 0z444 0z324 0z342 0z78 0z75 0z57 0z48

TGLA73 9 119 0z722 0z696 0z700

121 0z000 0z010 0z008

123 0z000 0z059 0z050

125 0z000 0z029 0z025

127 0z111 0z059 0z067

129 0z056 0z088 0z083

131 0z111 0z059 0z067 0z49 0z47 0z31 0z26

MGTG4B 4 125´* 0z111 0z049 0z058

127´* 0z611 0z843 0z808

129 0z278 0z108 0z134 0z33 0z30 0z16 0z29

AGLA293 5 220 0z944 0z931 0z933


According to Jamieson (1979), PE estimates

range from 0z05 for AGLA293 to 0z64 for

BM1824. According to Chakraborty et al.

(1988), estimates of PE ranked slightly different,

ranging from 0z00 (CSSM016) to 0z62 (BM1824).

Discussion

Moore et al. (1991) described a possible con-

servation of dinucleotide microsatellites

between closely related species. KuÈhn et al.

(1996) observed polymorphism for cattle micro-

satellites in the more distant species Cervus

elaphus, even though some primer sets failed to

amplify in this species. The aim of the present

investigation was to determine the efficacy of

cattle microsatellites to resolve paternity cases

in bison. Detectable PCR products were

obtained for 31 (94%) out of the 33 cattle primer

sets tested. Most alleles were identical in

mobility and size to those found in several

cattle breeds, but bison-specific alleles were

observed for 12 markers. Identification of

species-specific alleles allows the use of cattle

microsatellites for identification of bison ´cattle hybrids such as Beefalo (Penedo 1996).

No significant difference in allele frequencies

was observed between male and female plains

bison. There was no evidence of new bison

alleles among the five wood bison females,

although a larger sample of those needs to be

analysed to verify the distinctive position of

wood bison as indicated by Peden & Kraay

(1979).

Heterozygosity values were low by compar-

ison with studies using some of same markers in

Bos taurus breeds (Bates et al. 1996). Ritz et al.

(1996) also found bison to have the lowest

Table 1. Continued

Allele frequencies



222 0z056 0z069 0z067 0z12 0z12 0z05 0z04


TGLA227 18 73´* 1z000 1z000 1z000 0z00 0z00 0z00 0z00

TGLA126 20 111 0z111 0z098 0z100

113 0z111 0z451 0z400

117 0z556 0z245 0z292

121 0z056 0z059 0z058

123 0z166 0z137 0z142

125 0z000 0z010 0z008 0z72 0z68 0z48 0z42

TGLA122 21 137 0z000 0z029 0z025

139 0z000 0z010 0z008

141 0z500 0z510 0z509

147 0z278 0z314 0z308

149 0z222 0z137 0z150 0z62 0z56 0z35 0z34


MM8D3 2 116´* 0z166 0z236 0z225

118´* 0z056 0z118 0z108

120* 0z166 0z039 0z058

122 0z000 0z049 0z042

124 0z056 0z029 0z033

126 0z556 0z529 0z534 0z65 0z61 0z41 0z40

MM12E6 9 115 0z889 0z912 0z908

121 0z111 0z000 0z017

123 0z000 0z029 0z025

125 0z000 0z049 0z042

131 0z000 0z010 0z008 0z17 0z17 0z09 0z09

PEe for all microsatellites 0z99 0z99

*Bison-specific alleles compared to taurine are marked with an asterisk.aHeterozygosity (Nei 1973).bPIC value (Botstein et al. 1980).cPE according to Jamieson (1979).dPE according to Chakraborty et al. (1988).ePE cumulated (Jamieson 1994).


heterozygosity values in their study of the

Bovinae subfamily. The low level of genetic

diversity in bison possibly reflects a bottleneck

effect after the dramatic population reduction

that occurred in North America during the last

century. TGLA227, INRA023 and CSSM036

appear to be fixed in bison. The PIC values

were far below the calculated mean for dairy

cattle, but for some markers (TGLA57 and

MM8D3), these exceeded the estimates for beef

cattle.

Microsatellites will be increasingly used for

parentage testing in cattle and other domesti-

cated animals (Marklund et al. 1994; Glowatzki-

Mullis et al. 1995; Usha et al. 1995). The use of

microsatellites for parentage testing in bison is

not common, although it is clear from these data

that this would be an effective means for

breeders to maintain accurate pedigree records

and minimize inbreeding in their herds.

The estimates of PE were generally low for

the case with an alleged parent, as determined

by Jamieson (1979). The same markers (except

multiplex 3) used on three cattle breeds (Ger-

man Simmental, German Brown, and German

Black and White) by I. Russ (unpublished data)

and the StockMarksTM kit on American cattle

(Heyen et al. 1997) revealed much higher PE

values. Reduced levels of polymorphism or

fixation of allele for some markers caused the

lower values of PE. Nevertheless, the scores for

multiplex 4 are higher than in cattle.

Within a captive population, genotypes of all

males and females can be known. Allele

frequency differences between sexes influences

exclusionary power as described by Chakra-

borty et al. (1988). The PE values obtained by

this method were slightly different from Jamie-

son's PE value, except for CSSM016 in which

Chakraborty et al.'s (1988) PE value was 0

because of males being homozygous for the

same allele.

Only 60 bison were analysed for all 33 DNA

markers. The 30 remaining cows and 26 off-

spring born in Belgium were tested with a set of

nine bovine microsatellites. An agreement for

the use of this set of markers for cattle parentage

testing was reached during the XXVth Interna-

tional Conference on Animal Genetics of the

ISAG in Tours, France. The set of markers and

PE values on bison are given in Table 2. One of

these, TGLA 227, is monomorphic and contains

a bison-specific allele. This could be useful for

the identification of bison ´ cattle hybrids. The

cumulative PE values of 0z98 and 0z97 obtained

for the set of nine markers are similar to that

estimated for StockmarksTM kit on cattle.

Bison and cattle are estimated to have diverg-

ed about 1±1z4 million years ago (Loftus et al.

1994). The present study reveals good conserva-

tion of microsatellite flanking sequences

between the two species since divergence.

Allele frequencies of microsatellites that can

be amplified in both species will be helpful to

estimate genetic distances and lead to construc-

tion of phylogenetic trees. In this respect,

individual genotypes are available from the

authors.

It can be concluded that cattle microsatellites

are useful in bison for identification, parentage

testing and phylogenetic studies.

Acknowledgements

The authors thank J. F. d'Hoffschmidt from

Bison d'Ardenne for providing bison blood

samples, B. Morris and G. Kraay for making

available data on blood types of bison, and D.

Vanassche for excellent PCR work and allele

classification. Special thanks are due to M.C.T.

Penedo and L. Ritz for providing data for cattle

and bison microsatellites, and to K. Vanhove for

statistical analyses.

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Table 2. Exclusion probabilities (PEs) on bison for the

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Effectiveness of bovine microsatellites in resolving paternity cases in American bison, Bison bison L