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Method of parentage testing in North American bison, and domestic cattle using microsatellite loci

Imported: 17 Feb '17 | Published: 01 Aug '06

Robert D. Schnabel, James N. Derr

USPTO - Utility Patents

Abstract

A method for determining parentage of North American bison or domestic cattle offspring. In the method an offspring is tested to determine the alleles present in that offspring for selected loci. A pool of potential parents is also tested to determine which alleles of these loci are present in each parent. The likelihood that any potential parent is the parent of the offspring may then be determined by looking for the presence or absence of an allele in the offspring that is present in the parent or by some comparable method. The method may also be used to exclude all potential parents in a pool. Sixteen loci which may be used in such an analysis are BM1225, BM1706, BM17132, BM1905, BM2113, BM4440, BM720, BMS1862, BMS410, BMS510, BMS527, RM372, BMS1172, BMS2639, BM3628 and BMS2325. The method used to select these loci is also disclosed.

Description

This application claims priority from a provisional application filed on Jan. 11, 2002, having Ser. No. 60/347,792, which is incorporated herein by reference.

This invention was made with Government support under ‘Validation of 15 Microsatellites for Parentage Testing is North America’, NSF Grant No. DEB-9622126, ‘Identification of Domestic Cattle Hybrids in Wild Cattle’, NSF Grant No. DEB-9622126, and ‘Nuclear Gene Marker for Cattle’, NSF Grant No. DEB-9622126 awarded by the National Science Foundation. The Government has certain rights in this invention.

BACKGROUND OF THE INVENTION

The present invention relates to a method of determining parentage in bison and domestic cattle using distinct microsatellite loci.

Bison once numbered in the millions in North America but due to the population bottleneck experienced in the late 1800's, bison numbers were reduced to no more than 300 individuals by 1880 (Coder 1975; Dary 1989). Almost all of the bison alive today can be traced back to five populations that were used to repopulate most of the extant public and private herds (Coder 1975). Current semi-wild bison populations are fragmented among public parks and sanctuaries throughout the United States and Canada. However, the vast majority of bison today reside on private ranches where they are raised for meat production. Recently, Mommens et al. (1998) demonstrated that bovine microsatellites are better suited for parentage testing in bison than conventional blood typing due to a greater degree of variation. However, their sample was limited to a single herd located in Belgium, which probably does not represent the actual genetic variation found in bison in North America.

Currently, parentage testing in domestic animals is based on exclusionary techniques using genetic markers. An offspring is tested assuming one known parent and one or a limited number of candidate parents. If only one candidate parent is left non-excluded, that parent is assigned parentage to the offspring. Although one non-excluded parent may be the true parent, there exists the possibility that other non-excluded candidate parents exist in the population but were not considered. A likelihood based testing procedure is more appropriate for situations in which there are many candidate parents and obtaining a known parent is difficult. Using likelihood based procedures, all potential parents are considered as candidates and there is no need to identify a known parent prior to testing.

SUMMARY OF THE INVENTION

The purpose of this study was to characterize, standardize and provide validation for a set of highly polymorphic microsatellites for use in routine parentage testing in North American Bison and domestic cattle.

Fifteen bovine microsatellites were evaluated for use in parentage testing in 725 bison from 14 public populations, 178 bison from two private ranches and 107 domestic cattle from 5 different breeds. The number of alleles per locus ranged from 5 to 16 in bison and from 5 to 13 in cattle. On average, expected heterozygosity, polymorphism information content (PIC) and probability of exclusion values were slightly lower in bison than in cattle. A core set of 12 loci was further refined to produce a set of multiplexed markers suitable for routine parentage testing. Assuming one known parent, the core set of markers provides exclusion probabilities in bison of 0.9955 and in cattle of 0.9995 averaged across all populations or breeds tested. Tests of Hardy-Weinberg and linkage equilibrium showed only minor deviations. This core set of 12 loci represent a powerful and efficient method for determining parentage in North American bison and domestic cattle.

Further tests have also indicated that two additional loci of the 15 originally identified, BMS1172 and BMS2639, may also be suitable for parentage testing. Two other loci, BM3628 and BMS2325, have subsequently been identified as suitable loci through testing in the two private bison herds.

The above summary provides a general outline of the invention. For a better understanding of the invention and its advantages, reference may be made to the following description of exemplary embodiments.

DETAILED DESCRIPTION OF THE INVENTION

The present invention includes a method of determining parentage in bison or domestic cattle using microsatellite loci. These loci were selected as set forth below and may be used in any type of parentage testing in which allelic variation is used to determine the likelihood of parentage. Preferred methods of detecting the specific alleles in the offspring and potential parents are described below, but alternative methods may also be employed. When used with the methods described below, the indicated levels of certainty are achieved. Alternative methods may result in differences of certainty if the methods change the probability that allele assignments are correct. One skilled in the art will be able to select alternative methods of detecting specific alleles which result in a desired level of overall parentage certainly.

In a preferred embodiment, 12 loci, BM1225, BM1706, BM17132, BM1905, BM2113, BM4440, BM720, BMS1862, BMS410, BMS510, BMS527, RM372, are used. However, one skilled in the art will understand that paternity may be determined using only a subset of these loci. The full set or any subset may also be used with any other loci useful in determining parentage. The four additional loci later identified as acceptable for parentage testing, BMS1172, BMS2639, BM3628 and BMS2325, may also be used in testing. Based upon known or readily determinable allele types and frequencies in a given population for each loci, a set of loci comprising the above loci and/or any other known loci may be selected for parentage testing. In general, the more loci selected, the greater the certainty of any parentage assignment will be. However, the invention by no means requires the use of all of the 12 loci originally identified, not does it require that a total of 12 loci be used in every embodiment. In a preferred embodiment, at least two loci are selected from the 16 identified above.

The goal of the study leading to the present invention was to characterize, standardize and provide validation for a set of polymorphic microsatellites for use in routine parentage testing in North American bison and domestic cattle. Table 3 demonstrates that the exclusion probabilities found in bison and cattle for these loci are comparable to other loci previously described (Glowatzki-Mullis et al. 1995; Peelman et al. 1998; Heyen et al. 1997; Mommens et al. 1998). Additionally, in cattle the core set of markers produces similar exclusion probabilities to the commercially available StockMarks™ kit (PE Biosystems). However, in bison the core set of markers offer higher exclusion probabilities than either the StockMarks™ kit or the ISAG approved set of markers (Mommens et al. 1998).

In order to validate the use of these markers for parentage testing in bison, the guidelines set forth for selecting loci for human parentage testing were followed (Parentage Testing Committee, American Association of Blood Banks, 1997). A total of 121 offspring were tested from two separate private populations. In every case the loci exhibited normal co-dominant Mendelian inheritance with no evidence of null alleles or mutaions. Similar validation studies were conducted using the BM3628 and BMS2325 loci similar results.

The development of an allelic ladder, which is used for each genotyping run, fulfills the requirement of a known DNA control and makes it possible to directly compare samples that are run at different points in time or even on different machines. In the case of parentage testing of domestic animals, this is a desirable feature since offspring will be tested years apart and re-running parents each year would be inefficient and costly. An allelic ladder also increases consistency between laboratories since each genotype is assigned relative to a known standard. Locus BMS510 exhibited single base pair differences in bison. Normally this would preclude this locus from being used as a marker for parentage testing due to the difficulty in allele assignment reproducibility. However, this problem was overcome by sizing alleles relative to the allelic ladder. The minimum and maximum standard deviation of allele sizes for this locus was 0.06 and 0.25 bp respectively with an average over all the alleles of 0.09 bp. These values represent between gel deviations. The within gel standard deviation, averaged across alleles, is reduced to only 0.06 bp. Smith (1995) demonstrated that values in this range were highly unlikely to produce incorrect allele assignment when an allelic ladder is used.

In order to use allele frequencies to calculate genotype frequencies and exclusion probabilities, allele frequencies from the populations tested must be consistent with HW expectations. 903 bison from 14 public populations and two private populations represent an adequate sample with which to estimate allele frequencies. Tests of HWE, although showing minor deviations for some locus population combinations, did not yield consistent deviations for the testing methods employed. The number of HW deviations observed in this study is similar to other studies in humans. Hammond et al. (1994) found 11.5% (18/156), Edwards et al. (1992) found 11.6% (7/60) and Thomson et al. (1999) found 5.5% (2/36) of the possible locus-population-test combinations showed deviations, which is comparable to the 7.5% (71/942) found in the current study. The lack of consistency in the observed deviations leads us to conclude that these loci are in HWE for the populations tested.

Tests of genotypic disequillibrium showed no consistent deviations in the populations which were not expected a priori to show deviations. In a production setting such as with the HHP and ABR populations, genotypic disequillibrium is expected because a limited number of bulls are used for breeding. However, in these cases typically the entire population will be tested and departures from genotypic equilibrium will have little effect on the final parentage analysis. Therefore, we conclude that the observed deviations in HWE and genotypic equilibrium are small enough that they will not significantly affect the calculations of genotypic frequencies or multilocus probabilities from allele frequencies.

The advantages of likelihood based parentage assignment over exclusionary methods have been demonstrated by Slate et al. (2000) for natural populations and extended to captive production populations in the current study. Indeed, even with highly developed sets of markers such as those presented here, genotyping errors occur. A likelihood-based system to assign parentage allows the lab to identify potential errors or mutations and make corrections before parentage is rejected.

PCR based methods in conjunction with highly variable microsatellite loci and fluorescent based genotyping provide the technologies needed to establish a new standard for parentage testing. The core set of 12 microsatellites presented here along with 4 additional microsatellites offers a powerful battery of markers for both parentage testing and individual identification. These loci are preferably used as the core set of 12 or in combination with one or more of the 4 additional loci, but they may be combined in whole or in part with other loci without substantial loss of identification power. These markers when used in likelihood based parentage testing will help to refine breeding programs and allow for improved genetic management by accurate determination of pedigrees in both bison and cattle.

The invention may be better understood through reference to the specific examples which follow. Although only preferred embodiments of the invention are specifically described above and in the examples, it will be appreciated that modifications and variations of the invention are possible without departing from the spirit and intended scope of the invention.

EXAMPLES

Example 1

DNA Source

Fourteen public bison herds, two private bison herds and five cattle breeds were sampled. Sample sizes and population locations are listed in Table 1. These herds represent most of the major public herds that have played a role in populating private bison herds around the world. Therefore, the majority of the genetic variation present in extant bison herds should be contained within these public herds.

TABLE 1 Bison populations and domestic cattle breeds sampled. Sample Public Herds Abbreviation Location Size Antelope Island State Park AI Utah 67 Custer State Park CSP South Dakota 37 Elk Island National Park EIW Alberta 25 (woods) Elk Island National Park EIP Alberta 24 (plains) Fort Niobrara National Wildlife FN Nebraska 24 Refuge Finney Game Refuge GC Kansas 50 Henry Mountains HM Utah 21 Caprock Canyon State Park CCSP Texas 33 Mackenzei Bison Sanctuary MBS Canada 40 (woods) Maxwell Game Refuge MX Kansas 35 National Bison Range NBR Montana 38 Wind Cave National Park WC South Dakota 152 Wood Buffalo National Park WBNP Canada 21 (woods) Yellowstone National Park YNP Wyoming 158 Total 725 Private Herds Arrowhead Buffalo Ranch, Ltd. ABR Ohio 135 Hidden Hollow Preserve HHP Kentucky 43 Total 178 Cattle Breeds Angus AN 54 Hereford HE 16 Holstein HO 12 Shorthorn SH 12 Texas Longhorn TLH 13 Total 107

Example 2

DNA Extraction

Genomic DNA was isolated from white blood cells by proteinase K treatment followed by phenol chloroform extraction (Sambrook et al. 1989) or by using the SUPER QUICK-GENE DNA Isolation kit (Analytical Genetic Testing Center, Inc. Denver, Colo.). DNA was also extracted from hair follicles using the following procedure. Approximately 8–12 hair follicles were cut from the switch of the tail using a razor blade and digested for four hours at 55° C. in 200 μl lysis buffer (500 mM KCl, 100 mM Tris-HCl pH 8.0, 0.1 μg/ml gelatin, 0.45% Triton X-100, 0.45% Tween-20, 0.5 mg/ml proteinase K). After digestion, samples were centrifuged at 5,000 g for two minutes. The clear aqueous layer was then transferred to a new tube and 0.5 μl of 10 mg/ml RNase A was added. The sample was then extracted once with phenol/chloroform/isoamyl alcohol (25:24:1) followed by a chloroform extraction. DNA was ethanol precipitated then resuspended in 50 μl TE buffer (10 mM Tris-HCl, 1 mM EDTA pH 8.0).

Example 3

Loci

Bovine microsatellites were chosen from the USDA cattle mapping database (sol.marc.usda.gov) that fulfilled the following set of criteria in cattle:

    • 1. High PIC values, high heterozygosity and a large number of alleles
    • 2. Lack of known null alleles
    • 3. Loci non-syntenic or separated by more than 40 cM
    • 4. Allele size range
    • 5. Suitability for multiplex PCR.
      Primer sequences flanking 15 microsatellites that fulfilled these criteria were synthesized with a fluorescent label attached to the 5′ end of each forward primer (Table 2).

TABLE 2 Chromosomal location and fluorescent dye used for each of the 15 loci selected from the USDA database. Locus Chr.a Pos.a Dyeb BM1225 20 8.0 TET BM1706 16 80.6 6FAM BM17132 19 58.6 6FAM BM1905 23 64.3 TET BM2113 2 106.2 6FAM BM4440 2 55.0 TET BM720 13 38.6 TET BMS1117 21 9.9 HEX BMS1172 4 27.3 6FAM BMS1862 24 32.8 HEX BMS2639 18 57.0 6FAM BMS410 12 0.0 TET BMS510 28 22.1 HEX BMS527 1 55.9 6FAM RM372 8 19.1 HEX aBovine chromosome and relative position (cM). bABI fluorescent label used with forward primer.

Example 4

Multiplex PCR

Based on the results of genotyping approximately 500 bison and 50 cattle for these 15 loci, a core set of 12 loci were selected which could be amplified in two PCR reactions and co-loaded in a single lane of an ABI Prism377 sequencer or a single injection on an ABI Prism 310 capillary-based genetic analyzer. Core multiplex A consists of BMS510, BMS410, BM17132, RM372 and BMS527. Core multiplex B consists of BM4440, BM2113, BMS1862, BM1905, BM720, BM1706 and BM1225. PCR conditions for core multiplexes A and B are as follows: 25–100 ng template DNA, 10 mM Tris-HCl (pH 9.0), 50 mM KCl, 1% Triton®-X, 3.0 mM MgCl2, 500 μm dNTPs, 0.05–0.3 μm each primer, 1X MasterAmp PCR enhancer (Epicentre Technologies), and 0.5U Taq DNA polymerase (Promega) in a 5 μl reaction. Thermal cycle parameters for core multiplex A and B were 2 minutes 96° C. followed by 35 cycles of (15 seconds 96° C., 15 seconds 54° C., 5 seconds 72° C.) with a final extension step of 20 minutes at 72° C. using a GeneAmp® PCR 9700 thermocycler (PE Biosystems). In later experiments a total of 16 loci, including the BMS1172, BMS2639, BM3628 and BMS2325 were amplified.

Example 5

Genotyping

PCR products were separated on an ABI Prism 377 DNA Sequencer (ABI377) or an ABI Prism 310 Genetic Analyzer (ABI310)(PE Biosystems) and sized relative to an internal size standard (GS500, PE Biosystems or MAPMARKER LOW, Bioventures). Fluorescent signals from the dye labeled microsatellites were detected using GENESCAN 3.1 software (PE Biosystems). Genotypes were assigned using Genotyper 2.0 software (PE Biosystems) by assigning both an integer value and the actual decimal value (called size) to each peak. After the allelic ladder was developed, the ladder was included on each gel (ABI377) or with each group of samples (ABI310) and genotypes were assigned relative to the actual sequence sizes of the allelic ladder. Previous samples that were genotyped without the allelic ladder were re-assigned genotypes based on the true sequence size of each allele.

Example 6

Cloning and Sequencing

Approximately one half of the bison alleles at each locus were cloned and sequenced. Samples were amplified individually and cloned using either the Original TA Cloning Kit or the Topo TA Cloning kit (Invitrogen) as per the manufacturer's protocol. Approximately 10–20 positive clones from each ligation were picked and grown overnight in 3 ml Terrific Broth containing 50 μg/ml ampicilin. A standard alkali-lysis mini-prep procedure was used to recover plasmid DNA (Sambrook et al. 1989). Plasmid DNA was diluted 1:50 with TE buffer and used as a source of template DNA for PCR. Each positive clone was amplified via PCR and genotyped using the ABI310. Clones that sized identical to one of the original alleles of the animal were used to make glycerol stocks. Cloned alleles were sequenced using the Big-dye™ terminator cycle sequencing kit (PE Biosystems) and an ABI377 automated sequencer. Sequenced alleles were submitted to Genbank and have accession numbers AF213181 to AF213246. An allelic ladder was constructed by mixing equimolar amounts of DNA from the sequenced plasmids into a DNA mastermix. The combined plasmids were used as template DNA for the allelic ladder in each PCR multiplex.

Example 7

Data Analysis

Expected heterozygosity (Nei, 1987), exclusion probabilities and polymorphism information content (PIC) (Botstein et al, 1980) were calculated for each marker within each population. Two exclusion probabilities were calculated which correspond to different scenarios. Exclusion probability one (PE1) assumes genotypes are known for the offspring and a putative parent, but genotypes are not available for a known parent (one parent missing). Exclusion probability two (PE2) assumes genotypes are known for the offspring, one confirmed parent, and one putative parent (both parents genotyped). PE1 and PE2, as well as combined exclusion probabilities were calculated according to Jamieson & Taylor (1997). Tests of Hardy-Weinberg equilibrium (HWE) were performed using the program GENEPOP version 3.1d (Raymond and Rousset, 1995). Exact p-values were calculated for loci that had four alleles or less in a population. For loci that had more than four alleles present in a population, an unbiased estimate of the exact HW probability was calculated using the Markov chain method of Guo and Thompson (1992). Unbiased estimates of genotypic disequilibrium were calculated with GENEPOP using the Markov chain method. Parameters used for all Markov chain procedures were dememorization of 10,000 steps, 125 batches and 40,000 iterations per batch for a total Markov chain length of 5 million steps.

Example 8

Parentage Inference

Parentage testing was performed on the two pedigreed private bison herds to evaluate the actual effectiveness of the loci for determining parentage, verify Mendelian inheritance and check for the presence of null alleles. The accuracy of these pedigrees have previously been verified by genotyping over 200 microsatellites in these herds (unpublished data). The ABR sample contained 92 offspring and 44 potential parents. The HHP sample contained 29 offspring and 22 potential parents. Likelihood based parentage testing was performed using the program CERVUS 1.0 (Marshall et al., 1998) following the procedures outlined in the program. Analysis parameters used for simulations were as follows: 10,000 cycles, 45 candidate parents for the ABR herd and 22 candidate parents for the HHP herd, 95% of the candidate parents sampled, 100% of the loci typed, 1% typing error, 80% relaxed confidence and 95% strict confidence.

Unbiased expected heterozygosity, PIC, exclusion probabilities, allele frequencies, repeat length and the standard deviation in allele size calling are located in Table 4 and can be obtained via the internet at www.cvm.tamu.edu/derrlab/index.html. A total of 138 and 151 alleles were found in bison and domestic cattle respectively. The number of alleles per locus ranged from 5 to 16 in bison and from 5 to 13 in cattle. Of the 15 loci tested, 5 had a greater number of alleles in bison than in domestic cattle. For four of these loci, BM2113, BM1706, BMS1172 and BMS2639, this result is probably due to the limited number of cattle tested. According to published results, all four of these loci have an equal number of alleles or more in cattle compared to what was observed in bison (Stone et al. 1995; Bishop et al. 1994). The exception is BM1225 in which 16 alleles were observed in bison but cattle are reported to only have 11 alleles. Excluding BM4440 for the CCSP population, which was monomorphic, expected heterozygosities in bison ranged from 84.2% to 6.0% and from 85.4% to 39.8% for cattle. The overall mean heterozygosity across all populations and all markers was 62.17% for bison and 70.16% for cattle (Table 3). The only populations that failed to reach the 99% threshold for PE2 were Antelope Island and the CCSP population. This is most likely due to the fact that both of these herds were founded by a small number of individuals and have remained genetically isolated for much of their history (Coder 1975; Popov and Low 1950).

TABLE 3 Mean expected heterozygosity across all 15 loci and combined average exclusion probabilities for all 15 loci and the core set of 12 loci. Mean Expected All Loci Core Set Population Heterozygosity PE1 PE2 PE1 PE2 AI 0.4496 0.8622 0.9858 0.8612 0.9820 CSP 0.6818 0.9953 0.9999 0.9901 0.9997 EIP 0.6666 0.9938 0.9999 0.9894 0.9997 EIW 0.5541 0.9663 0.9989 0.9506 0.9974 FN 0.6602 0.9943 0.9999 0.9860 0.9996 GC 0.6521 0.9923 0.9999 0.9828 0.9994 HM 0.5757 0.9777 0.9991 0.9599 0.9973 CCSP 0.4160 0.8457 0.9796 0.7768 0.9570 MBS 0.6334 0.9893 0.9998 0.9838 0.9996 MX 0.6729 0.9956 0.9999 0.9916 0.9998 NBR 0.6542 0.9902 0.9998 0.9714 0.9988 WBNP 0.6759 0.9950 0.9999 0.9886 0.9997 WC 0.6630 0.9943 0.9999 0.9859 0.9995 YNP 0.6340 0.9898 0.9998 0.9813 0.9993 ABR 0.6981 0.9972 1.0000 0.9920 0.9998 HHP 0.6591 0.9956 0.9999 0.9920 0.9995 AN 0.6907 0.9965 1.0000 0.9934 0.9999 HE 0.6359 0.9839 0.9995 0.9662 0.9981 HO 0.7279 0.9978 1.0000 0.9930 0.9999 SH 0.7029 0.9971 1.0000 0.9930 0.9999 TLH 0.7507 0.9993 1.0000 0.9984 1.0000 Mean Bison 0.6217 0.9734 0.9976 0.9610 0.9955 Mean Cattle 0.7016 0.9949 0.9999 0.9888 0.9995

Example 9

Hardy-Weinberg & Genotypic Disequilibrium Tests

Calculation of genotype frequencies and exclusion probabilities from allele frequencies depend on the underlying assumptions of HWE. However, the errors associated with using allele frequencies to calculate genotype frequencies and exclusion probabilities should be minimal as long as there is approximate agreement with HW expectations.

In order to test Hardy-Weinberg assumptions, three distinct tests of HWE were performed with the difference being the alternate hypothesis to equilibrium. Each locus within each population was checked for HWE for a total of 314 comparisons (CCSP was monomorphic at BM4440). Eight percent (25/314) of the locus/population combinations showed significant departure from HWE at p<0.05 for the probability test. In order to more precisely identify these deviations, score tests (U-tests) (Rousset and Raymond 1995) were performed with the alternative hypothesis of either heterozygote excess or deficiency. When the alternative hypothesis was heterozygote excess, 4.1% (13/314) of the locus/population combinations showed significant deviations from HWE at p<0.05. When the alternative hypothesis was heterozygote deficiency 10.5% (33/314) of the locus/population combinations were significant at p<0.05. There was no consistency between the three tests to indicate any specific locus/population was in disequilibrium.

Non-random association of gametes to form genotypes could also affect using allele frequencies to calculate genotype frequencies. In natural populations this is most likely due to population sub-structuring. Tests of genotypic disequilibrium within populations resulted in 1876 comparisons. Three populations (Al, ABR and HHP) were not tested for genotypic disequilibrium since all three of these populations use a limited number of breeding bulls. When these populations were eliminated from consideration because of known breeding structure, 6.4% (120/1876) of the combinations were significant at p<0.05. Tests of genotypic disequilibrium across populations resulted in 105 comparisons. No locus pairs showed significant disequilibrium across populations at p<0.05 (Bonferoni corrected).

Example 10

Parentage Inference

Both the ABR and HHP pedigrees were used to check the inheritance of the markers and to evaluate the effectiveness of both the markers and the likelihood testing procedure in a production setting. A total of 121 offspring were used to evaluate the test's effectiveness. For each offspring, every reproductively capable animal in the population was considered as a potential parent, allowing for the possibility of missing parents. The first cycle of parentage analysis resulted in eliminating all potential parents that showed incompatibilities at more than one locus. Parents that showed mismatches at one locus were considered as potential parents to allow for the possibility of either a mutation or a genotyping error. The potential parents that were left were then considered as known parents and this additional information was used to re-test the offspring against the original set of potential parents. After the second round of parentage analysis in the ABR herd, 87% (80/92) of the offspring were unambiguously assigned parentage to the correct sire and dam. A total of 12 offspring were not assigned parentage after the second cycle because these 12 cows were purchased as bred heifers; therefore the sires were unavailable. After inspecting the results from the first cycle of parentage analysis, the correct dam was assigned with >95% confidence in each case where the sire was unavailable. Parentage analysis results for the HHP population were much the same as for ABR. Every offspring was unambiguously assigned parentage except two offspring whose sire was not sampled, in which case, the correct dam was assigned with >95% confidence.

REFERENCES

The following references are incorporated by reference herein.

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TABLE 4 Appendix A BM1225 Size1 Repeat2 Std. Dev.3 AI CSP EIP EIW FN GC HM JA MBS MX NBR WBNP WC YNP ABR HHP AN HE HO SH TLH 219 0.02 0.125 0.077 215 0.10 0.120 0.042 117 na 0.018 119 0.20 0.149 0.196 0.025 0.024 0.161 0.049 0.105 0.120 0.633 0.375 0.208 0.169 241 16 0.24 0.136 0.191 0.354 0.063 0.478 0.527 0.119 0.465 0.138 0.529 0.431 0.167 0.122 0.457 0.459 0.663 0.759 0.567 0.331 0.112 0.116 243 0.15 0.125 0.028 0.003 0.115 145 18 0.16 0.063 0.008 147 0.16 0.063 0.011 0.050 0.014 0.083 0.003 0.003 0.015 249 20 0.28 0.015 0.068 0.063 0.083 0.031 0.043 0.111 0.028 0.046 0.007 0.060 0.023 251 0.01 0.042 0.292 0.083 0.038 253 22 0.27 0.127 0.243 0.125 0.183 0.043 0.061 0.313 0.145 0.650 0.114 0.056 0.472 0.201 0.199 0.146 0.047 0.038 255 0.05 0.061 0.143 0.001 259 0.38 0.042 0.013 261 na 0.073 165 28 0.21 0.052 0.081 0.043 0.092 0.024 0.071 0.028 0.105 0.119 267 na 0.021 269 30 0.23 0.022 0.021 0.167 0.217 0.490 0.143 0.382 0.142 0.129 0.236 0.167 0.059 0.019 0.116 0.128 271 0.24 0.135 0.083 0.143 0.013 0.076 0.245 0.030 0.023 273 11 0.10 0.001 0.022 0.043 0.014 0.125 0.012 275 0.14 0.021 0.021 0.043 0.028 Het4 0.580 0.806 0.827 0.615 0.689 0.614 0.818 0.615 0.546 0.656 0.732 0.721 0.803 0.708 0.736 0.516 0.398 0.472 0.677 0.633 0.793 PIC5 0.354 0.773 0.801 0.589 0.636 0.560 0.786 0.529 0.512 0.610 0.690 0.680 0.775 0.652 0.708 0.503 0.361 0.357 0.589 0.697 0.249 PE16 0.075 0.433 0.491 0.230 0.270 0.227 0.456 0.186 0.167 0.147 0.329 0.319 0.439 0.283 0.354 0.160 0.078 0.103 0.220 0.234 0.406 PE27 0.210 0.611 0.664 0.412 0.444 0.383 0.633 0.319 0.318 0.422 0.509 0.503 0.616 0.457 0.540 0.331 0.201 0.176 0.368 0.409 0.584 BM1106 Size Repeat Std. Dev. AI CSP EIP EIW FN GC HM JA MBS MX NBR WBNP WC YNP ABR HHP AN HE HO SH TLH 232 11 0.14 0.246 0.054 0.104 0.560 0.146 0.150 0.100 0.136 0.112 0.200 0.316 0.267 0.174 0.076 0.060 0.302 234 0.11 0.013 0.042 0.035 236 na 0.083 238 14 0.12 0.614 0.527 0.771 0.540 0.667 0.700 0.900 0.803 0.663 0.786 0.658 0.595 0.510 0.747 0.112 0.372 0.119 0.375 0.451 240 na 0.013 242 na 0.003 0.031 0.071 244 0.01 0.004 0.063 0.042 0.041 0.115 246 16 0.06 0.095 0.016 0.016 249 na 0.048 0.018 250 20 0.15 0.082 0.104 0.010 0.061 0.013 0.016 0.036 0.015 0.023 0.491 0.406 0.167 0.042 252 0.10 0.037 0.176 0.011 0.080 0.188 0.140 0.150 0.016 0.071 0.016 0.146 0.090 0.035 0.167 0.500 0.113 0.292 0.346 254 0.18 0.149 0.020 0.018 0.024 0.261 0.025 0.060 0.167 0.083 0.346 256 0.16 0.120 0.125 0.035 Het 0.661 0.662 0.388 0.578 0.504 0.470 0.182 0.335 0.527 0.345 0.470 0.576 0.642 0.332 0.189 0.705 0.683 0.589 0.727 0.699 0.751 PIC 0.519 0.619 0.357 0.491 0.448 0.425 0.164 0.109 0.491 0.293 0.380 0.514 0.583 0.308 0.370 0.634 0.614 0.494 0.662 0.636 0.696 PE1 0.222 0.253 0.076 0.167 0.125 0.111 0.016 0.055 0.152 0.059 0.109 0.175 0.223 0.055 0.081 0.265 0.267 0.173 0.295 0.274 0.339 PE2 0.371 0.431 0.209 0.293 0.265 0.255 0.082 0.169 0.316 0.152 0.202 0.326 0.383 0.175 0.224 0.430 0.469 0.295 0.466 0.445 0.511 BM17132 Size Repeat Std. Dev. AI CSP EIP EIW FN GC HM JA MBS MX NBR WBNP WC YNP ABR HHP AN HE HO SH TLH  75 na 0.010  19 0.05 0.042 0.087 0.071 0.125  81 13 0.06 0.039 0.050  81 0.10 0.881 0.230 0.085 0.104 0.152 0.561 0.015 0.275 0.371 0.092 0.238 0.062 0.031 0.251 0.167 0.050 0.211  85 15 0.09 0.022 0.446 0.417 0.146 0.152 0.102 0.476 0.061 0.097 0.143 0.474 0.024 0.431 0.373 0.435 0.395 0.226 0.467 0.375 0.100 0.077  87 0.09 0.082 0.311 0.250 0.616 0.543 0.245 0.214 0.125 0.314 0.434 0.452 0.336 0.142 0.069 0.301 0.063 0.542 0.200 0.346  89 17 0.09 0.007 0.014 0.250 0.063 0.152 0.092 0.924 0.200 0.071 0.214 0.234 0.214 0.155 0.253 0.208 0.010 0.011  91 na 0.029 0.141 0.070  93 0.05 0.310  95 20 na 0.007 0.025 0.130 0.009  97 na 0.009 0.018  99 0.11 0.066 0.042 101 0.04 0.311 0.155 0.250 0.550 0.231 103 0.05 0.123 0.031 Het 0.218 0.656 0.701 0.551 0.642 0.609 0.639 0.143 0.768 0.704 0.582 0.675 0.649 0.776 0.663 0.702 0.395 0.671 0.765 0.650 0.315 PIC 0.206 0.582 0.619 0.513 0.691 0.554 0.558 0.135 0.725 0.641 0.437 0.636 0.573 0.739 0.597 0.615 0.757 0.605 0.712 0.604 0.125 PE1 0.024 0.217 0.267 0.165 0.221 0.199 0.199 0.010 0.566 0.269 0.167 0.268 0.209 0.384 0.236 0.264 0.410 0.245 0.551 0.243 0.564 PE2 0.111 0.368 0.434 0.316 0.197 0.360 0.346 0.070 0.544 0.434 0.284 0.438 0.355 0.564 0.392 0.428 0.598 0.410 0.530 0.421 0.542 BM1905 Size Repeat Std. Dev. AI CSP EIP EIW FN GC HM JA MBS MX NBR WBNP WC YNP ABR HHP AN HE HO SH TLH 110 0.47 0.063 0.013 0.024 0.038 173 12 0.07 0.022 0.236 0.260 0.896 0.870 0.170 0.403 0.109 0.769 0.314 0.171 0.619 0.172 0.064 0.496 0.116 124 na 0.058 176 14 0.45 0.246 0.709 0.604 0.130 0.720 0.592 0.469 0.141 0.557 0.579 0.310 0.311 0.795 0.158 0.779 0.019 0.063 178 0.15 0.102 0.219 0.331 0.125 0.423 180 16 0.11 0.007 0.148 0.039 0.292 0.215 182 0.09 0.030 0.146 0.021 0.038 0.026 0.141 0.010 184 18 0.08 0.694 0.028 0.021 0.990 0.422 0.038 0.071 0.224 0.018 0.116 0.105 0.125 0.042 186 0.27 0.019 0.123 0.208 0.083 0.038 188 0.24 0.028 0.602 0.563 0.333 0.333 0.269 192 na 0.042 194 na 0.028 198 25 0.10 0.057 0.017 0.083 0.083 0.017 Het 0.458 0.444 0.557 0.195 0.229 0.443 0.489 0.595 0.168 0.587 0.589 0.524 0.316 0.318 0.613 0.173 0.603 0.625 0.114 0.783 0.739 PIC 0.396 0.383 0.487 0.185 0.201 0.397 0.366 0.503 0.358 0.514 0.528 0.442 0.275 0.790 0.637 0.339 0.367 0.570 0.663 0.338 0.683 PE1 0.106 0.099 0.152 0.019 0.026 0.093 0.116 0.174 0.073 0.178 0.178 0.137 0.050 0.050 0.194 0.068 0.209 0.212 0.291 0.189 0.323 PE2 0.226 0.216 0.292 0.100 0.101 0.230 0.183 0.297 0.211 0.319 0.331 0.256 0.143 0.160 0.314 0.192 0.388 0.380 0.464 0.565 0.506 BM2113 Size Repeat Std. Dev. AI CSP EIP EIW FN GC HM JA MBS MX NBR WBNP WC YNP ABR HHP AN HE HO SH TLH 125 0.03 0.071 127 0.09 0.041 0.047 0.063 0.125 0.048 0.076 0.049 0.093 0.120 0.031 0.203 0.208 0.077 129 15 0.09 0.761 0.122 0.331 0.720 0.146 0.360 0.548 0.463 0.143 0.539 0.571 0.257 0.247 0.340 0.229 0.125 0.231 131 na 0.097 0.038 133 17 0.07 0.324 0.024 0.013 0.014 0.013 0.220 0.101 0.136 0.058 135 0.13 0.011 0.300 0.013 0.057 0.112 0.185 0.031 0.083 0.292 0.154 131 0.07 0.370 0.459 0.500 0.042 0.023 139 0.07 0.019 0.031 0.083 0.133 0.385 141 0.13 0.120 0.087 0.143 0.003 0.185 0.406 0.083 0.018 143 22 0.11 0.231 0.324 0.354 0.050 0.375 0.190 0.429 0.939 0.300 0.457 0.263 0.890 0.164 0.595 0.239 0.430 0.120 0.031 0.042 145 0.12 0.081 0.146 0.150 0.061 0.071 0.029 0.131 0.149 0.116 147 0.05 0.054 0.271 0.100 0.171 0.024 0.010 0.057 0.011 0.023 153 27 0.06 0.007 0.014 0.271 0.186 0.013 0.075 Het 0.363 0.761 0.696 0.458 0.747 0.725 0.522 0.115 0.677 0.728 0.614 0.621 0.820 0.569 0.781 0.719 0.772 0.621 0.692 0.766 0.775 PIC 0.306 0.728 0.625 0.424 0.698 0.671 0.405 0.107 0.619 0.691 0.548 0.572 0.792 0.510 0.747 0.668 0.731 0.516 0.638 0.709 0.728 PE1 0.061 0.377 0.253 0.103 0.332 0.297 0.135 0.027 0.256 0.331 0.194 0.214 0.461 0.169 0.196 0.305 0.373 0.102 0.271 0.147 0.376 PE2 0.156 0.555 0.412 0.261 0.510 0.470 0.215 0.054 0.423 0.515 0.347 0.393 0.616 0.320 0.376 0.481 0.554 0.139 0.450 0.524 0.536 BM4440 Size Repeat Std. Dev. AI CSP EIP EIW FN GC HM JA MBS MX NBR WBNP WC YNP ABR HHP AN HE HO SH TLH 121 na 0.025 123 0.19 0.007 0.027 0.063 0.146 0.167 0.120 0.038 0.113 0.066 0.125 0.032 0.038 0.035 0.185 0.344 0.458 0.457 0.269 125 15 0.22 0.015 0.230 0.104 0.271 0.104 0.030 0.405 1.030 0.188 0.147 0.197 0.250 0.342 0.566 0.313 0.244 296 0.053 0.154 127 0.31 0.716 0.027 0.375 0.188 0.229 0.590 0.071 0.150 0.118 0.429 0.150 0.049 0.266 0.146 0.198 129 11 0.25 0.246 0.581 0.208 0.333 0.333 0.190 0.405 0.439 0.279 0.039 0.400 0.560 0.120 0.299 0.477 131 0.21 0.001 0.103 0.219 0.063 0.146 0.070 0.119 0.175 0.162 0.276 0.050 0.026 0.016 0.131 0.023 0.111 0.083 0.016 133 19 0.27 0.003 0.023 0.021 0.021 0.013 0.324 0.469 0.157 0.167 0.115 137 na 0.019 139 0.21 0.019 0.167 141 na 0.053 143 24 0.01 0.176 0.016 0.030 0.023 0.037 0.208 0.55 0.038 145 0.12 0.031 0.231 141 0.81 0.009 0.063 0.125 0.154 149 na 0.031 0.042 Het 0.427 0.600 0.756 0.763 0.384 0.599 0.661 0.000 0.721 0.821 0.706 0.746 0.561 0.630 0.770 0.680 0.765 0.663 0.716 0.766 0.827 PIC 0.163 0.549 0.709 0.713 0.752 0.555 0.587 0.000 0.619 0.790 0.651 0.697 0.482 0.566 0.731 0.621 0.720 0.594 0.639 0.719 0.784 PE1 0.092 0.198 0.342 0.350 0.387 0.199 0.230 0.000 0.312 0.456 0.283 0.334 0.163 0.210 0.374 0.355 0.361 0.241 0.291 0.361 0.449 PE2 0.199 0.362 0.526 0.328 0.567 0.369 0.183 0.000 0.491 0.612 0.454 0.512 0.289 0.365 0.553 0.423 0.539 0.400 0.469 0.546 0.626 BM720 Size Repeat Std. Dev. AI CSP EIP EIW FN GC HM JA MBS MX NBR WBNP WC YNP ABR HHP AN HE HO SH TLH 203  9 0.04 0.054 0.174 0.015 0.004 0.116 209 na 0.115 213 0.08 0.095 0.052 0.167 0.029 0.091 0.224 0.166 0.097 0.023 0.009 0.031 215 0.02 0.042 0.083 0.115 217 0.05 0.500 0.083 0.333 0.135 219 0.05 0.125 0.035 221 0.06 0.167 223 19 0.11 0.022 0.189 0.083 0.152 0.521 0.024 0.128 0.105 0.124 0.131 0.211 0.089 0.142 225 0.11 0.143 0.152 0.022 0.092 0.015 0.132 0.193 0.003 0.239 0.093 227 21 0.02 0.061 0.054 0.438 0.543 0.239 0.052 0.524 0.474 0.294 0.081 0.474 0.102 0.267 0.067 0.213 0.009 0.063 0.083 229 22 0.10 0.455 0.297 0.375 0.087 0.391 0.229 0.286 0.094 0.250 0.324 0.622 0.184 0.257 0.307 0.164 0.070 0.167 0.031 231 23 0.09 0.453 0.054 0.104 0.065 0.174 0.146 0.578 0.039 0.081 0.132 0.047 0.429 0.384 0.157 0.156 0.167 0.041 233 0.03 0.014 0.068 0.070 0.157 0.313 0.167 0.081 0.038 235 0.05 0.012 0.281 0.031 0.154 237 0.06 0.019 0.281 0.125 0.083 0.423 239 0.05 0.037 0.292 Het 0.511 0.104 0.657 0.654 0.717 0.653 0.623 0.554 0.692 0.708 0.580 0.689 0.812 0.793 0.721 0.775 0.693 0.790 0.876 0.791 0.769 PIC 0.491 0.771 0.534 0.610 0.634 0.636 0.551 0.470 0.644 0.644 0.545 0.632 0.782 0.737 0.676 0.736 0.652 0.744 0.841 0.743 0.727 PE1 0.172 0.433 0.229 0.245 0.313 0.240 0.197 0.151 0.279 0.273 0.190 0.260 0.446 0.409 0.510 0.388 0.287 0.394 0.549 0.197 0.375 PE2 0.291 0.610 0.382 0.424 0.489 0.411 0.147 0.274 0.455 0.436 0.367 0.433 0.621 0.588 0.538 0.568 0.469 0.572 0.711 0.575 0.563 BM51117 Size Repeat Std. Dev. AI CSP EIP EIW FN GC HM JA MBS MX NBR WBNP WC YNP ABR HHP AN HE HO SH TLH  87 0.03 0.022 0.007 0.011 0.039 0.250 0.083  89 13 0.10 0.903 0.432 0.342 0.680 0.500 0.370 0.214 0.106 0.500 0.486 0.176 0.550 0.470 0.253 0.379 0.163  91 0.07 0.073 0.351 0.487 0.240 0.213 0.160 0.214 0.894 0.397 0.229 0.095 0.225 0.421 0.228 0.383 0.538  93 0.17 0.015 0.203 0.042 0.080 0.261 0.430 0.571 0.103 0.243 0.551 0.175 0.103 0.519 0.197 0.263 0.120 0.156 0.042 0.048 0.269  95 0.12 0.007 0.027 0.528 0.375 0.292 0.208 0.385  97 0.06 0.122 0.106 0.469 0.115 0.667 0.037  99 0.01 0.014 0.040 0.043 0.050 0.030 0.038 0.038 101 0.06 0.037 0.042 0.192 103 na 0.038 Het 0.179 0.653 0.537 0.478 0.641 0.654 0.389 0.191 0.585 0.656 0.618 0.672 0.593 0.617 0.673 0.622 0.618 0.625 0.723 0.514 0.745 PIC 0.169 0.577 0.428 0.414 0.370 0.387 0.517 0.172 0.494 0.591 0.568 0.560 0.505 0.545 0.605 0.555 0.548 0.536 0.634 0.456 0.691 PE1 0.016 0.215 0.141 0.112 0.209 0.224 0.169 0.018 0.169 0.226 0.208 0.201 0.177 0.188 0.240 0.199 0.199 0.189 0.284 0.133 0.127 PE2 0.089 0.363 0.235 0.257 0.362 0.375 0.385 0.056 0.290 0.385 0.382 0.362 0.101 0.334 0.356 0.154 0.349 0.329 0.452 0.278 0.508 BM51172 Size Repeat Std. Dev. AI CSP EIP EIW FN GC HM JA MBS MX NBR WBNP WC YNP ABR HHP AN HE HO SH TLH  86 0.10 0.029 0.176 0.030 0.015  88 13 0.11 0.157 0.108 0.292 0.040 0.083 0.290 0.095 0.015 0.038 0.214 0.392 0.095 0.392 0.015 0.207 0.122  90 14 0.13 0.067 0.473 0.333 0.760 0.646 0.490 0.313 0.015 0.738 0.686 0.162 0.595 0.294 0.627 0.481 0.451 0.500 0.500 0.500 0.308 0.131  92 15 0.09 0.208 0.020 0.014 0.003 0.004 0.333 0.406 0.161 0.173 0.038  94 0.09 0.006 0.028 0.250 0.125 0.077  96 0.10 0.139 0.094 0.083 0.042 0.115  98 na 0.024 100 0.10 0.297 0.208 0.063 0.050 0.015 0.016 0.057 0.149 0.095 0.162 0.022 0.139 0.085 102 20 0.12 0.067 0.167 0.200 0.060 0.333 0.138 0.122 0.190 0.003 0.203 0.083 0.183 104 0.11 0.709 0.122 0.090 0.071 0.591 0.145 0.117 0.053 0.159 Het 0.466 0.666 0.740 0.385 0.534 0.665 0.295 0.541 0.421 0.483 0.758 0.398 0.717 0.546 0.695 0.724 0.625 0.585 0.667 0.415 0.453 PIC 0.430 0.605 0.683 0.333 0.481 0.611 0.272 0.457 0.377 0.432 0.717 0.550 0.665 0.495 0.655 0.678 0.569 0.486 0.599 0.412 0.420 PE1 0.114 0.241 0.309 0.073 0.148 0.252 0.041 0.148 0.090 0.120 0.354 0.195 0.295 0.158 0.291 0.311 0.199 0.166 0.234 0.114 0.107 PE2 0.263 0.404 0.483 0.189 0.101 0.420 0.150 0.208 0.218 0.259 0.336 0.365 0.467 0.312 0.429 0.495 0.344 0.231 0.400 0.264 0.261 BM51862 Size Repeat Std. Dev. AI CSP EIP EIW FN GC HM JA MBS MX NBR WBNP WC YNP ABR HHP AN HE HO SH TLH 142  9 0.00 0.343 0.311 0.208 0.180 0.375 0.200 0.119 0.385 0.300 0.081 0.262 0.361 0.352 0.222 0.238 144 0.06 0.160 0.060 0.143 0.024 0.019 148 na 0.035 152 na 154 0.10 0.048 0.278 0.300 156 0.06 0.127 0.042 0.250 0.013 0.051 0.284 0.024 0.017 0.049 0.107 0.131 158 17 0.05 0.007 0.392 0.208 0.100 0.025 0.030 0.071 0.218 0.200 0.041 0.248 0.145 0.203 0.107 160 0.07 0.135 0.125 0.720 0.641 0.129 0.238 0.038 0.119 0.389 0.188 0.083 0.087 0.154 162 19 0.07 0.015 0.034 0.042 0.050 0.060 0.071 0.017 0.054 0.119 0.030 0.062 0.079 0.036 0.009 0.042 164 10 0.05 0.485 0.027 0.104 0.250 0.050 0.357 0.141 0.051 0.014 0.189 0.048 0.010 0.079 0.162 0.036 0.041 0.033 166 0.09 0.027 0.042 0.440 0.120 0.048 0.141 0.043 0.054 0.119 0.036 0.173 0.053 0.250 0.157 0.063 0.208 0.203 0.077 168 0.09 0.022 0.014 0.271 0.120 0.175 0.010 0.167 0.315 0.114 0.338 0.262 0.060 0.110 0.177 0.107 0.061 0.192 170 23 0.09 0.083 0.167 0.219 0.048 0.017 0.041 0.009 0.560 0.033 0.192 172 0.11 0.009 0.695 0.161 0.042 174 na 0.009 0.038 190 na 0.043 193 0.05 0.139 0.018 Het 0.632 0.703 0.825 0.731 0.757 0.828 0.800 0.526 0.768 0.821 0.762 0.834 0.741 0.793 0.842 0.840 0.734 0.492 0.634 0.702 0.354 PIC 0.563 0.649 0.793 0.631 0.709 0.801 0.764 0.465 0.731 0.791 0.719 0.803 0.704 0.764 0.319 0.808 0.683 0.443 0.627 0.654 0.317 PE1 0.212 0.283 0.466 0.321 0.346 0.480 0.424 0.136 0.378 0.463 0.260 0.481 0.341 0.425 0.310 0.492 0.316 0.123 0.260 0.294 0.507 PE2 0.361 0.457 0.610 0.503 0.525 0.653 0.604 0.276 0.559 0.618 0.538 0.660 0.519 0.605 0.679 0.664 0.491 0.271 0.435 0.476 0.676 BM52639 Size Repeat Std. Dev. AI CSP EIP EIW FN GC HM JA MBS MX NBR WBNP WC YNP ABR HHP AN HE HO SH TLH 156 na 0.018 164 14 0.12 0.021 0.175 0.083 165 0.17 0.015 0.380 0.063 0.015 0.013 0.358 0.094 0.417 0.250 0.162 168 0.03 0.239 0.135 0.370 0.313 0.400 0.143 0.424 0.050 0.265 0.081 0.167 0.253 0.194 0.197 0.125 0.083 0.192 170 17 0.13 0.664 0.324 0.304 0.340 0.146 0.040 0.381 0.482 0.309 0.203 0.286 0.291 0.389 0.261 0.150 172 0.12 0.022 0.338 0.217 0.340 0.125 0.230 0.476 0.061 0.362 0.221 0.149 0.262 0.345 0.391 0.130 0.425 0.216 0.405 0.167 0.125 0.017 174 19 0.09 0.015 0.022 0.060 0.183 0.160 0.175 0.118 0.459 0.024 0.023 0.088 0.028 0.313 0.083 0.192 176 0.11 0.045 0.027 0.060 0.138 0.140 0.132 0.138 0.044 0.081 0.071 0.007 0.129 0.035 178 21 0.22 0.031 0.020 0.042 0.030 0.119 0.103 0.061 0.175 0.066 0.156 0.125 0.011 180 0.10 0.301 0.031 0.175 0.038 184 na 0.024 186 0.08 0.095 0.037 0.364 0.029 0.025 190 na 0.027 0.039 Het 0.501 0.751 0.723 0.720 0.802 0.743 0.615 0.666 0.752 0.775 0.717 0.809 0.727 0.652 0.766 0.751 0.726 0.719 0.770 0.777 0.728 PIC 0.446 0.106 0.664 0.663 0.363 0.701 0.527 0.597 0.715 0.732 0.676 0.773 0.674 0.375 0.726 0.709 0.669 0.652 0.724 0.727 0.655 PE1 0.131 0.346 0.294 0.302 0.416 0.338 0.195 0.236 0.356 0.375 0.312 0.433 0.102 0.214 0.365 0.349 0.300 0.285 0.369 0.111 0.330 PE2 0.269 0.523 0.464 0.474 0.595 0.517 0.316 0.391 0.578 0.553 0.491 0.610 0.474 0.361 0.544 0.552 0.470 0.456 0.531 0.553 0.479 BM5410 Size Repeat Std. Dev. AI CSP EIP EIW FN GC HM JA MBS MX NBR WBNP WC YNP ABR HHP AN HE HO SH TLH  81 0.10 0.013 0.071 0.003  83 12 0.06 0.036 0.635 0.333 0.020 0.600 0.406 0.667 0.106 0.183 0.400 0.486 0.095 0.566 0.471 0.447 0.547 0.083 0.094 0.273 0.413 0.077  85 0.11 0.262 0.081 0.042 0.080 0.156 0.138 0.243 0.041 0.048 0.158 0.056 0.015 0.031 0.042 0.269  87 0.25 0.014 0.045 0.095 0.030 0.013 0.024 0.013 0.042  89 15 0.09 0.638 0.257 0.604 0.840 0.455 0.229 0.024 0.470 0.538 0.329 0.284 0.667 0.276 0.252 0.346 0.384 0.019  91 0.29 0.013 0.081 0.296 0.111 0.125 0.500  93 17 0.19 0.014 0.083 0.014 0.024 0.094 0.012 0.028 0.056 0.038  95 0.09 0.015 0.021 0.050 0.125 0.194 0.087 0.029 0.091 0.071 0.003 0.041 0.023 0.083 0.333 0.042  97 19 0.24 0.214 0.013 0.258 0.008  99 0.09 0.065 0.003 0.056 0.161 103 0.03 0.287 0.531 0.111 0.361 0.077 105 0.03 0.056 0.186 0.056 0.038 107 na 0.091 109 0.09 0.083 Het 0.519 0.327 0.527 0.287 0.543 0.739 0.506 0.617 0.653 0.617 0.670 0.519 0.581 0.670 0.669 0.559 0.803 0.671 0.800 0.766 0.676 PIC 0.454 0.464 0.459 0.269 0.436 0.695 0.430 0.534 0.611 0.608 0.616 0.512 0.510 0.601 0.610 0.453 0.775 0.626 0.747 0.719 0.617 PE1 0.136 0.142 0.138 0.041 0.147 0.131 0.129 0.194 0.247 0.237 0.256 0.162 0.167 0.293 0.253 0.156 0.445 0.262 0.401 0.364 0.257 PE2 0.269 0.279 0.251 0.152 0.241 0.511 0.271 0.311 0.425 0.392 0.424 0.395 0.388 0.383 0.415 0.269 0.621 0.444 0.580 0.347 0.428 BM5510 Size Repeat Std. Dev. AI CSP EIP EIW FN GC HM JA MBS MX NBR WBNP WC YNP ABR HHP AN HE HO SH TLH  82 na 0.040  84 na 0.045  88 0.14 0.094 0.077  90 0.25 0.015  91 12 0.08 0.969 0.471 0.130 0.625 0.229 0.310 0.214 0.303 0.637 0.386 0.399 0.452 0.682 0.365 0.395 0.114  92   12A 0.14 0.008 0.382 0.500 0.195 0.188 0.370 0.143 0.697 0.097 0.214 0.292 0.239 0.197 0.331 0.301 0.267 0.370 0.544 0.409 0.333 0.423  94   13A 0.15 0.074 0.043 0.104 0.229 0.100 0.310 0.150 0.229 0.069 0.119 0.105 0.036 0.105 0.256 0.065 0.042 0.154  95 14 0.06 0.023 0.074 0.326 0.083 0.354 0.220 0.333 0.050 0.171 0.250 0.190 0.095 0.197 0.199 0.163  96 0.05 0.009 0.091 0.333  98 0.04 0.037 0.039 0.045 0.042 0.192 100 na 0.038 102 0.06 0.031 0.045 0.071 104 0.06 0.472 0.903 0.125 106 0.01 0.046 0.273 0.063 0.035 108 na 0.091 Het 0.060 0.626 0.632 0.562 0.742 0.712 0.736 0.426 0.559 0.729 0.701 0.697 0.580 0.671 0.706 0.747 0.638 0.631 0.753 0.766 0.760 PIC 0.059 0.549 0.538 0.514 0.686 0.614 0.676 0.133 0.323 0.675 0.638 0.618 0.510 0.606 0.649 0.619 0.365 0.554 0.699 0.713 0.715 PE1 0.002 0.205 0.208 0.167 0.312 0.281 0.308 0.089 0.174 0.301 0.266 0.266 0.167 0.241 0.231 0.314 0.219 0.208 0.345 0.339 0.160 PE2 0.030 0.347 0.356 0.329 0.486 0.450 0.475 0.167 0.346 0.475 0.431 0.437 0.308 0.401 0.446 0.488 0.363 0.356 0.522 0.315 0.542 BM5523 Size Repeat Std. Dev. AI CSP EIP EIW FN GC HM JA MBS MX NBR WBNP WC YNP ABR HHP AN HE HO SH TLH 159 11 0.05 0.119 0.021 0.014 0.029 163 13 0.06 0.033 0.135 0.146 0.053 0.110 0.024 0.186 0.103 0.095 0.010 0.047 0.038 165 14 0.13 0.208 0.040 0.110 0.141 0.041 0.092 0.071 0.019 0.011 167 15 0.08 0.037 0.054 0.063 0.240 0.184 0.120 0.331 0.167 0.129 0.013 0.333 0.010 0.023 0.143 0.021 0.170 0.125 0.042 169 na 0.042 0.018 171 na 0.077 173 0.09 0.419 0.294 0.229 0.140 0.342 0.400 0.543 0.045 0.106 0.280 0.551 0.262 0.247 0.259 0.485 0.500 0.056 0.063 0.083 0.108 175 19 0.10 0.188 0.150 0.271 0.060 0.289 0.160 0.256 0.676 0.167 0.214 0.158 0.119 0.160 0.463 0.139 0.384 0.009 0.031 0.208 177 0.11 0.297 0.063 0.320 0.132 0.100 0.143 0.045 0.218 0.129 0.119 0.573 0.180 0.184 0.081 0.259 0.031 0.500 0.115 179 0.06 0.028 0.438 0.167 0.077 181 0.07 0.012 0.407 0.418 0.500 0.206 0.269 183 0.09 0.102 0.083 0.115 185 na 0.042 187 na 0.009 189 na 0.009 Het 0.660 0.762 0.610 0.727 0.135 0.770 0.605 0.558 0.787 0.809 0.648 0.787 0.587 0.674 0.892 0.602 0.745 0.621 0.695 0.684 0.308 PIC 0.594 0.716 0.772 0.668 0.702 0.738 0.553 0.476 0.743 0.715 0.611 0.746 0.525 0.620 0.650 0.516 0.701 0.514 0.643 0.621 0.763 PE1 0.218 0.350 0.431 0.298 0.316 0.386 0.195 0.138 0.791 0.433 0.247 0.196 0.177 0.256 0.283 0.185 0.114 0.199 0.279 0.160 0.424 PE2 0.393 0.527 0.608 0.466 0.513 0.570 0.132 0.284 0.571 0.611 0.429 0.575 0.326 0.424 0.456 0.316 0.523 0.774 0.439 0.435 0.602 RM372 Size Repeat Std. Dev. AI CSP EIP EIW FN GC HM JA MBS MX NBR WBNP WC YNP ABR HHP AN HE HO SH TLH 114  9 0.17 0.041 0.087 0.021 0.103 0.071 0.030 0.020 0.015 0.023 116 0.04 0.063 0.192 118 11 0.01 0.365 0.152 0.229 0.167 0.038 0.071 0.043 0.048 0.293 0.534 0.135 0.244 122 na 0.038 126 0.34 0.151 0.061 0.167 0.077 128 0.22 0.108 0.217 0.091 0.051 0.086 0.029 0.143 0.140 0.113 0.116 0.150 0.375 0.136 0.411 0.108 130 17 0.10 0.412 0.122 0.457 0.587 0.146 0.638 0.222 0.121 0.531 0.586 0.329 0.524 0.260 0.106 0.338 0.031 0.208 0.250 0.545 0.161 0.018 132 0.09 0.008 0.087 0.031 0.018 0.115 0.071 0.020 0.137 0.004 0.015 0.094 0.074 0.091 0.041 0.154 134 19 0.14 0.164 0.149 0.391 0.022 0.271 0.260 0.611 0.788 0.126 0.729 0.443 0.143 0.127 0.373 0.256 0.302 0.170 0.156 0.227 0.205 0.192 136 0.09 0.414 0.135 0.250 0.100 0.013 0.029 0.080 0.022 0.132 0.151 0.047 138 0.54 0.081 0.157 0.050 0.008 0.047 Het 0.633 0.797 0.622 0.599 0.791 0.528 0.557 0.359 0.656 0.596 0.673 0.680 0.803 0.757 0.774 0.811 0.793 0.763 0.639 0.741 0.315 PIC 0.555 0.767 0.335 0.548 0.743 0.462 0.489 0.328 0.623 0.545 0.610 0.641 0.773 0.712 0.737 0.776 0.754 0.721 0.574 0.684 0.778 PE1 0.201 0.429 0.189 0.195 0.391 0.140 0.151 0.064 0.260 0.194 0.247 0.277 0.437 0.149 0.383 0.440 0.404 0.363 0.213 0.915 0.430 PE2 0.341 0.609 0.324 0.360 0.572 0.175 0.294 0.185 0.446 0.357 0.405 0.462 0.614 0.526 0.562 0.613 0.584 0.543 0.379 0.494 0.601 1Allele size (does not include non-template adenine added to 3′ terminus by Taq polymerase) 2Number of repeats present in the sequenced bison allele. 3Standard deviation of called size assigned by Genescan software 4Expected heterozygosity 5Polymorphic information content 6Probability of excluding a putative parent when a confirmed parent's genotypes are unavailable. 7Probability of excluding a putative parent when a confirmed parent's genotypes are known.

Claims

1. A method of determining parentage of a North American bison or domestic cattle offspring comprising:
i) determining the alleles present in the offspring for selected microsatellite loci;
ii) determining the alleles present in sampled potential parents of the offspring for the same selected microsatellite loci;
iii) determining the likelihood that any potential parent is the actual parent of the offspring based upon the presence or absence of an allele for each of the selected loci in the offspring that is present in the potential parent;
wherein the selected loci comprise BM1225, BM1706, BM17132, BM1905, BM2113, BM4440, BM720, BMS1862, BMS410, BMS510, BMS527, RM372, BMS1172, BMS2639, BM3628 and BMS2325.
i) determining the alleles present in the offspring for selected microsatellite loci;
ii) determining the alleles present in sampled potential parents of the offspring for the same selected microsatellite loci;
iii) determining the likelihood that any potential parent is the actual parent of the offspring based upon the presence or absence of an allele for each of the selected loci in the offspring that is present in the potential parent;
wherein the selected loci comprise BM1225, BM1706, BM17132, BM1905, BM2113, BM4440, BM720, BMS1862, BMS410, BMS510, BMS527, RM372, BMS1172, BMS2639, BM3628 and BMS2325.
2. The method of claim 1, wherein the selected loci consist of BM1225, BM1706, BM17132, BM1905, BM2113, BM4440, BM720, BMS 1862, BMS410, BMS510, BMS527, RM372, BMS1172, BMS2639, BM3628 and BMS2325.