Exclusion probabilities of 22 bovine microsatellite markers in fluorescent multiplexes for semiautomated parentage testing

Heyen, D. W.; Beever, Jonathan E.; Da, Yang; Evert, R. E.; Green, C.; Bates, Stephen; Ziegle, Janet; Lewin, Harris A.

doi:10.1111/j.1365-2052.1997.t01-1-00057.x

Cited by 94 publications

(79 citation statements)

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“…Polymorphism information content ranged from 0.575 (SPS115, 8 alleles) to 0.816 (TGLA227, 12 alleles) with average value 0.713, which confirms a high polymorphism of each analyzed microsatellite. Our results are comparable to those of Holstein cattle found by Heyen et al (1997) in the USA, Visscher et al (2002) in the UK, or Czerneková et al (2006) in the Czech Republic, and higher than those published by Radko et al (2005) in Poland. Generally, the higher the heterozygosity, the higher the genetic variation of the population and its genetic polymorphism, and the more suitable is the marker for individual identification.…”

Section: Resultssupporting

confidence: 41%

“…Most of the studies (Heyen et al, 1997;Curi and Lopes, 2002;Visscher et al, 2002;Weller et al, 2004) were focused on paternity testing, as the genotyping of both parents and progeny would be too expensive for routine application. Weller et al (2004) tested the effects of inseminator, region, herd, sire and birth year on incorrect paternity by logistic and linear analysis.…”

Section: Resultsmentioning

confidence: 99%

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2022

Czech J. Anim. Sci.

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A set of 233 Holstein calves, their 233 dams and 44 sires from 4 large-sized herds was genotyped for 10 microsatellites recommended by ISAG for paternity/parentage testing. Heterozygosity of microsatellites ranged from 0.607 (SPS115) to 0.835 (TGLA227), and PIC from 0.575 (SPS115) to 0.816 (TGLA227) confirming a high polymorphism of each analysed locus. Their combined exclusion probability reached 0.999, which made them suitable and sufficiently accurate for parentage testing. A conflict between putative parents and calf in at least 2 markers with combined exclusion probability > 0.9 was required to reject parentage. The pedigree was considered incorrect in 25 (10.73%) out of the evaluated progeny/parent trios, of which in 10 samples the genotype of both parents did not match their offspring, and in 2 samples the putative dam was in conflict with the calf genotype. This result shows that the interchange of calves on farms with large-sized herds plays the role as important as the errors in sire identification, or recording mistakes.

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Section: Resultssupporting

confidence: 41%

Section: Resultsmentioning

confidence: 99%

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2022

Czech J. Anim. Sci.

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“…Genomic DNA was extracted from straws of frozen semen samples by a salting-out method adapted from Heyen et al [15]. The quantities of original DNA available were very small.…”

Section: Extraction and Amplification Of Dnamentioning

confidence: 99%

Linkage disequilibrium on chromosome 6 in Australian Holstein-Friesian cattle

Khatkar¹,

Thomson²,

Tammen³

et al. 2006

Genet. Sel. Evol.

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-We analysed linkage disequilibrium (LD) in Australian Holstein-Friesian cattle by genotyping a sample of 45 bulls for 15 closely-spaced microsatellites on two regions of BTA6 reported to carry important QTL for dairy traits. The order and distance of markers were based on the USDA-MARC linkage map. Frequencies of haplotypes were estimated using the E-M approach and a more computationally-intensive Bayesian approach as implemented in PHASE. LD was then estimated using the Hedrick multiallelic extension of Lewontin normalised coefficient D . Estimates of D from the two approaches were in close agreement (r = 0.91). The mean estimates of D for marker pairs with an inter-marker distance of less than 5 cM (n = 13) are 0.57 and 0.51, and for distances more than 20 cM (n = 44) are 0.29 and 0.17, estimated from the E-M and Bayesian approaches, respectively. The Malecot model was fitted for the exponential decline of LD with map distance between markers. The swept radii (the distance at which LD has declined to 1/e (∼37%) of its initial value) are 11.6 and 13.7 cM for the above two methods, respectively. The Malecot model was also fitted using map distance in Mb from the bovine integrated map (bovine location database, bLDB) in addition to cM from the MARC map. Overall, the results indicate a high level of LD on chromosome 6 in Australian dairy cattle.linkage disequilibrium / dairy cattle / markers / chromosome 6

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“…The level of polymorphic variation observed in bovine short tandem repeats (STRs) permits the use of relatively few loci to identify cattle and to determine their parentage [16,17]. Several well defined cattle STR panels are commercially available.…”

Section: Introductionmentioning

confidence: 99%

Compilation of a panel of informative single nucleotide polymorphisms for bovine identification in the Northern Irish cattle population

et al. 2010

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Background Animal identification is pivotal in governmental agricultural policy, enabling the management of subsidy payments, movement of livestock, test scheduling and control of disease. Advances in bovine genomics have made it possible to utilise inherent genetic variability to uniquely identify individual animals by DNA profiling, much as has been achieved with humans over the past 20 years. A DNA profiling test based on bi-allelic single nucleotide polymorphism (SNP) markers would offer considerable advantages over current short tandem repeat (STR) based industry standard tests, in that it would be easier to analyse and interpret. In this study, a panel of 51 genome-wide SNPs were genotyped across panels of semen DNA from 6 common breeds for the purposes of ascertaining allelic frequency. For SNPs on the same chromosome, the extent of linkage disequilbrium was determined from genotype data by Expectation Maximization (EM) algorithm. Minimum probabilities of unique identification were determined for each breed panel. The usefulness of this SNP panel was ascertained by comparison to the current bovine STR Stockmarks II assay. A statistically representative random sampling of bovine animals from across Northern Ireland was assembled for the purposes of determining the population allele frequency for these STR loci and subsequently, the minimal probability of unique identification they conferred in sampled bovine animals from Northern Ireland. Results 6 SNPs exhibiting a minor allele frequency of less than 0.2 in more than 3 of the breed panels were excluded. 2 Further SNPs were found to reside in coding areas of the cattle genome and were excluded from the final panel. The remaining 43 SNPs exhibited genotype frequencies which were in Hardy Weinberg Equilibrium. SNPs on the same chromosome were observed to have no significant linkage disequilibrium/allelic association. Minimal probabilities of uniquely identifying individual animals from each of the breeds were obtained and were observed to be superior to those conferred by the industry standard STR assay. Conclusions The 43 SNPs characterised herein may constitute a starting point for the development of a SNP based DNA identification test for European cattle.

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Exclusion probabilities of 22 bovine microsatellite markers in fluorescent multiplexes for semiautomated parentage testing

Cited by 94 publications

References 0 publications

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Linkage disequilibrium on chromosome 6 in Australian Holstein-Friesian cattle

Compilation of a panel of informative single nucleotide polymorphisms for bovine identification in the Northern Irish cattle population

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