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Query: UMLS:C0012872 (DNA marker)
 929 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Deoxyribonucleic acid-based tests were used to assign paternity to 625 calves from a multiple-sire breeding pasture. There was a large variability in calf output and a large proportion of young bulls that did not sire any offspring. Five of 27 herd sires produced over 50% of the calves, whereas 10 sires produced no progeny and 9 of these were yearling bulls. A comparison was made between the paternity results obtained when using a DNA marker panel with a high (0.999), cumulative parentage exclusion probability (P(E)) and those obtained when using a marker panel with a lower P(E) (0.956). A large percentage (67%) of the calves had multiple qualifying sires when using the lower resolution panel. Assignment of the most probable sire using a likelihood-based method based on genotypic information resolved this problem in approximately 80% of the cases, resulting in 75% agreement between the 2 marker panels. The correlation between weaning weight, on-farm EPD based on pedigrees inferred from the 2 marker panels was 0.94 for the 24 bulls that sired progeny. Partial progeny assignments inferred from the lower resolution panel resulted in the generation of EPD for bulls that actually sired no progeny according to the high-P(E) panel, although the Beef Improvement Federation accuracies of EPD for these bulls were never greater than 0.14. Simulations were performed to model the effect of loci number, minor allele frequency, and the number of offspring per bull on the accuracy of genetic evaluations based on parentage determinations derived from SNP marker panels. The SNP marker panels of 36 and 40 loci produced EPD with accuracies nearly identical to those EPD resulting from use of the true pedigree. However, in field situations where factors including variable calf output per sire, large sire cohorts, relatedness among sires, low minor allele frequencies, and missing data can occur concurrently, the use of marker panels with a larger number of SNP loci will be required to obtain accurate on-farm EPD.
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PMID:DNA-based paternity analysis and genetic evaluation in a large, commercial cattle ranch setting. 1787 82

Deoxyribonucleic acid from sires is usually not available from experiments aimed at QTL mapping for traits of the dam in cow-calf operations and free range sheep populations. In this study, methods to reconstruct sire genotypes using genotype information from large half-sib progeny were developed. The methods are based on 1) all offspring genotypes are compatible with more than 1 genotype for the sire, but 1 of the genotypes is more likely than the others when comparing the proportion of the different genotypes among offspring with its expected values assuming Mendelian inheritance, or 2) all offspring genotypes are compatible with just 1 possible genotype for the sire in the pedigree. A Monte Carlo simulation experiment was carried out to test the methods with 1 million replicates. A 99.7% correct sire genotype reconstruction was obtained with 30 offspring and a DNA marker with 3 or more alleles segregating at similar frequencies. Methods to test for incorrect paternity in half-sib offspring without DNA from the sire were also developed. A maximum likelihood method was developed to test for departure of Mendelian segregation due to a contaminating sire whose offspring are fully compatible with the genotype of the pedigree sire. A large number of offspring was needed to detect offspring from a contaminating sire (1,000 progeny for a power of 0.99 and proportion of true paternity of the pedigree of 0.80). Multi-marker methods were also developed for detection of paternity misidentification. Probabilities of detection of wrong paternity for a contaminating sire not sharing any alleles with the sire in the pedigree were 0.95 and 0.99 when using 5 and 10 markers in 30 half-sib offspring, respectively. The methods to infer the sire genotypes were tested with 49 progeny of a Merino ram whose genotype was inferred for 7 microsatellites. Methods to infer genotype of the sire are feasible, but QTL mapping experiments without DNA from the sires are more costly due to the need of genotyping markers in progeny for which the sire in the pedigree is homozygous.
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PMID:Inferring unknown genotypes of sires at codominant deoxyribonucleic acid markers in half-sib families. 1925 34