Factors Affecting Incorrect Paternity Assignment in the Israeli Holstein Population

Institute of Animal Sciences ARO, The Volcani Center, Bet Dagan 50250, Israel.
Journal of Dairy Science (Impact Factor: 2.57). 09/2004; 87(8):2627-40. DOI: 10.3168/jds.S0022-0302(04)73389-5
Source: PubMed


A total of 6040 Israeli Holstein cows from 181 Kibbutz herds listed as progeny of 11 sires were genotyped for 104 microsatellites. Seventeen markers were deleted due to a frequency of erroneous genotypes >1%, leaving 160,470 valid genotypes. Conflicts between the putative sire and daughter in at least 2 markers and for at least 10% of the markers genotyped per cow were required to reject paternity. Cows that did not meet the requirements for paternity confirmation or rejection were deleted from further analysis. The frequency of rejected paternity was 11.7%. The effects of recorded sire, birth year, geographical region, herd, and inseminator on the frequency of paternity rejection were analyzed with linear and nonlinear models. Only the effects of inseminator and recorded sire were significant in all models tested that included these effects. The main causes of incorrect paternity recording appear to be inseminator recording mistakes, and possibly mistakes with respect to semen labeling at the AI institutes. Incorrect paternity recording due to multiple inseminations by different sires could explain, at most, 20% of the paternity mistakes. Instituting a system of quality control, especially at the level of the inseminator, should reduce paternity errors to no more than 8%, and increase genetic progress by at least 1%.

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    • "Correct pedigree information is essential for performing genetic evaluations, as errors lead to incorrect estimates and low accuracies of estimated breeding values (see Maichomo et al., 2008). Pedigree errors of about 10% may lead to reductions in selection response of two to three percent in dairy cattle (Visscher et al., 2002), while different studies have reported observed pedigree errors of up to 23% in cattle in several countries (Christensen et al., 1982; Ron et al., 1996; Banos et al., 2001; Weller et al., 2004; Jiménez- Gamero et al., 2006). Microsatellite markers have been used extensively for parentage control in different species and are recommended by the International Society for Animal Genetics (ISAG) as they are highly abundant and informative, relatively inexpensive to use, and generate satisfactory results in tests for paternity exclusion (Luikart et al., 1999; Arruga et al., 2001; Curi and Lopes, 2002; Carneiro et al., 2007; Glowatzki-Mullis et al., 2007; Bolormaa et al., 2008; Reis et al., 2008; Carolino et al., 2009; Araújo et al., 2010; Stevanovic et al., 2010; Zhang et al., 2010; Adamov et al., 2011; Saberivand et al., 2011; Visser et al., 2011). "
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    ABSTRACT: Brazilian goats are generally kept in small herds and extensive rearing systems, mainly in the northeastern region of the country. Despite production improvement in recent years, the lack of pedigree control has affected genetic progress. This study aimed to validate a panel of 16 microsatellites for parentage testing in locally adapted and commercial goats breeds raised in Brazil, as well as to compare its efficiency with the panel recommended by the Brazilian Ministry of Agriculture, Livestock and Supplies (MAPA) in 2004. The number of alleles and expected heterozygosity (He) per marker ranged from four to 18, and from 0.051 to 0.831, respectively. Using all markers, 100% of parentage cases of the validation dataset were resolved with a strict confidence level of 95%. The 16 microsatellites panel showed adequate exclusion power (99.99%) and identity accuracy (99.99%). Suggestions for improvement of the marker panel endorsed by MAPA are provided.
    Genetics and Molecular Biology 03/2014; 37(1):54-60. DOI:10.1590/S1415-47572014000100010 · 1.20 Impact Factor
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    • "Also, we have observed that single nucleotide insertions or deletions within the amplified MS region can result in the rounding up or down of the called MS allele fragment size resulting in a 2 bp difference in the reported allele size. Therefore, the high inherent chance of genotyping errors has led several studies to suggest that 2 MS marker conflicts must exist for an animal to be excluded in parentage verification (Bonin et al., 2004; Weller et al., 2004; Baruch and Weller, 2008). In a comparison of a bovine parentage MS panel vs. a 32 SNP parentage panel (Heaton et al., 2002) employed for sire discovery for 287 calves from US beef and dairy farms, the SNP panel routinely outperformed the MS panel with the SNP panel assigning a sire at 100% probability 81.9% of the time vs. 38.3% of the time for the MS panel (Stewart Bauck, GeneSeek a Neogen Company, Pers. "
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    ABSTRACT: To assist cattle producers transition from microsatellite (MS) to single nucleotide polymorphism (SNP) genotyping for parental verification we previously devised an effective and inexpensive method to impute MS alleles from SNP haplotypes. While the reported method was verified with only a limited data set (N = 479) from Brown Swiss, Guernsey, Holstein, and Jersey cattle, some of the MS-SNP haplotype associations were concordant across these phylogenetically diverse breeds. This implied that some haplotypes predate modern breed formation and remain in strong linkage disequilibrium. To expand the utility of MS allele imputation across breeds, MS and SNP data from more than 8000 animals representing 39 breeds (Bos taurus and B. indicus) were used to predict 9410 SNP haplotypes, incorporating an average of 73 SNPs per haplotype, for which alleles from 12 MS markers could be accurately be imputed. Approximately 25% of the MS-SNP haplotypes were present in multiple breeds (N = 2 to 36 breeds). These shared haplotypes allowed for MS imputation in breeds that were not represented in the reference population with only a small increase in Mendelian inheritance inconsistancies. Our reported reference haplotypes can be used for any cattle breed and the reported methods can be applied to any species to aid the transition from MS to SNP genetic markers. While ~91% of the animals with imputed alleles for 12 MS markers had ≤1 Mendelian inheritance conflicts with their parents' reported MS genotypes, this figure was 96% for our reference animals, indicating potential errors in the reported MS genotypes. The workflow we suggest autocorrects for genotyping errors and rare haplotypes, by MS genotyping animals whose imputed MS alleles fail parentage verification, and then incorporating those animals into the reference dataset.
    Frontiers in Genetics 09/2013; 4:176. DOI:10.3389/fgene.2013.00176
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    • "However, not all sires were available for sampling and consequently were not analyzed . The misidentification rates are high compared to other livestock species (Crawford et al., 1993; Laughlin et al., 2003; Weller et al., 2004; Siwek and Knol, 2010), indicating the need to improve the identification system and genealogical data collection. The obtained non-exclusion probabilities and paternity test results indicated that this microsatellite panel is suitable for parentage testing animals from moderately inbred and structured populations, even when subjects are related (De Ungria et al., 2002; von Wurmb-Schwark et al., 2006; Wenk et al., 2006; Scarpetta et al., 2007), and could be used for pedigree reconstruction of Valle del Belice breed. "
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    ABSTRACT: The aim of this work was to develop and evaluate a PCR based microsatellite markers multiplex system for parentage verification of Sicilian Valle del Belice dairy sheep. A total of 85 samples of blood and hair were collected and genotyped for 24 microsatellite markers in multiplex electrophoresis runs. A total of 269 alleles were detected across the 24 loci investigated. The PIC considering all loci was equal to 0.736, showing that this microsatellite panel was very polymorphic and highly informative. A parentage test was performed on 64 families generated with multiple sires. Results indicated 20.3% and 29.7% misidentification rates for females and males, respectively. In 8 cases, out of 13 maternal exclusions, the real mother was identified among other females within the flock. The observed misidentification rates indicated the necessity of keeping more efficient collection of genealogical records, in order to properly control inbreeding or implement a breeding program. The parentage test presented here could be a helpful tool on verifying or even reconstructing the current pedigree data of Valle del Belice dairy sheep breed.
    Small Ruminant Research 05/2013; 113(1). DOI:10.1016/j.smallrumres.2013.03.021 · 1.13 Impact Factor
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