Development of SNP markers for individual identification and parentage test in a Japanese Black cattle population

Hara, Kazuhiro; Watabe, H.; Sasazaki, Shinji; Mukai, Fumio; Mannen, Hideyuki

doi:10.1111/j.1740-0929.2009.00720.x

Cited by 11 publications

(10 citation statements)

References 24 publications

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“…Previous studies designed strategies to sample the entire genetic diversity in beef cattle or purebred populations and simulated populations of purebred gene frequencies have been used to estimate the resolution and sensitivity of these methods in identifying individuals and in parental analysis (Table S7) (Heaton et al , 2002; Werner et al , 2004; López Herráez et al , 2005; Van Eenennaam et al , 2007; Baruch and Weller, 2008; Karniol et al , 2009; Allen et al , 2010; Hara et al , 2010a,b). …”

Section: Introductionmentioning

confidence: 99%

Comparison of the effectiveness of microsatellites and SNP panels for genetic identification, traceability and assessment of parentage in an inbred Angus herd

et al. 2013

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During the last decade, microsatellites (short tandem repeats or STRs) have been successfully used for animal genetic identification, traceability and paternity, although in recent year single nucleotide polymorphisms (SNPs) have been increasingly used for this purpose. An efficient SNP identification system requires a marker set with enough power to identify individuals and their parents. Genetic diagnostics generally include the analysis of related animals. In this work, the degree of information provided by SNPs for a consanguineous herd of cattle was compared with that provided by STRs. Thirty-six closely related Angus cattle were genotyped for 18 STRs and 116 SNPs. Cumulative SNPs exclusion power values (Q) for paternity and sample matching probability (MP) yielded values greater than 0.9998 and 4.32E−42, respectively. Generally 2–3 SNPs per STR were needed to obtain an equivalent Q value. The MP showed that 24 SNPs were equivalent to the ISAG (International Society for Animal Genetics) minimal recommended set of 12 STRs (MP ∼ 10−11). These results provide valuable genetic data that support the consensus SNP panel for bovine genetic identification developed by the Parentage Recording Working Group of ICAR (International Committee for Animal Recording).

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Section: Introductionmentioning

confidence: 99%

Comparison of the effectiveness of microsatellites and SNP panels for genetic identification, traceability and assessment of parentage in an inbred Angus herd

et al. 2013

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“…Parentage exclusion probabilities when both suspected parents' genotypes were known ( P E2 ) and parentage exclusion probabilities when only one suspected parent was genotyped ( P E1 ) were computed as described (Jamieson & Taylor 1997). Detail s of formulas of P I , P E2 and P E1 were described in our previous study (Hara et al . in press).…”

Section: Methodsmentioning

confidence: 99%

“…In our previous study, 29 SNP markers for Japanese Black cattle were developed by amplified fragment length polymorphisms (AFLP) method. The SNP panel possessed sufficient probability (2.73 × 10 −12 ) for individual identification in Japanese Black populations (Hara et al . in press).…”

Section: Introductionmentioning

confidence: 99%

Development of novel SNP system for individual and pedigree control in a Japanese Black cattle population using whole‐genome genotyping assay

Hara

Kon

Sasazaki

et al. 2010

Animal Science Journal

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Individual identification and parentage analysis using DNA markers are essential for assuring food identity and managing livestock population. The objective of this study was to develop a single nucleotide polymorphism (SNP) panel system for individual effective identification and parentage testing in a Japanese Black cattle population using BovineSNP50 BeadChip. On the basis of SNP frequencies, 60 unlinked informative SNPs were finally selected as candidate markers. The allelic frequencies for each SNP were estimated using additional individuals by PCR-RFLP (restriction fragment length polymorphism). A total of 87 SNP markers added in conjunction with previously developed 27 SNPs were evaluated to assess the utility of the test. The estimated identity power was 2.01 ¥ 10 -34 . Parentage exclusion probabilities, when both suspected parents' genotypes were known and when only one suspected parent was genotyped, were estimated as 0.99999997 and 0.99998010, respectively. This developed SNP panel was quite powerful and could successfully exclude false sires with a probability of >0.9999 even if the dam's genotype information was not obtained. The SNP system would contribute to management of the beef industry in Japan.

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“…1662 Harliziiis et al Several SNP panels have been developed and evaluated for parentage testing in cattle (Heaton et al, 2002;Van Eenennaam et al, 2007;Fisher et al, 2009;Hará et al, 2010). Single nucleotide polymorphism sets for parental verification have also been developed in pigs (Goffaux et al, 2005;Ballester et al, 2007;Rohrer et al, 2007).…”

Section: Introductionmentioning

confidence: 97%

A single nucleotide polymorphism set for paternal identification to reduce the costs of trait recording in commercial pig breeding1,2

Harlizius¹,

Lopes

Duijvesteijn³

et al. 2011

Journal of Animal Science

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In animal breeding, recording of correct pedigrees is essential to achieve genetic progress. Markers on DNA are useful to verify the on-farm pedigree records (parental verification) but can also be used to assign parents retrospectively (parental identification). This approach could reduce the costs of recording for traits with low incidence, such as those related to diseases or mortality. In this study, SNP were used to assign the true sires of 368 purebred animals from a Duroc-based sire line and 140 crossbred offspring from a commercial pig population. Some of the sires were closely related. There were 3 full sibs and 17 half sibs among the true fathers and 4 full sibs and 35 half sibs among all putative fathers. To define the number of SNP necessary, 5 SNP panels (40, 60, 80, 100, and 120 SNP) were assembled from the Illumina PorcineSNP60 Beadchip (Illumina, San Diego, CA) based on minor allele frequency (>0.3), high genotyping call rate (≥90%), and equal spacing across the genome. For paternal identification considering only the 66 true sires in the data set, 60 SNP resulted in 100% correct assignment of the sire. By including additional putative sires (n = 304), 80 SNP were sufficient for 100% correct assignment of the sire. The following criteria were derived to identify the correct sire for the current data set: the logarithm of odds (LOD) score for assigning the correct sire was ≥5, the number of mismatches was ≤1, and the difference in the LOD score between the first and the second most likely sire was >5. If the correct sire was not present among all putative sires, the mean LOD for the most likely sire was close to zero or negative when using 100 SNP. More SNP would be needed for paternal identification if the number of putative sires increased and the degree of relatedness was greater than in the data set used here. The threshold for the number of mismatches can be adjusted according to the practical situation to account for the trade-off between false negatives and false positives. The latter can be avoided efficiently, ensuring that the correct father is being sampled. Nevertheless, a restriction on the number of putative sires is advisable to reduce the risk of assigning close relatives.

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Development of SNP markers for individual identification and parentage test in a Japanese Black cattle population

Cited by 11 publications

References 24 publications

Comparison of the effectiveness of microsatellites and SNP panels for genetic identification, traceability and assessment of parentage in an inbred Angus herd

Comparison of the effectiveness of microsatellites and SNP panels for genetic identification, traceability and assessment of parentage in an inbred Angus herd

Development of novel SNP system for individual and pedigree control in a Japanese Black cattle population using whole‐genome genotyping assay

A single nucleotide polymorphism set for paternal identification to reduce the costs of trait recording in commercial pig breeding1,2

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