The Effect of Using DNA Obtained from Blood of Cattle with Genetic Chimerism on Illumina’s Beadchip Assay Performance

Open access

Abstract

Blood cell chimerism is a common phenomenon occurring in cattle coming from double or multiple parturitions and can be observed as two DNA profiles present in blood of each of twin born animals. In the era of genomics, a large number of animals is being genotyped with high throughput genotyping methods, which are giving limited insight into the performance of single markers and rather only statistical description of the results is available for a common user. This hampers the detailed analysis of the results obtained and direct identification of the causes of poorer performance of some samples. In this study we describe the influence of analysis of DNA obtained from blood samples of cattle with genetic chimerism on basic parameters of Infinium technology-based Illumina’s genotyping arrays. The results obtained may help to identify such samples, especially when no precise information about the animals’ origin is available

Anderson D., Billingham R.E., Lampkin G.H., Madawar P.B. (1951). The use of skingrafting to distinguish between monozygotic and dizygotic twins in cattle. Heredity, 5: 379-397.

Basrur P.K., Kanagawa H. (1969). Parallelism in chimeric ratios in heterosexual cattle twins. Genetics, 63: 419-425.

Buoen L.C., Zhang T.Q., Veber A.F., Ruth G.R. (1992). Non-freemartin rate in Holstein heterosexual twins. Am. Assoc. Bov. Pract. Confr., 1: 300-303.

Cady R.A., Van Vleck L.D. (1978). Factors affecting twinning and effects of twinning in Holstein dairy cattle. J. Anim. Sci., 46: 950-956.

Conlin L.K., Thiel B.D., Bonnemann C.G., Medne L., Ernst L.M., Zackai E.H., Deardorff M.A., Krantz I.D., Hakonarson H., Spinner N.B. (2010). Mechanisms of mosaicism, chimerism and uniparental disomy identified by single nucleotide polymorphism array analysis. Hum. Mol. Genet., 19: 1263-1275.

Craig D.W., Millis M.P., Di Stefano J.K. (2009). Genome-wide SNPgenotyping study using pooled DNAto identify candidate markers mediating susceptibility to end-stage renal disease attributed to Type 1 diabetes. Diabet. Med., 26: 1090-1098.

Fricke P.M. (2001). Review: Twinning in Dairy Cattle. Prof. Anim. Sci., 17: 61-67.

Hayes B.J., Bowman P.J., Chamberlain A.C., Verbyla K., Goddard M.E. (2009). Accuracy of genomic breeding values in multi-breed dairy cattle populations. Genet. Sel. Evol., 41: 51.

Holl H.M., Lear T.L., Nolen-Walston R.D., Slack J., Brooks S.A. (2013). Detection of two equine trisomies using SNP-CGH. Mamm. Genome, 24: 252-256.

Komisarek J., Dorynek Z.J. (2002). Genetic aspects of twinning in cattle. J. Appl. Genet., 43: 55-68.

Meaburn E., Butcher L.M., Liu L., Fernandes C., Hansen V., Al - Chalabi A., Plo- min R., Craig I., Schalkwyk L.C. (2005). Genotyping DNApools on microarrays: tackling the QTLproblem of large samples and large numbers of SNPs. BMC Genomics, 6: 52.

Metzger J., Philipp U., Lopes M.S.,da Camara Machado A., Felicetti M., Sil -vestrelli M., Distl O. (2013). Analysis of copy number variants by three detection algorithms and their association with body size in horses. BMC Genomics, 14: 487.

Nielen M., Schukken Y.H., Scholl D.T., Wilbrink H.J., Brand A. (1989). Twinning in dairy cattle:astudy of risk factors and effects. Theriogenology, 32: 845-862.

Niku M., Pessa-Morikawa T., Taponen J., Iivanainen A. (2007). Direct observation of hematopoietic progenitor chimerism in fetal freemartin cattle. BMC Vet. Res., 3: 29.

Peiris B.L., Ralph J., Lamont S.J., Dekkers J.C. (2011) Predicting allele frequencies in DNA pools using high density SNPgenotyping data. Anim. Genet., 42: 113-116.

Radko A., Słota E., Marczyńska J. (2010). Usefulness ofasupplementary set of microsatellite DNAmarkers for parentage testing in cattle. Pol. J. Vet. Sci., 13: 313-318.

Staaf J., Vallon - Christersson J., Lindgren D., Juliusson G., Rosenquist R., Hög lund M., Borg A., Ringnér M. (2008). Normalization of Illumina Infinium whole-genome SNPdata improves copy number estimates and allelic intensity ratios. BMC Bioinformatics, 9: 409.

Szyda J., Żarnecki A., Suchocki T., Kamiński S. (2011). Fitting and validating the genomic evaluation model to Polish Holstein-Friesian cattle. J. Appl. Genet., 52: 363-366.

Vigier B., Watrin F., Magre S., Tran D., Garrigou O., Forest M.G., Josso N. (1988). Anti-mullerian hormone and freemartinism: inhibition of germ cell development and induction of seminiferous cord-like structures in rat fetal ovaries exposed in vitro to purified bovine AMH. Reprod. Nutr. Dev., 28: 1113-1128.

Vigier B., Magre S., Charpentier G., Bezard J., Josso N. (1991). Anti-mullerian hormone and natural and experimental freemartin effect. Bull. Assoc. Anat., 75: 29-32.

Zhang T.Q., Buoen L.C., Seguin B.E., Ruth G.R., Weber A.F. (1994). Diagnosis of freemartinism in cattle: the need for clinical and cytogenetic evaluation. J. Am. Vet. Med. Assoc., 204: 1672-1675.

Annals of Animal Science

The Journal of National Research Institute of Animal Production

Journal Information


IMPACT FACTOR 2017: 1.018
5-year IMPACT FACTOR: 0.959



CiteScore 2017: 1.01

SCImago Journal Rank (SJR) 2017: 0.413
Source Normalized Impact per Paper (SNIP) 2017: 0.822

Metrics

All Time Past Year Past 30 Days
Abstract Views 0 0 0
Full Text Views 139 139 13
PDF Downloads 49 49 5