Acta Univ. Agric. Silvic. Mendelianae Brun. 2019, 67(5), 1183-1188 | DOI: 10.11118/actaun201967051183

Deviation Patterns of Observed and Expected Haplotype Blocks Associated with Potential Recessive Disorders in Tyrol Grey Cattle

Maulana Naji1, Cord Drögemüller2, Gábor Mészáros1, Johann Sölkner1
1 Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Gregor-Mendel-Str. 33, A-1180 Vienna, Austria
2 Institute of Genetics, Vetsuisse faculty, University of Bern, Bremgartenstrasse 109a, 3001 Bern, Switzerland

Confirmed by phenotypic records, several studies across different breeds in different locations have linked missing homozygous pattern with several defects in the functional system and recessive genetic disorders. Recessive genetic diseases are expressed when the recessive alleles appear in a homozygous state for an individual. One of the indicators to detect the recessive allele is through haplotypes, which have a normal frequency in the population, but never occur in the homozygous state. In this study, we used SNP genotypes of 220 Austrian Tyrol Grey cattle and 80 Italian Tyrol Grey cattle to identify the haplotype blocks (Hapblocks) that possibly carry genes causing recessive disorders. Hapblocks with missing homozygous state in the population were statistically tested as to whether this is very unlikely in Hardy-Weinberg equilibrium. Eight out of all hapblocks passing the threshold had functional genes which are crucial in maintaining the metabolism, production, reproduction, and health of the individuals. These hapblocks had a high frequency of above 13% but never appear in homozygous state. Thus, these are foreseen as potential source of genetic defects. Our finding in this analysis can be used as a reference for further study in haplotype analyses of inherited recessive disease for other cattle breeds.

Keywords: recessive disease, haplotype, missing homozygous, Tyrol Grey cattle
Grants and funding:

Maulana Naji was granted Erasmus Mundus Alfabet for his MSc and currently receiving Ernst Mach Grant PhD scholarship from OeAD GmbH.

Received: July 22, 2019; Accepted: August 23, 2019; Published: October 31, 2019  Show citation

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Naji, M., Drögemüller, C., Mészáros, G., & Sölkner, J. (2019). Deviation Patterns of Observed and Expected Haplotype Blocks Associated with Potential Recessive Disorders in Tyrol Grey Cattle. Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis, 67(5), 1183-1188. doi: 10.11118/actaun201967051183
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    References

    1. ALLEN-GIPSON, D. S., BLACKBURN, M. R., SCHNEIDER, D. J., ZHANG, H., BLUITT, D. L., JARRELL, J. C., YANOV, D., SISSON, J. H. and WYATT, T. A. 2011. Adenosine activation of A(2B) receptor(s) is essential for stimulated epithelial ciliary motility and clearance. Am. J. Physiol. Lung Cell. Mol. Physiol., 301(2): L171-L180. DOI: 10.1152/ajplung.00203.2010 Go to original source...
    2. CHARLIER, C., LI, W., HARLAND, C., LITTLEJOHN, M., COPPIETERS, W., CREAGH, F., DAVIS, S., DRUET, T., FAUX, P., GUILLAUME, F., KARIM, L., KEEHAN, M., KADRI, N. K., TAMMA, N., SPELMAN, R. and GEORGES, M. 2016. NGS-based reverse genetic screen for common embryonic lethal mutations compromising fertility in livestock. Genome Res., 26: 1333-1341. DOI: 10.1101/gr.207076.116 Go to original source...
    3. DE SOUZA, M. M., NICIURA, S. C. M., TIZIOTO, P. C., IBELLI, A. M. G., GASPARIN, G., ROCHA, M. I. P., BRESSANI, F. A., MALAGO-JR, W., DINIZ, W. J. S., DE OLIVEIRA, P. S. N., LIMA, A. O., MUDADU, M. A., BARIONI JUNIOR, W., COUTINHO, L. L. and REGITANO, L. C. A. 2016. Allele- and parent-of-origin-specific effects on expression of the KCNJ11 gene: A candidate for meat tenderness in cattle. Genet. Mol. Res., 15(3): gmr.15038549. Go to original source...
    4. DELANEAU, O., HOWIE, B., COX, A. J., ZAGURY, J.-F. and MARCHINI, J. 2017. Haplotype Estimation Using Sequencing Reads. Am. J. Hum. Genet., 93(4): 687-696. DOI: 10.1016/j.ajhg.2013.09.002 Go to original source...
    5. DROGEMULLER, C., REICHART, U., SEUBERLICH, T., OEVERMANN, A., BAUMGARTNER, M., KUHNI BOGHENBOR, K., STOFFEL, M. H., SYRING, C., MEYLAN, M., MULLER, S., MULLER, M., GREDLER, B., SOLKNER, J. and LEEB, T. 2011. An unusual splice defect in the mitofusin 2 gene (MFN2) is associated with degenerative axonopathy in Tyrolean Grey cattle. PloS One, 6(4): e18931. DOI: 10.1371/journal.pone.0018931 Go to original source...
    6. FRITZ, S., CAPITAN, A., DJARI, A., RODRIGUEZ, S. C., BARBAT, A., BAUR, A., GROHS, C., WEISS, B., BOUSSAHA, M., ESQUERRÉ, D., KLOPP, C., ROCHA, D. and BOICHARD, D. 2013. Detection of Haplotypes Associated with Prenatal Death in Dairy Cattle and Identification of Deleterious Mutations in GART, SHBG and SLC37A2. PLoS ONE, 8(6): e65550. DOI: 10.1371/journal.pone.0065550 Go to original source...
    7. HULLMANN, J. E., GRISANTI, L. A., MAKAREWICH, C. A., GAO, E., GOLD, J. I., CHUPRUN, J. K., TILLEY, D. G., HOUSER, S. R. and KOCH, W. J. 2014. GRK5-mediated exacerbation of pathological cardiac hypertrophy involves facilitation of nuclear NFAT activity. Circ. Res., 115: 976-985. DOI: 10.1161/CIRCRESAHA.116.304475 Go to original source...
    8. KALCHER, L., FÜRST, C. and EGGER-DANNER, C. 2018. Zentrale Arbeitsgemeinschaft österreichischer Rinderzüc: Jahresbericht 2017. Ried im Innkreis: Hammerer.
    9. KORZEKWA, A. J., MILEWSKI, R., LUPICKA, M. and SKARZYNSKI, D. J. 2016. Leukotriene production profiles and actions in the bovine endometrium during the oestrous cycle. Reprod. Fertil. Dev., 28(6): 682-689. DOI: 10.1071/RD14301 Go to original source...
    10. LI, F., CHEN, H., LEI, C. Z., REN, G., WANG, J., LI, Z. J. and WANG, J. Q. 2010. Novel SNPs of the bovine NUCB2 gene and their association with growth traits in three native Chinese cattle breeds. Mol. Biol. Rep., 37(1): 541-546. DOI: 10.1007/s11033-009-9732-y Go to original source...
    11. MURGIANO, L., JAGANNATHAN, V., BENAZZI, C., BOLCATO, M., BRUNETTI, B., MUSCATELLO, L. V., DITTMER, K., PIFFER, C., GENTILE, A. and DROGEMULLER, C. 2014. Deletion in the EVC2 gene causes chondrodysplastic dwarfism in Tyrolean Grey cattle. PloS One 9(7): e94861. DOI: 10.1371/journal.pone.0094861 Go to original source...
    12. MURGIANO, L., JAGANNATHAN, V., PIFFER, C., DIEZ-PRIETO, I., BOLCATO, M., GENTILE, A. and DRÖGEMÜLLER, C. 2016. A frameshift mutation in MOCOS is associated with familial renal syndrome (xanthinuria) in Tyrolean Grey cattle. BMC Vet. Res., 12: 276. DOI: 10.1186/s12917-016-0904-4 Go to original source...
    13. PANT, S. D., VERSCHOOR, C. P., SCHENKEL, F. S., YOU, Q., KELTON, D. F. and KARROW, N. A. 2014. Bovine CLEC7A genetic variants and their association with seropositivity in Johne's disease ELISA. Gene, 537(2): 302-307. DOI: 10.1016/j.gene.2013.12.020 Go to original source...
    14. PURCELL, S. and CHANG, C. 2017. PLINK [version]. [Program]. Copyright Christopher Chang.
    15. SAHANA, G., NIELSEN, U. S., AAMAND, G. P., LUND, M. S. and GULDBRANDTSEN, B. 2013. Novel harmful recessive haplotypes identified for fertility traits in Nordic Holstein cattle. PLoS ONE, 8(8): e82909. DOI: 10.1371/journal.pone.0082909 Go to original source...
    16. SÖLKNER, J., GREDLER, B., DRÖGEMÜLLER, C. and LEEB, T. 2009. Homozygosity mapping of a weaver-like disorder in Tyrol Grey cattle. In: Annual Conference of the European Association for Animal Production. August 24th-27th. Barcelona, Spain.
    17. UTSUNOMIYA, Y. T. and MILANESI, M. 2017. Package package for genome-wide haplotyping GHap. [Program].
    18. VAN RADEN, P. M., OLSON, K. M., NULL, D. J. and HUTCHISON, J. L. 2011. Harmful recessive effects on fertility detected by absence of homozygous haplotypes. J. Dairy Sci., 94(12): 6153-6161. DOI: 10.3168/jds.2011-4624 Go to original source...
    19. WALSH, C. P., DAVIES, A., BUTCHER, A. J., DOLPHIN, A. C. and KITMITTO, A. 2009. Three-dimensional structure of CaV3.1: comparison with the cardiac L-type voltage-gated calcium channel monomer architecture. J. Biol. Chem., 284: 22310-22321. DOI: 10.1074/jbc.M109.017152 Go to original source...
    20. WANG, X., LI, T., ZHAO, H. B. and KHATIB, H. 2013. Short communication: A mutation in the 3' untranslated region diminishes microRNA binding and alters expression of the OLR1 gene. J. Dairy Sci., 96(10): 6525-6528. DOI: 10.3168/jds.2013-6873 Go to original source...
    21. XU, L., ZHANG, L. P., YUAN, Z. R., GUO, L. P., ZHU, M., GAO, X., GAO, H. J., LI, J. Y. and XU, S. Z. 2013. Polymorphism of SREBP1 is associated with beef fatty acid composition in Simmental bulls. Genet. Mol. Res., GMR 12(4): 5802-5809. DOI: 10.4238/2013.November.22.7 Go to original source...
    22. ZHANG, Q., ZHAO, S., CHEN, H., ZHANG, L., ZHANG, L., LI, F. and WANG, X. 2011. SNP discovery and haplotype analysis in the bovine PRKAA2 gene. Mol. Biol. Rep., 38(3): 1551-1556. DOI: 10.1007/s11033-010-0263-3 Go to original source...
    23. ZHAO, F.-Q., ZHENG, Y.-C., WALL, E. H. and MCFADDEN, T. B. 2005. Cloning and expression of bovine sodium/glucose cotransporters. J. Dairy Sci., 88(1): 182-194. DOI: 10.3168/jds.S0022-0302(05)72677-1 Go to original source...

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