Research Article
BibTex RIS Cite

Year 2018, Volume: 65 Issue: 4, 387 - 393, 09.11.2018

Burak Karacaören

https://doi.org/10.1501/Vetfak_0000002872

Abstract

References

  • 1. Boehnke M, Langefeld CD (1998): Genetic association mapping based on discordant sib pairs: the discordantalleles test. Am J Hum Genet, 62, 950-961.
  • 2. Endelman JB (2011): Ridge regression and other kernels for genomic selection with R package rrBLUP. The Plant Genome, 4, 250-255.
  • 3. Everitt BS, Landau S, Leese M (2001): Cluster Analysis. National Academy Press, Washington, DC
  • 4. Gao H, Zhang T, Wu Y, et al (2014): Multiple-trait genome-wide association study based on principal component analysis for residual covariance matrix. Heredity, 113, 526-532.
  • 5. Gianola D, de los Campos G, Toro, MA, et al (2015). Do molecular markers inform about pleiotropy? Genetics, 201, 23-29.
  • 6. Goddard, ME, Kemper, KE, Macleod, IM, et al (2016): Genetics of complex traits: prediction of phenotype, identification of causal polymorphisms and genetic architecture. In Proc. R. Soc. B, 283, 20160569.
  • 7. Gratten J, Visscher PM (2016): Genetic pleiotropy in complex traits and diseases: implications for genomic medicine. Genom Med, 8, 78.
  • 8. Hartley SW, Monti S, Liu CT, et al (2012): Bayesian methods for multivariate modeling of pleiotropic SNP associations and genetic risk prediction. Front genet, 3, 176.
  • 9. Hill WG (2010): Understanding and using quantitative genetic variation. Philosophical Transactions of the Royal Society of London B: Biological Sciences, 365, 73-85.
  • 10. Karacaören B (2016): Investigations on Genetic Architecture of Hairy Loci in Dairy Cattle by Using Single and Whole Genome Regression Approaches. AsianAustralas j anim sci, 29, 938.
  • 11. Karacaören B, de Koning DJ, Velander I, et al (2010): Alternative association analyses on boar taint using discordant sib pairs experimental design. In 9th World Congress on Genetics Applied to Livestock Production, Leipzig, Germany. 743 p.
  • 12. Karacaören B. (2012): Some observations for discordant sib pair design using QTL-MAS 2010 dataset. Kafkas Vet Fak Derg, 18, 857-860.
  • 13. Leong W, Sun PY, Edmands S. (2017): Latitudinal clines in temperature and salinity tolerance in tidepool copepods. J. Hered, 109, 71-77.
  • 14. Liu J, Wan X, Ma S, Yang C. (2016): EPS: an empirical Bayes approach to integrating pleiotropy and tissuespecific information for prioritizing risk genes. Bioinformatics, 32, 1856-1864.
  • 15. Meuwissen THE, Hayes BJ, Goddard ME (2001): Prediction of total genetic value using genome wide dense marker maps. Genetics 157, 1819-1829.
  • 16. Moser G, Lee HS, Hayes BJ, et al (2015): Simultaneous discovery, estimation and prediction analysis of complex traits using a bayesian mixture model. PLoS. Genet. 11, e1004969.
  • 17. R Development Core Team (2013): R: A language and environmental for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
  • 18. Shriner D (2012): Moving toward system genetics through multiple trait analysis in genome-wide association studies. Front Genet, 3, 1.
  • 19. Solovieff N, Cotsapas C, Lee PH, et al (2013): Pleiotropy in complex traits: challenges and strategies. Nat Rev Genet, 14, 483-495.
  • 20. Storchova R, Gregorova S, Buckiova D, et al (2004) Genetic analysis of X-linked hybrid sterility in the house mouse. Mamm. Genome, 15, 515-524.
  • 21. Turner LM, Harr B. (2014): Genome-wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky-Muller interactions. Elife, 3, e02504.
  • 22. Usai MG, GaspaG, Macciotta NP, et al (2014): XVI th QTLMAS: simulated dataset and comparative analysis of submitted results for QTL mapping and genomic evaluation. In BMC proceedings (Vol. 8, No. 5, p. S1). BioMed Central.
  • 23. Visscher PM, Yang J (2016): A plethora of pleiotropy across complex traits. Nat Genet, 48, 707-708.
  • 24. Wang L, Oehlers SH, Espenschied ST, et al (2015): CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation. Genome biol, 16, 190.
  • 25. White, MA, Stubbings M, Dumont BL, et al (2012): Genetics and evolution of hybrid male sterility in house mice. Genetics, 191, 917-934.
  • 26. Yang J, Benyamin B, McEvoy BP, et al (2010): Common SNPs explain a large proportion of the heritability for human height. Nat Genet, 42, 565-569.
  • 27. Yu J, Pressoir G, Briggs WH, et al (2006): A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat genet, 38, 203-208

A genomic investigation on hybrid sterility in house mouse using a two stage model

Year 2018, Volume: 65 Issue: 4, 387 - 393, 09.11.2018

Burak Karacaören

https://doi.org/10.1501/Vetfak_0000002872

Abstract

Genome wide association studies (GWASs) commonly used to search for genetic variants associated with
quantitative traits. Pleiotropic effect of genes may cause the observed correlations among different phenotypes. This study proposed a
two stage multilocus model for pleiotropic GWAS using a Bayesian mixture model to take into account of both small and major gene
effects. The objectives of this study were to investigate if the two-stage model was useful for detecting pleiotropic genes using a
simulated data set and to investigate existence of pleiotropic genes for testis weight and testis gene expression levels in house mouse.
The analyses included relative testis weight and testis gene expression traits. The results showed that two stage model had higher power
to detect the pleiotropic QTL than the single marker model. It was also noted the possible economical impact of sampling informative
individuals for the GWAS analyses by observing genomic trends in the simulated dataset. Two stage model detected 50 and 53 major
SNP effects using first and the second principal components. Additive genetic variation explained by chromosome X was found to be
4% for the testis weight.  

Keywords

Bayesian mixture model genome wide association analyses pleiotropy

References

  • 1. Boehnke M, Langefeld CD (1998): Genetic association mapping based on discordant sib pairs: the discordantalleles test. Am J Hum Genet, 62, 950-961.
  • 2. Endelman JB (2011): Ridge regression and other kernels for genomic selection with R package rrBLUP. The Plant Genome, 4, 250-255.
  • 3. Everitt BS, Landau S, Leese M (2001): Cluster Analysis. National Academy Press, Washington, DC
  • 4. Gao H, Zhang T, Wu Y, et al (2014): Multiple-trait genome-wide association study based on principal component analysis for residual covariance matrix. Heredity, 113, 526-532.
  • 5. Gianola D, de los Campos G, Toro, MA, et al (2015). Do molecular markers inform about pleiotropy? Genetics, 201, 23-29.
  • 6. Goddard, ME, Kemper, KE, Macleod, IM, et al (2016): Genetics of complex traits: prediction of phenotype, identification of causal polymorphisms and genetic architecture. In Proc. R. Soc. B, 283, 20160569.
  • 7. Gratten J, Visscher PM (2016): Genetic pleiotropy in complex traits and diseases: implications for genomic medicine. Genom Med, 8, 78.
  • 8. Hartley SW, Monti S, Liu CT, et al (2012): Bayesian methods for multivariate modeling of pleiotropic SNP associations and genetic risk prediction. Front genet, 3, 176.
  • 9. Hill WG (2010): Understanding and using quantitative genetic variation. Philosophical Transactions of the Royal Society of London B: Biological Sciences, 365, 73-85.
  • 10. Karacaören B (2016): Investigations on Genetic Architecture of Hairy Loci in Dairy Cattle by Using Single and Whole Genome Regression Approaches. AsianAustralas j anim sci, 29, 938.
  • 11. Karacaören B, de Koning DJ, Velander I, et al (2010): Alternative association analyses on boar taint using discordant sib pairs experimental design. In 9th World Congress on Genetics Applied to Livestock Production, Leipzig, Germany. 743 p.
  • 12. Karacaören B. (2012): Some observations for discordant sib pair design using QTL-MAS 2010 dataset. Kafkas Vet Fak Derg, 18, 857-860.
  • 13. Leong W, Sun PY, Edmands S. (2017): Latitudinal clines in temperature and salinity tolerance in tidepool copepods. J. Hered, 109, 71-77.
  • 14. Liu J, Wan X, Ma S, Yang C. (2016): EPS: an empirical Bayes approach to integrating pleiotropy and tissuespecific information for prioritizing risk genes. Bioinformatics, 32, 1856-1864.
  • 15. Meuwissen THE, Hayes BJ, Goddard ME (2001): Prediction of total genetic value using genome wide dense marker maps. Genetics 157, 1819-1829.
  • 16. Moser G, Lee HS, Hayes BJ, et al (2015): Simultaneous discovery, estimation and prediction analysis of complex traits using a bayesian mixture model. PLoS. Genet. 11, e1004969.
  • 17. R Development Core Team (2013): R: A language and environmental for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
  • 18. Shriner D (2012): Moving toward system genetics through multiple trait analysis in genome-wide association studies. Front Genet, 3, 1.
  • 19. Solovieff N, Cotsapas C, Lee PH, et al (2013): Pleiotropy in complex traits: challenges and strategies. Nat Rev Genet, 14, 483-495.
  • 20. Storchova R, Gregorova S, Buckiova D, et al (2004) Genetic analysis of X-linked hybrid sterility in the house mouse. Mamm. Genome, 15, 515-524.
  • 21. Turner LM, Harr B. (2014): Genome-wide mapping in a house mouse hybrid zone reveals hybrid sterility loci and Dobzhansky-Muller interactions. Elife, 3, e02504.
  • 22. Usai MG, GaspaG, Macciotta NP, et al (2014): XVI th QTLMAS: simulated dataset and comparative analysis of submitted results for QTL mapping and genomic evaluation. In BMC proceedings (Vol. 8, No. 5, p. S1). BioMed Central.
  • 23. Visscher PM, Yang J (2016): A plethora of pleiotropy across complex traits. Nat Genet, 48, 707-708.
  • 24. Wang L, Oehlers SH, Espenschied ST, et al (2015): CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation. Genome biol, 16, 190.
  • 25. White, MA, Stubbings M, Dumont BL, et al (2012): Genetics and evolution of hybrid male sterility in house mice. Genetics, 191, 917-934.
  • 26. Yang J, Benyamin B, McEvoy BP, et al (2010): Common SNPs explain a large proportion of the heritability for human height. Nat Genet, 42, 565-569.
  • 27. Yu J, Pressoir G, Briggs WH, et al (2006): A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat genet, 38, 203-208
There are 27 citations in total.

Details

Primary Language English
Subjects Veterinary Surgery
Journal Section Research Article
Authors

Burak Karacaören

Publication Date November 9, 2018
Published in Issue Year 2018Volume: 65 Issue: 4

Cite

APA Karacaören, B. (2018). A genomic investigation on hybrid sterility in house mouse using a two stage model. Ankara Üniversitesi Veteriner Fakültesi Dergisi, 65(4), 387-393. https://doi.org/10.1501/Vetfak_0000002872
AMA Karacaören B. A genomic investigation on hybrid sterility in house mouse using a two stage model. Ankara Univ Vet Fak Derg. November 2018;65(4):387-393. doi:10.1501/Vetfak_0000002872
Chicago Karacaören, Burak. “A Genomic Investigation on Hybrid Sterility in House Mouse Using a Two Stage Model”. Ankara Üniversitesi Veteriner Fakültesi Dergisi 65, no. 4 (November 2018): 387-93. https://doi.org/10.1501/Vetfak_0000002872.
EndNote Karacaören B (November 1, 2018) A genomic investigation on hybrid sterility in house mouse using a two stage model. Ankara Üniversitesi Veteriner Fakültesi Dergisi 65 4 387–393.
IEEE B. Karacaören, “A genomic investigation on hybrid sterility in house mouse using a two stage model”, Ankara Univ Vet Fak Derg, vol. 65, no. 4, pp. 387–393, 2018, doi: 10.1501/Vetfak_0000002872.
ISNAD Karacaören, Burak. “A Genomic Investigation on Hybrid Sterility in House Mouse Using a Two Stage Model”. Ankara Üniversitesi Veteriner Fakültesi Dergisi 65/4 (November 2018), 387-393. https://doi.org/10.1501/Vetfak_0000002872.
JAMA Karacaören B. A genomic investigation on hybrid sterility in house mouse using a two stage model. Ankara Univ Vet Fak Derg. 2018;65:387–393.
MLA Karacaören, Burak. “A Genomic Investigation on Hybrid Sterility in House Mouse Using a Two Stage Model”. Ankara Üniversitesi Veteriner Fakültesi Dergisi, vol. 65, no. 4, 2018, pp. 387-93, doi:10.1501/Vetfak_0000002872.
Vancouver Karacaören B. A genomic investigation on hybrid sterility in house mouse using a two stage model. Ankara Univ Vet Fak Derg. 2018;65(4):387-93.