307
Views
1
CrossRef citations to date
0
Altmetric
Genetics

Identification of potential genomic regions for egg weight by a haplotype-based genome-wide association study using Bayesian methods

, , & ORCID Icon
Pages 251-257 | Received 22 Jul 2019, Accepted 15 Dec 2019, Published online: 26 Feb 2020

References

  • Boichard, D., G. Francois, B. Aurélia, C. Pascal, R. Marie-Noelle, Y. B. Marie, D. Tom, G. Lucie, C. Jean-Jacques, and L. Journaux. 2012. “Genomic Selection in French Dairy Cattle.” Animal Production Science 52 (3): 115–120.
  • Browning, B. L., and S. R. Browning. 2009. “A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals.” The American Journal of Human Genetics 84 (2): 210–223. doi:10.1016/j.ajhg.2009.01.005.
  • Brückner, K., J. P. Labrador, P. Scheiffele, A. Herb, P. H. Seeburg, and R. Klein. 1999. “EphrinB Ligands Recruit GRIP Family PDZ Adaptor Proteins into Raft Membrane Microdomains.” Neuron 22 (3): 511–524. doi:10.1016/S0896-6273(00)80706-0.
  • Cantor, R. M., K. Lange, and J. S. Sinsheimer. 2010. “Prioritizing GWAS Results: A Review of Statistical Methods and Recommendations for Their Application.” The American Journal of Human Genetics 86 (1): 6–22. doi:10.1016/j.ajhg.2009.11.017.
  • Cattaruzzi, G., S. Altamura, M. A. Tessari, A. Rustighi, V. Giancotti, C. Pucillo, and G. Manfioletti. 2007. “The Second AT-Hook of the Architectural Transcription Factor HMGA2 Is Determinant for Nuclear Localization and Function.” Nucleic Acids Research 35 (6): 1751–1760. doi:10.1093/nar/gkl1106.
  • Cuyabano, B. C. D., G. Su, and M. S. Lund. 2015. “Selection of Haplotype Variables from a High-Density Marker Map for Genomic Prediction.” Genetics Selection Evolution 47 (1): 61. doi:10.1186/s12711-015-0143-3.
  • Delgado, T. C. 2013. “Glutamate and GABA in Appetite Regulation.” Frontiers in Endocrinology 4: 103. doi:10.3389/fendo.2013.00103.
  • Garrick, D. J., and R. L. Fernando. 2013. “Implementing a QTL Detection Study (GWAS) Using Genomic Prediction Methodology.” In Genome-Wide Association Studies and Genomic Prediction, edited by C. Gondro, J. H. J. van der Werf, and B. Hayes, 275–298. Berlin: Springer Series.
  • Goraga, Z. S., M. K. Nassar, and G. A. Brockmann. 2012. “Quantitative Trait Loci Segregating in Crosses between New Hampshire and White Leghorn Chicken Lines: I. Egg Production Traits.” Animal Genetics 43 (2): 183–189. doi:10.1111/age.2012.43.issue-2.
  • Goto, T., A. Ishikawa, N. Goto, M. Nishibori, T. Umino, and M. Tsudzuki. 2014. “Mapping of Main-Effect and Epistatic Quantitative Trait Loci for Internal Egg Traits in an F2 Resource Population of Chickens.” The Journal of Poultry Science 51: 375–386. doi:10.2141/ jpsa.0140030.
  • Guilherme, A., N. A. Soriano, P. S. Furcinitti, and M. P. Czech. 2004. “Role of EHD1 and EHBP1 in Perinuclear Sorting and Insulin-Regulated GLUT4 Recycling in 3T3-L1 Adipocytes.” Journal of Biological Chemistry 279 (38): 40062–40075. doi:10.1074/jbc.M401918200.
  • Hansen, C., Y. Nengjun, Y. M. Zhang, X. Shizhong, J. Gavora, and H. H. Cheng. 2005. “Identification of QTL for Production Traits in Chickens.” Animal Biotechnology 16 (1): 67–79. doi:10.1081/ABIO-200055016.
  • Hess, M., T. Druet, A. Hess, and D. Garrick. 2017. “Fixed-Length Haplotypes Can Improve Genomic Prediction Accuracy in an Admixed Dairy Cattle Population.” Genetics Selection Evolution 49 (1): 54. doi:10.1186/s12711-017-0329-y.
  • Huang, D. W., B. T. Sherman, and R. A. Lempicki. 2009. “Systematic and Integrative Analysis of Large Gene Lists Using DAVID Bioinformatics Resources.” Nature Protocols 4 (1): 44–57. doi:10.1038/nprot.2008.211.
  • Karimi, Z., M. Sargolzaei, J. A. B. Robinson, and F. S. Schenkel. 2018. “Assessing Haplotype-Based Models for Genomic Evaluation in Holstein Cattle.” Canadian Journal of Animal Science 98 (4): 750–759.
  • Kerje, S., Ö. Carlborg, L. Jacobsson, K. Schütz, C. Hartmann, P. Jensen, and L. Andersson. 2003. “The Twofold Difference in Adult Size between the Red Junglefowl and White Leghorn Chickens Is Largely Explained by a Limited Number of QTLs.” Animal Genetics 34 (4): 264–274. doi:10.1046/j.1365-2052.2003.01000.x.
  • Kranis, A., A. A. Gheyas, C. Boschiero, F. Turner, S. Le Yu, R. T. Smith, A. Pirani, F. Brew, and P. Kaiser. 2013. “Development of a High Density 600K SNP Genotyping Array for Chicken.” BMC Genomics 14 (1): 59. doi:10.1186/1471-2164-14-59.
  • Kudinov, A. A., N. V. Dementieva, O. V. Mitrofanova, O. I. Stanishevskaya, E. S. Fedorova, T. A. Larkina, A. I. Mishina, K. V. Plemyashov, D. K. Griffin, and M. N. Romanov. 2019. “Genome-Wide Association Studies Targeting the Yield of Extraembryonic Fluid and Production Traits in Russian White Chickens.” BMC Genomics 20 (1): 270. doi:10.1186/s12864-019-5605-5.
  • Liao, R., X. Zhang, Q. Chen, Z. Wang, Q. Wang, C. Yang, and Y. Pan. 2016. “Genome‐wide Association Study Reveals Novel Variants for Growth and Egg Traits in Dongxiang Blue‐shelled and White Leghorn Chickens.” Animal Genetics 47 (5): 588–596. doi:10.1111/age.12456.
  • Liu, Z., C. Sun, Y. Yan, L. Guangqi, W. Guiqin, A. Liu, and N. Yang. 2018. “Genome-Wide Association Analysis of Age-Dependent Egg Weights in Chickens.” Frontiers in Genetics 9. doi:10.3389/fgene.2018.00128.
  • Meuwissen, T., B. Hayes, and M. Goddard. 2001. “Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps.” Genetics 157: 1819–1829.
  • Meuwissen, T. H. E., J. Odegard, I. Andersen-Ranberg, and E. Grindflek. 2014. “On the Distance of Genetic Relationships and the Accuracy of Genomic Prediction in Pig Breeding.” Genetics Selection Evolution 46 (1): 49. doi:10.1186/1297-9686-46-49.
  • Mi, H., X. Huang, A. Muruganujan, H. Tang, C. Mills, D. Kang, and P. D. Thomas. 2016. “PANTHER Version 11: Expanded Annotation Data from Gene Ontology and Reactome Pathways, and Data Analysis Tool Enhancements.” Nucleic Acids Research 45 (D1): D183–89. doi:10.1093/nar/gkw1138.
  • Niknafs, S., A. Nejati-Javaremi, H. Mehrabani-Yeganeh, and S. A. Fatemi. 2012. “Estimation of Genetic Parameters for Body Weight and Egg Production Traits in Mazandaran Native Chicken.” Tropical Animal Health and Production 44 (7): 1437–1443. doi:10.1007/s11250-012-0084-6.
  • Schneider, M. R., and W. Barendse. 2011. “Haplotype Analysis Improved Evidence for Candidate Genes for Intramuscular Fat Percentage from a Genome Wide Association Study of Cattle.” PloS One 6 (12): e29601. doi:10.1371/journal.pone.0029601.
  • Setou, M., D.-H. Seog, Y. Tanaka, Y. Kanai, Y. Takei, M. Kawagishi, and N. Hirokawa. 2002. “Glutamate-Receptor-Interacting Protein GRIP1 Directly Steers Kinesin to Dendrites.” Nature 417 (6884): 83. doi:10.1038/nature743.
  • Spalona, A., H. A. N. S. Ranvig, K. Cywa-Benko, A. Zanon, A. Sabbioni, I. Szalay, J. Benková, J. Baumgartner, and T. Szwaczkowski. 2007. “Population Size in Conservation of Local Chicken Breeds in Chosen European Countries.” Archiv Fur Geflugelkunde 71 (2): 49–55.
  • Sun, X., D. Habier, R. L. Fernando, D. J. Garrick, and J. C. M. Dekkers. 2011. “Genomic Breeding Value Prediction and QTL Mapping of QTLMAS2010 Data Using Bayesian Methods.” BMC Proceedings 5: S13. BioMed Central. doi:10.1186/1753-6561-5-S3-S13.
  • Tongsiri, S., M. G. Jeyaruban, and J. H. J. Van Der Werf. 2015. “Genetic Parameters for Egg Production Traits in Purebred and Hybrid Chicken in a Tropical Environment.” British Poultry Science 1–8. doi:10.1080/00071668.2015.1099614.
  • Tuiskula-Haavisto, M., D.-J. De Koning, M. Honkatukia, N. F. Schulman, A. Mäki-Tanila, and J. Vilkki. 2004. “Quantitative Trait Loci with Parent-of-Origin Effects in Chicken.” Genetics Research 84 (1): 57–66. doi:10.1017/S0016672304006950.
  • Tuiskula‐Haavisto, M., R. Mervi Honkatukia, M. S. Preisinger, D. J. De Koning, W. H. Wei, and J. Vilkki. 2011. “Quantitative Trait Loci Affecting Eggshell Traits in an F2 Population.” Animal Genetics 42 (3): 293–299. doi:10.1111/j.1365-2052.2010.02131.x.
  • Uemoto, Y., S. Sato, T. Kikuchi, S. Egawa, K. Kohira, H. Sakuma, S. Miyashita, S. Arata, T. Kojima, and K. Suzuki. 2017. “Genomic Evaluation Using SNP‐ and Haplotype‐based Genomic Relationship Matrices in a Closed Line of Duroc Pigs.” Animal Science Journal 88 (10): 1465–1474. doi:10.1111/asj.12805.
  • Villumsen, T. M., L. Janss, and M. S. Lund. 2009. “The Importance of Haplotype Length and Heritability Using Genomic Selection in Dairy Cattle.” Journal of Animal Breeding and Genetics 126 (1): 3–13. doi:10.1111/j.1439-0388.2008.00747.x.
  • Wolc, A., J. Arango, T. Jankowski, I. Dunn, P. Settar, J. E. Fulton, N. P. O’sullivan, R. Preisinger, R. L. Fernando, and D. J. Garrick. 2014. “Genome‐wide Association Study for Egg Production and Quality in Layer Chickens.” Journal of Animal Breeding and Genetics 131 (3): 173–182. doi:10.1111/jbg.2014.131.issue-3.
  • Wolc, A., J. Arango, P. Settar, J. E. Fulton, N. P. O’Sullivan, and J. C. M. Dekkers. 2018. “Genome Wide Association Study for Heat Stress Induced Mortality in a White Egg Layer Line.” Poultry Science 98 (1): 92–96. doi:10.3382/ps/pey403.
  • Wolc, A., J. Arango, P. Settar, J. E. Fulton, N. P. O’sullivan, R. Preisinger, D. Habier, R. Fernando, D. J. Garrick, and W. G. Hill. 2012. “Genome‐wide Association Analysis and Genetic Architecture of Egg Weight and Egg Uniformity in Layer Chickens.” Animal Genetics 43: 87–96. doi:10.1111/age.2012.43.issue-s1.
  • Wright, D., S. Kerje, H. Brändström, K. Schütz, A. Kindmark, L. Andersson, P. Jensen, and T. Pizzari. 2008. “The Genetic Architecture of a Female Sexual Ornament.” Evolution: International Journal of Organic Evolution 62 (1): 86–98. doi:10.1111/j.1558-5646.2007.00281.x.
  • Wu, Q., M. S. Clark, and R. D. Palmiter. 2012. “Deciphering a Neuronal Circuit that Mediates Appetite.” Nature 483 (7391): 594. doi:10.1038/nature10899.
  • Xu, Z., Q. Nie, and X. Zhang. 2013. “Overview of Genomic Insights into Chicken Growth Traits Based on Genome-Wide Association Study and MicroRNA Regulation.” Current Genomics 14 (2): 137–146. doi:10.2174/1389202911314020006.
  • Yousefi Zonuz, A., A. Alijani, H. Mohammadi, R. A. Rafat, and H. Daghigh Kia. 2013. “Estimation of Genetic Parameters for Productive and Reproductive Traits in Esfahan Native Chickens..” Journal of Livestock Science and Technologies 1 (1): 36–40.
  • Zeng, J. 2015. Whole Genome Analyses Accounting for Structures in Genotype Data. Ames: Iowa State University.
  • Zhang, H., Z. Wang, S. Wang, and L. Hui. 2012. “Progress of Genome Wide Association Study in Domestic Animals.” Journal of Animal Science and Biotechnology 3 (1): 26. doi:10.1186/2049-1891-3-26.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.