Assignments

Problem Sets

Topic Due Date File Key
Hardy Weinberg Equilibrium, Linkage Disequilibrium Friday, Oct. 9, 2015 HW1_HWE_LD_15.xlsx HW1_HWE_LD_15_s.xlsx
Inbreeding, Selection Monday, Oct. 19, 2015 HW2_INB_SEL_15.xlsx HW2_INB_SEL_15_s.xlsx
Means and Variances, Breeding Values, GMA Wednesday, Nov. 4, 2015 HW3_Means_Variances_15.xlsx HW3_Means_Variances_15_s.xlsx
Estimating Genetic Variances Tuesday, Nov. 10, 2015 HW4_PO_regression.xlsx HW4_PO_regression_s.xlsx
Nested Mating Design Wed., Nov. 18, 2015 HW5_Nested_2015.xlsx HW5_Nested_2015_s.xlsx

Supplemental Reading

pdf files of articles will be posted in Canvas

Article Questions

Mangin, B., F. Sandron, K. Henry, B. Devaux, G. Willems, P. Devaux, and E. Goudemand. 2015. Breeding patterns and cultivated beets origins by genetic diversity and linkage disequilibrium analyses. Theor Appl Genet, First online: 04 August 2015.

SR1_Questions.docx

Yan, J., T. Shah, M.L Warburton, E.S. Buckler, M.D. McMullen, et al. 2009. Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP Markers. PLoS ONE 4(12): e8451. doi:10.1371/journal.pone.0008451.

SR2_Yan_2009_maize_LD.docx

Morrell, P.L., E.S. Buckler, and J. Ross-Ibarra. 2012. Crop genomics: advances and applications. Nature Reviews Genetics 13: 85-96.

SR3_Morrell_2012_crop_genomics_review.docx

Longin, C.F.H., M. Gowda, J. Mühleisen, E. Ebmeyer, E. Kazman, R. Schachschneider, J. Schacht, M. Kirchhoff, Y. Zhao, J.C. Reif. 2013. Hybrid wheat: quantitative genetic parameters and consequences for the design of breeding programs. Theoretical and Applied Genetics 126(11): 2791-2801.

SR4_Longin_2013_Hybrid_Wheat.docx

El-Kassaby, Y.A., E.P. Cappa, C. Liewlaksaneeyanawin, J. Klápště, and M. Lstibůrek. 2011. Breeding without Breeding: Is a complete pedigree necessary for efficient breeding? PLoS One 6(10) e25737.

SR5_ El-Kasaby_2011_BWB.docx

Heffner, E.L., JL. Jannink, M.E. Sorrels. 2011. Genomic selection accuracy using multifamily prediction models in a wheat breeding program. The Plant Genome, 4: 65–75.

SR6_Heffner_wheat_GS.docx

Sonah et al., Combining Genome-wide Association and QTL Analysis: Opportunities and Challenges (ISB News Report, November 2014)

SR7_Sonah_2014_soybean_GWAS_QTL.docx

de Meijer, Etienne PM, Manuela Bagatta, Andrea Carboni, Paola Crucitti, VM Cristiana Moliterni, Paolo Ranalli, and Giuseppe Mandolino. 2003. The inheritance of chemical phenotype in Cannabis sativa L. Genetics 163, no. 1: 335-346.

SR8_deMeijer_2003_Cannabis.docx
Case Studies for Term Projects  

Bonnett, D.G., G.J. Rebetzke and W. Spielmeyer. 2005. Strategies for efficient implementation of molecular markers in wheat breeding. Molecular Breeding 15: 75-85.

 

Rabbi et al. 2014. High-resolution mapping of resistance to cassava mosaic geminiviruses in cassava using genotyping-by-sequencing and its implications for breeding. Virus Research 186: 87–96.

 

Sukumaran, S., et al. 2014. Genome‑wide association study for grain yield and related traits in an elite spring wheat population grown in temperate irrigated Environments. Theor Appl Genet 128: 353–363.

 

Poland JA, Brown PJ, Sorrells ME, Jannink J-L. 2012. Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach. PLoS ONE 7(2): e32253. doi:10.1371/journal.pone.0032253

 
Shearman J.R., D. Sangsrakru, N. Jomchai, P. Ruang-Areerate, C. Sonthirod, C. Naktang, K. Theerawattanasuk, S. Tragoonrung, and S. Tangphatsornruang. 2015. SNP identification from RNA sequencing and linkage map construction of rubber tree for anchoring the draft genome. PLoS One 10(4): e0121961. doi: 10.1371/journal.pone.0121961.