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United States Department of Agriculture

Agricultural Research Service

Research Project: BIOINFORMATIC METHODS AND TOOLS TO PREDICT SMALL GRAIN FIELD PERFORMANCE Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

Comparison of genomic, marker-assisted, and pedigree-BLUP selection methods to increase beta-glucan concentration in elite oat germplasm - (Peer Reviewed Journal)
Asoro, F., Newell, M., Beavis, W., Scott, M.P., Tinker, N., Jannink, J. 2013. Comparison of genomic, marker-assisted, and pedigree-BLUP selection methods to increase beta-glucan concentration in elite oat germplasm. Crop Science. 53(5):1894-1906.
Multiple trait genomic selection methods increase genetic value prediction accuracy - (Peer Reviewed Journal)
Jia, Y., Jannink, J. 2012. Multiple trait genomic selection methods increase genetic value prediction accuracy. Genetics. 192(4):1513-1522.
Effectiveness of genomic prediction of maize hybrid performance in different breeding populations and environments     Reprint Icon - (Peer Reviewed Journal)
Weber, V.S., Atlin, G.A., Hickey, J.M., Crossa, J., Jannink, J., Sorrells, M.E., Raman, B., Cairns, J.E., Tarekegne, A., Semagn, K., Beyene, Y., Grudloyma, P., Technow, F., Riedelsheimer, C., Melchinger, A.E. 2012. Effectiveness of genomic prediction of maize hybrid performance in different breeding populations and environments. Genes, Genomes, and Genomics. 2(11):1427-1436.
Shrinkage estimation of the realized relationship matrix     Reprint Icon - (Peer Reviewed Journal)
Endelman, J.B., Jannink, J. 2012. Shrinkage estimation of the realized relationship matrix. Genes, Genomes, and Genomics. 2(11):1405-1413.
Using genomic prediction to characterize environments and optimize prediction accuracy in applied breeding data - (Peer Reviewed Journal)
Heslot, N., Jannink, J., Sorrells, M. 2013. Using genomic prediction to characterize environments and optimize prediction accuracy in applied breeding data. Crop Science. 53(3):921-933.
The hordeum toolbox - the barley CAP genotype and phenotype resource - (Peer Reviewed Journal)
Blake, V.C., Kling, J.G., Hayes, P.M., Jannink, J., Jillella, S.R., Lee, J., Matthews, D.E., Chao, S., Close, T.J., Muehlbauer, G.J., Smith, K.P., Wise, R.P., Dickerson, J.A. 2012. The hordeum toolbox - the barley CAP genotype and phenotype resource. The Plant Genome. DOI: 10.385/plantgenome2012.03.0002.
Evaluation of genomic prediction methods for fusarium head blight resistance in wheat - (Peer Reviewed Journal)
Rutkoski, J., Benson, J., Jia, Y., Brown Guedira, G.L., Jannink, J., Sorrells, M. 2012. Evaluation of genomic prediction methods for fusarium head blight resistance in wheat. The Plant Genome. 5:51-61.
Potential and optimization of genomic selection for fusarium head blight resistance in six-row barley - (Peer Reviewed Journal)
Lorenz, A.J., Smith, K.P., Jannink, J. 2012. Potential and optimization of genomic selection for fusarium head blight resistance in six-row barley. Crop Science. 52(4):1609-1621. DOI: 10.2135/cropsci2011.09.0503.
Accuracy and training population design for genomic selection in elite north american oats - (Peer Reviewed Journal)
Asoro, F.G., Newell, M.A., Beavis, W.D., Jannink, J., Scott, M.P. 2011. Accuracy and training population design for genomic selection in elite north american oats. The Plant Genome. 4:132-144.
Factors affecting the power of haplotype markers in association studies - (Peer Reviewed Journal)
Hamblin, M., Jannink, J. 2011. Factors affecting the power of haplotype markers in association studies. The Plant Genome. 4:145-153.
Accuracy of genomic selection in barley breeding programs: a simulation study based on the real SNP data - (Peer Reviewed Journal)
(18-Apr-11)
Population genetics of genomics-based crop improvement methods - (Review Article)
Hamblin, M., Buckler Iv, E.S., Jannink, J. 2011. Population genetics of genomics-based crop improvement methods. Trends in Genetics. 27:98-106.
Genomic selection accuracy using multi-family prediction models in a wheat breeding program - (Peer Reviewed Journal)
Heffner, E., Jannink, J., Sorrells, M. 2011. Genomic selection accuracy using multi-family prediction models in a wheat breeding program. The Plant Genome. 4:65-75.
Population structure and linkage disequilibrium in oat (Avena sativa L.): implications for genome-wide association studies - (Peer Reviewed Journal)
Newell, M.A., Cook, D., Tinker, N.A., Jannink, J. 2010. Population structure and linkage disequilibrium in oat (Avena sativa L.): implications for genome-wide association studies. Theoretical and Applied Genetics. 122:623-632.
Performance of single nucleotide polymorphisms versus haplotypes for genome-wide association analysis in barley - (Peer Reviewed Journal)
Lorenz, A.J., Hamblin, M.T., Jannink, J. 2010. Performance of single nucleotide polymorphisms versus haplotypes for genome-wide association analysis in barley. PLoS Genetics. 5(II):e14079.
Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor - (Peer Reviewed Journal)
Swanson-Wagner, R.A., Eichten, S.R., Kumari, S., Tiffin, P., Stein, J.C., Ware, D., Springer, N.M. 2010. Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Research. 20(12):1689-1699.
Genomic selection in plant breeding: knowledge and prospects - (Review Article)
Lorenz, A.J., Chao, S., Asoro, F.G., Heffner, E.L., Hayashi, T., Iwata, H., Smith, K.P., Sorrells, M.E., Jannink, J. 2011. Genomic selection in plant breeding: knowledge and prospects. Advances in Agronomy. 110:77-123.
Digital gene expression signatures for maize development - (Peer Reviewed Journal)
Eveland, A.L., Nagasawa, N., Goldshmidt, A., Meyer, S., Beatty, M., Sakai, H., Ware, D., Jackson, D. 2010. Digital gene expression signatures for maize development. Plant Physiology. 154(3):1024-1039.
Assessment of power and false discovery in genome-wide association studies using the BarleyCAP germplasm - (Peer Reviewed Journal)
Bradbury, P., Parker, T., Hamblin, M.T., Jannink, J. 2010. Assessment of power and false discovery in genome-wide association studies using the BarleyCAP germplasm. Crop Science. 51:52-59.
Dynamics of long-term genomic selection - (Peer Reviewed Journal)
Jannink, J. 2010. Dynamics of long-term genomic selection. Genetics. 42:35.
Plant breeding with genomic selection: potential gain per unit time and cost - (Peer Reviewed Journal)
Heffner, E.L., Lorenz, A.J., Jannink, J., Sorrells, M.E. 2010. Plant breeding with genomic selection: potential gain per unit time and cost. Crop Science. 50:1681-1690.
Genomic selection in plant breeding: from theory to practice - (Peer Reviewed Journal)
Jannink, J., Lorenz, A.J., Iwata, H. 2010. Genomic selection in plant breeding: from theory to practice. Briefings in Functional Genomics and Proteomics. 9:166-177.
Marker genotype imputation in a low-marker-density panel with a high-marker-density reference panel: accuracy evaluation in barley breeding lines - (Peer Reviewed Journal)
Iwata, H., Jannink, J. 2010. Marker genotype imputation in a low-marker-density panel with a high-marker-density reference panel: accuracy evaluation in barley breeding lines. Crop Science. 50:1269-1278.
Whole genome association mapping of grain shape variation among Oryza sativa L. germplasms based on elliptic Fourier analysis - (Peer Reviewed Journal)
Iwata, H., Ebana, K., Uga, Y., Hayashi, T., Jannink, J. 2009. Whole genome association mapping of grain shape variation among Oryza sativa L. germplasms based on elliptic Fourier analysis. Theoretical and Applied Genetics. 114(8):1437-1449.
Population structure and linkage disequilibrium in US barley germplasm: implications for association mapping - (Peer Reviewed Journal)
Hamblin, M.T., Close, T.J., Bhat, P.R., Chao, S., Abraham, K., Blake, T., Brooks, W.S., Cooper, B., Griffey, C.A., Hayes, P.M., Hole, D.J., Horsley, R.D., Obert, D.E., Smith, K.P., Ullrich, S.E., Muehlbauer, G.J., Jannink, J. 2010. Population structure and linkage disequilibrium in US barley germplasm: implications for association mapping. Crop Science. 50:556-566.
Association-Based Genomic Selection in Cultivated Barley - (Peer Reviewed Journal)
Zhong, S., Dekkers, J., Jannink, J. 2009. Association-Based Genomic Selection in Cultivated Barley. Genetics. 182:355-364.
Marker imputation in barley association studies - (Peer Reviewed Journal)
Jannink, J., Iwata, H., Bhat, P.R., Chao, S., Wenzl, P., Muehlbauer, G.J. 2009. Marker imputation in barley association studies. The Plant Genome. 2:11-22.
Bayesian multilocus association mapping on ordinal and censored traits and its application to the analysis of genetic variation among Oryza sativa L. germplasms - (Peer Reviewed Journal)
Iwata, H., Ebana, K., Fukuoka, S., Hayashi, T., Jannink, J. 2009. Bayesian multilocus association mapping on ordinal and censored traits and its application to the analysis of genetic variation among Oryza sativa L. germplasms. Theoretical and Applied Genetics. 118(5):865-880.
New DArT markers for oat provide enhanced map coverage and global germplasm characterization - (Peer Reviewed Journal)
Tinker, N.A., Kilian, A., Rines, H.W., Bjornstad, A., Howarth, C.J., Jannink, J., Anderson, J.M., Rossnagel, B.G., Wight, C.P., Stuthman, D.D., Sorrells, M.E., Scoles, G.J., Eckstein, P.E., Ohm, H.W., Jackson, E.W., Tuvesson, S., Kolb, F.L., Molnar, S.J., Olsson, O., Carson, M.L., Ceplitis, A., Bonman, J.M., Federizzi, L., Langdon, T. 2009. New DArT markers for oat provide enhanced map coverage and global germplasm characterization. Biomed Central (BMC) Genomics. 10(39):1471-2164.
Association genetics in barley - (Peer Reviewed Journal)
Waugh, R., Muehlbauer, G.J., Jannink, J., Ramsay, L. 2009. Association genetics in barley. Current Opinion in Plant Biology. 12(2):218-222.
Genomic Selection for Crop Improvement - (Peer Reviewed Journal)
Heffner, E.L., Sorrells, M.E., Jannink, J. 2009. Genomic Selection for Crop Improvement. Crop Science. 49:1-12.
Impact of Dry Solids and Bile Acid Concentrations on Bile Acid Binding Capacity of Extruded Oat Cereals - (Peer Reviewed Journal)
Yao, N., Jannink, J., White, P.J., Alavi, S. 2008. Impact of Dry Solids and Bile Acid Concentrations on Bile Acid Binding Capacity of Extruded Oat Cereals. Journal of Agricultural and Food Chemistry. 56:8672-8679.
Last Modified: 11/25/2014
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