Projects

BIOINFORMATIC METHODS AND TOOLS TO PREDICT SMALL GRAIN FIELD PERFORMANCE Appropriated (D)   Accession Number: 413092

EVALUATING GENOMIC SELECTION FOR APPLIED PLANT BREEDING Reimbursable (R)   Accession Number: 418723

IMPROVING BARLEY AND WHEAT GERMPLASM FOR CHANGING ENVIRONMENTS Reimbursable (R)   Accession Number: 421067

POPULATION GENETIC RESEARCH IN SUPPORT OF BIOINFORMATIC METHODS TO PREDICT SMALL GRAIN FIELD PERFORMANCE Specific Cooperative Agreement (S)   Accession Number: 419711

Publications (Clicking on the reprint icon will take you to the publication reprint.)

SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species - (Peer Reviewed Journal)

Oliver, R.E., Tinker, N.A., Lazo, G.R., Chao, S., Jellen, E.N., Carson, M.L., Rines, H.W., Obert, D., Lutz, J.D., Shackelford, I., Korol, A.B., Wight, C., Gardner, K.M., Hattori, J., Beattie, A., Bjornstad, A., Bonman, J.M., Jannink, J., Mitchell Fetch, J.W., Harrison, S., Howarth, C.J., Ibrahim, A., Kolb, F.L., Mcmullen, M.S., Murphy, J.P., Ohm, H., Rossnagel, B.G., Yan, W., Miclaus, K.J., Hiller, J., Maughan, P.J., Redman-Hulse, R.R., Anderson, J.M., Islamovic, E., Jackson, E.W. 2013. SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species. PLoS One. 8:e58068.

Prediction of genetic values of multiple quantitative traits via multivariate random-effect regression model - (Peer Reviewed Journal) - (26-Sep-12)

Shrinkage estimation of the realized relationship matrix - (Peer Reviewed Journal) - (10-Sep-12)

Genomic selection in wheat using genotyping-by-sequencing - (Peer Reviewed Journal)

Poland, J.A., Endelman, J.B., Dawson, J., Rutkoski, J., Wu, S., Manes, Y., Dreisigacker, S., Crossa, J., Sanchez, H., Sorrells, M., Jannink, J. 2012. Genomic selection in wheat using genotyping-by-sequencing. The Plant Genome. VOL. 5, NO. 3 103:113.

Genomewide association study for beta-glucan content in North American elite oat - (Peer Reviewed Journal)

Asoro, F.G., Newell, M.A., Scott, M.P., Beavis, W.D., Jannink, J. 2013. Genomewide association study for beta-glucan content in North American elite oat. Crop Science. 53:542-553.

Genome-wide association study for oat (Avena sativa L.) beta-glucan concentration using germplasm of worldwide origin - (Peer Reviewed Journal)

Newell, M., Franco, A., Scott, M.P., White, P., Beavis, W., Jannink, J. 2012. Genome-wide association study for oat (Avena sativa L.) beta-glucan concentration using germplasm of worldwide origin. Theoretical and Applied Genetics. DOI: 10.1007/s00122-012-1945-0.

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) - (19-Apr-12)

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.

Development of high-density genetic maps for barley and wheat using a novel two enzyme genotyping-by-sequencing approach - (Peer Reviewed Journal)

Poland, J.A., Brown, P.J., Sorrells, M.E., Jannink, J. 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.

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.

Analysis of genetic diversity using SNP markers in oat - (Abstract Only)

Chao, S., Oliver, R.E., Lazo, G.R., Tinker, N., Jannink, J., Redman, R.R., Jackson, E.W. 2011. Analysis of genetic diversity using SNP markers in oat. Meeting Abstract. pg. 209.

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.

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.

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.

New DArT markers for oat provide enhanced map coverage and global germplasm characterization - (Peer Reviewed Journal)

Tinker, N.A., Kilian, A., Wright, C.P., Heller-Uszynska, K., Wenzl, P., Rines, H.W., Bjornstad, A., Howarth, C., Jannink, J., Anderson, J.M., Rossnagle, B.G., Stuthman, D.D., Sorrells, M.E., Jackson, E.W., Tuvesson, S., Kolb, F.L., Olsson, O., Federizzi, L.C., Carson, M.L., Ohm, H.W., Molnar, S.J., Scoles, G.J., Eckstein, P.E., Bonman, J.M., Ceplitis, A., Langdon, T. 2009. New DArT markers for oat provide enhanced map coverage and global germplasm characterization. BMC Medical Genetics. 10:39.

Selective Advance for Accelerated Development of Recombinant Inbred QTL Mapping Populations - (Peer Reviewed Journal)

Boddhireddy, P., Jannink, J., Nelson, J. 2009. Selective Advance for Accelerated Development of Recombinant Inbred QTL Mapping Populations. Crop Science. 49:1284-1294.

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.

Morphological Genetic Diversity of Worldwide Barley and Mega-Targets of Selection - (Peer Reviewed Journal)

Gutierrez, L., Nason, J.D., Jannink, J. 2009. Morphological Genetic Diversity of Worldwide Barley and Mega-Targets of Selection. Crop Science. 49:483-497.

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.

Overview of QTL detection in plants and tests for synergistic epistatic interactions - (Peer Reviewed Journal)

Jannink, J., Moreau, L., Charcosset, A., Charmet, G. 2008. Overview of QTL detection in plants and tests for synergistic epistatic interactions. Genetica. 136:225-236.

Size distributions of different orders of kernels within the oat spikelet - (Peer Reviewed Journal)

Doehlert, D.C., Jannink, J., Mcmullen, M.S. 2008. Size distributions of different orders of kernels within the oat spikelet. Crop Science. 48:298-340

QTL x Genetic Background Interaction: Application to Predicting Progeny Value - (Peer Reviewed Journal)

Jannink, J. 2007. Qtl x genetic background interaction: application to predicting progeny value. Euphytica. 161:61-69.

Using QTL results to discriminate among crosses based on their progeny mean and variance - (Peer Reviewed Journal)

Zhong, S., Jannink, J. 2007. Using QTL results to discriminate among crosses based on their progeny mean and variance. Genetics. 177:567-576.