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United States Department of Agriculture

Agricultural Research Service

Jean-Luc Jannink
Plant, Soil and Nutrition Research
RESEARCH GENETICIST (PLANTS)

Phone: (607) 255-5266
Fax: (607) 255-6683
USDA,REE,ARS,NAA
ROBERT W. HOLLEY CENTER, TOWER ROAD
ITHACA, NY, 14853-2901

Projects
Enhancing Breeding of Small Grains through Improved Bioinformatics
Appropriated (D)
  Accession Number: 424887
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 Reprint Icon will take you to the publication reprint.)
Assessing genomic selection prediction accuracy in a dynamic barley breeding - (Peer Reviewed Journal)
Sallam, A., Endelman, J., Jannink, J., Smith, K. 2014. Assessing genomic selection prediction accuracy in a dynamic barley breeding. The Plant Genome. DOI: 10.3835/plantgenome2014.05.0020.
Perspectives for genomic selection applications and research in plants - (Peer Reviewed Journal) - (23-Jul-14)
Genomic selection for quantitative adult plant stem rust resistance in wheat - (Peer Reviewed Journal)
Rutkoski, J.E., Sorrells, M., Poland, J.A., Singh, R.P., Huerta-Espino, J., Bhavani, S., Barbier, H., Rouse, M.N., Jannink, J. 2014. Genomic selection for quantitative adult plant stem rust resistance in wheat. The Plant Genome. DOI: 10.3835/plantgenome2014.02.0006.
Genetic mapping using genotyping-by-sequencing in the clonally-propagated cassava - (Peer Reviewed Journal)
Rabbi, I., Hamblin, M., Gedil, M., Kulakow, P., Ferguson, M., Ikpan, A.S., Ly, D., Jannink, J. 2014. Genetic mapping using genotyping-by-sequencing in the clonally-propagated cassava. Crop Science. DOI: 10.2135/cropsci2013.07.0482.
Genomic selection in plant breeding - (Book / Chapter)
Newell, M., Jannink, J. 2013. Genomic selection in plant breeding. In: Fleury, D., and Whitford, R., editors. Crop Breeding: Methods and Protocols. Humana Press, Springer New York, Heidelberg, Dordrecht, London. p. 117-130.
High-resolution mapping of resistance to cassava mosaic geminiviruses in cassava using genotyping-by-sequencing and its implications for breeding - (Peer Reviewed Journal)
Rabbi, I., Hamblin, M., Kumar, P., Gedil, M., Ikpan, A.S., Jannink, J., Kulakow, P. 2013. 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.
Integrating environmental covariates and crop modeling into the genomic selection framework to predict genotype by environment interactions - (Peer Reviewed Journal)
Heslot, N., Akdemir, D., Sorrells, M.E., Jannink, J. 2013. Integrating environmental covariates and crop modeling into the genomic selection framework to predict genotype by environment interactions. Theoretical and Applied Genetics. 127:463-480.
Micro-enzymatic evaluation of oat (Avena sativa L.) beta-glucan for high-throughput phenotyping - (Peer Reviewed Journal)
Newell, M.A., Kim, H., Asoro, F.G., Moran Lauter, A., White, P.J., Scott, M.P., Jannink, J. 2014. Micro-enzymatic evaluation of oat (Avena sativa L.) beta-glucan for high-throughput phenotyping. Cereal Chemistry. 91:183–188.
Genomic prediction in maize breeding populations with genotyping-by-sequencing - (Peer Reviewed Journal)
Crossa, J., Beyene, Y., Segman, K., Perez, P., Hickey, J.M., Chen, C., De Los Campos, G., Burgueno, J., Windhausen, V.S., Buckler IV, E.S., Jannink, J., Lopez Crua, M.A., Babu, R. 2013. Genomic prediction in maize breeding populations with genotyping-by-sequencing. Genes, Genomes, Genetics. DOI: 10.1534/g3.113.008227.
Impact of marker ascertainment bias on genomic selection accuracy and estimates of genetic diversity Reprint Icon - (Peer Reviewed Journal)
Heslot, N., Rutkoski, J., Poland, J.A., Jannink, J., Sorrells, M.E. 2013. Impact of marker ascertainment bias on genomic selection accuracy and estimates of genetic diversity. PLoS One. 8(9): e74612.
Genotype by environment interaction and the use of unbalanced historical data for genomic selection in an international wheat breeding program - (Peer Reviewed Journal)
Dawson, J.C., Endelman, J., Heslot, N., Crossa, J., Poland, J.A., Dreisigacker, S., Manes, Y., Sorrells, M., Jannink, J. 2013. Genotype by environment interaction and the use of unbalanced historical data for genomic selection in an international wheat breeding program. Field Crops Research. 154:12-22.
Optimal design of preliminary yield trials with genome-wide markers - (Peer Reviewed Journal)
Endelman, J., Atlin, G., Beyene, Y., Fentaye, K., Zhang, X., Sorrells, M., Jannink, J. 2014. Optimal design of preliminary yield trials with genome-wide markers. Crop Science. 54:48-59.
An algorithm for deciding the number of clusters and validating using simulated data with application to exploring crop population structure - (Peer Reviewed Journal)
Newell, M., Cook, D., Hofmann, H., Jannink, J. 2013. An algorithm for deciding the number of clusters and validating using simulated data with application to exploring crop population structure. Annals of Applied Statistics. 7:1898-1916.
Ensemble learning with trees and rules: supervised, semi-supervised, unsupervised - (Peer Reviewed Journal) - (14-Apr-13)
Genomic predictability of interconnected bi-parental maize populations Reprint Icon - (Peer Reviewed Journal)
Riedelsheimer, C., Endelman, J., Stange, M., Sorrells, M., Jannink, J., Melchinger, A. 2013. Genomic predictability of interconnected bi-parental maize populations. Genetics. 194:493-503.
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.
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.
The effects of relatedness and GxE interaction on prediction accuracies in genomic selection: a study in cassava - (Peer Reviewed Journal)
Ly, D., Hamblin, M., Rabbi, I., Gedli, M., Bakare, M., Gauch, H., Okechukwu, R., Dixon, A., Kulakow, P., Jannink, J. 2013. The effects of relatedness and GxE interaction on prediction accuracies in genomic selection: a study in cassava. Crop Science. 53(4):1312-1325.
Imputation of unordered markers and the impact on genomic selection accuracy Reprint Icon - (Peer Reviewed Journal)
Rutkoski, J., Poland, J.A., Jannink, J., Sorrells, M. 2013. Imputation of unordered markers and the impact on genomic selection accuracy. Genetics. 3(3):427-39.
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.
Genomic selection in wheat using genotyping-by-sequencing Reprint Icon - (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. 5(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. 125:1687-1696.
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.
Development of high-density genetic maps for barley and wheat using a novel two enzyme genotyping-by-sequencing approach Reprint Icon - (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 Reprint Icon - (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.
ARS News Articles
Last Modified: 12/22/2014
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