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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » People & Locations » Jean-Luc Jannink
Jean-Luc Jannink
Plant, Soil and Nutrition Research
Research Geneticist (Plants)

Phone: (607) 255-5266
Fax: (607) 255-6683

(Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)

Projects
Breeding Insight Phase 2: Expansion to Support More Diverse Plant and Animal Use Cases
Cooperative Agreement (A)
  Accession Number: 439262
Breeding Insight 3
Cooperative Agreement (A)
  Accession Number: 444969
Breeding for Intercropping
Cooperative Agreement (A)
  Accession Number: 445012
The Triticeae Toolbox (T3) - Breeding Process and Data Facilitation to Accelerate Genetic Gain and Discovery
In-House Appropriated (D)
  Accession Number: 445558
Oat Pangenome Project Data Sharing Agreement
Non-Funded Cooperative Agreement (N)
  Accession Number: 440183

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Genomic prediction for targeted populations of environments in oat (Avena sativa) Reprint Icon - (Peer Reviewed Journal)
Sandro, P., Bhatta, M., Bower, A., Carlson, S., Jannink, J., Waring, D.J., Birkett, C.L., Smith, K., Wiersma, J., Caffe, M., Kleinjan, J., Mcmullen, M.S., English, L., Gutierrez, L. 2024. Genomic prediction for targeted populations of environments in oat (Avena sativa). Crop and Pasture Science. Volume 75. https://doi.org/10.1071/CP23126.
Genetic analysis of cassava brown streak disease root necrosis using image analysis and genome-wide association studies Reprint Icon - (Peer Reviewed Journal)
Nandudu, L., Strock, C., Ogbonna, A., Kawuki, R., Jannink, J. 2024. Genetic analysis of cassava brown streak disease root necrosis using image analysis and genome-wide association studies. Frontiers in Plant Science. Voulume 15. https://doi.org/10.3389/fpls.2024.1360729.
Genetic complexity of cassava brown streak disease: insights from qPCR-based viral titer analysis and genome-wide association studies Reprint Icon - (Peer Reviewed Journal)
Nandudu, L., Sheat, S., Winter, S., Ogbonna, A., Kawuki, R., Jannink, J. 2024. Genetic complexity of cassava brown streak disease: insights from qPCR-based viral titer analysis and genome-wide association studies. Frontiers in Plant Science. Volume 15. https://doi.org/10.3389/fpls.2024.1365132.
Evaluating breeding for broad versus narrow adaptation for cassava in Nigeria using stochastic simulation Reprint Icon - (Peer Reviewed Journal)
Bakare, M.A., Kayondo, S., Kulakow, P., Rabbi, I., Jannink, J. 2023. Evaluating breeding for broad versus narrow adaptation for cassava in Nigeria using stochastic simulation. Crop Science. Volume 64, Issue 2 pp. 603-616. https://doi.org/10.1002/csc2.21170.
Genetic dissection of cassava brown streak disease in a genomic selection population Reprint Icon - (Peer Reviewed Journal)
Nandudu, L., Kawuki, R., Ogbonna, A., Kanaabi, M., Jannink, J. 2023. Genetic dissection of cassava brown streak disease in a genomic selection population. Frontiers in Plant Science. 13:1099409. https://doi.org/10.3389/fpls.2022.1099409.
Increasing cassava root yield: Additive-dominant genetic models for selection of parents and clones Reprint Icon - (Peer Reviewed Journal)
Braatz De Andrade, L.R., Bandeira E Sousa, M., Wolfe, M., Jannink, J., Vilela De Resende, M.D., Azevedo, C.F., De Oliveira, E.J. 2022. Increasing cassava root yield: Additive-dominant genetic models for selection of parents and clones. Frontiers in Plant Science. 13:1071156. https://doi.org/10.3389/fpls.2022.1071156.
Parsimonious genotype by environment interaction covariance models for cassava (Manihot esculenta) Reprint Icon - (Peer Reviewed Journal)
Bakare, M.A., Kayondo, I.S., Aghogho, C.I., Wolfe, M.D., Parkes, E.Y., Kulakow, P., Egesi, C., Jannink, J., Rabbi, I.Y. 2022. Parsimonious genotype by environment interaction covariance models for cassava (Manihot esculenta). Frontiers in Plant Science. 13:978248. https://doi.org/10.3389/fpls.2022.978248.
Skinny kelp (Saccharina angustissima) provides valuable genetics for the biomass improvement of farmed sugar kelp (Saccharina latissima) Reprint Icon - (Peer Reviewed Journal)
Li, Y., Umanzor, S., Ng, C., Huang, M., Marty-Rivera, M., Bailey, D., Aydlett, M., Jannink, J., Lindell, S., Yarish, C. 2022. Skinny kelp (Saccharina angustissima) provides valuable genetics for the biomass improvement of farmed sugar kelp (Saccharina latissima). Journal of Applied Phycology. 34:2551-2563. https://doi.org/10.1007/s10811-022-02811-1.
Towards equitable public sector plant breeding in the US Reprint Icon - (Peer Reviewed Journal)
Brzozowski, L., Hanson, S., Jannink, J., Meints, B., Moore, V., Tufan, H., Villwock, S. 2022. Towards equitable public sector plant breeding in the US. Crop Science. https://doi.org/10.1002/csc2.20800.
GrainGenes: A data-rich repository for small grains genetics and genomics Reprint Icon - (Peer Reviewed Journal)
Yao, E., Blake, V.C., Cooper, L., Wight, C.P., Michel, S., Cagirici, H.B., Lazo, G.R., Birkett, C., Waring, D.J., Jannink, J., Holmes, I., Waters, A.J., Eickholt, D.P., Sen, T.Z. 2022. GrainGenes: A data-rich repository for small grains genetics and genomics. Database: The Journal of Biological Databases and Curation. 2022. Article baac034. https://doi.org/10.1093/database/baac034.
Exploring genotype by environment interaction on cassava yield and yield related traits using classical statistical methods Reprint Icon - (Peer Reviewed Journal)
Bakare, M.A., Kayondo, I.S., Aghogho, C.I., Wolfe, M.D., Parkes, E.Y., Kulakow, P., Egesi, C., Rabbi, I.Y., Jannink, J. 2022. Exploring genotype by environment interaction on cassava yield and yield related traits using classical statistical methods. PLOS ONE. 17(7): Article e0268189. https://doi.org/10.1371/journal.pone.0268189.
Generalizable approaches for genomic prediction of metabolites in plants Reprint Icon - (Peer Reviewed Journal)
Brzozowski, L.J., Campbell, M.T., Hu, H., Caffee, M., Gutierrez, L., Smith, K.P., Sorrells, M.E., Gore, M., Jannink, J. 2022. Generalizable approaches for genomic prediction of metabolites in plants. The Plant Genome. 15: Article e20205. https://doi.org/10.1002/tpg2.20205.
Breedbase: a digital ecosystem for modern plant breeding Reprint Icon - (Peer Reviewed Journal)
Morales, N., Ogbonna, A.C., Ellerbrock, B.J., Bauchet, G.J., Tantikanjana, T., Tecle, I.Y., Powell, A.F., Lyon, D., Naama, M., Simoes, C.C., Saha, S., Hosmani, P., Flores, M., Panitz, N., Preble, R.S., Agbona, A., Rabbi, I., Kulakow, P., Peteti, P., Kawuki, R., Esuma, W., Kanaabi, M., Chelagant, D.M., Uba, E., Olojede, A., Onyeka, J., Shah, T., Karanja, M., Egesi, C., Tufan, H., Paterne, A., Asfaw, A., Jannink, J., Wolfe, M., Birkett, C.L., Hershberger, J.M., Gore, M.A., Robbins, K.R., Rife, T., Chaney, C., Poland, J., Arnaud, E., Laporte, M., Waring, D.J., Brown, A., Bayo, S., Uwimana, B., Akech, V., Yencho, C., De Boeck, B., Campos, H., Swennen, R., Edwards, J., Mueller, L.A., Kulembeka, H., Salum, K., Mrema, E. 2022. Breedbase: a digital ecosystem for modern plant breeding. G3, Genes/Genomes/Genetics. https://doi.org/10.1093/g3journal/jkac078.
Simulation of sugar kelp (Saccharina latissima) breeding guided by practices to accelerate genetic gains Reprint Icon - (Peer Reviewed Journal)
Huang, M., Robbins, K.R., Li, Y., Umanzor, S., Marty-Rivera, M., Bailey, D., Yarish, C., Lindell, S., Jannink, J. 2022. Simulation of sugar kelp (Saccharina latissima) breeding guided by practices to accelerate genetic gains. Genes, Genomes, Genetics. 12(3). https://doi.org/10.1093/g3journal/jkac186.
Selection for seed size has uneven effects on specialized metabolite abundance in oat (Avena sativa L.) Reprint Icon - (Peer Reviewed Journal)
Brzozowski, L.J., Hu, H., Campbell, M.T., Broeckling, C.D., Caffe, M., Gutierrez, L., Smith, K.P., Sorrells, M.E., Gore, M.A., Jannink, J. 2021. Selection for seed size has uneven effects on specialized metabolite abundance in oat (Avena sativa L.). Genes, Genomes, Genetics. 12(3): Article ejkab419. https://doi.org/10.1093/g3journal/jkab419.
A population based expression atlas provides insights into disease resistance and other physiological traits in cassava (Manihot esculenta Crantz) Reprint Icon - (Peer Reviewed Journal)
Ogbonna, A.C., Ramu, P., Esuma, W., Nandudu, L., Morales, N., Powell, A., Kawuki, R., Bauchet, G., Jannink, J., Mueller, L.A. 2021. A population based expression atlas provides insights into disease resistance and other physiological traits in cassava (Manihot esculenta Crantz). Scientific Reports. 11: Article e23520. https://doi.org/10.1038/s41598-021-02794-y.
Response to early generation genomic selection for yield in wheat Reprint Icon - (Peer Reviewed Journal)
Bonnett, D., Li, Y., Crossa, J., Dreisigacker, S., Basnet, B., Perez-Rodriguez, P., Alvarado, G., Jannink, J., Poland, J., Sorrells, M. 2022. Response to early generation genomic selection for yield in wheat. Frontiers in Plant Science. 12.718611. https://doi.org/10.3389/fpls.2021.718611.
Development of the Wheat Practical Haplotype Graph Database as a Resource for Genotyping Data Storage and Genotype Imputation Reprint Icon - (Peer Reviewed Journal)
Jordan, K., Bradbury, P., Miller, Z., Nyine, M., He, F., Guttieri, M.J., Brown Guedira, G.L., Buckler Iv, E.S., Jannink, J., Akhunov, E., Ward, B.P., Bai, G., Bowden, R.L., Fiedler, J.D., Faris, J.D. 2021. Development of the Wheat Practical Haplotype Graph Database as a Resource for Genotyping Data Storage and Genotype Imputation. G3 Genes/Genomes/Genetics. https://doi.org/10.1101/2021.06.10.447944.
Sexual dimorphism and the effect of wild introgressions on recombination in cassava (Manihot esculenta Crantz) breeding germplasm Reprint Icon - (Peer Reviewed Journal)
Chan, A.W., Villwock, S.S., Williams, A.L., Jannink, J. 2021. Sexual dimorphism and the effect of wild introgressions on recombination in cassava (Manihot esculenta Crantz) breeding germplasm. Genes, Genomes, Genetics. 12(1): Article jkab372. https://doi.org/10.1093/g3journal/jkab372.
Genome-wide association mapping and genomic prediction of yield-related traits and starch pasting properties in cassava Reprint Icon - (Peer Reviewed Journal)
Phumichai, C., Aiemnaka, P., Nathaison, P., Hunsawattanakul, S., Fungfoo, P., Rojanaridpiched, C., Vichukit, V., Kongsil, P., Kittipadakul, P., Sorrells, M.E., Wannarat, W., Chunwongse, J., Tongyoo, P., Kijkhunasatian, C., Chotineeranat, S., Piyachomkwan, K., Wolfe, M.D., Jannink, J. 2021. Genome-wide association mapping and genomic prediction of yield-related traits and starch pasting properties in cassava. Theoretical and Applied Genetics. 135:145-171. https://doi.org/10.1007/s00122-021-03956-2.
Multi-omics prediction of oat agronomic and seed nutritional traits across environments and in distantly related populations Reprint Icon - (Peer Reviewed Journal)
Hu, H., Campbell, M.T., Yeats, T.H., Zheng, X., Runcie, D.E., Covarrubias-Pazaran, G., Broeckling, C., Yao, L., Caffe-Treml, M., Jannink, J., Gutierrezlucia, Smith, K., Tanaka, J., Hoekenga, O., Sorrells, M.E., Gore, M.A. 2021. Multi-omics prediction of oat agronomic and seed nutritional traits across environments and in distantly related populations. Theoretical and Applied Genetics. 134:4043-4054. https://doi.org/10.1007/s00122-021-03946-4.
Data-driven decentralized breeding increases prediction accuracy in a challenging crop production environment Reprint Icon - (Peer Reviewed Journal)
De Sousa, K., Van Etten, J., Poland, J., Fadda, C., Jannink, J., Gebrehawaryat, Y., Lakew, B.F., Mengistu, D.K., Pe, M.E., Dell'Acqua, M., Solberg, S. 2021. Data-driven decentralized breeding increases prediction accuracy in a challenging crop production environment. Communications Biology. https://doi.org/10.1038/s42003-021-02463-w.
Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices Reprint Icon - (Peer Reviewed Journal)
Wolfe, M.D., Chan, A.W., Kulakow, P., Rabbi, I., Jannink, J. 2021. Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices. Genetics. 219(3). https://doi.org/10.1093/genetics/iyab122.
RNA polymerase mapping in plants identifies intergenic regulatory elements enriched in causal variants Reprint Icon - (Peer Reviewed Journal)
Lozano, R., Booth, G.T., Omar, B., Li, B., Buckler IV, E.S., Lis, J.T., Pino Del Carpio, D., Jannink, J. 2021. RNA polymerase mapping in plants identifies intergenic regulatory elements enriched in causal variants. Genes, Genomes, Genetics. jkab273. https://doi.org/10.1093/g3journal/jkab273.
Development of the Wheat Practical Haplotype Graph Database as a Resource for Genotyping Data Storage and Genotype Imputation Reprint Icon - (Pre-print Publication)
Jordan, K., Bradbury, P., Miller, Z., Nyine, M., He, F., Guttieri, M.J., Brown Guedira, G.L., Buckler Iv, E.S., Jannink, J., Akhunov, E., Ward, B.P., Bai, G., Bowden, R.L., Fiedler, J.D., Faris, J.D. 2021. Development of the Wheat Practical Haplotype Graph Database as a Resource for Genotyping Data Storage and Genotype Imputation. bioRxiv. https://doi.org/10.1101/2021.06.10.447944.
Outlook of cassava brown streak disease assessment: Perspectives of the screening methods of breeders and pathologists Reprint Icon - (Peer Reviewed Journal)
Ozimati, A.A., Esuma, W., Alicai, T., Jannink, J., Egesi, C., Kawuki, R. 2021. Outlook of cassava brown streak disease assessment: Perspectives of the screening methods of breeders and pathologists. Frontiers in Plant Science. 12:648436. https://doi.org/10.3389/fpls.2021.648436.
Multi-species genomics-enabled selection for improving agroecosystems across space and time Reprint Icon - (Peer Reviewed Journal)
Wolfe, M.D., Jannink, J., Kantar, M.B., Santantonio, N. 2021. Multi-species genomics-enabled selection for improving agroecosystems across space and time. Frontiers in Plant Science. 12:665349. https://doi.org/10.3389/fpls.2021.665349.
Improving genomic prediction for seed quality traits in oat (Avena sativa L.) using trait-specific relationship matrices Reprint Icon - (Peer Reviewed Journal)
Campbell, M.T., Hu, H., Yeats, T.H., Bzozowski, L.J., Caffe-Treml, M., Gutierrez, L., Smith, K.P., Sorrells, M.E., Gore, M.A., Jannink, J. 2021. Improving genomic prediction for seed quality traits in oat (Avena sativa L.) using trait-specific relationship matrices. Frontiers in Genetics. 12:643733. https://doi.org/10.3389/fgene.2021.643733.
Comparative analysis of morphometric traits of farmed sugar kelp and skinny kelp, Saccharina spp., strains from the Northwest Atlantic Reprint Icon - (Peer Reviewed Journal)
Umanzor, S., Li, Y., Bailey, D., Augyte, S., Huang, M., Marty-Rivera, M., Jannink, J., Yarish, C., Lindell, S. 2021. Comparative analysis of morphometric traits of farmed sugar kelp and skinny kelp, Saccharina spp., strains from the Northwest Atlantic. Journal of the World Aquaculture Society. 2021;1-10. https://doi.org/10.1111/jwas.12783.
Kelp, Saccharina spp, population genetics in New England, US, for guiding a breeding program of thermally resilient strains - (Peer Reviewed Journal)
Augyte, S., Jannink, J., Mao, X., Huang, M., Robbins, K., Hare, M., Umanzor, S., Marty-Rivera, M., Li, Y., Yarish, C., Lindell, S., Bailey, D. 2020. Kelp, Saccharina spp, population genetics in New England, US, for guiding a breeding program of thermally resilient strains. Bulletin of Fisheries Research Agency. 50:135-139.
Translating insights from the seed metabolome into improved prediction for lipid-composition traits in oat (Avena sativa L.) Reprint Icon - (Peer Reviewed Journal)
Campbell, M.T., Hu, H., Yeats, T.H., Caffe-Treml, M., Gutierrez, L., Smith, K.P., Sorrells, M.E., Gore, M.A., Jannink, J. 2021. Translating insights from the seed metabolome into improved prediction for lipid-composition traits in oat (Avena sativa L.). Genetics. 217(3):iyaa043. https://doi.org/10.1093/genetics/iyaa043.
Population genetics of sugar kelp in the Northwest Atlantic region using genome-wide markers Reprint Icon - (Peer Reviewed Journal)
Mao, X., Augyte, S., Huang, M., Hare, M.P., Bailey, D., Umanzor, S., Marty-Rivera, M., Robbins, K.R., Yarish, C., Lindell, S., Jannink, J. 2020. Population genetics of sugar kelp in the Northwest Atlantic region using genome-wide markers. Frontiers in Marine Science. 7:694. https://doi.org/10.3389/fmars.2020.00694.
Translating insights from the seed metabolome into improved prediction for healthful compounds in oat (Avena sativa L.) Reprint Icon - (Other)
Campbell, M.T., Hu, H., Yeats, T.H., Caffe-Treml, M., Gutierrez, L., Smith, K.P., Sorrells, M.E., Gore, M., Jannink, J. 2020. Translating insights from the seed metabolome into improved prediction for healthful compounds in oat (Avena sativa L.). bioRxiv. https://doi.org/10.1101/2020.07.06.190512.
Genome-wide association analysis reveals new insights into the genetic architecture of defensive, agro-morphological and quality-related traits in cassava Reprint Icon - (Peer Reviewed Journal)
Rabbi, I., Kayondo, S., Bauchet, G., Yusuf, M., Aghogho, C., Ogunpaimo, K., Uwugiaren, R., Smith, I., Peteri, P., Agbona, A., Parkes, E., Lydia, E., Wolfe, M., Jannink, J., Egesi, C., Kulakow, P. 2020. Genome-wide association analysis reveals new insights into the genetic architecture of defensive, agro-morphological and quality-related traits in cassava. Plant Molecular Biology. https://doi.org/10.1007/s11103-020-01038-3.
Improving root characterisation for genomic prediction in cassava Reprint Icon - (Peer Reviewed Journal)
Yonis, B., Pino Del Carpio, D., Wolfe, M., Jannink, J., Kulakow, P., Ismail, R. 2020. Improving root characterisation for genomic prediction in cassava. Scientific Reports. https://doi.org/10.1038/s41598-020-64963-9.
Using public databases for genomic prediction of tropical maize lines Reprint Icon - (Peer Reviewed Journal)
Morais, P., Akdemir, D., Rogerio Braatz De Andrade, L., Jannink, J., Fritsche-Neto, R., Borem, A., Alvez, F.C., Lyra, D.H., Granato, I.S. 2020. Using public databases for genomic prediction of tropical maize lines. Plant Breeding. 139(4):697-707. https://doi.org/10.1111/pbr.12827.
Incorporating selfing to purge deleterious alleles in a cassava genomic selection program Reprint Icon - (Other)
Somo, M., Jannink, J. 2020. Incorporating selfing to purge deleterious alleles in a cassava genomic selection program. bioRxiv. https://doi.org/10.1101/2020.04.04.025841.
Recurrent genomic selection for wheat grain fructans Reprint Icon - (Peer Reviewed Journal)
Veenstra, L.D., Poland, J., Jannink, J., Sorrells, M.E. 2020. Recurrent genomic selection for wheat grain fructans. Crop Science. 60(3):1499-1512. https://doi.org/10.1002/csc2.20130.
Genomic prediction and quantitative trait locus discovery in a cassava training population constructed from multiple breeding stages Reprint Icon - (Peer Reviewed Journal)
Somo, M., Kulembeka, H., Mtunda, K., Mrema, E., Salum, K., Wolfe, M., Rabbi, I., Egesi, C., Kawuki, R., Jannink, J., Ozimati, A., Lozano, R. 2020. Genomic prediction and quantitative trait locus discovery in a cassava training population constructed from multiple breeding stages. Crop Science. 60(2):896-913. https://doi.org/10.1002/csc2.20003.
Genetic correlation, genome-wide association and genomic prediction of portable NIRS predicted carotenoids in cassava roots Reprint Icon - (Peer Reviewed Journal)
Ikeogu, U.N., Akdemir, D., Wolfe, M.D., Okeke, U.G., Chinedozi, A., Jannink, J., Egesi, C.N. 2019. Genetic correlation, genome-wide association and genomic prediction of portable NIRS predicted carotenoids in cassava roots. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2019.01570.
Genome wide association study of 5 agronomic traits in olive (Olea europaea L.) Reprint Icon - (Peer Reviewed Journal)
Kaya, H.B., Akdemir, D., Lozano, R., Cetin, O., Kaya, H.S., Sahin, M., Smith, J.L., Bahattin, Y., Jannink, J. 2019. Genome wide association study of 5 agronomic traits in olive (Olea europaea L.). Scientific Reports. 9:18764. https://doi.org/10.1038/s41598-019-55338-w.
A new oat seed transcriptome identifies heritable temporal gene expression patterns in developing seeds of hexaploid oat Reprint Icon - (Peer Reviewed Journal)
Hu, H., Gutierrez-Gonzalez, J.L., Liu, X., Yeats, T.H., Garvin, D.F., Hoekenga, O.A., Sorrels, M.E., Gore, M.A., Jannink, J. 2020. A new oat seed transcriptome identifies heritable temporal gene expression patterns in developing seeds of hexaploid oat. Plant Biotechnology Journal. 18(5):1211-1222. https://doi.org/10.1111/pbi.13286.
Heritable temporal gene expression patterns correlate with metabolomic seed content in developing hexaploid oat seed Reprint Icon - (Peer Reviewed Journal)
Hu, H., Gutierrez-Gonzalez, J.J., Liu, X., Yeats, T.H., Garvin, D.F., Hoekenga, O.A., Sorrells, M.E., Gore, M.A., Jannink, J. 2019. Heritable temporal gene expression patterns correlate with metabolomic seed content in developing hexaploid oat seed. Plant Biotechnology Journal. 18:1211-1222. https://doi.org/10.1111/pbi.13286.
Historical introgressions from a wild relative of modern cassava improved important traits and may be under balancing selection Reprint Icon - (Peer Reviewed Journal)
Wolfe, M.D., Bauchet, G.J., Chan, A.W., Lozano, R., Ramu, P., Egesi, C., Kawuki, R., Kulakow, P., Rabbi, I., Jannink, J. 2019. Historical introgressions from a wild relative of modern cassava improved important traits and may be under balancing selection. Genetics. 213(4):1237-1253. https://doi.org/10.1534/genetics.119.302757.
GrainGenes: centralized small grain resources and digital platform for geneticists and breeders - (Peer Reviewed Journal)
Blake, V.C., Woodhouse, M.R., Lazo, G.R., Odell, S.G., Wight, C.W., Tinker, N.A., Wang, Y., Gu, Y.Q., Birkett, C.L., Jannink, J., Matthews, D.E., Hane, D.L., Michel, S.L., Yao, E., Sen, T.Z. 2019. GrainGenes: centralized small grain resources and digital platform for geneticists and breeders. Database: The Journal of Biological Databases and Curation. 2019.
A framework for genomics-informed ecophysiological modeling in plants Reprint Icon - (Peer Reviewed Journal)
Wang, D.R., Guadagno, C.R., Mao, X., Mackay, S.D., Pleban, J.R., Baker, J.R., Weinig, C., Jannink, J., Ewers, B.E. 2019. A framework for genomics-informed ecophysiological modeling in plants. Journal of Experimental Botany. 70(9):2561-2574. https://doi.org/10.1093/jxb/erz090.
High-throughput phenotyping platforms enhance genomic selection for wheat grain yield across populations and cycles in early stage Reprint Icon - (Peer Reviewed Journal)
Sun, J., Poland, J.A., Mondal, S., Crossa, J., Philomin, J., Singh, R.P., Rutkoski, J.E., Jannink, J., Crespo-Herrera, L., Velu, G., Huerta-Espino, J., Sorrels, M. 2019. High-throughput phenotyping platforms enhance genomic selection for wheat grain yield across populations and cycles in early stage. Theoretical and Applied Genetics. 132:1705–1720. https://doi.org/10.1007/s00122-019-03309-0.
Homeologous epistasis in wheat: the search for an immortal hybrid Reprint Icon - (Peer Reviewed Journal)
Santantonio, N., Jannink, J., Sorrels, M. 2019. Homeologous epistasis in wheat: the search for an immortal hybrid. Genetics. 211:1105-1122. https://doi.org/10.25386/genetics.6913253.
Multivariate genome-wide association analyses reveal the genetic basis of seed fatty acid composition in oat (Avena sativa L.) Reprint Icon - (Peer Reviewed Journal)
Carlson, M.O., Montilla-Bascon, G., Hoekenga, O.A., Tinker, N.A., Poland, J., Baseggio, M., Sorrels, M.E., Jannink, J., Gore, M., Yeats, T.H. 2019. Multivariate genome-wide association analyses reveal the genetic basis of seed fatty acid composition in oat (Avena sativa L.). Genes, Genomes, Genetics. 1-39. https://doi.org/10.1101/589952.
A statistical framework for detecting mislabeled and contaminated samples using shallow-depth sequence data Reprint Icon - (Peer Reviewed Journal)
Chan, A.W., Williams, A.L., Jannink, J. 2018. A statistical framework for detecting mislabeled and contaminated samples using shallow-depth sequence data. BMC Bioinformatics. 19:478. https://doi.org/10.1186/s12859-018-2512-8.
Prediction of subgenome additive and interaction effects in allohexaploid wheat Reprint Icon - (Peer Reviewed Journal)
Santantonia, N., Jannink, J., Sorrels, M. 2019. Prediction of subgenome additive and interaction effects in allohexaploid wheat. Genes, Genomes, Genetics. 9(3):685-698. https://doi.org/10.1534/g3.118.200613
A Low resolution epistasis mapping approach to identify chromosome arm interactions in allohexaploid wheat Reprint Icon - (Peer Reviewed Journal)
Santantonia, N., Jannink, J., Sorrels, M. 2018. A Low resolution epistasis mapping approach to identify chromosome arm interactions in allohexaploid wheat. Genes, Genomes, Genetics. 9:675-684. https://doi.org/10.25387/g3.7311797.
Training population optimization for prediction of cassava brown streak disease resistance in West African clones Reprint Icon - (Peer Reviewed Journal)
Ozimati, A., Kawuki, R., Esuma, W., Kayondo, I.S., Wolfe, M., Lozano, R., Rabbi, I., Kulakow, P., Jannink, J. 2018. Training population optimization for prediction of cassava brown streak disease resistance in West African clones. Genes, Genomes, Genetics. 8(12):3903-3913. https://doi.org/10.1534/g3.118.200710.
A low-cost automated system for high-throughput phenotyping of single oat seeds Reprint Icon - (Peer Reviewed Journal)
Clohessy, J.W., Pauli, D., Kreher, K.M., Buckler IV, E.S., Armstrong, P.R., Wu, T., Hoekenga, O.A., Jannink, J., Sorrells, M.E., Gore, M.A. 2018. A low-cost automated system for high-throughput phenotyping of single oat seeds. The Plant Phenome Journal. 1(1):1-13. https://doi.org/10.2135/tppj2018.07.0005.
Genetic variation and trait correlations in an East African cassava breeding population for genomic selection Reprint Icon - (Peer Reviewed Journal)
Ozimati, A., Kawuki, R., Esuma, W., Kayondo, S.I., Pariyo, A., Wolfe, M., Jannink, J. 2019. Genetic variation and trait correlations in an East African cassava breeding population for genomic selection. Crop Science. 59(2):460-473. https://doi.org/10.2135/cropsci2018.01.0060.
Influence of genotype and environment on wheat grain fructan content Reprint Icon - (Peer Reviewed Journal)
Veenstra, L.D., Santantonio, N., Jannink, J., Sorrells, M.E. 2018. Influence of genotype and environment on wheat grain fructan content. Crop Science. 59:190-198. https://doi.org/10.2135/cropsci2018.06.0363.
RNA polymerase mapping in plants identifies enhancers enriched in causal variants - (Review Article)
Lozano, R., Booth, G.T., Omar, B.Y., Li, B., Buckler IV, E.S., Lis, J.T., Jannink, J., Pino Del Carpio, D. 2018. RNA polymerase mapping in plants identifies enhancers enriched in causal variants. bioRxiv. https://doi.org/10.1101/376640.
Genome-wide association study of resistance to Cassava Green Mite pest and related traits in cassava Reprint Icon - (Peer Reviewed Journal)
Ezenwaka, L., Pino Del Carpio, D., Jannink, J., Rabbi, I., Danquah, E., Asante, I., Danquah, A., Blay, E., Egesi, C. 2018. Genome-wide association study of resistance to Cassava Green Mite pest and related traits in cassava. Crop Science. 58(5):1907-1918. https://doi.org/10.2135/cropsci2018.01.0024.
Association mapping in common bean revealed regions associated with Anthracnose and Angular Leaf Spot resistance Reprint Icon - (Peer Reviewed Journal)
Fritsche-Neto, R., Oliveira De Souza, T.L., Pereira, H.S., Claudio De Faria, L., Mela, L.C., Novaes, E., Brum, I.J., Jannink, J. 2019. Association mapping in common bean revealed regions associated with Anthracnose and Angular Leaf Spot resistance. Scientia Agricola. 76(4):321-327. http://doi.org/10.1590/1678-992X-2017-0306.
Accuracy of genomic selection to predict maize single-crosses obtained through different mating designs Reprint Icon - (Peer Reviewed Journal)
Fritsche-Neto, R., Akdemir, D., Jannink, J. 2018. Accuracy of genomic selection to predict maize single-crosses obtained through different mating designs. Theoretical and Applied Genetics. 131:1153-1162. https://doi.org/10.1007/s00122-018-3068-8
Dysregulation of expression correlates with rare allele burden and fitness loss in maize Reprint Icon - (Peer Reviewed Journal)
Kremling, K., Chen, S., Su, M., Jannink, J., Romay, M., Swarts, K., Lu, F., Lorant, A., Bradbury, P., Buckler IV, E.S. 2018. Dysregulation of expression correlates with rare allele burden and fitness loss in maize. Nature. 555:520-523. https://doi.org/10.1038/nature25966.
Genome-wide association studies and heritability estimation in the functional genomics era - (Book / Chapter)
Pino Del Carpio, D., Lozano, R., Wolfe, M., Jannink, J. 2018. Genome-wide association studies and heritability estimation in the functional genomics era. In: Population Genomics. Springer, Cam. Switzerland: Springer Nature. p. 1-65.
Improving genomic prediction in Cassava field experiments by accounting for interplot competition Reprint Icon - (Peer Reviewed Journal)
Elias, A., Rabbi, I., Kulakow, P., Jannink, J. 2018. Improving genomic prediction in Cassava field experiments by accounting for interplot competition. G3, Genes/Genomes/Genetics. https://doi.org/10.1534/g3.117.300354
Genome-wide association mapping and genomic prediction for CBSD resistance in Manihot esculenta Reprint Icon - (Peer Reviewed Journal)
Kayondo, I., Pino Del Carpio, D., Lozano, R., Ozimati, A., Wolfe, M., Baguma, Y., Gracen, V., Offei, S., Ferguson, M., Kawuki, R., Jannink, J. 2018. Genome-wide association mapping and genomic prediction for CBSD resistance in Manihot esculenta. Scientific Reports. 8:1549. https://doi.org/10.1038/s41598-018-19696-1.
Impact of mislabeling on genomic selection in cassava breeding Reprint Icon - (Peer Reviewed Journal)
Yabe, S., Iwata, H., Jannink, J. 2018. Impact of mislabeling on genomic selection in cassava breeding. Crop Science. 58:1470-1480. doi: 10.2135/cropsci2017.07.0442
Accuracies of univariate and multivariate genomic prediction models in African cassava Reprint Icon - (Peer Reviewed Journal)
Okeke, U., Akdemir, D., Rabbi, I., Kulakow, P., Jannink, J. 2017. Accuracies of univariate and multivariate genomic prediction models in African cassava. Genetics Selection Evolution. 49:88. https://doi.org/10.1186/s12711-017-0361-y
Rapid analyses of dry matter content and carotenoids in fresh cassava roots using a portable visible and near infrared spectrometer (Vis/NIRS) Reprint Icon - (Peer Reviewed Journal)
Ikeogu, U., Davrieux, F., Dufour, D., Ceballos, H., Egesi, C., Jannink, J. 2017. Rapid analyses of dry matter content and carotenoids in fresh cassava roots using a portable visible and near infrared spectrometer (Vis/NIRS). PLoS One. 12(12):e0188918. https://doi.org/10.1371/journal.pone.0188918
Improving genomic prediction in cassava field experiments using spatial analysis Reprint Icon - (Peer Reviewed Journal)
Elias, A., Rabbi, I., Kulakow, P., Jannink, J. 2018. Improving genomic prediction in cassava field experiments using spatial analysis. G3, Genes/Genomes/Genetics. 8:53-62. https://doi.org/10.1534/g3.117.300323
Locally epistatic models for genome-wide prediction and association by importance sampling Reprint Icon - (Peer Reviewed Journal)
Adkemir, D., Jannink, J., Isidro-Sanchez, J. 2017. Locally epistatic models for genome-wide prediction and association by importance sampling. Genetics Selection Evolution. 49:74. https://doi.org/10.1186/s12711-017-0348-8.
Resistance to multiple temperate and tropical stem and sheath diseases of rice Reprint Icon - (Peer Reviewed Journal)
Rosas, J., Martinez, S., Blanco, P., Perez De Vida, F., Bonnecarrere, V., Mosquera, G., Cruz, M., Garayochea, S., Monteverde, E., McCouch, S., German, S., Jannink, J., Gutierrez, L. 2017. Resistance to multiple temperate and tropical stem and sheath diseases of rice. The Plant Genome. 11(1). https://doi.org/10.3835/plantgenome2017.03.0029.
Whole-genome prediction of reaction norms to environmental stress in bread wheat (Triticum aestivum L.) by genomic random regression Reprint Icon - (Peer Reviewed Journal)
Ly, D., Huet, S., Gauffreteau, A., Rincent, R., Touzy, G., Mini, A., Jannink, J., Cormier, F., Paux, E., Lafarge, S., Le Gouis, J., Charmet, G. 2017. Whole-genome prediction of reaction norms to environmental stress in bread wheat (Triticum aestivum L.) by genomic random regression. Field Crops Research. 216:32-41. https://doi.org/10.1016/j.fcr.2017.08.020
Regional heritability mapping provides insights into dry matter (DM) content in African white and yellow cassava populations - (Peer Reviewed Journal)
Okeke, U., Akdemir, D., Rabbi, I., Kulakow, P., Jannink, J. 2017. Regional heritability mapping provides insights into dry matter (DM) content in African white and yellow cassava populations. The Plant Genome. 11(1):1-18. DOI:10/3835/plantgenome2017.06.0050
Prospects for genomic selection in cassava breeding Reprint Icon - (Peer Reviewed Journal)
Wolfe, M., Carpio, D., Alabi, O., Ezenwaka, L., Ikeogu, U., Kayondo, I., Lozano, R., Okeke, U., Ozimati, A., Williams, E., Egesi, C., Kawuki, R., Kulakow, P., Rabbi, I., Jannink, J. 2017. Prospects for genomic selection in cassava breeding. The Plant Genome. 10(3):1-19. doi: 10.3835/plantgenome2017.03.0015
Genome-wide association mapping of correlated traits in cassava: dry matter and total carotenoid content - (Peer Reviewed Journal)
Rabbi, I., Udoh, L., Wolfe, M., Parkes, E., Gedil, M., Dixon, A., Punna, R., Jannink, J., Kulakow, P. 2017. Genome-wide association mapping of correlated traits in cassava: dry matter and total carotenoid content. The Plant Genome. 10(3):1-14.
Multitrait, random regression, or simple repeatability model in high-throughput phenotyping data improve genomic prediction for wheat grain yield - (Peer Reviewed Journal)
Sun, J., Rutkoski, J., Poland, J., Crossa, J., Jannink, J., Sorrells, M. 2017. Multitrait, random regression, or simple repeatability model in high-throughput phenotyping data improve genomic prediction for wheat grain yield. The Plant Genome. 10(2):1-12.
Wheat fructans: A potential breeding target for nutritionally improved, climate-resilient varieties - (Peer Reviewed Journal)
Veenstra, L., Jannink, J., Sorrells, M. 2017. Wheat fructans: A potential breeding target for nutritionally improved, climate-resilient varieties. Crop Science. 57:1624-1640.
A simple language to script and simulate breeding schemes: the breeding scheme language - (Peer Reviewed Journal)
Yabe, S., Iwata, H., Jannink, J. 2017. A simple language to script and simulate breeding schemes: the breeding scheme language. Crop Science. 57(3):1347-1354.
Genome-enabled prediction models for yield related traits in chickpea - (Peer Reviewed Journal)
Roorkiwal, M., Rathore, A., Das, R., Singh, M., Jain, A., Srinivasan, S., Gaur, P., Chellapilla, B., Tripathi, S., Li, Y., Hickey, J., Lorenz, A., Sutton, T., Crossa, J., Jannink, J., Varshney, R. 2016. Genome-enabled prediction models for yield related traits in chickpea. Frontiers in Plant Science. 7:1666. doi:10.3389/fpls.2016.01666.
Breeding value of primary synthetic wheat genotypes for grain yield - (Peer Reviewed Journal)
Jafarzadeh, J., Bonnett, D., Jannink, J., Akdemir, D., Dreisigacker, S., Sorrells, M. 2016. Breeding value of primary synthetic wheat genotypes for grain yield. PLoS One. 11(9):e0162860.
Marker-based estimates reveal significant non-additive effects in clonally propagated cassava (Manihot esculenta): implications for the prediction of total genetic value and the selection of varieties - (Peer Reviewed Journal)
Wolfe, M.D., Kulakow, P., Rabbi, I.Y., Jannink, J. 2016. Marker-based estimates reveal significant non-additive effects in clonally propagated cassava (Manihot esculenta): implications for the prediction of total genetic value and the selection of varieties. G3, Genes/Genomes/Genetics. https://doi.org/10.1534/g3.116.033332.
Introduction to a special issue on genotype by environment interaction - (Peer Reviewed Journal)
De Leon, N., Jannink, J., Edwards, J.W., Kaeppler, S. 2016. Introduction to a special issue on genotype by environment interaction. Crop Science. 56:2081-2089.
Evaluating imputation algorithms for low-depth genotyping-by-sequencing (GBS) data - (Peer Reviewed Journal)
Chen, A.W., Hamblin, M.T., Jannink, J. 2016. Evaluating imputation algorithms for low-depth genotyping-by-sequencing (GBS) data. PLoS One. 11(8):e0160733.
Population genetics related to adaptation in elite oat germplasm - (Peer Reviewed Journal)
Esvelt Klos, K.L., Huang, Y., Babiker, E.M., Beattie, A., Bekele, W.A., Bjornstad, A., Bonman, J.M., Carson, M.L., Chao, S., Gnanesh, B.N., Harrison, S.A., Howarth, C.J., Hu, G., Ibrahim, A., Islamovic, E., Jackson, E.W., Jannink, J., Kolb, F.L., Mcmullen, M.S., Fetch, J.M., Murphy, J., Obert, D.E., Ohm, H.W., Rines, H.W., Rossnagel, B., Schuleter, J.A., Wight, C.P., Yan, W., Tinker, N.A. 2016. Population genetics related to adaptation in elite oat germplasm. The Plant Genome. 9(2):1-12. doi: 10.3835/plantgenome2015.10.0103.
Genome-wide association and prediction analysis in African cassava (Manihot esculenta) reveals the genetic architecture of resistance to cassava mosaic disease and prospects for rapid genetic improvement - (Peer Reviewed Journal)
Wolfe, M.D., Rabbi, I.Y., Egesi, C., Hamblin, M., Kawuki, R., Kulakow, P., Lozano, R., Del Carpio, D., Rumu, P., Jannink, J. 2016. Genome-wide association and prediction analysis in African cassava (Manihot esculenta) reveals the genetic architecture of resistance to cassava mosaic disease and prospects for rapid genetic improvement. Virus Research. 9. doi: 10.3835/plantgenome2015.11.0118.
Comparison of phenotyping methods for resistance to stem rot and aggregated sheath spot in rice - (Peer Reviewed Journal)
Rosas, J., Marthez, S., Bonnecarrere, V., Perezde Vida, F., Blanco, P., Malosetti, M., Jannink, J., Gutierrez, L. 2016. Comparison of phenotyping methods for resistance to stem rot and aggregated sheath spot in rice. Crop Science. 56:1619-1627.
Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement - (Peer Reviewed Journal)
Spindel, J., Begum, H., Akdemir, D., Collard, B., Redooa, E., Jannink, J., Mccouch, S. 2016. Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement. Heredity. 116:395-408.
An alternative covariance estimator to investigate genetic heterogeneity in populations - (Peer Reviewed Journal)
Heslot, N., Jannink, J. 2015. An alternative covariance estimator to investigate genetic heterogeneity in populations. Genetics Selection Evolution. 47:93 doi: 10.1186/s12711-0150171-Z.
Genomic prediction using phenotypes from pedigreed lines with no marker data - (Peer Reviewed Journal)
Ashraf, B., Edriss, V., Akdemir, D., Autrique, E., Bonnett, D., Crossa, J., Janss, L., Singh, R., Jannink, J. 2016. Genomic prediction using phenotypes from pedigreed lines with no marker data. Crop Science. 56(3):957-964.
The triticeae toolbox: combining phenotype and genotype data to advance small-grains breeding - (Peer Reviewed Journal)
Blake, V., Birkett, C.L., Matthews, D.E., Hane, D., Bradbury, P., Jannink, J. 2015. The triticeae toolbox: combining phenotype and genotype data to advance small-grains breeding. The Plant Genome. doi: 10.3835/PlantGenome2014.12.0099.
Identification and distribution of the NBS-LRR gene family in the cassava genome - (Peer Reviewed Journal)
Lozano, R., Hamblin, M., Prochnik, S., Jannink, J. 2015. Identification and distribution of the NBS-LRR gene family in the cassava genome. BMC Genomics. 16:360. doi: 10.1186/s12864-015-1554-9.
Optimization of genomic selection training populations with a genetic algorithm Reprint Icon - (Peer Reviewed Journal)
Akdemir, D., Sanchez, J., Jannink, J. 2015. Optimization of genomic selection training populations with a genetic algorithm. Genetics Selection Evolution. 47:38.
Increased prediction accuracy in wheat breeding trials using a marker x environment interaction genomic selection model Reprint Icon - (Peer Reviewed Journal)
Cruz, M., Crossa, J., Bonnett, D., Dreisigacker, S., Poland, J.A., Jannink, J., Singh, R., De Los Campos, G. 2015. Increased prediction accuracy in wheat breeding trials using a marker x environment interaction genomic selection model. Genes, Genomes, Genetics. 5(4):569-582.
Genomic selection & association mapping in rice: effect of trait genetic architecture, training population composition, marker number & statistical model on accuracy of rice genomic selection in elite, tropical rice breeding Reprint Icon - (Peer Reviewed Journal)
Spindel, J., Begum, H., Akdemir, D., Virk, P., Collard, B., Redona, E., Atlin, G., Jannink, J., Mccouch, S.R. 2015. Genomic selection & association mapping in rice: effect of trait genetic architecture, training population composition, marker number & statistical model on accuracy of rice genomic selection in elite, tropical rice breeding. PLoS Genetics. 11(6):e1005350.
Locally epistatic genomic relationship matrices for genomic association Reprint Icon - (Peer Reviewed Journal)
Akdemir, D., Jannink, J. 2015. Locally epistatic genomic relationship matrices for genomic association. Genetics. 199:857-871.
solGS: a web-based tool for genomic selection Reprint Icon - (Peer Reviewed Journal)
Tecle, I., Edwards, J., Menda, N., Egesi, C., Rabbi, I.Y., Kulakow, P., Kawuki, R., Jannink, J., Mueller, L.A. 2014. solGS: a web-based tool for genomic selection. BMC Bioinformatics. 15:398.
Efficient use of historical data for genomic selection: a case study of rust resistance in wheat - (Peer Reviewed Journal)
Rutkoski, J., Singh, R., Huerta-Espino, J., Bhavani, S., Poland, J.A., Jannink, J., Sorrells, M. 2015. Efficient use of historical data for genomic selection: a case study of rust resistance in wheat. The Plant Genome. (8). DOI: 10.3835/plantgenome2014.09.0046.
Training set optimization under population structure in genomic selection Reprint Icon - (Peer Reviewed Journal)
Isidro, J., Jannink, J., Akdemir, D., Poland, J., Heslot, N., Sorrells, M. 2015. Training set optimization under population structure in genomic selection. Theoretical and Applied Genetics. 128(1):145-158.
Genomic prediction in bi-parental tropical maize populations in water-stressed and well-watered environments using low density and GBS SNPs Reprint Icon - (Peer Reviewed Journal)
Zhang, X., Perez-Rodriquez, P., Kassa, S., Beyene, Y., Babu, R., Lopez Cruz, M., San Vicente, F., Olsen, M., Buckler IV, E.S., Jannink, J., Prasanna, B.M., Crossa, J. 2014. Genomic prediction in bi-parental tropical maize populations in water-stressed and well-watered environments using low density and GBS SNPs. Heredity. 114:291-299.
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. (8). DOI: 10.3835/plantgenome2014.05.0020.
Perspectives for genomic selection applications and research in plants Reprint Icon - (Peer Reviewed Journal)
Heslot, N., Jannink, J., Sorrells, M.E. 2014. Perspectives for genomic selection applications and research in plants. Crop Science. 55:1-12.
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 Reprint Icon - (Peer Reviewed Journal)
Akdemir, D., Jannink, J. 2014. Ensemble learning with trees and rules: supervised, semi-supervised, unsupervised. Intelligent Data Analysis (An International Journal). 18(5):857-872.
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. Genes, Genomes, and Genomics. 3(3):427-439.
Imputation of unordered markers and the impact on genomic selection accuracy - (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 - (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 - (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 - (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 - (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)
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.
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