Lewis Lukens

Lewis Lukens
Professor, Associate Chair



519-824-4120 x52304


B.A. Carleton College Northfield, MN USA;
Ph.D. University of Minnesota, St. Paul MN, USA


Crop Science Building


326 CRSC

We are investigating a variety of  questions in the areas of bioinformatics and quantitative genetics. Our research effort focuses on maize as well as other plant species.


BINF*6410 Bioinformatics Programming
BIOL*3300 Applied Bioinformatics
PLNT*6160 Advanced Plant Breeding II
PLNT*6260 Advanced Plant Genetics I
PLNT*6500 Applied Bioinformatics

Relevant Links:

Selected Publications:

So, D., Smith, A., Sparry, E. and Lukens, L., 2022. Genetics, not environment, contributed to winter wheat yield gains in Ontario, Canada. Theoretical and Applied Genetics, pp.1-16.

S Zhan, C Griswold, L Lukens Zea mays RNA-seq estimated transcript abundances are strongly affected by read mapping bias BMC genomics 22 (1), 1-12 2021

LD Cox, S Munholland, L Mats, H Zhu, WL Crosby, L Lukens, KP Pauls, ...The Induction of the Isoflavone Biosynthesis Pathway Is Associated with Resistance to Common Bacterial Blight in Phaseolus vulgaris L. Metabolites 11 (7), 433 1 2021

W Hargreaves, A N'Daiye, S Walkowiak, CJ Pozniak, K Wiebe, J Enns, ...The effects of crop attributes, selection, and recombination on Canadian bread wheat molecular variation The Plant Genome, e20099 2021

MAA Minow, L Lukens, V Rossi, J Colasanti Patterns of stability and change in the maize genome: a case study of small RNA transcriptomes in two recombinant inbred lines and their progenitors Genome 99 (999), 1-12 2021

MAA Minow, LM Ávila, L Lukens, V Rossi, J Colasanti Introgressed DNA within a Zea mays near-isogenic line displays lower levels of 24nt sRNA expression than the homologous region from the recurrent parent Genome 64 (12), 1091-1098 2021

B Waese-Perlman, A Pasha, C Ho, A Azhieh, Y Liu, A Sullivan, V Lau, ...  ePlant in 2021: New Species, Viewers, Data Sets, and Widgets bioRxiv 2021

MA House, CJ Swanton, LN Lukens The neonicotinoid insecticide thiamethoxam enhances expression of stress-response genes in Zea mays in an environmentally specific pattern Genome 64 (5), 567-579 1 2021

RM Whiting, S Torabi, L Lukens, M Eskandari Genomic regions associated with important seed quality traits in food-grade soybeans BMC plant biology 20 (1), 1-14 1 2020

E Raherison, MM Majidi, R Goessen, N Hughes, R Cuthbert, R Knox, ...Evidence for the accumulation of nonsynonymous mutations and favorable pleiotropic alleles during wheat breeding G3: Genes, Genomes, Genetics 10 (11), 4001-4011 2 2020

ME Cristescu, L Lukens Encouraging data sharing in Genome Genome 63 (11), iii-iii 2020

AG McKenzie‐Gopsill, S Amirsadeghi, HJ Earl, AMP Jones, L Lukens, ... Early physiological and biochemical responses of soyabean to neighbouring weeds under resource‐independent competition Weed Research 59 (4), 288-299 6 2019

VH Gonzalez, EA Lee, LL Lukens, CJ Swanton 13 2019 The relationship between floret number and plant dry matter accumulation varies with early season stress in maize (Zea mays L.) Field Crops Research 238, 129-138

JL Neyhart, D Sweeney, M Sorrells, C Kapp, KD Kephart, J Sherman, ...Registration of the S2MET barley mapping population for multi‐environment genomewide selection Journal of Plant Registrations 13 (2), 270-280 8 2019

M House, L Lukens Epialleles in Plant Breeding 2019 Epigenetics in Plants of Agronomic Importance: An Update Fundamentals and Applications …2019

LM Avila, W Obeidat, H Earl, X Niu, W Hargreaves, L Lukens (2018). Shared and genetically distinct Zea mays transcriptome responses to ongoing and past low temperature exposure  BMC genomics 19 (1), 761.

W Obeidat, L Avila, H Earl, L Lukens  (2018). Leaf spectral reflectance of maize seedlings and its relationship to cold tolerance Crop Science.

MAA Minow, LM Ávila, K Turner, E Ponzoni, I Mascheretti, FM Dussault, L Lukens..., (2018). Distinct gene networks modulate floral induction of autonomous maize and photoperiod-dependent teosinte, Journal of experimental botany 69 (12), 2937-2952 

JAF Coutin, S Munholland, A Silva, S Subedi, L Lukens, WL Crosby, ... (2017). Proanthocyanidin accumulation and transcriptional responses in the seed coat of cranberry beans (Phaseolus vulgaris L.) with different susceptibility to postharvest darkening. BMC plant biology 17 (1), 89 .

HW Kim, S Amirsadeghi, A McKenzie-Gopsill, M Afifi, G Bozzo, EA Lee, L Lukens, CJ Swanton (2016). Changes in light quality alter physiological responses of soybean to thiamethoxam. Planta 244 (3), 639-650. 

AG Mckenzie‐Gopsill, E Lee, L Lukens, CJ Swanton (2016). Rapid and early changes in morphology and gene expression in soya bean seedlings emerging in the presence of neighbouring weeds. Weed Research 56 (4), 267-273.

AG McKenzie-Gopsill, L Lukens, E Lee, CJ Swanton (2016). Does the presence of neighbouring weeds alter the expression of adaptive plasticity to subsequent drought stress in soybean? Field crops research 192, 144-153.

LM Avila, D Cerrudo, C Swanton, L Lukens (2016). Brevis plant1, a putative inositol polyphosphate 5-phosphatase, is required for internode elongation in maize. Journal of experimental botany 67 (5), 1577-1588.

J Gal, M Afifi, E Lee, L Lukens, CJ Swanton (2015). Detection of neighboring weeds alters soybean seedling roots and nodulation Weed Science 63 (4), 888-900. 

R Khanal, A Navabi, L Lukens (2015). Linkage map construction and quantitative trait loci (QTL) mapping using intermated vs. selfed recombinant inbred maize line (Zea mays L.). Canadian journal of plant science 95 (6), 1133-1144.

M Afifi, E Lee, L Lukens, C Swanton (2015). Maize (Zea mays) seeds can detect above‐ground weeds; thiamethoxam alters the view. Pest management science 71 (9), 1335-1345.

M Afifi, E Lee, L Lukens, C Swanton (2015). Thiamethoxam as a seed treatment alters the physiological response of maize (Zea mays) seedlings to neighbouring weeds. Pest management science 71 (4), 505-514. 

YM Bi, A Meyer, GS Downs, X Shi, A El-Kereamy, L Lukens, SJ Rothstein (2014). High throughput RNA sequencing of a hybrid maize and its parents shows different mechanisms responsive to nitrogen limitation. BMC genomics 15 (1), 77.

 A Reid, V Gonzalez, PH Sikkema, EA Lee, L Lukens, CJ Swanton (2014). Delaying weed control lengthens the anthesis-silking interval in maize. Weed science 62 (2), 326-3378.

G Larson, DR Piperno, RG Allaby, MD Purugganan, L Andersson, M Arroyo-Kalin, L Barton, C Climer Vigueira, T Denham, K Dobney, AN Doust, P Gepts, M Thomas P Gilbert, KJ Gremillion, L Lucas, Lewis Lukens (2014). Current perspectives and the future of domestication studies. Proceedings of the National Academy of Sciences, 201323964 231.

AN Doust, L Lukens, KM Olsen, M Mauro-Herrera, A Meyer, K Rogers (2014). Beyond the single gene: How epistasis and gene-by-environment effects influence crop domestication. Proceedings of the National Academy of Sciences, 201308940 32.

MA House, CK Griswold, LN Lukens (2014). Evidence for Selection on Gene Expression in Cultivated Rice (Oryza sativa). Molecular biology and evolution 31 (6), 1514-1525 12. 

GS Downs, C Liseron-Monfils, LN Lukens (2014). Regulatory motifs identified from a maize developmental coexpression network. Genome 2.

R Khanal, A Navabi, EA Lee, LN Lukens (2014). The Effect of Linkage on Genetic Variances within Biparental Simulated and Zea mays Populations. Crop Science 54 (6), 2481-2491 1.

M. House, L Lukens (2014). The role of germinally inherited epialleles in plant breeding. Epigenetics in Plants Agronomic Importance: Fundamentals and Applications 1-11.

Liseron-Monfils C., Y.M. Bi , G.S. Downs, W. Wu , T. Signorelli, G. Lu, X. Chen, E. Bondo, T. Zhu, L. Lukens, J. Colasanti, S. Rothstein and M. Raizada. (2013). Nitrogen transporter and assimilation genes exhibit developmental stage-selective expression in maize (Zea mays L.) associated with distinct cis-acting promoter motifs. Plant Signaling & Behavior. 8 (10): e26056.Doust, A.N.*, L. Lukens*, K.M. Olsen*, M. Mauro-Herrera and A. Meyer, K. Rogers. (2014) Beyond the single gene – do epistasis and gene-by-environment effects influence crop domestication? Proceedings of the National Academy of Sciences. * Equal contributors

Zhan, S. and L. Lukens. (2013). Protein-Coding cis-Natural Antisense Transcripts Have High and Broad Expression in Arabidopsis. Plant Physiology. 161 (4): 2171-2180.

Downs, G.S., Y.M. Bi, J. Colasanti, W. Wu, X. Chen, T. Zhu, S.J. Rothstein and L.N. Lukens. (2013). A Developmental Transcriptional Network for Maize Defines Coexpression Modules. Plant Physiology. 161 (4): 1830-1843.

Lukens, L. and G.S. Downs. (2012). Bioinformatics techniques for understanding and analyzing tree gene expression data. Genomics of Tree Crops. 17-38. DOI: 10.1007/978-1-4614-0920-5_2.

Moore, S. and L. Lukens. (2011). An evaluation of Arabidopsis thaliana hybrid traits and their genetic control. G3: Genes, Genomes, Genetics, 1: 571-579. DOI:10.1534/g3.111.001156.

Khanal, R., H. Earl, E. Lee, and L. Lukens (2011). Genetic architecture of flowering time and related traits in two early flowering maize lines. Crop Science, 51: 146-156.

L. Lukens and S. Zhan (2010). Plant bioinformatics and microarray technologies. Murray Moo-Young (ed). Comprehensive Biotechnology. 2nd ed. 4: 149-163.

Page, E.R., M. Tollenaar, E.A. Lee, L. Lukens and C.J. Swanton. (2010). Shade avoidance: an integral component of crop-weed competition. Weed Research. 50: 281-288.

Zhan, S. and L. Lukens. (2010). Identification of novel miRNAs and miRNA dependent developmental shifts of gene expression in Arabidopsis thaliana. PloS ONE. 5 (4). DOI: 10.1371/journal.pone.0010157.

Palomeque, L., L. Liu, W. Li, B. Hedges, E. Cober, M. Smid, L. Lukens and I. Rajcan. (2009). Validation of mega-environment universal and specific QTL associated with seed yield and agronomic traits in soybeans. Theoretical and Applied Genetics. 120: 997-1003.

Page, E., M. Tollenaar, E. Lee, L. Lukens and C.J. Swanton. (2009). Does the shade avoidance response underlie the critical period for weed control in maize (Zea mays L.)? Weed Research. 49: 563–571.

Page. E.R., M. Tollenaar, E.A. Lee, L. Lukens and C.J. Swanton. (2009). Timing, effect, and recovery from intraspecific competition in maize. Agronomy Journal. 102: 1007-1013.

Iniguez-Luy, F., L. Lukens, M. Farnham, R. Amasino and T. Osborn. (2008). Development of public immortal mapping populations, molecular markers, and linkage maps for rapid cycling /Brassica rapa/ and /B. oleracea/. Theoretical and Applied Genetics. 120: 131-43.

Lukens, L. and S. Zhan. (2007). The plant genome's methylation status and response to stress: Implications for plant improvement. Current Opinion in Plant Biology. 10: 317-322.

Lukens, L., J. C.Pires, E. Leon, R. D. Vogelzang, L. Oslach and T. Osborn. (2006). Patterns of sequence loss and cytosine methylation within a population of newly resynthesized Brassica napus allopolyploids. Plant Physiology. 140: 336-348.

Zhan, S., J. Horrocks, and L. Lukens. (2006). Islands of co-expressed neighbouring genes in Arabidopsis thaliana suggest higher order chromosome domains. Plant Journal. 45: 347-357

Ghosh, A. K., L. Lukens, D. Hunter and J.N. Strommer. (2006). European and Asian pears: SSR/PAGE-based analysis of commercially important North American cultivars. HortScience. 41: 304-309. PDF - 520 KB]

Parkin, I., S. Gulden, A. Sharpe, L. Lukens, T.C. Osborn and D.J. Lydiate. (2005). Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana. Genetics. 171: 765-781.

Wang, H., T. Nussbaum-Wagler, B. Li, Q. Zhao, Y. Vigouroux, M. Faller, K. Bomblies, L. Lukens and J. Doebley. (2005). The origin of the maize ear by regulatory evolution. Nature. 436: 714-719.