Julin N. Maloof

Julin Maloof

Position Title

Department of Plant Biology, College of Biological Sciences
Genome Center

2131 Life Sciences

Research Interests

How plants sense and respond to their neighbors

Light is essential for plant growth. Perhaps as a consequence, plants have an intricate set of photoreceptors and responses that they use to optimize their development and physiology to suit their light environment. We study the downstream mechanisms underlying these responses and how plants have evolved differences in their light perception and responses that allow them to thrive in different environments. We are interested in both the genetic and molecular basis of variation in light response as well as the adaptive consequences. A combination of molecular and quantitative genetics and genomics is used in Arabidopsis, Tomato, and Brassica

Grad Group Affiliations

  • Integrative Genetics and Genomics
  • Plant Biology

Specialties / Focus

  • Cell and Developmental Biology
  • Environmental and Integrative Biology
  • Integrated Genetics and Genomics
  • Model Plants
  • Molecular Biology, Biochemistry and Genomics
  • Plant Breeding
  • Quantitative and Population Genetics


  • BIS 181 Comparative Genomics, Fall Quarter
  • BIS 180L Genome Biology Lab, Spring Quarter


  • Maloof Lab http://malooflab.openwetware.org/

Honors and Awards

  • 2013 AAAS Fellow

    Professional Societies

    • Genetics Society of America
    • American Society of Plant Biologists
    • American Association for the Advancement of Science


    • 1989 BA Biology Haverford College
    • 1998 PhD Biochemistry University of California, San Francisco


    Filiault DL, Seymour DK, Maruthachalam R, Maloof JN. (2017) The Generation of Doubled Haploid Lines for QTL Mapping. Methods in molecular biology (Clifton, N.J.) 1610:39-57.

    Wang Z, Yang R, Devisetty UK, Maloof JN, Zuo Y, Li J, Shen Y, Zhao J, Bao M, Ning G. (2017) The Divergence of Flowering Time Modulated by FT/TFL1 Is Independent to Their Interaction and Binding Activities. Frontiers in plant science 8:697.

    Markelz RJC, Covington MF, Brock MT, Devisetty UK, Kliebenstein DJ, Weinig C, Maloof JN. (2017) Using RNA-Seq for Genomic Scaffold Placement, Correcting Assemblies, and Genetic Map Creation in a Common Brassica rapa Mapping Population. G3 (Bethesda, Md.) 7(7):2259-2270.

    Bucksch A, Atta-Boateng A, Azihou AF, Battogtokh D, Baumgartner A, Binder BM, Braybrook SA, Chang C, Coneva V, DeWitt TJ, Fletcher AG, Gehan MA, Diaz-Martinez DH, Hong L, Iyer-Pascuzzi AS, Klein LL, Leiboff S, Li M, Lynch JP, Maizel A, Maloof JN, Markelz RJC, Martinez CC, Miller LA, Mio W, Palubicki W, Poorter H, Pradal C, Price CA, Puttonen E, Reese JB, Rellán-Álvarez R, Spalding EP, Sparks EE, Topp CN, Williams JH, Chitwood DH. (2017) Morphological Plant Modeling: Unleashing Geometric and Topological Potential within the Plant Sciences. Frontiers in plant science 8:900.

    Rubin MJ, Brock MT, Davis AM, German ZM, Knapp M, Welch SM, Harmer SL, Maloof JN, Davis SJ, Weinig C. (2017) Circadian rhythms vary over the growing season and correlate with fitness components. Molecular ecology .

    Ranjan A, Budke JM, Rowland SD, Chitwood DH, Kumar R, Carriedo L, Ichihashi Y, Zumstein K, Maloof JN, Sinha NR. (2016) eQTL Regulating Transcript Levels Associated with Diverse Biological Processes in Tomato. Plant physiology 172(1):328-40.

    Fulop D, Ranjan A, Ofner I, Covington MF, Chitwood DH, West D, Ichihashi Y, Headland L, Zamir D, Maloof JN, Sinha NR. (2016) A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification. G3 (Bethesda, Md.) 6(10):3169-3184.

    Schrager-Lavelle A, Herrera LA, Maloof JN. (2016) Tomato phyE Is Required for Shade Avoidance in the Absence of phyB1 and phyB2. Frontiers in plant science 7:1275.

    Müller-Moulé P, Nozue K, Pytlak ML, Palmer CM, Covington MF, Wallace AD, Harmer SL, Maloof JN. (2016) YUCCA auxin biosynthetic genes are required for Arabidopsis shade avoidance. PeerJ 4:e2574.

    Müller NA, Wijnen CL, Srinivasan A, Ryngajllo M, Ofner I, Lin T, Ranjan A, West D, Maloof JN, Sinha NR, Huang S, Zamir D, Jiménez-Gómez JM. (2016) Domestication selected for deceleration of the circadian clock in cultivated tomato. Nature genetics 48(1):89-93.

    Brock MT, Lucas LK, Anderson NA, Rubin MJ, Markelz RJ, Covington MF, Devisetty UK, Chapple C, Maloof JN, Weinig C. (2016) Genetic architecture, biochemical underpinnings and ecological impact of floral UV patterning. Molecular ecology 25(5):1122-40.

    Carriedo LG, Maloof JN, Brady SM. (2016) Molecular control of crop shade avoidance. Current opinion in plant biology 30():151-8.

    Ranjan A, Budke JM, Rowland SD, Chitwood DH, Kumar R, Carriedo L, Ichihashi Y, Zumstein K, Maloof JN, Sinha NR. (2016) eQTL Regulating Transcript Levels Associated with Diverse Biological Processes in Tomato. Plant physiology 172(1):328-40.

    Fulop D, Ranjan A, Ofner I, Covington MF, Chitwood DH, West D, Ichihashi Y, Headland L, Zamir D, Maloof JN, Sinha NR. (2016) A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification. G3 (Bethesda, Md.) .

    Nguyen TT, Slaughter DC, Max N, Maloof JN, Sinha N. Structured Light-Based 3D Reconstruction System for Plants. Sensors. 2015 Jul 29;15(8):18587–612.

    Chitwood DH, Kumar R, Ranjan A, Pelletier JM, Townsley BT, Ichihashi Y, Martinez CC, Zumstein K, Harada JJ, Maloof JN, Sinha NR. (2015) Light-Induced Indeterminacy Alters Shade-Avoiding Tomato Leaf Morphology. Plant physiology 169(3):2030-47.

    Brady SM, Burow M, Busch W, Carlborg Ö, Denby KJ, Glazebrook J, Hamilton ES, Harmer SL, Haswell ES, Maloof JN, Springer NM, Kliebenstein DJ. Reassess the t Test: Interact with All Your Data via ANOVA. Plant Cell. 2015 Jul 28;tpc.15.00238.

    Baker RL, Leong WF, Brock MT, Markelz RJC, Covington MF, Devisetty UK, Edwards CE, Maloof J, Welch S, Weinig C. Modeling development and quantitative trait mapping reveal independent genetic modules for leaf size and shape. New Phytologist. 2015 Oct;208(1):257–68.

    Nozue K, Tat AV, Kumar Devisetty U, Robinson M, Mumbach MR, Ichihashi Y, Lekkala S, Maloof JN. Shade Avoidance Components and Pathways in Adult Plants Revealed by Phenotypic Profiling. PLoS Genet. 2015 Apr 15;11(4):e1004953.

    Fitz Gerald JN, Carlson AL, Smith E, Maloof JN, Weigel D, Chory J, Borevitz JO, Swanson RJ (2014). New Arabidopsis advanced intercross recombinant inbred lines reveal female control of nonrandom mating. Plant Physiol. 165(1):175–85. PMCID: PMC4012578

    Bolger A, Scossa F, Bolger ME, Lanz C, Maumus F, Tohge T, Quesneville H, Alseekh S, Sørensen I, Lichtenstein G, Fich EA, Conte M, Keller H, Schneeberger K, Schwacke R, Ofner I, Vrebalov J, Xu Y, Osorio S, Aflitos SA, Schijlen E, Jiménez-Gómez JM, Ryngajllo M, Kimura S, Kumar R, Koenig D, Headland LR, Maloof JN, Sinha N, van Ham RCHJ, Lankhorst RK, Mao L, Vogel A, Arsova B, Panstruga R, Fei Z, Rose JKC, Zamir D, Carrari F, Giovannoni JJ, Weigel D, Usadel B, Fernie AR. (2014) The genome of the stress-tolerant wild tomato species Solanum pennellii. Nat Genet. 46(9):1034–8.

    Devisetty UK, Covington MF, Tat AV, Lekkala S, Maloof JN (2014). Polymorphism Identification and Improved Genome Annotation of Brassica rapa through Deep RNA Sequencing. G3 (Bethesda).

    Ichihashi Y, Aguilar-Martínez JA, Farhi M, Chitwood DH, Kumar R, Millon LV, Peng J, Maloof JN, Sinha NR (2014). Evolutionary developmental transcriptomics reveals a gene network module regulating interspecific diversity in plant leaf shape. Proceedings of the National Academy of Sciences. 111(25):E2616–21. PMCID: PMC4078850

    Chitwood DH, Ranjan A, Kumar R, Ichihashi Y, Zumstein K, Headland LR, Ostria-Gallardo E, Aguilar-Martínez JA, Bush S, Carriedo L, Fulop D, Martinez CC, Peng J, Maloof JN, Sinha NR (2014). Resolving Distinct Genetic Regulators of Tomato Leaf Shape within a Heteroblastic and Ontogenetic Context. THE PLANT CELL.

    Ron M, Dorrity MW, de Lucas M, Toal T, Hernandez RI, Little SA, Maloof JN, Klibenstein DJ, Brady SM (2013). Identification of Novel Loci Regulating Inter-specific Variation in Root Morphology and Cellular Development in Tomato. Plant Physiol. PMCID: PMC3668068

    Chitwood DH, Ranjan A, Martinez CC, Headland LR, Thiem T, Kumar R, Covington MF, Hatcher T, Naylor DT, Zimmerman S, Downs N, Raymundo N, Buckler ES, Maloof JN, Aradhya M, Prins B, Li L, Myles S, Sinha NR (2014). A modern ampelography: a genetic basis for leaf shape and venation patterning in grape. Plant Physiol. 164(1):259–72. PMCID: PMC3875807

    Koenig D, Jiménez-Gómez JM, Kimura S, Fulop D, Chitwood DH, Headland LR, Kumar R, Covington MF, Devisetty UK, Tat AV, Tohge T, Bolger A, Schneeberger K, Ossowski S, Lanz C, Xiong G, Taylor-Teeples M, Brady SM, Pauly M, Weigel D, Usadel B, Fernie AR, Peng J, Sinha NR, Maloof JN (2013). Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. Proceedings of the National Academy of Sciences 110(28):E2655–62. PMCID: PMC3710864

    Chitwood DH, Kumar R, Headland LR, Ranjan A, Covington MF, Ichihashi Y, Fulop D, Jiménez-Gómez JM, Peng J, Maloof JN, Sinha NR (2013). A quantitative genetic basis for leaf morphology in a set of precisely defined tomato introgression lines. THE PLANT CELL (7):2465–81. PMCID: PMC3753377

    Chitwood DH, Maloof JN, Sinha NR (2013). Dynamic transcriptomic profiles between tomato and a wild relative reflect distinct developmental architectures. Plant Physiol. PMCID: PMC3668051

    Maloof JN, Nozue K, Mumbach MR, Palmer CM (2013). LeafJ: An ImageJ Plugin for Semi-automated Leaf Shape Measurement. JoVE. 2013;(71).

    Palmer CM, Bush SM, Maloof JN. Phenotypic and Developmental Plasticity in Plants. eLS. John Wiley & Sons. Ltd: Chichester; 2012. p. 1–9.

    Sharlach M, Dahlbeck D, Liu L, Chiu J, Jiménez-Gómez JM, Kimura S, Koenig D, Maloof JN, Sinha N, Minsavage GV, Jones JB, Stall RE, Staskawicz BJ (2012). Fine genetic mapping of RXopJ4, a bacterial spot disease resistance locus from Solanum pennellii LA716. Theor Appl Genet.

    Seymour, D. K., Filiault, D. L., Henry, I. M., Monson-Miller, J., Ravi, M., Pang, A., Comai, L., et al. (2012). Rapid creation of Arabidopsis doubled haploid lines for quantitative trait locus mapping. Proceedings of the National Academy of Sciences of the United States of America, 109(11), 4227–4232. doi:10.1073/pnas.1117277109

    Filiault, D. L., & Maloof, J. N. (2012). A Genome-Wide Association Study Identifies Variants Underlying the Arabidopsis thaliana Shade Avoidance Response. PLoS Genetics, 8(3), e1002589. doi:10.1371/journal.pgen.1002589

    Chitwood, D. H., Headland, L. R., Kumar, R., Peng, J., Maloof, J. N., & Sinha, N. R. (2012). The developmental trajectory of leaflet morphology in wild tomato species. PLANT PHYSIOLOGY. doi:10.1104/pp.111.192518

    Chitwood, D. H., Headland, L. R., Filiault, D. L., Kumar, R., Jiménez-Gómez, J. M., Schrager, A. V., Park, D. S., et al. (2012). Native Environment Modulates Leaf Size and Response to Simulated Foliar Shade across Wild Tomato Species. PloS one, 7(1), e29570. doi:10.1371/journal.pone.0029570

    Jiménez-Gómez, J. M., Corwin, J. A., Joseph, B., Maloof, J. N., & Kliebenstein, D. J. (2011). Genomic analysis of QTLs and genes altering natural variation in stochastic noise. PLoS Genetics, 7(9), e1002295. doi:10.1371/journal.pgen.1002295

    Arana, M. V., Marín-de la Rosa, N., Maloof, J. N., Blázquez, M. A. & Alabadí, D. Circadian oscillation of gibberellin signaling in Arabidopsis. Proc Natl Acad Sci U S A 108, 9292-9297 (2011).

    Kim, K., Shin, J., Lee, S. H., Kweon, H. S., Maloof, J. N. & Choi, G. Phytochromes inhibit hypocotyl negative gravitropism by regulating the development of endodermal amyloplasts through phytochrome-interacting factors. Proc Natl Acad Sci U S A 108, 1729-1734 (2011).

    Stewart, J. L., Maloof, J. N. & Nemhauser, J. L. PIF Genes Mediate the Effect of Sucrose on Seedling Growth Dynamics. PLoS One 6, e19894 (2011).

    Nozue, K., Harmer, S. L. & Maloof, J. N. Genomic Analysis of Circadian Clock-, Light-, and Growth-Correlated Genes Reveals PHYTOCHROME-INTERACTING FACTOR5 as a Modulator of Auxin Signaling in Arabidopsis. Plant Physiol 156, 357-372 (2011).

    Chang, C. S., Maloof, J. N. & Wu, S. H. COP1-mediated degradation of BBX22/LZF1 optimizes seedling development in Arabidopsis. Plant Physiol 156, 228-239 (2011).

    Holtan, H. E., Bandong, S., Marion, C. M., Adam, L., Tiwari, S., Shen, Y., Maloof, J. N., Maszle, D. R., Ohto, M. A., Preuss, S., Meister, R., Petracek, M., Repetti, P. P., Reuber, T. L., Ratcliffe, O. J. & Khanna, R. BBX32, An Arabidopsis B-box Protein, Functions in Light Signaling by Suppressing HY5-Regulated Gene Expression And Interacting with STH2. Plant Physiol (2011).

    Kerwin, R. E., Jimenez-Gomez, J. M., Fulop, D., Harmer, S. L., Maloof, J. N. & Kliebenstein, D. J. Network Quantitative Trait Loci Mapping of Circadian Clock Outputs Identifies Metabolic Pathway-to-Clock Linkages in Arabidopsis. Plant Cell 23, 471-485 (2011).

    Maloof JN. Recent advances in regulation of flowering. F1000 Biol Rep 2010 Feb 11

    Brock MT, Maloof JN, and Weinig C. Genes underlying quantitative variation in ecologically important traits: PIF4 (phytochrome interacting factor 4) is associated with variation in internode length, flowering time, and fruit set in Arabidopsis thaliana. Mol Ecol 2010 Mar; 19(6) 1187-99.

    Brock MT, Dechaine JM, Iniguez-Luy FL, Maloof JN, Stinchcombe JR, and Weinig C. Floral Genetic Architecture: An Examination of QTL Architecture Underlying Floral (Co)Variation Across Environments. Genetics 2010 Sep 13.

    Jiménez-Gómez JM, Wallace AD, and Maloof JN. Network analysis identifies ELF3 as a QTL for the shade avoidance response in Arabidopsis. PLoS Genet 2010 Sep 9; 6(9).

    Balasubramanian S, Schwartz C, Singh A, Warthmann N, Kim MC, Maloof JN, Loudet O, Trainer GT, Dabi T, Borevitz JO, Chory J, & Weigel D (2009). QTL Mapping in New Arabidopsis thaliana Advanced Intercross-Recombinant Inbred Lines. PLoS ONE 4: e4318.

    Jiménez-Gómez JM, & Maloof JN (2009). Plant research accelerates along the (bio)informatics superhighway: symposium on plant sensing, response and adaptation to the environment. EMBO Rep 10: 568-72.

    Jimenez-Gomez JM, & Maloof JN (2009). Sequence diversity in three tomato species: SNPs, markers, and molecular evolution. BMC Plant Biol 9: 85.

    Schwartz C, Balasubramanian S, Warthmann N, Michael TP, Lempe J, Sureshkumar S, Kobayashi Y, Maloof JN, Borevitz JO, Chory J, & Weigel D (2009). Cis-regulatory Changes at FLOWERING LOCUS T Mediate Natural Variation in Flowering Responses of Arabidopsis thaliana. Genetics

    Filiault DL, Wessinger CA, Dinneny JR, Lutes J, Borevitz JO, Weigel D, Chory J, & Maloof JN (2008). Amino acid polymorphisms in Arabidopsis phytochrome B cause differential responses to light. Proc Natl Acad Sci U S A 105: 3157-62.

    Nozue K, Covington MF, Duek PD, Lorrain S, Fankhauser C, Harmer SL, Maloof JN. (2007) Rhythmic growth explained by coincidence between internal and external cues. Nature 448:358-61

    Weinig C, Johnston JA, Willis CG, Maloof JN. (2007) Antagonistic multilevel selection on size and architecture in variable density settings. Evolution Int J Org Evolution 61:58-67

    Balasubramanian S, Sureshkumar S, Agrawal M, Michael TP, Wessinger C, Maloof JN, Clark R, Warthmann N, Chory J, Weigel D (2006). The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana. Nat Genet 38: 711-5.

    Nozue K, Maloof JN. (2006) Diurnal regulation of plant growth. Plant Cell Environ 29:396-408

    Maloof JN (2005) Small but not forgotten. Heredity 96: 1-2.

    Lu L, Lee YR, Pan R, Maloof JN, & Liu B (2005) An internal motor kinesin is associated with the Golgi apparatus and plays a role in trichome morphogenesis in Arabidopsis. Mol Biol Cell 16: 811-23.

    Wolyn DJ, Borevitz JO, Loudet O, Schwartz C, Maloof J, Ecker JR, Berry CC, Chory J (2004). Light-response quantitative trait loci identified with composite interval and eXtreme array mapping in Arabidopsis thaliana. Genetics 167: 907-17.

    Maloof JN (2004) Plant development: slowing root growth naturally. Curr Biol 14: R395-6.

    Maloof, J. N. (2003). QTL for plant growth and morphology. Curr Opin Plant Biol 6, 85-90.

    Nemhauser, J.L., Maloof, J.N., and Chory, J. (2003). Building integrated models of plant growth and development. Plant Physiol 132, 436-439.

    Maloof, J. N. (2003). Genomic approaches to analyzing natural variation in Arabidopsis thaliana. Curr Opin Genet Dev 13, 576-582.

    Nordborg, M, JO Borevitz, J Bergelson, CC Berry, J Chory, J Hagenblad, M Kreitman, JN Maloof, T Noyes, PJ Oefner, EA Stahl, D Weigel. 2002. The extent of linkage disequilibrium in Arabidopsis thaliana. Nature Genetics. 30:190-193

    Borevitz, JO, JN Maloof, J Lutes, T. Davi, JL Redfern, GT Trainer, JD Werner, T Asami, CC Berry, D Weigel, J Chory. 2002. Quantitative trait loci controlling light and hormone response in two accessions of Arabidopsis thaliana. Genetics. 160:683-69

    Friedrichsen, D. M., Nemhauser, J., Muramitsu, T., Maloof, J. N., Alonso, J., Ecker, J. R., Furuya, M., and Chory, J. (2002). Three redundant brassinosteroid early response genes encode putative bHLH transcription factors required for normal growth. Genetics 162, 1445-1456.

    Maloof, JN, JO Borevitz, T Dabi, J Lutes, RB Nehring, JL Redfern, GT Trainer, JM Wilson, T Asami, CC Berry, D Weigel, J Chory. 2001. Natural variation in light sensitivity of Arabidopsis thaliana. Nature Genetics. 29:441-446

    Maloof, J. N., Borevitz, J. O., Weigel, D., and Chory, J. (2000). Natural variation in phytochrome signaling. Semin Cell Dev Biol 11, 523-530.

    Maloof, J. N., Whangbo, J., Harris, J. M., Jongeward, G. D., and Kenyon, C. (1999). A Wnt signaling pathway controls hox gene expression and neuroblast migration in C. elegans. Development 126, 37-49.

    Maloof, J. N., and Kenyon, C. (1998). The Hox gene lin-39 is required during C. elegans vulval induction to select the outcome of Ras signaling. Development 125, 181-190.