Horticulture Department and the Center of Applied Genetic Technologies
Ph.D. (1998) Michigan State University

CAGT Room 124


2015-2020 NSF Plant Genome Research Program. “Exploitation of genetic and epigenetic variation in the regulation of tomato fruit quality traits”.

2014-2016 OARDC Research Enhancement Competitive Grants Program, Seed grant. “Expression, purification and characterization of the tomato fruit shape proteins SUN and OVATE”.

2013-2016 USDA National Institute of Food and Agriculture. “The regulation and improvement of fruit weight in fresh market tomato”.


Tomato Analyzer software application to study color, fruit and leaf morphology (

Trait ontology for fruits (terms and mathematical descriptors for each term), incorporated in SGN (

Tomato fruit morphology database, incorporated in SGN (

Gene expression profiles of tomato tissues and time points from genetic stocks ( D005, D006, D008, D009, D012.

Selected Publications:

R.J. Pattison, F. Csukasi, Y. Zheng, Z. Fei, E. van der Knaap, C. Catalá. 2015. Comprehensive tissue-specific transcriptome analysis reveals distinct regulatory programs during early tomato fruit development. Plant Physiol 168: 1684-1701.

Sun, L., G.R. Rodriguez, J.P. Clevenger, E. Illa-Berenguer, J. Lin, J. Blakeslee, W. Liu, Z. Fei, A. Wijeratne, T. Meulia, E. van der Knaap. 2015. Candidate gene selection and detailed morphological evaluations of fs8.1, a quantitative trait locus controlling tomato fruit shape. J Exp Bot 2015 Jul 14. pii: erv361.

Wu, S., J.P. Clevenger, L. Sun, S. Visa, Y. Kamiya, Y. Jikumaru, J. Blakeslee, E. van der Knaap. 2015. The control of tomato fruit elongation orchestrated by sun, ovate and fs8.1 in a wild relative of tomato. Plant Science 238: 95-104

Xu, C., K.L. Liberatore, C.A. MacAlister, Z. Huang, Y.H. Chu, K. Jiang, C. Brooks, M. Ogawa-Ohnishi, G. Xiong, M. Pauly, J. Van Eck, Y. Matsubayashi, E. van der Knaap, Z.B. Lippman. 2015. A cascade of arabinosyltransferases controls shoot meristem size in tomato. Nat Genet 47: 784-792.

Clevenger, J.P., J. Van Houten, M. Blackwood, G. R. Rodríguez, Y. Jikumaru, Y.Kamiya, M. Kusano, K. Saito, S. Visa, E. van der Knaap. 2015. Network analyses reveal shifts in transcript profiles and metabolites that accompany the expression of SUN and an elongated tomato fruit. Plant Physiol 168: 1164-1178.

Illa-Berenguer, E., J. Van Houten, Z. Huang, E. van der Knaap. 2015. Rapid and reliable identification of tomato fruit weight and locule number loci by QTL-seq. Theor Appl Genet 128: 1329-1342.

Blanca, J., J. Montero-Pau, C. Sauvage, G. Bauchet, E. Illa, M.J. Díez, D. Francis, M. Causse, E. van der Knaap, J. Cañizares. 2015. Genomic variation in the tomato, from wild ancestors to contemporary breeding accessions. BMC Genomics 16:257.

Visa, S., C. Cao, B.B. McSpadden Gardener, E. van der Knaap. 2014. Modeling of tomato fruits into nine shape categories using elliptic Fourier shape modeling and Bayesian classification of contour morphometric data. Euphytica 200: 429-439.

Van der Knaap, E., M. Chakrabarti, Y.H. Chu, J. Clevenger, E. Illa Berenguer, Z. Huang, N. Keyhaninejad, Q. Mu, L. Sun, Y. Wang, S. Wu. 2014. What lies beyond the eye: the molecular mechanisms regulating tomato fruit weight and shape. Frontiers in Plant Science 5: 227.

Liu, N., S. Wu, J. Van Houten, Y. Wang, B. Ding, Z. Fei, T.H. Clarke, J.W. Reed, E. van der Knaap. 2014. Down-regulation of AUXIN RESPONSE FACTORS 6 and 8 by microRNA 167 leads to floral development defects and female sterility in tomato. J Exp Bot 65:2507-2520.

Monforte, A.J., A.I. Diaz, A. Cano-Delgado, E. van der Knaap. 2014. The genetic basis of fruit morphology in horticultural crops: lessons from tomato and melon. J Exp Bot 65:4625-4637.

Chakrabarti, M., N. Zhang, C. Sauvage, S. Munos, J. Blanca, J. Canizares, M.J. Diez, R. Schneider, J. McClead, M. Mazurek, M. Causse and E. van der Knaap. 2013. A cytochrome P450 regulates a domestication trait in tomato. Proc Natl Acad Sci USA 110:17125-17130

De Franceschi P., T. Stegmeir, A. Cabrera, E. van der Knaap, U.R. Rosyara, A.M. Sebolt, L. Dondini, E. Dirlewanger, J. Quero-Garcia, J.A. Campoy and A.F. Iezzoni 2013. Cell Number Regulator genes in Prunus provide candidate genes for the control of fruit size in sweet and sour cherry. Mol Breeding 32: 311-326.

Rodríguez, G.R., H.J. Kim and E. van der Knaap 2013. Mapping of two suppressors of OVATE (sov) loci in tomato. Heredity 111: 256-264.

McCouch et al., 2013. Feeding the future. Nature 499: 23-24

Jiang, N., S. Visa, S. Wu and E. van der Knaap. 2013. Rider transposon insertion and phenotypic change in tomato. In: Topics in Current Genetics, Plant transposable elements – Impacts on genome structure and function. Eds: M.A. Grandbastien and J.M. Casacuberta. Springer, Heidelberg Germany.

Huang, Z., J. Van Houten, G. Gonzalez, H. Xiao and E. van der Knaap. 2013. Genome-wide identification, phylogeny and expression analysis of SUN, OFP and YABBY gene family in tomato. Mol Genet Genomics 288: 111-129.

Van der Knaap, E., C. Anderson and G.R. Rodriguez. 2013. Chapter 3, Diversity within cultivated tomato. In: Genetics, Genomics and Breeding of Tomato. Eds: B.E. Liedl, J.A. Labate, J.R. Stommel, A. Slade and C. Kole. CRC Press, Boca Raton FL, USA.

Grandillo, S., P. Termolino and E. van der Knaap. 2013. Chapter 6, Molecular mapping of complex traits in tomato. In: Genetics, Genomics and Breeding of Tomato. Eds: B.E. Liedl, J.A. Labate, J.R. Stommel, A. Slade and C. Kole. CRC Press, Boca Raton FL, USA.

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