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Faculty - Benildo G. de los Reyes









Benildo G. de los Reyes
Professor of Molecular Genetics
School of Biology and Ecology

Cooperating Professor
Dept. of Molecular and Biomedical Sciences

313 Hitchner Hall
Phone: (207) 581-2995
Fax: (207) 581-2537

Ph.D., Oklahoma State University, 1999

Research Topic

Plant stress physiology and biochemistry; Oxidative signaling; Gene regulation and genetic network modeling; Regulon engineering


Overview of Research

The multi-faceted defenses of plants against the physiological perturbations caused by environmental extremes are configured by integrative functioning of a large number of genes, operating through an intricately coordinated regulatory network.  Under this level of complexity, expressing the full stress tolerance potential of a plant requires fine-scale regulation of the transcriptome and proteome. Research in my laboratory is based on a combination of ‘empirical’ and ‘predictive’ paradigms of genetics and molecular biology with the long-term goals of understanding the: 1) Hierarchy of stress response regulatory networks at the transcriptional and post-transcriptional levels and how such networks configure the physiological and biochemical defenses at the cellular and whole-plant levels; 2) Regulatory cross talks that integrate biotic and abiotic stress response pathways; 3) Critical network hubs that determine phenotypic variation for complex stress-related traits; and 4) Genetic and epigenetic changes that lead to network rewiring during speciation and domestication.   We are addressing these goals by using reference plant species (Oryza sativa and Arabidopsis thaliana) with well-established genetic and genomic resources to conduct genome-enabled investigations facilitated by the  tools of transcriptomics (microarray, mRNA-SEQ, miRNA-Seq, and other NGS-based tools), forward genetics (transgenesis, mutagenesis, interspecific introgression), cellular physiology and biochemistry (protein-DNA and protein-protein interactions) and bioinformatics (regulatory network modeling, phylogenetic footprinting).


Representative Publications

Xu F, Park MR, Mohanty B, Herath V, Kitazumi A, Yun SJ, De los Reyes BG (2012) Cis-regulatory signatures of orthologous groups of stress-associated bZIP transcription factors from rice, sorghum and Arabidopsis based on phylogenetic footprints (Under review).

Mohanty B, Yeo HC, Wijaya E, De los Reyes BG, Lee D-Y (2012) Patterns of cis-element enrichment revealed potential regulatory modules involved in the regulation of low-oxygen response transcriptomes of rice and Arabidopsis (Under review).

Park MR, Baek S-H, De los Reyes BG, Yun SJ, Hasenstein KH (2012) Transcriptome profiling characterizes phosphate deficiency effects on carbohydrate metabolism in rice leaves. Journal of Plant Physiology 169:193-205.

Rioux R, Manmathan H, Jia Y, De los Reyes BG, Tavantzis S (2011) Comparative analysis of putative pathogenesis-related gene expression in two Rhizoctonia solani pathosystems. Current Genetics 57:391-408.

Park MR, Yun KY, Herath V, Mohanty B, Xu F, Bajic VB, Yun SJ, De los Reyes BG (2010) Supra-optimal expression of the cold-regulated OsMyb4 transcription factor in transgenic rice changes the complexity of transcriptional network with major effects on stress tolerance and panicle development. Plant Cell and Environment 33:2209-2230.

Yun KY, Park MR, Mohanty B, Herath V, Xu F, Mauleon R, Wijaya E, Bajic VB, Bruskiewich R, De los Reyes BG (2010) Transcriptional regulatory network triggered by oxidative signals configures the early response mechanisms of japonica rice to chilling stress. BMC Plant Biology 10:e16. [HIGHLY ACCESSED]

Zhang Y, XuanJ, De los ReyesBG,  Clarke R, Ressom HW (2010) Reconstruction of gene regulatory modules in cancer cell cycle by multi-source data integration. PLoSOne 5:4-e10268.

Ressom HW, Lakshman D, Yun SJ, Pramanik SK, De los Reyes BG (2009) Microarray data analysis using machine learning methods. In: Biosystems Engineering, A. Nag (editor), McGraw Hill Pub., pp. 1-32.

Zhang Y, Xuan J, De los Reyes BG, Clarke R, Ressom HW (2009) Reverse engineering module networks by PSO-RNN hybrid modeling. BMC Genomics 10:S15e.

Antoine W, De los Reyes BG, Miernyk JA, Stewart JM (2009) Molecular evolution of the plant SLT protein family. Icfai Journal of Genetics and Evolution 2:56-73.

Zhang Y, Xuan J, De los Reyes BG, Clarke R, Ressom HW (2008) Identification of network motifs for transcription factors by integrating multi-source biological data. BMC Bioinformatics 9:203e. [HIGHLY ACCESSED]

De los Reyes BG, Lakshman D, Yun SJ, Ressom H (2008) Agricultural genomics. In: Agricultural Biotechnology, A. Nag (editor), PHI Learning Private Ltd., pp. 55-88.

Irish BM, Corell JM, Feng C, Bentley T, De los Reyes BG (2007) Characterization of a resistance locus (Pfs-1) to the spinach downy mildew pathogen (Peronospora farinosa f. sp. spinaciae) and development and evaluation of a co-dominant molecular marker linked to Pfs1. Phytopathology 98:894-900.

Cheng C, Yun KY, Ressom H, Mohanty B, Bajic VB, Jia Y, Yun SJ, De los Reyes BG (2007) An early response regulatory cluster induced by low temperature and hydrogen peroxide in seedlings of chilling-tolerant japonica rice. BMC Genomics 8:e175.

Park MR, Baek SH, De los Reyes BG,Yun SJ (2007) Overexpression of a high-affinity transporter gene from tobacco (NtPT1) enhances phosphate uptake and accumulation in transgenic rice plants. Plant and Soil 292:259-269.

Ballou S, Yun KY, Cheng C, De los Reyes BG (2007) Cold sensitivity gradient in tuber-bearing Solanum based on physiological and transcript profiles. Crop Science 47:2027-2035.

Antoine W, Stewart JM, De los Reyes BG(2005) The rice homolog of the sodium/lithium tolerance (SLT1) gene functions as molecular chaperone in vitro. Physiologia Plantarum 125: 299-310.

Morsy MR, Almutairi AM, Gibbons J, Yun SJ, De los Reyes BG (2005) The OsLti6 genes encoding low-molecular-weight membrane proteins are differentially expressed in rice cultivars with contrasting sensitivity to low temperature. Gene 344:171-180.

Cho EA, Lee CA, Kim YS, Baek SH, De los Reyes BG, Yun SJ (2005) Expression of r-tocopherol methyltransferase improves tocopherol composition in lettuce (Latuca sativa L.). Molecules and Cells 19:16-22.

Choi DG, Yoo NH, Yu CH, De los Reyes BG, Yun SJ (2004) The activities of antioxidant enzymes in response to oxidative stresses and hormones in paraquat-tolerant Rehmannia glutinosa plants. Journal of Biochemistry and Molecular Biology 37:618-624.

McGrath JM, Shaw RS, De los Reyes BG, Weiland J (2004) Construction of a sugar beet BAC library from a hybrid that combines diverse traits. Plant Molecular Biology Reporter 22:23-28.

De los Reyes BG, Morsy M, Gibbons J, Varma TSN, Antoine W, McGrath JM, Halgren R, Redus M (2003) A snapshot of the low temperature stress transcriptome of developing rice seedlings (Oryza sativa L.) via ESTs from subtracted cDNA library. Theoretical and Applied Genetics 107:1071-1082.

De los Reyes BG, Myers SJ, McGrath JM (2003) Induction of glyoxylate cycle enzymes by stress as a marker for seedling vigor in sugar beet (Beta vulgaris L.). Molecular Genetics and Genomics 269:692-698.

De los Reyes BG, McGrath JM (2003) Cultivar-specific seedling vigor and expression of a putative oxalate oxidase germin-like protein in sugar beet (Beta vulgaris L.). Theoretical and Applied Genetics 107:54-61.

Multani DS, Khush GS, De los Reyes BG, Brar DS (2003) Alien gene introgression and development of monosomic alien addition lines from Oryza latifolia Desv. to rice, Oryza sativa L. Theoretical and Applied Genetics 107:395-405.

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