Dr. Amit Dhingra

Amit Dhingra

www.genomics.wsu.edu

Professor, Department of Horticulture. Ph.D. 2000, University of Delhi South Campus, India, and Rutgers, The State University of New Jersey.

Research

Horticultural crops have unique biology and are thus an intriguing study system Investigations in my research program are focused on understanding important biological phenomenon in horticultural crops. We integrate transcriptomics, molecular biology, plant physiology, functional and translational genomics approaches to identify gene(s) participating in a biological process. In collaboration with the in-house bioinformatics expertise in Rosaceae, the ultimate goal is to develop resources that will support the establishment of time saving and cost effective methodologies for effective horticultural crop improvement.

I have had a long standing interest in chloroplast genomics, plastid transformation and gene expression. The recently described ASAP methodology (Dhingra and Folta, 2005), which facilitates the rapid and economical sequencing of chloroplast genomes is being employed to resolve phylogenetic issues in plant Orders and Families. A bioinformatics resource for organelle genomics is being developed based on this method. Plastid transformation offers several benefits compared to nuclear integration of transgenes. Maternal inheritance of plastid genome in majority of crops mitigates concerns of transgene outcross. We are interested in extending this technology to tree fruit crops as an additional research resource and a novel product for the market.

An additional interest includes photobiology and photosynthesis engineering. We have recently described the effect of green light, considered to be a benign part of the light spectrum, on the plastid transcriptome. I am interested in the identification of green light response elements in the chloroplast genome. Photosynthetic efficiency can have a bearing on the biomass production in plants. We are interested in modifying Rubisco to tamper with its affinity for oxygen and efficiency of carbon dioxide capture for eventually improving biomass.

Selected Publications

Schaeffer SM, Christian R, Castro-Velasquez N, Hyden B, Lynch-Holm V, Dhingra A (2017) Comparative ultrastructure of fruit plastids in three genetically diverse genotypes of apple (Malus × domestica Borkh.) during development. Plant Cell Reports. doi:10.1007/s00299-017-2179-z

Ikiz D, Gallardo RK, Dhingra A, Hewitt S. (2017) Assessing consumers’ preferences and willingness to pay for novel sliced packed fresh pears: A latent class approach. Agribusiness. doi: 10.1002/agr.21532.

Hewitt, S., Kilian, B., Hari, R., Koepke, T., Sharpe, R., & Dhingra, A. (2017). Evaluation of multiple approaches to identify genome-wide polymorphisms in closely related genotypes of sweet cherry (Prunus avium L.). Computational and Structural Biotechnology Journal. doi:http://dx.doi.org/10.1016/j.csbj.2017.03.002

Lawrence NC, Hauvermale AL, Dhingra A, Burke IC (2017) Population structure and genetic diversity of Bromus tectorum within the small grain production region of the Pacific Northwest. Ecology and Evolution. doi: 10.1002/ece3.3386

Yin C, Schlatter D, Schroeder K, Mueth N, Prescott A, Dhingra A, Hulbert S, Paulitz TC (2017) Bacterial communities on wheat grown under long-term conventional tillage and no-till in the Pacific Northwest of the US. Phytobiomes. doi:10.1094/PBIOMES-09-16-0008-R

Zúñiga, C. E., Jarolmasjed, S., Sinha, R., Zhang, C., Kalcsits, L., Dhingra, A., & Sankaran, S. (2017). Spectrometric techniques for elemental profile analysis associated with bitter pit in apples. Postharvest Biology and Technology, 128, 121-129. doi:http://dx.doi.org/10.1016/j.postharvbio.2017.02.009 Zunigaetal_2017

Davis, G., Kanazawa, A, Schottler, M., Kohzuma, K., Froehlich, JE, Rutherford, W., Satoh-Cruz, M., Minhas, D., Dhingra, A. & Kramer, DM (2016). Limitations to Photosynthesis by Proton Motive Force-Induced Photosystem II Photodamage. eLife 5: e16921.

Schaeffer S, Hendrickson C, Fox R, Dhingra A (2016) Identification of Differentially Expressed Genes between ‘Honeycrisp’ and ‘Golden Delicious’ Apple Fruit Tissues Reveal Candidates for Crop Improvement. Horticulturae 2016, 2(3), 11; doi:10.3390/horticulturae2030011

Sharpe RM, Koepke T, Harper A, Grimes J, Galli M, Satoh-Cruz M, Kalyanaraman A, Evans K, Kramer D, Dhingra A (2016) CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites. PLoS One 11: e0152404

Strand, SD., Livingston, A., Satoh-Cruz, M., Koepke, T., Enlow, HM*., Fisher, N., Froehlich, JE., Cruz, JA., Minhas, D., Hixson, KK., Kohzuma, K., Lipton, M., Dhingra, A. and Kramer, D (2016). Defects in Expression of Chloroplast Proteins Leads to H2O2 Accumulation and Activation of Cyclic Electron Flow around Photosystem I. Frontiers in Plant Science 7 doi:10.3389/fpls.2016.02073.

Wang, J., Zhai, Y., Liu, W., Dhingra, A., Pappu, H. R., & Liu, Q. (2016). Structure and Genome Organization of Cherry Virus A (Capillovirus, Betaflexiviridae) from China Using Small RNA Sequencing. Genome announcements, 4(3). doi:10.1128/genomeA.00364-16

Bodah E, Porter L, Cordova B and Dhingra A (2015) Phenotypic Evaluation and Classification of Pea (Pisum sativum L.) Accessions and Commercial Cultivars for Fusarium Root Rot Resistance. Euphytica 208: 63-72.

Mandadi N., Hendrickson C., Savithri H.S., Thippeswamy R., Pai N.R., Javeed S., Verghese A., Rai A., Pappu A., Nagaraje G. and Dhingra A (2015) Genome sequences of Photorhabdus luminescens strains isolated from entomopathogenic nematodes from southern India. Genomics Data 6: 46-47.

Syamaladevi R, Adhikari A, Lupien SL, Dugan F, Bhunia K, Dhingra A & Sablani SS (2015) Ultraviolet-C light inactivation of Penicillium expansum on fruit surfaces, Food Control, 50: 297-303

Syamaladevi RM, Lupien SL, Bhuniaa K, Sablania SS, Dugan F, Rasco B, Killinger K, Dhingra A, Ross C (2014) UV-C light inactivation kinetics of Penicillium expansum on pearsurfaces: Influence on physicochemical and sensory quality during storage. Postharvest Biology and Technology 87:27-32

Koepke T, Schaeffer S, Harper A, Dicenta F, Edwards M, Henry RJ, Moller BL, Meisel L, Oraguzie N, Silva H, Sanchez-Perez R, Dhingra A (2013) Comparative genomics analysis in Prunoideae to identify biologically relevant polymorphisms. Plant Biotechnol J. doi:10.1111/pbi.12081

Koepke T, Dhingra A (2013) Rootstock scion somatogenetic interactions in perennial composite plants. Plant Cell Rep 32 (9):1321-1337. doi:10.1007/s00299-013-1471-9

Jiwan D, Roalson EH, Main D, Dhingra A (2013) Antisense expression of peach mildew resistance locus O (PpMlo1) gene confers cross-species resistance to powdery mildew in Fragaria x ananassa. Transgenic Res. doi:10.1007/s11248-013-9715-6

Garczynski SF, Coates BS, Unruh TR, Schaeffer S, Jiwan D, Koepke T, Dhingra A (2013) Application of Cydia pomonella expressed sequence tags: Identification and expression of three general odorant binding proteins in codling moth. Insect Sci 20 (5):559-574. doi:10.1111/j.1744-7917.2012.01560.x

KL Nicholson, N Tarlyn, T Armour, M Swanson and A Dhingra 2012. Effect of phyllotactic position and cultural treatments toward successful direct shoot organogenesis in dwarf ‘Pixie’ grapevine (Vitis vinifera L.). Plant Cell, Tissue and Organ Culture DOI: 10.1007/s11240-012-0173-2

Syamaladevi RM, Lu X, Sablani SS, Insan SK, Adhikari A, Killinger K, Rasco B, Dhingra A, Bandyopadhyay A, Annapure U (2012) Inactivation of Escherichia coli Population on Fruit Surfaces Using Ultraviolet-C Light: Influence of Fruit Surface Characteristics. Food and Bioprocess Technology DOI 10.1007/s11947-012-0989-0

A Fernandez I Marti, B Athanson, T Koepke, C Font I Forcada, A Dhingra, N Oraguzie. 2012 Genetic diversity and relatedness of sweet cherry (Prunus avium L.) cultivars based on single nucleotide polymorphic markers. Frontiers in Plant Science 3: 116.

K Kohzuma, CD Bosco, A Kanazawa, A Dhingra, W Nitschke, J Meurer and DM Kramer. 2012 Thioredoxin-insensitive plastid ATP synthase that performs moonlighting functions. Proceedings of the National Academy of Sciences USA DOI: 10.1073/pnas.1115728109

T Koepke, S Schaeffer, V Krishnan, D Jiwan, A Harper, M Whiting, N Oraguzie and A Dhingra. 2012 Rapid gene-based SNP and haplotype marker development in non-model eukaryotes using 3′UTR sequencing. BMC Genomics 13: 18.

R Ahmad, DE Parfitt, J Fass, E Ogundiwin, A Dhingra, TM Gradziel, D Lin, NA Joshi, P Martinez-Garcia and CH Crisosto. 2011 Whole genome sequencing of peach (Prunus persica L.) for SNP identification and selection. BMC Genomics. 12:569.

J Rosnow, S Offermann, J Park, T Okita, N Tarlyn, A Dhingra and G Edwards. 2011 In vitro cultures and regeneration of Bienertia sinuspersici (Chenopodiaceae) under increasing concentrations of sodium chloride and carbon dioxide. Plant Cell Reports 30:1541-53.

M Moore, N Hassan, M Gitzendanner, R Bruenn, M Croley, A Vandeventer, J Horn, A Dhingra, S Brockington, M Latvis, J Ramdial, R Alexandre, A Piedrahita, Z Xi, C Davis, P Soltis & D Soltis. 2011 Phylogenetic analysis of the plastid inverted repeat for 244 species: insights into deeper-level angiosperm relationships from a long, slowly evolving sequence region. International Journal of Plant Sciences 172: 541-558.

R Velasco, A Zharkikh, J Affourtit, A Dhingra, A Cestaro, A Kalyanaraman et al. 2010 The genome of the domesticated apple (Malus x domestica Borkh.). Nature Genetics 42: 833-839.

K Folta, MA Clancy, S Chamala, AM Brunings, A Dhingra, L Gomide, RJ Kulathinal, N Peres, TM Davis & WB Barbazuk. 2010 A transcript accounting from diverse tissues of a cultivated strawberry. The Plant Genome 3: 1-16.

A Livingston, JA Cruz, K Kohzuma, A Dhingra and DM Kramer. 2010 An Arabidopsis mutant with high cyclic electron flow around photosystem I (hcef) involving the NDH complex. Plant Cell 22: 221 – 233

S Brockington, R Alexandre, J Ramdial, M Moore, S Crawley, A Dhingra, K Hilu, D Soltis and P Soltis. 2009 Phylogeny of the Caryophyllales sensu lato: revising hypothesis on pollination biology and perianth differentiation in the core Caryophyllales. International Journal of Plant Sciences 170: 627-643

Md M Haque, A Kalyanaraman, A Dhingra, N Abu-Lail and K Graybeal. 2009 DNAJig: A new approach for building DNA nanostructures. IEEE International Conference on Bioinformatics & Biomedicine. Nov 1-4, Washington DC

B Sosinski, V Shulaev, A Dhingra, A Kalyanaraman, R Bumgarner, D Rokhsar, I Verde, R Velasco, A Abbot. 2009 Rosaceous Genome Sequencing: Perspectives and Progress. In: Folta KM and Gardner SE (eds) Genetics and Genomics of Rosaceae. Plant Genetics and Genomics: Crops and Models vol 6 pp 601 – 605

MD Logacheva, TH Samigullin, A Dhingra, AA Penin. 2008 Chloroplast genomics and phylogenetic analysis of Fagopyrum esculentum ssp ancestralis – a wild ancestor or cultivated buckwheat. BMC Plant Biology 8: 59

S Jian, P Soltis, M Gitzendanner, M Moore, R Li, T Hendry, Y Qiu, A Dhingra, C Bell, D Soltis. 2008. Resolving an ancient, rapid radiation in Saxifragales. Systematic Biology 57: 28-57