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CAHNRS Department of Horticulture Genomics Lab

Publications

2017

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

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

2016

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

2015

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

2014

Schaeffer S, Harper A, Raja R, Jaiswal P & Dhingra A (2014) Comparative analysis of predicted plastid-targeted proteomes of sequenced higher plant genomes. PLoS ONE 9(11): e112870. doi: 10.1371/journal.pone.0112870

Naveed K, Mitter N, Harper A, Dhingra A & Pappu HR (2014) Comparative Analysis of virus-specific small RNA profiles of three biologically distinct strains of Potato virus Y (PVY) in PVY-infected potato (Solanum tuberosum) cv. Russet Burbank. Virus Research 191:153–160.

Biesla B, Jiwan D, Fernandez-Marti A, Dhingra A and Rubio-Cabetas M (2014) Detection of SNP and validation of a SFP InDel (deletion) in inverted repeat region of the Prunus species chloroplast genome. Scientia Horticulturae168: 108-112. Bieslaetal2014

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 pear surfaces: Influence on physicochemical and sensory quality during storage. Postharvest Biology and Technology 87:27-32

2013

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. 11: 883-893 doi:10.1111/pbi.12081 Featured on the cover of September 2013 issue. KoepkeandSchaefferetal2013

Plant Biotechnology Journal

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 Jiwanetal2013

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

2012

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 Nicholsonetal_2012_PCTOC

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.

2011

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.

2010

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. Featured on the cover of the journal.

Naturegeneticscover

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

2009

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

2008

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

2007

A Dhingra A, VA James, HU Koop, MC Mok, R De Paepe, M Gallo, KM Folta. 2007. Tobacco – In: Kole C, Hall TC (eds) A Compendium of Transgenic Crop Plants. Blackwell Publishing, Oxford, UK. pp 1 – 56

2006

A Dhingra, DH Bies, KR Lehner and KM Folta. 2006. Green light adjusts the plastid transcriptome during early photomorphogenic development. Plant Physiology 142:1256-1266

KM Folta and A Dhingra. 2006. Transformation of strawberry: The basis for translational genomics in Rosaceae. In Vitro Cellular and Developmental Biology – Plant 42:482-490

MJ Moore, A Dhingra, PS Soltis, R Shaw, WG Farmerie, KM Folta and DS Soltis. 2006. Rapid and accurate pyrosequencing of angiosperm plastid genomes. BMC Plant Biology 6:17

KM Folta, A Dhingra, L Howard, P Stewart and CK Chandler. 2006. Characterization of LF9, an octaploid strawberry genetic line selected for rapid regeneration and transformation. Planta 224:1058-1067

2005-1996

KM Folta, A Dhingra, SA Maruhnich, DH Bies andJ Justice. 2005. Terrestrial and space applications of LEDs in regulating plant growth and development. Proceedings of Light Emitting Diodes 2005 Conference, San Diego, CA, October 17-20, 2005.

A Dhingra and KM Folta. 2005. ASAP: Amplification, sequencing and annotation of plastomes. BMC Genomics 6:176. (Highly accessed paper).

A Dhingra and H Daniell. 2005. Chloroplast transformation via organogenesis or somatic embryogenesis. Arabidopsis Protocols 2nd Ed. Methods in Molecular Biology 323 251- 269.

A Dhingra and H Daniell. 2004. Engineering of herbicide resistance pathways via plastid genetic engineering. In: Daniell H and Chase CD (eds), Molecular Biology of Plant Organelles, pp 491-512. Kluwer Academic Publishers.

A Dhingra, AR Portis Jr. and Henry Daniell. 2004. Enhanced translation of a chloroplast expressed RbcS gene restores SSU levels and photosynthesis in nuclear antisense RbcS plants. Proceedings of National Academy of Sciences, USA, 101:6315-6320.

H Daniell, O Ruiz and A Dhingra. 2004. Chloroplast transformation of higher plants. Methods in Molecular Biology 286:111-137.

S Kumar, A Dhingra and H Daniell. 2004. Plastid expressed betaine aldehyde dehydrogenase gene in carrot cultured cells, roots and leaves, confers enhanced salt tolerance. Plant Physiology 136:2843-2854.

S Kumar, A Dhingra and H Daniell. 2004. Stable transformation of the cotton plastid genome and maternal inheritance of transgenes. Plant Molecular Biology 56: 203-216.

A Dhingra, JP Khurana and AK Tyagi. 2004. Involvement of G-proteins and calmodulin in lightdependent control of the expression of (psbA, psaA and rbcL) in rice (Oryza sativa L.). Plant Science 166:163-168.

H Daniell and A Dhingra. 2002. Multigene engineering: Dawn of an exciting new era in plant biotechnology. Current Opinion in Biotechnology 13:136-141.

AK Tyagi, JP Khurana, AK Sharma, A Mohanty, A Dhingra, S Raghuvanshi and T Gaur. 2002. Mechanism of regulation of gene expression for chloroplast proteins. In: SK Sopory, R Oelmuller, SC Maheshwari (eds). Signal transduction in plants. Current advances, pp 297- 307. Kluwer Academic/Plenum Publishers, New York.

H Daniell, A Dhingra and LA Allison. 2002. Chloroplast Transformation: From Basic Molecular Biology to Biotechnology. Reviews in Plant Biotechnology and Biochemistry 1:1-20.

H Daniell, A Dhingra and A Fernandez San-Milan. 2001. Chloroplast transgenic approach for the production of antibodies, biopharmaceuticals and edible vaccines. In International Congress of Photosynthesis; Brisbane, Australia, 2001:S40-04.

AK Tyagi, A Dhingra, S Raghuvanshi. 2000. Light-regulated expression of photosynthesisrelated genes. In: M Yunus, U Pathre, P Mohanty (eds), Probing Photosynthesis: Mechanism, Regulation and Adaptation, pp 324-341.Taylor and Francis Publishers Ltd., London

M Grover, A Dhingra, AK Sharma, et al. 1999. Involvement of phytochrome, Ca2+ and phosphorylation in light-dependent control of transcript levels for plastid genes (psbA, psaA and rbcL) in rice (Oryza sativa L.). Physiologia Plantarum 105:701-707.

M Grover, AK Sharma, A Dhingra, et al. 1998. Regulation of plastid gene expression involves calcium and protein phosphatases/kinases for signal transduction. Plant Science 137:185- 190.

AK Tyagi, AK Sharma, M Grover, A Mohanty, A Dhingra, et. al. 1998. Investigations on expression and engineering of genes in rice. In: Gupta, P. K. (ed), Proceedings of the Symposium on Genetics and Biotechnology in crop improvement, pp 169-181. Rastogi Publications, Meerut, India.

AK Tyagi, A Sharma, S Bajaj, Anju, A Mohanty, A Dhingra, S Raghuvanshi, NR Chaudhury, S Mukherjee. 1997. Investigations on expression and engineering of plastid and nuclear genes in rice. In: Abstracts of General Meeting of the International Program on Rice Biotechnology, Malacca, Malaysia.

AK Tyagi, M Grover, A Sharma, CN Chowdhry, A Mohanty, A Dhingra, S Raghuvanshi, N Maheshwari, SC Maheshwari, NR Choudhury, S Mukherjee and VP Singh. 1996. Studies on expression and engineering of plastid and nuclear genes in rice. In: Abstracts of 5th Annual Meeting, National Rice Biotechnology Network, IARI, New Delhi.