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CAHNRS Department of Horticulture Genomics Lab

Publications

2018

Bielsa, B., Hewitt, S., Reyes-Chin-Wo, S., Jose Rubio-Cabetas, M., Dhingra, A. (2018) Identification of water use efficiency related genes in ‘Garnem’ almond-peach rootstock using time-course transcriptome analysis. PLoS ONE doi: 10.1371/journal.pone.0205493

2017

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

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.