doi: 10.1104/pp.16.00137, Valkonen, J. P. T., Keskitalo, M., Vasara, T., Pietilä, L., and Raman, D. K. V. (1996). *Correspondence: Satya Swathi Nadakuduti, nadakudu@msu.edu David S. Douches, douchesd@msu.edu, Front. doi: 10.1016/j.phytochem.2011.12.003. Genome-editin… Genomics has several practical applications in crop improvement. Efficient CRISPR/Cas9 genome editing of Phytoene desaturase in cassava. LC-MS analysis of solanidane glycoalkaloid diversity among tubers of four wild potato species and three cultivars (Solanum tuberosum). 15, 1509–1519. Nature 532:293. doi: 10.1038/nature.2016.19754, Waltz, E. (2018). CRISPR/Cas9 nuclease engineered to have a Cas9 protein and a guide RNA (gRNA) that is a fusion of CRISPR RNA (crRNA) and trans-activating crRNA (tracrRNA). Nearly 150 scientists and industrialists attended a recent meeting outside Cambridge to review progress in the application of genomics to crop plant improvement. %���� Silencing of multiple susceptibility genes (S-genes) by RNAi resulted in late blight resistance in potato (Sun et al., 2016). A., and Liu, D. R. (2016). doi: 10.1038/nbt0118-6b, Wang, S., Zhang, S., Wang, W., Xiong, X., Meng, F., and Cui, X. 7:11. doi: 10.1186/1471-2229-7-11, Dlugosz, E. M., Lenaghan, S. C., and Stewart, C. N. (2016). Plant Sci. Plants 1:15034. doi: 10.1038/NPLANTS.2015.34, El Kasmi, F., and Nishimura, M. T. (2016). Diploid and tetraploid Solanum chacoense genotypes that synthesize leptine glycoalkaloids and deter feeding by Colorado potato beetle. doi: 10.1080/13102818.2003.10817052, Bachem, C. W. B., Speckmann, G. J., Van der Linde Piet, C. G., Verheggen, F. T. M., Hunt, M. D., Steffens, J. C., et al. Self-compatibility allows fixing of gene edits and segregating out any insertions of foreign DNA from the process of transformation by selection in the progeny. By transient expression of reagents as plasmid DNA or via RNPs in potato protoplasts, mutagenized lines in all four alleles were regenerated with tubers that had the desired high amylopectin starch (Andersson et al., 2017, 2018). Antisense expression of polyphenol oxidase genes inhibits enzymatic browning in potato tubers. <>stream 14, 169–176. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). Changes in the steroidal alkaloid solasodine during development of Solanum nigrum and Solanum incanum. An overview of the factors affecting sugar content of potatoes. doi: 10.1371/journal.pone.0144591, Butler, N. M., Baltes, N. J., Voytas, D. F., and Douches, D. S. (2016). doi: 10.1080/07352689609701934, Voytas, D. F. (2013). View all doi: 10.1016/j.plantsci.2004.08.006, McKey, D., Elias, M., Pujol, M. E., and Duputié, A. (2018). Proc. Sharma, N. Seetharama, C.T. (2012). 60, 520–523. Potato steroidal glycoalkaloids: biosynthesis and genetic manipulation. 2020-12-19T15:41:07-08:00 StMYB44 negatively regulates phosphate transport by suppressing expression of PHOSPHATE1 in potato. doi: 10.1146/annurev-arplant-042811-105552, Waltz, E. (2015). 16, 844–855. Plant Biotechnol. Am. (2017). (2018). Phytochemistry 68, 327–334. 2020-12-19T15:41:07-08:00 67, 461–466. this is done by me and my team mates of Wayamba University Sri Lanka for our project.From now we decided to allow download this file.I would be greatful if you… Since Science named it as “Breakthrough of the Year” and Fortune magazine hailed it as “Biotech’s Billion Dollar Breakthrough” in 2003, RNAi has significantly gained prominence as the method of choice for researchers sleuthing the structure and function of important genes. (2017). doi: 10.1126/science.1193070, Ren, C., Liu, X., Zhang, Z., Wang, Y., Duan, W., Li, S., et al. Emerging fungal threats to animal, plant and ecosystem health. Using RNPs, possibility of integration of plasmid-derived DNA sequences or foreign DNA into the host genome can be eliminated. After 6–8 weeks, shoots emerge and are grown on shoot induction media. (2017). doi: 10.1038/ncomms14261, Lu, Y., and Zhu, J. K. (2017). A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. application/pdf As genomics becomes more widely used in agriculture, researchers and breeders are increasingly using Illumina technology to … doi: 10.1093/nar/gkt780, Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. Next, we discuss the challenges of genome-editing in clonally propagated polyploid crops and summarize the insights gained from case studies along with future prospects focused on enhancement of potato breeding using this technology. doi: 10.1007/s00299-016-2062-3, PubMed Abstract | CrossRef Full Text | Google Scholar. Polyploidy and vegetative reproduction are unique to plants, frequently found in a large number of important food crops including root and tuber crops, several perennial fruit crops as well as forage crops (McKey et al., 2010; Gemenet and Khan, 2017). J. Transcription activator-like effector nucleases (TALEN)-mediated targeted DNA insertion in potato plants. doi: 10.1016/j.cell.2015.09.038, Zetsche, B., Heidenreich, M., Mohanraju, P., Fedorova, I., Kneppers, J., Degennaro, E. M., et al. Breed. Genet. Plant Pathol. Potatoes for sustainable global food security. FIGURE 1. In this section, we describe recently developed plant sequence resources. Am. Rev. Rasthali genome. CRISPR/Cas9-mediated efficient editing in phytoene desaturase (PDS) demonstrates precise manipulation in banana cv. Potato Res. 12, 934–940. SSNs create double stranded breaks (DSBs) at the target locus and rely on cellular repair mechanisms to correct these breaks (Figure 1A). Gene editing could be used to create genetic variation that is identical to that already present in crop varieties grown in Europe; however, it would nonetheless be regulated due to this process-based approach. Plant genome engineering with sequence-specific nucleases. doi: 10.1126/science.aaf6395, Jung, J. H., and Altpeter, F. (2016). Nat. (A) Double stranded DNA (dsDNA) break repair in a cell occurs either by non-homologous end joining (NHEJ), where the cleaved DNA molecule is simply rejoined, often with indels in coding regions (green) that result in gene knock-out or by homologous recombination (HR), where a donor repair template (red) can be used for targeted knock-in experiments, where a single or few nucleotides alterations, insertion of an entire transgene or suites of transgenes can be made. doi: 10.1016/j.molp.2016.11.013, Ma, J., Xiang, H., Donnelly, D. J., Meng, F. R., Xu, H., Durnford, D., et al. Role of Bioinformatics in Crop Improvement . Nature 484, 186–194. Improving crops with gene editing provides a range of options: by altering only a few nucleotides from billions found in the genomes of living cells, altering the full allele or by inserting a new gene in a targeted region of the genome. Vlnv enzyme breaks down sucrose to the reducing sugars glucose and fructose in cold-stored potato tubers which form dark-pigmented bitter tasting products when processed at high temperatures (Sowokinos, 2001; Kumar et al., 2004; Matsuura-Endo et al., 2006). Nat. 24 Crop Sci. doi: 10.1111/j.1469-8137.2010.03210.x, Moehs, C. P., Allen, P. V., Friedman, M., and Belknap, W. R. (1997). Genome-editing systems have been utilized in a wide variety of plant species to characterize gene functions and improve agricultural traits. 15, 817–823. Annu. Efficient genome editing of wild strawberry genes, vector development and validation. Science 337, 816–821. The ultimate goal would be to develop new potato cultivars with low SGA levels in tubers while still maintaining high levels in above ground tissues for crop protection. 1–2 cm shoots are excised and transferred to root induction media. A definition of biotechnology from the U.S. Office of Technology Assessments reads, "Any technique that uses living organisms to make or modify products, to improve plants or animals, or to develop microorganisms for specific purposes.“ 7:1904. doi: 10.3389/fpls.2016.01904, Matsuura-Endo, C., Ohara-Takada, A., Chuda, Y., Ono, H., Yada, H., Yoshida, M., et al. Potato, (Solanum tuberosum Group Tuberosum L.) (2n = 4x = 48) represents one such heterozygous, polyploid crop that is clonally propagated by tubers. Phytochemistry 46, 489–494. Base editor constitutes fusion of nickase Cas9 (nCas9) with cytidine deaminase enabling the editing of single bases by C→T conversion of single-stranded target. 16, 1868–1877. Recently, an extracellular surface protein called receptor-like protein ELR (elicitin response) from the wild potato species, S. microdontum, has been reported to recognize an elicitin that is highly conserved in Phytophthora species offering a broad spectrum durable resistance to this pathogen (Du et al., 2015). J. Exp. The primary in vivo steroidal alkaloid glucosyltransferase from potato. 34, 372–377. Biotechnol. 113, 12619–12621. Plant Mol. B., Packer, M. S., Zuris, J. These genomics-based approaches aim to decipher the entire genome, including genic and ... 3.3. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. 56, 1412–1422. BMC Plant Biol. Reduced polyphenol oxidase gene expression and enzymatic browning in potato (Solanum tuberosum L.) with artificial microRNAs. doi: 10.1093/jxb/erx026, Zong, Y., Wang, Y., Li, C., Zhang, R., Chen, K., Ran, Y., et al. (2014). The three major methods of genetic transformation in plants are: Agrobacterium-mediated transformation, biolistics and protoplast transfection. Intracellular innate immune surveillance devices in plants and animals. A simple gateway-assisted construction system of TALEN genes for plant genome editing. 52, 1–15. Andersson, M., Turesson, H., Olsson, N., Fält, A. S., Olsson, P., Gonzalez, M. N., et al. While conventional breeding and genetic analysis are challenging in cultivated potato due to the above mentioned features, majority of diploid potatoes possess gametophytic self-incompatibility (SI). Loss of susceptibility as a novel breeding strategy for durable and broad-spectrum resistance. Plant Biotechnol. Reinventing potato as a diploid inbred line-based crop. Genomics 18, 89–99. Targeted mutagenesis in soybean using the CRISPR-Cas9 system. The major areas of genomics which are adopted for improvement of crops are: Tissue Culture Genetic Engineering Molecular diagnostics Molecular markers Development of … Biotechnol. (2016) with the permission of the copyright holder (John Wiley & Sons, Inc.). Indeed, the limiting step to the successful transformation of most of the major crops has not been transgene insertion itself, but rather the regeneration of viable … (2016). Genome manipulation in polyploid heterozygous crops include the task of simultaneously targeting multiple alleles and screening large number of transformants to recover multiallelic mutagenic lines. RNAi has the potential to beco… Effects of storage temperature on the contents of sugars and free amino acids in tubers from different potato cultivars and acrylamide in chips. CRISPR/Cas12a that has PAM requirement of “TTTN”, allowing targeting of AT rich regions, is emerging as equally effective alternative, implemented in various plants (Kim et al., 2017; Tang et al., 2017). (B) Agrobacterium-mediated plant transformation and regeneration in potato. 64, 327–350. Genome-editing will best be applied to potato improvement using diploid F1 hybrids. Winner of the Standing Ovation Award for “Best PowerPoint Templates” from Presentations Magazine. J. Agric. The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. However, SGAs also have positive impact as defensive allelochemicals deterring insect herbivores (Sinden et al., 1980; Sanford et al., 1990, 1997). Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato. Plant Biotechnol. 2015-01-31T09:48:26+05:30 In this review, we describe various genome-editing platforms available for plants, their delivery mechanisms and discuss the recent USDA and the European Union clarifications regarding regulatory aspects of gene-edited crops. Commun. Genome editing in maize directed by CRISPR-Cas9 ribonucleoprotein complexes. doi: 10.1021/jf00068a056, Sinden, S. L., Sanford, L. L., and Osman, S. F. (1980). J. (2018). B., and Wang, N. (2016). doi: 10.1016/j.phytochem.2006.10.025, McCue, K. F., Allen, P. V., Shepherd, L. V. T., Blake, A., Whitworth, J., Maccree, M. M., et al. The recent accumulation of nucleotide sequences of model plants, as well as of applied species such as crops and domestic animals, has provided fundamental information for the design of sequence-based research applications in functional genomics. Bioinformatics and Genomics Genomics is the study of complex sets of genes, their expression and the most vital role they play in biology. Nucleic Acids Res. Two approaches currently used to combat this disease are fungicide spraying and breeding for disease resistance. Biotechnol. Arican, E., and Gozukirmizi, N. (2003). doi: 10.1007/s11816-017-0448-5, Malnoy, M., Viola, R., Jung, M.-H., Koo, O.-J., Kim, S., Kim, J.-S., et al. More recently, adenine base editors have been developed that convert A→G (or T→C) (Gaudelli et al., 2017). 35, 438–440. Cas12a cleaves DNA at sites distal to PAM and introduces a staggered DSB with a 4–5-nt 5′ overhang, unlike blunt DSB by Cas9. Studies have shown differential levels of SGA accumulation among plant organs and developmental stages (Valkonen et al., 1996; Eltayeb et al., 1997; Friedman and McDonald, 1997). doi: 10.1038/s41477-018-0178-x, Kaur, N., Alok, A., Shivani, Kaur, N., Pandey, P., Awasthi, P., et al. 74, 15–21. Rep. 6:32289. doi: 10.1038/srep32289, Rommens, C. M., Ye, J., Richael, C., and Swords, K. (2006). doi: 10.1371/journal.pone.0177966, Nicolia, A., Proux-Wéra, E., Åhman, I., Onkokesung, N., Andersson, M., Andreasson, E., et al. For multiplexing, to target more than one gene at a time, Cas12a requires only a single RNA PolIII promoter to drive several crRNAs, whereas Cas9 requires relatively large constructs (Zetsche et al., 2017). Null segregants – progeny of the transgenic, edited parent that still retain the germline edit but lack the integrated T-DNA or other foreign sequence – are excempt from regulation. Nat. Plant Biotechnol. Tuber quality traits, such as reduced SGAs or potatoes with reduced bruising, are some of the traits that could be improved using genome-editing. Crit. However, limited progress has been made in other such crops including sweetpotato, strawberry, grapes, citrus, banana etc., In this review we summarize the developments in genome-editing platforms, delivery mechanisms applicable to plants and then discuss the recent developments in regulation of genome-edited crops in the United States and The European Union. Copyright © 2018 Nadakuduti, Buell, Voytas, Starker and Douches. Protoplast transformation and regeneration of plants from leaf protoplasts also can lead to somaclonal variation, which may have negative impact(s) on plant development. Cloning and expression of solanidine UDP-glucose glucosyltransferase from potato. (2018). (2016). Science 354:aaf6395. Crouch, K.K. Silencing of beta-carotene hydroxylase increases total carotenoid and beta-carotene levels in potato tubers. (2010). Genome-editing combined with inbred diploid line development would be a monumental shift in the potential for genetic improvement and opens up possibilities for creating a better potato breeding pipeline. Mol. Protoplasts facilitate direct delivery of DNA into cells with gene-editing reagents expressed as plasmid DNA for transient transformation. (2017). KPSB_A_976152_O Nat. Potato Res. 6:13. doi: 10.1186/1471-2229-6-13, Diretto, G., Welsch, R., Tavazza, R., Mourgues, F., Pizzichini, D., Beyer, P., et al. Applications of Structural Genomics in Crop Improve-ment. 7:10654. doi: 10.1038/ncomms10654, Chen, Y., Wang, Z., Ni, H., Xu, Y., Chen, Q., and Jiang, L. (2017). Genome-editing was successfully applied in diploid potato to overcome gametophytic SI by knocking-out the Stylar ribonuclease gene (S-RNase) (Ye et al., 2018). 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