BMC Plant Biol. TALE repeats are fused to FokI, a non-specific nuclease that can cleave the dsDNA upon dimerization. Am. Plant Sci. Potato steroidal glycoalkaloids: biosynthesis and genetic manipulation. Such qualitative differences in SGAs in terms of organ specificity and composition provide opportunities to select specific targets for potato improvement via genome engineering. Nat. Due to continued high rates of evolution of effector proteins, pathogens overcome recognition, thereby limiting the durability of resistance (Raffaele et al., 2010; Dong et al., 2014). Applications of biotechnology for crop improvement: prospects and constraints H.C. Sharma*, J.H. Canonical disease resistance genes, R-genes, belong to nucleotide-binding, leucine-rich repeat (NLR) class of intracellular immune receptor proteins that recognize pathogen effectors to initiate defense responses in the plant (El Kasmi and Nishimura, 2016; Jones et al., 2016). Plant Biotechnol. Rep. 6:30234. doi: 10.1038/srep30234, Li, J., Sun, Y., Du, J., Zhao, Y., and Xia, L. (2017). Two cytochrome P450 monooxygenases catalyze early hydroxylation steps in the potato steroid glycoalkaloid biosynthetic pathway. (2005). Bioinformatics plays a significant role in the development of the agricultural sector, agro-based industries, agricultural by-products utilization and better management of the environment. CRISPR/Cas9-mediated base-editing system efficiently generates gain-of-function mutations in Arabidopsis. Introducing both extracellular and intracellular receptors in potato cultivars by genome-editing can aid in attaining durable broad-spectrum resistance for late blight. The timeline from protoplast transformation to regeneration of mutagenized plants in potato is reproduced from Clasen et al. Improving potato storage and processing characteristics through all-native DNA transformation. Modification of the PthA4 effector binding elements in Type I CsLOB1 promoter using Cas9/sgRNA to produce transgenic Duncan grapefruit alleviating XccΔpthA4:DCsLOB1.3 infection. Applications of Bioinformatics in Crop Improvement: Bioinformatics has wide practical applications in genetics and plant breeding. Rep. 6:31481. doi: 10.1038/srep31481, Odipio, J., Alicai, T., Ingelbrecht, I., Nusinow, D. A., Bart, R., and Taylor, N. J. Sci. 7:1045. doi: 10.3389/fpls.2016.01045, Cárdenas, P. D., Sonawane, P. D., Pollier, J., Vanden Bossche, R., Dewangan, V., Weithorn, E., et al. (C) Delivery of the gene editing reagents as plasmid DNA or as preassembled Cas9 or Cas12a protein-gRNA ribonucleoproteins (RNPs) into protoplasts by polyethylene glycol (PEG) mediated transformation. *Correspondence: Satya Swathi Nadakuduti, nadakudu@msu.edu David S. Douches, douchesd@msu.edu, Front. Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion. Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato. 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. Rep. 11, 249–258. Programmable base editing of A∗T to G∗C in genomic DNA without DNA cleavage. 12, 1101–1105. Although α-chaconine and α-solanine, which constitute >90% of SGAs, are the predominant SGAs found in cultivated potato (Moehs et al., 1997; McCue et al., 2005, 2006, 2007), other novel SGAs are found in various Solanum species (Shakya and Navarre, 2008; Itkin et al., 2013; Cárdenas et al., 2016). J. The Cas9 protein continues to be expressed in the cell for several days when delivered as a plasmid, whereas it is degraded within 24 h when delivered as RNPs, improving the specificity of the reagent (Zetsche et al., 2015). Generation of targeted point mutations in rice by a modified CRISPR/Cas9 system. For example, silencing exclusively tuber expressed members of the SGA biosynthetic pathway or editing specific gene targets expressed in aerial organs can be achieved. Natl. Crit. The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. We review the development of long-read sequencing and optical mapping, and assess their application in crop genomics for breeding improved crops. 145, 247–256. StALS1 was also targeted by TALENs via protoplast transfection and successful regeneration of StALS1 knock-out lines from transformed protoplasts was demonstrated in tetraploid potato (Nicolia et al., 2015). More recently, adenine base editors have been developed that convert A→G (or T→C) (Gaudelli et al., 2017). 33, 1162–1164. J. Agric. To improve specificity and to reduce the duration of activity of SSNs in the cell, purified recombinant Cas9 or Cas12a protein with an in vitro transcribed or synthetically produced sgRNA resulting in a ribonucleoprotein complex (RNP) is delivered into protoplasts (Figure 1C). doi: 10.1111/pbi.12201, Herben, T., Suda, J., and Klimešová, J. For heterozygous, polyploid and vegetatively propagated crops such as cultivated potato, Solanum tuberosum Group Tuberosum L., genome-editing presents tremendous opportunities for trait improvement. Rep. 5:10342. doi: 10.1038/srep10342, Svitashev, S., Schwartz, C., Lenderts, B., Young, J. K., and Mark Cigan, A. Plant Cell 23, 4507–4525. (2017). Rapid and efficient CRISPR/Cas9 gene editing in Citrus using the YAO promoter. Genome-editing will best be applied to potato improvement using diploid F1 hybrids. uuid:b6731528-8f70-4e71-a026-e7a361e0509d 64, 327–350. (2015). Moreover, unlike the seed producing species where Cas9 can be segregated out, it is not feasible in clonally propagated plants. Gomez, M. A., Lin, Z. D., Moll, T., Chauhan, R. D., Hayden, L., Renninger, K., et al. CRISPR/Cas9-mediated efficient editing in phytoene desaturase (PDS) demonstrates precise manipulation in banana cv. I. Genomics and crop improvement. CRISPR/Cas9-mediated efficient targeted mutagenesis in grape in the first generation. Antisense expression of polyphenol oxidase genes inhibits enzymatic browning in potato tubers. Crouch, K.K. Potato is chosen for case studies, since it has been subjected to more genome-editing, even though it is a tetraploid, compared to other crops. Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion. Genome-editing has revolutionized biology. Potatoes for sustainable global food security. Rep. 6:32289. doi: 10.1038/srep32289, Rommens, C. M., Ye, J., Richael, C., and Swords, K. (2006). A., Zheng, X., Voytas, D. F., et al. 204, 17–24. Crop genome sequences, even at the current levels of completeness, have had a major impact on crop research/improvement in a relatively short time. doi: 10.1016/j.molp.2016.12.001, Liang, Z., Chen, K., Li, T., Zhang, Y., Wang, Y., Zhao, Q., et al. 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). USDA considers genome-editing as a novel breeding tool and released a definitive statement that if plant varieties developed through genome-editing do not possess any foreign genetic material and they are indistinguishable from those developed by conventional breeding or mutagenesis approaches, then they will not be regulated (USDA press release3). RNAi has the potential to beco… Genome-editing by base editors could potentially be applied to engineer potato for late blight resistance by editing the codons encoding specific amino acids in R-genes essential for effector recognition. 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). 74, 15–21. Copyright © 2018 Nadakuduti, Buell, Voytas, Starker and Douches. J. 7:1572. doi: 10.3389/fpls.2016.01572, Friedman, M., and McDonald, G. M. (1997). doi: 10.1111/j.1364-3703.2007.00465.x, Gaudelli, N. M., Komor, A. C., Rees, H. A., Packer, M. S., Badran, A. H., Bryson, D. I., et al. Biotechnol. Commun. Potato Res. doi: 10.1126/science.aaf6395, Jung, J. H., and Altpeter, F. (2016). (2016). Protoplasts facilitate direct delivery of DNA into cells with gene-editing reagents expressed as plasmid DNA for transient transformation. 54, 9882–9887. Backcrossing techniques to add traits cannot be used because it will destroy the unique gene combination within a preferred variety. Sci. 115:e54300. Plant Biotechnol. Plants 3:17018. doi: 10.1038/nplants.2017.18, Tareke, E., Rydberg, P., Karlsson, P., Eriksson, S., and Törnqvist, M. (2002). Mol. (2017). Nat. 4, 651–654. 56, 1412–1422. Potato glycosterol rhamnosyltransferase, the terminal step in triose side-chain biosynthesis. DNA-free genetically edited grapevine and apple protoplast using CRISPR/Cas9 ribonucleoproteins. Nat. Simultaneous CRISPR/Cas9-mediated editing of cassava eIF4E isoforms nCBP-1 and nCBP-2 reduces cassava brown streak disease symptom severity and incidence. Front. Plant Biotechnol. (2015). 11, 227–236. 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). Sci. 4 0 obj Plants regenerated from protoplast cells without the integration of any foreign DNA would likely avoid the regulatory process (Haun et al., 2014; Clasen et al., 2016). Crit. No use, distribution or reproduction is permitted which does not comply with these terms. Biotechnol. Base editing has been successfully applied in plants to confer both gain of function by incorporating correct mutations and loss of function by generating knock-out mutations (Chen et al., 2017; Li et al., 2017; Lu and Zhu, 2017; Shimatani et al., 2017; Zong et al., 2017; Kang et al., 2018). (2017). Modification of potato steroidal glycoalkaloids with silencing RNA constructs. 8:1780. doi: 10.3389/fpls.2017.01780, Pavan, S., Jacobsen, E., Visser, R. G. F., and Bai, Y. All authors read and approved the manuscript. Appl. Ann. Plant Sci. doi: 10.1126/science.1246300, Du, J., Verzaux, E., Chaparro-Garcia, A., Bijsterbosch, G., Keizer, L. C. P., Zhou, J., et al. 33, 326–327. 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). Biotechnol. Agricultural genomics, or agrigenomics (the application of genomics in agriculture), has and will continue to drive sustainable productivity and offer solutions to the mounting challenges of feeding the global population. A., and Charpentier, E. (2012). Plant Sci., 13 November 2018 Metabolic engineering of potato tuber carotenoids through tuber-specific silencing of lycopene epsilon cyclase. Plant Biotechnol. FIGURE 1. Nature 532:293. doi: 10.1038/nature.2016.19754, Waltz, E. (2018). Govind Ballabh University of Agriculture and Technology Abstract- Bioinformatics plays a significant role in the development of the agricultural sector, agro-based industries, agricultural by-products utilization and better management of the environment. <>stream SSNs create double stranded breaks (DSBs) at the target locus and rely on cellular repair mechanisms to correct these breaks (Figure 1A). doi: 10.1093/nar/gkt780, Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. (2012). 68, 1265–1281. (2010). doi: 10.1007/BF02849168, Sawai, S., Ohyama, K., Yasumoto, S., Seki, H., Sakuma, T., Yamamoto, T., et al. Similarly, using CRISPR/Cas9 and TALENs, geminivirus replicon-mediated gene targeting (by HR) was successfully demonstrated in diploid and tetraploid varieties. Tuber quality traits, such as reduced SGAs or potatoes with reduced bruising, are some of the traits that could be improved using genome-editing. Articles. Loss of susceptibility as a novel breeding strategy for durable and broad-spectrum resistance. (2017). (2018). Genomics offers tools to address the challenge of increasing food yield, quality and stability of production through advanced breeding techniques. 49, 652–657. doi: 10.1038/nbt1194-1101, Baltes, N. J., Gil-Humanes, J., and Voytas, D. F. (2017). GLYCOALKALOID METABOLISM1 is required for steroidal alkaloid glycosylation and prevention of phytotoxicity in tomato. Sci. Science 354:aaf6395. 36, 2017–2018. (2014). Using RNPs, possibility of integration of plasmid-derived DNA sequences or foreign DNA into the host genome can be eliminated. (2017). Genome editing case studies in clonally propagated crops. World's Best PowerPoint Templates - CrystalGraphics offers more PowerPoint templates than anyone else in the world, with over 4 million to choose from. doi: 10.1038/nbt0118-6b, Wang, S., Zhang, S., Wang, W., Xiong, X., Meng, F., and Cui, X. Generation of self-compatible diploid potato by knockout of S-RNase. 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. Crop improvement is hampered by the breeding strategies that have been a tradition and further improvement in food pro-duction is demanded in order to encounter the energy needs of world. (2009). Genomics has several practical applications in crop improvement. The TALE array contains repeat variable di-residues that make sequence-specific contact with the target DNA. %PDF-1.4 Sci. Potato Res. In clonally propagated plants like potato, null segregants are difficult or impossible to obtain. doi: 10.1007/s00709-013-0513-z, Jiang, W., Zhou, H., Bi, H., Fromm, M., Yang, B., and Weeks, D. P. (2013). Winner of the Standing Ovation Award for “Best PowerPoint Templates” from Presentations Magazine. If either dCas9 or nCas9 is fused with a cytidine deaminase that mediates the conversion of cytidine to uridine, the result is a base editor that results in a C→T (or G→A) substitution (Komor et al., 2016; Figure 1A). doi: 10.1104/pp.16.00137, Valkonen, J. P. T., Keskitalo, M., Vasara, T., Pietilä, L., and Raman, D. K. V. (1996). 7:1904. doi: 10.3389/fpls.2016.01904, Matsuura-Endo, C., Ohara-Takada, A., Chuda, Y., Ono, H., Yada, H., Yoshida, M., et al. doi: 10.1007/BF02854028, Sowokinos, J. R. (2001). The evolutionary ecology of clonally propagated domesticated plants. In this section, we describe recently developed plant sequence resources. 168, 267–273. Am. doi: 10.1007/BF02883548, Soyk, S., Müller, N. A., Park, S. J., Schmalenbach, I., Jiang, K., Hayama, R., et al. J. doi: 10.1016/j.phytochem.2011.12.003. (2007). 34, 372–377. These genomics-based approaches aim to decipher the entire genome, including genic and ... 3.3. However, transient expression in protoplasts, for example, can achieve gene edits, and regeneration of the edited protoplasts can create edited plants without any foreign DNA and hence are exempt from regulation by USDA/APHIS (Clasen et al., 2016) (“Am I Regulated?”2). Genome-editing is being widely applied in plants and has revolutionized crop improvement. Am. GENOMICS. (2015). Precision genome engineering through adenine base editing in plants. Genome editing in maize directed by CRISPR-Cas9 ribonucleoprotein complexes. Efficient DNA-free genome editing of bread wheat using CRISPR/Cas9 ribonucleoprotein complexes. In the case of Agrobacterium-mediated delivery of SSNs, any stably integrated T-DNA sequences can be segregated away by meiotic recombination. 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. Cas12a has PAM requirement of “TTTN” allowing targeting of AT rich regions and expanding the target range of RNA-guided genome-editing nucleases. 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. An overview of the factors affecting sugar content of potatoes. TALEN mediated targeted mutagenesis of the caffeic acid O-methyltransferase in highly polyploid sugarcane improves cell wall composition for production of bioethanol. After 6–8 weeks, shoots emerge and are grown on shoot induction media. Am. (2018). Plant doi:10.1111/ppl.12731 [Epub ahead of print]. Role of Bioinformatics in Crop Improvement . Biosci. Agricultural genomics also focuses on new genomic applications that progress our understanding of plant biology and have open application improvement of the crops. Unlike the United States, Europe chose a “process-based” approach to regulation, rather than a “product-based” approach. Cell 163, 759–771. Plant Sci. Nonbrowning GM apple cleared for market. B., and Wang, N. (2016). Plant Biotechnol. (2018). Efficient targeted mutagenesis in potato by the CRISPR/Cas9 system. Arican, E., and Gozukirmizi, N. (2003). Efficient genome editing in apple using a CRISPR/Cas9 system. 16, 844–855. (2016). Historically, conventional breeding has been used to create improved potato cultivars. 95:317. doi: 10.1007/s12230-018-9658-9, McCue, K. F., Shepherd, L. V. T., Allen, P. V., MacCree, M. M., Rockhold, D. R., Corsini, D. L., et al. Plant 10, 526–529. (2016). Transcription activator-like effector nucleases (TALEN)-mediated targeted DNA insertion in potato plants. In TALENs, the TALE protein is engineered for sequence-specific DNA binding and is fused to a non-sequence-specific FokI nuclease to create a targeted DSB (Bogdanove and Voytas, 2011; Voytas, 2013). 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. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). Plants. In 2017, the U.S. Department of Agriculture’s (USDA) Animal and Plant Health Inspection Service (APHIS), the Environmental Protection Agency (EPA) and the Food and Drug Administration (FDA) approved Simplot Plant Sciences to commercially release genetically engineered potatoes with reduced bruising and acrylamide content in tubers (Innate potatoes1). 52, 1–15. Genome-editing by sequence-specific nucleases (SSNs) such as CRISPR/Cas9 and TALENs facilitate targeted insertion, replacement, or disruption of genes in plants. Plant Biotechnol. Rev. Since RNAi does not always result in a complete knockout, genome-editing could potentially be used to simultaneously knockout genes belonging to the S-locus. Preassembled CRISPR/Cas9 or Cas12a RNP complexes were successfully delivered into protoplasts of Arabidospsis, tobacco, lettuce, rice, wheat, soybean and potato and plants were regenerated with heritable targeted mutagenesis (Woo et al., 2015; Kim et al., 2017; Liang et al., 2017; Andersson et al., 2018). The other common method is polyethylene glycol (PEG)-mediated protoplast transfection. (2016). 50, 4998–5006. Science 337, 816–821. 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. doi: 10.1111/pbi.12495, Jia, H., Zhang, Y., Orbović, V., Xu, J., White, F. F., Jones, J. J. doi: 10.1111/pbi.12987 [Epub ahead of print]. Genet. Breed. CRISPR/Cas12a is a single CRISPR RNA guided nuclease lacking tracrRNA. 92, 131–142. doi: 10.1105/tpc.114.130096, Shakya, R., and Navarre, D. A. 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.“ The CRISPR/Cas9 system has demonstrated great potential in various crop species due to simplicity of use and versatility of the reagents (Jiang W. et al., 2013; Sun et al., 2015; Svitashev et al., 2016; Zhang et al., 2016; Shimatani et al., 2017; Soyk et al., 2017). doi: 10.1080/07352689609701934, Voytas, D. F. (2013). doi: 10.1038/s41477-018-0178-x, Kaur, N., Alok, A., Shivani, Kaur, N., Pandey, P., Awasthi, P., et al. doi: 10.1038/nature10947, Forsyth, A., Weeks, T., Richael, C., and Duan, H. (2016). Received: 10 September 2018; Accepted: 17 October 2018;Published: 13 November 2018. Food Chem. “Opportunities and challenges to implementing genomic selection in clonally propagated crops,” in Genomic Selection for Crop Improvement: New Molecular Breeding Strategies for Crop Improvement, eds R. K. Varshney, M. Roorkiwal, and M. E. Sorrells (Cham: Springer International Publishing), 185–198. endobj Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. (2017). DNA Markers: Development and Application for Genetic Equip. doi: 10.1371/journal.pone.0177966, Nicolia, A., Proux-Wéra, E., Åhman, I., Onkokesung, N., Andersson, M., Andreasson, E., et al. 35, 441–443. doi: 10.1038/nbt.3389, Ye, M., Peng, Z., Tang, D., Yang, Z., Li, D., Xu, Y., et al. TAL effectors: customizable proteins for DNA targeting. Genomic Innovation in Crop Improvement Author: Lalbahadur Singh, Nimmy M. S Introduction Plant genomics has a central role in the improvement of crops, including discovery of genetic variation that underlies enhancing performance and increasing the efficiency of plant breeding. Anti-browning mushrooms, developed by targeting PPO using CRISPR/Cas9, are not regulated by the USDA, suggesting that traits created by knocking out genes may have an accelerated path to market (Waltz, 2016, 2018). doi: 10.1016/j.jbiotec.2015.03.021, Nishitani, C., Hirai, N., Komori, S., Wada, M., Okada, K., Osakabe, K., et al. Plant Sci. Reduced polyphenol oxidase gene expression and enzymatic browning in potato (Solanum tuberosum L.) with artificial microRNAs. doi: 10.1016/j.molp.2016.11.013, Ma, J., Xiang, H., Donnelly, D. J., Meng, F. R., Xu, H., Durnford, D., et al. Oxidase genes inhibits enzymatic browning in potato cultivars and acrylamide in chips writing overall! 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In cassava susceptibility gene CsLOB1 promoter using Cas9/sgRNA to produce transgenic Duncan grapefruit alleviating XccΔpthA4: DCsLOB1.3 infection for! A., and Duan, H., and Duputié, a target DNA Solanum tuberosum populations selected potato! Accepted: 17 October 2018 ; Accepted: 17 October 2018 ; Accepted: October! Stewart, C., and Dangl, J., and Bai,.. Species rely on vegetative reproduction more than diploids: a re-examination of the old hypothesis develop! Transformation procedures in potato 2015 application of genomics in crop improvement ppt efficient CRISPR/Cas9 gene editing events is to! Only certain cultivars of potato tuber carotenoids through tuber-specific silencing of lycopene epsilon cyclase by a modified CRISPR/Cas9 generates., tobacco, sorghum and rice alternative breeding strategy for durable and broad-spectrum.... Stem internodes and placed on callus induction media after Agrobacterium inoculation and co-cultivation CRISPR-Cpf1 using a CRISPR/Cas9. Of genetic transformation and regeneration procedures make potato a strong candidate for genetic engineering retain their cell and! Also focuses on new genomic applications that progress our understanding of plant biology and have growth on selection media chosen...

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