Abstract
Genome editing with artificially engineered nucleases is an advanced molecular technology for pursuing precise and effective genetic engineering. In this technology, engineered nucleases induce DNA double-strand breaks at targeted sites in a genome, stimulating the DNA repair system in cells, thus enabling site-directed mutagenesis. Genome editing using CRISPR (clustered regularly interspaced short palindromic repeats)/CRISPR-associated protein9 (Cas9), originating from a defence system of prokaryotes, is a powerful technology that is now being widely utilized in molecular research studies, as well as in breeding programmes of various plant species, including fruit trees, to impart either novel or enhanced traits to established commercial cultivars or to new cultivars/genotypes. Recently, several reports have demonstrated successful apple genome editing and the introduction of important traits, such as those for early flowering and reduced fire blight susceptibility, to popular commercial cultivars, such as ‘Gala’ and ‘Golden Delicious’. It is important to point out that these reports reveal that such genome-edited/mutant apple plants or cell lines do not carry foreign genes. Nevertheless, during the process of precise genome editing, the coexistence of various types of mutations referred to as “mosaic mutations” and off-target effects are major concerns. Therefore, to minimize such effects, selection of target sequences and estimation of off-target effects for CRISPR/Cas9 has been developed for many organisms, and these have also been employed for apple by using in silico analysis based on genome information. On the other hand, apple genome heterozygosity has led to difficulties in genome editing, as the complex genome of apple precludes the use of some of these basic techniques for genome editing. Therefore, further studies focused on genome information and culture techniques tailored for apple are needed. It will be highly critical for each apple cultivar in developing precise and efficient genome editing for apple. This chapter will provide an overview of current studies of genome editing in apple and will discern and explore how this strategy will provide insights into molecular breeding technologies for genetic improvement of the apple.
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References
Abu-Qaoud H, Skirvin RM, Chevreau E (1990) In vitro separation of chimeral pears into their component genotypes. Euphytica 48(2):189–196
Andersson M, Turesson H, Olsson N, Fält AS, Ohlsson P, Gonzalez MN, Samuelsson M, Hofvander P (2018) Genome editing in potato via CRISPR-Cas9 ribonucleoprotein delivery. Physiol Plant 164(4):378–384
Borejsza-Wysocka EE, Malnoy M, Meng X, Bonasera JM, Nissinen RM, Kim JF, Beer SV, Aldwinckle HS (2004) Silencing of apple proteins that interact with DspE, a pathogenicity effector from Erwinia amylovora, as a strategy to increase resistance to fire blight Acta Hortic 663:469–474
Bortesi L, Fischer R (2015) The CRISPR/Cas9 system for plant genome editing and beyond. Biotech Adv 33(1):41–52
Broothaerts W, Keulemans J, Van Nerum I (2004) Self-fertile apple resulting from S-RNase gene silencing. Plant Cell Rep 22(7):497–501
Čermák T, Baltes NJ, Čegan R, Zhang Y, Voytas DF (2015) High-frequency, precise modification of the tomato genome. Genome Biol 16(1):232. https://doi.org/10.1186/s13059-015-0796-9
Charrier A, Vergne E, Dousset N, Richer A, Petiteau A, Chevreau E (2019) Efficient targeted mutagenesis in apple and first time edition of pear using the CRISPR-Cas9 system. Front Plant Sci 10:40. https://doi.org/10.3389/fpls.2019.00040
Chen X, Li S, Zhang D, Han M, Jin X, Zhao C, Wang S, Xing L, Ma J, Ji J, An N (2019) Sequencing of a wild apple (Malus baccata) genome unravels the differences between cultivated and wild apple species regarding disease resistance and cold tolerance. G3: Genes Genomes Genet 9(7):2051–2060
Clasen BM, Stoddard TJ, Luo S, Demorest ZL, Li J, Cedrone F, Tibebu R, Davison S, Ray EE, Daulhac A, Coffman A, Yabandith A, Retterath A, Haun W, Baltes NJ, Mathis L, Voytas DF, Zhang F (2016) Improving cold storage and processing traits in potato through targeted gene knockout. Plant Biotech J 14(1):169–176
Crosby JA, Janick J, Pecknold PC, Goffreda JC, Korban SS (1994) ‘GoldRush’ apple. HortScience 29(7):827–828
Daccord N, Celton JM, Linsmith G, Becker C, Choisne N, Schijlen E, van de Geest H, Bianco L, Micheletti D, Velasco R, Pierro EAD, Gouzy J, Rees DJG, Guérif P, Muranty H, Durel CE, Laurens F, Lespinasse Y, Gaillard S, Aubourg S, Quesneville H, Weigel D, van de Weg E, Troggio M, Bucher E (2017) High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nat Genet 49(7):1099–1106. https://doi.org/10.1038/ng.3886
Dahan-Meir T, Filler-Hayut S, Melamed-Bessudo C, Bocobza S, Czosnek H, Aharoni A, Levy AA (2018) Efficient in planta gene targeting in tomato using geminiviral replicons and the CRISPR/Cas9 system. Plant J 95(1):5–16
Fu Y, Sander JD, Reyon D, Cascio VM, Joung JK (2014) Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotech 32(3):279–284
Gao C (2019) Precision plant breeding using genome editing technologies. Transgenic Res 28:53–55
Gil-Humanes J, Wang Y, Liang Z, Shan Q, Ozuna CV, Sánchez-León S, Baltes NJ, Starker C, Barro F, Gao C, Voytas DF (2017) High-efficiency gene targeting in hexaploid wheat using DNA replicons and CRISPR/Cas9. Plant J 89(6):1251–1262
Haeussler M, Schönig K, Eckert H, Eschstruth A, Mianné J, Renaud JB, Schneider-Maunoury S, Shkumatava A, Teboul L, Kent J, Joly JS, Concordet JP (2016) Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol 17(1):148. https://doi.org/10.1186/s13059-016-1012-2
Hayut SF, Bessudo CM, Levy AA (2017) Targeted recombination between homologous chromosomes for precise breeding in tomato. Nat Commun 8(1):15605. https://doi.org/10.1038/ncomms15605
Iwata H, Minamikawa MF, Kajiya-Kanegae H, Ishimori M, Hayashi T (2016) Genomics-assisted breeding in fruit trees. Breed Sci 66(1):100–115
James DJ, Passey AJ, Barbara DJ, Bevan M (1989) Genetic transformation of apple (Malus pumila Mill.) using a disarmed Ti-binary vector. Plant Cell Rep 7(8):658–661
Kamburova VS, Nikitina EV, Shermatov SE, Buriev ZT, Kumpatla SP, Emani C, Abdurakhmonov IY (2017) Genome editing in plants: an overview of tools aapplications. Int J Agron 2017: Article ID 7315351. https://doi.org/10.1155/2017/7315351
Kaur N, Alok A, Shivani KN, Pandey P, Awasthi P, Tiwari S (2018) CRISPR/Cas9-mediated efficient editing in phytoene desaturase (PDS) demonstrates precise manipulation in banana cv. Rasthali Genome Funct Integr Genomics 18(1):89–99
Kim H, Kim ST, Ryu J, Kang BC, Kim JS, Kim SG (2017) CRISPR/Cpf1-mediated DNA-free plant genome editing. Nat Commun 8(1):14406. https://doi.org/10.1038/ncomms14406
Kotoda N, Iwanami H, Takahashi S, Abe K (2006) Antisense expression of MdTFL1, a TFL1-like gene, reduces the juvenile phase in apple. J Am Soc Hortic Sci 131(1):74–81
Kunihisa M, Moriya S, Abe K, Okada K, Haji T, Hayashi T, Kawahara Y, Itoh R, Itoh T, Katayose Y, Kanamori H, Matsumoto T, Mori S, Sasaki H, Matsumoto T, Nishitani C, Terakami S, Yamamoto T (2016) Genomic dissection of a ‘Fuji’ apple cultivar: re-sequencing, SNP marker development, definition of haplotypes, and QTL detection. Breed Sci 66(4):499–515
Liang Z, Chen K, Li T, Zhang Y, Wang Y, Zhao Q, Liu J, Zhang H, Liu C, Ran Y, Gao C (2017) Efficient DNA-free genome editing of bread wheat using CRISPR/Cas9 ribonucleoprotein complexes. Nat Commun 8(1):14261. https://doi.org/10.1038/ncomms14261
Limera C, Sabbadini S, Sweet JB, Mezzetti B (2017) New biotechnological tools for the genetic improvement of major woody fruit species. Front Plant Sci 8:1418. https://doi.org/10.3389/fpls.2017.01418
Liu H, Ding Y, Zhou Y, Jin W, Xie K, Chen LL (2017) CRISPR-P 2.0: an improved CRISPR-Cas9 tool for genome editing in plants. Mol Plant 10(3):530–532
Liu X, Homma A, Sayadi J, Yang S, Ohashi J, Takumi T (2016) Sequence features associated with the cleavage efficiency of CRISPR/Cas9 system. Sci Rep 6:19675. https://doi.org/10.1038/srep19675
Malnoy M, Viola R, Jung MH, Koo OJ, Kim S, Kim JS, Velasco R, Nagamangala Kanchiswamy C (2016) DNA-free genetically edited grapevine and apple protoplast using CRISPR/Cas9 ribonucleoproteins. Front Plant Sci 7:1904. https://doi.org/10.3389/fpls.2016.01904
Mehravar M, Shirazi A, Nazari M, Banan M (2019) Mosaicism in CRISPR/Cas9-mediated genome editing. Dev Biol 445(2):156–162
Miki D, Zhang W, Zeng W, Feng Z, Zhu JK (2018) CRISPR/Cas9-mediated gene targeting in Arabidopsis using sequential transformation. Nat Commun 9(1):1967. https://doi.org/10.1038/s41467-018-04416-0
Milčevičová R, Gosch C, Halbwirth H, Stich K, Hanke MV, Peil A, Flachowsky H, Rozhon W, Jonak C, Oufir M, Hausman JF, Matušíková I, Fluch S, Wilhelm E (2010) Erwinia amylovora-induced defense mechanisms of two apple species that differ in susceptibility to fire blight. Plant Sci 179(1–2):60–67
Mimida N, Kotoda N, Ueda T, Igarashi M, Hatsuyama Y, Iwanami H, Moriya S, Abe K (2009) Four TFL1/CEN-like genes on distinct linkage groups show different expression patterns to regulate vegetative and reproductive development in apple (Malus× domestica Borkh.). Plant Cell Physiol 50(2): 394–412
Murata M, Nishimura M, Murai N, Haruta M, Homma S, Itoh Y (2001) A transgenic apple callus showing reduced polyphenol oxidase activity and lower browning potential. Biosci Biotech Biochem 65(2):383–388
Nakajima I, Ban Y, Azuma A, Onoue N, Moriguchi T, Yamamoto T, Toki S, Endo M (2017) CRISPR/Cas9-mediated targeted mutagenesis in grape. PLoS ONE 12(5):e0177966. https://doi.org/10.1371/journal.pone.0177966
Nishitani C, Hirai N, Komori S, Wada M, Okada K, Osakabe K, Yamamoto T, Osakabe Y (2016) Efficient genome editing in apple using a CRISPR/Cas9 system. Sci Rep 6:31481. https://doi.org/10.1038/srep31481
Norelli JL, Aldwinckle HS, Destéfano-Beltrán L, Jaynes JM (1994) Transgenic ‘Mailing 26’apple expressing the attacin E gene has increased resistance to Erwinia amylovora. Euphytica 77(1–2):123–128
Ohmori M, Yamane H, Osakabe K, Osakabe Y, Tao R (2020) Targeted mutagenesis of CENTRORADIALIS using CRISPR/Cas9 system through the improvement of genetic transformation efficiency of tetraploid highbush blueberry. J Hortic Sci Biotech. https://doi.org/10.1080/14620316.2020.1822760
Osakabe Y, Osakabe K (2015) Genome editing with engineered nucleases in plants. Plant Cell Physiol 56(3):389–400
Osakabe Y, Watanabe T, Sugano SS, Ueta R, Ishihara R, Shinozaki K, Osakabe K (2016) Optimization of CRISPR/Cas9 genome editing to modify abiotic stress responses in plants. Sci Rep 6:26685. https://doi.org/10.1038/srep26685
Osakabe Y, Liang Z, Ren C, Nishitani C, Osakabe K, Wada M, Komori S, Malnoy M, Velasco R, Poli M, Jung MH, Koo OJ, Viola R, Kanchiswamy CN (2018) CRISPR–Cas9-mediated genome editing in apple and grapevine. Nat Protoc 13(12):2844–2863
Pan C, Ye L, Qin L, Liu X, He Y, Wang J, Chen L, Lu G (2016) CRISPR/Cas9-mediated efficient and heritable targeted mutagenesis in tomato plants in the first and later generations. Sci Rep 6:24765. https://doi.org/10.1038/srep24765
Peer R, Rivlin G, Golobovitch S, Lapidot M, Gal-On A, Vainstein A, Tzfira T, Flaishman MA (2015) Targeted mutagenesis using zinc-finger nucleases in perennial fruit trees. Planta 241(4):941–951
Peng A, Chen S, Lei T, Xu L, He Y, Wu L, Yao L, Zou X (2017) Engineering canker-resistant plants through CRISPR/Cas9-targeted editing of the susceptibility gene CsLOB1 promoter in citrus. Plant Biotech J 15(12):1509–1519
Pompili V, Dalla Costa L, Piazza S, Pindo M, Malnoy M (2020) Reduced fire blight susceptibility in apple cultivars using a high-efficiency CRISPR/Cas9-FLP/FRT-based gene editing system. Plant Biotech J 18(3):845–858. https://doi.org/10.1111/pbi.13253
Puchta H, Fauser F (2013) Gene targeting in plants: 25 years later. Int J Dev Biol 57:629–637
Puite KJ, Schaart JG (1996) Genetic modification of the commercial apple cultivars Gala, Golden Delicious and Elstar via an Agrobacterium tumefaciens-mediated transformation method. Plant Sci 119:125–133
Ren C, Liu X, Zhang Z, Wang Y, Duan W, Li S, Liang Z (2016) CRISPR/Cas9-mediated efficient targeted mutagenesis in Chardonnay (Vitis vinifera L.). Sci Rep 6:32289. https://doi.org/10.1038/srep32289
Rong YS, Golic KG (2003) The homologous chromosome is an effective template for the repair of mitotic DNA double-strand breaks in Drosophila. Genetics 165(4):1831–1842
Rozov SM, Permyakova NV, Deineko EV (2019) The problem of the low rates of CRISPR/Cas9-mediated knock-ins in plants: Approaches and solutions. Int J Mol Sci 20(13):3371. https://doi.org/10.3390/ijms20133371
Seong ES, Song KJ (2008) Factors affecting the early gene transfer step in the development of transgenic ‘Fuji’ apple plants. Plant Grow Reg 54(2):89–95
Shannon S, Meeks-Wagner DR (1991) A mutation in the Arabidopsis TFL1 gene affects inflorescence meristem development. Plant Cell 3(9):877–892
Spiegel-Roy P (1990) Economic and agricultural impact of mutation breeding in fruit trees. Mut Breed Rev 5:1–26
Steinert J, Schiml S, Puchta H (2016) Homology-based double-strand break-induced genome engineering in plants. Plant Cell Rep 35(7):1429–1438
Subburaj S, Chung SJ, Lee C, Ryu SM, Kim DH, Kim JS, Bae S, Lee GJ (2016) Site-directed mutagenesis in Petunia × hybrida protoplast system using direct delivery of purified recombinant Cas9 ribonucleoproteins. Plant Cell Rep 35(7):1535–1544
Svitashev S, Schwartz C, Lenderts B, Young JK, Cigan AM (2016) Genome editing in maize directed by CRISPR–Cas9 ribonucleoprotein complexes. Nat Commun 7(1):13274. https://doi.org/10.1038/ncomms13274
Ueta R, Abe C, Watanabe T, Sugano SS, Ishihara R, Ezura H, Osakabe Y, Osakabe K (2017) Rapid breeding of parthenocarpic tomato plants using CRISPR/Cas9. Sci Rep 7:507. https://doi.org/10.1038/s41598-017-00501-4
Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Ri AD, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E, Eldredge G, Fitzgerald LM, Gutin N, Lanchbury G, Macalma T, Mitchell JT, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu VT, King ST, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater MM, Masiero S, Lasserre P, Lespinasse Y, Allan AC, Bus V, Chagné D, Crowhurst RN, Gleave AP, Lavezzo E, Fawcett JA, Proost S, Rouzé P, Sterck L, Toppo S, Lazzari B, Hellens RP, Durel C-E, Gutin A, Bumgarner R, Gardiner SE, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R (2010) The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet 42:833–839
Wada M, Ureshino A, Tanaka N, Komori S, Takahashi S, Kudo K, Bessho H (2009) Anatomical analysis by two approaches ensure the promoter activities of apple AFL genes. J Jpn Soc Hortic Sc 78(1):32–39
Wang M, Lu Y, Botella JR, Mao Y, Hua K, Zhu JK (2017) Gene targeting by homology-directed repair in rice using a geminivirus-based CRISP)R/Cas9 system. Mol Plant 10(7):1007–1010
Wang Z, Wang S, Li D, Zhang Q, Li L, Zhong C, Liu Y, Huang H (2018) Optimized paired-sgRNA/Cas9 cloning and expression cassette triggers high-efficiency multiplex genome editing in kiwifruit. Plant Biotech J 16(8):1424–1433
Woo JW, Kim J, Kwon SI, Corvalán C, Cho SW, Kim H, Kim SG, Kim ST, Choe S, Kim JS (2015) DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins. Nat Biotech 33(11):1162–1164
Xiao A, Cheng Z, Kong L, Zhu Z, Lin S, Gao G, Zhang B (2014) CasOT: a genome-wide Cas9/gRNA off-target searching tool. Bioinformatics 30(8):1180–1182
Zhang L, Hu J, Han X, Li J, Gao Y, Richards CM, Zhang C, Tian Y, Liu G, Gul H, Wang D, Tian Y, Yang C, Meng M, Yuan G, Kang G, Wu Y, Wang K, Zhang H, Wang D, Cong P (2019) A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour. Nat Commun 10:1494. https://doi.org/10.1038/s41467-019-09518-x
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Nishitani, C., Osakabe, K., Osakabe, Y. (2021). Genome Editing in Apple. In: Korban, S.S. (eds) The Apple Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-74682-7_10
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