Abstract
The fast-moving CRISPR technology has allowed plant scientists to manipulate plant genomes in a targeted manner. So far, most of the applications were focused on gene knocking out by creating indels. However, more precise genome editing tools are demanded to assist the introduction of functional single nucleotide polymorphisms (SNPs) in breeding programs. The CRISPR base editing tools were developed to meet this need. In this chapter, we present a cytidine deaminase base editing method for editing the point mutations that control the grain size and seed coat color in rice.
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References
**ek M, Chylinski K, Fonfara I, Hauer M, Doudna J, Charpentier E (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–821
Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339:819–823
Jiang W, Zhou H, Bi H, Fromm M, Yang B, Weeks DP (2013) Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucleic Acids Res 41:1–12
Yin X, Biswal AK, Dionora J, Perdigon KM, Balahadia CP, Mazumdar S, Chater C, Lin HC, Coe RA, Kretzschmar T, Gray JE, Quick WP, Bandyopadhyay A (2017) CRISPR-Cas9 and CRISPR-Cpf1 mediated targeting of a stomatal developmental gene EPFL9 in rice. Plant Cell Rep 36:1–13
Puchta H (2005) The repair of double-strand breaks in plants: mechanisms and consequences for genome evolution. J Exp Bot 56:1–14
Miki D, Zhang W, Zeng W, Feng Z, Zhu JK (2018) CRISPR/Cas9-mediated gene targeting in Arabidopsis using sequential transformation. Nat Commun 9:1967
Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR (2016) Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533:420–424
Komor AC, Badran AH (2017) Editing the genome without double-stranded DNA breaks. ACS Chem Biol 13:383–388
Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, Bryson DI, Liu DR (2017) Programmable base editing of A·T to G·C in genomic DNA without DNA cleavage. Nature 551:464–471
Zong Y, Wang Y, Li C, Zhang R, Chen K, Ran Y, Qiu J, Wang D, Gao C (2017) Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion. Nat Biotechnol 35:438–440
Hua K, Tao X, Yuan F, Wang D, Zhu JK (2018) Precise a·T to G·C base editing in the rice genome. Mol Plant 11:627–630
Kim JS (2018) Precision genome engineering through adenine and cytosine base editing. Nat Plants 4:148–151
Li H, Qin R, Liu X, Liao S, Xu R, Yang J, Wei P (2019) CRISPR/Cas9-mediated adenine base editing in rice genome. Rice Sci 26:125–128
Schellenberger V, Wang CW, Geething NC, Spink BJ, Campbell A, To W, Scholle MD, Yin Y, Yao Y, Bogin O, Cleland JL, Silverman J, Stemmer WP (2009) A recombinant polypeptide extends the in vivo half-life of peptides and proteins in a tunable manner. Nat Biotechnol 27:1186–1190
Dwivedi SL, Scheben A, Edwards D, Spillane C, Ortiz R (2017) Assessing and exploiting functional diversity in germplasm pools to enhance abiotic stress adaptation and yield in cereals and food legumes. Front Plant Sci 8:1461
Huq A, Akter S, Nou S, Kim HT, Jung YJ, Kang KK (2016) Identification of functional SNPs in genes and their effects on plant phenotypes. J Plant Biotechnol 43:1–11
Duan P, Rao Y, Zeng D, Yang Y, Xu R, Zhang B, Dong G, Qian Q, Li Y (2014) SMALL GRAIN 1, which encodes a mitogen-activated protein kinase kinase 4, influences grain size in rice. Plant J 77:547–557
**a X, **ao-Bo Z, Yong-Feng S, Hui-Mei W, Bao-Hua F, **ao-Hong L, Qi-Na L-XHS, Dan G, Yan H, Jian-Li W (2016) A point mutation in an F-box domain-containing protein is responsible for brown hull phenotype in rice. Rice Sci 23:1–8
Fang N, Xu R, Huang L, Zhang B, Duan P, Li N, Luo Y, Li Y (2016) Small grain 11 controls grain size, grain number and grain yield in rice. Rice 9:64
Lepiniec L, Debeaujon I, Routaboul JM, Baudry A, Pourcel L, Nesi N, Caboche M (2006) Genetics and biochemistry of seed flavonoids. Annu Rev Plant Biol 57:405–430
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Authors acknowledge International Rice Research Institute for funding.
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Tra, M.V.T., Yin, X., Bajal, I., Balahadia, C.P., Quick, W.P., Bandyopadhyay, A. (2021). Single Base Editing Using Cytidine Deaminase to Change Grain Size and Seed Coat Color in Rice. In: Bandyopadhyay, A., Thilmony, R. (eds) Rice Genome Engineering and Gene Editing. Methods in Molecular Biology, vol 2238. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1068-8_9
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DOI: https://doi.org/10.1007/978-1-0716-1068-8_9
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