CRISPR/Cas Systems: Opportunities and Challenges for Crop Breeding

Overview

Journal Plant Cell Rep

Publisher Springer

Date 2021 May 12

PMID 33977326

Citations 17

Authors

Sukumar Biswas

Dabing Zhang

Jianxin Shi

Affiliations

Soon will be listed here.

Abstract

Increasing crop production to meet the demands of a growing population depends largely on crop improvement through new plant-breeding techniques (NPBT) such as genome editing. CRISPR/Cas systems are NPBTs that enable efficient target-specific gene editing in crops, which is supposed to accelerate crop breeding in a way that is different from genetically modified (GM) technology. Herein, we review the applications of CRISPR/Cas systems in crop breeding focusing on crop domestication, heterosis, haploid induction, and synthetic biology, and summarize the screening methods of CRISPR/Cas-induced mutations in crops. We highlight the importance of molecular characterization of CRISPR/Cas-edited crops, and pay special attentions to emerging highly specific genome-editing tools such as base editors and prime editors. We also discuss future improvements of CRISPR/Cas systems for crop improvement.

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References

Ainley W, Sastry-Dent L, Welter M, Murray M, Zeitler B, Amora R . Trait stacking via targeted genome editing. Plant Biotechnol J. 2013; 11(9):1126-34. DOI: 10.1111/pbi.12107. View

Ali Z, Shami A, Sedeek K, Kamel R, Alhabsi A, Tehseen M . Fusion of the Cas9 endonuclease and the VirD2 relaxase facilitates homology-directed repair for precise genome engineering in rice. Commun Biol. 2020; 3(1):44. PMC: 6978410. DOI: 10.1038/s42003-020-0768-9. View

Aman R, Ali Z, Butt H, Mahas A, Aljedaani F, Khan M . RNA virus interference via CRISPR/Cas13a system in plants. Genome Biol. 2018; 19(1):1. PMC: 5755456. DOI: 10.1186/s13059-017-1381-1. View

Kunkel J . Nursing management of the head injured patient. Crit Care Update. 1981; 8(3):22-33. View

Anzalone A, Koblan L, Liu D . Genome editing with CRISPR-Cas nucleases, base editors, transposases and prime editors. Nat Biotechnol. 2020; 38(7):824-844. DOI: 10.1038/s41587-020-0561-9. View

Araki M, Ishii T . Towards social acceptance of plant breeding by genome editing. Trends Plant Sci. 2015; 20(3):145-9. DOI: 10.1016/j.tplants.2015.01.010. View

Arndell T, Sharma N, Langridge P, Baumann U, Watson-Haigh N, Whitford R . gRNA validation for wheat genome editing with the CRISPR-Cas9 system. BMC Biotechnol. 2019; 19(1):71. PMC: 6829922. DOI: 10.1186/s12896-019-0565-z. View

Baltes N, Voytas D . Enabling plant synthetic biology through genome engineering. Trends Biotechnol. 2014; 33(2):120-31. DOI: 10.1016/j.tibtech.2014.11.008. View

Birchler J, Yao H, Chudalayandi S, Vaiman D, Veitia R . Heterosis. Plant Cell. 2010; 22(7):2105-12. PMC: 2929104. DOI: 10.1105/tpc.110.076133. View

10.

Biswas S, Li R, Yuan Z, Zhang D, Zhao X, Shi J . Development of methods for effective identification of CRISPR/Cas9-induced indels in rice. Plant Cell Rep. 2019; 38(4):503-510. DOI: 10.1007/s00299-019-02392-3. View

11.

Biswas S, Li R, Hong J, Zhao X, Yuan Z, Zhang D . Effective identification of CRISPR/Cas9-induced and naturally occurred mutations in rice using a multiplex ligation-dependent probe amplification-based method. Theor Appl Genet. 2020; 133(8):2323-2334. DOI: 10.1007/s00122-020-03600-5. View

12.

Brauer E, Balcerzak M, Rocheleau H, Leung W, Schernthaner J, Subramaniam R . Genome Editing of a Deoxynivalenol-Induced Transcription Factor Confers Resistance to in Wheat. Mol Plant Microbe Interact. 2019; 33(3):553-560. DOI: 10.1094/MPMI-11-19-0332-R. View

13.

Butt H, Eid A, Momin A, Bazin J, Crespi M, Arold S . CRISPR directed evolution of the spliceosome for resistance to splicing inhibitors. Genome Biol. 2019; 20(1):73. PMC: 6489355. DOI: 10.1186/s13059-019-1680-9. View

14.

Butt H, Rao G, Sedeek K, Aman R, Kamel R, Mahfouz M . Engineering herbicide resistance via prime editing in rice. Plant Biotechnol J. 2020; 18(12):2370-2372. PMC: 7680537. DOI: 10.1111/pbi.13399. View

15.

cermak T, Baltes N, Cegan R, Zhang Y, Voytas D . High-frequency, precise modification of the tomato genome. Genome Biol. 2015; 16:232. PMC: 4635538. DOI: 10.1186/s13059-015-0796-9. View

16.

Chen K, Gao C . TALENs: customizable molecular DNA scissors for genome engineering of plants. J Genet Genomics. 2013; 40(6):271-9. DOI: 10.1016/j.jgg.2013.03.009. View

17.

Chen K, Wang Y, Zhang R, Zhang H, Gao C . CRISPR/Cas Genome Editing and Precision Plant Breeding in Agriculture. Annu Rev Plant Biol. 2019; 70:667-697. DOI: 10.1146/annurev-arplant-050718-100049. View

18.

Curtin S, Zhang F, Sander J, Haun W, Starker C, Baltes N . Targeted mutagenesis of duplicated genes in soybean with zinc-finger nucleases. Plant Physiol. 2011; 156(2):466-73. PMC: 3177250. DOI: 10.1104/pp.111.172981. View

19.

Curtin S, Xiong Y, Michno J, Campbell B, Stec A, cermak T . CRISPR/Cas9 and TALENs generate heritable mutations for genes involved in small RNA processing of Glycine max and Medicago truncatula. Plant Biotechnol J. 2017; 16(6):1125-1137. PMC: 5978873. DOI: 10.1111/pbi.12857. View

20.

Do P, Nguyen C, Bui H, Tran L, Stacey G, Gillman J . Demonstration of highly efficient dual gRNA CRISPR/Cas9 editing of the homeologous GmFAD2-1A and GmFAD2-1B genes to yield a high oleic, low linoleic and α-linolenic acid phenotype in soybean. BMC Plant Biol. 2019; 19(1):311. PMC: 6632005. DOI: 10.1186/s12870-019-1906-8. View