Selection of the high efficient sgRNA for CRISPR-Cas9 to edit herbicide related genes, PDS, ALS, and EPSPS in tomato

Applied Biological Chemistry - Tập 65 Số 1 - 2022
So Hee Yang1, Euyeon Kim1, Hyosun Park1, Yeonjong Koo1
1Department of Agricultural Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea

Tóm tắt

Abstract

Herbicide resistance is one of the main crop traits that improve farming methods and crop productivity. CRISPR-Cas9 can be applied to the development of herbicide-resistant crops based on a target site resistance mechanism, by editing genes encoding herbicide binding proteins. The sgRNAs capable of editing the target genes of herbicides, pds (phytoene desaturase), ALS (acetolactate synthase), and EPSPS (5-Enolpyruvylshikimate-3-phosphate synthase), were designed to use with the CRISPR-Cas9 system in tomato (Solanum lycopersicum cv. Micro-Tom). The efficiency of the sgRNAs was tested using Agrobacterium mediated transient expression in the tomato cotyledons. One sgRNA designed for editing the target site of PDS had no significant editing efficiency. However, three different sgRNAs designed for editing the target site of ALS had significant efficiency, and one of them, ALS2-P sgRNA, showed over 0.8% average efficiency in the cotyledon genome. The maximum efficiency of ALS2-P sgRNA was around 1.3%. An sgRNA for editing the target site of EPSPS had around 0.4% editing efficiency on average. The sgRNA efficiency testing provided confidence that editing of the target sites could be achieved in the transformation process. We confirmed that 19 independent transgenic tomatoes were successfully edited by ALS2_P or ALS1_W sgRNAs and two of them had three base deletion mutations, which are expected to have altered herbicide resistance. In this study, we demonstrated the usefulness of performing an sgRNA efficiency test before crop transformation, and confirmed that the CRISPR-Cas9 system is a valuable tool for breeding herbicide-resistant crops.

Từ khóa


Tài liệu tham khảo

Gressel J (2009) Evolving understanding of the evolution of herbicide resistance. Pest Manag Sci 65:1164–1173

Busi R, Vila-Aiub MM, Beckie HJ, Gaines TA, Goggin DE, Kaundun SS, Lacoste M, Neve P, Nissen SJ, Norsworthy JK, Renton M, Shaner DL, Tranel PJ, Wright T, Yu Q, Powles SB (2013) Herbicide-resistant weeds: from research and knowledge to future needs. Evol Appl 6:1218–1221

Sundstrom J, Albihn A, Boqvist S, Ljungvall K, Marstorp H, Martiin C, Nyberg K, Vagsholm I, Yuen J, Magnusson U (2014) Future threats to agricultural food production posed by environmental degradation, climate change, and animal and plant diseases—a risk analysis in three economic and climate settings. Food Secur 6:201–215

Heap I (2014) Global perspective of herbicide-resistant weeds. Pest Manag Sci 70:1306–1315

Green JM (2014) Current state of herbicides in herbicide-resistant crops. Pest Manag Sci 70:1351–1357

Gage KL, Krausz RF, Walters SA (2019) Emerging challenges for weed management in herbicide-resistant crops. Agriculture 9:180

Green JM, Owen MD (2011) Herbicide-resistant crops: utilities and limitations for herbicide-resistant weed management. J Agric Food Chem 59:5819–5829

Yi SY, Cui Y, Zhao Y, Liu ZD, Lin YJ, Zhou F (2016) A novel naturally occurring class i 5-enolpyruvylshikimate-3-phosphate synthase from Janibacter sp. confers high glyphosate tolerance to rice. Sci Rep 6:19104

Leino L, Tall T, Helander M, Saloniemi I, Saikkonen K, Ruuskanen S, Puigbo P (2021) Classification of the glyphosate target enzyme (5-enolpyruvylshikimate-3-phosphate synthase) for assessing sensitivity of organisms to the herbicide. J Hazard Mater 408:124556

Heap I, Duke SO (2018) Overview of glyphosate-resistant weeds worldwide. Pest Manag Sci 74:1040–1049

Jakeman DL, Mitchell DJ, Shuttleworth WA, Evans JNS (1998) On the mechanism of 5-enolpyruvylshikimate-3-phosphate synthase. Biochemistry-Us 37:12012–12019

Liu Y, Cao G, Chen R, Zhang S, Ren Y, Lu W, Wang J, Wang G (2015) Transgenic tobacco simultaneously overexpressing glyphosate N-acetyltransferase and 5-enolpyruvylshikimate-3-phosphate synthase are more resistant to glyphosate than those containing one gene. Transgenic Res 24:753–763

Le DT, Choi JD, Tran LS (2010) Amino acids conferring herbicide resistance in tobacco acetohydroxyacid synthase. GM Crops 1:62–67

Yu Q, Han H, Vila-Aiub MM, Powles SB (2010) AHAS herbicide resistance endowing mutations: effect on AHAS functionality and plant growth. J Exp Bot 61:3925–3934

Yu Q, Powles SB (2014) Resistance to AHAS inhibitor herbicides: current understanding. Pest Manag Sci 70:1340–1350

Sato H, Shimizu T, Kawai K, Kaku K, Arakawa A, Tachibana T, Takamizo T (2013) Herbicide-resistant tall fescue with cytoplasmic male sterility selected by a mutated rice acetolactate synthase gene. Crop Sci 53:201–207

Naing AH, Kyu SY, Pe PPW, Park KI, Lee JM, Lim KB, Kim CK (2019) Silencing of the phytoene desaturase (PDS) gene affects the expression of fruit-ripening genes in tomatoes. Plant Methods 15:110

Brausemann A, Gemmecker S, Koschmieder J, Ghisla S, Beyer P, Einsle O (2017) Structure of phytoene desaturase provides insights into herbicide binding and reaction mechanisms involved in carotene desaturation. Structure 25:1222–1232

Depka B, Jahns P, Trebst A (1998) Beta-carotene to zeaxanthin conversion in the rapid turnover of the D1 protein of photosystem II. FEBS Lett 424:267–270

Koschmieder J, Fehling-Kaschek M, Schaub P, Ghisla S, Brausemann A, Timmer J, Beyer P (2017) Plant-type phytoene desaturase: functional evaluation of structural implications. PLoS ONE 12:e0187628

Arias RS, Dayan FE, Michel A, Howell J, Scheffler BE (2006) Characterization of a higher plant herbicide-resistant phytoene desaturase and its use as a selectable marker. Plant Biotechnol J 4:263–273

Heap IM (1997) The occurrence of herbicide-resistant weeds worldwide. Pestic Sci 51:235–243

Kumar V, Bellinder RR, Gupta RK, Malik RK, Brainard DC (2008) Role of herbicide-resistant rice in promoting resource conservation technologies in rice-wheat cropping systems of India: a review. Crop Prot 27:290–301

Ogawa T, Kawahigashi H, Toki S, Handa H (2008) Efficient transformation of wheat by using a mutated rice acetolactate synthase gene as a selectable marker. Plant Cell Rep 2:1325–1331

Endo M, Toki S (2013) Creation of herbicide-tolerant crops by gene targeting. J Pestic Sci 38:49–59

Shaner DL (2000) The impact of glyphosate-tolerant crops on the use of other herbicides and on resistance management. Pest Manag Sci 56:320–326

Mannerlof M, Tuvesson S, Steen P, Tenning P (1997) Transgenic sugar beet tolerant to glyphosate. Euphytica 94:83–91

Castle LA, Siehl DL, Gorton R, Patten PA, Chen YH, Bertain S, Cho HJ, Duck N, Wong J, Liu DL, Lassner MW (2004) Discovery and directed evolution of a glyphosate tolerance gene. Science 304:1151–1154

Adli M (2018) The CRISPR tool kit for genome editing and beyond. Nat Commun 9:1911

Nishihara M, Higuchi A, Watanabe A, Tasaki K (2018) Application of the CRISPR/Cas9 system for modification of flower color in Torenia fournieri. BMC Plant Biol 18:331

Lone BA, Karna SKL, Ahmad F, Shahi N, Pokharel YR (2018) CRISPR/Cas9 system: a bacterial tailor for genomic engineering. Genet Res Int 2018:3797214

Ma X, Zhu Q, Chen Y, Liu YG (2016) CRISPR/Cas9 platforms for genome editing in plants: developments and applications. Mol Plant 29:961–974

Farooq R, Hussain K, Nazir S, Javed MR, Masood N (2018) CRISPR/Cas9; A robust technology for producing genetically engineered plants. Cell Mol Biol 64:31–38

Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F (2013) Genome engineering using the CRISPR-Cas9 system. Nat Protoc 8:2281–2308

Samanta MK, Dey A, Gayen S (2016) CRISPR/Cas9: an advanced tool for editing plant genomes. Transgenic Res 25:561–573

Wang Y, Geng L, Yuan M, Wei J, Jin C, Li M, Yu K, Zhang Y, Jin H, Wang E, Chai Z, Fu X, Li X (2017) Deletion of a target gene in Indica rice via CRISPR/Cas9. Plant Cell Rep 36:1333–1343

Toda E, Okamoto T (2020) CRISPR/Cas9-based genome editing using rice zygotes. Curr Protoc Plant Biol 5:e20111

Dong H, Huang Y, Wang K (2021) The development of herbicide resistance crop plants using CRISPR/Cas9-mediated gene editing. Genes 12:912

Lowder LG, Zhang D, Baltes NJ, Paul JW 3rd, Tang X, Zheng X, Voytas DF, Hsieh TF, Zhang Y, Qi Y (2015) A CRISPR/Cas9 toolbox for multiplexed plant genome editing and transcriptional regulation. Plant Physiol 169:971–985

Li C, Zhang R, Meng XB, Chen S, Zong Y, Lu CJ, Qiu JL, Chen YH, Li JY, Gao CX (2020) Targeted, random mutagenesis of plant genes with dual cytosine and adenine base editors. Nat Biotechnol 38:875–882

van der Vyver C, Conradie T, Kossmann J, Lloyd J (2013) In vitro selection of transgenic sugarcane callus utilizing a plant gene encoding a mutant form of acetolactate synthase. In Vitro Cell Dev-Pl 49(2):198–206

Mavrodiev EV, Dervinis C, Whitten WM, Gitzendanner MA, Kirst M, Kim S, Kinser TJ, Soltis PS, Soltis DE (2021) A new, simple, highly scalable, and efficient protocol for genomic DNA extraction from diverse plant taxa. Appl Plant Sci 9:e11413

Park J, Lim K, Kim JS, Bae S (2017) Cas-analyzer: an online tool for assessing genome editing results using NGS data. Bioinformatics 33:286–288

Thông tin
Thông tin xuất bản

Applied Biological Chemistry

Tập 65 Số 1

Thông tin tác giả