Abstract
Peanut (Arachis hypogaea L.) is an important global food crop, providing a valuable source of protein, oil and nutrition. The functional analysis of genes associated with yield traits is an important step in molecular breeding, which requires effective methods of genetic transformation. In this study, we applied the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 system in conjunction with Agrobacterium tumefaciens-mediated pollen tube transformation to create knockout mutants of the peanut MUTATOR-LIKE TRANSPOSABLE ELEMENT9A (AhMULE9A) gene, which plays an importantly regulatory role in response to Al stress in peanut. The gene mutations were identified by the analysis of genomic sequences flanking the sgRNA target sites. The sequencing of AhMULE9A mutations showed that eleven of the fifteen transgenics produced resulted in protein sequence changes, demonstrating the efficacy of this method for the production of targeted mutations in allotetraploid peanut.
Key message
This study highlights the efficiency and utility of CRISPR/Cas9 gene editing in peanut in conjunction with Agrobacterium tumefaciens-mediated pollen tube transformation.
Similar content being viewed by others
Data availability
Data sharing not applicable to this article as no datasets were generated or analyzed during the current study.
References
Andersson M, Turesson H, Nicolia A, Fält AS, Samuelsson M, Hofvander P (2017) Efficient targeted multiallelic mutagenesis in tetraploid potato (Solanum tuberosum) by transient CRISPR-Cas9 expression in protoplasts. Plant Cell Rep 36(1):117–128. https://doi.org/10.1007/s00299-016-2062-3
Bertioli DJ, Cannon SB, Froenicke L, Huang GD, Farmer AD, Cannon EKS, Liu X, Gao DY, Clevenger J, Dash S, Ren LH, Moretzsohn MC, Shirasawa K, Huang W, Vidigal B, Abernathy B, Chu Y, Niederhuth CE, Umale P, Araújo ACG, Kozik A, Kim KD, Burow MD, Varshney RK, Wang XJ, Zhang XY, Barkley N, Guimarães PM, Isobe S, Guo BZ, Liao BS, Stalker HT, Schmitz RJ, Scheffler BE, Leal-Bertioli SCM, Xun X, Jackson SA, Michelmore R, Ozias-Akins P (2016) The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut. Nat Genet 48(4):438–446. https://doi.org/10.1038/ng3517
Bertioli DJ, Jenkins J, Clevenger J, Dudchenko O, Gao D, Seijo G, Leal-Bertioli SCM, Ren LH, Farmer AD, Pandey MK, Samoluk SS, Abernathy B, Agarwal G, Ballén-Taborda C, Cameron C, Campbell J, Chavarro C, Chitikineni A, Chu Y, Dash S, Baidouri MEI, Guo BZ, Huang W, Kim KD, Korani W, Lanciano S, Lui CG, Mirouze M, Moretzsohn MC, Pham M, Shin JH, Shirasawa K, Sinharoy S, Sreedasyam A, Weeks NT, Zhang XY, Zheng Z, Sun ZQ, Froenicke L, Aiden EL, Michelmore R, Varshney RK, Corley Holbrook C, Cannon EKS, Scheffler BE, Grimwood J, Ozias-Akins P, Cannon SB, Jackson SA, Schmutz J (2019) The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nat Genet 51(5):877–884. https://doi.org/10.1038/s41588-019-0405-z
Cai YP, Chen L, Liu XJ, Guo C, Sun S, Wu CX, Jiang BJ, Han F, Hou WS (2018) CRISPR/Cas9-mediated targeted mutagenesis of GmFT2a delays flowering time in soya bean. Plant Biotechnol J 16(1):176–185
Char SN, Li RQ, Yang B (2019) CRISPR/Cas9 for mutagenesis in rice. In: Kumar S, Barone P, Smith M (eds) Transgenic plants, vol 1864. Humana Press, New York, pp 279–293. https://doi.org/10.1007/978-1-4939-8778-8_19
Chen XG, Lu XK, Shu N, Wang S, Wang JJ, Wang DL, Guo LX, Ye WW (2017) Targeted mutagenesis in cotton (Gossypium hirsutum L.) using the CRISPR/Cas9 system. Sci Rep 7:44304
Das DR, Horváth B, Kundu A, Kaló P, DasGupta M (2019) Functional conservation of CYCLOPS in crack entry legume Arachis hypogaea. Plant Sci 281:232–241. https://doi.org/10.1016/j.plantsci2018.12.003
Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation: version II. Plant Mol Biol Rep 1(4):19–21. https://doi.org/10.1007/BF02712670
Détain A, Bhowmik P, Leborgne-Castel N, Ochatt S (2022) Latest biotechnology tools and targets for improving abiotic stress tolerance in protein legumes. Environ Exp Bot 197:104824. https://doi.org/10.1016/j.envexpbot.2022.104824
Eckerstorfer MF, Engelhard M, Heissenberger A, Simon S, Teichmann H (2019) Plants developed by new genetic modification techniques—comparison of existing regulatory frameworks in the EU and non-EU countries. Front Bioeng Biotechnol 7:26. https://doi.org/10.3389/fbioe.2019.00026
Keshavareddy G, Kumar ARV, Ramu VS (2018) Methods of plant transformation: a review. Int J Curr Microbiol Appl Sci 7(07):2656–2668. https://doi.org/10.20546/ijcmas.2018.707.312
Kim YA, Moon H, Jin Park C (2019) CRISPR/Cas9-targeted mutagenesis of Os8N3 in rice to confer resistance to Xanthomonas oryzae pv. Oryzae. Rice 12(1):67. https://doi.org/10.1186/s12284-019-0325-7
Krishna G, Singh BK, Kim EK, Morya VK, Ramteke PW (2015) Progress in genetic engineering of peanut (Arachis hypogaea L.)—a review. Plant Biotechnol J 13(2):147–162. https://doi.org/10.1111/pbi.12339
Kumar R, Janila P, Vishwakarma MK, Khan AW, Manohar SS, Gangurde SS, Variath MT, Shasidhar Y, Pandey MK, Varshney RK (2020) Whole-genome resequencing‐based QTL–seq identified candidate genes and molecular markers for fresh seed dormancy in groundnut. Plant Biotechnol J 18(4):992–1003. https://doi.org/10.1111/pbi.13266
Kundu A, DasGupta M (2018) Silencing of putative cytokinin receptor histidine kinase1 inhibits both inception and differentiation of root nodules in Arachis hypogaea. Mol Plant Microbe Interact 31(2):187–199. https://doi.org/10.1094/MPMI-06-17-0144-R
Lawrenson T, Shorinola O, Stacey N, Li C, Ostergaard L, Patron N, Uauy C, Harwood W (2015) Induction of targeted, heritable mutations in barley and Brassica oleracea using RNA-guided Cas9 nuclease. Genome Biol 16:258. https://doi.org/10.1186/s13059-015-0826-7
Liao GT, Luo SZ, Li XY, Li AL, Mo YC, Wang AQ, Xiao D, He LF, Zhan J (2023) Identification and functional characterization of REGULATORY PARTICLE NON-ATPASE 1a-like (AhRPN1a-like) in peanuts during aluminum-induced programmed cell death. J Plant Physiol. https://doi.org/10.1016/j.jplph.2023.154079
Luo HY, Pandey MK, Khan AW, Guo JB, Wu B, Cai Y, Huang L, Zhou XJ, Chen YN, Chen WG, Liu N, Lei Y, Liao BS, Varshney RK, Jiang HF (2019) Discovery of genomic regions and candidate genes controlling shelling percentage using QTL-seq approach in cultivated peanut (Arachis hypogaea L.). Plant Biotechnol J 17(7):1248–1260. https://doi.org/10.1111/pbi.13050
Luo L, Wan Q, Zhang K, Zhang XR, Guo RJ, Wang C, Zheng CC, Liu FZ, Ding ZJ, Wan YS (2021) AhABI4s negatively regulate salt-stress response in peanut. Front Plant Sci 12:741641. https://doi.org/10.3389/fpls.2021.741641
Ma X, Zhang Q, Zhu Q, Liu W, Chen Y, Qiu R, Wang B, Yang ZF, Li HY, Lin YR, Xie YY, Shen RX, Chen SF, Wang Z, Chen YL, Guo JX, Chen LT, Zhao XC, Dong ZC (2015) A robust CRISPR/Cas9 system for convenient, high-efficiency multiplex genome editing in monocot and dicot plants. Mol Plant 8:1274–1284. https://doi.org/10.1016/j.molp.2015.04.007
Mallikarjuna G, Rao TSRB, Kirti PB (2016) Genetic engineering for peanut improvement: current status and prospects. Plant Cell Tissue Organ Cult 125(3):399–416. https://doi.org/10.1007/s11240-016-0966-9
Manghwar H, Li B, Ding X, Hussain A, Lindsey K, Zhang XL, Jin SX (2020) CRISPR/Cas systems in genome editing: methodologies and tools for sgRNA design, off-target evaluation, and strategies to mitigate off‐target effects. Adv Sci 7(6):1902312. https://doi.org/10.1002/advs201902312
Mehravar M, Shirazi A, Nazari M, Banan M (2019) Mosaicism in CRISPR/Cas9-mediated genome editing. Dev Biol 445(2):156–162. https://doi.org/10.1016/j.ydbio.2018.10.008
Neelakandan AK, Wright DA, Traore SM, Ma X, Subedi B, Veeramasu S, Spalding MH, He G (2022) Application of CRISPR/Cas9 system for efficient gene editing in peanut. Plants (Basel) 11(10):1361. https://doi.org/10.3390/plants11101361
Ortigosa A, Gimenez-Ibanez S, Leonhardt N, Solano R (2019) Design of a bacterial speck resistant tomato by CRISPR/Cas9-mediated editing of SlJAZ2. Plant Biotechnol J 17(3):665–673. https://doi.org/10.1111/pbi.13006
Pandey P, Mysore KS, Senthil-Kumar M (2022) Recent advances in plant gene silencing methods. Methods Mol Biol 2408:1–22. https://doi.org/10.1007/978-1-0716-1875-2_1
Puli COR, Akila CS, Pandit V, Konduru S, Kandi SR, Chinta S (2021) Peanut (Arachis hypogaea L.) transgenic plants for abiotic stress tolerance. In: Kavi Kishor PB, Rajam MV, Pullaiah T (eds) Genetically modified crops. Springer, Singapore, pp 139–173
Shan QW, Wang YP, Li J, Zhang Y, Chen KL, Liang Z, Zhang K, Liu JX, Xi JZJ, Qiu JL, Gao CX (2013) Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol 31:686–688. https://doi.org/10.1038/nbt.2650
Shi JR, Gao HR, Wang HY, Renee Lafitte H, Archibald RL, Yang MZ, Hakimi SM, Mo H, Habben JE (2017) ARGOS8 variants generated by CRISPR-Cas9 improve maize grain yield under field drought stress conditions. Plant Biotechnol J 15(2):207–216. https://doi.org/10.1111/pbi12603
Shi L, Li X, Xue L, Zhang J, Huang B, Sun Z, Zhang Z, Dai X, Han S, Dong W, Zhang X (2023) Creation of herbicide-resistance in allotetraploid peanut using CRISPR/Cas9-meditated cytosine base-editing. Plant Biotechnol J. https://doi.org/10.1111/pbi.14114
Shu HM, Luo ZL, Peng Z, Wang JP (2020) The application of CRISPR/Cas9 in hairy roots to explore the functions of AhNFR1 and AhNFR5 genes during peanut nodulation. BMC Plant Biol 20(1):417. https://doi.org/10.1186/s12870-020-02614-x
Sun XJ, Hu Z, Chen R, Jiang QY, Song GH, Zhang H, Xi YJ (2015) Targeted mutagenesis in soybean using the CRISPR-Cas9 system. Sci Rep 5(1):10342. https://doi.org/10.1038/srep10342
Svitashev S, Young JK, Schwartz C, Gao HR, Falco SC, Cigan AM (2015) Targeted mutagenesis, precise gene-editing, and site-specific gene insertion in maize using Cas9 and guide RNA. Plant Physiol 169:931–945
Tsai S, Zheng Z, Nguyen N, Liebers M, Topkar V, Thapar V, Wyvekens N, Khayter C, Iafrate AJ, Le LP, Aryee MJ, Joung JK (2015) GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nat Biotechnol 33:187–197. https://doi.org/10.1038/nbt.3117
Wang P, Zhang J, Sun L, Ma YZ, Xu J, Liang SJ, Deng JW, Tan JF, Zhang QH, Tu LL, Daniell H, Jin SX, Zhang XL (2018) High efficient multisites genome editing in allotetraploid cotton (Gossypium hirsutum) using CRISPR/Cas9 system. Plant Biotechnol J 16:137–150
Wang LJ, Chen SC, Peng AH, Xie Z, He YR, Zou XP (2019) CRISPR/Cas9-mediated editing of CsWRKY22 reduces susceptibility to Xanthomonas citri subsp. citri in Wanjincheng orange (Citrus Sinensis (L.) Osbeck). Plant Biotechnol Rep 13(5):501–510. https://doi.org/10.1007/s11816-019-00556-x
Wu J, Liu HM, Ren SC, Li PP, Li X, Lin L, Sun QF, Zhang L, Lin C, Wang YP (2022) Generating an oilseed rape mutant with non-abscising floral organs using CRISPR/Cas9 technology. Plant Physiol 190(3):1562–1565
Xing HL, Dong L, Wang ZP, Zhang HY, Han CY, Liu B, Wang XC, Chen QJ (2014) A CRISPR/Cas9 toolkit for multiplex genome editing in plants. BMC Plant Biol 14:327
Yang H, Luo L, Li YY, Li HD, Zhang XR, Zhang K, Zhu SQ, Li XL, Li YJ, Wan YS, Liu FZ (2023) Fine mapping of qAHPS07 and functional studies of AhRUVBL2 controlling pod size in peanut (Arachis hypogaea L.). Plant Biotechnol J. https://doi.org/10.1111/pbi14076
You J, Li DH, Yang L, Dossou SSK, Zhou R, Zhang YX, Wang LH (2022) CRISPR/Cas9-mediated efficient targeted mutagenesis in sesame (Sesamum indicum L.). Front Plant Sci 13:935825. https://doi.org/10.3389/fpls.2022.935825
Yuan M, Zhu J, Gong L, He L, Lee C, Han S, Chen C, He G (2019) Mutagenesis of FAD2 genes in peanut with CRISPR/Cas9 based gene editing. BMC Biotechnol 9(1):24
Zhang YW, Bai Y, Wu GH, Zou SH, Chen YF, Gao CX, Tang DZ (2017) Simultaneous modification of three homoeologs of TaEDR1 by genome editing enhances powdery mildew resistance in wheat. Plant J 91(4):714–724. https://doi.org/10.1111/tpj.13599
Zhang ZN, Ge XY, Luo XL, Wang P, Fan Q, Hu G, Xiao JL, Li FG, Wu JH (2018) Simultaneous editing of two copies of Gh14-3-3d confers enhanced transgene-clean plant defense against verticillium dahliae in allotetraploid upland cotton. Front Plant Sci 9:842. https://doi.org/10.3389/fpls2018.00842
Zhang M, Liu QL, Yang XP, Xu JH, Liu G, Yao XF, Ren RS, Xu J, Lou L (2020) CRISPR/Cas9-mediated mutagenesis of Clpsk1 in watermelon to confer resistance to Fusarium oxysporum f.sp. niveum. Plant Cell Rep 39(5):589–595. https://doi.org/10.1007/s00299-020-02516-0
Zhang L, Wang YZ, Li T, Qiu HM, Xia ZJ, Dong YS (2021) Target-specific mutations efficiency at multiple loci of CRISPR/Cas9 system using one sgRNA in soybean. Transgenic Res 30(1):51–62
Zhou M, Luo J, Xiao D, Wang AQ, He LF, Zhan J (2023) An efficient method for the production of transgenic peanut plants by pollen tube transformation mediated by Agrobacterium Tumefaciens. Plant Cell Tissue Organ Cult 152(1):207–214. https://doi.org/10.1007/s11240-022-02388-0
Zhuang WJ, Chen H, Yang M, Wang JP, Pandey MK, Zhang C, Chang WC, Zhang LS, Zhang XT, Tang RH, Garg V, Wang XJ, Tang HB, Chow CN, Wang JP, Deng Y, Wang DP, Khan AW, Yang Q, Cai TC, Bajaj P, Wu KC, Guo BZ, Zhang XY, Li JJ, Liang F, Hu J, Liao BS, Liu SY, Chitikineni A, Yan HS, Zheng YX, Shan SH, Liu QZ, Xie DY, Wang ZY, Khan SA, Ali N, Zhao CZ, Li XG, Luo ZL, Zhang SB, Zhuang RR, Peng Z, Wang SY, Mamadou G, Zhuang YH, Zhao ZF, Yu WC, Xiong FQ, Quan WP, Yuan M, Li Y, Zou HS, Xia H, Zha L, Fan JP, Yu JG, Xie WP, Yuan JQ, Chen K, Zhao SS, Chu WT, Chen YT, Sun PC, Meng FB, Zhuo T, Zhao YH, Li CJ, He GH, Zhao YL, Wang CC, Kavikishor PB, Pan RL, Paterson AH, Wang XY, Min R, Varshney RK (2019) The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication. Nat Genet 51(5):865–876. https://doi.org/10.1038/s41588-019-0402-2
Zischewski J, Fische R, Bortesi L (2017) Detection of on-target and off-target mutations generated by CRISPR/Cas9 and other sequence-specific nucleases. Biotechnol Adv 35(1):95–104. https://doi.org/10.1016/j.biotechadv.2016.12.003
Acknowledgements
This work was financially supported by the Central Guidance for Local Science and Technology Development Funds Projects (Grant No. ZY22096013), the Guangxi Natural Science Foundation (Grant No. 2022GXNSFAA035437), the Guangxi Innovation Team Project of Soybean and Oil Crops of Modern Agricultural Industrial Technology System of China (nycytxgxcxtd-20-02) and Training Program for 1000 Young and Middle-aged Key Teachers in Guangxi at 2019.
Funding
This study was funded by the Central Guidance for Local Science and Technology Development Funds Projects (Grant No. ZY22096013), the Guangxi Natural Science Foundation (Grant No. 2022GXNSFAA035437), the Guangxi Innovation Team Project of Soybean and Oil Crops of Modern Agricultural Industrial Technology System of China (nycytxgxcxtd-20-02) and Training Program for 1000 Young and Middle–aged Key Teachers in Guangxi at 2019.
Author information
Authors and Affiliations
Contributions
JZ conceived the experiments and revised this manuscript; ALL performed most of the experiments and wrote the manuscript; MZ, GTL, XYL performed some of the experiments; AQW, DX, LFH and JZ analyzed the data. All authors have read and agreed to the published version of the manuscript.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare no conflict of interest.
Additional information
Communicated by Sergio J. Ochatt.
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Li, A., Zhou, M., Liao, G. et al. CRISPR/Cas9 gene editing in peanut by Agrobacterium tumefaciens-mediated pollen tube transformation. Plant Cell Tiss Organ Cult 155, 883–892 (2023). https://doi.org/10.1007/s11240-023-02607-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11240-023-02607-2