CRISPR/Cas9-mediated multiple guide RNA-targeted mutagenesis in the potato.
Amylose
CAPS analysis
CRISPR/Cas9
GBSS
S. Tuberosum L
Journal
Transgenic research
ISSN: 1573-9368
Titre abrégé: Transgenic Res
Pays: Netherlands
ID NLM: 9209120
Informations de publication
Date de publication:
10 2023
10 2023
Historique:
received:
27
12
2022
accepted:
01
06
2023
medline:
27
10
2023
pubmed:
18
6
2023
entrez:
18
6
2023
Statut:
ppublish
Résumé
CRISPR/Cas9 technology has become the most efficient method for genome editing in many plant species, including important industrial crops such as potatoes. This study used three target regions (T1, T2, and T3) in gbss exon I, whose sequences were first inserted into the BbsI sites in the appropriate guide RNA (gRNA) vector (pEn-Chimera, pMR203, pMR204, and pMR205), and then localized between the AtU6 promoter and the gRNA scaffold sequence. Expression vectors were constructed by introducing gRNA genes into the pMR287 (pYUCas9Plus) plasmids using the MultiSite Gateway system by attR and attL sites. The three target regions of mutant potato lines were analyzed. The use of CRISPR/Cas9-mediated multiple guide RNA-targeted mutagenesis allowed tri- or tetra-allelic mutant potato lines to be generated. Multiple nucleotide substitutions and indels within and around the three target sites caused a frameshift mutation that led to a premature stop codon, resulting in the production of gbss-knockout plants. Mutation frequencies and analysis of mutation patterns suggested that the stably transformed Cas9/multiple guide RNA expression constructs used in this study can induce targeted mutations efficiently in the potato genome. Full knockout of the gbss gene was analyzed by CAPS, Sanger sequencing and iodine staining. The present study demonstrated successful CRISPR/Cas9-mediated multiple guide RNA-targeted mutagenesis in the potato gbss gene by Agrobacterium-mediated transformation, resulting in an amylose-free phenotype.
Identifiants
pubmed: 37330986
doi: 10.1007/s11248-023-00356-8
pii: 10.1007/s11248-023-00356-8
doi:
Substances chimiques
RNA, Guide, CRISPR-Cas Systems
0
Starch Synthase
EC 2.4.1.21
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
383-397Informations de copyright
© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.
Références
Abeuova LS, Kali BR, Rakhimzhanova AO, Bekkuzhina SS, Manabayeva SA (2020) High frequency direct shoot regeneration from Kazakh commercial potato cultivars. PeerJ 8:e9447. https://doi.org/10.7717/peerj.9447
doi: 10.7717/peerj.9447
pubmed: 32742778
pmcid: 7365135
Aboul-Maaty NA-F, Oraby HA-S (2019) Extraction of high-quality genomic DNA from different plant orders applying a modified CTAB-based method. Bull Natl Res Cent. https://doi.org/10.1186/s42269-019-0066-1
doi: 10.1186/s42269-019-0066-1
Andersson M, Trifonova A, Andersson AB, Johansson M, Bulow L, Hofvander P (2003) A novel selection system for potato transformation using a mutated AHAS gene. Plant Cell Rep 22(4):261–267. https://doi.org/10.1007/s00299-003-0684-8
doi: 10.1007/s00299-003-0684-8
pubmed: 14586551
Andersson M, Turesson H, Nicolia A, Fält A-S, Samuelsson M, Hofvander P (2016) 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
doi: 10.1007/s00299-016-2062-3
pubmed: 27699473
pmcid: 5206254
Andersson M, Turesson H, Olsson N, Fält A-S, Ohlsson P, Gonzalez MN, Samuelsson M, Hofvander P (2018a) Genome editing in potato via CRISPR-Cas9 ribonucleoprotein delivery. Physiol Plant. https://doi.org/10.1111/ppl.12731
doi: 10.1111/ppl.12731
pubmed: 29572864
Andersson M, Turesson H, Olsson N, Falt AS, Ohlsson P, Gonzalez MN, Samuelsson M, Hofvander P (2018b) Genome editing in potato via CRISPR-Cas9 ribonucleoprotein delivery. Physiol Plant 164(4):378–384. https://doi.org/10.1111/ppl.12731
doi: 10.1111/ppl.12731
pubmed: 29572864
Anzalone AV, Koblan LW, Liu DR (2020) Genome editing with CRISPR-Cas nucleases, base editors, transposases and prime editors. Nat Biotechnol 38(7):824–844. https://doi.org/10.1038/s41587-020-0561-9
doi: 10.1038/s41587-020-0561-9
pubmed: 32572269
Birch PRJ, Bryan G, Fenton B, Gilroy EM, Hein I, Jones JT, Prashar A, Taylor MA, Torrance L, Toth IK (2012) Crops that feed the world 8: potato: are the trends of increased global production sustainable? Food Secur 4(4):477–508. https://doi.org/10.1007/s12571-012-0220-1
doi: 10.1007/s12571-012-0220-1
Chilton MD, Currier TC, Farrand SK, Bendich AJ, Gordon MP, Nester EW (1974) Agrobacterium tumefaciens DNA and PS8 bacteriophage DNA not detected in crown gall tumors. Proc Natl Acad Sci USA 71:3672–3676
doi: 10.1073/pnas.71.9.3672
pubmed: 4530328
pmcid: 433838
Delcour JA, Bruneel C, Derde LJ, Gomand SV, Pareyt B, Putseys JA, Wilderjans E, Lamberts L (2010) Fate of starch in food processing: from raw materials to final food products. Annu Rev Food Sci Technol 1:87–111. https://doi.org/10.1146/annurev.food.102308.124211
doi: 10.1146/annurev.food.102308.124211
pubmed: 22129331
Fossi M, Amundson K, Kuppu S, Britt A, Comai L (2019) Regeneration of Solanum tuberosum plants from protoplasts induces widespread genome instability. Plant Physiol 180(1):78–86. https://doi.org/10.1104/pp.18.00906
doi: 10.1104/pp.18.00906
pubmed: 30792232
pmcid: 6501065
Hovenkamp-Hermelink J, Jacobsen E, Ponstein A, Visser R, Vos-Scheperkeuter G, Bijmolt E, De Vries J, Witholt B, Feenstra W (1987) Isolation of an amylose-free starch mutant of the potato (Solanum tuberosum L.). Theor Appl Genet 75:217–221
doi: 10.1007/BF00249167
https://new.stat.gov.kz (2022) Gross crop harvest in the Republic of Kazakhstan for 2022. https://newstatgovkz/ru/industries/business-statistics/stat-forrest-village-hunt-fish/publications/5099/?sphrase_id=39867
Hua D, Ma M, Ge G, Suleman M, Li H (2020) The role of cyanide-resistant respiration in Solanum tuberosum L. against high light stress. Plant Biol (stuttg) 22(3):425–432. https://doi.org/10.1111/plb.13098
doi: 10.1111/plb.13098
pubmed: 32052535
Johansen IE, Liu Y, Jorgensen B, Bennett EP, Andreasson E, Nielsen KL, Blennow A, Petersen BL (2019) High efficacy full allelic CRISPR/Cas9 gene editing in tetraploid potato. Sci Rep 9(1):17715. https://doi.org/10.1038/s41598-019-54126-w
doi: 10.1038/s41598-019-54126-w
pubmed: 31776399
pmcid: 6881354
Kamiya Y, Abe F, Mikami M, Endo M, Kawaura K (2020) A rapid method for detection of mutations induced by CRISPR/Cas9-based genome editing in common wheat. Plant Biotechnol (tokyo) 37(2):247–251. https://doi.org/10.5511/plantbiotechnology.20.0404b
doi: 10.5511/plantbiotechnology.20.0404b
pubmed: 32821233
Khlestkin VK, Peltek SE, Kolchanov NA (2017) Target genes for development of potato (Solanum tuberosum L.) cultivars with desired starch properties (review). Sel’skokhozyaistvennaya Biologiya 52(1):25–36. https://doi.org/10.15389/agrobiology.2017.1.25eng
doi: 10.15389/agrobiology.2017.1.25eng
Kozlov SS, Blennow A, Krivandin AV, Yuryev VP (2007) Structural and thermodynamic properties of starches extracted from GBSS and GWD suppressed potato lines. Int J Biol Macromol 40(5):449–460. https://doi.org/10.1016/j.ijbiomac.2006.11.001
doi: 10.1016/j.ijbiomac.2006.11.001
pubmed: 17188347
Kusano H, Ohnuma M, Mutsuro-Aoki H, Asahi T, Ichinosawa D, Onodera H, Asano K, Noda T, Horie T, Fukumoto K, Kihira M, Teramura H, Yazaki K, Umemoto N, Muranaka T, Shimada H (2018) Establishment of a modified CRISPR/Cas9 system with increased mutagenesis frequency using the translational enhancer dMac3 and multiple guide RNAs in potato. Sci Rep 8(1):13753. https://doi.org/10.1038/s41598-018-32049-2
doi: 10.1038/s41598-018-32049-2
pubmed: 30214055
pmcid: 6137036
Kusano H, Onodera H, Kihira M, Aoki H, Matsuzaki H, Shimada H (2016) A simple Gateway-assisted construction system of TALEN genes for plant genome editing. Sci Rep 6:30234. https://doi.org/10.1038/srep30234
doi: 10.1038/srep30234
pubmed: 27452606
pmcid: 4958979
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. https://doi.org/10.1016/j.molp.2017.01.003
doi: 10.1016/j.molp.2017.01.003
pubmed: 28089950
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25(4):402–408. https://doi.org/10.1006/meth.2001.1262
doi: 10.1006/meth.2001.1262
pubmed: 11846609
Makhotenko AV, Khromov AV, Snigir EA, Makarova SS, Makarov VV, Suprunova TP, Kalinina NO, Taliansky ME (2019) Functional analysis of coilin in virus resistance and stress tolerance of potato solanum tuberosum using CRISPR-Cas9 editing. Dokl Biochem Biophys 484(1):88–91. https://doi.org/10.1134/S1607672919010241
doi: 10.1134/S1607672919010241
pubmed: 31012023
Murashige T, Skoog F (1962) A revised medium for rapid growth and biosynthesis with tobacco tissue culture. Plant Physiol 15:473–497
doi: 10.1111/j.1399-3054.1962.tb08052.x
Naito Y, Hino K, Bono H, Ui-Tei K (2015) CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites. Bioinformatics 31(7):1120–1123. https://doi.org/10.1093/bioinformatics/btu743
doi: 10.1093/bioinformatics/btu743
pubmed: 25414360
Shure M, Wessle S, Fedoroff N (1983) Molecular identification and isolation of the Waxy locus in maize. Cell Res 35(1):225–233. https://doi.org/10.1016/0092-8674(83)90225-8
doi: 10.1016/0092-8674(83)90225-8
Toinga-Villafuerte S, Vales MI, Awika JM, Rathore KS (2022) CRISPR/Cas9-mediated mutagenesis of the granule-bound starch synthase gene in the potato variety yukon gold to obtain amylose-free starch in tubers. Int J Mol Sci. https://doi.org/10.3390/ijms23094640
doi: 10.3390/ijms23094640
pubmed: 35563030
pmcid: 9101600
Tussipkan D, Manabayeva SA (2021) Employing CRISPR/Cas technology for the improvement of potato and other tuber crops. Front Plant Sci 12:747476. https://doi.org/10.3389/fpls.2021.747476
doi: 10.3389/fpls.2021.747476
pubmed: 34764969
pmcid: 8576567
Veillet F, Chauvin L, Kermarrec MP, Sevestre F, Merrer M, Terret Z, Szydlowski N, Devaux P, Gallois JL, Chauvin JE (2019a) The Solanum tuberosum GBSSI gene: a target for assessing gene and base editing in tetraploid potato. Plant Cell Rep 38(9):1065–1080. https://doi.org/10.1007/s00299-019-02426-w
doi: 10.1007/s00299-019-02426-w
pubmed: 31101972
Veillet F, Perrot L, Chauvin L, Kermarrec MP, Guyon-Debast A, Chauvin JE, Nogue F, Mazier M (2019b) Transgene-free genome editing in tomato and potato plants using agrobacterium-mediated delivery of a CRISPR/Cas9 cytidine base editor. Int J Mol Sci. https://doi.org/10.3390/ijms20020402
doi: 10.3390/ijms20020402
pubmed: 30669298
pmcid: 6358797
Visser RG, Somhorst I, Kuipers GJ, Ruys NJ, Feenstra WJ, Jacobsen E (1991) Inhibition of the expression of the gene for granule-bound starch synthase in potato by antisense constructs. Mol Gen Genet 225(2):289–296
doi: 10.1007/BF00269861
pubmed: 2005870
Visser RGF, Suurs LCJM, Bruinenberg PM, Bleeker I, Jacobsen E (1997) Comparison between amylose-free and amylose containing potato starches. Starch Stärke 49(11):438–443. https://doi.org/10.1002/star.19970491103
doi: 10.1002/star.19970491103
Xu X, Visser RGF, Trindade LM (2014) Starch modification by biotechnology: state of art and perspectives. Starch Polym. https://doi.org/10.1016/B978-0-444-53730-0.00021-X
doi: 10.1016/B978-0-444-53730-0.00021-X