eISSN: 2221-6197 DOI: 10.31301/2221-6197

Organoleptic control of the knockout CRISPR/Cas editing in plants. A review

Year: 2024

Pages: 206-216

Number: Volume 17, issue 3

Type: scientific article

Summary:

Knockout CRISPR/Cas editing of plant genomes can be used both in model experiments aimed at the development of this technology, and in introducing targeted mutations to create plants s with new traits. Possibility to obtain information about the editing event in a quick and easy way accelerates getting the desired results. Organoleptic control of changes in the genome can indirectly serve this purpose by allowing visual or olfactic assessment. This can be achieved through a knockout of the phytoendesaturase gene, which causes albinism in plants, and the betaine aldehyde dehydrogenase 2 (BADH2) gene, which leads to a change in the metabolism of γ aminobutyric aldehyde and the synthesis of 2 acetyl-1-pyrroline, characterized by a strong aroma reminiscent of popcorn. The history of studying the BADH2 gene begins with the aromatic rice Oryza sativa of the basmati variety, which carries a natural mutation in this gene and thereby accumulates 2 acetyl-1-pyrroline. The BADH2 gene, characterized by high evolutionary conservatism, has been also sequenced in several plant species from different families. A number of gene edited crops have been produced by knockout of the BADH2 gene, including sorghum, peanuts, rapeseed, rice, and soybeans. In some cases, CRISPR/Cas knockout editing can be performed without inserting foreign DNA into the genome, thereby mimicking naturally occuring mutations. According to the laws of some countries, such plants are not considered GMOs.

Keywords:

CRISPR/Cas editing, rice, plants, betaine aldehyde dehydrogenase 2, BADH2, odor, fragrance, 2 acetyl 1 pyrroline

References:

  1. Bhatt V, Ramkumar TR, Barvkar V et al. Targeted disruption of OsBADH2 induces basmati aroma in the popular indica rice variety IR-64 using CRISPR/Cas9. Plant Physiology Reports. doi: 10.1007/s40502-025-00901-z
  2. Bigyan KC, Pandit R, Regmi R et al. Genetic basis of rice aroma gene and its application in rice genetics and breeding: A review. Russian Journal of Agricultural and Socio-Economic Sciences 111(3). 170-175. doi: 10.18551/rjoas.2021-03.20
  3. Bradbury LM, Fitzgerald TL, Henry RJ et al. The gene for fragrance in rice. Plant Biotechnol J. 2005. 3(3). 363-370. doi: 10.1111/j.1467-7652.2005.00131.x
  4. Brocker C, Vasiliou M, Carpenter S et al. Aldehyde dehydrogenase (ALDH) superfamily in plants: gene nomenclature and comparative genomics. Planta. 2013. 237(1). 189-210. doi: 10.1007/s00425-012-1749-0
  5. Bulle M, Venkatapuram AK, Abbagani S, Kirti PB. CRISPR/Cas9 based genome editing of Phytoene desaturase (PDS) gene in chilli pepper (Capsicum annuum). J Genet Eng Biotechnol. 2024. 22(2). 100380. doi: 10.1016/j.jgeb.2024.100380
  6. Buttery RG, Ling LC, Juliano BO. 2-Acetyl-1-Pyrroline: An Important Aroma Component of Cooked Rice. Chemistry and Industry (London). (23). 958-959.
  7. Buttery RG, Stern DJ, Ling LC. Studies on Flavor Volatiles of Some Sweet Corn Products. Agric. Food Chem. 1994. 42(3). 791–795. doi: 10.1021/jf00039a038
  8. Buttery RG, Turnbaugh JG, Ling LC. Contribution of volatiles to rice aroma. Agric. Food Chem. 1988. 36(5). 1006–1009. doi: 10.1021/jf00083a025
  9. Chandanshive S, Mathure S, Nadaf A. Multiple mutations in BADH2 gene reveal the novel fragrance allele in indica rice (Oryza sativa). J Genet. 2024. 103. 13. doi: 10.1007/s12041-024-01464-y
  10. Chen M, Wei X, Shao G et al. Fragrance of the rice grain achieved via artificial microRNA induced down regulation of OsBADH2. Plant Breeding. 2012. 131(5). 584-590. doi: 10.1111/j.1439-0523.2012.01989.x
  11. Cordeiro GM, Christopher MJ, Henry RJ et al. Identification of microsatellite markers for fragrance in rice by analysis of the rice genome sequence. Molecular Breeding. 2002. 9. 245–250. doi.org/10.1023/A:1020350725667
  12. Fitzgerald TL, Waters DL, Henry RJ. Betaine aldehyde dehydrogenase in plants. Plant Biol (Stuttg). 2009. 11(2). 119-130. doi: 10.1111/j.1438-8677.2008.00161.x
  13. Gerashchenkov GA, Rozhnova NA, Kuluev BR et al. Design of Guide RNA for CRISPR/Cas Plant Genome Editing. Molecular Biology. 2020. 54(1). 24-42. DOI: 10.1134/S0026893320010069
  14. Goff SA, Ricke D, Lan TH et al. A draft sequence of the rice genome (Oryza sativa ssp. japonica). Science. 2002. 296(5565). 92-100. doi: 10.1126/science.1068275
  15. He D, Zhou R, Huang C et al. Improvement of Flowering Stage in Japonica Rice Variety Jiahe212 by Using CRISPR/Cas9 System. Plants (Basel). 13(15). 2166. doi: 10.3390/plants13152166
  16. Henderson SW, Henderson ST, Goetz M et al. Efficient CRISPR/Cas9-Mediated Knockout of an Endogenous Phytoene Desaturase Gene in T1 Progeny of Apomictic Hieracium Enables New Strategies for Apomixis Gene Identification. Genes (Basel). 11(9). 1064. doi: 10.3390/genes11091064
  17. Huang Y, Huang L, Cheng M et al. , Li C, Zhou X, Ullah A, Sarfraz S, Khatab A, Xie G. Progresses in biosynthesis pathway, regulation mechanism and potential application of 2-acetyl-1-pyrroline in fragrant rice. Plant Physiol Biochem. 215.109047. doi: 10.1016/j.plaphy.2024.109047
  18. Hui S, Li H, Mawia AM et al. Production of aromatic three-line hybrid rice using novel alleles of BADH2. Plant Biotechnol J. 2022. 20(1). 59-74. doi: 10.1111/pbi.13695
  19. Imran M, Shafiq S, Ashraf U et al. Biosynthesis of 2-Acetyl-1-pyrroline in Fragrant Rice: Recent Insights into Agro-management, Environmental Factors, and Functional Genomics. J Agric Food Chem. 71(10). 4201-4215. doi: 10.1021/acs.jafc.2c07934
  20. Jin Q, Waters D, Cordeiro GM et al. A single nucleotide polymorphism (SNP) marker linked to the fragrance gene in rice (Oryza sativa). Plant Science. 2003. 165(2). 359-364. doi: 10.1016/S0168-9452(03)00195-X
  21. Juwattanasomran R, Somta P, Chankaew S et al. A SNP in GmBADH2 gene associates with fragrance in vegetable soybean variety "Kaori" and SNAP marker development for the fragrance. Theor Appl Genet. 122(3). 533-541. doi: 10.1007/s00122-010-1467-6
  22. Khandagale KS, Chavhan R, Nadaf AB. RNAi-mediated down regulation of BADH2 gene for expression of 2-acetyl-1-pyrroline in non-scented indica rice IR-64 (Oryza sativa). 3 Biotech. 2020. 10(4). 145. doi: 10.1007/s13205-020-2131-8
  23. Kuluev BR, Gumerova GR, Mikhaylova EV et al. Delivery of CRISPR/Cas components into higher plant cells for genome editing. Russian Journal of Plant Physiology. 2019. 66(5). 694-706. DOI: 10.1134/S102144371905011X
  24. Liao Y, Li M, Wu H et al. Generation of aroma in three-line hybrid rice through CRISPR/Cas9 editing of betaine aldehyde dehydrogenase2 (OsBADH2). Physiol Plant. 2024. 176(1). e doi: 10.1111/ppl.14206
  25. Mikhaylova EV, Khusnutdinov EA, Chemeris AV et al. Available Toolkits for CRISPR/CAS Genome Editing in Plants. Russian Journal of Plant Physiology. 69. 3. DOI:1134/S1021443722010137
  26. Niu X, Tang W, Huang W et al. RNAi-directed downregulation of OsBADH2 results in aroma (2-acetyl-1-pyrroline) production in rice (Oryza sativa). BMC Plant Biol. 2008. 8. 100. doi: 10.1186/1471-2229-8-100
  27. Okpala NE, Mo Z, Duan M et al. The genetics and biosynthesis of 2-acetyl-1-pyrroline in fragrant rice. Plant Physiol Biochem. 2019. 135. 272-276. doi: 10.1016/j.plaphy.2018.12.012
  28. Pavese V, Moglia A, Corredoira E et al. First Report of CRISPR/Cas9 Gene Editing in Castanea sativa Mill. Front Plant Sci. 25(12). 728516. doi: 10.3389/fpls.2021.728516
  29. Qian L, Jin H, Yang Q et al. A Sequence Variation in GmBADH2 Enhances Soybean Aroma and Is a Functional Marker for Improving Soybean Flavor. Int J Mol Sci. 23(8). 4116. doi: 10.3390/ijms23084116
  30. Senthil K, Rathinam M, Parashar M et al. Establishing a CRISPR/Cas9 genome editing framework in pigeonpea (Cajanus cajan L.) by targeting phytoene desaturase (PDS) gene disruption. J Genet Eng Biotechnol. 23(1). 100465. doi: 10.1016/j.jgeb.2025.100465
  31. Schieberle P. Quantitation of Important Roast-Smelling Odorants in Popcorn by Stable Isotope Dilution Assays and Model Studies on Flavor Formation during Popping. Agric. Food Chem. 1995. 43(9). 2442–2448. doi: 10.1021/jf00057a024
  32. Shan Q, Zhang Y, Chen K et al. Creation of fragrant rice by targeted knockout of the OsBADH2 gene using TALEN technology. Plant Biotechnol J. 13(6). 791-800. doi: 10.1111/pbi.12312
  33. Shi Y, Zhao G, Xu X et al. Discovery of a new fragrance allele and development of functional markers for identifying diverse fragrant genotypes in rice. Mol Breeding. 2014. 33. 701–708. doi.org/10.1007/s11032-013-9986-x
  34. Tian Y, Zhou Y, Gao G et al. Creation of Two-Line Fragrant Glutinous Hybrid Rice by Editing the Wx and OsBADH2 Genes via the CRISPR/Cas9 System. Int J Mol Sci. 24(1). 849. doi: 10.3390/ijms24010849
  35. Thimmaraju R, Bhagyalakshmi N, Narayan Ms et al. In vitro culture of Pandanus amaryllifolius and enhancement of 2‐acetyl‐1‐pyrroline, the major flavouring compound of aromatic rice, by precursor feeding of L‐proline. J Science Food Agriculture. 2005. 85(15). 2527-2534. DOI: 10.1002/jsfa.2286
  36. Usman B, Nawaz G, Zhao N et al. Generation of High Yielding and Fragrant Rice (Oryza sativa) Lines by CRISPR/Cas9 Targeted Mutagenesis of Three Homoeologs of Cytochrome P450 Gene Family and OsBADH2 and Transcriptome and Proteome Profiling of Revealed Changes Triggered by Mutations. Plants (Basel). 2020. 9(6). 788. doi: 10.3390/plants9060788
  37. Vaia G, Pavese V, Moglia A et al. Knockout of phytoene desaturase gene using CRISPR/Cas9 in highbush blueberry. Front Plant Sci. 13. 1074541. doi: 10.3389/fpls.2022.1074541
  38. Wakte K, Zanan R, Hinge V et al. Thirty-three years of 2-acetyl-1-pyrroline, a principal basmati aroma compound in scented rice (Oryza sativa): a status review. J Sci Food Agric. 2017. 97(2). 384-395. doi: 10.1002/jsfa.7875
  39. Wang Y, Liu X, Zheng X et al. Creation of aromatic maize by CRISPR/Cas. J Integr Plant Biol. 63(9). 1664-1670. doi: 10.1111/jipb.13105
  40. Wei X, Handoko DD, Pather L et al. Evaluation of 2-acetyl-1-pyrroline in foods, with an emphasis on rice flavour. Food Chem. 531-544. doi: 10.1016/j.foodchem.2017.04.005
  41. Wu J, Xu J, He A et al. Generating fragrant oilseed rape using CRISPR/Cas9-mediated gene editing. Plant Physiol. 197(1) kiae660. doi: 10.1093/plphys/kiae660
  42. Wu W, Miao R, Li Z et al. CRISPR/Cas9-mediated editing of BADH2 and Wx genes for the development of novel aromatic and soft-textured black and red rice. Physiol Plant. 177(2). e70194. doi: 10.1111/ppl.70194
  43. Xie H, Song M, Cao X et al. Breeding exceptionally fragrant soybeans for soy milk with strong aroma. J Integr Plant Biol. 66(4). 642-644. doi: 10.1111/jipb.13631
  44. Xue L, Qu P, Zhao H et al. Creation of fragrant peanut using CRISPR/Cas9. J Integr Plant Biol. 67(6). 1438-1440. doi: 10.1111/jipb.13864
  45. Yu J, Hu S, Wang J. et al. A draft sequence of the rice genome (Oryza sativa ssp. indica). Science. 2002. 296(5565). 79-92. doi: 10.1126/science.1068037
  46. Yundaeng C, Somta P, Tangphatsornruang S et al. A single base substitution in BADH/AMADH is responsible for fragrance in cucumber (Cucumis sativus), and development of SNAP markers for the fragrance. Theor Appl Genet. 128(9). 1881-1892. doi: 10.1007/s00122-015-2554-5
  47. Yundaeng C, Somta P, Tangphatsornruang S et al. Gene discovery and functional marker development for fragrance in sorghum (Sorghum bicolor (L.) Moench). Theor Appl Genet. 126(11). 2897-2906. doi: 10.1007/s00122-013-2180-z
  48. Zhang C, Yun P, Xia J et al. CRISPR/Cas9-mediated editing of Wx and BADH2 genes created glutinous and aromatic two-line hybrid rice. Mol Breed. 43(4). 24. doi: 10.1007/s11032-023-01368-2
  49. Zhang D, Tang S, Xie P et al. Creation of fragrant sorghum by CRISPR/Cas9. J Integr Plant Biol. 64(5). 961-964. doi: 10.1111/jipb.13232
  50. Zhang Y, He Q, Zhang S et al. De novo creation of popcorn-like fragrant foxtail millet. J Integr Plant Biol. 65(11). 2412-2415. doi: 10.1111/jipb.13556
  51. Zhao G, Deng L, Liu X et al. A mutation in CmoBADH results in the production of 2-acetyl-1-pyrroline, conferring a 'taro-like' aroma in Cucurbita moschata. Theor Appl Genet. 138(11). 265. doi: 10.1007/s00122-025-05050-3
Download pdf
up
eISSN: 2221-6197 DOI: 10.31301/2221-6197