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Enhancing climate resilience and ensuring food security with genome editing tools

Contact Info

Divison of Plant Physiology, ICAR-IARI, New Delhi - 110012

+91 9899426498

crispricar@gmail.com

Target Genes

Genes targeted in different crops for genome editing in this proposal


S.No. Crop Trait Gene SDN1/SDN2/Base editing/Prime editing Reference for the gene (Previous work done, if any)
1. Rice NUE, Photosynthesis & Yield DREB1C SDN1
2. Rice Drought and salt tolerance and yield DST SDN1
3. Rice Enhanced root development/ drought Tolerance OsRRS1 SDN1 Gao et al. (2023) New Phytologist 238(3): 1146-1162
4. Rice Blast resistance OsDjA2, OsERF104 and OsPi21 SDN1 Távora et al. (2022) Rice science 22(6): 535-544 Nawaz et al (2020) Genes 11(7):735
5. Rice Culm strength OsIIP4 SDN1 Zhang et al. (2018) Molecular Plants 11(1):163-174
6. Rice Yield GW2, GW5, TGW6 SDN1
7. Rice NUE ARE1, AAP3, AAP5 SDN1
8. Rice Bacterial blight resistance OsSWEET11, OsSWEET13, OsSWEET14, OsSWEET15 SDN1 Oliva et al., 2019
9. Rice Resistance to Blast disease SEC3A, MPK5 SDN1/SDN2 Ma et al. (2018); Xie and Yang (2013)
10. Rice Resistance to stunting disease of rice caused by Southern rice black-streaked dwarf virus eIF4G & OsAGO2 SDN1/SDN2 Wang et al. 2021
11. Rice Nematode resistance OsAAP6, OsHIPP20, OsFAD8 SDN1 Parriyar al. 2018, Radakovic et al. 2018, Dash et al. 2022
12 Rice Fe content HRZ1, HRZ2 SDN1/prime editing Aung et al. 2018
13 Rice Yield LOC_Os04g52590, LOC_Os04g52590 (OsRLCK159), and LOC_Os04g52210 (OsKS-3) SDN1 DOI: 10.1111/tpj.14062
DOI: 10.1266/ggs.16-00018
DOI: 10.1073/pnas.1310790110
14 Rice Bacterial blight disease Xa5 SDN2/prime editing Iyer and McCouch 2004; Iyer et al 2008; Yuan et al 2016
15. Rice erect leaf, erect panicle, yield br11, dep1 SDN2/prime editing (Morinaka et al., 2006), (Huang et al., 2009)
16. Rice Herbicide resistance als, epsps SDN2/prime editing (Sun et al., 2016), (Li et al., 2016)
17. Rice Yield Gn1a SDN1 (Li et al., 2016)
18. Rice Lodging resistant Sd1 SDN1 Hu et al., 2019
19. Rice NUE DNR1 SDN1 Zhang et al., 2021
20. Rice WUE EPFL9 SDN1 Yin et al., 2017
21. Rice Quality IPK1 SDN1 Ibrahima et al., 2022
22. Rice Yield OSD1, PAIR1, REC8, MTL1 SDN1 Xie et al., 2019
23. Rice Grain filling, earliness, and male sterility (targeting two-line hybrid system) SALT-RESPONSIVE ERF1 (SERF1), TMS5, and OsOPR7 SDN1 Schmidt et al 2014; Barman et al 2019; Zhou et al 2016; Pak et al 2021
24. Rice Dwarfness, grain yield, and culm strength OsCKX2 and Semi-dwarf (sd-1) SDN1 Spielmeyer et al 2002; Ashikari et al 2005; Tu et al 2022
25. Rice OsCKX2 SDN1 N.A.
26. Rice high-amylose SBEII N.A. N.A.
27. Wheat Nitrogen Use Efficiency BT (Bric-a-Brac/Tramtrack/Broad gene) SDN1 Arasu et al., 2016; O'Brien et al., 2016; Sevanthi et al., 2021
28. Wheat Nitrogen Use Efficiency NGT1 SDN1 Sawaki et al., 2013; Kiba et al., 2018; Li et al., 2021; Sevanthi et al., 2021
29. Wheat Nutrient (Nitrogen and Phosphorus) Use Efficiency SPX4 SDN1 Hu B., Jiang Z., Wang W. et al (2019) Nature Plants 5, 401-413
30. Wheat Heat stress tolerance Ortholog of ZmHsf1 in wheat SDN1 Qin et al., 2022
31. Wheat Nitrogen use efficiency Abnormal cytokinin response1, repressor1 (ARE1) SDN1 Zhang et al., 2021
32. Wheat Heat stress tolerance Proline Dehydrogenase (ProDH) SDN1 Guo et al., 2020
33. Wheat Biofortification of Fe and Zn Inositol Triphosphate Kinases (ITPK1) SDN1 Aggarwal et al., 2018; Karmakar et al., 2020
34. Wheat Resistant starch Starch branching enzyme (SBE) SDN1 Regina et al., 2006, 2015
35. Maize Haploid induction MTL, DMP SDN1 Kelliher, T. et al. (2017) Nature, 542:105-109. Li Y., Lin, Z. et al. (2021) Nature, 1571-1583
36. Maize Banded leaf and sheath blight resistance Zm FBL41 SDN1 Li et al., 2019
37. Maize High-amylose/low-glycemic maize ZmSBEIIb SDN1 Luo et al., 2022; Regina et al., 2015; Sun et al., 2017; Carciofi et al. 2012
38. Maize Low phytic acid, high amylose MIK,ITPK SDN1 N.A.
39. Maize Kernel number per plant ZmRRN2 SDN1
40. Pearl millet Phytic acid biosynthesis Inositol phosphate kinase (IPK1) SDN1 doi.org/10.1371/journal.pone.0193894
41. Pearl millet Grain yield ABCI-1 Repressor (ARE1) SDN1 doi.org/10.1038/s41467-017-02781-w
42. Pearl millet Herbicide tolerance EPSP gene and Acetolactate synthase (ALS) gene SDN1 EPSP, ALS
43. Pearl millet Shelf life Two Lipase genes: PgTAGLip1 and PgTAGLip2 SDN1 Lipase
44. Foxtail millet Grain yield ABCI-1 Repressor (ARE1) SDN1 doi.org/10.1038/s41467-017-02781-w
45. Foxtail millet Phytic acid biosynthesis Inositol phosphate kinase (IPK1) SDN1 doi.org/10.1371/journal.pone.0193894
46. Finger Millet Pollen development MATRILINEAL (SiMTL) SDN1 doi.org/10.1111/pbi.13584
47. Finger Millet Grain yield Cytohinin oxidase (CKX1 and CKX2), ABCI-1 Repressor (ARE1) SDN1 https://doi.org/10.1093/jxb/erz502
doi.org/10.1371/journal.pone.019td>
48. Finger Millet Phytic acid biosynthesis Inositol phosphate kinase (IPK1) SDN1 doi.org/10.1371/journal.pone.0193894
49. Finger Millet Drought stress tolerance MSI1, ONAC095, AHP, AHP3, AHP4, AHP, DREB2A-INTERACTING PROTEIN, ATAF1 SDN1 Alexandre et al. 2009, Huang et al. 2016, Nishiyama et al. 2013, Qin et al. 2008, Lu et al. 200
50. Sorghum Herbicide tolerance EPSP, ALS SDN1
51. Mustard Early flowering SET DOMAIN GROUP 8 (SDG8), FLOWERING LOCUS C (FLCs) SDN1 Jiang et al. 2018, Jeong et al. 2019
52. Mustard Self incompatibility SCR-methylation-inducing region 2, ZML1 SDN1
53. Mustard Male Sterility MS5 SDN1
54. Mustard Improved Yield & Seed shattering resistance ALCATRAZ (ALC) /JAGGED (JAG)/INDEHISCENT (IND) SDN1 Braatz et al. 2017, 2018; Zhai et al. 2019; Zaman et al. 2019
55. Mustard Flowering phenotype/ Yield increase APETELA 2 (AP2) SDN1 Zhang et al. 2018b
56. Mustard Improved oil yield/ Improved plant architecture REPRESSOR OF GA (RGA) SDN1/SDN2 Yan et al. 2021; Cheng et al. 2021
57. Mustard Seed yield ENHANCER3 OF DA1 (EOD3/CYP78A6) SDN1
58. Mustard Resistance to silique shattering; tolerance to Sclerotinia sclerotiorum Inflorescence Deficient in Abscission (IDA) SDN1
59. Mustard Oil content WRINKLED1 SDN1
60. Mustard Yield TCP homologs SDN1/SDN2
61. Mustard Aphid resistance CYP71A SDN1/SDN2 Lu et al. 2018
62. Mustard High oil content TTG1 SDN1 Zhao et al. 2019; Xie et al. 2020
63. Mustard Orobanche resistance Lateral Branched oxidoreductase (LBO) SDN1
64. Mustard Yield Cytokinin oxidase/dehydrogenase SDN1/SDN2 Bartina et al., 2011; Schwartz et al., 2017
65. Mustard Seed number BjCLV1 SDN1 Wang, G., ... Shen, J. (2021) Plant Biotechnol. J.
66. Mustard Orobanche resistance PDR1/PDR12 SDN1
67. Mustard Early flowering phenotype BnaSIP, BnaTFL1 SDN1 Ahmar et al. 2022, Sriboon et al. 2020
68. Mustard Increased number of seeds per silique BnaEOD3 SND-1 Khan et al. 2021
69. Groundnut High Oleate FAD2B SDN1/SDN2 Jung et al., 2000
70. Groundnut Low phytic acid content IPK 1 SDN1/SDN2 Ajay et al, 2016
71. Soybean Seed and oil yield GmSDP1 SDN1 Kanai et al. 2019
72. Soybean Seed yield + removal of pod shattering GmGA30x1+Pdh1 SDN1 Hu' et al 2022, Zhang et al. 2022
73. Soybean Insect Resistance GmUGT SDN1 Zhang et al. 2022
74. Soybean Oleic acid content FAD2-1A and FAD2-1B SDN1 Do et al., 2019
75. Soybean Resistance to Yellow Mosaic Disease
  • Flavonone-3-Hydroxylase
  • Flavone synthase
 SDN1 Zhang, P., Plant Biotechnology Journal, 18(6), 1384-1395
76. Soybean Drought, water logging, and salinity stress tolerance
  • Farnesyltransferase (Era1)
  • 1-Aminocyclopropane Carboxylate Synthase (ACS)
  • PARP1 poly(ADP-ribose) polymerase (PARP)
  • Ethylene Insensitive 2 (EIN2)
  • Fatty Acid Desaturase 3 (FAD3)
 SDN1/SDN2/Base editing/Prime editing
  • Ogata et al. (2017)
  • Vanderaurwa et al. (2007)
  • Li et al. (2022)
  • Naing et al. (2022)
  • Singh et al. (2011)
  • Singh et al. (2022)
77. Camelina sativa Improved oil content FATTY ACID DESATURASE 2 (FAD2) / FATTY ACID ELONGASE (FAE1) SDN1 Morineau et al., 2017; Jiang et al., 2017; Ozseyhan et al., 2018; Malik et al., 2018
78. Castor Non-toxic castor lines ricin and RCA N.A. N.A.
79. Chickpea Drought miR171-Scarecrow like SDN2 Yadav et al., 2022 (1)
80. Chickpea Fusarium wilt miR398-copper chaperone for superoxide dismutase module SDN2 Ph.D. thesis IARI (2) (Manuscript under preparation)
81. Chickpea Productivity JAGGED and SFL SDN1 Cai et al. 2021 Caballo et al. 2022
82. Chickpea Nutrition ARE SDN1 Zhang et al. 2021
83. Chickpea Nutrition CaSrGR1 SDN1 Chang et al 2019
84. Pigeonpea DH CENH3 SDN1 Ravi and Chan 2010
85. Pigeonpea Male Sterility DT1, MS1 SDN1 Zhang et al 2006 Gu et al 2014
86. Pigeonpea NUE ARE SDN1 Zhang et al. 2021
87. Pigeonpea Productivity CKXs, BSI, KIX SDN1 Liu et al 2020, Ge et al 2016, Ashikari et al 2005
88. Pigeonpea SMD EIF4e SDN1 Nieto et al., 2006
89. Pigeonpea Earliness TFL SDN1 Mir et al., 2012
90. Pigeonpea Lodging GoX20 SDN1 Shao et al 2020
91. Grasspea ODAP LsBOS, LsAAE3, LsCAS SDN1 Edward et al., 2023; Wang et al., 2021
92. Lentil Earliness and Lodging SVP GoX20 SDN1 Han et al., 2019; Zang et al., 2020
93. Faba bean Enhanced L-DOPA N.A. N.A. N.A.
94. Cotton (G. hirsutum) Fiber quality (length and strength) and drought tolerance GhADF1 SDN1 Wang et al., 2009; Qin et al., 2022
95. Cotton (G. hirsutum) Fiber quality (length and strength) and agronomic traits GhPHYA1 SDN1 Abdurakhmonov et al., 2014
96. Cotton (G. hirsutum) Cotton seed oil content and salt stress tolerance GhPEPC2 SDN1 Zhao et al., 2018
97. Cotton (G. hirsutum) Square and boll shedding tolerant N.A. N.A
98. Cotton (G. hirsutum) Square and boll shedding tolerant JOINTLESS SDN1
99. Jute (Corchorus olitorius) Improve fibre quality (reduced lignin & pectin in bast fibre) iCaffeoyl-CoA 3-O-methyltransferase (CCoAOMT) Cinnamyl alcohol dehydrogenase (CAD), rhamnose biosynthesis gene (RHM1) SDN1 editing Satya et al., 2021; Chakraborty et al., 2015, Sarkar et al (2017)
100. Jute (Corchorus olitorius) Resistance to short-day flowering for climate change adaptation Gibberellin receptor GID1C (GID1C), Protein TOPLESS (TPL) SDN1 editing Data et al. (2021)
101. Jute (Corchorus olitorius) Herbicide tolerance Acetolactate synthase (ALS) and EPSPS SDN1 editing Data et al. (2019)
102. Flax (Linum usitatissimum) Heat Stress Tolerance LusHSFA2a, LusHSFA2b, LusNAC003 SDN1 editing Saha et al. (2019)
103. Sugarcane Fatty acid accumulation OLE1, CYSO1, SDP1, TGD1 SDN1 Parajuli et al., 2019
104. Sugarcane Whip smut resistance ScCat1 SDN1 Wu et al., 2023
105. Sugarcane Reduced lignin content Caffeic acid O-methyltransferase SDN1 Jung and Altpeter, 2016
106. Sugarcane Herbicide resistance Acetolactate synthase (ALS) SDN1 Oz et al., 2021
107. Sugarcane Biomass modification F5H, CAD, PAL SDN1 Lakshmi et al., 2023
108. Sugarcane Abiotic stress tolerance HP4, DST, GA20 SDN1/SDN2 Ha et al. 2022, Santosh Kumar et al., 2020, Andrew-Peter-Leon et al., 2021
109. Sugarcane CAS9 free gene edited plants Deactivate CAS9 SDN1 Yang et al., 2023
110. Sugarcane Knockout of flowering Flowering Locus (FT) SDN1 Abe et al., 2005