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Table 1 Major HGT studies in monocots

From: Challenges and Perspectives in Homology-Directed Gene Targeting in Monocot Plants

No.Gene/AlleleMonocotHDR toolSelection markerHDR allele-associated markerHomologous donor length (bp) (5′ arm + 3′ arm)Gene targeting efficiencyReference 
Gene targeting without targeted DSBs
1waxy (Granule-Bound Starch Synthase gene knockout)riceT-DNAHptII (positive)/DT-A (negative)HptII (positive)6300 + 68000.94% (per total surviving calli)Terada et al. 2002 
2Acetolactate synthase (ALS) (W548 L and S627I)riceT-DNABispyrobac-sodium (BS) herbicide (positive)BS herbicide (positive)8092~ 3% (per total surviving calli)Endo et al. 2007 
3Alcohol dehydrogenase2 (Adh2)riceT-DNAHptII (positive)/DT-A (negative)HptII (positive)6200 + 60001.9% (per total surviving calli)Terada et al. 2007 
4GUS-HptII taggingriceT-DNAHptII (positive)/DT-A (negative)HptII (positive)3100 + 3100~ 5.3% (per total surviving calli)Yamauchi et al. 2009 
 α-subunit of anthranilate synthase gene (OASA2)riceT-DNATrp-analog 5MT (positive)Trp-analog 5MT (positive)7000 in total0.34% (per total surviving calli)Saika et al. 2011 
5Domains Rearranged Methylase 2 (OsDRM2), 70 bp targeted deletionriceT-DNAHptII (positive)/DT-A (negative)HptII (positive)3000 + 31001.9% (per total surviving calli)Moritoh et al. 2012 
OsDRM2, 3000 bp targeted deletionriceT-DNAHptII (positive)/DT-A (negative)HptII (positive)3000 + 30000.4% (per total surviving calli) 
6Repressor Of Silencing 1a (ROS1a)riceT-DNAHptII (positive)/DT-A (negative)HptII (positive)3000 + 30001.1% (per total surviving calli)Ono et al. 2012 
7waxyriceT-DNAHptII (positive)/DT-A (negative)HptII (positive)6800 + 57001.5% (per total surviving calli)Ozawa et al. 2012 
β1,2-Xylosyltransferase (XylT)riceT-DNAHptII (positive)/DT-A (negative)HptII (positive)5500 + 56001.8% (per total surviving calli) 
8OsRac1riceT-DNAHptII (positive)/DT-A (negative), Cre/loxP-based removal of HptIIHptII (positive), Cre/loxP-based removal of HptII3000 + 3000~ 5.3% (per total surviving calli)Dang et al. 2013 
Caffeic acid O-methyltransferase (CAOMT)riceT-DNAHptII (positive)/CodA (negative)HptII (positive)3700 + 6000~ 12.1% (per total surviving calli)Osakabe et al. 2014 
9ALS (W548 L and S627I)riceT-DNABS herbicide (positive) and HptII (positive)/DT-A (negative), piggyBac-based removal of HptIIBS herbicide (positive) and HptII (positive), piggyBac-based removal of HptII8092~ 6% (per total hygromycin-resistant calli)Nishizawa-Yokoi et al. 2015a 
cleistogamy 1 (Oscly1)riceT-DNABS herbicide (positive) and HptII (positive)/DT-A (negative), piggyBac-based removal of HptIIBS herbicide (positive) and HptII (positive), piggyBac-based removal of HptII6000~ 0.078% 
10waxyriceT-DNANptII (positive)/RNAi mediated anti-NptII (negative)NptII (positive)5000 + 51000.26% (per total surviving calli)Nishizawa-Yokoi et al. 2015b 
Glyoxalase I (OsGlb33)riceT-DNANptII (positive)/RNAi mediated anti-NptII (negative)NptII (positive)5400 + 62000.21% (per total surviving calli) 
Targeted DSB-based gene targetingSite-specific Nuclease
11Inositol-1,3,4,5,6-pentakisphosphate 2-kinase (IPK) and phosphinothricin acetyltransferase (PAT)MaizeSilicon carbide whiskers-mediated transformationBialaphos herbicide (positive)Bialaphos herbicide (positive)815 + 815?Shukla et al. 2009Meganucleases
12Synthetic DNAMaizeT-DNANptII and GFP (positive)NptII and GFP (positive)2992 + 12000.085% (True event per immature embryo)Ayar et al. 2013ZFNs
OsPDSriceBombardmentTransientTransient23 + 37 (single stranded oligos)6.9% (2/29 clones of PCR product, restriction digestion for enrichment of HDR productsShan et al. 2013CRISPR/Cas9
13Pre-intergrated GFPBarleyBombardmentGFP/YFP fluorescenceGFP/YFP fluorescence196 + 3342–3% (per total surviving calli)Budhagatapalli et al. 2015TALENs
14Acetolactate synthase (ALS) genes (ALS1 and ALS2)MaizeBombardmentChlorsulfuron and bialaphos (positive selection of ALS HDR events).bialaphos (positive selection of ALS HDR events).749 dsDNA donor and 127 single stranded oligo donor0.2% (dsDNA donor) and 0.35% (ssDNA donors)Svitashev et al. 2015CRISPR/Cas9
Upstream of the LIGULELESS1 (LIG1) geneBialaphos (positive)Bialaphos (positive)1099 + 10350.7% (meganulease) and 2.5–4.1 (CRISPR/Cas9)Meganuclease and CRISPR/Cas9
15OsALS (W548 L and S627I)riceBombardmentBS herbicide (positive)BS herbicide (positive)?1.4–6.3% (per total hygromycin tolerant calli)Li et al. 2016TALENs
16OsALS (W548 L and S627I)riceBombardment and T-DNAHygromycine and BS (positive)BS (positive)100 + 46 (330 bp interval)7.0–25% (number of perfect HDR events per total calli)Sun et al. 2016CRISPR/Cas9
17OsALS (W548 L and S627I)riceT-DNAHygromycine and BS (positive), lig4 backgroundBS (positive)329 + 6350.147–1.000% (number of perfect HDR events per total calli)Endo et al. 2016CRISPR/Cas9
18Nitrate transporter NRT1.1BriceBombardmentHygromycine (positive)None100 + 1006.72%Li et al. 2018aCRISPR/Cas9
19OsALS (W548 L and S627I)riceBombardmentHygromycine and BS (positive)BS (positive)97 bp left arm only or 97 + 1210.66% (only left homologous arm) and 1.22% (both arms)Li et al. 2018bCRISPR/Cpf1
20Wheat ubiquitin gene (TaUbi)wheatWDV replicon bombardmentGFP (positive)GFP748 + 7733.8% (per total protoplasts) and 5.74% (per total cells, normalized to scutela transformation efficiency)Gil-Humanes et al. 2017CRISPR/Cas9
Mildew Locus O (TaMLO)wheatWDV replicon bombardmentBFP (positive)BFP674 + 6476.4% (per total cells, normalized to scutela transformation efficiency)
5-enolypyruvylshikimate-3-phosphate synthase (TaEPSPS)wheatWDV replicon bombardmentdsRED (positive)dsRED210 + 6464.7% (per total cells, normalized to scutela transformation efficiency)
TaUbi and TaMLO, multiplexedwheatWDV replicon bombardmentGFP and BFP (positive)GFP and BFP748 + 773 (TaUbi) and 674 + 647 (TaMLO)1.1% (per total cells, normalized to scutela transformation efficiency)
TaUbi and TaEPSPS, multiplexedwheatWDV replicon bombardmentGFP and dsRED (positive)GFP and dsRED748 + 773 (TaUbi) and 210 + 646 (TaEPSPS)0.4% (per total cells, normalized to scutela transformation efficiency)
21OsACT and OsGSTRiceWDV replicon T-DNAGFP and kanamycin (positive)GFP and kanamycin500 + 500Cas9 overexpressed background: 19.4% (OsACT) and 7.7% (OsGST); WT background 8.5% (OsACT) and 4.7% (OsGST)Wang et al. 2017CRISPR/Cas9