Table 1 Major HGT studies in monocots
From: Challenges and Perspectives in Homology-Directed Gene Targeting in Monocot Plants
No. | Gene/Allele | Monocot | HDR tool | Selection marker | HDR allele-associated marker | Homologous donor length (bp) (5′ arm + 3′ arm) | Gene targeting efficiency | Reference |  |
|---|---|---|---|---|---|---|---|---|---|
Gene targeting without targeted DSBs | |||||||||
1 | waxy (Granule-Bound Starch Synthase gene knockout) | rice | T-DNA | HptII (positive)/DT-A (negative) | HptII (positive) | 6300 + 6800 | 0.94% (per total surviving calli) | Terada et al. 2002 |  |
2 | Acetolactate synthase (ALS) (W548 L and S627I) | rice | T-DNA | Bispyrobac-sodium (BS) herbicide (positive) | BS herbicide (positive) | 8092 | ~ 3% (per total surviving calli) | Endo et al. 2007 |  |
3 | Alcohol dehydrogenase2 (Adh2) | rice | T-DNA | HptII (positive)/DT-A (negative) | HptII (positive) | 6200 + 6000 | 1.9% (per total surviving calli) | Terada et al. 2007 |  |
4 | GUS-HptII tagging | rice | T-DNA | HptII (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) | rice | T-DNA | Trp-analog 5MT (positive) | Trp-analog 5MT (positive) | 7000 in total | 0.34% (per total surviving calli) | Saika et al. 2011 |  |
5 | Domains Rearranged Methylase 2 (OsDRM2), 70 bp targeted deletion | rice | T-DNA | HptII (positive)/DT-A (negative) | HptII (positive) | 3000 + 3100 | 1.9% (per total surviving calli) | Moritoh et al. 2012 |  |
OsDRM2, 3000 bp targeted deletion | rice | T-DNA | HptII (positive)/DT-A (negative) | HptII (positive) | 3000 + 3000 | 0.4% (per total surviving calli) |  | ||
6 | Repressor Of Silencing 1a (ROS1a) | rice | T-DNA | HptII (positive)/DT-A (negative) | HptII (positive) | 3000 + 3000 | 1.1% (per total surviving calli) | Ono et al. 2012 |  |
7 | waxy | rice | T-DNA | HptII (positive)/DT-A (negative) | HptII (positive) | 6800 + 5700 | 1.5% (per total surviving calli) | Ozawa et al. 2012 |  |
β1,2-Xylosyltransferase (XylT) | rice | T-DNA | HptII (positive)/DT-A (negative) | HptII (positive) | 5500 + 5600 | 1.8% (per total surviving calli) |  | ||
8 | OsRac1 | rice | T-DNA | HptII (positive)/DT-A (negative), Cre/loxP-based removal of HptII | HptII (positive), Cre/loxP-based removal of HptII | 3000 + 3000 | ~ 5.3% (per total surviving calli) | Dang et al. 2013 |  |
Caffeic acid O-methyltransferase (CAOMT) | rice | T-DNA | HptII (positive)/CodA (negative) | HptII (positive) | 3700 + 6000 | ~ 12.1% (per total surviving calli) | Osakabe et al. 2014 |  | |
9 | ALS (W548 L and S627I) | rice | T-DNA | BS herbicide (positive) and HptII (positive)/DT-A (negative), piggyBac-based removal of HptII | BS herbicide (positive) and HptII (positive), piggyBac-based removal of HptII | 8092 | ~ 6% (per total hygromycin-resistant calli) | Nishizawa-Yokoi et al. 2015a |  |
cleistogamy 1 (Oscly1) | rice | T-DNA | BS herbicide (positive) and HptII (positive)/DT-A (negative), piggyBac-based removal of HptII | BS herbicide (positive) and HptII (positive), piggyBac-based removal of HptII | 6000 | ~ 0.078% |  | ||
10 | waxy | rice | T-DNA | NptII (positive)/RNAi mediated anti-NptII (negative) | NptII (positive) | 5000 + 5100 | 0.26% (per total surviving calli) | Nishizawa-Yokoi et al. 2015b |  |
Glyoxalase I (OsGlb33) | rice | T-DNA | NptII (positive)/RNAi mediated anti-NptII (negative) | NptII (positive) | 5400 + 6200 | 0.21% (per total surviving calli) |  | ||
Targeted DSB-based gene targeting | Site-specific Nuclease | ||||||||
11 | Inositol-1,3,4,5,6-pentakisphosphate 2-kinase (IPK) and phosphinothricin acetyltransferase (PAT) | Maize | Silicon carbide whiskers-mediated transformation | Bialaphos herbicide (positive) | Bialaphos herbicide (positive) | 815 + 815 | ? | Shukla et al. 2009 | Meganucleases |
12 | Synthetic DNA | Maize | T-DNA | NptII and GFP (positive) | NptII and GFP (positive) | 2992 + 1200 | 0.085% (True event per immature embryo) | Ayar et al. 2013 | ZFNs |
OsPDS | rice | Bombardment | Transient | Transient | 23 + 37 (single stranded oligos) | 6.9% (2/29 clones of PCR product, restriction digestion for enrichment of HDR products | Shan et al. 2013 | CRISPR/Cas9 | |
13 | Pre-intergrated GFP | Barley | Bombardment | GFP/YFP fluorescence | GFP/YFP fluorescence | 196 + 334 | 2–3% (per total surviving calli) | Budhagatapalli et al. 2015 | TALENs |
14 | Acetolactate synthase (ALS) genes (ALS1 and ALS2) | Maize | Bombardment | Chlorsulfuron and bialaphos (positive selection of ALS HDR events). | bialaphos (positive selection of ALS HDR events). | 749 dsDNA donor and 127 single stranded oligo donor | 0.2% (dsDNA donor) and 0.35% (ssDNA donors) | Svitashev et al. 2015 | CRISPR/Cas9 |
Upstream of the LIGULELESS1 (LIG1) gene | Bialaphos (positive) | Bialaphos (positive) | 1099 + 1035 | 0.7% (meganulease) and 2.5–4.1 (CRISPR/Cas9) | Meganuclease and CRISPR/Cas9 | ||||
15 | OsALS (W548 L and S627I) | rice | Bombardment | BS herbicide (positive) | BS herbicide (positive) | ? | 1.4–6.3% (per total hygromycin tolerant calli) | Li et al. 2016 | TALENs |
16 | OsALS (W548 L and S627I) | rice | Bombardment and T-DNA | Hygromycine and BS (positive) | BS (positive) | 100 + 46 (330 bp interval) | 7.0–25% (number of perfect HDR events per total calli) | Sun et al. 2016 | CRISPR/Cas9 |
17 | OsALS (W548 L and S627I) | rice | T-DNA | Hygromycine and BS (positive), lig4 background | BS (positive) | 329 + 635 | 0.147–1.000% (number of perfect HDR events per total calli) | Endo et al. 2016 | CRISPR/Cas9 |
18 | Nitrate transporter NRT1.1B | rice | Bombardment | Hygromycine (positive) | None | 100 + 100 | 6.72% | Li et al. 2018a | CRISPR/Cas9 |
19 | OsALS (W548 L and S627I) | rice | Bombardment | Hygromycine and BS (positive) | BS (positive) | 97 bp left arm only or 97 + 121 | 0.66% (only left homologous arm) and 1.22% (both arms) | Li et al. 2018b | CRISPR/Cpf1 |
20 | Wheat ubiquitin gene (TaUbi) | wheat | WDV replicon bombardment | GFP (positive) | GFP | 748 + 773 | 3.8% (per total protoplasts) and 5.74% (per total cells, normalized to scutela transformation efficiency) | Gil-Humanes et al. 2017 | CRISPR/Cas9 |
Mildew Locus O (TaMLO) | wheat | WDV replicon bombardment | BFP (positive) | BFP | 674 + 647 | 6.4% (per total cells, normalized to scutela transformation efficiency) | |||
5-enolypyruvylshikimate-3-phosphate synthase (TaEPSPS) | wheat | WDV replicon bombardment | dsRED (positive) | dsRED | 210 + 646 | 4.7% (per total cells, normalized to scutela transformation efficiency) | |||
TaUbi and TaMLO, multiplexed | wheat | WDV replicon bombardment | GFP and BFP (positive) | GFP and BFP | 748 + 773 (TaUbi) and 674 + 647 (TaMLO) | 1.1% (per total cells, normalized to scutela transformation efficiency) | |||
TaUbi and TaEPSPS, multiplexed | wheat | WDV replicon bombardment | GFP and dsRED (positive) | GFP and dsRED | 748 + 773 (TaUbi) and 210 + 646 (TaEPSPS) | 0.4% (per total cells, normalized to scutela transformation efficiency) | |||
21 | OsACT and OsGST | Rice | WDV replicon T-DNA | GFP and kanamycin (positive) | GFP and kanamycin | 500 + 500 | Cas9 overexpressed background: 19.4% (OsACT) and 7.7% (OsGST); WT background 8.5% (OsACT) and 4.7% (OsGST) | Wang et al. 2017 | CRISPR/Cas9 |