Induced Genetic Variations in Fruit Trees Using New Breeding Tools: Food Security and Climate Resilience
Abstract
:1. Introduction
2. Tree Breeding under Climate Change
3. Mutagenesis as a Source of Genetic Variability in Tree Plants
TILLING as a Powerful Tool in Mutation Breeding
4. Genomics and Genetic Engineering Perspectives of Trees
5. Genome Editing in Precision Breeding
5.1. Principle and Types of CRISPR-Cas Systems
5.2. CRISPR/Cas Based GE Strategy in Trees
5.3. CRISPR-Mediated Genome Editing in Apples
5.4. CRISPR-Mediated Genome Editing in Banana
Cas Type | Organism | Size (Amino Acids) | Class/ Type | PAM Site | Altered PAM | Types of End | Mutations | Plants | References |
---|---|---|---|---|---|---|---|---|---|
SpCas9 | Streptococcus pyogenes | 1368–1424 | 2/II | NGG | -- | Blunt/ds or ss | -- | Many plant species | [92,115,116,117] |
SpCas9 VQR | S. pyogenes | 1372 | 2/II | NGA | Yes | Blunt/ds or ss | D1135V/R1335Q/T1337R | Rice | [118] |
SpCas9 EQR | S. pyogenes | 1372 | 2/II | NGAG | Yes | Blunt/ds or ss | D1135E/R1335Q/T1337R | - | [118] |
SpCas9 VRER | S. pyogenes | 1372 | 2/II | NGCG | Yes | Blunt/ds or ss | D1135V/G1218R/R1335E/T1337R | Rice | [118] |
SpCas9 D1135E | S. pyogenes | 1372 | 2/II | NAG/NGA | Yes | Blunt/ds or ss | D1135E | - | [117] |
SpCas9 QQR1 | S. pyogenes | 1372 | 2/II | NAAG | Yes | Blunt/ds or ss | G1218R/N1286Q/I1331F/D1332K/ R1333Q/R1335Q/T1337R | - | [119] |
SpCas9-NG | S. pyogenes | 1372 | 2/II | NG | Yes | Blunt/ds or ss | R1335V/L1111R/D1135V/G1218R/ E1219F/A1322R/T1337R | Arabidopsis and rice | [120] |
SpCas9-HF1 | S. pyogenes | 1368 | 2-II | NGG | Enhanced specificity | Blunt/ds or ss | N497A/R661A/Q695A/Q926A | Arabidopsis and rice | [121] |
eHF1-Cas9 | S. pyogenes | 1368 | 2-II | NGG | Enhanced specificity | Blunt/ds or ss | N497A/R661A/Q695A/K848A/ Q926A/K1003A/R1060A | Rice | [122] |
HiFi Cas9 | S. pyogenes | 1368 | 2-II | NGG | Enhanced specificity | Blunt/ds or ss | R691A | Rice | [123] |
XCas9 | S. pyogenes | 1368 | 2-II | NG, GAA & GAT | Enhanced specificity | Blunt/ds or ss | A262T/R324L/S409I/E480K/ E543D/M694I/E1219V | Rice | [124] |
dCas9 | S. pyogenes | 1368 | 2-II | NGG | No | Blunt/ds or ss | D10A/H840A | Arabidopsis and rice | [125,126] |
nCas9 | S. pyogenes | 1368 | 2-II | NG, GAA & GAT | Enhanced specificity | Blunt/ds or ss | D10A | Rice, tobacco | [127,128] |
SaCas9 | Staphylococcus aureus | 1053 | 2-II | NNGRRT | - | Blunt/ds or ss | - | Tobacco, rice, Arabidopsis and citrus | [129] |
SaCas9-KKH | S. aureus | 1053 | 2-II | NNNRRT | Enhanced specificity | Blunt/ds or ss | E782K/N968K/R1015H | Tobacco, rice, Arabidopsis and citrus | [130] |
BlatCas9 | Brevibacillus laterosporus | 1092 | 2-II | NNNNCND | Staggered/ds | - | Maize | [94] | |
FnCas9 | Francisella novicida | 1629 | 2B-II | NGG | - | Staggered/ds | - | Arabidopsis | [131] |
Cpf1 (Cas12a) | Prevotella & Franscisella | 1300 | 2-V | TTTN | - | Staggered/ds | - | Many plant species | [132,133] |
AsCas12a RR | Acidaminococcus | 1307 | 2-V | TYCV & CCCC | Yes | Staggered/ds | S542R/K607R | - | [134,135] |
AsCas12a RVR | Acidaminococcus | 1307 | 2-V | TATV | Yes | Staggered/ds | S542R/K548V/N552R | - | [135] |
LbCas12a | Lachnospiraceae bacterium | 1228 | 2-V | TTTV | - | Staggered/ds | - | Many plant species | [134] |
LbCas12a RR | Lachnospiraceae bacterium | 1228 | 2-V | TYCV & CCCC | Yes | Staggered/ds | G532R/K595R | Rice | [135] |
LbCas12a RVR | Lachnospiraceae bacterium | 1228 | 2-V | TATV | Yes | Staggered/ds | G532R/K538V/Y542R | Rice | [135] |
FnCas12a | F. novicida | 1300 | 2-V | TTV, TTTV & KYTV | - | Staggered/ds | - | Rice | [134] |
FnCas12a RR | F. novicida | 1300 | 2-V | TYCV & TCTV | Yes | Staggered/ds | N607R/K671R | Rice | [136] |
FnCas12a RVR | F. novicida | 1300 | 2-V | TWTV | Yes | Staggered/ds | N607R/K613V/N617R | Rice | [136] |
Cas12b | Alicyclobacillus, Acidoterrestris, Bacillus Thermoamylovorans, A. acidiphilus | 1100–1300 | 2-VB | TTTN | - | Staggered/ds | - | Many plant species | [137,138] |
Cas12X | Deltaproteobacteria | <1000 | 2-V | TTCN | - | Staggered/ds | - | - | [139,140] |
5.5. CRISPR-Mediated Genome Editing in Citrus
5.6. CRISPR-Mediated Genome Editing in Papaya
5.7. CRISPR-Mediated Genome Editing in Pear
5.8. Mitigation of Off-Target Mutations in GE Trees
5.8.1. GC Content of sgRNA
5.8.2. gRNA Length and Mismatches
5.8.3. Chemical Modification of gRNA
5.8.4. Concentration of Cas Protein/gRNA
5.8.5. Cas Protein Variants
Tree Species | Gene Target | Trait Modified | CRISPR-Cas System | Reference |
---|---|---|---|---|
Apple | PDS | Albino phenotype | CRISPR-Cas9 | [102,104,106] |
DIPM-1 DIPM-2 DIPM-4 | Fire blight | CRISPR-Cas9 | [103,107] | |
TFL1 | Early flowering | CRISPR-Cas9 | [106] | |
ALS | CRISPR-Cas9 | [39] | ||
CNGC2 | B. dothidea resistance | CRISPR-Cas9 | [108] | |
Detection of viruses and viroids | CRISPR-Cas12 | [109] | ||
Banana | PDS | Albino phenotype | CRISPR-Cas9 | [113,114] |
PDS | eBSV resistance | CRISPR-Cas9 | [141] | |
PDS | Albino phenotype | CRISPR-Cas9 | [142] | |
PDS | Albino phenotype | CRISPR-Cas12a | [142] | |
ACO1 | Fruit ripening | CRISPR-Cas9 | [143] | |
LCYε | β-carotene | CRISPR-Cas9 | [93] | |
GA20ox2 | Gibberlic acid biosynthesis | CRISPR-Cas9 | [145] | |
Cacao | TcNPR3 | Resistance to Phytophthora tropicalis | CRISPR-Cas9 | [177] |
Citrus | PDS | Albino phenotype | CRISPR-Cas9 | [146,147] |
LOB1 | Canker resistance | CRISPR-Cas9 | [149] | |
PDS | Albino phenotype | CRISPR-Cas12 | [148] | |
Papaya | Papain (PpalEPIC8) | Cysteine protease, P. palmivora resistance | CRISPR-Cas9 | [150] |
Ppal15kDa | P. palmivora resistance | CRISPR-Cas9 | [151] | |
Pear | TFL1 | Early flowering | CRISPR-Cas9 | [106] |
PDS and ALS | Albino and chlorsulfuron | CRISPR-Cas9 C-to-T BE | [39] | |
PbPAT14 | Dwarf and yellowing | CRISPR-Cas9 | [152] |
5.9. CRISPR Delivery Techniques and Vectors
5.10. Genome Editing Tools: Base, Prime and RNA Editors
5.10.1. Base Editors
5.10.2. Prime Editing
5.10.3. RNA Editing
6. Techniques to Estimate and Quantify the Mutation Rate
6.1. T7E1 Mismatch Cleavage Assay
6.2. High-Resolution Melting Assay
6.3. Sanger Sequencing
6.4. Next-Generation Sequencing
6.5. FLA-PCR (Fragment Analysis)
7. Critical Assessment of CRISPR-Cas Based GE in Fruit Trees
8. Biological and Regulatory Constraints to GE in Trees
9. Conclusions and Future Perspectives
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Common Name | Botanical Name | Variety | Mutagen Source | Country | Year of Registration |
---|---|---|---|---|---|
Almond | Prunus dulcis Mill. | Supernova | Gamma rays (30 Gy) | Italy | 1987 |
Apple | Malus pumila Mill. | Mori-hou-fu 3A | Gamma rays (30 Gy) | Japan | 1963 |
Senbatsu-Fuji-2-Kei | Gamma rays (60 Gy) | 1985 | |||
Belrene | EMS | France | 1970 | ||
Blackjoin BA 2 520 | Gamma rays (50 Gy) | 1970 | |||
Courtagold | 1972 | ||||
Courtavel | 1972 | ||||
Lysgolden | 1972 | ||||
Donghenghongpingguo | Gamma rays (250 Gy) | China | 1987 | ||
Dovar | X-rays (30–35 Gy) | Netherlands | 1978 | ||
Golden Haidegg | Gamma rays (50 Gy) | Austria | 1986 | ||
James Grieve Double Red | Gamma rays (62 Gy) | Czech Republic | 1995 | ||
McIntosh 8F-2-32 | Gamma rays | Canada | 1970 | ||
Shamrock | Gamma rays | Canada | 1986 | ||
Apricot | Prunus armeniaca L. | Early Blenheim | thermal neutrons (thN) | Canada | 1970 |
Banana | Musa paradisiaca L. | Klue Hom Thong KU1 | Gamma rays (25 Gy) | Thailand | 1985 |
Novaria | Gamma rays (60 Gy) | Malaysia | 1995 | ||
AL-BEELY | Gamma rays | Sudan | 2007 | ||
Pirama 1 | Gamma rays (30 Gy) | Indonesia | 2019 | ||
Fuxuan 01 | Gamma rays | China | 2005 | ||
Clementina | Citrus celementina L. | Nero | Fast neutron (6 Gy) | Spain | 2006 |
Neufina | 2010 | ||||
CLEMENVERD | Fast neutron (5 Gy) | Spain | |||
Ficus | Ficus benjamina L. | Golden King | X-rays (25 Gy) AND Gamma rays (20 Gy) | Belgium | 1980 |
Golden Princess | |||||
Fig | Ficus carica L. | Bol (Abundant) | Gamma rays (50–70 Gy) | Russian Federation | 1979 |
Grapefruit | Citrus paradisi Macf. | Rio Red | Thermal neutrons (thN) | United States | 1970 |
Star Ruby | 1984 | ||||
Indian Jujube | Ziziphus mauritiana Lamk. | Dao tien | MNH (0.02–0.04%) | Viet Nam | 1986 |
Ma hong | |||||
Japanese pear | Pyrus pyriforia Nak. | Gold Nijisseiki | Gamma rays (0.12–0.15 Gy) | Japan | 1991 |
Kotobuki Shinsui | Gamma rays (80 Gy) | 1997 | |||
Osa Gold | 1997 | ||||
Lemon | Citrus limon L. | Eureka 22 INTA | X-rays (10 Gy) | Argentina | 1987 |
Loquat | Eriobotrya japonica L. | Shiro-mogi | Gamma rays (200 Gy) | Japan | 1982 |
Mandarin | Citrus reticulata L. | Zhongyu 7 | Gamma rays (100 Gy) | China | 1985 |
Zhongyu 8 | 1986 | ||||
Hongju 420 | |||||
NIAB Kinnow | Gamma rays (20 Gy) | Pakistan | 2017 | ||
PAU Kinnow-1 | Gamma rays (30 Gy) | India | 2017 | ||
Mulberry | Morus alba L. | Sangfu 1 | Gamma rays (75 Gy) | China | 1974 |
Fuzaofeng | Gamma rays (5 Gy) | 1992 | |||
Ji 7681 | N2 laser | 1988 | |||
Fusang 10 | Gamma rays | 1980 | |||
Shansang 871 | Gamma rays (60 Gy) | 1994 | |||
Shigu 11-6 | Gamma rays (100 Gy) | 1995 | |||
Lala Berry | Colchicine | Japan | 2003 | ||
Pop Berry | Colchicine | 2004 | |||
S54 | EMS | India | 1974 | ||
Orange | Citrus sinensis L. | Hongju 418 | Gamma rays (100 Gy) | China | 1983 |
Xuegan 9-12-1 | |||||
Valencia 2 INTA | X-rays (20 Gy) | Argentina | 1987 | ||
IAC 2014 | Gamma rays (40 Gy) | Brazil | 2016 | ||
Papaya | Carica papaya L. | Pusa nanha | Gamma rays (150 Gy) | India | 1987 |
Peach | Prunus persica L. | Magnif 135 | Gamma rays | Argentina | 1968 |
Shaji 1 | CO2 laser | China | 1985 | ||
Shaji 2 | |||||
Fuku-ekubo | Gamma rays (30 Gy) | Japan | 1996 | ||
Shimizu Hakutou RS | 2004 | ||||
Plovdiv 6 | Gamma rays (10 Gy) | Bulgaria | 1981 | ||
Pear | Pyrus communis L. | Fuxiangyanghongdli | Gamma rays (2.5 Gy) | China | 1983 |
Chaofu 1 | 1989 | ||||
Chaofu 10 | |||||
Chaofu 10 | |||||
Chaofu 2 | |||||
Plum | Prunus domestica L. | Spurdente-Ferco | Gamma rays | France | 1988 |
Pomegranate | Punica granatum L. | Karabakh | Gamma rays (50–70 Gy) | Russian Federation | 1979 |
Khyrda | |||||
Sour cherry | Prunus cerasus L. | Plodorodnaya Michurina | X-rays | Russian Federation | 1977 |
Karlik Samorodka | Gamma rays | 1979 | |||
Polukarlik Orlovskoi Rannei | |||||
Polukarlik Turgenevki | |||||
Nishina Zao (DT2008) | Ion beams | Japan | 2009 | ||
Sweet cherry | Prunus avium L. | Compact Lambert | X-rays (40 Gy) | Canada | 1964 |
Compact Stella 35B-11 | 1974 | ||||
Van 2D-14-11 | 1972 | ||||
Lapins | X-rays | 1983 | |||
Lambert 2B-17-18-EC | X-rays (50 Gy) | 1972 | |||
Stella | 1968 | ||||
Stella 16A-7 | 1972 | ||||
Sunburst | 1983 | ||||
Sumste Samba | Gamma rays | 2000 | |||
ALDAMLA | Gamma rays (25 Gy) | Turkey | 2014 | ||
BURAK | Gamma rays (50 Gy) | ||||
Burlat C1 | Gamma rays | Italy | 1983 | ||
Nero II C1 | |||||
Ferrovia spur | X-rays (4 Gy) | 1992 | |||
Super 6 | Colchicine | Japan | 1997 | ||
Roman Nishiki | 2002 |
Country | Cartagena Protocol of Biosafety (CPB) Status | Regulations for Different GE Categories | ||
---|---|---|---|---|
SDN-1 | SDN-2 | SDN-3 | ||
Argentina | Non-ratified | Non-GMO | Cas-by-case decision | Non-GMO if no transgene |
Australia | Non-ratified | Non-GMO | GMO | Not clear |
Brazil | Ratified | Non-GMO (with previous consultation) | Cas-by-case decision | Non-GMO if no transgene |
Canada | Non-ratified | Case-by-case (based upon novelty) | ||
Chile | Non-ratified | Non-GMO (with previous consultation) | Non-GMO | Non-GMO if no transgene |
China | Ratified | Under review with new legislations | ||
Colombia | Ratified | Non-GMO (with previous consultation) | Non-GMO (Case-by-case decision) | Non-GMO if no transgene |
European Union | Ratified | GMO | ||
Guatemala El Salvador | Ratified | No clear regulations | ||
Honduras | Ratified | Case-by-case non-GMO | Non-GMO if no transgene | |
India | Ratified | Currently unclear (under discussion) | ||
Israel | Non-ratified | Non-GMO | Non-GMO if no transgene | |
Japan | Ratified | Non-GMO if no extracellular footprints were integrated into the organism genome | GMO (if extracellular footprints remain) | |
New Zealand | Ratified | GMO | ||
Norway | Ratified | Currently unclear (proposal under review) | ||
Paraguay | Ratified | Unclear (may vary Case-by-case) | ||
Russian Federation | Non-ratified | Unclear due to new expected policies | ||
South Africa | Non-ratified | Currently unclear (under discussion) | ||
Switzerland | Ratified | Currently unclear (under discussion) | ||
United States | Non-ratified | Case-by-case (USDA); clarification under discussion (FDA) |
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Sattar, M.N.; Iqbal, Z.; Al-Khayri, J.M.; Jain, S.M. Induced Genetic Variations in Fruit Trees Using New Breeding Tools: Food Security and Climate Resilience. Plants 2021, 10, 1347. https://doi.org/10.3390/plants10071347
Sattar MN, Iqbal Z, Al-Khayri JM, Jain SM. Induced Genetic Variations in Fruit Trees Using New Breeding Tools: Food Security and Climate Resilience. Plants. 2021; 10(7):1347. https://doi.org/10.3390/plants10071347
Chicago/Turabian StyleSattar, Muhammad Naeem, Zafar Iqbal, Jameel M. Al-Khayri, and S. Mohan Jain. 2021. "Induced Genetic Variations in Fruit Trees Using New Breeding Tools: Food Security and Climate Resilience" Plants 10, no. 7: 1347. https://doi.org/10.3390/plants10071347