TILLING in Cereal Crops for Allele Expansion and Mutation Detection by Using Modern Sequencing Technologies
Abstract
:1. Introduction
1.1. Background
1.2. TILLING and EcoTILLING
1.3. Generation of Induced Mutation for TILLING
1.4. Methods of Mutation Detection in TILLING
- The 3D pooling strategy allows for the observation of individual mutant plants and for the molecular recognition of mutation without requiring additional deconvolution of pools and additional sequencing steps;
- TbyS can be used to recognize single base alterations and their impact on specific traits;
- TbyS does not depend on fluorescent primers;
- TbyS enables flexible options for pooling techniques.
2. Application of TILLING in Cereal Crops
2.1. TILLING for Starch Synthesis
2.2. TILLING for Plant Architecture
2.3. TILLING for Disease Resistance
2.4. TILLING for Other Yield-Related Parameters
3. Prospect of TILLIING
3.1. Next-Generation Sequencing and TILLING
3.2. Importance of TbyS
3.3. Genome-Editing Technology and TILLING
4. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Species | Ploidy Level | Genotypes | Gene Name | No. of Genes | SNPs/Haplotypes | Methodology | Genome Size | Trait | Reference |
---|---|---|---|---|---|---|---|---|---|
Arabidopsis thaliana | 2x | 192 | DMMT2, DRM1C7, PIF2, AtWR | 5 | 55 (haplotypes) | CEL-1-PAGE | 125 MB | [30] | |
Triticum aestivum | 6x | 214 | VRN-A1 | 1 | CJE/Agarose | 17 GB | Vernalization | [31] | |
1787 | Pin a, Pin b | 2 | 15 | CEL-1-PAGE | Kernel hardness | [32] | |||
Oryza sativa | 2x | 48 | 14 | CEL-1-PAGE/UL | 400–430 MB | [33] | |||
48 | MYB1, TPP, ADF | 3 | Agarose gel | [34] | |||||
45 | 87 | - | CJE/Agarose gel | Boron toxicity | [35] | ||||
375 | OSCP17 | 1 | 38 | CJE/Agarose gel | Salt tolerance | [36] | |||
95 | 19 | 14 | CEL-1-PAGE | Drought tolerance | [37] | ||||
392 | osCPK17, osRMC, osNHX1, osHKTI;5, SalT | 5 | 69 | CEL-1-PAGE | Salt resistant | [38] | |||
512 | GBSSI, SSI, SSIIa, SSIIIa, SBEIa, SBEIIb | 6 | 23 | EcoTbyS | Starch synthesis | [39] | |||
Hordeum vulgare | 2x | 292 | Lhcb1 | 1 | 23 | CEL-1-PAGE | 5.3 GB | Chlorophyll protein | [40] |
210 | HSP17.8 | 1 | 11 | CEL-1-PAGE | Heat shock protein | [41] | |||
Brassica sp. | 2x 4x | 117 | FAE1-A8, FAE1-C3 | 2 | 18 | CEL-1-PAGE | 488–1544 MB 157 MB | Erucic acid content | [42] |
187 | accD, matK, rbcL, atp6 | 4 | 60 | CEL-1-PAGE | Organelle genome | [43] | |||
676 | Chloroplast DNA | 1 | 538 | EcoTbyS | Chloroplast DNA | [44] | |||
Solanum lycopersicum | 2x | 49 | GCH1, ADCS, ADCL1, ADCL2, FPGSp, FPGSm, GGH1, GGH2, GGH3 | 9 | CEL-1-PAGE | 950 MB | Folate biosynthesis | [45] | |
127 | ACS2, CoP1, CYC-B, MSH2, NAC-NOR, PHoT1, PHYA, PHYB, PSY1 | 9 | 54 | CEL-1-PAGE | Plant development | [46] | |||
Gossypium hirsutum | 4x | 277 | GhSus1At, GhSus1Dt, GhSus3At, GhSus4Dt, GhSus5Dt, GhSus6At, GhSus7Dt, GhSus8Dt | 8 | 24 | CEL-1-PAGE | 1724 MB | Sucrose synthesis | [47] |
Capsicum annum | 2x | 233 | eIF4E, I1F(iso)4E, eIF(iso)4G, eIF4G | 4 | 62 | CEL-1-PAGE | 3.48 GB | Virus resistance | [48] |
Populus nigra | 2x | 768 | CAD4, HCT1, C3H3, CCR7, 4CL3 | 5 | 84 | TbyS | Lignin biosynthesis | [49] | |
Glycine max | 2x | 25 | Gy1, Gy2, Gy3, Gy4, Gy5 | 5 | - | Agarose gel | 1.15 GB | Seed protein | [29] |
Olea europea | 2x | 96 | fad7 | 1 | 3 (haplotypes) | CEL-1-PAGE | Fatty acid enzyme | [50] | |
Beta vulgaris | 2x | 268 | BTC1, BVFL1, BvFT1 | 3 | 21 | CEL-1-PAGE | 714–758 MB | Winter hardiness | |
Jatropha curcas | 2x | 907 | AF, EUO6, EFO3, DQ98, EU10, EU22, EU39, EU23, EU21, DQ15, DQ66, SUSY11 | 12 | 86 | CEL-1-PAGE | 320.5 MB | Oil & stress tolerance | [51] |
Cicer arietinum | 2x | 192 | 1133 | Agarose gel | 738 MB | Seed weight | [28] |
Species | Ploidy | Mutagen | M2 Size | MF (Kb) | Mutation Detection Technology | Trait | Reference |
---|---|---|---|---|---|---|---|
Maize | 2x | EMS | 750 | 1/485 | CEL-1- PAGE | Chromomethylase | [85] |
Rice | 2x | EMS | - | 1/1000 | CEL-1- PAGE | [32] | |
768 | 1/294 | CEL-1-PAGE | [86] | ||||
6912 | 1/451 | CEL-I -Agarose gel | [33] | ||||
EMS | 2048 | 1/293 | TILLING by sequencing | Phytic acid metabolism | [87] | ||
Barley | 2x | EMS | 9216 | 1/1000 | dHPLC | Floral parts regulation | [81] |
EMS | 10,279 | 1/500 | CEL-1-PAGE | Fungus immunity | [88] | ||
NaN3 | 5600 | 1/374 | CEL-I-Agarose gel | Starch metabolism | [89] | ||
Wheat | 6x 4x | EMS | 2020 | 1/26 | HRM | Resistance against powdery mildew | [62] |
EMS | 4500 | 1/35,000 | TILLING by sequencing | [90] | |||
EMS | 10,000 | 1/24 | CEL-1, PAGE | Quality of starch | [76] | ||
EMS | 4500 | 1/84 | CEL-1-PAGE, HRM | Quality of starch | [63] | ||
EMS | 2610 | 1/34;1/47 | Agarose gel, PAGE | Development of spike | [91] | ||
EMS | 8000 | 1/40 | CEL-1-PAGE | Starch quality | [92] | ||
EMS | 3992 | HRM | Starch metabolism | [59] | |||
EMS | 1140 | 1/77 | CEL I- Agarose gel, dHPLC | Carotenoid metabolism | [93] | ||
EMS | 1532 | 1/92 | CEL-I | Waxy and lignin | [94] | ||
EMS | 733 | Exome sequencing | Plant height | [6] | |||
EMS | TILLING by Sequencing, CEL-1- PAGE | Thousand grain weight | [95] | ||||
EMS | 10,000 | TILLING by Electrophoresis | Gluten content | [96] | |||
EMS | 1122 | CEL-1-PAGE | Kernel hardness and starch | [97] |
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Irshad, A.; Guo, H.; Zhang, S.; Liu, L. TILLING in Cereal Crops for Allele Expansion and Mutation Detection by Using Modern Sequencing Technologies. Agronomy 2020, 10, 405. https://doi.org/10.3390/agronomy10030405
Irshad A, Guo H, Zhang S, Liu L. TILLING in Cereal Crops for Allele Expansion and Mutation Detection by Using Modern Sequencing Technologies. Agronomy. 2020; 10(3):405. https://doi.org/10.3390/agronomy10030405
Chicago/Turabian StyleIrshad, Ahsan, Huijun Guo, Shunlin Zhang, and Luxiang Liu. 2020. "TILLING in Cereal Crops for Allele Expansion and Mutation Detection by Using Modern Sequencing Technologies" Agronomy 10, no. 3: 405. https://doi.org/10.3390/agronomy10030405