Quantitative Epigenetics: A New Avenue for Crop Improvement
Abstract
:1. Introduction
2. Epialleles (Natural and Mutagen Induced)
3. Epigenetic Recombinant Inbred Lines (epiRILs)
3.1. Persistence of Epigenetic Modification in the epiRILs
3.2. Phenotypic Variation and Stability in the epiRILs
3.3. Epigenetic Basis of Heterosis
4. Development of Epigenetically Modified Population by Chemical Agents
5. Development of User-Friendly Epigenetic Markers
6. Quantitative Epigenetic Models for Complex Trait
7. EpiQTLs and Epigenome-Wide Association Study (EWAS)
8. Epigenome Editing Using Site-Specific Nucleases
9. Conclusions and Future Prospects
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Species (Common Name) | Family | Monocot/Eudicot | Genome Size (Mb) | Repeat Elements | CpG (%) | CpHpG (%) | CpHpH (%) | Reference |
---|---|---|---|---|---|---|---|---|
Arabidopsis thaliana (Arabidopsis) | Brassicaceae | Eudicot | 135 | 31,189 | 24.00 | 6.70 | 1.70 | [15] |
Beta vulgaris (beet) | Amaranthaaceae | Eudicot | 758 | 656,014 | 92.00 | 81.00 | 18.80 | [4] |
Brassica oleracea (cabbage) | Brassicaceae | Eudicot | 648 | 532,987 | 52.50 | 22.00 | 5.11 | [4] |
Brassica rapa (mustard) | Brassicaceae | Eudicot | 485 | 218,781 | 37.20 | 17.28 | 4.44 | [4] |
Cajanus cajan (pigeonpea) | Fabaceae | Eudicot | 833 | 1,127,729 | 70.23 | 54.60 | 9.87 | [19] |
Camellia sinensis (tea) | Theaceae | Eudicot | 3100 | 5,164,785 | 82.00 | 70.00 | 10.00 | [20] |
Cannabis sativa (canabis) | Cannabaceae | Eudicot | 818 | 376,401 | 75.50 | 65.00 | 8.72 | [4] |
Capsella rubella (pink shepherd’s purse) | Brassicaceae | Eudicot | 219 | 39,716 | 32.00 | 9.90 | 34.70 | [4] |
Cicer arietinum (chickpea) | Fabaceae | Eudicot | 738 | 853,514 | 93.00 | 89.00 | 38.00 | [21] |
Citrus clementina (clementine) | Rutaceae | Eudicot | 370 | 205,699 | 45.83 | 25.13 | 8.26 | [4] |
Cucumis sativus (cucumber) | Cucurbitaceae | Eudicot | 367 | 57,750 | 45.88 | 16.50 | 4.12 | [4] |
Eucalyptus grandis (rose gum) | Myrtaceae | Eudicot | 640 | 689,306 | 37.12 | 19.96 | 1.36 | [4] |
Fragaria vesca (strawberry) | Rosaceae | Eudicot | 240 | 129,500 | 48.35 | 20.63 | 2.32 | [4] |
Glycine max (soybean) | Fabaceae | Eudicot | 1115 | 38,581 | 63.20 | 38.40 | 4.10 | [22] |
Gossypium raimondii (cotton) | Malvaceae | Eudicot | 880 | 489,564 | 71.97 | 57.80 | 13.14 | [4] |
Lotus japonicus (birdsfoot trefoil) | Fabaceae | Eudicot | 472 | 160,505 | 67.75 | 36.59 | 8.66 | [4] |
Malus domestica (apple) | Rosaceae | Eudicot | 742 | 1,245,768 | 63.50 | 44.14 | 4.57 | [4] |
Manihot esculenta (cassava) | Euphorbiaceae | Eudicot | 742 | 258,416 | 51.53 | 30.38 | 1.90 | [4] |
Medicago truncatula (barrel clover) | Fabaceae | Eudicot | 465 | 375,003 | 59.80 | 16.94 | 5.09 | [4] |
Populus trichocarpa (poplar) | Salicaceae | Eudicot | 500 | 173,230 | 43.95 | 26.78 | 5.01 | [4] |
Prunus persica (peach) | Rosaceae | Eudicot | 265 | 95,678 | 50.18 | 19.59 | 3.64 | [4] |
Ricinus communis (castor bean) | Euphorbiaceae | Eudicot | 323 | 575,449 | 64.54 | 37.94 | 11.97 | [4] |
Solanaceae lycopersicum (tomato) | Solanaceae | Eudicot | 907 | 887,009 | 84.05 | 54.84 | 8.35 | [4] |
Solanaceae tuberosum (potato) | Solanaceae | Eudicot | 840 | 404,861 | 70.90 | 42.20 | 15.80 | [23] |
Vitis vinifera (grape vine) | Vitaceae | Eudicot | 487 | 449,466 | 45.95 | 20.43 | 1.15 | [4] |
Brachypodium distachyon (stiff brome) | Poaceae | Monocot | 352 | 51,793 | 49.17 | 19.17 | 1.41 | [4] |
Oryza sativa (rice) | Poaceae | Monocot | 430 | 447,163 | 54.70 | 37.30 | 12.00 | [16] |
Panicum hallii (Hall’s panicgrass) | Poaceae | Monocot | 550 | 154,970 | 56.28 | 29.97 | 2.43 | [4] |
Panicum virgatum (switchgrass) | Poaceae | Monocot | 1600 | 1,793,620 | 53.56 | 35.74 | 3.06 | [4] |
Setaria viridis (green foxtail) | Poaceae | Monocot | 515 | 372,068 | 44.49 | 23.25 | 1.56 | [4] |
Sorghum bicolor (sorghum) | Poaceae | Monocot | 730 | 397,003 | 84.75 | 73.25 | 5.81 | [4] |
Triticum aestivum (wheat) | Poaceae | Monocot | 17,000 | 3,968,974 | 53.30 | 3.48 | 1.41 | [17] |
Zea mays (maize) | Poaceae | Monocot | 2665 | 1,971,471 | 86.00 | 74.00 | 5.40 | [7] |
Species | Gene/Locus | Epigenetic Variation | Phenotypic Traits | References |
---|---|---|---|---|
Arabidopsis thaliana | SUP (SUPERMAN) | Mutagen induced | Increased numbers of stamens and carpels | [29] |
FWA (Flowering Wageningen) | Mutagen induced | Late flowering | [30] | |
PAI2 (Phosphoribosyl Anthranilate Isomerise) | Trans-acting (small RNAs) | Only gene expression affected; no specific phenotype | [43] | |
BAL1 | Mutagen induced | Dwarfing and elevated disease resistance | [31] | |
AG (AGAMOUS) | Mutagen induced | Affect flower structure | [44] | |
BNS (BONSAI) | ddm1-induced syndrome | Stunted growth | [45] | |
FOLT1(folate transporter 1) | Trans-acting (small RNAs) | Reduced fertility | [46] | |
QQS (Qua-Quine Starch) | Spontaneous | Higher starch accumulation | [47] | |
PPH (Pheophytin Pheophorbide Hydrolase) | Spontaneous | Inhibits leaf senescence | [33] | |
HISN6B (Histidinol-phosphate aminotransferase 1) | Spontaneous | Hybrid incompatibility | [48] | |
Zea Mays | r1 (red1) | Spontaneous | Reduced pigmentation | [49] |
b1(booster 1) | Spontaneous | Reduced pigmentation | [50] | |
pl1 (purple plant 1) | Spontaneous | Reduced pigmentation | [51] | |
p1 (pericarp color 1) | Spontaneous | Reduced pigmentation | [32] | |
lpa1(low phytic acid1) | Paramutagenic | High inorganic phosphate in seeds | [52] | |
Linaria vulgaris | Lcyc (Linaria cycliodea) | Spontaneous | Floral symmetry; dorsiventral flower axis | [38] |
Solanum lycopersicum | CNR (Colorless non-ripening) | Spontaneous | Normal fruit ripening | [39] |
VTE3 (Vitamin E) | Spontaneous | Tocopherol accumulation in fruit | [40] | |
Oryza sativa | D1 (Drawf1) | Spontaneous | Dwarf | [53] |
SPL14 (Squamosa Promoter binding protein-Like) | Spontaneous | Panicle branching and higher grain yield | [54] | |
FIE1 (Fertilization-Independent Endosperm 1) | Spontaneous | Dwarf | [55] | |
RAV6 [Related to Abscisic Acid Insensitive 3 (ABI3)/Viviparous1 (VP1) 6] | Spontaneous | Larger lamina inclination and smaller grain size | [56] | |
AK1 (Adenylate Kinase 1) | Spontaneous | Defects in photosynthetic capacity | [57] | |
ESP (Epigenetic Short Panicle) | Spontaneous | Short panicle | [58] | |
Elaeis guineensis | DEF1 (DEFICIENS) | Spontaneous | Mantled fruit | [59] |
Brassica rapa | SP11/SCR (S locus protein 11/S locus cystein rich) | Trans-acting (small RNAs) | Self-incompatibility | [42] |
Cucumis melo | CmWIP1 (WASP/N-WASP-interacting protein 1) | Transposon Insertion | Sex determination | [41] |
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Gahlaut, V.; Zinta, G.; Jaiswal, V.; Kumar, S. Quantitative Epigenetics: A New Avenue for Crop Improvement. Epigenomes 2020, 4, 25. https://doi.org/10.3390/epigenomes4040025
Gahlaut V, Zinta G, Jaiswal V, Kumar S. Quantitative Epigenetics: A New Avenue for Crop Improvement. Epigenomes. 2020; 4(4):25. https://doi.org/10.3390/epigenomes4040025
Chicago/Turabian StyleGahlaut, Vijay, Gaurav Zinta, Vandana Jaiswal, and Sanjay Kumar. 2020. "Quantitative Epigenetics: A New Avenue for Crop Improvement" Epigenomes 4, no. 4: 25. https://doi.org/10.3390/epigenomes4040025