Integrating Omics and Gene Editing Tools for Rapid Improvement of Traditional Food Plants for Diversified and Sustainable Food Security
Abstract
:1. Introduction
2. Importance of Traditional Food Plants
2.1. Diversity of Traditional Food Plants across the Globe
2.2. Traditional Food Plants Possess Important Nutritional Traits
2.3. Traditional Food Plants Show Varying Degrees of Tolerance to Stresses
2.4. Traditional Food Plants Ensure Stable and Sustainable Food Security
2.5. Traditional Food Plants Provide Alternative Sources of Income to the Farmers and Unorganized Workers
3. Multi-Omics Tools to Dissect Nutritional and Stress-Related Traits for Ensuring Sustainable Global Food Security
4. Examples of Application of Multi-Omics Tools to Traditional Food Plants
4.1. Lysine Biosynthesis in Amaranthus
4.2. Transcriptional Regulation of Anti-Nutritional Saponins in Chenopodium quinoa
4.3. Genetic Mechanism of Stress Tolerance in Manihot esculenta
4.4. Genetic Dissection of Pathogen Resistance and the Early Fruit Development and Evolution in Physalis
4.5. Detection of Genes Regulating Uptake and Storage of Micronutrients in Traditional Food Plants
4.6. Unraveling the Mechanism behind High Amount of α-Linolenic Acid and Salinity Tolerance in Portulaca oleracea
4.7. Higher Accumulation of Lycopene in Elaeagnus
4.8. Nutritional Composition of Dioscorea, a Neglected Staple Tuber Crop of the Indigenous Communities
4.9. Transcriptional Basis of Lipid Biosynthesis in Salvia, a Wonder Seed for the 21st Century
4.10. The Adansonia digitata Contains More Vitamin C Than Oranges
5. Integrating Omics and Gene Editing Tools for Improvement/Domestication of Traditional Food Plants
6. Recent Successful Examples of Gene Editing and Translational Genomics in Traditional Food Plants
7. Challenges to Translational Genomics Using Gene Editing Technology/Tools
8. Conclusions and Future Perspectives
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
AOCC | African Orphan Crops Consortium |
Cas9 | CRISPR-Associated Protein 9 |
CFF | Crops For the Future |
CRISPR-Cas9 | Clustered Regularly Interspaced Short Palindromic Repeat-Associated Protein 9 |
DGE | Differential Gene Expression |
DNA | Deoxyribonucleic Acid |
FAO | Food and Agricultural Organization |
GC | Gas Chromatography |
gRNA | Guide ribonucleic Acid |
HDR | Homology Directed Recombination |
HPLC | High Performance Liquid Chromatography |
ICP-MS | Inductively Coupled Plasma Mass Spectroscopy |
ICRAF | International Council for Research in Agroforestry |
mRNA | Messenger Ribonucleic Acid |
NCBI | National Center for Biotechnology Information |
NHEJ | Non-Homologous End Joining |
PEG | Poly Ethylene Glycol |
sgRNA | Single Guide Ribonucleic Acid |
RNA | Ribonucleic Acid |
RT-PCR | Real-Time Polymerase Chain Reaction |
QTLs | Quantitative Trait Locus |
TALENs | Transcriptional Activator-Like Effector Nucleases |
TFPs | Traditional Food Plants |
Trex2 | Three prime Repair Exonuclease 2 |
ZFNs | Zinc Finger Nucleases |
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Sl. No. | Traditional Food Plant | Occurrence and Traditional Use | Important Nutritional and Stress Resilient Traits |
---|---|---|---|
1 | Lolium perenne (Perennial ryegrass, Poaceae) | Used as a cereal in North America, Southern countries of Europe, North Africa, Middle East and towards the eastern sides of Central Asia [84]. | The seed has a nutritional value similar to oats (Avena sativa) and contains gluten which is an important trait of baked food [84]. |
2 | Cleome gynandra (Stinkweed, Capparaceae) | It is an important vegetable in rural areas of several African countries [85]. | Rich in linoleic acid and amino acids content such as glutamic acid, aspartic acid, arginine, tyrosine, histidine and lysine [85]. The C4 photosynthetic pathway helps them to survive in dry and hot conditions [86]. Adapted to several types of soils and can grow in humid, semiarid and arid climates [87]. |
3 | Basella alba (Vine spinach, Basellaceae) | Used throughout temperate regions and the tropics [88]. | Leaves are rich in calcium, fiber, fat, protein and carbohydrates [89]. They are extremely heat tolerant and are also adapted to a variety of soils and climates [90]. |
4 | Vigna subterranea (Bambara groundnut, Fabaceae) | An important indigenous crop in sub-Saharan African countries such as South Africa, Senegal and Kenya, and Madagascar [91]. | Drought and pest resistant, able to survive in poor soils. Rich in protein whereas fat content is low [92]. Rich in essential sulfur-containing amino acids such as Methionine and provides a good amount of fiber, iron, potassium and calcium [93]. |
5 | Chlorophytum comosum (Spider plant, Asparagaceae) | Iran [94]. | Tubers are rich in carbohydrates, fiber and calcium [94]. |
6 | Corchorus spp. (Mallow, Malvaceae) | In India, Africa and the Middle East, it has been a popular vegetable since ancient times [95]. | The leaves are a good source of calcium, iron, beta carotene, vitamin C and α-tocopherol. Plants also show antioxidant activity [96]. |
7 | Macrotyloma uniflorum (Horse gram, Fabaceae) | Cultivated in Asian countries, especially India and Myanmar, and African countries [97]. | Adapted to drought and poor fertile solid conditions. A potential source of nutrients such as protein, iron and calcium [97]. |
8 | Fagopyrum tataricum, F. esculentum (Buckwheat, Polygonaceae) | Found on a large scale in Asian and Southeast Asian countries. It was spread from China to Japan and Korea. It is also consumed in Russia, Sweden, Europe and North America [98]. | Proteins are rich in essential amino acid lysine [98]. |
9 | Brassica carinata (Ethiopian mustard, Brassicaceae) | Consumed all over the world and considered important food crops in European countries, India, Japan and China [99]. It is an important green leafy vegetable in Zambia and in most parts of tropical Africa [100]. | High levels of glutamic acid, arginine and proline [99]. |
10 | Colocasia esculenta (Taro, Araceae) | It is found all over the Pacific islands and other parts of the world. Africa is the bulk producer of taro, followed by Asia and Oceania [101]. | Rich in small starch grains and proteins. Nutritive than other tubers and rich in vitamins (thiamine, vitamin C, niacin and riboflavin) and minerals (iron, phosphorus and calcium). Taro corms have a high quantity of magnesium and potassium; also a good source of carotene [102]. |
11 | Boscia senegalensis (Aizen plant, Capparaceae) | Native to the Sahel region of Africa [103]. | Protein contains a considerable quantity of tryptophan and arginine. Zinc and iron are present at a relatively high level [104]. High degree of drought resistance [105]. It is highly drought tolerant and can perform very well poor soil conditions [103]. |
12 | Sphenostylis stenocarpa (African yam bean, Fabaceae) | Cultivated in different regions of African countries [106]. | The legume and tuber of the plant is edible. Adapted to wide range of climatic, geographical and edaphic conditions [106]. They have a short growing period [107]. |
13 | Telfairia occidentalis (Fluted guard, Cucurbitaceae) | The crop is extensively cultivated in southern Nigeria [108]. | Leafy vegetable with oil-rich leaves. Its nutritious seeds are also consumed as they are a good source of minerals and proteins [108]. |
14 | Digitaria exilis (Fonio millet, Poaceae) | Cultivated throughout West Africa [109]. | Rich in minerals, vitamins, carbohydrates, protein, fiber and iron. Another advantage is that it is gluten free [110]. Grows in poor-fertile soil and rain-deficient areas [111]. Long storage life without preservatives [109]. |
15 | Crotalaria brevidens (Rattle pod, Fabaceae) | Widely consumed and cultivated in East Africa and West Africa [112]. | Good source of β-carotene, ascorbate, folic acid, riboflavin, iron, calcium and magnesium [59]. They have nitrogen fixing capacity, drought tolerance, produce seeds under tropical conditions and are suitable for intercropping [112]. |
16 | Dacryodes edulis (African pear, Burseraceae) | Cultivated in Guinea and widely in other tropical parts of Africa [113]. | Edible fruits contain lipid, protein, vitamins and minerals such as potassium, calcium, magnesium, iron, zinc, copper and selenium [113,114,115]. |
17 | Treculia africana (African breadfruit, Moraceae) | Cultivated in Nigeria and Africa as a whole [116]. | Seeds are highly nutritious because of the presence of minerals such as potassium, magnesium and calcium, vitamins, fats, proteins and carbohydrates [117]. Grows in marginal areas where other species may not be able to grow [116]. |
18 | Momordica balsamina (Balsam apple, Cucurbitaceae) | Indegenous to the countries of tropical Africa, Arabia, Asia and Australia. Widely distributed in Swaziland, Namibia, Botswana and the provinces of South Africa [118]. | Leaves are rich in protein and fat. They have higher values of minerals such as calcium, magnesium and iron [119]. Leaves also contain 17 amino acids [118]. |
19 | Adansonia digitata (Baobab, Malvaceae) | Distributed throughout the drier parts of Africa, Namibia, Ethiopia, Sudan and Sahara [120]. | Contains vitamin B2/Riboflavin, calcium, phosphorus, iron, vitamin A and vitamin C. It contains almost 10 times more vitamin C than oranges [121]. It is drought tolerant and can tolerate various ranges of pH. It can also grow in calcareous soils and rocky hillsides [120]. |
20 | Berchemia discolour (Bird plum, Rhamnaceae) | Indigenous Southern African fruit tree species. Widely distributed in the regions of northern, eastern, central and southern Africa [122]. | The dry pulp is a rich source of calcium, carbohydrates, iron, sodium, potassium and magnesium [122]. |
21 | Heinsia crinita (Bush apple, Rubiaceae) | Indigenous to West Africa, especially the southern part of Nigeria [123]. | Rich in calcium, magnesium, potassium, iron and zinc [123]. |
22 | Psophocarpus tetragonolobus (Winged beans, Fabaceae) | It grows widely in Malaysia, Indonesia, the Philippines, Bangladesh, Thailand, Sri Lanka, India, Myanmar and African countries [124]. | Seeds, pods, tubers, foliage and flowers are nutritious [124] and contain higher crude protein [125]. It has adequate quantity of minerals such as P, K, Ca, S, Na, Mg, Mn, Fe, B, Sr, Zn, Ba, Cu and Cr, and vitamins such as vitamin A, vitamin B1, vitamin B2, vitamin B3, vitamin B6, vitamin B9, vitamin C and vitamin E [126]. It is suitable to be grown in hot, humid conditions and possess nitrogen fixation capacity [127]. |
23 | Tropaeolum tuberosum (Mashua, Tropaeolaceae) | Traditional subsistence tuber crops indigenous to the Andean highlands [128]. | It can be grown in poor soils without pesticides and fertilizers [128]. They have a high level of protein with an ideal balance of essential amino acids. More content of vitamin C and provitamin A (equivalents of Retinol) than other Andean tubers. Rich in magnesium, phosphorus, iron and zinc [129]. |
24 | Oxalis tuberosa (Oca, Oxalidaceae) | Second important tuber crop in Bolivia and Peru. Cultivated as an important crop in Central Andes, Chile, Argentina, Ecuador, Bolivia and Peru [130]. | Iron- and calcium-rich tubers [131]. Notable quantities of fructo-oligosaccharides reported [130]. |
25 | Smallanthus sonchifolius (Yacon, Asteraceae) | Cultivated in Bolívia, Peru, Czech Republic, Argentina, Italy, Brazil, Ecuador, Korea, Japan, New Zealand and the United States [132]. | Rich in fructooligosaccharides that are good for colon health. They are extremely hardy plants and adapted to cold and hot conditions [133]. |
26 | Chenopodium pallidicaule (Cañiwa, Amaranthaceae) | Majorly grown in Bolivian and Peruvian Altiplano [134]. | Exceptional protein quantity and quality and grains are enriched with micronutrients such as calcium and iron [134]. The nutritional value is equivalent to milk proteins [135]. Gross et al. [136] recognized that it has a balanced amino acid composition and 15.3% protein content. It does not have saponins, which gives a bitter taste and hence it is possible to consume directly without washing. Drought- and frost-resistant plants, well adapted to rocky and poor nutrient soil [134]. |
27 | Lablab purpureus (Hyacinth bean, Fabaceae) | Third high priority vegetable in the south-western and central regions of Bangladesh [137]. Cultivated as a minor crop in tropical regions of Asia and Africa [138] | Extremely resilient to drought-prone areas. A good source of vegetable protein and also a potent source of fats, carbohydrates, fibers and minerals such as phosphorus, calcium and iron [139]. |
28 | Sclerocarya birrea (Marula, Anacardiaceae) | African fruit tree [140]. | Seeds contain sufficient amounts of calcium, phosphorus, magnesium, iron, potassium and copper. Seed edible part has 36.4% of protein, with high levels of cysteine and methionine. Fruits are rich in ascorbic acid and juice extracts contain 33 types of sesquiterpene hydrocarbons [140]. |
29 | Amorphophallus paeoniifolius (Elephant foot yam, Araceae) | Cultivated in Southeast Asian countries such as Malaysia, the Philippines and Indonesia [141]. | Multiple edible parts such as leaves, rhizomes and petioles. Immunity booster and rich in carbohydrates, phenols, alkaloids, tannins, flavones, steroids, coumarins, vitamins, minerals and antioxidants [142]. |
30 | Solanum quitoense (Lulo, Solanaceae) | Majorly cultivated and consumed in Columbia, Ecuador and Central America [143]. | Carotenoid content of fruit is high. Very low fat content but rich in proteins [143]. |
31 | Senna tora (Sickle pod, Caesalpiniaceae) | India [144]. | Its leaves consist of lipids, crude fiber, crude protein and minerals (iron, calcium, cobalt sodium, zinc, magnesium, manganese and potassium) [144]. Sickle pods hold great potential as a source of medicine, minerals. They exhibit drought tolerance [145]. |
32 | Ziziphus jujuba (Buckthorns, Rhamnaceae) | Widely distributed in Europe, Southern and Eastern Asia and Australia [146]. | They grow in different soils and are resistant to alkalinity and salinity, and better adapted to arid regions. They contain high amounts of fructose and fiber. Jujube fruit is rich in unsaturated fatty acids especially linoleic acid (omega-6). They are rich in vitamin C also. Excellent source of magnesium, phosphorus, potassium, sodium and zinc [146,147]. |
33 | Pyrus pyrifolia (Asian pear, Rosaceae) | It is cultivated throughout Central and South China, Russia, Korea, Japan, Vietnam, Thailand, India, Indonesia and the Philippines. As of recently, it is also cultivated in Australia, New Zealand, the USA and Europe (Italy, France) [148]. | Abundant in vitamin B and minerals [148]. |
34 | Achyranthes bidentata (Ox knee, Amaranthaceae) | Grown as cereal in Korea, Vietnam and China. In India and China, leaves and seeds are consumed [149]. | Seeds are rich in proteins and minerals such as iron, calcium, phosphorus, potassium and magnesium. It contains 1.6 times higher quantity of vitamin E than Amaranthus seeds [149]. |
35 | Setaria italica (Foxtail millet, Poaceae) | China, India and other Asian countries [150]. | Great tolerance to drought and can grow in arid and barren lands [150]. |
36 | Grewia asiatica (Phalsa, Malvaceae) | Various parts of South Asia including Cambodia, Philippines and Laos [151]. | Rich in vitamin A, vitamin C, minerals and fiber. Can grow nicely under water-deficient conditions [152]. |
37 | Aegle marmelos (Bael, Rutaceae) | Cultivated throughout India, Nepal, Tibet, Sri Lanka, Laos, Thailand, Malaysia, Phillipines, Vietnam and Myanmar [153]. | Potent source of vitamins (A, B, C, folate) and minerals, antioxidants, dietary fiber, amino acids and bioactive compounds [153]. They are adapted to high salinity conditions [154]. |
38 | Carissa carandas (Koranda, Apocynaceae) | India [155]. | Rich source of vitamin C, iron, calcium and phosphorus [155]. They are xerophytic and suitable for growing in dry land [156]. |
39 | Artocarpus heterophyllus (Jackfruit, Moraceae) | Majorly cultivated in tropical regions of Burma, Sri Lanka, Indonesia, Malaysia, Jamaica, India, Mauritius, Brazil, East Africa, Seychelles and Rodrigues Island [157]. | Fruits are rich in carbohydrates and vitamins such as A, C and folic acid. Rich in calcium and magnesium [158]. Tolerant to water deficit conditions [157]. |
40 | Ullucus tuberosus (Olluco, Basellaceae) | Peru, Ecuador, Colombia, Venezuela and northwestern Argentina [159]. | Resistant against frost and drought and can perform in poor soils. Lower in fat than corn [159]. |
41 | Arracacia xanthorrhiza (Arracacha, Apiaceae) | It is found in South American Countries such as Ecuador, Colombia, Brazil and Venezuela [160]. | Adapted to mesothermic, montane, day length regimes and tropical frost-free conditions [160]. |
42 | Morinda citrifolia (Indian mulberry, Rubiaceae) | Native to Southeast Asia and Australia and widely distributed globally [161]. | Vitamins such as ascorbic acid and provitamin A, amino acids such as aspartic acid, mineral and an alkaloid, xeronine, are detected in its fruits [162]. The plant shows tolerance to a number of stresses such as drought, water logging and salinity [161]. |
43 | Canavalia gladiata (Sword bean, Leguminosae) | They are cultivated on a limited scale in Asia, West Indies, Africa and South America [163]. | Seed coat of the sword bean is rich in gallic acid and other derivatives [164]. Seeds are a rich source of sodium, potassium and calcium [165]. The crude protein content of sword beans is high. Some cultivars are fairly resistant to drought [163]. |
44 | Lupinus mutabilis (Tarwi, Leguminosae) | Distributed widely in the Andes, Venezuela, Colombia, Ecuador, Peru and Bolivia, Australia, Germany, New Zealand, Poland and the United Kingdom [166]. | Seeds have high protein and lipid content whereas fiber and carbohydrate content are lower compared to other lupin species [167]. It has adaptability to temperate and cold climates. It can grow on marginal land and low fertility soils [168]. |
45 | Limonia acidissima (Wood Apple, Rutaceae) | Native to India but also cultivated in Bangladesh, Pakistan and Sri Lanka [169]. | The fruits are rich in β-carotene, vitamin B, vitamin C, thiamine and riboflavin. Fruit pulp is enriched with citric acid, other fruit acids, mucilage and minerals. Other compounds such as alkaloids, coumarins, fatty acids and sterols are also detected in its fruits [169]. It is well adapted to drier conditions and thus shows a greater stress tolerance [170]. |
46 | Cordia myxa (Indian Cherry, Boraginaceae) | It is found globally especially in the tropics. It grows naturally in India, Myanmar and Afghanistan [171]. | It displays drought tolerance and because of that it can easily grow in arid and semi-arid regions [171]. |
47 | Carissa carandas (Karonda, Apocynaceae) | The plant is distributed in various parts of the world such as Nepal, Afghanistan, India, Sri Lanka, Java, Malaysia, Myanmar, Pakistan, Australia and South Africa [172]. | Fruits are rich in calcium, iron, vitamin C, vitamin A [173]. The plant shows drought tolerance [172]. |
48 | Lepidium meyenii (Maca, Brassicaceae) | Nutritionally highly valuable and is native to Peru [174]. | It contains good quantities of fiber, essential amino acids, fatty acids, vitamin C and minerals such as copper, iron and calcium [175]. |
49 | Pastinaca sativa (Parsnips, Apiaceae) | It is commonly found in old fields, roadsides and woodland edges in North America [176]. | Rich in vitamins and minerals; particularly rich in potassium [176]. It shows drought tolerance [177]. |
50 | Xanthosoma sagittifolium (American taro, Araceae) | Traditionally used as a tuber crop, native to Nigeria and tropical Africa [178]. | Good source of carbohydrates and starch. Superior in terms of their protein digestibility and mineral composition such as calcium, phosphorus and magnesium [178]. |
51 | Colocasia antiquorum (Taro, Araceae) | Widely consumed throughout the world especially Africa, Asia, the West Indies and South America [179]. | The corms are full of anthocyanins [179]. They are salt tolerant [180]. |
52 | Nelumbo nucifera (Lotus, Nymphaeaceae) | Creeping rhizomes are found throughout India; also found in China and Japan [181]. | It is a good source of protein and total carbohydrates and possesses high calorific value. It also contains higher quantities of essential minerals such as Na, K, Mg, Fe, Co, Zn and P [182]. Exhibits flooding tolerance [183]. |
53 | Plectranthus rotundifolius (Spreng, Lamiaceae) | Eaten for its edible tubers, native to tropical Africa. Grown in Africa and South East Asia [184]. | It contains higher mineral content than potato, sweet potato and cassava [185]. Highly tolerant to drought [186]. |
54 | Triticum monococcum (Einkorn wheat, Poaceae) | It has been an ancient staple food crop for many years. However, it is presently cultivated only in the Mediterranean region and continental Europe [187]. | Not very good in dietary fiber but it contains good amounts of proteins, unsaturated fatty acids, zinc and iron. It contains antioxidant compounds such as carotenoids, tocols and conjugated polyphenols [187]. They exhibit tolerance to salinity and frost [188]. |
55 | Triticum dicoccon (Emmer wheat, Poaceae) | Used as a cereal crop in the Middle- East, Central and West Asia and Europe [189]. | Rich in proteins, carbohydrates and minerals, poor in fats [189]. Shows drought tolerance [190]. |
56 | Triticum spelta (Dinkel wheat, Poaceae) | It has been an important staple food in parts of Europe in the ancient past [191]. | High vitamin content [191] and rich source of iron, zinc, copper, magnesium, potassium, sodium and selenium [192]. They have high flooding tolerance [193]. |
57 | Eleusine coracana (Finger millet, Poaceae) | It is produced in India, Niger, Mali, Burkina Faso, Chad and China [194]. | It is rich in calcium, dietary fiber, protein, minerals, phenolics and vitamins such as thiamine and riboflavin. It contains a good quantity of iron and amino acids such as methionine, isoleucine, leucine and phenylalanine [194]. They are tolerant to drought, pests and pathogens [195]. |
58 | Panicum sumatrense (Little millet, Poaceae) | Found in the Caucasus, China, India and Malaysia [196]. | Rich in micronutrients such as calcium and iron. They also contain high dietary fiber content and essential amino acids and have low glycemic index [196]. It also shows considerable tolerance against drought, salinity stresses and diseases. |
59 | Panicum miliaceum (Proso millet, Poaceae) | Produced in China, Russia, India and some countries of Eastern Europe and North America [197]. | The protein contains essential amino acids such as leucine, isoleucine and methionine than wheat [197]. They are drought tolerant [198]. |
60 | Pennisetum glaucum (Pearl millet, Poaceae) | An important cereal in arid and semiarid regions of Asia and Africa [199]. | It has high levels of calcium, iron, zinc, lipids and amino acids. Contains omega-9, omega-6 and omega-3 fatty acids. The tannins and phytates act as strong antioxidants [200,201]. It has a low glycemic index and it is a gluten-free crop. They are extremely drought-tolerant [202]. |
61 | Brosimum alicastrum (Breadnut, Moraceae) | Grown in southern Mexico [203]. | The flour obtained from the seeds is characterized by high protein, dietary fiber and micronutrient content. They are drought tolerant [204]. |
62 | Artocarpus altilis (Breadfruit, Moraceae) | It is an important food in the Pacific [205]. | Rich in fiber, protein, magnesium, potassium, phosphorus, thiamine (B1) and niacin (B3). They have tolerance to salinity and can grow on coralline soils and atolls [206]. |
63 | Mucuna pruriens (Velvet bean, Fabaceae) | Cultivated in Southeast Asian countries, including India and Sri Lanka, and Central South American countries as a legume for its seeds [207]. | The seeds are rich in dietary fiber and proteins [207]. They grow well in less fertile soil and show adaptation to drought conditions and acidified soils [208]. |
64 | Pachira aquatica (Malabar Chestnut, Bombacaceae) | Native to Southern Mexico, Guyana and Northeastern Brazil and introduced in other areas such as Guangdong, Southern Yunnan and Taiwan as a cultivated plant [209]. | Seeds contain a high amount of lipids, proteins with high amounts of essential amino acids such as tryptophan, threonine and phenylalanine/tyrosine [210]. Seeds contain more phosphate, magnesium, zinc, iron and copper than some fruits and other starchy foods [209]. |
65 | Strychnos cocculoides (Monkey orange, Loganiaceae) | The species is native to Botswana, Kenya, Namibia, South Africa, Tanzania, Uganda, Zambia and Zimbabwe [211]. | Adapted to drought prone and semi-arid areas. The vitamin C content of the fruits varies from 34.2 mg/100 g to 88 mg/100 g. Considered an essential source of iron [212]. |
Sl. No. | Traditional Food Plant | Distribution | Important Nutritional and Stress Resilient Traits | Exceptionally Notable Character | Applications of Different Omics Technologies |
---|---|---|---|---|---|
1. | Eleusine coracana (L.) Gaertn. (Finger millets, Poaceae) | Majorly produced in Mali, Niger, India, Burkina Faso and China [194]. | Tolerant to pathogens and pests. Drought resistant. Rich in minerals such as calcium and iron, vitamins, protein, dietary fiber and phenolics [194,195]. | Minerals and micronutrients are superior to rice and wheat [268]. | 1. Using genomics tools, Nirgude et al. [269] reported higher expression of opaque2 (regulate seed storage proteins), calcium transporters and calmodulin gene (calcium storage) and Kumar et al. [270] discussed allele mining strategies for PiKh and Pi21 genes that show resistance against Pyricularia oryzae blast disease. 2. Using transcriptomics, expression of several genes such as calcium transporters (CaX, CDPKs, CBPs) are reported [271]. Several transcription factors such as MYB, MYC, WRKY and ZFD were detected during drought stress [195]. 3. Proteomics study led to the identification of a calcium-binding protein, calreticulin [272]. Anatala et al. [273] reported heat shock proteins (HSPs), storage proteins and late embryogenesis abundant (LEA) during drought stress. |
2 | Setaria italica (L.) P. Beauv. (Foxtail millet, Poaceae) | Majorly cultivated in Asian countries such as India and China [150]. | Great drought tolerant potential and grows well in barren and arid land [150]. | Rich in essential amino acids, vitamin B, protein and micro elements [274]. | 1. Lata et al. [275] and Shi et al. [276] reported POD precursors, late embryogenesis abundant (LEAs) and aquaporins for drought tolerance by using transcriptomics. Phospholipid hydroperoxide glutathione peroxidase (PHGPX), ascorbate peroxidase (APX) and catalase 1 (CAT1) during salinity tolerance were reported using transcriptomics by Sreenivasulu et al. [277]. |
3. | Moringa oleifera Lam. (Drumstick, Moringaceae) | Distributed mainly in Middle Eastern, African and Asian countries [278]. | It has high micronutrient and vitamin content. It also shows antioxidant and medicinal activities. They can withstand occasional waterlogged conditions and adapt to hot and semi-arid conditions [279]. They are tolerant to heat, cold, salinity, nutrient starvation, variable light conditions and water deficiency [280]. | Rich in micronutrients and vitamin A [279]. | 1. WRKY transcription factors for various abiotic stress tolerance and copies of Cys2His2 zinc finger motifs (C2H2), APETALA2/ethylene-responsive element-binding protein (AP2-EREBP), C3H transcription factors for drought and cold resistance were reported [280]. High-throughput sequencing technology reported microRNAs related to biotic and abiot stress tolerance [281]. Nutritional component-related genes such as Vacuolar iron transporters (VIT), calreticulin for calcium storage, Zinc transporters, magnesium transporter and genes for vitamin C biosynthesis recognised [282]. 2. Flavonoid compounds and rutinoside sugar compounds were detected using metabolomics by Makita [283]. |
4. | Chenopodium quinoa Willd. (Quinoa, Amaranthaceae) | Cultivated as an important crop since ancient times in various parts of North-Altiplano, South and Central Chile [284]. | Rich source of minerals such as magnesium, iron, calcium, copper, potassium, zinc and phosphorus [66]. They have antioxidant activity (e.g., polyphenols) and rich in vitamins such as Vit. A, B1, B2, B9, C and E, lipids, proteins rich in essential amino acids particularly methionine and lysine, dietary fiber and carbohydrates [285]. They have extreme agro-ecological adaptability [286]. | Higher mineral content than maize and barley including calcium, magnesium, iron, copper, potassium, phosphorus and zinc [66]. | 1. Draft gene sequence and genes related to abiotic stress and nutrients were identified [287]. 2. Xyloglucan endotransglucosylase genes, an expansion A7-like gene and Ethylene Responsive Factor (ERF) genes were found to be downregulated in salt-tolerant plants [288]. 3. Sobota et al. [289] reported albumin and globulins through proteomics. 4. Root cell membrane’s potential, net H+, Na+ and K+ fluxes during salinity adaptation through ionomics study [290]. |
5. | Vigna unguiculata (L.) Walp. (Cow pea, Fabaceae) | Cultivated across Africa, Southeast Asia, Latin Southern and the United States of America. It is not widely cultivated in Europe but used in some Mediterranean countries [291]. | Rich in proteins and carbohydrates [292]. Proteins are rich in lysine and tryptophan amino acids [293]. Shows considerable adaptation to the warm climate with adequate rainfall [292]. | High quantity of folic acid and low quantity of antinutrients [294]. | 1. Up-regulated expression of chalcone isomerase and chalcone synthase in the salt-tolerant plants were reported [295]. 2. Sugars, proline, galactinol and quercetin were identified as osmolytes during osmotic stress using metabolomics [296]. 3. Identified amino acids which are related to glycolysis and tricarboxylic acid cycle [297]. 4. Lutein and beta carotene were reported using metabolomics [298]. |
6. | Vigna radiata (L.) R. Wilczek (Mungbean, Leguminosae) | African regions, South and Southeast Asia [299]. | Drought resistant. Higher iron and folate content [299]. | Rich in digestible protein quantity than other pulses [300]. | 1. Eight flavonoids (vitexin, isovitexin, rutin, kaempferol 3-O-rutinoside, isoquercitrin, genistein, daidzein and isorhamnetin) and two phenolics were reported using metabolomics [299]. |
7. | Sorghum bicolor (L.) Moench(Sorghum, Poaceae) | Major food in semi-arid tropical temperatures of African and Asian regions [301]. | Suitable for cultivation in dry areas and poor soil conditions [302]. Gluten-free cereal that is rich in antioxidants and phenolic compounds [303]. | Gluten-free grains [303,304]. | 1. Quantitative trait loci for sorghum polyphenols were recognized [302]. 2. Increased expression of Late Embryogenesis Abundant (LEA), delta 1-pyrroline-5-carboxylate synthase 2 (P5CS2) and high-affinity K+ transporter 1 (HKT1) for drought tolerance [305]. Salinity and osmotic stress tolerance genes reported [306]. 3. Presence of fructose, galactose, lactose, cellobiose and sedoheptulose as an osmotic protectant were detected using metabolomics [307]. 4. Glutathione-S transferases and l-ascorbate peroxidase during salinity stress identified [308]. |
8. | Manihot esculenta Crantz. (Cassava, Euphorbiaceae) | Used by different communities all over the world, mainly tropical and subtropical areas [309]. | Adapted to marginal soil conditions and erratic rain. Carbohydrate and protein rich [310]. | Rich source of energy [311]. | 1. Using genomics, carotenoid markers on chromosome 1 and candidate genes for carotenoid (phytoene synthase) and starch biosynthesis were reported [312]. 2. Identification of starch biosynthesis genes [310]. Expression profiling and characterization of drought responsive Abscisic acid (ABA)-responsive element (ABRE)-binding factors (ABFs) [313]. Upregulation of 1300 genes during drought stress [314]. Transcription factors related to heat stress (A3, heat-shock transcription factor 21 and a homeobox-leucine zipper protein ATHB12) and dehydration tolerance (ERD1, RD19, RD22 precursor, drought-induced protein Di19-like) were reported [315]. WRKY genes related to abiotic stress tolerance [316]. 3. Proteomics—ATP synthase subunit beta, Rubisco activase (RCA), Rubisco, phosphoglycerate, chaperone peroxiredoxin, heat shock protein, glutathione transferase profiling during cold stress [317]. |
9. | Amaranthus hypochondriacus L., Amaranthus viridis L. (Amaranth, Amaranthaceae) | Consumed in China since ancient times. Central America, South America. It is also used in Africa and Caribbean [318]. | Leaves and seeds are rich in quality proteins and its quantity is higher than maize. Proteins contain higher amounts of amino acid lysine and sulfur containing amino acids [319]. Amaranth oil contains unsaturated linolenic fatty acid which is good for human health [320]. | High quality protein with rich lysine content in leaves and seed [319]. | 1. Gene annotation of lysine biosynthetic pathway and expression analysis was analyzed [321]. 2. Chloroplast chaperones, Rubisco large subunit, cytochrome b6f, oxygen evolving complexes and ascorbate peroxidase expression variation during drought stress were studied [322]. 3. Lutein and beta carotene detection [298]. |
10. | Sesuvium portulacastrum (L.) L. (Shoreline purslane, Aizoaceae) | Locally consumed in various regions of India, South East Asia, Philippines [323]. | Salt, drought and oxidative stress tolerance. Salty taste and fleshy nature of leaves [324]. | Rich source of sodium [323]. | 1. Identified Late embryogenesis abundant 2 as the gene for salt and drought tolerance [324]. Fructose-1,6-bisphosphate aldolase gene (FBA) for abiotic stress tolerance was isolated [325]. 2. Copper (Cu), iron (Fe), manganese (Mn) and zinc (Zn) accumulation during salinity tolerance was reported [326]. |
11. | Ipomoea batatas (L.) Lam. (Sweet potato, Convolvulaceae) | Consumed throughout the world. Asia and Pacific islands produce 92 % of the world’s sweet potato supply [327]. | It is pest and disease tolerant and adapted to high moisture conditions. Rich in complex carbohydrates, vitamin A, vitamin C, Fe and K. Orange-fleshed sweet potatoes are one of the storehouses of beta-carotene. It is a highly resistant crop [327]. | Rich source of beta carotene [327]. | 1. APX, manganese-dependent superoxide dismutase (MnSOD), LEA, early responsive to dehydration (ERD), sodium/hydrogen antiporter (NHX), aquaporin (AQP), vacuolar calcium ion transporter (CAX), metallothionein (MT), betaine aldehyde dehydrogenase (BADH), pyrophosphatase (PPase), catalase (CAT), polyphenol oxidases (PPO), ABRE-binding protein (AREB) during abiotic stress tolerance reported [328]. 2. Amino acids, carbohydrates and flavonoids were detected using metabolomics [329]. Βeta-carotene content [330]. |
12. | Ipomoea imperati (Vahl) Griseb. (Beach morning glory, Convolvulaceae) | Distributed in coastline all over the world [331]. Consumed by local communities for the underground tuber. | Salinity tolerant and grows well in poor nutrient soil [331]. | Rich in sodium [331]. | 1. Expression profiling of AP2/EREBP, bHLH, HD-ZIP and MYB transcription factors during salinity tolerance reported [331]. |
13. | Dioscorea spp. (Yam, Dioscoreaceae) | Tropical and subtropical Countries. Major food in Africa [309]. | Great source of fiber, potassium, manganese, copper and antioxidants. They also exhibit abiotic stress tolerance [332]. | Vitamin C and potassium rich [333]. | 1. Metabolite profiling revealed amino acid content, malic acid content, fatty acids and phosphate content [332]. 2. Genome sequencing revealed the hybrid origin of Dioscorea rotundata from D. prehensilis (wild rainforest plant) and Dioscorea abyssinica (Savannah adapted plant) [334]. |
14. | Portulaca oleracea L. (Common purslane, Portulacaceae) | Distributed all around the world such as New Zealand, Canada, America, temperate countries of Europe, Australia and is highly abundant in India [335]. | It contains high amounts of α-linolenic acid and oxalic acid in their leaves which are highly health beneficial [336]. It is also rich in carbohydrates, protein, minerals (calcium, magnesium, sodium and potassium), vitamin C, carotene, riboflavin, thiamine and nicotinic acid. It is well adapted to dry and salinity conditions, therefore ideal for arid areas [337]. | High amount of alpha-linolenic acid and oxalic acid in the leaves [336]. | Metabolomics study reported 6 amino acids, 22 phenolic compounds, 16 alkaloids and 11 fatty acids [338]. α-linolenic acid accounted for about 40 % to 60 % of total fatty acid [339]. |
15. | Physalis peruviana L. (Wild tomatillos, Solanaceae) | A cultural staple of Mexico, Central America, South Africa, North America and Europe [340]. | They have carotenoids, minerals and vitamin-rich fruits and seeds and show adaptability towards various environmental conditions [341,342]. | Carotenoid and vitamin-rich fruits and seeds [341]. | Metabolomic profiling reported lutein as the most abundant carotenoid (64.61 µg/g at the half-ripe stage) and the presence of gamma carotenoid (rare in fruits) [343]. |
16. | Rumex vesicarius L. (Ruby dock, Polygonaceae) | Cultivated in North Indian states as a vegetable [344]. | Rich in phenols, ascorbic acid, α-tocopherol and β-carotene [345]. | Vitamin rich [345]. | Metabolomic study reported 13 Phenolic compounds, ascorbic acid, α-tocopherol and β-carotene content and 6-C-glucosyl-naringenin identified as the key phenolic compound which have high antioxidant capacity [345]. |
17. | Corylus avellana L. (Hazelnuts, Betulaceae) | Consumed by human civilizations from Mesolithic time onwards and cultivated worldwide especially in Spain, Turkey and Italy, United States and Canada [346,347]. | Rich source of starch, protein, lipids, vitamin E and C, potassium, phosphorus, magnesium and calcium [348]. | Rich in malic acid and unsaturated fatty acids [349]. | Reported higher concentration of palmitic acid which prevents metabolic syndromes such as diabetes [350]. |
18. | Avena sativa L. (Oats, Poaceae) | Consumed in developing as well as developed countries [351]. | Nutritionally rich, traditionally used cereal crops as a major protein diet in cold climate countries including Northern Europe [352]. Better adapted to acid soils and variable soil types than other grain cereal crops [351]. | High dietary fiber content and 78–81.5% unsaturated fatty acids out of 5–9 % lipids [353]. | 1. Barley yellow dwarf virus tolerance QTL on chromosome 3C using genome wide association study was reported [354]. 2. Presence of polyamines detected during osmotic stress detected [355]. |
19. | Bacopa monnieri (L.) Pennell. (Brahmi, Plantaginaceae) | Sri Lanka, India, Nepal, China, Taiwan, Vietnam and Pakistan. Traditionally used as a medicinal plant from ancient times onwards [356]. | Rich in Fe, Mg and Zn. Studies have proven the ability of Brahmi to enhance memory. They grow well in Marshy areas [356]. | Rich source of microelements [356]. | 1. De novo assembly of transcriptome and draft chloroplast genome from RNAseq data [357]. 2. Proline content elevation during osmotic stress [358]. |
20 | Elaeagnus umbellata Thunb. (Autumn olive, Elaeagnaceae) | Berries consumed in tropical and temperate Asia. Nowadays it is available in European countries also [65]. | The berries are a rich source of lycopene and possess 10 times higher quantity of lycopene in their fruits than tomatoes [359]. They are rich in β-cryptoxanthin, α-cryptoxanthin, lutein, β-carotene, phytofluene and phytoene and vitamins. Exhibit drought tolerance, temperature tolerance and high tolerance to pruning. Can grow in high-saline soils [65]. | Ten times higher quantity of lycopene in their fruit than tomato [65]. | 1. Phytoene Synthase (EutPSY) gene expression correlation with lycopene [360]. 2. Sugar metabolism-related enzymes (R-amylase, UGPase, phosphoglucomutase, acid invertase and triose-phosphate isomerase) and carotenoid biosynthesis-related proteins (Acetyl-CoA C-acetyltransferase, IPP isomerase and dimethylallyl diphosphate) reported [361]. |
21. | Porteresia coarctata (Roxb.) Tateoka(Wild rice, Poaceae) | India, Sri Lanka, Bangladesh and Myanmar [362]. | Grows in saline estuaries and is adapted to salinity [362]. | With increase in salinity stress, carbohydrate and ash content increases [363]. | Elevation of proteins related to photosynthesis such as Rubisco large subunit, Rubisco small subunit and light harvesting complex-chlorophyll a, b reported during salinity [362]. |
22. | Atriplex lentiformis (Torr.) S.Watson(Quail Bush, Chenopodiaceae) | South western United States and northern Mexico [290]. | Good salinity adaptation capacity [290]. | Rich source of sodium [364]. | 1. Studied the H+-ATPase activity of plasma membranes during salinity stress, which leads the plant for K+ retention and Na+ exclusion for better salt tolerance [290]. |
23 | Fagopyrum esculentum Moench (Buckwheat, Polygonaceae) | Worldwide distribution [365]. | Grows in hilly areas and marginal ecosystems [365]. Rich in sulfur containing amino acids such as cysteine and methionine than any cereal. Fatless, gluten-free grains that are rich in starch and minerals such as Ca, Mo, S and vitamins [352,366]. | Excellent quality of protein with a high amount of essential amino acid lysine [98]. | 1. Draft genome of buckwheat was developed and the same study identified expression of three granule bound starch synthase (GBSS) genes [287]. 2. Differential expression of sugar biosynthesis and metabolism-related genes in F. esculentum and F. tataricum [367]. |
24 | Panicum miliaceum L. (Proso millet, Poaceae) | It is cultivated widely in Asian countries, some African countries and the Middle East [368]. | More efficient in water usage, because it shows the C4 pathway, hence suitable for cultivation in dry areas. High productivity in low input soil and marginal lands [263]. Rich in both major nutrients and minor nutrients such as phenolics, minerals and vitamins. Gluten-free grain [197]. | Richer in essential amino acids than wheat [197]. | 1. Genes related to C4 mechanisms such as carbonic anhydrase (CA), NAD dependent malic enzyme (NAD-ME) and NADP- malic enzyme (NADP-ME) [369]. 2. Protein related to metabolisms such as polysaccharide and starch [370]. 3. Nearly 48 metabolites including several primary metabolites and five phenolic acids were detected [371]. |
25 | Sclerocarya birrea (A.Rich.) Hochst. (Marula, Anacardiaceae) | Popular African tree [140]. | Ascorbic acid-, arginine- and glutamine-rich fruits [140]. | Highest level of arginine and ascorbic acid [140]. | 1. Draft genome reported and identified genes involved in starch biosynthesis pathway [265]. |
26 | Ziziphus jujuba Mill. (Chinese jujube, Rhamnaceae) | Mainly cultivated in Asian countries [372]. | Salt tolerant and drought tolerant [373]. Good source of phenolics, vitamin C, triterpenic acids, flavonoids and polysaccharides [374]. | Rich in unsaturated fatty acid, especially omega-6 fatty acid [375]. | 1. Expression of 5269 differentially expressed genes during salinity were recognized and among them, 2540 were downregulated and 2729 were upregulated [373]. Expression profiling of genes during heat stress led to identification of heat responsive factors [374].Expression profiling of three UDP-glucose flavonoid 3-O-glucosyltransferase (UFGT), responsible for anthocyanin accumulation in fruit peel [376]. |
27 | Dacryodes edulis (G.Don.) H.J.Lam (African pear, bush pear, Burseraceae) | Cultivated in tropical countries of Africa [113]. | Rich source of protein, vitamins and lipids [113]. | Selenium content is high compared to other crops reported with selenium. Beta-carotene is higher than papaya, avocado and amaranth. They are rich in potassium [114]. | NA |
28 | Basella alba L. (Vine spinach, Basellaceae) | Tropical Asian countries [89]. | Heat- and drought-tolerant plants, high quantities of vitamin A, C, iron and calcium are present [89]. | Leaves are rich in calcium [89]. | NA |
29 | Solanum quitoense Lam. (Lulo, Solanaceae) | South American countries and nowadays found in European countries also [377]. | Adapted to shady areas and rich in vitamins [377]. | Rich in carotenoids [143]. | NA |
30 | Chenopodium pallidicaule Aellen (Cañiwa, Amaranthaceae) | Mainly cultivated in Bolivia and Peru [378]. | Disease and pest resistant. Adapted to salinity, heat and drought tolerance. Rich in protein [378]. | Exceptional protein content and quality, equivalent to that of milk proteins. Balanced amino acid composition [135]. | NA |
31 | Adansonia digitata L. (Baobab, Malvaceae) | Tropical African countries [120]. | Adapted to arid and semi-arid conditions and rich source of vitamin A and C [120]. | Fruit pulp vitamin C is almost ten times that of oranges [121]. | Performed profiling of proteins, amino acids and minerals [121]. |
32 | Strychnos cocculoides Baker (Monkey orange, Loganiaceae) | America, African and South tropic Asian regions [379]. | Adapted to warm climate conditions [379]. Rich in iron, zinc and vitamin C [212]. | Essential source of iron [212]. | N/A |
33 | Panicum sumatrense Roth(Little millet, Poaceae) | Tropical region of Asia and Africa [368]. | Grow with minimal requirements and adapted to harsh environmental conditions and rich in micronutrients [368]. | Grains are a good source of iron and calcium [196]. | 1. Complete chloroplast genome was sequenced [380]. 2. RNa sequences were performed and differential gene expression at the time of drought and salinity stress also studied. At the time of drought stress, 241 DGEs were upregulated and 134 DGEs were downregulated [381]. |
Domesticated Crop|Related Traditional Plant (S) | Gene | Wild Trait | Domestication Trait | Function of the Gene | Reference (s) |
---|---|---|---|---|---|
Fragaria vesca|Pyrus pyrifolia, Rubus fruticosus, R. spectabilis, R. occidentalis [459]. | TERMINAL FLOWER 1 Homologue KSN (TFL1) | Non-frequent flowering. | Continuous flowering. | Flowering repression. Establishment of a continuous flowering habit. | [437,460,461] |
Hordeum vulgare|H. murinum [462], H. brachyantherum, H. jubatum [463]. | nud (nud) | Palea and lemma hulls are tightly adhered to the caryopsis which results in hulled seeds. | Reduced organ adhesion between the caryopsis and the hull. | Controls caryopsis and is involved in the lipid biosynthesis pathway. | [437,464] |
SIX-ROWED SPIKE1 (VRS1) | Two-rowed inflorescences. | Change in inflorescence architecture from two-rowed to six-rowed spikelet. | Loss of function of Vrs1 results in the conversion of the rudimentary lateral two-rowed spikelet in barley into a fully developed six-rowed fertile spikelet. | [437,465] | |
Photoperiod-H1 (Ppd-H1) | Early flowering. | Delayed flowering time. | Candidate gene for leaf size and flowering time in the barley population. | [437,466] | |
RESISTANT TO RALSTONIA SOLANACEARUM 2 (RRS2) | Low leaf scald resistance. | Increased leaf scald resistance. | Resistance gene to fungal pathogen Rhynchosporium secalis which causes leaf scald disease. | [437,467] | |
EARLY FLOWERING3 (ELF3) | Late flowering. | Earlier flowering time. | Part of a circadian clock input pathway. Can regulate the initiation of flowering independently of phyB. | [437,468] | |
INTERMEDIUM-C (INT-C) | Tillering and sterile lateral spikelets. | Increased expression causes suppression of tillering and male fertility in lateral spikelets. | Regulation of shoot system development. Mutation of the gene is correlated with lateral spikelet fertility phenotypes. | [437,469].. | |
Oryza sativa|O. latifolia, O. glumaepatula [470]. | PROSTRATE GROWTH1 (PROG1) | Prostrate growth. | Asymmetrical growth of the tiller base leading to erect growth. | Inactive prog1 results in the conversion of prostrate to erect growth habit in domesticated rice. | [437,471] |
SHATTERING4-1 (SH4-1) | Easily shatters seeds. | Lack of an abscission layer leads to seed non-shattering. | Responsible for rice grain shattering. | [437,472,473] | |
BLACK HULL4 (BH4) | Black hull. | White hull. | Controls black hull color. | [437,474] | |
Red pericarp (Rc) | Red pericarp. | White pericarp (absence of anthocyanin). | Required for red pericarp in rice- proanthocyanin synthesis-related gene. | [437,475] | |
AMMONIUM TRANSPORTER1;1 (AMT1;1) | Poor nitrogen uptake mechanism. | Modified nitrogen uptake and response. | It is a high affinity ammonium transporter which may be involved in ammonium uptake from the soil. | [437,476] | |
LIGULELESS1 (LG1) | Open the panicle and easily shatter seeds. | Altered panicle growth results in closed panicles and reduced shattering. | Controls laminar joint formation between leaf blade and leaf sheath and controls ligule and auricle development. | [437,477] | |
BETAINE ALDEHYDE DEHYDROGENASE2 (BADH2) | Non-fragrant grains. | Fragrant grains. | Plays a key role in the accumulation of a fragrant compound, 2-acetyl-1-pyrroline (2AP). An inactive BADH2 promotes fragrance in rice. | [437,478] | |
GRAIN WIDTH5 (GW5/SW5)) | Small sized seeds. | Increase seed size by increasing the cell number of the outer glume layer. | Controls rice grain width and weight. | [437,479] | |
GRANULE BOUND STARCH SYNTHASE I (Waxy; GBSSI) | Non-glutinous grains. | Glutinous grains. | It controls amylose synthesis in the endosperm. | [437,480,481] | |
GRAIN SIZE3 (GS3) | Short grain. | Long grain phenotype. | Contributes to seed or grain size. | [437,482] | |
SHATTERING1 (Sh1) | Shattering. | Reduction in shattering. | Controls shattering. | [437,472] | |
HEADINGDATE1 (HD1) | Early flowering. | Delayed flowering time. | A regulator of the florigen gene Hd3a. | [437,483] | |
Quantitative trait locus of seed shattering on chromosome 1 (qSH1) | Shattering seeds. | Loss of seed shattering because of the absence of an abscission layer. | Regulates seed shattering. | [472,484] | |
Zea mays|Setaria italica, Lolium perenne, Digitaria exilis, Avena sativa, Secale cereale [485]. | teosinte glume architecture 1 (Tga1) | Hard glume. | Softer glume. | Represses branching. | [437,486,487,488,489] |
zea agamous-like1 (Zagl1) | Small female ear. | Increase in female ear length. | Role in flowering time and ear size. | [437] | |
ramosa1 (ra1) | Many branches with multiple ears on each branch and tassel at the tip of the branch. | Affects kernel organization, altered inflorescence architecture. | Regulate the inflorescence branching systems. | [437,490] | |
PROLAMIN BINDING FACTOR (PBF) | Less protein storage. | Altered prolamin protein levels in seeds. | Controls the expression of seed storage protein (zein) genes. | [437] | |
teosinte branched 1 (TB1) | Many branches with multiple ears on each branch and tassel at the tip of the branch. | Increased expression causes short, ear-tipped branches. | It is involved in apical dominance. It has a significant role in repression of axillary organs. | [437,487,489,491]. | |
SHATTERING 1-5.1, SHATTERING1-5.2 (Sh1-5.1-Sh1-5.2) | Easily shattering. | Non-shattering phenotype because of lack of abscission layer. | It plays a key role in establishment of the abscission layer and is responsible for grain shattering. | [437,472] | |
BARREN STALK1 (BA1) | Presence of axillary meristem. | Prevents axillary meristem development. | Modulates maize inflorescence. Regulates vegetative lateral meristem. | [437,492] | |
CO, CO-LIKE and TIMING OF CAB1 (CCT) | Late flowering. | Lower expression leads to earlier flowering. | CO, CO-like and TIMING OF CAB1 modulate flowering time. | [437,493,494] | |
MADS19 (zmm19) | Kernels without glume covering. | Ectopic expression in inflorescences leads to kernels covered by glumes. | Loss of the MADS19 results in larger glumes. | [437,495] | |
SUGARY1 (Su1) | Non-sweet taste. | Altered starch biosynthesis, sugary sweet taste. | Key role in starch biosynthetic process | [437,496,497] | |
SHATTERING1 (Sh1) | Shattering phenotype. | Non-shattering phenotype because of lack of abscission layer. | Promotes grain shattering through an abscission layer. | [437,472] | |
Glycine max|Canavalia ensiformis, C. gladiata, Lupinus mutabilis, Cajanus cajan, Phaseolus mungo, P. vulgaris, P. aconitifolius, P. calcaratus, P. lunatus, Vigna unguiculata, Lens culinaris, Vicia faba, Lathyrus sativus, Cyamopsis tetragonolobus, Dolichos lablab, Arachis hypogaea [498,499]. | TERMINAL FLOWER1b (TFL1b) | Indeterminate shoots. | Determinate shoots end with terminal inflorescence. | Maintains indeterminate growth of cells in the shoot apical meristem. | [437] |
Setaria italica|S. faberi, S. viridis, S. pumila, Panicum glaucum, P. miliaceum [500]. | GRANULE BOUND STARCH SYNTHASE I (GBSSI) | Non-glutinous grains. | Glutinous grains. | The gene is involved in starch biosynthesis. | [437,501,502] |
Solanum lycopersicum|S. quitoense, S. macrocarpon, Physalis prunisa, P. minima [446,503]. | FASCIATED (FAS) | Small fruit size. | Increased cell proliferation leads to larger fruit. | Promotes cell size growth. | [437,504] |
fruit weight 2.2 (FW2.2) | Lower number of locules. | Increase in locule number in fruit. | Regulates fruit size. | [437,505,506] | |
OVATE (OVATE) | Non-expansive fruit neck region. | Expansion of the fruit and fruit shape determination. | Key regulator of fruit shape. | [437,507] | |
SUN (SUN) | Fruit is not elongated. | Increased growth resulting in elongated fruit. | Major gene controlling the elongated fruit shape. | [437,508] | |
LOCULE NUMBER (LC) | Fruits have two locules. | Fruits have 3–4 locules instead of 2 locules. | Control fruit shape. | [437,504] | |
Vitis vinifera|Cissus discolor, C. s mollissima, Cayratia pedata, Ampelocissus latifolia [509]. | myb-related transcription factor (MYBA1) | Dark colored berry. | Lack of anthocyanins lead to white berry color. | Controls the last steps in the anthocyanins biosynthesis pathway. | [437,510] |
myb-related transcription factor (MYBA2) | Dark colored berry. | Lack of anthocyanins lead to white berry color. | Control the anthocyanin biosynthesis pathway. | [437] |
Sl. No. | Crop Name | Method of Gene Editing | Target Gene and Effect of Mutation after Editing | References |
---|---|---|---|---|
1 | Solanum lycopersicum L. | CRISPR/Cas9 system via Agrobacterium- mediated transformation and TALEN. | Anthocyanin mutant 1 (ANT1)—resulted in deep purple colored plant tissues. | [526] |
CRISPR/Cas9 system via Agrobacterium- mediated transformation. | Mildew resistance locus O (MLO)—powdery mildew-resistant plant. | [527] | ||
2 | Solanum tuberosum L. | CRISPR/Cas9 system via Agrobacterium- mediated transformation. | Acetolactate synthase1 (ALS1)—resulted in reduced herbicide susceptibility. | [528] |
CRISPR/Cas9 system PEG mediated protoplast transfection. | Granule bound starch synthase (GBSS)—resulted in absence of amylase enzyme. | [529] | ||
3 | Zea mays L. | CRISPR/Cas9 system via particle bombardment transformation. | ALS1, ALS2—resulted in chlorsulfuron-resistant plants. | [513] |
CRISPR/Cas9 system via particle bombardment transformation. | Auxin-regulated gene involved in organ size (ARGOS8)—resulted in decreased ethylene response and increased grain yield under stress conditions. | [530] | ||
CRISPR/Cas9 system via Agrobacterium- mediated transformation. | Thermosensitive genic male-sterile 5 (TMS5)-resulted in male sterility. | [531] | ||
TALEN via PEG-mediated transformation. | Phytoene desaturase (PDS), Inositol-pentakisphosphate 2-kinase (IPK1A), Isopentenyl phosphate kinase (IPK), Multidrug resistance-associated protein 4 (MRP4)—resulted in mutation of the genes. | [532] | ||
CRISPR/Cas9 system via PEG-mediated transformation. | Inositol phosphate kinase (IPK)—resulted in mutation. | [532] | ||
CRISPR/Cas9 system. | G protein β subunit (Gβ)—resulted in an autoimmune response. | [533] | ||
CRISPR/Cas9 system. | Waxy—resulted in waxy corn hybrids. | [534] | ||
CRISPR/Cas9 system via Agrobacterium- mediated transformation. | Gibberellin-Oxidase20-3 (GA20ox3)—resulted in semi dwarf plants. | [535] | ||
4 | Oryza sativa L. | CRISPR/Cas9 system via particle bombardment transformation. | ALS—resulted in herbicide resistance. | [536] |
CRISPR/Cpf1 system via particle bombardment transformation. | Chlorophyllide-a oxygenase (COA1) -resulted in precise gene insertions and indel mutations. | [537] | ||
CRISPR/Cas9 system via particle bombardment transformation. | Nitrate transporter 1.1 (NRT1.1B)—resulted in improved nitrogen use efficiency. | [538] | ||
CRISPR/Cas9 system via PEG mediated transformation. | Drooping leaf (DL)—resulted in a drooping leaf phenotype. | [539] | ||
5 | Triticum aestivum L. | CRISPR/Cas9 system via Agrobacterium- mediated transformation. | Grain width (GASR7)—resulted in mutations. | [531] |
CRISPR/Cas9 system via particle bombardment transformation. | Grain weight (GW)—resulted in mutation of the gene. | [540] | ||
6 | Malus domestica Borkh. | CRISPR/Cas9 system via PEG mediated transformation. | DIPM-1, DIPM-2 and DIPM-4—resulted in mutation of the genes.. | [516] |
7 | Vitis vinifera L. | CRISPR/Cas9 system via PEG mediated transformation. | (MLO-7)—Resulted inmutations of the gene. | [516] |
8 | Brassica oleracea L. | CRISPR/Cas9 system via PEG mediated transformation. | FRIGIDA (FRI) and phytoene desaturase (PDS)—resulted in the mutations of the genes. | [541] |
9 | Cucumis sativus L. | CRISPR/Cas9 system via Agrobacterium- mediated transformation. | WPP domain-interacting protein 1 (WIP1)—resulted in development of gynoecious phenotype with upper node having only female flowers. | [542] |
CRISPR/Cas9 system via Agrobacterium- mediated transformation. | Eukaryotic translation initiation factor 4E (eIF4E)—resulted in resistance against vein yellowing virus (ipomovirus), Zucchini yellow mosaic virus and Papaya ringspot mosaic virus-W (potyviruses). | [515] | ||
10 | Solanum nigrum L. | CRISPR/Cas9 system via Agrobacterium-mediated transformation. | Gravity response gene (Lazy1)—resulted in downward growth of the stem. | [543] |
11 | Brassica rapa L. | CRISPR/Cas9 system via PEG mediated transformation. | FRI and PDS genes—resulted in the mutations of the genes. | [541] |
12 | Musa x paradisiaca L. | CRISPR/Cas9 system via PEG mediated transformation. | PDS—resulted in mutation of the gene. | [544] |
13. | Nicotiana tabacum L. | CRISPR/Cas9 system. | PDS—resulted in albino phenotype. | [545] |
14 | Setaria viridis (L.) P. Beauv. | CRISPR/Cas9_Trex2 system via Agrobacterium-mediated transformation. | Domains rearranged methylase (Drm1) and male sterile 45 (Ms45)— resulted in the mutations of the genes. | [546] |
CRISPR/Cas9 system. | Less Shattering1 (Les1)—reduced shattering. | [547] | ||
15 | Medicago truncatula Gaertn. | CRISPR/Cas9 system via Agrobacterium- mediated transformation. | Hua enhancer1 (Hen1)—results in a shrunken, shriveled seed phenotype. | [548] |
CRISPR/Cas9 system via Agrobacterium- mediated transformation. | PDS—resulted in albino phenotypes. | [549] | ||
16 | Vigna unguiculata (L.) Walp. | CRISPR/Cas9 system via Agrobacterium- mediated transformation. | Meiosis gene (SPO11-1)—infertile phenotype. | [550] |
CRISPR/Cas9 system via Agrobacterium- mediated transformation. | Symbiosis receptor-like kinase (SYMRK)—resulted in blockage of nodule formation. | [525] | ||
17 | Cicer arietinum L. | CRISPR/Cas9 system via PEG mediated transformation. | 4-coumarate ligase (4CL) and Reveille 7 (RVE7) genes—resulted in mutations of the genes. | [551] |
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Kumar, A.; Anju, T.; Kumar, S.; Chhapekar, S.S.; Sreedharan, S.; Singh, S.; Choi, S.R.; Ramchiary, N.; Lim, Y.P. Integrating Omics and Gene Editing Tools for Rapid Improvement of Traditional Food Plants for Diversified and Sustainable Food Security. Int. J. Mol. Sci. 2021, 22, 8093. https://doi.org/10.3390/ijms22158093
Kumar A, Anju T, Kumar S, Chhapekar SS, Sreedharan S, Singh S, Choi SR, Ramchiary N, Lim YP. Integrating Omics and Gene Editing Tools for Rapid Improvement of Traditional Food Plants for Diversified and Sustainable Food Security. International Journal of Molecular Sciences. 2021; 22(15):8093. https://doi.org/10.3390/ijms22158093
Chicago/Turabian StyleKumar, Ajay, Thattantavide Anju, Sushil Kumar, Sushil Satish Chhapekar, Sajana Sreedharan, Sonam Singh, Su Ryun Choi, Nirala Ramchiary, and Yong Pyo Lim. 2021. "Integrating Omics and Gene Editing Tools for Rapid Improvement of Traditional Food Plants for Diversified and Sustainable Food Security" International Journal of Molecular Sciences 22, no. 15: 8093. https://doi.org/10.3390/ijms22158093