More than half of the publishers listed alongside IntechOpen (18 out of 30) are Social Science and Humanities publishers. IntechOpen is an exception to this as a leader in not only Open Access content but Open Access content across all scientific disciplines, including Physical Sciences, Engineering and Technology, Health Sciences, Life Science, and Social Sciences and Humanities.
\\n\\n
Our breakdown of titles published demonstrates this with 47% PET, 31% HS, 18% LS, and 4% SSH books published.
\\n\\n
“Even though ItechOpen has shown the potential of sci-tech books using an OA approach,” other publishers “have shown little interest in OA books.”
\\n\\n
Additionally, each book published by IntechOpen contains original content and research findings.
\\n\\n
We are honored to be among such prestigious publishers and we hope to continue to spearhead that growth in our quest to promote Open Access as a true pioneer in OA book publishing.
Simba Information has released its Open Access Book Publishing 2020 - 2024 report and has again identified IntechOpen as the world’s largest Open Access book publisher by title count.
\n\n
Simba Information is a leading provider for market intelligence and forecasts in the media and publishing industry. The report, published every year, provides an overview and financial outlook for the global professional e-book publishing market.
\n\n
IntechOpen, De Gruyter, and Frontiers are the largest OA book publishers by title count, with IntechOpen coming in at first place with 5,101 OA books published, a good 1,782 titles ahead of the nearest competitor.
\n\n
Since the first Open Access Book Publishing report published in 2016, IntechOpen has held the top stop each year.
\n\n\n\n
More than half of the publishers listed alongside IntechOpen (18 out of 30) are Social Science and Humanities publishers. IntechOpen is an exception to this as a leader in not only Open Access content but Open Access content across all scientific disciplines, including Physical Sciences, Engineering and Technology, Health Sciences, Life Science, and Social Sciences and Humanities.
\n\n
Our breakdown of titles published demonstrates this with 47% PET, 31% HS, 18% LS, and 4% SSH books published.
\n\n
“Even though ItechOpen has shown the potential of sci-tech books using an OA approach,” other publishers “have shown little interest in OA books.”
\n\n
Additionally, each book published by IntechOpen contains original content and research findings.
\n\n
We are honored to be among such prestigious publishers and we hope to continue to spearhead that growth in our quest to promote Open Access as a true pioneer in OA book publishing.
\n\n
\n\n
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1. Introduction
Nitrogen is the most abundant (78%) of the atmosphere in gaseous form as an N2 molecule. But it is not directly available to the plants for their growth and development [1]. It is the foremost important major essential nutrient element involved in the physiological processes in plants. Globally, nitrogen deficiency is a crucial growth-limiting factor for plants, especially under abiotic stresses. The nitrogen use efficiency (NUE) is defined as the output of any crop plant per unit of nitrogen applied under a specific set of soil and climatic conditions [2]. Agronomist usually considers the amount of rough rice produced per unit of nitrogen applied as the efficiency of nitrogen, but physiologist defined it as the amount of rough rice produced per unit of nitrogen absorbed [3, 4]. The latter is also termed as N utilization efficiency. Apparent N recovery is based on N uptake measurement in the above-ground plant parts and assumes that fertilized and control crops absorb the same amount of soil N. On the other hand, physiological and agronomic efficiencies are based on grain yield rather than total dry matter production. However, the enhancement of NUE under an abiotic stressful environment has paramount importance to the future rice breeder.
Rice (Oryza sativa L.) is grown in a wide range of ecosystems from the tropic to the temperate regions, but productivity is severely tormented by various abiotic stresses [5, 6]. Farmers may encounter flooding or waterlogging if heavy rain occurs immediately after seeding before or after transplanting. The flooding can cause complete crop failure because of the high sensitivity of rice to anaerobic conditions caused by flooding during germination [7, 8]. There are various forms of flooding caused by directly from heavy rains and/or flooding from adjacent rivers, leading to drastic reductions in rice yield, ranging from 0.5 to 2.0 t ha−1 [9]. Flash floods are relatively short durations, prevailing some days to a couple of weeks. Apart from this, stagnant flooding (30–50 cm water depth) may occur at any time of the monsoon. Sometimes, the stagnant flooding may have coincidence with the flash flood resulting in severe impacts on rice production. In deepwater areas, stagnant water present from 0.5 m to a few meters in the field, usually for 4-6 months. The depth of water in some of these deepwater areas can exceed 4 m as in floating-rice areas. Rice breeders have been trying to develop a unique rice variety having specific adaptive traits to tackle these types of floods [10, 11, 12]. Recently, the Bangladesh Rice Research Institute has developed a deepwater rice variety, BRRI dhan91, for the deepwater ecosystem. However, the application of nitrogenous fertilizer is very challenging to the deepwater rice field and the NUE of this ecosystem is not yet been well investigated.
Another one among the most important abiotic stresses is drought. Despite the importance of drought as a major factor in yield reduction in rainfed ecosystems, few efforts have been made to develop high-yielding drought-tolerant rice variety. Impending rice production will experience a range of drought stress. The root architectural plasticity is taken into accounts as a very important characteristic to confer tolerance to drought stress [13]. Deciphering the genetic and molecular mechanisms controlling root phenotypic plasticity is important for effective screening, selection and rice breeding efforts. Despite the likely genetic complexity behind the regulation of trait expression in line with environmental conditions, phenotypic plasticity is heritable and selectable. The QTLs have been identified incur for plasticity in aerenchyma development and lateral root growth in response to drought stress in rice [14]. These QTLs can be used in advanced breeding for the development of a drought-tolerant rice variety. Due to global climate change, rice crops will face diverse stresses, including prolonged drought stress, poor soil fertility, and unpredictable rainfall. Rice establishment, either by transplanting or direct seeding, depends upon the rainfall pattern. Therefore, the identification of root phenotypic plasticity traits suitable for adaptation to the particular range of conditions faced by rice crops, as well as the genetic regions responsible for those plasticity traits, may facilitate selection for wide adaptation of rice genotypes to variable conditions to confer sustainable yield. Quantification of root architectural plasticity possesses significant value to detect which root traits may play the pivotal roles in rice adaptability to drought. It is reported that the most plastic genotypes in root traits may show the most yield stability under various dynamics of drought stress [11]. In this regard, many drought-tolerant cultivars, like N22 and Moroberekan, have been selected from rainfed ecosystems through traditional processes. These cultivars harbor genes for tolerance to abiotic stresses, including a wide range of drought [15]. But due to their low yield potential and poor grain quality, farmers and consumers are reluctant to prefer these cultivars. This provides a unique opportunity for rice breeders to develop high-yielding drought-tolerant varieties.
Salinity is another major abiotic stress that is globally distributed in both irrigated and non-irrigated areas [16, 17]. On a global basis, salinity stress ranked second after the drought [18]. Salt stress affects many aspects of rice growth and development, especially during seed germination and seedling growth [19]. It is one of the most prevalent environmental threats to global agricultural productivity, especially in arid and semi-arid climates, where population growth, water shortage and land degradation are major concerns [1, 20]. Salt-affected soils are identified by high electrical conductivity (EC), sodium adsorption ratio (SAR) and pH, calcareousness, poor organic matter, less biological activity and imbalance in physical soil conditions. Salinity causes toxicities of ions like Na+ and Cl−, osmotic stress and ionic imbalance to the root zone or in the soil body, including soil impermeability [21], resulting in nutrient uptake problems in rice plant. Salt stress is the osmotic stress expressed on seedling to the reproductive stage when they are growing under high saline conditions. The N is the essential element for the synthesis of chlorophyll, amino acids, nucleic acids, and proteins. Reduction in plant dry matter is sometimes observed under severe NaCl salt stress and N deficiency. This phenomenon possibly happens because of the decrease in sugar or starch accumulation [1, 22]. The NUE of nitrogenous fertilizers in saline soil depends upon its mineralization pattern, soil salinity levels, soil texture, temperature, freshwater irrigation and soil pH [23]. As NUE for rice plants under salt-affected soils is relatively lower than those on normal soils, the judicious use of nitrogenous fertilizer application in saline soil is needed. Breeders involved in salinity tolerant rice, it is groundbreaking news that the over-expression of PHYTOCHROME-INTERACTING FACTOR-LIKE14 (OsPIL14), or loss of function of the DELLA protein SLENDER RICE1 (SLR1), accelerate mesocotyl and root growth under salt stress and minimize the sensitivity to NaCl-induced hindrance of seedling growth in rice [17].
2. Crop establishment methods under abiotic stress
Crop establishment under abiotic stress is crucial for farmers, even though farmers are coping with this stress condition. There are many more abiotic stresses; out of those, we will discuss only flooding, drought and salinity stress.
2.1 Crop establishment under flooding stress
Proper rice establishment is significantly important in flood-prone areas because of its sensitivity to flooding during germination (Figure 1) and early seedling stage relative to other growth stages [24, 25]. In most areas of Asia, irrigated rice is established by transplanting of seedlings into puddle soil [26, 27], after which the fields are flooded for a prolonged time and recession of water is done before harvesting. Puddling gives some advantages such as it reduces water loss by percolation, assists weed control through destroying weeds, burying weed seeds and maintaining anaerobic conditions that impede weed germination, and makes the soil soft for transplanting [28, 29]. In many rainfed areas of Bangladesh and the eastern part of India, water deposits in the field to around 30 cm or more within a few days after the onset of the rainy season, making the farmers to transplant taller and older seedlings being their only viable option in their hand [30]. Many variations in direct-seeding are being practiced depending on water availability and field conditions [29]. Due to increasing labor scarcity and cost, however, the need to shift a more suitable establishment method with much lower labor requirement than manual transplanting is conducted. This can be achieved by changing to mechanical transplanting or direct-seeding, which also enable timelier planting/seeding and improved crop stand [31]. Researchers in China [32], South Asia [33], and Australia [34] reported that rice could be successfully grown using dry-seeding. Dry-seeding rice has been developed as an alternative establishment method of rice that alters labor requirements and other inputs while increasing or maintaining economic productivity and alleviating soil degradation problems in cropping systems [35, 36].
Figure 1.
Crop establishment methods and seed management options under early flooding stress using anaerobic germination (AG) potential rice genotypes in direct-seeded rice (DSR) system under field condition.
The three basic methods of direct seeding are water seeding (broadcasting seed into standing water), dry-seeding and wet-seeding [31]. In wet seeded rice (WSR), the pre-germinated seeds are broadcasted or sown in rows on the saturated soil surface, typically after puddling. Dry-seeding involves broadcasting or preferably drilling the seed into non-puddled soil, usually after dry tillage [31]. Water seeding involves pre-germinated rice seeds broadcast in standing water and is practiced in some cooler areas like in California, Central Asia and Australia [30]. The main advantage of this method is that the standing water suppresses the majority of weed species. This is common in temperate irrigated areas, but could potentially be adapted in flood-prone rainfed lowlands in the tropical area where farmers can practice early sowing without waiting for a complete recession of floodwater, to minimize the risk of delayed maturity and late-season drought [26]. Once the rice crop has been established in direct-seeded systems and based on water availability, the field is flooded to suppress weed growth and water depth is then maintained at 5–10 cm through most of the season, later water is gradually drained prior to harvest [30]. The type and degree of adoption of alternative rice crop establishment methods to puddling and manual transplanting vary across Asia. In some parts of South East Asia (Philippines, Malaysia, and Vietnam) and Sri Lanka, transplanting has been replaced in large areas by wet-seeding on puddled soil [2, 26]. In the more developed East Asian countries, like Japan and South Korea, transplanting in puddled soil using specialized machinery has been a common practice for many years, and there is now emerging interest in mechanical transplanting into either puddle or non-puddle/dry tilled soil in parts of India. In parts of South Asia, especially in the rice-wheat systems of north-west India, dry-seeding of rice is at the early stages of adoption. The same seed drill can also be used for sowing other crops; thus, dry-seeding may be more conducive to the mechanization of rice establishment than the use of a single purpose mechanical transplanters in regions where farmers also grow non-rice crops [37].
The establishment methods involving puddling have several disadvantages, including higher tillage costs, adverse effects on soil structure for upland crops grown in rotation with rice, and high water requirement for crop establishment. Irrigation cost for crop establishment can be reduced by avoiding puddling, with or without a change in the crop establishment method. For example, both mechanical transplanting and wet-seeding can be done in non-puddled soil after saturating the soil (after dry tillage or no-tillage) [38]. Dry-seeding into dry or moist soil, can further reduce the water requirement for crop establishment, with or without prior dry tillage as for transplanted and wet seeded rice. Nevertheless, direct-seeded rice in the field for 2–3 weeks is longer than transplanted rice, increasing the length of the irrigation season. It has been observed that the extraction of water is more uniform across depths with direct-seeded rice because of better root growth than with transplanted rice [39]. At the early stage of crop growth, up to 60 days after sowing (DAS) growth rate is relatively higher in DSR and WSR than transplanted rice, having more plant density per unit area compared to transplanting [40].
2.2 Crop establishment under drought stress
Drought is an environmental occurrence imposed by the synergistic effect of hydrological, climatic, and natural forces that result in insouciant precipitation for agricultural production over a long period [41]. Globally drought severity is one of the serious concerns because of its immense impacts [42]. The frequency and severity of global drought remain omnipresent and the incidence or extremity of drought has been increasing globally, such as in the Mediterranean region [43], Central China [44], and Africa [45]. Drought is a major constraint to rice production worldwide, as it can occur for varying lengths of time and intensity at any stage of rice growth and development. With the increasing human population and depleting water resources, the development of drought-tolerant rice is of supreme importance to minimizing rice yield losses from drought stress [46]. The major obstacle of rain-fed rice production is drought [47]. Irrigated conditions induce shallow root systems to uptake the resources from the top layer of the soil, whereas rain-fed conditions favor a deep and robust root system, needed to extract the water and nutrients from a wider volume of soil [48]. Three common types of drought can be found for rice production: early water scarcity that causes a delay in seedling establishment through transplanting, mild sporadic stress having cumulative effects, and late stress affecting long duration varieties [49].
Drought stress induces different physiological and biochemical changes in rice at various developmental stages [50]. It is reported that the plant acclimatized to drought stress through modification of its roots into thicker and longer to uptake nutrient and water from a relatively higher depth of soil and it is found that assimilates are translocated to roots instead of shoots in response to drought stress [51]. In contrast, some researchers opined that root growth in rice decreases under drought stress [52]. These findings show that the response of roots to water stress is highly dependent on the rice genotype, period and intensity of stress [53]. The impact of drought stress on rice yield also depends on the growth stages, with the seedling, tillering, flowering, but if rice plant faces severe drought at the panicle initiation stage might be the most sensitive stage resulting huge loss in yield [54].
2.2.1 Role of root to uptake water under drought
As roots uptake water and nutrients from the soil; hence, the morphological and physiological characteristics of roots play a vital role in determining shoot growth, successive development and ultimate crop production [55]. The access of water to a plant is measured by its root system, root properties, root structure, and distribution of root and rootlets, so improving root traits to expedite the uptake of soil moisture and uphold the productivity under drought stress is of paramount interest [56, 57]. Herbaceous plants like rice have a root system comprised of coarse roots, which include the primary roots that originate from the taproot system and the nodal/seminal roots of fibrous root systems, easily distinguishable from the finer lateral roots [58]. Moisture deficiency can be recovered through modification of the root-shoot ratio and maintain leaf gourd cell-mediated process under drought stress [59]. The optimal dry matter partitioning theory proposes that a plant distributes the assimilates among its different parts for optimum growth and development [60]. It further suggests that the shoot ratio and some other signaling processes may change the ratio to balance the assimilates that alter plant growth even the plants produce certain root for adaptation [61]. Roots having a small diameter and a high specific root length expedite the surface area of roots in contact with soil water and also increase the influx of the xylem through the apoplastic pathway [62, 63]. Moreover, the decrease in root diameter also assists in enhancing water access and upraises the productivity of plants under drought stress [64].
Agronomic adjustments to root plasticity may occur when plant combat with multiple resources limitation [65]. Root architecture varying with rice seedling establishment methods; dry direct seeding prone to more edaphic stresses than irrigated transplanted methods [31]. Moreover, the adjustments in high yield potential among genotypes showing the highest degree of root plasticity may be due to genetic potentiality rather than functional adjustments. Undesirable traits to drought stress such as tall plant height and very early flowering have been reported previously, later in high-yielding, medium-duration drought-tolerant rice varieties developed [66, 67]. So the exact identification and fine-mapping of the QTLs governing the root plasticity traits identified [68]. The positive plasticity values noticed in response to stress indicate that the growth of that particular root trait was increased due to stress application. This response is distinct from an allometric response, in which larger root biomass is related to larger shoot size, because though root growth increased under drought stress but shoot growth down-regulated under stress [68]. The genotypes showing most root-plasticity have positive correlations for root architectural traits between and drought suggest that the most root-plastic genotypes would consistently show a plastic response in different drought environments either in transplanting or direct seeding or in other soil types [68]. The genotypes having the most root-plasticity under drought also would show a relatively greater degree of plasticity under low phosphorus content soil, depending on the soil depth [68]. Combinations of multiple root plasticity traits in response to drought and/or low-phosphorus have been related to genotypic variation for adaptation to various environments [69]. It is reported that no single functional parameter was strongly incurred to trends in root plasticity or yield [68]. In line with root architectural plasticity, traits such as root anatomy, water use efficiency, and phenology has been reported to be related to more stable plant establishment across versatile environments in various species [70, 71]. In the case of rice, phenological plasticity in response to drought may be difficult to assess because rice exhibited delayed flowering under drought, and this delay can be reduced by plasticity in root architectural traits, which improve moisture uptake. A set of QTLs has been identified related to root architectural plasticity traits and phenotypic plasticity traits in rice, resulting in getting a better understanding of rice establishment under drought stress [68].
2.3 Crop establishment under salinity stress
Generally, rice plants are very sensitive to salinity stress during the early stages of seedling establishment, post-germination and reproductive stage and relatively less sensitive during tillering and grain filling stages [72, 73]. Under salinity altering in the shoot to root ratio as a consequence of root length reduction was supposed to be the avoidance mechanism of the seedlings from salt stress. Salinity accumulates the toxic ion in plants, causing a mineral imbalance. The essential ions are reduced and do not meet the demand resulting in hindrance in normal physiological activities of rice plants. High salt stress impedes the seed germination process, while low salt stress induces seed dormancy [74]. To cope with such stress conditions, seeds develop a mechanism of maintaining low water potential, other specific avoidance, escaping, or tolerance mechanisms to protect the damage by salt stress [75]. Salinity limits germination in a number of ways. From reducing the osmotic potential of soil, which makes a decline in water imbibitions by seed [74] to the creation of ionic toxicity, which alters enzymatic action involved in nucleic acid metabolism. Other effects of salt stress on seed germination include changes in the metabolic process of protein [76]. Seeds are usually more sensitive to salt stress due to close association to the surface of the soil. Accumulation of NaCl to a toxic level in soil, ionic stress decreases the rate of germination [77]. Seed could not absorb water properly because of lower water potential induced by salt stress resulting in toxic effects to the developing embryo and delay in the germination process [78]. The average time of seed germination depends on salinity severity and genotype’s inherent quality. There is a strong negative co-relationship between the strength of salinity stress and the rate of germination [79]. Salinity exhibits an immense effect on the germination index and seed size [80]. Small-sized seeds show a relatively higher germination index than large size seeds under salinity stress. Salinity has a negative effect on germination percentage, rate of germination and germination speed [81]. After germination, in successive growth of the seedling, salinity reduces shoot and root dry matter production in rice genotypes [82], and the magnitude of reduction increased with increasing salinity level (Table 1).
Genotype
Salinity level (dS m−1)
0
5
10
15
0
5
10
15
Shoot dry weight (g/10 plants)
Root dry weight (g/10 plants)
IR20
0.060
0.05 (17)
0.028 (53)
0.016 (73)
0.068
0.048 (29)
0.036 (47)
0.016 (76)
POKKALI
0.134
0.116 (13)
0.064 (52)
0.044 (67)
0.152
0.076 (50)
0.026 (83)
0.018 (88)
IR29
0.140
0.07 (50)
0.036 (74)
0.014 (90)
0.06
0.048 (20)
0.022 (63)
0.012 (80)
NERICA 1
0.084
0.064 (24)
0.024 (71)
0.008 (90)
0.054
0.038 (30)
0.018 (67)
0.01 (82)
NERICA 5
0.076
0.054 (29)
0.032 (58)
0.02 (74)
0.13
0.056 (57)
0.016 (88)
0.004 (97)
NERICA 12
0.092
0.068 (26)
0.046 (50)
0.028 (70)
0.062
0.04 (35)
0.024 (61)
0.01 (84)
NERICA 19
0.054
0.038 (30)
0.014 (74)
0.004 (93)
0.036
0.028 (22)
0.002 (94)
0.0 (100)
IWAII
0.090
0.068 (24)
0.032 (64)
0.02 (78)
0.068
0.046 (32)
0.028 (59)
0.016 (76)
Table 1.
Effect of salinity on shoot and root dry weight (g/10 plants) of different rice varieties [82].
Values in parenthesis indicate percent reduction to respective controls.
2.3.1 Plant physiology under salinity
Higher amounts of salt in the soil cause a serious threat to various metabolic processes of plants, which results in a reduction of crop yield. Soil salinity limits the uptake of essential ions into the plants resulting in metabolic disorder leading to downstream in plant growth rate [83]. Excess salt concentration in the root zone of plants causes a change in plant water potential. Salinity causes a reduction in turgor pressure in plant cells due to less water uptake by the plants. Insufficient water limit cell division and regulation of stomatal aperture, which lead to low photosynthesis rate and in severe case causes plant tissues death [84]. Aside from this, reduction in turgor pressure causes stomatal closure, resulting reduction in gaseous exchange of transpiration [20]. Salinity causes other physiological disorders, like changes in membrane permeability, leading to misfolding of membrane proteins [85] and suppression of the photosynthesis [86]. Reduction in enzymatic activities and photopigments causes a lowering of photosynthesis rate [87]. Many plant physiological and biochemical processes, photosynthesis [88], water conductance through stomata [75, 89] are affected by salinity, resulting in an adverse effect on biological processes and crop yield reduction.
2.3.2 Plant anatomical change under salinity stress
Rice adopts various strategies in response to salinity through their anatomical modification, which allows them to cope with the stress. Plants with growth in high salt concentration have more thickness of leaves [90], epidermis, cell walls and cuticles. The higher the salt concentrations, the higher the mesophyll cell layers and cell size up to some extend [91], due to more elasticity in the cell wall at high turgor pressure [92]. Salinity expedites the density of stomata at the lower side of leaves [93] with increased palisade tissues [94]; however, salinity downregulates the number of cells per leaf. Salinity reduces the number of stomata on the surface of the epidermis [95], vessels number [94]. However, salinity accelerates subrinization inside the roots resulting in hindrance in nutrient uptake from soil [96]. In rice, it is reported that stem diameter was reduced [97], while trichome and stomata density increased. Salt stress reduced cell size, the epidermal thickness of leaves, apical meristem, diameter of the cortex and central cylinder [98]. Salinity induced thickening of exodermis and endodermis [99] and assist in developing sclerenchymatous tissues [98]. Once the seed has germinated, the next goal for the plant is an establishment. Salinity causes a reduction in crop establishment by reducing shoot growth, sealing leaf development and expansion, reducing the growth of internodes and inducing abscission of leaf [91, 100]. Salinity causes some complexity to plants, like osmotic stress, ion toxicity and nutrient imbalance, which are detected as the most prominent reasons for a reduction in crop growth, resulting in crop failure in severe cases. Nonetheless, different developmental stages like germination, vegetative growth, flowering, spikelet’s setting and grain filling of rice behave differently with salinity. It is reported that salinity decreased biomass and leaf area in rice [101].
3. QTLs and genes of nitrogen use efficiency
In soil, inorganic nitrogen is available for plants as nitrate (NO3−) in aerobic upland condition and ammonium (NH4+) in flooded wetland or acidic soils. Nitrogen use efficiency (NUE) is a complex trait that is controlled by multiple genes. Many genes and/QTLs associated with NUE have been identified in rice. Studying and understanding the mechanisms of N utilization at a molecular level may help to improve rice varieties for N deficiency tolerance under different abiotic stresses. Researchers [102] identified 14 putative QTLs for NUE components and 63 QTLs for 12 physiological and agronomic characteristics with six hotspot regions using 174 recombinant inbred lines derived from the IR64/Azucena cross at the vegetative phase in the hydroponic Yoshida solution with three different N concentrations: 1X (standard), 1/4X and 1/8X. In line with this, it is reported that eight QTLs for plant height in hydroponics with two N supply levels in the Yoshida culture solution and 13 QTLs for plant height in a soil mediated experiment with two N supply treatments [103]. Twelve QTLs were detected for root weight, 14 for shoot weight and 12 for biomass from 239 rice recombinant inbreed lines (RILs) derived from a cross between two indica parents (Zhenshan97/Minghui63) under hydroponics medium using two N treatments [104]. In another pot experiment, seven QTLs were identified associated with nitrogen use and the yield on chromosome 3 [105]. Three candidate genes Os05g0208000, Os07g0617800 and Os10g0189600 were identified through fine-mapping of four QTLs located on chromosomes 5, 7 and 10 accelerated yield performance under low N level [106].
Five QTLs were identified on chromosomes 1, 2, 7 and 11 for grain yield (GY) using 127 RILs derived from the cross Zhanshan 97/Minghui 63 [107]. The phenotypic and genetic associations between grain NUE and GY are positive and highly significant; thus, QTLs for both NUE and GY could be used to trigger NUE and GY in a breeding program [108]. Seven QTLs for the glutamine synthetase (GS1) protein content and six QTLs for the NADH-GOGAT protein content were detected using backcross inbred lines between Nipponbare and Kasalath. Some of these QTLs were fined mapped to get a structural gene for GS1 from chromosome 2 and chromosome 1 [109]. A QTL on chromosome 2 activates cytosolic GS1 for protein synthesis in older leaves, resulting in more active tillers during the vegetative stage and a more panicle number and total panicle weight [110]. Using 166 RIL populations, 22 single QTLs and 58 pairs of epistatic QTLs associated with physiological NUE in rice have been identified [111]. With the same mapping population, 28 main effect QTLs and 23 pairs of epistatic QTLs were detected [112]. It is reported that [113], using 38 chromosome segment substitution lines derived from a cross between “Koshihikari,” a japonica variety, and “Kasalath,” an indica variety, identified a major QTL qRL6.1 on the long arm of chromosome 6 associated with root elongation under deficient and sufficient NH4+ condition. The “Kasalath” allele at this QTL region promoted significant root elongation. The marker interval was C11635–P3A2 and phenotypic variance explained by this QTL was 76.4%.
A set of RILs grown in four different seasons in two locations with three nitrogen fertilization treatments was analyzed for QTL for grain yield components and two main effect QTLs were detected viz., grain yield per panicle on chromosome 4 and grain number per panicle on chromosome 12 under N zero level [114]. Four QTLs for trait differences of plant height and heading date between two N levels have been mapped on chromosomes 2 and 8 co-locating with reported QTLs for NUE [111]. In response to low nitrogen application for two years, 33 QTL have been identified in RIL population, out of which only ten QTLs were consistent under low N [115]. QTL mapping for NUE and nitrogen deficiency tolerance traits in RIL population for two years resulted in four common QTL on chromosomes 1, 3, 4 and 7 [116].
From a recombinant inbred population, 20 single QTLs (S-QTLs) and 58 pairs of epistatic loci (E-QTLs) were detected for the nitrogen concentration of grain, nitrogen concentration of straw, the nitrogen content of shoot, harvest index, grain yield, straw yield and physiological nitrogen use efficiency (PNUE) [117]. Researchers [118] identified seven chromosomal regions using 40 introgression lines (ILs) derived from a cross between “Ilpumbyeo,” a temperate japonica variety, and “Moroberekan,” a tropical japonica accession from seedlings grown in 0, 250 and 500 μM NH4+. Among them, the qRW6 QTL was detected on the long arm of chromosome 6 associated with root weight in temperate japonica.
Recently, a group of scientists reported [119] about a main effect QTL qRDWN6XB (Table 2) on the long arm of chromosome 6, which positively confers tolerance to N deficiency in the Indica rice variety XieqingzaoB, was identified using a chromosomal segment substitution line population using Zhonghui9308 and XieqingzaoB. Nine candidate genes were found in this region through fine mapping. Out of these genes, Os06g15910 was seemed to be a strong candidate gene associated with root system improvement under low N status. However, putative QTLs/genes needed for multiple abiotic stress tolerance, NUE and associated novel traits in rice could be discovered through a holistic breeding approach (Figure 2).
Major QTLs/genes associated with nitrogen use efficiency under abiotic stresses.
Figure 2.
Holistic breeding approach for multiple abiotic stress tolerance in rice. F = flooding, D = drought, S = salinity, QTLs = quantitative trait loci.
4. Hybrid rice production under abiotic stress
Adverse environmental conditions like abiotic factors, triggering abiotic stresses, run a key role in determining the productivity of rice yields. Biologically, abiotic stress is considered as a substantial deviation from the model environments in which plants are grown, inhibiting them from expressing their complete genetic potential regarding growth, development and reproduction [120]. Agriculture production in Bangladesh is dwindled mainly due to biotic and abiotic stresses. Abiotic stress ubiquitously affects the crop growth and development process worldwide. Hence, these are one of major areas of concern to fulfill the required food demand [121, 122]. The major abiotic stresses, drought, flooding, salinity are making the risks to food and nutritional security from tropics to temperate regions worldwide. Drought affects plants in numerous ways like it affects plant growth, yield, membrane integrity, pigment content, osmotic adjustments, water relations and photosynthetic activity [123]. Over the last three decades, the temperature of the country has increased significantly. It is estimated that by 2030, 2050 and 2100, the temperature may increase around 1, 1.4 and 2.4°C, respectively [124]. This is significant as an increased temperature reduces the yield of rice. Therefore, the country is in a risky situation in meeting future challenges concerning food security.
Bangladesh is facing salinity intrusion into the arable agricultural lands. The decline in rice yield under judiciously salt-affected soils is anticipated to be 68 percent [126]. Due to global warming, the rise in sea levels, surplus irrigation without appropriate drainage in the inland area under salt stress is growing. Flash flood and cold injury also cause rice production loss almost every year in Bangladesh. Rainfed conditions in Bangladesh are quite complex, where multiple stresses frequently prevail and even follow in quick succession within a single cropping season. Two or more abiotic stresses often coexist in many rainfed lowland and saline areas of Bangladesh. Most of the rainfed areas in Bangladesh are often occurred by multiple abiotic stresses such as flooding, drought and salinity even within the same cropping season near the coastal areas. Therefore, we need to breed new hybrid rice varieties that could tolerate more than one abiotic stress and yield high under normal favorable rainfed conditions as well.
Northern districts of Bangladesh are cold prone areas of the country. Usually, Boro (winter) rice is seriously affected by cold during the seedling and flowering stage. Seedling mortality sometimes goes up to 90%, especially in the northern part of the country. In recent years, more than 2.0 million hectares of rice crops in the cold prune area of Bangladesh have been seriously affected by extreme cold stress, causing partial to total yield loss, especially in the northern part of the country. In the haor areas of Bangladesh, early planted Boro rice has to face cold stress at the reproductive stages (Panicle initiation to flowering). If the mean temperature goes down below 20°C for more than 5-6 days during the reproductive stage of the hybrid rice plant associated with spikelet sterility, cause serious yield damage.
In particular, abiotic stresses significantly constrain rice production in Bangladesh and the frequency of these stresses is, unfortunately, likely to increase with climate change. Hybrid rice breeding programs around the world have preemptively responded by breeding stress-tolerant rice varieties. By manipulating the heritable variation present in the germplasm, we can develop abiotic stress-tolerant cultivars through breeding techniques, but it is a cumbersome and time-consuming process. The slow progress is due to the complexity of the problem involving environmental conditions and the genetic system. The development of stress-tolerant hybrid rice varieties has gained momentum among the breeders in the recent past. The development of hybrid rice with inbuilt stress tolerance is most desirable to increase the production capacity of rice under saline conditions.
Climate change has affected Bangladeshi agriculture a lot. The most pronounced effects of climate change are the heat stress, periodic drought conditions, and salinity intrusion in coastal belts due to sudden flood and flash flood in major rice-growing areas of Bangladesh. In the last couple of decades, the salinity affected area increased drastically in Bangladesh (Table 3). Due to periodic drought and saline water intrusion in the coastal belt, the already existing problem of high amounts of salts in the upper surface soil has intensified. In the future, efforts should be directed to develop climate-smart hybrid rice, which can perform stably under diverse environmental conditions. Nonetheless, China is now feeding 20 percent of the world’s population from only 10 percent of the world’s arable land where hybrid rice covers around 57 percent of the total cultivated rice area [125]. They have achieved this success by adopting research on region-based and stress-tolerant hybrid rice development. Their way of success was not so smooth, but eventually, they overcome all the obstacles. On the other hand, rice is called “the life of the people of Bangladesh.” No obvious alternative crop can replace rice presently. Initially, after the introduction of hybrid rice in Bangladesh in 1998, the area under hybrid rice cultivation significantly increased, but not up to the mark. Currently, only 7.48 percent of the total rice area is under hybrid rice cultivation in Bangladesh [126]. We have released hybrid rice for a favorable environment. It is now worldwide accepted that hybrid rice can give 15-20% more yield compared to inbred high yielding rice cultivars. Therefore, the development of abiotic stress tolerant hybrid rice is the demand of the time to sustain food security.
Years
Salinity class and salt affected area (000’ha)
Total (000’ha)
S1 (2.0–4.0 dS/m)
S2 (4.1.0–8.0 dS/m)
S3 + S4 (8.1–16.0 dS/m)
S5 (>16.0 dS/m)
1973
287.37
426.43
79.75
39.9
833.45
2000
289.76
307.20
336.58
87.14
1020.75
2009
328.43
274.22
351.69
101.92
1056.26
Table 3.
Extent of soil salinity during the last four decades (1973–2009) in coastal areas of Bangladesh.
Source: Soil Resources Development Institute (2010).
5. Future outlook and conclusions
Among the essential nutrient elements, nitrogen has a paramount importance for rice growth and development in natural ecosystems. To promote optimum N nutrition for the higher rice yield, it is important to explore the possible variability in NUE in rice genotypes. Understanding the molecular mechanisms of variable NUE in rice genotypes would help to develop NUE in the elite rice variety under abiotic stressful conditions using traditional and molecular plant breeding methods, including genome editing. Global climate change plunges world rice production toward various abiotic stress. Flooding, drought and salinity are correlated to cause problems in rice production. If rice seedlings experience flooding during the vegetative stage, they may suffer from terminal drought during the reproductive stage, depending on the ecosystems. Likewise, periodic drought conditions may upregulate the existing salinity stress through intensification of a high amount of salt layer on the upper surface soil. Therefore, there is a dire need to adopt a holistic approach to address the problems of abiotic stresses for future rice breeding. Genomics and post-genomics approaches have high potentials for dissecting underlying molecular mechanisms in differential NUE in rice genotypes. With the help of molecular mapping, fine-tuning of target QTLs, genome editing of a number of major and minor QTLs associated with abiotic stress tolerance in rice have been detected in recent years. Further enhanced research endeavors are now underway toward the development of more tolerant rice varieties to abiotic stresses. The identified QTLs are valuable resources for marker-assisted selection (MAS) to develop elite rice genotypes tolerant to flood, drought and salinity. Novel approaches are needed to apply for accelerating the mitigation of the problems of abiotic stresses in rice such as marker-assisted breeding (MAB), rapid generation advance (RGA), gene editing and transgenic technology. Attempts should be taken to develop abiotic stress-tolerant rice varieties, which can perform in a sustainable manner in a wide range of environmental conditions. Identified QTLs and rice germplasms tolerant to abiotic stresses could be explored to understand the molecular genetics of flooding, drought and salt tolerance in rice. New genes involved in abiotic stress tolerance are needed to be identified. There is a need for strategic research on molecular breeding and agronomic aspects to enhance the resilience of global rice production. To achieve these goals, capacity building of rice scientists, farmers and other stakeholders involved in developing abiotic stress-tolerant rice variety might help to increase the desired NUE in rice.
\n',keywords:"abiotic stress, crop establishment, climate change, QTLs, food security",chapterPDFUrl:"https://cdn.intechopen.com/pdfs/73418.pdf",chapterXML:"https://mts.intechopen.com/source/xml/73418.xml",downloadPdfUrl:"/chapter/pdf-download/73418",previewPdfUrl:"/chapter/pdf-preview/73418",totalDownloads:715,totalViews:0,totalCrossrefCites:0,totalDimensionsCites:1,totalAltmetricsMentions:3,impactScore:0,impactScorePercentile:30,impactScoreQuartile:2,hasAltmetrics:1,dateSubmitted:"May 27th 2020",dateReviewed:"September 15th 2020",datePrePublished:"October 15th 2020",datePublished:"March 3rd 2021",dateFinished:"October 1st 2020",readingETA:"0",abstract:"Nitrogenous fertilizer has remarkably improved rice (Oryza sativa L.) yield across the world since its discovery by Haber-Bosch process. Due to climate change, future rice production will likely experience a wide range of environmental plasticity. Nitrogen use efficiency (NUE) is an important trait to confer adaptability across various abiotic stresses such as flooding, drought and salinity. The problem with the increased N application often leads to a reduction in NUE. New solutions are needed to simultaneously increase yield and maximize the NUE of rice. Despite the differences among flooding, salinity and drought, these three abiotic stresses lead to similar responses in rice plants. To develop abiotic stress tolerant rice varieties, speed breeding seems a plausible novel approach. Approximately 22 single quantitative trait loci (QTLs) and 58 pairs of epistatic QTLs are known to be closely associated with NUE in rice. The QTLs/genes for submergence (SUB1A) tolerance, anaerobic germination (AG, TPP7) potential and deepwater flooding tolerance (SK1, SK2) are identified. Furthermore, phytochrome-interacting factor-like14 (OsPIL14), or loss of function of the slender rice1 (SLR1) genes enhance salinity tolerance in rice seedlings. This review updates our understanding of the molecular mechanisms of abiotic stress tolerance and discusses possible approaches for developing N-efficient rice variety.",reviewType:"peer-reviewed",bibtexUrl:"/chapter/bibtex/73418",risUrl:"/chapter/ris/73418",book:{id:"9669",slug:"recent-advances-in-rice-research"},signatures:"Satyen Mondal, Jamil Hasan, Priya Lal Biswas, Emam Ahmed, Tuhin Halder, Md. Panna Ali, Amina Khatun, Muhammad Nasim, Tofazzal Islam, Evangelina S. Ella and Endang M. Septiningsih",authors:[{id:"266125",title:"Prof.",name:"Tofazzal",middleName:null,surname:"Islam",fullName:"Tofazzal Islam",slug:"tofazzal-islam",email:"tofazzalislam@yahoo.com",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",institution:null},{id:"322243",title:"Dr.",name:"Satyen",middleName:null,surname:"Mondal",fullName:"Satyen Mondal",slug:"satyen-mondal",email:"satyen1981@gmail.com",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",institution:null},{id:"322253",title:"Dr.",name:"Jamil",middleName:null,surname:"Hasan",fullName:"Jamil Hasan",slug:"jamil-hasan",email:"jamilbrri@yahoo.com",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",institution:null},{id:"329440",title:"Dr.",name:"Priya Lal",middleName:null,surname:"Biswas",fullName:"Priya Lal Biswas",slug:"priya-lal-biswas",email:"priyalal.biswas@yahoo.com",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",institution:{name:"Bangladesh Rice Research Institute",institutionURL:null,country:{name:"Bangladesh"}}},{id:"329441",title:"MSc.",name:"Emam",middleName:null,surname:"Ahmed",fullName:"Emam Ahmed",slug:"emam-ahmed",email:"emam.brri@gmail.com",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",institution:{name:"Bangladesh Rice Research Institute",institutionURL:null,country:{name:"Bangladesh"}}},{id:"329442",title:"MSc.",name:"Tuhin",middleName:null,surname:"Halder",fullName:"Tuhin Halder",slug:"tuhin-halder",email:"tuhin.brri@gmail.com",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",institution:{name:"Bangladesh Rice Research Institute",institutionURL:null,country:{name:"Bangladesh"}}},{id:"329443",title:"Dr.",name:"Amina",middleName:null,surname:"Khatun",fullName:"Amina Khatun",slug:"amina-khatun",email:"aminabrri@gmail.com",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",institution:{name:"Bangladesh Rice Research Institute",institutionURL:null,country:{name:"Bangladesh"}}},{id:"329445",title:"Dr.",name:"Muhammad",middleName:null,surname:"Nasim",fullName:"Muhammad Nasim",slug:"muhammad-nasim",email:"nasimbrri@gmail.com",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",institution:{name:"Bangladesh Rice Research Institute",institutionURL:null,country:{name:"Bangladesh"}}},{id:"329448",title:"Dr.",name:"Evangelina S.",middleName:null,surname:"Ella",fullName:"Evangelina S. Ella",slug:"evangelina-s.-ella",email:"E.Ella@irri.org",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",institution:{name:"International Rice Research Institute",institutionURL:null,country:{name:"Philippines"}}},{id:"329450",title:"Dr.",name:"Md. Panna",middleName:null,surname:"Ali",fullName:"Md. Panna Ali",slug:"md.-panna-ali",email:"panna.entom@brri.gov.bd",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",institution:{name:"Bangladesh Rice Research Institute",institutionURL:null,country:{name:"Bangladesh"}}},{id:"331022",title:"Dr.",name:"Endang M.",middleName:null,surname:"Septiningsih",fullName:"Endang M. Septiningsih",slug:"endang-m.-septiningsih",email:"eseptiningsih@tamu.edu",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",institution:null}],sections:[{id:"sec_1",title:"1. Introduction",level:"1"},{id:"sec_2",title:"2. Crop establishment methods under abiotic stress",level:"1"},{id:"sec_2_2",title:"2.1 Crop establishment under flooding stress",level:"2"},{id:"sec_3_2",title:"2.2 Crop establishment under drought stress",level:"2"},{id:"sec_3_3",title:"2.2.1 Role of root to uptake water under drought",level:"3"},{id:"sec_5_2",title:"2.3 Crop establishment under salinity stress",level:"2"},{id:"sec_5_3",title:"2.3.1 Plant physiology under salinity",level:"3"},{id:"sec_6_3",title:"2.3.2 Plant anatomical change under salinity stress",level:"3"},{id:"sec_9",title:"3. QTLs and genes of nitrogen use efficiency",level:"1"},{id:"sec_10",title:"4. Hybrid rice production under abiotic stress",level:"1"},{id:"sec_11",title:"5. Future outlook and conclusions",level:"1"}],chapterReferences:[{id:"B1",body:'Murtaza G, Azooz MM, Murtaza B, Usman Y, Saqib M. Nitrogen-use-efficiency (NUE) in plants under NaCl stress. Salt Stress in Plants: Signalling, Omics and Adaptations. 2014.p. 415-437. 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Compatible solute engineering in plants for abiotic stress tolerance - role of glycine betaine. Current Genomics. 2013; 14: 157-165'},{id:"B123",body:'Benjamin JG, Nielsen DC. Water deficit effects on root distribution of soybean, field pea and chickpea. Field Crops Research. 2006; 97:248-253'},{id:"B124",body:'Amin MR, Zhang J, Yang M. Effects of climate change on the yield and cropping area of major food crops: A case of Bangladesh. Sustainability. 2015; 7:898-915. DOI: 10.3390/su7010898'},{id:"B125",body:'Yuan LP. Development of hybrid rice to ensure food security. Rice Sci. 2014; 21(1):1−2'},{id:"B126",body:'Krishi Dairy. Dhaka: Agriculture Information Services (AIS), Ministry of agriculture, the government of the people’s republic of Bangladesh; 2016'}],footnotes:[],contributors:[{corresp:"yes",contributorFullName:"Satyen Mondal",address:"satyen1981@gmail.com",affiliation:'
Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Bangladesh
'},{corresp:null,contributorFullName:"Evangelina S. Ella",address:null,affiliation:'
International Rice Research Institute, Manila, Philippines
'},{corresp:null,contributorFullName:"Endang M. Septiningsih",address:null,affiliation:'
Texas A&M University, USA
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1. Introduction
Located in the back of eyeball, the retina is a soft and transparent membrane attached to the inner surface of the choroid and forms part of the central nervous system. The retina can sense light stimuli, convert the light signals it receives into electrical signals, and then transmit them to the cerebral cortex through the optic nerve to form vision [1]. The retina is mainly composed of pigment epithelial cells, photoreceptor cells, bipolar cells, horizontal cells, amacrine cells, ganglion cells, and Müller glial cells [2]. Different neuron types form different layers, and the orderly arranged nuclei and synaptic regions are alternately arranged, forming a complex and orderly layered structure of the retina [3].
Our early research on the retina, derived only from human fetal retinal tissue [4, 5], faced significant challenges due to access difficulties and ethical issues [6]. Beyond that, most of what we know about the retina comes from studying animal retinas, but human and animal retinas differ in composition and function. For example, most mammals have only two types of cone photoreceptors that express S-opsin or M-opsin [7, 8], while humans have a third type that expresses L-opsin [9]; mice, the main subjects of our study, have a higher proportion of rods than humans [10], whose vision is determined by the density of cones in the macula and fovea [11, 12]. Therefore, it is of great significance to develop appropriate human retinal models to supplement animal models.
The establishment of human embryonic stem cell (ESC) lines [13] and the emergence of induced pluripotent stem cell (iPSC) technology [14] have turned our attention to cell research. Early 2D differentiation protocols used exogenous signaling molecules, Wnt antagonist DKK1 and bone morphogenetic protein (BMP) antagonist Noggin, to guide pluripotent stem cells to an anterior neural fate [15, 16, 17] and to differentiate into various types of retinal cells, including retinal pigment epithelial (RPE) cells, photoreceptors, and ganglion cells [18, 19, 20, 21, 22, 23, 24, 25]. However, 2D differentiation is far from interpreting retinal development in vivo. Retinal development and maturation are regulated by a series of interacting signal networks, such as factors secreted by RPE that promote photoreceptor maturation. Early retinal differentiation produced a single cell type [19, 20, 21, 22] and lacked the necessary interaction between cells. Therefore, we still need to find a more perfect model of human retina.
This breakthrough was achieved by constructing a 3D differentiation procedure. Through 3D differentiation, we can obtain retinal organoids that are highly reducible to the development process and complex structure of the retina, which we vividly call it “retina in a dish.” In this chapter, we review the development of retinal organoids and show their application in today’s life science research.
2. Overview of retinal organoids
In 2011, Sassi’s team used mouse embryonic stem cells (mESCs) to construct the first true retinal organoid through a 3D differentiation procedure [26]. In the following year, human retinal organoids were created [27], which is of epoch-making significance, meaning that human research on retinal development and retinal diseases has entered a new stage, and retinal organoids also provide a new and most potential tool for the treatment of retinal degeneration diseases.
During neurogenesis in vertebrates, the development of the retina can be roughly divided into two stages, the appearance of the optic cup structure and the orderly differentiation of seven types of retinal cells. In the first stage, the forebrain splits to form two secondary brain vesicles: telencephalon and diencephalon. In the diencephalon, eye field region first bulges outward to form the optic vesicle, and the distal vesicle invaginates to form the double-layer optic cup, which further develops into the outer retinal pigment epithelium and the inner neural retina (NR) (Figure 1a) [28, 29, 30, 31, 32]. In the second stage, the inner pluripotent retinal progenitor cells (RPCs) sequentially differentiate into retinal ganglion cells (RGCs), cone photoreceptors, horizontal cells, amacrine cells, rod photoreceptors, bipolar cells and Müller glia cells (Figure 1b) [33]. The cone and rod are connected to the retinal pigment epithelium and together form the outer nuclear layer (ONL). After extending to the outer plexiform layer (OPL), they form synapses with bipolar cells and horizontal cells in the inner nuclear layer (INL). On the other side of the inner nuclear layer, bipolar cells, amacrine cells, and ganglion cells form the synaptic networks of the inner plexiform layer (IPL). Müller glial cells span the whole layer of the retina, from the retinal pigment epithelium to the ganglion cell layer (GCL) (Figure 1c) [34, 35].
Figure 1.
Overview of retina. (a) the first stage of retinal development: The formation of double—Layer optic cup structure. (b) the second stage of retinal development: Retinal progenitor cells (RPCs) differentiate into seven types of retinal cells. (c) Structure of the retina.
Retinal development in vivo is regulated by a series of transcription factors, signal transduction factors and cell surface factors. In vitro, differentiation of retinal organoids is also a programmed process that mimics development in vivo by adding various signaling molecules in stages. First, stem cells proliferate and aggregate (Figure 2A), inducing the formation of embryoid body (EB) (Figure 2B) and neuroepithelium (Figure 2C), which appear as translucent bright rings under a microscope (Figure 2D). And then, they develop into optic vesicles (Figure 2E), followed by neuroretinas (Figure 2F), which in turn differentiate into seven types of retinal cells. The sequence of retinal cell types is consistent with in vivo development [36]. After differentiation, the cells undergo spontaneous nuclear migration, forming pinnacles and finally arranged into layered structures, in which the ganglion cells are located in the inner layer of the retinal organoid and the photoreceptors are located in the outer layer of the retinal organoid [26, 27]. Since RPE is usually a mass of cells not adjacent to the neuroretina and is not derived from the floating culture of optic vesicles, we do not consider it to be part of the retinoid organoid in this paper. With the continuous development of differentiation technology, photoreceptors in organoids become more and more mature, which is manifested by the appearance of outer segments and photosensitivity [37, 38].
Figure 2.
The differentiation of retinal organoids. (A) Growing human embryonic stem cells (H9). (B) Embryoid bodies (EB) at day 9 of differentiation. (C) Neuroepithelium appear at day 12. (D) Neuroepithelium appear as translucent bright rings at day 12. (E) Optic vesicle/cup at day 21. (F) Neural retinal (NR) region at day 26. Scale bars: 1000 μm (A, D, and E); 400 μm (B and C); 200 μm (F). All photos are provided by Dr. Ze-Hua Xu.
3. Differentiation of retinal organoids
The development of retinal organoid technology is the result of continuous attempts and innovations by a large number of researchers. Here, we try to review the progress of retinal organoids differentiation in the past ten years (Figure 3).
Figure 3.
Progress in retinal organoid differentiation over the decade.
3.1 Diversity of differentiation methods
There are various differentiation methods for retinal organoids, but in terms of differentiation steps, there are mainly two differentiation schemes (Figure 4). The first is a classic 3D differentiation protocol from Sassi’s team [26, 27]. The stem cells were dissociated and reassembled in a serum-free and low-growth factor medium (SFEBq culture, or serum-free culture of embryoid body-like aggregates with quick aggregation), and forced to form an embryoid body (EB) in a 96-well V-shaped plate. They were then stimulated by the addition of Matrigel to differentiate into neuroepithelial cells and subsequently into retinal progenitor cells and double-layer optic cup structures [27]. The cells were in suspension culture during the whole process of differentiation, and the formation of optic cups and the differentiation of neuroretina were self-organized [27]. 3D differentiation protocol is complicated in the early stage of differentiation, but it has a higher degree of reduction in the retinal development process, including the occurrence of optic cups invagination, the appearance of ciliary marginal stem cells at the NR-RPE boundary [39], and the establishment of dorsal-ventral (D-V) polarity [40].
Figure 4.
Two main methods of retinal organoid differentiation.
The second differentiation method combines 2D culture and 3D culture (2D/3D) [37, 41, 42, 43, 44, 45, 46], and the difference is mainly reflected in the early stage of neural induction. It has been reported that pluripotent stem cells can differentiate into the retina even when they are simply fused together [41, 42]. In this differentiation scheme, the stem cells were divided into small pieces by enzymatic hydrolysis [37] or mechanical methods [41, 43, 45] to form aggregates. The aggregates were cultured on a plate coated with Matrigel or floated in medium in the form of lumps of Matrigel/PSCs [43, 45]. After it differentiated into neuroepithelium and optic vesicles, the latter were separated for suspension culture and further differentiated into retinal organoids. This approach bypasses EB formation stage and induces optic vesicle formation by endogenous production of inducer molecules from aggregated cells, avoiding the aggregation step of SFEBq method and the need of Wnt/BMP antagonist [47]. These studies suggest that cell-cell and cell-extracellular matrix interactions are key to inducing retinal organoids differentiation in the early stage of stem cell differentiation.
With the improvement of differentiation methods, the structure of retinal organoids has been improved. Photoreceptors can reach advanced maturity, characterized by the formation of the inner and outer segments and connecting cilia of photoreceptors, the appearance of photosensitivity [37, 44], the expression of photoreceptor neurotransmitters, and the formation of synaptic bands [38, 44]. By adjusting the differentiation method, we can also change the proportion of cells in organoids, such as retinal organoids rich in cones or RGCs [45, 46], which is good for cell transplantation. Oxygen is also an important factor in regulating the differentiation of retinal organoids, and hypoxic conditions (5%) effectively produce vesicles and cups as well as more mature neuroretinas [48]. Another study showed that high oxygen (40%) promoted the formation of NR in EB, as well as the generation, migration and maturation of retinal ganglion cells during metaphase differentiation [49]. The co-culture of RPE with retinal organoids promoted the differentiation of photoreceptors [50], while the co-culture with brain organoids promoted the axon extension of RGCs [51]. More encouragingly, researchers have differentiated human brain organoids with bilaterally symmetric vesicles [52].
3.2 Modulation of signaling molecules
Retinal development requires the regulation of a series of signaling molecules. Similarly, by adding different signaling molecules, retinal organoids differentiation can be regulated in vitro. Dickkopf-related protein 1 (DKK-1), a Wnt signaling pathway antagonist, salvages the self-organizing ability of stem cells to differentiate into retinal progenitor cells [53]. Insulin-like growth factor 1 (IGF-1) regulates the formation of retinal organoids and promotes the formation of the correct retinal lamellar structure by various retinal cells [54, 55]. In the absence of IGF-1, retinal lamination was absent at the early stage of differentiation, while photoreceptors decreased and retinal ganglion cells increased at the late stage of differentiation [55]. Addition of docosahexaenoic acid and fibroblast growth factor 1 can specifically promote the maturation of photoreceptors including cones [56]. Replacement of widely used all-trans retinoic acid with 9-cis-retinoic acid in culture medium promoted the expression of rod photoreceptors rhodopsin and the maturation of mitochondrial morphology [57, 58]. COCO protein can block BMP/TGFβ/Wnt signaling pathway, enhance photoreceptor precursors, and promote s-cone differentiation and inner segment protuberances formation [59, 60]. During retinal development, s-cone appear first, followed by L/M-cones. This time transition from the designation of the s-cone to the production of the L/M-cone is controlled by thyroid hormone (TH) signaling [61].
3.3 Combination of organoid technology and tissue engineering technology
There is also a lot of innovative research that combines retinal organoid technology with emerging materials technology. The use of bioreactors improved retinal stratification and increased the production of photoreceptors with cilia and new outer segments [62]. In static culture, the development of retinal organoids may be limited by oxygen and nutrient diffusion, and rotating-wall vessel (RWV) bioreactors can accelerate and improve the growth and differentiation of retinal organoids [63]. The spherical structure of retinal organoids limits its interaction with host RPE and the remaining neuroretinas during transplantation. In order to create a planar retinal organoid, a biodegradable scaffold was developed that mimics the extracellular matrix of neuroretinas [64]. Retina-on-a-chip is a new microphysiological model of the human retina that integrates seven different basic retinal cell types and provides vascular-like perfusion to retinal organoids [65]. Arrayed bottom-lined micropores composed of bionic hydrogels, facilitated rapid retinoid tissue formation from mESCs aggregates in an efficient and routine manner [66]. Automated microfluidic devices with significantly reduced shear stress can maintain the long-term survival of retinal organoids [67]. For details of some other differentiation improvements [68, 69, 70, 71], please refer to Figure 3.
4. Applications of retinal organoids
As a three-dimensional multicellular structure formed by self-organization in vitro, retinal organoids can reproduce the development process of retina in vivo to some extent, and can be used to summarize some structural and functional characteristics of human retina. Meanwhile, they are the most promising tools for retinal disease research (Figure 5).
Figure 5.
Applications of retinal organoids.
4.1 Retinal organoids as disease models
The reprogramming technique enables iPSCs-derived retinal organoids to retain the patient’s genetic characteristics, allowing us to study a variety of retinal diseases in detail in a dish. To date, retinitis pigmentosa (RP), Laber congenital amaurosis (LCA), retinoblastoma (RB) and some other retinal diseases (Table 1) have been reproduced in dishes using retinal organoid technology [47, 98].
Photoreceptors have significant defects in morphology, localization, transcription profile and electrophysiological activity; shorted cilium was found in patient retinal organoids
Reduced levels of full-length TRNT1 protein and expression of a truncated smaller protein; autophagy was defective, with abnormal accumulation of LC3-II and elevated oxidative stress levels
Two distinct populations of s-opsin expressing photoreceptors emerge; one population more representative of typical cones, and the other of rod/cone intermediates
RP is a relatively common hereditary retinal disorder characterized by night blindness and progressive loss of visual field [99]. LCA, the main disease leading to congenital blindness in infants, accounts for more than 5% of hereditary retinopathy, with complete loss of binocular cone and rod function within 1 year after birth [100]. Both diseases have been reported to be associated with multiple pathogenic genes. By differentiating different genetically-mutated stem cell lines into retinal organoids [101], we can observe their disease phenotypes in dishes, including photoreceptor degeneration, ciliary morphology disorder, and various functional impairment at molecular levels. Retinoblastoma is the most common intraocular malignancy in children [102]. The main cause of retinoblastoma is the loss of RB1 gene expression [103]. RB1 gene is a tumor suppressor gene, but the mechanism of RB1 deletion leading to retinal cancer is not clear, one of the key questions is the origin of RB cancer. By constructing RB models based on retinal organoids [104], we successfully observed tumorigenesis in retinal organoids and demonstrated that RB originates from ARR3 positive precursors of mature cones during development [90]. Other disease models, such as s-cone syndrome, rod-cone dystrophy, Macular telangiectasia type 2, microphthalmia, Stargardt disease, X-linked juvenile cleft retina, have also contributed to our understanding of retinal diseases.
4.2 Retinal organoids as tools for therapeutic research
4.2.1 Gene therapy
Identification of pathogenic genes promotes the generation of animal models and elucidates the physiological functions of gene products to a certain extent, thus promoting the development of gene therapy. So far, most research has focused on saving retinal organoid disease phenotypes through gene editing of patient-specific induced pluripotent stem cells [72, 73, 87, 97, 105, 106]. However, this strategy cannot be applied to patients. Adeno-associated virus (AAV) show great promise as a gene therapy vector for a wide range of retinal diseases. For example, AAV-mediated gene augmentation has successfully treated LCA caused by RPE65 mutations [107]. AAV-mediated gene therapy based on retinal organoids has also shown promising results in the laboratory [81, 82, 108]. In addition, gene therapies such as antisense morpholino and antisense oligonucleotides (AONs) have also been reported (Table 2).
ROs
Gene therapy
Result
Reference
CEP290-LCA-Optic Cups
Antisense morpholino
Effectively blocked aberrant splicing and restored expression of full-length CEP290, restoring normal cilia-based protein trafficking
Hereditary retinal degenerative diseases such as RP, Stargardt’s disease and LCA are the leading cause of incurable blindness. The vision loss associated with these diseases is caused by the death of photoreceptors in the retina. Existing treatments, including neuroprotection and gene therapy, require the presence of endogenous photoreceptors. In addition, due to the complex mechanism of retinal degeneration diseases, especially RP, it has been found that there are multiple genes with multiple mutation modes, and treatment methods focusing on a single mutation are extremely difficult technically and economically. Thus, transplant-based photoreceptor cell replacement becomes an attractive therapeutic strategy for restoring visual function and, if successful, could be applied to a wide range of retinal degenerative diseases.
Research on retinal cell transplantation dates back to 2006 [109]. Mice were able to effectively integrate rod photoreceptor precursor cells isolated from juvenile mice retinas into the ONL. These cells can further differentiate in the host retina and exhibit morphological characteristics typical of mature photoreceptors, such as inner and outer segments, while expressing molecules necessary for light transduction, forming synaptic connections with downstream cells, generating light responses and promoting visual function [109, 110, 111, 112, 113, 114, 115]. These results demonstrate the feasibility of photoreceptor transplantation as a therapeutic strategy for restoring visual acuity after retinal degeneration.
However, this cannot be applied to the treatment of retinal diseases in humans. There are ethical challenges to primary photoreceptors transplantation, but stem cell-based photoreceptors can avoid this problem. It has been shown that photoreceptor cells derived from stem cells can be integrated into mouse retinas, restoring the animal’s response to light [116, 117]. This is far from enough, until the appearance of retinal organoids, retinal cell transplantation and clinical transformation have made a breakthrough.
Transplantation of retinal organoids, mainly photoreceptors, is also a process of constant exploration [118]. The safety and effectiveness of transplantation, the enrichment and purification of transplanted cells, the effects of retinal organoids at different stages of development and host retinas with different degrees of degeneration on the efficiency of transplantation, and the evaluation of cell integration and function after transplantation are all issues that need to be explored.
Table 3 gives a brief summary of some retinal organoid transplantation cases in recent years. There are two transplantation methods: one is to digest the retinal organ into a single cell, from which the photoreceptor cells are purified and enriched, and the transplantation is carried out in the form of cell suspension. Another method is to strip the photoreceptor layer from the retinal organ and transplant it in thin slices. This method is more difficult to operate, because it is difficult to maintain the correct shape and polarity of the retina when it is transplanted into the eye of the host, and appropriate transplantation instruments need to be designed. The implant may contain some interneurons that block the connection between photoreceptor cells and the remaining inner layer of the retina in the host, and there are eye size requirements in the host animal. The implant is usually performed in rats, cats and non-human primates. In general, we have gained a lot from the exploration of retinal organ transplantation. A number of studies have shown that transplanted cells or tissues can survive in the host eye for a long time, migrate and integrate into the correct location. Integrated cells can further differentiate and mature in vivo, presenting typical cell structures, such as internal and external segments, and expressing corresponding cell markers and synaptic markers. In some studies, the formation of synaptic connections between host and graft and improvement of host visual function were also observed. In the host, transplanted cells or tissues are electrically excitatory [136], indicating their potential for restoring visual function. Through behavioral and electrophysiological experiments, we found that the host can not only slow down the progressive visual loss to some extent, but also show a relatively significant recovery of visual function [127, 130, 131, 134, 135, 137, 138]. These are exciting results and suggest that cell replacement therapy based on retinal organoids is a promising treatment that will bring light to patients with retinal diseases.
Graft/Host
Transplantation method
Transplantation result
Reference
Rhodopsin-GFP-mESC-ROs-rod precursors/adult mice with retinal degeneration
Cell suspension
Transplanted cells integrate within the degenerated retinas of mice and mature into outer segment-bearing photoreceptors
Transplanted retinal tissue differentiated into a series of retinal cell types, including rod and cone photoreceptors that formed structured outer nuclear layers; formation of host-graft synaptic connections
hESC-ROs-retinal sheets /mice of end-stage retinal degeneration with immunodeficiency
Retinal tissue
Long-term survival and well-structured graft photoreceptor layer maturation without rejection or tumor formation; formation of host-graft synaptic connections
hESC-ROs(30–65 days of differentiation)-retinal sheets/immunodeficient rho S334ter-3 rats
Retinal tissue
The transplanted sheets differentiated, integrated, and produced functional photoreceptors and other retinal cells; maturation of the transplanted retinal cells created visual improvements; the donor cells were synaptically active
CD73+ photoreceptor precursors can be isolated in large numbers and transplanted into rat eyes, showing capacity to survive and mature in close proximity to host inner retina (hiPSC-derived retinal cells did not appear to migrate to host ONL)
The CRX+ cells settled next to the inner nuclear layer and made connections with the inner neurons of the host retina, and approximately one-third of them expressed the pan cone marker, Arrestin 3, indicating further maturation upon integration into the host retina
The transplanted organoids survived more than 7 months; developed photoreceptors with inner and outer segments, and other retinal cells; and were well-integrated within the host
hiPSC-ROs-retinal sheets with PLGA scaffolds/rhesus monkey
Retinal tissue
With sufficient graft-host contact provided by the scaffold, the transplanted tissues survived for up to 1 year without tumorigenesis; Histological examinations indicated survival, further maturation, and migration
mESC-ROs-retinal progenitor cells (RPC)/mice with retinal degeneration
Cell suspension
RPC grafts form active synaptic networks within sites of ADR that functionally integrate with the retinal neuron populations and that resemble physiological patterns of neural circuits to the normal retina
Drug development focuses on screening, a process that requires cell models. The closer the cell model was to the physiological state, the more accurate the screening was. Therefore, organoids are undoubtedly a better choice for drug screening. Some ocular supplements, vitamin E, lutein, astaxanthin, and anthocyanin, have been reported to protect retinal photoreceptor degeneration induced by 4-hydroxytamoxifen (4-OHT) and light [139]. Few studies have successfully screened effective drugs using retinal organoids. In addition, there are some studies using retinal organoids as screening tools to explore the membrane transport effects of some microbial opsin [140]. These results suggest that retinal organoids can be used to validate the effectiveness of some therapeutic products and drug molecules.
5. Limitations and deficiencies
In recent years, although the technology of retinal organoids has made great progress, it is still beyond the reach of our existing tools and technologies to construct retinal organoids with the same structure and physiological functions as the mature retina in vivo. Our research on retinal organoids is still in its infancy and there are some limitations to overcome.
Long-term maintenance of retinal organoids depends on oxygen and nutrients, and in our existing culture system, oxygen diffusion limits the size of retinal organoids and the development of their internal cells, especially ganglion cells. Currently, we are trying to introduce a combination of tissue engineering techniques to solve this problem, such as the use of bioreactors and retinal chips [62, 63, 65]. The absence of vascular system also limits the long-term maintenance of organoids. Microglia are the resident immune cells of the central nervous system and are particularly important for the development of the retina, which can regulate the survival of neurons and prune synapses [141]. Co-differentiation of retinal organoids and vascular tissues or microglia in a dish is challenging because they come from different germ layers. The retina develops from the ectoderm, while vascular tissue-associated cells and microglia originate from the mesoderm. Therefore, we usually choose to achieve the complexity of retinal organoids through co-culture. In recent years, the realization of vascular structure in human brain has made some progress. After transplantation of human cerebral organs into the cerebral cortex of mice, the growth of blood vessels in mice was induced to increase the survival and maturation of cells [142]. In vitro, a study found that ectopic expression of human ETS variant 2 (ETV2) in hESCs can form a complex vascular-like network in human cortical organs and promote the maturation of organoid function [143]. In the future, we also expect that 3D printing of vascular tissue [144] and co-culture with mesodermal progenitor cells [145] will make the differentiation system of retinal organoids more perfect. For the retina in a petri dish to function, the most important point is to establish synaptic connections and form functional circuits. While our differentiated retina can form synaptic connections now, it’s not nearly as good as the complex network of synapses in the retina in vivo. Even retinal organoids derived from normal stem cell lines respond poorly to light. This may be due to the gradual degeneration of ganglion cells during late differentiation and lack of connection to the brain, which hindrance our assessment of retinal functional circuits. It may also be associated with limited growth of the outer segment due to the lack of direct interaction with RPE. Retinal organoid technology has solved the problem of cell-cell interaction, but in organisms, tissue-to-tissue and organ-to-organ interactions remain important for development. For example, the relationship of the retina to the lens, ciliary body and cornea, and the relationship of the retina to the brain.
6. Conclusions
It’s an exciting time, and technological advances have made a lot of things possible. Retinal organoids are our research tools for overcoming retinal diseases. It allows us to further understand the development and maturation of the retina, reproduce disease pathology and phenotypes in vitro, and explore the feasibility of gene therapy. In addition, it provides us with cells for cell transplantation and drug screening. We have enjoyed the great benefits brought by retinal organoids. However, their defects and deficiencies are also prominent, which is the direction we need to work towards. There is still a long way to go in the development of retinal organoids, and we expect that technological breakthroughs will enable us to advance to the next level in this field in the future.
Acknowledgments
We thank Dr. Ze-Hua Xu for providing photos of retinal organoid differentiation.
\n',keywords:"retinal organoids, retinal differentiation, disease models, retinal degenerative diseases, transplant",chapterPDFUrl:"https://cdn.intechopen.com/pdfs/81318.pdf",chapterXML:"https://mts.intechopen.com/source/xml/81318.xml",downloadPdfUrl:"/chapter/pdf-download/81318",previewPdfUrl:"/chapter/pdf-preview/81318",totalDownloads:38,totalViews:0,totalCrossrefCites:0,dateSubmitted:"January 29th 2022",dateReviewed:"March 4th 2022",datePrePublished:"April 16th 2022",datePublished:null,dateFinished:"April 16th 2022",readingETA:"0",abstract:"Retinal organoids (ROs) are 3D tissue structures derived from embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs) in vitro, which characterize the structure and function of retina to a certain extent. Since 2011, mouse and human retinal organoids have been available, opening up new avenues for retinal development, disease and regeneration research. Over the decade, great progress has been made in the development of retinal organoids, which is reflected in the improvement of differentiation efficiency and development degree. At the same time, retinal organoids also show broad application prospects, which are widely used in the construction of disease models. On this basis, the mechanism of disease, drug screening and retinal regeneration therapy have been explored. Although retinal organoids have a bright future, the deficiency of their structure and function, the limitations of differentiation and culture, and the difference compared with embryonic retina still remain to be solved.",reviewType:"peer-reviewed",bibtexUrl:"/chapter/bibtex/81318",risUrl:"/chapter/ris/81318",signatures:"Jing Yuan and Zi-Bing Jin",book:{id:"11430",type:"book",title:"Organoids",subtitle:null,fullTitle:"Organoids",slug:null,publishedDate:null,bookSignature:"Assistant Prof. Manash K. Paul",coverURL:"https://cdn.intechopen.com/books/images_new/11430.jpg",licenceType:"CC BY 3.0",editedByType:null,isbn:"978-1-80355-769-4",printIsbn:"978-1-80355-768-7",pdfIsbn:"978-1-80355-770-0",isAvailableForWebshopOrdering:!0,editors:[{id:"319365",title:"Assistant Prof.",name:"Manash K.",middleName:null,surname:"Paul",slug:"manash-k.-paul",fullName:"Manash K. Paul"}],productType:{id:"1",title:"Edited Volume",chapterContentType:"chapter",authoredCaption:"Edited by"}},authors:null,sections:[{id:"sec_1",title:"1. Introduction",level:"1"},{id:"sec_2",title:"2. Overview of retinal organoids",level:"1"},{id:"sec_3",title:"3. Differentiation of retinal organoids",level:"1"},{id:"sec_3_2",title:"3.1 Diversity of differentiation methods",level:"2"},{id:"sec_4_2",title:"3.2 Modulation of signaling molecules",level:"2"},{id:"sec_5_2",title:"3.3 Combination of organoid technology and tissue engineering technology",level:"2"},{id:"sec_7",title:"4. Applications of retinal organoids",level:"1"},{id:"sec_7_2",title:"4.1 Retinal organoids as disease models",level:"2"},{id:"sec_8_2",title:"4.2 Retinal organoids as tools for therapeutic research",level:"2"},{id:"sec_8_3",title:"Table 2.",level:"3"},{id:"sec_9_3",title:"Table 3.",level:"3"},{id:"sec_11_2",title:"4.3 Retinal organoids for drug screening",level:"2"},{id:"sec_13",title:"5. Limitations and deficiencies",level:"1"},{id:"sec_14",title:"6. Conclusions",level:"1"},{id:"sec_15",title:"Acknowledgments",level:"1"}],chapterReferences:[{id:"B1",body:'Demb JB, Singer JH. Functional circuitry of the retina. Annual Review of Vision Science. 2015;1:263-289. DOI: 10.1146/annurev-vision-082114-035334'},{id:"B2",body:'Reese BE. Development of the retina and optic pathway. Vision Research. 2011;51:613-632. DOI: 10.1016/j.visres.2010.07.010'},{id:"B3",body:'Masland RH. The neuronal organization of the retina. Neuron. 2012;76:266-280. 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Retinal cells integrate into the outer nuclear layer and differentiate into mature photoreceptors after subretinal transplantation into adult mice. Experimental Eye Research. 2008;86:691-700. DOI: 10.1016/j.exer.2008.01.018'},{id:"B111",body:'Lakowski J, Baron M, Bainbridge J, Barber AC, Pearson RA, Ali RR, et al. Cone and rod photoreceptor transplantation in models of the childhood retinopathy Leber congenital amaurosis using flow-sorted Crx-positive donor cells. Human Molecular Genetics. 2010;19:4545-4559. DOI: 10.1093/hmg/ddq378'},{id:"B112",body:'Eberle D, Schubert S, Postel K, Corbeil D, Ader M. Increased integration of transplanted CD73-positive photoreceptor precursors into adult mouse retina. Investigative Ophthalmology & Visual Science. 2011;52:6462-6471. DOI: 10.1167/iovs.11-7399'},{id:"B113",body:'Pearson RA, Barber AC, Rizzi M, Hippert C, Xue T, West EL, et al. Restoration of vision after transplantation of photoreceptors. Nature. 2012;485:99-103. 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Defining the integration capacity of embryonic stem cell-derived photoreceptor precursors. Stem Cells. 2012;30:1424-1435. DOI: 10.1002/stem.1123'},{id:"B118",body:'Jin ZB, Gao ML, Deng WL, Wu KC, Sugita S, Mandai M, et al. Stemming retinal regeneration with pluripotent stem cells. Progress in Retinal and Eye Research. 2019;69:38-56. DOI: 10.1016/j.preteyeres.2018.11.003'},{id:"B119",body:'Gonzalez-Cordero A, West EL, Pearson RA, Duran Y, Carvalho LS, Chu CJ, et al. Photoreceptor precursors derived from three-dimensional embryonic stem cell cultures integrate and mature within adult degenerate retina. Nature Biotechnology. 2013;31:741-747. DOI: 10.1038/nbt.2643'},{id:"B120",body:'Decembrini S, Koch U, Radtke F, Moulin A, Arsenijevic Y. Derivation of traceable and transplantable photoreceptors from mouse embryonic stem cells. Stem Cell Reports. 2014;2:853-865. DOI: 10.1016/j.stemcr.2014.04.010'},{id:"B121",body:'Assawachananont J, Mandai M, Okamoto S, Yamada C, Eiraku M, Yonemura S, et al. Transplantation of embryonic and induced pluripotent stem cell-derived 3D retinal sheets into retinal degenerative mice. Stem Cell Reports. 2014;2:662-674. DOI: 10.1016/j.stemcr.2014.03.011'},{id:"B122",body:'Shirai H, Mandai M, Matsushita K, Kuwahara A, Yonemura S, Nakano T, et al. Transplantation of human embryonic stem cell-derived retinal tissue in two primate models of retinal degeneration. Proceedings of the National Academy of Sciences of the United States of America. 2016;113:E81-E90. DOI: 10.1073/pnas.1512590113'},{id:"B123",body:'Santos-Ferreira T, Volkner M, Borsch O, Haas J, Cimalla P, Vasudevan P, et al. Stem cell-derived photoreceptor transplants differentially integrate into mouse models of cone-rod dystrophy. Investigative Ophthalmology & Visual Science. 2016;57:3509-3520. DOI: 10.1167/iovs.16-19087'},{id:"B124",body:'Kruczek K, Gonzalez-Cordero A, Goh D, Naeem A, Jonikas M, Blackford SJI, et al. Differentiation and transplantation of embryonic stem cell-derived cone photoreceptors into a mouse model of end-stage retinal degeneration. Stem Cell Reports. 2017;8:1659-1674. DOI: 10.1016/j.stemcr.2017.04.030'},{id:"B125",body:'Zhu J, Reynolds J, Garcia T, Cifuentes H, Chew S, Zeng X, et al. Generation of transplantable retinal photoreceptors from a current good manufacturing practice-manufactured human induced pluripotent stem cell line. Stem Cells Translational Medicine. 2018;7:210-219. DOI: 10.1002/sctm.17-0205'},{id:"B126",body:'Iraha S, Tu HY, Yamasaki S, Kagawa T, Goto M, Takahashi R, et al. Establishment of Immunodeficient retinal degeneration model mice and functional maturation of human ESC-derived retinal sheets after transplantation. Stem Cell Reports. 2018;10:1059-1074. DOI: 10.1016/j.stemcr.2018.01.032'},{id:"B127",body:'McLelland BT, Lin B, Mathur A, Aramant RB, Thomas BB, Nistor G, et al. Transplanted hESC-derived retina organoid sheets differentiate, integrate, and improve visual function in retinal degenerate rats. Investigative Ophthalmology & Visual Science. 2018;59:2586-2603. DOI: 10.1167/iovs.17-23646'},{id:"B128",body:'Gagliardi G, Ben M’Barek K, Chaffiol A, Slembrouck-Brec A, Conart JB, Nanteau C, et al. Characterization and transplantation of CD73-positive photoreceptors isolated from human iPSC-derived retinal organoids. Stem Cell Reports. 2018;11:665-680. DOI: 10.1016/j.stemcr.2018.07.005'},{id:"B129",body:'Collin J, Zerti D, Queen R, Santos-Ferreira T, Bauer R, Coxhead J, et al. CRX expression in pluripotent stem cell-derived photoreceptors Marks a transplantable subpopulation of early cones. Stem Cells. 2019;37:609-622. DOI: 10.1002/stem.2974'},{id:"B130",body:'Zou T, Gao L, Zeng Y, Li Q , Li Y, Chen S, et al. Organoid-derived C-kit (+)/SSEA4(−) human retinal progenitor cells promote a protective retinal microenvironment during transplantation in rodents. Nature Communications. 2019;10:1205. DOI: 10.1038/s41467-019-08961-0'},{id:"B131",body:'Garita-Hernandez M, Lampic M, Chaffiol A, Guibbal L, Routet F, Santos-Ferreira T, et al. Restoration of visual function by transplantation of optogenetically engineered photoreceptors. Nature Communications. 2019;10:4524. DOI: 10.1038/s41467-019-12330-2'},{id:"B132",body:'Eastlake K, Wang W, Jayaram H, Murray-Dunning C, Carr AJF, Ramsden CM, et al. Phenotypic and functional characterization of Muller glia isolated from induced pluripotent stem cell-derived retinal organoids: Improvement of retinal ganglion cell function upon transplantation. Stem Cells Translational Medicine. 2019;8:775-784. DOI: 10.1002/sctm.18-0263'},{id:"B133",body:'Singh RK, Occelli LM, Binette F, Petersen-Jones SM, Nasonkin IO. Transplantation of human embryonic stem cell-derived retinal tissue in the subretinal space of the cat eye. Stem Cells and Development. 2019;28:1151-1166. DOI: 10.1089/scd.2019.0090'},{id:"B134",body:'Lin B, McLelland BT, Aramant RB, Thomas BB, Nistor G, Keirstead HS, et al. Retina organoid transplants develop photoreceptors and improve visual function in RCS rats with RPE dysfunction. Investigative Ophthalmology & Visual Science. 2020;61:34. DOI: 10.1167/iovs.61.11.34'},{id:"B135",body:'Ribeiro J, Procyk CA, West EL, O’Hara-Wright M, Martins MF, Khorasani MM, et al. Restoration of visual function in advanced disease after transplantation of purified human pluripotent stem cell-derived cone photoreceptors. Cell Reports. 2021;35:109022. DOI: 10.1016/j.celrep.2021.109022'},{id:"B136",body:'Luo Z, Xian B, Li K, Li K, Yang R, Chen M, et al. Biodegradable scaffolds facilitate epiretinal transplantation of hiPSC-derived retinal neurons in nonhuman primates. Acta Biomaterialia. 2021;134:289-301. DOI: 10.1016/j.actbio.2021.07.040'},{id:"B137",body:'He XY, Zhao CJ, Xu H, Chen K, Bian BS, Gong Y, et al. Synaptic repair and vision restoration in advanced degenerating eyes by transplantation of retinal progenitor cells. Stem Cell Reports. 2021;16:1805-1817. DOI: 10.1016/j.stemcr.2021.06.002'},{id:"B138",body:'Thomas BB, Lin B, Martinez-Camarillo JC, Zhu D, McLelland BT, Nistor G, et al. Co-grafts of human embryonic stem cell derived retina organoids and retinal pigment epithelium for retinal reconstruction in Immunodeficient retinal degenerate Royal College of surgeons rats. Frontiers in Neuroscience. 2021;15:752958. DOI: 10.3389/fnins.2021.752958'},{id:"B139",body:'Ito SI, Onishi A, Takahashi M. Chemically-induced photoreceptor degeneration and protection in mouse iPSC-derived three-dimensional retinal organoids. Stem Cell Research. 2017;24:94-101. DOI: 10.1016/j.scr.2017.08.018'},{id:"B140",body:'Garita-Hernandez M, Guibbal L, Toualbi L, Routet F, Chaffiol A, Winckler C, et al. Optogenetic light sensors in human retinal organoids. Frontiers in Neuroscience. 2018;12:789. DOI: 10.3389/fnins.2018.00789'},{id:"B141",body:'Rathnasamy G, Foulds WS, Ling E-A, Kaur C. Retinal microglia—A key player in healthy and diseased retina. Progress in Neurobiology. 2019;173:18-40'},{id:"B142",body:'Mansour AA, Gonçalves JT, Bloyd CW, Li H, Fernandes S, Quang D, et al. An in vivo model of functional and vascularized human brain organoids. Nature Biotechnology. 2018;36:432-441'},{id:"B143",body:'Cakir B, Xiang Y, Tanaka Y, Kural MH, Parent M, Kang Y-J, et al. Engineering of human brain organoids with a functional vascular-like system. Nature Methods. 2019;16:1169-1175'},{id:"B144",body:'Richards D, Jia J, Yost M, Markwald R, Mei Y. 3D bioprinting for vascularized tissue fabrication. Annals of Biomedical Engineering. 2017;45:132-147. DOI: 10.1007/s10439-016-1653-z'},{id:"B145",body:'Worsdorfer P, Dalda N, Kern A, Kruger S, Wagner N, Kwok CK, et al. Generation of complex human organoid models including vascular networks by incorporation of mesodermal progenitor cells. Scientific Reports. 2019;9:15663. DOI: 10.1038/s41598-019-52204-7'}],footnotes:[],contributors:[{corresp:null,contributorFullName:"Jing Yuan",address:null,affiliation:'
Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Laboratory, Beijing, China
Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Science Key Laboratory, Beijing, China
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His interests include tomography, digital signal processing and instrumentation for metrology and imaging. He is a fellow of the Software Sustainability Institute, promoting best-practices for embedded software and signal processing firmware. While his current work focuses on logic synthesis for FPGAs, he developed an all-digital array of single-photon avalanche diodes (SPADs) with a readout suitable for optical communications or metrology as a direct optical to digital converter. He has recently completed a historical analysis of avalanche multiplication and the internal photoelectric effect covering the period 1900 to 1969. 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ASICs can provide us with high-speed computation in the case of digital circuits. For example, central processing units, graphics processing units, field-programmable gate arrays, and custom-made digital signal processors are examples of ASICs and the transistors they are fabricated from. We can use that same technology—complementary metal-oxide semiconductor processes—to implement high-precision sensing of or interfacing to the world through analog-to-digital converters, digital-to-analog converters, custom image sensors, and highly integrated micron-scale sensors such as magnetometers, accelerometers, and microelectromechanical machines. ASIC technologies—now transitioning toward magneto-resistive and phase-changing materials—also offer digital memory capacities that have aided our technological progress. Combining these domains, we have moved toward big data analytics and the new era of artificial intelligence and machine learning. 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To achieve this, single-photon avalanche diodes (SPADs) can be implemented in complementary metal-oxide-semiconductor (CMOS) technologies and have already been investigated in several topologies for VLC. The digital nature of SPADs removes the design effort used for low-noise, high-gain but high-bandwidth analogue circuits. We therefore present one of these circuit topologies, along with some common design and performance metrics. 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In this chapter, the nature of the photon is discussed along with what physical mechanisms allow detection of single-photons using solid-state semiconductor-based technologies. By restricting the scope of this chapter to near-infrared, visible and near-ultraviolet detection we can focus upon the internal photoelectric effect. Likewise, by concentrating on single-photon semiconductor detectors, we can focus upon the carrier-multiplication gain that has allowed sensitivity to approach the single-photon level. This chapter and the references herein aim to provide a historical account and full literature review of key, early developments in the history of photodiodes (PDs), avalanche photodiodes (APDs), single-photon avalanche diodes (SPADs), other Geiger-mode avalanche photodiodes (GM-APDs) and silicon photo-multipliers (Si-PMs). As there are overlaps with the historical development of the transistor (1940s), we find that development of the p-n junction and the observation of noise from distinct crystal lattice or doping imperfections – called “microplasmas” – were catalysts for innovation. The study of microplasmas, and later dedicated structures acting as known-area, uniform-breakdown artificial microplasmas, allowed the avalanche gain mechanism to be observed, studied and utilised.",signatures:"Edward M.D. Fisher",authors:[{id:"199505",title:"Dr.",name:"Edward",surname:"Fisher",fullName:"Edward Fisher",slug:"edward-fisher",email:"emd.fisher@gmail.com"}],book:{id:"6286",title:"Photon Counting",slug:"photon-counting-fundamentals-and-applications",productType:{id:"1",title:"Edited Volume"}}},{id:"65560",title:"Introductory Chapter: ASIC Technologies and Design Techniques",slug:"introductory-chapter-asic-technologies-and-design-techniques",abstract:null,signatures:"Edward M.D. Fisher",authors:[{id:"199505",title:"Dr.",name:"Edward",surname:"Fisher",fullName:"Edward Fisher",slug:"edward-fisher",email:"emd.fisher@gmail.com"}],book:{id:"7189",title:"Application Specific Integrated Circuits",slug:"application-specific-integrated-circuits-technologies-digital-systems-and-design-methodologies",productType:{id:"1",title:"Edited Volume"}}}],collaborators:[{id:"111050",title:"Prof.",name:"Mohamed",surname:"Himdi",slug:"mohamed-himdi",fullName:"Mohamed Himdi",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",biography:null,institutionString:null,institution:{name:"Institute of Electronics and Telecommunications of Rennes",institutionURL:null,country:{name:"France"}}},{id:"190463",title:"Ph.D. Student",name:"Waleed",surname:"Sethi",slug:"waleed-sethi",fullName:"Waleed Sethi",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",biography:null,institutionString:null,institution:{name:"King Saud University",institutionURL:null,country:{name:"Saudi Arabia"}}},{id:"202731",title:"Dr.",name:"Hamsakutty",surname:"Vettikalladi",slug:"hamsakutty-vettikalladi",fullName:"Hamsakutty Vettikalladi",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",biography:null,institutionString:null,institution:null},{id:"202732",title:"Dr.",name:"Habib",surname:"Fathallah",slug:"habib-fathallah",fullName:"Habib Fathallah",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",biography:null,institutionString:null,institution:null},{id:"205656",title:"Dr.",name:"Ali",surname:"Shahpari",slug:"ali-shahpari",fullName:"Ali Shahpari",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",biography:null,institutionString:null,institution:null},{id:"208236",title:"Dr.",name:"Isiaka",surname:"Alimi",slug:"isiaka-alimi",fullName:"Isiaka Alimi",position:null,profilePictureURL:"https://mts.intechopen.com/storage/users/208236/images/system/208236.jpg",biography:"Isiaka A. Alimi received his Ph.D. in Telecommunications Engineering from the University of Aveiro, Portugal. He was with the Federal Radio Corporation of Nigeria as a senior engineer (RF transmission and management) and the Department of Electrical and Electronics Engineering, Federal University of Technology, Akure, Nigeria, as a lecturer. He is currently a researcher at the Instituto de Telecomunicações, Aveiro, Portugal, where he has been participating in various R&D activities. He has authored/co-authored more than forty technical papers, nine book chapters, and has co-edited one book. His research interests include optical communications, microwave photonics, network security, fixed-mobile broadband (wired and wireless technologies) convergence, and their applications for effective resources management in access networks. 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Monteiro obtained the “Licenciatura” diploma in Electronics and Telecommunications Engineering at the University of Aveiro in 1988. In 1990, he obtained his M.Sc. diploma in Electronic Engineering from the University of Wales UK, and his Ph.D. in Electrical Engineering, at the University of Aveiro, in 1999. Presently, he is an Associate Professor at the University of Aveiro and a Senior Researcher at the Instituto de Telecomunicações. His main research interests include Optical Communication Networks and Microwave Photonics. He tutored and co-tutored successfully more than 14 Ph.D.’s, having participated in more than 28 research projects (national and international). He has authored/co-authored more than 18 patent applications and over 110 papers in journals and 380 conference contributions. 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Since 2014, he has been the dean of the Doctoral School, University of Aveiro. Dr. Teixeira has worked at several industrial organizations, including Nokia Siemens Networks, Coriant, and PICadvanced, a startup in photonics that he cofounded that employs more than forty highly skilled persons. He holds eleven patents and has published more than 400 papers. He has supervised more than seventy MSc and fifteen Ph.D. students and has participated in more than thirty-five national and international projects.",institutionString:"Universidade de Aveiro",institution:null}]},generic:{page:{slug:"open-access-funding",title:"Open Access Funding",intro:"
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Please note that this list is not a definitive one and is updated regularly. To suggest possible modifications or the inclusion of your institution/funder, please contact us at funders@intechopen.com
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Please be aware that you must be a member, or grantee, of the institutions/funders listed in order to apply for their Open Access publication funds.
Open Access publication costs can often be designated directly in the grants or in specific budgets allocated for that purpose. Many of the most important funding organisations encourage, and even request, that the projects they fund are made available at no cost to the wider public. IntechOpen strives to maintain excellent relationships with these funders and ensures compliance with mandates.
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In order to help Authors identify appropriate funding agencies and institutions, we have created a list, based on extensive research on various OA resources (including ROARMAP and SHERPA/JULIET) of organizations that have funds available. Before consulting our list we encourage you to petition your own institution or organization for Open Access funds or check the specifications of your grant with your funder to ascertain if publication costs are included. Where you are in receipt of a grant you should clarify:
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Does your institution already have a budget for covering Open Access publication costs?
\n\t
Does your grant list Open Access publication fees as legitimate direct/indirect costs?
\n
\n\n
If you are associated with any of the institutions in our list below, you can apply to receive OA publication funds by following the instructions provided in the links. Please consult the Open Access policies or grant Terms and Conditions of any institution with which you are linked to explore ways to cover your publication costs (also accessible by clicking on the link in their title).
\n\n
Please note that this list is not a definitive one and is updated regularly. To suggest possible modifications or the inclusion of your institution/funder, please contact us at funders@intechopen.com
\n\n
Please be aware that you must be a member, or grantee, of the institutions/funders listed in order to apply for their Open Access publication funds.
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At the beginning of humification, the significant decrease in the intensity of the band located at 1735 cm–1 shows that lignin is affected at the first stage of the composting process. At the end of the humification, the band located toward 3450–3420 cm–1 at the beginning of the process undergoes a systematic shift (Δν of the order of 10 cm–1) toward lower wave numbers. The band located at 1660–1650 cm–1 on the Fourier transform infrared spectroscopy (FTIR) spectra before composting shifts systematically toward 1640 cm–1 at the end of humification. This phenomenon can be used as index of compost maturity. 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Soil is a non-renewable natural resources on which the whole human society is dependent for various goods and services. The intensive, and unsustainable anthropogenic practices along with the rapid growth of the human population have led to continuous expansion and concern for the degradation of soil. The agricultural soil is exposed to a plethora of contaminants, the most significant contaminant among them is heavy metals. The major sources of heavy metal contamination are associated with agriculture, industries, and mining. The increase of heavy metal contents in the soil system affects all organisms via biomagnification. In this chapter, we will review various conventional and contemporary physical or chemical and biological techniques for remediation of contaminated soil. 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He completed a one-year Post-Doctoral Fellowship awarded by the DFAIT (Foreign Affairs and International Trade Canada) at the Institute of Biomedical Engineering of the University of New Brunswick (Canada) in 2010. Currently, he is Professor in the Faculty of Electrical Engineering (UFU). He has authored and co-authored more than 200 peer-reviewed publications in Biomedical Engineering. He has been a researcher of The National Council for Scientific and Technological Development (CNPq-Brazil) since 2009. He has served as an ad-hoc consultant for CNPq, CAPES (Coordination for the Improvement of Higher Education Personnel), FINEP (Brazilian Innovation Agency), and other funding bodies on several occasions. He was the Secretary of the Brazilian Society of Biomedical Engineering (SBEB) from 2015 to 2016, President of SBEB (2017-2018) and Vice-President of SBEB (2019-2020). 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