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Society for Advancement of Rice Research, Directorate of Rice Research, Hyderabad, India 60

Breeding For Yield Potential and Enhanced Productivity Across Different Rice Ecologies Through Green Super Rice (GSR) Breeding Strategy Jauhar Ali1, Jian Long Xu2, Yongming Gao2, Marfel Fontanilla1, Zhi Kang Li1,2 1International Rice Research Institute, Philippines (IRRI), Philippines; and 2Chinese Academy of Agricultural Sciences (CAAS), Beijing, China. Email: [email protected]

Abstract

Breeding for increased yield potential under irrigated conditions is one of the major challenges for several decades. Through an innovative green super rice (GSR) breeding strategy, we have been successful in developing several high yielding cultivars with tolerance to multiple abiotic stresses. We discuss on the success story of one such cultivar i.e. GSR IR1-8-S6-S3-Y2 (IRIS 179-880151, HHZ8-SAL6-SAL3-Y2). This cultivar was identified as the highest yielder especially in the dry season at IRRI successively in preliminary yield trials, replicated 2-year yield trials and demonstration trials. Its yields were impressive in physiological trials with 11-12% more yields than checks. The yields under large on farm trials in 2012 as direct seeded (DS) rice at Victoria (7.34 t/ha) in comparison to NSIC Rc222 (IRRI 154) (5.2 t/ha) and at Bae of Laguna province and Infanta, Quezon clearly demonstrated its superiority over the checks. This GSR was also preferred by the farmers for both its taste and quality. The same line showed a moderate tolerance to salinity (6-10 d/Sm) at Infanta, Quezon, Philippines and to drought at reproductive stage (~ 75k Pascals) during DS 2010, 2011 and 2012 at IRRI. Likewise, in a submergence screening trial at IRRI during DS 2012, it showed a phenotypic acceptability score of 4.2 and was comparable to the submergence tolerant check (IRRI149). GSR IR1-8-S6-S3-Y2 cultivar stood first with 6.31 t/ha mean grain yield amongst 905 elite rice materials from different breeding programs within IRRI and PhilRice tested over five locations under the stage 2 (DS 2012) of multi-environment testing (MET) of the Global Rice Science Partnership (GRiSP). GSR IR1-8-S6-S3-Y2 was thus demonstrated to be a resilient green super rice cultivar that can withstand drought, salinity and submergence without compromising on grain yield and quality. Success of these findings may be attributed to the rigorous early generation screening of backcross population under multiple abiotic stress conditions and later stringent selection scheme for higher grain yields over low input (lesser water and fertilizers), drought and irrigated conditions. The breeding efficiency of this strategy increases multi-fold upon design QTL pyramiding approach whereby favourable non-allelic QTLs and networks from ILs belonging to different donors can be combined into a common recipient background. Keywords: Yield, productivity, rice ecologies, green super rice Introduction Rice is one of the world’s most important food crop with a total production of 685 million tonnes from 158 million hectares with an average productivity of 4.32 t/ha. Asia has nearly 90% of the total rice area and production; Asia also consumes what it produces. Recent liking of rice crop in Africa has lead to un-precedented milled rice imports to the tune of 4.4 mt annually creating an increased pressure on Asian rice farming. The global rise in rice production and productivity since the early 1960s has been primarily due the introduction of semidwarf varieties. The introduction of the ‘miracle rice’ to large parts of Asia

through the modern rice breeding initiated by Peter Jennings at IRRI, Philippines had paid rich dividends to keep the hunger away (Jennings 1964). Rice breeding for increased yields was primarily enhanced due the introduction of semi-dwarf SD1 gene into rice varieties making them more responsive to fertilizers. Mostly the breeders had followed pedigree breeding from single (elite x elite) or multiple crosses especially to incorporate disease and insect pest resistance. Much of these varieties could not bring about the desired trait and yield improvement except a few instances like IR36, IR64, IR66 or IR72. However, the traditional conventional breeding through crosses with elite x elite

International Dialogue on Perception and Prospects of Designer Rice 61

or elite x traditional landrace followed through pedigree breeding had enabled rice breeder across Asia to develop thousands of rice varieties. An investigation on the parentages of all crossed materials indicates that we have only utilized 10% of the available germplasm collections. The yield could not surpass beyond a level of 10 t/ha under tropical irrigated lowlands (Peng et al 1999). Yoshida et al (1981) had estimated the potential yield to 15.9 t/ha in such environments based on total incident solar radiation during the growing season. Breeding programs concentrated on irrigated lowland rice primarily trying to manipulate plant architecture. This ideotype breeding approach was useful to identify plant types that are theoretically efficient on the basis of physiology and plant morphology (Donald 1968). Breeders were looking into plant type traits rather than on yield itself and was being followed in most cereal crops (Rasmusso 1991). Dingkuhn et al (1991) had suggested 25% increase in yield potential based on simulation modeling studies by modifying the following traits: (i) enhanced leaf growth combined with reduced tillering during early vegetative growth; (ii) reduced leaf growth and greater foliar N concentration during late vegetative and reproductive growth; (iii) a steeper slope of the vertical N concentration gradient in the leaf canopy with a greater proportion of total leaf N in the upper leaves; (iv) increased carbohydrate storage capacity in stems; and (v) a greater reproductive sink capacity and an extended grain filling period. Khush (1995) had proposed new plant type (NPT) concept to break the yield barrier. Such NPT ideotype has low tillering capacity (3-4 tillers when direct seeded); few unproductive tillers; 200-250 grains per panicle; a plant height of 90-100 cm; thick and sturdy stems; 100-130 days growth duration; and increased harvest index (Peng et al 1994). First generation NPT breeding work was initiated in 1989 primarily using tropical japonica bulu rices as its base to capture the low tillering trait, large panicles, thick stems, vigorous root system and short stature (Khush 1995). Within a span of five years the first generation NPTs were grown in replicated observational trials. As desired the NPT lines had large panicles, few unproductive tillers and lodging resistance but the desired grain yield was not achieved due to low biomass production and poor grain filling. Further efforts to improve the NPT by crossing these first generation NPTs with elite indica rices resulted in the release of NSIC Rc158 in Philippines. Despite the release of the second generation of NPT lines, the yield increase was not significant over the indica check varieties (Peng et al 2008). Physiological studies had shown that to get 10% increase in grain yield in dry season under irrigated lowlands, the following traits are essentially: 330 panicles per m2, 150 spikelets per panicle, 80% grain filling, 25 mg grain weight (oven dry), 22 t/ha above ground total biomass (at 14% moisture

content) and 50% harvest index (Peng and Khush 2003). IRRI’s NPT program stimulated breeders across globe to pursue ideotype breeding. Development of bushy plant type varieties i.e. Guichao and Teqing that had high early vigor with shading tolerance and were amenable to high planting density in 1980’s became popular in southern China (Huang 2001). Another variety Shennong 265 that had a combination of erect plant type and growth vigor was widely grown in Liaoning Province (Yang et al 1996). China further established a national project on “super rice” in 1996 to increase the national average rice yield to 6.9 t/ha by 2010 and to 7.5 t/ha by 2030 (Cheng et al 1998, 2007). Yuan (2001) laid emphasis that super rice should produce 100 kg grain/ha/day. In general, both hybrid and varietal breeding programs in the past concentrated on exploiting the genetic response to higher inputs. Approaches to increase rice production There are two fundamental approaches to increase the rice production. One of the major approaches is that of breeders and physiologists who have been trying for decades to raise the genetic yield potential of the rice crop through changing the plant architecture and making it morpho-physiologically efficient in utilizing the high inputs under intensive irrigated ecologies. The second approach is to enhance the overall resilience of the varieties by increasing the fitness of breeding lines, enabling them to grow in varied rice production systems without compromising on higher grain yield and grain quality. By this second approach, it is possible to increase the overall productivity both under stressed and normal conditions. In the past, rice breeders focused their attention only on stressed or irrigated conditions. Even under the stressed condition, they concentrated on one target trait at a time, for instance drought tolerant rice or submergence. It is well known that the abiotic stresses like drought are quite cyclic in nature and they never repeat in each season and year. In reality, normal years and favorable seasons are encountered in between stressed seasons at random. However, lack of such varieties that would perform well under both stressed and normal conditions has led to yield fluctuations. Perhaps this is also the reason why in the rainfed environments, the land races are still considered as the best cultivars. Unfortunately, these land races are not the best yielders under normal as well as under stressed conditions but they give reasonably stable but moderate yields that is firmly relied by the farmers. We therefore, initiated a breeding strategy that would promote resilience into rice varieties right at the beginning of the breeding cycle making it more nutrient water use efficient lines besides withstanding varied abiotic and biotic stresses for a given ecosystem. Such resilient rice is labeled as green super rice (GSR). GSR is now the basis of a concept to develop rice varieties and hybrids that require less chemical inputs


and irrigation water and that possess key survival traits for complex abiotic and biotic stress conditions encompassing the varied rice-growing situations without compromising high yield and grain quality. GSR breeding using Huang Hua Zhan (HHZ) (recurrent parent) and 16 donors is discussed here to highlight this innovative breeding strategy. GSR breeding and evaluation Sixteen donors (Table 1) were crossed with HHZ and their respective F1s were then backcrossed once with HHZ, later selfed and seeds were bulked to create sixteen BC1F2 bulk populations. Three rounds of screenings were carried out after transplanting of 21d old seedling beginning with 2008 wet season using these bulk populations to varied abiotic stresses like drought for one month (irrigation water ceased until harvest), low inputs (LI) (without any fertilizers, pesticides or herbicides application except one manual weeding at active tillering stage), salinity seedling level screening with simple nutrient addition program (SNAP) culture solution at 18 d/Sm), submergence (14 d seedling are submerged in 1-m depth of fresh water for 21 days), anaerobic germination (direct seeded and immediately submerged in water with 10 cm depth for 21 days), and irrigated condition (with site specific nutrient management). In all such screenings, surviving plants that showed superior performance over the checks and the recipient parent (i.e. HHZ) were selected (Fig. 1) (Ali et al 2012). This evaluation can be extended to any biotic or abiotic stress as long to select superior transgressive segregants. Under field and controlled conditions, especially lines in back cross nursery preliminary and replicated yield trials, and derived genotyping populations were further screened

for biotic stresses like bacterial blight, blast, bacterial leaf streak, sheath blight and tungro virus. Screening for varied abiotic and biotic stresses at BC1F2 resulted in 845-trait specific ILs derived from 16 donors in HHZ background. All of them were genotyped with SSR and SNP markers. These ILs will be used for designed QTL pyramiding to combine different target traits into one line using the molecular data. Many of the identified promising lines were highly tolerant to drought, salinity, submergence, and low input conditions as compared to the respective tolerant checks IR 74371-70-1-1, FL478, IR49830 and PSBRc82, and under normal irrigated conditions. Many were also identified to be tolerant to biotic stresses like bacterial leaf blight, blast, and sheath blight. A new MET (multi-environment test) was initiated in 2011 under the Global Rice Science Partnership (GRiSP) to establish a systematic, sequential, multistage and MET system for elite breeding lines managed through one entity. Materials for the MET comprised of irrigated breeding lines from IRRI and collaborating national institutions like PhilRice. The trial was conducted in a row-column design with two replications as per the MET protocol (IRRI 2011). There were two modules based on the flowering of entries – module 1 for very early/early (≤90 days) and module 2 for medium/late (> 90 days). A total of 605 materials from different breeding programs were tested in MET1 in DS 2011. Only 15 IRRI bred GSR materials were entered for module 1. Further, five of these promising GSR materials were promoted to stage 2 of MET in DS 2012 based on superior yield performance over 100 elite entries including checks i.e. IRRI104, 105,123, 153 and 154.

Table 1. Two batches of 16 populations developed using 16 donors from 7 countries introgressed into the recipient parent, Huang-Hua-Zhan (HHZ) Batch Popolation Donor Country of origin Generation (DS 2012) 1 HHZ5 OM1723 Vietnam (I) BC1F9 1 HHZ8 Phalguna India (I) BC1F9 1 HHZ9 IR50 IRRI (I), Philippines BC1F9 1 HHZ11 IR64 IRRI (I), Philippines BC1F9 1 HHZ12 Teqing China (I) BC1F9 1 HHZ15 PSB Rc66 Philippines (I) BC1F9 1 HHZ17 CDR22 India (I) BC1F9 1 HHZ19 PSB Rc28 Philippines (I) BC1F9 2 HHZ1 Yue-Xiang-Zhan China (I) BC1F8 2 HHZ2 Khazar Iran (I) BC1F8 2 HHZ3 OM1706 Vietnam (I) BC1F8 2 HHZ6 IRAT352 CIAT (upland), Brazil BC1F8 2 HHZ10 Zhong 413 China (I) BC1F8 2 HHZ14 R644 China (I) BC1F8 2 HHZ16 IR58025B IRRI (I), Philippines BC1F8 2 HHZ18 Bg304 Sri Lanka (I) BC1F8


Figure 1. IRRI-GSR breeeding progream and strategy


Table 2. Green super rice (GSR) lines in Huanghuazhan background nominate to national cooperative trial of the Philippines

GSR Lines NCT Nomination Maturity Plant ht. Traits Designation Year/ Season Categories (days) (cm) Irrigated category HHZ 8-SAL6-SAL3-Y2 2011DS IRLL: TPR 105 87 YIG,LI,ST,DT,SubT,ZnD HHZ 2-Y3-Y1-Y1 2012DS IRLL: TPR 115 95 YIG HHZ 5 SAL6-SAL3-DT1 2012DS IRLL: TPR 105 79 YIG,LI,ST,DT,SubT PSB Rc82 - - - - - NSIC Rc222 - - - - - Special purpose category (ps) HHZ 12-DT10-SAL1-DT1 2011DS SPC: Aromatic 115 87 YIG,LI,ST,DT HHZ 5 SAL8-DT3-SUB1 2012DS SPC: multi-trait 110 81 DT,ST,SubT Adverse condition (ac) HHZ 1-Y4-Y1 2011DS AC: Saline 110 87 ST,LI,DT,YIG HHZ 5-SAL14-SAL2-Y2 2011DS AC: Upland 115 82 DT,YIG HHZ 12-SAL2-Y3-Y2 2011DS AC: Upland 110 92 DT,YIG,LI NISC Rc184(NCT-ST Ck) - Salinity check PSB Rc18 Sub1 Submergence check IRRI 119 Submergence check IRRI 149 - Submergence check

GSR Lines Grain Yields (t/ha @

14% MC) IRRI sub tank On-farm (2012 DS)

Designation

DS 2010-

11

WS2010-11

LI (4 seaso

ns)

Rainfed (DS 2010-

11)

Drought (2010-

11)

Salinity (DS 2012)

TQ

Submergence score (DS Was

2012

Bae Laguna

(zinc def)

Victoria Laguna (HY

envt) Irrigated category HHZ 8-SAL6-SAL3-Y2 7.38 5.6 3.32 5.28 1.79 5.09 4.2 4.34 7.37 HHZ 2-Y3-Y1-Y1 6.76 5.06 2.6 4.02 0.29 - - - - HHZ 5 SAL6-SAL3-DT1 7.16 5.3 3.1 4.77 0.96 - 5 - - PSB Rc82 6.57 5.35 3.81 4.93 1.47 - - 4.06 - NSIC Rc222 6.77 5.03 3.55 4.66 0.46 - - 4.02 5.2 Special purpose category (ps) HHZ 12-DT10-SAL1-DT1 7.68 5.21 3.74 5.68 1.6 5.06 - 4.09 5.95 HHZ 5 SAL8-DT3-SUB1 5.96 5.46 3.25 4.74 1.95 5.11 5 - - Adverse condition (ac) HHZ 1-Y4-Y1 - 6 5.48 5.42 no data 5.6 3 - - HHZ 5-SAL14-SAL2-Y2 6.88 5.32 2.95 4.8 2.29 5.38 - 3.47 6.3 HHZ 12-SAL2-Y3-Y2 6.7 6.26 3.12 4.92 1.91 - - - NISC Rc184(NCT-ST Ck) 4.75 - - - PSB Rc18 Sub1 6.2 - - IRRI 119 2.8 - - IRRI 149 4.1 - -


We have provided all the 16 partners in the national agricultural research partners in Asia and Africa with the second generation of 83 IRRI-bred GSR materials in two batches for further evaluation and utilization. The third generation of GSR materials is currently being developed in this background with designed QTL pyramiding to further enhance the grain yield and resilience. Performance appraisal of GSR Rainfed ecosystems especially in India, Bangladesh, Indonesia, Vietnam and Lao PDR require varieties materials that possess such multiple abiotic stress tolerance. Therefore the use of high yielding green super rice will show more durability to changing weather conditions and will be stable and provide insurance against varying pests to the resource poor rice farmers in both irrigated and rainfed conditions. We found GSR-

IR1-8-S6-S3-Y2 (IRIS 179-880151), to be highly adaptive as its recipient parent Huang Hua Zhan but with improved traits like higher yields (~1 t/ha) and tolerance to salinity, drought, submergence and site specific low in put nutrient conditions over its recipient parent and thus validated the strength of this novel breeding strategy (Fig. 2) (Table 2-4). Similar yield improvements could be achieved by drought tolerant ILs over its IR64 recipient parent especially under irrigated and drought conditions (Guan et al 2011). It was relatively easy to enhance the yields of these ILs over its recipient parent especially for irrigated and stressed conditions, as the selection strategy eliminated poor yielders despite possessing improved stress resistance (Ali et al 2006). A compensation mechanism was also noticed when material highly tolerant to submergence was screened under drought as they were mostly susceptible to it and vice versa.

Table 3. Multiple abiotic stress tolerant ILs developed from 16 donors introgressed into Huanghuazhan recipient background and nominated to NCT using IRRI- GSR breeding scheme. Target traits Number of ILs

Produced from BN

Selected at PYT& RYT

Nominated to MET & NCT

Drought tolerance (DT) 613 79 21

High yield under low-input (LI) 370 27 3

Salinity tolerance (SAL) 502 73 18

Submergence tolerance (SUB) 128 13 2

High yield under irrigated (Y) 576 100 27

Drought tolerance and high yield under low-input 246 15 2

Drought tolerance and salinity tolerance 326 19 5

Drought and submergence tolerance 82 6

Drought tolerance and high yield 382 40 11

High yield under low-input and salinity tolerance 274 10 1

High yield under low-input and submergence tolerance 38 0

High yield under low-input 178 1

Salinity and submergence tolerance 60 9

Salinity tolerance and high yield 292 42 8

Submergence tolerance and high yield 101 5 1

Drought, salinity and submergence tolerance 35 3 2

Drought and salinity tolerance and high yield 154 9

Drought and submergence tolerance and high yield 58 3

High yield under low-input, salinity and SUB 20 0

High yield under low-input, salinity tolerance 117 0

High yield under low-input and submergence tolerance 36 0

Salinity and submergence tolerance 39 2

Total: 845 146 40 IL = Introgression lines; BN = backcross nursery; PYT = preliminary yield trial; RYT = replicated yield trial; NCT = national cooperative testing (Philippines); MET = Multi-environment test (IRRI)


Figure 2. High yielding multiple abiotic stress tolerant green super rice (GSR) cultivars developed and bred at IRRI possessing desirable cooking quality traits: top - GSR IR1-12-D10-S1-D1 and bottom - GSR IR1-8-S6-S3-Y2.


Table 4. Performance of some IRRI bred GSR entries under stage 2 (module 1 early duration with 100 elite lines) of multi-environment testing (MET) during 2012DS. Name Location (yield in t/ha) Mean

yield Yield rank*

Yield stability

N.Ecija Isabela Agusan Bohol IRRI (t/ha) index (rank)* GSR IR1-8-S6-S3-Y2 8.86 7.2 4.32 5.2 5.97 6.31 1 3 GSR IR1-1-Y4-Y1 8.22 7.21 3.74 4.81 4.97 5.79 28 65 GSR IR1-8-S9-D2-Y1 7.52 6.39 3.94 4.75 5.03 5.53 68 61 GSR IR1-12-Y4-DT 1-Y1 7.99 5.44 3.95 2.76 5.81 5.19 89 97 GSR IR1-12-D10-S1-D1 8.04 5.45 4.58 4.94 5.12 5.62 47 38 IRRI 104(PSRBc10) 7.4 5.98 4.06 4.91 5.74 5.61 49 50 IRRI 105 (PSRBc18) 8.18 6.36 3.75 4.66 4.86 5.56 63 57 IRRI 123(PSRBc82) 7.26 5.48 4.57 4.79 4.9 5.91 18 68 IRRI 153(Mestiso21) 6.76 5.86 4.37 5.85 5.48 5.66 42 78 IRRI 154 (NSIC Rc222) 9.06 5.35 4.51 4.82 4.98 5.74 34 75

*Ranks are out of 100 entries tested in the module 1 of MET stage 2 in DS2012

Interestingly, drought tolerant screenings favored selection for salinity tolerance in the introgression lines. Recently, Wang et al (2012) found existence of genetic overlaps at 14 QTL for drought and salinity tolerance. In our study, unless the introgression lines possessed tolerance to most abiotic stresses in the highest possible levels across all screenings compared to recipient and donor parents or checks, they were not advanced any further. Forty ILs that were found to be tolerant to multiple abiotic and biotic stress were nominated to the national cooperative testing (NCT) of the Philippines and MET under GRiSP of IRRI using GSR breeding approach (Table 2-4). The new GSR breeding strategy allowed us to identify several ILs that were found to be superior in its stable yield performance under three conditions i.e. irrigated, drought or site specific low in put nutrient conditions within a short period of five years (Fig. 2) (Ali et al 2012). As expected we had observed relatively fewer ILs (17) that had combined three target abiotic traits out of 146 identified for preliminary and replicated yield trials and only two were nominated to the NCT and MET. In MET stage 2 trials under GRiSP with IRRI bred GSR cultivars during DS 2011 and WS 2011, GSR-IR1-8-S6-S3-Y2 stood first in the MET with 7% and 10% yield advantage over the best check IRRI123 and IRRI154 (NSIC222) (Table 4). Out of 100 entries studied, this cultivar ranked 3rd for yield stability index (YSI) with highest grain yield of 6.31t/ha in comparison to IRRI123 with YSI of 68 and grain yield of 5.91 t/ha. Multiple abiotic stress traits in such cultivars can fit them very well in varied rice ecosystems but they seem to do better under irrigated and rainfed lowlands. If these types of cultivars with multiple abiotic stress tolerances are deployed in target rainfed and irrigated conditions, perhaps we can usher second green revolution in the resource poor rainfed lowlands (Fig. 2). We expect

this cultivar to perform better in the NCT trials of the Philippines and qualify for its release earliest by wet season of 2013 for general cultivation. This cultivar has already been shared with other national partners across Asia and Africa and soon we will be able to confirm its wide scale adaptation and yield stability. This new GSR breeding methodology has been proven to be successful on account of two major reasons, first being a massive introgression breeding effort with appropriate cross tolerance screening and selection techniques that has brought out the known and hidden genetic diversity from a large number of donors into elite adaptable varietal backgrounds. Early generation screening of backcross populations for multiple abiotic stress conditions and later stringent selection scheme to identify promising entries across three different rice growing conditions i.e. irrigated, drought and low input had favoured the selection of resilient genotypes.

Thus, we had increased the fitness of the genotypes to varied rice growing conditions. New analytical tools (Zhang et al 2011) allowed us to detect genetic complex networks for tolerances to major abiotic and biotic stresses that complement favorably in the tolerant ILs. Secondly, a few rounds of designed QTL pyramiding approach with use of SSR and SNP markers can make these ILs still powerful to pool up the favorable QTLs from several donors into common adaptable varietal backgrounds. Currently, we are utilizing molecular sequencing tools (de novo genome sequencing for parental lines and ILs with BGI, Shenzen) for the newly developed first batch of 512 HHZ ILs with tolerances to many abiotic and biotic stresses. Further use of omic study tools including epigenomics should soon enable us to unravel the complex genetic networks that govern these tolerances.


ACKNOWLEDGEMENT Drs S Peng and J Krishna, IRRI are duly acknowledged for their physiological evaluation of the key GSR breeding materials. Dr Redona is acknowledged for evaluating GSR advance breeding materials under MET. REFERENCE Ali J, Xu JL, Gao YM, Fontanilla MA and Li ZK.

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Citation: Ali J, Xu JL Gao Y, Fontanilla M, Li ZK. 2013. Breeding for yield potential and enhanced productivity across different rice ecologies through green super rice (GSR) breeding strategy. In: Muralidharan K and Siddiq EA, eds. 2013. International Dialogue on Perception and Prospects of Designer Rice. Society for Advancement of Rice Research, Directorate of Rice Research, Hyderabad 500 030, India, pp 60-68.

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