Modesto Amante

International Rice Research Institute, Лос-Баньос, Calabarzon, Philippines

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Publications (15)40.66 Total impact

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    ABSTRACT: Availability of irrigation water is becoming a major limiting factor in rice cultivation. Production in rainfed areas is affected in particular by drought events, as these areas are commonly planted to high-yielding drought-susceptible rice (Oryza sativa L.) varieties. The use of bulk segregant analysis (BSA), taking grain yield (GY) as a selection criterion, has resulted in the identification of several large-effect QTL. A QTL mapping study was undertaken on a BC1F3:4 population developed from the cross IR55419-04/2*TDK1 with the aim of identifying large-effect QTL in the background of TDK1, a popular variety from Lao PDR. The study identified three QTL--qDTY3.1 (RM168-RM468), qDTY6.1 (RM586-RM217), and qDTY6.2 (RM121-RM541)--for grain yield under drought. qDTY3.1 and qDTY6.1, showed consistent effect across seasons under lowland drought-stress conditions while qDTY6.1 and qDTY6.2 showed effect under both upland and lowland drought conditions. The test of QTL effect, conducted through a QTL class analysis, showed the complimentary nature of qDTY3.1 and qDTY6.1. Both QTL showed specific patterns of effect across different maturity groups within the mapping population and higher stability for grain yield was seen across stress levels for lines with both QTLs as compared to those with single or no QTL. The study offers a clear understanding of large-effect QTL for grain yield under drought and the effects of these both as individual QTL and in various combinations. The study also opens up an opportunity to develop a drought-tolerant version of TDK1 through marker-assisted backcross breeding and has led to a large-scale QTL pyramiding program aiming to combine these QTL with Sub1 in the background of TDK1 as recipient variety.
    BMC Genetics 02/2014; 15(1):16. · 2.81 Impact Factor
  • Molecular Breeding 06/2012; 30:1767–1779. · 3.25 Impact Factor
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    ABSTRACT: The genetic basis of high grain yield under reproductive-stage drought was studied using an F3-derived population generated from the cross of upland rice (Oryza sativa L.) cultivars Vandana and Way Rarem. Contributed by the susceptible parent Way Rarem, locus qDTY 12.1 was hypothesized to have interaction with loci from the Vandana genome to enhance the grain yield of tolerant line Vandana under drought. A test of the digenic interaction of qDTY 12.1 showed that two loci, qDTY 2.3 on chromosome 2 and qDTY 3.2 on chromosome 3, significantly increased the yield and harvest index of qDTY 12.1 -positive lines under severe upland and lowland drought conditions. qDTY 2.3 and qDTY 3.2 , in interaction with qDTY 12.1 , reduced days to flowering and plant height of qDTY 12.1 -positive lines under stress and non-stress conditions in upland. BC2F3-derived backcross inbred lines (BILs) were used to validate these results and identify new quantitative trait loci. Lines with qDTY 2.3 and qDTY 12.1 showed increased yield over Way Rarem under severe and moderate stress conditions, in upland. IR84996-50-4-B-4, a selection from one of the BILs, yielded more than the popular drought-tolerant cultivars Apo, UPLRi7, and IR74371-54-1-1 under severe stress conditions. Introgressed segments from Vandana also improved yield under non-stress conditions. The results indicate that digenic interac-tions can explain the genetic control of complex quantitative traits such as grain yield under drought, and a few interacting loci with large effects on grain yield or yield-related traits may enhance drought response across a wide range of genetic backgrounds and environments when introgressed together.
    Molecular Breeding 05/2012; · 3.25 Impact Factor
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    ABSTRACT: Fine-mapping studies on four QTLs, qDTY(2.1), qDTY(2.2), qDTY(9.1) and qDTY(12.1), for grain yield (GY) under drought were conducted using four different backcross-derived populations screened in 16 experiments from 2006 to 2010. Composite and bayesian interval mapping analyses resolved the originally identified qDTY(2.1) region of 42.3 cM into a segment of 1.6 cM, the qDTY(2.2) region of 31.0 cM into a segment of 6.7 cM, the qDTY(9.1) region of 32.1 cM into two segments of 9.4 and 2.4 cM and the qDTY(12.1) region of 10.6 cM into two segments of 3.1 and 0.4 cM. Two of the four QTLs (qDTY(9.1) and qDTY(12.1)) having effects under varying degrees of stress severity showed the presence of more than one region within the original QTL. The study found the presence of a donor allele at RM262 within qDTY(2.1) and RM24334 within qDTY(9.1) showing a negative effect on GY under drought, indicating the necessity of precise fine mapping of QTL regions before using them in marker-assisted selection (MAS). However, the presence of sub-QTLs together in close vicinity to each other provides a unique opportunity to breeders to introgress such regions together as a unit into high-yielding drought-susceptible varieties through MAS.
    Theoretical and Applied Genetics 02/2012; 125(1):155-69. · 3.66 Impact Factor
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    ABSTRACT: Fine-mapping studies on four QTLs, qDTY 2.1 , qDTY 2.2 , qDTY 9.1 and qDTY 12.1 , for grain yield (GY) under drought were conducted using four different backcross-derived populations screened in 16 experiments from 2006 to 2010. Composite and Bayesian interval mapping anal-yses resolved the originally identified qDTY 2.1 region of 42.3 cM into a segment of 1.6 cM, the qDTY 2.2 region of 31.0 cM into a segment of 6.7 cM, the qDTY 9.1 region of 32.1 cM into two segments of 9.4 and 2.4 cM and the qDTY 12.1 region of 10.6 cM into two segments of 3.1 and 0.4 cM. Two of the four QTLs (qDTY 9.1 and qDTY 12.1) having effects under varying degrees of stress severity showed the presence of more than one region within the original QTL. The study found the presence of a donor allele at RM262 within qDTY 2.1 and RM24334 within qDTY 9.1 showing a negative effect on GY under drought, indicating the necessity of precise fine mapping of QTL regions before using them in marker-assisted selection (MAS). However, the presence of sub-QTLs together in close vicinity to each other provides a unique opportunity to breeders to introgress such regions together as a unit into high-yielding drought-susceptible varieties through MAS.
    Theoretical and Applied Genetics 02/2012; · 3.66 Impact Factor
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    ABSTRACT: The genetic basis of high grain yield under reproductive-stage drought was studied using an F3-derived population generated from the cross of upland rice (Oryza sativa L.) cultivars Vandana and Way Rarem. Contributed by the susceptible parent Way Rarem, locus qDTY 12.1 was hypothesized to have interaction with loci from the Vandana genome to enhance the grain yield of tolerant line Vandana under drought. A test of the digenic interaction of qDTY 12.1 showed that two loci, qDTY 2.3 on chromosome 2 and qDTY 3.2 on chromosome 3, significantly increased the yield and harvest index of qDTY 12.1 -positive lines under severe upland and lowland drought conditions. qDTY 2.3 and qDTY 3.2 , in interaction with qDTY 12.1 , reduced days to flowering and plant height of qDTY 12.1 -positive lines under stress and non-stress conditions in upland. BC2F3-derived backcross inbred lines (BILs) were used to validate these results and identify new quantitative trait loci. Lines with qDTY 2.3 and qDTY 12.1 showed increased yield over Way Rarem under severe and moderate stress conditions, in upland. IR84996-50-4-B-4, a selection from one of the BILs, yielded more than the popular drought-tolerant cultivars Apo, UPLRi7, and IR74371-54-1-1 under severe stress conditions. Introgressed segments from Vandana also improved yield under non-stress conditions. The results indicate that digenic interac-tions can explain the genetic control of complex quantitative traits such as grain yield under drought, and a few interacting loci with large effects on grain yield or yield-related traits may enhance drought response across a wide range of genetic backgrounds and environments when introgressed together.
    Molecular Breeding 01/2012; · 3.25 Impact Factor
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    ABSTRACT: Drought is a major abiotic stress factor limiting rice production in rainfed areas. In this study we identified a large-effect quantitative trait locus (QTL) associated with grain yield under stress in five different populations on chromosome 1. The effect of this QTL was further confirmed and characterized in five backcross populations in a total of sixteen stress and non-stress trials during 2006 and 2008. In all the stress trials (eight in total) qDTY1.1 showed strong association with grain yield explaining on average 58% of the genetic variation in the trait. Homozygotes for the tolerant parent allele (Apo) yielded on average 27% more than the susceptible parent allele (IR64) homozygotes. Using an Apo/ 3* IR64 population, the peak of this QTL (qDTY1.1) was mapped to an interval between RM486 and RM472 at 162.8 cM at a LOD score of 9.26. qDTY1.1 was strongly associated with plant height in all the environments; this was probably due to the presence of the sd1 locus in this genomic region. In a Vandana/ 3* IR64 population segregating for sd1, a strong relation between plant height and yield under stress was observed. The observed relation between increased height and drought tolerance is likely due to tight linkage between qDTY1.1 and sd1 and not due to pleiotrophy of sd1. Thus there is a possibility of combining reduced plant height and drought tolerance in rice. The large and consistent effect of qDTY1.1 across several genetic backgrounds and environments makes it a potential strong candi-date for use in molecular breeding of rice for drought tolerance.
    Molecular Breeding 09/2011; · 3.25 Impact Factor
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    ABSTRACT: The seasonal and annual variability of sensible heat flux (H), latent heat flux (LE), evapotranspiration (ET), crop coefficient (Kc) and crop water productivity (WPET) were investigated under two different rice environments, flooded and aerobic soil conditions, using the eddy covariance (EC) technique during 2008-2009 cropping periods. Since we had only one EC system for monitoring two rice environments, we had to move the system from one location to the other every week. In total, we had to gap-fill an average of 50-60% of the missing weekly data as well as those values rejected by the quality control tests in each rice field in all four cropping seasons. Although the EC method provides a direct measurement of LE, which is the energy used for ET, we needed to correct the values of H and LE to close the energy balance using the Bowen ratio closure method before we used LE to estimate ET. On average, the energy balance closure before correction was 0.72 ± 0.06 and it increased to 0.99 ± 0.01 after correction. The G in both flooded and aerobic fields was very low. Likewise, the energy involved in miscellaneous processes such as photosynthesis, respiration and heat storage in the rice canopy was not taken into consideration. Average for four cropping seasons, flooded rice fields had 19% more LE than aerobic fields whereas aerobic rice fields had 45% more H than flooded fields. This resulted in a lower Bowen ratio in flooded fields (0.14 ± 0.03) than in aerobic fields (0.24 ± 0.01). For our study sites, evapotranspiration was primarily controlled by net radiation. The aerobic rice fields had lower growing season ET rates (3.81 ± 0.21 mm d-1) than the flooded rice fields (4.29 ± 0.23 mm d-1), most probably due to the absence of ponded water and lower leaf area index of aerobic rice. Likewise, the crop coefficient, Kc, of aerobic rice was significantly lower than that of flooded rice. For aerobic rice, Kc values were 0.95 ± 0.01 for the vegetative stage, 1.00 ± 0.01 for the reproductive stage, 0.97 ± 0.04 for the ripening stage and 0.88 ± 0.03 for the fallow period, whereas, for flooded rice, Kc values were 1.04 ± 0.04 for the vegetative stage, 1.11 ± 0.05 for the reproductive stage, 1.04 ± 0.05 for the ripening stage and 0.93 ± 0.06 for the fallow period. The average annual ET was 1301 mm for aerobic rice and 1440 mm for flooded rice. This corresponds to about 11% lower total evapotranspiration in aerobic fields than in flooded fields. However, the crop water productivity (WPET) of aerobic rice (0.42 ± 0.03 g grain kg-1 water) was significantly lower than that of flooded rice (1.26 ± 0.26 g grain kg-1 water) because the grain yields of aerobic rice were very low since they were subjected to water stress. The results of this investigation showed significant differences in energy balance and evapotranspiration between flooded and aerobic rice ecosystems. Aerobic rice is one of the promising water-saving technologies being developed to lower the water requirements of the rice crop to address the issues of water scarcity. This information should be taken into consideration in evaluating alternative water-saving technologies for environmentally sustainable rice production systems.
    Agricultural Water Management 03/2011; 98(9):1417-1430. · 2.33 Impact Factor
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    ABSTRACT: R ice grown under flooded conditions, usually referred to as lowland rice, occupies 55% of the world rice area while producing 75% of world rice (Dobermann and Fairhurst, 2000). However, lowland rice production is being threatened by a grow-ing water scarcity worldwide (Tuong and Bouman, 2003). By 2025, a "physical water scarcity" is projected for more than 2 mil-lion ha of dry-season lowland rice and 13 million ha of wet-season lowland rice in Asia, and an "economic water scarcity" is expected to hamper most of Asia's 22 million ha of dry-season lowland rice (Tuong and Bouman, 2003). Some areas that are currently planted to lowland rice are likely to experience interruptions of water supply or even to revert to primarily rainfed production. The increasing water scarcity highlights the need to improve the water productivity of rice, and its ability to tolerate periods of water shortage, to ensure adequate food for future generations. Aerobic rice is a promising approach for dealing with the emerging water shortage and maintaining sustainable rice produc-tion. Aerobic rice is a relatively new production system in which specially developed varieties are direct seeded and grown in non-puddled and nonfl ooded aerobic soils. It can be either irrigated or ABSTRACT Aerobic rice is a production system in which rice is direct seeded and grown in nonpuddled and nonfl ooded aerobic soils. Aerobic rice varieties need to be developed to cope with the increas-ing water scarcity in tropical Asia. Advanced breeding lines were evaluated in 24 yield trials under both nonstressed and stressed aerobic soil conditions in 4 yr (2005–2008) to assess the effi cacy of the two-stress-level screening protocol and selection strategies for develop-ing aerobic rice and to identify genotypes that are high yielding and drought tolerant. Twenty-six genotypes outyielded the reference varieties Apo and UPLRi-7 by more than 10% under both nonstress and stress conditions. High harvest index (HI) and vegetative vigor accounted for the increased yield of the newly developed geno-types. On average, the drought stress reduced grain yield by 60%, HI by 50%, and plant height by 12 cm and delayed fl owering by 3 d. There was a low genetic correlation for yield across the two stress levels, and indirect selection under one stress level was not predicted to be effective in improving grain yield under the other, suggest-ing that screening genotypes under both non-stress and stress conditions for yield is needed to develop aerobic-adapted varieties combining high yield potential with drought tolerance. The elite germplasm identifi ed in this study is likely to be useful to farmers in water-short irrigated and rainfed areas in the tropics.
    Crop Science 01/2010; 50:2268-2276. · 1.51 Impact Factor
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    ABSTRACT: An F(4:5) population of 490 recombinant inbred lines (RILs) from the cross Apo/(2*)Swarna was used to detect quantitative trait loci (QTL) with large effects on grain yield under drought stress using bulk-segregant analysis (BSA). Swarna is an important rainfed lowland rice variety grown on millions of hectares in Asia, but is highly susceptible to drought and aerobic soil conditions. Apo is an aerobic-adapted variety with moderate tolerance to drought. Two rice microsatellite (RM) markers, RM324, and RM416, located on chromosomes 2 and 3, respectively, were shown via BSA to be strongly associated with yield under lowland drought stress. The effects of these QTL were tested in a total of eight hydrological environments over a period of 3 years. The QTL linked to RM416 (DTY(3.1)) had a large effect on grain yield under severe lowland drought stress, explaining about 31% of genetic variance for the trait (P < 0.0001). It also explained considerable variance for yield under mild stress in lowland conditions and aerobic environments. To our knowledge this is the first reported QTL that has a large effect on yield in both lowland drought and aerobic environments. The QTL linked to RM324 (DTY(2.1)) had a highly significant effect on grain yield in lowland drought stress (R(2) = 13-16%) and in two aerobic trials. The effect of these QTL on grain yield was verified to be not mainly due to phenology differences. Effects of DTY(3.1) on yield under stress have been observed in several other rice mapping populations studied at IRRI. Results of this study indicate that BSA is an effective method of identifying QTL alleles with large effects on rice yield under severe drought stress. The Apo alleles for these large-effect QTL for grain yield under drought and aerobic conditions may be immediately exploited in marker-assisted-breeding to improve the drought tolerance of Swarna.
    Theoretical and Applied Genetics 10/2009; 120(1):177-90. · 3.66 Impact Factor
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    ABSTRACT: The seasonal fluxes of heat, moisture and CO2 were investigated under two different rice environments: flooded and aerobic soil conditions, using the eddy covariance technique during 2008 dry season. The fluxes were correlated with the microclimate prevalent in each location. This study was intended to monitor the environmental impact, in terms of C budget and heat exchange, of shifting from lowland rice production to aerobic rice cultivation as an alternative to maintain crop productivity under water scarcity.
    Agricultural and Forest Meteorology 10/2009; 149(10):1737-1750. · 3.89 Impact Factor
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    ABSTRACT: Drought is a major production constraint in rainfed rice (Oryza sativa L.). Lack of effective selection criteria is a major limitation hampering progress in breeding for drought tolerance. In an earlier report, we showed in two populations that one cycle of direct selection was effective in increasing grain yield under stress. In the present study, we retested the efficiency of direct selection for grain yield under drought stress in rice using four populations derived from crossing upland-adapted, drought-tolerant varieties (Apo, Vandana) to high-yielding, lowland-adapted, drought-susceptible varieties (IR64, IR72). Each population was subjected to two cycles of divergent selection either under drought stress in upland or under nonstress conditions in lowland conditions. Following selection, approximately 40 high-yielding lines selected under each protocol from each population, along with a set of unselected lines, were evaluated in a series of selection response trials over a range of moisture levels. Significant response to direct selection under stress was realized in 9 out of 15 combinations of populations and stress environments, and in 6 of the 7 severe stress trials. Averaging over all the populations and stress environments, the stress-selected lines had a yield advantage of 25 and 37% over nonstress-selected and random lines, respectively. In contrast to this, under nonstress, the nonstress-selected lines had an average yield advantage of only 7 and 13% over stress-selected and random lines, respectively. Direct selection in managed stress trials during dry seasons gave significant response (25% on average relative to indirect selection in nonstress conditions) under naturally occurring wet season stress. In addition, direct selection under stress in upland gave an average gain of 16 and 45% over nonstress-selected and random lines, respectively, under stress in lowland. The yield advantage of the stress-selected lines appears to result mainly from maintenance of higher harvest index. These results show that direct selection for grain yield under stress is effective and does not reduce yield potential. Overall, this is the first report in rice demonstrating that (a) selection under managed drought stress in the dry season can result in yield gains under natural stress in the wet season, and (b) that selection under upland drought stress can, at least under the conditions of the present study, result in gains under lowland drought conditions.
    Field Crops Research. 01/2008;
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    ABSTRACT: Traditionally, upland rice is grown in Asia in low-input, subsistence systems. More productive upland systems, using more fertilizer and improved varieties, are emerging in China and Philippines, and could contribute to productivity increases in rainfed environments in other countries. Here, we evaluate, on-station and on-farm, the yield under upland management of improved indica upland cultivars selected for yield under high-fertility conditions. These cultivars are compared with traditional and improved tropical japonica upland varieties, and with elite indica high-yielding varieties (HYV) developed for irrigated lowland production, to characterize the features of varieties that produce high yields in favorable upland environments. Forty-four improved and traditional varieties and experimental lines were evaluated in irrigated lowland, non-stressed upland, moderately stressed upland, severely water-stressed upland, and low-fertility upland environments in southern Luzon, Philippines. Correlations between yields in non-stress and mild-stress environments were low but positive. Some cultivars, like IR55423-01, were among the highest yielding under both conditions, indicating that high yield and moderate water-stress tolerance can be combined. Upland-selected indica varieties yielded 3.56 t ha−1 in favorable upland environments on-station in southern Luzon, outperforming improved tropical japonica and irrigated varieties by 23 and 69%, respectively. They were also the highest-yielding class in infertile, acid soils. The improved upland indica cultivars are about 110 cm tall under favorable upland conditions and maintain a harvest index of nearly 0.4, or about one-third higher than other cultivar types. The best upland-adapted rice varieties produced average yields on-farm of 3.3 and 4.1 t ha−1 in southern Luzon and Yunnan, respectively, outyielding traditional checks by 30–50% with moderate N application. Screening under both high-fertility, non-stress conditions and moderate reproductive-stage stress appears to be needed to develop cultivars combining high-yield potential with drought tolerance. Upland-adapted indica cultivars offer a new approach to increasing productivity and reducing risk in Asian rainfed rice systems.
    Field Crops Research. 01/2006;
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    ABSTRACT: Osmotic adjustment is one of several characters putatively associated with drought tolerance in rice. Indica cultivars are known to have a greater capacity for osmotic adjustment than japonica cultivars. We developed an advanced back-cross population using an indica donor, IR62266-42-6-2, to introgress osmotic adjustment into an elite japonica cultivar, IR60080-46A. One hundred and fifty BC(3)F(3) families were genotyped using microsatellites and RFLP markers, and a few candidate genes. We evaluated osmotic adjustment in these lines under greenhouse conditions using the re-hydration technique. Using the composite interval mapping technique, we detected 14 QTLs located on chromosomes 1, 2, 3, 4, 5, 7, 8 and 10 that together explained 58% of the phenotypic variability. Most, but not all, of the alleles with positive effects came from the donor parent. On chromosome 8, two QTLs were associated in repulsion. The QTL locations were in good agreement with previous studies on this trait on rice and in other cereals. Some BC(3)F(3) lines carried the favorable alleles at the two markers flanking up to four QTLs. Intercrossing these lines followed by marker-aided selection in their progenies will be necessary to recover lines with levels of osmotic adjustment equal to the donor parent. The advanced back-cross strategy appeared to be an appropriate method to accelerate the process of introgressing interesting traits into elite material.
    Theoretical and Applied Genetics 12/2003; 107(7):1288-96. · 3.66 Impact Factor
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    ABSTRACT: Seasonal rainfall in the Philippines is known to be modulated by ENSO phenomenon, with El Niño frequently contributing to reduced rainfall and drought while La Niña resulting in excessive rainfalls, floods and more intense typhoons. The alterations in rainfall patterns can have considerable feedback on solar radiation, air temperature, and soil moisture which can affect the ecosystem CO2 exchange. In this paper, we assessed the effects of the ENSO events (2008–mid 2010) on the seasonal climate conditions and determined how it affected the gross primary production (GPP), ecosystem respiration (Re), and net ecosystem production (NEP) of two contrasting rice environments: flooded and non-flooded.The 2008 dry season (DS) was under a La Niña event while the 2008 wet season (WS) was a neutral one with strong tropical cyclones associated during the wet season. The 2009DS was also La Niña while the 2009WS was El Niño; however, the northern part of the Philippines experienced strong tropical cyclones. The 2010DS was under an El Niño event.The La Niña in 2008DS resulted in about 15% lower solar radiation (SR), 0.3 °C lower air temperature (Ta) and 60% higher precipitation compared to the 28-year climate normal patterns. Both flooded and non-flooded rice fields had lower NEP in 2008 DS (164 and 14 g C m−2, respectively) than in 2008 WS (295 and 82 g C m−2, respectively) because the climate anomaly resulted in SR – driven decrease in GPP. The La Niña in 2009DS even resulted in 0.2 °C lower air temperature and 40% more precipitation than the 2008DS La Niña. This cooler temperature resulted in lower Re in flooded rice fields while the higher precipitation resulted in higher GPP in non-flooded fields since the climate was favorable for the growth of the aerobic rice, the ratoon crops and the weeds. This climate anomaly benefitted both flooded and non-flooded rice fields by increasing NEP (351 and 218 g C m−2, respectively). However, NEP decreased in 2009WS in both flooded and non-flooded rice fields (225 and 39 g C m−2, respectively) due to the devastating effects of the strong tropical cyclones that hit the northern part of the Philippines. On the other hand, the El Niño event during 2010DS resulted in about 6% higher solar radiation, 0.4 °C higher air temperature and 67% lower precipitation than the 28-year climate normal pattern. The NEP of flooded and non-flooded rice fields were closely similar at 187 and 174 g C m−2, respectively. This climate anomaly resulted in Ta – driven increase in Re, as well as vapor pressure deficit (VPD) – driven decrease in GPP in flooded rice fields. The GPP and Re in non-flooded rice fields were less sensitive to higher VPD and higher Ta, respectively. It appears that the net ecosystem CO2 exchange in non-flooded rice field was less sensitive to an El Niño event.
    Field Crops Research 134:80–94. · 2.47 Impact Factor