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Genome-wide association study (GWAS) was performed for 16 agronomic traits including nitrogen use efficiency (NUE) and yield-related components using a panel of 190 mainly japonica rice varieties and a set of 38 390 single nucleotide polymorphism (SNP) markers. This panel was evaluated under rainfed upland conditions in Madagascar in two consecutive cropping seasons with two contrasted nitrogen input levels. Using another set of five grain traits, we identified previously known genes (GW5, GS3, Awn1 and Glabrous1), thus validating the pertinence and accuracy of our datasets for GWAS. A total of 369 significant associations were detected between SNPs and agronomic traits, gathered into 46 distinct haplotype groups and 28 isolated markers. Few association signals were identified for the complex quantitative trait NUE, however, larger number of quantitative trait loci (QTLs) were detected for its component traits, with 10 and 2 association signals for nitrogen utilization efficiency and nitrogen uptake efficiency, respectively. Several detected association signals co-localized with genes involved in nitrogen transport or nitrogen remobilization within 100 kb. The present study thus confirmed the potential of GWAS to identify candidate genes and new loci associated with agronomic traits. However, because of the quantitative and complex nature of NUE-related traits, GWAS might have not captured a large number of QTLs with limited effects.

Indigenous upland rice is a staple food for local people in the North and Northeast regions of Thailand. As a result, variations of grain yield and GxE interactions have been utilized for wider adaptability of upland rice varieties. A high yielding genotype that performs well under a good yielding environment as well as in poor environments is greatly needed. Our experiment, therefore, aimed to identify high potential indigenous upland rice varieties for grain yield and yield stability under rainfed conditions. Fifty upland rice genotypes were evaluated from 2013 to 2015, in which a randomized complete block design with three replications was laid out over the three years. Based on grain yield, eight indigenous upland rice varieties, including ULR026, ULR042, ULR075, ULR078, ULR080, ULR081, ULR089 and ULR105; demonstrated superior performance, high yield stability, and greater adaptability over the other varieties, including the Sew Mae Jan check variety. Additional qualities of the superior varieties included high amylose content (ULR081 and ULR075), high aroma (ULR078), and intermediate gelatinization temperature test (GT) (ULR078, ULR026, and ULR105). The participatory varietal selection (PVS) test for farmer(s) acceptance, and promotion of these varieties under rainfed conditions will be further studied.

Keeping in view the expanding environmental pollution and irrigation water deficit, a pot experiment was performed for the upland (Huyou2, Hanyou737) and paddy rice cultivars (Taigeng8; Yixiang2292), to study soil liming effects on methane (CH4) and nitrous oxide (N2O) emission, bioavailability and accumulation of Cd, Pb in upland and paddy rice. Upland rice reduced 90% of soil CH4 emission as compared to paddy conditions. Soil CH4 emission decreased by 45% and 39% with dolomite, and it reduced by 35% and 33% with lime treatment both in upland and paddy conditions, respectively. Soil N2O emission decreased by 44% and 52% with dolomite, and with the lime application, it was reduced by 37% and 44% for both upland and paddy conditions respectively. Reduction in soil DTPA-extractable Cd was between 37-53% and 43–80% with dolomite and 16–37% and 24–72% Cd decreased with lime application in upland and paddy conditions respectively. Soil DTPA-extractable Pb reduced by 27–44% and 25–53% with dolomite and 16–40% and 11–42% with soil-applied lime in upland and paddy conditions, respectively. Cd accumulation in rice grain was decreased by 47–88% and 62–79% with dolomite and 31–86% and 45–52% reduction by lime application in upland and paddy rice respectively. Rice grain Pb reduced by 58–91% and 66–78% with dolomite application and 32–71% and 44–71% with lime in upland and paddy rice, respectively. Our results showed that soil liming significantly reduced soil N2O and CH4 emission and Cd, Pb accumulation in rice grain, but dolomite was more effective as compared to lime. Altogether, results of this study suggest that upland rice can be cultivated in Cd Pb polluted soils with least soil CH4 emission. Cd and Pb toxicity, accumulation, and N2O emission in upland rice can be minimized by soil liming of 3 g kg−1 and optimizing the nutrients composition of the soil.

Shortfall of rain that creates drought like situation in non-irrigated agriculture system often limits rice production, necessitating introduction of drought tolerance trait into the cultivar of interest. The mechanism governing drought tolerance is, however, largely unknown, particularly the involvement of miRNAs, the master regulators of biochemical events. In this regard, response study on a drought tolerant rice variety KMJ 1-12-3 to 20% PEG (osmolality- 315 mOsm/kg) as drought stress revealed significant changes in abundance of several conserved miRNAs targeting transcription factors like homeodomain-leucine zipper, MADS box family protein, C2H2 zinc finger protein and Myb, well known for their importance in drought tolerance in plants. The response study also revealed significant PEG-induced decrease in abundance of the miRNAs targeting cyclin A, cyclin-dependent kinase, guanine nucleotide exchange factor, GTPase-activating protein, 1-aminocyclopropane-1-carboxylic acid oxidase and indole-3-acetic beta-glucosyl transferase indicating miRNA-regulated role of the cell cycle regulators, G-protein signalling and the plant hormones ethylene and IAA in drought tolerance in plants. The study confirmed the existence of four novel miRNAs, including osa-miR12470, osa-miR12471, osa-miR12472 and osa-miR12473, and the targets of three of them could be successfully validated. The PEG-induced decrease in abundance of the novel miRNAs osa-miR12470 and osa-miR12473 targeting RNA dependent RNA polymerase and equilibrative nucleoside transporter, respectively suggested an overall increase in both degradation and synthesis of nucleic acids in plants challenged with drought stress. The drought-responsive miRNAs identified in the study may be proved useful in introducing the trait in the rice cultivars of choice by manipulation of their cellular abundance.

Nutrient deficiencies are considered major constraints to rice production in sub-Saharan Africa (SSA), but a systematic, continent-wide analysis of these constraints is lacking. The objective of this study was to assess responses of rice yields to macronutrients (N, P, and K) across major rice production systems [irrigated lowland rice (IL), rainfed lowland rice (RL), and rainfed upland rice (RU)] and diverse agro-ecological zones (semi-arid, sub-humid, humid, and highlands) in SSA. Diagnostic trials were conducted in 17 countries in 18–60 farmers' fields in each of 30 sites (totaling 1037 farmers' fields), of which 12 sites were in IL, 15 in RL and 3 in RU. All trials had an NPK treatment, and three treatments in which either nitrogen (N), phosphorus (P), or potassium (K) was omitted from the NPK treatment (minus N, P, and K plots). The trials were conducted during one or two seasons. Regression between yields in the NPK and minus N plots was used for calculating N fertilizer requirement, following the approach used for the development of a nutrient management decision support tool for rice (RiceAdvice) in SSA. Site mean yields in the NPK treatment ranged from 1.4 to 7.3 t ha−1. On average, these yields were 1.1 t ha−1 higher than farmers' yields previously observed in the same sites. N was generally the most limiting nutrient, followed by P. Rice yields without N, P, and K were 68, 84, and 89% of yields in the NPK treatment, and were positively correlated with those in the NPK treatment irrespective of production systems and agro-ecological zone (AEZ). Results from a regression model across sites indicated that achieving 3, 5, and 7 t ha−1 requires N fertilizer application at an average rate of 56, 91, and 122 kg N ha−1, respectively. However, there was significant treatment by site interaction on rice yield. Site mean yields were significantly lower without N, P, and K in 93, 60, and 50% of sites as compared to the NPK treatment. Yield response to macronutrients varied across sites and was not related to production system, nor AEZ. Results from this study will help further improvement of RiceAdvice for providing decision support tailored to the particular site, zone, or production system, thereby closing yield gaps, improving fertilizer nutrient efficiency and preventing negative environmental consequences of fertilizer use.

Drought resistance is required in rice breeding to address the challenge of frequent droughts. However, the evolutionary mechanism of rice drought resistance is not fully understood. We investigated the genetic differentiation between upland and lowland rice domesticated in agro-ecosystems with contrasting water–soil conditions using genome-wide SNPs. We estimated morphological differences among upland and lowland rice in drought resistance and productivity through common garden experiments. Upland rice had better drought resistance but poorer productivity. The negative correlations between traits of drought resistance and productivity are attributed to the underlying genetic trade-offs through tight linkages (e.g., DCA1 and OsCesA7) or pleiotropic effects (e.g., LAX1). The genetic trade-offs are common and greatly shape the evolution of drought resistance in upland rice. In genomic regions associated with both productivity and drought resistance, signs of balancing selection were detected in upland rice, while signs of directional selection were detected in lowland rice, potentially contributing to their adaptive differentiation. Signs of balancing selection in upland rice resulted from bi-directional selection during its domestication in drought-prone upland agro-ecosystems. Using genome-wide association analysis, we identified several valuable quantitative trait loci associated with drought resistance, for which highly differentiated genes should be considered candidates. Bi-directional selection breaking tight linkages by accumulating recombination events would be applicable in breeding water-saving and drought-resistance rice.

The Community-based Upland PalayCheck System under the Upland Rice Development Program was used as a platform of implementation. It has eight (8) KeyChecks as farmers’ best practices and technologies in upland rice production. The study described the socio-demographic profile, institutional factors, biophysical factors, and economic factors of the farmer respondents. Moreover, it described the perceived effectiveness of Farmers’ Field School (FFS) on Upland PalayCheck System, upland community seed banking, and community-based upland palayamanan. Also, the relevance, comparability, traceability, and ease of the practice of the technologies and practices under the Upland PalayCheck System were determined. Also, respondents’ rice production practices and the percentage of adoption under the Upland PalayCheck System were assessed. Furthermore, factors that influence the level of adoption of the Upland PalayChck System were determined. Barangay Kilig and Caragasan were selected as the locale of the study because these were the pilot site of the project in the municipality. The study was conducted through a survey questionnaire and focus group discussions. Respondents were active participants of FFS on the Upland PalayCheck System. Qualitative data were analyzed through SPSS, however, thematic analysis was done to analyzed the reasons of respondents. The result shows that there were more female farmers in the area. Thus, the introduction of technologies should be more gender sensitive. Moreover, the majority of them were elementary level and have limited access to training except for the said FFS. These farmers were mostly owners of their land and the majority manage more than 2 ha. Thus, they need more capital in their farm operation. Also, they get their capital from cooperatives and microfinance which may bring them deep indebtedness if they do not get a good yield. Also, farming was their major source of income in the area. Therefore, they should have given other ventures in agriculture for a living. Furthermore, they get technical advice mostly from technical experts radio and leaflets. However, extension contact was only at least once a month due to the large proportion of extension workers over a number of farmers. Furthermore, the majority of the upland areas of the farmers were low soil fertility. Also, the majority of their field received low precipitation resulting in drought. Nevertheless, upland rice farming can be considered as a good alternative crop in the uplands because of its promising higher average selling price at 25.48% of premium varieties. However, seldom of them were selling their products because it is more for their food consumption. The latest average yield (2.40 t/ha) of farmer respondents was greater than the previous average yield in the municipality (>1.0/ha). Farmers Field School (FFS) on the Upland Community-based Palayaman System was used as a platform to disseminate the objectives of the URDP. The level of effectiveness of farmers on Upland FFS, CSB, and Upland Palayamanan was also assessed. The result shows that the conduct of Upland FFS and overall impressions to URDP were agreed to be very effective. Respondents stated that they gained more knowledge of upland rice farming and increase their yield. Moreover, they have learned to address their problems in upland rice production.

Crop rotations in today’s swidden systems of Northern Thailand typically include five to ten years of fallow. Regarding ecosystem functions, these systems are relatively close to secondary forests when compared to modern agricultural systems; but they are under pressure for intensification, i.e. shortened fallow periods. In general, criteria are needed to decide whether fallow duration can be reduced, safeguarding ecosystem restoration and provision of food and income for farmers. Acknowledging that a comprehensive assessment would cover multiple aspects, our study focuses on the role of fallow duration on tree structural and biodiversity related variables. We studied recovery indicators of tree communities at two potential broad-leaved forest climax sites that differ in soils, forest type and agricultural intensification: An intensive system of one-year upland rice, then one- to two-year maize cultivation with synthetic inputs followed by six years fallow; and an extensive system with one-year upland rice cultivation without agrochemicals and ten years fallow. Contrasting systems were chosen to test the applicability of our indicators, not to compare their management practices. From 2010 to 2011, eight variables related to stand structure and tree diversity were either monitored or surveyed in chronosequence plots of 6 × 50 m representing different fallow ages. For each variable, means per fallow year were compared by least squares means (LS-means), and quadratic regressions from mixed models were fitted. Significant differences between LS-means and optima of regressions served to distinguish fallow stages and served as indicators of recovery and system stability. Stepwise multiple regressions confirmed fallow age as main determinant for most variables. Numbers of tree species and diversity index recovered to levels of the previous rotation within the respective fallow time, but in both systems were far from climax communities, probably due to seed-bank depletion and shift toward resprouting species. While species dominance changed over time in the extensive system, the intensive system was dominated by a single species. In the extensive system only tree density passed a peak during the fallow period, while biomass-related variables approached plateaus. In combination with the replacement of early fallow species, this points to the onset of competition and transition between successional stages. For the intensive system, no structural variable passed a maximum. With only one of eight indicators on the extensive site fulfilling the statistical criterion of passing a peak during the prevailing fallow time, reducing fallow periods is not recommended for our cases. Generally, combining LS-means and quadratic regression allowed assessing fallow duration based on distinct successional stages at different sites. The approach should include various relevant site-specific indicators, in our case representing biomass and carbon storage, species and structural diversity, considered crucial for both sites.

A total of 17 simple sequence repeat (SSR) markers linked to QTLs (qDTYs) governing grain yield under reproductive stage (RS) drought stress were used to assess the genetic relationship and prospecting new donors for qDTYs among 32 popular upland rice genotypes. These SSR markers generated a total of 36 alleles with an average allele count of 2.1 per locus. Polymorphic information content value of the markers ranged from 0.376 to 0.662 with an average value of 0.484. The expected heterozyogosity ranged from 0.381 to 0.632. STRUCTURE analysis divided the 32 genotypes into three sub-populations. Subsequent phenotyping revealed that all the tolerant genotypes were grouped into one sub-population, whereas the moderately tolerant and susceptible genotypes were grouped into separate sub-populations. Phylogenetic tree constructed by the unweighted neighbour-joining method also divided the genotypes into three clusters. The grouping pattern of genotypes into the clusters was similar to that into the STRUCTURE analysis, on the basis of drought tolerance level. The average value of genetic dissimilarity coefficient among the genotypes was observed to be 0.486. Furthermore, by combining genotyping data with phenotyping data, 16 new donors for 6 qDTYs were identified. Keywords: drought screening, genetic relationship, population structure, qDTY donor, upland rice, grain yield

In this study, 13 rice husk (RH) varieties from 4 agro-ecological zones in Uganda were characterized, NaOH-pretreated, and evaluated for their potential utilization as precursors for production of bio-oil, ash, char, and activated carbon for selected applications. RH varieties were characterized through particle size analysis, bulk density, proximate and ultimate analyses, specific surface area, pore volume, as well as lignocellulosic and inorganic compositions. Selected RH varieties were subsequently pretreated at NaOH concentrations of 1–4%w/v, using pretreatment ratios of 5 g RH: 40 mL NaOH. Properties varied among RH varieties, suiting them as feedstocks for different applications. Upland rice husk varieties are more suited precursors for production of bio-oil, and activated carbon due to their relatively lower ash content, higher specific surface area, as well as higher volatile matter and fixed carbon contents. Upland rice husks could as well be employed in the preparation of electrodes for electrochemical devices, due to their relatively higher specific surface area. A high ash content (21–32% dry basis) of lowland rice husks presents good prospects for their calcination, since larger amounts of rice husk ash could be obtained, and employed in different applications. Lowland rice husk varieties could also be more suited precursors for production of char for soil amendment, due to their relatively higher ash content, which subsequently increases their char yields. However, alkaline pretreatment of rice husks using 2–4%w/v NaOH can reduce the ash content by as much as 74–93%, depending on the rice husk variety, which paves way for utilizing rice husks with a high ash content in different applications. Aside from ash reduction, the enhanced specific surface area (1.2–1.7 m2 g−1), volatile matter (68–79%db) and fixed carbon (19–24%db) contents of NaOH-pretreated rice husks suggests they are more suited feedstocks than when employed in their raw form, for production of bio-oil, as well as activated carbon.

The increase in emission of greenhouse gases (GHGs) due to anthropogenic perturbation in both the agricultural and natural eco-systems are degrading the environmental quality. Conventional tillage (CT) and residue burning/removal exacerbates the land degradation and GHG emission, and the impacts are much more in the upland ecosystem than valley lands. Therefore, the aim of the present study was to evaluate the energy budget, and carbon footprint (CF) of no-till (NT) and mulches under the upland rice (Oryza sativa)–mustard (Brassica campestris var. toria) cropping system over CT based system to develop a clean production technology for improving the environmental quality and conservingnatural resources. The novelty of the study is that integrated effect of NT, diverse mulches and cropping system effect has been considered together as a conservation measure for sustainable and clean agricultural practice over those of CT based technologies. The experiment comprised of two tillage systems as the main-plot and four mulch types as the sub-plot treatments under a split-plot design. Two tillage systems included: 1. CT-RI: CT with 100% residue incorporation (RI), and 2. NT-RR: NT with 100% residue retention (RR). Four mulch types included: 1. rice straw mulch (SM), 2. green manure (GM) - Gliricidia sp. (a leguminous shrub) mulch, 3. brown manuring (BM) mulch [cowpea (Vigna unguiculata) grown as an intercrop and killed with a spray of 2, 4-D, 40 days after sowing (DAS)] and 4. no mulch (NM) control. The adoption of NT-RR significantly (p = 0.05) reduced the energy use (16,727 MJ/ha) and the cost of production (INR 54,271/ha, 1 US$ = 64.46 INR) compared with those under CT-RI (27,630 MJ/ha and INR 76,903/ha, respectively). Thus, NT-RR also increased the energy use efficiency (EUE), energy productivity (EP), net returns, and reduced CF of the system compared with those under CT-RI. Use of different mulches also increased the energy use efficiency, system productivity, and net returnscompared with those under NM. The total CO2-e emission (CF) was higher under CT-RI (2307 kg CO2-e/ha) as compared to those under NT-RR (2013 kg CO2-e/ha). The savings of fossil fuel from less number of tillage operations and also low emissions associated with energy consumed in manufacture, transport, repair and use of machines contributed to the lowest GWP under NT-RR. Thus, the study supports and recommended that the NT-RR with BM is an environmentally safe and clean production technology for enhancing the energy use efficiency, reducing the CF and cost of production of direct-seeded upland rice-mustard cropping system in India and similar agro-eco-regions elsewhere in the rice based cropping system in the world.

A vast upland area in Madagascar remains uncultivated because of erratic rainfall and because of the low fertility of the soils that are highly weathered and depleted in available phosphorus (P). This study was set up to identify to what extent farmyard manure (FYM) can overcome P deficiency and increase the use efficiency of mineral P (TSP). Rainfed rice was grown with soybean in rotation (two fields) in three subsequent seasons with factorial supplies of FYM and TSP (both applied in planting hole) with blanket N&K doses. The low and unresponsive rice grain yields (

Luang Prabang Province is located within the area recognized as the center of rice (Oryza sativa L.) diversity in Lao PDR. This study reported on grain quality characteristics of 60 upland rice seed samples sharing 49 variety names collected from 6 villages in Luang Prabang in 2015. Most of the samples has non-pigmented pericarp, while red pericarp was found in four samples and purple in five samples. Almost all of the samples were of large grain type, with glutinous endosperm in 70% and non-glutinous endosperm in 30%. The brown (unpolished) rice was found with a wide range of grain nutritional quality, including protein (9.2% ± 0.9%), Fe (15.9 ± 6.9 mg/kg), Zn (19.6 ± 2.1 mg/kg), anthocyanin (0.774 ± 0.880 mg/g), and anti-oxidative capacity (2.071 ± 1.373 mg/g). The varieties sharing similar names had similar morphological characteristics but varied in nutritional concentration, with required confirmation in genetic variation analysis. This study found that some rice varieties with high grain quality may benefit the farmers directly or could be used in varietal improvement programs.

The National Agricultural Research Organisation (NARO), Uganda, under the ATAAS Project and the University of Pretoria.

The objective of the present study was to evaluate agronomic biofortification with nitrogen (N) and selenium (Se) with the aim of increasing the daily Se intake by the population and the nutritional quality of the grain. A randomized block experimental design with a 5 × 2 factorial scheme was used; the factors were the five levels of N (0, 20, 40, 80, and 120 kg ha−1), applied as topdressing fertilization, and the two levels of Se (0 and 25 g ha−1). The reserve protein fractions in the seeds, glutelin, and globulin increased significantly when Se application was combined with N fertilization. Grain Se content varied from 0.03 to 0.35 mg kg−1, which was within the food safety limit of 0.3 mg kg−1 established by the Codex Alimentarius. The estimated daily Se intake originating from Se-biofortified rice varied between 2.05 and 24.7 μg per day, representing an increase from 3.72% to 44.9% of the daily Se requirement. Because the recommended Se daily intake for adults is 55 μg per day, the present study presents relevant information about agronomic biofortification to increase Se concentrations in edible plant parts, with possible benefits to human health.

Rice is one of the staple food crops and is a profitable smallholder cash crop in Zambia. It has the potential to contribute significantly to increased incomes and employment among rural producers. However, rice is the only staple crop in the country for which domestic production does not meet or exceed domestic demand. Low productivity is one of the factors that contribute to this. One necessary step towards addressing this problem is the identification of land with greatest potential for rice production, as well as the identification of land-based limitations which might be overcome by improved management. The aim of this study was to develop a land suitability index for rainfed paddy rice production reflecting expert opinion and published studies based on climatic, topographic and soil properties. Land suitability was evaluated using a method which accounts for important multiple factors, and which considers their joint effect in terms of a hierarchical model of constraints. The suitability classes were ranked according to the FAO land suitability classification as: Highly Suitable (S1), Moderately Suitable (S2), Marginally Suitable (S3), Currently Not Suitable (N2), and Permanently Not Suitable (N1). Results showed that there is limited potential for rainfed paddy rice production in Zambia with

Little is known about the impact of the combined application of intercropping and arbuscular mycorrhizal fungus (AMF) on the plant growth and Cd accumulation in the two intercropped plants. A greenhouse pot experiment was performed to investigate the effects of intercropping (IC) and AMF-Glomus versiforme (GV) on the growth, photosynthesis, Cd accumulation and antioxidant activities in the two intercropped plants-upland rice and Cd hyperaccumulator Sphagneticola calendulacea (L.) Pruski in the soils added with 5 mg Cd kg-1. It was found that the GV inoculation and the combined treatment of IC and GV (IC + GV) significantly (p < 0.05) increased the biomasses and the P contents of upland rice and S. calendulacea. In addition, the Cd concentrations and uptakes of plants in IC, GV and IC + GV treatments were significantly (p < 0.05) dropped in upland rice but increased in S. calendulacea compared with the monocropping control, and the compound treatment showed better effect on decreasing Cd accumulation in upland rice (especially grains) and increasing Cd uptake by S. calendulacea compared with the single intercropping or AMF treatment. Moreover, IC, GV and IC + GV treatments significantly (p < 0.05) improved the net photosynthetic rate, stomatal conductance and transpiration rate of the two intercropped plants. Finally, IC, GV and IC + GV treatments all significantly increased the catalase activities and total antioxidant capacities, while decreased the malondialdehyde contents in upland rice and S. calendulacea. The present work could provide a feasible strategy for safe production of upland rice and phytoremediation of Cd contaminated soils.

Analysis of rice microarray data indicated that a gene encoding for chalcone isomerase2 (OsCHI2) showed upregulation in response to abiotic stress. Hence, we isolated OsCHI2 from a popular drought tolerant upland rice variety Nagina22 and developed transgenic plants of a drought stress sensitive rice cv. Pusa Sugandh 2 expressing OsCHI2 under the control of stress inducible promoter AtRd29A and further studied their response to different abiotic stresses. Stable chromosomal integration of transgene was confirmed in the transgenic plants through PCR, Southern hybridization and expression analysis. Physio-biochemical studies revealed that the Rd29A::OsCHI2 transgenic rice plants upheld higher relative water content, more photosynthetic pigments and proline with lower relative electrolyte leakage and less malondialdehyde content as compared to WT plants under abiotic stresses. Quantitative RT-PCR analysis demonstrated that the expression level of the transgene in the OsCHI2 transgenic lines was higher than WT plants under stress conditions. Stress-inducible expression of OsCHI2 also enhanced transcript abundance of structural genes of flavonoids biosynthesis pathway leading to higher production of flavonoids under abiotic stresses in the transgenic plants. In brief, our results demonstrated that OsCHI2 is not only capable of modulating flavonoid metabolism but also can impart enhanced adaptation to different abiotic stresses other than heat stress.

Mineral fertilizer input is indispensable to offset yield stagnation in rainfed upland rice production in sub-Saharan Africa (SSA). The present study is the first attempt to perform a meta-analysis based on a Bayesian approach with the objective of quantitatively assessing the impact of mineral fertilizer application on upland rice yield and quantifying the effects of soil type and precipitation on the yield response to mineral fertilizer application. The data were gathered from 13 field studies on the rice variety NERICA 4 in 8 SSA countries, which provided a total of 151 paired observations. The yield gain with fertilizer application (YG) varied considerably, ranging from –0.8 to 3.0 t ha−1, with an average of 0.6 t ha−1. Based on the empirical relationships among the datasets, the total precipitation during the cropping season, N fertilizer application rate, and binarized soil type (i.e., low clay [≤ 20 %] and high clay [> 20 %]) were selected as key factors for the determination of YG. High clay soils exhibited higher YG than low clay soils did (i.e., 0.87 vs. 0.37 t ha−1, respectively). The relationships of YG with the N fertilizer application rate and precipitation were modeled for each soil type using a Bayesian approach. The results of the Markov chain Monte Carlo simulation indicated that greater precipitation improved YG with high credibility irrespective of soil type. Additionally, a greater rate of N fertilizer application in high clay soil also improved YG with high credibility, while its contribution to YG in low clay soil was inferior. These results highlight the need to develop a field-specific nutrient management strategy for rainfed upland rice with a focus on fine-tuning the N fertilizer input based on the soil texture and expected precipitation for improving upland rice yield and nutrient use efficiency in SSA. The Bayesian procedure offers a new approach for the meta-analysis of the yield response to mineral fertilizers as affected by biophysical factors. However, including more data points in the database and additional factors in the data analysis are warranted to improve the model predictability and reliability.

Nutrient deficiencies limit rice production in sub-Saharan Africa. The conventional recommended remedy for this is the soil application of fertilizers composed of the macro-nutrients, N, P and K, whereas crop micronutrient requirements are neglected. This leads to nutrient mining and diminished fertiliser use efficiency. Application of micronutrients along with recommended NPK fertiliser rates can prevent nutrient mining and boost rice yields. In this study, we assessed the productivity and profitability of different soil- and foliar-applied micronutrients in 30 on-farm trials per year for two consecutive years (2015, 2016) in Tanzania, East Africa. Five locally available foliar formulations (combinations of macro- and micronutrients or micronutrients alone) and soil application of micronutrients (3−2−7.5−10 Zn-B-Mg-S kg ha–1) were assessed under two NPK-fertilization regimes (80−17.5−33.2 and 0−0−0 kg N-P-K ha–1) in three rice growing environments (RGEs): Irrigated Lowland (IL), Rainfed Lowland (RL), and Rainfed Upland (RU). The effect of foliar and soil applied micronutrients on yield was consistent in IL but was highly variable in the RL and RU conditions across years. The soil application of micronutrients in the absence of NPK was ineffective in any of the RGEs. In IL, without NPK, foliar application alone increased yield by 0.3−0.4 t ha–1, compared to control (3.1 t ha–1). Only NPK application increased yield by 1 t ha–1, while NPK and micronutrients application increased yield by 1.5 t ha–1, compared to control. The benefit-cost (B:C) ratio for NPK with soil applied micronutrients was 4–4.5 compared to NPK application alone. In RL, application of NPK alone increased yield in 2015 from 2.7 to 5.0 t ha–1 while NPK and soil applied micronutrients application increased yield to 6.8 t ha–1. However, a drought incidence in 2016 nullified this effect. With NPK, two foliar products (F2 and F3) increased yield significantly by 1 t ha–1. The highest B:C ratio was obtained with soil applied micronutrients (B:C of 14), and two of the foliar products obtained a B:C ratio of 7 and 7.2, respectively. In RU, no significant yield differences were observed among treatments in any year, likely due to drought. Foliar application was effective only under drought-free conditions across the rice growing environments. This study demonstrated that soil applied micronutrients together with NPK significantly increased yields in IL and RL in the absence of drought-stress. Application of macronutrients is a likely prerequisite for maximizing the benefits of applying micronutrients to increase rice yields in Tanzania.

Despite increasing pressure on land, many hill tribe communities in Northern Thailand practice traditional swidden agriculture with long fallow periods that allow the soil to recover from cropping. To determine the most appropriate time for a new cropping cycle, farmers, in a collective decision making process, often use presence or numbers of tree species considered as soil fertility indicators. In Nong Khao, a case study village in Mae Hong Son district, we investigated in how far abundance of indicator tree species found during vegetation surveys corresponded to measured soil fertility parameters and whether an extended list of indicator species could improve prediction of these soil properties. During interviews, farmers listed 11 tree species considered indicators for good upland rice and vegetable soil, unsuitable soil for upland rice, or hard soil. Abundances of indicator species as well as of other species found during comprehensive botanical inventories on 135 plots of different fallow ages were introduced into regression models to predict soil fertility parameters measured on the inventoried plots. Both models – including only indicator species versus all species found in the inventories – were compared regarding their predictive power for soil properties. Soil organic matter (SOM), pH, plant available phosphorus (Pav) – related to farmers’ criteria ‘good soil’ or 'unsuitable for rice cropping’ – as well as bulk density (BD, for ‘hard soil’), changed significantly during the fallow period, from initial maxima towards temporary pessima in years 6 to 7, followed by recovery towards year ten. Most indicator species, like Macaranga denticulata for enhanced Pav or Dalbergia cultrata for high SOM, were clearly related to the soil quality characteristics attributed to them by farmers. Including all inventoried tree species significantly improved predictions of measured soil parameters by ΔAIC > |2|. Ten additional species from the surveys had potential as additional indicator species. Our approach to relate indicator species to measured soil parameters is generic across areas, while soil parameters are site-specific. Applicability of our approach to link environmental parameters to indicator species could be extended if further criteria considered important by farmers such as weed suppression, represented by tree structure parameters, would complement soil fertility.

Worldwide, approximately 27 million ha of rice are grown in upland rather than paddy fields, and is subject to drought stress. To counter this stress, it is desirable to breed new rice cultivars with improved drought tolerance. For breeding purposes, especially for breeding upland rice, it is desirable to develop a simple and accurate method to evaluate rice drought tolerance. We describe a new method that can be used to evaluate efficiently the drought tolerance degree (DTD) of upland rice cultivars, and call it the DTD method. DTD is defined as the mean of the ratios of green leaf length to total leaf length of the top three leaves in every rice seedling after drought treatment, and thus takes values from zero to one. To test whether the DTD method works effectively to evaluate drought tolerance of upland rice cultivars, we determined the DTD values of 13 upland rice cultivars showing varying degrees of drought tolerance in drought-tolerance trials. The idr1-1 mutant, which displayed the strongest drought tolerance of the 13 cultivars as identified by drought-tolerance trials under severe drought stress, had the highest DTD value and 297-28, displaying the weakest drought tolerance, had the lowest DTD value. Further analyses of water potential, survival rate, panicles per plant, spikelets per panicle, seed setting rate, yield per plant, and contents of proline, chlorophyll, and malondialdehyde (MDA) indicated that DTD values are in general correlated with the values of these traits, making this new method useful for assessing the drought tolerance of upland rice cultivars. These results show that the DTD method is a simple, direct and relatively accurate evaluation method for drought-tolerance breeding of upland rice. Keywords: Upland rice, Breeding, Drought tolerance degree (DTD), New evaluation method

Iron (Fe) is an essential nutrient for plants but under high concentrations, such as that found naturally in clay and waterlogged soils, its toxic effect can limit production. This study aimed to investigate the stress tolerance responses exhibited by different rice cultivars. Both lowland and upland cultivars were grown under excess Fe and hypoxic conditions. Lowland cultivars showed higher Fe accumulation in roots compared with upland cultivars suggesting the use of different strategies to tolerate excess Fe. The upland Canastra cultivar displayed a mechanism to limit iron translocation from roots to the shoots, minimizing leaf oxidative stress induced by excess Fe. Conversely, the cultivar Curinga invested in the increase of R1/A, as an alternative drain of electrons. However, the higher iron accumulation in the leaves, was not necessarily related to high toxicity. Nutrient uptake and/or utilization mechanisms in rice plants are in accordance with their needs, which may be defined in relation to crop environments. Alterations in the biochemical parameters of photosynthesis suggest that photosynthesis in rice under excess Fe is primarily limited by biochemical processes rather than by diffusional limitations, particularly in the upland cultivars. The electron transport rate, carboxylation efficiency and electron excess dissipation by photorespiration demonstrate to be good indicators of iron tolerance. Altogether, these chemical and molecular patterns suggests that rice plants grown under excess Fe exhibit gene expression reprogramming in response to the Fe excess per se and in response to changes in photosynthesis and nutrient levels to maintain growth under stress.

Black beetles (BB: Heteronychus spp.: Coleoptera, Scarabaeidae) are serious constraints to upland rice production in the Madagascar central highlands. From 2002 to 2007 we compared the effects of two soil management and two fertilization modalities in an upland rice-based cropping system on soil macrofauna abundance, diversity and BB damage to rice crops and yield. This cropping system involved a 2-year rotation of upland rice the first year, followed by common bean the second year, with oat as a relay crop under both conventional tillage (CT) and no-tillage soil management (NT), each under both organic (OF) and mineral fertilization (MF). All four modalities (CT-OF; CT-MF; NT-OF and NT-MF) were managed under two plant protection levels (seed dressing with imidacloprid + thiram vs no seed dressing). Herbivorous/detritivorous beetles were the most abundant soil biota, respectively representing more than two-thirds and half of all macrofauna at the outset of the experiment and 4 years later, with the BB Heteronychus arator rugifrons (Fairmaire) being the dominant pest species (herbivore). The Shannon diversity index was reduced significantly between the beginning and the end of the experiment 4 years later, while it was only marginally affected by soil management, fertilization and seed dressing regimes at both sampling dates. Throughout the study period, seed dressing resulted in a significant reduction in BB damage, and in a significantly higher rice grain yield as compared to control. NT management did not enable seed dressing discontinuation based on grain yield and BB damage level after 3 and 4 years of this practice, respectively. In this respect, CT-MF management ranked best in the absence of seed dressing. The reasons for the poor performance of NT management in the studied cropping system as compared to the same strategy used in other systems reported in earlier studies are discussed. (Resume d'auteur)

Family farms in the tropics mainly rely on rainfed agriculture. Water availability is limited to rainfall and is one of the main constraints to crop productivity. Conservation agriculture (CA) is promoted as an alternative that, among other functions, enhances water infiltration and limits evaporation from the soil thanks to a mulch of crop residues left on the soil surface. These functions are assumed to reduce the water availability constraint by limiting water stress during crop growth. But the variability of rainfall distribution combined with the wide range of agroecological conditions and the variety of crop husbandries in the tropics makes it difficult to evaluate the efficiency of mulching. The aim of this study was to capture the variability through a simple modeling approach using the crop growth model PYE-CA, which requires a limited set of parameters and a virtual experiment (VE). We applied our approach to a case study of upland rice in the Lake Alaotra region in Madagascar, where rainfall distribution is highly variable. The VE used a 17-year series of weather data with a range of soil water conditions, sowing dates, and growth and yield limitations that cover the variability of agroecological conditions and management systems in the study area. The VE revealed that variable successions of wet and dry episodes during the rainy season resulted in both water stress and an increase in deep drainage. In the majority of conditions simulated, enhancing water infiltration through CA mainly increased water loss through drainage. However, better water infiltration may also reduce the production risks involved in early sowing or crop intensification, thereby offering new opportunities to farmers. As an alternative to time consuming and labor intensive experimentation, we propose a suitable modeling approach to identify the main drivers of rainfall × crop interactions that could be extrapolated to other regions in the tropics.

International audience; Although Sierra Leone aims to improve the livelihoods of its rice-farming households, the effect of specific policy changes on diverse households remains an open question. This study presents a household model that simulates strategies of production and consumption for rice-farming households in Sierra Leone. It accounts for non-separability between household production and consumption decisions, accounts for resource constraints, and uses a risk-adjusted measure of welfare. The model simulated the effects of three policy scenarios seeking to improve food consumption and calculated production, consumption and socio-economic indicators. The scenarios included: 1) subsidizing rice seed costs, 2) subsidizing palm oil production costs, and 3) subsidizing the conversion of lowlands into land suitable for rice production. The model was applied to four representative rice-farming households in northern Sierra Leone that differed in their land resources and rice consumption. The four household types included: 1) Upland_intensive, 2) Lowland_intensive, 3) Upland_extensive, and 4) Lowland_extensive. Results show that extensive lowland-based households had the lowest rice consumption (54 kg capita−1 year-1) and caloric intake (843 Kcal capita−1 day−1) in comparison with the other household types. Subsidizing rice seed costs in the lowlands, compared to the baseline scenario, improved rice consumption across the households by 15–34%, and farm income by 12–57%. Regardless of the scenario, differences in caloric intake, in comparison to the baseline scenario, were less than differences in rice consumption, thus indicating substitution effects between the different foods (vegetables, cereals, oils, and sweet potatoes). A maximum caloric increase of 16% was achieved by subsidizing palm oil production costs. Subsidizing lowland conversion for rice cultivation improved rice consumption mainly through the subsidy’s positive effect on rice production, which in turn effected self-consumption. Depending on the scenario, the increase in household income was mainly because of an increase in upland rice area, an increase in rice sowing rates, an increase in cash, or a specialization in lowland rice combined with planting a cash crop.

This study followed up on results of an integrated rodent management program that was implemented from 2010 to 2011 in 18 treatment and 18 control villages in three provinces of Northern Laos. The program's impact on reducing rodent damage to upland rice was reported previously. Here, we focused on the efficiency with which upland villagers applied the proposed rodent control methods (snap traps, biological control using the protozoan parasite Sarcocystis singaporensis, community hunts) by comparing control effort (inputs) to an output of more than 73,000 rodents (mainly black rats) culled in Houphanh (HP) province. We also hypothesized that rice yields of a given crop year (2009) could predict rat damage in the three provinces in following years (2010, 2011). A survey of flowering of bamboo and fagacean ‘nut’ trees in 2011 was used to check for a potential influence of flowering events on rodent infestation. Using regression analysis we observed that efficiency (cumulative culls method−1) of snap traps and biological control decreased significantly with increasing field size of upland rice fields, while the opposite trend was apparent with regard to paddy fields. Numbers of rodents culled by hunting and trapping increased with rising numbers of hunting villagers, but culls household−1 declined with increasing village size. We developed multiple regression models that predicted rodent culls by the paddy/upland rice area ratio and rodent control effort and explained >90% of the variation. Rat damage to wet season rice in 2010 and 2011 (and rodent culls ha−1) increased with increasing village rice yields of 2009, while the treatments' regression line was positioned at a 5.5% lower rat damage level, in parallel to the controls. Integration of the observed relationships using the General Linear Model (GLM) allowed predicting rat damage under different treatment and seasonal scenarios. Surprisingly, 99.8% of the variation in rodent culls ha−1 in HP could be explained by a combination of rodent control effort, rice productivity, and flowering events. Herewith, we provide predictive and explanatory models that could be useful for future rodent management in the uplands. The observed relationships are discussed in view of potential forecasting of chronic rodent infestation and, ultimately, outbreaks.

Rice (Oryza spp.) is the major staple food for most countries in West Africa, but local production does not meet demand. Rice is grown mainly by smallholder farmers, and yields are generally low with high temporal and spatial variability. Low yields have been attributed to unfavorable climate conditions, poor soil quality, and sub-optimum agricultural practices. The objectives of this study were to assess variation in yields of three major rice production systems (irrigated lowland, rainfed lowland, and upland) across three climatic zones (semi-arid, sub-humid, and humid), and identify factors affecting that variation. We analyzed data on yield, climate, soil, and agricultural practices for 1305 farmers’ fields at 22 sites in 11 West African countries between 2012 and 2014. A boundary function approach was used to determine attainable yields. Random forest algorithm was used to identify factors responsible for yield variation. Average rice yield was 4.1, 2.0, and 1.5 t ha−1 in irrigated lowland, rainfed lowland, and rainfed upland systems, respectively, with maximum attainable yields of 8.3, 6.5, and 4.0 t ha−1. Yield difference between attainable and average yield tended to be higher in irrigated and rainfed lowland systems. In those two systems, yields were highest in the semi-arid zone, while no difference in yields among climatic zones was apparent for upland rice. High rice yields were associated with high solar radiation, high maximum temperature, intermediate air humidity, multiple split nitrogen (N) fertilizer applications, high frequency of weeding operations, the use of certified seeds, and well-leveled fields in the irrigated lowland system. Minimum temperature, solar radiation, rainfall, construction of field bunds, varietal choice, and the frequency of weeding operations were determinants of rice yield variation in the rainfed lowland system. Varietal choice, bird control, and frequency of weeding operations affected rice yields in the upland system. Improving access to inputs, improving input use efficiencies, and site-specific management strategies are recommended as priority interventions to boost rice yields at regional scale independent of production system and climatic zone.

In the central highlands of Madagascar, blast, a serious fungal disease of rice caused by Magnaporthe oryzae, was shown to be less severe in conservation agriculture (CA) than in conventional tillage (CT) cropping systems. To assess the effects of CA cropping systems on rice susceptibility to blast and to understand the mechanisms involved, an experiment was conducted over three growing seasons in two sites (at high and mid-altitude). Two fertilization treatments, one with mineral nitrogen (N) fertilizer, and one without, were studied in interaction with two different cropping systems (CA/CT) and two rice varieties that differ in their susceptibility to blast. The performances of the two cropping systems were assessed, and results showed that yields were no higher in the CA or were lower than in CT cropping systems. The effects of the treatments on upland rice crop growth were measured by leaf N content as an indicator of N crop status, and leaf area index (LAI) as an indicator of canopy density. In all years at both sites, leaf N content during early growth stages was higher in the CT than in the CA cropping system. The LAI was lower in the CA than in the CT cropping system at the high altitude site in all three years, and in two out of three seasons at the middle altitude site. Overall, when the level of blast was high, blast was less severe in the CA cropping system and with no N fertilizer. Leaf N content and LAI were used as intermediate explanatory variables in the statistical analyses, and one or the other or both always masked the effect of the cropping system or of N fertilization. Our results show that leaf N content during early growth stages masks the effect of the cropping system on leaf blast severity. When the LAI is strongly affected by the cropping system, it also masks the effect of the cropping system on the severity of leaf and panicle blast. Very often both variables masked the effects of the cropping system and of N fertilization. These findings should help improve disease management by modifying fertilization practices and crop nutrition in conservation agriculture cropping systems.

The efficacy of vapor-phase (VP) upland rice vinegar (URV) was investigated as a bio-fumigant for maize, to reduce consumer health risks associated with spore and toxin formation by Aspergillus flavus . Complete reduction of mycelial growth occurred with in vitro VP exposure to URV (containing 0.0017 mmol/L acetic acid) or with VP exposure to pure acetic acid (PAA) (containing 0.0023 mmol/L acetic acid). No significant differences were observed between the two materials after 90 min exposures. Using gas chromatography-mass spectrometry (GC-MS), URV vapor was shown to contain volatiles having antifungal activities. These are identified as isoamylalcohol, 1-butanol, 3-methyl-, acetate and β-phenylethyl acetate. It is suggested these volatiles increase the antifungal effectiveness of URV. Exposure to VP-URV (containing 0.0043 mmol/L AA) for 5 h completely eliminated viable spores of A. flavus on maize seeds (23% moisture content) previously inoculated with 4.43 ± 0.28 log spores/g). At the same time, aflatoxin production decreased, as VP-URV exposure increased. Hence, VP-URV is shown to be an effective control agent for A. flavus mycelial growth and aflatoxin formation on maize, so effectively reducing the potential for consumer health risks due to this widespread fungus.

With the shortage of water resources and environmental pollution caused by unreasonable fertilization, the research on water-nutrition interaction has become a hot topic. However, the synergistic effects of effects of phosphorus (P) application rates and irrigation schedules on grain yield and quality of paddy rice and upland rice were less studied. Field experiments were conducted on upland rice (japonica Zhonghan 3) and paddy rice (japonica yangfujing 8) under three P (P2O5) application rates, 50 (low amount, LP), 100 (normal amount, NP) and 150 kg ha −1 (high amount, HP) and two irrigation schedules, bare-dry (BD) and continuous flooding (CF, control). BD with HP and CF with HP were conducive to the highest yield of upland rice, but there was no significant difference between NP and HP for two varieties except for paddy rice under BD. The head rice rate of upland rice and paddy rice was the highest at LP under BD and CF, but there was no significant difference between NP and LP. The setback viscosity was the lowest and the breakdown viscosity was the highest for two varieties under BD with LP and under CF with NP, however, NP had no significant difference for two varieties compared to LP under BD and compared to HP under CF. Compared with CF, BD reduced grain yield, improved processing quality and appearance quality. The results suggested that bare-dry combined with normal P application for upland rice cultivation and continuous flooding combined with normal P application for paddy rice cultivation are promising options for increasing grain yield, processing quality and cooking quality.

Topsoil is the most sensitive to land management practices, and the application of fire has been used for clearing the land and burning crop residues in highlands. Thus, investigating the topsoil organic carbon density (SOCD) is crucial to improve the understanding of its impact. Four sites of highland maize-upland rice systems in the Mae Chaem Basin, Chiang Mai Province, Thailand were selected as study areas and investigated for two years . At each site, burnt and unburnt soil samples were collected separately from depths of 0–10, 10–20, and 20–30 cm. Results showed that burnt soil contained higher SOCD than unburnt soil, with average values of 75.0 and 71.4 Mg C ha−1, respectively; however, a significant difference was not detected. The SOCD of burnt soils increased in the first growing season after the burning 5 months due to the large amounts of ashes and black carbon left after the fire and decreased in the second growing season after the burning 10 months. Burning caused the fluctuation of SOCD, resulting in a slight increase of SOCD in burnt soils by 0.19 Mg C ha−1 year−1, whereas it steadily increased by 2.04 Mg C ha−1 year−1 in unburnt soils across the maize-upland rice system. This study pointed out that burning may not sustain the SOCD in the long term, especially in the highlands.

Understanding the community composition and diversity of arbuscular mycorrhizal fungi (AMF) in agricultural ecosystems is important for exploring their potential for use in sustainable crop production. In this study, we collected rice root samples from upland rice fields under different agricultural practices in four districts of Bangladesh (Khagrachori, Rangamati, Chattogram, and Bandarban) to estimate the AMF colonization rate and to investigate the taxonomic diversity and community composition of indigenous AMF by high-throughput Illumina amplicon sequencing. The AMF colonization rates of the rice root samples ranged between 14 and 47%, and were positively correlated with the soil pH (4.58–5.93), suggesting that more AMF colonization is likely to form under slightly acidic conditions. This result suggests that AMF colonization rate in upland rice roots might be affected by soil pH; however, no significant correlation with soil available phosphorus contents was observed. In total, eight different AMF genera were detected by amplicon sequencing. Glomus and Paraglomus were found to be the dominant genera in all the regions, followed by Scutellospora, Acaulospora, Claroideoglomus, Diversispora, Gigaspora, and Archaeospora. Shannon’s diversity index and Pielou’s evenness were significantly higher in the Bandarban district than the other districts, whereas Faith’s phylogenetic diversity and richness showed no significant difference between the four districts. The beta diversities of AMF community composition based on the Bray-Curtis dissimilarities were significantly differentiated among the districts. The soil available phosphorus contents were significantly correlated with the AMF beta diversities between the four districts. This is the first study to report on the AMF community composition and diversity in upland rice roots and on how AMF communities are affected by the soil chemical properties in different locations in Bangladesh.

Genetic improvement has been given high priority in rice research for development in sub-Saharan Africa (SSA). This paper provides an overview of historical efforts of genetic improvement in SSA focused on improving rice productivity. It further describes yield gain of new rice varieties evaluated in recent field experiments in four selected breeding target domains, and summarizes adoption studies on rice varieties. Efforts to develop rice varieties adapted to diverse rice production systems in SSA have been made by several research organizations, including national agricultural research institutes, bilateral organizations, and three CGIAR centers. The efforts have resulted in the release of around 570 rice varieties in 10 major rice-producing SSA countries by 2020. Among these varieties, the most well-known are interspecfic upland rice varieties “New Rice for Africa (NERICA)” that were developed from crosses between improved Oryza sativa tropical japonica and Oryza glaberrima varieties. However, recent field assessements demonstrated that upland rice yield can be further improved through introduction of upland indica materials from Asia. In contrast, lowland interspecific rice varieties out-yielded the previously released improved O. sativa varieties in selected SSA countries. Field assessments in Senegal and Madagascar did not demonstrate the yield advantage of the recently-developed varieties including hybrids over best performing ones released before. The adoption level of improved varieties in terms of share of area occupied by improved varieties in 18 SSA countries was 40 % in 2008 with old varieties that were released before 2000 being dominant and 7% of the total rice area occupied by NERICA varieties. Especially in irrigated and rainfed lowland rice systems, the majority of dominant varieties were still those introduced from Asia. Panel data between 2002 and 2019 from the Senegal River Valley also confirmed this, and Sahel 108, which was introduced from Asia and released in Senegal in 1994, accounted for >70 % of the total rice area in both the wet and dry seasons in 2019. The implications of this review for future rice genetic improvement and varietal replacement in SSA are discussed.

Intercropping of hyperaccumulators with crops is a promising measure to enhance phytoremediation without impeding agricultural production. A Cd-hyperaccumulator, Solanum nigrum L. (S. nigrum), was intercropped with upland rice in a pot and rhizo-box experiment with Cd-contaminated soil to evaluate the combined effects of intercropping and arbuscular mycorrhizal fungi on plant growth and Cd accumulation. The results showed that, compared with monoculture, the combined treatments markedly decreased Cd concentration in rice parts, with the lowest Cd concentration in brown rice (reducing by 64.5%). The spatial distribution of root surface area and DTPA-Cd in the rhizo-box indicated competitive Cd uptake by neighbouring S. nigrum. Moreover, the combined treatments reduced Nramp5 expression but increased HMA3 levels in rice roots, leading to lower bioaccumulation and transfer coefficients. Additionally, fewer secreted organic acids and a higher rhizosphere pH were observed in rice. Conversely, the combined treatments promoted biomass, root length, root surface area, and decreased the rhizosphere pH in S. nigrum, thus increasing the Cd accumulation. Although the intercropping system with AMF inoculation notably reduced rice yield, the land-use efficiency was higher. These results provided insights into the role of AMF in the upland rice/S. nigrum system and demonstrated an alternative system for Cd phytoremediation.

This study examines the molecular response of upland rice when exposed to different inorganic arsenic (iAs) species. One-week-old upland rice (Oryza sativa indica DOURADOAGULHA) seedlings were separately exposed to 100 μM arsenite [As(III)] and arsenate [As(V)] in hydroponic culture for 12 h. Genome-wide transcriptomic analysis revealed that 2983 and 1844 genes were responsive under As(III) and As(V) stresses, respectively. There were 915 shared genes between As(III) and As(V) treatments. Arsenic stress induced changes in complicated gene regulatory pathway of upland rice seedlings, including transcriptional regulation, hormone signaling, redox, transporters and detoxification process. In upland rice separately exposed to As(III) and As(V) for 12, 24, 48 and 72 h, qRT-PCR analysis showed that WRKY4, bHLH and AP2-EREBP associated with transcriptional regulation were significantly down-regulated, while NAC [NAM (no apical meristem), ATAF (Arabidopsis thaliana activating factor) and CUC (cup-shaped cotyledon)] transcription factor was up-regulated. The hormone signaling related gene OZG2, the redox related genes encoding Prx, GST, oxidoreductase and cytochrome P450, the transporter process related genes OsABCC9 and ZIP3 were affected under As stress. Under As(III) and As(V) treatments for 1 and 3 d, the malondialdehyde (MDA) contents in upland rice were increased, while catalase (CAT), peroxidase (POD), superoxide dismutase (SOD) and glutathione reductase (GR) contents were significantly declined. In addition, transcriptomic analysis showed that the genes encoding SOD, Prx, Grx and TrxR were mostly down-regulated. In conclusion, the combination of transcriptome and physiological response may provide a deeper understanding about the molecular mechanism in the response to As in upland rice.

Agricultural management practices are frequently non conservative and can lead to substantial loss of soil organic carbon and soil fertility, but for many regions in Africa the knowledge is very limited. To study the effect of local agricultural practices on soil organic carbon content and to explore effective ways to increase soil carbon storage, field experiments were conducted on an upland rice soil (Lixisol) in northern Benin in West Africa. The treatments comprised two tillage systems (no-tillage, and manual tillage), two rice straw managements (no rice straw, and rice straw mulch at 3 Mg ha ⿿1 ) and three nitrogen fertilizer levels (no nitrogen, 60 kg ha ⿿1 , 120 kg ha ⿿1 ). Phosphorus and potassium fertilizers were applied to be non-limiting at 40 kg P 2 O 5 ha ⿿1 and 40 kg K 2 O ha ⿿1 per cropping season. Heterotrophic respiration was higher in manual tillage than no-tillage, and higher in mulched than in non-mulched treatments. Under the current management practices (manual tillage, with no residue and no nitrogen fertilization) in upland rice fields in northern Benin, the carbon added as aboveground biomass and root biomass was not enough to compensate for the loss of carbon from organic matter decomposition, rendering the upland rice fields as net sources of atmospheric CO 2 . With no-tillage, 3 Mg ha ⿿1 of rice straw mulch and 60 kg N ha ⿿1 , the soil carbon balance was approximately zero. With no other changes in management practices, an increase in nitrogen level from 60 kg N ha ⿿1 to 120 kg N ha ⿿1 resulted in a positive soil carbon balance. Considering the high cost of inorganic nitrogen fertilizer and the potential risk of soil and air pollution often associated with intensive fertilizer use, implementation of no-tillage combined with application of 3 Mg ha ⿿1 of rice straw mulch and 60 kg N ha ⿿1 could be recommended to the smallholder farmers to compensate for the loss of carbon from organic matter decomposition in upland rice fields in northern Benin.

With the rapidly increasing demand of rice globally, there is an urgent need to develop management strategies to improve the yields of rice crops, while at the same time minimize the possible adverse climatic impacts arising from greenhouse gas emissions from paddy fields. In this study, we investigated the influence of amendment application (steel slag and sulfate), rice cultivars (super rice cultivar, Qiuyou 6, and common rice cultivar, Hesheng 10), and cultivation methods (hand cultivation, machine cultivation, throwing cultivation) on rice yield, soil properties, as well as CH 4 and N 2 O emissions in a subtropical paddy field in southeast China. When compared to the controls, mean CH 4 emissions were significantly lower in the steel slag amendment and sulfate amendment plots by 66.1% and 23.1%, respectively, but significantly higher in the machine cultivation plots by 26.6% ( P 2 O emissions from the super rice, machine cultivation, and throwing cultivation plots than those from the controls by 133.4%, 45.8%, and 172.2%, respectively ( P 4 and N 2 O emissions, the total global warming potential per unit yield was significantly lower in the plots amended with steel slag and sulfate than in the controls. Moreover, we found that steel slag application, machine cultivation and throwing cultivation were able to increase crop yield significantly ( P

Made available in DSpace on 2018-11-26T16:32:43Z (GMT). No. of bitstreams: 0 Previous issue date: 2016-03-01 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG) National Research University Programme of Thailand's Commission on Higher Education Dithizone (DTZ) staining is a rapid, simple, and inexpensive method that allows the histochemical localization of Zn. In this study, we evaluated genotypic variation in Zn concentration in brown rice grown in the field using atomic absorption spectrophotometer (AAS) as DTZ staining quantified using ImageJ software. We used dehusked grains from upland rice accessions widely cultivated in Brazil. The DTZ staining showed that the concentration of Zn varied within and between rice grains. The staining intensity index (Y) provided differences in localization of Zn across the grain regions. Zn concentration in brown rice varied in multiple regression analysis, showing major differences in index weighted by stained area of each region (YAW) for the embryo, endosperm, and aleurone, especially in the endosperm and aleurone regions due to a large portion of the area in the kernel. The total YAW among rice accessions was positively correlated with Zn concentration in grains by chemical analysis. The DTZ staining associated with imageJ software is a promising to estimate Zn concentration in different grain tissues. Thus,. this method may be useful for rapid screening of rice germplasms. (C) 2015 Elsevier Ltd. All rights reserved. Chiang Mai Univ, Fac Agr, Dept Plant Sci & Nat Resources, Div Agron, Chiang Mai 50200, Thailand Univ Fed Lavras, Dept Soil Sci, POB 3037, BR-37200000 Lavras, MG, Brazil Chiang Mai Univ, Lanna Rice Res Ctr, Chiang Mai 50200, Thailand Sao Paulo State Univ, Fac Sci & Engn, Biosyst Engn, BR-17602496 Tupa, SP, Brazil Univ Fed Lavras, Dept Plant Pathol, POB 3037, BR-37200000 Lavras, MG, Brazil Sao Paulo State Univ, Fac Sci & Engn, Biosyst Engn, BR-17602496 Tupa, SP, Brazil

In Senegal, the peri-urban Niayes region has biophysical and socio-economic potential to contribute to national food security. Peri-urban agriculture highly contributes to the local food supply, but one potential constraint to expansion is soil suitability for new crops. We examined the suitability of soils for the cultivation of upland rice (Oryza sativa L.), cassava (Manihot esculenta Crantz), and groundnut (Arachis hypogaea L.) in a peri-urban wetland outside of Dakar. The selected crops are central to local diets. Study sites were located along a toposequence. We evaluated soil suitability metrics for these three crops based on physical and chemical characteristics. The results show that soil texture varied from sandy to sandy loam. The organic matter concentration varied between 0 g kg−1 and 2 g kg−1. Total nitrogen and organic carbon had low values in all sites except in S4 while macronutrients (Ca, Mg, Na, and K) varied across sites. Calcium was the most abundant cation in the soils; followed by Mg, Na, and K. Based on these factors, we found that there is high suitability for groundnut production in peri-urban Dakar, slight potential for cassava, and marginal or poor suitability for rice production. It attempts to fill the knowledge gap with new data for soil suitability in research development (R&D) in Senegalese agriculture. The same approach could be applied in other areas when introducing new crops for diversification.

An integrated rodent management program was tested in outbreak-prone areas in three provinces of the Northern uplands of Laos (Luangprabang, Phongsaly, Houaphanh). In each province, it was replicated in six villages and associated upland rice fields; six neighboring villages served as negative controls. The program started end of 2010 and aimed at protecting the wet season rice harvest of 2011 against rodent damage. Rodent control techniques included sustained trapping, rodent-proofing of grain stores, rodent hunts and village sanitation campaigns, and biological rodent control using the protozoan parasite Sarcocystis singaporensis . The measures were embedded in a community approach, which was coordinated by provincial and district agricultural officers. Compared to the control villages, which showed on average 10.9% rat damage to ripening upland rice before harvest in 2011, and to the situation of the previous year (12.8%), rat damage was significantly reduced to an average of 4.3% in rice fields of the treatment villages. The incidence of rat-infested rice storage huts dropped significantly from an average of 86% in 2010 to 3.5% in 2011 in the treatment villages. Villagers from Houaphanh culled a total of 73,088 rodents over a period of about nine months, which included mainly black rats ( Rattus rattus ). Because the program phased out before harvest in 2011, potential losses due to rodents were predicted based on yield-damage relationships of the crop year 2010. The predicted average reduction of yield loss for 2011 was 55%, or 417.6 kg ha −1 , in the treatment villages when compared to the controls. The program implemented principles of ecologically-based rodent management (EBRM), the components of which are discussed. In conclusion, EBRM could be helpful in stemming as what was observed as high chronic rodent populations in the uplands of Laos. True outbreaks will require development of a suitable forecast system.

Magnaporthe oryzae (Mo) damages rice leaf, and Thichoderma asperellum (Ta) is a potential biological agent against rice blast. The aims were to identify a reduction of leaf blast severity (LBS), induction of biochemical defense, growth promotion, physiological changes, and modulation of four genes, promoted by four Ta isolates and Ta pool (mixed four Ta isolates). Assay 1 (A1) tested Ta, applied by soil drenched (D) or foliar spraying (S), and evaluated LBS and enzyme activity after challenge inoculation (ChI). Assay 2 (A2) detected growth promotion and physiological changes (A, E, gs, and WUE) when Ta was applied by seed treatment (ST). In assay 3 (A3), plants were treated with Ta by D and S and evaluated after ChI for physiological changes, total chlorophyll content, antioxidant enzymes, and gene expression. In A1, all treatments suppressed leaf blast, and Ta (Ufra.T06) promoted CHI, GLU, LOX, and PAL activities in all applications form. In A2, the Ta pool promoted increases of 52%, 12,24%, 90%, and 40% in A, E, gs, and WUE, respectively. In A3, the Ta pool suppressed LBS by 89% and modulated J10sPR10 and LOX-RLL expression by increasing 35% and 474%, respectively. Ta pool is a stable combination for a multiple function biological agent and should be inserted in integrated rice management.

The study of water-nitrogen (N) interaction to improve crop drought resistance and reduce environmental pollution has increasingly become a hot topic. However, the response of yield and quality of paddy rice and upland rice to N nutrition under different irrigation regimes is little known. Continuous flooding cultivation (CF, control) and bare-dry cultivation (BD) were used to cultivate paddy rice cultivar Yangjing 687 (japonica) and upland rice cultivar Zhonghan 3 (japonica), and 3 N application rates, 140 (low N, LN), 210 (normal N, NN) and 280 kg ha−1(high N, HN), were set for each irrigation regime. The results showed that under BD and CF irrigation regimes, the yield of paddy rice was the highest at NN, while that of upland rice was the highest at BD with NN and at CF with HN, breakdown viscosity was the highest and setback viscosity was the lowest for paddy rice at LN and for upland rice at NN. Increasing N application, the chalky kernels percentage and the chalkiness of upland rice increased first and then decreased, while that of paddy rice decreased under BD and increased under CF. Compared with CF, BD made the seed setting percentage and 1000-grain weight of upland rice and paddy rice different, and improved the appearance and nutritional quality of upland rice. The correlation between the cooking and nutritional quality and leaf N content of upland rice was lower than that of paddy rice. These results suggest that the yield and cooking quality of upland rice were high under BD with NN, and the paddy rice yield was high under BD with NN or CF with NN.

Sustainability of conventional agricultural production systems is threatened by triple challenges of energy and environmental crises, deteriorating natural resources bases, and declining farm profitability. Current agricultural management practices (energy-intensive, inefficient external and natural input use, and crop biomass burning) are negatively impacting the ecosystem services which are the principal drivers for food security and human survival. Hence, there is a need to shift from unsustainable production practices to cleaner production systems. Energy use, carbon footprint (CF), and economic sustainability are important indicators of any clean production systems. Thus, a hypothesis was formulated that no-till (NT) cultivation along with mulching can provide an environmentally clean crop production practice that can enhance energy use efficiency, economic profitability, and reduce the CF. Therefore, the present experiment was conducted for four consecutive years (2012–15) to evaluate the energy budget, CF, and economics of NT along with bio-mulching for a cleaner upland rice production system. The experiment comprised of two tillage practices i.e., conventional tillage (CT) and NT in main plots and four bio- mulches in subplots i.e., rice straw mulch (RSM), Gliricidia sepium mulch (GLM), brown manuring mulch (BMM) of cowpea (Vigna unguiculata), and no mulch (NM) as a control. Results revealed that the adoption of NT curtailed energy use by 48.50%, specific energy by 49.63%, CF by 16.48%, and cost of cultivation by 35% in addition to enhancing energy use efficiency and benefit to cost ratio in comparison to CT. It was also observed that mulching, particularly the BMM, boosted the energy use efficiency, economic productivity, net returns, and benefit to cost ratio over NM. The results suggested that NT with BMM is an environmentally clean production technology to enhance the energy use efficiency, besides reducing the CF of direct-seeded upland rice production system in the Eastern Himalayas and similar eco-regions of the world.

Rice blast (Magnaporthe oryzae) can cause large losses in crop yields, especially in upland rice systems. Avirulent strains of M. oryzae can induce resistance to subsequent attacks by virulent strains in plants. This study aimed to investigate the defense responses in upland rice challenged with a virulent strain of M. oryzae after acclimation with an avirulent strain. The avirulent strain decreased rice blast severity in the challenged plants. Induced resistance was characterized by a hypersensitive response and early accumulation of phenolic compounds. Scanning electron microscopy showed that M. oryzae conidia germinate and form appressoria, but do not colonize leaf tissues. The activities of pathogenesis-related proteins, total phenolic compounds, and salicylic acid (SA) were affected by acclimation to the avirulent strain. The activities of β-1,3-glucanase, phenylalanine ammonia-lyase, and peroxidase, as well as the SA levels explained most of the variability in the rice plant responses to M. oryzae. In addition, OsXa13, OsMAPKKK74, OsAOS2, OsACO7, and OsMAS1 expression was modulated depending on the virulence of the M. oryzae strains. This modulation in gene expression is critical for infection and some of these mechanisms are targeted by effectors, resulting in enhanced susceptibility and pathogen infection. These results have practical importance in plant-pathogen interaction studies to identify resistance-relevant mechanisms against M. oryzae in upland rice.

Rice yield responses forecast (YIELDCAST) is a very useful decision support tool in climate adaptation in Sahel, where crops are purely rainfed climate-stressors sensitive. This study aims to construct upland rice yield responses forecasting algebraic formulation code referred as YIELDCAST by using gene-expression programming (GEP) based on observed rainfall and temperatures data (1979–2011), and forcing with global climate model (GCM) downscaled outputs under CO2 emission scenarios SR-A1B, A2 and B1 (2012–2100) over Bobo-Dioulasso, a Sahelian region. Statistically, GEP is a capable tool to downscale climate variables in the region (R = 0.746−0.949), and construct reliable rice YIELDCAST tool (R = 0.930; MSE = 0.037 ton/ha; MAE = 0.155 ton/ha, RSE = 0.137 ton/ha). Yields forecasted (2012–2100) showed a noticeable statistically significant difference between scenarios; however, fluctuating with no substantial increase (average below 1.60 ton/ha); suggesting that the increase observed in temperatures and decrease in rains will either reduced or hindered yield to largely increase in Sahel. With no such YIELDCAST tool to support adaptation decision, Sahel will still be under the trap of the broad array of adaptation strategy, which is a trial and error, less specific and costly. The model can help anticipate adaptation decision support on-farm water management, shift to suitable planting periods, and use of improved drought resistant and short duration varieties adapted to a local weather pattern.

Leaf blast caused by Magnaporthe oryzae is among the major diseases that limit rice productivity in the world, and control of the disease occurs, basically, through the application of fungicides. Control methods such as the application of growth promoting rhizobacteria could be inserted in the integrated management of rice blast. The objective of this work was to evaluate the potential of four liquid formulations containing Pseudomonas fluorescens (BRM 32111) and Burkholderia pyrrocina (BRM 32113) to suppress leaf blast, under field conditions. The trials were conducted at Embrapa Rice and Beans, between December 2018 and April 2019. The experiments were performed in a randomized block containing 7 treatments, 4 replicates. The treatments consisted of microbiolized seeds and sprays at 14 and 21 days after planting with: Formulation 11 + BRM 32,113 (T1); Formulation 32 + BRM 32,113 (T2); Formulation 11 + BRM 32,111 (T3): Formulation 20 + BRM 32,111 (T4); BRM 32,111 (T5); BRM 32,113 (T6) and Absolute control (water – T7). Severity of leaf blast and panicle, gas exchange and grain yield were evaluated. Plants treated with P. fluorescens (T3, T4 and T5) or B. pyrrocinia (T1, T2 and T6) presented 49%, 39%, 60%, 15% increase in the assimilation rate of CO2 (A), transpiration (E), stomatal conductance (gs) and internal CO2 concentration (Ci), respectively. All treatments were efficient in suppressing leaf and panicle blast and in promoting biomass increase in 55%. The yields of T1, T4, T5 and T6 treatments increased 481, 424, 688 and 427 kg ha−1, respectively. Our results indicate that the formulated rhizobacteria have the potential to be included in the integrated management for blast control in rice fields.

Increasing water scarcity and rapid socio-economic development are driving farmers in Asia to transform traditionally flooded rice cropping systems into non-flooded crop production. The management of earthworms in non-flooded rice fields appears to be a promising strategy to support residue recycling and mitigate greenhouse gas (GHG) emissions triggered by residue amendment. We conducted a field experiment on non-flooded rainfed rice fields, with and without residue amendment. In-situ mesocosms were inoculated with endogeic earthworms (Metaphire sp.), with either low (ET1: 150 individuals m−2), or high density (ET2: 450 individuals m−2), and a control (ET0: no earthworms). We measured GHG emissions (methane (CH4); nitrous oxide (N2O); carbon dioxide (CO2)) twice a week during the cropping season with static chambers. Effects of earthworms on yield and root growth were additionally assessed. Earthworms offset the enormous increase of CH4 emissions induced by straw amendment (from 4.6 ± 5 to 75.3 ± 46 kg CH4-C ha−1 in ET0). Earthworm activity significantly reduced CH4 release, particularly at ET2, by more than one-third (to 22 ± 15 kg CH4-C ha−1). In contrast, earthworm inoculation did not affect N2O emission. Straw amendment more than doubled the global warming potential (GWP). Earthworms reduced GWP by 39% at low (ET1) and 55% at high densities (ET2). Earthworm activity reduced root mass density under conditions of straw amendment but did not affect yield. Earthworms can significantly reduce detrimental effects of rice crop residue amendment on GHG release under upland rice production. Organic carbon (C) might be preserved in earthworm casts and thereby limit C availability for CH4 production. At the same time, earthworm activity might increase methanotrophic CH4 consumption, due to improved soil aeration or less root exudates. Consequently, earthworms have a strong potential for regulating ecosystem functions related to rice straw decomposition, nutrient allocation and thus GHG reduction.

Lowland and upland rice, as for two ecotypes, that have been exhibited different tolerance levels under hypoxia conditions. However, the molecular mechanisms underlying rice root hypoxia tolerance between them are not fully understood. This study was performed to assess the morphological, physiological and transcriptional changes of roots in one lowland rice YueFu (YF) and one upland rice IRAT109 (IR) genotype. A morpho-physiological analysis revealed that compared to IR, YF showed less reduction of root length, root and shoot biomass, formed more aerenchyma in the root, and kept more oxygen influxes in root under hypoxia conditions. Indole-3-acetic acid (IAA) fluxes patterns exhibited a different response to hypoxia in YF and IR. The contents of IAA, ethylene and hydrogen peroxide were significantly increased in YF and IR, but nitric oxide significantly increased only in YF under hypoxic conditions. Subsequently, transcriptome analysis revealed that more differentially expressed genes (DEGs) were identified to respond to hypoxia in YF than IR. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that DEGs in both genotypes enriched in energy metabolism, aerenchyma formation, reactive oxygen species, and cell wall modification, whereas more related DEGs in YF significantly enriched in these pathways than IR. The specific DEGs in YF especially enriched in phytohormone metabolism and signaling, such as auxin, jasmonic acid, and ethylene, but the specific DEGs in IR especially enriched in photosynthesis. All these results demonstrate that YF is more tolerant to hypoxia than IR, and elucidate some specific mechanisms underlying the differential hypoxia tolerance in lowland and upland rice. This study has provided valuable candidate genes for genetic improvement of rice in adapting to hypoxia stress.