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Nitrogen (N) fertilizers are widely used worldwide to increase agricultural productivity. However, significant N losses contributing to air and water pollution ultimately reduce the nitrogen use efficiency (NUE) of crops. Numerous research studies have emphasized the use of a low dose of N fertilizer, but few have focused on screening N-efficient rice genotypes. This study aimed to identify and screen ten rice genotypes that are N-use-efficient under different N fertilization treatments using the surface placement of neem-oil-coated urea: N0 (control), N60 (½ of recommended N), and N120 (recommended N) for two consecutive years (2020 and 2021) under a split plot design. In both growing seasons, the application of N120 yielded the highest panicles m−2 (PAN = 453), filled grains panicle−1 (FGP = 133), leaf area index (LAI = 5.47), tillers m−2 (TILL = 541), grain yield t ha−1 (GY = 5.5) and harvest index (HI = 45.4%) by the genotype ‘Nidhi’, being closely followed by the genotype ‘Daya’. Four genotypes (‘Nidhi’, ‘Daya’, ‘PB 1728’ and ‘Nagina 22’), out of the ten genotypes evaluated, responded well to different fertilization treatments with N with respect to the grain yield efficiency index (GYEI ≥ 1). Regarding N fertilization, N60 and N120 recorded the highest increase in PAN (28.5%; 41.4%), FGP (29.5%; 39.3%), test weight (29.5%; 45.3%), LAI at 30 days after transplanting (DAT) (143.7%; 223.3%), and LAI at 60 DAT (61.6%; 70.1%) when compared with N0. Furthermore, the application of N60 and N120 improved GY and HI by 47.6% and 59.4%, and 3.4% and 6.2%, respectively, over N0. Nitrogen addition (N60 and N120) also significantly increased the chlorophyll content at 60 DAT (8.8%; 16.3%), TILL at 60 DAT (22.9%; 46.2%), TILL at harvest (28%; 41.4%), respectively, over N0. Overall, our research findings clearly indicate that ‘Nidhi’ and ‘Daya’ could be efficient candidates for improved nitrogen use, grain yield and GYEI in the Indo-Gangetic plains of India.

Rice is often grown as multiple crops in one year, with reduced tillage upland cropping following flooded cropping gaining prominence due to water use, soil degradation and labour demands. This study explored whether a deep rather than shallow rooting rice cultivar grown in a flooded cropping cycle, benefited deeper root growth of follow-on rice in an upland, reduced tillage cropping cycle. In a greenhouse study, a simulated flooded paddy was planted with deep (Black Gora) and shallow (IR64) root cultivars and a plant-free control. Artificial plough pans were made in between the topsoil and subsoil to form different treatments with no plough pan (0.35 MPa), soft plough pan (1.03 MPa) and hard plough pan (1.70 MPa). After harvest of this ‘first season’ rice, the soil was drained and undisturbed to simulate zero-tillage upland, with a photoperiod insensitive variety (BRRI Dhan 28) planted. Root length, root surface area, root volume, root diameter, number of root tips and branches were measured. The number of roots penetrating the plough pan was measured from camera images and X-ray CT. The overall root length density (RLD), root surface area, number of root tips and branching of BRRI Dhan 28 did not vary between plough pan and no plough pan treatments. Compared to the shallow rooting rice genotype, the deep rooting rice genotype as a ‘first season’ crop promoted 19 % greater RLD, 34 % greater surface area and 29 % more branching of BRRI Dhan 28 in the subsoil. In the topsoil, however, BRRI Dhan 28 had 28 % greater RLD, 35 % greater surface area and 43 % more branching for the shallow rather deep rooting genotype planted in the ‘first season’. The results suggest that rice cultivar selection for a paddy cycle affects root growth of a follow-on rice crop grown under no-till, with benefits to subsoil access from deep rooting cultivars and topsoil proliferation for shallow rooting cultivars.

High throughput phenotyping and quantitative genetics have enabled researchers to identify genetic regions, or markers, associated with changes in phenotype. However, going from GWAS markers to candidate genes is still challenging. When selecting candidate genes for ionomic GWAS markers, we curated a collection of well-known ionomic genes (KIG) experimentally shown to alter plant elemental uptake and their orthologs in 10 crop species: 2066 genes total. Yet when compared to ionomic GWAS markers, over 90% of significant markers were not linked to a KIG - indicating the list is incomplete and many causal genes are unknown. Continuing to use only functional annotations as candidate selection criteria will keep efforts biased toward well-known genes and hinder the characterization of unknown genes. We propose an unbiased computational approach that compares analogous GWAS markers from multiple species and searches for conserved genes linked to trait markers. Like the KIG list, we expect many of these unknown candidate genes to have orthologs in other species. By leveraging the evolutionary relationship of these conserved genes, rather than prior knowledge and gene annotations, this method: 1) finds more candidate genes than we expect from random chance, 2) selects and prioritizes candidates in poorly annotated species, and 3) includes unknown genes in the results. With this approach, we now have an unbiased list of gene candidates across 19 ionomic traits in model species and crop species to verify in future experiments.

Aims Cracks and biopores in compacted soil such as plough pans could aid deep rooting, mitigating constraints to seasonal upland use of paddy fields for rice production. This research investigated how soil macropores through a simulated plough pan affects root growth of contrasting deep and shallow rooting rice genotypes. Methods Deep rooting Black Gora and shallow rooting IR64 rice varieties were grown in packed cores of unsaturated soil in a controlled greenhouse. Simulated biopores and cracks (macropores) were inserted through the plough pan to form treatments with no macropores, biopores, cracks, and combined cracks and biopores. Different root parameters such as root length density (RLD), root volume, root diameter, number of root tips and branches were measured. The number of roots was calculated manually, including the number of roots growing through macropores in the plough pan layer. Results Plough pans with macropores had 25–32% more roots than with no macropores. RLD was 55% greater in the plough pan layer if cracks were present compared to biopores. Conversely, RLD was 26% less in subsoil if the plough pan had cracks compared to biopores. Different root parameters were greatly influenced by the presence of macropores in the plough pan, and deep-rooted Black Gora produced 81% greater RLD, 30% more root numbers and 103% more branching than the shallow rooted rice genotype IR64 within the plough pan layer. Conclusions Macropores greatly improve rice root growth through plough pans for a deep rooting but not a shallow rooting rice variety. Whereas cracks produce a greater number of roots in the plough pan, biopores result in greater root branching and root numbers deeper in subsoil.

Key message Identification of a large number of QTL and candidate genes for sodium accumulation in a field grown population of rice derived from theaus subpopulation. Abstract Rice (Oryza sativa L.) is a globally important cereal crop. Sodium (Na+) and potassium (K+) are the major monovalent ions which affect rice growth, and exploring their uptake mechanisms will be useful for understanding rice biology. Since the balance of Na+ and K+ plays a significant role in adaptation of rice to salinity, that biology might inform the search for tolerance. In this study, the Na+ and K+ concentration and Na+/K+ ratio in grains and shoots were analyzed in the Bengal and Assam Aus Panel grown in field conditions under continuously flooded (CF) and alternate wetting and drying (AWD) irrigation. Overall, AWD irrigation significantly reduced the Na+ concentration and increased the K+ concentration in shoots and grains compared to the plants grown under CF. Genome-wide association mapping was conducted on Na+, K+ concentration and Na+/K+ ratio with 2 million SNPs using an efficient mixed model. Only QTLs which contained more than two significant SNPs (p + concentration and Na+/K+ ratio across all traits and field conditions, with 48 QTLs found in multiple traits and/or water conditions. Four notable QTLs (one each on chromosomes 1 and 11, two on chromosome 2) and the haplotype variants of four candidate genes (OsHKT1;5, OsNHX2, LOC_Os02g32490 and OsFAD2_1) are discussed. The QTLs/candidate genes identified here could be useful for breeding rice that accumulates lower concentrations of sodium.

The survival of the extensive livestock system, the practice for most farmers in the livestock industry in Ghana depends heavily on the natural pastures as forage resource. To efficiently use the rangelands, knowledge of the species composition, especially that of poisonous plants is essential. Documented knowledge in Ghana is scanty; documentation and dissemination of the knowledge resource would enable a wider access and wider benefit to stakeholders. A study was conducted in Ghana on poisonous plants with the aim to discover the existence and diversity of poisonous plants and associated antidotes affecting livestock for documentation and preservation of knowledge. 70 different items were cited; 22 were poisonous plants for which antidotes were not cited, 28 were poisonous plants with known antidotes and 32 antidotes. There were 575 citations of plants from 194 reported cases of suspected plant poisoning, categorized as poisonous plants for which no antidotes were cited (146), poisonous plants with cited antidotes (147) and antidotes (282). 50 plants species were identified and belonged to 29 plant families. Some plants were known only by local names. There was an extensive knowledge of the diversity of poisonous plants and antidotes within the ecological zones along with possible antidotes.

A key target for the improvement of Oryza sativa (rice) is the development of heat-tolerant varieties. This necessitates the development of high-throughput methodologies for the screening of heat tolerance. Progress has been made to this end via visual scoring and chlorophyll fluorescence; however, these approaches demand large infrastructural investments to expose large populations of adult plants to heat stress. To address this bottleneck, we investigated the response of the maximum quantum efficiency of photosystem II (PSII) to rapidly increasing temperatures in excised leaf segments of juvenile rice plants. Segmented models explained the majority of the observed variation in response. Coefficients from these models, i.e. critical temperature (Tcrit ) and the initial response (m1 ), were evaluated for their usability for forecasting adult heat tolerance, measured as the vegetative heat tolerance of adult rice plants through visual (stay-green) and chlorophyll fluorescence (ɸPSII) approaches. We detected substantial variation in heat tolerance of a randomly selected set of indica rice varieties. Both Tcrit and m1 were associated with measured heat tolerance in adult plants, highlighting their usability as high-throughput proxies. Variation in heat tolerance was associated with daytime respiration but not with photosynthetic capacity, highlighting a role for the non-photorespiratory release of CO2 in heat tolerance. To date, this represents the first published instance of genetic variation in these key gas-exchange traits being quantified in response to heat stress in a diverse set of rice accessions. These results outline an efficient strategy for screening heat tolerance and accentuate the need to focus on reduced rates of respiration to improve heat tolerance in rice.

Alternate wetting and drying (AWD) technique has been developed and evaluated on rice (Oryza sativa) systems in several countries worldwide for increasing water use efficiency and reducing negative effects of permanent flooding, like the increase in methane emissions and arsenic availability in soil. In this study, a paddy field experiment was carried out for two years to evaluate the application in Northern Italy rice area of a moderate AWD, i.e. only implemented during the vegetative phase of the crop and ponded water maintained thereafter, compared with Continuous Flooding (CF) system. The adaptability of 12 European commercial rice cultivars to AWD was investigated in terms of crop phenology, morphological traits, root production, nitrogen (N) uptake, yield, milled rice yield and microelement concentration in grains. Results showed substantial (40.7 %) water saving probably favoured by the presence of a shallow water table. In these pedoclimatic conditions, very limited effects of a mild AWD on crop status and final productivity were recorded and the commercial cultivars did not display significant different adaptabilities to the water stress. Moreover, AWD decreased arsenic (As) concentration in grain but increased grain Cadmium (Cd) being the degree of such a response dependent upon the variety, suggesting that the genotype plays an important role in this aspect of adaptation to AWD. info:eu-repo/semantics/acceptedVersion

The aus rice variety group originated in stress-prone regions and is a promising source for the development of new stress-tolerant rice cultivars. In this study, an aus panel (~220 genotypes) was evaluated in field trials under well-watered and drought conditions and in the greenhouse (basket, herbicide and lysimeter studies) to investigate relationships between grain yield and root architecture, and to identify component root traits behind the composite trait of deep root growth. In the field trials, high and stable grain yield was positively related to high and stable deep root growth (r = 0.16), which may indicate response to within-season soil moisture fluctuations (i.e., plasticity). When dissecting component traits related to deep root growth (including angle, elongation and branching), the number of nodal roots classified as 'large-diameter' was positively related to deep root growth (r = 0.24), and showed the highest number of colocated genome-wide association study (GWAS) peaks with grain yield under drought. The role of large-diameter nodal roots in deep root growth may be related to their branching potential. Two candidate loci that colocated for yield and root traits were identified that showed distinct haplotype distributions between contrasting yield/stability groups and could be good candidates to contribute to rice improvement.

Aims Cracks and biopores in compacted soil such as plough pans could aid deep rooting, mitigating constraints to seasonal upland use of paddy fields for rice production. This research investigated how soil macropores through a simulated plough pan affects root growth of contrasting deep and shallow rooting rice genotypes.Methods Deep rooting Black Gora and shallow rooting IR64 rice varieties were grown in packed cores of unsaturated soil in a controlled greenhouse. Artificial biopores and cracks (macropores) were inserted through the plough pan to form treatments with no macropores, biopores, cracks, and combined cracks and biopores. Different root parameters such as root length density (RLD), root volume, root diameter, number of root tips and branches were measured. The number of roots was calculated manually, including the number of roots growing through macropores in the plough pan layer.Results Plough pans with macropores had 25-32 % more roots than with no macropores. RLD was 55 % greater in the plough pan layer if cracks were present compared to biopores. Conversely, RLD was 26 % less in subsoil if the plough pan had cracks compared to biopores. Different root parameters were greatly influenced by the presence of macropores in the plough pan, and deep-rooted Black Gora produced 81% greater RLD, 30 % more root numbers and 103 % more branching than the shallow rooted rice genotype IR64 within the plough pan layer.Conclusions Macropores greatly improve rice root growth through plough pans for a deep rooting but not shallow rooting rice variety. Whereas cracks produce a greater number of roots in the plough pan, biopores result in greater root branching and root numbers deeper in subsoil.

Iron (Fe) deficiency is one of the common causes of anaemia in humans. Improving grain Fe in rice, therefore, could have a positive impact for humans worldwide, especially for those people who consume rice as a staple food. In this study, 225-269 accessions of the Bengal and Assam Aus Panel (BAAP) were investigated for their accumulation of grain Fe in two consecutive years in a field experiment under alternative wetting and drying (AWD) and continuous flooded (CF) irrigation. AWD reduced straw Fe by 40% and grain Fe by 5.5-13%. Genotype differences accounted for 35% of the variation in grain Fe, while genotype by irrigation interaction accounted for 12% of the variation in straw and grain Fe in year 1, with no significant interactions detected in year 2. Twelve rice accessions were identified as having high grain Fe for both years regardless of irrigation treatment, half of which were from BAAP

International audience; Many rice-growing areas are affected by high concentrations of arsenic (As). Rice varieties that prevent As uptake and/or accumulation can mitigate As threats to human health. Genomic selection is known to facilitate rapid selection of superior genotypes for complex traits. We explored the predictive ability (PA) of genomic prediction with single-environment models, accounting or not for trait-specific markers, multi-environment models, and multi-trait and multi-environment models, using the genotypic (1600K SNPs) and phenotypic (grain As content, grain yield and days to flowering) data of the Bengal and Assam Aus Panel. Under the base-line single-environment model, PA of up to 0.707 and 0.654 was obtained for grain yield and grain As content, respectively; the three prediction methods (Bayesian Lasso, genomic best linear unbiased prediction and reproducing kernel Hilbert spaces) were considered to perform similarly, and marker selection based on linkage disequilibrium allowed to reduce the number of SNP to 17K, without negative effect on PA of genomic predictions. Single-environment models giving distinct weight to trait-specific markers in the genomic relationship matrix outperformed the base-line models up to 32%. Multi-environment models, accounting for genotype × environment interactions, and multi-trait and multi-environment models outperformed the base-line models by up to 47% and 61%, respectively. Among the multi-trait and multi-environment models, the Bayesian multi-output regressor stacking function obtained the highest predictive ability (0.831 for grain As) with much higher efficiency for computing time. These findings pave the way for breeding for As-tolerance in the progenies of biparental crosses involving members of the Bengal and Assam Aus Panel. Genomic prediction can also be applied to breeding for other complex traits under multiple environments.

It has been estimated that up to 90% of human exposure to cadmium is through food, and that cadmium within rice grains can be a major contributor to that dietary source. In this study genome wide association mapping was conducted on the Bengal and Assam Aus Panel (BAAP) of rice to identify quantitative trait loci and candidate genes for lowering grain cadmium. Field experiments were conducted over two years under two different irrigation systems: continually flooded and alternate wetting and drying (AWD). There was significant effects of water treatment, genotype, and genotype by water treatment interaction. Importantly, AWD increased grain cadmium, on average, by 49.6% and 108.8% in year 1 and 2 respectively. There was between 4.6 and 28 fold variation in cadmium concentration. A total of 58 QTLs were detected but no loci are clearly specific to one water regime despite approximately 20% of variation attributable to genotype by water regime interaction. A number of QTLs were consistent across most water treatments and years. These included QTLs on chromosome 7 (7.23–7.61, 8.93–9.04, and 29.12–29.14 Mbp), chromosome 5 (8.66–8.72 Mbp), and chromosome 9 (11.46–11.64 Mbp). Further analysis of the loci on chromosome 7 (8.93–9.04 Mbp), identified the candidate gene OsNRAMP1, where cultivars with a deletion upstream of the gene had higher concentrations of cadmium compared to the cultivars that did not have the deletion. The distribution of alleles within the BAAP suggest this QTL is easily detected in this population because it is composed of aus cultivars. Local genome cluster analysis suggest high Cd alleles are uncommon, but should be avoided in breeding. Supplementary Information The online version contains supplementary material available at (10.1007/s10681-020-02752-1).

In the last six decades, the consumption of reactive nitrogen (Nr) in the form of fertilizer in India has been growing rapidly, whilst the nitrogen use efficiency (NUE) of cropping systems has been decreasing. These trends have led to increasing environmental losses of Nr, threatening the quality of air, soils, and fresh waters, and thereby endangering climate-stability, ecosystems, and human-health. Since it has been suggested that the fertilizer consumption of India may double by 2050, there is an urgent need for scientific research to support better nitrogen management in Indian agriculture. In order to share knowledge and to develop a joint vision, experts from the UK and India came together for a conference and workshop on “Challenges and Opportunities for Agricultural Nitrogen Science in India.” The meeting concluded with three core messages: (1) Soil stewardship is essential and legumes need to be planted in rotation with cereals to increase nitrogen fixation in areas of limited Nr availability. Synthetic symbioses and plastidic nitrogen fixation are possibly disruptive technologies, but their potential and implications must be considered. (2) Genetic diversity of crops and new technologies need to be shared and exploited to reduce N losses and support productive, sustainable agriculture livelihoods. (3) The use of leaf color sensing shows great potential to reduce nitrogen fertilizer use (by 10–15%). This, together with the usage of urease inhibitors in neem-coated urea, and better management of manure, urine, and crop residues, could result in a 20–25% improvement in NUE of India by 2030.

Paddy soils in Bangladesh experience extensive irrigation with groundwater and surface water, both having variable geochemical constituents. The soils also have topological variations across the landscape. To understand the geochemical variability in the soils as affected by the different sources of irrigation water and the topographical variability, cultivation zones of paddy soils irrigated with both groundwater (n = 904) and surface water (n = 281) across Bangladesh were sampled and analyzed for a suit of seventeen geochemical elements. This study also assessed the extent and distribution of arsenic and the other geochemical elements in the paddy soils (n = 1209) as well as in a set of neighboring non-paddy soils (n = 235) within the different inundation land types (highland, medium highland-1, medium highland-2, medium lowland, lowland and very lowland) of Bangladesh. The mean concentrations of aluminum (26,000 mg/kg), cobalt (13 mg/kg), copper (32 mg/kg), iron (28,250 mg/kg), lead (18 mg/kg), magnesium (8050 mg/kg), molybdenum (1.02 mg/kg), nickel (41 mg/kg), potassium (4870 mg/kg), sodium (750 mg/kg) and zinc (70 mg/kg) in the surface water-irrigated paddy soils were found to be significantly (0.001 ≥ p ≤ 0.05) higher compared to the concentrations in the soils irrigated with groundwater (23,400; 12; 28; 25,650; 17; 7000; 0.96; 36; 4350; 600; and 62 mg/kg, respectively). Therefore, surface water used for paddy irrigation could increase the inputs of a number of toxic elements in the paddy soils having potential risk of crop contamination. Arsenic in the paddy and non-paddy soils varied significantly (F = 24.74, p F = 3.42, p

The AWD is an irrigation technology for rice cultivation, consisting in implementing alternate draining and flooded periods over the growing season, that delivers multiple environmental benefits, such as reduced water consumption, CH4 emissions and arsenic (As) grain content, but can be offset by yield losses. The trade-offs between the agronomic and environmental effects of AWD are crop context-dependent and they also vary among the different versions of AWD studied. Therefore, the implementation of a safe AWD needs to be preceded by studies conducted within a specific rice cropping system. A two-year field experiment was conducted to assess the effect of AWD on grain yield, As and heavy metal content in grains, and greenhouse gas emissions in nine representative European rice cultivars grown in a Mediterranean growing area. The experiment was performed in a split-plot design with four replications. The study revealed a significant cultivar effect on the agronomic response to AWD. Among the studied cultivars, one of them performed as tolerant to AWD while a group formed by four cultivars showed slight non-significant yield decline. AWD significantly reduced CH4 emissions and the global warming potential by 90% being such a large mitigation capacity explained by the negligible N2O emissions found in both water treatments. Finally, the implementation of AWD significantly reduced by ca. 40% As grain concentration but increased cadmium content, though the levels remained below the recommended thresholds. Further, AWD increased key nutritional elements like cupper, selenium, and zinc. In conclusion, this study confirms that AWD can be safely implemented in Mediterranean rice cultivation conditions with limited or null yield impact while obtaining the associated environmental benefits of this practice info:eu-repo/semantics/acceptedVersion

Many rice-growing areas are affected by high concentrations of arsenic (As). Rice varieties that prevent As uptake and/or accumulation can mitigate As threats to human health. Genomic selection is known to facilitate rapid selection of superior genotypes for complex traits. We explored the predictive ability (PA) of genomic prediction with single-environment models, accounting or not for trait-specific markers, multi-environment models, and multi-trait and multi-environment models, using the genotypic (1600 K SNP) and phenotypic (grain arsenic content, grain yield and days to flowering, observed under two irrigation systems over two years) data of the Bengal and Assam Aus Panel (BAAP). Under the base-line single environment model, PA of up to 0.707 and 0.654 was obtained for grain yield and grain As respectively, the three prediction methods (BL, GBLUP and RKHS) considered performed similarly, and marker selection based on linkage disequilibrium allowed to reduce the number of SNP to 17 K, without negative effect on PA of genomic predictions. Single environment models giving distinct weight to trait-specific markers in the genomic relationship matrix outperformed the base-line models up to 32%. Multi-environment models, accounting for G × E interactions, and multi-trait and multi-environment models outperformed the base-line models by up to 47% and 61%, respectively. Among the multi-trait and multi-environment models, the Bayesian multi-output regressor stacking function obtained the highest PA (0.831 for grain As) with much higher efficiency for computing time. These findings pave the way for breeding for As-tolerance in the progenies of biparental crosses involving members of the BAAP. It also applies to breeding for other complex traits evaluated under multiple environments.

Manganese (Mn) is an essential trace element for plants and commonly contributes to human health; however, the understanding of the genes controlling natural variation in Mn in crop plants is limited. Here, the integration of two of genome-wide association study approaches was used to increase the identification of valuable quantitative trait loci (QTL) and candidate genes responsible for the concentration of grain Mn across 389 diverse rice cultivars grown in Arkansas and Texas, USA, in multiple years. Single-trait analysis was initially performed using three different SNP datasets. As a result, significant loci could be detected using the high-density SNP dataset. Based on the 5.2 M SNP dataset, major QTLs were located on chromosomes 3 and 7 for Mn containing six candidate genes. In addition, the phenotypic data of grain Mn concentration were combined from three flooded-field experiments from the two sites and 3 years using multi-experiment analysis based on the 5.2 M SNP dataset. Two previous QTLs on chromosome 3 were identified across experiments, whereas new Mn QTLs were identified that were not found in individual experiments, on chromosomes 3, 4, 9 and 11. OsMTP8.1 was identified in both approaches and is a good candidate gene that could be controlling grain Mn concentration. This work demonstrates the utilisation of multi-experiment analysis to identify constitutive QTLs and candidate genes associated with the grain Mn concentration. Hence, the approach should be advantageous to facilitate genomic breeding programmes in rice and other crops considering QTLs and genes associated with complex traits in natural populations.

As the global population grows, demand on food production will also rise. For rice, one limiting factor effecting production could be availability of fresh water, hence adoption of techniques that decrease water usage while maintaining or increasing crop yield are needed. Alternative wetting and drying (AWD) is one of these techniques. AWD is a method by which the level of water within a rice field cycles between being flooded and nonflooded during the growth period of the rice crop. The degree to which AWD affects cultivars differently has not been adequately addressed to date. In this study, 22 rice cultivars, mostly landraces of the aus subpopulation, plus some popular improved indica cultivars from Bangladesh, were tested for their response to AWD across three different field sites in Bangladesh. Grain and shoot elemental concentrations were determined at harvest. Overall, AWD slightly increased grain mass and harvest index compared to plants grown under continually flooded (CF) conditions. Plants grown under AWD had decreased concentrations of nitrogen in their straw compared to plants grown under CF. The concentration of elements in the grain were also affected when plants were grown under AWD compared to CF: Nickel, copper, cadmium and iron increased, but sodium, potassium, calcium, cobalt, phosphorus, molybdenum and arsenic decreased in the grains of plants grown under AWD. However, there was some variation in these patterns across different sites. Analysis of variance revealed no significant cultivar × treatment interaction, or site × cultivar × treatment interaction, for any of the plant mass traits. Of the elements analyzed, only grain cadmium concentrations were significantly affected by treatment × cultivar interactions. These data suggest that there is no genetic adaptation amongst the cultivars screened for response to AWD, except for grain cadmium concentration and imply that breeding specifically for AWD is not needed.

As the world’s population increases, demands on staple crops like rice (Oryza sativa L.) will also increase, requiring additional fresh water supplies for irrigation of rice fields. Safe alternate wetting and drying (AWD) is a water management technique that is being adopted across a number of countries to reduce the water input for rice cultivation. The impact of AWD on plant growth, yield and grain quality is not well understood. A field trial of AWD was conducted at Mymensingh, Bangladesh over two boro (dry) seasons using eight field plots, four under AWD and four continuously flooded (CF). This manuscript describes the results of check cultivar BRRI dhan28 which was replicated in 35–40 rows per plot giving a total of 140–160 replicates per treatment. A study on the soil solution concentration of many elements indicated that manganese, iron, zinc, and arsenic were different under AWD conditions compared to CF on a number of sampling time points, but did not show a pattern related to the AWD treatment. A survey of soil strength using a penetrometer detected a small, but statistically significant, hardening of the surface soil of the AWD plots. At harvest the shoot and grain mass was significantly greater for the plants grown under AWD (9.0-9.4% and 12.0-15.4%, respectively) with the plants grown under AWD having a greater number of productive tillers. Physiological examination in the first year showed that although AWD decreased (∼21%) leaf elongation rate (LER) of recently transplanted seedlings during the first drying cycle, subsequent drying cycles did not affect LER, while tillering was slightly increased by AWD and there was evidence of higher leaf abscisic acid (ABA) in AWD plants. In the second year analysis of six phytohormones revealed that AWD increased plant foliar isopentenyladenine (iP) concentrations by 37% while leaf trans-zeatin concentrations decreased (36%) compared to CF plants. The elemental composition of the shoots and grains was also examined. In both years AWD decreased grain concentration of sulphur (by 4% and 15%), calcium (by 6% and 9%), iron (by 11% and 16%), and arsenic (by 14% and 26%), while it increased the grain concentration of manganese (by 19% and 28%), copper (by 81% and 37%), and cadmium (by 28% and 67%). These results indicate that plants grown under safe AWD conditions at this site have an increased grain mass compared to plants grown under CF, and this may be partly due to a high number of productive tillers. AWD decreases the concentration of arsenic in the grains in this site, but it elevates the concentration of cadmium.

Made available in DSpace on 2020-12-10T19:59:24Z (GMT). No. of bitstreams: 0 Previous issue date: 2020-02-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) FAPEG-Goias Research Foundation FAPEMA-Maranhao Research Foundation United Kingdom, Biotechnology and Biological Sciences Research Council In weathered tropical soil, low nutrient use efficiency can lead to agricultural systems becoming unsustainable. Therefore, tropical agriculture is highly dependent on ecosystem services, such as nutrient recycling and carbon sequestration, to enhance soil fertility, increase nutrient uptake, and facilitate sustainable production of agricultural goods. This research aimed to find the balance between sustainability and profitability of tropical agriculture by evaluating the changes in soil caused by the ecosystem services provided by the biomass of leguminous trees (Gliricidia) and assessing how these changes (associated with potassium) can affect nitrogen-use efficiency and maize yield. An experiment was conducted testing the impact of Glircidia biomass addition vs. bare soil, with or without addition of both nitrogen and/or potassium. Changes in soil organic matter, (SOM) base cations sum, soil resistance, N uptake, N-use efficiency, and maize yield were evaluated. Gliricidia biomass, when used with N and K, contributed to increasing SOM by 5.0 g/kg and the sum of base cations by 1458. 65 kg/ha in the 0-30 cm layer. Moreover, grain yield was increased by approximately 70% in the treatments with Gliricidia when compared to treatments without biomass where yield was very low. In bare soil, the additional yield of 1.5 tons/ha would not be enough to convince farmers to change slash and burn to conventional bare soil systems. Our results showed that leguminous trees, such as Gliricidia, might contribute to ensuring sustainable agricultural intensification in humid tropical soils with low natural fertility by providing ecosystem services such as biomass production, carbon sequestration, base cation recycling, and increased N acquisition. These findings might be an important strategy to replace the common slash-and-burn-system and preserve the rainforest against the traditional shifting cultivation system. In contrast, the conventional system with bare soil showed that the addition of nitrogen was unfeasible, mainly in conditions of high rainfall precipitation. In these circumstances, the use of potassium may increase nitrogen-use efficiency only when biomass is not used. Sao Paulo State Univ, Coll Agr Sci, Dept Crop Sci, BR-18610307 Botucatu, SP, Brazil Univ Estadual Maranhao, Postgrad Program Agroecol, BR-65000000 Sao Luis, Maranhao, Brazil Fed Inst Educ Sci & Technol Piaui, BR-64860000 Urucui, Piaui, Brazil Univ Fed Maranhao, Dept Biol, BR-65080805 Sao Luis, Maranhao, Brazil Univ Aberdeen, Inst Biol & Environm Sci, Aberdeen AB24 3UU, Scotland Univ Nottingham, Sch Biosci, Sutton Bonington Campus, Loughborough LE12 5RD, Leics, England Sao Paulo State Univ, Coll Agr Sci, Dept Crop Sci, BR-18610307 Botucatu, SP, Brazil FAPESP: 2015/50305-8 FAPEG-Goias Research Foundation: 201510267001479 FAPEMA-Maranhao Research Foundation: RCUK-02771/16 United Kingdom, Biotechnology and Biological Sciences Research Council: BB/N013201/1

Background Rice is a global staple crop, being the main calorific component of many people living subsistence livelihoods. Rice can accumulate toxic elements such as arsenic, with the crop water management strongly affecting uptake. This study utilises the Bengal and Assam Aus Panel to conduct genome wide association (GWA) mapping for arsenic in shoots and grains of rice grown over 2 years under continually flooded (CF) and alternate wetting and drying (AWD). The aim was to assess genotype by water management interaction, identify quantitative trait loci (QTL) for arsenic accumulation, and propose candidate genes for lowering grain arsenic. Results AWD significantly reduced grain arsenic across all cultivars on average by 15.7 and 15.1% in year 1 and 2 respectively and shoot arsenic by 27.0% compared to the plants grown under CF. There was a weak cultivar by treatment interaction for grain for arsenic. All traits were strongly influenced by cultivar. GWA mapping identified a large number of 74 individual QTLs for arsenic, with six QTLs showing stability across years and/or water treatments. Three of the loci (one on chromosome 3, one on chromosome 4, and one on chromosome 5) were investigated in detail using an approach of clustering cultivars that had similar haplotypes for the QTL regions and then looking at the phenotypic values across the clusters. Two of the identified QTLs co-localised with known genes involved in arsenic accumulation, including Lsi2 which has not previously been reported to underlie a grain arsenic QTL. Conclusions This study has identified a number of novel QTLs for arsenic accumulation, as well as cultivars that consistently accumulate less arsenic over multiple field traits. The use of a haplotype clustering approach after GWA mapping has allowed for the effect, in terms of arsenic accumulation, to be determined for cultivars that share similar genomic sequence. Allocating nine high yielding Bangladeshi cultivars to these clusters has identified the potential of utilising these QTLs in breeding programmes; for example, incorporation of the QTL on chromosome 5 should decrease grain arsenic in elite high yielding Bangladeshi cultivars by 10% in all high yielding cultivars studied. Electronic supplementary material The online version of this article (10.1186/s12284-019-0307-9) contains supplementary material, which is available to authorized users.

Water saving techniques, such as alternate wetting and drying (AWD), are becoming a necessity in modern rice farming because of climate change mitigation and growing water use scarcity. Reducing water can vastly reduce methane (CH4) emissions; however, this net climate benefit may be offset by enhanced carbon dioxide (CO2) emissions from soil. The main aims of this study were: to determine the effects of AWD on yield and ecosystem C dynamics, and to establish the underlying mechanistic basis for observed trends in net ecosystem C gain or loss in an Italian rice paddy. We investigated the effects of conventional water management (i.e. conventionally flooded paddy; CF) and AWD on biomass accumulation (aboveground, belowground, grain), key ecosystem C fluxes (net ecosystem exchange (NEE), net primary productivity (NPP), gross primary productivity (GPP), ecosystem respiration (ER), autotrophic respiration (RA), heterotrophic respiration (RH)), and soil organic matter (SOM) decay for four common commercial European rice cultivars. The most significant finding was that neither treatment nor cultivar affected NEE, GPP, ER or SOM decomposition. RA was the dominant contributor to ER for both CF and AWD treatments. Cultivar and treatment affected the total biomass of the rice plants; specifically, with greater root production in CF compared to AWD. Importantly, there was no effect of treatment on the overall yield for any cultivar. Possibly, the wetting-drying cycles may have been insufficient to allow substantial soil C metabolism or there was a lack of labile substrate in the soil. These results imply that AWD systems may not be at risk of enhancing soil C loss, making it a viable solution for climate change mitigation and water conservation. Although more studies are needed, the initial outlook for AWD in Europe is positive; with no net loss of soil C from SOM decomposition, whilst also maintaining yield., Graphical abstract Unlabelled Image, Highlights • Alternate wetting and drying does not enhance carbon loss in European rice paddies. • Aerobic conditions do not increase soil organic matter decomposition. • Periods of drought do not affect rice yields in four European rice cultivars. • Alternate wetting and drying reduces rice root production.

The root-knot nematode Meloidogyne graminicola is a serious pest in rice affecting production in many rice growing areas. Natural host resistance is an attractive control strategy because the speed of the parasite’s life cycle and the broad host range it attacks make other control measures challenging. Although resistance has been found in the domesticated African rice Oryza glaberrima and the wild rice species O. longistaminata, the introgression of resistance genes to Asian rice O. sativa is challenging. Resistance due to a major gene in O. sativa would greatly aid breeding. Recently two accessions resistant to M. graminicola have been identified in a screen of 332 diverse O. sativa cultivars. In this study, these two resistant cultivars, LD 24 (an indica from Sri Lanka) and Khao Pahk Maw (an aus from Thailand), were crossed with a moderately susceptible cultivar, Vialone Nano (a temperate japonica from Italy). Approximately 175 F2 progeny of both populations were screened for susceptibility to M. graminicola infection. Between 20 and 23 individuals with highest and lowest galls per plants were pooled to make susceptible and resistant bulks which were sequenced to conduct bulked segregant analysis using the QTL-seq method. This revealed a nematode resistance locus from 23 Mbp to the bottom of rice chromosome 11 in both crosses suggesting a rare introgression of the same locus is responsible for resistance in both cultivars. While this information can be used in marker-assisted breeding, analysis of available SNP data revealed candidate loci and genes worthy of further investigation for gene identification.

© 2018, The Author(s). Background and aims: Alternate wetting and drying (AWD) saves water in paddy rice production but could influence soil physical conditions and root growth. This study investigated the interaction between contrasting rice genotypes, soil structure and mechanical impedance influenced by hydraulic stresses typical of AWD. Methods: Contrasting rice genotypes, IR64 and deeper-rooting Black Gora were grown in various soil conditions for 2 weeks. For the AWD treatments the soil was either maintained in a puddled state, equilibrated to −5kPa (WET), or dried to −50kPa and then rewetted at the water potential of −5kPa (DRY-WET). There was an additional manipulated macropore structure treatment, i.e. the soil was broken into aggregates, packed into cores and equilibrated to −5kPa (REPACKED). A flooded treatment (puddled soil remained flooded until harvest) was set as a control (FLOODED). Soil bulk density, penetration resistance and X-ray Computed Tomography (CT) derived macropore structure were measured. Total root length, root surface area, root volume, average diameter, and tip number were determined by WinRhizo. Results: AWD induced formation of macropores and slightly increased soil mechanical impedance. The total root length of the AWD and REPACKED treatments were 1.7–2.2 and 3.5–4.2 times greater than that of the FLOODED treatment. There was no significant difference between WET and DRY-WET treatments. The differences between genotypes were minimal. Conclusions: AWD influenced soil physical properties and some root characteristics of rice seedlings, but drying soil initially to −50kPa versus −5kPa had no impact. Macropores formed intentionally from repacking caused a large change in root characteristics.

Root traits such as root angle and hair length influence resource acquisition particularly for immobile nutrients like phosphorus (P). Here, we attempted to modify root angle in rice by disrupting the OsAUX1 auxin influx transporter gene in an effort to improve rice P acquisition efficiency. We show by X-ray microCT imaging that root angle is altered in the osaux1 mutant, causing preferential foraging in the top soil where P normally accumulates, yet surprisingly, P acquisition efficiency does not improve. Through closer investigation, we reveal that OsAUX1 also promotes root hair elongation in response to P limitation. Reporter studies reveal that auxin response increases in the root hair zone in low P environments. We demonstrate that OsAUX1 functions to mobilize auxin from the root apex to the differentiation zone where this signal promotes hair elongation when roots encounter low external P. We conclude that auxin and OsAUX1 play key roles in promoting root foraging for P in rice., Plant root architecture can adapt to different nutrient conditions in the soil. Here Giri et al. show that the rice auxin influx carrier AUX1 mobilizes auxin from the root apex to the differentiation zone and promotes root hair elongation when roots encounter low external phosphate.

Root traits such as root angle and hair length influence resource acquisition particularly for immobile nutrients like phosphorus (P). Here, we attempted to modify root angle in rice by disrupting the OsAUX1 auxin influx transporter gene in an effort to improve rice P acquisition efficiency. We show by X-ray microCT imaging that root angle is altered in the osaux1 mutant, causing preferential foraging in the top soil where P normally accumulates, yet surprisingly, P acquisition efficiency does not improve. Through closer investigation, we reveal that OsAUX1 also promotes root hair elongation in response to P limitation. Reporter studies reveal that auxin response increases in the root hair zone in low P environments. We demonstrate that OsAUX1 functions to mobilize auxin from the root apex to the differentiation zone where this signal promotes hair elongation when roots encounter low external P. We conclude that auxin and OsAUX1 play key roles in promoting root foraging for P in rice.

Highlight Assessing gall numbers in 331 cultivars of a rice diversity panel has identified two resistant landraces, 11 quantitative trait loci and good candidate genes for resistance to Meloidogyne graminicola., The root-knot nematode Meloidogyne graminicola is one of the most serious nematode pests worldwide and represents a major constraint on rice production. While variation in the susceptibility of Asian rice (Oryza sativa) exists, so far no strong and reliable resistance has been reported. Quantitative trait loci for partial resistance have been reported but no underlying genes have been tagged or cloned. Here, 332 accessions of the Rice Diversity Panel 1 were assessed for gall formation, revealing large variation across all subpopulations of rice and higher susceptibility in temperate japonica accessions. Accessions Khao Pahk Maw and LD 24 appeared to be resistant, which was confirmed in large pot experiments where no galls were observed. Detailed observations on these two accessions revealed no nematodes inside the roots 2 days after inoculation and very few females after 17 days (5 in Khao Pahk Maw and 100 in the susceptible controls). These two cultivars appear ideal donors for breeding root-knot nematode resistance. A genome-wide association study revealed 11 quantitative trait loci, two of which are close to epistatic loci detected in the Bala x Azucena population. The discussion highlights a small number of candidate genes worth exploring further, in particular many genes with lectin domains and genes on chromosome 11 with homology to the Hordeum Mla locus.

As research on roots intensifies due to the growing realization that a better understanding of their function and genetics offers important strategies for tackling the global challenge set by increased population, climate change, and food security, it is important to present new developments in the area. This special issue features articles offered by contributors to a session on that subject at the Society of Experimental Biology Annual Meeting in Prague in 2015 which was sponsored by European Union project called EURoot (www.EURoot.eu). The review by Berg et al. (2016) reviews current knowledge on the role of microorganisms in the phyllosphere (above ground), rhizosphere (soil close to roots), and endosphere (inside the plant) in plant growth, development, and function and highlights the need to consider metaorganisms which are co-evolved assemblages of plant and microbes working together. The work argues for a change in consideration of what a plant is and highlights the diversity of the microorganisms involved, the transmission between plants, the importance of endophytes, and several unexpected functions and metabolic outcomes of the biological interactions of the metaorganism. The first survey of the drought response of roots at the transcriptome level was the subject of a review by Janiak et al. (2016). Since it is the root that initially experiences and signals drought to the plant, this is a valuable collation of literature which highlights the important role of several classes of transcription factors, the downstream targets, and the interplay with hormones and other signalling molecules. A related review by Shabala et al. (2016) focuses on the role of membrane transporters in the sensing and response to soil-based plant stresses first experienced by the root—those of drought, salinity, and flooding, emphasizing specific genes with promise for conferring tolerance. It highlights the importance of maintaining membrane potential and ATP production during stress and the role of reactive oxygen species and cytosolic Ca2+ and K+ in signalling responses while also detailing the role of ion transporters in the response to these stresses. Current root research has placed a lot of effort into improving phenotyping that is either more accurate, more high throughput or more relevant. Addressing these issues, Wasson et al. (2016) provide details of a new portable fluorescence spectroscopy imaging system that can be used in the phenotyping of roots that improves accuracy and speed and reduces costs. Importantly, this is applied to a crop (wheat) grown in the field which is the most relevant environment in which to phenotype roots, but where root research is rarely conducted due to the high variation and high labour requirements. Another major thrust of root research is the development and improvement of models that can aid in the characterization of plant form and function and help produce better target traits for specific crop improvements. Kalogiros et al. (2016) describes a density-based model of root growth that can back-calculate root parameters based on images taken at one time point. The authors show that the model predicts root traits with high accuracy in a diverse panel of Brasica rapa, and suggest that the model will be useful in identifying genotypes with efficient root systems in phenotyping screens even if they have incomplete image data. Concentrating more on root function, a model of nutrient uptake by root hairs is presented by Daly et al. (2016). Using data from X-ray Computed Tomography the authors model the distance into the bulk soil that is required for root hairs to be ineffective (and hence for root hair distribution to be irrelevant) and find that, for relatively immobile nutrients like phosphorus, it is less for saturated soil (1.1mm) than partially saturated soil (1.4mm). Two further papers consider the role of root hairs. Bengough et al. (2016) used time-lapse photography of a root hairless mutant of maize and its wild type to calculate the anchorage force afforded by root hairs. It provides an insight into the role of root hairs in anchoring roots and shows the considerable advantage they provide in allowing penetration of weak and medium penetration-resistance soils, but not hard soils. Using a root hairless barley mutant and its wild type, Kwasniewski et al. (2016) investigated the role of the root hair in the signalling of drought stress. They used a transcriptomics approach. The results suggest that, while the mutant showed most of the typical responses to drought, they appear to have less of the responses associated with root to shoot stress signalling, suggesting a role for root hairs in drought perception and/or signalling. The pattern of gene expression in different tissues of the root was investigated by Optiz et al. (2016). These authors split the maize root into four different sections, being the tip, the elongation zone, and then the cortex and stele of the mature zone. The transcriptomic responses to PEG-induced drought were different in these sections, highlighting their different roles and reactions for sensing, signalling, and responding to drought. Another article details the effect of drought on gene regulation, but this time on the methylation status of genes. Chwialkowska et al. (2016) assessed the methylome of the leaves and roots of barley seedlings exposed to drought and after recovery using Methylation Sensitive Amplification Polymorphism Sequencing. The results showed evidence of methylation and demethylation in response to drought which was balanced in leaves but was dominated by methylation in roots where recovery to the pre-drought state appeared slower. One further article focuses on gene expression. Tai et al. (2016) used transcriptomics and anatomical measurement to differentiate three different types of maize root, the embryonic primary and seminal roots, and the post-embryonic crown roots. Although gene expression differences were relatively small (in the order of 1% of genes differentially expressed between root types), global expression profiling suggests that those genes that were different between tissues reveal differences in root function. Researchers from the same laboratory as above (Zhang et al., 2016) have investigated the role of two genes known to be involved in lateral and seminal root production in maize, RUM1 (ROOTLESS WITH UNDETECTABLE MERISTEM 1) and its homeologue RUL1 (RUM1-like 1), both of which are regulators of auxin signalling. While both genes have similar molecular properties, the expression of RUL1 is much lower than that of RUM1 while the authors reveal a RUM1-associated protein 1 (RAP1) that specifically interacts with RUM1 but not with RUL1 suggesting that RUM1 and RUL1 are at least partially associated with different molecular networks. The gene RUM1 also featured in one of two papers that examine the detection and/or utility of quantitative trait loci (QTLs) detected for root system architecture traits. In Salvi et al. (2016), three QTLs for the number of roots were detected in maize introgression lines, with two of these being above excellent candidate genes, RUM1 and RTCS (rootless concerning crown and seminal roots). In durum wheat, Maccaferri et al. (2016) used two linkage mapping populations and one genome-wide association panel (with about 90K markers) to identify root trait QTLs, revealing several genomic regions with clusters of QTLs for root length and number or root angle detected by both mapping approaches. In both of these papers the authors discuss the implications of these QTLs for breeding. Genome-wide association mapping was used in rice for the final two papers of this special issue. A total of 196 accessions were assessed for root and shoot growth under low phosphorus by Mori et al. (2016) revealing major differences in root efficiency of phosphorus uptake (amount of P taken up per unit of root surface area). Detailed physiology revealed several-fold differences in root efficiency between cultivars while mapping revealed, among others, a QTL on chromosome 11 with major potential for crop improvement. Finally, Dimkpa et al. (2016) screened 330 rice accessions for resistance to the root-knot nematode Meloidogyne graminicola revealing 11 QTLs and some notable candidate genes. They also discovered two rice landraces with complete resistance to the nematode which was confirmed in separate, large-pot experiments in two independent laboratories, providing excellent breeding strategies for improving resistance to this soil-borne pest that severely impacts root growth and function. Together these reviews and original research papers provide a glimpse into some of the issues and methodologies that are occupying root scientists at the current time.

While the impact of arsenic in irrigated agriculture has become a major environmental concern in Bangladesh, to date there is still a limited understanding of arsenic in Bangladeshi paddy soils at a landscape level. A soil survey was conducted across ten different physiographic regions of Bangladesh, which encompassed six types of geomorphology (Bil, Brahmaputra floodplain, Ganges floodplain, Meghna floodplain, Karatoya-Bangali floodplain and Pleistocene terrace). A total of 1209 paddy soils and 235 matched non-paddy soils were collected. The source of irrigation water (groundwater and surface water) was also recorded. The concentrations of arsenic and sixteen other elements were determined in the soil samples. The concentration of arsenic was higher in paddy soils compared to non-paddy soils, with soils irrigated with groundwater being higher in arsenic than those irrigated with surface water. There was a clear difference between the Holocene floodplains and the Pleistocene terraces, with Holocene floodplain soils being higher in arsenic and other elements. The results suggest that arsenic is most likely associated with less well weathered/leached soils, suggesting it is either due to the geological newness of Holocene sediments or differences between the sources of sediments, which gives rise to the arsenic problems in Bangladeshi soils.

Rice plants grown on soils with elevated arsenic have been shown to have increased arsenic content in their grains. To gain a better understanding of the likelihood of high grain arsenic in rice grown in different soils, it is important to understand the factors affecting the bioavailability and mobility of arsenic. Paddy soils from six different physiographic regions of Bangladesh were collected, and diffusive gradients in thin-films (DGT) were used to assess the porewater and solid phase arsenic. While significant differences were identified in total soil arsenic (1.4-9.8mg/kg), porewater arsenic ((As)Csoln) (5.6-64.7μg/l), labile arsenic ((As)CDGT) (6.3-77.6μg/l), and solid phase pool of arsenic ((As)Kd) (52-1057l/kg), importantly arsenic resupply capacity was not different between the physiographic regions. All soils had a high ratio of DGT to porewater arsenic (~1), this in conjunction with the porewater arsenic values and the high (As)Kd values suggesting a large solid phase pool of arsenic capable of contributing towards the resupply/transport of the labile pool of arsenic in the soil porewater. This indicates that there is less difference in soil arsenic availability than might be predicted based solely on total soil arsenic content between the physiographic regions.

Human activities have massively altered the global nitrogen (N) cycle, doubling annual production of reactive N (Nr) compounds from atmospheric dinitrogen (N2). The use of 120 Mt year−1 fertilizer N, with a global terrestrial/atmospheric N fixation of 285 Mt year−1, has provided huge benefits for global food production. However, nitrogen use efficiency (NUE) of the world food system is only ∼15%. The lost Nr creates a cascade of air and water pollution and greenhouse gas emissions, until it is eventually denitrified back to N2. India clearly illustrates a dual N challenge for food and environment, consuming 17 Mt of N fertilizer annually (14% of the global total), which has increased since 1970 at 6% year−1 approximately. Emissions of nitrogen oxides (NOx) from combustion sources are also increasing rapidly at 6.5% year−1 currently. By comparison, population growth rate is lower (2% year−1), while ammonia (NH3) emission increase is even less (1%), pertaining to smaller changes in livestock numbers. At current rate, Indian NOx emissions will exceed NH3 emissions by 2055. India currently loses Nr worth US$10 billion year−1 as fertilizer value, while costs of Nr to health, ecosystems, and climate are estimated at US$75 (38–151) billion year−1. Only a small fraction of the Indian population consumes animal products, hence per capita Nr use and pollution is much less than in many developed countries. However, rates of meat consumption are increasing. While published projections from the UN Food and Agriculture Organization anticipate a doubling of South Asian fertilizer consumption from 2006 to 2050 (equivalent to 1.9% year−1 increase), these projections lack transparency and require reevaluation. In practice, the future nitrogen cycle for India will depend on scientific advances in agronomy, genetics and environment, and the extent to which government and society grasp the emerging opportunities for optimizing N management.

In a large scale survey of rice grains from markets (13 countries) and fields (6 countries), a total of 1578 rice grain samples were analysed for lead. From the market collected samples, only 0.6% of the samples exceeded the Chinese and EU limit of 0.2 μg g − 1 lead in rice (when excluding samples collected from known contaminated/mine impacted regions). When evaluating the rice grain samples against the Food and Drug Administration's (FDA) provisional total tolerable intake (PTTI) values for children and pregnant women, it was found that only people consuming large quantities of rice were at risk of exceeding the PTTI from rice alone. Furthermore, 6 field experiments were conducted to evaluate the proportion of the variation in lead concentration in rice grains due to genetics. A total of 4 of the 6 field experiments had significant differences between genotypes, but when the genotypes common across all six field sites were assessed, only 4% of the variation was explained by genotype, with 9.5% and 11% of the variation explained by the environment and genotype by environment interaction respectively. Further work is needed to identify the sources of lead contamination in rice, with detailed information obtained on the locations and environments where the rice is sampled, so that specific risk assessments can be performed.

Root research requires high throughput phenotyping methods that provide meaningful information on root depth if the full potential of the genomic revolution is to be translated into strategies that maximise the capture of water deep in soils by crops. A very simple, low cost method of assessing root depth of seedlings using a layer of herbicide (TRIK or diuron) buried 25 or 30 cm deep in soil-filled boxes of varying size is described that is suitable for screening hundreds or thousands of rice accessions in controlled environment conditions. Variation in cultivar sensitivity to the herbicide when injected into pots was detected but considered small in relation to the variation detected when the herbicide was buried. Using 32 rice cultivars previously characterised for root traits in rhizotron and hydroponic systems, 80% of variation in herbicide score at 35 days was explained by cultivar and herbicide score correlated strongly with rooting depth traits. Using 139 genotypes of the Bala × Azucena mapping population, heritability for herbicide symptoms reached 55% and quantitative trait loci were detected which match those previously reported in this population. In repeated experiments using different soils, the method did not always perform to its maximum potential (in terms of speed of symptom development or discrimination between cultivars). This was not due to degradation or reduced bio-availability of the herbicide in the soil but is believed to be due to the soil water content and water release characteristics as it relates to plant water use. Therefore, when using this technique, thorough preliminary experiments to determine the best water application regime for the particular combination of soil and environmental conditions are required. The method should be applicable to seedling stage screening of rice and other crops.

Summary Six varieties of rice were exposed to low and high levels of arsenic in the same soil. Their individual responses of expressing phytochelatins have been correlated to inorganic arsenic uptake, transport, and accumulation in the rice grain., Rice has the predilection to take up arsenic in the form of methylated arsenic (o-As) and inorganic arsenic species (i-As). Plants defend themselves using i-As efflux systems and the production of phytochelatins (PCs) to complex i-As. Our study focused on the identification and quantification of phytochelatins by HPLC-ICP-MS/ESI-MS, relating them to the several variables linked to As exposure. GSH, 11 PCs, and As–PC complexes from the roots of six rice cultivars (Italica Carolina, Dom Sofid, 9524, Kitrana 508, YRL-1, and Lemont) exposed to low and high levels of i-As were compared with total, i-As, and o-As in roots, shoots, and grains. Only Dom Sofid, Kitrana 508, and 9524 were found to produce higher levels of PCs even when exposed to low levels of As. PCs were only correlated to i-As in the roots (r=0.884, P

Hybrid recognition in the genus Fragaria (strawberry, Rosaceae) is difficult when based on morphological characteristics since there is great similarity among Fragaria species, even between different ploidy levels. This study aimed to identify and characterise an alloheptaploid hybrid (2n = 7x = 49) Fragaria for the first time in the genus from Europe (Germany, Bavaria) using different techniques. The hybrid was documented based on the evidence obtained from ploidy levels using flow cytometric measurement of nuclear DNA content, identification of the parental origin using 14 RAPD primers, fertility assessment from artificial crosses and fruit set level. RAPD analysis showed that the hybrid shared five species-specific markers with diploid F. vesca, and three with hexaploid F. moschata, indicating these species to be the most likely parents. The mean fluorescent intensity reflected by nuclear DNA in the putative hybrid (703) fell within the range accepted for heptaploidy in Fragaria, while the corr...