Chlorophyll fluorescence-based high-throughput phenotyping facilitates the genetic dissection of photosynthetic heat tolerance in African (Oryza glaberrima) and Asian (Oryza sativa) rice.

Rising temperatures and extreme heat events threaten rice production. Half of the global population relies on rice for basic nutrition, and therefore developing heat-tolerant rice is essential. During vegetative development, reduced photosynthetic rates can limit growth and the capacity to store soluble carbohydrates. The photosystem II (PSII) complex is a particularly heat-labile component of photosynthesis. We have developed a high-throughput chlorophyll fluorescence-based screen for photosynthetic heat tolerance capable of screening hundreds of plants daily. Through measuring the response of maximum PSII efficiency to increasing temperature, this platform generates data for modelling the PSII-temperature relationship in large populations in a small amount of time. Coefficients from these models (photosynthetic heat tolerance traits) demonstrated high heritabilities across African (Oryza glaberrima) and Asian (Oryza sativa, Bengal Assam Aus Panel) rice diversity sets, highlighting valuable genetic variation accessible for breeding. Genome-wide association studies were performed across both species for these traits, representing the first documented attempt to characterize the genetic basis of photosynthetic heat tolerance in any species to date. A total of 133 candidate genes were highlighted. These were significantly enriched with genes whose predicted roles suggested influence on PSII activity and the response to stress. We discuss the most promising candidates for improving photosynthetic heat tolerance in rice.

Superior Haplotypes for Early Root Vigor Traits in Rice Under Dry Direct Seeded Low Nitrogen Condition Through Genome Wide Association Mapping.

Water and land resources have been aggressively exploited in the recent decades to meet the growing demands for food. The changing climate has prompted rice scientists and farmers of the tropics and subtropics to adopt the direct seeded rice (DSR) system. DSR system of rice cultivation significantly reduces freshwater consumption and labor requirements, while increasing system productivity, resource use efficiency, and reducing greenhouse gas emissions. Early root vigor is an essential trait required in an ideal DSR system of rice cultivation to ensure a good crop stand, adequate uptake of water, nutrients and compete with weeds. The aus subpopulation which is adapted for DSR was evaluated to understand the biology of early root growth under limited nitrogen conditions over two seasons under two-time points (14 and 28 days). The correlation study identified a positive association between shoot dry weight and root dry weight. The genome-wide association study was conducted on root traits of 14 and 28 days with 2 million single-nucleotide polymorphisms (SNPs) using an efficient mixed model. QTLs over a significant threshold of p < 0.0001 and a 10% false discovery rate were selected to identify genes involved in root growth related to root architecture and nutrient acquisition from 97 QTLs. Candidate genes under these QTLs were explored. On chromosome 4, around 30 Mbp are two important peptide transporters (PTR5 and PTR6) involved in mobilizing nitrogen in the root during the early vegetative stage. In addition, several P transporters and expansin genes with superior haplotypes are discussed. A novel QTL from 21.12 to 21.46 Mb on chromosome 7 with two linkage disequilibrium (LD) blocks governing root length at 14 days were identified. The QTLs/candidate genes with superior haplotype for early root vigor reported here could be explored further to develop genotypes for DSR conditions.

Identification of genomic loci regulating grain iron content in aus rice under two irrigation management systems.

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 aus subgroup 3 which prominently comes from Bangladesh. On average, subgroup 3 had higher grain Fe than the other four subgroups of aus. Genome-wide association mapping identified 6 genomic loci controlling natural variation of grain Fe concentration in plants grown under AWD. For one QTL, nicotianamine synthase OsNAS3 is proposed as candidate for controlling natural variation of grain Fe in rice. The BAAP contains three haplotypes of OsNAS3 where one haplotype (detected in 31% of the individuals) increased grain Fe up to 11%. Haplotype analysis of this gene in rice suggests that the ability to detect the QTL is enhanced in the BAAP because the high Fe allele is balanced in aus, unlike indica and japonica subgroups.

Aus rice root architecture variation contributing to grain yield under drought suggests a key role of nodal root diameter class.

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.

Genome-wide association mapping of sodium and potassium concentration in rice grains and shoots under alternate wetting and drying and continuously flooded irrigation.

KEY MESSAGE: Identification of a large number of QTL and candidate genes for sodium accumulation in a field grown population of rice derived from the aus subpopulation. 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 < 0.0001) and where at least one of these significant SNPs passed a 10% false discovery rate were reported. A total of 106 QTLs were identified as being associated with Na+ 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.

Genetic loci regulating cadmium content in rice grains.

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).

Genome-wide association mapping for grain manganese in rice (Oryza sativa L.) using a multi-experiment approach.

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.

Genome-Wide Association Mapping for Salt Tolerance of Rice Seedlings Grown in Hydroponic and Soil Systems Using the Bengal and Assam Aus Panel.

Salinity is a major abiotic stress which inhibits rice production in coastal, arid and semi-aid areas in many countries, such as India and Bangladesh. Identification of salt tolerant cultivars, quantitative trait loci (QTLs) and genes is essential for breeding salt tolerant rice. The aus subpopulation of rice is considered to have originated predominantly from Bangladesh and India and have rich genetic diversity with wide variation in abiotic stress resistance. The objective of this study was to identify QTLs, and subsequently candidate genes using cultivars from the aus subpopulation and compare the results of two different seedling stage screening methods. Salt tolerance at the rice seedling stage was evaluated on 204 rice accessions from the Bengal and Assam Aus Panel (BAAP) grown in both hydroponics and soil under control and salt stress conditions. Ten salt related traits of stress symptoms, plant growth and the content of sodium and potassium were measured. Three cultivars, BRRI dhan 47, Goria, and T 1 showed more salt tolerance than the tolerant check Pokkali in both systems. Genome-wide association mapping was conducted on salt indices traits with 2 million SNPs using an efficient mixed model (EMMA) controlling population structure and kinship, and a significance threshold of P < 0.0001 was used to determine significant SNPs. A total of 97 and 74 QTLs associated with traits in hydroponic and soil systems were identified, respectively, including 11 QTLs identified in both systems. A total of 65 candidate genes were found including a well-known major gene OsHKT1;5. The most significant QTL was detected at around 40 Mb on chromosome 1 coinciding with two post-translational modifications SUMOylation genes (OsSUMO1 and OsSUMO2), this QTL was investigated. The salt tolerance rice cultivars and QTLs/genes identified here will provide useful information for future studies on genetics and breeding salt tolerant rice.

Rapid temperature responses of photosystem II efficiency forecast genotypic variation in rice vegetative heat tolerance.

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.

Ecosystem services for intensification of agriculture, with emphasis on increased nitrogen ecological use efficiency.

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.

QTL-seq reveals a major root-knot nematode resistance locus on chromosome 11 in rice (Oryza sativa L.).

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.

Genetic loci regulating arsenic content in rice grains when grown flooded or under alternative wetting and drying irrigation.

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.

Spatial Effects and GWA Mapping of Root Colonization Assessed in the Interaction Between the Rice Diversity Panel 1 and an Arbuscular Mycorrhizal Fungus.

If water saving methods of rice management are to be adopted, the interaction between rice plants and arbuscular mycorrhizal (AM) fungi will grow in agronomic significance. As yet there are very few studies on the interaction between rice and AM fungi and none on host genetics. A subset 334 cultivars from the Rice Diversity Panel 1 were grown in 250 L boxes filled with phosphorus (P) deficient aerobic soil without addition, with added rock phosphate and with rock phosphate and the AM fungus Rhizophagus irregularis. Statistical analysis of position of plants revealed a positive effect of their neighbors on their dry weight which was stronger in the presence of rock phosphate and even stronger with rock phosphate and AM fungi. A weak but significant difference in the response of cultivars to AM fungus treatment in terms of shoot dry weight (SDW) was revealed. Neighbor hyphal colonization was positively related to a plant's hyphal colonization, providing insights into the way a network of AM fungi interact with multiple hosts. Hyphal colonization ranged from 21 to 89%, and 42% of the variation was explained by rice genotype. Colonization was slightly lower in aus cultivars than other rice subgroups and high in cultivars from the Philippines. Genome wide association (GWA) mapping for hyphal colonization revealed 23 putative quantitative trait loci (QTLs) indicating there is an opportunity to investigate the impact of allelic variation in rice on AM fungal colonization. Using published transcriptomics data for AM response in rice, some promising candidate genes are revealed under these QTLs being a calcium/calmodulin serine/threonine protein kinase at 4.9 Mbp on chromosome 1, two ammonium transporters genes at 24.6 Mbp on chromosome 2 and a cluster of subtilisin genes at 1.2 Mbp on chromosome 4. Future studies should concentrate on the biological significance of genetic variation in rice for AM colonization.

Genome Wide Association Mapping of Grain and Straw Biomass Traits in the Rice Bengal and Assam Aus Panel (BAAP) Grown Under Alternate Wetting and Drying and Permanently Flooded Irrigation.

Growing demand for staple crops like rice will need to be achieved predominately through agricultural intensification and more efficient use of inputs. To meet this demand it is essential that the genetic diversity within rice is fully utilized. The aus subpopulation is considered an underappreciated resource within that diversity. A new rice panel, the Bengal and Assam Aus Panel (BAAP) of 266 aus accessions was generated with ∼2 million informative SNPs obtained using skim sequencing at ∼4× depth. The BAAP was grown in the field in Bangladesh in the 'boro' season under both continuously flooded and Alternate Wetting and Drying (AWD) irrigation during 2013 and 2014 in Mymensingh and during 2014 in Madhupur. Heading date, grain mass, straw biomass and harvest index were measured. The majority (94%) of BAAP accessions flowered within a relatively small window of 10 days. The AWD irrigation treatment generally caused an increase in grain mass, but no significant genotype by treatment interactions were detected for this trait. Shoot biomass was the only trait that showed evidence of genotype by treatment interaction. The average LD (Linkage Disequilibrium) decay across the genome was 243 Kbp. Genome wide association mapping revealed 115 quantitative trait loci (QTLs). There was little evidence of QTLs specific to the irrigation treatment, and only a few QTLs co-localized with known genes. However, some QTLs were detected across multiple sites and years. These QTLs should be targets for breeding, and include a region around 2.2 Mbp on chromosome 1, a large region in the middle of chromosome 7 and two regions on chromosome 11 (∼10 Mbp and ∼29 Mbp). The BAAP appears to be a valuable addition to the growing collection of GWA mapping populations of rice.

Interaction between contrasting rice genotypes and soil physical conditions induced by hydraulic stresses typical of alternate wetting and drying irrigation of soil.

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 -5 kPa (WET), or dried to -50 kPa and then rewetted at the water potential of -5 kPa (DRY-WET). There was an additional manipulated macropore structure treatment, i.e. the soil was broken into aggregates, packed into cores and equilibrated to -5 kPa (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 -50 kPa versus -5 kPa had no impact. Macropores formed intentionally from repacking caused a large change in root characteristics.

Physiographical variability in arsenic dynamics 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 (AsCsoln) (5.6-64.7µg/l), labile arsenic (AsCDGT) (6.3-77.6µg/l), and solid phase pool of arsenic (AsKd) (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 AsKd 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.

Biomass and elemental concentrations of 22 rice cultivars grown under alternate wetting and drying conditions at three field sites in Bangladesh.

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.

Arsenic in Bangladeshi soils related to physiographic region, paddy management, and mirco- and macro-elemental status.

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.

Genetic and root phenotype diversity in Sri Lankan rice landraces may be related to drought resistance.

BACKGROUND: The development of relatively cheap and high throughput methods of genotyping and phenotyping plants offers the opportunity to explore local germplasm more thoroughly than before and should accelerate the identification of sources of genetic variation suitable for breeding. In this study, 135 Sri Lankan accessions, mostly identified as landraces, for which data was available at the International Rice Research Institute on drought scores were genotyped using a 384 SNP array and assessed for root depth using a newly developed buried herbicide method. Roots of 36 accessions were assessed using hydroponics and 12 using soil-filled rhizotrons to establish if variation in herbicide score could be attributed to root traits. RESULTS: Population structure based on the SNPs using STRUCTURE revealed six groups, being tropical japonica, aus and four indica subpopulations. Three of these indica subpopulations do not seem to be represented in the Rice Diversity Panel I (RDP1) of 372 global rice accessions and appear to represent genetic diversity so far poorly studied by the global scientific community. The herbicide score was highly discriminatory between landraces and correlated very strongly with hydroponic and rhizotron root traits. The mean herbicide score strongly differentiated between landraces according to the province and the latitude from which they were collected. It also differed between subpopulations, being high in indica 2 and tropical japonica and low in indica 1 and aus. Drought scores suggest that indica 2 is more drought resistant than the other groups. Correlations indicate that those landraces with high herbicide scores are more drought resistant in the vegetative stage. The landrace Niyan Wee, whose name in Sinhalese means "drought rice" belongs to the indica 2 subgroup, has high herbicide scores and deep roots. CONCLUSIONS: Niyan Wee and other cultivars within the indica 2 subgroup should be a valuable source of breeding for drought resistance at least partly because of their superior root traits, not normally associated with the indica rice cultivars.

A genome-wide association study of a global rice panel reveals resistance in Oryza sativa to root-knot nematodes.

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 <1 in LD 24, in comparison with >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.