Genotypic variation in element concentrations in brown rice from Yunnan landraces in China

A tale of two metals: Biofortification of rice grains with iron and zinc

Iron (Fe) and zinc (Zn) are essential micronutrients needed by virtually all living organisms, including plants and humans, for proper growth and development. Due to its capacity to easily exchange electrons, Fe is important for electron transport in mitochondria and chloroplasts. Fe is also necessary for chlorophyll synthesis. Zn is a cofactor for several proteins, including Zn-finger transcription factors and redox metabolism enzymes such as copper/Zn superoxide dismutases. In humans, Fe participates in oxygen transport, electron transport, and cell division whereas Zn is involved in nucleic acid metabolism, apoptosis, immunity, and reproduction. Rice (Oryza sativa L.) is one of the major staple food crops, feeding over half of the world's population. However, Fe and Zn concentrations are low in rice grains, especially in the endosperm, which is consumed as white rice. Populations relying heavily on rice and other cereals are prone to Fe and Zn deficiency. One of the most cost-effective solutions to this problem is biofortification, which increases the nutritional value of crops, mainly in their edible organs, without yield reductions. In recent years, several approaches were applied to enhance the accumulation of Fe and Zn in rice seeds, especially in the endosperm. Here, we summarize these attempts involving transgenics and mutant lines, which resulted in Fe and/or Zn biofortification in rice grains. We review rice plant manipulations using ferritin genes, metal transporters, changes in the nicotianamine/phytosiderophore pathway (including biosynthetic genes and transporters), regulators of Fe deficiency responses, and other mutants/overexpressing lines used in gene characterization that resulted in Fe/Zn concentration changes in seeds. This review also discusses research gaps and proposes possible future directions that could be important to increase the concentration and bioavailability of Fe and Zn in rice seeds without the accumulation of deleterious elements. We also emphasize the need for a better understanding of metal homeostasis in rice, the importance of evaluating yield components of plants containing transgenes/mutations under field conditions, and the potential of identifying genes that can be manipulated by gene editing and other nontransgenic approaches.

Can 2,4-D promote the hormesis effect in upland rice?

This study aimed to evaluate the influence of low doses of 2,4-D on the agronomic traits of upland rice applied at different stages of crop growth. The work was carried out in a randomized completly blocks, and consisted of the application of 5 low doses of the 2,4-D herbicide (0, 0.68, 1.36, 2.04, 3.40 and 5.44 g acid equivalent (e.a.) ha-1) in two stages of rice development (tillering and floral differentiation). Nitrogen contentes in leaves, SPAD index and yield are higher when low doses of 2,4-D is applied in the tillering stage. Application of 2,4-D at a dose of 2.04 g a.e ha-1 results in a 19% increase in the number of spikelet per panicle. On the other hand, there is no effect of the application of low doses of 2,4-D on height, number of stems, active tillering and weight of 100 seeds. Our results contribute to increase knowledge of the hormesis effect in plants in order to increase crop yield.

NILs of Cold Tolerant Japonica Cultivar Exhibited New QTLs for Mineral Elements in Rice

Chilling stress at booting stage can cause floret deterioration and sterility by limiting the supply of food chain and the accumulation of essential mineral elements resulting in reduction of yield and grain quality attributes in rice. Genomic selection of chilling tolerant rice with reference to the accumulation of mineral elements will have great potential to cope with malnutrition and food security in times of climate change. Therefore, a study was conducted to explore the genomic determinants of cold tolerance and mineral elements content in near-isogenic lines (NILs) of japonica rice subjected to chilling stress at flowering stage. Detailed morphological analysis followed by quantitative analysis of 17 mineral elements revealed that the content of phosphorus (P, 3,253 mg/kg) and potassium (K, 2,485 mg/kg) were highest while strontium (Sr, 0.26 mg/kg) and boron (B, 0.34 mg/kg) were lowest among the mineral elements. The correlation analysis revealed extremely positive correlation of phosphorus (P) and copper (Cu) with most of the cold tolerance traits. Among all the effective ear and the second leaf length correlation was significant with half of the mineral elements. As a result of comparative analysis, some QTLs (qBRCC-1, qBRCIC-2, qBRZC-6, qBRCHC-6, qBRMC-6, qBRCIC-6a, qBRCIC-6b, qBRCHC-6, and qBRMC-6) identified for calcium (Ca), zinc (Zn), chromium (Cr) and magnesium (Mg) on chromosome number 1, 2, and 6 while, a novel QTL (qBCPC-1) was identified on chromosome number 1 for P element only. These findings provided bases for the identification of candidate genes involved in mineral accumulation and cold tolerance in rice at booting stage.

Can the application of low doses of paraquat induce the hormesis effect in upland rice?

This study aimed to verify the effects of the application of paraquat low doses on the agronomic traits of upland rice in two different application modes. The treatments consisted of a combination of 6 low doses of the paraquat (0; 20; 40; 60; 80 and 120 g a.i. ha^-1) and 2 application modes of low doses a) single application performed between active tillering and floral differentiation b) application split into four applications, the first being carried out at the beginning of active tillering, the second being carried out between active tillering and floral differentiation, the third application carried out after floral differentiation and the fourth application carried out after flowering with 25% of the dose in each application. The application of low doses of paraquat does not promote the hormesis effect of upland rice. The increase in the frequency of the plant to the herbicide caused by the splitting of applications negatively affected the plant height, number of spikelets per panicle, yield, leaf nitrogen and sulfur as the low doses levels were increased. On the other hand, there is no influence of paraquat low doses levels when single applied to the agronomic traits of upland rice.

Genetic architecture of root and shoot ionomes in rice (Oryza sativa L.)

KEY MESSAGE

Association analysis for ionomic concentrations of 20 elements identified independent genetic factors underlying the root and shoot ionomes of rice, providing a platform for selecting and dissecting causal genetic variants. Understanding the genetic basis of mineral nutrient acquisition is key to fully describing how terrestrial organisms interact with the non-living environment. Rice (Oryza sativa L.) serves both as a model organism for genetic studies and as an important component of the global food system. Studies in rice ionomics have primarily focused on above ground tissues evaluated from field-grown plants. Here, we describe a comprehensive study of the genetic basis of the rice ionome in both roots and shoots of 6-week-old rice plants for 20 elements using a controlled hydroponics growth system. Building on the wealth of publicly available rice genomic resources, including a panel of 373 diverse rice lines, 4.8 M genome-wide single-nucleotide polymorphisms, single- and multi-marker analysis pipelines, an extensive tome of 321 candidate genes and legacy QTLs from across 15 years of rice genetics literature, we used genome-wide association analysis and biparental QTL analysis to identify 114 genomic regions associated with ionomic variation. The genetic basis for root and shoot ionomes was highly distinct; 78 loci were associated with roots and 36 loci with shoots, with no overlapping genomic regions for the same element across tissues. We further describe the distribution of phenotypic variation across haplotypes and identify candidate genes within highly significant regions associated with sulfur, manganese, cadmium, and molybdenum. Our analysis provides critical insight into the genetic basis of natural phenotypic variation for both root and shoot ionomes in rice and provides a comprehensive resource for dissecting and testing causal genetic variants.

Identification of Promising RILs for High Grain Zinc Through Genotype × Environment Analysis and Stable Grain Zinc QTL Using SSRs and SNPs in Rice (Oryza sativa L.)

Polished rice is one of the commonly consumed staple foods across the world. However, it contains limited nutrients especially iron (Fe) and zinc (Zn). To identify promising recombinant inbred lines (RILs) for grain Zn and single plant yield, 190 RILs developed from PR116 and Ranbir Basmati were evaluated in two environments (E1 and E2). A subset of 44 contrasting RILs for grain Zn was screened in another two environments (E3 and E4). Phenotypic data was collected for 10 traits, viz., days to 50% flowering, plant height, panicle length, number of tillers, single plant yield (SPY), test weight, Fe and Zn in brown (IBR, ZBR), and polished rice (IPR, ZPR). Stepwise regression analysis of trait data in 190 RILs and a subset of 44 RILs revealed the interdependence of ZPR, ZBR, IPR, and IBR and the negative association of grain Zn with single plant yield. Based on the additive main effect and multiplicative interaction (AMMI) and genotype and genotype × environment interaction (GGE) analyses of the subset of 44 RILs across four environments (E1-E4), six promising RILs were identified for ZPR with >28 ppm. Mapping of 190 RILs with 102 simple sequence repeats (SSRs) resulted in 13 QTLs for best linear unbiased estimates (BLUEs) of traits including advantage over check (AOC). Using genotype-based sequencing (GBS), the subset of 44 RILs was mapped with 1035 single-nucleotide polymorphisms (SNPs) and 21 QTLs were identified. More than 100 epistatic interactions were observed. A major QTL qZPR.1.1 (PV 37.84%) and another QTL qZPR.11.1 (PV 15.47%) were identified for grain Zn in polished rice. A common major QTL (qZBR.2.1 and qZPR.2.1) was also identified on chromosome 2 for grain Zn content across SSR and SNP maps. Two potential candidate genes related to transporters were identified based on network analyses in the genomic regions of QTL < 3 Mb. The RILs identified for grain Zn and SPY were nominated for national evaluation as under rice biofortification, and two QTLs identified based on BLUEs could be used in the rice biofortification breeding programs.

Transporter genes identified in landraces associated with high zinc in polished rice through panicle transcriptome for biofortification

Polished rice is poor source of micronutrients, however wide genotypic variability exists for zinc uptake and remobilization and zinc content in brown and polished grains in rice. Two landraces (Chittimutyalu and Kala Jeera Joha) and one popular improved variety (BPT 5204) were grown under zinc sufficient soil and their analyses showed high zinc in straw of improved variety, but high zinc in polished rice in landraces suggesting better translocation ability of zinc into the grain in landraces. Transcriptome analyses of the panicle tissue showed 41182 novel transcripts across three samples. Out of 1011 differentially expressed exclusive transcripts by two landraces, 311 were up regulated and 534 were down regulated. Phosphate transporter-exporter (PHO), proton-coupled peptide transporters (POT) and vacuolar iron transporter (VIT) showed enhanced and significant differential expression in landraces. Out of 24 genes subjected to quantitative real time analyses for confirmation, eight genes showed significant differential expression in landraces. Through mapping, six rice microsatellite markers spanning the genomic regions of six differentially expressed genes were validated for their association with zinc in brown and polished rice using recombinant inbred lines (RIL) of BPT 5204/Chittimutyalu. Thus, this study reports repertoire of genes associated with high zinc in polished rice and a proof concept for deployment of transcriptome information for validation in mapping population and its use in marker assisted selection for biofortification of rice with zinc.

Cell wall targeted in planta iron accumulation enhances biomass conversion and seed iron concentration in Arabidopsis and rice

Conversion of nongrain biomass into liquid fuel is a sustainable approach to energy demands as global population increases. Previously, we showed that iron can act as a catalyst to enhance the degradation of lignocellulosic biomass for biofuel production. However, direct addition of iron catalysts to biomass pretreatment is diffusion-limited, would increase the cost and complexity of biorefinery unit operations and may have deleterious environmental impacts. Here, we show a new strategy for in planta accumulation of iron throughout the volume of the cell wall where iron acts as a catalyst in the deconstruction of lignocellulosic biomass. We engineered CBM-IBP fusion polypeptides composed of a carbohydrate-binding module family 11 (CBM11) and an iron-binding peptide (IBP) for secretion into Arabidopsis and rice cell walls. CBM-IBP transformed Arabidopsis and rice plants show significant increases in iron accumulation and biomass conversion compared to respective controls. Further, CBM-IBP rice shows a 35% increase in seed iron concentration and a 40% increase in seed yield in greenhouse experiments. CBM-IBP rice potentially could be used to address iron deficiency, the most common and widespread nutritional disorder according to the World Health Organization.

A study on toxic and essential elements in rice from the Republic of Kazakhstan: comparing the level of contamination in rice from the European Community

Selected toxic elements (total As, Cd, Cr, Hg, Pb, Sr, U and V) and essential elements (Co, Cu, Fe, Mn and Zn) were analyzed using an inductively coupled plasma mass spectrometry (ICP-MS) in unpolished and milled rice collected from Kazakhstan and milled rice from Spain and Portugal to evaluate the potential health risk to the population. Arsenic species (arsenite, arsenate, arsenobetaine, dimethylarsinate and monomethilarsonate) were analyzed using HPLC-IC-MS. From 146 samples analyzed, none of them exceeded the maximum limit set by the European Legislation for Cd or Pb or values recommended by the Codex Alimentarius. Concentrations of Sr, U and V were below LOD and those of Hg, Pb, Co and Cr between <LOD and 0.54 mg/kg (highest concentration of Cr) in milled rice. Portuguese rice samples contained the highest mean concentration of As, Hg, Pb, Co, Cr, Cu, Mn and Zn. The highest mean of arsenobetaine (0.001 mg/kg), dimethylarsinate (0.27 mg/kg) and monomethilarsonate (0.02 mg/kg) was found in Spanish rice and that of arsenite (0.30 mg/kg) in Kazakh rice. Inorganic As in samples from Kazakhstan was above the ML (0.2 mg/kg) proposed by FAO/WHO, but in seven samples from Spain and in four from Portugal were above the limit. The estimated weekly intake of total or inorganic As(III, V), Cd, Hg and Pb for rice consumption by Kazakh, Spanish and Portuguese adults and children was lower than the provisional tolerable weekly intake established by Joint FAO/WHO Expert Committee on Food Additives and the European Food Safety Authority.

Development of an iron-enriched high-yieldings indica rice cultivar by introgression of a high-iron trait from transgenic iron-biofortified rice

Low level of iron in staple food crops is one reason for the predominance of iron-deficiency anemia in developing countries. Most of the iron in rice grains accumulates in the outer aleurone layer and embryo, which are removed during milling, and the edible endosperm contains very low amounts of iron. In an effort to increase iron nutrition, we report here the transgene introgression of a high-iron trait into a high-yielding indica rice cultivar. The ferritin gene from soybean (soyfer1) was introduced into rice plants through interbreeding between soybean ferritin-overexpressing transgenic IR68144 and the high-yielding cultivar Swarna. The stable integration of the soyfer1 gene was confirmed in the BC2F4 generation, and the hybrid seeds showed 2.6-fold soybean ferritin gene expression over the recurrent parent Swarna. The hybrid milled seeds revealed a 2.54-fold increase in iron and 1.54-fold increase in zinc compared to Swarna. Agronomic data and an SSR marker analysis of the hybrid rice plants were taken into account for NIL character identification.

Genome wide association mapping of grain arsenic, copper, molybdenum and zinc in rice (Oryza sativa L.) grown at four international field sites

The mineral concentrations in cereals are important for human health, especially for individuals who consume a cereal subsistence diet. A number of elements, such as zinc, are required within the diet, while some elements are toxic to humans, for example arsenic. In this study we carry out genome-wide association (GWA) mapping of grain concentrations of arsenic, copper, molybdenum and zinc in brown rice using an established rice diversity panel of ∼300 accessions and 36.9 k single nucleotide polymorphisms (SNPs). The study was performed across five environments: one field site in Bangladesh, one in China and two in the US, with one of the US sites repeated over two years. GWA mapping on the whole dataset and on separate subpopulations of rice revealed a large number of loci significantly associated with variation in grain arsenic, copper, molybdenum and zinc. Seventeen of these loci were detected in data obtained from grain cultivated in more than one field location, and six co-localise with previously identified quantitative trait loci. Additionally, a number of candidate genes for the uptake or transport of these elements were located near significantly associated SNPs (within 200 kb, the estimated global linkage disequilibrium previously employed in this rice panel). This analysis highlights a number of genomic regions and candidate genes for further analysis as well as the challenges faced when mapping environmentally-variable traits in a highly genetically structured diversity panel.

Zinc - an indispensable micronutrient

Availability of Zn to plant is hampered by its immobile nature and adverse soil conditions. Thus, Zn deficiency is observed even though high amount is available in soil. Root-shoot barrier, a major controller of zinc transport in plant is highly affected by changes in the anatomical structure of conducting tissue and adverse soil conditions like pH, clay content, calcium carbonate content, etc. Zn deficiency results in severe yield losses and in acute cases plant death. Zn deficiency in edible plant parts results in micronutrient malnutrition leading to stunted growth and improper sexual development in humans. To overcome this problem several strategies have been used to enrich Zn availability in edible plant parts, including nutrient management, biotechnological tools, and classical and molecular breeding approaches.

Profiling the ionome of rice and its use in discriminating geographical origins at the regional scale, China

Element profile was investigated for their use to trace the geographical origin of rice (Oryza sativa L.) samples. The concentrations of 13 elements (calcium (Ca), potassium (K), magnesium (Mg), phosphorus (P), boron (B), manganese (Mn), iron (Fe), nickel (Ni), copper (Cu), arsenic (As), selenium (Se), molybdenum (Mo), and cadmium (Cd)) were determined in the rice samples by inductively coupled plasma optical emission and mass spectrometry. Most of the essential elements for human health in rice were within normal ranges except for Mo and Se. Mo concentrations were twice as high as those in rice from Vietnam and Spain. Meanwhile, Se concentrations were three times lower in the whole province compared to the Chinese average level of 0.088 mg/kg. About 12% of the rice samples failed the Chinese national food safety standard of 0.2 mg/kg for Cd. Combined with the multi-elemental profile in rice, the principal component analysis (PCA), discriminant function analysis (DFA) and Fibonacci index analysis (FIA) were applied to discriminate geographical origins of the samples. Results indicated that the FIA method could achieve a more effective geographical origin classification compared with PCA and DFA, due to its efficiency in making the grouping even when the elemental variability was so high that PCA and DFA showed little discriminatory power. Furthermore, some elements were identified as the most powerful indicators of geographical origin: Ca, Ni, Fe and Cd. This suggests that the newly established methodology of FIA based on the ionome profile can be applied to determine the geographical origin of rice.

Diversity of macro- and micronutrients in the seeds of lentil landraces

Increasing the amount of bioavailable mineral elements in plant foods would help to improve the nutritional status of populations in developing countries. Legume seeds have the potential to provide many essential nutrients. It is important to have information on genetic variations among different lentil populations so that plant breeding programs can use new varieties in cross-breeding programs. The main objective of this study was to characterize the micro- and macronutrient concentrations of lentil landraces seeds collected from South-Eastern Turkey. We found impressive variation in the micro- and macroelement concentrations in 39 lentil landraces and 7 cultivars. We investigated the relationships of traits by correlation analysis and principal component analysis (PCA). The concentrations of several minerals, particularly Zn, were positively correlated with other minerals, suggesting that similar pathways or transporters control the uptake and transport of these minerals. Some genotypes had high mineral and protein content and potential to improve the nutritional value of cultivated lentil. Cross-breeding of numerous lentil landraces from Turkey with currently cultivated varieties could improve the levels of micro- and macronutrients of lentil and may contribute to the worldwide lentil quality breeding program.

Iron biofortification in rice: it's a long way to the top

Rice and most staple cereals contain low iron (Fe) levels, most of which is lost during grain processing. Populations with monotonous diets consisting mainly of cereals are especially prone to Fe deficiency, which affects about two billion people. Supplementation or food fortification programs have not always been successful. Crop Fe fertilization is also not very effective due to Fe soil insolubility. An alternative solution is Fe biofortification by generating cultivars that efficiently mobilize, uptake and translocate Fe to the edible parts. Here, we review the strategies used for the Fe biofortification of rice, including conventional breeding and directed genetic modification, which offer the most rapid way to develop Fe-rich rice plants. While classical breeding is able to modify the contents of inhibitors of Fe absorption, transgenic approaches have focused on enhanced Fe uptake from soil, xylem and phloem loading and grain sink strength. A comprehensive table is provided in which the percentages of the recommended dietary Fe intake reached by independently developed transgenic plants are calculated. In this review we also emphasize that the discovery of new QTLs and genes related to Fe biofortification is extremely important, but interdisciplinary research is needed for future success in this area.

Effect of zinc sulfate fortification in germinated brown rice on seed zinc concentration, bioavailability, and seed germination

Rice is the staple food for more than half of the world's population and, hence, the main source of a vital micronutrient, zinc (Zn). Unfortunately, the bioavailability of Zn from rice is very low not only due to low content but also due to the presence of some antinutrients such as phytic acid. We investigated the effect of germination and Zn fortification treatment on Zn bioavailability of brown rice from three widely grown cultivars using the Caco-2 cell model to find a suitable fortification level for producing germinated brown rice. The results of this study showed that Zn content in brown rice increased significantly (p < 0.05) as the external Zn concentrations increased from 25 to 250 mg/L. In contrast, no significant influence (p > 0.05) on germination percentage of rice was observed when the Zn supply was lower than 150 mg/L. Zn fortification during the germination process has a significant impact on the Zn content and finally Zn bioavailability. These findings may result from the lower molar ratio of phytic acid to Zn and higher Zn content in Zn fortified germinated brown rice, leading to more bioavailable Zn. Likewise, a significant difference (p < 0.05) was found among cultivars with respect to the capacity for Zn accumulation and Zn bioavailability; these results might be attributed to the difference in the molar ratio of phytic acid to Zn and the concentration of Zn among the cultivars evaluated. Based on global intake of Zn among the world population, we recommend germinated brown rice fortified with 100 mg/L ZnSO(4) as a suitable concentration to use in the germination process, which contains high Zn concentration and Zn bioavailability. In the current study, the cultivar Bing91185 fortified with Zn through the germination process contained a high amount as well as bioavailable Zn, which was identified as the most promising cultivar for further evaluation to determine its efficiency as an improved source of Zn for target populations.

Profiling and association mapping of grain metabolites in a subset of the core collection of Chinese rice germplasm (Oryza sativa L.)

In this study, metabolic profiles of a set of 48 rice germplasms from the Chinese core collection were obtained by gas chromatography and time-of-flight mass spectrometry (GC-TOF-MS). Forty-one metabolites were identified and relatively quantified according to the internal standard (IS). Wide ranges of variations for all metabolites were observed among rice accessions. The maximum/minimum ratios varied from 4.73 to 211.36. The metabolites were categorized into seven groups based on their chemical characteristics. Clustering analysis and a correlation network showed that most of the metabolites had variations among rice accessions in the same direction. Using 218 molecular markers, association mapping was conducted to identify the chromosomal loci influencing the concentrations of identified metabolites. Twenty markers were identified associating with the concentrations of 29 metabolites [-lg(P) > 3]. Allelic effects were investigated in detail in two markers (RM315 and RM541) as examples.